usage: __main__.py [-h] [--labels_list LABELS_LIST]
[--reorder_txt REORDER_TXT] [--lookup_table LOOKUP_TABLE]
[--name_axis] [--axis_text_size X_SIZE Y_SIZE]
[--axis_text_angle X_ANGLE Y_ANGLE] [--colormap COLORMAP]
[--display_legend] [--legend_min_max MIN MAX]
[--write_values FONT_SIZE DECIMAL] [--histogram FILENAME]
[--nb_bins NB_BINS] [--exclude_zeros]
[--chord_chart FILENAME]
[--percentile_threshold PERCENTILE_THRESHOLD]
[--angle_threshold ANGLE_THRESHOLD] [--alpha ALPHA]
[--text_size TEXT_SIZE] [--text_distance TEXT_DISTANCE]
[--log] [--show_only] [-v [{DEBUG,INFO,WARNING}]] [-f]
in_matrix out_png
Script to display a connectivity matrix and adjust the desired visualization.
Made to work with scil_tractogram_segment_bundles_for_connectivity.py and
scil_connectivity_reorder_rois.py.
This script can either display the axis labels as:
- Coordinates (0..N)
- Labels (using --labels_list)
- Names (using --labels_list and --lookup_table)
Examples of labels_list.txt and lookup_table.json can be found in the
freesurfer_flow output (https://github.com/scilus/freesurfer_flow)
If the matrix was made from a bigger matrix using
scil_connectivity_reorder_rois.py, provide the text file(s), using
--labels_list and/or --reorder_txt.
The chord chart is always displaying parting in the order they are defined
(clockwise), the color is attributed in that order following a colormap. The
thickness of the line represent the 'size/intensity', the greater the value is
the thicker the line will be. In order to hide the low values, two options are
available:
- Angle threshold + alpha, any connections with a small angle on the chord
chart will be slightly transparent to increase the focus on bigger
connections.
- Percentile, hide any connections with a value below that percentile
positional arguments:
in_matrix Connectivity matrix in numpy (.npy) format.
out_png Output filename for the connectivity matrix figure.
options:
-h, --help show this help message and exit
--log Apply a base 10 logarithm to the matrix.
--show_only Do not save the figure, simply display it.
-v [{DEBUG,INFO,WARNING}]
Produces verbose output depending on the provided level.
Default level is warning, default when using -v is info.
-f Force overwriting of the output files.
Naming options:
--labels_list LABELS_LIST
List saved by the decomposition script,
must contain labels rather than coordinates (.txt).
--reorder_txt REORDER_TXT
File with two rows (x/y) listing the ordering (.txt).
--lookup_table LOOKUP_TABLE
Lookup table with the label number as keys and the name as values (.json).
Matplotlib options:
--name_axis Use the provided info/files to name axis.
--axis_text_size X_SIZE Y_SIZE
Font size of the X and Y axis labels. [(10, 10)]
--axis_text_angle X_ANGLE Y_ANGLE
Text angle of the X and Y axis labels. [(90, 0)]
--colormap COLORMAP Colormap to use for the matrix. [viridis]
--display_legend Display the colorbar next to the matrix.
--legend_min_max MIN MAX
Manually define the min/max of the legend.
--write_values FONT_SIZE DECIMAL
Write the values at the center of each node.
The font size and the rouding parameters can be adjusted.
Histogram options:
--histogram FILENAME Compute and display/save an histogram of weights.
--nb_bins NB_BINS Number of bins to use for the histogram.
--exclude_zeros Exclude the zeros from the histogram.
Chord chart options:
--chord_chart FILENAME
Compute and display/save a chord chart of weigth.
--percentile_threshold PERCENTILE_THRESHOLD
Discard connections below that percentile.[0]
--angle_threshold ANGLE_THRESHOLD
Angle below that theshold will be transparent.
Use --alpha to set opacity. Value typicallybetween 0.1 and 5 degrees. [1]
--alpha ALPHA Opacity for the smaller angle on the chord (0-1). [0.9]
--text_size TEXT_SIZE
Size of the font for the parcels name/number [10].
--text_distance TEXT_DISTANCE
Distance from the center so the parcels name/number do not overlap
with the diagram [1.1].