SCTrack package

Submodules

• SCTrack.base module
  • Cell
    • Cell.area
    • Cell.available_range
    • Cell.bbox
    • Cell.branch_id
    • Cell.cell_id
    • Cell.center
    • Cell.change_mitosis_flag()
    • Cell.contours
    • Cell.d_long
    • Cell.d_short
    • Cell.draw()
    • Cell.feature
    • Cell.is_accurate_matched
    • Cell.is_be_matched
    • Cell.move()
    • Cell.move_speed
    • Cell.parent
    • Cell.polygon_area()
    • Cell.polygon_centroid()
    • Cell.r_long
    • Cell.r_short
    • Cell.region
    • Cell.set_branch_id()
    • Cell.set_cell_id()
    • Cell.set_feature()
    • Cell.set_match_status()
    • Cell.set_parent_id()
    • Cell.set_region()
    • Cell.set_status()
    • Cell.set_track_id()
    • Cell.status
    • Cell.track_id
    • Cell.update_region()
    • Cell.update_speed()
    • Cell.vector
  • CellStatus
  • MatchStatus
    • MatchStatus.LossMatch
    • MatchStatus.Matched
    • MatchStatus.Unmatched
  • NoneTypeFilter()
  • Rectangle
    • Rectangle.area
    • Rectangle.draw()
    • Rectangle.isInclude()
    • Rectangle.isIntersect()
  • SingleInstance
    • SingleInstance.init_flag
  • TreeStatus
    • TreeStatus.add_M_count()
    • TreeStatus.add_exist_time()
    • TreeStatus.check_division_window()
    • TreeStatus.enter_mitosis()
    • TreeStatus.exit_mitosis()
    • TreeStatus.exit_mitosis_time
    • TreeStatus.get_status()
    • TreeStatus.is_in_division_window()
    • TreeStatus.is_mitosis_enter
    • TreeStatus.predict_M_len
    • TreeStatus.reset_M_count()
    • TreeStatus.reset_division_window()
    • TreeStatus.set_matched_status()
    • TreeStatus.status
    • TreeStatus.sub_division_window()
  • Vector
    • Vector.EuclideanDistance()
    • Vector.cos
    • Vector.cosDistance()
    • Vector.cosSimilar()
    • Vector.module
  • warningFilter()
• SCTrack.config module
• SCTrack.feature module
  • Feature
  • FeatureExtractor
    • FeatureExtractor.GetAreaByVector()
    • FeatureExtractor.add_cell()
    • FeatureExtractor.area()
    • FeatureExtractor.bbox()
    • FeatureExtractor.cells
    • FeatureExtractor.convert_dtype()
    • FeatureExtractor.coord2counter()
    • FeatureExtractor.coordinate2mask()
    • FeatureExtractor.ellipse_points()
    • FeatureExtractor.extract()
    • FeatureExtractor.get_cell_image()
    • FeatureExtractor.get_cell_list()
    • FeatureExtractor.get_regions()
    • FeatureExtractor.get_roi_from_coord()
    • FeatureExtractor.get_roi_from_mask()
    • FeatureExtractor.set_cell_image()
    • FeatureExtractor.show()
  • Mask
    • Mask.center
    • Mask.mask
  • feature_extract()
  • get_frame_by_index()
  • imread()
• SCTrack.generate_tracking_stack module
  • JsonParser
    • JsonParser.get_coords_by_frame_index()
    • JsonParser.get_coords_by_frame_name()
    • JsonParser.get_frame_name_by_index()
    • JsonParser.parse_json()
  • Mask
    • Mask.center
    • Mask.mask
  • RefinedParser
    • RefinedParser.get_stack()
    • RefinedParser.parse_id()
    • RefinedParser.parse_position()
  • Stack
  • coord2counter()
  • coordinate2mask()
  • csv2mask()
  • extractRoiFromImg()
  • link()
• SCTrack.prepare module
  • DetectionParser
    • DetectionParser.get_frame_names()
    • DetectionParser.get_region_attr()
    • DetectionParser.get_regions_by_frame()
  • convert_dtype()
  • draw_bbox()
  • json2box()
• SCTrack.reclassification module
  • TreeParser
    • TreeParser.bfs()
    • TreeParser.check_ctype_exit()
    • TreeParser.check_ctype_start()
    • TreeParser.check_mitosis_start()
    • TreeParser.get_child()
    • TreeParser.get_lineage_dict()
    • TreeParser.parse_g1_g2()
    • TreeParser.parse_lineage()
    • TreeParser.parse_lineage_branch_id()
    • TreeParser.parse_lineage_phase()
    • TreeParser.parse_mitosis()
    • TreeParser.parse_mitosis_error()
    • TreeParser.parse_s()
    • TreeParser.record_cell_division_count()
    • TreeParser.search_root_node()
    • TreeParser.set_cell_id()
    • TreeParser.smooth_type()
  • find_combinations_objects()
  • pares_single_tree()
  • paste()
  • relink_tree()
  • run()
  • run_track()
  • track_tree_to_TRA()
  • track_tree_to_mask()
  • track_tree_to_table()
  • track_trees_to_json()
• SCTrack.sctrack module
  • main()
• SCTrack.t_error module
  • ErrorMatchMitosis
  • InsertError
  • MatchFailed
  • MitosisError
  • NodeExistError
  • StatusError
• SCTrack.template module
• SCTrack.track module
  • start_track()
• SCTrack.tracker module
  • CellNode
    • CellNode.STATUS
    • CellNode.get_branch_id()
    • CellNode.get_children()
    • CellNode.get_parent()
    • CellNode.get_status()
    • CellNode.get_track_id()
    • CellNode.get_tree_status()
    • CellNode.identifier
    • CellNode.nid
    • CellNode.set_branch_id()
    • CellNode.set_children()
    • CellNode.set_parent()
    • CellNode.set_status()
    • CellNode.set_track_id()
    • CellNode.set_tree_status()
  • Checker
    • Checker.check()
  • Match
    • Match.calcAreaSimilar()
    • Match.calcCosDistance()
    • Match.calcCosSimilar()
    • Match.calcEuclideanDistance()
    • Match.calcIoU()
    • Match.calcIoU_roughly()
    • Match.compareDicSimilar()
    • Match.compareMcySimilar()
    • Match.compareShapeSimilar()
    • Match.normalize()
  • Matcher
    • Matcher.add_child_node()
    • Matcher.calc_similar()
    • Matcher.calc_sorted_value()
    • Matcher.check_iou()
    • Matcher.draw_bbox()
    • Matcher.get_similar_sister()
    • Matcher.is_mitosis_start()
    • Matcher.match_candidates()
    • Matcher.match_duplicate_child()
    • Matcher.match_one()
    • Matcher.match_similar()
    • Matcher.match_single_cell()
    • Matcher.predict_next_position()
    • Matcher.select_mitosis_cells()
    • Matcher.select_single_child()
  • Tracker
    • Tracker.add_node()
    • Tracker.check_track()
    • Tracker.draw_bbox()
    • Tracker.get_current_tree()
    • Tracker.handle_duplicate_match()
    • Tracker.id_distributor()
    • Tracker.init_tracking_tree()
    • Tracker.rematch()
    • Tracker.track()
    • Tracker.track_near_frame()
    • Tracker.track_near_frame_mult_thread()
    • Tracker.track_tree_to_json()
    • Tracker.update_speed()
    • Tracker.visualize_single_tree()
    • Tracker.visualize_to_tif()
  • TrackingTree
    • TrackingTree.add_node()
    • TrackingTree.auto_update_last_layer()
    • TrackingTree.branch_id_distributor()
    • TrackingTree.change_mitosis_flag()
    • TrackingTree.get_childs()
    • TrackingTree.get_parent()
    • TrackingTree.last_layer
    • TrackingTree.last_layer_cell
    • TrackingTree.update_last_layer()
  • get_cell_line_from_tree()
• SCTrack.utils module
  • convert_dtype()
  • mask_seq_to_json()
  • mask_tif_to_json()
  • mask_to_coords()
  • mask_to_json()
  • readTif()
  • tif2png()
  • time_it()

Module contents