pyIDI

pyidi is a python package for displacement identification from raw video.

Currently the pyIDI method works with Photron .cih and .cihx files, however, numpy.ndarray can also be passed as cih_file argument. If an array is passed, it must have a shape of: (n time points, image height, image width).

The basic usage of the package is presented.

Loading the video

First create the pyIDI object:

video = pyidi.pyIDI('filename.cih')

Setting the points

Displacements are computed for certain points or certain regions of interest that are represented by a point.

Points must be of shape n_points x 2:

points = [[1, 2],
          [1, 5],
          [2, 10]]

where the first column indicates indices along axis 0, and the second column indices along axis 1.

The points must be passed to pyIDI object:

video.set_points(points=points)

If the points are not known, a Point selection UI or newer Napari image viewer can be used to select the points.

Setting the method

The method for displacement identification must be selected:

video.set_method(method='sof') # Simplified optical flow method

After the method is selected, the arguments can be configured. Note that the docstring is now showing the required arguments for the selected method.

video.method.configure(*args, **kwargs)

For more details on the available methods, see the currently implemented Displacement identification methods.

Get displacement

Finally, displacements can be identified:

displacements = video.get_displacements()

Saved analysis

The settings of the analysis and the identified displacements are saved in a directory next to the loaded cih_file.

Directory content before the analysis:

  • video_to_analyze.cih

Directory content after the analysis:

  • video_to_analyze.cih

  • video_to_analyze_pyidi_analysis

    • analysis_001

      • points.pkl
      • results.pkl
      • settings.txt

Loading saved analysis

The saved analysis can be loaded using the load_analysis function:

analysis_path = 'video_to_analyze_pyidi_analysis/analysis_001'

video_loaded, info_dict = pyidi.load_analysis(analysis_path)

Now we can access the video_loaded attributes, e.g.:

video_loaded.displacements