Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | W _ __call__() (lib.utilities.FunctionLogger method) __enter__() (lib.utilities.MultithreadedCopier method) __exit__() (lib.utilities.MultithreadedCopier method) __Init__() (lib.utilities.Exporter method) _assemble_blocks() (lib.data_handling.data_converter.Constructor method) _check_cluster_number() (lib.data_handling.mf_parser.MinfluxFilter method) _construct_record() (lib.data_handling.data_converter.Constructor method) _convert_results_to_df() (lib.data_handling.data_postprocessing.PostProcessorFacade method) _define_color_scheme() (lib.plotting.style.Style method) _dict_to_line_mapping() (lib.data_handling.data_analysis.Fit method) _do_global_fit() (lib.data_handling.data_analysis.Fit method) _do_local_fit() (lib.data_handling.data_analysis.Fit method) _estimate_initial_values() (lib.data_handling.data_analysis.Estimators method) _find_bkps() (lib.data_handling.mf_parser.MinfluxFilter method) _find_ext() (lib.data_handling.data_analysis.Estimators method) _find_files() (lib.data_handling.mf_parser.MinfluxParser method) _find_state_clusters() (lib.data_handling.mf_parser.MinfluxFilter method) _generate_lighter_shades() (lib.plotting.style.Style method) _generate_params() (lib.simulation.MINFLUXMonteCarlo.MCSimulation method) _generate_points() (lib.simulation.MINFLUXMonteCarlo.MCSimulation method) _get_background_estimate() (lib.data_handling.data_analysis.AnalysisRoutines method) _get_beta_estimate() (lib.data_handling.data_converter.Constructor method) _get_bgr_estimate() (lib.data_handling.data_converter.Constructor method) _get_bgr_photons() (lib.simulation.setup.Sample method) _get_brightness_estimate() (lib.data_handling.data_converter.Constructor method) _get_fixed_curvature() (lib.data_handling.data_analysis.AnalysisRoutines method) _get_kappa_estimate() (lib.data_handling.data_analysis.AnalysisRoutines method) _get_metrics() (lib.data_handling.data_analysis.Study method) _get_moving_avg_segments() (lib.data_handling.data_preprocessing.Extractor method) _get_sig_photons() (lib.simulation.setup.Sample method) _get_std_layout_single() (lib.plotting.artefacts.Figures method) _label_cluster() (lib.data_handling.mf_parser.MinfluxFilter method) _line_to_nan_mapping() (lib.data_handling.data_analysis.Fit method) _load_as_frame() (lib.data_handling.mf_parser.MinfluxParser method) _load_processed_file() (in module lib.data_handling.mf_parser) _load_processed_files() (lib.data_handling.mf_parser.MinfluxPostProcessing method) _map_clusters_on_states() (lib.data_handling.mf_parser.MinfluxFilter method) _moving_average() (lib.utilities.BaseFunc method) _plot_fit() (lib.data_handling.data_analysis.MinfluxAnalysis method) _read_otto() (lib.data_handling.mf_parser.MinfluxParser method) _read_philip() (lib.data_handling.mf_parser.MinfluxParser method) _read_thomas() (lib.data_handling.mf_parser.MinfluxParser method) _sanity_check() (lib.simulation.psf_models.PSFmodel method) _save_frame() (lib.data_handling.mf_parser.MinfluxFilter method) (lib.data_handling.mf_parser.MinfluxParser method) _segment_frame() (lib.data_handling.mf_parser.MinfluxFilter method) _set_params() (lib.data_handling.data_preprocessing.Extractor method) _set_rcparams() (lib.plotting.style.Style method) _state_id_pre_assignment() (lib.data_handling.mf_parser.MinfluxFilter method) _transform_frame() (lib.data_handling.mf_parser.MinfluxParser method) _transform_otto() (lib.data_handling.mf_parser.MinfluxParser method) _transform_philip() (lib.data_handling.mf_parser.MinfluxParser method) _transform_thomas() (lib.data_handling.mf_parser.MinfluxParser method) A add_blinking() (lib.simulation.setup.Sample method) add_figures() (lib.plotting.artefacts.Artefacts method) AIRY_FACTOR (in module lib.constants) ALPHA (in module lib.constants) AnalysisRoutines (class in lib.data_handling.data_analysis) analyze() (lib.simulation.MINFLUXMonteCarlo.MCSimulation method) append() (lib.data_handling.data_analysis.Results method) (lib.plotting.artefacts.Artefacts method) (lib.simulation.measurement.Pattern method) Artefacts (class in lib.plotting.artefacts) assign_chunk_id() (lib.data_handling.data_analysis.MinfluxAnalysis method) B Background (class in lib.simulation.psf_models) BACKGROUND_RATE (in module lib.constants) backgroundPSF() (lib.simulation.setup.Instrument method) BaseFunc (class in lib.utilities) bgr_model() (lib.simulation.setup.Setup method) bin_frame() (lib.data_handling.mf_parser.MinfluxFilter method) BLEACH_IDX (in module lib.constants) BLINKING (in module lib.constants) BLOCK_SIZE (in module lib.constants) C calculate_norms() (lib.utilities.BaseFunc method) check_residuals() (lib.data_handling.data_analysis.Fit method) clone() (lib.simulation.setup.Sample method) Configuration (class in lib.utilities) construct_trace() (lib.simulation.setup.Trace method) Constructor (class in lib.data_handling.data_converter) Converter (class in lib.data_handling.utilities) (class in lib.utilities) copy() (lib.utilities.MultithreadedCopier method) CPSegmentation_Figures (class in lib.plotting.artefacts) create_artists() (lib.plotting.style.ImageHandler method) D DATA_DIR (in module lib.config) default() (lib.utilities.NumpyArrayEncoder method) despine_axes() (lib.plotting.style.Style method) DET_PSF (in module lib.constants) Detection (class in lib.simulation.psf_models) DETECTION_FWHM (in module lib.constants) detectionPSF() (lib.simulation.setup.Instrument method) DIMENSIONS (in module lib.constants) do_fit() (lib.data_handling.data_analysis.Fit method) do_sanity_check() (lib.utilities.Configuration method) drop_axes() (lib.plotting.style.Style method) DWELL_TIME (in module lib.constants) E effBgr() (lib.simulation.setup.Instrument method) effPSF() (lib.simulation.setup.Instrument method) emissionPSF() (lib.simulation.setup.Instrument method) Estimators (class in lib.data_handling.data_analysis) evaluate_data() (lib.data_handling.data_analysis.EvaluationFacade method) EvaluationFacade (class in lib.data_handling.data_analysis) EXC_PSF (in module lib.constants) Experiment (class in lib.simulation.experiment) ExperimentGenerator (class in lib.simulation.experiment) Exporter (class in lib.utilities) Extractor (class in lib.data_handling.data_preprocessing) F fig_check_residuals() (lib.plotting.artefacts.Residual_Figures method) fig_COM_movement() (lib.plotting.artefacts.Minflux_Figures method) fig_correlation_matrix() (lib.plotting.artefacts.Meta_Analysis_Figures method) fig_correlations() (lib.plotting.artefacts.Meta_Analysis_Figures method) fig_count_histogram() (lib.plotting.artefacts.Minflux_Figures method) fig_diagnostics() (lib.plotting.artefacts.CPSegmentation_Figures method) fig_distance_histogram() (lib.plotting.artefacts.Minflux_Figures method) fig_distance_precision() (lib.plotting.artefacts.Minflux_Figures method) fig_distance_wrt_time() (lib.plotting.artefacts.Minflux_Figures method) fig_estimated_distances() (lib.plotting.artefacts.Meta_Analysis_Figures method) fig_filter_statistics() (lib.plotting.artefacts.Filter_Figures method) fig_individual_batch_histograms() (lib.plotting.artefacts.Meta_Analysis_Figures method) fig_NALM_analysis() (lib.plotting.artefacts.NALM_Figures method) fig_pos_brightness() (lib.plotting.artefacts.Minflux_Figures method) fig_power_balance() (lib.plotting.artefacts.Meta_Analysis_Figures method) fig_raw_trace() (lib.plotting.artefacts.Trace_Figures method) fig_segmented_trace() (lib.plotting.artefacts.Trace_Figures method) fig_tracking() (lib.plotting.artefacts.Minflux_Figures method) fig_visibility() (lib.plotting.artefacts.Minflux_Figures method) figsize() (in module lib.plotting.style) Figures (class in lib.plotting.artefacts) Filter (class in lib.data_handling.data_filtering) filter_data() (lib.data_handling.data_filtering.Filter method) filter_directory() (lib.data_handling.mf_parser.MinfluxFilterFacade method) filter_experiments() (in module lib.data_handling.data_filtering) Filter_Figures (class in lib.plotting.artefacts) filter_frame() (lib.data_handling.mf_parser.MinfluxFilter method) filter_single_file() (in module lib.data_handling.data_filtering) filter_single_minflux_file() (in module lib.data_handling.mf_parser) find_files() (lib.utilities.BaseFunc method) Fit (class in lib.data_handling.data_analysis) fit_chunk() (lib.data_handling.data_analysis.MinfluxAnalysis method) flatten_list() (lib.utilities.BaseFunc method) FOV, [1] FunctionLogger (class in lib.utilities) FWHM, [1] G generate_data() (lib.simulation.MINFLUXMonteCarlo.MCSimulation method) generate_sample() (lib.simulation.setup.SampleGenerator method) get_angles() (lib.simulation.measurement.PointLinearPhasePattern method) get_array_from_tif() (lib.data_handling.data_preprocessing.Extractor method) get_bleach_idx() (lib.data_handling.data_preprocessing.Extractor method) get_c0s() (lib.simulation.measurement.PointLinearPhasePattern method) get_CE() (lib.data_handling.data_analysis.Estimators method) get_CRB_scan() (lib.simulation.experiment.ExperimentGenerator method) get_default() (lib.simulation.experiment.ExperimentGenerator method) get_even_clusters() (lib.data_handling.data_postprocessing.PostProcessor method) get_experiments() (lib.data_handling.data_converter.Constructor method) get_FE() (lib.data_handling.data_analysis.Estimators method) get_figsize() (lib.plotting.style.Style method) get_generator() (lib.simulation.measurement.PatternGenerator method) get_git_root() (lib.utilities.BaseFunc method) get_harmonic_estimate() (lib.data_handling.data_analysis.Fit method) get_HE() (lib.data_handling.data_analysis.Estimators method) get_initial_guess() (lib.data_handling.data_analysis.Estimators method) get_kvec() (lib.simulation.measurement.PointLinearPhasePattern method) get_MLE() (lib.data_handling.data_analysis.Estimators method) (lib.data_handling.data_analysis.Fit method) get_model() (lib.simulation.setup.Setup method) get_pattern() (lib.simulation.measurement.Measurement method) (lib.simulation.measurement.MinfluxPatternGenerator method) (lib.simulation.measurement.PhasePatternGenerator method) get_phases() (lib.simulation.measurement.MinfluxPattern method) (lib.simulation.measurement.PointLinearPhasePattern method) get_photons() (lib.simulation.setup.Sample method) get_positions() (lib.simulation.measurement.PointLinearPhasePattern method) get_rand_positions() (lib.simulation.setup.SampleGenerator method) get_taylor_estimate() (lib.data_handling.data_analysis.Fit method) get_taylorE() (lib.data_handling.data_analysis.Estimators method) get_trace() (lib.simulation.setup.Setup method) getCramerRaoBound() (lib.simulation.MINFLUXMonteCarlo.MCAnalysis method) getFisherMatrix() (lib.simulation.MINFLUXMonteCarlo.MCAnalysis method) getInverseFisherMatrix() (lib.simulation.MINFLUXMonteCarlo.MCAnalysis method) getMLE() (lib.simulation.MINFLUXMonteCarlo.MCAnalysis method) getPSF() (lib.simulation.psf_models.Background method) (lib.simulation.psf_models.Detection method) (lib.simulation.psf_models.PSFmodel method) (lib.simulation.psf_models.standingWave method) grid_data() (lib.data_handling.data_analysis.MinfluxAnalysis method) H handle_ticks() (lib.plotting.style.Style method) HARMONIC_analysis() (lib.data_handling.data_analysis.AnalysisRoutines method) harmonic_model() (lib.data_handling.data_analysis.Estimators method) hide_axes() (lib.plotting.style.Style method) I id_generator() (lib.utilities.Labeler method) ImageHandler (class in lib.plotting.style) Importer (class in lib.utilities) Instrument (class in lib.simulation.setup) interpret_prompt() (lib.simulation.experiment.Experiment method) is_bleached() (lib.simulation.setup.Sample method) ITERATION_DEPTH (in module lib.constants) J join_array() (lib.data_handling.utilities.Converter method) join_dict_values() (lib.utilities.BaseFunc method) K KAPPA_analysis() (lib.data_handling.data_analysis.AnalysisRoutines method) L Labeler (class in lib.utilities) LAMBDA (in module lib.constants) lib module lib.config module lib.constants module lib.data_handling module lib.data_handling.data_analysis module lib.data_handling.data_converter module lib.data_handling.data_filtering module lib.data_handling.data_postprocessing module lib.data_handling.data_preprocessing module lib.data_handling.mf_parser module lib.data_handling.utilities module lib.plotting module lib.plotting.artefacts module lib.plotting.style module lib.simulation module lib.simulation.experiment module lib.simulation.measurement module lib.simulation.MINFLUXMonteCarlo module lib.simulation.psf_models module lib.simulation.setup module lib.utilities module LIGHT_FACTOR (in module lib.constants) load() (lib.simulation.experiment.Experiment method) load_json() (lib.utilities.Importer method) load_yaml() (lib.utilities.Importer method) Log (class in lib.simulation.experiment) (class in lib.utilities) log_function_call() (lib.utilities.FunctionLogger method) log_to_database() (lib.utilities.Log method) loglike_objective() (lib.data_handling.data_analysis.Estimators method) Loglikelihood() (lib.simulation.MINFLUXMonteCarlo.MCAnalysis method) lsqs_objective() (lib.data_handling.data_analysis.Estimators method) M match_pattern() (lib.utilities.BaseFunc method) max_quad_model() (lib.data_handling.data_analysis.Estimators method) MCAnalysis (class in lib.simulation.MINFLUXMonteCarlo) MCSimulation (class in lib.simulation.MINFLUXMonteCarlo) Measurement (class in lib.simulation.measurement) MEASUREMENT_MODE (in module lib.constants) meta_analysis() (lib.data_handling.data_postprocessing.MetaAnalysis method) Meta_Analysis_Figures (class in lib.plotting.artefacts) MetaAnalysis (class in lib.data_handling.data_postprocessing) MF_ParserFacade (class in lib.data_handling.mf_parser) min_hexa_model() (lib.data_handling.data_analysis.Estimators method) min_poly_model() (lib.data_handling.data_analysis.Estimators method) min_quad_model() (lib.data_handling.data_analysis.Estimators method) MINFLUX, [1] Minflux_Figures (class in lib.plotting.artefacts) MinfluxAnalysis (class in lib.data_handling.data_analysis) MinfluxFilter (class in lib.data_handling.data_filtering) (class in lib.data_handling.mf_parser) MinfluxFilterFacade (class in lib.data_handling.mf_parser) MinfluxParser (class in lib.data_handling.mf_parser) MinfluxPattern (class in lib.simulation.measurement) MinfluxPatternGenerator (class in lib.simulation.measurement) MinfluxPostProcessing (class in lib.data_handling.mf_parser) MinfluxProcessor (class in lib.data_handling.mf_parser) MinfluxProcessorFacade (class in lib.data_handling.mf_parser) MLE() (in module lib.simulation.MINFLUXMonteCarlo) MLE_analysis() (lib.data_handling.data_analysis.AnalysisRoutines method) mod_fit() (in module lib.simulation.MINFLUXMonteCarlo) model() (lib.simulation.MINFLUXMonteCarlo.MCAnalysis method) module lib lib.config lib.constants lib.data_handling lib.data_handling.data_analysis lib.data_handling.data_converter lib.data_handling.data_filtering lib.data_handling.data_postprocessing lib.data_handling.data_preprocessing lib.data_handling.mf_parser lib.data_handling.utilities lib.plotting lib.plotting.artefacts lib.plotting.style lib.simulation lib.simulation.experiment lib.simulation.measurement lib.simulation.MINFLUXMonteCarlo lib.simulation.psf_models lib.simulation.setup lib.utilities MOLECULE_BRIGHTNESS (in module lib.constants) MultifluxPostProcessing (class in lib.simulation.MINFLUXMonteCarlo) MultithreadedCopier (class in lib.utilities) N NALM, [1] NALM_Figures (class in lib.plotting.artefacts) nan_mask_list() (lib.utilities.BaseFunc method) NUMBER_OF_MOLECULES (in module lib.constants) NUMERICAL_APERTURE (in module lib.constants) NumpyArrayEncoder (class in lib.utilities) O objective_hess() (lib.data_handling.data_analysis.Estimators method) objective_jac() (lib.data_handling.data_analysis.Estimators method) OUTPUT_DIR (in module lib.config) P pairwise_distances_jax() (in module lib.simulation.MINFLUXMonteCarlo) parse_directory() (lib.data_handling.mf_parser.MF_ParserFacade method) parse_single_file() (in module lib.data_handling.mf_parser) partition_array() (lib.data_handling.utilities.Converter method) partition_record() (lib.data_handling.utilities.Converter method) Pattern (class in lib.simulation.measurement) PatternGenerator (class in lib.simulation.measurement) perform() (lib.data_handling.data_analysis.Study method) (lib.simulation.experiment.Experiment method) pgf_with_latex (in module lib.plotting.style) PhasePatternGenerator (class in lib.simulation.measurement) PHOTON_BUDGET (in module lib.constants) pick_lines_from_record() (lib.simulation.experiment.Record method) PIXEL_NUMBER (in module lib.constants) plot_imarray() (lib.plotting.artefacts.Trace_Figures method) plot_segmented_trace() (lib.plotting.artefacts.Trace_Figures method) PointLinearPhasePattern (class in lib.simulation.measurement) POLY_analysis() (lib.data_handling.data_analysis.AnalysisRoutines method) post_filtering() (lib.data_handling.mf_parser.MinfluxFilterFacade method) post_process() (lib.simulation.MINFLUXMonteCarlo.MultifluxPostProcessing method) post_process_minflux() (lib.data_handling.mf_parser.MinfluxPostProcessing method) postprocess_data() (lib.data_handling.data_postprocessing.PostProcessorFacade method) postprocess_single_file() (in module lib.data_handling.data_postprocessing) PostProcessor (class in lib.data_handling.data_postprocessing) PostProcessorFacade (class in lib.data_handling.data_postprocessing) process_batch() (in module lib.data_handling.mf_parser) process_group() (in module lib.data_handling.data_postprocessing) (in module lib.data_handling.mf_parser) (in module lib.simulation.MINFLUXMonteCarlo) process_minflux() (lib.data_handling.mf_parser.MinfluxProcessorFacade method) process_results() (lib.data_handling.data_postprocessing.PostProcessor method) process_single_file() (lib.data_handling.mf_parser.MinfluxProcessor method) Protocol (class in lib.simulation.experiment) PSF, [1] PSFgenerator (class in lib.simulation.psf_models) PSFmodel (class in lib.simulation.psf_models) R Record (class in lib.simulation.experiment) register_entity() (lib.simulation.experiment.Log method) register_function() (lib.utilities.FunctionLogger method) remove_trailing_zeros() (lib.utilities.BaseFunc method) remove_tuple_outliers() (lib.data_handling.mf_parser.MinfluxFilter method) REPETITIONS (in module lib.constants) rerun_f() (lib.utilities.FunctionLogger method) reshape_record() (lib.data_handling.utilities.Converter method) Residual_Figures (class in lib.plotting.artefacts) Results (class in lib.data_handling.data_analysis) ROOT_DIR (in module lib.config) run() (lib.simulation.MINFLUXMonteCarlo.MCSimulation method) S Sample (class in lib.simulation.setup) SampleGenerator (class in lib.simulation.setup) save() (lib.simulation.experiment.Experiment method) save_as_tif() (lib.simulation.experiment.Experiment method) save_fig() (lib.plotting.artefacts.Figures method) save_figures() (lib.plotting.artefacts.Artefacts method) save_log() (lib.simulation.experiment.Log method) SCAN_RANGE (in module lib.constants) script_name (in module lib.plotting.artefacts) (in module lib.plotting.style) (in module lib.simulation.experiment) (in module lib.simulation.MINFLUXMonteCarlo) segment_frame() (lib.data_handling.mf_parser.MinfluxFilter method) set_image() (lib.plotting.style.ImageHandler method) set_params() (lib.utilities.Configuration method) set_style() (lib.plotting.style.Style method) Setup (class in lib.simulation.setup) SHRINK_FACTOR (in module lib.constants) SIG_TO_FWHM (in module lib.constants) signal_model() (lib.simulation.setup.Setup method) SINGLE_MOLECULE_PHOTON_BUDGET (in module lib.constants) SMLM, [1] stamp() (lib.utilities.Labeler method) standingWave (class in lib.simulation.psf_models) Status (class in lib.utilities) STED_FACTOR (in module lib.constants) STORM, [1] Study (class in lib.data_handling.data_analysis) study_single_file() (in module lib.data_handling.data_analysis) Style (class in lib.plotting.style) SUPERPOSITION_TYPE (in module lib.constants) T terminate() (lib.utilities.FunctionLogger method) to_tuple() (lib.utilities.BaseFunc method) to_yaml() (lib.utilities.Converter method) Trace (class in lib.simulation.setup) Trace_Figures (class in lib.plotting.artefacts) truncate_record() (lib.simulation.experiment.Record method) U unregister_entity() (lib.simulation.experiment.Log method) update() (lib.plotting.style.Style method) (lib.simulation.experiment.Experiment method) W weighted_median() (lib.utilities.BaseFunc method) WINDOW_analysis() (lib.data_handling.data_analysis.AnalysisRoutines method) write_json() (lib.utilities.Exporter method) write_to_log() (lib.simulation.experiment.Log method) write_yaml() (lib.utilities.Exporter method)