In [1]:

    

import sys
import brainbox as bb
from matplotlib import pyplot as plt
import scipy.spatial.distance as dist
import scipy.cluster.hierarchy as clh


    

In [2]:

    

in_path = '/data1/abide/Out/Remote/some_failed/out'
out_path = '/data1/abide/Analysis/Remote/some_missing'
metric = 'stability_maps'


    

In [3]:

    

file_dict = bb.fileOps.grab_files(in_path, '.nii.gz', sub=metric)


    

    




I will be pulling files from /data1/abide/Out/Remote/some_failed/out/stability_maps

In [4]:

    

array_dict = bb.dataOps.read_files(file_dict)


    

    




I found 607 files to load.
 100.0 % done 0.00 seconds to go.
We are done

In [6]:

    

result_list = []
for n_id in range(10):
    sys.stdout.write('\rRunning network {}.'.format(n_id))
    sys.stdout.flush()
    
    eucl = dist.squareform(dist.pdist(array_dict[metric][..., n_id], 'euclidean'))
    Y = clh.linkage(eucl, method='ward')
    result_list.append((eucl, Y))


    

    




Running network 9.

In [8]:

    

f = plt.figure(figsize=(18, 50))
order_net = None
for n_id in range(10):
    n_id += 1
    sys.stdout.write('\rRunning network {}.'.format(n_id))
    sys.stdout.flush()
    (eucl, Y) = result_list[n_id-1]
    ax = f.add_subplot(5,2,n_id)
    subdend = bb.visuOps.add_subplot_axes(ax, [0, 0.71, 1, 0.29])
    submat = bb.visuOps.add_subplot_axes(ax, [0, 0, 1, 0.7])
    if order_net:
        Y = result_list[order_net][1]
    
    Z1 = clh.dendrogram(Y, ax=subdend)
    if order_net:
        subdend.matshow(np.ones((100,20)), aspect='auto')

    idx = Z1['leaves']
    tmp = eucl[idx, :]
    D = tmp[:, idx]
    a = submat.matshow(-D, aspect='auto')
    submat.set_xticks([])
    submat.set_yticks([])
    subdend.set_xticks([])
    subdend.set_yticks([])
    ax.set_xticks([])
    ax.set_yticks([])
    ax.set_title('Network {}'.format(n_id))
f.suptitle('Stability Maps')


    

    




Running network 10.





    
Out[8]:





<matplotlib.text.Text at 0x13b7af50>






    

In [7]: