sarcgraph.sg.SarcGraph.zdisc_tracking

SarcGraph.zdisc_tracking(file_path=None, raw_frames=None, segmented_zdiscs=None, sigma=1.0, min_length=8, tp_depth=4.0, full_track_ratio=0.75, skip_merging=False, save_output=True)[source]

Track detected Z-Discs in a video. The input could be the address to a video/image sample (file_path), raw frames as a numpy array (raw_frames), or segmented zdiscs information in a pandas datafram (segmented_zdiscs)e. If the function is run with no inputs, it will search for ‘raw-frames.npy’, or ‘segmented-zdiscs.csv’ in the specified output directory SarcGraph().output_dir.

Parameters:

  • file_path (str) – The address of an image or a video file to be loaded

  • raw_frames (np.ndarray, shape=(frames, dim_1, dim_2, channels)) – Raw input image or video given as a 4 dimensional array

  • segmented_zdiscs (pd.DataFrame) – Information of all detected zdiscs in every frame.

  • sigma (float) – Standard deviation for Gaussian kernel, by default 1.0

  • min_length (int) – Minimum length for zdisc contours measured in pixels, by default 8

  • tp_depth (float, optional) – the maximum distance features can move between frames, by default 4.0

  • full_track_ratio (float, optional) – by default 0.75

  • skip_merging (bool, optional) – skipping the merging step will result in fewer fully tracked zdiscs, by default False

  • save_output (bool) – by default True

Returns:

tracked zdiscs information. Columns are 'frame' (frame number), 'x' and 'y' (zdiscs center position), 'p1_x', 'p1_y', 'p2_x', 'p2_y' (zdiscs end points positions), and 'particle' (id of each tracked zdisc).

Return type:

pd.DataFrame

Notes

See also

sarcgraph.sg.SarcGraph.zdisc_segmentation(), sarcgraph.sg.SarcGraph._merge_tracked_zdiscs()