freesurfer-volume-reader/examples/barplot.py

import argparse

from matplotlib import pyplot
import pandas
import seaborn

from freesurfer_volume_reader import freesurfer


def generate_freesurfer_mode_label(row):
    mri_sequences = ['T1' if row['T1_input'] else None,
                     row['analysis_id'].split('_')[0] if row['analysis_id'] else None]
    return ' & '.join(filter(None, mri_sequences))


def main():
    argparser = argparse.ArgumentParser()
    argparser.add_argument('--subject', required=True)
    argparser.add_argument('--subjects-dir', dest='subjects_dir_path', required=True)
    args = argparser.parse_args()
    volume_frame = pandas.concat(
        f.read_volumes_dataframe() for f in
        freesurfer.HippocampalSubfieldsVolumeFile.find(args.subjects_dir_path))
    volume_frame['subfield_segmentation_mode'] = volume_frame.apply(
        generate_freesurfer_mode_label, axis=1)
    volume_frame = volume_frame[volume_frame['subject'] == args.subject]
    volume_frame.to_csv('hippocampal_subfield_volumes_{}.csv'.format(args.subject), index=False)
    volume_frame.drop(columns=['subject', 'T1_input', 'analysis_id'], inplace=True)
    print(volume_frame)
    volume_frame.sort_values(['subfield_segmentation_mode', 'subfield'], inplace=True)
    seaborn.set(font_scale=0.3)
    volume_frame_subfields = volume_frame[volume_frame['subfield'] != 'Whole_hippocampus']
    for hemisphere in ['left', 'right']:
        pyplot.ylim(0, 750)
        plot_ax = seaborn.barplot(data=volume_frame_subfields[volume_frame_subfields['hemisphere']
                                                              == hemisphere],
                                  x='subfield', y='volume_mm^3',
                                  hue='subfield_segmentation_mode')
        plot_ax.set_title('Hippocampal Subfield Volumes of Subject {}'.format(args.subject)
                          + '\n{} Hemisphere'.format(str.capitalize(hemisphere)))
        pyplot.savefig('hippocampal_subfield_volumes_{}_{}.png'.format(args.subject, hemisphere))
        pyplot.clf()
    seaborn.set(font_scale=0.4)
    plot_ax = seaborn.barplot(data=volume_frame[volume_frame['subfield'] == 'Whole_hippocampus'],
                              x='hemisphere', y='volume_mm^3',
                              hue='subfield_segmentation_mode')
    plot_ax.set_title('Hippocampal Volume of Subject {}'.format(args.subject))
    pyplot.savefig('hippocampal_volume_{}.png'.format(args.subject))


if __name__ == '__main__':
    main()