def label_fusion(target_path, atlas_img_path_list, atlas_lab_path_list, out_file, probabilities, params_list):
out_dir = os.path.dirname(out_file)
out_name = os.path.basename(out_file).split(os.extsep, 1)[0]
if params_list[0] == 'Joint':
jointfusion_path = os.path.join(os.environ['ANTSPATH'], 'jointfusion')
prob_dir = os.path.join(out_dir, out_name)
prob_path = os.path.join(prob_dir, 'prob%d.nii.gz')
cmdline = [jointfusion_path, '3', '1']
cmdline += ['-g'] + atlas_img_path_list
cmdline += ['-tg', target_path]
cmdline += ['-l'] + atlas_lab_path_list
cmdline += ['-m', 'Joint']
cmdline += [item for sublist in zip(['-rp', '-rs'], params_list[1:]) for item in sublist]
if probabilities:
os.makedirs(prob_dir)
cmdline += ['-p', prob_path]
cmdline += [out_file]
else:
python_path = os.path.join(os.environ['HOME'], 'anaconda', 'envs', 'sitkpy', 'bin', 'python')
mod_path = os.path.join(os.environ['HOME'], 'CODE', 'mod_py')
nlwv_path = os.path.join(mod_path, 'pblf_py.py')
cmdline = [python_path, '-u', nlwv_path]
cmdline += ['--atlas_img_list'] + atlas_img_path_list
cmdline += ['--target_img', target_path]
cmdline += ['--atlas_lab_list'] + atlas_lab_path_list
cmdline += ['--method'] + params_list[:2]
cmdline += [item for sublist in zip(['--patch_radius', '--search_radius', '--fusion_radius', '--struct_sim', '--normalization',], params_list[2:]) for item in sublist]
if probabilities:
cmdline += ['--probabilities']
cmdline += ['--out_file', out_file]
# launch
qsub_launcher = Launcher(' '.join(cmdline))
qsub_launcher.name = "{}_joint".format(out_name)
qsub_launcher.folder = out_dir
# qsub_launcher.queue = 'short.q'
qsub_launcher.queue = 'default.q'
return qsub_launcher.run()
'--metric',
'MeanSquares[{},{},{}]'.format(args.use_labels[2], lab_path,
w_lab)
])
cmdline.extend(
['--convergence', '[{},1e-9,15]'.format('x'.join(its_syn))])
cmdline.extend(['--smoothing-sigmas', smooth_sig])
cmdline.extend(['--shrink-factors', shrink_fac])
#
# mask
if args.template_mask is not None:
cmdline.extend(['--masks', args.template_mask[0]])
#
# launch
print "Launching registration of file {}".format(img_file)
name_list.append(img_file.split(os.extsep, 1)[0])
launcher.add(name_list[-1], ' '.join(cmdline), args.out_dir[0])
launcher.run(name_list[-1])
print "Waiting for registration jobs to finish..."
launcher.wait()
print "Registration finished."
for i_img in range(Nimg):
est_path = os.path.join(args.est_dir[0], est_files[i_img])
gtr_path = os.path.join(args.gtr_dir[0], gtr_files[i_img])
out_path = os.path.join(tmp_dir, est_names[i_img])
out_paths.append(out_path)
cmdline = "%s 3 %s DiceAndMinDistSum %s %s" % (imagemath_path, out_path,
est_path, gtr_path)
qsub_launcher = Launcher(cmdline)
print("Launching Dice evaluation job for labels %s" % est_names[i_img])
launcher.add(est_names[i_img], cmdline, tmp_dir)
launcher.run(est_names[i_img])
print "Waiting for Dice evaluation jobs to finish..."
launcher.wait()
print "Dice evaluation finished."
subj_dices = dict([])
label_dices = dict([])
for i, out_path in enumerate(out_paths):
# Read per-label Dice
check_file_repeat(out_path + '.csv')
f = open(out_path + '.csv', 'r')
args.reg_dir[0], file_name + args.in_deform_intfix[0] +
'1InverseWarp.nii.gz')
]
cmdline += [
'--output',
os.path.join(args.out_dir[0],
file.split('.nii.gz')[0] + args.out_suffix[0])
]
#
# launch
print "Launching warping of file {}".format(file)
qsub_launcher = Launcher(' '.join(cmdline))
qsub_launcher.name = file.split('.nii.gz')[0]
qsub_launcher.folder = args.out_dir[0]
qsub_launcher.queue = 'short.q'
job_id = qsub_launcher.run()
if is_hpc:
wait_jobs += [job_id]
# Wait for the jobs to finish (in cluster)
if is_hpc:
print "Waiting for warping jobs to finish..."
call(wait_jobs)
print "Warping finished."
args.target_deform_intfix[0] + '1Warp.nii.gz')
]
cmdline += [
'--transform',
os.path.join(
args.target_reg_dir[0], target_name +
args.target_linear_intfix[0] + '0GenericAffine.mat')
]
cmdline += [
'--output',
os.path.join(
args.out_dir[0],
atlas_file.split(os.extsep, 1)[0] + args.out_suffix[0])
]
#
# launch
job_name = atlas_file.split(os.extsep, 1)[0]
print "Launching warping of file {}".format(job_name)
launcher.add(job_name, ' '.join(cmdline), args.out_dir[0])
launcher.run(job_name)
# Wait for the jobs to finish (in cluster)
print "Waiting for warping jobs to finish..."
launcher.wait()
print "Warping finished."