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<title>SelfiSys: Assess the Impact of Systematic Effects in Galaxy Surveys &mdash; SelfiSys /Users/hoellinger/Library/CloudStorage/Dropbox/travail/these/science/code/SELFI/selfisys/src/ documentation</title>
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<p class="caption" role="heading"><span class="caption-text">API Documentation</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="selfisys.hiddenbox.html">hiddenbox</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox"><code class="docutils literal notranslate"><span class="pre">HiddenBox</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Npop"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Npop</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Ntimesteps"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Ntimesteps</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.Psingle"><code class="docutils literal notranslate"><span class="pre">HiddenBox.Psingle</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.compute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.compute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.evaluate"><code class="docutils literal notranslate"><span class="pre">HiddenBox.evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_neglect_lightcone"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_neglect_lightcone</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.force_recompute_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.force_recompute_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.gravity_on"><code class="docutils literal notranslate"><span class="pre">HiddenBox.gravity_on</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.load_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.load_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.make_data"><code class="docutils literal notranslate"><span class="pre">HiddenBox.make_data()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.modified_selfi"><code class="docutils literal notranslate"><span class="pre">HiddenBox.modified_selfi</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.prefix_mocks"><code class="docutils literal notranslate"><span class="pre">HiddenBox.prefix_mocks</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.reset_survey"><code class="docutils literal notranslate"><span class="pre">HiddenBox.reset_survey()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.setup_only"><code class="docutils literal notranslate"><span class="pre">HiddenBox.setup_only</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_recompute_pool"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_recompute_pool()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.switch_setup"><code class="docutils literal notranslate"><span class="pre">HiddenBox.switch_setup()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.hiddenbox.html#selfisys.hiddenbox.HiddenBox.update"><code class="docutils literal notranslate"><span class="pre">HiddenBox.update()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.normalise_hb.html">normalise_hb</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.normalise_hb.html#selfisys.normalise_hb.define_normalisation"><code class="docutils literal notranslate"><span class="pre">define_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation"><code class="docutils literal notranslate"><span class="pre">worker_normalisation()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_public"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_public()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.normalise_hb.html#selfisys.normalise_hb.worker_normalisation_wrapper"><code class="docutils literal notranslate"><span class="pre">worker_normalisation_wrapper()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.prior.html">prior</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.logposterior_hyperparameters_parallel"><code class="docutils literal notranslate"><span class="pre">logposterior_hyperparameters_parallel()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.perform_prior_optimisation_and_plot"><code class="docutils literal notranslate"><span class="pre">perform_prior_optimisation_and_plot()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior"><code class="docutils literal notranslate"><span class="pre">planck_prior</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.mean"><code class="docutils literal notranslate"><span class="pre">planck_prior.mean</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.inv_covariance"><code class="docutils literal notranslate"><span class="pre">planck_prior.inv_covariance</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.Nbin_max"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_max</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.Nbin_min"><code class="docutils literal notranslate"><span class="pre">planck_prior.Nbin_min</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.compute"><code class="docutils literal notranslate"><span class="pre">planck_prior.compute()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.load"><code class="docutils literal notranslate"><span class="pre">planck_prior.load()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.logpdf"><code class="docutils literal notranslate"><span class="pre">planck_prior.logpdf()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.sample"><code class="docutils literal notranslate"><span class="pre">planck_prior.sample()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.planck_prior.save"><code class="docutils literal notranslate"><span class="pre">planck_prior.save()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.prior.html#selfisys.prior.worker_class"><code class="docutils literal notranslate"><span class="pre">worker_class()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.selection_functions.html">selection_functions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.init_selection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.init_selection()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.lognormals_z_to_x"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.lognormals_z_to_x()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.multiple_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.multiple_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.one_lognormal_z"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.one_lognormal_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection.r_grid"><code class="docutils literal notranslate"><span class="pre">LognormalSelection.r_grid()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.selfi_interface.html">selfi_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.selfi_interface.html#selfisys.selfi_interface.PrintMessage"><code class="docutils literal notranslate"><span class="pre">PrintMessage()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.selfi_interface.html#selfisys.selfi_interface.indent"><code class="docutils literal notranslate"><span class="pre">indent()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.selfi_interface.html#selfisys.selfi_interface.unindent"><code class="docutils literal notranslate"><span class="pre">unindent()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.sbmy_interface.html">sbmy_interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.sbmy_interface.html#selfisys.sbmy_interface.compute_Phi"><code class="docutils literal notranslate"><span class="pre">compute_Phi()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.sbmy_interface.html#selfisys.sbmy_interface.generate_white_noise_Field"><code class="docutils literal notranslate"><span class="pre">generate_white_noise_Field()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.sbmy_interface.html#selfisys.sbmy_interface.get_power_spectrum_from_cosmo"><code class="docutils literal notranslate"><span class="pre">get_power_spectrum_from_cosmo()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.sbmy_interface.html#selfisys.sbmy_interface.handle_time_stepping"><code class="docutils literal notranslate"><span class="pre">handle_time_stepping()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.sbmy_interface.html#selfisys.sbmy_interface.setup_sbmy_parfiles"><code class="docutils literal notranslate"><span class="pre">setup_sbmy_parfiles()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.grf.html">grf</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.grf.html#selfisys.grf.primordial_grf"><code class="docutils literal notranslate"><span class="pre">primordial_grf()</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="selfisys.utils.html">selfisys.utils package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.examples_utils">selfisys.utils.examples_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.examples_utils.clear_large_plot"><code class="docutils literal notranslate"><span class="pre">clear_large_plot()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.logger">selfisys.utils.logger module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.CustomLogger"><code class="docutils literal notranslate"><span class="pre">CustomLogger</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.CustomLogger.diagnostic"><code class="docutils literal notranslate"><span class="pre">CustomLogger.diagnostic()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.CustomLoggerHandler.emit"><code class="docutils literal notranslate"><span class="pre">CustomLoggerHandler.emit()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.INDENT"><code class="docutils literal notranslate"><span class="pre">INDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.PrintDiagnostic"><code class="docutils literal notranslate"><span class="pre">PrintDiagnostic()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.PrintError"><code class="docutils literal notranslate"><span class="pre">PrintError()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.PrintInfo"><code class="docutils literal notranslate"><span class="pre">PrintInfo()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.PrintLeftType"><code class="docutils literal notranslate"><span class="pre">PrintLeftType()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.PrintWarning"><code class="docutils literal notranslate"><span class="pre">PrintWarning()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.UNINDENT"><code class="docutils literal notranslate"><span class="pre">UNINDENT()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.logger.getCustomLogger"><code class="docutils literal notranslate"><span class="pre">getCustomLogger()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.low_level">selfisys.utils.low_level module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.low_level.stderr_redirector"><code class="docutils literal notranslate"><span class="pre">stderr_redirector()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.low_level.stdout_redirector"><code class="docutils literal notranslate"><span class="pre">stdout_redirector()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.parser">selfisys.utils.parser module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.bool_sh"><code class="docutils literal notranslate"><span class="pre">bool_sh()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.check_files_exist"><code class="docutils literal notranslate"><span class="pre">check_files_exist()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.intNone"><code class="docutils literal notranslate"><span class="pre">intNone()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.joinstrs"><code class="docutils literal notranslate"><span class="pre">joinstrs()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.joinstrs_only"><code class="docutils literal notranslate"><span class="pre">joinstrs_only()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.parser.safe_npload"><code class="docutils literal notranslate"><span class="pre">safe_npload()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.path_utils">selfisys.utils.path_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.path_utils.file_names_evaluate"><code class="docutils literal notranslate"><span class="pre">file_names_evaluate()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.path_utils.get_file_names"><code class="docutils literal notranslate"><span class="pre">get_file_names()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.plot_examples">selfisys.utils.plot_examples module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_examples.plot_comoving_distance_redshift"><code class="docutils literal notranslate"><span class="pre">plot_comoving_distance_redshift()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_examples.plot_galaxy_field_slice"><code class="docutils literal notranslate"><span class="pre">plot_galaxy_field_slice()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_examples.plot_power_spectrum"><code class="docutils literal notranslate"><span class="pre">plot_power_spectrum()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_examples.plot_selection_functions_def_in_z"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions_def_in_z()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_examples.redshift_distance_conversion"><code class="docutils literal notranslate"><span class="pre">redshift_distance_conversion()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_examples.relative_error_analysis"><code class="docutils literal notranslate"><span class="pre">relative_error_analysis()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.plot_params">selfisys.utils.plot_params module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.get_offset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.get_offset()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_scientific"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_scientific()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.ScalarFormatterForceFormat_11.set_useOffset"><code class="docutils literal notranslate"><span class="pre">ScalarFormatterForceFormat_11.set_useOffset()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.create_all_colormaps"><code class="docutils literal notranslate"><span class="pre">create_all_colormaps()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.create_colormap"><code class="docutils literal notranslate"><span class="pre">create_colormap()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.dynamic_text_scaling"><code class="docutils literal notranslate"><span class="pre">dynamic_text_scaling()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.get_contours"><code class="docutils literal notranslate"><span class="pre">get_contours()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.reset_plotting"><code class="docutils literal notranslate"><span class="pre">reset_plotting()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_params.setup_plotting"><code class="docutils literal notranslate"><span class="pre">setup_plotting()</span></code></a></li>
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</li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.plot_utils">selfisys.utils.plot_utils module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_C"><code class="docutils literal notranslate"><span class="pre">plot_C()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_fisher"><code class="docutils literal notranslate"><span class="pre">plot_fisher()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_gradients"><code class="docutils literal notranslate"><span class="pre">plot_gradients()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_histogram"><code class="docutils literal notranslate"><span class="pre">plot_histogram()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks"><code class="docutils literal notranslate"><span class="pre">plot_mocks()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_mocks_compact"><code class="docutils literal notranslate"><span class="pre">plot_mocks_compact()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_observations"><code class="docutils literal notranslate"><span class="pre">plot_observations()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_prior_and_posterior_covariances"><code class="docutils literal notranslate"><span class="pre">plot_prior_and_posterior_covariances()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_reconstruction"><code class="docutils literal notranslate"><span class="pre">plot_reconstruction()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plot_selection_functions"><code class="docutils literal notranslate"><span class="pre">plot_selection_functions()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.plot_utils.plotly_3d"><code class="docutils literal notranslate"><span class="pre">plotly_3d()</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.timestepping">selfisys.utils.timestepping module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.timestepping.merge_nTS"><code class="docutils literal notranslate"><span class="pre">merge_nTS()</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.tools">selfisys.utils.tools module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.tools.cosmo_vector_to_Simbelmyne_dict"><code class="docutils literal notranslate"><span class="pre">cosmo_vector_to_Simbelmyne_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.tools.cosmo_vector_to_class_dict"><code class="docutils literal notranslate"><span class="pre">cosmo_vector_to_class_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.tools.custom_stat"><code class="docutils literal notranslate"><span class="pre">custom_stat()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.tools.fisher_rao"><code class="docutils literal notranslate"><span class="pre">fisher_rao()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.tools.get_k_max"><code class="docutils literal notranslate"><span class="pre">get_k_max()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.tools.get_summary"><code class="docutils literal notranslate"><span class="pre">get_summary()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.tools.none_or_bool_or_str"><code class="docutils literal notranslate"><span class="pre">none_or_bool_or_str()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.tools.params_ids_to_Simbelmyne_dict"><code class="docutils literal notranslate"><span class="pre">params_ids_to_Simbelmyne_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.tools.sample_omega_from_prior"><code class="docutils literal notranslate"><span class="pre">sample_omega_from_prior()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.tools.summary_to_score"><code class="docutils literal notranslate"><span class="pre">summary_to_score()</span></code></a></li>
</ul>
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<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.workers">selfisys.utils.workers module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.workers.Simbelmyne_worker"><code class="docutils literal notranslate"><span class="pre">Simbelmyne_worker()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.workers.evaluate_gradient_of_Symbelmyne"><code class="docutils literal notranslate"><span class="pre">evaluate_gradient_of_Symbelmyne()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="selfisys.utils.html#selfisys.utils.workers.worker_gradient_Symbelmyne"><code class="docutils literal notranslate"><span class="pre">worker_gradient_Symbelmyne()</span></code></a></li>
</ul>
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<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils">Module contents</a></li>
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<p class="caption" role="heading"><span class="caption-text">Contribute</span></p>
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<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>
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<section id="selfisys-assess-the-impact-of-systematic-effects-in-galaxy-surveys">
<h1>SelfiSys: Assess the Impact of Systematic Effects in Galaxy Surveys<a class="headerlink" href="#selfisys-assess-the-impact-of-systematic-effects-in-galaxy-surveys" title="Link to this heading"></a></h1>
<a class="reference external image-reference" href="https://arxiv.org/abs/2412.04443"><img alt="arXiv" src="https://img.shields.io/badge/astro--ph.CO-arxiv%3A2412.04443-B31B1B.svg" />
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<a class="reference external image-reference" href="https://github.com/hoellin/selfisys_public/releases"><img alt="GitHub Release" src="https://img.shields.io/github/v/tag/hoellin/selfisys_public.svg?label=version" />
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<a class="reference external image-reference" href="https://github.com/hoellin/selfisys_public/commits/main"><img alt="Last Commit" src="https://img.shields.io/github/last-commit/hoellin/selfisys_public" />
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<a class="reference external image-reference" href="https://github.com/hoellin/selfisys_public/blob/main/LICENSE"><img alt="License" src="https://img.shields.io/badge/License-GPLv3-blue.svg" />
</a>
<p><strong>SelfiSys</strong> is a Python package designed to address the issue of model misspecification in field-based, implicit likelihood cosmological inference.</p>
<p>It leverages the inferred initial matter power spectrum, enabling a thorough diagnosis of systematic effects in large-scale spectroscopic galaxy surveys.</p>
<section id="key-features">
<h2>Key Features<a class="headerlink" href="#key-features" title="Link to this heading"></a></h2>
<ul class="simple">
<li><dl class="simple">
<dt><strong>Custom hidden-box forward models</strong></dt><dd><p>We provide a <cite>HiddenBox</cite> class to simulate realistic spectroscopic galaxy surveys. It accommodates fully non-linear gravitational evolution, and incorporates multiple systematic effects observed in real-world survey, e.g., misspecified galaxy bias, survey mask, selection functions, dust extinction, line interlopers, or inaccurate gravity solver.</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt><strong>Diagnosis of systematic effects</strong></dt><dd><p>Diagnose the impact of systematic effects using the inferred initial matter power spectrum, prior to performing cosmological inference.</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt><strong>Cosmological inference</strong></dt><dd><p>Perform inference of cosmological parameters using Approximate Bayesian Computation (ABC) with a Population Monte Carlo (PMC) sampler.</p>
</dd>
</dl>
</li>
</ul>
<p>For practical examples demonstrating how to use SelfiSys, visit the <a class="reference external" href="https://github.com/hoellin/selfisys_examples">SelfiSys Examples Repository</a>.</p>
</section>
<section id="references">
<h2>References<a class="headerlink" href="#references" title="Link to this heading"></a></h2>
<p>If you use the SelfiSys package in your research, please cite the following paper and feel free to <a class="reference external" href="mailto:tristan&#46;hoellinger&#37;&#52;&#48;iap&#46;fr">contact the authors</a> for feedback, collaboration opportunities, or other inquiries.</p>
<p><strong>Diagnosing Systematic Effects Using the Inferred Initial Power Spectrum</strong>
<em>Hoellinger, T. and Leclercq, F., arXiv e-prints</em>, 2024
<a class="reference external" href="https://arxiv.org/abs/2412.04443">arXiv:2412.04443</a>
<a class="reference external" href="https://arxiv.org/abs/2412.04443">[astro-ph.CO]</a>
<a class="reference external" href="https://ui.adsabs.harvard.edu/abs/arXiv:2412.04443">[ADS]</a>
<a class="reference external" href="https://arxiv.org/pdf/2412.04443">[pdf]</a></p>
</section>
<section id="contributors">
<h2>Contributors<a class="headerlink" href="#contributors" title="Link to this heading"></a></h2>
<ul>
<li><p><strong>Tristan Hoellinger</strong>
<a class="reference external" href="mailto:tristan&#46;hoellinger&#37;&#52;&#48;iap&#46;fr">tristan<span>&#46;</span>hoellinger<span>&#64;</span>iap<span>&#46;</span>fr</a></p>
<p>Principal developer and maintainer, Institut d’Astrophysique de Paris (IAP).</p>
</li>
</ul>
</section>
<section id="license">
<h2>License<a class="headerlink" href="#license" title="Link to this heading"></a></h2>
<p>This software is distributed under the GPLv3 Licence. Please review the <a class="reference external" href="https://github.com/hoellin/selfisys_public/blob/main/LICENSE">LICENSE</a> file in the repository to understand the terms of use and ensure compliance. By downloading and using this software, you agree to the terms of the licence.</p>
</section>
<section id="requirements">
<h2>Requirements<a class="headerlink" href="#requirements" title="Link to this heading"></a></h2>
<p>The code is written in Python 3.10 and depends on the following packages:</p>
<ul class="simple">
<li><p><a class="reference external" href="https://pyselfi.readthedocs.io/en/latest/">pySELFI</a>: Python implementation of the Simulator Expansion for Likelihood-Free Inference.</p></li>
<li><p><a class="reference external" href="https://simbelmyne.readthedocs.io/en/latest/">Simbelmynë</a>: A hierarchical probabilistic simulator for generating synthetic galaxy survey data.</p></li>
<li><p><a class="reference external" href="https://elfi.readthedocs.io/en/latest/">ELFI</a>: A statistical software package for likelihood-free inference, implementing Approximate Bayesian Computation (ABC) with a Population Monte Carlo (PMC) sampler.</p></li>
</ul>
<p>A comprehensive list of dependencies, along with installation instructions, will be provided in a future release.</p>
<div class="toctree-wrapper compound">
<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></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></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>
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<li class="toctree-l1"><a class="reference internal" href="selfisys.selection_functions.html">selection_functions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.selection_functions.html#selfisys.selection_functions.LognormalSelection"><code class="docutils literal notranslate"><span class="pre">LognormalSelection</span></code></a></li>
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<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>
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<li class="toctree-l1"><a class="reference internal" href="selfisys.grf.html">grf</a><ul>
<li class="toctree-l2"><a class="reference internal" href="selfisys.grf.html#selfisys.grf.primordial_grf"><code class="docutils literal notranslate"><span class="pre">primordial_grf()</span></code></a></li>
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<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></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.logger">selfisys.utils.logger module</a></li>
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<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.timestepping">selfisys.utils.timestepping module</a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.tools">selfisys.utils.tools module</a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils.workers">selfisys.utils.workers module</a></li>
<li class="toctree-l2"><a class="reference internal" href="selfisys.utils.html#module-selfisys.utils">Module contents</a></li>
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