DiatomTrack.gui package

Submodules

DiatomTrack.gui.editor module

class DiatomTrack.gui.editor.TrackEditor(tracks, video_path)

Bases: object

Main GUI window of the DiatomTrack editor for manual editing and review.

apply_zoom(image)

Apply zoom on current frame.

build_tree()

Build the forest in the tree widget.

canvas_double_right(event)

Select and highlight closest object in canvas upon double right click.

close_window()

Confirm abrupt exit.

down_arrow_press(*args)

Jump one frame backward upon down arrow press.

draw_overlay(image)

Draw the corresponding overlay on the current video frame for all activated information.

draw_rectangle(event)

Draw rectangle overlay to mark out zoomed area.

end_rectangle(*args)

Set dimensions of rectangle and refresh parameters, canvas and tree.

expand_tree()

Expand all trees.

expand_tree_children(parent)

Expand a tree.

faster_video(*args)

Accelerate video playback.

find_age_line_points(row)

Find end points for drawing the side / age / theca marker lines of the cells.

find_trace_line_points(item)

Find the line points of the long axis to draw the trace of an object for the last 10 frames’ position.

finish()

Close window to progress orderly to the next step.

flip_cell()

Flip assigned age of selected track’s / cell’s children if applicable.

flip_frustule()

Flip the thecae / side assignment for the selected tree item.

flip_selected_cell()

Flip assigned age of the selected cell / track.

get_color(item)

Get a random RGB tuple from an objects id.

highlight_track()

Toggle highliting of the selected track in video.

jump_to_frame(*args)

Jump to a frame in the video and update corresponding widgets and overlay.

jump_to_time(*args)

Jump to a timestamp in the video and update corresponding widgets and overlay.

left_arrow_press(*args)

Jump video backward upon left arrow press.

listbox_double_click(*args)

Jump to double clicked frame in standard listbox view.

listbox_right_click(*args)

Remove selected item from listbox when moving tracks in the forest.

manual_update_canvas()

Update video canvas for cases not covered by update_canvas / manual interventions.

merge()

Merge selected tree items if not occuring in the same frame.

play_video()

Toggle video playback.

remove()

Remove items from tree by setting ‘show’ column to 0 in the dataframe and display them in the sparate deleted listbox.

remove_restore_short()

Automatically remove or restore all tracks that are short (len==1).

reset_zoom(*args)

Reset video zoom and rebuild tree.

restart_video()

Jump to first frame of video.

restore()

Restore elements that were removed from the tree by setting the ‘show’ column to 1 in the dataframe.

right_arrow_press(*args)

Jump video forward upon right arrow press.

scrub(val)

Enable scrubbing of the video scrollbar.

shift_overlay(*args)

Toggle overlay with button press.

slower_video(*args)

Decelerate video playback.

spacebar_press(*args)

Start / stop video playback upon spacebar press.

split()

Split selected tree item / track at selected frame in listbox.

start_rectangle(event)

Start drwaing a rectangle as overlay in the canvas upon left click.

swap_tracklets()

Swap two selected tracks at the selected frame (assign everything after the frame to the other).

toggle_cell_age()

Toggle cell age overlay modes.

toggle_frustule_age()

Toggle theca age overlay modes.

toggle_id()

Toggle between shown id for the objects in the frame.

toggle_merge()

Toggle merge mode of tree items.

toggle_move()

Move tracks within a tree or the forest if not overlapping.

toggle_overlay()

Toggle the drawn overlay in video.

toggle_trace()

Toggle trace overlay for last frames.

toggle_tree(*args)

Toggle between showing only selected tree and all trees.

tree_current()

Toggle tree to only show up to current frame.

tree_double_click(*args)

Show only tree of double clicked item in overlay and forest.

tree_double_right(*args)

Reset selected tree and rebuild forest.

tree_select(*args)

Populate list box with frames upon selecting a tree item and highlight the object in the video frame if applicable.

tree_set_limit(*args)

Limit tree to frame that is set in widget.

tree_zoom()

Only show trees in current video zoom.

ui_init(name)

Initialize all window widgets.

Parameters:

name (str) – Name of the experiment for window naming.

Return type:

None.

up_arrow_press(*args)

Jump one frame forward upon up arrow press.

update_canvas()

Update video canvas and associated parameters if not currently drawing rectangle and video is still playing.

update_frame_number(frame)

Update the frame number widget.

update_speed_display()

Update the speed multiplier widget.

update_time(seconds)

Update the video time widget.

window_exception()

Exit immediately.

DiatomTrack.gui.load module

class DiatomTrack.gui.load.ReadSegmentationWindow(file)

Bases: object

Class containing window and reading of segmentation data.

close_window()

Confirm abrupt exit.

read_file()

Read the data from file.

window_exception()

Exit immediately.

class DiatomTrack.gui.load.ReadTrackVideoWindow(file)

Bases: object

Class containing window and extraction of tracking data from track video file.

close_window()

Confirm abrupt exit.

read_file()

Open video and extract metadata to dataframe.

window_exception()

Exit immediately.

class DiatomTrack.gui.load.ReadTrackWindow(file)

Bases: object

Class containing window and reading of tracking data.

close_window()

Confirm abrupt exit.

read_file()

Read data from csv to dataframe.

window_exception()

Exit immediately.

DiatomTrack.gui.load.read_seg(name)

Create and close window for reading of segmentation data.

Parameters:

name (str) – Path to file.

Returns:

The segmentation data (contours).

Return type:

dict

DiatomTrack.gui.load.read_track(name)

Create and close window for reading of tracking data.

Parameters:

name (str) – Path to file.

Returns:

The tracking data.

Return type:

Pandas dataframe

DiatomTrack.gui.load.read_tvf(name)

Create and close window for extraction of tracking data from tvf.

Parameters:

name (str) – Path to video file.

Returns:

• Pandas dataframe – The tracking data.

• name (str) – Path to video file.

DiatomTrack.gui.parser module

class DiatomTrack.gui.parser.ParserDirectory

Bases: object

GUI for parsing initial directories for processing from scratch.

close_window()

Confirm abrupt exit.

invoke_confirm(event)

Invoke the Ok button with Return to progress.

parse()

Parse and check inputs and close window if no error.

reset_inputs()

Reset all input fields.

select_saving()

Select the directory for saving.

select_source()

Select the image directory.

select_states()

Select the model states.

skip_window()

Skip this window and go to the next step.

window_exception()

Exit immediately.

class DiatomTrack.gui.parser.ParserEditor

Bases: object

GUI for parsing directories and files for editor.

close_window()

Confirm abrupt exit.

invoke_confirm(event)

Invoke the Ok button with Return to progress.

parse()

Parse and check inputs and close window if no error.

reset_inputs()

Reset all input fields.

select_saving()

Select directory for saving.

select_track()

Select track data.

select_track_video()

Select track video file.

select_video()

Select video file.

window_exception()

Exit immediately.

class DiatomTrack.gui.parser.ParserSkip

Bases: object

GUI for parsing directories for processing from tracking.

close_window()

Confirm abrupt exit.

invoke_confirm(event)

Invoke the Ok button with Return to progress.

parse()

Parse and check inputs and close window if no error.

reset_inputs()

Reset all input fields.

select_saving()

Select directory for saving.

select_segmentation()

Select segmentation data.

select_states()

Select model states.

select_video()

Select video file.

skip_window()

Skip this window and go to the next step.

window_exception()

Exit immediately.

class DiatomTrack.gui.parser.ParserTrack

Bases: object

GUI for parsing tracking parameters.

close_window()

Confirm abrupt exit.

invoke_confirm(event)

Invoke the Ok button with Return to progress.

parse()

Parse and check inputs and close window if no error.

reset_inputs()

Reset all input fields.

window_exception()

Exit immediately.

DiatomTrack.gui.parser.parse_editor()

Get the file and saving information for the editor.

Returns:

Paths to video, track data or combined as track video file, and save directory, and save name.

Return type:

tuple

DiatomTrack.gui.parser.parse_segmentation()

Get the paths and directories for segmentation and additional information, None if parsing / step is skipped.

Returns:

Parsed directories, paths and parameters, or None.

Return type:

tuple or None

DiatomTrack.gui.parser.parse_tracker()

Get the tracking parameters.

Returns:

• age (int) – Maximum frames an object may be undetected.

• offset (int) – The maximum distance in Euclidean tracking.

• split (int) – The maximum distance to consider splitting.

• gap (int) – The maximum distance for matching after detection gap.

DiatomTrack.gui.save module

class DiatomTrack.gui.save.SaveData(destination_directory, name, video_file, dataframe, original_dataframe, start_time, counts)

Bases: object

The class containing the window for final saving of data.

close_window()

Confirm abrupt exit.

parse()

Parse and check input parameters.

save()

Core function of the window activated upon button press. Activate the saving process.

save_df()

Save dataframe as csv and loop to next step.

save_metadata_video()

Save video and dataframe as metadata in custom track video file.

save_odf()

Save original dataframe as csv and loop to next step.

save_statistics()

Save process statistics and loop to next step.

save_tvf()

Save track video file and close window (and program).

select_saving()

Select directory to save in.

window_exception()

Exit immediately.

Module contents