Nisnap SPM_SEGMENT (Carles/Jordi)

nisnap.py

import pyxnat 
from nisnap import xnat, snap 
from glob import glob 
import os.path as op 
methods = ['T1', 'T1_FLAIR', 'T1_T2', 'T1_maskT1T2'] 
 
x = pyxnat.Interface(config='/home/grg/.xnat_goperto_ci.cfg') 
dd = '/mnt/projects/Segmentation_ALFA_PLUS_IRENE'  
subjects2 = sorted([int(e.split('/')[-1]) for e in glob(op.join(dd, 'segmentacions_T1', '*'))]) 
subjects = sorted([int(e['subject_label']) for e in x.array.experiments(project_id='ALFA_PLUS', 
                                                                        columns=['subject_label'])]) 
subjects = sorted(set(subjects2).intersection(subjects)) 
experiments = [] 
for e in subjects: 
    exp = x.array.experiments(subject_label=e, project_id='ALFA_PLUS').data[0]['ID'] 
    experiments.append((e, exp)) 
     
d = {'SPM12_SEGMENT_T2T1_COREG3': 'T2T1_COREG3', 
     'SPM12_SEGMENT_COREG' : 'T1_COREG', 
     'SPM12_SEGMENT_T2T1_COREG6': 'T2T1_G33342', 
     'SPM12_SEGMENT_T2T1_COREG7': 'T2T1_G33342_no_denoising', 
     'SPM12_SEGMENT_T2T1_COREG8': 'T2T1_COREG3_no_denoising'} 
 
carles = True 
jordi = True 
 
for i, (s, e) in enumerate(experiments[25:]): 
    print(i, s,e) 
    if jordi: 
        for k, v in d.items(): 
            xnat.plot_segment('/home/grg/.xnat_goperto_ci.cfg', experiment_id=e, axes='x', 
                opacity=40, slices=list(range(139,197,3)), rowsize=5, figsize=(10,10), 
                resource_name=k, savefig='/tmp/snapshots/%s_%s.png'%(s, v), animated=False, cache=False) 
 
    if carles: 
        for m in methods: 
            cfiles = sorted(glob(op.join(dd, 'segmentacions_%s'%m, str(s), 'c*T1_ALFA1_%s.nii'%s))) 
            t1 = glob(op.join(dd, 'T1', str(s), 'T1_ALFA1_%s.nii'%s))[0] 
            print(t1, cfiles)    
            snap.plot_segment(cfiles, bg=t1, axes='x', savefig='/tmp/snapshots/%s_%s.png'%(s, m), 
                slices=list(range(139,197,3)), rowsize=5, opacity=40, figsize=(10,10))