Initial commit: v0.1.0

2025-06-07 16:41:11 +00:00 · 2025-01-10 17:03:16 +01:00 · 2025-01-10 17:03:16 +01:00 · c041384662
commit c041384662
172 changed files with 45744 additions and 0 deletions
--- a/docs/_modules/selfisys/utils/low_level.html
+++ b/docs/_modules/selfisys/utils/low_level.html
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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>
+<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>
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+<p class="caption" role="heading"><span class="caption-text">References</span></p>
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+</ul>
+
+        </div>
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+
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+          <li class="breadcrumb-item"><a href="../../index.html">Module code</a></li>
+      <li class="breadcrumb-item active">selfisys.utils.low_level</li>
+      <li class="wy-breadcrumbs-aside">
+      </li>
+  </ul>
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+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+             
+  <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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