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import os.path as op
import numpy as np

import mne
from mne.datasets import sample

from jumeg import get_jumeg_path
from jumeg.connectivity import (get_label_distances,
                                plot_grouped_connectivity_circle)
import yaml

from nilearn import plotting

data_path = sample.data_path()
subjects_dir = data_path + '/subjects'
subject = 'sample'

parc = 'aparc'

yaml_fname = get_jumeg_path() + '/data/desikan_%s_cortex_based_grouping.yaml' % parc
label_distances_fname = get_jumeg_path() + '/data/desikan_%s_label_com_distances.npy' % parc

labels_fname = get_jumeg_path() + '/data/desikan_label_names.yaml'
with open(labels_fname, 'r') as f:
    label_names = yaml.safe_load(f)['label_names']

replacer_dict_fname = get_jumeg_path() + '/data/replacer_dictionaries.yaml'
with open(replacer_dict_fname, 'r') as f:
    replacer_dict = yaml.safe_load(f)['replacer_dict_aparc']

# load the distances matrix
con = np.load(label_distances_fname)
node_order_size = con.shape[0]

# forget long range connections, plot short neighbouring connections
neighbor_range = 30.  # millimetres
con[con > neighbor_range] = 0.

plot_grouped_connectivity_circle(yaml_fname, con, label_names,
                                 labels_mode='cortex_only',
                                 node_order_size=node_order_size,
                                 replacer_dict=replacer_dict,
                                 out_fname='label_com_distances_circle_%0.1f_%s.png' % (neighbor_range, parc),
                                 colorbar_pos=(0.1, 0.1),
                                 n_lines=None, colorbar=True,
                                 colormap='Reds')

# compute the distances between COM's of the labels
_, coords, _, _ = get_label_distances(subject, subjects_dir, parc=parc)

# compute the degree
degs = mne.connectivity.degree(con, threshold_prop=1)

# show the label ROIs using Nilearn plotting
fig = plotting.plot_connectome(np.zeros((node_order_size, node_order_size)),
                               coords, node_size=20, edge_threshold='99%',
                               node_color='cornflowerblue',
                               display_mode='ortho',
                               title='%s' % parc)


# fig.savefig('%s_label_distances_based_degrees.png' % parc)
fig.savefig('%s_labels_degrees.png' % parc)
Script to plot label distances on circle and connectome plots.
