usage: __main__.py [-h]
[--random_coloring SEED | --uniform_coloring R G B | --local_coloring | --color_dict JSON | --color_from_streamlines KEY | --color_from_points KEY]
[--shape {line,tube}] [--width WIDTH]
[--subsample SUBSAMPLE] [--downsample DOWNSAMPLE]
[--background R G B] [-v [{DEBUG,INFO,WARNING}]]
in_bundles [in_bundles ...]
Visualize bundles.
Example usages:
# Visualize streamlines as tubes, each bundle with a different color
>>> scil_viz_bundle.py path_to_bundles/ --shape tube --random_coloring 1337
# Visualize a tractogram with each streamlines drawn as lines, colored with
# their local orientation, but only load 1 in 10 streamlines
>>> scil_viz_bundle.py tractogram.trk --shape line --subsample 10
# Visualize CSTs as large tubes and color them from a list of colors in a file
>>> scil_viz_bundle.py path_to_bundles/CST_* --width 0.5
--color_dict colors.json
positional arguments:
in_bundles List of tractography files supported by nibabel.
options:
-h, --help show this help message and exit
--shape {line,tube} Display streamlines either as lines or tubes.
[Default: tube]
--width WIDTH Width of tubes or lines representing streamlines
[Default: 0.25]
--subsample SUBSAMPLE
Only load 1 in N streamlines.
[Default: 1]
--downsample DOWNSAMPLE
Downsample streamlines to N points.
[Default: None]
--background R G B RBG values [0, 255] of the color of the background.
[Default: [0, 0, 0]]
-v [{DEBUG,INFO,WARNING}]
Produces verbose output depending on the provided level.
Default level is warning, default when using -v is info.
Colouring options:
--random_coloring SEED
Assign a random color to bundles.
--uniform_coloring R G B
Assign a uniform color to streamlines.
--local_coloring Assign coloring to streamlines depending on their local orientations.
--color_dict JSON JSON file containing colors for each bundle.
Bundle filenames are indicated as keys and colors as values.
A 'default' key and value can be included.
--color_from_streamlines KEY
Extract a color per streamline from the data_per_streamline property of the tractogram at the specified key.
--color_from_points KEY
Extract a color per point from the data_per_point property of the tractogram at the specified key.