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/tools.html
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+  <title>selfisys.utils.tools &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>
+<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>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="../../../CONTRIBUTING.html#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>
+
+        </div>
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="../../../index.html">SelfiSys</a>
+      </nav>
+
+      <div class="wy-nav-content">
+        <div class="rst-content style-external-links">
+          <div role="navigation" aria-label="Page navigation">
+  <ul class="wy-breadcrumbs">
+      <li><a href="../../../index.html" class="icon icon-home" aria-label="Home"></a></li>
+          <li class="breadcrumb-item"><a href="../../index.html">Module code</a></li>
+      <li class="breadcrumb-item active">selfisys.utils.tools</li>
+      <li class="wy-breadcrumbs-aside">
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+             
+  <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>
+
+</pre></div>
+
+           </div>
+          </div>
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+
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