Index

_

__init__() (align method) (alignParameters method) (autoreg method) (autoregParameters method) (BasePlotter method) (butter method) (butterParameters method) (Cache method) (CellTracker method) (crosscorr method) (crosscorrParameters method) (detrend method) (detrendParameters method) (dsignal method) (dsignalParameters method) (FeatureCalculator method) (fft method) (fftParameters method) (findpeaks method) (findpeaksParameters method) (gpsignal method) (gpsignalParameters method) (interpolate method) (interpolateParameters method) (mi method) (miParameters method) (ParametersABC method) (Parser method) (PostProcessABC method) (ProcessABC method) (savgol method) (savgolParameters method) (standardscaler method) (standardscalerParameters method) (StepABC method) (Template method) (TemplateParameters method)

A

accumulate() (in module agora.io.utils) add_index_levels() (in module agora.utils.kymograph) add_to_collection() (in module agora.abc) agora module agora.abc module agora.io module agora.io.decorators module agora.io.utils module agora.logging module agora.track_abc module agora.utils module agora.utils.association module agora.utils.cast module agora.utils.indexing module agora.utils.kymograph module agora.utils.merge module

aliby module aliby.bin module aliby.io module aliby.lineage module aliby.tile module aliby.tile.traps module aliby.track module aliby.track.cell_tracker module aliby.track.utils module aliby.utils module align (class in postprocessor.core.multisignal.align) alignParameters (class in postprocessor.core.multisignal.align) apply_merges() (in module agora.utils.merge) area() (in module extraction.core.functions.cell) assign_lbls() (CellTracker method) autoreg (class in postprocessor.core.processes.autoreg) autoreg_periodogram() (autoreg method) autoregParameters (class in postprocessor.core.processes.autoreg)

B

background_max5() (in module extraction.core.functions.trap) BasePlotter (class in postprocessor.routines.plottingabc) bidirectional_retainment_filter() (in module agora.utils.kymograph)

butter (class in postprocessor.core.processes.butter) butterfilter() (butter method) butterParameters (class in postprocessor.core.processes.butter)

C

Cache (class in agora.io.utils) calc_baryangles() (in module aliby.track.utils) calc_barycentre() (in module aliby.track.utils) calc_barydists() (in module aliby.track.utils) calc_dtfeats() (CellTracker method) calc_feat_ndarray() (CellTracker method) calc_feats_from_mask() (CellTracker method) (FeatureCalculator method) calc_trapfeats() (CellTracker method) (FeatureCalculator method)

CellTracker (class in aliby.track.cell_tracker) check_type_recursive() (in module agora.abc) classical_periodogram() (fft method) cluster_kymograph() (in module agora.utils.kymograph) compare_indices() (in module agora.utils.indexing) compare_pred_truth_lols() (in module aliby.track.utils) conical_volume() (in module extraction.core.functions.cell) crosscorr (class in postprocessor.core.multisignal.crosscorr) crosscorrParameters (class in postprocessor.core.multisignal.crosscorr)

D

detrend (class in postprocessor.core.processes.detrend) detrendParameters (class in postprocessor.core.processes.detrend) df_extend_nan() (in module postprocessor.core.multisignal.align) df_shift() (in module postprocessor.core.multisignal.align)

div0() (in module extraction.core.functions.math_utils) drop_level() (in module agora.utils.kymograph) drop_mother_label() (in module agora.utils.kymograph) dsignal (class in postprocessor.core.processes.dsignal) dsignalParameters (class in postprocessor.core.processes.dsignal)

E

eccentricity() (in module extraction.core.functions.cell) estimate_gr() (in module postprocessor.core.processes.gpsignal) extract_header() (in module logfile_parser.swainlab_parser) extraction module extraction.core module extraction.core.functions module extraction.core.functions.cell module extraction.core.functions.custom module

extraction.core.functions.custom.localisation module extraction.core.functions.distributors module extraction.core.functions.loaders module extraction.core.functions.math_utils module extraction.core.functions.trap module extraction.core.functions.versioning module extraction.local_data_loaders module

F

FeatureCalculator (class in agora.track_abc) fft (class in postprocessor.core.processes.fft) fftParameters (class in postprocessor.core.processes.fft) fields_to_dict_or_table() (in module logfile_parser.swainlab_parser) filt_cluster() (in module agora.utils.kymograph) findpeaks (class in postprocessor.core.processes.findpeaks) findpeaksParameters (class in postprocessor.core.processes.findpeaks) fit_autoreg() (autoreg method) from_yaml() (alignParameters class method) (autoregParameters class method) (butterParameters class method) (crosscorrParameters class method) (detrendParameters class method) (dsignalParameters class method) (fftParameters class method) (findpeaksParameters class method) (gpsignalParameters class method) (interpolateParameters class method) (miParameters class method) (ParametersABC class method) (savgolParameters class method) (standardscalerParameters class method) (TemplateParameters class method)

G

gauss3D() (in module extraction.core.functions.custom.localisation) generate_palette_map() (in module postprocessor.routines.plot_utils) get_examples_dir() (in module logfile_parser.legacy) get_feats2use() (CellTracker method) get_index_as_np() (in module agora.utils.kymograph) get_legacy_log_example_interface() (in module logfile_parser.legacy) get_logfile_grammars_dir() (in module logfile_parser.legacy) get_mother_ilocs_from_daughters() (in module agora.utils.kymograph) get_mothers_from_another_df() (in module agora.utils.kymograph)

get_new_lbls() (CellTracker method) get_nfeats_from_model() (in module aliby.track.cell_tracker) get_parameters() (in module postprocessor.core.abc) get_process() (in module postprocessor.core.abc) get_sha() (in module extraction.core.functions.versioning) get_store_path() (in module agora.io.utils) gpsignal (class in postprocessor.core.processes.gpsignal) gpsignalParameters (class in postprocessor.core.processes.gpsignal) GrammarNotFound group_merges() (in module agora.utils.merge)

H

half_ceil() (in module aliby.tile.traps) half_floor() (in module aliby.tile.traps)

HeaderEndNotFound heatmap() (in module postprocessor.routines.heatmap) histogram() (in module postprocessor.routines.histogram)

I

identify_trap_locations() (in module aliby.tile.traps) imBackground() (in module extraction.core.functions.trap) imread() (in module agora.io.utils)

interpolate (class in postprocessor.core.processes.interpolate) interpolateParameters (class in postprocessor.core.processes.interpolate) intersection_matrix() (in module agora.utils.kymograph)

J

join_tracks_pair() (in module agora.utils.merge)

L

load() (in module extraction.local_data_loaders) load_1z() (in module extraction.local_data_loaders) load_cellfuns() (in module extraction.core.functions.loaders) load_cellfuns_core() (in module extraction.core.functions.loaders) load_custom_args() (in module extraction.core.functions.loaders) load_funs() (in module extraction.core.functions.loaders) load_paired_images() (in module extraction.local_data_loaders) load_redfuns() (in module extraction.core.functions.loaders) load_tiled_image() (in module extraction.local_data_loaders)

load_trapfuns() (in module extraction.core.functions.loaders) logfile_parser module logfile_parser.legacy module logfile_parser.logfile_parser module logfile_parser.swainlab_parser module lol_to_adj() (in module aliby.track.utils)

M

matlab_style_gauss2D() (in module extraction.core.functions.custom.localisation) max2p5pc() (in module extraction.core.functions.cell) max5px() (in module extraction.core.functions.cell) mean() (in module extraction.core.functions.cell) mean_plot() (in module postprocessor.routines.mean_plot) median() (in module extraction.core.functions.cell) median_plot() (in module postprocessor.routines.median_plot) melt_reset() (in module agora.utils.kymograph) merge_association() (in module agora.utils.merge) mi (class in postprocessor.core.multisignal.mi) min_maj_approximation() (in module extraction.core.functions.cell) miParameters (class in postprocessor.core.multisignal.mi) module agora agora.abc agora.io agora.io.decorators agora.io.utils agora.logging agora.track_abc agora.utils agora.utils.association agora.utils.cast agora.utils.indexing agora.utils.kymograph agora.utils.merge aliby aliby.bin aliby.io aliby.lineage aliby.tile aliby.tile.traps aliby.track aliby.track.cell_tracker aliby.track.utils aliby.utils extraction extraction.core extraction.core.functions extraction.core.functions.cell extraction.core.functions.custom extraction.core.functions.custom.localisation extraction.core.functions.distributors extraction.core.functions.loaders extraction.core.functions.math_utils extraction.core.functions.trap extraction.core.functions.versioning extraction.local_data_loaders logfile_parser logfile_parser.legacy logfile_parser.logfile_parser logfile_parser.swainlab_parser postprocessor postprocessor.core postprocessor.core.abc postprocessor.core.functions postprocessor.core.multisignal postprocessor.core.multisignal.align postprocessor.core.multisignal.crosscorr postprocessor.core.multisignal.mi postprocessor.core.processes postprocessor.core.processes.autoreg postprocessor.core.processes.butter postprocessor.core.processes.detrend postprocessor.core.processes.dsignal postprocessor.core.processes.fft postprocessor.core.processes.findpeaks postprocessor.core.processes.gpsignal postprocessor.core.processes.interpolate postprocessor.core.processes.savgol postprocessor.core.processes.standardscaler postprocessor.core.processes.template postprocessor.routines postprocessor.routines.heatmap postprocessor.routines.histogram postprocessor.routines.mean_plot postprocessor.routines.median_plot postprocessor.routines.plot_utils postprocessor.routines.plottingabc postprocessor.routines.single_birth_plot postprocessor.routines.single_plot

N

non_uniform_savgol() (in module postprocessor.core.processes.savgol)

nuc_conv_3d() (in module extraction.core.functions.custom.localisation) nuc_est_conv() (in module extraction.core.functions.custom.localisation)

O

optimise_ar_order() (autoreg method)

P

ParametersABC (class in agora.abc) parametrized() (in module agora.io.utils) parse() (Parser method) parse_fields() (in module logfile_parser.swainlab_parser) parse_from_grammar() (in module logfile_parser.swainlab_parser) parse_from_swainlab_grammar() (in module logfile_parser.swainlab_parser) parse_table() (in module logfile_parser.swainlab_parser) parse_x() (in module logfile_parser.swainlab_parser) ParseError Parser (class in logfile_parser.logfile_parser) pick_baryfun() (in module aliby.track.utils) plot() (BasePlotter method) PostProcessABC (class in postprocessor.core.abc) postprocessor module postprocessor.core module postprocessor.core.abc module postprocessor.core.functions module postprocessor.core.multisignal module postprocessor.core.multisignal.align module postprocessor.core.multisignal.crosscorr module postprocessor.core.multisignal.mi module postprocessor.core.processes module postprocessor.core.processes.autoreg module postprocessor.core.processes.butter module postprocessor.core.processes.detrend module

postprocessor.core.processes.dsignal module postprocessor.core.processes.fft module postprocessor.core.processes.findpeaks module postprocessor.core.processes.gpsignal module postprocessor.core.processes.interpolate module postprocessor.core.processes.savgol module postprocessor.core.processes.standardscaler module postprocessor.core.processes.template module postprocessor.routines module postprocessor.routines.heatmap module postprocessor.routines.histogram module postprocessor.routines.mean_plot module postprocessor.routines.median_plot module postprocessor.routines.plot_utils module postprocessor.routines.plottingabc module postprocessor.routines.single_birth_plot module postprocessor.routines.single_plot module predict_proba_from_ndarray() (CellTracker method) probabilities_from_impair() (CellTracker method) ProcessABC (class in agora.abc)

R

reduce_z() (in module extraction.core.functions.distributors) repr_obj() (in module agora.io.utils) run() (align method) (autoreg method) (butter method) (crosscorr method) (detrend method) (fft method) (findpeaks method) (mi method) (standardscaler method)

run_tp() (CellTracker method)

S

savgol (class in postprocessor.core.processes.savgol) savgolParameters (class in postprocessor.core.processes.savgol) scale_feats() (CellTracker method) (FeatureCalculator method) segment_traps() (in module aliby.tile.traps) single_birth_plot() (in module postprocessor.routines.single_birth_plot) single_plot() (in module postprocessor.routines.single_plot) slices_from_spans() (in module agora.utils.kymograph) small_peaks_conv() (in module extraction.core.functions.custom.localisation)

sort_association() (in module agora.utils.merge) spherical_volume() (in module extraction.core.functions.cell) split_df() (in module agora.utils.kymograph) standard_filtering() (in module agora.utils.kymograph) standardscaler (class in postprocessor.core.processes.standardscaler) standardscalerParameters (class in postprocessor.core.processes.standardscaler) std() (in module extraction.core.functions.cell) StepABC (class in agora.abc) switch_case_nfeats() (in module aliby.track.cell_tracker)

T

table_to_df() (in module logfile_parser.swainlab_parser) Template (class in postprocessor.core.processes.template) TemplateParameters (class in postprocessor.core.processes.template) timed() (in module agora.io.utils) timer() (in module agora.logging) to_dict() (alignParameters method) (autoregParameters method) (butterParameters method) (crosscorrParameters method) (detrendParameters method) (dsignalParameters method) (fftParameters method) (findpeaksParameters method) (gpsignalParameters method) (interpolateParameters method) (miParameters method) (ParametersABC method) (savgolParameters method) (standardscalerParameters method) (TemplateParameters method)

to_legacy() (in module logfile_parser.legacy) to_yaml() (alignParameters method) (autoregParameters method) (butterParameters method) (crosscorrParameters method) (detrendParameters method) (dsignalParameters method) (fftParameters method) (findpeaksParameters method) (gpsignalParameters method) (interpolateParameters method) (miParameters method) (ParametersABC method) (savgolParameters method) (standardscalerParameters method) (TemplateParameters method) trap_apply() (in module extraction.core.functions.distributors)

U

union_find() (in module agora.utils.merge) update() (alignParameters method) (autoregParameters method) (butterParameters method) (crosscorrParameters method) (detrendParameters method) (dsignalParameters method) (fftParameters method) (findpeaksParameters method) (gpsignalParameters method) (interpolateParameters method) (miParameters method) (ParametersABC method) (savgolParameters method) (standardscalerParameters method) (TemplateParameters method)

V

validate_association() (in module agora.utils.indexing)

volume() (in module extraction.core.functions.cell)