DiatomTrack package

Subpackages

• DiatomTrack.core package
  • Submodules
  • DiatomTrack.core.assignment module
    • associate()
    • associate_secondary()
    • calculate_iou()
    • euclid_batch()
    • iou_batch()
    • linear_assignment()
  • DiatomTrack.core.segmentation module
    • run_segmentation()
    • segmentation()
    • segmentation_setup()
  • DiatomTrack.core.tracker module
    • DiatomTrack
      • DiatomTrack.get_state()
      • DiatomTrack.summarize()
      • DiatomTrack.update()
    • KalmanTracker
      • KalmanTracker.count
      • KalmanTracker.get_predictions()
      • KalmanTracker.get_state()
      • KalmanTracker.predict()
      • KalmanTracker.summarize()
      • KalmanTracker.tree
      • KalmanTracker.update()
    • track()
    • tracks_to_dataframe()
  • Module contents
• DiatomTrack.gui package
  • Submodules
  • DiatomTrack.gui.editor module
    • TrackEditor
      • TrackEditor.apply_zoom()
      • TrackEditor.build_tree()
      • TrackEditor.canvas_double_right()
      • TrackEditor.close_window()
      • TrackEditor.down_arrow_press()
      • TrackEditor.draw_overlay()
      • TrackEditor.draw_rectangle()
      • TrackEditor.end_rectangle()
      • TrackEditor.expand_tree()
      • TrackEditor.expand_tree_children()
      • TrackEditor.faster_video()
      • TrackEditor.find_age_line_points()
      • TrackEditor.find_trace_line_points()
      • TrackEditor.finish()
      • TrackEditor.flip_cell()
      • TrackEditor.flip_frustule()
      • TrackEditor.flip_selected_cell()
      • TrackEditor.get_color()
      • TrackEditor.highlight_track()
      • TrackEditor.jump_to_frame()
      • TrackEditor.jump_to_time()
      • TrackEditor.left_arrow_press()
      • TrackEditor.listbox_double_click()
      • TrackEditor.listbox_right_click()
      • TrackEditor.manual_update_canvas()
      • TrackEditor.merge()
      • TrackEditor.play_video()
      • TrackEditor.remove()
      • TrackEditor.remove_restore_short()
      • TrackEditor.reset_zoom()
      • TrackEditor.restart_video()
      • TrackEditor.restore()
      • TrackEditor.right_arrow_press()
      • TrackEditor.scrub()
      • TrackEditor.shift_overlay()
      • TrackEditor.slower_video()
      • TrackEditor.spacebar_press()
      • TrackEditor.split()
      • TrackEditor.start_rectangle()
      • TrackEditor.swap_tracklets()
      • TrackEditor.toggle_cell_age()
      • TrackEditor.toggle_frustule_age()
      • TrackEditor.toggle_id()
      • TrackEditor.toggle_merge()
      • TrackEditor.toggle_move()
      • TrackEditor.toggle_overlay()
      • TrackEditor.toggle_trace()
      • TrackEditor.toggle_tree()
      • TrackEditor.tree_current()
      • TrackEditor.tree_double_click()
      • TrackEditor.tree_double_right()
      • TrackEditor.tree_select()
      • TrackEditor.tree_set_limit()
      • TrackEditor.tree_zoom()
      • TrackEditor.ui_init()
      • TrackEditor.up_arrow_press()
      • TrackEditor.update_canvas()
      • TrackEditor.update_frame_number()
      • TrackEditor.update_speed_display()
      • TrackEditor.update_time()
      • TrackEditor.window_exception()
  • DiatomTrack.gui.load module
    • ReadSegmentationWindow
      • ReadSegmentationWindow.close_window()
      • ReadSegmentationWindow.read_file()
      • ReadSegmentationWindow.window_exception()
    • ReadTrackVideoWindow
      • ReadTrackVideoWindow.close_window()
      • ReadTrackVideoWindow.read_file()
      • ReadTrackVideoWindow.window_exception()
    • ReadTrackWindow
      • ReadTrackWindow.close_window()
      • ReadTrackWindow.read_file()
      • ReadTrackWindow.window_exception()
    • read_seg()
    • read_track()
    • read_tvf()
  • DiatomTrack.gui.parser module
    • ParserDirectory
      • ParserDirectory.close_window()
      • ParserDirectory.invoke_confirm()
      • ParserDirectory.parse()
      • ParserDirectory.reset_inputs()
      • ParserDirectory.select_saving()
      • ParserDirectory.select_source()
      • ParserDirectory.select_states()
      • ParserDirectory.skip_window()
      • ParserDirectory.window_exception()
    • ParserEditor
      • ParserEditor.close_window()
      • ParserEditor.invoke_confirm()
      • ParserEditor.parse()
      • ParserEditor.reset_inputs()
      • ParserEditor.select_saving()
      • ParserEditor.select_track()
      • ParserEditor.select_track_video()
      • ParserEditor.select_video()
      • ParserEditor.window_exception()
    • ParserSkip
      • ParserSkip.close_window()
      • ParserSkip.invoke_confirm()
      • ParserSkip.parse()
      • ParserSkip.reset_inputs()
      • ParserSkip.select_saving()
      • ParserSkip.select_segmentation()
      • ParserSkip.select_states()
      • ParserSkip.select_video()
      • ParserSkip.skip_window()
      • ParserSkip.window_exception()
    • ParserTrack
      • ParserTrack.close_window()
      • ParserTrack.invoke_confirm()
      • ParserTrack.parse()
      • ParserTrack.reset_inputs()
      • ParserTrack.window_exception()
    • parse_editor()
    • parse_segmentation()
    • parse_tracker()
  • DiatomTrack.gui.save module
    • SaveData
      • SaveData.close_window()
      • SaveData.parse()
      • SaveData.save()
      • SaveData.save_df()
      • SaveData.save_metadata_video()
      • SaveData.save_odf()
      • SaveData.save_statistics()
      • SaveData.save_tvf()
      • SaveData.select_saving()
      • SaveData.window_exception()
  • Module contents
• DiatomTrack.model package
  • Submodules
  • DiatomTrack.model.model module
    • UNet
      • UNet.forward()
  • Module contents
• DiatomTrack.utils package
  • Submodules
  • DiatomTrack.utils.DataUtils module
    • InitializeDataPredict
    • SegDatasetPredict
    • cv_imread()
    • cvtColor()
    • resize()
  • DiatomTrack.utils.Transforms module
    • Normalize
    • ToTensor
  • DiatomTrack.utils.contours module
    • contour_filter()
    • contour_filter_process()
    • contours_to_properties()
    • contours_to_rectangles()
    • convert_array_to_rectangle()
    • convert_contour_to_array()
    • rotation_boundary()
  • Module contents

Submodules

DiatomTrack.main module

DiatomTrack.main.main()

Start DiatomTrack. First user input is parsed. Then images are segmented, cells tracked and editor opened based on input.

Return type:

None.

Module contents