Initial commit: v0.1.0

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# Contributing to SelfiSys
We welcome contributions to the SelfiSys repository! Please follow these guidelines when contributing.
---
## Reporting Issues
If you find a bug or have a suggestion, please open an issue in the [GitHub repository](https://github.com/hoellin/selfisys_public). Include as much detail as possible:
- Steps to reproduce the issue
- Expected vs. actual behaviour
- Relevant error messages or logs (if applicable)
- Suggestions for improvement (if applicable)
If you are unsure whether your issue is a bug or have questions about the code, you are welcome to open an issue for discussion.
## Submitting Contributions
1. Fork the repository and create a new branch for your changes.
2. Ensure your contributions are well-documented and adhere to the highest coding standards.
3. Test your changes thoroughly before submitting:
- Ensure Jupyter notebooks run without errors from top to bottom.
- Validate new functionality or fixes using appropriate test cases.
4. Before submitting a pull request, synchronise your fork with the main repository to incorporate upstream changes.
- Add the main repository as a remote.
```bash
git remote add upstream https://github.com/hoellin/selfisys_public.git
```
- Fetch the latest changes from the upstream repository.
```bash
git fetch upstream
```
- Merge the changes into your local repository.
```bash
git merge upstream/main
```
5. Open a pull request describing your changes to the main repository.
## Style Guidelines
Follow best practices for Python coding and Jupyter notebooks.
### Python code
Refer to the [PEP 8 Style Guide](https://pep8.org/) for Python coding standards.
### Jupyter Notebooks
- Use clear and concise Markdown cells to explain code and results.
- Avoid leaving unnecessary output (e.g., debugging print statements).
- Ensure notebooks are runnable from top to bottom.
- For tips on creating clean and effective Jupyter notebooks, see [Jupyter Notebook Best Practices](https://realpython.com/jupyter-notebook-best-practices/).
---
## Questions?
If you have any questions or need further clarification, feel free to [contact the authors](mailto:tristan.hoellinger@iap.fr).

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# SelfiSys: Assess the Impact of Systematic Effects in Galaxy Surveys
[![arXiv](https://img.shields.io/badge/astro--ph.CO-arxiv%3A2412.04443-B31B1B.svg?style=flat)](https://arxiv.org/abs/2412.04443)
[![GPLv3 license](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://github.com/hoellin/selfisys_public/blob/main/LICENSE)
[![GitHub version](https://img.shields.io/github/tag/hoellin/selfisys_public.svg?label=version)](https://github.com/hoellin/selfisys_public)
[![GitHub last commit](https://img.shields.io/github/last-commit/hoellin/selfisys_public.svg)](https://github.com/hoellin/selfisys_public/commits/main)
**SelfiSys** is a Python package designed to address the issue of model misspecification in field-based, implicit likelihood cosmological inference.
It leverages the inferred initial matter power spectrum, enabling a thorough diagnosis of systematic effects in large-scale spectroscopic galaxy surveys.
## Key Features
- **Custom hidden-box forward models**
We provide a `HiddenBox` class to simulate realistic spectroscopic galaxy surveys. It accommodates fully non-linear gravitational evolution, and incorporates multiple systematic effects observed in real-world survey, e.g., misspecified galaxy bias, survey mask, selection functions, dust extinction, line interlopers, or inaccurate gravity solver.
- **Diagnosis of systematic effects**
Diagnose the impact of systematic effects using the inferred initial matter power spectrum, prior to performing cosmological inference.
- **Cosmological inference**
Perform inference of cosmological parameters using Approximate Bayesian Computation (ABC) with a Population Monte Carlo (PMC) sampler.
---
## Documentation
The documentation, including a detailed API reference, is available at [hoellin.github.io/selfisys_public](https://hoellin.github.io/selfisys_public/).
For practical examples demonstrating how to use SelfiSys, visit the [SelfiSys Examples Repository](https://github.com/hoellin/selfisys_examples).
## Contributors
- **Tristan Hoellinger**, [tristan.hoellinger@iap.fr](mailto:tristan.hoellinger@iap.fr)
Principal developer and maintainer, Institut dAstrophysique de Paris (IAP).
For information on contributing, refer to [CONTRIBUTING.md](CONTRIBUTING.md).
## References
If you use the SelfiSys package in your research, please cite the following paper and feel free to [contact the authors](mailto:tristan.hoellinger@iap.fr) for feedback, collaboration opportunities, or other inquiries.
**Diagnosing Systematic Effects Using the Inferred Initial Power Spectrum**
*Hoellinger, T. and Leclercq, F., 2024*
[arXiv:2412.04443](https://arxiv.org/abs/2412.04443) [[astro-ph.CO]](https://arxiv.org/abs/2412.04443) [[ADS]](https://ui.adsabs.harvard.edu/abs/arXiv:2412.04443) [[pdf]](https://arxiv.org/pdf/2412.04443)
BibTeX entry for citation:
```bibtex
@ARTICLE{hoellinger2024diagnosing,
author = {Hoellinger, Tristan and Leclercq, Florent},
title = "{Diagnosing Systematic Effects Using the Inferred Initial Power Spectrum}",
journal = {arXiv e-prints},
keywords = {Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics},
year = 2024,
month = dec,
eid = {arXiv:2412.04443},
pages = {arXiv:2412.04443},
doi = {10.48550/arXiv.2412.04443},
archivePrefix = {arXiv},
eprint = {2412.04443},
primaryClass = {astro-ph.CO},
adsurl = {https://ui.adsabs.harvard.edu/abs/2024arXiv241204443H},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
```
## Requirements
The code is written in Python 3.10 and depends on the following packages:
- [`pySELFI`](https://pyselfi.readthedocs.io/en/latest/): Python implementation of the Simulator Expansion for Likelihood-Free Inference.
- [`Simbelmynë`](https://simbelmyne.readthedocs.io/en/latest/): A hierarchical probabilistic simulator for generating synthetic galaxy survey data.
- [`ELFI`](https://elfi.readthedocs.io/en/latest/): A statistical software package for likelihood-free inference, implementing in particular Approximate Bayesian Computation (ABC) with a Population Monte Carlo (PMC) sampler.
A comprehensive list of dependencies, including version specifications to ensure reproducibility, will be provided in a yaml file, along with installation instructions, in a future release.
---
## License
This software is distributed under the GPLv3 Licence. Please review the [LICENSE](https://github.com/hoellin/selfisys_public/blob/main/LICENSE) file in the repository to understand the terms of use and ensure compliance. By downloading and using this software, you agree to the terms of the licence.

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# References
If you use the SelfiSys package in your research, please cite the following paper and feel free to [contact the authors](mailto:tristan.hoellinger@iap.fr) for feedback, collaboration opportunities, or other inquiries.
**Diagnosing Systematic Effects Using the Inferred Initial Power Spectrum**
*Hoellinger, T. and Leclercq, F., 2024*
[arXiv:2412.04443](https://arxiv.org/abs/2412.04443) [[astro-ph.CO]](https://arxiv.org/abs/2412.04443) [[ADS]](https://ui.adsabs.harvard.edu/abs/arXiv:2412.04443) [[pdf]](https://arxiv.org/pdf/2412.04443)
BibTeX entry for citation:
```bibtex
@ARTICLE{hoellinger2024diagnosing,
author = {Hoellinger, Tristan and Leclercq, Florent},
title = "{Diagnosing Systematic Effects Using the Inferred Initial Power Spectrum}",
journal = {arXiv e-prints},
keywords = {Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics},
year = 2024,
month = dec,
eid = {arXiv:2412.04443},
pages = {arXiv:2412.04443},
doi = {10.48550/arXiv.2412.04443},
archivePrefix = {arXiv},
eprint = {2412.04443},
primaryClass = {astro-ph.CO},
adsurl = {https://ui.adsabs.harvard.edu/abs/2024arXiv241204443H},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
```
Other references relevant to the SelfiSys pipeline and cited in the code are listed below.
- **[jasche2010bayesian]**
Jasche, J., Kitaura, F. S., Wandelt, B. D., and Enßlin, T. A., “Bayesian power-spectrum inference for large-scale structure data”, <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 406, no. 1, OUP, pp. 6085, 2010. [doi:10.1111/j.1365-2966.2010.16610.x](https://doi.org/10.48550/arXiv.0911.2493).
- **[gil2015power]**
Gil-Marín, H., “The power spectrum and bispectrum of SDSS DR11 BOSS galaxies - I. Bias and gravity”, <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 451, no. 1, OUP, pp. 539580, 2015. [doi:10.1093/mnras/stv961](https://doi.org/10.48550/arXiv.1407.5668).
- **[howlett2015clustering]**
Howlett, C., Ross, A. J., Samushia, L., Percival, W. J., and Manera, M., “The clustering of the SDSS main galaxy sample - II. Mock galaxy catalogues and a measurement of the growth of structure from redshift space distortions at z = 0.15”, <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 449, no. 1, OUP, pp. 848866, 2015. [doi:10.1093/mnras/stu2693](https://doi.org/10.48550/arXiv.1409.3238).
- **[leclercq2019primordial]**
Florent Leclercq, Wolfgang Enzi, Jens Jasche, Alan Heavens, Primordial power spectrum and cosmology from black-box galaxy surveys, Monthly Notices of the Royal Astronomical Society, Volume 490, Issue 3, December 2019, Pages 42374253, [doi:10.1093/mnras/stz2718](https://doi.org/10.1093/mnras/stz2718).
- **[hoellinger2024diagnosing]**
Hoellinger, T. and Leclercq, F., “Diagnosing Systematic Effects Using the Inferred Initial Power Spectrum”, <i>arXiv e-prints</i>, Art. no. arXiv:2412.04443, 2024. [doi.org:10.48550/arXiv.2412.04443](https://doi.org/10.48550/arXiv.2412.04443).

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<li class="toctree-l1"><a class="reference internal" href="selfisys.hiddenbox.html">hiddenbox</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox"><code class="docutils literal notranslate"><span class="pre">HiddenBox</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Npop"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Npop</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Ntimesteps"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Ntimesteps</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Psingle"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Psingle</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.compute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.compute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.evaluate"><code class="docutils literal notranslate"><span class="pre">HiddenBox.evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_neglect_lightcone"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_neglect_lightcone</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_recompute_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_recompute_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.gravity_on"><code class="docutils literal notranslate"><span class="pre">HiddenBox.gravity_on</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.load_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.load_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.make_data"><code class="docutils literal notranslate"><span class="pre">HiddenBox.make_data()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.modified_selfi"><code class="docutils literal notranslate"><span class="pre">HiddenBox.modified_selfi</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.prefix_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.prefix_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.reset_survey"><code class="docutils literal notranslate"><span class="pre">HiddenBox.reset_survey()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.setup_only"><code class="docutils literal notranslate"><span class="pre">HiddenBox.setup_only</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_recompute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_recompute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_setup"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_setup()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.update"><code class="docutils literal notranslate"><span class="pre">HiddenBox.update()</span></code></a></li>
</ul>
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</ul>
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<li class="toctree-l1"><a class="reference internal" href="selfisys.normalise_hb.html">normalise_hb</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.normalise_hb.html#selfisys.normalise_hb.define_normalisation"><code class="docutils literal notranslate"><span class="pre">define_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation"><code class="docutils literal notranslate"><span class="pre">worker_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_public"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_public()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_wrapper"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_wrapper()</span></code></a></li>
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<li class="toctree-l1"><a class="reference internal" href="selfisys.prior.html">prior</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.logposterior_hyperparameters_parallel"><code class="docutils literal notranslate"><span class="pre">logposterior_hyperparameters_parallel()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.perform_prior_optimisation_and_plot"><code class="docutils literal notranslate"><span class="pre">perform_prior_optimisation_and_plot()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior"><code class="docutils literal notranslate"><span class="pre">planck_prior</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.mean"><code class="docutils literal notranslate"><span class="pre">planck_prior.mean</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.inv_covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.inv_covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.Nbin_max"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_max</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.Nbin_min"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_min</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.compute"><code class="docutils literal notranslate"><span class="pre">planck_prior.compute()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.load"><code class="docutils literal notranslate"><span class="pre">planck_prior.load()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.logpdf"><code class="docutils literal notranslate"><span class="pre">planck_prior.logpdf()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.sample"><code class="docutils literal notranslate"><span class="pre">planck_prior.sample()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.save"><code class="docutils literal notranslate"><span class="pre">planck_prior.save()</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.worker_class"><code class="docutils literal notranslate"><span class="pre">worker_class()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.selection_functions.html">selection_functions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.init_selection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.init_selection()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.lognormals_z_to_x"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.lognormals_z_to_x()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.r_grid"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.r_grid()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.selfi_interface.html">selfi_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.selfi_interface.html#selfisys.selfi_interface.PrintMessage"><code class="docutils literal notranslate"><span class="pre">PrintMessage()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.selfi_interface.html#selfisys.selfi_interface.indent"><code class="docutils literal notranslate"><span class="pre">indent()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.selfi_interface.html#selfisys.selfi_interface.unindent"><code class="docutils literal notranslate"><span class="pre">unindent()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.sbmy_interface.html">sbmy_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.sbmy_interface.html#selfisys.sbmy_interface.compute_Phi"><code class="docutils literal notranslate"><span class="pre">compute_Phi()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.sbmy_interface.html#selfisys.sbmy_interface.generate_white_noise_Field"><code class="docutils literal notranslate"><span class="pre">generate_white_noise_Field()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.sbmy_interface.html#selfisys.sbmy_interface.get_power_spectrum_from_cosmo"><code class="docutils literal notranslate"><span class="pre">get_power_spectrum_from_cosmo()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.sbmy_interface.html#selfisys.sbmy_interface.handle_time_stepping"><code class="docutils literal notranslate"><span class="pre">handle_time_stepping()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.sbmy_interface.html#selfisys.sbmy_interface.setup_sbmy_parfiles"><code class="docutils literal notranslate"><span class="pre">setup_sbmy_parfiles()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.grf.html">grf</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.grf.html#selfisys.grf.primordial_grf"><code class="docutils literal notranslate"><span class="pre">primordial_grf()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.utils.html">selfisys.utils package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.examples_utils">selfisys.utils.examples_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.examples_utils.clear_large_plot"><code class="docutils literal notranslate"><span class="pre">clear_large_plot()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.logger">selfisys.utils.logger module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.CustomLogger"><code class="docutils literal notranslate"><span class="pre">CustomLogger</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.CustomLogger.diagnostic"><code class="docutils literal notranslate"><span class="pre">CustomLogger.diagnostic()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler.emit"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler.emit()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.INDENT"><code class="docutils literal notranslate"><span class="pre">INDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.PrintDiagnostic"><code class="docutils literal notranslate"><span class="pre">PrintDiagnostic()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.PrintError"><code class="docutils literal notranslate"><span class="pre">PrintError()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.PrintInfo"><code class="docutils literal notranslate"><span class="pre">PrintInfo()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.PrintLeftType"><code class="docutils literal notranslate"><span class="pre">PrintLeftType()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.PrintWarning"><code class="docutils literal notranslate"><span class="pre">PrintWarning()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.UNINDENT"><code class="docutils literal notranslate"><span class="pre">UNINDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.getCustomLogger"><code class="docutils literal notranslate"><span class="pre">getCustomLogger()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.low_level">selfisys.utils.low_level module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.low_level.stderr_redirector"><code class="docutils literal notranslate"><span class="pre">stderr_redirector()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.low_level.stdout_redirector"><code class="docutils literal notranslate"><span class="pre">stdout_redirector()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.parser">selfisys.utils.parser module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.bool_sh"><code class="docutils literal notranslate"><span class="pre">bool_sh()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.check_files_exist"><code class="docutils literal notranslate"><span class="pre">check_files_exist()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.intNone"><code class="docutils literal notranslate"><span class="pre">intNone()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.joinstrs"><code class="docutils literal notranslate"><span class="pre">joinstrs()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.joinstrs_only"><code class="docutils literal notranslate"><span class="pre">joinstrs_only()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.safe_npload"><code class="docutils literal notranslate"><span class="pre">safe_npload()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.path_utils">selfisys.utils.path_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.path_utils.file_names_evaluate"><code class="docutils literal notranslate"><span class="pre">file_names_evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.path_utils.get_file_names"><code class="docutils literal notranslate"><span class="pre">get_file_names()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.plot_examples">selfisys.utils.plot_examples module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_examples.plot_comoving_distance_redshift"><code class="docutils literal notranslate"><span class="pre">plot_comoving_distance_redshift()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_examples.plot_galaxy_field_slice"><code class="docutils literal notranslate"><span class="pre">plot_galaxy_field_slice()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_examples.plot_power_spectrum"><code class="docutils literal notranslate"><span class="pre">plot_power_spectrum()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_examples.plot_selection_functions_def_in_z"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions_def_in_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_examples.redshift_distance_conversion"><code class="docutils literal notranslate"><span class="pre">redshift_distance_conversion()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_examples.relative_error_analysis"><code class="docutils literal notranslate"><span class="pre">relative_error_analysis()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.plot_params">selfisys.utils.plot_params module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.get_offset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.get_offset()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_scientific"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_scientific()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_useOffset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_useOffset()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.create_all_colormaps"><code class="docutils literal notranslate"><span class="pre">create_all_colormaps()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.create_colormap"><code class="docutils literal notranslate"><span class="pre">create_colormap()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.dynamic_text_scaling"><code class="docutils literal notranslate"><span class="pre">dynamic_text_scaling()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.get_contours"><code class="docutils literal notranslate"><span class="pre">get_contours()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.reset_plotting"><code class="docutils literal notranslate"><span class="pre">reset_plotting()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.setup_plotting"><code class="docutils literal notranslate"><span class="pre">setup_plotting()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.plot_utils">selfisys.utils.plot_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_C"><code class="docutils literal notranslate"><span class="pre">plot_C()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_fisher"><code class="docutils literal notranslate"><span class="pre">plot_fisher()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_gradients"><code class="docutils literal notranslate"><span class="pre">plot_gradients()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_histogram"><code class="docutils literal notranslate"><span class="pre">plot_histogram()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks"><code class="docutils literal notranslate"><span class="pre">plot_mocks()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks_compact"><code class="docutils literal notranslate"><span class="pre">plot_mocks_compact()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_observations"><code class="docutils literal notranslate"><span class="pre">plot_observations()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_prior_and_posterior_covariances"><code class="docutils literal notranslate"><span class="pre">plot_prior_and_posterior_covariances()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_reconstruction"><code class="docutils literal notranslate"><span class="pre">plot_reconstruction()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_selection_functions"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plotly_3d"><code class="docutils literal notranslate"><span class="pre">plotly_3d()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.timestepping">selfisys.utils.timestepping module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.timestepping.merge_nTS"><code class="docutils literal notranslate"><span class="pre">merge_nTS()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.tools">selfisys.utils.tools module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.tools.cosmo_vector_to_Simbelmyne_dict"><code class="docutils literal notranslate"><span class="pre">cosmo_vector_to_Simbelmyne_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.tools.cosmo_vector_to_class_dict"><code class="docutils literal notranslate"><span class="pre">cosmo_vector_to_class_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.tools.custom_stat"><code class="docutils literal notranslate"><span class="pre">custom_stat()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.tools.fisher_rao"><code class="docutils literal notranslate"><span class="pre">fisher_rao()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.tools.get_k_max"><code class="docutils literal notranslate"><span class="pre">get_k_max()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.tools.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.tools.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.tools.params_ids_to_Simbelmyne_dict"><code class="docutils literal notranslate"><span class="pre">params_ids_to_Simbelmyne_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.tools.sample_omega_from_prior"><code class="docutils literal notranslate"><span class="pre">sample_omega_from_prior()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.tools.summary_to_score"><code class="docutils literal notranslate"><span class="pre">summary_to_score()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.workers">selfisys.utils.workers module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.workers.Simbelmyne_worker"><code class="docutils literal notranslate"><span class="pre">Simbelmyne_worker()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.workers.evaluate_gradient_of_Symbelmyne"><code class="docutils literal notranslate"><span class="pre">evaluate_gradient_of_Symbelmyne()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.workers.worker_gradient_Symbelmyne"><code class="docutils literal notranslate"><span class="pre">worker_gradient_Symbelmyne()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils">Module contents</a></li>
</ul>
</li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Contribute</span></p>
<ul class="current">
<li class="toctree-l1 current"><a class="current reference internal" href="#">Contributing to SelfiSys</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#reporting-issues">Reporting Issues</a></li>
<li class="toctree-l2"><a class="reference internal" href="#submitting-contributions">Submitting Contributions</a></li>
<li class="toctree-l2"><a class="reference internal" href="#style-guidelines">Style Guidelines</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#python-code">Python code</a></li>
<li class="toctree-l3"><a class="reference internal" href="#jupyter-notebooks">Jupyter Notebooks</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#questions">Questions?</a></li>
</ul>
</li>
</ul>
<p class="caption" role="heading"><span class="caption-text">References</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="REFERENCES.html">References</a></li>
</ul>
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<li class="breadcrumb-item active">Contributing to SelfiSys</li>
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<section id="contributing-to-selfisys">
<h1>Contributing to SelfiSys<a class="headerlink" href="#contributing-to-selfisys" title="Link to this heading"></a></h1>
<p>We welcome contributions to the SelfiSys repository! Please follow these guidelines when contributing.</p>
<hr class="docutils" />
<section id="reporting-issues">
<h2>Reporting Issues<a class="headerlink" href="#reporting-issues" title="Link to this heading"></a></h2>
<p>If you find a bug or have a suggestion, please open an issue in the <a class="reference external" href="https://github.com/hoellin/selfisys_public">GitHub repository</a>. Include as much detail as possible:</p>
<ul class="simple">
<li><p>Steps to reproduce the issue</p></li>
<li><p>Expected vs. actual behaviour</p></li>
<li><p>Relevant error messages or logs (if applicable)</p></li>
<li><p>Suggestions for improvement (if applicable)</p></li>
</ul>
<p>If you are unsure whether your issue is a bug or have questions about the code, you are welcome to open an issue for discussion.</p>
</section>
<section id="submitting-contributions">
<h2>Submitting Contributions<a class="headerlink" href="#submitting-contributions" title="Link to this heading"></a></h2>
<ol class="arabic">
<li><p>Fork the repository and create a new branch for your changes.</p></li>
<li><p>Ensure your contributions are well-documented and adhere to the highest coding standards.</p></li>
<li><p>Test your changes thoroughly before submitting:</p>
<ul class="simple">
<li><p>Ensure Jupyter notebooks run without errors from top to bottom.</p></li>
<li><p>Validate new functionality or fixes using appropriate test cases.</p></li>
</ul>
</li>
<li><p>Before submitting a pull request, synchronise your fork with the main repository to incorporate upstream changes.</p>
<ul>
<li><p>Add the main repository as a remote.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>remote<span class="w"> </span>add<span class="w"> </span>upstream<span class="w"> </span>https://github.com/hoellin/selfisys_public.git
</pre></div>
</div>
</li>
<li><p>Fetch the latest changes from the upstream repository.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>fetch<span class="w"> </span>upstream
</pre></div>
</div>
</li>
<li><p>Merge the changes into your local repository.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>merge<span class="w"> </span>upstream/main
</pre></div>
</div>
</li>
</ul>
</li>
<li><p>Open a pull request describing your changes to the main repository.</p></li>
</ol>
</section>
<section id="style-guidelines">
<h2>Style Guidelines<a class="headerlink" href="#style-guidelines" title="Link to this heading"></a></h2>
<p>Follow best practices for Python coding and Jupyter notebooks.</p>
<section id="python-code">
<h3>Python code<a class="headerlink" href="#python-code" title="Link to this heading"></a></h3>
<p>Refer to the <a class="reference external" href="https://pep8.org/">PEP 8 Style Guide</a> for Python coding standards.</p>
</section>
<section id="jupyter-notebooks">
<h3>Jupyter Notebooks<a class="headerlink" href="#jupyter-notebooks" title="Link to this heading"></a></h3>
<ul class="simple">
<li><p>Use clear and concise Markdown cells to explain code and results.</p></li>
<li><p>Avoid leaving unnecessary output (e.g., debugging print statements).</p></li>
<li><p>Ensure notebooks are runnable from top to bottom.</p></li>
<li><p>For tips on creating clean and effective Jupyter notebooks, see <a class="reference external" href="https://realpython.com/jupyter-notebook-best-practices/">Jupyter Notebook Best Practices</a>.</p></li>
</ul>
</section>
</section>
<hr class="docutils" />
<section id="questions">
<h2>Questions?<a class="headerlink" href="#questions" title="Link to this heading"></a></h2>
<p>If you have any questions or need further clarification, feel free to <a class="reference external" href="mailto:tristan&#46;hoellinger&#37;&#52;&#48;iap&#46;fr">contact the authors</a>.</p>
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<title>SelfiSys: Assess the Impact of Systematic Effects in Galaxy Surveys &mdash; SelfiSys /Users/hoellinger/Library/CloudStorage/Dropbox/travail/these/science/code/SELFI/selfisys/src/ documentation</title>
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<p class="caption" role="heading"><span class="caption-text">API Documentation</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="selfisys.hiddenbox.html">hiddenbox</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox"><code class="docutils literal notranslate"><span class="pre">HiddenBox</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Npop"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Npop</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Ntimesteps"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Ntimesteps</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Psingle"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Psingle</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.compute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.compute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.evaluate"><code class="docutils literal notranslate"><span class="pre">HiddenBox.evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_neglect_lightcone"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_neglect_lightcone</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_recompute_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_recompute_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.gravity_on"><code class="docutils literal notranslate"><span class="pre">HiddenBox.gravity_on</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.load_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.load_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.make_data"><code class="docutils literal notranslate"><span class="pre">HiddenBox.make_data()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.modified_selfi"><code class="docutils literal notranslate"><span class="pre">HiddenBox.modified_selfi</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.prefix_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.prefix_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.reset_survey"><code class="docutils literal notranslate"><span class="pre">HiddenBox.reset_survey()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.setup_only"><code class="docutils literal notranslate"><span class="pre">HiddenBox.setup_only</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_recompute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_recompute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_setup"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_setup()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.update"><code class="docutils literal notranslate"><span class="pre">HiddenBox.update()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.normalise_hb.html">normalise_hb</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.normalise_hb.html#selfisys.normalise_hb.define_normalisation"><code class="docutils literal notranslate"><span class="pre">define_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation"><code class="docutils literal notranslate"><span class="pre">worker_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_public"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_public()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_wrapper"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_wrapper()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.prior.html">prior</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.logposterior_hyperparameters_parallel"><code class="docutils literal notranslate"><span class="pre">logposterior_hyperparameters_parallel()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.perform_prior_optimisation_and_plot"><code class="docutils literal notranslate"><span class="pre">perform_prior_optimisation_and_plot()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior"><code class="docutils literal notranslate"><span class="pre">planck_prior</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.mean"><code class="docutils literal notranslate"><span class="pre">planck_prior.mean</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.inv_covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.inv_covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.Nbin_max"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_max</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.Nbin_min"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_min</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.compute"><code class="docutils literal notranslate"><span class="pre">planck_prior.compute()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.load"><code class="docutils literal notranslate"><span class="pre">planck_prior.load()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.logpdf"><code class="docutils literal notranslate"><span class="pre">planck_prior.logpdf()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.sample"><code class="docutils literal notranslate"><span class="pre">planck_prior.sample()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.save"><code class="docutils literal notranslate"><span class="pre">planck_prior.save()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.worker_class"><code class="docutils literal notranslate"><span class="pre">worker_class()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.selection_functions.html">selection_functions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.init_selection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.init_selection()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.lognormals_z_to_x"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.lognormals_z_to_x()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.r_grid"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.r_grid()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.selfi_interface.html">selfi_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.selfi_interface.html#selfisys.selfi_interface.PrintMessage"><code class="docutils literal notranslate"><span class="pre">PrintMessage()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.selfi_interface.html#selfisys.selfi_interface.indent"><code class="docutils literal notranslate"><span class="pre">indent()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.selfi_interface.html#selfisys.selfi_interface.unindent"><code class="docutils literal notranslate"><span class="pre">unindent()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.sbmy_interface.html">sbmy_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.sbmy_interface.html#selfisys.sbmy_interface.compute_Phi"><code class="docutils literal notranslate"><span class="pre">compute_Phi()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.sbmy_interface.html#selfisys.sbmy_interface.generate_white_noise_Field"><code class="docutils literal notranslate"><span class="pre">generate_white_noise_Field()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.sbmy_interface.html#selfisys.sbmy_interface.get_power_spectrum_from_cosmo"><code class="docutils literal notranslate"><span class="pre">get_power_spectrum_from_cosmo()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.sbmy_interface.html#selfisys.sbmy_interface.handle_time_stepping"><code class="docutils literal notranslate"><span class="pre">handle_time_stepping()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.sbmy_interface.html#selfisys.sbmy_interface.setup_sbmy_parfiles"><code class="docutils literal notranslate"><span class="pre">setup_sbmy_parfiles()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.grf.html">grf</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.grf.html#selfisys.grf.primordial_grf"><code class="docutils literal notranslate"><span class="pre">primordial_grf()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.utils.html">selfisys.utils package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.examples_utils">selfisys.utils.examples_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.examples_utils.clear_large_plot"><code class="docutils literal notranslate"><span class="pre">clear_large_plot()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.logger">selfisys.utils.logger module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.CustomLogger"><code class="docutils literal notranslate"><span class="pre">CustomLogger</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.CustomLogger.diagnostic"><code class="docutils literal notranslate"><span class="pre">CustomLogger.diagnostic()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler.emit"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler.emit()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.INDENT"><code class="docutils literal notranslate"><span class="pre">INDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.PrintDiagnostic"><code class="docutils literal notranslate"><span class="pre">PrintDiagnostic()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.PrintError"><code class="docutils literal notranslate"><span class="pre">PrintError()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.PrintInfo"><code class="docutils literal notranslate"><span class="pre">PrintInfo()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.PrintLeftType"><code class="docutils literal notranslate"><span class="pre">PrintLeftType()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.PrintWarning"><code class="docutils literal notranslate"><span class="pre">PrintWarning()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.UNINDENT"><code class="docutils literal notranslate"><span class="pre">UNINDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.getCustomLogger"><code class="docutils literal notranslate"><span class="pre">getCustomLogger()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.low_level">selfisys.utils.low_level module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.low_level.stderr_redirector"><code class="docutils literal notranslate"><span class="pre">stderr_redirector()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.low_level.stdout_redirector"><code class="docutils literal notranslate"><span class="pre">stdout_redirector()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.parser">selfisys.utils.parser module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.bool_sh"><code class="docutils literal notranslate"><span class="pre">bool_sh()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.check_files_exist"><code class="docutils literal notranslate"><span class="pre">check_files_exist()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.intNone"><code class="docutils literal notranslate"><span class="pre">intNone()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.joinstrs"><code class="docutils literal notranslate"><span class="pre">joinstrs()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.joinstrs_only"><code class="docutils literal notranslate"><span class="pre">joinstrs_only()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.safe_npload"><code class="docutils literal notranslate"><span class="pre">safe_npload()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.path_utils">selfisys.utils.path_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.path_utils.file_names_evaluate"><code class="docutils literal notranslate"><span class="pre">file_names_evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.path_utils.get_file_names"><code class="docutils literal notranslate"><span class="pre">get_file_names()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.plot_examples">selfisys.utils.plot_examples module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_examples.plot_comoving_distance_redshift"><code class="docutils literal notranslate"><span class="pre">plot_comoving_distance_redshift()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_examples.plot_galaxy_field_slice"><code class="docutils literal notranslate"><span class="pre">plot_galaxy_field_slice()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_examples.plot_power_spectrum"><code class="docutils literal notranslate"><span class="pre">plot_power_spectrum()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_examples.plot_selection_functions_def_in_z"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions_def_in_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_examples.redshift_distance_conversion"><code class="docutils literal notranslate"><span class="pre">redshift_distance_conversion()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_examples.relative_error_analysis"><code class="docutils literal notranslate"><span class="pre">relative_error_analysis()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.plot_params">selfisys.utils.plot_params module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.get_offset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.get_offset()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_scientific"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_scientific()</span></code></a></li>
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<section id="selfisys-assess-the-impact-of-systematic-effects-in-galaxy-surveys">
<h1>SelfiSys: Assess the Impact of Systematic Effects in Galaxy Surveys<a class="headerlink" href="#selfisys-assess-the-impact-of-systematic-effects-in-galaxy-surveys" title="Link to this heading"></a></h1>
<p><a class="reference external" href="https://arxiv.org/abs/2412.04443"><img alt="arXiv" src="https://img.shields.io/badge/astro--ph.CO-arxiv%3A2412.04443-B31B1B.svg?style=flat" /></a>
<a class="reference external" href="https://github.com/hoellin/selfisys_public/blob/main/LICENSE"><img alt="GPLv3 license" src="https://img.shields.io/badge/License-GPLv3-blue.svg" /></a>
<a class="reference external" href="https://github.com/hoellin/selfisys_public"><img alt="GitHub version" src="https://img.shields.io/github/tag/hoellin/selfisys_public.svg?label=version" /></a>
<a class="reference external" href="https://github.com/hoellin/selfisys_public/commits/main"><img alt="GitHub last commit" src="https://img.shields.io/github/last-commit/hoellin/selfisys_public.svg" /></a></p>
<p><strong>SelfiSys</strong> is a Python package designed to address the issue of model misspecification in field-based, implicit likelihood cosmological inference.</p>
<p>It leverages the inferred initial matter power spectrum, enabling a thorough diagnosis of systematic effects in large-scale spectroscopic galaxy surveys.</p>
<section id="key-features">
<h2>Key Features<a class="headerlink" href="#key-features" title="Link to this heading"></a></h2>
<ul class="simple">
<li><p><strong>Custom hidden-box forward models</strong></p></li>
</ul>
<p>We provide a <code class="docutils literal notranslate"><span class="pre">HiddenBox</span></code> class to simulate realistic spectroscopic galaxy surveys. It accommodates fully non-linear gravitational evolution, and incorporates multiple systematic effects observed in real-world survey, e.g., misspecified galaxy bias, survey mask, selection functions, dust extinction, line interlopers, or inaccurate gravity solver.</p>
<ul class="simple">
<li><p><strong>Diagnosis of systematic effects</strong></p></li>
</ul>
<p>Diagnose the impact of systematic effects using the inferred initial matter power spectrum, prior to performing cosmological inference.</p>
<ul class="simple">
<li><p><strong>Cosmological inference</strong></p></li>
</ul>
<p>Perform inference of cosmological parameters using Approximate Bayesian Computation (ABC) with a Population Monte Carlo (PMC) sampler.</p>
</section>
<hr class="docutils" />
<section id="documentation">
<h2>Documentation<a class="headerlink" href="#documentation" title="Link to this heading"></a></h2>
<p>The documentation, including a detailed API reference, is available at <a class="reference external" href="https://hoellin.github.io/selfisys_public/">hoellin.github.io/selfisys_public</a>.</p>
<p>For practical examples demonstrating how to use SelfiSys, visit the <a class="reference external" href="https://github.com/hoellin/selfisys_examples">SelfiSys Examples Repository</a>.</p>
</section>
<section id="contributors">
<h2>Contributors<a class="headerlink" href="#contributors" title="Link to this heading"></a></h2>
<ul class="simple">
<li><p><strong>Tristan Hoellinger</strong>, <a class="reference external" href="mailto:tristan&#46;hoellinger&#37;&#52;&#48;iap&#46;fr">tristan<span>&#46;</span>hoellinger<span>&#64;</span>iap<span>&#46;</span>fr</a><br />
Principal developer and maintainer, Institut dAstrophysique de Paris (IAP).</p></li>
</ul>
<p>For information on contributing, refer to <a class="reference internal" href="CONTRIBUTING.html"><span class="std std-doc">CONTRIBUTING.md</span></a>.</p>
</section>
<section id="references">
<h2>References<a class="headerlink" href="#references" title="Link to this heading"></a></h2>
<p>If you use the SelfiSys package in your research, please cite the following paper and feel free to <a class="reference external" href="mailto:tristan&#46;hoellinger&#37;&#52;&#48;iap&#46;fr">contact the authors</a> for feedback, collaboration opportunities, or other inquiries.</p>
<p><strong>Diagnosing Systematic Effects Using the Inferred Initial Power Spectrum</strong>
<em>Hoellinger, T. and Leclercq, F., 2024</em>
<a class="reference external" href="https://arxiv.org/abs/2412.04443">arXiv:2412.04443</a> <a class="reference external" href="https://arxiv.org/abs/2412.04443">[astro-ph.CO]</a> <a class="reference external" href="https://ui.adsabs.harvard.edu/abs/arXiv:2412.04443">[ADS]</a> <a class="reference external" href="https://arxiv.org/pdf/2412.04443">[pdf]</a></p>
<p>BibTeX entry for citation:</p>
<div class="highlight-bibtex notranslate"><div class="highlight"><pre><span></span><span class="nc">@ARTICLE</span><span class="p">{</span><span class="nl">hoellinger2024diagnosing</span><span class="p">,</span>
<span class="w"> </span><span class="na">author</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{Hoellinger, Tristan and Leclercq, Florent}</span><span class="p">,</span>
<span class="w"> </span><span class="na">title</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">&quot;{Diagnosing Systematic Effects Using the Inferred Initial Power Spectrum}&quot;</span><span class="p">,</span>
<span class="w"> </span><span class="na">journal</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{arXiv e-prints}</span><span class="p">,</span>
<span class="w"> </span><span class="na">keywords</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics}</span><span class="p">,</span>
<span class="w"> </span><span class="na">year</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="m">2024</span><span class="p">,</span>
<span class="w"> </span><span class="na">month</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="nv">dec</span><span class="p">,</span>
<span class="w"> </span><span class="na">eid</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{arXiv:2412.04443}</span><span class="p">,</span>
<span class="w"> </span><span class="na">pages</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{arXiv:2412.04443}</span><span class="p">,</span>
<span class="w"> </span><span class="na">doi</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{10.48550/arXiv.2412.04443}</span><span class="p">,</span>
<span class="na">archivePrefix</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{arXiv}</span><span class="p">,</span>
<span class="w"> </span><span class="na">eprint</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{2412.04443}</span><span class="p">,</span>
<span class="na">primaryClass</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{astro-ph.CO}</span><span class="p">,</span>
<span class="w"> </span><span class="na">adsurl</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{https://ui.adsabs.harvard.edu/abs/2024arXiv241204443H}</span><span class="p">,</span>
<span class="w"> </span><span class="na">adsnote</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{Provided by the SAO/NASA Astrophysics Data System}</span>
<span class="p">}</span>
</pre></div>
</div>
</section>
<section id="requirements">
<h2>Requirements<a class="headerlink" href="#requirements" title="Link to this heading"></a></h2>
<p>The code is written in Python 3.10 and depends on the following packages:</p>
<ul class="simple">
<li><p><a class="reference external" href="https://pyselfi.readthedocs.io/en/latest/"><code class="docutils literal notranslate"><span class="pre">pySELFI</span></code></a>: Python implementation of the Simulator Expansion for Likelihood-Free Inference.</p></li>
<li><p><a class="reference external" href="https://simbelmyne.readthedocs.io/en/latest/"><code class="docutils literal notranslate"><span class="pre">Simbelmynë</span></code></a>: A hierarchical probabilistic simulator for generating synthetic galaxy survey data.</p></li>
<li><p><a class="reference external" href="https://elfi.readthedocs.io/en/latest/"><code class="docutils literal notranslate"><span class="pre">ELFI</span></code></a>: A statistical software package for likelihood-free inference, implementing in particular Approximate Bayesian Computation (ABC) with a Population Monte Carlo (PMC) sampler.</p></li>
</ul>
<p>A comprehensive list of dependencies, including version specifications to ensure reproducibility, will be provided in a yaml file, along with installation instructions, in a future release.</p>
</section>
<hr class="docutils" />
<section id="license">
<h2>License<a class="headerlink" href="#license" title="Link to this heading"></a></h2>
<p>This software is distributed under the GPLv3 Licence. Please review the <a class="reference external" href="https://github.com/hoellin/selfisys_public/blob/main/LICENSE">LICENSE</a> file in the repository to understand the terms of use and ensure compliance. By downloading and using this software, you agree to the terms of the licence.</p>
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<li class="toctree-l2"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox"><code class="docutils literal notranslate"><span class="pre">HiddenBox</span></code></a><ul>
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<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.compute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.compute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.evaluate"><code class="docutils literal notranslate"><span class="pre">HiddenBox.evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_neglect_lightcone"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_neglect_lightcone</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_recompute_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_recompute_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.gravity_on"><code class="docutils literal notranslate"><span class="pre">HiddenBox.gravity_on</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.load_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.load_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.make_data"><code class="docutils literal notranslate"><span class="pre">HiddenBox.make_data()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.modified_selfi"><code class="docutils literal notranslate"><span class="pre">HiddenBox.modified_selfi</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.prefix_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.prefix_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.reset_survey"><code class="docutils literal notranslate"><span class="pre">HiddenBox.reset_survey()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.setup_only"><code class="docutils literal notranslate"><span class="pre">HiddenBox.setup_only</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_recompute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_recompute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_setup"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_setup()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.update"><code class="docutils literal notranslate"><span class="pre">HiddenBox.update()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.normalise_hb.html">normalise_hb</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.normalise_hb.html#selfisys.normalise_hb.define_normalisation"><code class="docutils literal notranslate"><span class="pre">define_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation"><code class="docutils literal notranslate"><span class="pre">worker_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_public"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_public()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_wrapper"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_wrapper()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.prior.html">prior</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.logposterior_hyperparameters_parallel"><code class="docutils literal notranslate"><span class="pre">logposterior_hyperparameters_parallel()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.perform_prior_optimisation_and_plot"><code class="docutils literal notranslate"><span class="pre">perform_prior_optimisation_and_plot()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior"><code class="docutils literal notranslate"><span class="pre">planck_prior</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.mean"><code class="docutils literal notranslate"><span class="pre">planck_prior.mean</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.inv_covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.inv_covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.Nbin_max"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_max</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.Nbin_min"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_min</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.compute"><code class="docutils literal notranslate"><span class="pre">planck_prior.compute()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.load"><code class="docutils literal notranslate"><span class="pre">planck_prior.load()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.logpdf"><code class="docutils literal notranslate"><span class="pre">planck_prior.logpdf()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.sample"><code class="docutils literal notranslate"><span class="pre">planck_prior.sample()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.save"><code class="docutils literal notranslate"><span class="pre">planck_prior.save()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.worker_class"><code class="docutils literal notranslate"><span class="pre">worker_class()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.selection_functions.html">selection_functions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.init_selection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.init_selection()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.lognormals_z_to_x"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.lognormals_z_to_x()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.r_grid"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.r_grid()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.selfi_interface.html">selfi_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.selfi_interface.html#selfisys.selfi_interface.PrintMessage"><code class="docutils literal notranslate"><span class="pre">PrintMessage()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.selfi_interface.html#selfisys.selfi_interface.indent"><code class="docutils literal notranslate"><span class="pre">indent()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.selfi_interface.html#selfisys.selfi_interface.unindent"><code class="docutils literal notranslate"><span class="pre">unindent()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.sbmy_interface.html">sbmy_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.sbmy_interface.html#selfisys.sbmy_interface.compute_Phi"><code class="docutils literal notranslate"><span class="pre">compute_Phi()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.sbmy_interface.html#selfisys.sbmy_interface.generate_white_noise_Field"><code class="docutils literal notranslate"><span class="pre">generate_white_noise_Field()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.sbmy_interface.html#selfisys.sbmy_interface.get_power_spectrum_from_cosmo"><code class="docutils literal notranslate"><span class="pre">get_power_spectrum_from_cosmo()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.sbmy_interface.html#selfisys.sbmy_interface.handle_time_stepping"><code class="docutils literal notranslate"><span class="pre">handle_time_stepping()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.sbmy_interface.html#selfisys.sbmy_interface.setup_sbmy_parfiles"><code class="docutils literal notranslate"><span class="pre">setup_sbmy_parfiles()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.grf.html">grf</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.grf.html#selfisys.grf.primordial_grf"><code class="docutils literal notranslate"><span class="pre">primordial_grf()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.utils.html">selfisys.utils package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.examples_utils">selfisys.utils.examples_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.examples_utils.clear_large_plot"><code class="docutils literal notranslate"><span class="pre">clear_large_plot()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.logger">selfisys.utils.logger module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.CustomLogger"><code class="docutils literal notranslate"><span class="pre">CustomLogger</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.CustomLogger.diagnostic"><code class="docutils literal notranslate"><span class="pre">CustomLogger.diagnostic()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler.emit"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler.emit()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.INDENT"><code class="docutils literal notranslate"><span class="pre">INDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.PrintDiagnostic"><code class="docutils literal notranslate"><span class="pre">PrintDiagnostic()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.PrintError"><code class="docutils literal notranslate"><span class="pre">PrintError()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.PrintInfo"><code class="docutils literal notranslate"><span class="pre">PrintInfo()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.PrintLeftType"><code class="docutils literal notranslate"><span class="pre">PrintLeftType()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.PrintWarning"><code class="docutils literal notranslate"><span class="pre">PrintWarning()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.UNINDENT"><code class="docutils literal notranslate"><span class="pre">UNINDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.getCustomLogger"><code class="docutils literal notranslate"><span class="pre">getCustomLogger()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.low_level">selfisys.utils.low_level module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.low_level.stderr_redirector"><code class="docutils literal notranslate"><span class="pre">stderr_redirector()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.low_level.stdout_redirector"><code class="docutils literal notranslate"><span class="pre">stdout_redirector()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.parser">selfisys.utils.parser module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.bool_sh"><code class="docutils literal notranslate"><span class="pre">bool_sh()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.check_files_exist"><code class="docutils literal notranslate"><span class="pre">check_files_exist()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.intNone"><code class="docutils literal notranslate"><span class="pre">intNone()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.joinstrs"><code class="docutils literal notranslate"><span class="pre">joinstrs()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.joinstrs_only"><code class="docutils literal notranslate"><span class="pre">joinstrs_only()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.safe_npload"><code class="docutils literal notranslate"><span class="pre">safe_npload()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.path_utils">selfisys.utils.path_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.path_utils.file_names_evaluate"><code class="docutils literal notranslate"><span class="pre">file_names_evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.path_utils.get_file_names"><code class="docutils literal notranslate"><span class="pre">get_file_names()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.plot_examples">selfisys.utils.plot_examples module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_examples.plot_comoving_distance_redshift"><code class="docutils literal notranslate"><span class="pre">plot_comoving_distance_redshift()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_examples.plot_galaxy_field_slice"><code class="docutils literal notranslate"><span class="pre">plot_galaxy_field_slice()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_examples.plot_power_spectrum"><code class="docutils literal notranslate"><span class="pre">plot_power_spectrum()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_examples.plot_selection_functions_def_in_z"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions_def_in_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_examples.redshift_distance_conversion"><code class="docutils literal notranslate"><span class="pre">redshift_distance_conversion()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_examples.relative_error_analysis"><code class="docutils literal notranslate"><span class="pre">relative_error_analysis()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.plot_params">selfisys.utils.plot_params module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.get_offset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.get_offset()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_scientific"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_scientific()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_useOffset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_useOffset()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.create_all_colormaps"><code class="docutils literal notranslate"><span class="pre">create_all_colormaps()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.create_colormap"><code class="docutils literal notranslate"><span class="pre">create_colormap()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.dynamic_text_scaling"><code class="docutils literal notranslate"><span class="pre">dynamic_text_scaling()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.get_contours"><code class="docutils literal notranslate"><span class="pre">get_contours()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.reset_plotting"><code class="docutils literal notranslate"><span class="pre">reset_plotting()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.setup_plotting"><code class="docutils literal notranslate"><span class="pre">setup_plotting()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.plot_utils">selfisys.utils.plot_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_C"><code class="docutils literal notranslate"><span class="pre">plot_C()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_fisher"><code class="docutils literal notranslate"><span class="pre">plot_fisher()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_gradients"><code class="docutils literal notranslate"><span class="pre">plot_gradients()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_histogram"><code class="docutils literal notranslate"><span class="pre">plot_histogram()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks"><code class="docutils literal notranslate"><span class="pre">plot_mocks()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks_compact"><code class="docutils literal notranslate"><span class="pre">plot_mocks_compact()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_observations"><code class="docutils literal notranslate"><span class="pre">plot_observations()</span></code></a></li>
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<section id="references">
<h1>References<a class="headerlink" href="#references" title="Link to this heading"></a></h1>
<p>If you use the SelfiSys package in your research, please cite the following paper and feel free to <a class="reference external" href="mailto:tristan&#46;hoellinger&#37;&#52;&#48;iap&#46;fr">contact the authors</a> for feedback, collaboration opportunities, or other inquiries.</p>
<p><strong>Diagnosing Systematic Effects Using the Inferred Initial Power Spectrum</strong>
<em>Hoellinger, T. and Leclercq, F., 2024</em>
<a class="reference external" href="https://arxiv.org/abs/2412.04443">arXiv:2412.04443</a> <a class="reference external" href="https://arxiv.org/abs/2412.04443">[astro-ph.CO]</a> <a class="reference external" href="https://ui.adsabs.harvard.edu/abs/arXiv:2412.04443">[ADS]</a> <a class="reference external" href="https://arxiv.org/pdf/2412.04443">[pdf]</a></p>
<p>BibTeX entry for citation:</p>
<div class="highlight-bibtex notranslate"><div class="highlight"><pre><span></span><span class="nc">@ARTICLE</span><span class="p">{</span><span class="nl">hoellinger2024diagnosing</span><span class="p">,</span>
<span class="w"> </span><span class="na">author</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{Hoellinger, Tristan and Leclercq, Florent}</span><span class="p">,</span>
<span class="w"> </span><span class="na">title</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">&quot;{Diagnosing Systematic Effects Using the Inferred Initial Power Spectrum}&quot;</span><span class="p">,</span>
<span class="w"> </span><span class="na">journal</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{arXiv e-prints}</span><span class="p">,</span>
<span class="w"> </span><span class="na">keywords</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics}</span><span class="p">,</span>
<span class="w"> </span><span class="na">year</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="m">2024</span><span class="p">,</span>
<span class="w"> </span><span class="na">month</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="nv">dec</span><span class="p">,</span>
<span class="w"> </span><span class="na">eid</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{arXiv:2412.04443}</span><span class="p">,</span>
<span class="w"> </span><span class="na">pages</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{arXiv:2412.04443}</span><span class="p">,</span>
<span class="w"> </span><span class="na">doi</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{10.48550/arXiv.2412.04443}</span><span class="p">,</span>
<span class="na">archivePrefix</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{arXiv}</span><span class="p">,</span>
<span class="w"> </span><span class="na">eprint</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{2412.04443}</span><span class="p">,</span>
<span class="na">primaryClass</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{astro-ph.CO}</span><span class="p">,</span>
<span class="w"> </span><span class="na">adsurl</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{https://ui.adsabs.harvard.edu/abs/2024arXiv241204443H}</span><span class="p">,</span>
<span class="w"> </span><span class="na">adsnote</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{Provided by the SAO/NASA Astrophysics Data System}</span>
<span class="p">}</span>
</pre></div>
</div>
<p>Other references relevant to the SelfiSys pipeline and cited in the code are listed below.</p>
<ul class="simple">
<li><p><strong>[jasche2010bayesian]</strong>
Jasche, J., Kitaura, F. S., Wandelt, B. D., and Enßlin, T. A., “Bayesian power-spectrum inference for large-scale structure data”, <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 406, no. 1, OUP, pp. 6085, 2010. <a class="reference external" href="https://doi.org/10.48550/arXiv.0911.2493">doi:10.1111/j.1365-2966.2010.16610.x</a>.</p></li>
<li><p><strong>[gil2015power]</strong>
Gil-Marín, H., “The power spectrum and bispectrum of SDSS DR11 BOSS galaxies - I. Bias and gravity”, <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 451, no. 1, OUP, pp. 539580, 2015. <a class="reference external" href="https://doi.org/10.48550/arXiv.1407.5668">doi:10.1093/mnras/stv961</a>.</p></li>
<li><p><strong>[howlett2015clustering]</strong>
Howlett, C., Ross, A. J., Samushia, L., Percival, W. J., and Manera, M., “The clustering of the SDSS main galaxy sample - II. Mock galaxy catalogues and a measurement of the growth of structure from redshift space distortions at z = 0.15”, <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 449, no. 1, OUP, pp. 848866, 2015. <a class="reference external" href="https://doi.org/10.48550/arXiv.1409.3238">doi:10.1093/mnras/stu2693</a>.</p></li>
<li><p><strong>[leclercq2019primordial]</strong>
Florent Leclercq, Wolfgang Enzi, Jens Jasche, Alan Heavens, Primordial power spectrum and cosmology from black-box galaxy surveys, Monthly Notices of the Royal Astronomical Society, Volume 490, Issue 3, December 2019, Pages 42374253, <a class="reference external" href="https://doi.org/10.1093/mnras/stz2718">doi:10.1093/mnras/stz2718</a>.</p></li>
<li><p><strong>[hoellinger2024diagnosing]</strong>
Hoellinger, T. and Leclercq, F., “Diagnosing Systematic Effects Using the Inferred Initial Power Spectrum”, <i>arXiv e-prints</i>, Art. no. arXiv:2412.04443, 2024. <a class="reference external" href="https://doi.org/10.48550/arXiv.2412.04443">doi.org:10.48550/arXiv.2412.04443</a>.</p></li>
</ul>
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<li class="toctree-l3"><a class="reference internal" href="../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_max"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_max</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_min"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_min</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.prior.html#selfisys.prior.planck_prior.compute"><code class="docutils literal notranslate"><span class="pre">planck_prior.compute()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.prior.html#selfisys.prior.planck_prior.load"><code class="docutils literal notranslate"><span class="pre">planck_prior.load()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.prior.html#selfisys.prior.planck_prior.logpdf"><code class="docutils literal notranslate"><span class="pre">planck_prior.logpdf()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.prior.html#selfisys.prior.planck_prior.sample"><code class="docutils literal notranslate"><span class="pre">planck_prior.sample()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.prior.html#selfisys.prior.planck_prior.save"><code class="docutils literal notranslate"><span class="pre">planck_prior.save()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../selfisys.prior.html#selfisys.prior.worker_class"><code class="docutils literal notranslate"><span class="pre">worker_class()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../selfisys.selection_functions.html">selection_functions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.init_selection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.init_selection()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.lognormals_z_to_x"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.lognormals_z_to_x()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.r_grid"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.r_grid()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../selfisys.selfi_interface.html">selfi_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../selfisys.selfi_interface.html#selfisys.selfi_interface.PrintMessage"><code class="docutils literal notranslate"><span class="pre">PrintMessage()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../selfisys.selfi_interface.html#selfisys.selfi_interface.indent"><code class="docutils literal notranslate"><span class="pre">indent()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../selfisys.selfi_interface.html#selfisys.selfi_interface.unindent"><code class="docutils literal notranslate"><span class="pre">unindent()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../selfisys.sbmy_interface.html">sbmy_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../selfisys.sbmy_interface.html#selfisys.sbmy_interface.compute_Phi"><code class="docutils literal notranslate"><span class="pre">compute_Phi()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../selfisys.sbmy_interface.html#selfisys.sbmy_interface.generate_white_noise_Field"><code class="docutils literal notranslate"><span class="pre">generate_white_noise_Field()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../selfisys.sbmy_interface.html#selfisys.sbmy_interface.get_power_spectrum_from_cosmo"><code class="docutils literal notranslate"><span class="pre">get_power_spectrum_from_cosmo()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../selfisys.sbmy_interface.html#selfisys.sbmy_interface.handle_time_stepping"><code class="docutils literal notranslate"><span class="pre">handle_time_stepping()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../selfisys.sbmy_interface.html#selfisys.sbmy_interface.setup_sbmy_parfiles"><code class="docutils literal notranslate"><span class="pre">setup_sbmy_parfiles()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../selfisys.grf.html">grf</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../selfisys.grf.html#selfisys.grf.primordial_grf"><code class="docutils literal notranslate"><span class="pre">primordial_grf()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../selfisys.utils.html">selfisys.utils package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../selfisys.utils.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="../selfisys.utils.html#module-selfisys.utils.examples_utils">selfisys.utils.examples_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.examples_utils.clear_large_plot"><code class="docutils literal notranslate"><span class="pre">clear_large_plot()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../selfisys.utils.html#module-selfisys.utils.logger">selfisys.utils.logger module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.logger.CustomLogger"><code class="docutils literal notranslate"><span class="pre">CustomLogger</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.logger.CustomLogger.diagnostic"><code class="docutils literal notranslate"><span class="pre">CustomLogger.diagnostic()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler.emit"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler.emit()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.logger.INDENT"><code class="docutils literal notranslate"><span class="pre">INDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.logger.PrintDiagnostic"><code class="docutils literal notranslate"><span class="pre">PrintDiagnostic()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.logger.PrintError"><code class="docutils literal notranslate"><span class="pre">PrintError()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.logger.PrintInfo"><code class="docutils literal notranslate"><span class="pre">PrintInfo()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.logger.PrintLeftType"><code class="docutils literal notranslate"><span class="pre">PrintLeftType()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.logger.PrintWarning"><code class="docutils literal notranslate"><span class="pre">PrintWarning()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.logger.UNINDENT"><code class="docutils literal notranslate"><span class="pre">UNINDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.logger.getCustomLogger"><code class="docutils literal notranslate"><span class="pre">getCustomLogger()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../selfisys.utils.html#module-selfisys.utils.low_level">selfisys.utils.low_level module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.low_level.stderr_redirector"><code class="docutils literal notranslate"><span class="pre">stderr_redirector()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.low_level.stdout_redirector"><code class="docutils literal notranslate"><span class="pre">stdout_redirector()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../selfisys.utils.html#module-selfisys.utils.parser">selfisys.utils.parser module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.parser.bool_sh"><code class="docutils literal notranslate"><span class="pre">bool_sh()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.parser.check_files_exist"><code class="docutils literal notranslate"><span class="pre">check_files_exist()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.parser.intNone"><code class="docutils literal notranslate"><span class="pre">intNone()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.parser.joinstrs"><code class="docutils literal notranslate"><span class="pre">joinstrs()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.parser.joinstrs_only"><code class="docutils literal notranslate"><span class="pre">joinstrs_only()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.parser.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.parser.safe_npload"><code class="docutils literal notranslate"><span class="pre">safe_npload()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../selfisys.utils.html#module-selfisys.utils.path_utils">selfisys.utils.path_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.path_utils.file_names_evaluate"><code class="docutils literal notranslate"><span class="pre">file_names_evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.path_utils.get_file_names"><code class="docutils literal notranslate"><span class="pre">get_file_names()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../selfisys.utils.html#module-selfisys.utils.plot_examples">selfisys.utils.plot_examples module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_examples.plot_comoving_distance_redshift"><code class="docutils literal notranslate"><span class="pre">plot_comoving_distance_redshift()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_examples.plot_galaxy_field_slice"><code class="docutils literal notranslate"><span class="pre">plot_galaxy_field_slice()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_examples.plot_power_spectrum"><code class="docutils literal notranslate"><span class="pre">plot_power_spectrum()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_examples.plot_selection_functions_def_in_z"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions_def_in_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_examples.redshift_distance_conversion"><code class="docutils literal notranslate"><span class="pre">redshift_distance_conversion()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_examples.relative_error_analysis"><code class="docutils literal notranslate"><span class="pre">relative_error_analysis()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../selfisys.utils.html#module-selfisys.utils.plot_params">selfisys.utils.plot_params module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.get_offset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.get_offset()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_scientific"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_scientific()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_useOffset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_useOffset()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_params.create_all_colormaps"><code class="docutils literal notranslate"><span class="pre">create_all_colormaps()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_params.create_colormap"><code class="docutils literal notranslate"><span class="pre">create_colormap()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_params.dynamic_text_scaling"><code class="docutils literal notranslate"><span class="pre">dynamic_text_scaling()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_params.get_contours"><code class="docutils literal notranslate"><span class="pre">get_contours()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_params.reset_plotting"><code class="docutils literal notranslate"><span class="pre">reset_plotting()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_params.setup_plotting"><code class="docutils literal notranslate"><span class="pre">setup_plotting()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../selfisys.utils.html#module-selfisys.utils.plot_utils">selfisys.utils.plot_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_utils.plot_C"><code class="docutils literal notranslate"><span class="pre">plot_C()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_utils.plot_fisher"><code class="docutils literal notranslate"><span class="pre">plot_fisher()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_utils.plot_gradients"><code class="docutils literal notranslate"><span class="pre">plot_gradients()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_utils.plot_histogram"><code class="docutils literal notranslate"><span class="pre">plot_histogram()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks"><code class="docutils literal notranslate"><span class="pre">plot_mocks()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks_compact"><code class="docutils literal notranslate"><span class="pre">plot_mocks_compact()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_utils.plot_observations"><code class="docutils literal notranslate"><span class="pre">plot_observations()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_utils.plot_prior_and_posterior_covariances"><code class="docutils literal notranslate"><span class="pre">plot_prior_and_posterior_covariances()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_utils.plot_reconstruction"><code class="docutils literal notranslate"><span class="pre">plot_reconstruction()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_utils.plot_selection_functions"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.plot_utils.plotly_3d"><code class="docutils literal notranslate"><span class="pre">plotly_3d()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../selfisys.utils.html#module-selfisys.utils.timestepping">selfisys.utils.timestepping module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.timestepping.merge_nTS"><code class="docutils literal notranslate"><span class="pre">merge_nTS()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../selfisys.utils.html#module-selfisys.utils.tools">selfisys.utils.tools module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.tools.cosmo_vector_to_Simbelmyne_dict"><code class="docutils literal notranslate"><span class="pre">cosmo_vector_to_Simbelmyne_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.tools.cosmo_vector_to_class_dict"><code class="docutils literal notranslate"><span class="pre">cosmo_vector_to_class_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.tools.custom_stat"><code class="docutils literal notranslate"><span class="pre">custom_stat()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.tools.fisher_rao"><code class="docutils literal notranslate"><span class="pre">fisher_rao()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.tools.get_k_max"><code class="docutils literal notranslate"><span class="pre">get_k_max()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.tools.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.tools.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.tools.params_ids_to_Simbelmyne_dict"><code class="docutils literal notranslate"><span class="pre">params_ids_to_Simbelmyne_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.tools.sample_omega_from_prior"><code class="docutils literal notranslate"><span class="pre">sample_omega_from_prior()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.tools.summary_to_score"><code class="docutils literal notranslate"><span class="pre">summary_to_score()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../selfisys.utils.html#module-selfisys.utils.workers">selfisys.utils.workers module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.workers.Simbelmyne_worker"><code class="docutils literal notranslate"><span class="pre">Simbelmyne_worker()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.workers.evaluate_gradient_of_Symbelmyne"><code class="docutils literal notranslate"><span class="pre">evaluate_gradient_of_Symbelmyne()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../selfisys.utils.html#selfisys.utils.workers.worker_gradient_Symbelmyne"><code class="docutils literal notranslate"><span class="pre">worker_gradient_Symbelmyne()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../selfisys.utils.html#module-selfisys.utils">Module contents</a></li>
</ul>
</li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Contribute</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../CONTRIBUTING.html">Contributing to SelfiSys</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../CONTRIBUTING.html#reporting-issues">Reporting Issues</a></li>
<li class="toctree-l2"><a class="reference internal" href="../CONTRIBUTING.html#submitting-contributions">Submitting Contributions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../CONTRIBUTING.html#style-guidelines">Style Guidelines</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../CONTRIBUTING.html#python-code">Python code</a></li>
<li class="toctree-l3"><a class="reference internal" href="../CONTRIBUTING.html#jupyter-notebooks">Jupyter Notebooks</a></li>
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<li class="toctree-l2"><a class="reference internal" href="../CONTRIBUTING.html#questions">Questions?</a></li>
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<p class="caption" role="heading"><span class="caption-text">References</span></p>
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<h1>All modules for which code is available</h1>
<ul><li><a href="selfisys/grf.html">selfisys.grf</a></li>
<li><a href="selfisys/hiddenbox.html">selfisys.hiddenbox</a></li>
<li><a href="selfisys/normalise_hb.html">selfisys.normalise_hb</a></li>
<li><a href="selfisys/prior.html">selfisys.prior</a></li>
<li><a href="selfisys/sbmy_interface.html">selfisys.sbmy_interface</a></li>
<li><a href="selfisys/selection_functions.html">selfisys.selection_functions</a></li>
<li><a href="selfisys/selfi_interface.html">selfisys.selfi_interface</a></li>
<li><a href="selfisys/setup_model.html">selfisys.setup_model</a></li>
<li><a href="selfisys/utils/examples_utils.html">selfisys.utils.examples_utils</a></li>
<li><a href="selfisys/utils/logger.html">selfisys.utils.logger</a></li>
<li><a href="selfisys/utils/low_level.html">selfisys.utils.low_level</a></li>
<li><a href="selfisys/utils/parser.html">selfisys.utils.parser</a></li>
<li><a href="selfisys/utils/path_utils.html">selfisys.utils.path_utils</a></li>
<li><a href="selfisys/utils/plot_examples.html">selfisys.utils.plot_examples</a></li>
<li><a href="selfisys/utils/plot_params.html">selfisys.utils.plot_params</a></li>
<li><a href="selfisys/utils/plot_utils.html">selfisys.utils.plot_utils</a></li>
<li><a href="selfisys/utils/timestepping.html">selfisys.utils.timestepping</a></li>
<li><a href="selfisys/utils/tools.html">selfisys.utils.tools</a></li>
<li><a href="selfisys/utils/workers.html">selfisys.utils.workers</a></li>
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<title>selfisys.grf &mdash; SelfiSys /Users/hoellinger/Library/CloudStorage/Dropbox/travail/these/science/code/SELFI/selfisys/src/ documentation</title>
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<p class="caption" role="heading"><span class="caption-text">API Documentation</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.hiddenbox.html">hiddenbox</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox"><code class="docutils literal notranslate"><span class="pre">HiddenBox</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Npop"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Npop</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Ntimesteps"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Ntimesteps</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Psingle"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Psingle</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.compute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.compute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.evaluate"><code class="docutils literal notranslate"><span class="pre">HiddenBox.evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_neglect_lightcone"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_neglect_lightcone</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_recompute_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_recompute_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.gravity_on"><code class="docutils literal notranslate"><span class="pre">HiddenBox.gravity_on</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.load_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.load_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.make_data"><code class="docutils literal notranslate"><span class="pre">HiddenBox.make_data()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.modified_selfi"><code class="docutils literal notranslate"><span class="pre">HiddenBox.modified_selfi</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.prefix_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.prefix_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.reset_survey"><code class="docutils literal notranslate"><span class="pre">HiddenBox.reset_survey()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.setup_only"><code class="docutils literal notranslate"><span class="pre">HiddenBox.setup_only</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_recompute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_recompute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_setup"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_setup()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.update"><code class="docutils literal notranslate"><span class="pre">HiddenBox.update()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.normalise_hb.html">normalise_hb</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.normalise_hb.html#selfisys.normalise_hb.define_normalisation"><code class="docutils literal notranslate"><span class="pre">define_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation"><code class="docutils literal notranslate"><span class="pre">worker_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_public"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_public()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_wrapper"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_wrapper()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.prior.html">prior</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.logposterior_hyperparameters_parallel"><code class="docutils literal notranslate"><span class="pre">logposterior_hyperparameters_parallel()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.perform_prior_optimisation_and_plot"><code class="docutils literal notranslate"><span class="pre">perform_prior_optimisation_and_plot()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior"><code class="docutils literal notranslate"><span class="pre">planck_prior</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.mean"><code class="docutils literal notranslate"><span class="pre">planck_prior.mean</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.inv_covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.inv_covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_max"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_max</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_min"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_min</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.compute"><code class="docutils literal notranslate"><span class="pre">planck_prior.compute()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.load"><code class="docutils literal notranslate"><span class="pre">planck_prior.load()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.logpdf"><code class="docutils literal notranslate"><span class="pre">planck_prior.logpdf()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.sample"><code class="docutils literal notranslate"><span class="pre">planck_prior.sample()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.save"><code class="docutils literal notranslate"><span class="pre">planck_prior.save()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.worker_class"><code class="docutils literal notranslate"><span class="pre">worker_class()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.selection_functions.html">selection_functions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.init_selection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.init_selection()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.lognormals_z_to_x"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.lognormals_z_to_x()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.r_grid"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.r_grid()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.selfi_interface.html">selfi_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.selfi_interface.html#selfisys.selfi_interface.PrintMessage"><code class="docutils literal notranslate"><span class="pre">PrintMessage()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.selfi_interface.html#selfisys.selfi_interface.indent"><code class="docutils literal notranslate"><span class="pre">indent()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.selfi_interface.html#selfisys.selfi_interface.unindent"><code class="docutils literal notranslate"><span class="pre">unindent()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.sbmy_interface.html">sbmy_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.compute_Phi"><code class="docutils literal notranslate"><span class="pre">compute_Phi()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.generate_white_noise_Field"><code class="docutils literal notranslate"><span class="pre">generate_white_noise_Field()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.get_power_spectrum_from_cosmo"><code class="docutils literal notranslate"><span class="pre">get_power_spectrum_from_cosmo()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.handle_time_stepping"><code class="docutils literal notranslate"><span class="pre">handle_time_stepping()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.setup_sbmy_parfiles"><code class="docutils literal notranslate"><span class="pre">setup_sbmy_parfiles()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.grf.html">grf</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.grf.html#selfisys.grf.primordial_grf"><code class="docutils literal notranslate"><span class="pre">primordial_grf()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.utils.html">selfisys.utils package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.examples_utils">selfisys.utils.examples_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.examples_utils.clear_large_plot"><code class="docutils literal notranslate"><span class="pre">clear_large_plot()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.logger">selfisys.utils.logger module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.CustomLogger"><code class="docutils literal notranslate"><span class="pre">CustomLogger</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.CustomLogger.diagnostic"><code class="docutils literal notranslate"><span class="pre">CustomLogger.diagnostic()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler.emit"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler.emit()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.INDENT"><code class="docutils literal notranslate"><span class="pre">INDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.PrintDiagnostic"><code class="docutils literal notranslate"><span class="pre">PrintDiagnostic()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.PrintError"><code class="docutils literal notranslate"><span class="pre">PrintError()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.PrintInfo"><code class="docutils literal notranslate"><span class="pre">PrintInfo()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.PrintLeftType"><code class="docutils literal notranslate"><span class="pre">PrintLeftType()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.PrintWarning"><code class="docutils literal notranslate"><span class="pre">PrintWarning()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.UNINDENT"><code class="docutils literal notranslate"><span class="pre">UNINDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.getCustomLogger"><code class="docutils literal notranslate"><span class="pre">getCustomLogger()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.low_level">selfisys.utils.low_level module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.low_level.stderr_redirector"><code class="docutils literal notranslate"><span class="pre">stderr_redirector()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.low_level.stdout_redirector"><code class="docutils literal notranslate"><span class="pre">stdout_redirector()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.parser">selfisys.utils.parser module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.bool_sh"><code class="docutils literal notranslate"><span class="pre">bool_sh()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.check_files_exist"><code class="docutils literal notranslate"><span class="pre">check_files_exist()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.intNone"><code class="docutils literal notranslate"><span class="pre">intNone()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.joinstrs"><code class="docutils literal notranslate"><span class="pre">joinstrs()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.joinstrs_only"><code class="docutils literal notranslate"><span class="pre">joinstrs_only()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
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<h1>Source code for selfisys.grf</h1><div class="highlight"><pre>
<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="c1"># Copyright (C) 2024 Tristan Hoellinger</span>
<span class="c1"># Distributed under the GNU General Public License v3.0 (GPLv3).</span>
<span class="c1"># See the LICENSE file in the root directory for details.</span>
<span class="c1"># SPDX-License-Identifier: GPL-3.0-or-later</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="n">__author__</span> <span class="o">=</span> <span class="s2">&quot;Tristan Hoellinger&quot;</span>
<span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;0.1.0&quot;</span>
<span class="n">__date__</span> <span class="o">=</span> <span class="s2">&quot;2024&quot;</span>
<span class="n">__license__</span> <span class="o">=</span> <span class="s2">&quot;GPLv3&quot;</span>
<span class="sd">&quot;&quot;&quot;Tools for generating Gaussian random fields from given power spectra.</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="kn">from</span> <span class="nn">selfisys.utils.logger</span> <span class="kn">import</span> <span class="n">getCustomLogger</span>
<span class="n">logger</span> <span class="o">=</span> <span class="n">getCustomLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>
<div class="viewcode-block" id="primordial_grf">
<a class="viewcode-back" href="../../selfisys.grf.html#selfisys.grf.primordial_grf">[docs]</a>
<span class="k">def</span> <span class="nf">primordial_grf</span><span class="p">(</span>
<span class="n">L</span><span class="p">,</span>
<span class="n">N</span><span class="p">,</span>
<span class="n">seedphases</span><span class="p">,</span>
<span class="n">fname_powerspectrum</span><span class="p">,</span>
<span class="n">fname_outputinitialdensity</span><span class="p">,</span>
<span class="n">force_sim</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
<span class="n">return_g</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
<span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
<span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Generate a Gaussian random field from a specified input power</span>
<span class="sd"> spectrum.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> L : float</span>
<span class="sd"> Side length of the simulation box in Mpc/h.</span>
<span class="sd"> N : int</span>
<span class="sd"> Grid resolution (number of cells per dimension).</span>
<span class="sd"> seedphases : int</span>
<span class="sd"> Seed for random phase generation (for reproducibility).</span>
<span class="sd"> fname_powerspectrum : str</span>
<span class="sd"> File path to the input power spectrum.</span>
<span class="sd"> fname_outputinitialdensity : str</span>
<span class="sd"> File path to store the generated initial density field.</span>
<span class="sd"> force_sim : bool, optional</span>
<span class="sd"> If True, regenerate the GRF even if the output file exists.</span>
<span class="sd"> Default is False.</span>
<span class="sd"> return_g : bool, optional</span>
<span class="sd"> If True, return the GRF as a numpy array. Default is False.</span>
<span class="sd"> verbose : int, optional</span>
<span class="sd"> Verbosity level (0 = silent, 1 = progress, 2 = detailed).</span>
<span class="sd"> Default is 0.</span>
<span class="sd"> Raises</span>
<span class="sd"> ------</span>
<span class="sd"> OSError</span>
<span class="sd"> If the power spectrum file cannot be read.</span>
<span class="sd"> RuntimeError</span>
<span class="sd"> If an unexpected error occurs during power spectrum reading.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> numpy.ndarray or None</span>
<span class="sd"> The GRF data if `return_g` is True, otherwise None.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">from</span> <span class="nn">os.path</span> <span class="kn">import</span> <span class="n">exists</span>
<span class="kn">from</span> <span class="nn">gc</span> <span class="kn">import</span> <span class="n">collect</span>
<span class="kn">from</span> <span class="nn">pysbmy.power</span> <span class="kn">import</span> <span class="n">PowerSpectrum</span>
<span class="kn">from</span> <span class="nn">pysbmy.field</span> <span class="kn">import</span> <span class="n">Field</span>
<span class="c1"># Skip simulation if output already exists and overwrite is not requested</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">force_sim</span> <span class="ow">and</span> <span class="n">exists</span><span class="p">(</span><span class="n">fname_outputinitialdensity</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">pysbmy.field</span> <span class="kn">import</span> <span class="n">read_basefield</span>
<span class="k">if</span> <span class="n">verbose</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">fname_outputinitialdensity</span><span class="si">}</span><span class="s2"> already exists. Skipping simulation.&quot;</span><span class="p">)</span>
<span class="k">return</span> <span class="n">read_basefield</span><span class="p">(</span><span class="n">fname_outputinitialdensity</span><span class="p">)</span><span class="o">.</span><span class="n">data</span> <span class="k">if</span> <span class="n">return_g</span> <span class="k">else</span> <span class="kc">None</span>
<span class="c1"># Read the power spectrum</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">P</span> <span class="o">=</span> <span class="n">PowerSpectrum</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">fname_powerspectrum</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">OSError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
<span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Unable to read power spectrum file: </span><span class="si">{</span><span class="n">fname_powerspectrum</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="k">raise</span>
<span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
<span class="n">logger</span><span class="o">.</span><span class="n">exception</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Unexpected error while reading power spectrum: </span><span class="si">{</span><span class="n">e</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="k">raise</span>
<span class="c1"># Generate the Gaussian random field</span>
<span class="k">if</span> <span class="n">verbose</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
<span class="n">g</span> <span class="o">=</span> <span class="n">Field</span><span class="o">.</span><span class="n">GRF</span><span class="p">(</span><span class="n">L</span><span class="p">,</span> <span class="n">L</span><span class="p">,</span> <span class="n">L</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">N</span><span class="p">,</span> <span class="n">N</span><span class="p">,</span> <span class="n">N</span><span class="p">,</span> <span class="n">P</span><span class="p">,</span> <span class="mf">1e3</span><span class="p">,</span> <span class="n">seedphases</span><span class="p">)</span> <span class="c1"># a_init = 1e3</span>
<span class="k">else</span><span class="p">:</span>
<span class="kn">from</span> <span class="nn">selfisys.utils.low_level</span> <span class="kn">import</span> <span class="n">stdout_redirector</span>
<span class="kn">from</span> <span class="nn">io</span> <span class="kn">import</span> <span class="n">BytesIO</span>
<span class="c1"># Suppress standard output to avoid cluttering logs</span>
<span class="k">with</span> <span class="n">BytesIO</span><span class="p">()</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
<span class="k">with</span> <span class="n">stdout_redirector</span><span class="p">(</span><span class="n">f</span><span class="p">):</span>
<span class="n">g</span> <span class="o">=</span> <span class="n">Field</span><span class="o">.</span><span class="n">GRF</span><span class="p">(</span><span class="n">L</span><span class="p">,</span> <span class="n">L</span><span class="p">,</span> <span class="n">L</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">N</span><span class="p">,</span> <span class="n">N</span><span class="p">,</span> <span class="n">N</span><span class="p">,</span> <span class="n">P</span><span class="p">,</span> <span class="mf">1e3</span><span class="p">,</span> <span class="n">seedphases</span><span class="p">)</span>
<span class="c1"># Write the field to disk</span>
<span class="n">g</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">fname_outputinitialdensity</span><span class="p">)</span>
<span class="n">field</span> <span class="o">=</span> <span class="n">g</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span> <span class="k">if</span> <span class="n">return_g</span> <span class="k">else</span> <span class="kc">None</span>
<span class="c1"># Free memory</span>
<span class="k">del</span> <span class="n">g</span>
<span class="n">collect</span><span class="p">()</span>
<span class="k">return</span> <span class="n">field</span></div>
</pre></div>
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<p class="caption" role="heading"><span class="caption-text">API Documentation</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.hiddenbox.html">hiddenbox</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox"><code class="docutils literal notranslate"><span class="pre">HiddenBox</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Npop"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Npop</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Ntimesteps"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Ntimesteps</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Psingle"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Psingle</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.compute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.compute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.evaluate"><code class="docutils literal notranslate"><span class="pre">HiddenBox.evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_neglect_lightcone"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_neglect_lightcone</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_recompute_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_recompute_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.gravity_on"><code class="docutils literal notranslate"><span class="pre">HiddenBox.gravity_on</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.load_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.load_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.make_data"><code class="docutils literal notranslate"><span class="pre">HiddenBox.make_data()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.modified_selfi"><code class="docutils literal notranslate"><span class="pre">HiddenBox.modified_selfi</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.prefix_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.prefix_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.reset_survey"><code class="docutils literal notranslate"><span class="pre">HiddenBox.reset_survey()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.setup_only"><code class="docutils literal notranslate"><span class="pre">HiddenBox.setup_only</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_recompute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_recompute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_setup"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_setup()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.update"><code class="docutils literal notranslate"><span class="pre">HiddenBox.update()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.normalise_hb.html">normalise_hb</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.normalise_hb.html#selfisys.normalise_hb.define_normalisation"><code class="docutils literal notranslate"><span class="pre">define_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation"><code class="docutils literal notranslate"><span class="pre">worker_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_public"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_public()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_wrapper"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_wrapper()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.prior.html">prior</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.logposterior_hyperparameters_parallel"><code class="docutils literal notranslate"><span class="pre">logposterior_hyperparameters_parallel()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.perform_prior_optimisation_and_plot"><code class="docutils literal notranslate"><span class="pre">perform_prior_optimisation_and_plot()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior"><code class="docutils literal notranslate"><span class="pre">planck_prior</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.mean"><code class="docutils literal notranslate"><span class="pre">planck_prior.mean</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.inv_covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.inv_covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_max"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_max</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_min"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_min</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.compute"><code class="docutils literal notranslate"><span class="pre">planck_prior.compute()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.load"><code class="docutils literal notranslate"><span class="pre">planck_prior.load()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.logpdf"><code class="docutils literal notranslate"><span class="pre">planck_prior.logpdf()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.sample"><code class="docutils literal notranslate"><span class="pre">planck_prior.sample()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.save"><code class="docutils literal notranslate"><span class="pre">planck_prior.save()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.worker_class"><code class="docutils literal notranslate"><span class="pre">worker_class()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.selection_functions.html">selection_functions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.init_selection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.init_selection()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.lognormals_z_to_x"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.lognormals_z_to_x()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.r_grid"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.r_grid()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.selfi_interface.html">selfi_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.selfi_interface.html#selfisys.selfi_interface.PrintMessage"><code class="docutils literal notranslate"><span class="pre">PrintMessage()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.selfi_interface.html#selfisys.selfi_interface.indent"><code class="docutils literal notranslate"><span class="pre">indent()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.selfi_interface.html#selfisys.selfi_interface.unindent"><code class="docutils literal notranslate"><span class="pre">unindent()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.sbmy_interface.html">sbmy_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.compute_Phi"><code class="docutils literal notranslate"><span class="pre">compute_Phi()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.generate_white_noise_Field"><code class="docutils literal notranslate"><span class="pre">generate_white_noise_Field()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.get_power_spectrum_from_cosmo"><code class="docutils literal notranslate"><span class="pre">get_power_spectrum_from_cosmo()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.handle_time_stepping"><code class="docutils literal notranslate"><span class="pre">handle_time_stepping()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.setup_sbmy_parfiles"><code class="docutils literal notranslate"><span class="pre">setup_sbmy_parfiles()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.grf.html">grf</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.grf.html#selfisys.grf.primordial_grf"><code class="docutils literal notranslate"><span class="pre">primordial_grf()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.utils.html">selfisys.utils package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.examples_utils">selfisys.utils.examples_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.examples_utils.clear_large_plot"><code class="docutils literal notranslate"><span class="pre">clear_large_plot()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.logger">selfisys.utils.logger module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.CustomLogger"><code class="docutils literal notranslate"><span class="pre">CustomLogger</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.CustomLogger.diagnostic"><code class="docutils literal notranslate"><span class="pre">CustomLogger.diagnostic()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler.emit"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler.emit()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.INDENT"><code class="docutils literal notranslate"><span class="pre">INDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.PrintDiagnostic"><code class="docutils literal notranslate"><span class="pre">PrintDiagnostic()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.PrintError"><code class="docutils literal notranslate"><span class="pre">PrintError()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.PrintInfo"><code class="docutils literal notranslate"><span class="pre">PrintInfo()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.PrintLeftType"><code class="docutils literal notranslate"><span class="pre">PrintLeftType()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.PrintWarning"><code class="docutils literal notranslate"><span class="pre">PrintWarning()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.UNINDENT"><code class="docutils literal notranslate"><span class="pre">UNINDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.getCustomLogger"><code class="docutils literal notranslate"><span class="pre">getCustomLogger()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.low_level">selfisys.utils.low_level module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.low_level.stderr_redirector"><code class="docutils literal notranslate"><span class="pre">stderr_redirector()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.low_level.stdout_redirector"><code class="docutils literal notranslate"><span class="pre">stdout_redirector()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.parser">selfisys.utils.parser module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.bool_sh"><code class="docutils literal notranslate"><span class="pre">bool_sh()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.check_files_exist"><code class="docutils literal notranslate"><span class="pre">check_files_exist()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.intNone"><code class="docutils literal notranslate"><span class="pre">intNone()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.joinstrs"><code class="docutils literal notranslate"><span class="pre">joinstrs()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.joinstrs_only"><code class="docutils literal notranslate"><span class="pre">joinstrs_only()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.safe_npload"><code class="docutils literal notranslate"><span class="pre">safe_npload()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.path_utils">selfisys.utils.path_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.path_utils.file_names_evaluate"><code class="docutils literal notranslate"><span class="pre">file_names_evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.path_utils.get_file_names"><code class="docutils literal notranslate"><span class="pre">get_file_names()</span></code></a></li>
</ul>
</li>
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<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11</span></code></a><ul>
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<h1>Source code for selfisys.normalise_hb</h1><div class="highlight"><pre>
<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="c1"># Copyright (C) 2024 Tristan Hoellinger</span>
<span class="c1"># Distributed under the GNU General Public License v3.0 (GPLv3).</span>
<span class="c1"># See the LICENSE file in the root directory for details.</span>
<span class="c1"># SPDX-License-Identifier: GPL-3.0-or-later</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="n">__author__</span> <span class="o">=</span> <span class="s2">&quot;Tristan Hoellinger&quot;</span>
<span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;0.1.0&quot;</span>
<span class="n">__date__</span> <span class="o">=</span> <span class="s2">&quot;2024&quot;</span>
<span class="n">__license__</span> <span class="o">=</span> <span class="s2">&quot;GPLv3&quot;</span>
<span class="sd">&quot;&quot;&quot;Tools to define normalisation constants for the hidden box.&quot;&quot;&quot;</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Tuple</span><span class="p">,</span> <span class="n">Dict</span><span class="p">,</span> <span class="n">Any</span>
<span class="kn">from</span> <span class="nn">selfisys.global_parameters</span> <span class="kn">import</span> <span class="n">MIN_K_NORMALISATION</span>
<span class="kn">from</span> <span class="nn">selfisys.hiddenbox</span> <span class="kn">import</span> <span class="n">HiddenBox</span>
<div class="viewcode-block" id="worker_normalisation">
<a class="viewcode-back" href="../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation">[docs]</a>
<span class="k">def</span> <span class="nf">worker_normalisation</span><span class="p">(</span>
<span class="n">hidden_box</span><span class="p">:</span> <span class="n">HiddenBox</span><span class="p">,</span>
<span class="n">params</span><span class="p">:</span> <span class="n">Tuple</span><span class="p">[</span><span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">],</span> <span class="nb">list</span><span class="p">,</span> <span class="nb">list</span><span class="p">,</span> <span class="nb">bool</span><span class="p">],</span>
<span class="p">)</span> <span class="o">-&gt;</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Worker function to compute the normalisation constants,</span>
<span class="sd"> compatible with Python multiprocessing.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> hidden_box : HiddenBox</span>
<span class="sd"> Instance of the HiddenBox class.</span>
<span class="sd"> params : tuple</span>
<span class="sd"> A tuple containing (cosmo, seedphase, seednoise, force).</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> phi : ndarray</span>
<span class="sd"> Computed summary statistics.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="p">(</span>
<span class="n">cosmo</span><span class="p">,</span>
<span class="n">seedphase</span><span class="p">,</span>
<span class="n">seednoise</span><span class="p">,</span>
<span class="n">force</span><span class="p">,</span>
<span class="p">)</span> <span class="o">=</span> <span class="n">params</span>
<span class="n">name</span> <span class="o">=</span> <span class="p">(</span>
<span class="s2">&quot;norm&quot;</span>
<span class="o">+</span> <span class="s2">&quot;__&quot;</span>
<span class="o">+</span> <span class="s2">&quot;_&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="nb">str</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">s</span><span class="p">))</span> <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">seedphase</span><span class="p">])</span>
<span class="o">+</span> <span class="s2">&quot;__&quot;</span>
<span class="o">+</span> <span class="s2">&quot;_&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="nb">str</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">s</span><span class="p">))</span> <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">seednoise</span><span class="p">])</span>
<span class="p">)</span>
<span class="k">if</span> <span class="n">hidden_box</span><span class="o">.</span><span class="n">verbosity</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
<span class="n">hidden_box</span><span class="o">.</span><span class="n">_PrintMessage</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="s2">&quot;Running simulation...&quot;</span><span class="p">)</span>
<span class="n">hidden_box</span><span class="o">.</span><span class="n">_indent</span><span class="p">()</span>
<span class="n">phi</span> <span class="o">=</span> <span class="n">hidden_box</span><span class="o">.</span><span class="n">make_data</span><span class="p">(</span>
<span class="n">cosmo</span><span class="p">,</span>
<span class="n">name</span><span class="p">,</span>
<span class="n">seedphase</span><span class="p">,</span>
<span class="n">seednoise</span><span class="p">,</span>
<span class="n">force</span><span class="p">,</span>
<span class="n">force</span><span class="p">,</span>
<span class="n">force</span><span class="p">,</span>
<span class="n">force</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">hidden_box</span><span class="o">.</span><span class="n">_unindent</span><span class="p">()</span>
<span class="k">elif</span> <span class="n">hidden_box</span><span class="o">.</span><span class="n">verbosity</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
<span class="kn">from</span> <span class="nn">selfisys.utils.low_level</span> <span class="kn">import</span> <span class="p">(</span>
<span class="n">stdout_redirector</span><span class="p">,</span>
<span class="p">)</span>
<span class="kn">from</span> <span class="nn">io</span> <span class="kn">import</span> <span class="n">BytesIO</span>
<span class="n">f</span> <span class="o">=</span> <span class="n">BytesIO</span><span class="p">()</span>
<span class="k">with</span> <span class="n">stdout_redirector</span><span class="p">(</span><span class="n">f</span><span class="p">):</span>
<span class="n">phi</span> <span class="o">=</span> <span class="n">hidden_box</span><span class="o">.</span><span class="n">make_data</span><span class="p">(</span>
<span class="n">cosmo</span><span class="p">,</span>
<span class="n">name</span><span class="p">,</span>
<span class="n">seedphase</span><span class="p">,</span>
<span class="n">seednoise</span><span class="p">,</span>
<span class="n">force</span><span class="p">,</span>
<span class="n">force</span><span class="p">,</span>
<span class="n">force</span><span class="p">,</span>
<span class="n">force</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">f</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="k">else</span><span class="p">:</span>
<span class="kn">from</span> <span class="nn">selfisys.utils.low_level</span> <span class="kn">import</span> <span class="p">(</span>
<span class="n">stdout_redirector</span><span class="p">,</span>
<span class="n">stderr_redirector</span><span class="p">,</span>
<span class="p">)</span>
<span class="kn">from</span> <span class="nn">io</span> <span class="kn">import</span> <span class="n">BytesIO</span>
<span class="n">f</span> <span class="o">=</span> <span class="n">BytesIO</span><span class="p">()</span>
<span class="n">g</span> <span class="o">=</span> <span class="n">BytesIO</span><span class="p">()</span>
<span class="k">with</span> <span class="n">stdout_redirector</span><span class="p">(</span><span class="n">f</span><span class="p">),</span> <span class="n">stderr_redirector</span><span class="p">(</span><span class="n">g</span><span class="p">):</span>
<span class="n">phi</span> <span class="o">=</span> <span class="n">hidden_box</span><span class="o">.</span><span class="n">make_data</span><span class="p">(</span>
<span class="n">cosmo</span><span class="p">,</span>
<span class="n">name</span><span class="p">,</span>
<span class="n">seedphase</span><span class="p">,</span>
<span class="n">seednoise</span><span class="p">,</span>
<span class="n">force</span><span class="p">,</span>
<span class="n">force</span><span class="p">,</span>
<span class="n">force</span><span class="p">,</span>
<span class="n">force</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">f</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="n">g</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="k">return</span> <span class="n">phi</span></div>
<div class="viewcode-block" id="worker_normalisation_wrapper">
<a class="viewcode-back" href="../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_wrapper">[docs]</a>
<span class="k">def</span> <span class="nf">worker_normalisation_wrapper</span><span class="p">(</span><span class="n">args</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Wrapper function for the worker_normalisation function.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> args : tuple</span>
<span class="sd"> A tuple containing (hidden_box, params).</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> phi : ndarray</span>
<span class="sd"> Computed summary statistics.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">hidden_box</span><span class="p">,</span> <span class="n">params</span> <span class="o">=</span> <span class="n">args</span>
<span class="k">return</span> <span class="n">worker_normalisation</span><span class="p">(</span><span class="n">hidden_box</span><span class="p">,</span> <span class="n">params</span><span class="p">)</span></div>
<div class="viewcode-block" id="worker_normalisation_public">
<a class="viewcode-back" href="../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_public">[docs]</a>
<span class="k">def</span> <span class="nf">worker_normalisation_public</span><span class="p">(</span>
<span class="n">hidden_box</span><span class="p">,</span>
<span class="n">cosmo</span><span class="p">:</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">],</span>
<span class="n">N</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
<span class="n">i</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
<span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Run the i-th simulation required to compute the normalisation</span>
<span class="sd"> constants.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> hidden_box : HiddenBox</span>
<span class="sd"> Instance of the HiddenBox class.</span>
<span class="sd"> cosmo : dict</span>
<span class="sd"> Cosmological and some infrastructure parameters.</span>
<span class="sd"> N : int</span>
<span class="sd"> Total number of realisations required.</span>
<span class="sd"> i : int</span>
<span class="sd"> Index of the simulation to be computed.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">params</span> <span class="o">=</span> <span class="p">(</span>
<span class="n">cosmo</span><span class="p">,</span>
<span class="p">[</span>
<span class="n">i</span><span class="p">,</span>
<span class="n">hidden_box</span><span class="o">.</span><span class="n">_HiddenBox__global_seednorm</span><span class="p">,</span>
<span class="p">],</span>
<span class="p">[</span>
<span class="n">i</span> <span class="o">+</span> <span class="n">N</span><span class="p">,</span>
<span class="n">hidden_box</span><span class="o">.</span><span class="n">_HiddenBox__global_seednorm</span><span class="p">,</span>
<span class="p">],</span>
<span class="kc">False</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">worker_normalisation</span><span class="p">(</span><span class="n">hidden_box</span><span class="p">,</span> <span class="n">params</span><span class="p">)</span></div>
<div class="viewcode-block" id="define_normalisation">
<a class="viewcode-back" href="../../selfisys.normalise_hb.html#selfisys.normalise_hb.define_normalisation">[docs]</a>
<span class="k">def</span> <span class="nf">define_normalisation</span><span class="p">(</span>
<span class="n">hidden_box</span><span class="p">:</span> <span class="n">HiddenBox</span><span class="p">,</span>
<span class="n">Pbins</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
<span class="n">cosmo</span><span class="p">:</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">],</span>
<span class="n">N</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
<span class="n">min_k_norma</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="n">MIN_K_NORMALISATION</span><span class="p">,</span>
<span class="n">npar</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
<span class="n">force</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
<span class="p">)</span> <span class="o">-&gt;</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Define the normalisation constants for the HiddenBox instance.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> hidden_box : HiddenBox</span>
<span class="sd"> Instance of the HiddenBox class.</span>
<span class="sd"> Pbins : ndarray</span>
<span class="sd"> Array of P bin values.</span>
<span class="sd"> cosmo : dict</span>
<span class="sd"> Cosmological and infrastructure parameters.</span>
<span class="sd"> N : int</span>
<span class="sd"> Number of realisations required.</span>
<span class="sd"> min_k_norma : float, optional</span>
<span class="sd"> Minimum k value to compute the normalisation constants.</span>
<span class="sd"> npar : int, optional</span>
<span class="sd"> Number of parallel processes to use. Default is 1.</span>
<span class="sd"> force : bool, optional</span>
<span class="sd"> If True, force recomputation. Default is False.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> norm_csts : ndarray</span>
<span class="sd"> Normalisation constants for the HiddenBox instance.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">import</span> <span class="nn">tqdm.auto</span> <span class="k">as</span> <span class="nn">tqdm</span>
<span class="kn">from</span> <span class="nn">multiprocessing</span> <span class="kn">import</span> <span class="n">Pool</span>
<span class="n">hidden_box</span><span class="o">.</span><span class="n">_PrintMessage</span><span class="p">(</span>
<span class="mi">0</span><span class="p">,</span>
<span class="s2">&quot;Defining normalisation constants...&quot;</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">hidden_box</span><span class="o">.</span><span class="n">_indent</span><span class="p">()</span>
<span class="n">indices</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">Pbins</span> <span class="o">&gt;</span> <span class="n">min_k_norma</span><span class="p">)</span>
<span class="n">tasks</span> <span class="o">=</span> <span class="p">[</span>
<span class="p">(</span>
<span class="n">hidden_box</span><span class="p">,</span>
<span class="p">(</span>
<span class="n">cosmo</span><span class="p">,</span>
<span class="p">[</span>
<span class="n">i</span><span class="p">,</span>
<span class="n">hidden_box</span><span class="o">.</span><span class="n">_HiddenBox__global_seednorm</span><span class="p">,</span>
<span class="p">],</span>
<span class="p">[</span>
<span class="n">i</span> <span class="o">+</span> <span class="n">N</span><span class="p">,</span>
<span class="n">hidden_box</span><span class="o">.</span><span class="n">_HiddenBox__global_seednorm</span><span class="p">,</span>
<span class="p">],</span>
<span class="n">force</span><span class="p">,</span>
<span class="p">),</span>
<span class="p">)</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">N</span><span class="p">)</span>
<span class="p">]</span>
<span class="n">ncors</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">cpu_count</span><span class="p">()</span>
<span class="n">nprocs</span> <span class="o">=</span> <span class="nb">min</span><span class="p">(</span><span class="n">npar</span><span class="p">,</span> <span class="n">ncors</span><span class="p">)</span>
<span class="n">norm_csts_list</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="n">hidden_box</span><span class="o">.</span><span class="n">_Npop</span><span class="p">,</span> <span class="n">N</span><span class="p">))</span>
<span class="k">if</span> <span class="n">npar</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
<span class="k">with</span> <span class="n">Pool</span><span class="p">(</span><span class="n">nprocs</span><span class="p">)</span> <span class="k">as</span> <span class="n">p</span><span class="p">:</span>
<span class="k">for</span> <span class="n">j</span><span class="p">,</span> <span class="n">val</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span>
<span class="n">tqdm</span><span class="o">.</span><span class="n">tqdm</span><span class="p">(</span>
<span class="n">p</span><span class="o">.</span><span class="n">imap</span><span class="p">(</span>
<span class="n">worker_normalisation_wrapper</span><span class="p">,</span>
<span class="n">tasks</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">total</span><span class="o">=</span><span class="n">N</span><span class="p">,</span>
<span class="p">)</span>
<span class="p">):</span>
<span class="n">norm_csts_list</span><span class="p">[:,</span> <span class="n">j</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span>
<span class="p">[</span>
<span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span>
<span class="n">val</span><span class="p">[</span><span class="n">i</span> <span class="o">*</span> <span class="n">hidden_box</span><span class="o">.</span><span class="n">Psingle</span> <span class="p">:</span> <span class="p">(</span><span class="n">i</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="o">*</span> <span class="n">hidden_box</span><span class="o">.</span><span class="n">Psingle</span><span class="p">][</span><span class="n">indices</span><span class="p">]</span>
<span class="p">)</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">hidden_box</span><span class="o">.</span><span class="n">_Npop</span><span class="p">)</span>
<span class="p">]</span>
<span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">for</span> <span class="n">j</span><span class="p">,</span> <span class="n">val</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span>
<span class="n">tqdm</span><span class="o">.</span><span class="n">tqdm</span><span class="p">(</span>
<span class="nb">map</span><span class="p">(</span>
<span class="n">worker_normalisation_wrapper</span><span class="p">,</span>
<span class="n">tasks</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">total</span><span class="o">=</span><span class="n">N</span><span class="p">,</span>
<span class="p">)</span>
<span class="p">):</span>
<span class="n">val</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">val</span><span class="p">)</span>
<span class="n">norm_csts_list</span><span class="p">[:,</span> <span class="n">j</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span>
<span class="p">[</span>
<span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">val</span><span class="p">[</span><span class="n">i</span> <span class="o">*</span> <span class="n">hidden_box</span><span class="o">.</span><span class="n">Psingle</span> <span class="p">:</span> <span class="p">(</span><span class="n">i</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="o">*</span> <span class="n">hidden_box</span><span class="o">.</span><span class="n">Psingle</span><span class="p">][</span><span class="n">indices</span><span class="p">])</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">hidden_box</span><span class="o">.</span><span class="n">_Npop</span><span class="p">)</span>
<span class="p">]</span>
<span class="p">)</span>
<span class="n">norm_csts</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">norm_csts_list</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">hidden_box</span><span class="o">.</span><span class="n">_unindent</span><span class="p">()</span>
<span class="n">hidden_box</span><span class="o">.</span><span class="n">_PrintMessage</span><span class="p">(</span>
<span class="mi">0</span><span class="p">,</span>
<span class="s2">&quot;Defining normalisation constants done.&quot;</span><span class="p">,</span>
<span class="p">)</span>
<span class="k">return</span> <span class="n">norm_csts</span></div>
</pre></div>
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<p class="caption" role="heading"><span class="caption-text">API Documentation</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.hiddenbox.html">hiddenbox</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox"><code class="docutils literal notranslate"><span class="pre">HiddenBox</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Npop"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Npop</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Ntimesteps"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Ntimesteps</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Psingle"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Psingle</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.compute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.compute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.evaluate"><code class="docutils literal notranslate"><span class="pre">HiddenBox.evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_neglect_lightcone"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_neglect_lightcone</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_recompute_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_recompute_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.gravity_on"><code class="docutils literal notranslate"><span class="pre">HiddenBox.gravity_on</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.load_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.load_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.make_data"><code class="docutils literal notranslate"><span class="pre">HiddenBox.make_data()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.modified_selfi"><code class="docutils literal notranslate"><span class="pre">HiddenBox.modified_selfi</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.prefix_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.prefix_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.reset_survey"><code class="docutils literal notranslate"><span class="pre">HiddenBox.reset_survey()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.setup_only"><code class="docutils literal notranslate"><span class="pre">HiddenBox.setup_only</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_recompute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_recompute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_setup"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_setup()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.update"><code class="docutils literal notranslate"><span class="pre">HiddenBox.update()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.normalise_hb.html">normalise_hb</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.normalise_hb.html#selfisys.normalise_hb.define_normalisation"><code class="docutils literal notranslate"><span class="pre">define_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation"><code class="docutils literal notranslate"><span class="pre">worker_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_public"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_public()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_wrapper"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_wrapper()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.prior.html">prior</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.logposterior_hyperparameters_parallel"><code class="docutils literal notranslate"><span class="pre">logposterior_hyperparameters_parallel()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.perform_prior_optimisation_and_plot"><code class="docutils literal notranslate"><span class="pre">perform_prior_optimisation_and_plot()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior"><code class="docutils literal notranslate"><span class="pre">planck_prior</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.mean"><code class="docutils literal notranslate"><span class="pre">planck_prior.mean</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.inv_covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.inv_covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_max"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_max</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_min"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_min</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.compute"><code class="docutils literal notranslate"><span class="pre">planck_prior.compute()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.load"><code class="docutils literal notranslate"><span class="pre">planck_prior.load()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.logpdf"><code class="docutils literal notranslate"><span class="pre">planck_prior.logpdf()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.sample"><code class="docutils literal notranslate"><span class="pre">planck_prior.sample()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.save"><code class="docutils literal notranslate"><span class="pre">planck_prior.save()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.worker_class"><code class="docutils literal notranslate"><span class="pre">worker_class()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.selection_functions.html">selection_functions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.init_selection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.init_selection()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.lognormals_z_to_x"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.lognormals_z_to_x()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.r_grid"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.r_grid()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.selfi_interface.html">selfi_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.selfi_interface.html#selfisys.selfi_interface.PrintMessage"><code class="docutils literal notranslate"><span class="pre">PrintMessage()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.selfi_interface.html#selfisys.selfi_interface.indent"><code class="docutils literal notranslate"><span class="pre">indent()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.selfi_interface.html#selfisys.selfi_interface.unindent"><code class="docutils literal notranslate"><span class="pre">unindent()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.sbmy_interface.html">sbmy_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.compute_Phi"><code class="docutils literal notranslate"><span class="pre">compute_Phi()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.generate_white_noise_Field"><code class="docutils literal notranslate"><span class="pre">generate_white_noise_Field()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.get_power_spectrum_from_cosmo"><code class="docutils literal notranslate"><span class="pre">get_power_spectrum_from_cosmo()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.handle_time_stepping"><code class="docutils literal notranslate"><span class="pre">handle_time_stepping()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.setup_sbmy_parfiles"><code class="docutils literal notranslate"><span class="pre">setup_sbmy_parfiles()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.grf.html">grf</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.grf.html#selfisys.grf.primordial_grf"><code class="docutils literal notranslate"><span class="pre">primordial_grf()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.utils.html">selfisys.utils package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.examples_utils">selfisys.utils.examples_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.examples_utils.clear_large_plot"><code class="docutils literal notranslate"><span class="pre">clear_large_plot()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.logger">selfisys.utils.logger module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.CustomLogger"><code class="docutils literal notranslate"><span class="pre">CustomLogger</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.CustomLogger.diagnostic"><code class="docutils literal notranslate"><span class="pre">CustomLogger.diagnostic()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler.emit"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler.emit()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.INDENT"><code class="docutils literal notranslate"><span class="pre">INDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.PrintDiagnostic"><code class="docutils literal notranslate"><span class="pre">PrintDiagnostic()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.PrintError"><code class="docutils literal notranslate"><span class="pre">PrintError()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.PrintInfo"><code class="docutils literal notranslate"><span class="pre">PrintInfo()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.PrintLeftType"><code class="docutils literal notranslate"><span class="pre">PrintLeftType()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.PrintWarning"><code class="docutils literal notranslate"><span class="pre">PrintWarning()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.UNINDENT"><code class="docutils literal notranslate"><span class="pre">UNINDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.getCustomLogger"><code class="docutils literal notranslate"><span class="pre">getCustomLogger()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.low_level">selfisys.utils.low_level module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.low_level.stderr_redirector"><code class="docutils literal notranslate"><span class="pre">stderr_redirector()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.low_level.stdout_redirector"><code class="docutils literal notranslate"><span class="pre">stdout_redirector()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.parser">selfisys.utils.parser module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.bool_sh"><code class="docutils literal notranslate"><span class="pre">bool_sh()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.check_files_exist"><code class="docutils literal notranslate"><span class="pre">check_files_exist()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.intNone"><code class="docutils literal notranslate"><span class="pre">intNone()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.joinstrs"><code class="docutils literal notranslate"><span class="pre">joinstrs()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.joinstrs_only"><code class="docutils literal notranslate"><span class="pre">joinstrs_only()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.safe_npload"><code class="docutils literal notranslate"><span class="pre">safe_npload()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.path_utils">selfisys.utils.path_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.path_utils.file_names_evaluate"><code class="docutils literal notranslate"><span class="pre">file_names_evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.path_utils.get_file_names"><code class="docutils literal notranslate"><span class="pre">get_file_names()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.plot_examples">selfisys.utils.plot_examples module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_examples.plot_comoving_distance_redshift"><code class="docutils literal notranslate"><span class="pre">plot_comoving_distance_redshift()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_examples.plot_galaxy_field_slice"><code class="docutils literal notranslate"><span class="pre">plot_galaxy_field_slice()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_examples.plot_power_spectrum"><code class="docutils literal notranslate"><span class="pre">plot_power_spectrum()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_examples.plot_selection_functions_def_in_z"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions_def_in_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_examples.redshift_distance_conversion"><code class="docutils literal notranslate"><span class="pre">redshift_distance_conversion()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_examples.relative_error_analysis"><code class="docutils literal notranslate"><span class="pre">relative_error_analysis()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.plot_params">selfisys.utils.plot_params module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.get_offset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.get_offset()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_scientific"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_scientific()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_useOffset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_useOffset()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.create_all_colormaps"><code class="docutils literal notranslate"><span class="pre">create_all_colormaps()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.create_colormap"><code class="docutils literal notranslate"><span class="pre">create_colormap()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.dynamic_text_scaling"><code class="docutils literal notranslate"><span class="pre">dynamic_text_scaling()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.get_contours"><code class="docutils literal notranslate"><span class="pre">get_contours()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.reset_plotting"><code class="docutils literal notranslate"><span class="pre">reset_plotting()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.setup_plotting"><code class="docutils literal notranslate"><span class="pre">setup_plotting()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.plot_utils">selfisys.utils.plot_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_C"><code class="docutils literal notranslate"><span class="pre">plot_C()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_fisher"><code class="docutils literal notranslate"><span class="pre">plot_fisher()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_gradients"><code class="docutils literal notranslate"><span class="pre">plot_gradients()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_histogram"><code class="docutils literal notranslate"><span class="pre">plot_histogram()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks"><code class="docutils literal notranslate"><span class="pre">plot_mocks()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks_compact"><code class="docutils literal notranslate"><span class="pre">plot_mocks_compact()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_observations"><code class="docutils literal notranslate"><span class="pre">plot_observations()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_prior_and_posterior_covariances"><code class="docutils literal notranslate"><span class="pre">plot_prior_and_posterior_covariances()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_reconstruction"><code class="docutils literal notranslate"><span class="pre">plot_reconstruction()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_selection_functions"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plotly_3d"><code class="docutils literal notranslate"><span class="pre">plotly_3d()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.timestepping">selfisys.utils.timestepping module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.timestepping.merge_nTS"><code class="docutils literal notranslate"><span class="pre">merge_nTS()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.tools">selfisys.utils.tools module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.cosmo_vector_to_Simbelmyne_dict"><code class="docutils literal notranslate"><span class="pre">cosmo_vector_to_Simbelmyne_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.cosmo_vector_to_class_dict"><code class="docutils literal notranslate"><span class="pre">cosmo_vector_to_class_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.custom_stat"><code class="docutils literal notranslate"><span class="pre">custom_stat()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.fisher_rao"><code class="docutils literal notranslate"><span class="pre">fisher_rao()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.get_k_max"><code class="docutils literal notranslate"><span class="pre">get_k_max()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.params_ids_to_Simbelmyne_dict"><code class="docutils literal notranslate"><span class="pre">params_ids_to_Simbelmyne_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.sample_omega_from_prior"><code class="docutils literal notranslate"><span class="pre">sample_omega_from_prior()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.summary_to_score"><code class="docutils literal notranslate"><span class="pre">summary_to_score()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.workers">selfisys.utils.workers module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.workers.Simbelmyne_worker"><code class="docutils literal notranslate"><span class="pre">Simbelmyne_worker()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.workers.evaluate_gradient_of_Symbelmyne"><code class="docutils literal notranslate"><span class="pre">evaluate_gradient_of_Symbelmyne()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.workers.worker_gradient_Symbelmyne"><code class="docutils literal notranslate"><span class="pre">worker_gradient_Symbelmyne()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils">Module contents</a></li>
</ul>
</li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Contribute</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../CONTRIBUTING.html">Contributing to SelfiSys</a><ul>
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<h1>Source code for selfisys.selection_functions</h1><div class="highlight"><pre>
<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="c1"># Copyright (C) 2024 Tristan Hoellinger</span>
<span class="c1"># Distributed under the GNU General Public License v3.0 (GPLv3).</span>
<span class="c1"># See the LICENSE file in the root directory for details.</span>
<span class="c1"># SPDX-License-Identifier: GPL-3.0-or-later</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="n">__author__</span> <span class="o">=</span> <span class="s2">&quot;Tristan Hoellinger&quot;</span>
<span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;0.1.0&quot;</span>
<span class="n">__date__</span> <span class="o">=</span> <span class="s2">&quot;2024&quot;</span>
<span class="n">__license__</span> <span class="o">=</span> <span class="s2">&quot;GPLv3&quot;</span>
<span class="sd">&quot;&quot;&quot;Selection functions to simulate galaxy populations.</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">from</span> <span class="nn">gc</span> <span class="kn">import</span> <span class="n">collect</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">import</span> <span class="nn">h5py</span>
<div class="viewcode-block" id="LognormalSelection">
<a class="viewcode-back" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection">[docs]</a>
<span class="k">class</span> <span class="nc">LognormalSelection</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Class to generate radial selection functions.&quot;&quot;&quot;</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
<span class="bp">self</span><span class="p">,</span>
<span class="n">L</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">selection_params</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">survey_mask_path</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">local_select_path</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">size</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Initialise the LognormalSelection object.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> L : float</span>
<span class="sd"> Size of the simulation box (in Mpc/h). If not provided, it</span>
<span class="sd"> must be set before calling init_selection and using</span>
<span class="sd"> grid-dependent methods.</span>
<span class="sd"> selection_params : tuple of arrays</span>
<span class="sd"> Parameters for the selection functions (ss, mm, rr).</span>
<span class="sd"> Required for calling init_selection.</span>
<span class="sd"> survey_mask_path : str or None</span>
<span class="sd"> Path to the survey mask file. Required for calling</span>
<span class="sd"> init_selection.</span>
<span class="sd"> local_select_path : str</span>
<span class="sd"> Path where the selection function will be saved. Required</span>
<span class="sd"> for calling init_selection.</span>
<span class="sd"> size : int, optional</span>
<span class="sd"> Number of grid points along each axis. If not provided, it</span>
<span class="sd"> must be set before using grid-dependent methods.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="bp">self</span><span class="o">.</span><span class="n">L</span> <span class="o">=</span> <span class="n">L</span>
<span class="bp">self</span><span class="o">.</span><span class="n">selection_params</span> <span class="o">=</span> <span class="n">selection_params</span>
<span class="bp">self</span><span class="o">.</span><span class="n">survey_mask_path</span> <span class="o">=</span> <span class="n">survey_mask_path</span>
<span class="bp">self</span><span class="o">.</span><span class="n">local_select_path</span> <span class="o">=</span> <span class="n">local_select_path</span>
<span class="bp">self</span><span class="o">.</span><span class="n">size</span> <span class="o">=</span> <span class="n">size</span>
<div class="viewcode-block" id="LognormalSelection.r_grid">
<a class="viewcode-back" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.r_grid">[docs]</a>
<span class="k">def</span> <span class="nf">r_grid</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Compute the grid of radial distances in the simulation box.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> ndarray</span>
<span class="sd"> 3D array of radial distances from the origin.</span>
<span class="sd"> Raises</span>
<span class="sd"> ------</span>
<span class="sd"> AttributeError</span>
<span class="sd"> If the &#39;size&#39; attribute is not defined.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">size</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span>
<span class="s2">&quot;The attribute &#39;size&#39; must be defined to compute the radial grid.&quot;</span>
<span class="p">)</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">L</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span><span class="s2">&quot;The attribute &#39;L&#39; must be defined to compute the radial grid.&quot;</span><span class="p">)</span>
<span class="n">range1d</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">L</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">size</span><span class="p">,</span> <span class="n">endpoint</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
<span class="n">xx</span><span class="p">,</span> <span class="n">yy</span><span class="p">,</span> <span class="n">zz</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">meshgrid</span><span class="p">(</span><span class="n">range1d</span><span class="p">,</span> <span class="n">range1d</span><span class="p">,</span> <span class="n">range1d</span><span class="p">)</span>
<span class="n">x0</span> <span class="o">=</span> <span class="n">y0</span> <span class="o">=</span> <span class="n">z0</span> <span class="o">=</span> <span class="mf">0.0</span>
<span class="n">r</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">((</span><span class="n">xx</span> <span class="o">-</span> <span class="n">x0</span><span class="p">)</span> <span class="o">**</span> <span class="mi">2</span> <span class="o">+</span> <span class="p">(</span><span class="n">yy</span> <span class="o">-</span> <span class="n">y0</span><span class="p">)</span> <span class="o">**</span> <span class="mi">2</span> <span class="o">+</span> <span class="p">(</span><span class="n">zz</span> <span class="o">-</span> <span class="n">z0</span><span class="p">)</span> <span class="o">**</span> <span class="mi">2</span><span class="p">)</span> <span class="o">+</span> <span class="mf">1e-10</span>
<span class="k">return</span> <span class="n">r</span></div>
<div class="viewcode-block" id="LognormalSelection.one_lognormal">
<a class="viewcode-back" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal">[docs]</a>
<span class="nd">@staticmethod</span>
<span class="k">def</span> <span class="nf">one_lognormal</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">std</span><span class="p">,</span> <span class="n">mean</span><span class="p">,</span> <span class="n">rescale</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Rescaled log-normal distribution.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> x : ndarray</span>
<span class="sd"> Input array.</span>
<span class="sd"> std : float</span>
<span class="sd"> Standard deviation of the distribution.</span>
<span class="sd"> mean : float</span>
<span class="sd"> Mean of the distribution.</span>
<span class="sd"> rescale : float, optional</span>
<span class="sd"> Rescaling factor. If None, the distribution is normalised</span>
<span class="sd"> such that its maximum value is 1.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> ndarray</span>
<span class="sd"> Log-normal distribution evaluated at x.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">mu</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">mean</span><span class="o">**</span><span class="mi">2</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">std</span><span class="o">**</span><span class="mi">2</span> <span class="o">+</span> <span class="n">mean</span><span class="o">**</span><span class="mi">2</span><span class="p">))</span>
<span class="n">sig2</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="mi">1</span> <span class="o">+</span> <span class="n">std</span><span class="o">**</span><span class="mi">2</span> <span class="o">/</span> <span class="n">mean</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span>
<span class="n">lognorm</span> <span class="o">=</span> <span class="p">(</span><span class="mi">1</span> <span class="o">/</span> <span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="mi">2</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="p">)</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">sig2</span><span class="p">)</span> <span class="o">*</span> <span class="n">x</span><span class="p">))</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span>
<span class="o">-</span><span class="p">((</span><span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="o">-</span> <span class="n">mu</span><span class="p">)</span> <span class="o">**</span> <span class="mi">2</span> <span class="o">/</span> <span class="p">(</span><span class="mi">2</span> <span class="o">*</span> <span class="n">sig2</span><span class="p">))</span>
<span class="p">)</span>
<span class="k">if</span> <span class="n">rescale</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">return</span> <span class="n">lognorm</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">lognorm</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="n">lognorm</span> <span class="o">*</span> <span class="n">rescale</span></div>
<div class="viewcode-block" id="LognormalSelection.multiple_lognormal">
<a class="viewcode-back" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal">[docs]</a>
<span class="k">def</span> <span class="nf">multiple_lognormal</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span><span class="p">,</span> <span class="n">mask</span><span class="p">,</span> <span class="n">ss</span><span class="p">,</span> <span class="n">ll</span><span class="p">,</span> <span class="n">rr</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Compute multiple log-normal distributions.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> x : ndarray</span>
<span class="sd"> Input array.</span>
<span class="sd"> mask : ndarray or None</span>
<span class="sd"> Survey mask C(n).</span>
<span class="sd"> ss : array_like</span>
<span class="sd"> Standard deviations for each distribution.</span>
<span class="sd"> ll : array_like</span>
<span class="sd"> Means for each distribution.</span>
<span class="sd"> rr : array_like</span>
<span class="sd"> Rescaling factors for each distribution.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> list of ndarray</span>
<span class="sd"> List of log-normal distributions.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="n">mask</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">mask</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">ones_like</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
<span class="k">return</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">one_lognormal</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">s</span><span class="p">,</span> <span class="n">l</span><span class="p">,</span> <span class="n">r</span><span class="p">)</span> <span class="o">*</span> <span class="n">mask</span> <span class="k">for</span> <span class="n">s</span><span class="p">,</span> <span class="n">l</span><span class="p">,</span> <span class="n">r</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">ss</span><span class="p">,</span> <span class="n">ll</span><span class="p">,</span> <span class="n">rr</span><span class="p">)]</span></div>
<div class="viewcode-block" id="LognormalSelection.one_lognormal_z">
<a class="viewcode-back" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal_z">[docs]</a>
<span class="nd">@staticmethod</span>
<span class="k">def</span> <span class="nf">one_lognormal_z</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">sig2</span><span class="p">,</span> <span class="n">mu</span><span class="p">,</span> <span class="n">rescale</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Compute a log-normal distribution in redshift.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> x : ndarray</span>
<span class="sd"> Input array.</span>
<span class="sd"> sig2 : float</span>
<span class="sd"> Variance of the distribution.</span>
<span class="sd"> mu : float</span>
<span class="sd"> Mean of the distribution.</span>
<span class="sd"> rescale : float, optional</span>
<span class="sd"> Rescaling factor.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> ndarray</span>
<span class="sd"> Log-normal distribution evaluated at x.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">lognorm</span> <span class="o">=</span> <span class="p">(</span><span class="mi">1</span> <span class="o">/</span> <span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="mi">2</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="p">)</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">sig2</span><span class="p">)</span> <span class="o">*</span> <span class="n">x</span><span class="p">))</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span>
<span class="o">-</span><span class="p">((</span><span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="o">-</span> <span class="n">mu</span><span class="p">)</span> <span class="o">**</span> <span class="mi">2</span> <span class="o">/</span> <span class="p">(</span><span class="mi">2</span> <span class="o">*</span> <span class="n">sig2</span><span class="p">))</span>
<span class="p">)</span>
<span class="k">return</span> <span class="n">lognorm</span> <span class="o">*</span> <span class="n">rescale</span> <span class="k">if</span> <span class="n">rescale</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">lognorm</span></div>
<div class="viewcode-block" id="LognormalSelection.multiple_lognormal_z">
<a class="viewcode-back" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal_z">[docs]</a>
<span class="k">def</span> <span class="nf">multiple_lognormal_z</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span><span class="p">,</span> <span class="n">mask</span><span class="p">,</span> <span class="n">ss</span><span class="p">,</span> <span class="n">mm</span><span class="p">,</span> <span class="n">rr</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Compute multiple rescaled lognormal distributions as functions</span>
<span class="sd"> of redshift.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> x : ndarray</span>
<span class="sd"> Input array (redshifts).</span>
<span class="sd"> mask : ndarray or None</span>
<span class="sd"> Survey mask C(n).</span>
<span class="sd"> ss : array_like</span>
<span class="sd"> Standard deviations of the lognormal distributions.</span>
<span class="sd"> mm : array_like</span>
<span class="sd"> Means of the lognormal distributions.</span>
<span class="sd"> rr : array_like</span>
<span class="sd"> Rescaling factors for each distribution.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> list of ndarray</span>
<span class="sd"> List of log-normal distributions.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="n">mask</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">mask</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">ones_like</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
<span class="n">res</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">maxima</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">s</span><span class="p">,</span> <span class="n">m</span><span class="p">,</span> <span class="n">r</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">ss</span><span class="p">,</span> <span class="n">mm</span><span class="p">,</span> <span class="n">rr</span><span class="p">):</span>
<span class="n">mu</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">m</span><span class="o">**</span><span class="mi">2</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">s</span><span class="o">**</span><span class="mi">2</span> <span class="o">+</span> <span class="n">m</span><span class="o">**</span><span class="mi">2</span><span class="p">))</span>
<span class="n">sig2</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="mi">1</span> <span class="o">+</span> <span class="n">s</span><span class="o">**</span><span class="mi">2</span> <span class="o">/</span> <span class="n">m</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span>
<span class="n">maxima</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">sig2</span> <span class="o">/</span> <span class="mi">2</span> <span class="o">-</span> <span class="n">mu</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="mi">2</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span> <span class="o">*</span> <span class="n">sig2</span><span class="p">)))</span>
<span class="n">res</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">one_lognormal_z</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">sig2</span><span class="p">,</span> <span class="n">mu</span><span class="p">,</span> <span class="n">rescale</span><span class="o">=</span><span class="n">r</span><span class="p">)</span> <span class="o">*</span> <span class="n">mask</span><span class="p">)</span>
<span class="nb">max</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">maxima</span><span class="p">)</span>
<span class="n">res</span> <span class="o">=</span> <span class="p">[</span><span class="n">r</span> <span class="o">/</span> <span class="nb">max</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">res</span><span class="p">]</span>
<span class="k">return</span> <span class="n">res</span></div>
<div class="viewcode-block" id="LognormalSelection.lognormals_z_to_x">
<a class="viewcode-back" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.lognormals_z_to_x">[docs]</a>
<span class="k">def</span> <span class="nf">lognormals_z_to_x</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">xx</span><span class="p">,</span> <span class="n">mask</span><span class="p">,</span> <span class="n">params</span><span class="p">,</span> <span class="n">spline</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Convert log-normal distributions from redshift to distance.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> xx : array-like</span>
<span class="sd"> Comoving distances at which to evaluate the distributions.</span>
<span class="sd"> mask : ndarray or None</span>
<span class="sd"> Survey mask C(n).</span>
<span class="sd"> params : tuple of arrays</span>
<span class="sd"> Parameters for the distributions (ss, mm, rr).</span>
<span class="sd"> spline : UnivariateSpline</span>
<span class="sd"> Linear interpolator for the distance-redshift relation.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> tuple</span>
<span class="sd"> Tuple containing redshifts and list of distributions.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">ss</span><span class="p">,</span> <span class="n">mm</span><span class="p">,</span> <span class="n">rr</span> <span class="o">=</span> <span class="n">params</span>
<span class="n">zs</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">maximum</span><span class="p">(</span><span class="mf">1e-4</span><span class="p">,</span> <span class="n">spline</span><span class="p">(</span><span class="n">xx</span><span class="p">))</span>
<span class="n">res</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">multiple_lognormal_z</span><span class="p">(</span><span class="n">zs</span><span class="p">,</span> <span class="n">mask</span><span class="p">,</span> <span class="n">ss</span><span class="p">,</span> <span class="n">mm</span><span class="p">,</span> <span class="n">rr</span><span class="p">)</span>
<span class="k">return</span> <span class="n">zs</span><span class="p">,</span> <span class="n">res</span></div>
<div class="viewcode-block" id="LognormalSelection.init_selection">
<a class="viewcode-back" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.init_selection">[docs]</a>
<span class="k">def</span> <span class="nf">init_selection</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">reset</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Initialise the radial selection functions.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> reset : bool, optional</span>
<span class="sd"> Whether to reset the selection function.</span>
<span class="sd"> Raises</span>
<span class="sd"> ------</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="nb">any</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">survey_mask_path</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">local_select_path</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">]):</span>
<span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span>
<span class="s2">&quot;Some attributes are missing to initialise the selection function.&quot;</span>
<span class="p">)</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">local_select_path</span><span class="p">)</span> <span class="ow">or</span> <span class="n">reset</span><span class="p">:</span>
<span class="kn">from</span> <span class="nn">scipy.interpolate</span> <span class="kn">import</span> <span class="n">UnivariateSpline</span>
<span class="kn">from</span> <span class="nn">classy</span> <span class="kn">import</span> <span class="n">Class</span>
<span class="kn">from</span> <span class="nn">astropy.cosmology</span> <span class="kn">import</span> <span class="n">FlatLambdaCDM</span>
<span class="kn">from</span> <span class="nn">selfisys.utils.tools</span> <span class="kn">import</span> <span class="n">cosmo_vector_to_class_dict</span>
<span class="kn">from</span> <span class="nn">selfisys.global_parameters</span> <span class="kn">import</span> <span class="n">omegas_gt</span>
<span class="kn">from</span> <span class="nn">selfisys.utils.plot_utils</span> <span class="kn">import</span> <span class="n">plot_selection_functions</span>
<span class="c1"># Redshift-distance relation</span>
<span class="n">redshifts_upper_bound</span> <span class="o">=</span> <span class="mf">3.0</span>
<span class="n">zz</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">redshifts_upper_bound</span><span class="p">,</span> <span class="mi">10_000</span><span class="p">)</span>
<span class="n">cosmo</span> <span class="o">=</span> <span class="n">FlatLambdaCDM</span><span class="p">(</span><span class="n">H0</span><span class="o">=</span><span class="mi">100</span> <span class="o">*</span> <span class="n">omegas_gt</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">Ob0</span><span class="o">=</span><span class="n">omegas_gt</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">Om0</span><span class="o">=</span><span class="n">omegas_gt</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
<span class="n">d</span> <span class="o">=</span> <span class="n">cosmo</span><span class="o">.</span><span class="n">comoving_distance</span><span class="p">(</span><span class="n">zz</span><span class="p">)</span><span class="o">.</span><span class="n">value</span> <span class="o">/</span> <span class="mf">1e3</span> <span class="c1"># -&gt; Gpc/h</span>
<span class="n">spline</span> <span class="o">=</span> <span class="n">UnivariateSpline</span><span class="p">(</span><span class="n">d</span><span class="p">,</span> <span class="n">zz</span><span class="p">,</span> <span class="n">k</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">s</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<span class="c1"># Plot the selection functions</span>
<span class="n">L</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">L</span> <span class="o">/</span> <span class="mf">1e3</span>
<span class="n">Lcorner</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span> <span class="o">*</span> <span class="n">L</span>
<span class="n">zcorner</span> <span class="o">=</span> <span class="n">zz</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">argmin</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">d</span> <span class="o">-</span> <span class="n">Lcorner</span><span class="p">))]</span>
<span class="c1"># Get linear growth factor from CLASS</span>
<span class="n">cosmo_dict</span> <span class="o">=</span> <span class="n">cosmo_vector_to_class_dict</span><span class="p">(</span><span class="n">omegas_gt</span><span class="p">)</span>
<span class="n">cosmo_class</span> <span class="o">=</span> <span class="n">Class</span><span class="p">()</span>
<span class="n">cosmo_class</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="n">cosmo_dict</span><span class="p">)</span>
<span class="n">cosmo_class</span><span class="o">.</span><span class="n">compute</span><span class="p">()</span>
<span class="n">Dz</span> <span class="o">=</span> <span class="n">cosmo_class</span><span class="o">.</span><span class="n">get_background</span><span class="p">()[</span><span class="s2">&quot;gr.fac. D&quot;</span><span class="p">]</span>
<span class="n">redshifts</span> <span class="o">=</span> <span class="n">cosmo_class</span><span class="o">.</span><span class="n">get_background</span><span class="p">()[</span><span class="s2">&quot;z&quot;</span><span class="p">]</span>
<span class="n">cosmo_class</span><span class="o">.</span><span class="n">struct_cleanup</span><span class="p">()</span>
<span class="n">cosmo_class</span><span class="o">.</span><span class="n">empty</span><span class="p">()</span>
<span class="c1"># Define the axis for the plot</span>
<span class="n">xx</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mf">1e-5</span><span class="p">,</span> <span class="n">Lcorner</span><span class="p">,</span> <span class="mi">1000</span><span class="p">)</span>
<span class="n">zz</span><span class="p">,</span> <span class="n">res</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">lognormals_z_to_x</span><span class="p">(</span>
<span class="n">xx</span><span class="p">,</span>
<span class="kc">None</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">selection_params</span><span class="p">,</span>
<span class="n">spline</span><span class="p">,</span>
<span class="p">)</span>
<span class="c1"># Call auxiliary plotting routine</span>
<span class="n">plot_selection_functions</span><span class="p">(</span>
<span class="n">xx</span><span class="p">,</span>
<span class="n">res</span><span class="p">,</span>
<span class="kc">None</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">selection_params</span><span class="p">,</span>
<span class="n">L</span><span class="p">,</span>
<span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span> <span class="o">*</span> <span class="n">L</span><span class="p">,</span>
<span class="n">zz</span><span class="o">=</span><span class="n">zz</span><span class="p">,</span>
<span class="n">zcorner</span><span class="o">=</span><span class="n">zcorner</span><span class="p">,</span>
<span class="n">path</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">local_select_path</span><span class="p">[:</span><span class="o">-</span><span class="mi">3</span><span class="p">]</span> <span class="o">+</span> <span class="s2">&quot;.png&quot;</span><span class="p">,</span>
<span class="p">)</span>
<span class="c1"># Compute the selection function and save it to disk</span>
<span class="n">survey_mask</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">survey_mask_path</span><span class="p">)</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">survey_mask_path</span> <span class="k">else</span> <span class="kc">None</span>
<span class="n">r</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">r_grid</span><span class="p">()</span> <span class="o">/</span> <span class="mf">1e3</span> <span class="c1"># Convert to Gpc/h</span>
<span class="n">_</span><span class="p">,</span> <span class="n">select_fct</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">lognormals_z_to_x</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">survey_mask</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">selection_params</span><span class="p">,</span> <span class="n">spline</span><span class="p">)</span>
<span class="k">with</span> <span class="n">h5py</span><span class="o">.</span><span class="n">File</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">local_select_path</span><span class="p">,</span> <span class="s2">&quot;w&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
<span class="n">f</span><span class="o">.</span><span class="n">create_dataset</span><span class="p">(</span><span class="s2">&quot;select_fct&quot;</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">select_fct</span><span class="p">)</span>
<span class="k">del</span> <span class="n">survey_mask</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span> <span class="n">d</span><span class="p">,</span> <span class="n">zz</span><span class="p">,</span> <span class="n">spline</span><span class="p">,</span> <span class="n">select_fct</span>
<span class="n">collect</span><span class="p">()</span></div>
</div>
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<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.modified_selfi"><code class="docutils literal notranslate"><span class="pre">HiddenBox.modified_selfi</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.prefix_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.prefix_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.reset_survey"><code class="docutils literal notranslate"><span class="pre">HiddenBox.reset_survey()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.setup_only"><code class="docutils literal notranslate"><span class="pre">HiddenBox.setup_only</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_recompute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_recompute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_setup"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_setup()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.update"><code class="docutils literal notranslate"><span class="pre">HiddenBox.update()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.normalise_hb.html">normalise_hb</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.normalise_hb.html#selfisys.normalise_hb.define_normalisation"><code class="docutils literal notranslate"><span class="pre">define_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation"><code class="docutils literal notranslate"><span class="pre">worker_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_public"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_public()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_wrapper"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_wrapper()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.prior.html">prior</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.logposterior_hyperparameters_parallel"><code class="docutils literal notranslate"><span class="pre">logposterior_hyperparameters_parallel()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.perform_prior_optimisation_and_plot"><code class="docutils literal notranslate"><span class="pre">perform_prior_optimisation_and_plot()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior"><code class="docutils literal notranslate"><span class="pre">planck_prior</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.mean"><code class="docutils literal notranslate"><span class="pre">planck_prior.mean</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.inv_covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.inv_covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_max"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_max</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_min"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_min</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.compute"><code class="docutils literal notranslate"><span class="pre">planck_prior.compute()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.load"><code class="docutils literal notranslate"><span class="pre">planck_prior.load()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.logpdf"><code class="docutils literal notranslate"><span class="pre">planck_prior.logpdf()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.sample"><code class="docutils literal notranslate"><span class="pre">planck_prior.sample()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.save"><code class="docutils literal notranslate"><span class="pre">planck_prior.save()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.worker_class"><code class="docutils literal notranslate"><span class="pre">worker_class()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.selection_functions.html">selection_functions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.init_selection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.init_selection()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.lognormals_z_to_x"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.lognormals_z_to_x()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.r_grid"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.r_grid()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.selfi_interface.html">selfi_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.selfi_interface.html#selfisys.selfi_interface.PrintMessage"><code class="docutils literal notranslate"><span class="pre">PrintMessage()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.selfi_interface.html#selfisys.selfi_interface.indent"><code class="docutils literal notranslate"><span class="pre">indent()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.selfi_interface.html#selfisys.selfi_interface.unindent"><code class="docutils literal notranslate"><span class="pre">unindent()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.sbmy_interface.html">sbmy_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.compute_Phi"><code class="docutils literal notranslate"><span class="pre">compute_Phi()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.generate_white_noise_Field"><code class="docutils literal notranslate"><span class="pre">generate_white_noise_Field()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.get_power_spectrum_from_cosmo"><code class="docutils literal notranslate"><span class="pre">get_power_spectrum_from_cosmo()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.handle_time_stepping"><code class="docutils literal notranslate"><span class="pre">handle_time_stepping()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.setup_sbmy_parfiles"><code class="docutils literal notranslate"><span class="pre">setup_sbmy_parfiles()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.grf.html">grf</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.grf.html#selfisys.grf.primordial_grf"><code class="docutils literal notranslate"><span class="pre">primordial_grf()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.utils.html">selfisys.utils package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.examples_utils">selfisys.utils.examples_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.examples_utils.clear_large_plot"><code class="docutils literal notranslate"><span class="pre">clear_large_plot()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.logger">selfisys.utils.logger module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.CustomLogger"><code class="docutils literal notranslate"><span class="pre">CustomLogger</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.CustomLogger.diagnostic"><code class="docutils literal notranslate"><span class="pre">CustomLogger.diagnostic()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler.emit"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler.emit()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.INDENT"><code class="docutils literal notranslate"><span class="pre">INDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.PrintDiagnostic"><code class="docutils literal notranslate"><span class="pre">PrintDiagnostic()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.PrintError"><code class="docutils literal notranslate"><span class="pre">PrintError()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.PrintInfo"><code class="docutils literal notranslate"><span class="pre">PrintInfo()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.PrintLeftType"><code class="docutils literal notranslate"><span class="pre">PrintLeftType()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.PrintWarning"><code class="docutils literal notranslate"><span class="pre">PrintWarning()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.UNINDENT"><code class="docutils literal notranslate"><span class="pre">UNINDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.getCustomLogger"><code class="docutils literal notranslate"><span class="pre">getCustomLogger()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.low_level">selfisys.utils.low_level module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.low_level.stderr_redirector"><code class="docutils literal notranslate"><span class="pre">stderr_redirector()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.low_level.stdout_redirector"><code class="docutils literal notranslate"><span class="pre">stdout_redirector()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.parser">selfisys.utils.parser module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.bool_sh"><code class="docutils literal notranslate"><span class="pre">bool_sh()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.check_files_exist"><code class="docutils literal notranslate"><span class="pre">check_files_exist()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.intNone"><code class="docutils literal notranslate"><span class="pre">intNone()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.joinstrs"><code class="docutils literal notranslate"><span class="pre">joinstrs()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.joinstrs_only"><code class="docutils literal notranslate"><span class="pre">joinstrs_only()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.safe_npload"><code class="docutils literal notranslate"><span class="pre">safe_npload()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.path_utils">selfisys.utils.path_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.path_utils.file_names_evaluate"><code class="docutils literal notranslate"><span class="pre">file_names_evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.path_utils.get_file_names"><code class="docutils literal notranslate"><span class="pre">get_file_names()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.plot_examples">selfisys.utils.plot_examples module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_examples.plot_comoving_distance_redshift"><code class="docutils literal notranslate"><span class="pre">plot_comoving_distance_redshift()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_examples.plot_galaxy_field_slice"><code class="docutils literal notranslate"><span class="pre">plot_galaxy_field_slice()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_examples.plot_power_spectrum"><code class="docutils literal notranslate"><span class="pre">plot_power_spectrum()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_examples.plot_selection_functions_def_in_z"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions_def_in_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_examples.redshift_distance_conversion"><code class="docutils literal notranslate"><span class="pre">redshift_distance_conversion()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_examples.relative_error_analysis"><code class="docutils literal notranslate"><span class="pre">relative_error_analysis()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.plot_params">selfisys.utils.plot_params module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.get_offset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.get_offset()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_scientific"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_scientific()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_useOffset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_useOffset()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.create_all_colormaps"><code class="docutils literal notranslate"><span class="pre">create_all_colormaps()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.create_colormap"><code class="docutils literal notranslate"><span class="pre">create_colormap()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.dynamic_text_scaling"><code class="docutils literal notranslate"><span class="pre">dynamic_text_scaling()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.get_contours"><code class="docutils literal notranslate"><span class="pre">get_contours()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.reset_plotting"><code class="docutils literal notranslate"><span class="pre">reset_plotting()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.setup_plotting"><code class="docutils literal notranslate"><span class="pre">setup_plotting()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.plot_utils">selfisys.utils.plot_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_C"><code class="docutils literal notranslate"><span class="pre">plot_C()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_fisher"><code class="docutils literal notranslate"><span class="pre">plot_fisher()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_gradients"><code class="docutils literal notranslate"><span class="pre">plot_gradients()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_histogram"><code class="docutils literal notranslate"><span class="pre">plot_histogram()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks"><code class="docutils literal notranslate"><span class="pre">plot_mocks()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks_compact"><code class="docutils literal notranslate"><span class="pre">plot_mocks_compact()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_observations"><code class="docutils literal notranslate"><span class="pre">plot_observations()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_prior_and_posterior_covariances"><code class="docutils literal notranslate"><span class="pre">plot_prior_and_posterior_covariances()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_reconstruction"><code class="docutils literal notranslate"><span class="pre">plot_reconstruction()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_selection_functions"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plotly_3d"><code class="docutils literal notranslate"><span class="pre">plotly_3d()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.timestepping">selfisys.utils.timestepping module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.timestepping.merge_nTS"><code class="docutils literal notranslate"><span class="pre">merge_nTS()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.tools">selfisys.utils.tools module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.cosmo_vector_to_Simbelmyne_dict"><code class="docutils literal notranslate"><span class="pre">cosmo_vector_to_Simbelmyne_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.cosmo_vector_to_class_dict"><code class="docutils literal notranslate"><span class="pre">cosmo_vector_to_class_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.custom_stat"><code class="docutils literal notranslate"><span class="pre">custom_stat()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.fisher_rao"><code class="docutils literal notranslate"><span class="pre">fisher_rao()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.get_k_max"><code class="docutils literal notranslate"><span class="pre">get_k_max()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.params_ids_to_Simbelmyne_dict"><code class="docutils literal notranslate"><span class="pre">params_ids_to_Simbelmyne_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.sample_omega_from_prior"><code class="docutils literal notranslate"><span class="pre">sample_omega_from_prior()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.summary_to_score"><code class="docutils literal notranslate"><span class="pre">summary_to_score()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.workers">selfisys.utils.workers module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.workers.Simbelmyne_worker"><code class="docutils literal notranslate"><span class="pre">Simbelmyne_worker()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.workers.evaluate_gradient_of_Symbelmyne"><code class="docutils literal notranslate"><span class="pre">evaluate_gradient_of_Symbelmyne()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.workers.worker_gradient_Symbelmyne"><code class="docutils literal notranslate"><span class="pre">worker_gradient_Symbelmyne()</span></code></a></li>
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<h1>Source code for selfisys.selfi_interface</h1><div class="highlight"><pre>
<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="c1"># Copyright (C) 2024 Tristan Hoellinger</span>
<span class="c1"># Distributed under the GNU General Public License v3.0 (GPLv3).</span>
<span class="c1"># See the LICENSE file in the root directory for details.</span>
<span class="c1"># SPDX-License-Identifier: GPL-3.0-or-later</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="n">__author__</span> <span class="o">=</span> <span class="s2">&quot;Tristan Hoellinger&quot;</span>
<span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;0.1.0&quot;</span>
<span class="n">__date__</span> <span class="o">=</span> <span class="s2">&quot;2024&quot;</span>
<span class="n">__license__</span> <span class="o">=</span> <span class="s2">&quot;GPLv3&quot;</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd">Provides simple wrappers around pyselfi.utils functions for the SelfiSys</span>
<span class="sd">pipeline.</span>
<span class="sd">&quot;&quot;&quot;</span>
<div class="viewcode-block" id="PrintMessage">
<a class="viewcode-back" href="../../selfisys.selfi_interface.html#selfisys.selfi_interface.PrintMessage">[docs]</a>
<span class="k">def</span> <span class="nf">PrintMessage</span><span class="p">(</span><span class="n">required_verbosity</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">message</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">verbosity</span><span class="p">:</span> <span class="nb">int</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Print a message to standard output using pyselfi.utils.PrintMessage.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> required_verbosity : int</span>
<span class="sd"> The verbosity level required to display the message.</span>
<span class="sd"> message : str</span>
<span class="sd"> The actual message to display.</span>
<span class="sd"> verbosity : int</span>
<span class="sd"> The current verbosity level (0=quiet, 1=normal, 2=debug).</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">from</span> <span class="nn">pyselfi.utils</span> <span class="kn">import</span> <span class="n">PrintMessage</span> <span class="k">as</span> <span class="n">PSMessage</span>
<span class="k">if</span> <span class="n">verbosity</span> <span class="o">&gt;=</span> <span class="n">required_verbosity</span><span class="p">:</span>
<span class="n">PSMessage</span><span class="p">(</span><span class="mi">3</span><span class="p">,</span> <span class="n">message</span><span class="p">)</span></div>
<div class="viewcode-block" id="indent">
<a class="viewcode-back" href="../../selfisys.selfi_interface.html#selfisys.selfi_interface.indent">[docs]</a>
<span class="k">def</span> <span class="nf">indent</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Indent the standard output using pyselfi.utils.&quot;&quot;&quot;</span>
<span class="kn">from</span> <span class="nn">pyselfi.utils</span> <span class="kn">import</span> <span class="n">INDENT</span>
<span class="n">INDENT</span><span class="p">()</span></div>
<div class="viewcode-block" id="unindent">
<a class="viewcode-back" href="../../selfisys.selfi_interface.html#selfisys.selfi_interface.unindent">[docs]</a>
<span class="k">def</span> <span class="nf">unindent</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Unindent the standard output using pyselfi.utils.&quot;&quot;&quot;</span>
<span class="kn">from</span> <span class="nn">pyselfi.utils</span> <span class="kn">import</span> <span class="n">UNINDENT</span>
<span class="n">UNINDENT</span><span class="p">()</span></div>
</pre></div>
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<p class="caption" role="heading"><span class="caption-text">API Documentation</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.hiddenbox.html">hiddenbox</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox"><code class="docutils literal notranslate"><span class="pre">HiddenBox</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Npop"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Npop</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Ntimesteps"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Ntimesteps</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Psingle"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Psingle</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.compute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.compute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.evaluate"><code class="docutils literal notranslate"><span class="pre">HiddenBox.evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_neglect_lightcone"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_neglect_lightcone</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_recompute_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_recompute_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.gravity_on"><code class="docutils literal notranslate"><span class="pre">HiddenBox.gravity_on</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.load_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.load_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.make_data"><code class="docutils literal notranslate"><span class="pre">HiddenBox.make_data()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.modified_selfi"><code class="docutils literal notranslate"><span class="pre">HiddenBox.modified_selfi</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.prefix_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.prefix_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.reset_survey"><code class="docutils literal notranslate"><span class="pre">HiddenBox.reset_survey()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.setup_only"><code class="docutils literal notranslate"><span class="pre">HiddenBox.setup_only</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_recompute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_recompute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_setup"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_setup()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.update"><code class="docutils literal notranslate"><span class="pre">HiddenBox.update()</span></code></a></li>
</ul>
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</ul>
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<li class="toctree-l1"><a class="reference internal" href="../../selfisys.normalise_hb.html">normalise_hb</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.normalise_hb.html#selfisys.normalise_hb.define_normalisation"><code class="docutils literal notranslate"><span class="pre">define_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation"><code class="docutils literal notranslate"><span class="pre">worker_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_public"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_public()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_wrapper"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_wrapper()</span></code></a></li>
</ul>
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<li class="toctree-l1"><a class="reference internal" href="../../selfisys.prior.html">prior</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.logposterior_hyperparameters_parallel"><code class="docutils literal notranslate"><span class="pre">logposterior_hyperparameters_parallel()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.perform_prior_optimisation_and_plot"><code class="docutils literal notranslate"><span class="pre">perform_prior_optimisation_and_plot()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior"><code class="docutils literal notranslate"><span class="pre">planck_prior</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.mean"><code class="docutils literal notranslate"><span class="pre">planck_prior.mean</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.inv_covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.inv_covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_max"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_max</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_min"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_min</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.compute"><code class="docutils literal notranslate"><span class="pre">planck_prior.compute()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.load"><code class="docutils literal notranslate"><span class="pre">planck_prior.load()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.logpdf"><code class="docutils literal notranslate"><span class="pre">planck_prior.logpdf()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.sample"><code class="docutils literal notranslate"><span class="pre">planck_prior.sample()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.planck_prior.save"><code class="docutils literal notranslate"><span class="pre">planck_prior.save()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.prior.html#selfisys.prior.worker_class"><code class="docutils literal notranslate"><span class="pre">worker_class()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.selection_functions.html">selection_functions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.init_selection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.init_selection()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.lognormals_z_to_x"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.lognormals_z_to_x()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.r_grid"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.r_grid()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.selfi_interface.html">selfi_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.selfi_interface.html#selfisys.selfi_interface.PrintMessage"><code class="docutils literal notranslate"><span class="pre">PrintMessage()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.selfi_interface.html#selfisys.selfi_interface.indent"><code class="docutils literal notranslate"><span class="pre">indent()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.selfi_interface.html#selfisys.selfi_interface.unindent"><code class="docutils literal notranslate"><span class="pre">unindent()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.sbmy_interface.html">sbmy_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.compute_Phi"><code class="docutils literal notranslate"><span class="pre">compute_Phi()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.generate_white_noise_Field"><code class="docutils literal notranslate"><span class="pre">generate_white_noise_Field()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.get_power_spectrum_from_cosmo"><code class="docutils literal notranslate"><span class="pre">get_power_spectrum_from_cosmo()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.handle_time_stepping"><code class="docutils literal notranslate"><span class="pre">handle_time_stepping()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.setup_sbmy_parfiles"><code class="docutils literal notranslate"><span class="pre">setup_sbmy_parfiles()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.grf.html">grf</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.grf.html#selfisys.grf.primordial_grf"><code class="docutils literal notranslate"><span class="pre">primordial_grf()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../selfisys.utils.html">selfisys.utils package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.examples_utils">selfisys.utils.examples_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.examples_utils.clear_large_plot"><code class="docutils literal notranslate"><span class="pre">clear_large_plot()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.logger">selfisys.utils.logger module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.CustomLogger"><code class="docutils literal notranslate"><span class="pre">CustomLogger</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.CustomLogger.diagnostic"><code class="docutils literal notranslate"><span class="pre">CustomLogger.diagnostic()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler.emit"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler.emit()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.INDENT"><code class="docutils literal notranslate"><span class="pre">INDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.PrintDiagnostic"><code class="docutils literal notranslate"><span class="pre">PrintDiagnostic()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.PrintError"><code class="docutils literal notranslate"><span class="pre">PrintError()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.PrintInfo"><code class="docutils literal notranslate"><span class="pre">PrintInfo()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.PrintLeftType"><code class="docutils literal notranslate"><span class="pre">PrintLeftType()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.PrintWarning"><code class="docutils literal notranslate"><span class="pre">PrintWarning()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.UNINDENT"><code class="docutils literal notranslate"><span class="pre">UNINDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.logger.getCustomLogger"><code class="docutils literal notranslate"><span class="pre">getCustomLogger()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.low_level">selfisys.utils.low_level module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.low_level.stderr_redirector"><code class="docutils literal notranslate"><span class="pre">stderr_redirector()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.low_level.stdout_redirector"><code class="docutils literal notranslate"><span class="pre">stdout_redirector()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.parser">selfisys.utils.parser module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.bool_sh"><code class="docutils literal notranslate"><span class="pre">bool_sh()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.check_files_exist"><code class="docutils literal notranslate"><span class="pre">check_files_exist()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.intNone"><code class="docutils literal notranslate"><span class="pre">intNone()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.joinstrs"><code class="docutils literal notranslate"><span class="pre">joinstrs()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.joinstrs_only"><code class="docutils literal notranslate"><span class="pre">joinstrs_only()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.parser.safe_npload"><code class="docutils literal notranslate"><span class="pre">safe_npload()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.path_utils">selfisys.utils.path_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.path_utils.file_names_evaluate"><code class="docutils literal notranslate"><span class="pre">file_names_evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.path_utils.get_file_names"><code class="docutils literal notranslate"><span class="pre">get_file_names()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.plot_examples">selfisys.utils.plot_examples module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_examples.plot_comoving_distance_redshift"><code class="docutils literal notranslate"><span class="pre">plot_comoving_distance_redshift()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_examples.plot_galaxy_field_slice"><code class="docutils literal notranslate"><span class="pre">plot_galaxy_field_slice()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_examples.plot_power_spectrum"><code class="docutils literal notranslate"><span class="pre">plot_power_spectrum()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_examples.plot_selection_functions_def_in_z"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions_def_in_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_examples.redshift_distance_conversion"><code class="docutils literal notranslate"><span class="pre">redshift_distance_conversion()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_examples.relative_error_analysis"><code class="docutils literal notranslate"><span class="pre">relative_error_analysis()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.plot_params">selfisys.utils.plot_params module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.get_offset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.get_offset()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_scientific"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_scientific()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_useOffset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_useOffset()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.create_all_colormaps"><code class="docutils literal notranslate"><span class="pre">create_all_colormaps()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.create_colormap"><code class="docutils literal notranslate"><span class="pre">create_colormap()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.dynamic_text_scaling"><code class="docutils literal notranslate"><span class="pre">dynamic_text_scaling()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.get_contours"><code class="docutils literal notranslate"><span class="pre">get_contours()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.reset_plotting"><code class="docutils literal notranslate"><span class="pre">reset_plotting()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_params.setup_plotting"><code class="docutils literal notranslate"><span class="pre">setup_plotting()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.plot_utils">selfisys.utils.plot_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_C"><code class="docutils literal notranslate"><span class="pre">plot_C()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_fisher"><code class="docutils literal notranslate"><span class="pre">plot_fisher()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_gradients"><code class="docutils literal notranslate"><span class="pre">plot_gradients()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_histogram"><code class="docutils literal notranslate"><span class="pre">plot_histogram()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks"><code class="docutils literal notranslate"><span class="pre">plot_mocks()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks_compact"><code class="docutils literal notranslate"><span class="pre">plot_mocks_compact()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_observations"><code class="docutils literal notranslate"><span class="pre">plot_observations()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_prior_and_posterior_covariances"><code class="docutils literal notranslate"><span class="pre">plot_prior_and_posterior_covariances()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_reconstruction"><code class="docutils literal notranslate"><span class="pre">plot_reconstruction()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plot_selection_functions"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.plot_utils.plotly_3d"><code class="docutils literal notranslate"><span class="pre">plotly_3d()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.timestepping">selfisys.utils.timestepping module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.timestepping.merge_nTS"><code class="docutils literal notranslate"><span class="pre">merge_nTS()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.tools">selfisys.utils.tools module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.cosmo_vector_to_Simbelmyne_dict"><code class="docutils literal notranslate"><span class="pre">cosmo_vector_to_Simbelmyne_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.cosmo_vector_to_class_dict"><code class="docutils literal notranslate"><span class="pre">cosmo_vector_to_class_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.custom_stat"><code class="docutils literal notranslate"><span class="pre">custom_stat()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.fisher_rao"><code class="docutils literal notranslate"><span class="pre">fisher_rao()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.get_k_max"><code class="docutils literal notranslate"><span class="pre">get_k_max()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.params_ids_to_Simbelmyne_dict"><code class="docutils literal notranslate"><span class="pre">params_ids_to_Simbelmyne_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.sample_omega_from_prior"><code class="docutils literal notranslate"><span class="pre">sample_omega_from_prior()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.tools.summary_to_score"><code class="docutils literal notranslate"><span class="pre">summary_to_score()</span></code></a></li>
</ul>
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<li class="toctree-l2"><a class="reference internal" href="../../selfisys.utils.html#module-selfisys.utils.workers">selfisys.utils.workers module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.workers.Simbelmyne_worker"><code class="docutils literal notranslate"><span class="pre">Simbelmyne_worker()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.workers.evaluate_gradient_of_Symbelmyne"><code class="docutils literal notranslate"><span class="pre">evaluate_gradient_of_Symbelmyne()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../selfisys.utils.html#selfisys.utils.workers.worker_gradient_Symbelmyne"><code class="docutils literal notranslate"><span class="pre">worker_gradient_Symbelmyne()</span></code></a></li>
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<h1>Source code for selfisys.setup_model</h1><div class="highlight"><pre>
<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="c1"># Copyright (C) 2024 Tristan Hoellinger</span>
<span class="c1"># Distributed under the GNU General Public License v3.0 (GPLv3).</span>
<span class="c1"># See the LICENSE file in the root directory for details.</span>
<span class="c1"># SPDX-License-Identifier: GPL-3.0-or-later</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="n">__author__</span> <span class="o">=</span> <span class="s2">&quot;Tristan Hoellinger&quot;</span>
<span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;0.1.0&quot;</span>
<span class="n">__date__</span> <span class="o">=</span> <span class="s2">&quot;2024&quot;</span>
<span class="n">__license__</span> <span class="o">=</span> <span class="s2">&quot;GPLv3&quot;</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd">Set up parameters related to the grid and the fiducial power spectrum.</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="kn">import</span> <span class="nn">os.path</span>
<span class="kn">import</span> <span class="nn">gc</span>
<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Optional</span><span class="p">,</span> <span class="n">NamedTuple</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">from</span> <span class="nn">h5py</span> <span class="kn">import</span> <span class="n">File</span>
<span class="kn">from</span> <span class="nn">pysbmy.power</span> <span class="kn">import</span> <span class="n">PowerSpectrum</span><span class="p">,</span> <span class="n">FourierGrid</span><span class="p">,</span> <span class="n">get_Pk</span>
<span class="kn">from</span> <span class="nn">selfisys.utils.logger</span> <span class="kn">import</span> <span class="n">getCustomLogger</span>
<span class="kn">from</span> <span class="nn">selfisys.utils.tools</span> <span class="kn">import</span> <span class="n">get_k_max</span>
<span class="n">logger</span> <span class="o">=</span> <span class="n">getCustomLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>
<div class="viewcode-block" id="ModelSetup">
<a class="viewcode-back" href="../../selfisys.setup_model.html#selfisys.setup_model.ModelSetup">[docs]</a>
<span class="k">class</span> <span class="nc">ModelSetup</span><span class="p">(</span><span class="n">NamedTuple</span><span class="p">):</span>
<span class="n">size</span><span class="p">:</span> <span class="nb">int</span>
<span class="n">L</span><span class="p">:</span> <span class="nb">float</span>
<span class="n">P</span><span class="p">:</span> <span class="nb">int</span>
<span class="n">S</span><span class="p">:</span> <span class="nb">int</span>
<span class="n">G_sim_path</span><span class="p">:</span> <span class="nb">str</span>
<span class="n">G_ss_path</span><span class="p">:</span> <span class="nb">str</span>
<span class="n">Pbins_bnd</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span>
<span class="n">Pbins</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span>
<span class="n">k_s</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span>
<span class="n">P_ss_obj_path</span><span class="p">:</span> <span class="nb">str</span>
<span class="n">P_0</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span>
<span class="n">planck_Pk</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span></div>
<div class="viewcode-block" id="setup_model">
<a class="viewcode-back" href="../../selfisys.setup_model.html#selfisys.setup_model.setup_model">[docs]</a>
<span class="k">def</span> <span class="nf">setup_model</span><span class="p">(</span>
<span class="n">workdir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
<span class="n">params_planck</span><span class="p">:</span> <span class="nb">dict</span><span class="p">,</span>
<span class="n">params_P0</span><span class="p">:</span> <span class="nb">dict</span><span class="p">,</span>
<span class="n">size</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">256</span><span class="p">,</span>
<span class="n">L</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">3600.0</span><span class="p">,</span>
<span class="n">S</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">100</span><span class="p">,</span>
<span class="n">N_exact</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">8</span><span class="p">,</span>
<span class="n">Pinit</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">50</span><span class="p">,</span>
<span class="n">trim_threshold</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">100</span><span class="p">,</span>
<span class="n">minval</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">float</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
<span class="n">maxval</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">float</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
<span class="n">force</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
<span class="p">)</span> <span class="o">-&gt;</span> <span class="n">ModelSetup</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Set up the model by computing or loading necessary grids and</span>
<span class="sd"> parameters.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> workdir : str</span>
<span class="sd"> Directory where the results will be stored.</span>
<span class="sd"> params_planck : dict</span>
<span class="sd"> Parameters for the Planck 2018 cosmology.</span>
<span class="sd"> params_P0 : dict</span>
<span class="sd"> Parameters for the normalisation power spectrum.</span>
<span class="sd"> size : int</span>
<span class="sd"> Number of elements in each direction of the box.</span>
<span class="sd"> L : float</span>
<span class="sd"> Comoving length of the box in Mpc/h.</span>
<span class="sd"> S : int</span>
<span class="sd"> Number of support wavenumbers for the input power spectra.</span>
<span class="sd"> N_exact : int</span>
<span class="sd"> Number of support wavenumbers matching the Fourier grid.</span>
<span class="sd"> Pinit : int</span>
<span class="sd"> Maximum number of bins for the summaries.</span>
<span class="sd"> trim_threshold : int</span>
<span class="sd"> Minimum number of modes required per bin.</span>
<span class="sd"> minval : float, optional</span>
<span class="sd"> Minimum k value for the summaries.</span>
<span class="sd"> maxval : float, optional</span>
<span class="sd"> Maximum k value for the summaries.</span>
<span class="sd"> force : bool</span>
<span class="sd"> If True, forces recomputation of the inputs.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> ModelSetup</span>
<span class="sd"> A named tuple containing:</span>
<span class="sd"> - size (int): Number of elements in each direction of the box.</span>
<span class="sd"> - L (float): Comoving length of the box in Mpc/h.</span>
<span class="sd"> - P (int): Number of bins for the summaries.</span>
<span class="sd"> - S (int): Number of support wavenumbers for input powerspectra.</span>
<span class="sd"> - G_sim_path (str): Path to the full Fourier grid file.</span>
<span class="sd"> - G_ss_path (str): Path to the Fourier grid for summaries file.</span>
<span class="sd"> - Pbins_bnd (np.ndarray): Boundaries of summary bins.</span>
<span class="sd"> - Pbins (np.ndarray): Centres of the bins for the summaries.</span>
<span class="sd"> - k_s (np.ndarray): Support wavenumbers for input power spectra.</span>
<span class="sd"> - P_ss_obj_path (str): Path to the summary power spectrum file.</span>
<span class="sd"> - P_0 (np.ndarray): Normalisation power spectrum values.</span>
<span class="sd"> - planck_Pk (np.ndarray): Planck 2018 power spectrum values.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="c1"># Check input parameters</span>
<span class="k">if</span> <span class="n">N_exact</span> <span class="o">&lt;</span> <span class="mi">0</span> <span class="ow">or</span> <span class="n">N_exact</span> <span class="o">&gt;</span> <span class="n">S</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;Parameter &#39;N_exact&#39; must be between 0 and &#39;S&#39;.&quot;</span><span class="p">)</span>
<span class="c1"># Define file paths</span>
<span class="n">G_sim_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">workdir</span><span class="p">,</span> <span class="s2">&quot;G_sim.h5&quot;</span><span class="p">)</span>
<span class="n">k_s_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">workdir</span><span class="p">,</span> <span class="s2">&quot;k_s.npy&quot;</span><span class="p">)</span>
<span class="n">G_ss_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">workdir</span><span class="p">,</span> <span class="s2">&quot;G_ss.h5&quot;</span><span class="p">)</span>
<span class="n">P_ss_obj_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">workdir</span><span class="p">,</span> <span class="s2">&quot;P_ss_obj.h5&quot;</span><span class="p">)</span>
<span class="n">P_0_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">workdir</span><span class="p">,</span> <span class="s2">&quot;P_0.npy&quot;</span><span class="p">)</span>
<span class="n">theta_planck_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">workdir</span><span class="p">,</span> <span class="s2">&quot;theta_planck.npy&quot;</span><span class="p">)</span>
<span class="n">Pbins_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">workdir</span><span class="p">,</span> <span class="s2">&quot;Pbins.npy&quot;</span><span class="p">)</span>
<span class="n">Pbins_bnd_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">workdir</span><span class="p">,</span> <span class="s2">&quot;Pbins_bnd.npy&quot;</span><span class="p">)</span>
<span class="c1"># Compute or load the full Fourier grid</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">G_sim_path</span><span class="p">)</span> <span class="ow">or</span> <span class="n">force</span><span class="p">:</span>
<span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">&quot;Computing Fourier grid...&quot;</span><span class="p">)</span>
<span class="n">G_sim</span> <span class="o">=</span> <span class="n">FourierGrid</span><span class="p">(</span><span class="n">L</span><span class="p">,</span> <span class="n">L</span><span class="p">,</span> <span class="n">L</span><span class="p">,</span> <span class="n">size</span><span class="p">,</span> <span class="n">size</span><span class="p">,</span> <span class="n">size</span><span class="p">)</span>
<span class="n">G_sim</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">G_sim_path</span><span class="p">)</span>
<span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">&quot;Computing Fourier grid done.&quot;</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">&quot;Loading Fourier grid.&quot;</span><span class="p">)</span>
<span class="n">G_sim</span> <span class="o">=</span> <span class="n">FourierGrid</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">G_sim_path</span><span class="p">)</span>
<span class="c1"># Determine minimum and maximum k values</span>
<span class="k">if</span> <span class="n">minval</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">minval</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">G_sim</span><span class="o">.</span><span class="n">k_modes</span><span class="p">[</span><span class="n">G_sim</span><span class="o">.</span><span class="n">k_modes</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">])</span>
<span class="k">if</span> <span class="n">maxval</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">maxval</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span> <span class="o">*</span> <span class="n">size</span> <span class="o">/</span> <span class="n">L</span> <span class="c1"># 1D Nyquist frequency</span>
<span class="c1"># Compute or load support wavenumbers for the input power spectrum</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">k_s_path</span><span class="p">)</span> <span class="ow">or</span> <span class="n">force</span><span class="p">:</span>
<span class="n">logger</span><span class="o">.</span><span class="n">diagnostic</span><span class="p">(</span><span class="s2">&quot;Computing input power spectrum support wavenumbers...&quot;</span><span class="p">)</span>
<span class="n">k_s</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="n">S</span><span class="p">)</span>
<span class="n">sorted_knorms</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">G_sim</span><span class="o">.</span><span class="n">k_modes</span><span class="o">.</span><span class="n">flatten</span><span class="p">())</span>
<span class="n">unique_indices</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">unique</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">round</span><span class="p">(</span><span class="n">sorted_knorms</span><span class="p">,</span> <span class="mi">5</span><span class="p">),</span> <span class="n">return_index</span><span class="o">=</span><span class="kc">True</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
<span class="n">sorted_knorms_corrected</span> <span class="o">=</span> <span class="n">sorted_knorms</span><span class="p">[</span><span class="n">unique_indices</span><span class="p">]</span>
<span class="n">k_s</span><span class="p">[:</span><span class="n">N_exact</span><span class="p">]</span> <span class="o">=</span> <span class="n">sorted_knorms_corrected</span><span class="p">[</span><span class="mi">1</span> <span class="p">:</span> <span class="n">N_exact</span> <span class="o">+</span> <span class="mi">1</span><span class="p">]</span>
<span class="n">k_s_max</span> <span class="o">=</span> <span class="n">get_k_max</span><span class="p">(</span><span class="n">L</span><span class="p">,</span> <span class="n">size</span><span class="p">)</span>
<span class="n">k_s</span><span class="p">[</span><span class="n">N_exact</span><span class="p">:]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">logspace</span><span class="p">(</span>
<span class="n">np</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">sorted_knorms_corrected</span><span class="p">[</span><span class="n">N_exact</span><span class="p">]),</span>
<span class="n">np</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">k_s_max</span><span class="p">),</span>
<span class="n">S</span> <span class="o">-</span> <span class="n">N_exact</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span>
<span class="p">)[</span><span class="mi">1</span><span class="p">:]</span>
<span class="n">np</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="n">k_s_path</span><span class="p">,</span> <span class="n">k_s</span><span class="p">)</span>
<span class="n">logger</span><span class="o">.</span><span class="n">diagnostic</span><span class="p">(</span><span class="s2">&quot;Computing input power spectrum support wavenumbers done.&quot;</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">logger</span><span class="o">.</span><span class="n">diagnostic</span><span class="p">(</span><span class="s2">&quot;Loading input power spectrum support wavenumbers.&quot;</span><span class="p">)</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">k_s</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">k_s_path</span><span class="p">)</span>
<span class="k">except</span> <span class="p">(</span><span class="ne">IOError</span><span class="p">,</span> <span class="ne">FileNotFoundError</span><span class="p">)</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
<span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Failed to load k_s from </span><span class="si">{</span><span class="n">k_s_path</span><span class="si">}</span><span class="s2">: </span><span class="si">{</span><span class="n">e</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="k">raise</span>
<span class="c1"># Initialise Pbins</span>
<span class="n">Pbins_left_bnds_init</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">logspace</span><span class="p">(</span>
<span class="n">np</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">minval</span><span class="p">),</span> <span class="n">np</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">maxval</span><span class="p">),</span> <span class="n">Pinit</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">float32</span>
<span class="p">)</span>
<span class="n">Pbins_left_bnds_init</span> <span class="o">=</span> <span class="n">Pbins_left_bnds_init</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="c1"># Compute or load Fourier grid for the summaries</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">G_ss_path</span><span class="p">)</span> <span class="ow">or</span> <span class="n">force</span><span class="p">:</span>
<span class="n">G_ss</span> <span class="o">=</span> <span class="n">FourierGrid</span><span class="p">(</span>
<span class="n">L</span><span class="p">,</span>
<span class="n">L</span><span class="p">,</span>
<span class="n">L</span><span class="p">,</span>
<span class="n">size</span><span class="p">,</span>
<span class="n">size</span><span class="p">,</span>
<span class="n">size</span><span class="p">,</span>
<span class="n">k_modes</span><span class="o">=</span><span class="n">Pbins_left_bnds_init</span><span class="p">,</span>
<span class="n">kmax</span><span class="o">=</span><span class="n">maxval</span><span class="p">,</span>
<span class="n">trim_bins</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="n">trim_threshold</span><span class="o">=</span><span class="n">trim_threshold</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">G_ss</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">G_ss_path</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">G_ss</span> <span class="o">=</span> <span class="n">FourierGrid</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">G_ss_path</span><span class="p">)</span>
<span class="n">P</span> <span class="o">=</span> <span class="n">G_ss</span><span class="o">.</span><span class="n">NUM_MODES</span>
<span class="c1"># Compute or load Pbins and Pbins_bnd</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">Pbins_path</span><span class="p">)</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">Pbins_bnd_path</span><span class="p">)</span> <span class="ow">or</span> <span class="n">force</span><span class="p">:</span>
<span class="n">k_ss_max_offset</span> <span class="o">=</span> <span class="n">Pbins_left_bnds_init</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">-</span> <span class="n">Pbins_left_bnds_init</span><span class="p">[</span><span class="o">-</span><span class="mi">2</span><span class="p">]</span>
<span class="n">logger</span><span class="o">.</span><span class="n">diagnostic</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;k_ss_max_offset: </span><span class="si">{</span><span class="n">k_ss_max_offset</span><span class="si">:</span><span class="s2">.5f</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="n">Pbins_bnd</span> <span class="o">=</span> <span class="n">G_ss</span><span class="o">.</span><span class="n">k_modes</span>
<span class="n">Pbins_bnd</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">([</span><span class="n">Pbins_bnd</span><span class="p">,</span> <span class="p">[</span><span class="n">Pbins_bnd</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="n">k_ss_max_offset</span><span class="p">]])</span>
<span class="n">Pbins</span> <span class="o">=</span> <span class="p">(</span><span class="n">Pbins_bnd</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span> <span class="o">+</span> <span class="n">Pbins_bnd</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span> <span class="o">/</span> <span class="mi">2</span>
<span class="n">np</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="n">Pbins_path</span><span class="p">,</span> <span class="n">Pbins</span><span class="p">)</span>
<span class="n">np</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="n">Pbins_bnd_path</span><span class="p">,</span> <span class="n">Pbins_bnd</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">Pbins</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">Pbins_path</span><span class="p">)</span>
<span class="n">Pbins_bnd</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">Pbins_bnd_path</span><span class="p">)</span>
<span class="k">except</span> <span class="p">(</span><span class="ne">IOError</span><span class="p">,</span> <span class="ne">FileNotFoundError</span><span class="p">)</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
<span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Failed to load Pbins or Pbins_bnd: </span><span class="si">{</span><span class="n">e</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="k">raise</span>
<span class="c1"># Compute or load BBKS spectrum for normalisation</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">P_0_path</span><span class="p">)</span> <span class="ow">or</span> <span class="n">force</span><span class="p">:</span>
<span class="n">P_0</span> <span class="o">=</span> <span class="n">get_Pk</span><span class="p">(</span><span class="n">k_s</span><span class="p">,</span> <span class="n">params_P0</span><span class="p">)</span>
<span class="n">np</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="n">P_0_path</span><span class="p">,</span> <span class="n">P_0</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">P_0</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">P_0_path</span><span class="p">)</span>
<span class="k">except</span> <span class="p">(</span><span class="ne">IOError</span><span class="p">,</span> <span class="ne">FileNotFoundError</span><span class="p">)</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
<span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Failed to load P_0 from </span><span class="si">{</span><span class="n">P_0_path</span><span class="si">}</span><span class="s2">: </span><span class="si">{</span><span class="n">e</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="k">raise</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">P_ss_obj_path</span><span class="p">)</span> <span class="ow">or</span> <span class="n">force</span><span class="p">:</span>
<span class="n">P_0_ss</span> <span class="o">=</span> <span class="n">get_Pk</span><span class="p">(</span><span class="n">G_ss</span><span class="o">.</span><span class="n">k_modes</span><span class="p">,</span> <span class="n">params_P0</span><span class="p">)</span>
<span class="n">P_ss_obj</span> <span class="o">=</span> <span class="n">PowerSpectrum</span><span class="o">.</span><span class="n">from_FourierGrid</span><span class="p">(</span><span class="n">G_ss</span><span class="p">,</span> <span class="n">powerspectrum</span><span class="o">=</span><span class="n">P_0_ss</span><span class="p">,</span> <span class="n">cosmo</span><span class="o">=</span><span class="n">params_P0</span><span class="p">)</span>
<span class="n">P_ss_obj</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">P_ss_obj_path</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">P_ss_obj</span> <span class="o">=</span> <span class="n">PowerSpectrum</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">P_ss_obj_path</span><span class="p">)</span>
<span class="c1"># Compute or load Planck power spectrum</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">theta_planck_path</span><span class="p">)</span> <span class="ow">or</span> <span class="n">force</span><span class="p">:</span>
<span class="n">planck_Pk</span> <span class="o">=</span> <span class="n">get_Pk</span><span class="p">(</span><span class="n">k_s</span><span class="p">,</span> <span class="n">params_planck</span><span class="p">)</span>
<span class="n">np</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="n">theta_planck_path</span><span class="p">,</span> <span class="n">planck_Pk</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">planck_Pk</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">theta_planck_path</span><span class="p">)</span>
<span class="k">except</span> <span class="p">(</span><span class="ne">IOError</span><span class="p">,</span> <span class="ne">FileNotFoundError</span><span class="p">)</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
<span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Failed to load theta_planck from </span><span class="si">{</span><span class="n">theta_planck_path</span><span class="si">}</span><span class="s2">: </span><span class="si">{</span><span class="n">e</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="k">raise</span>
<span class="c1"># Clean up</span>
<span class="k">del</span> <span class="n">G_sim</span><span class="p">,</span> <span class="n">G_ss</span><span class="p">,</span> <span class="n">P_ss_obj</span><span class="p">,</span> <span class="n">Pbins_left_bnds_init</span>
<span class="n">gc</span><span class="o">.</span><span class="n">collect</span><span class="p">()</span>
<span class="k">return</span> <span class="n">ModelSetup</span><span class="p">(</span>
<span class="n">size</span><span class="p">,</span>
<span class="n">L</span><span class="p">,</span>
<span class="n">P</span><span class="p">,</span>
<span class="n">S</span><span class="p">,</span>
<span class="n">G_sim_path</span><span class="p">,</span>
<span class="n">G_ss_path</span><span class="p">,</span>
<span class="n">Pbins_bnd</span><span class="p">,</span>
<span class="n">Pbins</span><span class="p">,</span>
<span class="n">k_s</span><span class="p">,</span>
<span class="n">P_ss_obj_path</span><span class="p">,</span>
<span class="n">P_0</span><span class="p">,</span>
<span class="n">planck_Pk</span><span class="p">,</span>
<span class="p">)</span></div>
<div class="viewcode-block" id="compute_alpha_cv">
<a class="viewcode-back" href="../../selfisys.setup_model.html#selfisys.setup_model.compute_alpha_cv">[docs]</a>
<span class="k">def</span> <span class="nf">compute_alpha_cv</span><span class="p">(</span>
<span class="n">workdir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
<span class="n">k_s</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
<span class="n">size</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
<span class="n">L</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span>
<span class="n">window_fct_path</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
<span class="n">force</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
<span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Compute the cosmic variance parameter alpha_cv.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> workdir : str</span>
<span class="sd"> Directory where the results will be stored.</span>
<span class="sd"> k_s : np.ndarray</span>
<span class="sd"> Support wavenumbers.</span>
<span class="sd"> size : int</span>
<span class="sd"> Number of elements in each direction of the box.</span>
<span class="sd"> L : float</span>
<span class="sd"> Comoving length of the box in Mpc/h.</span>
<span class="sd"> window_fct_path : str, optional</span>
<span class="sd"> Path to the window function file.</span>
<span class="sd"> force : bool</span>
<span class="sd"> If True, forces recomputation of the inputs.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">from</span> <span class="nn">scipy.optimize</span> <span class="kn">import</span> <span class="n">curve_fit</span>
<span class="n">alpha_cv_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">workdir</span><span class="p">,</span> <span class="s2">&quot;alpha_cv.npy&quot;</span><span class="p">)</span>
<span class="n">alpha_cv_eff_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">workdir</span><span class="p">,</span> <span class="s2">&quot;alpha_cv_eff.npy&quot;</span><span class="p">)</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">alpha_cv_path</span><span class="p">)</span> <span class="ow">or</span> <span class="n">force</span><span class="p">:</span>
<span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">&quot;Computing cosmic variance alpha_cv...&quot;</span><span class="p">)</span>
<span class="n">k_s_bnd</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">([</span><span class="n">k_s</span><span class="p">,</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">inf</span><span class="p">]])</span>
<span class="n">G_sim</span> <span class="o">=</span> <span class="n">FourierGrid</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">workdir</span><span class="p">,</span> <span class="s2">&quot;G_sim.h5&quot;</span><span class="p">))</span><span class="o">.</span><span class="n">k_modes</span><span class="o">.</span><span class="n">flatten</span><span class="p">()</span>
<span class="n">knorms</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">G_sim</span><span class="p">)</span>
<span class="n">Nks</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">histogram</span><span class="p">(</span><span class="n">knorms</span><span class="p">,</span> <span class="n">bins</span><span class="o">=</span><span class="n">k_s_bnd</span><span class="p">)</span>
<span class="k">del</span> <span class="n">knorms</span><span class="p">,</span> <span class="n">G_sim</span>
<span class="n">nyquist_frequency</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span> <span class="o">*</span> <span class="n">size</span> <span class="o">/</span> <span class="n">L</span>
<span class="n">idx_nyquist</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">searchsorted</span><span class="p">(</span><span class="n">k_s</span><span class="p">,</span> <span class="n">nyquist_frequency</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">cubic_func</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">a</span><span class="p">):</span>
<span class="k">return</span> <span class="n">a</span> <span class="o">*</span> <span class="n">x</span><span class="o">**</span><span class="mi">3</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">popt</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">curve_fit</span><span class="p">(</span><span class="n">cubic_func</span><span class="p">,</span> <span class="n">k_s</span><span class="p">[:</span><span class="n">idx_nyquist</span><span class="p">],</span> <span class="n">Nks</span><span class="p">[:</span><span class="n">idx_nyquist</span><span class="p">])</span>
<span class="k">except</span> <span class="ne">RuntimeError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
<span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Curve fitting failed: </span><span class="si">{</span><span class="n">e</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="k">raise</span>
<span class="n">alpha_cv</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="mi">1</span> <span class="o">/</span> <span class="n">popt</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="n">np</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="n">alpha_cv_path</span><span class="p">,</span> <span class="n">alpha_cv</span><span class="p">)</span>
<span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Computing cosmic variance alpha_cv done. alpha_cv = </span><span class="si">{</span><span class="n">alpha_cv</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="k">if</span> <span class="n">window_fct_path</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="c1"># Compute alpha_cv with approximate correction for the effective volume</span>
<span class="n">nnz</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">with</span> <span class="n">File</span><span class="p">(</span><span class="n">window_fct_path</span><span class="p">,</span> <span class="s2">&quot;r&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
<span class="k">for</span> <span class="n">ipop</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">3</span><span class="p">):</span>
<span class="n">mask</span> <span class="o">=</span> <span class="n">f</span><span class="p">[</span><span class="s2">&quot;select_fct&quot;</span><span class="p">][:][</span><span class="n">ipop</span><span class="p">]</span>
<span class="n">nnz</span> <span class="o">+=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">mask</span><span class="p">)</span>
<span class="n">nnz_size</span> <span class="o">=</span> <span class="n">nnz</span> <span class="o">**</span> <span class="p">(</span><span class="mi">1</span> <span class="o">/</span> <span class="mf">3.0</span><span class="p">)</span> <span class="c1"># Side length of a cube containing nnz voxels</span>
<span class="n">eff_L</span> <span class="o">=</span> <span class="n">nnz_size</span> <span class="o">*</span> <span class="n">L</span> <span class="o">/</span> <span class="n">size</span>
<span class="n">alpha_cv_eff</span> <span class="o">=</span> <span class="n">alpha_cv</span> <span class="o">*</span> <span class="p">(</span><span class="n">L</span> <span class="o">/</span> <span class="n">eff_L</span><span class="p">)</span> <span class="o">**</span> <span class="mf">1.5</span>
<span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Effective length: </span><span class="si">{</span><span class="n">eff_L</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="mf">1e-3</span><span class="si">}</span><span class="s2"> Gpc/h&quot;</span><span class="p">)</span>
<span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Effective volume: </span><span class="si">{</span><span class="p">(</span><span class="n">eff_L</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="mf">1e-3</span><span class="p">)</span><span class="w"> </span><span class="o">**</span><span class="w"> </span><span class="mi">3</span><span class="si">}</span><span class="s2"> (Gpc/h)^3&quot;</span><span class="p">)</span>
<span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;alpha_cv_eff = </span><span class="si">{</span><span class="n">alpha_cv_eff</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="n">np</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="n">alpha_cv_eff_path</span><span class="p">,</span> <span class="n">alpha_cv_eff</span><span class="p">)</span>
<span class="n">gc</span><span class="o">.</span><span class="n">collect</span><span class="p">()</span></div>
</pre></div>
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<p class="caption" role="heading"><span class="caption-text">API Documentation</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.hiddenbox.html">hiddenbox</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox"><code class="docutils literal notranslate"><span class="pre">HiddenBox</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Npop"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Npop</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Ntimesteps"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Ntimesteps</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Psingle"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Psingle</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.compute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.compute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.evaluate"><code class="docutils literal notranslate"><span class="pre">HiddenBox.evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_neglect_lightcone"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_neglect_lightcone</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_recompute_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_recompute_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.gravity_on"><code class="docutils literal notranslate"><span class="pre">HiddenBox.gravity_on</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.load_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.load_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.make_data"><code class="docutils literal notranslate"><span class="pre">HiddenBox.make_data()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.modified_selfi"><code class="docutils literal notranslate"><span class="pre">HiddenBox.modified_selfi</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.prefix_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.prefix_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.reset_survey"><code class="docutils literal notranslate"><span class="pre">HiddenBox.reset_survey()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.setup_only"><code class="docutils literal notranslate"><span class="pre">HiddenBox.setup_only</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_recompute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_recompute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_setup"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_setup()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.update"><code class="docutils literal notranslate"><span class="pre">HiddenBox.update()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.normalise_hb.html">normalise_hb</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.define_normalisation"><code class="docutils literal notranslate"><span class="pre">define_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation"><code class="docutils literal notranslate"><span class="pre">worker_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_public"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_public()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_wrapper"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_wrapper()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.prior.html">prior</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.logposterior_hyperparameters_parallel"><code class="docutils literal notranslate"><span class="pre">logposterior_hyperparameters_parallel()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.perform_prior_optimisation_and_plot"><code class="docutils literal notranslate"><span class="pre">perform_prior_optimisation_and_plot()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior"><code class="docutils literal notranslate"><span class="pre">planck_prior</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.mean"><code class="docutils literal notranslate"><span class="pre">planck_prior.mean</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.inv_covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.inv_covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_max"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_max</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_min"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_min</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.compute"><code class="docutils literal notranslate"><span class="pre">planck_prior.compute()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.load"><code class="docutils literal notranslate"><span class="pre">planck_prior.load()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.logpdf"><code class="docutils literal notranslate"><span class="pre">planck_prior.logpdf()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.sample"><code class="docutils literal notranslate"><span class="pre">planck_prior.sample()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.save"><code class="docutils literal notranslate"><span class="pre">planck_prior.save()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.worker_class"><code class="docutils literal notranslate"><span class="pre">worker_class()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.selection_functions.html">selection_functions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.init_selection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.init_selection()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.lognormals_z_to_x"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.lognormals_z_to_x()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.r_grid"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.r_grid()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.selfi_interface.html">selfi_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.PrintMessage"><code class="docutils literal notranslate"><span class="pre">PrintMessage()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.indent"><code class="docutils literal notranslate"><span class="pre">indent()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.unindent"><code class="docutils literal notranslate"><span class="pre">unindent()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.sbmy_interface.html">sbmy_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.compute_Phi"><code class="docutils literal notranslate"><span class="pre">compute_Phi()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.generate_white_noise_Field"><code class="docutils literal notranslate"><span class="pre">generate_white_noise_Field()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.get_power_spectrum_from_cosmo"><code class="docutils literal notranslate"><span class="pre">get_power_spectrum_from_cosmo()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.handle_time_stepping"><code class="docutils literal notranslate"><span class="pre">handle_time_stepping()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.setup_sbmy_parfiles"><code class="docutils literal notranslate"><span class="pre">setup_sbmy_parfiles()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.grf.html">grf</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.grf.html#selfisys.grf.primordial_grf"><code class="docutils literal notranslate"><span class="pre">primordial_grf()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.utils.html">selfisys.utils package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.examples_utils">selfisys.utils.examples_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.examples_utils.clear_large_plot"><code class="docutils literal notranslate"><span class="pre">clear_large_plot()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.logger">selfisys.utils.logger module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLogger"><code class="docutils literal notranslate"><span class="pre">CustomLogger</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLogger.diagnostic"><code class="docutils literal notranslate"><span class="pre">CustomLogger.diagnostic()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler.emit"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler.emit()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.INDENT"><code class="docutils literal notranslate"><span class="pre">INDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintDiagnostic"><code class="docutils literal notranslate"><span class="pre">PrintDiagnostic()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintError"><code class="docutils literal notranslate"><span class="pre">PrintError()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintInfo"><code class="docutils literal notranslate"><span class="pre">PrintInfo()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintLeftType"><code class="docutils literal notranslate"><span class="pre">PrintLeftType()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintWarning"><code class="docutils literal notranslate"><span class="pre">PrintWarning()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.UNINDENT"><code class="docutils literal notranslate"><span class="pre">UNINDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.getCustomLogger"><code class="docutils literal notranslate"><span class="pre">getCustomLogger()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.low_level">selfisys.utils.low_level module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.low_level.stderr_redirector"><code class="docutils literal notranslate"><span class="pre">stderr_redirector()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.low_level.stdout_redirector"><code class="docutils literal notranslate"><span class="pre">stdout_redirector()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.parser">selfisys.utils.parser module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.bool_sh"><code class="docutils literal notranslate"><span class="pre">bool_sh()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.check_files_exist"><code class="docutils literal notranslate"><span class="pre">check_files_exist()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.intNone"><code class="docutils literal notranslate"><span class="pre">intNone()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.joinstrs"><code class="docutils literal notranslate"><span class="pre">joinstrs()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.joinstrs_only"><code class="docutils literal notranslate"><span class="pre">joinstrs_only()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.safe_npload"><code class="docutils literal notranslate"><span class="pre">safe_npload()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.path_utils">selfisys.utils.path_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.path_utils.file_names_evaluate"><code class="docutils literal notranslate"><span class="pre">file_names_evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.path_utils.get_file_names"><code class="docutils literal notranslate"><span class="pre">get_file_names()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.plot_examples">selfisys.utils.plot_examples module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_comoving_distance_redshift"><code class="docutils literal notranslate"><span class="pre">plot_comoving_distance_redshift()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_galaxy_field_slice"><code class="docutils literal notranslate"><span class="pre">plot_galaxy_field_slice()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_power_spectrum"><code class="docutils literal notranslate"><span class="pre">plot_power_spectrum()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_selection_functions_def_in_z"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions_def_in_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.redshift_distance_conversion"><code class="docutils literal notranslate"><span class="pre">redshift_distance_conversion()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.relative_error_analysis"><code class="docutils literal notranslate"><span class="pre">relative_error_analysis()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.plot_params">selfisys.utils.plot_params module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.get_offset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.get_offset()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_scientific"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_scientific()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_useOffset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_useOffset()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.create_all_colormaps"><code class="docutils literal notranslate"><span class="pre">create_all_colormaps()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.create_colormap"><code class="docutils literal notranslate"><span class="pre">create_colormap()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.dynamic_text_scaling"><code class="docutils literal notranslate"><span class="pre">dynamic_text_scaling()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.get_contours"><code class="docutils literal notranslate"><span class="pre">get_contours()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.reset_plotting"><code class="docutils literal notranslate"><span class="pre">reset_plotting()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.setup_plotting"><code class="docutils literal notranslate"><span class="pre">setup_plotting()</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.plot_utils">selfisys.utils.plot_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_C"><code class="docutils literal notranslate"><span class="pre">plot_C()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_fisher"><code class="docutils literal notranslate"><span class="pre">plot_fisher()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_gradients"><code class="docutils literal notranslate"><span class="pre">plot_gradients()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_histogram"><code class="docutils literal notranslate"><span class="pre">plot_histogram()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks"><code class="docutils literal notranslate"><span class="pre">plot_mocks()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks_compact"><code class="docutils literal notranslate"><span class="pre">plot_mocks_compact()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_observations"><code class="docutils literal notranslate"><span class="pre">plot_observations()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_prior_and_posterior_covariances"><code class="docutils literal notranslate"><span class="pre">plot_prior_and_posterior_covariances()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_reconstruction"><code class="docutils literal notranslate"><span class="pre">plot_reconstruction()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_selection_functions"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plotly_3d"><code class="docutils literal notranslate"><span class="pre">plotly_3d()</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.timestepping">selfisys.utils.timestepping module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.timestepping.merge_nTS"><code class="docutils literal notranslate"><span class="pre">merge_nTS()</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.tools">selfisys.utils.tools module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.cosmo_vector_to_Simbelmyne_dict"><code class="docutils literal notranslate"><span class="pre">cosmo_vector_to_Simbelmyne_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.cosmo_vector_to_class_dict"><code class="docutils literal notranslate"><span class="pre">cosmo_vector_to_class_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.custom_stat"><code class="docutils literal notranslate"><span class="pre">custom_stat()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.fisher_rao"><code class="docutils literal notranslate"><span class="pre">fisher_rao()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.get_k_max"><code class="docutils literal notranslate"><span class="pre">get_k_max()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.params_ids_to_Simbelmyne_dict"><code class="docutils literal notranslate"><span class="pre">params_ids_to_Simbelmyne_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.sample_omega_from_prior"><code class="docutils literal notranslate"><span class="pre">sample_omega_from_prior()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.summary_to_score"><code class="docutils literal notranslate"><span class="pre">summary_to_score()</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.workers">selfisys.utils.workers module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.workers.Simbelmyne_worker"><code class="docutils literal notranslate"><span class="pre">Simbelmyne_worker()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.workers.evaluate_gradient_of_Symbelmyne"><code class="docutils literal notranslate"><span class="pre">evaluate_gradient_of_Symbelmyne()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.workers.worker_gradient_Symbelmyne"><code class="docutils literal notranslate"><span class="pre">worker_gradient_Symbelmyne()</span></code></a></li>
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<h1>Source code for selfisys.utils.examples_utils</h1><div class="highlight"><pre>
<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="c1"># Copyright (C) 2024 Tristan Hoellinger</span>
<span class="c1"># Distributed under the GNU General Public License v3.0 (GPLv3).</span>
<span class="c1"># See the LICENSE file in the root directory for details.</span>
<span class="c1"># SPDX-License-Identifier: GPL-3.0-or-later</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="n">__author__</span> <span class="o">=</span> <span class="s2">&quot;Tristan Hoellinger&quot;</span>
<span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;0.1.0&quot;</span>
<span class="n">__date__</span> <span class="o">=</span> <span class="s2">&quot;2024&quot;</span>
<span class="n">__license__</span> <span class="o">=</span> <span class="s2">&quot;GPLv3&quot;</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd">This module provides utility functions for the examples.</span>
<span class="sd">&quot;&quot;&quot;</span>
<div class="viewcode-block" id="clear_large_plot">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.examples_utils.clear_large_plot">[docs]</a>
<span class="k">def</span> <span class="nf">clear_large_plot</span><span class="p">(</span><span class="n">fig</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Clear a figure to free up memory.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> fig : matplotlib.figure.Figure</span>
<span class="sd"> The figure to clear.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">from</span> <span class="nn">IPython.display</span> <span class="kn">import</span> <span class="n">clear_output</span>
<span class="k">del</span> <span class="n">fig</span>
<span class="n">clear_output</span><span class="p">()</span></div>
</pre></div>
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<p class="caption" role="heading"><span class="caption-text">API Documentation</span></p>
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<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.hiddenbox.html">hiddenbox</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox"><code class="docutils literal notranslate"><span class="pre">HiddenBox</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Npop"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Npop</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Ntimesteps"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Ntimesteps</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Psingle"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Psingle</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.compute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.compute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.evaluate"><code class="docutils literal notranslate"><span class="pre">HiddenBox.evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_neglect_lightcone"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_neglect_lightcone</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_recompute_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_recompute_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.gravity_on"><code class="docutils literal notranslate"><span class="pre">HiddenBox.gravity_on</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.load_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.load_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.make_data"><code class="docutils literal notranslate"><span class="pre">HiddenBox.make_data()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.modified_selfi"><code class="docutils literal notranslate"><span class="pre">HiddenBox.modified_selfi</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.prefix_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.prefix_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.reset_survey"><code class="docutils literal notranslate"><span class="pre">HiddenBox.reset_survey()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.setup_only"><code class="docutils literal notranslate"><span class="pre">HiddenBox.setup_only</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_recompute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_recompute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_setup"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_setup()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.update"><code class="docutils literal notranslate"><span class="pre">HiddenBox.update()</span></code></a></li>
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<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.normalise_hb.html">normalise_hb</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.define_normalisation"><code class="docutils literal notranslate"><span class="pre">define_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation"><code class="docutils literal notranslate"><span class="pre">worker_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_public"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_public()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_wrapper"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_wrapper()</span></code></a></li>
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<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.prior.html">prior</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.logposterior_hyperparameters_parallel"><code class="docutils literal notranslate"><span class="pre">logposterior_hyperparameters_parallel()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.perform_prior_optimisation_and_plot"><code class="docutils literal notranslate"><span class="pre">perform_prior_optimisation_and_plot()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior"><code class="docutils literal notranslate"><span class="pre">planck_prior</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.mean"><code class="docutils literal notranslate"><span class="pre">planck_prior.mean</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.inv_covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.inv_covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_max"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_max</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.compute"><code class="docutils literal notranslate"><span class="pre">planck_prior.compute()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.load"><code class="docutils literal notranslate"><span class="pre">planck_prior.load()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.logpdf"><code class="docutils literal notranslate"><span class="pre">planck_prior.logpdf()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.sample"><code class="docutils literal notranslate"><span class="pre">planck_prior.sample()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.save"><code class="docutils literal notranslate"><span class="pre">planck_prior.save()</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.worker_class"><code class="docutils literal notranslate"><span class="pre">worker_class()</span></code></a></li>
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<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.selection_functions.html">selection_functions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.init_selection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.init_selection()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.lognormals_z_to_x"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.lognormals_z_to_x()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.r_grid"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.r_grid()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.selfi_interface.html">selfi_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.PrintMessage"><code class="docutils literal notranslate"><span class="pre">PrintMessage()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.indent"><code class="docutils literal notranslate"><span class="pre">indent()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.unindent"><code class="docutils literal notranslate"><span class="pre">unindent()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.sbmy_interface.html">sbmy_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.compute_Phi"><code class="docutils literal notranslate"><span class="pre">compute_Phi()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.generate_white_noise_Field"><code class="docutils literal notranslate"><span class="pre">generate_white_noise_Field()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.get_power_spectrum_from_cosmo"><code class="docutils literal notranslate"><span class="pre">get_power_spectrum_from_cosmo()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.handle_time_stepping"><code class="docutils literal notranslate"><span class="pre">handle_time_stepping()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.setup_sbmy_parfiles"><code class="docutils literal notranslate"><span class="pre">setup_sbmy_parfiles()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.grf.html">grf</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.grf.html#selfisys.grf.primordial_grf"><code class="docutils literal notranslate"><span class="pre">primordial_grf()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.utils.html">selfisys.utils package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.examples_utils">selfisys.utils.examples_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.examples_utils.clear_large_plot"><code class="docutils literal notranslate"><span class="pre">clear_large_plot()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.logger">selfisys.utils.logger module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLogger"><code class="docutils literal notranslate"><span class="pre">CustomLogger</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLogger.diagnostic"><code class="docutils literal notranslate"><span class="pre">CustomLogger.diagnostic()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler.emit"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler.emit()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.INDENT"><code class="docutils literal notranslate"><span class="pre">INDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintDiagnostic"><code class="docutils literal notranslate"><span class="pre">PrintDiagnostic()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintError"><code class="docutils literal notranslate"><span class="pre">PrintError()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintInfo"><code class="docutils literal notranslate"><span class="pre">PrintInfo()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintLeftType"><code class="docutils literal notranslate"><span class="pre">PrintLeftType()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintWarning"><code class="docutils literal notranslate"><span class="pre">PrintWarning()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.UNINDENT"><code class="docutils literal notranslate"><span class="pre">UNINDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.getCustomLogger"><code class="docutils literal notranslate"><span class="pre">getCustomLogger()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.low_level">selfisys.utils.low_level module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.low_level.stderr_redirector"><code class="docutils literal notranslate"><span class="pre">stderr_redirector()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.low_level.stdout_redirector"><code class="docutils literal notranslate"><span class="pre">stdout_redirector()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.parser">selfisys.utils.parser module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.bool_sh"><code class="docutils literal notranslate"><span class="pre">bool_sh()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.check_files_exist"><code class="docutils literal notranslate"><span class="pre">check_files_exist()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.intNone"><code class="docutils literal notranslate"><span class="pre">intNone()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.joinstrs"><code class="docutils literal notranslate"><span class="pre">joinstrs()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.joinstrs_only"><code class="docutils literal notranslate"><span class="pre">joinstrs_only()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.safe_npload"><code class="docutils literal notranslate"><span class="pre">safe_npload()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.path_utils">selfisys.utils.path_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.path_utils.file_names_evaluate"><code class="docutils literal notranslate"><span class="pre">file_names_evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.path_utils.get_file_names"><code class="docutils literal notranslate"><span class="pre">get_file_names()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.plot_examples">selfisys.utils.plot_examples module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_comoving_distance_redshift"><code class="docutils literal notranslate"><span class="pre">plot_comoving_distance_redshift()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_galaxy_field_slice"><code class="docutils literal notranslate"><span class="pre">plot_galaxy_field_slice()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_power_spectrum"><code class="docutils literal notranslate"><span class="pre">plot_power_spectrum()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_selection_functions_def_in_z"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions_def_in_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.redshift_distance_conversion"><code class="docutils literal notranslate"><span class="pre">redshift_distance_conversion()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.relative_error_analysis"><code class="docutils literal notranslate"><span class="pre">relative_error_analysis()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.plot_params">selfisys.utils.plot_params module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.get_offset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.get_offset()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_scientific"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_scientific()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_useOffset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_useOffset()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.create_all_colormaps"><code class="docutils literal notranslate"><span class="pre">create_all_colormaps()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.create_colormap"><code class="docutils literal notranslate"><span class="pre">create_colormap()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.dynamic_text_scaling"><code class="docutils literal notranslate"><span class="pre">dynamic_text_scaling()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.get_contours"><code class="docutils literal notranslate"><span class="pre">get_contours()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.reset_plotting"><code class="docutils literal notranslate"><span class="pre">reset_plotting()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.setup_plotting"><code class="docutils literal notranslate"><span class="pre">setup_plotting()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.plot_utils">selfisys.utils.plot_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_C"><code class="docutils literal notranslate"><span class="pre">plot_C()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_fisher"><code class="docutils literal notranslate"><span class="pre">plot_fisher()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_gradients"><code class="docutils literal notranslate"><span class="pre">plot_gradients()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_histogram"><code class="docutils literal notranslate"><span class="pre">plot_histogram()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks"><code class="docutils literal notranslate"><span class="pre">plot_mocks()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks_compact"><code class="docutils literal notranslate"><span class="pre">plot_mocks_compact()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_observations"><code class="docutils literal notranslate"><span class="pre">plot_observations()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_prior_and_posterior_covariances"><code class="docutils literal notranslate"><span class="pre">plot_prior_and_posterior_covariances()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_reconstruction"><code class="docutils literal notranslate"><span class="pre">plot_reconstruction()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_selection_functions"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plotly_3d"><code class="docutils literal notranslate"><span class="pre">plotly_3d()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.timestepping">selfisys.utils.timestepping module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.timestepping.merge_nTS"><code class="docutils literal notranslate"><span class="pre">merge_nTS()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.tools">selfisys.utils.tools module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.cosmo_vector_to_Simbelmyne_dict"><code class="docutils literal notranslate"><span class="pre">cosmo_vector_to_Simbelmyne_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.cosmo_vector_to_class_dict"><code class="docutils literal notranslate"><span class="pre">cosmo_vector_to_class_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.custom_stat"><code class="docutils literal notranslate"><span class="pre">custom_stat()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.fisher_rao"><code class="docutils literal notranslate"><span class="pre">fisher_rao()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.get_k_max"><code class="docutils literal notranslate"><span class="pre">get_k_max()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.params_ids_to_Simbelmyne_dict"><code class="docutils literal notranslate"><span class="pre">params_ids_to_Simbelmyne_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.sample_omega_from_prior"><code class="docutils literal notranslate"><span class="pre">sample_omega_from_prior()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.summary_to_score"><code class="docutils literal notranslate"><span class="pre">summary_to_score()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.workers">selfisys.utils.workers module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.workers.Simbelmyne_worker"><code class="docutils literal notranslate"><span class="pre">Simbelmyne_worker()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.workers.evaluate_gradient_of_Symbelmyne"><code class="docutils literal notranslate"><span class="pre">evaluate_gradient_of_Symbelmyne()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.workers.worker_gradient_Symbelmyne"><code class="docutils literal notranslate"><span class="pre">worker_gradient_Symbelmyne()</span></code></a></li>
</ul>
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<h1>Source code for selfisys.utils.logger</h1><div class="highlight"><pre>
<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="c1"># Copyright (C) 2024 Tristan Hoellinger</span>
<span class="c1"># Distributed under the GNU General Public License v3.0 (GPLv3).</span>
<span class="c1"># See the LICENSE file in the root directory for details.</span>
<span class="c1"># SPDX-License-Identifier: GPL-3.0-or-later</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="n">__author__</span> <span class="o">=</span> <span class="s2">&quot;Tristan Hoellinger&quot;</span>
<span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;0.1.0&quot;</span>
<span class="n">__date__</span> <span class="o">=</span> <span class="s2">&quot;2024&quot;</span>
<span class="n">__license__</span> <span class="o">=</span> <span class="s2">&quot;GPLv3&quot;</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd">Logger routines for the SelfiSys package.</span>
<span class="sd">The printing routines and colours are adapted from the Simbelmynë</span>
<span class="sd">comological solver (https://simbelmyne.readthedocs.io/en/latest).</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="kn">import</span> <span class="nn">sys</span>
<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">cast</span>
<span class="kn">import</span> <span class="nn">logging</span>
<span class="kn">from</span> <span class="nn">selfisys</span> <span class="kn">import</span> <span class="n">DEFAULT_VERBOSE_LEVEL</span>
<span class="c1"># Global variables for fonts</span>
<span class="n">FONT_BOLDRED</span> <span class="o">=</span> <span class="s2">&quot;</span><span class="se">\033</span><span class="s2">[1;31m&quot;</span>
<span class="n">FONT_BOLDGREEN</span> <span class="o">=</span> <span class="s2">&quot;</span><span class="se">\033</span><span class="s2">[1;32m&quot;</span>
<span class="n">FONT_BOLDYELLOW</span> <span class="o">=</span> <span class="s2">&quot;</span><span class="se">\033</span><span class="s2">[1;33m&quot;</span>
<span class="n">FONT_BOLDCYAN</span> <span class="o">=</span> <span class="s2">&quot;</span><span class="se">\033</span><span class="s2">[1;36m&quot;</span>
<span class="n">FONT_BOLDGREY</span> <span class="o">=</span> <span class="s2">&quot;</span><span class="se">\033</span><span class="s2">[1;37m&quot;</span>
<span class="n">FONT_LIGHTPURPLE</span> <span class="o">=</span> <span class="s2">&quot;</span><span class="se">\033</span><span class="s2">[38;5;147m&quot;</span>
<span class="n">FONT_NORMAL</span> <span class="o">=</span> <span class="s2">&quot;</span><span class="se">\033</span><span class="s2">[00m&quot;</span>
<span class="c1"># Global variables for verbosity</span>
<span class="n">ERROR_VERBOSITY</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">INFO_VERBOSITY</span> <span class="o">=</span> <span class="mi">1</span>
<span class="n">WARNING_VERBOSITY</span> <span class="o">=</span> <span class="mi">2</span>
<span class="n">DIAGNOSTIC_VERBOSITY</span> <span class="o">=</span> <span class="mi">3</span>
<span class="n">DEBUG_VERBOSITY</span> <span class="o">=</span> <span class="mi">4</span>
<span class="n">DIAGNOSTIC_LEVEL</span> <span class="o">=</span> <span class="mi">15</span>
<span class="n">logging</span><span class="o">.</span><span class="n">addLevelName</span><span class="p">(</span><span class="n">DIAGNOSTIC_LEVEL</span><span class="p">,</span> <span class="s2">&quot;DIAGNOSTIC&quot;</span><span class="p">)</span>
<span class="n">G__ind__</span> <span class="o">=</span> <span class="mi">0</span> <span class="c1"># Global variable for logger indentation</span>
<div class="viewcode-block" id="INDENT">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.logger.INDENT">[docs]</a>
<span class="k">def</span> <span class="nf">INDENT</span><span class="p">():</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Indents the current level of outputs.&quot;&quot;&quot;</span>
<span class="k">global</span> <span class="n">G__ind__</span>
<span class="n">G__ind__</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">return</span> <span class="n">G__ind__</span></div>
<div class="viewcode-block" id="UNINDENT">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.logger.UNINDENT">[docs]</a>
<span class="k">def</span> <span class="nf">UNINDENT</span><span class="p">():</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Unindents the current level of outputs.&quot;&quot;&quot;</span>
<span class="k">global</span> <span class="n">G__ind__</span>
<span class="n">G__ind__</span> <span class="o">-=</span> <span class="mi">1</span>
<span class="k">return</span> <span class="n">G__ind__</span></div>
<div class="viewcode-block" id="PrintLeftType">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintLeftType">[docs]</a>
<span class="k">def</span> <span class="nf">PrintLeftType</span><span class="p">(</span><span class="n">message_type</span><span class="p">,</span> <span class="n">FONT_COLOR</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Prints the type of output to screen.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> message_type (string) : type of message</span>
<span class="sd"> FONT_COLOR (string) : font color for this type of message</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">from</span> <span class="nn">time</span> <span class="kn">import</span> <span class="n">localtime</span><span class="p">,</span> <span class="n">strftime</span>
<span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span>
<span class="s2">&quot;[&quot;</span>
<span class="o">+</span> <span class="n">strftime</span><span class="p">(</span><span class="s2">&quot;%H:%M:%S&quot;</span><span class="p">,</span> <span class="n">localtime</span><span class="p">())</span>
<span class="o">+</span> <span class="s2">&quot;|&quot;</span>
<span class="o">+</span> <span class="n">FONT_COLOR</span>
<span class="o">+</span> <span class="n">message_type</span>
<span class="o">+</span> <span class="n">FONT_NORMAL</span>
<span class="o">+</span> <span class="s2">&quot;]&quot;</span>
<span class="p">)</span>
<span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;==&quot;</span> <span class="o">*</span> <span class="n">G__ind__</span><span class="p">)</span>
<span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;|&quot;</span><span class="p">)</span></div>
<div class="viewcode-block" id="PrintInfo">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintInfo">[docs]</a>
<span class="k">def</span> <span class="nf">PrintInfo</span><span class="p">(</span><span class="n">message</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Prints an information to screen.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> message (string) : message</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="n">DEFAULT_VERBOSE_LEVEL</span> <span class="o">&gt;=</span> <span class="n">INFO_VERBOSITY</span><span class="p">:</span>
<span class="n">PrintLeftType</span><span class="p">(</span><span class="s2">&quot;INFO &quot;</span><span class="p">,</span> <span class="n">FONT_BOLDCYAN</span><span class="p">)</span>
<span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">{}</span><span class="se">\n</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">message</span><span class="p">))</span>
<span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span></div>
<div class="viewcode-block" id="PrintDiagnostic">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintDiagnostic">[docs]</a>
<span class="k">def</span> <span class="nf">PrintDiagnostic</span><span class="p">(</span><span class="n">verbosity</span><span class="p">,</span> <span class="n">message</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Prints a diagnostic to screen.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> verbosity (int) : verbosity of the message</span>
<span class="sd"> message (string) : message</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="n">DEFAULT_VERBOSE_LEVEL</span> <span class="o">&gt;=</span> <span class="n">verbosity</span><span class="p">:</span>
<span class="n">PrintLeftType</span><span class="p">(</span><span class="s2">&quot;DIAGNOSTIC&quot;</span><span class="p">,</span> <span class="n">FONT_BOLDGREY</span><span class="p">)</span>
<span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">{}</span><span class="se">\n</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">message</span><span class="p">))</span></div>
<div class="viewcode-block" id="PrintWarning">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintWarning">[docs]</a>
<span class="k">def</span> <span class="nf">PrintWarning</span><span class="p">(</span><span class="n">message</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Prints a warning to screen.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> message (string) : message</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="n">DEFAULT_VERBOSE_LEVEL</span> <span class="o">&gt;=</span> <span class="n">WARNING_VERBOSITY</span><span class="p">:</span>
<span class="n">PrintLeftType</span><span class="p">(</span><span class="s2">&quot;WARNING &quot;</span><span class="p">,</span> <span class="n">FONT_BOLDYELLOW</span><span class="p">)</span>
<span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">FONT_BOLDYELLOW</span> <span class="o">+</span> <span class="n">message</span> <span class="o">+</span> <span class="n">FONT_NORMAL</span> <span class="o">+</span> <span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span></div>
<div class="viewcode-block" id="PrintError">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintError">[docs]</a>
<span class="k">def</span> <span class="nf">PrintError</span><span class="p">(</span><span class="n">message</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Prints an error to screen.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> message (string) : message</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="n">DEFAULT_VERBOSE_LEVEL</span> <span class="o">&gt;=</span> <span class="n">ERROR_VERBOSITY</span><span class="p">:</span>
<span class="n">PrintLeftType</span><span class="p">(</span><span class="s2">&quot;ERROR &quot;</span><span class="p">,</span> <span class="n">FONT_BOLDRED</span><span class="p">)</span>
<span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">FONT_BOLDRED</span> <span class="o">+</span> <span class="n">message</span> <span class="o">+</span> <span class="n">FONT_NORMAL</span> <span class="o">+</span> <span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span></div>
<div class="viewcode-block" id="CustomLoggerHandler">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler">[docs]</a>
<span class="k">class</span> <span class="nc">CustomLoggerHandler</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">Handler</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Custom logging handler to redirect Python logger messages to custom</span>
<span class="sd"> print functions, with support for verbosity levels in debug</span>
<span class="sd"> messages.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<div class="viewcode-block" id="CustomLoggerHandler.emit">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler.emit">[docs]</a>
<span class="k">def</span> <span class="nf">emit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">record</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Emit a log record.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">log_message</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">record</span><span class="p">)</span>
<span class="n">log_level</span> <span class="o">=</span> <span class="n">record</span><span class="o">.</span><span class="n">levelno</span>
<span class="k">if</span> <span class="n">log_level</span> <span class="o">&gt;=</span> <span class="n">logging</span><span class="o">.</span><span class="n">ERROR</span><span class="p">:</span>
<span class="n">PrintError</span><span class="p">(</span><span class="n">log_message</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">log_level</span> <span class="o">&gt;=</span> <span class="n">logging</span><span class="o">.</span><span class="n">WARNING</span><span class="p">:</span>
<span class="n">PrintWarning</span><span class="p">(</span><span class="n">log_message</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">log_level</span> <span class="o">&gt;=</span> <span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">:</span>
<span class="n">PrintInfo</span><span class="p">(</span><span class="n">log_message</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">log_level</span> <span class="o">==</span> <span class="n">DIAGNOSTIC_LEVEL</span><span class="p">:</span>
<span class="c1"># Retrieve verbosity level from the record</span>
<span class="n">verbosity</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">record</span><span class="p">,</span> <span class="s2">&quot;verbosity&quot;</span><span class="p">,</span> <span class="n">DIAGNOSTIC_VERBOSITY</span><span class="p">)</span>
<span class="n">PrintDiagnostic</span><span class="p">(</span><span class="n">verbosity</span><span class="o">=</span><span class="n">verbosity</span><span class="p">,</span> <span class="n">message</span><span class="o">=</span><span class="n">log_message</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">log_level</span> <span class="o">&gt;=</span> <span class="n">logging</span><span class="o">.</span><span class="n">DEBUG</span><span class="p">:</span>
<span class="n">PrintDiagnostic</span><span class="p">(</span><span class="n">verbosity</span><span class="o">=</span><span class="n">DEBUG_VERBOSITY</span><span class="p">,</span> <span class="n">message</span><span class="o">=</span><span class="n">log_message</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="c1"># Fallback for other levels</span>
<span class="n">PrintInfo</span><span class="p">(</span><span class="n">log_message</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">handleError</span><span class="p">(</span><span class="n">record</span><span class="p">)</span></div>
</div>
<div class="viewcode-block" id="CustomLogger">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLogger">[docs]</a>
<span class="k">class</span> <span class="nc">CustomLogger</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">Logger</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Custom logger class supporting custom verbosity levels in diagnostic</span>
<span class="sd"> messages.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<div class="viewcode-block" id="CustomLogger.diagnostic">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLogger.diagnostic">[docs]</a>
<span class="k">def</span> <span class="nf">diagnostic</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">msg</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="n">verbosity</span><span class="o">=</span><span class="n">DIAGNOSTIC_VERBOSITY</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Log a message with DIAGNOSTIC level.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> msg : str</span>
<span class="sd"> The message to log.</span>
<span class="sd"> verbosity : int, optional</span>
<span class="sd"> The verbosity level required to log this message.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">isEnabledFor</span><span class="p">(</span><span class="n">DIAGNOSTIC_LEVEL</span><span class="p">):</span>
<span class="c1"># Pass verbosity as part of the extra argument</span>
<span class="n">extra</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;extra&quot;</span><span class="p">,</span> <span class="p">{})</span>
<span class="n">extra</span><span class="p">[</span><span class="s2">&quot;verbosity&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">verbosity</span>
<span class="n">kwargs</span><span class="p">[</span><span class="s2">&quot;extra&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">extra</span>
<span class="bp">self</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">DIAGNOSTIC_LEVEL</span><span class="p">,</span> <span class="n">msg</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
</div>
<span class="n">logging</span><span class="o">.</span><span class="n">setLoggerClass</span><span class="p">(</span><span class="n">CustomLogger</span><span class="p">)</span>
<div class="viewcode-block" id="getCustomLogger">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.logger.getCustomLogger">[docs]</a>
<span class="k">def</span> <span class="nf">getCustomLogger</span><span class="p">(</span><span class="n">name</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">CustomLogger</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Get as CustomLogger instance to use the custom printing routines.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> name : str</span>
<span class="sd"> The name of the logger.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> logger : logging.Logger</span>
<span class="sd"> The custom logger instance.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">logging</span><span class="o">.</span><span class="n">setLoggerClass</span><span class="p">(</span><span class="n">CustomLogger</span><span class="p">)</span>
<span class="n">logger</span> <span class="o">=</span> <span class="n">cast</span><span class="p">(</span><span class="n">CustomLogger</span><span class="p">,</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="n">name</span><span class="p">))</span> <span class="c1"># cast for type checkers and PyLance</span>
<span class="n">logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">DEBUG</span><span class="p">)</span> <span class="c1"># Set the desired base logging level</span>
<span class="n">handler</span> <span class="o">=</span> <span class="n">CustomLoggerHandler</span><span class="p">()</span>
<span class="n">formatter</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">Formatter</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">FONT_LIGHTPURPLE</span><span class="si">}</span><span class="s2">(%(name)s)</span><span class="si">{</span><span class="n">FONT_NORMAL</span><span class="si">}</span><span class="s2"> %(message)s&quot;</span><span class="p">)</span>
<span class="n">handler</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">formatter</span><span class="p">)</span>
<span class="c1"># Attach the handler to the logger if not already present</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">logger</span><span class="o">.</span><span class="n">handlers</span><span class="p">:</span>
<span class="n">logger</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">handler</span><span class="p">)</span>
<span class="k">return</span> <span class="n">logger</span></div>
</pre></div>
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<title>selfisys.utils.low_level &mdash; SelfiSys /Users/hoellinger/Library/CloudStorage/Dropbox/travail/these/science/code/SELFI/selfisys/src/ documentation</title>
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<p class="caption" role="heading"><span class="caption-text">API Documentation</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.hiddenbox.html">hiddenbox</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox"><code class="docutils literal notranslate"><span class="pre">HiddenBox</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Npop"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Npop</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Ntimesteps"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Ntimesteps</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Psingle"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Psingle</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.compute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.compute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.evaluate"><code class="docutils literal notranslate"><span class="pre">HiddenBox.evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_neglect_lightcone"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_neglect_lightcone</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_recompute_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_recompute_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.gravity_on"><code class="docutils literal notranslate"><span class="pre">HiddenBox.gravity_on</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.load_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.load_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.make_data"><code class="docutils literal notranslate"><span class="pre">HiddenBox.make_data()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.modified_selfi"><code class="docutils literal notranslate"><span class="pre">HiddenBox.modified_selfi</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.prefix_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.prefix_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.reset_survey"><code class="docutils literal notranslate"><span class="pre">HiddenBox.reset_survey()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.setup_only"><code class="docutils literal notranslate"><span class="pre">HiddenBox.setup_only</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_recompute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_recompute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_setup"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_setup()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.update"><code class="docutils literal notranslate"><span class="pre">HiddenBox.update()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.normalise_hb.html">normalise_hb</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.define_normalisation"><code class="docutils literal notranslate"><span class="pre">define_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation"><code class="docutils literal notranslate"><span class="pre">worker_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_public"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_public()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_wrapper"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_wrapper()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.prior.html">prior</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.logposterior_hyperparameters_parallel"><code class="docutils literal notranslate"><span class="pre">logposterior_hyperparameters_parallel()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.perform_prior_optimisation_and_plot"><code class="docutils literal notranslate"><span class="pre">perform_prior_optimisation_and_plot()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior"><code class="docutils literal notranslate"><span class="pre">planck_prior</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.mean"><code class="docutils literal notranslate"><span class="pre">planck_prior.mean</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.inv_covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.inv_covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_max"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_max</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_min"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_min</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.compute"><code class="docutils literal notranslate"><span class="pre">planck_prior.compute()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.load"><code class="docutils literal notranslate"><span class="pre">planck_prior.load()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.logpdf"><code class="docutils literal notranslate"><span class="pre">planck_prior.logpdf()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.sample"><code class="docutils literal notranslate"><span class="pre">planck_prior.sample()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.save"><code class="docutils literal notranslate"><span class="pre">planck_prior.save()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.worker_class"><code class="docutils literal notranslate"><span class="pre">worker_class()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.selection_functions.html">selection_functions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.init_selection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.init_selection()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.lognormals_z_to_x"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.lognormals_z_to_x()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.r_grid"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.r_grid()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.selfi_interface.html">selfi_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.PrintMessage"><code class="docutils literal notranslate"><span class="pre">PrintMessage()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.indent"><code class="docutils literal notranslate"><span class="pre">indent()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.unindent"><code class="docutils literal notranslate"><span class="pre">unindent()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.sbmy_interface.html">sbmy_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.compute_Phi"><code class="docutils literal notranslate"><span class="pre">compute_Phi()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.generate_white_noise_Field"><code class="docutils literal notranslate"><span class="pre">generate_white_noise_Field()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.get_power_spectrum_from_cosmo"><code class="docutils literal notranslate"><span class="pre">get_power_spectrum_from_cosmo()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.handle_time_stepping"><code class="docutils literal notranslate"><span class="pre">handle_time_stepping()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.setup_sbmy_parfiles"><code class="docutils literal notranslate"><span class="pre">setup_sbmy_parfiles()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.grf.html">grf</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.grf.html#selfisys.grf.primordial_grf"><code class="docutils literal notranslate"><span class="pre">primordial_grf()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.utils.html">selfisys.utils package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.examples_utils">selfisys.utils.examples_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.examples_utils.clear_large_plot"><code class="docutils literal notranslate"><span class="pre">clear_large_plot()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.logger">selfisys.utils.logger module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLogger"><code class="docutils literal notranslate"><span class="pre">CustomLogger</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLogger.diagnostic"><code class="docutils literal notranslate"><span class="pre">CustomLogger.diagnostic()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler.emit"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler.emit()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.INDENT"><code class="docutils literal notranslate"><span class="pre">INDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintDiagnostic"><code class="docutils literal notranslate"><span class="pre">PrintDiagnostic()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintError"><code class="docutils literal notranslate"><span class="pre">PrintError()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintInfo"><code class="docutils literal notranslate"><span class="pre">PrintInfo()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintLeftType"><code class="docutils literal notranslate"><span class="pre">PrintLeftType()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintWarning"><code class="docutils literal notranslate"><span class="pre">PrintWarning()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.UNINDENT"><code class="docutils literal notranslate"><span class="pre">UNINDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.getCustomLogger"><code class="docutils literal notranslate"><span class="pre">getCustomLogger()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.low_level">selfisys.utils.low_level module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.low_level.stderr_redirector"><code class="docutils literal notranslate"><span class="pre">stderr_redirector()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.low_level.stdout_redirector"><code class="docutils literal notranslate"><span class="pre">stdout_redirector()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.parser">selfisys.utils.parser module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.bool_sh"><code class="docutils literal notranslate"><span class="pre">bool_sh()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.check_files_exist"><code class="docutils literal notranslate"><span class="pre">check_files_exist()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.intNone"><code class="docutils literal notranslate"><span class="pre">intNone()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.joinstrs"><code class="docutils literal notranslate"><span class="pre">joinstrs()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.joinstrs_only"><code class="docutils literal notranslate"><span class="pre">joinstrs_only()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.safe_npload"><code class="docutils literal notranslate"><span class="pre">safe_npload()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.path_utils">selfisys.utils.path_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.path_utils.file_names_evaluate"><code class="docutils literal notranslate"><span class="pre">file_names_evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.path_utils.get_file_names"><code class="docutils literal notranslate"><span class="pre">get_file_names()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.plot_examples">selfisys.utils.plot_examples module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_comoving_distance_redshift"><code class="docutils literal notranslate"><span class="pre">plot_comoving_distance_redshift()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_galaxy_field_slice"><code class="docutils literal notranslate"><span class="pre">plot_galaxy_field_slice()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_power_spectrum"><code class="docutils literal notranslate"><span class="pre">plot_power_spectrum()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_selection_functions_def_in_z"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions_def_in_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.redshift_distance_conversion"><code class="docutils literal notranslate"><span class="pre">redshift_distance_conversion()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.relative_error_analysis"><code class="docutils literal notranslate"><span class="pre">relative_error_analysis()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.plot_params">selfisys.utils.plot_params module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11</span></code></a><ul>
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<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_useOffset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_useOffset()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.dynamic_text_scaling"><code class="docutils literal notranslate"><span class="pre">dynamic_text_scaling()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.reset_plotting"><code class="docutils literal notranslate"><span class="pre">reset_plotting()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_C"><code class="docutils literal notranslate"><span class="pre">plot_C()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_fisher"><code class="docutils literal notranslate"><span class="pre">plot_fisher()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_gradients"><code class="docutils literal notranslate"><span class="pre">plot_gradients()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_histogram"><code class="docutils literal notranslate"><span class="pre">plot_histogram()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks"><code class="docutils literal notranslate"><span class="pre">plot_mocks()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks_compact"><code class="docutils literal notranslate"><span class="pre">plot_mocks_compact()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_observations"><code class="docutils literal notranslate"><span class="pre">plot_observations()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_prior_and_posterior_covariances"><code class="docutils literal notranslate"><span class="pre">plot_prior_and_posterior_covariances()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_reconstruction"><code class="docutils literal notranslate"><span class="pre">plot_reconstruction()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_selection_functions"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plotly_3d"><code class="docutils literal notranslate"><span class="pre">plotly_3d()</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.timestepping">selfisys.utils.timestepping module</a><ul>
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<h1>Source code for selfisys.utils.low_level</h1><div class="highlight"><pre>
<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="c1"># Copyright (C) 2024 Tristan Hoellinger</span>
<span class="c1"># Distributed under the GNU General Public License v3.0 (GPLv3).</span>
<span class="c1"># See the LICENSE file in the root directory for details.</span>
<span class="c1"># SPDX-License-Identifier: GPL-3.0-or-later</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="n">__author__</span> <span class="o">=</span> <span class="s2">&quot;Tristan Hoellinger&quot;</span>
<span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;0.1.0&quot;</span>
<span class="n">__date__</span> <span class="o">=</span> <span class="s2">&quot;2024&quot;</span>
<span class="n">__license__</span> <span class="o">=</span> <span class="s2">&quot;GPLv3&quot;</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd">Tools to deal with low-level operations such as redirecting stdout from</span>
<span class="sd">C code.</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="kn">from</span> <span class="nn">contextlib</span> <span class="kn">import</span> <span class="n">contextmanager</span>
<span class="kn">import</span> <span class="nn">platform</span>
<span class="kn">import</span> <span class="nn">ctypes</span>
<span class="kn">import</span> <span class="nn">io</span>
<span class="kn">import</span> <span class="nn">os</span><span class="o">,</span> <span class="nn">sys</span>
<span class="kn">import</span> <span class="nn">tempfile</span>
<span class="n">libc</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">CDLL</span><span class="p">(</span><span class="kc">None</span><span class="p">)</span>
<span class="k">if</span> <span class="n">platform</span><span class="o">.</span><span class="n">system</span><span class="p">()</span> <span class="o">==</span> <span class="s2">&quot;Darwin&quot;</span><span class="p">:</span> <span class="c1"># macOS</span>
<span class="n">stdout_symbol</span> <span class="o">=</span> <span class="s2">&quot;__stdoutp&quot;</span>
<span class="n">stderr_symbol</span> <span class="o">=</span> <span class="s2">&quot;__stderrp&quot;</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">stdout_symbol</span> <span class="o">=</span> <span class="s2">&quot;stdout&quot;</span>
<span class="n">stderr_symbol</span> <span class="o">=</span> <span class="s2">&quot;stderr&quot;</span>
<span class="n">c_stdout</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="o">.</span><span class="n">in_dll</span><span class="p">(</span><span class="n">libc</span><span class="p">,</span> <span class="n">stdout_symbol</span><span class="p">)</span>
<span class="n">c_stderr</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="o">.</span><span class="n">in_dll</span><span class="p">(</span><span class="n">libc</span><span class="p">,</span> <span class="n">stderr_symbol</span><span class="p">)</span>
<span class="c1"># Taken from:</span>
<span class="c1"># https://eli.thegreenplace.net/2015/redirecting-all-kinds-of-stdout-in-python/</span>
<div class="viewcode-block" id="stdout_redirector">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.low_level.stdout_redirector">[docs]</a>
<span class="nd">@contextmanager</span>
<span class="k">def</span> <span class="nf">stdout_redirector</span><span class="p">(</span><span class="n">stream</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;A context manager that redirects stdout to the given stream. For</span>
<span class="sd"> instance, this can be used to redirect C code stdout to None (to</span>
<span class="sd"> avoid cluttering the log, e.g., when using tqdm).</span>
<span class="sd"> Args:</span>
<span class="sd"> stream (file-like object): The stream to which stdout should be</span>
<span class="sd"> redirected.</span>
<span class="sd"> Example:</span>
<span class="sd"> &gt;&gt;&gt; with stdout_redirector(stream):</span>
<span class="sd"> &gt;&gt;&gt; print(&quot;Hello world!&quot;) # Will be printed to stream</span>
<span class="sd"> &gt;&gt;&gt; # instead of stdout.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="c1"># The original fd stdout points to. Usually 1 on POSIX systems.</span>
<span class="n">original_stdout_fd</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">fileno</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">_redirect_stdout</span><span class="p">(</span><span class="n">to_fd</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Redirect stdout to the given file descriptor.&quot;&quot;&quot;</span>
<span class="c1"># Flush the C-level buffer stdout</span>
<span class="n">libc</span><span class="o">.</span><span class="n">fflush</span><span class="p">(</span><span class="n">c_stdout</span><span class="p">)</span>
<span class="c1"># Flush and close sys.stdout - also closes the file descriptor (fd)</span>
<span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="c1"># Make original_stdout_fd point to the same file as to_fd</span>
<span class="n">os</span><span class="o">.</span><span class="n">dup2</span><span class="p">(</span><span class="n">to_fd</span><span class="p">,</span> <span class="n">original_stdout_fd</span><span class="p">)</span>
<span class="c1"># Create a new sys.stdout that points to the redirected fd</span>
<span class="n">sys</span><span class="o">.</span><span class="n">stdout</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">TextIOWrapper</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">fdopen</span><span class="p">(</span><span class="n">original_stdout_fd</span><span class="p">,</span> <span class="s2">&quot;wb&quot;</span><span class="p">))</span>
<span class="c1"># Save a copy of the original stdout fd in saved_stdout_fd</span>
<span class="n">saved_stdout_fd</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">dup</span><span class="p">(</span><span class="n">original_stdout_fd</span><span class="p">)</span>
<span class="k">try</span><span class="p">:</span>
<span class="c1"># Create a temporary file and redirect stdout to it</span>
<span class="n">tfile</span> <span class="o">=</span> <span class="n">tempfile</span><span class="o">.</span><span class="n">TemporaryFile</span><span class="p">(</span><span class="n">mode</span><span class="o">=</span><span class="s2">&quot;w+b&quot;</span><span class="p">)</span>
<span class="n">_redirect_stdout</span><span class="p">(</span><span class="n">tfile</span><span class="o">.</span><span class="n">fileno</span><span class="p">())</span>
<span class="c1"># Yield to caller, then redirect stdout back to the saved fd</span>
<span class="k">yield</span>
<span class="n">_redirect_stdout</span><span class="p">(</span><span class="n">saved_stdout_fd</span><span class="p">)</span>
<span class="c1"># Copy contents of temporary file to the given stream</span>
<span class="n">tfile</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span>
<span class="n">tfile</span><span class="o">.</span><span class="n">seek</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">io</span><span class="o">.</span><span class="n">SEEK_SET</span><span class="p">)</span>
<span class="n">stream</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">tfile</span><span class="o">.</span><span class="n">read</span><span class="p">())</span>
<span class="k">finally</span><span class="p">:</span>
<span class="n">tfile</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="n">os</span><span class="o">.</span><span class="n">close</span><span class="p">(</span><span class="n">saved_stdout_fd</span><span class="p">)</span></div>
<span class="c1"># Adapted from:</span>
<span class="c1"># https://eli.thegreenplace.net/2015/redirecting-all-kinds-of-stdout-in-python/</span>
<div class="viewcode-block" id="stderr_redirector">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.low_level.stderr_redirector">[docs]</a>
<span class="nd">@contextmanager</span>
<span class="k">def</span> <span class="nf">stderr_redirector</span><span class="p">(</span><span class="n">stream</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;A context manager that redirects stderr to the given stream.</span>
<span class="sd"> For instance, this can be used to redirect C code stderr to None (to</span>
<span class="sd"> avoid cluttering the log, e.g., when using tqdm).</span>
<span class="sd"> Use with caution.</span>
<span class="sd"> Args:</span>
<span class="sd"> stream (file-like object): The stream to which stdout should be</span>
<span class="sd"> redirected.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="c1"># The original fd stdout points to. Usually 1 on POSIX systems.</span>
<span class="n">original_stderr_fd</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">fileno</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">_redirect_stderr</span><span class="p">(</span><span class="n">to_fd</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Redirect stderr to the given file descriptor.&quot;&quot;&quot;</span>
<span class="c1"># Flush the C-level buffer stderr</span>
<span class="n">libc</span><span class="o">.</span><span class="n">fflush</span><span class="p">(</span><span class="n">c_stderr</span><span class="p">)</span>
<span class="c1"># Flush and close sys.stderr - also closes the file descriptor (fd)</span>
<span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="c1"># Make original_stderr_fd point to the same file as to_fd</span>
<span class="n">os</span><span class="o">.</span><span class="n">dup2</span><span class="p">(</span><span class="n">to_fd</span><span class="p">,</span> <span class="n">original_stderr_fd</span><span class="p">)</span>
<span class="c1"># Create a new sys.stderr that points to the redirected fd</span>
<span class="n">sys</span><span class="o">.</span><span class="n">stderr</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">TextIOWrapper</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">fdopen</span><span class="p">(</span><span class="n">original_stderr_fd</span><span class="p">,</span> <span class="s2">&quot;wb&quot;</span><span class="p">))</span>
<span class="c1"># Save a copy of the original stdout fd in saved_stdout_fd</span>
<span class="n">saved_stderr_fd</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">dup</span><span class="p">(</span><span class="n">original_stderr_fd</span><span class="p">)</span>
<span class="k">try</span><span class="p">:</span>
<span class="c1"># Create a temporary file and redirect stdout to it</span>
<span class="n">tfile</span> <span class="o">=</span> <span class="n">tempfile</span><span class="o">.</span><span class="n">TemporaryFile</span><span class="p">(</span><span class="n">mode</span><span class="o">=</span><span class="s2">&quot;w+b&quot;</span><span class="p">)</span>
<span class="n">_redirect_stderr</span><span class="p">(</span><span class="n">tfile</span><span class="o">.</span><span class="n">fileno</span><span class="p">())</span>
<span class="c1"># Yield to caller, then redirect stdout back to the saved fd</span>
<span class="k">yield</span>
<span class="n">_redirect_stderr</span><span class="p">(</span><span class="n">saved_stderr_fd</span><span class="p">)</span>
<span class="c1"># Copy contents of temporary file to the given stream</span>
<span class="n">tfile</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span>
<span class="n">tfile</span><span class="o">.</span><span class="n">seek</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">io</span><span class="o">.</span><span class="n">SEEK_SET</span><span class="p">)</span>
<span class="n">stream</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">tfile</span><span class="o">.</span><span class="n">read</span><span class="p">())</span>
<span class="k">finally</span><span class="p">:</span>
<span class="n">tfile</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="n">os</span><span class="o">.</span><span class="n">close</span><span class="p">(</span><span class="n">saved_stderr_fd</span><span class="p">)</span></div>
</pre></div>
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<title>selfisys.utils.parser &mdash; SelfiSys /Users/hoellinger/Library/CloudStorage/Dropbox/travail/these/science/code/SELFI/selfisys/src/ documentation</title>
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<p class="caption" role="heading"><span class="caption-text">API Documentation</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.hiddenbox.html">hiddenbox</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox"><code class="docutils literal notranslate"><span class="pre">HiddenBox</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Npop"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Npop</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Ntimesteps"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Ntimesteps</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Psingle"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Psingle</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.compute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.compute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.evaluate"><code class="docutils literal notranslate"><span class="pre">HiddenBox.evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_neglect_lightcone"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_neglect_lightcone</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_recompute_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_recompute_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.gravity_on"><code class="docutils literal notranslate"><span class="pre">HiddenBox.gravity_on</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.load_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.load_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.make_data"><code class="docutils literal notranslate"><span class="pre">HiddenBox.make_data()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.modified_selfi"><code class="docutils literal notranslate"><span class="pre">HiddenBox.modified_selfi</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.prefix_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.prefix_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.reset_survey"><code class="docutils literal notranslate"><span class="pre">HiddenBox.reset_survey()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.setup_only"><code class="docutils literal notranslate"><span class="pre">HiddenBox.setup_only</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_recompute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_recompute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_setup"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_setup()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.update"><code class="docutils literal notranslate"><span class="pre">HiddenBox.update()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.normalise_hb.html">normalise_hb</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.define_normalisation"><code class="docutils literal notranslate"><span class="pre">define_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation"><code class="docutils literal notranslate"><span class="pre">worker_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_public"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_public()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_wrapper"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_wrapper()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.prior.html">prior</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.logposterior_hyperparameters_parallel"><code class="docutils literal notranslate"><span class="pre">logposterior_hyperparameters_parallel()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.perform_prior_optimisation_and_plot"><code class="docutils literal notranslate"><span class="pre">perform_prior_optimisation_and_plot()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior"><code class="docutils literal notranslate"><span class="pre">planck_prior</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.mean"><code class="docutils literal notranslate"><span class="pre">planck_prior.mean</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.inv_covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.inv_covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_max"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_max</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_min"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_min</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.compute"><code class="docutils literal notranslate"><span class="pre">planck_prior.compute()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.load"><code class="docutils literal notranslate"><span class="pre">planck_prior.load()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.logpdf"><code class="docutils literal notranslate"><span class="pre">planck_prior.logpdf()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.sample"><code class="docutils literal notranslate"><span class="pre">planck_prior.sample()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.save"><code class="docutils literal notranslate"><span class="pre">planck_prior.save()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.worker_class"><code class="docutils literal notranslate"><span class="pre">worker_class()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.selection_functions.html">selection_functions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.init_selection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.init_selection()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.lognormals_z_to_x"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.lognormals_z_to_x()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.r_grid"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.r_grid()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.selfi_interface.html">selfi_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.PrintMessage"><code class="docutils literal notranslate"><span class="pre">PrintMessage()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.indent"><code class="docutils literal notranslate"><span class="pre">indent()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.unindent"><code class="docutils literal notranslate"><span class="pre">unindent()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.sbmy_interface.html">sbmy_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.compute_Phi"><code class="docutils literal notranslate"><span class="pre">compute_Phi()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.generate_white_noise_Field"><code class="docutils literal notranslate"><span class="pre">generate_white_noise_Field()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.get_power_spectrum_from_cosmo"><code class="docutils literal notranslate"><span class="pre">get_power_spectrum_from_cosmo()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.handle_time_stepping"><code class="docutils literal notranslate"><span class="pre">handle_time_stepping()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.setup_sbmy_parfiles"><code class="docutils literal notranslate"><span class="pre">setup_sbmy_parfiles()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.grf.html">grf</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.grf.html#selfisys.grf.primordial_grf"><code class="docutils literal notranslate"><span class="pre">primordial_grf()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.utils.html">selfisys.utils package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.examples_utils">selfisys.utils.examples_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.examples_utils.clear_large_plot"><code class="docutils literal notranslate"><span class="pre">clear_large_plot()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.logger">selfisys.utils.logger module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLogger"><code class="docutils literal notranslate"><span class="pre">CustomLogger</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLogger.diagnostic"><code class="docutils literal notranslate"><span class="pre">CustomLogger.diagnostic()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler.emit"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler.emit()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.INDENT"><code class="docutils literal notranslate"><span class="pre">INDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintDiagnostic"><code class="docutils literal notranslate"><span class="pre">PrintDiagnostic()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintError"><code class="docutils literal notranslate"><span class="pre">PrintError()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintInfo"><code class="docutils literal notranslate"><span class="pre">PrintInfo()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintLeftType"><code class="docutils literal notranslate"><span class="pre">PrintLeftType()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintWarning"><code class="docutils literal notranslate"><span class="pre">PrintWarning()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.UNINDENT"><code class="docutils literal notranslate"><span class="pre">UNINDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.getCustomLogger"><code class="docutils literal notranslate"><span class="pre">getCustomLogger()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.low_level">selfisys.utils.low_level module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.low_level.stderr_redirector"><code class="docutils literal notranslate"><span class="pre">stderr_redirector()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.low_level.stdout_redirector"><code class="docutils literal notranslate"><span class="pre">stdout_redirector()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.parser">selfisys.utils.parser module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.bool_sh"><code class="docutils literal notranslate"><span class="pre">bool_sh()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.check_files_exist"><code class="docutils literal notranslate"><span class="pre">check_files_exist()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.intNone"><code class="docutils literal notranslate"><span class="pre">intNone()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.joinstrs"><code class="docutils literal notranslate"><span class="pre">joinstrs()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.joinstrs_only"><code class="docutils literal notranslate"><span class="pre">joinstrs_only()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.safe_npload"><code class="docutils literal notranslate"><span class="pre">safe_npload()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.path_utils">selfisys.utils.path_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.path_utils.file_names_evaluate"><code class="docutils literal notranslate"><span class="pre">file_names_evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.path_utils.get_file_names"><code class="docutils literal notranslate"><span class="pre">get_file_names()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.plot_examples">selfisys.utils.plot_examples module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_comoving_distance_redshift"><code class="docutils literal notranslate"><span class="pre">plot_comoving_distance_redshift()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_galaxy_field_slice"><code class="docutils literal notranslate"><span class="pre">plot_galaxy_field_slice()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_power_spectrum"><code class="docutils literal notranslate"><span class="pre">plot_power_spectrum()</span></code></a></li>
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</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.plot_params">selfisys.utils.plot_params module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.get_offset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.get_offset()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_scientific"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_scientific()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_useOffset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_useOffset()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.create_all_colormaps"><code class="docutils literal notranslate"><span class="pre">create_all_colormaps()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.create_colormap"><code class="docutils literal notranslate"><span class="pre">create_colormap()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.dynamic_text_scaling"><code class="docutils literal notranslate"><span class="pre">dynamic_text_scaling()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.reset_plotting"><code class="docutils literal notranslate"><span class="pre">reset_plotting()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.setup_plotting"><code class="docutils literal notranslate"><span class="pre">setup_plotting()</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.plot_utils">selfisys.utils.plot_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_C"><code class="docutils literal notranslate"><span class="pre">plot_C()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_histogram"><code class="docutils literal notranslate"><span class="pre">plot_histogram()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks_compact"><code class="docutils literal notranslate"><span class="pre">plot_mocks_compact()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_observations"><code class="docutils literal notranslate"><span class="pre">plot_observations()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_prior_and_posterior_covariances"><code class="docutils literal notranslate"><span class="pre">plot_prior_and_posterior_covariances()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_selection_functions"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plotly_3d"><code class="docutils literal notranslate"><span class="pre">plotly_3d()</span></code></a></li>
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<h1>Source code for selfisys.utils.parser</h1><div class="highlight"><pre>
<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="c1"># Copyright (C) 2024 Tristan Hoellinger</span>
<span class="c1"># Distributed under the GNU General Public License v3.0 (GPLv3).</span>
<span class="c1"># See the LICENSE file in the root directory for details.</span>
<span class="c1"># SPDX-License-Identifier: GPL-3.0-or-later</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="n">__author__</span> <span class="o">=</span> <span class="s2">&quot;Tristan Hoellinger&quot;</span>
<span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;0.1.0&quot;</span>
<span class="n">__date__</span> <span class="o">=</span> <span class="s2">&quot;2024&quot;</span>
<span class="n">__license__</span> <span class="o">=</span> <span class="s2">&quot;GPLv3&quot;</span>
<span class="sd">&quot;&quot;&quot;Utility functions for parsing command-line arguments.</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">from</span> <span class="nn">argparse</span> <span class="kn">import</span> <span class="n">ArgumentParser</span><span class="p">,</span> <span class="n">ArgumentTypeError</span>
<div class="viewcode-block" id="joinstrs">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.parser.joinstrs">[docs]</a>
<span class="k">def</span> <span class="nf">joinstrs</span><span class="p">(</span><span class="n">list_of_strs</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Join a list of strings into a single string.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> list_of_strs : list of str</span>
<span class="sd"> List of strings to join.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> str</span>
<span class="sd"> Concatenated string.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="s2">&quot;&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">list_of_strs</span> <span class="k">if</span> <span class="n">x</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">])</span></div>
<div class="viewcode-block" id="joinstrs_only">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.parser.joinstrs_only">[docs]</a>
<span class="k">def</span> <span class="nf">joinstrs_only</span><span class="p">(</span><span class="n">list_of_strs</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Join a list of strings into a single string, ignoring all</span>
<span class="sd"> non-string elements such as None values.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> list_of_strs : list of str</span>
<span class="sd"> List of strings to join.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> str</span>
<span class="sd"> Concatenated string.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="s2">&quot;&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">list_of_strs</span> <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="o">==</span> <span class="nb">str</span><span class="p">])</span></div>
<div class="viewcode-block" id="check_files_exist">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.parser.check_files_exist">[docs]</a>
<span class="k">def</span> <span class="nf">check_files_exist</span><span class="p">(</span><span class="n">files</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Check if all files in the list exist.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> files : list of str</span>
<span class="sd"> List of file paths to check.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> bool</span>
<span class="sd"> True if all files exist, False otherwise.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="nb">all</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">f</span><span class="p">)</span> <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">files</span><span class="p">)</span></div>
<div class="viewcode-block" id="none_or_bool_or_str">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.parser.none_or_bool_or_str">[docs]</a>
<span class="k">def</span> <span class="nf">none_or_bool_or_str</span><span class="p">(</span><span class="n">value</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Convert a string to None, bool, or str.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> value : str</span>
<span class="sd"> String to convert.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> None, bool, or str</span>
<span class="sd"> Converted value.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="n">value</span> <span class="o">==</span> <span class="s2">&quot;None&quot;</span> <span class="ow">or</span> <span class="n">value</span> <span class="o">==</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">return</span> <span class="kc">None</span>
<span class="k">elif</span> <span class="n">value</span> <span class="o">==</span> <span class="s2">&quot;True&quot;</span><span class="p">:</span>
<span class="k">return</span> <span class="kc">True</span>
<span class="k">elif</span> <span class="n">value</span> <span class="o">==</span> <span class="s2">&quot;False&quot;</span><span class="p">:</span>
<span class="k">return</span> <span class="kc">False</span>
<span class="k">return</span> <span class="n">value</span></div>
<div class="viewcode-block" id="intNone">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.parser.intNone">[docs]</a>
<span class="k">def</span> <span class="nf">intNone</span><span class="p">(</span><span class="n">value</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Convert a string to None or int.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> value : str</span>
<span class="sd"> String to convert.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> None or int</span>
<span class="sd"> Converted value.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="n">value</span> <span class="o">==</span> <span class="s2">&quot;None&quot;</span> <span class="ow">or</span> <span class="n">value</span> <span class="o">==</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">return</span> <span class="kc">None</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="nb">int</span><span class="p">(</span><span class="n">value</span><span class="p">)</span></div>
<div class="viewcode-block" id="safe_npload">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.parser.safe_npload">[docs]</a>
<span class="k">def</span> <span class="nf">safe_npload</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Load a numpy array from a file.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> path : str</span>
<span class="sd"> Path to the file to load.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> None or np.ndarray</span>
<span class="sd"> Loaded array or None if the file does not exist.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="n">val</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">allow_pickle</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="k">if</span> <span class="n">val</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">val</span> <span class="o">==</span> <span class="s2">&quot;None&quot;</span> <span class="ow">or</span> <span class="n">val</span> <span class="o">==</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">return</span> <span class="kc">None</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="n">val</span></div>
<div class="viewcode-block" id="bool_sh">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.parser.bool_sh">[docs]</a>
<span class="k">def</span> <span class="nf">bool_sh</span><span class="p">(</span><span class="n">value</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Convert a string to a boolean.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> value : str</span>
<span class="sd"> String to convert.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> bool</span>
<span class="sd"> Converted value.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="n">value</span> <span class="o">==</span> <span class="s2">&quot;True&quot;</span><span class="p">:</span>
<span class="k">return</span> <span class="kc">True</span>
<span class="k">elif</span> <span class="n">value</span> <span class="o">==</span> <span class="s2">&quot;False&quot;</span><span class="p">:</span>
<span class="k">return</span> <span class="kc">False</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">raise</span> <span class="n">ArgumentTypeError</span><span class="p">(</span><span class="s2">&quot;Boolean value expected.&quot;</span><span class="p">)</span></div>
</pre></div>
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<title>selfisys.utils.path_utils &mdash; SelfiSys /Users/hoellinger/Library/CloudStorage/Dropbox/travail/these/science/code/SELFI/selfisys/src/ documentation</title>
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<p class="caption" role="heading"><span class="caption-text">API Documentation</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.hiddenbox.html">hiddenbox</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox"><code class="docutils literal notranslate"><span class="pre">HiddenBox</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Npop"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Npop</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Ntimesteps"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Ntimesteps</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Psingle"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Psingle</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.compute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.compute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.evaluate"><code class="docutils literal notranslate"><span class="pre">HiddenBox.evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_neglect_lightcone"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_neglect_lightcone</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_recompute_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_recompute_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.gravity_on"><code class="docutils literal notranslate"><span class="pre">HiddenBox.gravity_on</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.load_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.load_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.make_data"><code class="docutils literal notranslate"><span class="pre">HiddenBox.make_data()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.modified_selfi"><code class="docutils literal notranslate"><span class="pre">HiddenBox.modified_selfi</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.prefix_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.prefix_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.reset_survey"><code class="docutils literal notranslate"><span class="pre">HiddenBox.reset_survey()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.setup_only"><code class="docutils literal notranslate"><span class="pre">HiddenBox.setup_only</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_recompute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_recompute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_setup"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_setup()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.update"><code class="docutils literal notranslate"><span class="pre">HiddenBox.update()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.normalise_hb.html">normalise_hb</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.define_normalisation"><code class="docutils literal notranslate"><span class="pre">define_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation"><code class="docutils literal notranslate"><span class="pre">worker_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_public"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_public()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_wrapper"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_wrapper()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.prior.html">prior</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.logposterior_hyperparameters_parallel"><code class="docutils literal notranslate"><span class="pre">logposterior_hyperparameters_parallel()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.perform_prior_optimisation_and_plot"><code class="docutils literal notranslate"><span class="pre">perform_prior_optimisation_and_plot()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior"><code class="docutils literal notranslate"><span class="pre">planck_prior</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.mean"><code class="docutils literal notranslate"><span class="pre">planck_prior.mean</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.inv_covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.inv_covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_max"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_max</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_min"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_min</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.compute"><code class="docutils literal notranslate"><span class="pre">planck_prior.compute()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.load"><code class="docutils literal notranslate"><span class="pre">planck_prior.load()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.logpdf"><code class="docutils literal notranslate"><span class="pre">planck_prior.logpdf()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.sample"><code class="docutils literal notranslate"><span class="pre">planck_prior.sample()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.save"><code class="docutils literal notranslate"><span class="pre">planck_prior.save()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.worker_class"><code class="docutils literal notranslate"><span class="pre">worker_class()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.selection_functions.html">selection_functions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.init_selection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.init_selection()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.lognormals_z_to_x"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.lognormals_z_to_x()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.r_grid"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.r_grid()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.selfi_interface.html">selfi_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.PrintMessage"><code class="docutils literal notranslate"><span class="pre">PrintMessage()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.indent"><code class="docutils literal notranslate"><span class="pre">indent()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.unindent"><code class="docutils literal notranslate"><span class="pre">unindent()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.sbmy_interface.html">sbmy_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.compute_Phi"><code class="docutils literal notranslate"><span class="pre">compute_Phi()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.generate_white_noise_Field"><code class="docutils literal notranslate"><span class="pre">generate_white_noise_Field()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.get_power_spectrum_from_cosmo"><code class="docutils literal notranslate"><span class="pre">get_power_spectrum_from_cosmo()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.handle_time_stepping"><code class="docutils literal notranslate"><span class="pre">handle_time_stepping()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.setup_sbmy_parfiles"><code class="docutils literal notranslate"><span class="pre">setup_sbmy_parfiles()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.grf.html">grf</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.grf.html#selfisys.grf.primordial_grf"><code class="docutils literal notranslate"><span class="pre">primordial_grf()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.utils.html">selfisys.utils package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.examples_utils">selfisys.utils.examples_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.examples_utils.clear_large_plot"><code class="docutils literal notranslate"><span class="pre">clear_large_plot()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.logger">selfisys.utils.logger module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLogger"><code class="docutils literal notranslate"><span class="pre">CustomLogger</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLogger.diagnostic"><code class="docutils literal notranslate"><span class="pre">CustomLogger.diagnostic()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler.emit"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler.emit()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.INDENT"><code class="docutils literal notranslate"><span class="pre">INDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintDiagnostic"><code class="docutils literal notranslate"><span class="pre">PrintDiagnostic()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintError"><code class="docutils literal notranslate"><span class="pre">PrintError()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintInfo"><code class="docutils literal notranslate"><span class="pre">PrintInfo()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintLeftType"><code class="docutils literal notranslate"><span class="pre">PrintLeftType()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintWarning"><code class="docutils literal notranslate"><span class="pre">PrintWarning()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.UNINDENT"><code class="docutils literal notranslate"><span class="pre">UNINDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.getCustomLogger"><code class="docutils literal notranslate"><span class="pre">getCustomLogger()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.low_level">selfisys.utils.low_level module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.low_level.stderr_redirector"><code class="docutils literal notranslate"><span class="pre">stderr_redirector()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.low_level.stdout_redirector"><code class="docutils literal notranslate"><span class="pre">stdout_redirector()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.parser">selfisys.utils.parser module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.bool_sh"><code class="docutils literal notranslate"><span class="pre">bool_sh()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.check_files_exist"><code class="docutils literal notranslate"><span class="pre">check_files_exist()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.intNone"><code class="docutils literal notranslate"><span class="pre">intNone()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.joinstrs"><code class="docutils literal notranslate"><span class="pre">joinstrs()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.joinstrs_only"><code class="docutils literal notranslate"><span class="pre">joinstrs_only()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.safe_npload"><code class="docutils literal notranslate"><span class="pre">safe_npload()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.path_utils">selfisys.utils.path_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.path_utils.file_names_evaluate"><code class="docutils literal notranslate"><span class="pre">file_names_evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.path_utils.get_file_names"><code class="docutils literal notranslate"><span class="pre">get_file_names()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.plot_examples">selfisys.utils.plot_examples module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_comoving_distance_redshift"><code class="docutils literal notranslate"><span class="pre">plot_comoving_distance_redshift()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_galaxy_field_slice"><code class="docutils literal notranslate"><span class="pre">plot_galaxy_field_slice()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_power_spectrum"><code class="docutils literal notranslate"><span class="pre">plot_power_spectrum()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_selection_functions_def_in_z"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions_def_in_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.redshift_distance_conversion"><code class="docutils literal notranslate"><span class="pre">redshift_distance_conversion()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.relative_error_analysis"><code class="docutils literal notranslate"><span class="pre">relative_error_analysis()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.plot_params">selfisys.utils.plot_params module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11</span></code></a><ul>
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<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_C"><code class="docutils literal notranslate"><span class="pre">plot_C()</span></code></a></li>
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<h1>Source code for selfisys.utils.path_utils</h1><div class="highlight"><pre>
<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="c1"># Copyright (C) 2024 Tristan Hoellinger</span>
<span class="c1"># Distributed under the GNU General Public License v3.0 (GPLv3).</span>
<span class="c1"># See the LICENSE file in the root directory for details.</span>
<span class="c1"># SPDX-License-Identifier: GPL-3.0-or-later</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="n">__author__</span> <span class="o">=</span> <span class="s2">&quot;Tristan Hoellinger&quot;</span>
<span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;0.1.0&quot;</span>
<span class="n">__date__</span> <span class="o">=</span> <span class="s2">&quot;2024&quot;</span>
<span class="n">__license__</span> <span class="o">=</span> <span class="s2">&quot;GPLv3&quot;</span>
<span class="sd">&quot;&quot;&quot;Helper functions to handle paths and file names.</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="k">def</span> <span class="nf">_get_prefix</span><span class="p">(</span><span class="n">prefix_mocks</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">suffix</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">sim_id</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">d</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">p</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Get file prefix.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> prefix_mocks : str | None</span>
<span class="sd"> Prefix for the mock data files. If None, defaults to base</span>
<span class="sd"> suffix.</span>
<span class="sd"> suffix : str</span>
<span class="sd"> Base suffix for the file name (e.g., &quot;mocks&quot; or &quot;g&quot;).</span>
<span class="sd"> sim_id : int, optional</span>
<span class="sd"> Simulation ID. Used if d and p are not provided.</span>
<span class="sd"> d : int, optional</span>
<span class="sd"> Direction index.</span>
<span class="sd"> p : int, optional</span>
<span class="sd"> Simulation index. If both d and p are provided, they take</span>
<span class="sd"> precedence over sim_id.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> str</span>
<span class="sd"> Formatted file name string.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">prefix</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">prefix_mocks</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">suffix</span><span class="si">}</span><span class="s2">&quot;</span> <span class="k">if</span> <span class="n">prefix_mocks</span> <span class="k">else</span> <span class="n">suffix</span>
<span class="k">if</span> <span class="n">d</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">p</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">return</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">prefix</span><span class="si">}</span><span class="s2">_d</span><span class="si">{</span><span class="n">d</span><span class="si">}</span><span class="s2">_p</span><span class="si">{</span><span class="n">p</span><span class="si">}</span><span class="s2">.h5&quot;</span>
<span class="k">return</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">prefix</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">sim_id</span><span class="si">}</span><span class="s2">.h5&quot;</span>
<div class="viewcode-block" id="get_file_names">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.path_utils.get_file_names">[docs]</a>
<span class="k">def</span> <span class="nf">get_file_names</span><span class="p">(</span>
<span class="n">fsimdir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
<span class="n">sim_id</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
<span class="n">sim_params</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
<span class="n">TimeSteps</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">int</span><span class="p">],</span>
<span class="n">prefix_mocks</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
<span class="n">gravity_on</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
<span class="n">return_g</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
<span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Generate file paths for a given simulation ID and parameters.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> fsimdir : str</span>
<span class="sd"> Path to the simulation directory.</span>
<span class="sd"> sim_id : int</span>
<span class="sd"> Simulation ID.</span>
<span class="sd"> sim_params : str</span>
<span class="sd"> Simulation parameters.</span>
<span class="sd"> TimeSteps : list of int</span>
<span class="sd"> List of time steps.</span>
<span class="sd"> prefix_mocks : str | None</span>
<span class="sd"> Prefix for mock data files. If None, defaults to &quot;mocks&quot;.</span>
<span class="sd"> gravity_on : bool, optional</span>
<span class="sd"> Whether gravity is active. Default is True.</span>
<span class="sd"> return_g : bool, optional</span>
<span class="sd"> If True, return the file name for the observed galaxy field.</span>
<span class="sd"> Default is False.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> dict</span>
<span class="sd"> Dictionary containing simulation inputs / outputs file paths.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">datadir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">fsimdir</span><span class="p">,</span> <span class="s2">&quot;data&quot;</span><span class="p">)</span>
<span class="n">names</span> <span class="o">=</span> <span class="p">{</span>
<span class="s2">&quot;fname_cosmo&quot;</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">datadir</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;input_cosmo_</span><span class="si">{</span><span class="n">sim_id</span><span class="si">}</span><span class="s2">.json&quot;</span><span class="p">),</span>
<span class="s2">&quot;fname_power_spectrum&quot;</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">datadir</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;input_power_</span><span class="si">{</span><span class="n">sim_id</span><span class="si">}</span><span class="s2">.h5&quot;</span><span class="p">),</span>
<span class="s2">&quot;fname_outputinitialdensity&quot;</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">datadir</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;initial_density_</span><span class="si">{</span><span class="n">sim_id</span><span class="si">}</span><span class="s2">.h5&quot;</span><span class="p">),</span>
<span class="s2">&quot;fname_mocks&quot;</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">datadir</span><span class="p">,</span> <span class="n">_get_prefix</span><span class="p">(</span><span class="n">prefix_mocks</span><span class="p">,</span> <span class="s2">&quot;mocks&quot;</span><span class="p">,</span> <span class="n">sim_id</span><span class="p">)),</span>
<span class="s2">&quot;fname_g&quot;</span><span class="p">:</span> <span class="p">(</span>
<span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">datadir</span><span class="p">,</span> <span class="n">_get_prefix</span><span class="p">(</span><span class="n">prefix_mocks</span><span class="p">,</span> <span class="s2">&quot;g&quot;</span><span class="p">,</span> <span class="n">sim_id</span><span class="p">))</span> <span class="k">if</span> <span class="n">return_g</span> <span class="k">else</span> <span class="kc">None</span>
<span class="p">),</span>
<span class="s2">&quot;fname_simparfile&quot;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
<span class="s2">&quot;fname_whitenoise&quot;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
<span class="s2">&quot;seedname_whitenoise&quot;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
<span class="s2">&quot;fnames_outputLPTdensity&quot;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
<span class="s2">&quot;fnames_outputrealspacedensity&quot;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
<span class="s2">&quot;fnames_outputdensity&quot;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
<span class="s2">&quot;fname_simlogs&quot;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
<span class="p">}</span>
<span class="k">if</span> <span class="n">gravity_on</span><span class="p">:</span>
<span class="n">names</span><span class="o">.</span><span class="n">update</span><span class="p">(</span>
<span class="p">{</span>
<span class="s2">&quot;fname_simparfile&quot;</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">datadir</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;sim_</span><span class="si">{</span><span class="n">sim_id</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">),</span>
<span class="s2">&quot;fname_whitenoise&quot;</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
<span class="n">datadir</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;initial_density_white_noise_</span><span class="si">{</span><span class="n">sim_id</span><span class="si">}</span><span class="s2">.h5&quot;</span>
<span class="p">),</span>
<span class="s2">&quot;seedname_whitenoise&quot;</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">datadir</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;initial_density_wn_</span><span class="si">{</span><span class="n">sim_id</span><span class="si">}</span><span class="s2">_seed&quot;</span><span class="p">),</span>
<span class="s2">&quot;fnames_outputLPTdensity&quot;</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">datadir</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;output_density_</span><span class="si">{</span><span class="n">sim_id</span><span class="si">}</span><span class="s2">.h5&quot;</span><span class="p">),</span>
<span class="s2">&quot;fname_simlogs&quot;</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">datadir</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;logs_sim_</span><span class="si">{</span><span class="n">sim_id</span><span class="si">}</span><span class="s2">.txt&quot;</span><span class="p">),</span>
<span class="p">}</span>
<span class="p">)</span>
<span class="k">if</span> <span class="n">sim_params</span><span class="o">.</span><span class="n">startswith</span><span class="p">((</span><span class="s2">&quot;split&quot;</span><span class="p">,</span> <span class="s2">&quot;custom&quot;</span><span class="p">)):</span>
<span class="n">names</span><span class="p">[</span><span class="s2">&quot;fnames_outputdensity&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span>
<span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">datadir</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;output_density_</span><span class="si">{</span><span class="n">sim_id</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2">.h5&quot;</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">TimeSteps</span><span class="p">[::</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="p">]</span>
<span class="n">names</span><span class="p">[</span><span class="s2">&quot;fnames_outputrealspacedensity&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span>
<span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">datadir</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;output_realdensity_</span><span class="si">{</span><span class="n">sim_id</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2">.h5&quot;</span><span class="p">)</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">TimeSteps</span><span class="p">[::</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="p">]</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">names</span><span class="p">[</span><span class="s2">&quot;fnames_outputdensity&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">datadir</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;output_density_</span><span class="si">{</span><span class="n">sim_id</span><span class="si">}</span><span class="s2">.h5&quot;</span><span class="p">)]</span>
<span class="n">names</span><span class="p">[</span><span class="s2">&quot;fnames_outputrealspacedensity&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span>
<span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">datadir</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;output_realdensity_</span><span class="si">{</span><span class="n">sim_id</span><span class="si">}</span><span class="s2">.h5&quot;</span><span class="p">)</span>
<span class="p">]</span>
<span class="k">return</span> <span class="n">names</span></div>
<div class="viewcode-block" id="file_names_evaluate">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.path_utils.file_names_evaluate">[docs]</a>
<span class="k">def</span> <span class="nf">file_names_evaluate</span><span class="p">(</span>
<span class="n">simdir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
<span class="n">sd</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
<span class="n">d</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
<span class="n">i</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
<span class="n">sim_params</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
<span class="n">TimeSteps</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">int</span><span class="p">],</span>
<span class="n">prefix_mocks</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
<span class="n">abc</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
<span class="n">gravity_on</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
<span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Generate file paths for the given simulation id and parameters.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> simdir : str</span>
<span class="sd"> Path to the simulation directory.</span>
<span class="sd"> sd : str</span>
<span class="sd"> Path to the simulation directory for the given direction.</span>
<span class="sd"> d : int</span>
<span class="sd"> Direction index (-1 for mock data, 0 for the expansion point, or</span>
<span class="sd"> 1 to S).</span>
<span class="sd"> i : int</span>
<span class="sd"> Simulation index.</span>
<span class="sd"> sim_params : str</span>
<span class="sd"> Simulation parameters.</span>
<span class="sd"> TimeSteps : list of int</span>
<span class="sd"> List of time steps.</span>
<span class="sd"> prefix_mocks : str | None</span>
<span class="sd"> Prefix for mock data files. If None, defaults to &quot;mocks&quot;.</span>
<span class="sd"> abc : bool, optional</span>
<span class="sd"> If True, appends the ABC index to the white noise path.</span>
<span class="sd"> gravity_on : bool, optional</span>
<span class="sd"> Whether gravity is active. Default is True.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> dict</span>
<span class="sd"> Dictionary containing simulation inputs / outputs file paths.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">names</span> <span class="o">=</span> <span class="p">{</span>
<span class="s2">&quot;fname_power_spectrum&quot;</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">sd</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;input_power_d</span><span class="si">{</span><span class="n">d</span><span class="si">}</span><span class="s2">.h5&quot;</span><span class="p">),</span>
<span class="s2">&quot;fname_outputinitialdensity&quot;</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">sd</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;initial_density_d</span><span class="si">{</span><span class="n">d</span><span class="si">}</span><span class="s2">_p</span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2">.h5&quot;</span><span class="p">),</span>
<span class="s2">&quot;fname_mocks&quot;</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">sd</span><span class="p">,</span> <span class="n">_get_prefix</span><span class="p">(</span><span class="n">prefix_mocks</span><span class="p">,</span> <span class="s2">&quot;mocks&quot;</span><span class="p">,</span> <span class="n">d</span><span class="o">=</span><span class="n">d</span><span class="p">,</span> <span class="n">p</span><span class="o">=</span><span class="n">i</span><span class="p">)),</span>
<span class="s2">&quot;fname_simlogs&quot;</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">sd</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;logs_sim_d</span><span class="si">{</span><span class="n">d</span><span class="si">}</span><span class="s2">_p</span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2">.txt&quot;</span><span class="p">),</span>
<span class="s2">&quot;fname_simparfile&quot;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
<span class="s2">&quot;fname_whitenoise&quot;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
<span class="s2">&quot;seedname_whitenoise&quot;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
<span class="s2">&quot;fnames_outputLPTdensity&quot;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
<span class="s2">&quot;fnames_outputrealspacedensity&quot;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
<span class="s2">&quot;fnames_outputdensity&quot;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
<span class="s2">&quot;fname_g&quot;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
<span class="p">}</span>
<span class="k">if</span> <span class="n">gravity_on</span><span class="p">:</span>
<span class="n">dir_wn</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">simdir</span><span class="p">,</span> <span class="s2">&quot;..&quot;</span><span class="p">,</span> <span class="s2">&quot;wn&quot;</span><span class="p">)</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">abc</span> <span class="k">else</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">simdir</span><span class="p">,</span> <span class="s2">&quot;wn&quot;</span><span class="p">,</span> <span class="n">abc</span><span class="p">)</span>
<span class="n">names</span><span class="o">.</span><span class="n">update</span><span class="p">(</span>
<span class="p">{</span>
<span class="s2">&quot;fname_simparfile&quot;</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">sd</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;sim_d</span><span class="si">{</span><span class="n">d</span><span class="si">}</span><span class="s2">_p</span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">),</span>
<span class="s2">&quot;fname_whitenoise&quot;</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">dir_wn</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;initial_density_white_p</span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2">.h5&quot;</span><span class="p">),</span>
<span class="s2">&quot;seedname_whitenoise&quot;</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">dir_wn</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;initial_density_white_p</span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">),</span>
<span class="s2">&quot;fnames_outputLPTdensity&quot;</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">sd</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;output_density_d</span><span class="si">{</span><span class="n">d</span><span class="si">}</span><span class="s2">_p</span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2">.h5&quot;</span><span class="p">),</span>
<span class="p">}</span>
<span class="p">)</span>
<span class="k">if</span> <span class="n">sim_params</span><span class="o">.</span><span class="n">startswith</span><span class="p">((</span><span class="s2">&quot;split&quot;</span><span class="p">,</span> <span class="s2">&quot;custom&quot;</span><span class="p">)):</span>
<span class="n">names</span><span class="p">[</span><span class="s2">&quot;fnames_outputrealspacedensity&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span>
<span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">sd</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;output_realdensity_d</span><span class="si">{</span><span class="n">d</span><span class="si">}</span><span class="s2">_p</span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">j</span><span class="si">}</span><span class="s2">.h5&quot;</span><span class="p">)</span> <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="n">TimeSteps</span><span class="p">[::</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="p">]</span>
<span class="n">names</span><span class="p">[</span><span class="s2">&quot;fnames_outputdensity&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span>
<span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">sd</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;output_density_d</span><span class="si">{</span><span class="n">d</span><span class="si">}</span><span class="s2">_p</span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">j</span><span class="si">}</span><span class="s2">.h5&quot;</span><span class="p">)</span> <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="n">TimeSteps</span><span class="p">[::</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="p">]</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">names</span><span class="p">[</span><span class="s2">&quot;fnames_outputrealspacedensity&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span>
<span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">sd</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;output_realdensity_d</span><span class="si">{</span><span class="n">d</span><span class="si">}</span><span class="s2">_p</span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2">.h5&quot;</span><span class="p">)</span>
<span class="p">]</span>
<span class="n">names</span><span class="p">[</span><span class="s2">&quot;fnames_outputdensity&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">sd</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;output_density_d</span><span class="si">{</span><span class="n">d</span><span class="si">}</span><span class="s2">_p</span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2">.h5&quot;</span><span class="p">)]</span>
<span class="k">return</span> <span class="n">names</span></div>
</pre></div>
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<p class="caption" role="heading"><span class="caption-text">API Documentation</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.hiddenbox.html">hiddenbox</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox"><code class="docutils literal notranslate"><span class="pre">HiddenBox</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Npop"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Npop</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Psingle"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Psingle</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.compute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.compute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.evaluate"><code class="docutils literal notranslate"><span class="pre">HiddenBox.evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_neglect_lightcone"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_neglect_lightcone</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_recompute_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_recompute_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.gravity_on"><code class="docutils literal notranslate"><span class="pre">HiddenBox.gravity_on</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.load_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.load_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.make_data"><code class="docutils literal notranslate"><span class="pre">HiddenBox.make_data()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.modified_selfi"><code class="docutils literal notranslate"><span class="pre">HiddenBox.modified_selfi</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.prefix_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.prefix_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.reset_survey"><code class="docutils literal notranslate"><span class="pre">HiddenBox.reset_survey()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.setup_only"><code class="docutils literal notranslate"><span class="pre">HiddenBox.setup_only</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_recompute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_recompute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_setup"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_setup()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.update"><code class="docutils literal notranslate"><span class="pre">HiddenBox.update()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.normalise_hb.html">normalise_hb</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.define_normalisation"><code class="docutils literal notranslate"><span class="pre">define_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation"><code class="docutils literal notranslate"><span class="pre">worker_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_public"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_public()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_wrapper"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_wrapper()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.prior.html">prior</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.logposterior_hyperparameters_parallel"><code class="docutils literal notranslate"><span class="pre">logposterior_hyperparameters_parallel()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.perform_prior_optimisation_and_plot"><code class="docutils literal notranslate"><span class="pre">perform_prior_optimisation_and_plot()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior"><code class="docutils literal notranslate"><span class="pre">planck_prior</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.mean"><code class="docutils literal notranslate"><span class="pre">planck_prior.mean</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.inv_covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.inv_covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_max"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_max</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_min"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_min</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.compute"><code class="docutils literal notranslate"><span class="pre">planck_prior.compute()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.load"><code class="docutils literal notranslate"><span class="pre">planck_prior.load()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.logpdf"><code class="docutils literal notranslate"><span class="pre">planck_prior.logpdf()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.sample"><code class="docutils literal notranslate"><span class="pre">planck_prior.sample()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.save"><code class="docutils literal notranslate"><span class="pre">planck_prior.save()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.worker_class"><code class="docutils literal notranslate"><span class="pre">worker_class()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.selection_functions.html">selection_functions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.init_selection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.init_selection()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.lognormals_z_to_x"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.lognormals_z_to_x()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.r_grid"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.r_grid()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.selfi_interface.html">selfi_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.PrintMessage"><code class="docutils literal notranslate"><span class="pre">PrintMessage()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.indent"><code class="docutils literal notranslate"><span class="pre">indent()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.unindent"><code class="docutils literal notranslate"><span class="pre">unindent()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.sbmy_interface.html">sbmy_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.compute_Phi"><code class="docutils literal notranslate"><span class="pre">compute_Phi()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.generate_white_noise_Field"><code class="docutils literal notranslate"><span class="pre">generate_white_noise_Field()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.get_power_spectrum_from_cosmo"><code class="docutils literal notranslate"><span class="pre">get_power_spectrum_from_cosmo()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.handle_time_stepping"><code class="docutils literal notranslate"><span class="pre">handle_time_stepping()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.setup_sbmy_parfiles"><code class="docutils literal notranslate"><span class="pre">setup_sbmy_parfiles()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.grf.html">grf</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.grf.html#selfisys.grf.primordial_grf"><code class="docutils literal notranslate"><span class="pre">primordial_grf()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.utils.html">selfisys.utils package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.examples_utils">selfisys.utils.examples_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.examples_utils.clear_large_plot"><code class="docutils literal notranslate"><span class="pre">clear_large_plot()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.logger">selfisys.utils.logger module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLogger"><code class="docutils literal notranslate"><span class="pre">CustomLogger</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLogger.diagnostic"><code class="docutils literal notranslate"><span class="pre">CustomLogger.diagnostic()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler.emit"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler.emit()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.INDENT"><code class="docutils literal notranslate"><span class="pre">INDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintDiagnostic"><code class="docutils literal notranslate"><span class="pre">PrintDiagnostic()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintError"><code class="docutils literal notranslate"><span class="pre">PrintError()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintInfo"><code class="docutils literal notranslate"><span class="pre">PrintInfo()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintLeftType"><code class="docutils literal notranslate"><span class="pre">PrintLeftType()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintWarning"><code class="docutils literal notranslate"><span class="pre">PrintWarning()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.UNINDENT"><code class="docutils literal notranslate"><span class="pre">UNINDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.getCustomLogger"><code class="docutils literal notranslate"><span class="pre">getCustomLogger()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.low_level">selfisys.utils.low_level module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.low_level.stderr_redirector"><code class="docutils literal notranslate"><span class="pre">stderr_redirector()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.low_level.stdout_redirector"><code class="docutils literal notranslate"><span class="pre">stdout_redirector()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.parser">selfisys.utils.parser module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.bool_sh"><code class="docutils literal notranslate"><span class="pre">bool_sh()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.check_files_exist"><code class="docutils literal notranslate"><span class="pre">check_files_exist()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.intNone"><code class="docutils literal notranslate"><span class="pre">intNone()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.joinstrs"><code class="docutils literal notranslate"><span class="pre">joinstrs()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.joinstrs_only"><code class="docutils literal notranslate"><span class="pre">joinstrs_only()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.safe_npload"><code class="docutils literal notranslate"><span class="pre">safe_npload()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.path_utils">selfisys.utils.path_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.path_utils.file_names_evaluate"><code class="docutils literal notranslate"><span class="pre">file_names_evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.path_utils.get_file_names"><code class="docutils literal notranslate"><span class="pre">get_file_names()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.plot_examples">selfisys.utils.plot_examples module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_comoving_distance_redshift"><code class="docutils literal notranslate"><span class="pre">plot_comoving_distance_redshift()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_galaxy_field_slice"><code class="docutils literal notranslate"><span class="pre">plot_galaxy_field_slice()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_power_spectrum"><code class="docutils literal notranslate"><span class="pre">plot_power_spectrum()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_selection_functions_def_in_z"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions_def_in_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.redshift_distance_conversion"><code class="docutils literal notranslate"><span class="pre">redshift_distance_conversion()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.relative_error_analysis"><code class="docutils literal notranslate"><span class="pre">relative_error_analysis()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.plot_params">selfisys.utils.plot_params module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.get_offset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.get_offset()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_scientific"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_scientific()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_useOffset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_useOffset()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.create_all_colormaps"><code class="docutils literal notranslate"><span class="pre">create_all_colormaps()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.create_colormap"><code class="docutils literal notranslate"><span class="pre">create_colormap()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.dynamic_text_scaling"><code class="docutils literal notranslate"><span class="pre">dynamic_text_scaling()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.get_contours"><code class="docutils literal notranslate"><span class="pre">get_contours()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.reset_plotting"><code class="docutils literal notranslate"><span class="pre">reset_plotting()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.setup_plotting"><code class="docutils literal notranslate"><span class="pre">setup_plotting()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.plot_utils">selfisys.utils.plot_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_C"><code class="docutils literal notranslate"><span class="pre">plot_C()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_fisher"><code class="docutils literal notranslate"><span class="pre">plot_fisher()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_gradients"><code class="docutils literal notranslate"><span class="pre">plot_gradients()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_histogram"><code class="docutils literal notranslate"><span class="pre">plot_histogram()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks"><code class="docutils literal notranslate"><span class="pre">plot_mocks()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks_compact"><code class="docutils literal notranslate"><span class="pre">plot_mocks_compact()</span></code></a></li>
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<h1>Source code for selfisys.utils.plot_examples</h1><div class="highlight"><pre>
<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="c1"># Copyright (C) 2024 Tristan Hoellinger</span>
<span class="c1"># Distributed under the GNU General Public License v3.0 (GPLv3).</span>
<span class="c1"># See the LICENSE file in the root directory for details.</span>
<span class="c1"># SPDX-License-Identifier: GPL-3.0-or-later</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="n">__author__</span> <span class="o">=</span> <span class="s2">&quot;Tristan Hoellinger&quot;</span>
<span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;0.1.0&quot;</span>
<span class="n">__date__</span> <span class="o">=</span> <span class="s2">&quot;2024&quot;</span>
<span class="n">__license__</span> <span class="o">=</span> <span class="s2">&quot;GPLv3&quot;</span>
<span class="sd">&quot;&quot;&quot;Visualisation utilities for the exploratory examples in SelfiSys.</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
<span class="kn">from</span> <span class="nn">selfisys.utils.plot_params</span> <span class="kn">import</span> <span class="o">*</span>
<span class="c1"># Configure global plotting settings</span>
<span class="n">setup_plotting</span><span class="p">()</span>
<div class="viewcode-block" id="plot_power_spectrum">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_power_spectrum">[docs]</a>
<span class="k">def</span> <span class="nf">plot_power_spectrum</span><span class="p">(</span>
<span class="n">G_sim</span><span class="p">,</span> <span class="n">true_P</span><span class="p">,</span> <span class="n">k_s</span><span class="p">,</span> <span class="n">planck_Pk</span><span class="p">,</span> <span class="n">Pbins</span><span class="p">,</span> <span class="n">Pbins_bnd</span><span class="p">,</span> <span class="n">size</span><span class="p">,</span> <span class="n">L</span><span class="p">,</span> <span class="n">wd</span><span class="p">,</span> <span class="n">title</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">display</span><span class="o">=</span><span class="kc">True</span>
<span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Plot a power spectrum over Fourier modes, its linear interpolation</span>
<span class="sd"> over specified support points, and a given binning for comparison.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> G_sim : pysbmy.power.FourierGrid</span>
<span class="sd"> Fourier grid object containing the `k_modes` attribute.</span>
<span class="sd"> true_P : pysbmy.power.PowerSpectrum</span>
<span class="sd"> Power spectrum object containing the `powerspectrum` attribute.</span>
<span class="sd"> k_s : array-like</span>
<span class="sd"> Support points in k-space.</span>
<span class="sd"> planck_Pk : array-like</span>
<span class="sd"> Power spectrum values at the support points.</span>
<span class="sd"> Pbins : array-like</span>
<span class="sd"> Centres of the Φ bins in k-space.</span>
<span class="sd"> Pbins_bnd : array-like</span>
<span class="sd"> Boundaries of the Φ bins in k-space.</span>
<span class="sd"> size : float</span>
<span class="sd"> Box size in number of grid cells.</span>
<span class="sd"> L : float</span>
<span class="sd"> Box length in Mpc/h.</span>
<span class="sd"> wd : str</span>
<span class="sd"> Working directory path for saving the figure.</span>
<span class="sd"> title : str, optional</span>
<span class="sd"> Title for the figure. Default is None.</span>
<span class="sd"> display : bool, optional</span>
<span class="sd"> Whether to display the figure. Default is True.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> None</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">from</span> <span class="nn">selfisys.utils.logger</span> <span class="kn">import</span> <span class="n">PrintInfo</span>
<span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">(</span><span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">15</span><span class="p">,</span> <span class="mi">5</span><span class="p">))</span>
<span class="c1"># Plot power spectrum data</span>
<span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">G_sim</span><span class="o">.</span><span class="n">k_modes</span><span class="p">,</span> <span class="n">true_P</span><span class="o">.</span><span class="n">powerspectrum</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="sa">r</span><span class="s2">&quot;$P(k)$ (over all modes)&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">k_s</span><span class="p">,</span> <span class="n">planck_Pk</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="sa">r</span><span class="s2">&quot;$P(k)$ (binnedlinear interpolation)&quot;</span><span class="p">,</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;dashed&quot;</span><span class="p">)</span>
<span class="c1"># Configure axes</span>
<span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;$k\,[h/\mathrm</span><span class="si">{Mpc}</span><span class="s2">]$&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;$[{\rm Mpc}/h]^3$&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">xscale</span><span class="p">(</span><span class="s2">&quot;log&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">yscale</span><span class="p">(</span><span class="s2">&quot;log&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">xlim</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">clip</span><span class="p">(</span><span class="n">k_s</span><span class="o">.</span><span class="n">min</span><span class="p">()</span> <span class="o">-</span> <span class="mf">2e-4</span><span class="p">,</span> <span class="mf">1e-4</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span> <span class="n">k_s</span><span class="o">.</span><span class="n">max</span><span class="p">())</span>
<span class="n">plt</span><span class="o">.</span><span class="n">ylim</span><span class="p">(</span><span class="mf">1e1</span><span class="p">,</span> <span class="mf">1e5</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">grid</span><span class="p">(</span><span class="n">which</span><span class="o">=</span><span class="s2">&quot;both&quot;</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="s2">&quot;y&quot;</span><span class="p">)</span>
<span class="c1"># Plot vertical lines for support points and binning</span>
<span class="n">plt</span><span class="o">.</span><span class="n">vlines</span><span class="p">(</span><span class="n">k_s</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="n">ymin</span><span class="o">=</span><span class="mf">1e1</span><span class="p">,</span> <span class="n">ymax</span><span class="o">=</span><span class="mf">1e5</span><span class="p">,</span> <span class="n">colors</span><span class="o">=</span><span class="s2">&quot;green&quot;</span><span class="p">,</span> <span class="n">linestyles</span><span class="o">=</span><span class="s2">&quot;dotted&quot;</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mf">0.6</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axvline</span><span class="p">(</span>
<span class="n">k_s</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span>
<span class="n">color</span><span class="o">=</span><span class="s2">&quot;green&quot;</span><span class="p">,</span>
<span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;dotted&quot;</span><span class="p">,</span>
<span class="n">linewidth</span><span class="o">=</span><span class="mf">0.6</span><span class="p">,</span>
<span class="n">label</span><span class="o">=</span><span class="sa">r</span><span class="s2">&quot;$\boldsymbol{\uptheta}$ support points&quot;</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">vlines</span><span class="p">(</span>
<span class="n">Pbins</span><span class="p">,</span>
<span class="n">ymin</span><span class="o">=</span><span class="mf">1e1</span><span class="p">,</span>
<span class="n">ymax</span><span class="o">=</span><span class="mf">5e2</span><span class="p">,</span>
<span class="n">colors</span><span class="o">=</span><span class="s2">&quot;red&quot;</span><span class="p">,</span>
<span class="n">linestyles</span><span class="o">=</span><span class="s2">&quot;dashed&quot;</span><span class="p">,</span>
<span class="n">linewidth</span><span class="o">=</span><span class="mf">0.5</span><span class="p">,</span>
<span class="n">label</span><span class="o">=</span><span class="sa">r</span><span class="s2">&quot;$\boldsymbol{\Phi}$ bin centres&quot;</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">vlines</span><span class="p">(</span>
<span class="n">Pbins_bnd</span><span class="p">,</span>
<span class="n">ymin</span><span class="o">=</span><span class="mf">1e1</span><span class="p">,</span>
<span class="n">ymax</span><span class="o">=</span><span class="mf">1e2</span> <span class="o">/</span> <span class="mi">2</span><span class="p">,</span>
<span class="n">colors</span><span class="o">=</span><span class="s2">&quot;blue&quot;</span><span class="p">,</span>
<span class="n">linestyles</span><span class="o">=</span><span class="s2">&quot;dashed&quot;</span><span class="p">,</span>
<span class="n">linewidth</span><span class="o">=</span><span class="mf">0.5</span><span class="p">,</span>
<span class="n">label</span><span class="o">=</span><span class="sa">r</span><span class="s2">&quot;$\boldsymbol{\Phi}$ bin boundaries&quot;</span><span class="p">,</span>
<span class="p">)</span>
<span class="c1"># Plot the Nyquist frequency</span>
<span class="n">nyquist_freq</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span> <span class="o">*</span> <span class="n">size</span> <span class="o">/</span> <span class="n">L</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axvline</span><span class="p">(</span>
<span class="n">nyquist_freq</span><span class="p">,</span> <span class="n">ymax</span><span class="o">=</span><span class="mi">1</span> <span class="o">/</span> <span class="mf">6.0</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s2">&quot;orange&quot;</span><span class="p">,</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;-&quot;</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="s2">&quot;Nyquist&quot;</span>
<span class="p">)</span>
<span class="c1"># Add legend, optional title, and save the figure</span>
<span class="n">plt</span><span class="o">.</span><span class="n">legend</span><span class="p">(</span><span class="n">loc</span><span class="o">=</span><span class="s2">&quot;upper center&quot;</span><span class="p">,</span> <span class="n">bbox_to_anchor</span><span class="o">=</span><span class="p">(</span><span class="mf">0.5</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.2</span><span class="p">),</span> <span class="n">ncol</span><span class="o">=</span><span class="mi">3</span><span class="p">)</span>
<span class="k">if</span> <span class="n">title</span><span class="p">:</span>
<span class="n">plt</span><span class="o">.</span><span class="n">title</span><span class="p">(</span><span class="n">title</span><span class="p">)</span>
<span class="n">output_dir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">wd</span><span class="p">,</span> <span class="s2">&quot;Figures&quot;</span><span class="p">)</span>
<span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">output_dir</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">output_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">output_dir</span><span class="p">,</span> <span class="s2">&quot;summary.pdf&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">bbox_inches</span><span class="o">=</span><span class="s2">&quot;tight&quot;</span><span class="p">)</span>
<span class="n">PrintInfo</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Figure saved to: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="k">if</span> <span class="n">display</span><span class="p">:</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
<span class="n">plt</span><span class="o">.</span><span class="n">close</span><span class="p">()</span></div>
<div class="viewcode-block" id="relative_error_analysis">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.relative_error_analysis">[docs]</a>
<span class="k">def</span> <span class="nf">relative_error_analysis</span><span class="p">(</span>
<span class="n">G_sim</span><span class="p">,</span> <span class="n">true_P</span><span class="p">,</span> <span class="n">k_s</span><span class="p">,</span> <span class="n">planck_Pk</span><span class="p">,</span> <span class="n">Pbins</span><span class="p">,</span> <span class="n">Pbins_bnd</span><span class="p">,</span> <span class="n">size</span><span class="p">,</span> <span class="n">L</span><span class="p">,</span> <span class="n">wd</span><span class="p">,</span> <span class="n">display</span><span class="o">=</span><span class="kc">True</span>
<span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Compute and plot the relative error between the interpolated and</span>
<span class="sd"> true power spectra.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> G_sim : pysbmy.power.FourierGrid</span>
<span class="sd"> Fourier grid object containing the `k_modes` attribute.</span>
<span class="sd"> true_P : pysbmy.power.PowerSpectrum</span>
<span class="sd"> Power spectrum object containing the `powerspectrum` attribute.</span>
<span class="sd"> k_s : array-like</span>
<span class="sd"> Support points in k-space.</span>
<span class="sd"> planck_Pk : array-like</span>
<span class="sd"> Power spectrum values at the support points.</span>
<span class="sd"> Pbins : array-like</span>
<span class="sd"> Centres of the Φ bins in k-space.</span>
<span class="sd"> Pbins_bnd : array-like</span>
<span class="sd"> Boundaries of the Φ bins in k-space.</span>
<span class="sd"> size : float</span>
<span class="sd"> Box size in number of grid cells.</span>
<span class="sd"> L : float</span>
<span class="sd"> Box length in Mpc/h.</span>
<span class="sd"> wd : str</span>
<span class="sd"> Working directory path for saving the figure.</span>
<span class="sd"> display : bool, optional</span>
<span class="sd"> Whether to display the figure. Default is True.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> None</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">from</span> <span class="nn">scipy.interpolate</span> <span class="kn">import</span> <span class="n">InterpolatedUnivariateSpline</span>
<span class="kn">from</span> <span class="nn">selfisys.utils.logger</span> <span class="kn">import</span> <span class="n">PrintInfo</span>
<span class="c1"># Interpolate the power spectrum</span>
<span class="n">spline</span> <span class="o">=</span> <span class="n">InterpolatedUnivariateSpline</span><span class="p">(</span><span class="n">k_s</span><span class="p">,</span> <span class="n">planck_Pk</span><span class="p">,</span> <span class="n">k</span><span class="o">=</span><span class="mi">5</span><span class="p">)</span>
<span class="n">rec_Pk</span> <span class="o">=</span> <span class="n">spline</span><span class="p">(</span><span class="n">G_sim</span><span class="o">.</span><span class="n">k_modes</span><span class="p">[</span><span class="mi">1</span><span class="p">:])</span>
<span class="n">true_spectrum</span> <span class="o">=</span> <span class="n">true_P</span><span class="o">.</span><span class="n">powerspectrum</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span>
<span class="n">xx</span> <span class="o">=</span> <span class="n">G_sim</span><span class="o">.</span><span class="n">k_modes</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span>
<span class="c1"># Compute relative errors</span>
<span class="n">rel_err</span> <span class="o">=</span> <span class="p">(</span><span class="n">rec_Pk</span> <span class="o">-</span> <span class="n">true_spectrum</span><span class="p">)</span> <span class="o">/</span> <span class="n">true_spectrum</span>
<span class="n">indices_all</span> <span class="o">=</span> <span class="nb">slice</span><span class="p">(</span><span class="kc">None</span><span class="p">)</span>
<span class="n">indices_nyquist</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">((</span><span class="n">xx</span> <span class="o">&gt;=</span> <span class="n">k_s</span><span class="o">.</span><span class="n">min</span><span class="p">())</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">xx</span> <span class="o">&lt;=</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span> <span class="o">*</span> <span class="n">size</span> <span class="o">/</span> <span class="n">L</span><span class="p">))[</span><span class="mi">0</span><span class="p">]</span>
<span class="n">indices_k2e1</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">xx</span> <span class="o">&lt;=</span> <span class="mf">2e-1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
<span class="n">max_relerr</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">rel_err</span><span class="p">[</span><span class="n">indices_all</span><span class="p">]))</span>
<span class="n">max_relerr_nyquist</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">rel_err</span><span class="p">[</span><span class="n">indices_nyquist</span><span class="p">]))</span>
<span class="n">max_relerr_2e1</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">rel_err</span><span class="p">[</span><span class="n">indices_k2e1</span><span class="p">]))</span>
<span class="c1"># Create the figure</span>
<span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">(</span><span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">15</span><span class="p">,</span> <span class="mi">5</span><span class="p">))</span>
<span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span>
<span class="n">xx</span><span class="p">,</span>
<span class="n">rel_err</span><span class="p">,</span>
<span class="n">label</span><span class="o">=</span><span class="sa">r</span><span class="s2">&quot;$\left(P_\textrm</span><span class="si">{interp}</span><span class="s2">-P_{\mathrm</span><span class="si">{true}</span><span class="s2">}\right)/P_{\mathrm</span><span class="si">{true}</span><span class="s2">}$&quot;</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;$k\,[h/\mathrm</span><span class="si">{Mpc}</span><span class="s2">]$&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s2">&quot;Relative error&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">xscale</span><span class="p">(</span><span class="s2">&quot;log&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">xlim</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">clip</span><span class="p">(</span><span class="n">k_s</span><span class="o">.</span><span class="n">min</span><span class="p">()</span> <span class="o">-</span> <span class="mf">2e-4</span><span class="p">,</span> <span class="mf">1e-4</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span> <span class="n">k_s</span><span class="o">.</span><span class="n">max</span><span class="p">())</span>
<span class="n">plt</span><span class="o">.</span><span class="n">ylim</span><span class="p">(</span><span class="o">-</span><span class="mf">0.1</span><span class="p">,</span> <span class="mf">0.1</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">grid</span><span class="p">(</span><span class="n">which</span><span class="o">=</span><span class="s2">&quot;both&quot;</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="s2">&quot;y&quot;</span><span class="p">)</span>
<span class="c1"># Vertical lines for binning and support points</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axvline</span><span class="p">(</span>
<span class="n">x</span><span class="o">=</span><span class="n">Pbins</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
<span class="n">color</span><span class="o">=</span><span class="s2">&quot;red&quot;</span><span class="p">,</span>
<span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;dashed&quot;</span><span class="p">,</span>
<span class="n">linewidth</span><span class="o">=</span><span class="mf">0.5</span><span class="p">,</span>
<span class="n">label</span><span class="o">=</span><span class="sa">r</span><span class="s2">&quot;$\boldsymbol\Phi$ bin centres&quot;</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axvline</span><span class="p">(</span><span class="n">x</span><span class="o">=</span><span class="n">Pbins</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="n">color</span><span class="o">=</span><span class="s2">&quot;red&quot;</span><span class="p">,</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;dashed&quot;</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mf">0.5</span><span class="p">)</span>
<span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">Pbins</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]:</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axvline</span><span class="p">(</span><span class="n">x</span><span class="o">=</span><span class="n">k</span><span class="p">,</span> <span class="n">ymax</span><span class="o">=</span><span class="mi">1</span> <span class="o">/</span> <span class="mf">6.0</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s2">&quot;red&quot;</span><span class="p">,</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;dashed&quot;</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mf">0.5</span><span class="p">)</span>
<span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">k_s</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]:</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axvline</span><span class="p">(</span><span class="n">x</span><span class="o">=</span><span class="n">k</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s2">&quot;green&quot;</span><span class="p">,</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;dotted&quot;</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mf">0.6</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axvline</span><span class="p">(</span>
<span class="n">x</span><span class="o">=</span><span class="n">k_s</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span>
<span class="n">color</span><span class="o">=</span><span class="s2">&quot;green&quot;</span><span class="p">,</span>
<span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;dotted&quot;</span><span class="p">,</span>
<span class="n">linewidth</span><span class="o">=</span><span class="mf">0.6</span><span class="p">,</span>
<span class="n">label</span><span class="o">=</span><span class="sa">r</span><span class="s2">&quot;$\boldsymbol\uptheta$ support points&quot;</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axvline</span><span class="p">(</span>
<span class="n">x</span><span class="o">=</span><span class="n">Pbins_bnd</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
<span class="n">ymax</span><span class="o">=</span><span class="mi">1</span> <span class="o">/</span> <span class="mf">3.0</span><span class="p">,</span>
<span class="n">color</span><span class="o">=</span><span class="s2">&quot;blue&quot;</span><span class="p">,</span>
<span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;dashed&quot;</span><span class="p">,</span>
<span class="n">linewidth</span><span class="o">=</span><span class="mf">0.5</span><span class="p">,</span>
<span class="n">label</span><span class="o">=</span><span class="sa">r</span><span class="s2">&quot;$\boldsymbol\Phi$ bin boundaries&quot;</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axvline</span><span class="p">(</span><span class="n">x</span><span class="o">=</span><span class="n">Pbins_bnd</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="n">ymax</span><span class="o">=</span><span class="mi">1</span> <span class="o">/</span> <span class="mf">3.0</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s2">&quot;blue&quot;</span><span class="p">,</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;dashed&quot;</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mf">0.5</span><span class="p">)</span>
<span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">Pbins_bnd</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]:</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axvline</span><span class="p">(</span><span class="n">x</span><span class="o">=</span><span class="n">k</span><span class="p">,</span> <span class="n">ymax</span><span class="o">=</span><span class="mi">1</span> <span class="o">/</span> <span class="mf">12.0</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s2">&quot;blue&quot;</span><span class="p">,</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;dashed&quot;</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mf">0.5</span><span class="p">)</span>
<span class="c1"># Nyquist and fundamental frequencies</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axvline</span><span class="p">(</span>
<span class="n">x</span><span class="o">=</span><span class="mi">2</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span> <span class="o">/</span> <span class="n">L</span><span class="p">,</span>
<span class="n">ymax</span><span class="o">=</span><span class="mi">1</span> <span class="o">/</span> <span class="mf">6.0</span><span class="p">,</span>
<span class="n">color</span><span class="o">=</span><span class="s2">&quot;orange&quot;</span><span class="p">,</span>
<span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;-&quot;</span><span class="p">,</span>
<span class="n">linewidth</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
<span class="n">label</span><span class="o">=</span><span class="s2">&quot;Fundamental mode&quot;</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axvline</span><span class="p">(</span>
<span class="n">x</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">pi</span> <span class="o">*</span> <span class="n">size</span> <span class="o">/</span> <span class="n">L</span><span class="p">,</span>
<span class="n">ymax</span><span class="o">=</span><span class="mi">1</span> <span class="o">/</span> <span class="mf">6.0</span><span class="p">,</span>
<span class="n">color</span><span class="o">=</span><span class="s2">&quot;orange&quot;</span><span class="p">,</span>
<span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;--&quot;</span><span class="p">,</span>
<span class="n">linewidth</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
<span class="n">label</span><span class="o">=</span><span class="s2">&quot;Nyquist&quot;</span><span class="p">,</span>
<span class="p">)</span>
<span class="c1"># Add title, legend, and save the figure</span>
<span class="n">plt</span><span class="o">.</span><span class="n">legend</span><span class="p">(</span><span class="n">loc</span><span class="o">=</span><span class="s2">&quot;upper center&quot;</span><span class="p">,</span> <span class="n">bbox_to_anchor</span><span class="o">=</span><span class="p">(</span><span class="mf">0.5</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.2</span><span class="p">),</span> <span class="n">ncol</span><span class="o">=</span><span class="mi">3</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">title</span><span class="p">(</span>
<span class="s2">&quot;Relative error between interpolated and true Planck 2018 power spectrum</span><span class="se">\n</span><span class="s2">&quot;</span>
<span class="sa">f</span><span class="s2">&quot;over the </span><span class="si">{</span><span class="n">G_sim</span><span class="o">.</span><span class="n">k_modes</span><span class="o">.</span><span class="n">size</span><span class="si">}</span><span class="s2"> modes of the Fourier grid (max: </span><span class="si">{</span><span class="n">max_relerr</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="mi">100</span><span class="si">:</span><span class="s2">.3f</span><span class="si">}</span><span class="se">\\</span><span class="s2">%)&quot;</span>
<span class="p">)</span>
<span class="n">output_dir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">wd</span><span class="p">,</span> <span class="s2">&quot;Figures&quot;</span><span class="p">)</span>
<span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">output_dir</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">output_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">output_dir</span><span class="p">,</span> <span class="s2">&quot;summary_relerr.pdf&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">bbox_inches</span><span class="o">=</span><span class="s2">&quot;tight&quot;</span><span class="p">)</span>
<span class="n">PrintInfo</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Figure saved to: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="c1"># Print summary of relative errors</span>
<span class="n">PrintInfo</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Max relative error over all support points: </span><span class="si">{</span><span class="n">max_relerr</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="mi">100</span><span class="si">:</span><span class="s2">.3f</span><span class="si">}</span><span class="s2">%&quot;</span><span class="p">)</span>
<span class="n">PrintInfo</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Max relative error up to 1D Nyquist frequency: </span><span class="si">{</span><span class="n">max_relerr_nyquist</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="mi">100</span><span class="si">:</span><span class="s2">.3f</span><span class="si">}</span><span class="s2">%&quot;</span><span class="p">)</span>
<span class="n">PrintInfo</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Max relative error up to k = 2e-1: </span><span class="si">{</span><span class="n">max_relerr_2e1</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="mi">100</span><span class="si">:</span><span class="s2">.3f</span><span class="si">}</span><span class="s2">%&quot;</span><span class="p">)</span>
<span class="k">if</span> <span class="n">display</span><span class="p">:</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
<span class="n">plt</span><span class="o">.</span><span class="n">close</span><span class="p">()</span></div>
<div class="viewcode-block" id="plot_comoving_distance_redshift">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_comoving_distance_redshift">[docs]</a>
<span class="k">def</span> <span class="nf">plot_comoving_distance_redshift</span><span class="p">(</span>
<span class="n">zz</span><span class="p">,</span> <span class="n">cosmo</span><span class="p">,</span> <span class="n">means_com</span><span class="p">,</span> <span class="n">L</span><span class="p">,</span> <span class="n">Lcorner</span><span class="p">,</span> <span class="n">wd</span><span class="p">,</span> <span class="n">colours_list</span><span class="o">=</span><span class="n">COLOUR_LIST</span><span class="p">,</span> <span class="n">display</span><span class="o">=</span><span class="kc">True</span>
<span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Plot comoving distance as a function of redshift, highlighting key</span>
<span class="sd"> scales.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> zz : array-like</span>
<span class="sd"> Redshift range for the plot.</span>
<span class="sd"> cosmo : astropy.cosmology object</span>
<span class="sd"> Cosmology instance for calculating comoving distances.</span>
<span class="sd"> means_com : array-like</span>
<span class="sd"> Mean comoving distances of selection functions.</span>
<span class="sd"> L : float</span>
<span class="sd"> Box side length in Gpc/h.</span>
<span class="sd"> Lcorner : float</span>
<span class="sd"> Diagonal of the box (sqrt(3) * L) in Gpc/h.</span>
<span class="sd"> wd : str</span>
<span class="sd"> Working directory for saving figures.</span>
<span class="sd"> colours_list : list</span>
<span class="sd"> List of colours for selection function annotations.</span>
<span class="sd"> display : bool, optional</span>
<span class="sd"> Whether to display the figure. Default is True.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">d</span> <span class="o">=</span> <span class="n">cosmo</span><span class="o">.</span><span class="n">comoving_distance</span><span class="p">(</span><span class="n">zz</span><span class="p">)</span> <span class="o">/</span> <span class="mf">1e3</span> <span class="c1"># Convert to Gpc/h</span>
<span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">(</span><span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">12</span><span class="p">,</span> <span class="mf">5.2</span><span class="p">))</span>
<span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">zz</span><span class="p">,</span> <span class="n">d</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="s2">&quot;Comoving distance&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axhline</span><span class="p">(</span>
<span class="n">L</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s2">&quot;black&quot;</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;--&quot;</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="sa">rf</span><span class="s2">&quot;$L = </span><span class="si">{</span><span class="n">L</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2">\textrm</span><span class="se">{{</span><span class="s2"> Gpc</span><span class="se">}}</span><span class="s2">/h$&quot;</span>
<span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axhline</span><span class="p">(</span>
<span class="n">Lcorner</span><span class="p">,</span>
<span class="n">color</span><span class="o">=</span><span class="s2">&quot;orange&quot;</span><span class="p">,</span>
<span class="n">linewidth</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;--&quot;</span><span class="p">,</span>
<span class="n">label</span><span class="o">=</span><span class="sa">rf</span><span class="s2">&quot;$L_\textrm</span><span class="se">{{</span><span class="s2">corner</span><span class="se">}}</span><span class="s2"> = </span><span class="si">{</span><span class="n">Lcorner</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2">\textrm</span><span class="se">{{</span><span class="s2"> Gpc</span><span class="se">}}</span><span class="s2">/h$&quot;</span><span class="p">,</span>
<span class="p">)</span>
<span class="c1"># Annotate key redshifts</span>
<span class="n">d_np</span> <span class="o">=</span> <span class="n">d</span><span class="o">.</span><span class="n">value</span>
<span class="n">z_L</span> <span class="o">=</span> <span class="n">zz</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">argmin</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">d_np</span> <span class="o">-</span> <span class="n">L</span><span class="p">))]</span>
<span class="n">z_corner</span> <span class="o">=</span> <span class="n">zz</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">argmin</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">d_np</span> <span class="o">-</span> <span class="n">Lcorner</span><span class="p">))]</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axvline</span><span class="p">(</span><span class="n">z_L</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s2">&quot;black&quot;</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mf">0.5</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.5</span><span class="p">,</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;-&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axvline</span><span class="p">(</span><span class="n">z_corner</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s2">&quot;orange&quot;</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mf">0.5</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.5</span><span class="p">,</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;-&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">text</span><span class="p">(</span><span class="n">z_L</span><span class="p">,</span> <span class="mf">1.07</span> <span class="o">*</span> <span class="n">d_np</span><span class="o">.</span><span class="n">max</span><span class="p">(),</span> <span class="sa">rf</span><span class="s2">&quot;$z(L) = </span><span class="si">{</span><span class="n">z_L</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2">$&quot;</span><span class="p">,</span> <span class="n">fontsize</span><span class="o">=</span><span class="n">GLOBAL_FS_TINY</span> <span class="o">-</span> <span class="mi">2</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">text</span><span class="p">(</span>
<span class="n">z_corner</span><span class="p">,</span>
<span class="mf">1.07</span> <span class="o">*</span> <span class="n">d_np</span><span class="o">.</span><span class="n">max</span><span class="p">(),</span>
<span class="sa">rf</span><span class="s2">&quot;$z(\sqrt</span><span class="se">{{</span><span class="s2">3</span><span class="se">}}</span><span class="s2">\,L) = </span><span class="si">{</span><span class="n">z_corner</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2">$&quot;</span><span class="p">,</span>
<span class="n">fontsize</span><span class="o">=</span><span class="n">GLOBAL_FS_TINY</span> <span class="o">-</span> <span class="mi">2</span><span class="p">,</span>
<span class="p">)</span>
<span class="c1"># Annotate the selection functions&#39; means</span>
<span class="n">z_means</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">zz</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">argmin</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">d_np</span> <span class="o">-</span> <span class="n">m</span><span class="p">))]</span> <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="n">means_com</span><span class="p">])</span>
<span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">z_mean</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">z_means</span><span class="p">):</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axvline</span><span class="p">(</span><span class="n">z_mean</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="n">colours_list</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;--&quot;</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">text</span><span class="p">(</span>
<span class="n">z_mean</span> <span class="o">-</span> <span class="mf">0.07</span><span class="p">,</span>
<span class="n">L</span> <span class="o">+</span> <span class="mf">0.2</span><span class="p">,</span>
<span class="sa">rf</span><span class="s2">&quot;$z(\mu_</span><span class="se">{{</span><span class="si">{</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="si">}</span><span class="se">}}</span><span class="s2"> = </span><span class="si">{</span><span class="n">means_com</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2">) = </span><span class="si">{</span><span class="n">z_mean</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2">$&quot;</span><span class="p">,</span>
<span class="n">fontsize</span><span class="o">=</span><span class="n">GLOBAL_FS_TINY</span> <span class="o">-</span> <span class="mi">2</span><span class="p">,</span>
<span class="n">rotation</span><span class="o">=</span><span class="mi">90</span><span class="p">,</span>
<span class="p">)</span>
<span class="c1"># Add labels, legend, and save the figure</span>
<span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="s2">&quot;Redshift $z$&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;Comoving distance [Gpc$/h$]&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">grid</span><span class="p">(</span><span class="n">which</span><span class="o">=</span><span class="s2">&quot;both&quot;</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="s2">&quot;both&quot;</span><span class="p">,</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;-&quot;</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mf">0.3</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s2">&quot;gray&quot;</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.5</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">legend</span><span class="p">()</span>
<span class="n">plt</span><span class="o">.</span><span class="n">tight_layout</span><span class="p">()</span>
<span class="n">plt</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">wd</span><span class="si">}</span><span class="s2">selection_functions_z.pdf&quot;</span><span class="p">,</span> <span class="n">bbox_inches</span><span class="o">=</span><span class="s2">&quot;tight&quot;</span><span class="p">,</span> <span class="n">dpi</span><span class="o">=</span><span class="mi">300</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">wd</span><span class="si">}</span><span class="s2">selection_functions_z.png&quot;</span><span class="p">,</span> <span class="n">bbox_inches</span><span class="o">=</span><span class="s2">&quot;tight&quot;</span><span class="p">,</span> <span class="n">dpi</span><span class="o">=</span><span class="mi">300</span><span class="p">,</span> <span class="n">transparent</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="k">if</span> <span class="n">display</span><span class="p">:</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
<span class="n">plt</span><span class="o">.</span><span class="n">close</span><span class="p">()</span></div>
<div class="viewcode-block" id="redshift_distance_conversion">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.redshift_distance_conversion">[docs]</a>
<span class="k">def</span> <span class="nf">redshift_distance_conversion</span><span class="p">(</span>
<span class="n">zz</span><span class="p">,</span> <span class="n">cosmo</span><span class="p">,</span> <span class="n">means_com</span><span class="p">,</span> <span class="n">L</span><span class="p">,</span> <span class="n">Lcorner</span><span class="p">,</span> <span class="n">xx</span><span class="p">,</span> <span class="n">wd</span><span class="p">,</span> <span class="n">colours_list</span><span class="o">=</span><span class="n">COLOUR_LIST</span><span class="p">,</span> <span class="n">display</span><span class="o">=</span><span class="kc">True</span>
<span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Plot the conversion between comoving distance and redshift; return</span>
<span class="sd"> the redshifts corresponding to the selection functions&#39; means.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> zz : array-like</span>
<span class="sd"> Redshift range for the plot.</span>
<span class="sd"> cosmo : astropy.cosmology object</span>
<span class="sd"> Cosmology instance for calculating comoving distances.</span>
<span class="sd"> means_com : array-like</span>
<span class="sd"> Mean comoving distances of selection functions.</span>
<span class="sd"> L : float</span>
<span class="sd"> Box side length in Gpc/h.</span>
<span class="sd"> Lcorner : float</span>
<span class="sd"> Diagonal of the box (sqrt(3) * L) in Gpc/h.</span>
<span class="sd"> xx : array-like</span>
<span class="sd"> Comoving distances at which to compute redshift.</span>
<span class="sd"> wd : str</span>
<span class="sd"> Working directory for saving figures.</span>
<span class="sd"> colours_list : list</span>
<span class="sd"> List of colours for selection function annotations.</span>
<span class="sd"> display : bool, optional</span>
<span class="sd"> Whether to display the figure. Default is True.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> spline : scipy.interpolate.UnivariateSpline</span>
<span class="sd"> Linear interpolator to convert comoving distances to redshifts.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">from</span> <span class="nn">scipy.interpolate</span> <span class="kn">import</span> <span class="n">UnivariateSpline</span>
<span class="c1"># Convert comoving distances to redshifts using a linear interpolation</span>
<span class="n">d_np</span> <span class="o">=</span> <span class="p">(</span><span class="n">cosmo</span><span class="o">.</span><span class="n">comoving_distance</span><span class="p">(</span><span class="n">zz</span><span class="p">)</span> <span class="o">/</span> <span class="mf">1e3</span><span class="p">)</span><span class="o">.</span><span class="n">value</span> <span class="c1"># Gpc/h</span>
<span class="n">spline</span> <span class="o">=</span> <span class="n">UnivariateSpline</span><span class="p">(</span><span class="n">d_np</span><span class="p">,</span> <span class="n">zz</span><span class="p">,</span> <span class="n">k</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">s</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<span class="n">z_x</span> <span class="o">=</span> <span class="n">spline</span><span class="p">(</span><span class="n">xx</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">(</span><span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">12</span><span class="p">,</span> <span class="mi">5</span><span class="p">))</span>
<span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">xx</span><span class="p">,</span> <span class="n">z_x</span><span class="p">)</span>
<span class="c1"># Annotate key scales</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axvline</span><span class="p">(</span>
<span class="n">L</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s2">&quot;black&quot;</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;--&quot;</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="sa">rf</span><span class="s2">&quot;$L = </span><span class="si">{</span><span class="n">L</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2">\textrm</span><span class="se">{{</span><span class="s2"> Gpc</span><span class="se">}}</span><span class="s2">/h$&quot;</span>
<span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axhline</span><span class="p">(</span><span class="n">spline</span><span class="p">(</span><span class="n">L</span><span class="p">),</span> <span class="n">color</span><span class="o">=</span><span class="s2">&quot;black&quot;</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;--&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axvline</span><span class="p">(</span>
<span class="n">Lcorner</span><span class="p">,</span>
<span class="n">color</span><span class="o">=</span><span class="s2">&quot;orange&quot;</span><span class="p">,</span>
<span class="n">linewidth</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;--&quot;</span><span class="p">,</span>
<span class="n">label</span><span class="o">=</span><span class="sa">rf</span><span class="s2">&quot;$L_\textrm</span><span class="se">{{</span><span class="s2">corner</span><span class="se">}}</span><span class="s2"> = </span><span class="si">{</span><span class="n">Lcorner</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2">\textrm</span><span class="se">{{</span><span class="s2"> Gpc</span><span class="se">}}</span><span class="s2">/h$&quot;</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axhline</span><span class="p">(</span><span class="n">spline</span><span class="p">(</span><span class="n">Lcorner</span><span class="p">),</span> <span class="n">color</span><span class="o">=</span><span class="s2">&quot;orange&quot;</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;--&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">text</span><span class="p">(</span><span class="n">L</span> <span class="o">+</span> <span class="mf">0.08</span><span class="p">,</span> <span class="n">spline</span><span class="p">(</span><span class="n">L</span><span class="p">)</span> <span class="o">-</span> <span class="mf">0.14</span><span class="p">,</span> <span class="sa">rf</span><span class="s2">&quot;$z(L) = </span><span class="si">{</span><span class="n">spline</span><span class="p">(</span><span class="n">L</span><span class="p">)</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2">$&quot;</span><span class="p">,</span> <span class="n">fontsize</span><span class="o">=</span><span class="n">GLOBAL_FS_TINY</span> <span class="o">-</span> <span class="mi">2</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">text</span><span class="p">(</span>
<span class="n">Lcorner</span> <span class="o">-</span> <span class="mf">1.2</span><span class="p">,</span>
<span class="n">spline</span><span class="p">(</span><span class="n">Lcorner</span><span class="p">)</span> <span class="o">-</span> <span class="mf">0.17</span><span class="p">,</span>
<span class="sa">rf</span><span class="s2">&quot;$z(\sqrt</span><span class="se">{{</span><span class="s2">3</span><span class="se">}}</span><span class="s2">\,L) = </span><span class="si">{</span><span class="n">spline</span><span class="p">(</span><span class="n">Lcorner</span><span class="p">)</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2">$&quot;</span><span class="p">,</span>
<span class="n">fontsize</span><span class="o">=</span><span class="n">GLOBAL_FS_TINY</span> <span class="o">-</span> <span class="mi">2</span><span class="p">,</span>
<span class="p">)</span>
<span class="c1"># Annotate the selection functions&#39; means</span>
<span class="n">z_means</span> <span class="o">=</span> <span class="n">spline</span><span class="p">(</span><span class="n">means_com</span><span class="p">)</span>
<span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">z_mean</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">z_means</span><span class="p">):</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axvline</span><span class="p">(</span><span class="n">means_com</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">color</span><span class="o">=</span><span class="n">colours_list</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;--&quot;</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axhline</span><span class="p">(</span><span class="n">z_mean</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="n">colours_list</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;--&quot;</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">text</span><span class="p">(</span>
<span class="n">L</span> <span class="o">+</span> <span class="mf">0.08</span><span class="p">,</span>
<span class="n">z_mean</span> <span class="o">-</span> <span class="mf">0.14</span><span class="p">,</span>
<span class="sa">rf</span><span class="s2">&quot;$z(\mu_</span><span class="se">{{</span><span class="si">{</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="si">}</span><span class="se">}}</span><span class="s2"> = </span><span class="si">{</span><span class="n">means_com</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2">) = </span><span class="si">{</span><span class="n">z_mean</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2">$&quot;</span><span class="p">,</span>
<span class="n">fontsize</span><span class="o">=</span><span class="n">GLOBAL_FS_TINY</span> <span class="o">-</span> <span class="mi">2</span><span class="p">,</span>
<span class="p">)</span>
<span class="c1"># Add labels, legend, and save the figure</span>
<span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;Comoving distance [Gpc$/h$]&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s2">&quot;Redshift $z$&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">grid</span><span class="p">(</span><span class="n">which</span><span class="o">=</span><span class="s2">&quot;both&quot;</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="s2">&quot;both&quot;</span><span class="p">,</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;-&quot;</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mf">0.3</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s2">&quot;gray&quot;</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.5</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">legend</span><span class="p">()</span>
<span class="n">plt</span><span class="o">.</span><span class="n">tight_layout</span><span class="p">()</span>
<span class="n">plt</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">wd</span><span class="si">}</span><span class="s2">redshift_distance_conversion.pdf&quot;</span><span class="p">,</span> <span class="n">bbox_inches</span><span class="o">=</span><span class="s2">&quot;tight&quot;</span><span class="p">,</span> <span class="n">dpi</span><span class="o">=</span><span class="mi">300</span><span class="p">)</span>
<span class="k">if</span> <span class="n">display</span><span class="p">:</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
<span class="n">plt</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="k">return</span> <span class="n">spline</span></div>
<div class="viewcode-block" id="plot_selection_functions_def_in_z">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_selection_functions_def_in_z">[docs]</a>
<span class="k">def</span> <span class="nf">plot_selection_functions_def_in_z</span><span class="p">(</span>
<span class="n">xx_of_zs</span><span class="p">,</span>
<span class="n">res</span><span class="p">,</span>
<span class="n">res_mis</span><span class="p">,</span>
<span class="n">z_means</span><span class="p">,</span>
<span class="n">cosmo</span><span class="p">,</span>
<span class="n">L</span><span class="p">,</span>
<span class="n">stds_z</span><span class="p">,</span>
<span class="n">wd</span><span class="p">,</span>
<span class="n">display</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Plot radial lognormal (in redshift) selection functions against</span>
<span class="sd"> comoving distances.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> xx_of_zs : array-like</span>
<span class="sd"> Comoving distances mapped from redshift.</span>
<span class="sd"> res : list of array-like</span>
<span class="sd"> Selection functions for the well-specified model.</span>
<span class="sd"> res_mis : list of array-like</span>
<span class="sd"> Selection functions for the mis-specified model.</span>
<span class="sd"> z_means : array-like</span>
<span class="sd"> Mean redshifts of every galaxy population.</span>
<span class="sd"> cosmo : object</span>
<span class="sd"> Cosmology object.</span>
<span class="sd"> L : float</span>
<span class="sd"> Box side length in comoving distance units.</span>
<span class="sd"> stds_z : array-like</span>
<span class="sd"> Standard deviations of redshift distributions.</span>
<span class="sd"> wd : str</span>
<span class="sd"> Working directory for saving figures.</span>
<span class="sd"> display : bool, optional</span>
<span class="sd"> Whether to display the figure. Default is True.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> None</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">from</span> <span class="nn">matplotlib.ticker</span> <span class="kn">import</span> <span class="n">FormatStrFormatter</span>
<span class="n">colours_list</span> <span class="o">=</span> <span class="n">COLOUR_LIST</span><span class="p">[:</span> <span class="nb">len</span><span class="p">(</span><span class="n">res</span><span class="p">)]</span>
<span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">(</span><span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span> <span class="mi">5</span><span class="p">))</span>
<span class="c1"># Plot well-specified selection functions</span>
<span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">r</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">res</span><span class="p">):</span>
<span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">xx_of_zs</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="n">colours_list</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
<span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">xx_of_zs</span><span class="p">,</span> <span class="n">res</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="n">color</span><span class="o">=</span><span class="s2">&quot;black&quot;</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="s2">&quot;Model A&quot;</span><span class="p">)</span>
<span class="c1"># Plot mis-specified selection functions</span>
<span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">r_mis</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">res_mis</span><span class="p">):</span>
<span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">xx_of_zs</span><span class="p">,</span> <span class="n">r_mis</span><span class="p">,</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;--&quot;</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="n">colours_list</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
<span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">xx_of_zs</span><span class="p">,</span> <span class="n">res_mis</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;--&quot;</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s2">&quot;black&quot;</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="s2">&quot;Model B&quot;</span><span class="p">)</span>
<span class="c1"># Define x-ticks and labels</span>
<span class="n">xticks</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span> <span class="o">*</span> <span class="n">L</span><span class="p">]</span>
<span class="n">xtick_labels</span> <span class="o">=</span> <span class="p">[</span><span class="sa">r</span><span class="s2">&quot;$0$&quot;</span><span class="p">,</span> <span class="sa">r</span><span class="s2">&quot;$\sqrt 3\,L \simeq </span><span class="si">{:.2f}</span><span class="s2">$&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span> <span class="o">*</span> <span class="n">L</span><span class="p">)]</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axvline</span><span class="p">(</span><span class="n">L</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s2">&quot;black&quot;</span><span class="p">,</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;-&quot;</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">zorder</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<span class="c1"># Annotate populations</span>
<span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">mean</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">z_means</span><span class="p">):</span>
<span class="n">std</span> <span class="o">=</span> <span class="n">stds_z</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="n">mu</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">mean</span><span class="o">**</span><span class="mi">2</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">mean</span><span class="o">**</span><span class="mi">2</span> <span class="o">+</span> <span class="n">std</span><span class="o">**</span><span class="mi">2</span><span class="p">))</span>
<span class="n">sig2</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="mi">1</span> <span class="o">+</span> <span class="n">std</span><span class="o">**</span><span class="mi">2</span> <span class="o">/</span> <span class="n">mean</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span>
<span class="n">mode</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">mu</span> <span class="o">-</span> <span class="n">sig2</span><span class="p">)</span>
<span class="n">dmode</span> <span class="o">=</span> <span class="n">cosmo</span><span class="o">.</span><span class="n">comoving_distance</span><span class="p">(</span><span class="n">mode</span><span class="p">)</span><span class="o">.</span><span class="n">value</span> <span class="o">/</span> <span class="mf">1e3</span>
<span class="n">dmean</span> <span class="o">=</span> <span class="n">cosmo</span><span class="o">.</span><span class="n">comoving_distance</span><span class="p">(</span><span class="n">mean</span><span class="p">)</span><span class="o">.</span><span class="n">value</span> <span class="o">/</span> <span class="mf">1e3</span>
<span class="n">xticks</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="n">dmean</span><span class="p">])</span>
<span class="n">xtick_labels</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">dmean</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">])</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axvline</span><span class="p">(</span><span class="n">dmean</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="n">colours_list</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;-.&quot;</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axvline</span><span class="p">(</span><span class="n">dmode</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="n">colours_list</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;-&quot;</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axvline</span><span class="p">(</span>
<span class="n">mode</span><span class="p">,</span>
<span class="n">color</span><span class="o">=</span><span class="n">colours_list</span><span class="p">[</span><span class="n">i</span><span class="p">],</span>
<span class="n">alpha</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
<span class="n">linewidth</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="n">label</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;Population </span><span class="si">{</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">,</span>
<span class="p">)</span>
<span class="c1"># Configure axes, labels, ticks, legend</span>
<span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;$r\,[{\rm Gpc}/h]$&quot;</span><span class="p">,</span> <span class="n">fontsize</span><span class="o">=</span><span class="n">GLOBAL_FS_LARGE</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;$R_i(r)$&quot;</span><span class="p">,</span> <span class="n">fontsize</span><span class="o">=</span><span class="n">GLOBAL_FS_LARGE</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">xticks</span><span class="p">(</span><span class="n">xticks</span><span class="p">,</span> <span class="n">xtick_labels</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">tick_params</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="s2">&quot;x&quot;</span><span class="p">,</span> <span class="n">which</span><span class="o">=</span><span class="s2">&quot;major&quot;</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="mi">8</span><span class="p">,</span> <span class="n">labelsize</span><span class="o">=</span><span class="n">GLOBAL_FS_SMALL</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">tick_params</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="s2">&quot;y&quot;</span><span class="p">,</span> <span class="n">which</span><span class="o">=</span><span class="s2">&quot;major&quot;</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="mi">8</span><span class="p">,</span> <span class="n">labelsize</span><span class="o">=</span><span class="n">GLOBAL_FS_SMALL</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">grid</span><span class="p">(</span><span class="n">which</span><span class="o">=</span><span class="s2">&quot;both&quot;</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="s2">&quot;both&quot;</span><span class="p">,</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;-&quot;</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mf">0.4</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s2">&quot;gray&quot;</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.5</span><span class="p">)</span>
<span class="n">maxs</span> <span class="o">=</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">r</span><span class="p">)</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">res</span><span class="p">]</span>
<span class="n">yticks</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">maxs</span>
<span class="n">plt</span><span class="o">.</span><span class="n">yticks</span><span class="p">(</span><span class="n">yticks</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">gca</span><span class="p">()</span><span class="o">.</span><span class="n">yaxis</span><span class="o">.</span><span class="n">set_major_formatter</span><span class="p">(</span><span class="n">FormatStrFormatter</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%.2f</span><span class="s2">&quot;</span><span class="p">))</span>
<span class="n">legend</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">legend</span><span class="p">(</span><span class="n">frameon</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">loc</span><span class="o">=</span><span class="s2">&quot;upper right&quot;</span><span class="p">,</span> <span class="n">fontsize</span><span class="o">=</span><span class="n">GLOBAL_FS_LARGE</span><span class="p">)</span>
<span class="n">legend</span><span class="o">.</span><span class="n">get_frame</span><span class="p">()</span><span class="o">.</span><span class="n">set_edgecolor</span><span class="p">(</span><span class="s2">&quot;white&quot;</span><span class="p">)</span>
<span class="k">for</span> <span class="n">lh</span> <span class="ow">in</span> <span class="n">legend</span><span class="o">.</span><span class="n">legend_handles</span><span class="p">:</span>
<span class="n">lh</span><span class="o">.</span><span class="n">set_alpha</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">tight_layout</span><span class="p">()</span>
<span class="n">plt</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">wd</span><span class="si">}</span><span class="s2">selection_functions_com.pdf&quot;</span><span class="p">,</span> <span class="n">bbox_inches</span><span class="o">=</span><span class="s2">&quot;tight&quot;</span><span class="p">,</span> <span class="n">dpi</span><span class="o">=</span><span class="mi">300</span><span class="p">)</span>
<span class="k">if</span> <span class="n">display</span><span class="p">:</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
<span class="n">plt</span><span class="o">.</span><span class="n">close</span><span class="p">()</span></div>
<div class="viewcode-block" id="plot_galaxy_field_slice">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_galaxy_field_slice">[docs]</a>
<span class="k">def</span> <span class="nf">plot_galaxy_field_slice</span><span class="p">(</span><span class="n">g</span><span class="p">,</span> <span class="n">size</span><span class="p">,</span> <span class="n">L</span><span class="p">,</span> <span class="n">wd</span><span class="p">,</span> <span class="n">id_obs</span><span class="p">,</span> <span class="n">limits</span><span class="o">=</span><span class="s2">&quot;minmax&quot;</span><span class="p">,</span> <span class="n">display</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Plot a 2D slice of the observed field.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> g : ndarray</span>
<span class="sd"> 2D array representing the observed field slice.</span>
<span class="sd"> size : int</span>
<span class="sd"> Number of grid points along each axis.</span>
<span class="sd"> L : float</span>
<span class="sd"> Size of the simulation box (in Mpc/h).</span>
<span class="sd"> wd : str</span>
<span class="sd"> Working directory for saving output files.</span>
<span class="sd"> id_obs : int or str</span>
<span class="sd"> Identifier for the observation, used in file naming.</span>
<span class="sd"> limits : str, optional</span>
<span class="sd"> Colormap scaling method. Options: &#39;minmax&#39;, &#39;truncate&#39;, &#39;max&#39;.</span>
<span class="sd"> display : bool, optional</span>
<span class="sd"> Whether to display the figure. Default is True.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">from</span> <span class="nn">mpl_toolkits.axes_grid1</span> <span class="kn">import</span> <span class="n">make_axes_locatable</span>
<span class="kn">from</span> <span class="nn">matplotlib</span> <span class="kn">import</span> <span class="n">colors</span>
<span class="c1"># Define colormap and set scaling limits</span>
<span class="n">GalaxyMap</span> <span class="o">=</span> <span class="n">create_colormap</span><span class="p">(</span><span class="s2">&quot;GalaxyMap&quot;</span><span class="p">)</span>
<span class="k">if</span> <span class="n">limits</span> <span class="o">==</span> <span class="s2">&quot;max&quot;</span><span class="p">:</span>
<span class="n">maxcol</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">g</span><span class="p">))</span>
<span class="n">mincol</span> <span class="o">=</span> <span class="o">-</span><span class="n">maxcol</span>
<span class="n">cmap</span> <span class="o">=</span> <span class="n">GalaxyMap</span>
<span class="k">elif</span> <span class="n">limits</span> <span class="o">==</span> <span class="s2">&quot;truncate&quot;</span><span class="p">:</span>
<span class="n">maxcol</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">([</span><span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="o">-</span><span class="n">g</span><span class="p">),</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">g</span><span class="p">)])</span>
<span class="n">mincol</span> <span class="o">=</span> <span class="o">-</span><span class="n">maxcol</span>
<span class="n">cmap</span> <span class="o">=</span> <span class="s2">&quot;PiYG&quot;</span>
<span class="k">elif</span> <span class="n">limits</span> <span class="o">==</span> <span class="s2">&quot;minmax&quot;</span><span class="p">:</span>
<span class="n">maxcol</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">g</span><span class="p">)</span>
<span class="n">mincol</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">g</span><span class="p">)</span>
<span class="n">cmap</span> <span class="o">=</span> <span class="n">GalaxyMap</span>
<span class="n">divnorm</span> <span class="o">=</span> <span class="n">colors</span><span class="o">.</span><span class="n">TwoSlopeNorm</span><span class="p">(</span><span class="n">vmin</span><span class="o">=</span><span class="n">mincol</span><span class="p">,</span> <span class="n">vcenter</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">vmax</span><span class="o">=</span><span class="n">maxcol</span><span class="p">)</span>
<span class="c1"># Plot</span>
<span class="n">fig</span><span class="p">,</span> <span class="n">ax</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">(</span><span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">6</span><span class="p">,</span> <span class="mi">6</span><span class="p">))</span>
<span class="n">im</span> <span class="o">=</span> <span class="n">ax</span><span class="o">.</span><span class="n">imshow</span><span class="p">(</span><span class="n">g</span><span class="p">,</span> <span class="n">norm</span><span class="o">=</span><span class="n">divnorm</span><span class="p">,</span> <span class="n">cmap</span><span class="o">=</span><span class="n">cmap</span><span class="p">)</span>
<span class="n">ax</span><span class="o">.</span><span class="n">invert_yaxis</span><span class="p">()</span> <span class="c1"># Place origin at bottom-left</span>
<span class="n">ax</span><span class="o">.</span><span class="n">spines</span><span class="p">[[</span><span class="s2">&quot;top&quot;</span><span class="p">,</span> <span class="s2">&quot;right&quot;</span><span class="p">,</span> <span class="s2">&quot;left&quot;</span><span class="p">,</span> <span class="s2">&quot;bottom&quot;</span><span class="p">]]</span><span class="o">.</span><span class="n">set_visible</span><span class="p">(</span><span class="kc">False</span><span class="p">)</span>
<span class="n">divider</span> <span class="o">=</span> <span class="n">make_axes_locatable</span><span class="p">(</span><span class="n">ax</span><span class="p">)</span>
<span class="n">cax</span> <span class="o">=</span> <span class="n">divider</span><span class="o">.</span><span class="n">append_axes</span><span class="p">(</span><span class="s2">&quot;right&quot;</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="s2">&quot;5%&quot;</span><span class="p">,</span> <span class="n">pad</span><span class="o">=</span><span class="mf">0.1</span><span class="p">)</span>
<span class="n">cbar</span> <span class="o">=</span> <span class="n">fig</span><span class="o">.</span><span class="n">colorbar</span><span class="p">(</span><span class="n">im</span><span class="p">,</span> <span class="n">cax</span><span class="o">=</span><span class="n">cax</span><span class="p">)</span>
<span class="n">cbar</span><span class="o">.</span><span class="n">outline</span><span class="o">.</span><span class="n">set_visible</span><span class="p">(</span><span class="kc">False</span><span class="p">)</span>
<span class="n">ticks</span> <span class="o">=</span> <span class="p">[</span><span class="n">mincol</span><span class="p">,</span> <span class="n">mincol</span> <span class="o">/</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">maxcol</span> <span class="o">/</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">2</span> <span class="o">*</span> <span class="n">maxcol</span> <span class="o">/</span> <span class="mi">3</span><span class="p">,</span> <span class="n">maxcol</span><span class="p">]</span>
<span class="n">cbar</span><span class="o">.</span><span class="n">set_ticks</span><span class="p">(</span><span class="n">ticks</span><span class="p">)</span>
<span class="n">cbar</span><span class="o">.</span><span class="n">set_ticklabels</span><span class="p">([</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">x</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2">&quot;</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">ticks</span><span class="p">],</span> <span class="n">size</span><span class="o">=</span><span class="n">GLOBAL_FS_SMALL</span><span class="p">)</span>
<span class="n">cbar</span><span class="o">.</span><span class="n">set_label</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;$\delta_\textrm</span><span class="si">{g}</span><span class="s2">$&quot;</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="n">GLOBAL_FS</span><span class="p">)</span>
<span class="n">ax</span><span class="o">.</span><span class="n">set_xticks</span><span class="p">(</span>
<span class="p">[</span><span class="n">size</span> <span class="o">*</span> <span class="n">i</span> <span class="o">/</span> <span class="mf">4.0</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">5</span><span class="p">)],</span> <span class="p">[</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">L</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="mf">1e-3</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="n">i</span><span class="w"> </span><span class="o">/</span><span class="w"> </span><span class="mi">4</span><span class="si">:</span><span class="s2">.1f</span><span class="si">}</span><span class="s2">&quot;</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">5</span><span class="p">)]</span>
<span class="p">)</span>
<span class="n">ax</span><span class="o">.</span><span class="n">set_yticks</span><span class="p">(</span>
<span class="p">[</span><span class="n">size</span> <span class="o">*</span> <span class="n">i</span> <span class="o">/</span> <span class="mf">4.0</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">5</span><span class="p">)],</span> <span class="p">[</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">L</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="mf">1e-3</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="n">i</span><span class="w"> </span><span class="o">/</span><span class="w"> </span><span class="mi">4</span><span class="si">:</span><span class="s2">.1f</span><span class="si">}</span><span class="s2">&quot;</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">5</span><span class="p">)]</span>
<span class="p">)</span>
<span class="n">ax</span><span class="o">.</span><span class="n">set_xlabel</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;Gpc/$h$&quot;</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="n">GLOBAL_FS</span><span class="p">)</span>
<span class="n">ax</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;Gpc/$h$&quot;</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="n">GLOBAL_FS</span><span class="p">)</span>
<span class="c1"># Save or display</span>
<span class="k">if</span> <span class="n">display</span><span class="p">:</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">plt</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">wd</span><span class="si">}</span><span class="s2">Figures/g_</span><span class="si">{</span><span class="n">id_obs</span><span class="si">}</span><span class="s2">.png&quot;</span><span class="p">,</span> <span class="n">bbox_inches</span><span class="o">=</span><span class="s2">&quot;tight&quot;</span><span class="p">,</span> <span class="n">dpi</span><span class="o">=</span><span class="mi">300</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">wd</span><span class="si">}</span><span class="s2">Figures/g_</span><span class="si">{</span><span class="n">id_obs</span><span class="si">}</span><span class="s2">.pdf&quot;</span><span class="p">,</span> <span class="n">bbox_inches</span><span class="o">=</span><span class="s2">&quot;tight&quot;</span><span class="p">,</span> <span class="n">dpi</span><span class="o">=</span><span class="mi">300</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">close</span><span class="p">()</span></div>
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<p class="caption" role="heading"><span class="caption-text">API Documentation</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.hiddenbox.html">hiddenbox</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox"><code class="docutils literal notranslate"><span class="pre">HiddenBox</span></code></a><ul>
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<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Ntimesteps"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Ntimesteps</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Psingle"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Psingle</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.compute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.compute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.evaluate"><code class="docutils literal notranslate"><span class="pre">HiddenBox.evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_neglect_lightcone"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_neglect_lightcone</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_recompute_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_recompute_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.gravity_on"><code class="docutils literal notranslate"><span class="pre">HiddenBox.gravity_on</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.load_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.load_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.make_data"><code class="docutils literal notranslate"><span class="pre">HiddenBox.make_data()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.modified_selfi"><code class="docutils literal notranslate"><span class="pre">HiddenBox.modified_selfi</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.prefix_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.prefix_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.reset_survey"><code class="docutils literal notranslate"><span class="pre">HiddenBox.reset_survey()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.setup_only"><code class="docutils literal notranslate"><span class="pre">HiddenBox.setup_only</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_recompute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_recompute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_setup"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_setup()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.update"><code class="docutils literal notranslate"><span class="pre">HiddenBox.update()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.normalise_hb.html">normalise_hb</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.define_normalisation"><code class="docutils literal notranslate"><span class="pre">define_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation"><code class="docutils literal notranslate"><span class="pre">worker_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_public"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_public()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_wrapper"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_wrapper()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.prior.html">prior</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.logposterior_hyperparameters_parallel"><code class="docutils literal notranslate"><span class="pre">logposterior_hyperparameters_parallel()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.perform_prior_optimisation_and_plot"><code class="docutils literal notranslate"><span class="pre">perform_prior_optimisation_and_plot()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior"><code class="docutils literal notranslate"><span class="pre">planck_prior</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.mean"><code class="docutils literal notranslate"><span class="pre">planck_prior.mean</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.inv_covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.inv_covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_max"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_max</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_min"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_min</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.compute"><code class="docutils literal notranslate"><span class="pre">planck_prior.compute()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.load"><code class="docutils literal notranslate"><span class="pre">planck_prior.load()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.logpdf"><code class="docutils literal notranslate"><span class="pre">planck_prior.logpdf()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.sample"><code class="docutils literal notranslate"><span class="pre">planck_prior.sample()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.save"><code class="docutils literal notranslate"><span class="pre">planck_prior.save()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.worker_class"><code class="docutils literal notranslate"><span class="pre">worker_class()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.selection_functions.html">selection_functions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.init_selection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.init_selection()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.lognormals_z_to_x"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.lognormals_z_to_x()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.r_grid"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.r_grid()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.selfi_interface.html">selfi_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.PrintMessage"><code class="docutils literal notranslate"><span class="pre">PrintMessage()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.indent"><code class="docutils literal notranslate"><span class="pre">indent()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.unindent"><code class="docutils literal notranslate"><span class="pre">unindent()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.sbmy_interface.html">sbmy_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.compute_Phi"><code class="docutils literal notranslate"><span class="pre">compute_Phi()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.generate_white_noise_Field"><code class="docutils literal notranslate"><span class="pre">generate_white_noise_Field()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.get_power_spectrum_from_cosmo"><code class="docutils literal notranslate"><span class="pre">get_power_spectrum_from_cosmo()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.handle_time_stepping"><code class="docutils literal notranslate"><span class="pre">handle_time_stepping()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.setup_sbmy_parfiles"><code class="docutils literal notranslate"><span class="pre">setup_sbmy_parfiles()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.grf.html">grf</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.grf.html#selfisys.grf.primordial_grf"><code class="docutils literal notranslate"><span class="pre">primordial_grf()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.utils.html">selfisys.utils package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.examples_utils">selfisys.utils.examples_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.examples_utils.clear_large_plot"><code class="docutils literal notranslate"><span class="pre">clear_large_plot()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.logger">selfisys.utils.logger module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLogger"><code class="docutils literal notranslate"><span class="pre">CustomLogger</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLogger.diagnostic"><code class="docutils literal notranslate"><span class="pre">CustomLogger.diagnostic()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler.emit"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler.emit()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.INDENT"><code class="docutils literal notranslate"><span class="pre">INDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintDiagnostic"><code class="docutils literal notranslate"><span class="pre">PrintDiagnostic()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintError"><code class="docutils literal notranslate"><span class="pre">PrintError()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintInfo"><code class="docutils literal notranslate"><span class="pre">PrintInfo()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintLeftType"><code class="docutils literal notranslate"><span class="pre">PrintLeftType()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintWarning"><code class="docutils literal notranslate"><span class="pre">PrintWarning()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.UNINDENT"><code class="docutils literal notranslate"><span class="pre">UNINDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.getCustomLogger"><code class="docutils literal notranslate"><span class="pre">getCustomLogger()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.low_level">selfisys.utils.low_level module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.low_level.stderr_redirector"><code class="docutils literal notranslate"><span class="pre">stderr_redirector()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.low_level.stdout_redirector"><code class="docutils literal notranslate"><span class="pre">stdout_redirector()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.parser">selfisys.utils.parser module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.bool_sh"><code class="docutils literal notranslate"><span class="pre">bool_sh()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.check_files_exist"><code class="docutils literal notranslate"><span class="pre">check_files_exist()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.intNone"><code class="docutils literal notranslate"><span class="pre">intNone()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.joinstrs"><code class="docutils literal notranslate"><span class="pre">joinstrs()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.joinstrs_only"><code class="docutils literal notranslate"><span class="pre">joinstrs_only()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.safe_npload"><code class="docutils literal notranslate"><span class="pre">safe_npload()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.path_utils">selfisys.utils.path_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.path_utils.file_names_evaluate"><code class="docutils literal notranslate"><span class="pre">file_names_evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.path_utils.get_file_names"><code class="docutils literal notranslate"><span class="pre">get_file_names()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.plot_examples">selfisys.utils.plot_examples module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_comoving_distance_redshift"><code class="docutils literal notranslate"><span class="pre">plot_comoving_distance_redshift()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_galaxy_field_slice"><code class="docutils literal notranslate"><span class="pre">plot_galaxy_field_slice()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_power_spectrum"><code class="docutils literal notranslate"><span class="pre">plot_power_spectrum()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_selection_functions_def_in_z"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions_def_in_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.redshift_distance_conversion"><code class="docutils literal notranslate"><span class="pre">redshift_distance_conversion()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.relative_error_analysis"><code class="docutils literal notranslate"><span class="pre">relative_error_analysis()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.plot_params">selfisys.utils.plot_params module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.get_offset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.get_offset()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_scientific"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_scientific()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_useOffset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_useOffset()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.create_all_colormaps"><code class="docutils literal notranslate"><span class="pre">create_all_colormaps()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.create_colormap"><code class="docutils literal notranslate"><span class="pre">create_colormap()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.dynamic_text_scaling"><code class="docutils literal notranslate"><span class="pre">dynamic_text_scaling()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.get_contours"><code class="docutils literal notranslate"><span class="pre">get_contours()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.reset_plotting"><code class="docutils literal notranslate"><span class="pre">reset_plotting()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.setup_plotting"><code class="docutils literal notranslate"><span class="pre">setup_plotting()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.plot_utils">selfisys.utils.plot_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_C"><code class="docutils literal notranslate"><span class="pre">plot_C()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_fisher"><code class="docutils literal notranslate"><span class="pre">plot_fisher()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_gradients"><code class="docutils literal notranslate"><span class="pre">plot_gradients()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_histogram"><code class="docutils literal notranslate"><span class="pre">plot_histogram()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks"><code class="docutils literal notranslate"><span class="pre">plot_mocks()</span></code></a></li>
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<h1>Source code for selfisys.utils.plot_params</h1><div class="highlight"><pre>
<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="c1"># Copyright (C) 2024 Tristan Hoellinger</span>
<span class="c1"># Distributed under the GNU General Public License v3.0 (GPLv3).</span>
<span class="c1"># See the LICENSE file in the root directory for details.</span>
<span class="c1"># SPDX-License-Identifier: GPL-3.0-or-later</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="n">__author__</span> <span class="o">=</span> <span class="s2">&quot;Tristan Hoellinger&quot;</span>
<span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;0.1.0&quot;</span>
<span class="n">__date__</span> <span class="o">=</span> <span class="s2">&quot;2024&quot;</span>
<span class="n">__license__</span> <span class="o">=</span> <span class="s2">&quot;GPLv3&quot;</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd">Plotting utilities and custom colormaps for the SelfiSys package.</span>
<span class="sd">This module provides custom Matplotlib settings, formatter classes, and</span>
<span class="sd">colormaps used for visualising results in the SelfiSys project.</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="c1"># Global font sizes</span>
<span class="n">GLOBAL_FS</span> <span class="o">=</span> <span class="mi">20</span>
<span class="n">GLOBAL_FS_LARGE</span> <span class="o">=</span> <span class="mi">22</span>
<span class="n">GLOBAL_FS_XLARGE</span> <span class="o">=</span> <span class="mi">24</span>
<span class="n">GLOBAL_FS_SMALL</span> <span class="o">=</span> <span class="mi">18</span>
<span class="n">GLOBAL_FS_TINY</span> <span class="o">=</span> <span class="mi">16</span>
<span class="n">COLOUR_LIST</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;C4&quot;</span><span class="p">,</span> <span class="s2">&quot;C5&quot;</span><span class="p">,</span> <span class="s2">&quot;C6&quot;</span><span class="p">,</span> <span class="s2">&quot;C7&quot;</span><span class="p">]</span>
<div class="viewcode-block" id="reset_plotting">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.plot_params.reset_plotting">[docs]</a>
<span class="k">def</span> <span class="nf">reset_plotting</span><span class="p">():</span>
<span class="kn">import</span> <span class="nn">matplotlib</span> <span class="k">as</span> <span class="nn">mpl</span>
<span class="n">mpl</span><span class="o">.</span><span class="n">rcParams</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">mpl</span><span class="o">.</span><span class="n">rcParamsDefault</span><span class="p">)</span></div>
<div class="viewcode-block" id="setup_plotting">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.plot_params.setup_plotting">[docs]</a>
<span class="k">def</span> <span class="nf">setup_plotting</span><span class="p">():</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Configure Matplotlib plotting settings for consistent appearance.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
<span class="kn">import</span> <span class="nn">importlib.resources</span>
<span class="k">with</span> <span class="n">importlib</span><span class="o">.</span><span class="n">resources</span><span class="o">.</span><span class="n">open_text</span><span class="p">(</span><span class="s2">&quot;selfisys&quot;</span><span class="p">,</span> <span class="s2">&quot;preamble.tex&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
<span class="n">preamble</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">read</span><span class="p">()</span>
<span class="c1"># Dictionary with rcParams settings</span>
<span class="n">rcparams</span> <span class="o">=</span> <span class="p">{</span>
<span class="s2">&quot;font.family&quot;</span><span class="p">:</span> <span class="s2">&quot;serif&quot;</span><span class="p">,</span>
<span class="s2">&quot;font.size&quot;</span><span class="p">:</span> <span class="n">GLOBAL_FS</span><span class="p">,</span> <span class="c1"># Base font size</span>
<span class="s2">&quot;axes.titlesize&quot;</span><span class="p">:</span> <span class="n">GLOBAL_FS_XLARGE</span><span class="p">,</span>
<span class="s2">&quot;axes.labelsize&quot;</span><span class="p">:</span> <span class="n">GLOBAL_FS_LARGE</span><span class="p">,</span>
<span class="s2">&quot;axes.linewidth&quot;</span><span class="p">:</span> <span class="mf">1.0</span><span class="p">,</span>
<span class="s2">&quot;xtick.labelsize&quot;</span><span class="p">:</span> <span class="n">GLOBAL_FS_SMALL</span><span class="p">,</span>
<span class="s2">&quot;ytick.labelsize&quot;</span><span class="p">:</span> <span class="n">GLOBAL_FS_SMALL</span><span class="p">,</span>
<span class="s2">&quot;xtick.major.width&quot;</span><span class="p">:</span> <span class="mf">1.2</span><span class="p">,</span>
<span class="s2">&quot;ytick.major.width&quot;</span><span class="p">:</span> <span class="mf">1.2</span><span class="p">,</span>
<span class="s2">&quot;xtick.minor.width&quot;</span><span class="p">:</span> <span class="mf">1.0</span><span class="p">,</span>
<span class="s2">&quot;ytick.minor.width&quot;</span><span class="p">:</span> <span class="mf">1.0</span><span class="p">,</span>
<span class="s2">&quot;xtick.direction&quot;</span><span class="p">:</span> <span class="s2">&quot;in&quot;</span><span class="p">,</span>
<span class="s2">&quot;ytick.direction&quot;</span><span class="p">:</span> <span class="s2">&quot;in&quot;</span><span class="p">,</span>
<span class="s2">&quot;xtick.major.pad&quot;</span><span class="p">:</span> <span class="mi">5</span><span class="p">,</span>
<span class="s2">&quot;xtick.minor.pad&quot;</span><span class="p">:</span> <span class="mi">5</span><span class="p">,</span>
<span class="s2">&quot;ytick.major.pad&quot;</span><span class="p">:</span> <span class="mi">5</span><span class="p">,</span>
<span class="s2">&quot;ytick.minor.pad&quot;</span><span class="p">:</span> <span class="mi">5</span><span class="p">,</span>
<span class="s2">&quot;legend.fontsize&quot;</span><span class="p">:</span> <span class="n">GLOBAL_FS_SMALL</span><span class="p">,</span>
<span class="s2">&quot;legend.title_fontsize&quot;</span><span class="p">:</span> <span class="n">GLOBAL_FS_LARGE</span><span class="p">,</span>
<span class="s2">&quot;figure.titlesize&quot;</span><span class="p">:</span> <span class="n">GLOBAL_FS_XLARGE</span><span class="p">,</span>
<span class="s2">&quot;figure.dpi&quot;</span><span class="p">:</span> <span class="mi">300</span><span class="p">,</span>
<span class="s2">&quot;grid.color&quot;</span><span class="p">:</span> <span class="s2">&quot;gray&quot;</span><span class="p">,</span>
<span class="s2">&quot;grid.linestyle&quot;</span><span class="p">:</span> <span class="s2">&quot;dotted&quot;</span><span class="p">,</span>
<span class="s2">&quot;grid.linewidth&quot;</span><span class="p">:</span> <span class="mf">0.6</span><span class="p">,</span>
<span class="s2">&quot;lines.linewidth&quot;</span><span class="p">:</span> <span class="mi">2</span><span class="p">,</span>
<span class="s2">&quot;lines.markersize&quot;</span><span class="p">:</span> <span class="mi">8</span><span class="p">,</span>
<span class="s2">&quot;text.usetex&quot;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
<span class="s2">&quot;text.latex.preamble&quot;</span><span class="p">:</span> <span class="n">preamble</span><span class="p">,</span>
<span class="p">}</span>
<span class="c1"># Update rcParams</span>
<span class="n">plt</span><span class="o">.</span><span class="n">rcParams</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">rcparams</span><span class="p">)</span></div>
<div class="viewcode-block" id="dynamic_text_scaling">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.plot_params.dynamic_text_scaling">[docs]</a>
<span class="k">def</span> <span class="nf">dynamic_text_scaling</span><span class="p">(</span><span class="n">fig_height</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Dynamically scale text sizes based on the vertical height of the</span>
<span class="sd"> figure.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> fig_height : float</span>
<span class="sd"> Height of the figure in inches.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> dict</span>
<span class="sd"> Dictionary of scaled font sizes for consistent appearance.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">scaling_factor</span> <span class="o">=</span> <span class="n">fig_height</span> <span class="o">/</span> <span class="mf">6.0</span> <span class="c1"># Reference height is 6 inches</span>
<span class="k">return</span> <span class="p">{</span>
<span class="s2">&quot;font.size&quot;</span><span class="p">:</span> <span class="n">GLOBAL_FS</span> <span class="o">*</span> <span class="n">scaling_factor</span><span class="p">,</span>
<span class="s2">&quot;axes.titlesize&quot;</span><span class="p">:</span> <span class="n">GLOBAL_FS_XLARGE</span> <span class="o">*</span> <span class="n">scaling_factor</span><span class="p">,</span>
<span class="s2">&quot;axes.labelsize&quot;</span><span class="p">:</span> <span class="n">GLOBAL_FS_LARGE</span> <span class="o">*</span> <span class="n">scaling_factor</span><span class="p">,</span>
<span class="s2">&quot;xtick.labelsize&quot;</span><span class="p">:</span> <span class="n">GLOBAL_FS_SMALL</span> <span class="o">*</span> <span class="n">scaling_factor</span><span class="p">,</span>
<span class="s2">&quot;ytick.labelsize&quot;</span><span class="p">:</span> <span class="n">GLOBAL_FS_SMALL</span> <span class="o">*</span> <span class="n">scaling_factor</span><span class="p">,</span>
<span class="s2">&quot;legend.fontsize&quot;</span><span class="p">:</span> <span class="n">GLOBAL_FS_SMALL</span> <span class="o">*</span> <span class="n">scaling_factor</span><span class="p">,</span>
<span class="s2">&quot;legend.title_fontsize&quot;</span><span class="p">:</span> <span class="n">GLOBAL_FS_LARGE</span> <span class="o">*</span> <span class="n">scaling_factor</span><span class="p">,</span>
<span class="s2">&quot;figure.titlesize&quot;</span><span class="p">:</span> <span class="n">GLOBAL_FS_XLARGE</span> <span class="o">*</span> <span class="n">scaling_factor</span><span class="p">,</span>
<span class="p">}</span></div>
<div class="viewcode-block" id="ScalarFormatterForceFormat_11">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11">[docs]</a>
<span class="k">class</span> <span class="nc">ScalarFormatterForceFormat_11</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Custom scalar formatter to enforce a specific number format with an</span>
<span class="sd"> offset.</span>
<span class="sd"> This formatter displays tick labels with one decimal place and</span>
<span class="sd"> includes the offset notation for powers of ten.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">useOffset</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">useMathText</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">useLocale</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">matplotlib.ticker</span> <span class="kn">import</span> <span class="n">ScalarFormatter</span>
<span class="bp">self</span><span class="o">.</span><span class="n">formatter</span> <span class="o">=</span> <span class="n">ScalarFormatter</span><span class="p">(</span>
<span class="n">useOffset</span><span class="o">=</span><span class="n">useOffset</span><span class="p">,</span> <span class="n">useMathText</span><span class="o">=</span><span class="n">useMathText</span><span class="p">,</span> <span class="n">useLocale</span><span class="o">=</span><span class="n">useLocale</span>
<span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">formatter</span><span class="o">.</span><span class="n">set_powerlimits</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>
<span class="k">def</span> <span class="fm">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">val</span><span class="p">,</span> <span class="n">pos</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">formatter</span><span class="o">.</span><span class="fm">__call__</span><span class="p">(</span><span class="n">val</span><span class="p">,</span> <span class="n">pos</span><span class="p">)</span>
<div class="viewcode-block" id="ScalarFormatterForceFormat_11.set_scientific">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_scientific">[docs]</a>
<span class="k">def</span> <span class="nf">set_scientific</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">b</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">formatter</span><span class="o">.</span><span class="n">set_scientific</span><span class="p">(</span><span class="n">b</span><span class="p">)</span></div>
<div class="viewcode-block" id="ScalarFormatterForceFormat_11.set_useOffset">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_useOffset">[docs]</a>
<span class="k">def</span> <span class="nf">set_useOffset</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">b</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">formatter</span><span class="o">.</span><span class="n">set_useOffset</span><span class="p">(</span><span class="n">b</span><span class="p">)</span></div>
<div class="viewcode-block" id="ScalarFormatterForceFormat_11.get_offset">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.get_offset">[docs]</a>
<span class="k">def</span> <span class="nf">get_offset</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">offset</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">formatter</span><span class="o">.</span><span class="n">get_offset</span><span class="p">()</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">formatter</span><span class="o">.</span><span class="n">orderOfMagnitude</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">return</span> <span class="sa">r</span><span class="s2">&quot;$\times 10^{</span><span class="si">%+d</span><span class="s2">}$&quot;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">formatter</span><span class="o">.</span><span class="n">orderOfMagnitude</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="sa">r</span><span class="s2">&quot;$\times 10^{+0}$&quot;</span></div>
</div>
<div class="viewcode-block" id="get_contours">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.plot_params.get_contours">[docs]</a>
<span class="k">def</span> <span class="nf">get_contours</span><span class="p">(</span><span class="n">Z</span><span class="p">,</span> <span class="n">nBins</span><span class="p">,</span> <span class="n">confLevels</span><span class="o">=</span><span class="p">(</span><span class="mf">0.3173</span><span class="p">,</span> <span class="mf">0.0455</span><span class="p">,</span> <span class="mf">0.0027</span><span class="p">)):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Compute contour levels for given confidence levels.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> Z : ndarray</span>
<span class="sd"> 2D histogram or density estimate.</span>
<span class="sd"> nBins : int</span>
<span class="sd"> Number of bins along one axis.</span>
<span class="sd"> confLevels : tuple of float</span>
<span class="sd"> Confidence levels for which to compute contour levels.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> chainLevels : ndarray</span>
<span class="sd"> Contour levels corresponding to the provided confidence levels.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="n">Z</span> <span class="o">=</span> <span class="n">Z</span> <span class="o">/</span> <span class="n">Z</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>
<span class="n">nContourLevels</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">confLevels</span><span class="p">)</span>
<span class="n">chainLevels</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">ones</span><span class="p">(</span><span class="n">nContourLevels</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
<span class="n">histOrdered</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">Z</span><span class="o">.</span><span class="n">flat</span><span class="p">)</span>
<span class="n">histCumulative</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">cumsum</span><span class="p">(</span><span class="n">histOrdered</span><span class="p">)</span>
<span class="n">nBinsFlat</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span> <span class="n">nBins</span><span class="o">**</span><span class="mi">2</span><span class="p">,</span> <span class="n">nBins</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span>
<span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nContourLevels</span><span class="p">):</span>
<span class="n">temp</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">interp</span><span class="p">(</span><span class="n">confLevels</span><span class="p">[</span><span class="n">l</span><span class="p">],</span> <span class="n">histCumulative</span><span class="p">,</span> <span class="n">nBinsFlat</span><span class="p">)</span>
<span class="n">chainLevels</span><span class="p">[</span><span class="n">nContourLevels</span> <span class="o">-</span> <span class="mi">1</span> <span class="o">-</span> <span class="n">l</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">interp</span><span class="p">(</span><span class="n">temp</span><span class="p">,</span> <span class="n">nBinsFlat</span><span class="p">,</span> <span class="n">histOrdered</span><span class="p">)</span>
<span class="k">return</span> <span class="n">chainLevels</span></div>
<div class="viewcode-block" id="create_colormap">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.plot_params.create_colormap">[docs]</a>
<span class="k">def</span> <span class="nf">create_colormap</span><span class="p">(</span><span class="n">name</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Create a custom colormap based on the specified name.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> name : str</span>
<span class="sd"> The name of the colormap to create.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> ListedColormap</span>
<span class="sd"> The requested custom colormap.</span>
<span class="sd"> Raises</span>
<span class="sd"> ------</span>
<span class="sd"> ValueError</span>
<span class="sd"> If the specified colormap name is not recognised.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">from</span> <span class="nn">matplotlib</span> <span class="kn">import</span> <span class="n">cm</span><span class="p">,</span> <span class="n">colors</span><span class="p">,</span> <span class="n">colormaps</span>
<span class="k">if</span> <span class="n">name</span> <span class="o">==</span> <span class="s2">&quot;GalaxyMap&quot;</span><span class="p">:</span>
<span class="c1"># Colormap for slices through galaxy density fields</span>
<span class="n">Ndots</span> <span class="o">=</span> <span class="mi">2</span><span class="o">**</span><span class="mi">13</span>
<span class="n">stretch_top</span> <span class="o">=</span> <span class="mf">0.5</span>
<span class="n">truncate_bottom</span> <span class="o">=</span> <span class="mf">0.0</span>
<span class="n">stretch_bottom</span> <span class="o">=</span> <span class="mf">1.0</span>
<span class="n">top</span> <span class="o">=</span> <span class="n">cm</span><span class="o">.</span><span class="n">get_cmap</span><span class="p">(</span><span class="s2">&quot;RdPu&quot;</span><span class="p">,</span> <span class="n">Ndots</span><span class="p">)</span>
<span class="n">top</span> <span class="o">=</span> <span class="n">colors</span><span class="o">.</span><span class="n">LinearSegmentedColormap</span><span class="o">.</span><span class="n">from_list</span><span class="p">(</span><span class="s2">&quot;&quot;</span><span class="p">,</span> <span class="p">[</span><span class="s2">&quot;white&quot;</span><span class="p">,</span> <span class="n">top</span><span class="p">(</span><span class="mf">0.5</span><span class="p">),</span> <span class="n">top</span><span class="p">(</span><span class="mf">1.0</span><span class="p">)])</span>
<span class="n">bottom</span> <span class="o">=</span> <span class="n">cm</span><span class="o">.</span><span class="n">get_cmap</span><span class="p">(</span><span class="s2">&quot;Greens_r&quot;</span><span class="p">,</span> <span class="n">Ndots</span><span class="p">)</span>
<span class="n">bottom</span> <span class="o">=</span> <span class="n">colors</span><span class="o">.</span><span class="n">LinearSegmentedColormap</span><span class="o">.</span><span class="n">from_list</span><span class="p">(</span><span class="s2">&quot;&quot;</span><span class="p">,</span> <span class="p">[</span><span class="n">bottom</span><span class="p">(</span><span class="mi">0</span><span class="p">),</span> <span class="n">bottom</span><span class="p">(</span><span class="mf">0.5</span><span class="p">),</span> <span class="s2">&quot;white&quot;</span><span class="p">])</span>
<span class="n">interp_top</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">Ndots</span><span class="p">)</span> <span class="o">**</span> <span class="n">stretch_top</span>
<span class="n">interp_bottom</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="n">truncate_bottom</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">Ndots</span><span class="p">)</span> <span class="o">**</span> <span class="n">stretch_bottom</span>
<span class="n">cols_galaxy</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vstack</span><span class="p">((</span><span class="n">bottom</span><span class="p">(</span><span class="n">interp_bottom</span><span class="p">),</span> <span class="n">top</span><span class="p">(</span><span class="n">interp_top</span><span class="p">)))</span>
<span class="k">return</span> <span class="n">colors</span><span class="o">.</span><span class="n">ListedColormap</span><span class="p">(</span><span class="n">cols_galaxy</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s2">&quot;GalaxyMap&quot;</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">name</span> <span class="o">==</span> <span class="s2">&quot;GradientMap&quot;</span><span class="p">:</span>
<span class="c1"># Colormap for gradient matrices</span>
<span class="n">Ndots</span> <span class="o">=</span> <span class="mi">2</span><span class="o">**</span><span class="mi">13</span>
<span class="n">stretch_bottom</span> <span class="o">=</span> <span class="mf">6.0</span>
<span class="n">stretch_top</span> <span class="o">=</span> <span class="mi">1</span> <span class="o">/</span> <span class="mf">2.5</span>
<span class="n">truncate_bottom</span> <span class="o">=</span> <span class="mf">0.35</span>
<span class="n">bottom</span> <span class="o">=</span> <span class="n">cm</span><span class="o">.</span><span class="n">get_cmap</span><span class="p">(</span><span class="s2">&quot;BuGn_r&quot;</span><span class="p">,</span> <span class="n">Ndots</span><span class="p">)</span>
<span class="n">top</span> <span class="o">=</span> <span class="n">cm</span><span class="o">.</span><span class="n">get_cmap</span><span class="p">(</span><span class="s2">&quot;RdPu&quot;</span><span class="p">,</span> <span class="n">Ndots</span><span class="p">)</span>
<span class="n">interp_top</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">Ndots</span><span class="p">)</span> <span class="o">**</span> <span class="n">stretch_top</span>
<span class="n">interp_bottom</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="n">truncate_bottom</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">Ndots</span><span class="p">)</span> <span class="o">**</span> <span class="n">stretch_bottom</span>
<span class="n">newcolors</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vstack</span><span class="p">((</span><span class="n">bottom</span><span class="p">(</span><span class="n">interp_bottom</span><span class="p">),</span> <span class="n">top</span><span class="p">(</span><span class="n">interp_top</span><span class="p">)))</span>
<span class="k">return</span> <span class="n">colors</span><span class="o">.</span><span class="n">ListedColormap</span><span class="p">(</span><span class="n">newcolors</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s2">&quot;GradientMap&quot;</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">name</span> <span class="o">==</span> <span class="s2">&quot;CovarianceMap&quot;</span><span class="p">:</span>
<span class="c1"># Colormap for the diagonal blocks of covariance matrices</span>
<span class="n">Ndots</span> <span class="o">=</span> <span class="mi">2</span><span class="o">**</span><span class="mi">15</span>
<span class="n">stretch_top_1</span> <span class="o">=</span> <span class="mf">0.3</span>
<span class="n">stretch_top_2</span> <span class="o">=</span> <span class="mf">1.0</span>
<span class="n">stretch_bottom</span> <span class="o">=</span> <span class="mf">0.2</span>
<span class="n">middle</span> <span class="o">=</span> <span class="mf">0.4</span> <span class="c1"># Middle of the positive scale, between 0 and 1</span>
<span class="n">cmap_name</span> <span class="o">=</span> <span class="s2">&quot;BrBG&quot;</span>
<span class="n">top</span> <span class="o">=</span> <span class="n">colormaps</span><span class="p">[</span><span class="n">cmap_name</span><span class="p">]</span>
<span class="n">bottom</span> <span class="o">=</span> <span class="n">colormaps</span><span class="p">[</span><span class="n">cmap_name</span><span class="p">]</span>
<span class="n">interp_top</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">(</span>
<span class="p">(</span>
<span class="n">middle</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">Ndots</span> <span class="o">//</span> <span class="mi">2</span><span class="p">)</span> <span class="o">**</span> <span class="n">stretch_top_1</span> <span class="o">+</span> <span class="mf">0.5</span><span class="p">,</span>
<span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">middle</span><span class="p">)</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">Ndots</span> <span class="o">//</span> <span class="mi">2</span><span class="p">)</span> <span class="o">**</span> <span class="n">stretch_top_2</span> <span class="o">+</span> <span class="mf">0.5</span> <span class="o">+</span> <span class="n">middle</span><span class="p">,</span>
<span class="p">)</span>
<span class="p">)</span>
<span class="n">interp_bottom</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="n">Ndots</span><span class="p">)</span> <span class="o">**</span> <span class="n">stretch_bottom</span> <span class="o">-</span> <span class="mf">0.5</span>
<span class="n">newcolors</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vstack</span><span class="p">((</span><span class="n">bottom</span><span class="p">(</span><span class="n">interp_bottom</span><span class="p">),</span> <span class="n">top</span><span class="p">(</span><span class="n">interp_top</span><span class="p">)))</span>
<span class="k">return</span> <span class="n">colors</span><span class="o">.</span><span class="n">ListedColormap</span><span class="p">(</span><span class="n">newcolors</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s2">&quot;CovarianceMap&quot;</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">name</span> <span class="o">==</span> <span class="s2">&quot;FullCovarianceMap&quot;</span><span class="p">:</span>
<span class="c1"># Colormap for full covariance matrices</span>
<span class="n">Ndots</span> <span class="o">=</span> <span class="mi">2</span><span class="o">**</span><span class="mi">15</span>
<span class="n">stretch_top_1</span> <span class="o">=</span> <span class="mf">0.3</span>
<span class="n">stretch_top_2</span> <span class="o">=</span> <span class="mf">1.0</span>
<span class="n">middle_top</span> <span class="o">=</span> <span class="mf">0.4</span> <span class="c1"># Middle of the positive scale, between 0 and 1</span>
<span class="n">stretch_bottom_1</span> <span class="o">=</span> <span class="mf">1.0</span>
<span class="n">stretch_bottom_2</span> <span class="o">=</span> <span class="mf">5.0</span>
<span class="n">middle_bottom</span> <span class="o">=</span> <span class="mf">0.7</span> <span class="c1"># Middle of the negative scale, between 0 and 1</span>
<span class="n">colname</span> <span class="o">=</span> <span class="s2">&quot;PRGn_r&quot;</span> <span class="c1"># Options: &quot;PRGn&quot;, &quot;PRGn_r&quot;, &quot;BrBG&quot;, &quot;PuOr&quot;</span>
<span class="n">top</span> <span class="o">=</span> <span class="n">colormaps</span><span class="p">[</span><span class="n">colname</span><span class="p">]</span>
<span class="n">bottom</span> <span class="o">=</span> <span class="n">colormaps</span><span class="p">[</span><span class="n">colname</span><span class="p">]</span>
<span class="n">interp_top</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">(</span>
<span class="p">(</span>
<span class="n">middle_top</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">Ndots</span> <span class="o">//</span> <span class="mi">2</span><span class="p">)</span> <span class="o">**</span> <span class="n">stretch_top_1</span> <span class="o">+</span> <span class="mf">0.5</span><span class="p">,</span>
<span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">middle_top</span><span class="p">)</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">Ndots</span> <span class="o">//</span> <span class="mi">2</span><span class="p">)</span> <span class="o">**</span> <span class="n">stretch_top_2</span>
<span class="o">+</span> <span class="mf">0.5</span>
<span class="o">+</span> <span class="n">middle_top</span><span class="p">,</span>
<span class="p">)</span>
<span class="p">)</span>
<span class="n">interp_bottom</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">(</span>
<span class="p">(</span>
<span class="n">middle_bottom</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">Ndots</span> <span class="o">//</span> <span class="mi">2</span><span class="p">)</span> <span class="o">**</span> <span class="n">stretch_bottom_1</span> <span class="o">-</span> <span class="mf">0.5</span><span class="p">,</span>
<span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">middle_bottom</span><span class="p">)</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">Ndots</span> <span class="o">//</span> <span class="mi">2</span><span class="p">)</span> <span class="o">**</span> <span class="n">stretch_bottom_2</span>
<span class="o">-</span> <span class="mf">0.5</span>
<span class="o">+</span> <span class="n">middle_bottom</span><span class="p">,</span>
<span class="p">)</span>
<span class="p">)</span>
<span class="n">newcolors</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vstack</span><span class="p">((</span><span class="n">bottom</span><span class="p">(</span><span class="n">interp_bottom</span><span class="p">),</span> <span class="n">top</span><span class="p">(</span><span class="n">interp_top</span><span class="p">)))</span>
<span class="k">return</span> <span class="n">colors</span><span class="o">.</span><span class="n">ListedColormap</span><span class="p">(</span><span class="n">newcolors</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s2">&quot;FullCovarianceMap&quot;</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">name</span> <span class="o">==</span> <span class="s2">&quot;Blues_Reds&quot;</span><span class="p">:</span>
<span class="c1"># Additional colormap combining blues and reds</span>
<span class="n">top</span> <span class="o">=</span> <span class="n">cm</span><span class="o">.</span><span class="n">get_cmap</span><span class="p">(</span><span class="s2">&quot;Reds_r&quot;</span><span class="p">,</span> <span class="mi">128</span><span class="p">)</span>
<span class="n">bottom</span> <span class="o">=</span> <span class="n">cm</span><span class="o">.</span><span class="n">get_cmap</span><span class="p">(</span><span class="s2">&quot;Blues&quot;</span><span class="p">,</span> <span class="mi">128</span><span class="p">)</span>
<span class="n">newcolors</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vstack</span><span class="p">((</span><span class="n">top</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mf">0.7</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">128</span><span class="p">)),</span> <span class="n">bottom</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">128</span><span class="p">))))</span>
<span class="k">return</span> <span class="n">colors</span><span class="o">.</span><span class="n">ListedColormap</span><span class="p">(</span><span class="n">newcolors</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s2">&quot;Blues_Reds&quot;</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">name</span> <span class="o">==</span> <span class="s2">&quot;Purples_Oranges&quot;</span><span class="p">:</span>
<span class="c1"># Additional colormap combining purples and oranges</span>
<span class="n">top</span> <span class="o">=</span> <span class="n">cm</span><span class="o">.</span><span class="n">get_cmap</span><span class="p">(</span><span class="s2">&quot;Oranges_r&quot;</span><span class="p">,</span> <span class="mi">128</span><span class="p">)</span>
<span class="n">bottom</span> <span class="o">=</span> <span class="n">cm</span><span class="o">.</span><span class="n">get_cmap</span><span class="p">(</span><span class="s2">&quot;Purples&quot;</span><span class="p">,</span> <span class="mi">128</span><span class="p">)</span>
<span class="n">newcolors</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vstack</span><span class="p">((</span><span class="n">top</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mf">0.7</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">128</span><span class="p">)),</span> <span class="n">bottom</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">128</span><span class="p">))))</span>
<span class="k">return</span> <span class="n">colors</span><span class="o">.</span><span class="n">ListedColormap</span><span class="p">(</span><span class="n">newcolors</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s2">&quot;Purples_Oranges&quot;</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Colormap &#39;</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">&#39; is not defined.&quot;</span><span class="p">)</span></div>
<div class="viewcode-block" id="create_all_colormaps">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.plot_params.create_all_colormaps">[docs]</a>
<span class="k">def</span> <span class="nf">create_all_colormaps</span><span class="p">():</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Create all custom colormaps.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> colormaps : dict</span>
<span class="sd"> Dictionary containing all custom colormaps.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">colormaps_dict</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">colormap_names</span> <span class="o">=</span> <span class="p">[</span>
<span class="s2">&quot;GalaxyMap&quot;</span><span class="p">,</span>
<span class="s2">&quot;GradientMap&quot;</span><span class="p">,</span>
<span class="s2">&quot;CovarianceMap&quot;</span><span class="p">,</span>
<span class="s2">&quot;FullCovarianceMap&quot;</span><span class="p">,</span>
<span class="s2">&quot;Blues_Reds&quot;</span><span class="p">,</span>
<span class="s2">&quot;Purples_Oranges&quot;</span><span class="p">,</span>
<span class="p">]</span>
<span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">colormap_names</span><span class="p">:</span>
<span class="n">colormaps_dict</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">create_colormap</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>
<span class="k">return</span> <span class="n">colormaps_dict</span></div>
</pre></div>
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<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.hiddenbox.html">hiddenbox</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox"><code class="docutils literal notranslate"><span class="pre">HiddenBox</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Npop"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Npop</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Psingle"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Psingle</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.compute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.compute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.evaluate"><code class="docutils literal notranslate"><span class="pre">HiddenBox.evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_neglect_lightcone"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_neglect_lightcone</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_recompute_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_recompute_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.gravity_on"><code class="docutils literal notranslate"><span class="pre">HiddenBox.gravity_on</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.load_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.load_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.make_data"><code class="docutils literal notranslate"><span class="pre">HiddenBox.make_data()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.modified_selfi"><code class="docutils literal notranslate"><span class="pre">HiddenBox.modified_selfi</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.prefix_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.prefix_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.reset_survey"><code class="docutils literal notranslate"><span class="pre">HiddenBox.reset_survey()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.setup_only"><code class="docutils literal notranslate"><span class="pre">HiddenBox.setup_only</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_setup"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_setup()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.update"><code class="docutils literal notranslate"><span class="pre">HiddenBox.update()</span></code></a></li>
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<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.normalise_hb.html">normalise_hb</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.define_normalisation"><code class="docutils literal notranslate"><span class="pre">define_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation"><code class="docutils literal notranslate"><span class="pre">worker_normalisation()</span></code></a></li>
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<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.prior.html">prior</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.logposterior_hyperparameters_parallel"><code class="docutils literal notranslate"><span class="pre">logposterior_hyperparameters_parallel()</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior"><code class="docutils literal notranslate"><span class="pre">planck_prior</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.mean"><code class="docutils literal notranslate"><span class="pre">planck_prior.mean</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.covariance</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.init_selection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.init_selection()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.lognormals_z_to_x"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.lognormals_z_to_x()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.r_grid"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.r_grid()</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.indent"><code class="docutils literal notranslate"><span class="pre">indent()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.unindent"><code class="docutils literal notranslate"><span class="pre">unindent()</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.compute_Phi"><code class="docutils literal notranslate"><span class="pre">compute_Phi()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.generate_white_noise_Field"><code class="docutils literal notranslate"><span class="pre">generate_white_noise_Field()</span></code></a></li>
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<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.grf.html">grf</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.grf.html#selfisys.grf.primordial_grf"><code class="docutils literal notranslate"><span class="pre">primordial_grf()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.utils.html">selfisys.utils package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.examples_utils">selfisys.utils.examples_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.examples_utils.clear_large_plot"><code class="docutils literal notranslate"><span class="pre">clear_large_plot()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.logger">selfisys.utils.logger module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLogger"><code class="docutils literal notranslate"><span class="pre">CustomLogger</span></code></a><ul>
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<h1>Source code for selfisys.utils.timestepping</h1><div class="highlight"><pre>
<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="c1"># Copyright (C) 2024 Tristan Hoellinger</span>
<span class="c1"># Distributed under the GNU General Public License v3.0 (GPLv3).</span>
<span class="c1"># See the LICENSE file in the root directory for details.</span>
<span class="c1"># SPDX-License-Identifier: GPL-3.0-or-later</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="n">__author__</span> <span class="o">=</span> <span class="s2">&quot;Tristan Hoellinger&quot;</span>
<span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;0.1.0&quot;</span>
<span class="n">__date__</span> <span class="o">=</span> <span class="s2">&quot;2024&quot;</span>
<span class="n">__license__</span> <span class="o">=</span> <span class="s2">&quot;GPLv3&quot;</span>
<span class="sd">&quot;&quot;&quot;Tools for time-stepping.</span>
<span class="sd">&quot;&quot;&quot;</span>
<div class="viewcode-block" id="merge_nTS">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.timestepping.merge_nTS">[docs]</a>
<span class="k">def</span> <span class="nf">merge_nTS</span><span class="p">(</span><span class="n">ts_path_list</span><span class="p">,</span> <span class="n">merged_path</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Merge multiple time-stepping objects into a single file.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> ts_path_list : list of str</span>
<span class="sd"> Paths to the individual time-stepping files to be merged.</span>
<span class="sd"> merged_path : str</span>
<span class="sd"> Path to save the merged time-stepping file.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> None</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">from</span> <span class="nn">h5py</span> <span class="kn">import</span> <span class="n">File</span>
<span class="kn">from</span> <span class="nn">numpy</span> <span class="kn">import</span> <span class="n">concatenate</span>
<span class="kn">from</span> <span class="nn">pysbmy.timestepping</span> <span class="kn">import</span> <span class="n">read_timestepping</span>
<span class="c1"># Read individual time-stepping objects</span>
<span class="n">ts</span> <span class="o">=</span> <span class="p">[</span><span class="n">read_timestepping</span><span class="p">(</span><span class="n">ts_path</span><span class="p">)</span> <span class="k">for</span> <span class="n">ts_path</span> <span class="ow">in</span> <span class="n">ts_path_list</span><span class="p">]</span>
<span class="k">with</span> <span class="n">File</span><span class="p">(</span><span class="n">merged_path</span><span class="p">,</span> <span class="s2">&quot;w&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">hf</span><span class="p">:</span>
<span class="c1"># Write scalar attributes</span>
<span class="n">hf</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s2">&quot;/info/scalars/nsteps&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">sum</span><span class="p">(</span><span class="n">tsi</span><span class="o">.</span><span class="n">nsteps</span> <span class="k">for</span> <span class="n">tsi</span> <span class="ow">in</span> <span class="n">ts</span><span class="p">)</span>
<span class="n">hf</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s2">&quot;/info/scalars/nkicks&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">sum</span><span class="p">(</span><span class="n">tsi</span><span class="o">.</span><span class="n">nkicks</span> <span class="k">for</span> <span class="n">tsi</span> <span class="ow">in</span> <span class="n">ts</span><span class="p">)</span>
<span class="n">hf</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s2">&quot;/info/scalars/ndrifts&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">sum</span><span class="p">(</span><span class="n">tsi</span><span class="o">.</span><span class="n">ndrifts</span> <span class="k">for</span> <span class="n">tsi</span> <span class="ow">in</span> <span class="n">ts</span><span class="p">)</span>
<span class="n">hf</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s2">&quot;/info/scalars/ai&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ts</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">ai</span>
<span class="n">hf</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s2">&quot;/info/scalars/af&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ts</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">af</span>
<span class="c1"># Merge and write datasets</span>
<span class="n">hf</span><span class="o">.</span><span class="n">create_dataset</span><span class="p">(</span><span class="s2">&quot;/scalars/forces&quot;</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">concatenate</span><span class="p">([</span><span class="n">tsi</span><span class="o">.</span><span class="n">forces</span> <span class="k">for</span> <span class="n">tsi</span> <span class="ow">in</span> <span class="n">ts</span><span class="p">]))</span>
<span class="n">hf</span><span class="o">.</span><span class="n">create_dataset</span><span class="p">(</span><span class="s2">&quot;/scalars/snapshots&quot;</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">concatenate</span><span class="p">([</span><span class="n">tsi</span><span class="o">.</span><span class="n">snapshots</span> <span class="k">for</span> <span class="n">tsi</span> <span class="ow">in</span> <span class="n">ts</span><span class="p">]))</span>
<span class="n">hf</span><span class="o">.</span><span class="n">create_dataset</span><span class="p">(</span><span class="s2">&quot;/scalars/aKickBeg&quot;</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">concatenate</span><span class="p">([</span><span class="n">tsi</span><span class="o">.</span><span class="n">aKickBeg</span> <span class="k">for</span> <span class="n">tsi</span> <span class="ow">in</span> <span class="n">ts</span><span class="p">]))</span>
<span class="n">hf</span><span class="o">.</span><span class="n">create_dataset</span><span class="p">(</span><span class="s2">&quot;/scalars/aKickEnd&quot;</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">concatenate</span><span class="p">([</span><span class="n">tsi</span><span class="o">.</span><span class="n">aKickEnd</span> <span class="k">for</span> <span class="n">tsi</span> <span class="ow">in</span> <span class="n">ts</span><span class="p">]))</span>
<span class="n">hf</span><span class="o">.</span><span class="n">create_dataset</span><span class="p">(</span><span class="s2">&quot;/scalars/aDriftBeg&quot;</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">concatenate</span><span class="p">([</span><span class="n">tsi</span><span class="o">.</span><span class="n">aDriftBeg</span> <span class="k">for</span> <span class="n">tsi</span> <span class="ow">in</span> <span class="n">ts</span><span class="p">]))</span>
<span class="n">hf</span><span class="o">.</span><span class="n">create_dataset</span><span class="p">(</span><span class="s2">&quot;/scalars/aDriftEnd&quot;</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">concatenate</span><span class="p">([</span><span class="n">tsi</span><span class="o">.</span><span class="n">aDriftEnd</span> <span class="k">for</span> <span class="n">tsi</span> <span class="ow">in</span> <span class="n">ts</span><span class="p">]))</span>
<span class="n">hf</span><span class="o">.</span><span class="n">create_dataset</span><span class="p">(</span><span class="s2">&quot;/scalars/aiKick&quot;</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">concatenate</span><span class="p">([</span><span class="n">tsi</span><span class="o">.</span><span class="n">aiKick</span> <span class="k">for</span> <span class="n">tsi</span> <span class="ow">in</span> <span class="n">ts</span><span class="p">]))</span>
<span class="n">hf</span><span class="o">.</span><span class="n">create_dataset</span><span class="p">(</span><span class="s2">&quot;/scalars/afKick&quot;</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">concatenate</span><span class="p">([</span><span class="n">tsi</span><span class="o">.</span><span class="n">afKick</span> <span class="k">for</span> <span class="n">tsi</span> <span class="ow">in</span> <span class="n">ts</span><span class="p">]))</span>
<span class="c1"># Handle `aDrift` merging with overlap adjustments</span>
<span class="n">aDrift_data</span> <span class="o">=</span> <span class="n">concatenate</span><span class="p">(</span>
<span class="p">[</span>
<span class="p">[</span><span class="n">ts</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">aDrift</span><span class="p">[</span><span class="mi">0</span><span class="p">]],</span> <span class="c1"># Initial drift</span>
<span class="n">concatenate</span><span class="p">(</span>
<span class="p">[</span><span class="n">concatenate</span><span class="p">([</span><span class="n">tsi</span><span class="o">.</span><span class="n">aDrift</span><span class="p">[</span><span class="mi">1</span><span class="p">:],</span> <span class="p">[</span><span class="n">tsi</span><span class="o">.</span><span class="n">aDrift</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]]])</span> <span class="k">for</span> <span class="n">tsi</span> <span class="ow">in</span> <span class="n">ts</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]]</span>
<span class="p">),</span> <span class="c1"># Intermediate drifts</span>
<span class="n">ts</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">aDrift</span><span class="p">[</span><span class="mi">1</span><span class="p">:],</span> <span class="c1"># Final drift</span>
<span class="p">]</span>
<span class="p">)</span>
<span class="n">hf</span><span class="o">.</span><span class="n">create_dataset</span><span class="p">(</span><span class="s2">&quot;/scalars/aDrift&quot;</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">aDrift_data</span><span class="p">)</span>
<span class="c1"># Handle `aSnapshotSave` merging</span>
<span class="n">aSnapshotSave_data</span> <span class="o">=</span> <span class="n">concatenate</span><span class="p">(</span>
<span class="p">[</span><span class="n">ts</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">aSnapshotSave</span><span class="p">]</span> <span class="o">+</span> <span class="p">[</span><span class="n">tsi</span><span class="o">.</span><span class="n">aSnapshotSave</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span> <span class="k">for</span> <span class="n">tsi</span> <span class="ow">in</span> <span class="n">ts</span><span class="p">[</span><span class="mi">1</span><span class="p">:]]</span>
<span class="p">)</span>
<span class="n">hf</span><span class="o">.</span><span class="n">create_dataset</span><span class="p">(</span><span class="s2">&quot;/scalars/aSnapshotSave&quot;</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">aSnapshotSave_data</span><span class="p">)</span>
<span class="n">hf</span><span class="o">.</span><span class="n">create_dataset</span><span class="p">(</span><span class="s2">&quot;/scalars/aiDrift&quot;</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">concatenate</span><span class="p">([</span><span class="n">tsi</span><span class="o">.</span><span class="n">aiDrift</span> <span class="k">for</span> <span class="n">tsi</span> <span class="ow">in</span> <span class="n">ts</span><span class="p">]))</span>
<span class="n">hf</span><span class="o">.</span><span class="n">create_dataset</span><span class="p">(</span><span class="s2">&quot;/scalars/afDrift&quot;</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">concatenate</span><span class="p">([</span><span class="n">tsi</span><span class="o">.</span><span class="n">afDrift</span> <span class="k">for</span> <span class="n">tsi</span> <span class="ow">in</span> <span class="n">ts</span><span class="p">]))</span>
<span class="n">hf</span><span class="o">.</span><span class="n">create_dataset</span><span class="p">(</span><span class="s2">&quot;/scalars/aKick&quot;</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">concatenate</span><span class="p">([</span><span class="n">tsi</span><span class="o">.</span><span class="n">aKick</span> <span class="k">for</span> <span class="n">tsi</span> <span class="ow">in</span> <span class="n">ts</span><span class="p">]))</span></div>
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<p class="caption" role="heading"><span class="caption-text">API Documentation</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.hiddenbox.html">hiddenbox</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox"><code class="docutils literal notranslate"><span class="pre">HiddenBox</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Npop"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Npop</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Ntimesteps"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Ntimesteps</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Psingle"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Psingle</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.compute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.compute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.evaluate"><code class="docutils literal notranslate"><span class="pre">HiddenBox.evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_neglect_lightcone"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_neglect_lightcone</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_recompute_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_recompute_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.gravity_on"><code class="docutils literal notranslate"><span class="pre">HiddenBox.gravity_on</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.load_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.load_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.make_data"><code class="docutils literal notranslate"><span class="pre">HiddenBox.make_data()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.modified_selfi"><code class="docutils literal notranslate"><span class="pre">HiddenBox.modified_selfi</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.prefix_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.prefix_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.reset_survey"><code class="docutils literal notranslate"><span class="pre">HiddenBox.reset_survey()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.setup_only"><code class="docutils literal notranslate"><span class="pre">HiddenBox.setup_only</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_recompute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_recompute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_setup"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_setup()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.update"><code class="docutils literal notranslate"><span class="pre">HiddenBox.update()</span></code></a></li>
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<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.normalise_hb.html">normalise_hb</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.define_normalisation"><code class="docutils literal notranslate"><span class="pre">define_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation"><code class="docutils literal notranslate"><span class="pre">worker_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_public"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_public()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_wrapper"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_wrapper()</span></code></a></li>
</ul>
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<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.prior.html">prior</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.logposterior_hyperparameters_parallel"><code class="docutils literal notranslate"><span class="pre">logposterior_hyperparameters_parallel()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.perform_prior_optimisation_and_plot"><code class="docutils literal notranslate"><span class="pre">perform_prior_optimisation_and_plot()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior"><code class="docutils literal notranslate"><span class="pre">planck_prior</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.mean"><code class="docutils literal notranslate"><span class="pre">planck_prior.mean</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.inv_covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.inv_covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_max"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_max</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_min"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_min</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.compute"><code class="docutils literal notranslate"><span class="pre">planck_prior.compute()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.load"><code class="docutils literal notranslate"><span class="pre">planck_prior.load()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.logpdf"><code class="docutils literal notranslate"><span class="pre">planck_prior.logpdf()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.sample"><code class="docutils literal notranslate"><span class="pre">planck_prior.sample()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.save"><code class="docutils literal notranslate"><span class="pre">planck_prior.save()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.worker_class"><code class="docutils literal notranslate"><span class="pre">worker_class()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.selection_functions.html">selection_functions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.init_selection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.init_selection()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.lognormals_z_to_x"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.lognormals_z_to_x()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.r_grid"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.r_grid()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.selfi_interface.html">selfi_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.PrintMessage"><code class="docutils literal notranslate"><span class="pre">PrintMessage()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.indent"><code class="docutils literal notranslate"><span class="pre">indent()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.unindent"><code class="docutils literal notranslate"><span class="pre">unindent()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.sbmy_interface.html">sbmy_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.compute_Phi"><code class="docutils literal notranslate"><span class="pre">compute_Phi()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.generate_white_noise_Field"><code class="docutils literal notranslate"><span class="pre">generate_white_noise_Field()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.get_power_spectrum_from_cosmo"><code class="docutils literal notranslate"><span class="pre">get_power_spectrum_from_cosmo()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.handle_time_stepping"><code class="docutils literal notranslate"><span class="pre">handle_time_stepping()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.setup_sbmy_parfiles"><code class="docutils literal notranslate"><span class="pre">setup_sbmy_parfiles()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.grf.html">grf</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.grf.html#selfisys.grf.primordial_grf"><code class="docutils literal notranslate"><span class="pre">primordial_grf()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.utils.html">selfisys.utils package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.examples_utils">selfisys.utils.examples_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.examples_utils.clear_large_plot"><code class="docutils literal notranslate"><span class="pre">clear_large_plot()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.logger">selfisys.utils.logger module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLogger"><code class="docutils literal notranslate"><span class="pre">CustomLogger</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLogger.diagnostic"><code class="docutils literal notranslate"><span class="pre">CustomLogger.diagnostic()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler.emit"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler.emit()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.INDENT"><code class="docutils literal notranslate"><span class="pre">INDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintDiagnostic"><code class="docutils literal notranslate"><span class="pre">PrintDiagnostic()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintError"><code class="docutils literal notranslate"><span class="pre">PrintError()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintInfo"><code class="docutils literal notranslate"><span class="pre">PrintInfo()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintLeftType"><code class="docutils literal notranslate"><span class="pre">PrintLeftType()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintWarning"><code class="docutils literal notranslate"><span class="pre">PrintWarning()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.UNINDENT"><code class="docutils literal notranslate"><span class="pre">UNINDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.getCustomLogger"><code class="docutils literal notranslate"><span class="pre">getCustomLogger()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.low_level">selfisys.utils.low_level module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.low_level.stderr_redirector"><code class="docutils literal notranslate"><span class="pre">stderr_redirector()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.low_level.stdout_redirector"><code class="docutils literal notranslate"><span class="pre">stdout_redirector()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.parser">selfisys.utils.parser module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.bool_sh"><code class="docutils literal notranslate"><span class="pre">bool_sh()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.check_files_exist"><code class="docutils literal notranslate"><span class="pre">check_files_exist()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.intNone"><code class="docutils literal notranslate"><span class="pre">intNone()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.joinstrs"><code class="docutils literal notranslate"><span class="pre">joinstrs()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.joinstrs_only"><code class="docutils literal notranslate"><span class="pre">joinstrs_only()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.safe_npload"><code class="docutils literal notranslate"><span class="pre">safe_npload()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.path_utils">selfisys.utils.path_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.path_utils.file_names_evaluate"><code class="docutils literal notranslate"><span class="pre">file_names_evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.path_utils.get_file_names"><code class="docutils literal notranslate"><span class="pre">get_file_names()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.plot_examples">selfisys.utils.plot_examples module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_comoving_distance_redshift"><code class="docutils literal notranslate"><span class="pre">plot_comoving_distance_redshift()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_galaxy_field_slice"><code class="docutils literal notranslate"><span class="pre">plot_galaxy_field_slice()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_power_spectrum"><code class="docutils literal notranslate"><span class="pre">plot_power_spectrum()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_selection_functions_def_in_z"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions_def_in_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.redshift_distance_conversion"><code class="docutils literal notranslate"><span class="pre">redshift_distance_conversion()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.relative_error_analysis"><code class="docutils literal notranslate"><span class="pre">relative_error_analysis()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.plot_params">selfisys.utils.plot_params module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.get_offset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.get_offset()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_scientific"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_scientific()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_useOffset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_useOffset()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.create_all_colormaps"><code class="docutils literal notranslate"><span class="pre">create_all_colormaps()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.create_colormap"><code class="docutils literal notranslate"><span class="pre">create_colormap()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.dynamic_text_scaling"><code class="docutils literal notranslate"><span class="pre">dynamic_text_scaling()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.get_contours"><code class="docutils literal notranslate"><span class="pre">get_contours()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.reset_plotting"><code class="docutils literal notranslate"><span class="pre">reset_plotting()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.setup_plotting"><code class="docutils literal notranslate"><span class="pre">setup_plotting()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.plot_utils">selfisys.utils.plot_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_C"><code class="docutils literal notranslate"><span class="pre">plot_C()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_fisher"><code class="docutils literal notranslate"><span class="pre">plot_fisher()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_gradients"><code class="docutils literal notranslate"><span class="pre">plot_gradients()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_histogram"><code class="docutils literal notranslate"><span class="pre">plot_histogram()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks"><code class="docutils literal notranslate"><span class="pre">plot_mocks()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks_compact"><code class="docutils literal notranslate"><span class="pre">plot_mocks_compact()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_observations"><code class="docutils literal notranslate"><span class="pre">plot_observations()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_prior_and_posterior_covariances"><code class="docutils literal notranslate"><span class="pre">plot_prior_and_posterior_covariances()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_reconstruction"><code class="docutils literal notranslate"><span class="pre">plot_reconstruction()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plot_selection_functions"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_utils.plotly_3d"><code class="docutils literal notranslate"><span class="pre">plotly_3d()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.timestepping">selfisys.utils.timestepping module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.timestepping.merge_nTS"><code class="docutils literal notranslate"><span class="pre">merge_nTS()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.tools">selfisys.utils.tools module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.cosmo_vector_to_Simbelmyne_dict"><code class="docutils literal notranslate"><span class="pre">cosmo_vector_to_Simbelmyne_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.cosmo_vector_to_class_dict"><code class="docutils literal notranslate"><span class="pre">cosmo_vector_to_class_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.custom_stat"><code class="docutils literal notranslate"><span class="pre">custom_stat()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.fisher_rao"><code class="docutils literal notranslate"><span class="pre">fisher_rao()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.get_k_max"><code class="docutils literal notranslate"><span class="pre">get_k_max()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.params_ids_to_Simbelmyne_dict"><code class="docutils literal notranslate"><span class="pre">params_ids_to_Simbelmyne_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.sample_omega_from_prior"><code class="docutils literal notranslate"><span class="pre">sample_omega_from_prior()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.tools.summary_to_score"><code class="docutils literal notranslate"><span class="pre">summary_to_score()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.workers">selfisys.utils.workers module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.workers.Simbelmyne_worker"><code class="docutils literal notranslate"><span class="pre">Simbelmyne_worker()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.workers.evaluate_gradient_of_Symbelmyne"><code class="docutils literal notranslate"><span class="pre">evaluate_gradient_of_Symbelmyne()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.workers.worker_gradient_Symbelmyne"><code class="docutils literal notranslate"><span class="pre">worker_gradient_Symbelmyne()</span></code></a></li>
</ul>
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<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils">Module contents</a></li>
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<h1>Source code for selfisys.utils.tools</h1><div class="highlight"><pre>
<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="c1"># Copyright (C) 2024 Tristan Hoellinger</span>
<span class="c1"># Distributed under the GNU General Public License v3.0 (GPLv3).</span>
<span class="c1"># See the LICENSE file in the root directory for details.</span>
<span class="c1"># SPDX-License-Identifier: GPL-3.0-or-later</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="n">__author__</span> <span class="o">=</span> <span class="s2">&quot;Tristan Hoellinger&quot;</span>
<span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;0.1.0&quot;</span>
<span class="n">__date__</span> <span class="o">=</span> <span class="s2">&quot;2024&quot;</span>
<span class="n">__license__</span> <span class="o">=</span> <span class="s2">&quot;GPLv3&quot;</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd">Utilities for the SelfiSys package, including tools for cosmological</span>
<span class="sd">parameter handling, power spectrum computations, and prior sampling.</span>
<span class="sd">&quot;&quot;&quot;</span>
<div class="viewcode-block" id="none_or_bool_or_str">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.tools.none_or_bool_or_str">[docs]</a>
<span class="k">def</span> <span class="nf">none_or_bool_or_str</span><span class="p">(</span><span class="n">value</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Convert string representations of None, True, and False to their</span>
<span class="sd"> respective Python objects; otherwise, return the input value.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="n">value</span> <span class="o">==</span> <span class="s2">&quot;None&quot;</span><span class="p">:</span>
<span class="k">return</span> <span class="kc">None</span>
<span class="k">if</span> <span class="n">value</span> <span class="o">==</span> <span class="s2">&quot;True&quot;</span><span class="p">:</span>
<span class="k">return</span> <span class="kc">True</span>
<span class="k">if</span> <span class="n">value</span> <span class="o">==</span> <span class="s2">&quot;False&quot;</span><span class="p">:</span>
<span class="k">return</span> <span class="kc">False</span>
<span class="k">return</span> <span class="n">value</span></div>
<div class="viewcode-block" id="get_k_max">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.tools.get_k_max">[docs]</a>
<span class="k">def</span> <span class="nf">get_k_max</span><span class="p">(</span><span class="n">L</span><span class="p">,</span> <span class="n">size</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Compute the maximum wavenumber for a given box size.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> L : float</span>
<span class="sd"> Size of the box in Mpc/h.</span>
<span class="sd"> size : int</span>
<span class="sd"> Number of grid cells along each dimension.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> float</span>
<span class="sd"> Maximum wavenumber in h/Mpc.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">from</span> <span class="nn">numpy</span> <span class="kn">import</span> <span class="n">pi</span><span class="p">,</span> <span class="n">sqrt</span>
<span class="k">return</span> <span class="nb">int</span><span class="p">(</span><span class="mf">1e3</span> <span class="o">*</span> <span class="n">sqrt</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span> <span class="o">*</span> <span class="n">pi</span> <span class="o">*</span> <span class="n">size</span> <span class="o">/</span> <span class="n">L</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="o">*</span> <span class="mf">1e-3</span></div>
<div class="viewcode-block" id="custom_stat">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.tools.custom_stat">[docs]</a>
<span class="k">def</span> <span class="nf">custom_stat</span><span class="p">(</span><span class="n">vec</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Compute a custom statistic for use with</span>
<span class="sd"> `scipy.stats.binned_statistic`.</span>
<span class="sd"> Assumes the data power spectrum is inverse-Gamma distributed (as in</span>
<span class="sd"> [jasche2010bayesian] and [leclercq2019primordial]). Returns &quot;NaN&quot;</span>
<span class="sd"> for vectors with insufficient elements, as expected by</span>
<span class="sd"> `scipy.stats.binned_statistic`.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> vec : array-like</span>
<span class="sd"> Input vector for computation.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> float or str</span>
<span class="sd"> Custom statistic or NaN if input is invalid.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">vec</span><span class="p">)</span> <span class="o">&lt;=</span> <span class="mi">2</span> <span class="ow">or</span> <span class="nb">sum</span><span class="p">(</span><span class="n">vec</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">return</span> <span class="s2">&quot;NaN&quot;</span>
<span class="k">return</span> <span class="nb">sum</span><span class="p">(</span><span class="n">vec</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">vec</span><span class="p">)</span> <span class="o">-</span> <span class="mi">2</span><span class="p">)</span></div>
<div class="viewcode-block" id="cosmo_vector_to_Simbelmyne_dict">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.tools.cosmo_vector_to_Simbelmyne_dict">[docs]</a>
<span class="k">def</span> <span class="nf">cosmo_vector_to_Simbelmyne_dict</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">kmax</span><span class="o">=</span><span class="mf">1.4</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Convert a vector of cosmological parameters into a dictionary</span>
<span class="sd"> compatible with `pysbmy`.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> x : array-like</span>
<span class="sd"> Vector of cosmological parameters.</span>
<span class="sd"> kmax : float, optional</span>
<span class="sd"> Maximum wavenumber for the power spectrum computation.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> dict</span>
<span class="sd"> Dictionary of cosmological parameters compatible with `pysbmy`.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">from</span> <span class="nn">selfisys.global_parameters</span> <span class="kn">import</span> <span class="n">WHICH_SPECTRUM</span>
<span class="k">return</span> <span class="p">{</span>
<span class="s2">&quot;h&quot;</span><span class="p">:</span> <span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
<span class="s2">&quot;Omega_r&quot;</span><span class="p">:</span> <span class="mf">0.0</span><span class="p">,</span>
<span class="s2">&quot;Omega_q&quot;</span><span class="p">:</span> <span class="mf">1.0</span> <span class="o">-</span> <span class="n">x</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span>
<span class="s2">&quot;Omega_b&quot;</span><span class="p">:</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
<span class="s2">&quot;Omega_m&quot;</span><span class="p">:</span> <span class="n">x</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span>
<span class="s2">&quot;m_ncdm&quot;</span><span class="p">:</span> <span class="mf">0.0</span><span class="p">,</span>
<span class="s2">&quot;Omega_k&quot;</span><span class="p">:</span> <span class="mf">0.0</span><span class="p">,</span>
<span class="s2">&quot;tau_reio&quot;</span><span class="p">:</span> <span class="mf">0.066</span><span class="p">,</span>
<span class="s2">&quot;n_s&quot;</span><span class="p">:</span> <span class="n">x</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span>
<span class="s2">&quot;sigma8&quot;</span><span class="p">:</span> <span class="n">x</span><span class="p">[</span><span class="mi">4</span><span class="p">],</span>
<span class="s2">&quot;w0_fld&quot;</span><span class="p">:</span> <span class="o">-</span><span class="mf">1.0</span><span class="p">,</span>
<span class="s2">&quot;wa_fld&quot;</span><span class="p">:</span> <span class="mf">0.0</span><span class="p">,</span>
<span class="s2">&quot;k_max&quot;</span><span class="p">:</span> <span class="n">kmax</span><span class="p">,</span>
<span class="s2">&quot;WhichSpectrum&quot;</span><span class="p">:</span> <span class="n">WHICH_SPECTRUM</span><span class="p">,</span>
<span class="p">}</span></div>
<div class="viewcode-block" id="cosmo_vector_to_class_dict">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.tools.cosmo_vector_to_class_dict">[docs]</a>
<span class="k">def</span> <span class="nf">cosmo_vector_to_class_dict</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">lmax</span><span class="o">=</span><span class="mi">2500</span><span class="p">,</span> <span class="n">kmax</span><span class="o">=</span><span class="mf">1.4</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Convert a vector of cosmological parameters into a dictionary</span>
<span class="sd"> compatible with `classy`.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> x : array-like</span>
<span class="sd"> Vector of cosmological parameters.</span>
<span class="sd"> lmax : int, optional</span>
<span class="sd"> Maximum multipole for the power spectrum computation.</span>
<span class="sd"> kmax : float, optional</span>
<span class="sd"> Maximum wavenumber for the power spectrum computation.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> dict</span>
<span class="sd"> Dictionary of cosmological parameters compatible with `classy`.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="p">{</span>
<span class="s2">&quot;output&quot;</span><span class="p">:</span> <span class="s2">&quot;lCl mPk&quot;</span><span class="p">,</span>
<span class="s2">&quot;l_max_scalars&quot;</span><span class="p">:</span> <span class="n">lmax</span><span class="p">,</span>
<span class="s2">&quot;lensing&quot;</span><span class="p">:</span> <span class="s2">&quot;no&quot;</span><span class="p">,</span>
<span class="s2">&quot;N_ncdm&quot;</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span>
<span class="s2">&quot;P_k_max_h/Mpc&quot;</span><span class="p">:</span> <span class="n">kmax</span><span class="p">,</span>
<span class="s2">&quot;h&quot;</span><span class="p">:</span> <span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
<span class="s2">&quot;Omega_b&quot;</span><span class="p">:</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
<span class="s2">&quot;Omega_m&quot;</span><span class="p">:</span> <span class="n">x</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span>
<span class="s2">&quot;n_s&quot;</span><span class="p">:</span> <span class="n">x</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span>
<span class="s2">&quot;sigma8&quot;</span><span class="p">:</span> <span class="n">x</span><span class="p">[</span><span class="mi">4</span><span class="p">],</span>
<span class="p">}</span></div>
<div class="viewcode-block" id="params_ids_to_Simbelmyne_dict">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.tools.params_ids_to_Simbelmyne_dict">[docs]</a>
<span class="k">def</span> <span class="nf">params_ids_to_Simbelmyne_dict</span><span class="p">(</span><span class="n">params_vals</span><span class="p">,</span> <span class="n">params_ids</span><span class="p">,</span> <span class="n">fixed</span><span class="p">,</span> <span class="n">kmax</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Convert a list of cosmological parameters into a dictionary</span>
<span class="sd"> compatible with `pysbmy`.</span>
<span class="sd"> Fixed parameters remain unchanged unless overridden by</span>
<span class="sd"> `params_vals`.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> params_vals : array-like</span>
<span class="sd"> Values of the parameters to be modified.</span>
<span class="sd"> params_ids : array-like</span>
<span class="sd"> Indices of the parameters to be modified.</span>
<span class="sd"> fixed : array-like</span>
<span class="sd"> Base values of the parameters.</span>
<span class="sd"> kmax : float</span>
<span class="sd"> Maximum wavenumber for the power spectrum computation.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> dict</span>
<span class="sd"> Dictionary of cosmological parameters compatible with `pysbmy`.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">from</span> <span class="nn">numpy</span> <span class="kn">import</span> <span class="n">copy</span>
<span class="n">x</span> <span class="o">=</span> <span class="n">copy</span><span class="p">(</span><span class="n">fixed</span><span class="p">)</span>
<span class="n">x</span><span class="p">[</span><span class="n">params_ids</span><span class="p">]</span> <span class="o">=</span> <span class="n">params_vals</span>
<span class="k">return</span> <span class="n">cosmo_vector_to_Simbelmyne_dict</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">kmax</span><span class="o">=</span><span class="n">kmax</span><span class="p">)</span></div>
<div class="viewcode-block" id="get_summary">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.tools.get_summary">[docs]</a>
<span class="k">def</span> <span class="nf">get_summary</span><span class="p">(</span><span class="n">params_vals</span><span class="p">,</span> <span class="n">params_ids</span><span class="p">,</span> <span class="n">Omegas_fixed</span><span class="p">,</span> <span class="n">bins</span><span class="p">,</span> <span class="n">normalisation</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">kmax</span><span class="o">=</span><span class="mf">1.4</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Compute the normalised power spectrum summary for a given parameter</span>
<span class="sd"> set.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> params_vals : array-like</span>
<span class="sd"> Parameter values to update.</span>
<span class="sd"> params_ids : array-like</span>
<span class="sd"> Indices of the parameters to update.</span>
<span class="sd"> Omegas_fixed : array-like</span>
<span class="sd"> Fixed base values of parameters.</span>
<span class="sd"> bins : array-like</span>
<span class="sd"> Power spectrum bins.</span>
<span class="sd"> normalisation : float, optional</span>
<span class="sd"> Normalisation factor for the summary.</span>
<span class="sd"> kmax : float, optional</span>
<span class="sd"> Maximum wavenumber for power spectrum computation.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> array</span>
<span class="sd"> Normalised power spectrum summary.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">from</span> <span class="nn">pysbmy.power</span> <span class="kn">import</span> <span class="n">get_Pk</span>
<span class="kn">from</span> <span class="nn">numpy</span> <span class="kn">import</span> <span class="n">array</span>
<span class="n">phi</span> <span class="o">=</span> <span class="n">get_Pk</span><span class="p">(</span><span class="n">bins</span><span class="p">,</span> <span class="n">params_ids_to_Simbelmyne_dict</span><span class="p">(</span><span class="n">params_vals</span><span class="p">,</span> <span class="n">params_ids</span><span class="p">,</span> <span class="n">Omegas_fixed</span><span class="p">,</span> <span class="n">kmax</span><span class="p">))</span>
<span class="k">return</span> <span class="n">array</span><span class="p">(</span><span class="n">phi</span><span class="p">)</span> <span class="o">/</span> <span class="n">normalisation</span> <span class="k">if</span> <span class="n">normalisation</span> <span class="k">else</span> <span class="n">array</span><span class="p">(</span><span class="n">phi</span><span class="p">)</span></div>
<div class="viewcode-block" id="summary_to_score">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.tools.summary_to_score">[docs]</a>
<span class="k">def</span> <span class="nf">summary_to_score</span><span class="p">(</span><span class="n">params_ids</span><span class="p">,</span> <span class="n">omega0</span><span class="p">,</span> <span class="n">F0</span><span class="p">,</span> <span class="n">F0_inv</span><span class="p">,</span> <span class="n">f0</span><span class="p">,</span> <span class="n">dw_f0</span><span class="p">,</span> <span class="n">C0_inv</span><span class="p">,</span> <span class="n">phi</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Compute the Fisher score.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> params_ids : array-like</span>
<span class="sd"> Indices of the parameters.</span>
<span class="sd"> omega0 : array-like</span>
<span class="sd"> Cosmological parameters at the expansion point.</span>
<span class="sd"> F0 : array-like</span>
<span class="sd"> Fisher information matrix.</span>
<span class="sd"> F0_inv : array-like</span>
<span class="sd"> Inverse Fisher information matrix.</span>
<span class="sd"> f0 : array-like</span>
<span class="sd"> Mean model at the expansion point.</span>
<span class="sd"> dw_f0 : array-like</span>
<span class="sd"> Derivative of the mean model.</span>
<span class="sd"> C0_inv : array-like</span>
<span class="sd"> Inverse covariance matrix.</span>
<span class="sd"> phi : array-like</span>
<span class="sd"> Observed summary.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> array</span>
<span class="sd"> Fisher score.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="n">omega0</span><span class="p">[</span><span class="n">params_ids</span><span class="p">]</span> <span class="o">+</span> <span class="n">F0_inv</span> <span class="o">@</span> <span class="n">dw_f0</span><span class="o">.</span><span class="n">T</span> <span class="o">@</span> <span class="n">C0_inv</span> <span class="o">@</span> <span class="p">(</span><span class="n">phi</span> <span class="o">-</span> <span class="n">f0</span><span class="p">)</span></div>
<div class="viewcode-block" id="fisher_rao">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.tools.fisher_rao">[docs]</a>
<span class="k">def</span> <span class="nf">fisher_rao</span><span class="p">(</span><span class="n">Com</span><span class="p">,</span> <span class="n">Com_obs</span><span class="p">,</span> <span class="n">F0</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Compute the Fisher-Rao distance between two summaries.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> Com : array-like</span>
<span class="sd"> Computed summary.</span>
<span class="sd"> Com_obs : array-like</span>
<span class="sd"> Observed summary.</span>
<span class="sd"> F0 : array-like</span>
<span class="sd"> Fisher information matrix.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> float</span>
<span class="sd"> Fisher-Rao distance.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">from</span> <span class="nn">numpy</span> <span class="kn">import</span> <span class="n">sqrt</span>
<span class="n">diff</span> <span class="o">=</span> <span class="n">Com</span> <span class="o">-</span> <span class="n">Com_obs</span>
<span class="k">return</span> <span class="n">sqrt</span><span class="p">(</span><span class="n">diff</span><span class="o">.</span><span class="n">T</span> <span class="o">@</span> <span class="n">F0</span> <span class="o">@</span> <span class="n">diff</span><span class="p">)</span></div>
<div class="viewcode-block" id="sample_omega_from_prior">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.tools.sample_omega_from_prior">[docs]</a>
<span class="k">def</span> <span class="nf">sample_omega_from_prior</span><span class="p">(</span><span class="n">nsample</span><span class="p">,</span> <span class="n">omega_mean</span><span class="p">,</span> <span class="n">omega_cov</span><span class="p">,</span> <span class="n">params_ids</span><span class="p">,</span> <span class="n">seed</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Sample cosmological parameters from a prior distribution.</span>
<span class="sd"> Ensures physical validity by clipping values to [eps, 1-eps].</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> nsample : int</span>
<span class="sd"> Number of samples to draw.</span>
<span class="sd"> omega_mean : array-like</span>
<span class="sd"> Prior mean vector.</span>
<span class="sd"> omega_cov : array-like</span>
<span class="sd"> Prior covariance matrix.</span>
<span class="sd"> params_ids : array-like</span>
<span class="sd"> Indices of the parameters to sample.</span>
<span class="sd"> seed : int, optional</span>
<span class="sd"> Seed for the random number generator.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> array</span>
<span class="sd"> Sampled cosmological parameters.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">from</span> <span class="nn">numpy</span> <span class="kn">import</span> <span class="n">array</span><span class="p">,</span> <span class="n">ix_</span><span class="p">,</span> <span class="n">clip</span>
<span class="kn">from</span> <span class="nn">numpy.random</span> <span class="kn">import</span> <span class="n">default_rng</span>
<span class="k">if</span> <span class="n">seed</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;A seed value is mandatory.&quot;</span><span class="p">)</span>
<span class="n">rng</span> <span class="o">=</span> <span class="n">default_rng</span><span class="p">(</span><span class="n">seed</span><span class="p">)</span>
<span class="n">OO_unbounded</span> <span class="o">=</span> <span class="n">rng</span><span class="o">.</span><span class="n">multivariate_normal</span><span class="p">(</span>
<span class="n">array</span><span class="p">(</span><span class="n">omega_mean</span><span class="p">)[</span><span class="n">params_ids</span><span class="p">],</span>
<span class="n">array</span><span class="p">(</span><span class="n">omega_cov</span><span class="p">)[</span><span class="n">ix_</span><span class="p">(</span><span class="n">params_ids</span><span class="p">,</span> <span class="n">params_ids</span><span class="p">)],</span>
<span class="n">nsample</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">eps</span> <span class="o">=</span> <span class="mf">1e-5</span>
<span class="k">return</span> <span class="n">clip</span><span class="p">(</span><span class="n">OO_unbounded</span><span class="p">,</span> <span class="n">eps</span><span class="p">,</span> <span class="mi">1</span> <span class="o">-</span> <span class="n">eps</span><span class="p">)</span></div>
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<title>selfisys.utils.workers &mdash; SelfiSys /Users/hoellinger/Library/CloudStorage/Dropbox/travail/these/science/code/SELFI/selfisys/src/ documentation</title>
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<p class="caption" role="heading"><span class="caption-text">API Documentation</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.hiddenbox.html">hiddenbox</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox"><code class="docutils literal notranslate"><span class="pre">HiddenBox</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Npop"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Npop</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Ntimesteps"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Ntimesteps</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Psingle"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Psingle</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.compute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.compute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.evaluate"><code class="docutils literal notranslate"><span class="pre">HiddenBox.evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_neglect_lightcone"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_neglect_lightcone</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_recompute_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_recompute_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.gravity_on"><code class="docutils literal notranslate"><span class="pre">HiddenBox.gravity_on</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.load_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.load_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.make_data"><code class="docutils literal notranslate"><span class="pre">HiddenBox.make_data()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.modified_selfi"><code class="docutils literal notranslate"><span class="pre">HiddenBox.modified_selfi</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.prefix_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.prefix_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.reset_survey"><code class="docutils literal notranslate"><span class="pre">HiddenBox.reset_survey()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.setup_only"><code class="docutils literal notranslate"><span class="pre">HiddenBox.setup_only</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_recompute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_recompute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_setup"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_setup()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.update"><code class="docutils literal notranslate"><span class="pre">HiddenBox.update()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.normalise_hb.html">normalise_hb</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.define_normalisation"><code class="docutils literal notranslate"><span class="pre">define_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation"><code class="docutils literal notranslate"><span class="pre">worker_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_public"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_public()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_wrapper"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_wrapper()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.prior.html">prior</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.logposterior_hyperparameters_parallel"><code class="docutils literal notranslate"><span class="pre">logposterior_hyperparameters_parallel()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.perform_prior_optimisation_and_plot"><code class="docutils literal notranslate"><span class="pre">perform_prior_optimisation_and_plot()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior"><code class="docutils literal notranslate"><span class="pre">planck_prior</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.mean"><code class="docutils literal notranslate"><span class="pre">planck_prior.mean</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.inv_covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.inv_covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_max"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_max</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.Nbin_min"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_min</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.compute"><code class="docutils literal notranslate"><span class="pre">planck_prior.compute()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.load"><code class="docutils literal notranslate"><span class="pre">planck_prior.load()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.logpdf"><code class="docutils literal notranslate"><span class="pre">planck_prior.logpdf()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.sample"><code class="docutils literal notranslate"><span class="pre">planck_prior.sample()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.planck_prior.save"><code class="docutils literal notranslate"><span class="pre">planck_prior.save()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.prior.html#selfisys.prior.worker_class"><code class="docutils literal notranslate"><span class="pre">worker_class()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.selection_functions.html">selection_functions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.init_selection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.init_selection()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.lognormals_z_to_x"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.lognormals_z_to_x()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.r_grid"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.r_grid()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.selfi_interface.html">selfi_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.PrintMessage"><code class="docutils literal notranslate"><span class="pre">PrintMessage()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.indent"><code class="docutils literal notranslate"><span class="pre">indent()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.selfi_interface.html#selfisys.selfi_interface.unindent"><code class="docutils literal notranslate"><span class="pre">unindent()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.sbmy_interface.html">sbmy_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.compute_Phi"><code class="docutils literal notranslate"><span class="pre">compute_Phi()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.generate_white_noise_Field"><code class="docutils literal notranslate"><span class="pre">generate_white_noise_Field()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.get_power_spectrum_from_cosmo"><code class="docutils literal notranslate"><span class="pre">get_power_spectrum_from_cosmo()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.handle_time_stepping"><code class="docutils literal notranslate"><span class="pre">handle_time_stepping()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.sbmy_interface.html#selfisys.sbmy_interface.setup_sbmy_parfiles"><code class="docutils literal notranslate"><span class="pre">setup_sbmy_parfiles()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.grf.html">grf</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.grf.html#selfisys.grf.primordial_grf"><code class="docutils literal notranslate"><span class="pre">primordial_grf()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../selfisys.utils.html">selfisys.utils package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.examples_utils">selfisys.utils.examples_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.examples_utils.clear_large_plot"><code class="docutils literal notranslate"><span class="pre">clear_large_plot()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.logger">selfisys.utils.logger module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLogger"><code class="docutils literal notranslate"><span class="pre">CustomLogger</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLogger.diagnostic"><code class="docutils literal notranslate"><span class="pre">CustomLogger.diagnostic()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler.emit"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler.emit()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.INDENT"><code class="docutils literal notranslate"><span class="pre">INDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintDiagnostic"><code class="docutils literal notranslate"><span class="pre">PrintDiagnostic()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintError"><code class="docutils literal notranslate"><span class="pre">PrintError()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintInfo"><code class="docutils literal notranslate"><span class="pre">PrintInfo()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintLeftType"><code class="docutils literal notranslate"><span class="pre">PrintLeftType()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.PrintWarning"><code class="docutils literal notranslate"><span class="pre">PrintWarning()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.UNINDENT"><code class="docutils literal notranslate"><span class="pre">UNINDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.logger.getCustomLogger"><code class="docutils literal notranslate"><span class="pre">getCustomLogger()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.low_level">selfisys.utils.low_level module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.low_level.stderr_redirector"><code class="docutils literal notranslate"><span class="pre">stderr_redirector()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.low_level.stdout_redirector"><code class="docutils literal notranslate"><span class="pre">stdout_redirector()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.parser">selfisys.utils.parser module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.bool_sh"><code class="docutils literal notranslate"><span class="pre">bool_sh()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.check_files_exist"><code class="docutils literal notranslate"><span class="pre">check_files_exist()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.intNone"><code class="docutils literal notranslate"><span class="pre">intNone()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.joinstrs"><code class="docutils literal notranslate"><span class="pre">joinstrs()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.joinstrs_only"><code class="docutils literal notranslate"><span class="pre">joinstrs_only()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.parser.safe_npload"><code class="docutils literal notranslate"><span class="pre">safe_npload()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.path_utils">selfisys.utils.path_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.path_utils.file_names_evaluate"><code class="docutils literal notranslate"><span class="pre">file_names_evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.path_utils.get_file_names"><code class="docutils literal notranslate"><span class="pre">get_file_names()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.plot_examples">selfisys.utils.plot_examples module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_comoving_distance_redshift"><code class="docutils literal notranslate"><span class="pre">plot_comoving_distance_redshift()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_galaxy_field_slice"><code class="docutils literal notranslate"><span class="pre">plot_galaxy_field_slice()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_power_spectrum"><code class="docutils literal notranslate"><span class="pre">plot_power_spectrum()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.plot_selection_functions_def_in_z"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions_def_in_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.redshift_distance_conversion"><code class="docutils literal notranslate"><span class="pre">redshift_distance_conversion()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_examples.relative_error_analysis"><code class="docutils literal notranslate"><span class="pre">relative_error_analysis()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../../../selfisys.utils.html#module-selfisys.utils.plot_params">selfisys.utils.plot_params module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.get_offset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.get_offset()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_scientific"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_scientific()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="../../../selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_useOffset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_useOffset()</span></code></a></li>
</ul>
</li>
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<h1>Source code for selfisys.utils.workers</h1><div class="highlight"><pre>
<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="c1"># Copyright (C) 2024 Tristan Hoellinger</span>
<span class="c1"># Distributed under the GNU General Public License v3.0 (GPLv3).</span>
<span class="c1"># See the LICENSE file in the root directory for details.</span>
<span class="c1"># SPDX-License-Identifier: GPL-3.0-or-later</span>
<span class="c1"># ----------------------------------------------------------------------</span>
<span class="n">__author__</span> <span class="o">=</span> <span class="s2">&quot;Tristan Hoellinger&quot;</span>
<span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;0.1.0&quot;</span>
<span class="n">__date__</span> <span class="o">=</span> <span class="s2">&quot;2024&quot;</span>
<span class="n">__license__</span> <span class="o">=</span> <span class="s2">&quot;GPLv3&quot;</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd">Routines for parameter inference and gradient evaluation in the SelfiSys</span>
<span class="sd">pipeline.</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="kn">import</span> <span class="nn">gc</span>
<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Any</span><span class="p">,</span> <span class="n">Tuple</span><span class="p">,</span> <span class="n">List</span>
<span class="kn">from</span> <span class="nn">selfisys.utils.logger</span> <span class="kn">import</span> <span class="n">getCustomLogger</span>
<span class="n">logger</span> <span class="o">=</span> <span class="n">getCustomLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>
<div class="viewcode-block" id="Simbelmyne_worker">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.workers.Simbelmyne_worker">[docs]</a>
<span class="k">def</span> <span class="nf">Simbelmyne_worker</span><span class="p">(</span><span class="n">args</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Tuple</span><span class="p">[</span><span class="nb">float</span><span class="p">,</span> <span class="n">Any</span><span class="p">]:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Worker function used for implicit likelihood inference of</span>
<span class="sd"> cosmological parameters.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> args : tuple</span>
<span class="sd"> A tuple of arguments to be unpacked for the worker routine:</span>
<span class="sd"> (index, param_val, param_id, fsimdir, k_s, Pbins_bnd,</span>
<span class="sd"> selection_params, norm_csts, P_ss_obj_path, obs_density,</span>
<span class="sd"> lin_bias, noise, survey_mask_path, G_sim_path, G_ss_path, Np0,</span>
<span class="sd"> Npm0, seedphase_init, seednoise_init, size, L,</span>
<span class="sd"> radial_selection, sim_params, wd, batch_idx, dbg, modeldir,</span>
<span class="sd"> local_mask_prefix, TimeStepDistribution, indices_steps_cumul,</span>
<span class="sd"> eff_redshifts, poolname_abc, setup_only, prefix_mocks).</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> tuple</span>
<span class="sd"> (param_val, Phi) where param_val is the parameter value used,</span>
<span class="sd"> and Phi is the resulting summary from evaluating the model.</span>
<span class="sd"> Raises</span>
<span class="sd"> ------</span>
<span class="sd"> OSError</span>
<span class="sd"> If file I/O (reading or writing mock data) fails.</span>
<span class="sd"> RuntimeError</span>
<span class="sd"> For unexpected errors in the worker routine.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">from</span> <span class="nn">pathlib</span> <span class="kn">import</span> <span class="n">Path</span>
<span class="k">try</span><span class="p">:</span>
<span class="p">(</span>
<span class="n">index</span><span class="p">,</span>
<span class="n">param_val</span><span class="p">,</span>
<span class="n">param_id</span><span class="p">,</span>
<span class="n">fsimdir</span><span class="p">,</span>
<span class="n">k_s</span><span class="p">,</span>
<span class="n">Pbins_bnd</span><span class="p">,</span>
<span class="n">selection_params</span><span class="p">,</span>
<span class="n">norm_csts</span><span class="p">,</span>
<span class="n">P_ss_obj_path</span><span class="p">,</span>
<span class="n">obs_density</span><span class="p">,</span>
<span class="n">lin_bias</span><span class="p">,</span>
<span class="n">noise</span><span class="p">,</span>
<span class="n">survey_mask_path</span><span class="p">,</span>
<span class="n">G_sim_path</span><span class="p">,</span>
<span class="n">G_ss_path</span><span class="p">,</span>
<span class="n">Np0</span><span class="p">,</span>
<span class="n">Npm0</span><span class="p">,</span>
<span class="n">seedphase_init</span><span class="p">,</span>
<span class="n">seednoise_init</span><span class="p">,</span>
<span class="n">size</span><span class="p">,</span>
<span class="n">L</span><span class="p">,</span>
<span class="n">radial_selection</span><span class="p">,</span>
<span class="n">sim_params</span><span class="p">,</span>
<span class="n">wd</span><span class="p">,</span>
<span class="n">batch_idx</span><span class="p">,</span>
<span class="n">dbg</span><span class="p">,</span>
<span class="n">modeldir</span><span class="p">,</span>
<span class="n">local_mask_prefix</span><span class="p">,</span>
<span class="n">TimeStepDistribution</span><span class="p">,</span>
<span class="n">indices_steps_cumul</span><span class="p">,</span>
<span class="n">eff_redshifts</span><span class="p">,</span>
<span class="n">poolname_abc</span><span class="p">,</span>
<span class="n">setup_only</span><span class="p">,</span>
<span class="n">prefix_mocks</span><span class="p">,</span>
<span class="p">)</span> <span class="o">=</span> <span class="n">args</span>
<span class="n">spectrum_name</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">seedphase_init</span> <span class="o">+</span> <span class="n">index</span><span class="p">)</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">seednoise_init</span> <span class="o">+</span> <span class="n">index</span><span class="p">))</span>
<span class="n">pooldir</span> <span class="o">=</span> <span class="p">(</span>
<span class="n">fsimdir</span> <span class="o">+</span> <span class="s2">&quot;/pool/d&quot;</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">poolname_abc</span> <span class="k">else</span> <span class="n">fsimdir</span> <span class="o">+</span> <span class="s2">&quot;/pool/&quot;</span> <span class="o">+</span> <span class="n">poolname_abc</span> <span class="o">+</span> <span class="s2">&quot;/d&quot;</span>
<span class="p">)</span>
<span class="n">simdir_d</span> <span class="o">=</span> <span class="n">pooldir</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">spectrum_name</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot;/&quot;</span>
<span class="n">Path</span><span class="p">(</span><span class="n">simdir_d</span><span class="p">)</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="k">if</span> <span class="n">prefix_mocks</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">fname_mocks</span> <span class="o">=</span> <span class="p">(</span>
<span class="n">simdir_d</span> <span class="o">+</span> <span class="s2">&quot;mocks_d&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">spectrum_name</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot;_p&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">batch_idx</span> <span class="o">+</span> <span class="n">index</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot;.h5&quot;</span>
<span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">fname_mocks</span> <span class="o">=</span> <span class="p">(</span>
<span class="n">simdir_d</span>
<span class="o">+</span> <span class="n">prefix_mocks</span>
<span class="o">+</span> <span class="s2">&quot;_mocks_d&quot;</span>
<span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">spectrum_name</span><span class="p">)</span>
<span class="o">+</span> <span class="s2">&quot;_p&quot;</span>
<span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">batch_idx</span> <span class="o">+</span> <span class="n">index</span><span class="p">)</span>
<span class="o">+</span> <span class="s2">&quot;.h5&quot;</span>
<span class="p">)</span>
<span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">fname_mocks</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">h5py</span> <span class="kn">import</span> <span class="n">File</span>
<span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">&quot;Mock file </span><span class="si">%s</span><span class="s2"> found, loading existing data...&quot;</span><span class="p">,</span> <span class="n">fname_mocks</span><span class="p">)</span>
<span class="k">with</span> <span class="n">File</span><span class="p">(</span><span class="n">fname_mocks</span><span class="p">,</span> <span class="s2">&quot;r&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
<span class="n">Phi</span> <span class="o">=</span> <span class="n">f</span><span class="p">[</span><span class="s2">&quot;Phi&quot;</span><span class="p">][:]</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">&quot;No existing mock file at </span><span class="si">%s</span><span class="s2">, generating new data...&quot;</span><span class="p">,</span> <span class="n">fname_mocks</span><span class="p">)</span>
<span class="kn">from</span> <span class="nn">numpy.random</span> <span class="kn">import</span> <span class="n">normal</span>
<span class="kn">from</span> <span class="nn">numpy</span> <span class="kn">import</span> <span class="n">shape</span><span class="p">,</span> <span class="nb">max</span>
<span class="kn">from</span> <span class="nn">selfisys.global_parameters</span> <span class="kn">import</span> <span class="n">BASELINE_SEEDNORM</span><span class="p">,</span> <span class="n">omegas_gt</span>
<span class="kn">from</span> <span class="nn">selfisys.utils.tools</span> <span class="kn">import</span> <span class="n">get_k_max</span>
<span class="kn">from</span> <span class="nn">selfisys.hiddenbox</span> <span class="kn">import</span> <span class="n">HiddenBox</span>
<span class="kn">from</span> <span class="nn">selfisys.utils.tools</span> <span class="kn">import</span> <span class="n">get_summary</span>
<span class="n">P</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">Pbins_bnd</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">BB_selfi</span> <span class="o">=</span> <span class="n">HiddenBox</span><span class="p">(</span>
<span class="n">k_s</span><span class="o">=</span><span class="n">k_s</span><span class="p">,</span>
<span class="n">P_ss_path</span><span class="o">=</span><span class="n">P_ss_obj_path</span><span class="p">,</span>
<span class="n">Pbins_bnd</span><span class="o">=</span><span class="n">Pbins_bnd</span><span class="p">,</span>
<span class="n">theta2P</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">P</span><span class="o">=</span><span class="n">P</span> <span class="o">*</span> <span class="n">shape</span><span class="p">(</span><span class="n">selection_params</span><span class="p">)[</span><span class="mi">1</span><span class="p">],</span> <span class="c1"># P * Npop</span>
<span class="n">size</span><span class="o">=</span><span class="n">size</span><span class="p">,</span>
<span class="n">L</span><span class="o">=</span><span class="n">L</span><span class="p">,</span>
<span class="n">G_sim_path</span><span class="o">=</span><span class="n">G_sim_path</span><span class="p">,</span>
<span class="n">G_ss_path</span><span class="o">=</span><span class="n">G_ss_path</span><span class="p">,</span>
<span class="n">Np0</span><span class="o">=</span><span class="n">Np0</span><span class="p">,</span>
<span class="n">Npm0</span><span class="o">=</span><span class="n">Npm0</span><span class="p">,</span>
<span class="n">fsimdir</span><span class="o">=</span><span class="n">wd</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span>
<span class="n">modeldir</span><span class="o">=</span><span class="n">modeldir</span><span class="p">,</span>
<span class="n">noise_std</span><span class="o">=</span><span class="n">noise</span><span class="p">,</span>
<span class="n">radial_selection</span><span class="o">=</span><span class="n">radial_selection</span><span class="p">,</span>
<span class="n">selection_params</span><span class="o">=</span><span class="n">selection_params</span><span class="p">,</span>
<span class="n">observed_density</span><span class="o">=</span><span class="n">obs_density</span><span class="p">,</span>
<span class="n">linear_bias</span><span class="o">=</span><span class="n">lin_bias</span><span class="p">,</span>
<span class="n">norm_csts</span><span class="o">=</span><span class="n">norm_csts</span><span class="p">,</span>
<span class="n">survey_mask_path</span><span class="o">=</span><span class="n">survey_mask_path</span><span class="p">,</span>
<span class="n">local_mask_prefix</span><span class="o">=</span><span class="n">local_mask_prefix</span><span class="p">,</span>
<span class="n">sim_params</span><span class="o">=</span><span class="n">sim_params</span><span class="p">,</span>
<span class="n">TimeStepDistribution</span><span class="o">=</span><span class="n">TimeStepDistribution</span><span class="p">,</span>
<span class="n">TimeSteps</span><span class="o">=</span><span class="n">indices_steps_cumul</span><span class="p">,</span>
<span class="n">eff_redshifts</span><span class="o">=</span><span class="n">eff_redshifts</span><span class="p">,</span>
<span class="n">seedphase</span><span class="o">=</span><span class="n">seedphase_init</span><span class="p">,</span>
<span class="n">seednoise</span><span class="o">=</span><span class="n">seednoise_init</span><span class="p">,</span>
<span class="n">fixnoise</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
<span class="n">seednorm</span><span class="o">=</span><span class="n">BASELINE_SEEDNORM</span><span class="p">,</span>
<span class="n">reset</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
<span class="n">save_frequency</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span>
<span class="n">verbosity</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">k_max</span> <span class="o">=</span> <span class="n">get_k_max</span><span class="p">(</span><span class="n">L</span><span class="p">,</span> <span class="n">size</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
<span class="n">logger</span><span class="o">.</span><span class="n">critical</span><span class="p">(</span><span class="s2">&quot;Error instantiating HiddenBox: </span><span class="si">%s</span><span class="s2">&quot;</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">e</span><span class="p">))</span>
<span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s2">&quot;Failed to set up HiddenBox.&quot;</span><span class="p">)</span> <span class="kn">from</span> <span class="nn">e</span>
<span class="c1"># Evaluate the param -&gt; &#39;theta&#39; using some get_summary logic</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">theta</span> <span class="o">=</span> <span class="n">get_summary</span><span class="p">(</span><span class="n">param_val</span><span class="p">,</span> <span class="n">param_id</span><span class="p">,</span> <span class="n">omegas_gt</span><span class="p">,</span> <span class="n">k_s</span><span class="p">,</span> <span class="n">kmax</span><span class="o">=</span><span class="n">k_max</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span>
<span class="n">max_tries</span> <span class="o">=</span> <span class="mi">10</span>
<span class="n">perturb_std</span> <span class="o">=</span> <span class="mf">1e-8</span>
<span class="n">param_val_init</span> <span class="o">=</span> <span class="n">param_val</span>
<span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span>
<span class="s2">&quot;get_summary failed for param_val=</span><span class="si">%s</span><span class="s2">. Trying small perturbations...&quot;</span><span class="p">,</span> <span class="n">param_val</span>
<span class="p">)</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">max_tries</span><span class="p">):</span>
<span class="n">param_val</span> <span class="o">=</span> <span class="n">normal</span><span class="p">(</span><span class="n">param_val_init</span><span class="p">,</span> <span class="n">perturb_std</span><span class="p">)</span>
<span class="n">logger</span><span class="o">.</span><span class="n">diagnostic</span><span class="p">(</span><span class="s2">&quot;Attempt #</span><span class="si">%d</span><span class="s2">: param_val=</span><span class="si">%s</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">i</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span> <span class="n">param_val</span><span class="p">)</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">theta</span> <span class="o">=</span> <span class="n">get_summary</span><span class="p">(</span><span class="n">param_val</span><span class="p">,</span> <span class="n">param_id</span><span class="p">,</span> <span class="n">omegas_gt</span><span class="p">,</span> <span class="n">k_s</span><span class="p">,</span> <span class="n">kmax</span><span class="o">=</span><span class="n">k_max</span><span class="p">)</span>
<span class="n">logger</span><span class="o">.</span><span class="n">diagnostic</span><span class="p">(</span>
<span class="s2">&quot;Success with param_val=</span><span class="si">%s</span><span class="s2"> on attempt #</span><span class="si">%d</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">param_val</span><span class="p">,</span> <span class="n">i</span> <span class="o">+</span> <span class="mi">1</span>
<span class="p">)</span>
<span class="k">break</span>
<span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span>
<span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="n">max_tries</span> <span class="o">-</span> <span class="mi">1</span><span class="p">:</span>
<span class="n">logger</span><span class="o">.</span><span class="n">critical</span><span class="p">(</span>
<span class="s2">&quot;All attempts to get_summary failed for param_val=</span><span class="si">%s</span><span class="s2">&quot;</span><span class="p">,</span>
<span class="n">param_val_init</span><span class="p">,</span>
<span class="p">)</span>
<span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s2">&quot;get_summary repeatedly failed.&quot;</span><span class="p">)</span>
<span class="k">continue</span>
<span class="kn">from</span> <span class="nn">io</span> <span class="kn">import</span> <span class="n">BytesIO</span>
<span class="kn">from</span> <span class="nn">selfisys.utils.low_level</span> <span class="kn">import</span> <span class="n">stderr_redirector</span><span class="p">,</span> <span class="n">stdout_redirector</span>
<span class="n">cosmo_vect</span> <span class="o">=</span> <span class="n">omegas_gt</span>
<span class="n">cosmo_vect</span><span class="p">[</span><span class="n">param_id</span><span class="p">]</span> <span class="o">=</span> <span class="n">param_val</span>
<span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">&quot;Evaluating model with HPC redirection, setup_only=</span><span class="si">%s</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">setup_only</span><span class="p">)</span>
<span class="n">f</span> <span class="o">=</span> <span class="n">BytesIO</span><span class="p">()</span>
<span class="n">g</span> <span class="o">=</span> <span class="n">BytesIO</span><span class="p">()</span>
<span class="k">try</span><span class="p">:</span>
<span class="k">with</span> <span class="n">stderr_redirector</span><span class="p">(</span><span class="n">f</span><span class="p">):</span>
<span class="k">with</span> <span class="n">stdout_redirector</span><span class="p">(</span><span class="n">g</span><span class="p">):</span>
<span class="k">if</span> <span class="n">setup_only</span><span class="p">:</span>
<span class="n">BB_selfi</span><span class="o">.</span><span class="n">switch_setup</span><span class="p">()</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">BB_selfi</span><span class="o">.</span><span class="n">switch_recompute_pool</span><span class="p">(</span><span class="n">prefix_mocks</span><span class="o">=</span><span class="n">prefix_mocks</span><span class="p">)</span>
<span class="n">Phi</span> <span class="o">=</span> <span class="n">BB_selfi</span><span class="o">.</span><span class="n">evaluate</span><span class="p">(</span>
<span class="n">theta</span><span class="p">,</span>
<span class="n">spectrum_name</span><span class="p">,</span>
<span class="n">seedphase_init</span> <span class="o">+</span> <span class="n">index</span><span class="p">,</span>
<span class="n">seednoise_init</span> <span class="o">+</span> <span class="n">index</span><span class="p">,</span>
<span class="n">i</span><span class="o">=</span><span class="n">batch_idx</span> <span class="o">+</span> <span class="n">index</span><span class="p">,</span>
<span class="n">thetaIsP</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="n">remove_sbmy</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="n">force_powerspectrum</span><span class="o">=</span><span class="n">dbg</span><span class="p">,</span>
<span class="n">force_parfiles</span><span class="o">=</span><span class="n">dbg</span><span class="p">,</span>
<span class="n">check_output</span><span class="o">=</span><span class="n">dbg</span><span class="p">,</span>
<span class="n">abc</span><span class="o">=</span><span class="n">poolname_abc</span><span class="p">,</span>
<span class="n">cosmo_vect</span><span class="o">=</span><span class="n">cosmo_vect</span><span class="p">,</span>
<span class="p">)</span>
<span class="k">if</span> <span class="n">setup_only</span><span class="p">:</span>
<span class="n">BB_selfi</span><span class="o">.</span><span class="n">switch_setup</span><span class="p">()</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">BB_selfi</span><span class="o">.</span><span class="n">switch_recompute_pool</span><span class="p">(</span><span class="n">prefix_mocks</span><span class="o">=</span><span class="n">prefix_mocks</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
<span class="n">logger</span><span class="o">.</span><span class="n">critical</span><span class="p">(</span><span class="s2">&quot;Error while evaluating model: </span><span class="si">%s</span><span class="s2">&quot;</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">e</span><span class="p">))</span>
<span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s2">&quot;Simbelmyne_worker model evaluation failed.&quot;</span><span class="p">)</span> <span class="kn">from</span> <span class="nn">e</span>
<span class="k">finally</span><span class="p">:</span>
<span class="n">g</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="n">f</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">&quot;Returning param_val=</span><span class="si">%s</span><span class="s2"> with resulting Phi of shape </span><span class="si">%s</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">param_val</span><span class="p">,</span> <span class="n">Phi</span><span class="o">.</span><span class="n">shape</span><span class="p">)</span>
<span class="k">return</span> <span class="n">param_val</span><span class="p">,</span> <span class="n">Phi</span>
<span class="k">except</span> <span class="ne">OSError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
<span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">&quot;File I/O error in Simbelmyne_worker: </span><span class="si">%s</span><span class="s2">&quot;</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">e</span><span class="p">))</span>
<span class="k">raise</span>
<span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
<span class="n">logger</span><span class="o">.</span><span class="n">critical</span><span class="p">(</span><span class="s2">&quot;Unexpected error in Simbelmyne_worker: </span><span class="si">%s</span><span class="s2">&quot;</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">e</span><span class="p">))</span>
<span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s2">&quot;Simbelmyne_worker HPC run failed.&quot;</span><span class="p">)</span> <span class="kn">from</span> <span class="nn">e</span>
<span class="k">finally</span><span class="p">:</span>
<span class="n">gc</span><span class="o">.</span><span class="n">collect</span><span class="p">()</span></div>
<div class="viewcode-block" id="worker_gradient_Symbelmyne">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.workers.worker_gradient_Symbelmyne">[docs]</a>
<span class="k">def</span> <span class="nf">worker_gradient_Symbelmyne</span><span class="p">(</span>
<span class="n">coeff</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span>
<span class="n">delta_x</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span>
<span class="n">omega</span><span class="p">,</span>
<span class="n">param_index</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
<span class="n">k_s</span><span class="p">,</span>
<span class="n">delta</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span>
<span class="n">kmax</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span>
<span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Worker function for evaluating the gradient of the power spectrum</span>
<span class="sd"> using finite differences.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> coeff : float</span>
<span class="sd"> Coefficient for the finite difference.</span>
<span class="sd"> delta_x : float</span>
<span class="sd"> Step size in the parameter space.</span>
<span class="sd"> omega : ndarray</span>
<span class="sd"> Base cosmological parameter vector.</span>
<span class="sd"> param_index : int</span>
<span class="sd"> Index of the parameter being varied.</span>
<span class="sd"> k_s : ndarray</span>
<span class="sd"> Array of wavenumbers.</span>
<span class="sd"> delta : float</span>
<span class="sd"> Denominator for finite differences (scaled).</span>
<span class="sd"> kmax : float</span>
<span class="sd"> Maximum wavenumber for power spectrum.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> ndarray</span>
<span class="sd"> The gradient of the power spectrum wrt the specified parameter.</span>
<span class="sd"> Raises</span>
<span class="sd"> ------</span>
<span class="sd"> RuntimeError</span>
<span class="sd"> If the gradient evaluation fails.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">from</span> <span class="nn">pysbmy.power</span> <span class="kn">import</span> <span class="n">get_Pk</span>
<span class="kn">from</span> <span class="nn">selfisys.utils.tools</span> <span class="kn">import</span> <span class="n">cosmo_vector_to_Simbelmyne_dict</span>
<span class="n">omega_new</span> <span class="o">=</span> <span class="n">omega</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">omega_new</span><span class="p">[</span><span class="n">param_index</span><span class="p">]</span> <span class="o">+=</span> <span class="n">delta_x</span>
<span class="n">ps</span> <span class="o">=</span> <span class="n">get_Pk</span><span class="p">(</span><span class="n">k_s</span><span class="p">,</span> <span class="n">cosmo_vector_to_Simbelmyne_dict</span><span class="p">(</span><span class="n">omega_new</span><span class="p">,</span> <span class="n">kmax</span><span class="o">=</span><span class="n">kmax</span><span class="p">))</span>
<span class="n">contrib_to_grad</span> <span class="o">=</span> <span class="p">(</span><span class="n">coeff</span> <span class="o">*</span> <span class="n">ps</span><span class="p">)</span> <span class="o">/</span> <span class="n">delta</span>
<span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">contrib_to_grad</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
<span class="n">logger</span><span class="o">.</span><span class="n">critical</span><span class="p">(</span><span class="s2">&quot;Error in worker_gradient_Symbelmyne: </span><span class="si">%s</span><span class="s2">&quot;</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">e</span><span class="p">))</span>
<span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s2">&quot;worker_gradient_Symbelmyne failed.&quot;</span><span class="p">)</span> <span class="kn">from</span> <span class="nn">e</span>
<span class="k">finally</span><span class="p">:</span>
<span class="n">gc</span><span class="o">.</span><span class="n">collect</span><span class="p">()</span></div>
<div class="viewcode-block" id="evaluate_gradient_of_Symbelmyne">
<a class="viewcode-back" href="../../../selfisys.utils.html#selfisys.utils.workers.evaluate_gradient_of_Symbelmyne">[docs]</a>
<span class="k">def</span> <span class="nf">evaluate_gradient_of_Symbelmyne</span><span class="p">(</span>
<span class="n">omega</span><span class="p">,</span>
<span class="n">param_index</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
<span class="n">k_s</span><span class="p">,</span>
<span class="n">coeffs</span><span class="p">:</span> <span class="n">List</span><span class="p">[</span><span class="nb">float</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mi">2</span> <span class="o">/</span> <span class="mf">3.0</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span> <span class="o">/</span> <span class="mf">12.0</span><span class="p">],</span>
<span class="n">deltas_x</span><span class="p">:</span> <span class="n">List</span><span class="p">[</span><span class="nb">float</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mf">0.01</span><span class="p">,</span> <span class="mf">0.02</span><span class="p">],</span>
<span class="n">delta</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">1e-2</span><span class="p">,</span>
<span class="n">kmax</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">1.4</span><span class="p">,</span>
<span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Estimate the gradient of CLASS with respect to the cosmological</span>
<span class="sd"> parameters using central finite differences of arbitrary order.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> omega : ndarray</span>
<span class="sd"> Base cosmological parameter vector.</span>
<span class="sd"> param_index : int</span>
<span class="sd"> Index of the parameter to differentiate against.</span>
<span class="sd"> k_s : ndarray</span>
<span class="sd"> Wavenumbers for the power spectrum.</span>
<span class="sd"> coeffs : list of float, optional</span>
<span class="sd"> Coefficients for the finite-difference scheme, typically</span>
<span class="sd"> [2/3, -1/12] etc. Default is [2/3.0, -1/12.0].</span>
<span class="sd"> deltas_x : list of float, optional</span>
<span class="sd"> Step sizes. The corresponding negative steps are generated</span>
<span class="sd"> automatically. Default is [0.01, 0.02].</span>
<span class="sd"> delta : float, optional</span>
<span class="sd"> Scale for the finite difference in the denominator. Default is</span>
<span class="sd"> 1e-2.</span>
<span class="sd"> kmax : float, optional</span>
<span class="sd"> Maximum wavenumber for the power spectrum. Default is 1.4.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> ndarray</span>
<span class="sd"> The gradient of the power spectrum wrt the specified parameter.</span>
<span class="sd"> Raises</span>
<span class="sd"> ------</span>
<span class="sd"> RuntimeError</span>
<span class="sd"> If the gradient evaluation fails.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">from</span> <span class="nn">multiprocessing</span> <span class="kn">import</span> <span class="n">Pool</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">grad</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">k_s</span><span class="p">))</span>
<span class="n">full_coeffs</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">((</span><span class="o">-</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">coeffs</span><span class="p">)[::</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="n">coeffs</span><span class="p">))</span>
<span class="n">deltas_x_full</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">((</span><span class="o">-</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">deltas_x</span><span class="p">)[::</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="n">deltas_x</span><span class="p">))</span>
<span class="n">tasks</span> <span class="o">=</span> <span class="p">[</span>
<span class="p">(</span><span class="n">c</span><span class="p">,</span> <span class="n">dx</span><span class="p">,</span> <span class="n">omega</span><span class="p">,</span> <span class="n">param_index</span><span class="p">,</span> <span class="n">k_s</span><span class="p">,</span> <span class="n">delta</span><span class="p">,</span> <span class="n">kmax</span><span class="p">)</span>
<span class="k">for</span> <span class="n">c</span><span class="p">,</span> <span class="n">dx</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">full_coeffs</span><span class="p">,</span> <span class="n">deltas_x_full</span><span class="p">)</span>
<span class="p">]</span>
<span class="n">logger</span><span class="o">.</span><span class="n">diagnostic</span><span class="p">(</span><span class="s2">&quot;Starting parallel HPC for gradient, tasks=</span><span class="si">%d</span><span class="s2">&quot;</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">tasks</span><span class="p">))</span>
<span class="k">with</span> <span class="n">Pool</span><span class="p">()</span> <span class="k">as</span> <span class="n">mp_pool</span><span class="p">:</span>
<span class="n">results</span> <span class="o">=</span> <span class="n">mp_pool</span><span class="o">.</span><span class="n">starmap</span><span class="p">(</span><span class="n">worker_gradient_Symbelmyne</span><span class="p">,</span> <span class="n">tasks</span><span class="p">)</span>
<span class="k">for</span> <span class="n">contrib</span> <span class="ow">in</span> <span class="n">results</span><span class="p">:</span>
<span class="n">grad</span> <span class="o">+=</span> <span class="n">contrib</span>
<span class="n">logger</span><span class="o">.</span><span class="n">diagnostic</span><span class="p">(</span><span class="s2">&quot;Gradient evaluation completed. Shape=</span><span class="si">%s</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">grad</span><span class="o">.</span><span class="n">shape</span><span class="p">)</span>
<span class="k">return</span> <span class="n">grad</span>
<span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
<span class="n">logger</span><span class="o">.</span><span class="n">critical</span><span class="p">(</span><span class="s2">&quot;Unexpected error in evaluate_gradient_of_Symbelmyne: </span><span class="si">%s</span><span class="s2">&quot;</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">e</span><span class="p">))</span>
<span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s2">&quot;evaluate_gradient_of_Symbelmyne failed.&quot;</span><span class="p">)</span> <span class="kn">from</span> <span class="nn">e</span>
<span class="k">finally</span><span class="p">:</span>
<span class="n">gc</span><span class="o">.</span><span class="n">collect</span><span class="p">()</span></div>
</pre></div>
</div>
</div>
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# Contributing to SelfiSys
We welcome contributions to the SelfiSys repository! Please follow these guidelines when contributing.
---
## Reporting Issues
If you find a bug or have a suggestion, please open an issue in the [GitHub repository](https://github.com/hoellin/selfisys_public). Include as much detail as possible:
- Steps to reproduce the issue
- Expected vs. actual behaviour
- Relevant error messages or logs (if applicable)
- Suggestions for improvement (if applicable)
If you are unsure whether your issue is a bug or have questions about the code, you are welcome to open an issue for discussion.
## Submitting Contributions
1. Fork the repository and create a new branch for your changes.
2. Ensure your contributions are well-documented and adhere to the highest coding standards.
3. Test your changes thoroughly before submitting:
- Ensure Jupyter notebooks run without errors from top to bottom.
- Validate new functionality or fixes using appropriate test cases.
4. Before submitting a pull request, synchronise your fork with the main repository to incorporate upstream changes.
- Add the main repository as a remote.
```bash
git remote add upstream https://github.com/hoellin/selfisys_public.git
```
- Fetch the latest changes from the upstream repository.
```bash
git fetch upstream
```
- Merge the changes into your local repository.
```bash
git merge upstream/main
```
5. Open a pull request describing your changes to the main repository.
## Style Guidelines
Follow best practices for Python coding and Jupyter notebooks.
### Python code
Refer to the [PEP 8 Style Guide](https://pep8.org/) for Python coding standards.
### Jupyter Notebooks
- Use clear and concise Markdown cells to explain code and results.
- Avoid leaving unnecessary output (e.g., debugging print statements).
- Ensure notebooks are runnable from top to bottom.
- For tips on creating clean and effective Jupyter notebooks, see [Jupyter Notebook Best Practices](https://realpython.com/jupyter-notebook-best-practices/).
---
## Questions?
If you have any questions or need further clarification, feel free to [contact the authors](mailto:tristan.hoellinger@iap.fr).

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# SelfiSys: Assess the Impact of Systematic Effects in Galaxy Surveys
[![arXiv](https://img.shields.io/badge/astro--ph.CO-arxiv%3A2412.04443-B31B1B.svg?style=flat)](https://arxiv.org/abs/2412.04443)
[![GPLv3 license](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://github.com/hoellin/selfisys_public/blob/main/LICENSE)
[![GitHub version](https://img.shields.io/github/tag/hoellin/selfisys_public.svg?label=version)](https://github.com/hoellin/selfisys_public)
[![GitHub last commit](https://img.shields.io/github/last-commit/hoellin/selfisys_public.svg)](https://github.com/hoellin/selfisys_public/commits/main)
**SelfiSys** is a Python package designed to address the issue of model misspecification in field-based, implicit likelihood cosmological inference.
It leverages the inferred initial matter power spectrum, enabling a thorough diagnosis of systematic effects in large-scale spectroscopic galaxy surveys.
## Key Features
- **Custom hidden-box forward models**
We provide a `HiddenBox` class to simulate realistic spectroscopic galaxy surveys. It accommodates fully non-linear gravitational evolution, and incorporates multiple systematic effects observed in real-world survey, e.g., misspecified galaxy bias, survey mask, selection functions, dust extinction, line interlopers, or inaccurate gravity solver.
- **Diagnosis of systematic effects**
Diagnose the impact of systematic effects using the inferred initial matter power spectrum, prior to performing cosmological inference.
- **Cosmological inference**
Perform inference of cosmological parameters using Approximate Bayesian Computation (ABC) with a Population Monte Carlo (PMC) sampler.
---
## Documentation
The documentation, including a detailed API reference, is available at [hoellin.github.io/selfisys_public](https://hoellin.github.io/selfisys_public/).
For practical examples demonstrating how to use SelfiSys, visit the [SelfiSys Examples Repository](https://github.com/hoellin/selfisys_examples).
## Contributors
- **Tristan Hoellinger**, [tristan.hoellinger@iap.fr](mailto:tristan.hoellinger@iap.fr)
Principal developer and maintainer, Institut dAstrophysique de Paris (IAP).
For information on contributing, refer to [CONTRIBUTING.md](CONTRIBUTING.md).
## References
If you use the SelfiSys package in your research, please cite the following paper and feel free to [contact the authors](mailto:tristan.hoellinger@iap.fr) for feedback, collaboration opportunities, or other inquiries.
**Diagnosing Systematic Effects Using the Inferred Initial Power Spectrum**
*Hoellinger, T. and Leclercq, F., 2024*
[arXiv:2412.04443](https://arxiv.org/abs/2412.04443) [[astro-ph.CO]](https://arxiv.org/abs/2412.04443) [[ADS]](https://ui.adsabs.harvard.edu/abs/arXiv:2412.04443) [[pdf]](https://arxiv.org/pdf/2412.04443)
BibTeX entry for citation:
```bibtex
@ARTICLE{hoellinger2024diagnosing,
author = {Hoellinger, Tristan and Leclercq, Florent},
title = "{Diagnosing Systematic Effects Using the Inferred Initial Power Spectrum}",
journal = {arXiv e-prints},
keywords = {Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics},
year = 2024,
month = dec,
eid = {arXiv:2412.04443},
pages = {arXiv:2412.04443},
doi = {10.48550/arXiv.2412.04443},
archivePrefix = {arXiv},
eprint = {2412.04443},
primaryClass = {astro-ph.CO},
adsurl = {https://ui.adsabs.harvard.edu/abs/2024arXiv241204443H},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
```
## Requirements
The code is written in Python 3.10 and depends on the following packages:
- [`pySELFI`](https://pyselfi.readthedocs.io/en/latest/): Python implementation of the Simulator Expansion for Likelihood-Free Inference.
- [`Simbelmynë`](https://simbelmyne.readthedocs.io/en/latest/): A hierarchical probabilistic simulator for generating synthetic galaxy survey data.
- [`ELFI`](https://elfi.readthedocs.io/en/latest/): A statistical software package for likelihood-free inference, implementing in particular Approximate Bayesian Computation (ABC) with a Population Monte Carlo (PMC) sampler.
A comprehensive list of dependencies, including version specifications to ensure reproducibility, will be provided in a yaml file, along with installation instructions, in a future release.
---
## License
This software is distributed under the GPLv3 Licence. Please review the [LICENSE](https://github.com/hoellin/selfisys_public/blob/main/LICENSE) file in the repository to understand the terms of use and ensure compliance. By downloading and using this software, you agree to the terms of the licence.

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# References
If you use the SelfiSys package in your research, please cite the following paper and feel free to [contact the authors](mailto:tristan.hoellinger@iap.fr) for feedback, collaboration opportunities, or other inquiries.
**Diagnosing Systematic Effects Using the Inferred Initial Power Spectrum**
*Hoellinger, T. and Leclercq, F., 2024*
[arXiv:2412.04443](https://arxiv.org/abs/2412.04443) [[astro-ph.CO]](https://arxiv.org/abs/2412.04443) [[ADS]](https://ui.adsabs.harvard.edu/abs/arXiv:2412.04443) [[pdf]](https://arxiv.org/pdf/2412.04443)
BibTeX entry for citation:
```bibtex
@ARTICLE{hoellinger2024diagnosing,
author = {Hoellinger, Tristan and Leclercq, Florent},
title = "{Diagnosing Systematic Effects Using the Inferred Initial Power Spectrum}",
journal = {arXiv e-prints},
keywords = {Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics},
year = 2024,
month = dec,
eid = {arXiv:2412.04443},
pages = {arXiv:2412.04443},
doi = {10.48550/arXiv.2412.04443},
archivePrefix = {arXiv},
eprint = {2412.04443},
primaryClass = {astro-ph.CO},
adsurl = {https://ui.adsabs.harvard.edu/abs/2024arXiv241204443H},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
```
Other references relevant to the SelfiSys pipeline and cited in the code are listed below.
- **[jasche2010bayesian]**
Jasche, J., Kitaura, F. S., Wandelt, B. D., and Enßlin, T. A., “Bayesian power-spectrum inference for large-scale structure data”, <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 406, no. 1, OUP, pp. 6085, 2010. [doi:10.1111/j.1365-2966.2010.16610.x](https://doi.org/10.48550/arXiv.0911.2493).
- **[gil2015power]**
Gil-Marín, H., “The power spectrum and bispectrum of SDSS DR11 BOSS galaxies - I. Bias and gravity”, <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 451, no. 1, OUP, pp. 539580, 2015. [doi:10.1093/mnras/stv961](https://doi.org/10.48550/arXiv.1407.5668).
- **[howlett2015clustering]**
Howlett, C., Ross, A. J., Samushia, L., Percival, W. J., and Manera, M., “The clustering of the SDSS main galaxy sample - II. Mock galaxy catalogues and a measurement of the growth of structure from redshift space distortions at z = 0.15”, <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 449, no. 1, OUP, pp. 848866, 2015. [doi:10.1093/mnras/stu2693](https://doi.org/10.48550/arXiv.1409.3238).
- **[leclercq2019primordial]**
Florent Leclercq, Wolfgang Enzi, Jens Jasche, Alan Heavens, Primordial power spectrum and cosmology from black-box galaxy surveys, Monthly Notices of the Royal Astronomical Society, Volume 490, Issue 3, December 2019, Pages 42374253, [doi:10.1093/mnras/stz2718](https://doi.org/10.1093/mnras/stz2718).
- **[hoellinger2024diagnosing]**
Hoellinger, T. and Leclercq, F., “Diagnosing Systematic Effects Using the Inferred Initial Power Spectrum”, <i>arXiv e-prints</i>, Art. no. arXiv:2412.04443, 2024. [doi.org:10.48550/arXiv.2412.04443](https://doi.org/10.48550/arXiv.2412.04443).

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SelfiSys: Assess the Impact of Systematic Effects in Galaxy Surveys
===================================================================
.. image:: https://img.shields.io/badge/astro--ph.CO-arxiv%3A2412.04443-B31B1B.svg
:target: https://arxiv.org/abs/2412.04443
:alt: arXiv
.. image:: https://img.shields.io/github/v/tag/hoellin/selfisys_public.svg?label=version
:target: https://github.com/hoellin/selfisys_public/releases
:alt: GitHub Release
.. image:: https://img.shields.io/github/last-commit/hoellin/selfisys_public
:target: https://github.com/hoellin/selfisys_public/commits/main
:alt: Last Commit
.. image:: https://img.shields.io/badge/License-GPLv3-blue.svg
:target: https://github.com/hoellin/selfisys_public/blob/main/LICENSE
:alt: License
**SelfiSys** is a Python package designed to address the issue of model misspecification in field-based, implicit likelihood cosmological inference.
It leverages the inferred initial matter power spectrum, enabling a thorough diagnosis of systematic effects in large-scale spectroscopic galaxy surveys.
Key Features
------------
- **Custom hidden-box forward models**
We provide a `HiddenBox` class to simulate realistic spectroscopic galaxy surveys. It accommodates fully non-linear gravitational evolution, and incorporates multiple systematic effects observed in real-world survey, e.g., misspecified galaxy bias, survey mask, selection functions, dust extinction, line interlopers, or inaccurate gravity solver.
- **Diagnosis of systematic effects**
Diagnose the impact of systematic effects using the inferred initial matter power spectrum, prior to performing cosmological inference.
- **Cosmological inference**
Perform inference of cosmological parameters using Approximate Bayesian Computation (ABC) with a Population Monte Carlo (PMC) sampler.
For practical examples demonstrating how to use SelfiSys, visit the `SelfiSys Examples Repository <https://github.com/hoellin/selfisys_examples>`_.
References
----------
If you use the SelfiSys package in your research, please cite the following paper and feel free to `contact the authors <mailto:tristan.hoellinger@iap.fr>`_ for feedback, collaboration opportunities, or other inquiries.
**Diagnosing Systematic Effects Using the Inferred Initial Power Spectrum**
*Hoellinger, T. and Leclercq, F., arXiv e-prints*, 2024
`arXiv:2412.04443 <https://arxiv.org/abs/2412.04443>`_
`[astro-ph.CO] <https://arxiv.org/abs/2412.04443>`_
`[ADS] <https://ui.adsabs.harvard.edu/abs/arXiv:2412.04443>`_
`[pdf] <https://arxiv.org/pdf/2412.04443>`_
Contributors
------------
- **Tristan Hoellinger**
`tristan.hoellinger@iap.fr <mailto:tristan.hoellinger@iap.fr>`_
Principal developer and maintainer, Institut dAstrophysique de Paris (IAP).
License
-------
This software is distributed under the GPLv3 Licence. Please review the `LICENSE <https://github.com/hoellin/selfisys_public/blob/main/LICENSE>`_ file in the repository to understand the terms of use and ensure compliance. By downloading and using this software, you agree to the terms of the licence.
Requirements
------------
The code is written in Python 3.10 and depends on the following packages:
- `pySELFI <https://pyselfi.readthedocs.io/en/latest/>`_: Python implementation of the Simulator Expansion for Likelihood-Free Inference.
- `Simbelmynë <https://simbelmyne.readthedocs.io/en/latest/>`_: A hierarchical probabilistic simulator for generating synthetic galaxy survey data.
- `ELFI <https://elfi.readthedocs.io/en/latest/>`_: A statistical software package for likelihood-free inference, implementing Approximate Bayesian Computation (ABC) with a Population Monte Carlo (PMC) sampler.
A comprehensive list of dependencies, along with installation instructions, will be provided in a future release.
.. toctree::
:maxdepth: 2
:caption: API Documentation
selfisys.hiddenbox
selfisys.normalise_hb
selfisys.prior
selfisys.selection_functions
selfisys.selfi_interface
selfisys.sbmy_interface
selfisys.grf
selfisys.utils
.. toctree::
:maxdepth: 2
:caption: Contribute
../../CONTRIBUTING.md
.. toctree::
:maxdepth: 2
:caption: References
../../REFERENCES.md

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global_parameters
=================
.. automodule:: selfisys.global_parameters
:members:
:undoc-members:
:show-inheritance:

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grf
===
.. automodule:: selfisys.grf
:members:
:undoc-members:
:show-inheritance:

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hiddenbox
=========
.. automodule:: selfisys.hiddenbox
:members:
:undoc-members:
:show-inheritance:

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normalise_hb
============
.. automodule:: selfisys.normalise_hb
:members:
:undoc-members:
:show-inheritance:

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prior
=====
.. automodule:: selfisys.prior
:members:
:undoc-members:
:show-inheritance:

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selfisys package
================
Subpackages
-----------
.. toctree::
:maxdepth: 4
selfisys.utils
Submodules
----------
selfisys.global\_parameters module
----------------------------------
.. automodule:: selfisys.global_parameters
:members:
:undoc-members:
:show-inheritance:
selfisys.grf module
-------------------
.. automodule:: selfisys.grf
:members:
:undoc-members:
:show-inheritance:
selfisys.hiddenbox module
-------------------------
.. automodule:: selfisys.hiddenbox
:members:
:undoc-members:
:show-inheritance:
selfisys.normalise\_hb module
-----------------------------
.. automodule:: selfisys.normalise_hb
:members:
:undoc-members:
:show-inheritance:
selfisys.prior module
---------------------
.. automodule:: selfisys.prior
:members:
:undoc-members:
:show-inheritance:
selfisys.sbmy\_interface module
-------------------------------
.. automodule:: selfisys.sbmy_interface
:members:
:undoc-members:
:show-inheritance:
selfisys.selection\_functions module
------------------------------------
.. automodule:: selfisys.selection_functions
:members:
:undoc-members:
:show-inheritance:
selfisys.selfi\_interface module
--------------------------------
.. automodule:: selfisys.selfi_interface
:members:
:undoc-members:
:show-inheritance:
selfisys.setup\_model module
----------------------------
.. automodule:: selfisys.setup_model
:members:
:undoc-members:
:show-inheritance:
Module contents
---------------
.. automodule:: selfisys
:members:
:undoc-members:
:show-inheritance:

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sbmy_interface
==============
.. automodule:: selfisys.sbmy_interface
:members:
:undoc-members:
:show-inheritance:

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selection_functions
===================
.. automodule:: selfisys.selection_functions
:members:
:undoc-members:
:show-inheritance:

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selfi_interface
===============
.. automodule:: selfisys.selfi_interface
:members:
:undoc-members:
:show-inheritance:

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setup_model
===========
.. automodule:: selfisys.setup_model
:members:
:undoc-members:
:show-inheritance:

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selfisys.utils package
======================
Submodules
----------
selfisys.utils.examples\_utils module
-------------------------------------
.. automodule:: selfisys.utils.examples_utils
:members:
:undoc-members:
:show-inheritance:
selfisys.utils.logger module
----------------------------
.. automodule:: selfisys.utils.logger
:members:
:undoc-members:
:show-inheritance:
selfisys.utils.low\_level module
--------------------------------
.. automodule:: selfisys.utils.low_level
:members:
:undoc-members:
:show-inheritance:
selfisys.utils.parser module
----------------------------
.. automodule:: selfisys.utils.parser
:members:
:undoc-members:
:show-inheritance:
selfisys.utils.path\_utils module
---------------------------------
.. automodule:: selfisys.utils.path_utils
:members:
:undoc-members:
:show-inheritance:
selfisys.utils.plot\_examples module
------------------------------------
.. automodule:: selfisys.utils.plot_examples
:members:
:undoc-members:
:show-inheritance:
selfisys.utils.plot\_params module
----------------------------------
.. automodule:: selfisys.utils.plot_params
:members:
:undoc-members:
:show-inheritance:
selfisys.utils.plot\_utils module
---------------------------------
.. automodule:: selfisys.utils.plot_utils
:members:
:undoc-members:
:show-inheritance:
selfisys.utils.timestepping module
----------------------------------
.. automodule:: selfisys.utils.timestepping
:members:
:undoc-members:
:show-inheritance:
selfisys.utils.tools module
---------------------------
.. automodule:: selfisys.utils.tools
:members:
:undoc-members:
:show-inheritance:
selfisys.utils.workers module
-----------------------------
.. automodule:: selfisys.utils.workers
:members:
:undoc-members:
:show-inheritance:
Module contents
---------------
.. automodule:: selfisys.utils
:members:
:undoc-members:
:show-inheritance:

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/* Compatability shim for jQuery and underscores.js.
*
* Copyright Sphinx contributors
* Released under the two clause BSD licence
*/
/**
* small helper function to urldecode strings
*
* See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
*/
jQuery.urldecode = function(x) {
if (!x) {
return x
}
return decodeURIComponent(x.replace(/\+/g, ' '));
};
/**
* small helper function to urlencode strings
*/
jQuery.urlencode = encodeURIComponent;
/**
* This function returns the parsed url parameters of the
* current request. Multiple values per key are supported,
* it will always return arrays of strings for the value parts.
*/
jQuery.getQueryParameters = function(s) {
if (typeof s === 'undefined')
s = document.location.search;
var parts = s.substr(s.indexOf('?') + 1).split('&');
var result = {};
for (var i = 0; i < parts.length; i++) {
var tmp = parts[i].split('=', 2);
var key = jQuery.urldecode(tmp[0]);
var value = jQuery.urldecode(tmp[1]);
if (key in result)
result[key].push(value);
else
result[key] = [value];
}
return result;
};
/**
* highlight a given string on a jquery object by wrapping it in
* span elements with the given class name.
*/
jQuery.fn.highlightText = function(text, className) {
function highlight(node, addItems) {
if (node.nodeType === 3) {
var val = node.nodeValue;
var pos = val.toLowerCase().indexOf(text);
if (pos >= 0 &&
!jQuery(node.parentNode).hasClass(className) &&
!jQuery(node.parentNode).hasClass("nohighlight")) {
var span;
var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
if (isInSVG) {
span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
} else {
span = document.createElement("span");
span.className = className;
}
span.appendChild(document.createTextNode(val.substr(pos, text.length)));
node.parentNode.insertBefore(span, node.parentNode.insertBefore(
document.createTextNode(val.substr(pos + text.length)),
node.nextSibling));
node.nodeValue = val.substr(0, pos);
if (isInSVG) {
var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
var bbox = node.parentElement.getBBox();
rect.x.baseVal.value = bbox.x;
rect.y.baseVal.value = bbox.y;
rect.width.baseVal.value = bbox.width;
rect.height.baseVal.value = bbox.height;
rect.setAttribute('class', className);
addItems.push({
"parent": node.parentNode,
"target": rect});
}
}
}
else if (!jQuery(node).is("button, select, textarea")) {
jQuery.each(node.childNodes, function() {
highlight(this, addItems);
});
}
}
var addItems = [];
var result = this.each(function() {
highlight(this, addItems);
});
for (var i = 0; i < addItems.length; ++i) {
jQuery(addItems[i].parent).before(addItems[i].target);
}
return result;
};
/*
* backward compatibility for jQuery.browser
* This will be supported until firefox bug is fixed.
*/
if (!jQuery.browser) {
jQuery.uaMatch = function(ua) {
ua = ua.toLowerCase();
var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
/(webkit)[ \/]([\w.]+)/.exec(ua) ||
/(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
/(msie) ([\w.]+)/.exec(ua) ||
ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
[];
return {
browser: match[ 1 ] || "",
version: match[ 2 ] || "0"
};
};
jQuery.browser = {};
jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
}

914
docs/_static/basic.css vendored Normal file
View file

@ -0,0 +1,914 @@
/*
* Sphinx stylesheet -- basic theme.
*/
/* -- main layout ----------------------------------------------------------- */
div.clearer {
clear: both;
}
div.section::after {
display: block;
content: '';
clear: left;
}
/* -- relbar ---------------------------------------------------------------- */
div.related {
width: 100%;
font-size: 90%;
}
div.related h3 {
display: none;
}
div.related ul {
margin: 0;
padding: 0 0 0 10px;
list-style: none;
}
div.related li {
display: inline;
}
div.related li.right {
float: right;
margin-right: 5px;
}
/* -- sidebar --------------------------------------------------------------- */
div.sphinxsidebarwrapper {
padding: 10px 5px 0 10px;
}
div.sphinxsidebar {
float: left;
width: 230px;
margin-left: -100%;
font-size: 90%;
word-wrap: break-word;
overflow-wrap : break-word;
}
div.sphinxsidebar ul {
list-style: none;
}
div.sphinxsidebar ul ul,
div.sphinxsidebar ul.want-points {
margin-left: 20px;
list-style: square;
}
div.sphinxsidebar ul ul {
margin-top: 0;
margin-bottom: 0;
}
div.sphinxsidebar form {
margin-top: 10px;
}
div.sphinxsidebar input {
border: 1px solid #98dbcc;
font-family: sans-serif;
font-size: 1em;
}
div.sphinxsidebar #searchbox form.search {
overflow: hidden;
}
div.sphinxsidebar #searchbox input[type="text"] {
float: left;
width: 80%;
padding: 0.25em;
box-sizing: border-box;
}
div.sphinxsidebar #searchbox input[type="submit"] {
float: left;
width: 20%;
border-left: none;
padding: 0.25em;
box-sizing: border-box;
}
img {
border: 0;
max-width: 100%;
}
/* -- search page ----------------------------------------------------------- */
ul.search {
margin-top: 10px;
}
ul.search li {
padding: 5px 0;
}
ul.search li a {
font-weight: bold;
}
ul.search li p.context {
color: #888;
margin: 2px 0 0 30px;
text-align: left;
}
ul.keywordmatches li.goodmatch a {
font-weight: bold;
}
/* -- index page ------------------------------------------------------------ */
table.contentstable {
width: 90%;
margin-left: auto;
margin-right: auto;
}
table.contentstable p.biglink {
line-height: 150%;
}
a.biglink {
font-size: 1.3em;
}
span.linkdescr {
font-style: italic;
padding-top: 5px;
font-size: 90%;
}
/* -- general index --------------------------------------------------------- */
table.indextable {
width: 100%;
}
table.indextable td {
text-align: left;
vertical-align: top;
}
table.indextable ul {
margin-top: 0;
margin-bottom: 0;
list-style-type: none;
}
table.indextable > tbody > tr > td > ul {
padding-left: 0em;
}
table.indextable tr.pcap {
height: 10px;
}
table.indextable tr.cap {
margin-top: 10px;
background-color: #f2f2f2;
}
img.toggler {
margin-right: 3px;
margin-top: 3px;
cursor: pointer;
}
div.modindex-jumpbox {
border-top: 1px solid #ddd;
border-bottom: 1px solid #ddd;
margin: 1em 0 1em 0;
padding: 0.4em;
}
div.genindex-jumpbox {
border-top: 1px solid #ddd;
border-bottom: 1px solid #ddd;
margin: 1em 0 1em 0;
padding: 0.4em;
}
/* -- domain module index --------------------------------------------------- */
table.modindextable td {
padding: 2px;
border-collapse: collapse;
}
/* -- general body styles --------------------------------------------------- */
div.body {
min-width: 360px;
max-width: 800px;
}
div.body p, div.body dd, div.body li, div.body blockquote {
-moz-hyphens: auto;
-ms-hyphens: auto;
-webkit-hyphens: auto;
hyphens: auto;
}
a.headerlink {
visibility: hidden;
}
a:visited {
color: #551A8B;
}
h1:hover > a.headerlink,
h2:hover > a.headerlink,
h3:hover > a.headerlink,
h4:hover > a.headerlink,
h5:hover > a.headerlink,
h6:hover > a.headerlink,
dt:hover > a.headerlink,
caption:hover > a.headerlink,
p.caption:hover > a.headerlink,
div.code-block-caption:hover > a.headerlink {
visibility: visible;
}
div.body p.caption {
text-align: inherit;
}
div.body td {
text-align: left;
}
.first {
margin-top: 0 !important;
}
p.rubric {
margin-top: 30px;
font-weight: bold;
}
img.align-left, figure.align-left, .figure.align-left, object.align-left {
clear: left;
float: left;
margin-right: 1em;
}
img.align-right, figure.align-right, .figure.align-right, object.align-right {
clear: right;
float: right;
margin-left: 1em;
}
img.align-center, figure.align-center, .figure.align-center, object.align-center {
display: block;
margin-left: auto;
margin-right: auto;
}
img.align-default, figure.align-default, .figure.align-default {
display: block;
margin-left: auto;
margin-right: auto;
}
.align-left {
text-align: left;
}
.align-center {
text-align: center;
}
.align-default {
text-align: center;
}
.align-right {
text-align: right;
}
/* -- sidebars -------------------------------------------------------------- */
div.sidebar,
aside.sidebar {
margin: 0 0 0.5em 1em;
border: 1px solid #ddb;
padding: 7px;
background-color: #ffe;
width: 40%;
float: right;
clear: right;
overflow-x: auto;
}
p.sidebar-title {
font-weight: bold;
}
nav.contents,
aside.topic,
div.admonition, div.topic, blockquote {
clear: left;
}
/* -- topics ---------------------------------------------------------------- */
nav.contents,
aside.topic,
div.topic {
border: 1px solid #ccc;
padding: 7px;
margin: 10px 0 10px 0;
}
p.topic-title {
font-size: 1.1em;
font-weight: bold;
margin-top: 10px;
}
/* -- admonitions ----------------------------------------------------------- */
div.admonition {
margin-top: 10px;
margin-bottom: 10px;
padding: 7px;
}
div.admonition dt {
font-weight: bold;
}
p.admonition-title {
margin: 0px 10px 5px 0px;
font-weight: bold;
}
div.body p.centered {
text-align: center;
margin-top: 25px;
}
/* -- content of sidebars/topics/admonitions -------------------------------- */
div.sidebar > :last-child,
aside.sidebar > :last-child,
nav.contents > :last-child,
aside.topic > :last-child,
div.topic > :last-child,
div.admonition > :last-child {
margin-bottom: 0;
}
div.sidebar::after,
aside.sidebar::after,
nav.contents::after,
aside.topic::after,
div.topic::after,
div.admonition::after,
blockquote::after {
display: block;
content: '';
clear: both;
}
/* -- tables ---------------------------------------------------------------- */
table.docutils {
margin-top: 10px;
margin-bottom: 10px;
border: 0;
border-collapse: collapse;
}
table.align-center {
margin-left: auto;
margin-right: auto;
}
table.align-default {
margin-left: auto;
margin-right: auto;
}
table caption span.caption-number {
font-style: italic;
}
table caption span.caption-text {
}
table.docutils td, table.docutils th {
padding: 1px 8px 1px 5px;
border-top: 0;
border-left: 0;
border-right: 0;
border-bottom: 1px solid #aaa;
}
th {
text-align: left;
padding-right: 5px;
}
table.citation {
border-left: solid 1px gray;
margin-left: 1px;
}
table.citation td {
border-bottom: none;
}
th > :first-child,
td > :first-child {
margin-top: 0px;
}
th > :last-child,
td > :last-child {
margin-bottom: 0px;
}
/* -- figures --------------------------------------------------------------- */
div.figure, figure {
margin: 0.5em;
padding: 0.5em;
}
div.figure p.caption, figcaption {
padding: 0.3em;
}
div.figure p.caption span.caption-number,
figcaption span.caption-number {
font-style: italic;
}
div.figure p.caption span.caption-text,
figcaption span.caption-text {
}
/* -- field list styles ----------------------------------------------------- */
table.field-list td, table.field-list th {
border: 0 !important;
}
.field-list ul {
margin: 0;
padding-left: 1em;
}
.field-list p {
margin: 0;
}
.field-name {
-moz-hyphens: manual;
-ms-hyphens: manual;
-webkit-hyphens: manual;
hyphens: manual;
}
/* -- hlist styles ---------------------------------------------------------- */
table.hlist {
margin: 1em 0;
}
table.hlist td {
vertical-align: top;
}
/* -- object description styles --------------------------------------------- */
.sig {
font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace;
}
.sig-name, code.descname {
background-color: transparent;
font-weight: bold;
}
.sig-name {
font-size: 1.1em;
}
code.descname {
font-size: 1.2em;
}
.sig-prename, code.descclassname {
background-color: transparent;
}
.optional {
font-size: 1.3em;
}
.sig-paren {
font-size: larger;
}
.sig-param.n {
font-style: italic;
}
/* C++ specific styling */
.sig-inline.c-texpr,
.sig-inline.cpp-texpr {
font-family: unset;
}
.sig.c .k, .sig.c .kt,
.sig.cpp .k, .sig.cpp .kt {
color: #0033B3;
}
.sig.c .m,
.sig.cpp .m {
color: #1750EB;
}
.sig.c .s, .sig.c .sc,
.sig.cpp .s, .sig.cpp .sc {
color: #067D17;
}
/* -- other body styles ----------------------------------------------------- */
ol.arabic {
list-style: decimal;
}
ol.loweralpha {
list-style: lower-alpha;
}
ol.upperalpha {
list-style: upper-alpha;
}
ol.lowerroman {
list-style: lower-roman;
}
ol.upperroman {
list-style: upper-roman;
}
:not(li) > ol > li:first-child > :first-child,
:not(li) > ul > li:first-child > :first-child {
margin-top: 0px;
}
:not(li) > ol > li:last-child > :last-child,
:not(li) > ul > li:last-child > :last-child {
margin-bottom: 0px;
}
ol.simple ol p,
ol.simple ul p,
ul.simple ol p,
ul.simple ul p {
margin-top: 0;
}
ol.simple > li:not(:first-child) > p,
ul.simple > li:not(:first-child) > p {
margin-top: 0;
}
ol.simple p,
ul.simple p {
margin-bottom: 0;
}
aside.footnote > span,
div.citation > span {
float: left;
}
aside.footnote > span:last-of-type,
div.citation > span:last-of-type {
padding-right: 0.5em;
}
aside.footnote > p {
margin-left: 2em;
}
div.citation > p {
margin-left: 4em;
}
aside.footnote > p:last-of-type,
div.citation > p:last-of-type {
margin-bottom: 0em;
}
aside.footnote > p:last-of-type:after,
div.citation > p:last-of-type:after {
content: "";
clear: both;
}
dl.field-list {
display: grid;
grid-template-columns: fit-content(30%) auto;
}
dl.field-list > dt {
font-weight: bold;
word-break: break-word;
padding-left: 0.5em;
padding-right: 5px;
}
dl.field-list > dd {
padding-left: 0.5em;
margin-top: 0em;
margin-left: 0em;
margin-bottom: 0em;
}
dl {
margin-bottom: 15px;
}
dd > :first-child {
margin-top: 0px;
}
dd ul, dd table {
margin-bottom: 10px;
}
dd {
margin-top: 3px;
margin-bottom: 10px;
margin-left: 30px;
}
.sig dd {
margin-top: 0px;
margin-bottom: 0px;
}
.sig dl {
margin-top: 0px;
margin-bottom: 0px;
}
dl > dd:last-child,
dl > dd:last-child > :last-child {
margin-bottom: 0;
}
dt:target, span.highlighted {
background-color: #fbe54e;
}
rect.highlighted {
fill: #fbe54e;
}
dl.glossary dt {
font-weight: bold;
font-size: 1.1em;
}
.versionmodified {
font-style: italic;
}
.system-message {
background-color: #fda;
padding: 5px;
border: 3px solid red;
}
.footnote:target {
background-color: #ffa;
}
.line-block {
display: block;
margin-top: 1em;
margin-bottom: 1em;
}
.line-block .line-block {
margin-top: 0;
margin-bottom: 0;
margin-left: 1.5em;
}
.guilabel, .menuselection {
font-family: sans-serif;
}
.accelerator {
text-decoration: underline;
}
.classifier {
font-style: oblique;
}
.classifier:before {
font-style: normal;
margin: 0 0.5em;
content: ":";
display: inline-block;
}
abbr, acronym {
border-bottom: dotted 1px;
cursor: help;
}
.translated {
background-color: rgba(207, 255, 207, 0.2)
}
.untranslated {
background-color: rgba(255, 207, 207, 0.2)
}
/* -- code displays --------------------------------------------------------- */
pre {
overflow: auto;
overflow-y: hidden; /* fixes display issues on Chrome browsers */
}
pre, div[class*="highlight-"] {
clear: both;
}
span.pre {
-moz-hyphens: none;
-ms-hyphens: none;
-webkit-hyphens: none;
hyphens: none;
white-space: nowrap;
}
div[class*="highlight-"] {
margin: 1em 0;
}
td.linenos pre {
border: 0;
background-color: transparent;
color: #aaa;
}
table.highlighttable {
display: block;
}
table.highlighttable tbody {
display: block;
}
table.highlighttable tr {
display: flex;
}
table.highlighttable td {
margin: 0;
padding: 0;
}
table.highlighttable td.linenos {
padding-right: 0.5em;
}
table.highlighttable td.code {
flex: 1;
overflow: hidden;
}
.highlight .hll {
display: block;
}
div.highlight pre,
table.highlighttable pre {
margin: 0;
}
div.code-block-caption + div {
margin-top: 0;
}
div.code-block-caption {
margin-top: 1em;
padding: 2px 5px;
font-size: small;
}
div.code-block-caption code {
background-color: transparent;
}
table.highlighttable td.linenos,
span.linenos,
div.highlight span.gp { /* gp: Generic.Prompt */
user-select: none;
-webkit-user-select: text; /* Safari fallback only */
-webkit-user-select: none; /* Chrome/Safari */
-moz-user-select: none; /* Firefox */
-ms-user-select: none; /* IE10+ */
}
div.code-block-caption span.caption-number {
padding: 0.1em 0.3em;
font-style: italic;
}
div.code-block-caption span.caption-text {
}
div.literal-block-wrapper {
margin: 1em 0;
}
code.xref, a code {
background-color: transparent;
font-weight: bold;
}
h1 code, h2 code, h3 code, h4 code, h5 code, h6 code {
background-color: transparent;
}
.viewcode-link {
float: right;
}
.viewcode-back {
float: right;
font-family: sans-serif;
}
div.viewcode-block:target {
margin: -1px -10px;
padding: 0 10px;
}
/* -- math display ---------------------------------------------------------- */
img.math {
vertical-align: middle;
}
div.body div.math p {
text-align: center;
}
span.eqno {
float: right;
}
span.eqno a.headerlink {
position: absolute;
z-index: 1;
}
div.math:hover a.headerlink {
visibility: visible;
}
/* -- printout stylesheet --------------------------------------------------- */
@media print {
div.document,
div.documentwrapper,
div.bodywrapper {
margin: 0 !important;
width: 100%;
}
div.sphinxsidebar,
div.related,
div.footer,
#top-link {
display: none;
}
}

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docs/_static/css/badge_only.css vendored Normal file
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.clearfix{*zoom:1}.clearfix:after,.clearfix:before{display:table;content:""}.clearfix:after{clear:both}@font-face{font-family:FontAwesome;font-style:normal;font-weight:400;src:url(fonts/fontawesome-webfont.eot?674f50d287a8c48dc19ba404d20fe713?#iefix) format("embedded-opentype"),url(fonts/fontawesome-webfont.woff2?af7ae505a9eed503f8b8e6982036873e) format("woff2"),url(fonts/fontawesome-webfont.woff?fee66e712a8a08eef5805a46892932ad) format("woff"),url(fonts/fontawesome-webfont.ttf?b06871f281fee6b241d60582ae9369b9) format("truetype"),url(fonts/fontawesome-webfont.svg?912ec66d7572ff821749319396470bde#FontAwesome) format("svg")}.fa:before{font-family:FontAwesome;font-style:normal;font-weight:400;line-height:1}.fa:before,a .fa{text-decoration:inherit}.fa:before,a .fa,li .fa{display:inline-block}li .fa-large:before{width:1.875em}ul.fas{list-style-type:none;margin-left:2em;text-indent:-.8em}ul.fas li .fa{width:.8em}ul.fas li .fa-large:before{vertical-align:baseline}.fa-book:before,.icon-book:before{content:"\f02d"}.fa-caret-down:before,.icon-caret-down:before{content:"\f0d7"}.fa-caret-up:before,.icon-caret-up:before{content:"\f0d8"}.fa-caret-left:before,.icon-caret-left:before{content:"\f0d9"}.fa-caret-right:before,.icon-caret-right:before{content:"\f0da"}.rst-versions{position:fixed;bottom:0;left:0;width:300px;color:#fcfcfc;background:#1f1d1d;font-family:Lato,proxima-nova,Helvetica Neue,Arial,sans-serif;z-index:400}.rst-versions a{color:#2980b9;text-decoration:none}.rst-versions .rst-badge-small{display:none}.rst-versions .rst-current-version{padding:12px;background-color:#272525;display:block;text-align:right;font-size:90%;cursor:pointer;color:#27ae60}.rst-versions .rst-current-version:after{clear:both;content:"";display:block}.rst-versions .rst-current-version .fa{color:#fcfcfc}.rst-versions .rst-current-version .fa-book,.rst-versions .rst-current-version .icon-book{float:left}.rst-versions .rst-current-version.rst-out-of-date{background-color:#e74c3c;color:#fff}.rst-versions .rst-current-version.rst-active-old-version{background-color:#f1c40f;color:#000}.rst-versions.shift-up{height:auto;max-height:100%;overflow-y:scroll}.rst-versions.shift-up .rst-other-versions{display:block}.rst-versions .rst-other-versions{font-size:90%;padding:12px;color:grey;display:none}.rst-versions .rst-other-versions hr{display:block;height:1px;border:0;margin:20px 0;padding:0;border-top:1px solid #413d3d}.rst-versions .rst-other-versions dd{display:inline-block;margin:0}.rst-versions .rst-other-versions dd a{display:inline-block;padding:6px;color:#fcfcfc}.rst-versions .rst-other-versions .rtd-current-item{font-weight:700}.rst-versions.rst-badge{width:auto;bottom:20px;right:20px;left:auto;border:none;max-width:300px;max-height:90%}.rst-versions.rst-badge .fa-book,.rst-versions.rst-badge .icon-book{float:none;line-height:30px}.rst-versions.rst-badge.shift-up .rst-current-version{text-align:right}.rst-versions.rst-badge.shift-up .rst-current-version .fa-book,.rst-versions.rst-badge.shift-up .rst-current-version .icon-book{float:left}.rst-versions.rst-badge>.rst-current-version{width:auto;height:30px;line-height:30px;padding:0 6px;display:block;text-align:center}@media screen and (max-width:768px){.rst-versions{width:85%;display:none}.rst-versions.shift{display:block}}#flyout-search-form{padding:6px}

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/*
* Base JavaScript utilities for all Sphinx HTML documentation.
*/
"use strict";
const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([
"TEXTAREA",
"INPUT",
"SELECT",
"BUTTON",
]);
const _ready = (callback) => {
if (document.readyState !== "loading") {
callback();
} else {
document.addEventListener("DOMContentLoaded", callback);
}
};
/**
* Small JavaScript module for the documentation.
*/
const Documentation = {
init: () => {
Documentation.initDomainIndexTable();
Documentation.initOnKeyListeners();
},
/**
* i18n support
*/
TRANSLATIONS: {},
PLURAL_EXPR: (n) => (n === 1 ? 0 : 1),
LOCALE: "unknown",
// gettext and ngettext don't access this so that the functions
// can safely bound to a different name (_ = Documentation.gettext)
gettext: (string) => {
const translated = Documentation.TRANSLATIONS[string];
switch (typeof translated) {
case "undefined":
return string; // no translation
case "string":
return translated; // translation exists
default:
return translated[0]; // (singular, plural) translation tuple exists
}
},
ngettext: (singular, plural, n) => {
const translated = Documentation.TRANSLATIONS[singular];
if (typeof translated !== "undefined")
return translated[Documentation.PLURAL_EXPR(n)];
return n === 1 ? singular : plural;
},
addTranslations: (catalog) => {
Object.assign(Documentation.TRANSLATIONS, catalog.messages);
Documentation.PLURAL_EXPR = new Function(
"n",
`return (${catalog.plural_expr})`
);
Documentation.LOCALE = catalog.locale;
},
/**
* helper function to focus on search bar
*/
focusSearchBar: () => {
document.querySelectorAll("input[name=q]")[0]?.focus();
},
/**
* Initialise the domain index toggle buttons
*/
initDomainIndexTable: () => {
const toggler = (el) => {
const idNumber = el.id.substr(7);
const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`);
if (el.src.substr(-9) === "minus.png") {
el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`;
toggledRows.forEach((el) => (el.style.display = "none"));
} else {
el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`;
toggledRows.forEach((el) => (el.style.display = ""));
}
};
const togglerElements = document.querySelectorAll("img.toggler");
togglerElements.forEach((el) =>
el.addEventListener("click", (event) => toggler(event.currentTarget))
);
togglerElements.forEach((el) => (el.style.display = ""));
if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler);
},
initOnKeyListeners: () => {
// only install a listener if it is really needed
if (
!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS &&
!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS
)
return;
document.addEventListener("keydown", (event) => {
// bail for input elements
if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return;
// bail with special keys
if (event.altKey || event.ctrlKey || event.metaKey) return;
if (!event.shiftKey) {
switch (event.key) {
case "ArrowLeft":
if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break;
const prevLink = document.querySelector('link[rel="prev"]');
if (prevLink && prevLink.href) {
window.location.href = prevLink.href;
event.preventDefault();
}
break;
case "ArrowRight":
if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break;
const nextLink = document.querySelector('link[rel="next"]');
if (nextLink && nextLink.href) {
window.location.href = nextLink.href;
event.preventDefault();
}
break;
}
}
// some keyboard layouts may need Shift to get /
switch (event.key) {
case "/":
if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break;
Documentation.focusSearchBar();
event.preventDefault();
}
});
},
};
// quick alias for translations
const _ = Documentation.gettext;
_ready(Documentation.init);

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const DOCUMENTATION_OPTIONS = {
VERSION: '/Users/hoellinger/Library/CloudStorage/Dropbox/travail/these/science/code/SELFI/selfisys/src/',
LANGUAGE: 'en',
COLLAPSE_INDEX: false,
BUILDER: 'html',
FILE_SUFFIX: '.html',
LINK_SUFFIX: '.html',
HAS_SOURCE: true,
SOURCELINK_SUFFIX: '.txt',
NAVIGATION_WITH_KEYS: false,
SHOW_SEARCH_SUMMARY: true,
ENABLE_SEARCH_SHORTCUTS: true,
};

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!function(e){var t={};function r(n){if(t[n])return t[n].exports;var o=t[n]={i:n,l:!1,exports:{}};return e[n].call(o.exports,o,o.exports,r),o.l=!0,o.exports}r.m=e,r.c=t,r.d=function(e,t,n){r.o(e,t)||Object.defineProperty(e,t,{enumerable:!0,get:n})},r.r=function(e){"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(e,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(e,"__esModule",{value:!0})},r.t=function(e,t){if(1&t&&(e=r(e)),8&t)return e;if(4&t&&"object"==typeof e&&e&&e.__esModule)return e;var n=Object.create(null);if(r.r(n),Object.defineProperty(n,"default",{enumerable:!0,value:e}),2&t&&"string"!=typeof e)for(var o in e)r.d(n,o,function(t){return e[t]}.bind(null,o));return n},r.n=function(e){var t=e&&e.__esModule?function(){return e.default}:function(){return e};return r.d(t,"a",t),t},r.o=function(e,t){return Object.prototype.hasOwnProperty.call(e,t)},r.p="",r(r.s=4)}({4:function(e,t,r){}});

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const themeFlyoutDisplay = "hidden";
const themeVersionSelector = true;
const themeLanguageSelector = true;
if (themeFlyoutDisplay === "attached") {
function renderLanguages(config) {
if (!config.projects.translations.length) {
return "";
}
// Insert the current language to the options on the selector
let languages = config.projects.translations.concat(config.projects.current);
languages = languages.sort((a, b) => a.language.name.localeCompare(b.language.name));
const languagesHTML = `
<dl>
<dt>Languages</dt>
${languages
.map(
(translation) => `
<dd ${translation.slug == config.projects.current.slug ? 'class="rtd-current-item"' : ""}>
<a href="${translation.urls.documentation}">${translation.language.code}</a>
</dd>
`,
)
.join("\n")}
</dl>
`;
return languagesHTML;
}
function renderVersions(config) {
if (!config.versions.active.length) {
return "";
}
const versionsHTML = `
<dl>
<dt>Versions</dt>
${config.versions.active
.map(
(version) => `
<dd ${version.slug === config.versions.current.slug ? 'class="rtd-current-item"' : ""}>
<a href="${version.urls.documentation}">${version.slug}</a>
</dd>
`,
)
.join("\n")}
</dl>
`;
return versionsHTML;
}
function renderDownloads(config) {
if (!Object.keys(config.versions.current.downloads).length) {
return "";
}
const downloadsNameDisplay = {
pdf: "PDF",
epub: "Epub",
htmlzip: "HTML",
};
const downloadsHTML = `
<dl>
<dt>Downloads</dt>
${Object.entries(config.versions.current.downloads)
.map(
([name, url]) => `
<dd>
<a href="${url}">${downloadsNameDisplay[name]}</a>
</dd>
`,
)
.join("\n")}
</dl>
`;
return downloadsHTML;
}
document.addEventListener("readthedocs-addons-data-ready", function (event) {
const config = event.detail.data();
const flyout = `
<div class="rst-versions" data-toggle="rst-versions" role="note">
<span class="rst-current-version" data-toggle="rst-current-version">
<span class="fa fa-book"> Read the Docs</span>
v: ${config.versions.current.slug}
<span class="fa fa-caret-down"></span>
</span>
<div class="rst-other-versions">
<div class="injected">
${renderLanguages(config)}
${renderVersions(config)}
${renderDownloads(config)}
<dl>
<dt>On Read the Docs</dt>
<dd>
<a href="${config.projects.current.urls.home}">Project Home</a>
</dd>
<dd>
<a href="${config.projects.current.urls.builds}">Builds</a>
</dd>
<dd>
<a href="${config.projects.current.urls.downloads}">Downloads</a>
</dd>
</dl>
<dl>
<dt>Search</dt>
<dd>
<form id="flyout-search-form">
<input
class="wy-form"
type="text"
name="q"
aria-label="Search docs"
placeholder="Search docs"
/>
</form>
</dd>
</dl>
<hr />
<small>
<span>Hosted by <a href="https://about.readthedocs.org/?utm_source=&utm_content=flyout">Read the Docs</a></span>
</small>
</div>
</div>
`;
// Inject the generated flyout into the body HTML element.
document.body.insertAdjacentHTML("beforeend", flyout);
// Trigger the Read the Docs Addons Search modal when clicking on the "Search docs" input from inside the flyout.
document
.querySelector("#flyout-search-form")
.addEventListener("focusin", () => {
const event = new CustomEvent("readthedocs-search-show");
document.dispatchEvent(event);
});
})
}
if (themeLanguageSelector || themeVersionSelector) {
function onSelectorSwitch(event) {
const option = event.target.selectedIndex;
const item = event.target.options[option];
window.location.href = item.dataset.url;
}
document.addEventListener("readthedocs-addons-data-ready", function (event) {
const config = event.detail.data();
const versionSwitch = document.querySelector(
"div.switch-menus > div.version-switch",
);
if (themeVersionSelector) {
let versions = config.versions.active;
if (config.versions.current.hidden || config.versions.current.type === "external") {
versions.unshift(config.versions.current);
}
const versionSelect = `
<select>
${versions
.map(
(version) => `
<option
value="${version.slug}"
${config.versions.current.slug === version.slug ? 'selected="selected"' : ""}
data-url="${version.urls.documentation}">
${version.slug}
</option>`,
)
.join("\n")}
</select>
`;
versionSwitch.innerHTML = versionSelect;
versionSwitch.firstElementChild.addEventListener("change", onSelectorSwitch);
}
const languageSwitch = document.querySelector(
"div.switch-menus > div.language-switch",
);
if (themeLanguageSelector) {
if (config.projects.translations.length) {
// Add the current language to the options on the selector
let languages = config.projects.translations.concat(
config.projects.current,
);
languages = languages.sort((a, b) =>
a.language.name.localeCompare(b.language.name),
);
const languageSelect = `
<select>
${languages
.map(
(language) => `
<option
value="${language.language.code}"
${config.projects.current.slug === language.slug ? 'selected="selected"' : ""}
data-url="${language.urls.documentation}">
${language.language.name}
</option>`,
)
.join("\n")}
</select>
`;
languageSwitch.innerHTML = languageSelect;
languageSwitch.firstElementChild.addEventListener("change", onSelectorSwitch);
}
else {
languageSwitch.remove();
}
}
});
}
document.addEventListener("readthedocs-addons-data-ready", function (event) {
// Trigger the Read the Docs Addons Search modal when clicking on "Search docs" input from the topnav.
document
.querySelector("[role='search'] input")
.addEventListener("focusin", () => {
const event = new CustomEvent("readthedocs-search-show");
document.dispatchEvent(event);
});
});

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/*
* This script contains the language-specific data used by searchtools.js,
* namely the list of stopwords, stemmer, scorer and splitter.
*/
var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
/* Non-minified version is copied as a separate JS file, if available */
/**
* Porter Stemmer
*/
var Stemmer = function() {
var step2list = {
ational: 'ate',
tional: 'tion',
enci: 'ence',
anci: 'ance',
izer: 'ize',
bli: 'ble',
alli: 'al',
entli: 'ent',
eli: 'e',
ousli: 'ous',
ization: 'ize',
ation: 'ate',
ator: 'ate',
alism: 'al',
iveness: 'ive',
fulness: 'ful',
ousness: 'ous',
aliti: 'al',
iviti: 'ive',
biliti: 'ble',
logi: 'log'
};
var step3list = {
icate: 'ic',
ative: '',
alize: 'al',
iciti: 'ic',
ical: 'ic',
ful: '',
ness: ''
};
var c = "[^aeiou]"; // consonant
var v = "[aeiouy]"; // vowel
var C = c + "[^aeiouy]*"; // consonant sequence
var V = v + "[aeiou]*"; // vowel sequence
var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0
var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1
var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1
var s_v = "^(" + C + ")?" + v; // vowel in stem
this.stemWord = function (w) {
var stem;
var suffix;
var firstch;
var origword = w;
if (w.length < 3)
return w;
var re;
var re2;
var re3;
var re4;
firstch = w.substr(0,1);
if (firstch == "y")
w = firstch.toUpperCase() + w.substr(1);
// Step 1a
re = /^(.+?)(ss|i)es$/;
re2 = /^(.+?)([^s])s$/;
if (re.test(w))
w = w.replace(re,"$1$2");
else if (re2.test(w))
w = w.replace(re2,"$1$2");
// Step 1b
re = /^(.+?)eed$/;
re2 = /^(.+?)(ed|ing)$/;
if (re.test(w)) {
var fp = re.exec(w);
re = new RegExp(mgr0);
if (re.test(fp[1])) {
re = /.$/;
w = w.replace(re,"");
}
}
else if (re2.test(w)) {
var fp = re2.exec(w);
stem = fp[1];
re2 = new RegExp(s_v);
if (re2.test(stem)) {
w = stem;
re2 = /(at|bl|iz)$/;
re3 = new RegExp("([^aeiouylsz])\\1$");
re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
if (re2.test(w))
w = w + "e";
else if (re3.test(w)) {
re = /.$/;
w = w.replace(re,"");
}
else if (re4.test(w))
w = w + "e";
}
}
// Step 1c
re = /^(.+?)y$/;
if (re.test(w)) {
var fp = re.exec(w);
stem = fp[1];
re = new RegExp(s_v);
if (re.test(stem))
w = stem + "i";
}
// Step 2
re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
if (re.test(w)) {
var fp = re.exec(w);
stem = fp[1];
suffix = fp[2];
re = new RegExp(mgr0);
if (re.test(stem))
w = stem + step2list[suffix];
}
// Step 3
re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
if (re.test(w)) {
var fp = re.exec(w);
stem = fp[1];
suffix = fp[2];
re = new RegExp(mgr0);
if (re.test(stem))
w = stem + step3list[suffix];
}
// Step 4
re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
re2 = /^(.+?)(s|t)(ion)$/;
if (re.test(w)) {
var fp = re.exec(w);
stem = fp[1];
re = new RegExp(mgr1);
if (re.test(stem))
w = stem;
}
else if (re2.test(w)) {
var fp = re2.exec(w);
stem = fp[1] + fp[2];
re2 = new RegExp(mgr1);
if (re2.test(stem))
w = stem;
}
// Step 5
re = /^(.+?)e$/;
if (re.test(w)) {
var fp = re.exec(w);
stem = fp[1];
re = new RegExp(mgr1);
re2 = new RegExp(meq1);
re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
w = stem;
}
re = /ll$/;
re2 = new RegExp(mgr1);
if (re.test(w) && re2.test(w)) {
re = /.$/;
w = w.replace(re,"");
}
// and turn initial Y back to y
if (firstch == "y")
w = firstch.toLowerCase() + w.substr(1);
return w;
}
}

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pre { line-height: 125%; }
td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
.highlight .hll { background-color: #ffffcc }
.highlight { background: #f8f8f8; }
.highlight .c { color: #3D7B7B; font-style: italic } /* Comment */
.highlight .err { border: 1px solid #FF0000 } /* Error */
.highlight .k { color: #008000; font-weight: bold } /* Keyword */
.highlight .o { color: #666666 } /* Operator */
.highlight .ch { color: #3D7B7B; font-style: italic } /* Comment.Hashbang */
.highlight .cm { color: #3D7B7B; font-style: italic } /* Comment.Multiline */
.highlight .cp { color: #9C6500 } /* Comment.Preproc */
.highlight .cpf { color: #3D7B7B; font-style: italic } /* Comment.PreprocFile */
.highlight .c1 { color: #3D7B7B; font-style: italic } /* Comment.Single */
.highlight .cs { color: #3D7B7B; font-style: italic } /* Comment.Special */
.highlight .gd { color: #A00000 } /* Generic.Deleted */
.highlight .ge { font-style: italic } /* Generic.Emph */
.highlight .ges { font-weight: bold; font-style: italic } /* Generic.EmphStrong */
.highlight .gr { color: #E40000 } /* Generic.Error */
.highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
.highlight .gi { color: #008400 } /* Generic.Inserted */
.highlight .go { color: #717171 } /* Generic.Output */
.highlight .gp { color: #000080; font-weight: bold } /* Generic.Prompt */
.highlight .gs { font-weight: bold } /* Generic.Strong */
.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
.highlight .gt { color: #0044DD } /* Generic.Traceback */
.highlight .kc { color: #008000; font-weight: bold } /* Keyword.Constant */
.highlight .kd { color: #008000; font-weight: bold } /* Keyword.Declaration */
.highlight .kn { color: #008000; font-weight: bold } /* Keyword.Namespace */
.highlight .kp { color: #008000 } /* Keyword.Pseudo */
.highlight .kr { color: #008000; font-weight: bold } /* Keyword.Reserved */
.highlight .kt { color: #B00040 } /* Keyword.Type */
.highlight .m { color: #666666 } /* Literal.Number */
.highlight .s { color: #BA2121 } /* Literal.String */
.highlight .na { color: #687822 } /* Name.Attribute */
.highlight .nb { color: #008000 } /* Name.Builtin */
.highlight .nc { color: #0000FF; font-weight: bold } /* Name.Class */
.highlight .no { color: #880000 } /* Name.Constant */
.highlight .nd { color: #AA22FF } /* Name.Decorator */
.highlight .ni { color: #717171; font-weight: bold } /* Name.Entity */
.highlight .ne { color: #CB3F38; font-weight: bold } /* Name.Exception */
.highlight .nf { color: #0000FF } /* Name.Function */
.highlight .nl { color: #767600 } /* Name.Label */
.highlight .nn { color: #0000FF; font-weight: bold } /* Name.Namespace */
.highlight .nt { color: #008000; font-weight: bold } /* Name.Tag */
.highlight .nv { color: #19177C } /* Name.Variable */
.highlight .ow { color: #AA22FF; font-weight: bold } /* Operator.Word */
.highlight .w { color: #bbbbbb } /* Text.Whitespace */
.highlight .mb { color: #666666 } /* Literal.Number.Bin */
.highlight .mf { color: #666666 } /* Literal.Number.Float */
.highlight .mh { color: #666666 } /* Literal.Number.Hex */
.highlight .mi { color: #666666 } /* Literal.Number.Integer */
.highlight .mo { color: #666666 } /* Literal.Number.Oct */
.highlight .sa { color: #BA2121 } /* Literal.String.Affix */
.highlight .sb { color: #BA2121 } /* Literal.String.Backtick */
.highlight .sc { color: #BA2121 } /* Literal.String.Char */
.highlight .dl { color: #BA2121 } /* Literal.String.Delimiter */
.highlight .sd { color: #BA2121; font-style: italic } /* Literal.String.Doc */
.highlight .s2 { color: #BA2121 } /* Literal.String.Double */
.highlight .se { color: #AA5D1F; font-weight: bold } /* Literal.String.Escape */
.highlight .sh { color: #BA2121 } /* Literal.String.Heredoc */
.highlight .si { color: #A45A77; font-weight: bold } /* Literal.String.Interpol */
.highlight .sx { color: #008000 } /* Literal.String.Other */
.highlight .sr { color: #A45A77 } /* Literal.String.Regex */
.highlight .s1 { color: #BA2121 } /* Literal.String.Single */
.highlight .ss { color: #19177C } /* Literal.String.Symbol */
.highlight .bp { color: #008000 } /* Name.Builtin.Pseudo */
.highlight .fm { color: #0000FF } /* Name.Function.Magic */
.highlight .vc { color: #19177C } /* Name.Variable.Class */
.highlight .vg { color: #19177C } /* Name.Variable.Global */
.highlight .vi { color: #19177C } /* Name.Variable.Instance */
.highlight .vm { color: #19177C } /* Name.Variable.Magic */
.highlight .il { color: #666666 } /* Literal.Number.Integer.Long */

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/*
* Sphinx JavaScript utilities for the full-text search.
*/
"use strict";
/**
* Simple result scoring code.
*/
if (typeof Scorer === "undefined") {
var Scorer = {
// Implement the following function to further tweak the score for each result
// The function takes a result array [docname, title, anchor, descr, score, filename]
// and returns the new score.
/*
score: result => {
const [docname, title, anchor, descr, score, filename, kind] = result
return score
},
*/
// query matches the full name of an object
objNameMatch: 11,
// or matches in the last dotted part of the object name
objPartialMatch: 6,
// Additive scores depending on the priority of the object
objPrio: {
0: 15, // used to be importantResults
1: 5, // used to be objectResults
2: -5, // used to be unimportantResults
},
// Used when the priority is not in the mapping.
objPrioDefault: 0,
// query found in title
title: 15,
partialTitle: 7,
// query found in terms
term: 5,
partialTerm: 2,
};
}
// Global search result kind enum, used by themes to style search results.
class SearchResultKind {
static get index() { return "index"; }
static get object() { return "object"; }
static get text() { return "text"; }
static get title() { return "title"; }
}
const _removeChildren = (element) => {
while (element && element.lastChild) element.removeChild(element.lastChild);
};
/**
* See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping
*/
const _escapeRegExp = (string) =>
string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
const _displayItem = (item, searchTerms, highlightTerms) => {
const docBuilder = DOCUMENTATION_OPTIONS.BUILDER;
const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
const contentRoot = document.documentElement.dataset.content_root;
const [docName, title, anchor, descr, score, _filename, kind] = item;
let listItem = document.createElement("li");
// Add a class representing the item's type:
// can be used by a theme's CSS selector for styling
// See SearchResultKind for the class names.
listItem.classList.add(`kind-${kind}`);
let requestUrl;
let linkUrl;
if (docBuilder === "dirhtml") {
// dirhtml builder
let dirname = docName + "/";
if (dirname.match(/\/index\/$/))
dirname = dirname.substring(0, dirname.length - 6);
else if (dirname === "index/") dirname = "";
requestUrl = contentRoot + dirname;
linkUrl = requestUrl;
} else {
// normal html builders
requestUrl = contentRoot + docName + docFileSuffix;
linkUrl = docName + docLinkSuffix;
}
let linkEl = listItem.appendChild(document.createElement("a"));
linkEl.href = linkUrl + anchor;
linkEl.dataset.score = score;
linkEl.innerHTML = title;
if (descr) {
listItem.appendChild(document.createElement("span")).innerHTML =
" (" + descr + ")";
// highlight search terms in the description
if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js
highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
}
else if (showSearchSummary)
fetch(requestUrl)
.then((responseData) => responseData.text())
.then((data) => {
if (data)
listItem.appendChild(
Search.makeSearchSummary(data, searchTerms, anchor)
);
// highlight search terms in the summary
if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js
highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
});
Search.output.appendChild(listItem);
};
const _finishSearch = (resultCount) => {
Search.stopPulse();
Search.title.innerText = _("Search Results");
if (!resultCount)
Search.status.innerText = Documentation.gettext(
"Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories."
);
else
Search.status.innerText = Documentation.ngettext(
"Search finished, found one page matching the search query.",
"Search finished, found ${resultCount} pages matching the search query.",
resultCount,
).replace('${resultCount}', resultCount);
};
const _displayNextItem = (
results,
resultCount,
searchTerms,
highlightTerms,
) => {
// results left, load the summary and display it
// this is intended to be dynamic (don't sub resultsCount)
if (results.length) {
_displayItem(results.pop(), searchTerms, highlightTerms);
setTimeout(
() => _displayNextItem(results, resultCount, searchTerms, highlightTerms),
5
);
}
// search finished, update title and status message
else _finishSearch(resultCount);
};
// Helper function used by query() to order search results.
// Each input is an array of [docname, title, anchor, descr, score, filename, kind].
// Order the results by score (in opposite order of appearance, since the
// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically.
const _orderResultsByScoreThenName = (a, b) => {
const leftScore = a[4];
const rightScore = b[4];
if (leftScore === rightScore) {
// same score: sort alphabetically
const leftTitle = a[1].toLowerCase();
const rightTitle = b[1].toLowerCase();
if (leftTitle === rightTitle) return 0;
return leftTitle > rightTitle ? -1 : 1; // inverted is intentional
}
return leftScore > rightScore ? 1 : -1;
};
/**
* Default splitQuery function. Can be overridden in ``sphinx.search`` with a
* custom function per language.
*
* The regular expression works by splitting the string on consecutive characters
* that are not Unicode letters, numbers, underscores, or emoji characters.
* This is the same as ``\W+`` in Python, preserving the surrogate pair area.
*/
if (typeof splitQuery === "undefined") {
var splitQuery = (query) => query
.split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu)
.filter(term => term) // remove remaining empty strings
}
/**
* Search Module
*/
const Search = {
_index: null,
_queued_query: null,
_pulse_status: -1,
htmlToText: (htmlString, anchor) => {
const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html');
for (const removalQuery of [".headerlink", "script", "style"]) {
htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() });
}
if (anchor) {
const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`);
if (anchorContent) return anchorContent.textContent;
console.warn(
`Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.`
);
}
// if anchor not specified or not found, fall back to main content
const docContent = htmlElement.querySelector('[role="main"]');
if (docContent) return docContent.textContent;
console.warn(
"Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template."
);
return "";
},
init: () => {
const query = new URLSearchParams(window.location.search).get("q");
document
.querySelectorAll('input[name="q"]')
.forEach((el) => (el.value = query));
if (query) Search.performSearch(query);
},
loadIndex: (url) =>
(document.body.appendChild(document.createElement("script")).src = url),
setIndex: (index) => {
Search._index = index;
if (Search._queued_query !== null) {
const query = Search._queued_query;
Search._queued_query = null;
Search.query(query);
}
},
hasIndex: () => Search._index !== null,
deferQuery: (query) => (Search._queued_query = query),
stopPulse: () => (Search._pulse_status = -1),
startPulse: () => {
if (Search._pulse_status >= 0) return;
const pulse = () => {
Search._pulse_status = (Search._pulse_status + 1) % 4;
Search.dots.innerText = ".".repeat(Search._pulse_status);
if (Search._pulse_status >= 0) window.setTimeout(pulse, 500);
};
pulse();
},
/**
* perform a search for something (or wait until index is loaded)
*/
performSearch: (query) => {
// create the required interface elements
const searchText = document.createElement("h2");
searchText.textContent = _("Searching");
const searchSummary = document.createElement("p");
searchSummary.classList.add("search-summary");
searchSummary.innerText = "";
const searchList = document.createElement("ul");
searchList.setAttribute("role", "list");
searchList.classList.add("search");
const out = document.getElementById("search-results");
Search.title = out.appendChild(searchText);
Search.dots = Search.title.appendChild(document.createElement("span"));
Search.status = out.appendChild(searchSummary);
Search.output = out.appendChild(searchList);
const searchProgress = document.getElementById("search-progress");
// Some themes don't use the search progress node
if (searchProgress) {
searchProgress.innerText = _("Preparing search...");
}
Search.startPulse();
// index already loaded, the browser was quick!
if (Search.hasIndex()) Search.query(query);
else Search.deferQuery(query);
},
_parseQuery: (query) => {
// stem the search terms and add them to the correct list
const stemmer = new Stemmer();
const searchTerms = new Set();
const excludedTerms = new Set();
const highlightTerms = new Set();
const objectTerms = new Set(splitQuery(query.toLowerCase().trim()));
splitQuery(query.trim()).forEach((queryTerm) => {
const queryTermLower = queryTerm.toLowerCase();
// maybe skip this "word"
// stopwords array is from language_data.js
if (
stopwords.indexOf(queryTermLower) !== -1 ||
queryTerm.match(/^\d+$/)
)
return;
// stem the word
let word = stemmer.stemWord(queryTermLower);
// select the correct list
if (word[0] === "-") excludedTerms.add(word.substr(1));
else {
searchTerms.add(word);
highlightTerms.add(queryTermLower);
}
});
if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js
localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" "))
}
// console.debug("SEARCH: searching for:");
// console.info("required: ", [...searchTerms]);
// console.info("excluded: ", [...excludedTerms]);
return [query, searchTerms, excludedTerms, highlightTerms, objectTerms];
},
/**
* execute search (requires search index to be loaded)
*/
_performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => {
const filenames = Search._index.filenames;
const docNames = Search._index.docnames;
const titles = Search._index.titles;
const allTitles = Search._index.alltitles;
const indexEntries = Search._index.indexentries;
// Collect multiple result groups to be sorted separately and then ordered.
// Each is an array of [docname, title, anchor, descr, score, filename, kind].
const normalResults = [];
const nonMainIndexResults = [];
_removeChildren(document.getElementById("search-progress"));
const queryLower = query.toLowerCase().trim();
for (const [title, foundTitles] of Object.entries(allTitles)) {
if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) {
for (const [file, id] of foundTitles) {
const score = Math.round(Scorer.title * queryLower.length / title.length);
const boost = titles[file] === title ? 1 : 0; // add a boost for document titles
normalResults.push([
docNames[file],
titles[file] !== title ? `${titles[file]} > ${title}` : title,
id !== null ? "#" + id : "",
null,
score + boost,
filenames[file],
SearchResultKind.title,
]);
}
}
}
// search for explicit entries in index directives
for (const [entry, foundEntries] of Object.entries(indexEntries)) {
if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) {
for (const [file, id, isMain] of foundEntries) {
const score = Math.round(100 * queryLower.length / entry.length);
const result = [
docNames[file],
titles[file],
id ? "#" + id : "",
null,
score,
filenames[file],
SearchResultKind.index,
];
if (isMain) {
normalResults.push(result);
} else {
nonMainIndexResults.push(result);
}
}
}
}
// lookup as object
objectTerms.forEach((term) =>
normalResults.push(...Search.performObjectSearch(term, objectTerms))
);
// lookup as search terms in fulltext
normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms));
// let the scorer override scores with a custom scoring function
if (Scorer.score) {
normalResults.forEach((item) => (item[4] = Scorer.score(item)));
nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item)));
}
// Sort each group of results by score and then alphabetically by name.
normalResults.sort(_orderResultsByScoreThenName);
nonMainIndexResults.sort(_orderResultsByScoreThenName);
// Combine the result groups in (reverse) order.
// Non-main index entries are typically arbitrary cross-references,
// so display them after other results.
let results = [...nonMainIndexResults, ...normalResults];
// remove duplicate search results
// note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept
let seen = new Set();
results = results.reverse().reduce((acc, result) => {
let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(',');
if (!seen.has(resultStr)) {
acc.push(result);
seen.add(resultStr);
}
return acc;
}, []);
return results.reverse();
},
query: (query) => {
const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query);
const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms);
// for debugging
//Search.lastresults = results.slice(); // a copy
// console.info("search results:", Search.lastresults);
// print the results
_displayNextItem(results, results.length, searchTerms, highlightTerms);
},
/**
* search for object names
*/
performObjectSearch: (object, objectTerms) => {
const filenames = Search._index.filenames;
const docNames = Search._index.docnames;
const objects = Search._index.objects;
const objNames = Search._index.objnames;
const titles = Search._index.titles;
const results = [];
const objectSearchCallback = (prefix, match) => {
const name = match[4]
const fullname = (prefix ? prefix + "." : "") + name;
const fullnameLower = fullname.toLowerCase();
if (fullnameLower.indexOf(object) < 0) return;
let score = 0;
const parts = fullnameLower.split(".");
// check for different match types: exact matches of full name or
// "last name" (i.e. last dotted part)
if (fullnameLower === object || parts.slice(-1)[0] === object)
score += Scorer.objNameMatch;
else if (parts.slice(-1)[0].indexOf(object) > -1)
score += Scorer.objPartialMatch; // matches in last name
const objName = objNames[match[1]][2];
const title = titles[match[0]];
// If more than one term searched for, we require other words to be
// found in the name/title/description
const otherTerms = new Set(objectTerms);
otherTerms.delete(object);
if (otherTerms.size > 0) {
const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase();
if (
[...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0)
)
return;
}
let anchor = match[3];
if (anchor === "") anchor = fullname;
else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname;
const descr = objName + _(", in ") + title;
// add custom score for some objects according to scorer
if (Scorer.objPrio.hasOwnProperty(match[2]))
score += Scorer.objPrio[match[2]];
else score += Scorer.objPrioDefault;
results.push([
docNames[match[0]],
fullname,
"#" + anchor,
descr,
score,
filenames[match[0]],
SearchResultKind.object,
]);
};
Object.keys(objects).forEach((prefix) =>
objects[prefix].forEach((array) =>
objectSearchCallback(prefix, array)
)
);
return results;
},
/**
* search for full-text terms in the index
*/
performTermsSearch: (searchTerms, excludedTerms) => {
// prepare search
const terms = Search._index.terms;
const titleTerms = Search._index.titleterms;
const filenames = Search._index.filenames;
const docNames = Search._index.docnames;
const titles = Search._index.titles;
const scoreMap = new Map();
const fileMap = new Map();
// perform the search on the required terms
searchTerms.forEach((word) => {
const files = [];
const arr = [
{ files: terms[word], score: Scorer.term },
{ files: titleTerms[word], score: Scorer.title },
];
// add support for partial matches
if (word.length > 2) {
const escapedWord = _escapeRegExp(word);
if (!terms.hasOwnProperty(word)) {
Object.keys(terms).forEach((term) => {
if (term.match(escapedWord))
arr.push({ files: terms[term], score: Scorer.partialTerm });
});
}
if (!titleTerms.hasOwnProperty(word)) {
Object.keys(titleTerms).forEach((term) => {
if (term.match(escapedWord))
arr.push({ files: titleTerms[term], score: Scorer.partialTitle });
});
}
}
// no match but word was a required one
if (arr.every((record) => record.files === undefined)) return;
// found search word in contents
arr.forEach((record) => {
if (record.files === undefined) return;
let recordFiles = record.files;
if (recordFiles.length === undefined) recordFiles = [recordFiles];
files.push(...recordFiles);
// set score for the word in each file
recordFiles.forEach((file) => {
if (!scoreMap.has(file)) scoreMap.set(file, {});
scoreMap.get(file)[word] = record.score;
});
});
// create the mapping
files.forEach((file) => {
if (!fileMap.has(file)) fileMap.set(file, [word]);
else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word);
});
});
// now check if the files don't contain excluded terms
const results = [];
for (const [file, wordList] of fileMap) {
// check if all requirements are matched
// as search terms with length < 3 are discarded
const filteredTermCount = [...searchTerms].filter(
(term) => term.length > 2
).length;
if (
wordList.length !== searchTerms.size &&
wordList.length !== filteredTermCount
)
continue;
// ensure that none of the excluded terms is in the search result
if (
[...excludedTerms].some(
(term) =>
terms[term] === file ||
titleTerms[term] === file ||
(terms[term] || []).includes(file) ||
(titleTerms[term] || []).includes(file)
)
)
break;
// select one (max) score for the file.
const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w]));
// add result to the result list
results.push([
docNames[file],
titles[file],
"",
null,
score,
filenames[file],
SearchResultKind.text,
]);
}
return results;
},
/**
* helper function to return a node containing the
* search summary for a given text. keywords is a list
* of stemmed words.
*/
makeSearchSummary: (htmlText, keywords, anchor) => {
const text = Search.htmlToText(htmlText, anchor);
if (text === "") return null;
const textLower = text.toLowerCase();
const actualStartPosition = [...keywords]
.map((k) => textLower.indexOf(k.toLowerCase()))
.filter((i) => i > -1)
.slice(-1)[0];
const startWithContext = Math.max(actualStartPosition - 120, 0);
const top = startWithContext === 0 ? "" : "...";
const tail = startWithContext + 240 < text.length ? "..." : "";
let summary = document.createElement("p");
summary.classList.add("context");
summary.textContent = top + text.substr(startWithContext, 240).trim() + tail;
return summary;
},
};
_ready(Search.init);

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/* Highlighting utilities for Sphinx HTML documentation. */
"use strict";
const SPHINX_HIGHLIGHT_ENABLED = true
/**
* highlight a given string on a node by wrapping it in
* span elements with the given class name.
*/
const _highlight = (node, addItems, text, className) => {
if (node.nodeType === Node.TEXT_NODE) {
const val = node.nodeValue;
const parent = node.parentNode;
const pos = val.toLowerCase().indexOf(text);
if (
pos >= 0 &&
!parent.classList.contains(className) &&
!parent.classList.contains("nohighlight")
) {
let span;
const closestNode = parent.closest("body, svg, foreignObject");
const isInSVG = closestNode && closestNode.matches("svg");
if (isInSVG) {
span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
} else {
span = document.createElement("span");
span.classList.add(className);
}
span.appendChild(document.createTextNode(val.substr(pos, text.length)));
const rest = document.createTextNode(val.substr(pos + text.length));
parent.insertBefore(
span,
parent.insertBefore(
rest,
node.nextSibling
)
);
node.nodeValue = val.substr(0, pos);
/* There may be more occurrences of search term in this node. So call this
* function recursively on the remaining fragment.
*/
_highlight(rest, addItems, text, className);
if (isInSVG) {
const rect = document.createElementNS(
"http://www.w3.org/2000/svg",
"rect"
);
const bbox = parent.getBBox();
rect.x.baseVal.value = bbox.x;
rect.y.baseVal.value = bbox.y;
rect.width.baseVal.value = bbox.width;
rect.height.baseVal.value = bbox.height;
rect.setAttribute("class", className);
addItems.push({ parent: parent, target: rect });
}
}
} else if (node.matches && !node.matches("button, select, textarea")) {
node.childNodes.forEach((el) => _highlight(el, addItems, text, className));
}
};
const _highlightText = (thisNode, text, className) => {
let addItems = [];
_highlight(thisNode, addItems, text, className);
addItems.forEach((obj) =>
obj.parent.insertAdjacentElement("beforebegin", obj.target)
);
};
/**
* Small JavaScript module for the documentation.
*/
const SphinxHighlight = {
/**
* highlight the search words provided in localstorage in the text
*/
highlightSearchWords: () => {
if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight
// get and clear terms from localstorage
const url = new URL(window.location);
const highlight =
localStorage.getItem("sphinx_highlight_terms")
|| url.searchParams.get("highlight")
|| "";
localStorage.removeItem("sphinx_highlight_terms")
url.searchParams.delete("highlight");
window.history.replaceState({}, "", url);
// get individual terms from highlight string
const terms = highlight.toLowerCase().split(/\s+/).filter(x => x);
if (terms.length === 0) return; // nothing to do
// There should never be more than one element matching "div.body"
const divBody = document.querySelectorAll("div.body");
const body = divBody.length ? divBody[0] : document.querySelector("body");
window.setTimeout(() => {
terms.forEach((term) => _highlightText(body, term, "highlighted"));
}, 10);
const searchBox = document.getElementById("searchbox");
if (searchBox === null) return;
searchBox.appendChild(
document
.createRange()
.createContextualFragment(
'<p class="highlight-link">' +
'<a href="javascript:SphinxHighlight.hideSearchWords()">' +
_("Hide Search Matches") +
"</a></p>"
)
);
},
/**
* helper function to hide the search marks again
*/
hideSearchWords: () => {
document
.querySelectorAll("#searchbox .highlight-link")
.forEach((el) => el.remove());
document
.querySelectorAll("span.highlighted")
.forEach((el) => el.classList.remove("highlighted"));
localStorage.removeItem("sphinx_highlight_terms")
},
initEscapeListener: () => {
// only install a listener if it is really needed
if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return;
document.addEventListener("keydown", (event) => {
// bail for input elements
if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return;
// bail with special keys
if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return;
if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) {
SphinxHighlight.hideSearchWords();
event.preventDefault();
}
});
},
};
_ready(() => {
/* Do not call highlightSearchWords() when we are on the search page.
* It will highlight words from the *previous* search query.
*/
if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords();
SphinxHighlight.initEscapeListener();
});

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