Index

Symbols

--gt-track-path traccuracy command line option --install-completion traccuracy command line option --out-path traccuracy command line option

--pred-track-path traccuracy command line option --show-completion traccuracy command line option

A

AOGMMetrics (class in traccuracy.metrics) (class in traccuracy.metrics._ctc)

B

BasicMetrics (class in traccuracy.metrics) (class in traccuracy.metrics._basic)

C

CellCycleAccuracy (class in traccuracy.metrics) (class in traccuracy.metrics._cca) CHOTAMetric (class in traccuracy.metrics) (class in traccuracy.metrics._chota) classify_basic_errors() (in module traccuracy.track_errors) (in module traccuracy.track_errors._basic) clear_annotations() (traccuracy._tracking_graph.TrackingGraph method) (traccuracy.TrackingGraph method) CompleteTracks (class in traccuracy.metrics) (class in traccuracy.metrics._complete_tracks) compute() (traccuracy.metrics._base.Metric method) (traccuracy.metrics._basic.BasicMetrics method) (traccuracy.metrics._cca.CellCycleAccuracy method) (traccuracy.metrics._chota.CHOTAMetric method) (traccuracy.metrics._complete_tracks.CompleteTracks method) (traccuracy.metrics._ctc.AOGMMetrics method) (traccuracy.metrics._ctc.CTCMetrics method) (traccuracy.metrics._divisions.DivisionMetrics method) (traccuracy.metrics._track_overlap.TrackOverlapMetrics method) (traccuracy.metrics.AOGMMetrics method) (traccuracy.metrics.BasicMetrics method) (traccuracy.metrics.CellCycleAccuracy method) (traccuracy.metrics.CHOTAMetric method) (traccuracy.metrics.CompleteTracks method) (traccuracy.metrics.CTCMetrics method) (traccuracy.metrics.DivisionMetrics method) (traccuracy.metrics.TrackOverlapMetrics method)

compute_mapping() (traccuracy.matchers._base.Matcher method) (traccuracy.matchers._ctc.CTCMatcher method) (traccuracy.matchers._iou.IOUMatcher method) (traccuracy.matchers._point.PointMatcher method) (traccuracy.matchers._point_seg.PointSegMatcher method) (traccuracy.matchers.CTCMatcher method) (traccuracy.matchers.IOUMatcher method) (traccuracy.matchers.PointMatcher method) (traccuracy.matchers.PointSegMatcher method) compute_overlap() (in module traccuracy.matchers._compute_overlap) compute_overlap_3D() (in module traccuracy.matchers._compute_overlap) CTC_FALSE_NEG (traccuracy._tracking_graph.EdgeFlag attribute) (traccuracy._tracking_graph.NodeFlag attribute) (traccuracy.EdgeFlag attribute) (traccuracy.NodeFlag attribute) CTC_FALSE_POS (traccuracy._tracking_graph.EdgeFlag attribute) (traccuracy._tracking_graph.NodeFlag attribute) (traccuracy.EdgeFlag attribute) (traccuracy.NodeFlag attribute) ctc_to_graph() (in module traccuracy.loaders._ctc) CTC_TRUE_POS (traccuracy._tracking_graph.NodeFlag attribute) (traccuracy.NodeFlag attribute) CTCMatcher (class in traccuracy.matchers) (class in traccuracy.matchers._ctc) CTCMetrics (class in traccuracy.metrics) (class in traccuracy.metrics._ctc)

D

Division

DivisionMetrics (class in traccuracy.metrics) (class in traccuracy.metrics._divisions)

E

Edge EdgeFlag (class in traccuracy) (class in traccuracy._tracking_graph) edges (traccuracy._tracking_graph.TrackingGraph property) (traccuracy.TrackingGraph property) end_frame (traccuracy._tracking_graph.TrackingGraph attribute) (traccuracy.TrackingGraph attribute)

evaluate_ctc_events() (in module traccuracy.track_errors) (in module traccuracy.track_errors._ctc) evaluate_division_events() (in module traccuracy.track_errors) (in module traccuracy.track_errors._divisions) export_graphs_to_geff() (in module traccuracy.utils)

F

F1 Score False negative False positive FALSE_NEG (traccuracy._tracking_graph.EdgeFlag attribute) (traccuracy._tracking_graph.NodeFlag attribute) (traccuracy.EdgeFlag attribute) (traccuracy.NodeFlag attribute) FALSE_POS (traccuracy._tracking_graph.EdgeFlag attribute) (traccuracy._tracking_graph.NodeFlag attribute) (traccuracy.EdgeFlag attribute) (traccuracy.NodeFlag attribute)

FN_DIV (traccuracy._tracking_graph.NodeFlag attribute) (traccuracy.NodeFlag attribute) FP_DIV (traccuracy._tracking_graph.NodeFlag attribute) (traccuracy.NodeFlag attribute) frame_key (traccuracy._tracking_graph.TrackingGraph attribute) (traccuracy.TrackingGraph attribute)

G

get_corrected_division_graphs_with_delta() (in module traccuracy.utils) get_divisions() (traccuracy._tracking_graph.TrackingGraph method) (traccuracy.TrackingGraph method) get_edge_errors() (in module traccuracy.track_errors._ctc) get_edges_with_flag() (traccuracy._tracking_graph.TrackingGraph method) (traccuracy.TrackingGraph method) get_equivalent_skip_edge() (in module traccuracy.utils) get_gt_pred_match() (traccuracy.matchers._matched.Matched method) (traccuracy.matchers.Matched method) get_gt_pred_matches() (traccuracy.matchers._matched.Matched method) (traccuracy.matchers.Matched method) get_labels_with_overlap() (in module traccuracy.matchers) (in module traccuracy.matchers._compute_overlap) get_lineages() (traccuracy._tracking_graph.TrackingGraph method) (traccuracy.TrackingGraph method) get_location() (traccuracy._tracking_graph.TrackingGraph method) (traccuracy.TrackingGraph method) get_merges() (traccuracy._tracking_graph.TrackingGraph method) (traccuracy.TrackingGraph method)

get_nodes_with_flag() (traccuracy._tracking_graph.TrackingGraph method) (traccuracy.TrackingGraph method) get_pred_gt_match() (traccuracy.matchers._matched.Matched method) (traccuracy.matchers.Matched method) get_pred_gt_matches() (traccuracy.matchers._matched.Matched method) (traccuracy.matchers.Matched method) get_skip_edges() (traccuracy._tracking_graph.TrackingGraph method) (traccuracy.TrackingGraph method) get_tracklets() (traccuracy._tracking_graph.TrackingGraph method) (traccuracy.TrackingGraph method) get_vertex_errors() (in module traccuracy.track_errors._ctc) get_weighted_edge_error_sum() (in module traccuracy.metrics._ctc) get_weighted_error_sum() (in module traccuracy.metrics._ctc) get_weighted_vertex_error_sum() (in module traccuracy.metrics._ctc) graph_bbox_and_labels() (in module traccuracy.matchers._compute_overlap) GT_DIR traccuracy command line option

H

has_value() (traccuracy._tracking_graph.NodeFlag class method) (traccuracy.NodeFlag class method)

I

info (traccuracy.matchers._base.Matcher property) (traccuracy.matchers._ctc.CTCMatcher property) (traccuracy.matchers._iou.IOUMatcher property) (traccuracy.matchers._point.PointMatcher property) (traccuracy.matchers._point_seg.PointSegMatcher property) (traccuracy.matchers.CTCMatcher property) (traccuracy.matchers.IOUMatcher property) (traccuracy.matchers.PointMatcher property) (traccuracy.matchers.PointSegMatcher property) (traccuracy.metrics._base.Metric property) (traccuracy.metrics._basic.BasicMetrics property) (traccuracy.metrics._cca.CellCycleAccuracy property) (traccuracy.metrics._chota.CHOTAMetric property) (traccuracy.metrics._complete_tracks.CompleteTracks property) (traccuracy.metrics._ctc.AOGMMetrics property) (traccuracy.metrics._ctc.CTCMetrics property) (traccuracy.metrics._divisions.DivisionMetrics property) (traccuracy.metrics._track_overlap.TrackOverlapMetrics property) (traccuracy.metrics.AOGMMetrics property) (traccuracy.metrics.BasicMetrics property) (traccuracy.metrics.CellCycleAccuracy property) (traccuracy.metrics.CHOTAMetric property) (traccuracy.metrics.CompleteTracks property) (traccuracy.metrics.CTCMetrics property) (traccuracy.metrics.DivisionMetrics property) (traccuracy.metrics.TrackOverlapMetrics property)

INTERTRACK_EDGE (traccuracy._tracking_graph.EdgeFlag attribute) (traccuracy.EdgeFlag attribute) IOUMatcher (class in traccuracy.matchers) (class in traccuracy.matchers._iou) is_skip_edge() (traccuracy._tracking_graph.TrackingGraph method) (traccuracy.TrackingGraph method)

L

Lineage load_ctc_data() (in module traccuracy.loaders) (in module traccuracy.loaders._ctc) load_geff_data() (in module traccuracy.loaders) (in module traccuracy.loaders._geff) load_point_data() (in module traccuracy.loaders) (in module traccuracy.loaders._point) load_tiffs() (in module traccuracy.loaders) (in module traccuracy.loaders._ctc)

location_keys (traccuracy._tracking_graph.TrackingGraph attribute) (traccuracy.TrackingGraph attribute) LOG (in module traccuracy.metrics._chota) logger (in module traccuracy._tracking_graph) (in module traccuracy.loaders._ctc) (in module traccuracy.matchers._base) (in module traccuracy.metrics._divisions) (in module traccuracy.track_errors._basic) (in module traccuracy.track_errors._ctc)

M

match_iou() (in module traccuracy.matchers._iou) match_point_to_seg() (in module traccuracy.matchers._point_seg) Matched (class in traccuracy.matchers) (class in traccuracy.matchers._matched) Matcher (class in traccuracy.matchers._base) matching_type (traccuracy.matchers._matched.Matched property) (traccuracy.matchers.Matched property) MATCHING_TYPES (in module traccuracy.metrics._base) Metric (class in traccuracy.metrics._base) MIN_BUFFER_CORRECT (traccuracy._tracking_graph.NodeFlag attribute) (traccuracy.NodeFlag attribute) MIN_BUFFER_CORRECT_SKIP (traccuracy._tracking_graph.NodeFlag attribute) (traccuracy.NodeFlag attribute) module traccuracy traccuracy._run_metrics traccuracy._tracking_graph traccuracy.loaders traccuracy.loaders._ctc traccuracy.loaders._geff traccuracy.loaders._point traccuracy.matchers traccuracy.matchers._base traccuracy.matchers._compute_overlap traccuracy.matchers._ctc traccuracy.matchers._iou traccuracy.matchers._matched traccuracy.matchers._point traccuracy.matchers._point_seg traccuracy.metrics traccuracy.metrics._base traccuracy.metrics._basic traccuracy.metrics._cca traccuracy.metrics._chota traccuracy.metrics._complete_tracks traccuracy.metrics._ctc traccuracy.metrics._divisions traccuracy.metrics._results traccuracy.metrics._track_overlap traccuracy.track_errors traccuracy.track_errors._basic traccuracy.track_errors._ctc traccuracy.track_errors._divisions traccuracy.utils

N

Node NodeFlag (class in traccuracy) (class in traccuracy._tracking_graph) nodes (traccuracy._tracking_graph.TrackingGraph property) (traccuracy.TrackingGraph property)

nodes_by_frame (traccuracy._tracking_graph.TrackingGraph attribute) (traccuracy.TrackingGraph attribute) NON_SPLIT (traccuracy._tracking_graph.NodeFlag attribute) (traccuracy.NodeFlag attribute)

P

Parent cell PointMatcher (class in traccuracy.matchers) (class in traccuracy.matchers._point) PointSegMatcher (class in traccuracy.matchers) (class in traccuracy.matchers._point_seg)

Precision PRED_DIR traccuracy command line option Predecessor

R

Recall remove_flag_from_edge() (traccuracy._tracking_graph.TrackingGraph method) (traccuracy.TrackingGraph method) remove_flag_from_node() (traccuracy._tracking_graph.TrackingGraph method) (traccuracy.TrackingGraph method)

Results (class in traccuracy.metrics) (class in traccuracy.metrics._results) run_metrics() (in module traccuracy) (in module traccuracy._run_metrics)

S

save_results_json() (in module traccuracy.utils) set_flag_on_all_edges() (traccuracy._tracking_graph.TrackingGraph method) (traccuracy.TrackingGraph method) set_flag_on_all_nodes() (traccuracy._tracking_graph.TrackingGraph method) (traccuracy.TrackingGraph method) set_flag_on_edge() (traccuracy._tracking_graph.TrackingGraph method) (traccuracy.TrackingGraph method) set_flag_on_node() (traccuracy._tracking_graph.TrackingGraph method) (traccuracy.TrackingGraph method) signature (in module traccuracy.matchers._compute_overlap)

Skip Edges SKIP_FALSE_NEG (traccuracy._tracking_graph.EdgeFlag attribute) (traccuracy.EdgeFlag attribute) SKIP_FALSE_POS (traccuracy._tracking_graph.EdgeFlag attribute) (traccuracy.EdgeFlag attribute) SKIP_TRUE_POS (traccuracy._tracking_graph.EdgeFlag attribute) (traccuracy.EdgeFlag attribute) start_frame (traccuracy._tracking_graph.TrackingGraph attribute) (traccuracy.TrackingGraph attribute) Successor

T

to_dict() (traccuracy.metrics._results.Results method) (traccuracy.metrics.Results method) TP_DIV (traccuracy._tracking_graph.NodeFlag attribute) (traccuracy.NodeFlag attribute) TP_DIV_SKIP (traccuracy._tracking_graph.NodeFlag attribute) (traccuracy.NodeFlag attribute) traccuracy module traccuracy command line option --gt-track-path --install-completion --out-path --pred-track-path --show-completion GT_DIR PRED_DIR traccuracy._run_metrics module traccuracy._tracking_graph module traccuracy.loaders module traccuracy.loaders._ctc module traccuracy.loaders._geff module traccuracy.loaders._point module traccuracy.matchers module traccuracy.matchers._base module traccuracy.matchers._compute_overlap module traccuracy.matchers._ctc module traccuracy.matchers._iou module traccuracy.matchers._matched module traccuracy.matchers._point module

traccuracy.matchers._point_seg module traccuracy.metrics module traccuracy.metrics._base module traccuracy.metrics._basic module traccuracy.metrics._cca module traccuracy.metrics._chota module traccuracy.metrics._complete_tracks module traccuracy.metrics._ctc module traccuracy.metrics._divisions module traccuracy.metrics._results module traccuracy.metrics._track_overlap module traccuracy.track_errors module traccuracy.track_errors._basic module traccuracy.track_errors._ctc module traccuracy.track_errors._divisions module traccuracy.utils module TrackingGraph (class in traccuracy) (class in traccuracy._tracking_graph) Tracklet TrackOverlapMetrics (class in traccuracy.metrics) (class in traccuracy.metrics._track_overlap) True positive TRUE_POS (traccuracy._tracking_graph.EdgeFlag attribute) (traccuracy._tracking_graph.NodeFlag attribute) (traccuracy.EdgeFlag attribute) (traccuracy.NodeFlag attribute)

V

version (traccuracy.metrics._results.Results property) (traccuracy.metrics.Results property)

W

WC_DIV (traccuracy._tracking_graph.NodeFlag attribute) (traccuracy.NodeFlag attribute)

WRONG_SEMANTIC (traccuracy._tracking_graph.EdgeFlag attribute) (traccuracy.EdgeFlag attribute)