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pyIDI

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).

Note

In version 0.30.0, the argument cih_file was renamed to input_file. This was done because we introduced the VideoReader class, which can read multiple file formats such as .cih, .cihx, .avi, .mp4, .png, .jpg, numpy.ndarray etc.

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
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