def warp_label(path_label, folder_label, file_label, fname_src, fname_transfo, path_out):
# read label file and check if file exists
sct.printv('\nRead label file...', param.verbose)
template_label_ids, template_label_names, template_label_file = read_label_file(path_label+folder_label, file_label)
# create output folder
sct.run('mkdir '+path_out+folder_label, param.verbose)
# Warp label
for i in xrange(0, len(template_label_file)):
fname_label = path_label+folder_label+template_label_file[i]
# check if file exists
# sct.check_file_exist(fname_label)
# apply transfo
sct.run('sct_apply_transfo -i '+fname_label+' -o '+path_out+folder_label+template_label_file[i] +' -d '+fname_src+' -w '+fname_transfo+' -x '+get_interp(template_label_file[i]), param.verbose)
# Copy list.txt
sct.run('cp '+path_label+folder_label+param.file_info_label+' '+path_out+folder_label, 0)
def get_fractional_volume_per_label(atlas_folder, file_label, nb_RL_labels=15):
"""This function takes as input the path to the folder containing an atlas and the name of the file gathering the
labels' file name of this atlas.
It returns, in the following order:
- a list of the labels' ID,
- a list of the labels' name,
- a 1D-numpy array containing the fractional volume of each label in the same order as the previous lists."""
import sct_extract_metric
import nibabel
import numpy
[label_id, label_name,
label_file] = sct_extract_metric.read_label_file(atlas_folder, file_label)
nb_label = len(label_file)
fract_volume_per_lab = numpy.zeros((nb_label))
# compute fractional volume for each label
for i_label in range(0, nb_label):
fract_volume_per_lab[i_label] = numpy.sum(
nibabel.load(atlas_folder + label_file[i_label]).get_data())
# gather right and left sides
# nb_non_RL_labels = nb_label - (2*nb_RL_labels) # number of labels that are not paired side-wise
fract_volume_per_lab_RL_gatehered = numpy.zeros((nb_RL_labels))
label_name_RL_gatehered = []
for i_label in range(0, nb_RL_labels):
ind_ID_first_side = label_id.index(i_label)
ind_ID_other_side = label_id.index(i_label + nb_RL_labels)
fract_volume_per_lab_RL_gatehered[i_label] = fract_volume_per_lab[
ind_ID_first_side] + fract_volume_per_lab[ind_ID_other_side]
label_name_RL_gatehered.append(label_name[ind_ID_first_side].replace(
'left', '').replace('right', '').strip())
# # add labels that are not paired side-wise
# for i_label in range(0, nb_non_RL_labels):
# fract_volume_per_lab_RL_gatehered[nb_RL_labels+i_label] = fract_volume_per_lab[2 * nb_RL_labels + i_label]
# label_name_RL_gatehered.append(label_name[2 * nb_RL_labels + i_label].strip())
return label_id, label_name, fract_volume_per_lab, label_name_RL_gatehered, fract_volume_per_lab_RL_gatehered
def get_nb_voxel_in_WM(atlas_folder, file_label):
"""This function takes as input the path to the folder containing an atlas and the name of the file gathering the
labels' file name of this atlas. It returns the number of voxels including at least one label."""
import sct_extract_metric
import nibabel
import numpy
[label_id, label_name, label_file] = sct_extract_metric.read_label_file(atlas_folder, file_label)
nb_label = len(label_file)
# sum of all the labels
sum_all_labels = nibabel.load(atlas_folder + label_file[0]).get_data()
for i_label in range(1, nb_label):
sum_all_labels = numpy.add(sum_all_labels, nibabel.load(atlas_folder + label_file[i_label]).get_data())
# count the number of non-zero voxels
nb_voxel_in_WM = numpy.count_nonzero(sum_all_labels)
return nb_voxel_in_WM
def get_fractional_volume_per_label(atlas_folder, file_label, nb_RL_labels=15):
"""This function takes as input the path to the folder containing an atlas and the name of the file gathering the
labels' file name of this atlas.
It returns, in the following order:
- a list of the labels' ID,
- a list of the labels' name,
- a 1D-numpy array containing the fractional volume of each label in the same order as the previous lists."""
import sct_extract_metric
import nibabel
import numpy
[label_id, label_name, label_file] = sct_extract_metric.read_label_file(atlas_folder, file_label)
nb_label = len(label_file)
fract_volume_per_lab = numpy.zeros((nb_label))
# compute fractional volume for each label
for i_label in range(0, nb_label):
fract_volume_per_lab[i_label] = numpy.sum(nibabel.load(atlas_folder + label_file[i_label]).get_data())
# gather right and left sides
# nb_non_RL_labels = nb_label - (2*nb_RL_labels) # number of labels that are not paired side-wise
fract_volume_per_lab_RL_gatehered = numpy.zeros((nb_RL_labels))
label_name_RL_gatehered = []
for i_label in range(0, nb_RL_labels):
ind_ID_first_side = label_id.index(i_label)
ind_ID_other_side = label_id.index(i_label + nb_RL_labels)
fract_volume_per_lab_RL_gatehered[i_label] = fract_volume_per_lab[ind_ID_first_side] + fract_volume_per_lab[ind_ID_other_side]
label_name_RL_gatehered.append(label_name[ind_ID_first_side].replace('left', '').replace('right', '').strip())
# # add labels that are not paired side-wise
# for i_label in range(0, nb_non_RL_labels):
# fract_volume_per_lab_RL_gatehered[nb_RL_labels+i_label] = fract_volume_per_lab[2 * nb_RL_labels + i_label]
# label_name_RL_gatehered.append(label_name[2 * nb_RL_labels + i_label].strip())
return label_id, label_name, fract_volume_per_lab, label_name_RL_gatehered, fract_volume_per_lab_RL_gatehered
def compute_fract_vol_per_lab(atlas_folder, file_label):
atlas_folder = '/Users/slevy_local/spinalcordtoolbox/dev/atlas/validate_atlas/cropped_atlas/'
file_label = 'info_label.txt'
[label_id, label_name,
label_file] = sct_extract_metric.read_label_file(atlas_folder, file_label)
nb_label = len(label_file)
fract_volume_per_lab = numpy.zeros((nb_label))
# compute fractional volume for each label
for i_label in range(0, nb_label):
fract_volume_per_lab[i_label] = numpy.sum(
nibabel.load(atlas_folder + label_file[i_label]).get_data())
print 'Labels\'name:'
print label_name
print '\nCorresponding fractional volume:'
print fract_volume_per_lab
return label_name, fract_volume_per_lab
def compute_fract_vol_per_lab(atlas_folder, file_label):
atlas_folder = '/Users/slevy_local/spinalcordtoolbox/dev/atlas/validate_atlas/cropped_atlas/'
file_label = 'info_label.txt'
[label_id, label_name, label_file] = sct_extract_metric.read_label_file(atlas_folder, file_label)
nb_label = len(label_file)
fract_volume_per_lab = numpy.zeros((nb_label))
# compute fractional volume for each label
for i_label in range(0, nb_label):
fract_volume_per_lab[i_label] = numpy.sum(nibabel.load(os.path.join(atlas_folder, label_file[i_label)]).get_data())
print 'Labels\'name:'
print label_name
print '\nCorresponding fractional volume:'
print fract_volume_per_lab
return label_name, fract_volume_per_lab
def get_nb_voxel_in_WM(atlas_folder, file_label):
"""This function takes as input the path to the folder containing an atlas and the name of the file gathering the
labels' file name of this atlas. It returns the number of voxels including at least one label."""
import sct_extract_metric
import nibabel
import numpy
[label_id, label_name,
label_file] = sct_extract_metric.read_label_file(atlas_folder, file_label)
nb_label = len(label_file)
# sum of all the labels
sum_all_labels = nibabel.load(atlas_folder + label_file[0]).get_data()
for i_label in range(1, nb_label):
sum_all_labels = numpy.add(
sum_all_labels,
nibabel.load(atlas_folder + label_file[i_label]).get_data())
# count the number of non-zero voxels
nb_voxel_in_WM = numpy.count_nonzero(sum_all_labels)
return nb_voxel_in_WM
def warp_label(path_label, folder_label, file_label, fname_src, fname_transfo,
path_out):
# read label file and check if file exists
sct.printv('\nRead label file...', param.verbose)
template_label_ids, template_label_names, template_label_file = read_label_file(
path_label + folder_label, file_label)
# create output folder
sct.run('mkdir ' + path_out + folder_label, param.verbose)
# Warp label
for i in xrange(0, len(template_label_file)):
fname_label = path_label + folder_label + template_label_file[i]
# check if file exists
# sct.check_file_exist(fname_label)
# apply transfo
sct.run(
'sct_apply_transfo -i ' + fname_label + ' -o ' + path_out +
folder_label + template_label_file[i] + ' -d ' + fname_src +
' -w ' + fname_transfo + ' -x ' +
get_interp(template_label_file[i]), param.verbose)
# Copy list.txt
sct.run(
'cp ' + path_label + folder_label + param.file_info_label + ' ' +
path_out + folder_label, 0)
def warp_label(path_label, folder_label, file_label, fname_src, fname_transfo, path_out):
"""
Warp label files according to info_label.txt file
:param path_label:
:param folder_label:
:param file_label:
:param fname_src:
:param fname_transfo:
:param path_out:
:return:
"""
# read label file and check if file exists
sct.printv('\nRead label file...', param.verbose)
try:
template_label_ids, template_label_names, template_label_file, combined_labels_ids, combined_labels_names, combined_labels_id_groups, clusters_apriori = read_label_file(path_label + folder_label, file_label)
except Exception as error:
sct.printv('\nWARNING: Cannot warp label ' + folder_label + ': ' + str(error), 1, 'warning')
# raise
# try:
# template_label_ids, template_label_names, template_label_file, combined_labels_ids, combined_labels_names, combined_labels_id_groups = read_label_file(path_label+folder_label, file_label)
# except Exception:
# import traceback
# sct.printv('\nERROR: ' + traceback.format_exc(), 1, 'error')
else:
# create output folder
if not os.path.exists(path_out + folder_label):
os.makedirs(path_out + folder_label)
# Warp label
for i in xrange(0, len(template_label_file)):
fname_label = path_label + folder_label + template_label_file[i]
# check if file exists
# sct.check_file_exist(fname_label)
# apply transfo
sct.run('sct_apply_transfo -i ' + fname_label + ' -o ' + path_out + folder_label + template_label_file[i] + ' -d ' + fname_src + ' -w ' + fname_transfo + ' -x ' + get_interp(template_label_file[i]), param.verbose)
# Copy list.txt
sct.run('cp ' + path_label + folder_label + param.file_info_label + ' ' + path_out + folder_label, 0)
def warp_label(path_label, folder_label, file_label, fname_src, fname_transfo, path_out):
"""
Warp label files according to info_label.txt file
:param path_label:
:param folder_label:
:param file_label:
:param fname_src:
:param fname_transfo:
:param path_out:
:return:
"""
# read label file and check if file exists
sct.printv('\nRead label file...', param.verbose)
try:
template_label_ids, template_label_names, template_label_file, combined_labels_ids, combined_labels_names, combined_labels_id_groups, clusters_apriori = read_label_file(path_label + folder_label, file_label)
except Exception as error:
sct.printv('\nWARNING: Cannot warp label '+folder_label+': '+str(error), 1, 'warning')
# raise
# try:
# template_label_ids, template_label_names, template_label_file, combined_labels_ids, combined_labels_names, combined_labels_id_groups = read_label_file(path_label+folder_label, file_label)
# except Exception:
# import traceback
# sct.printv('\nERROR: ' + traceback.format_exc(), 1, 'error')
else:
# create output folder
sct.run('mkdir '+path_out+folder_label, param.verbose)
# Warp label
for i in xrange(0, len(template_label_file)):
fname_label = path_label+folder_label+template_label_file[i]
# check if file exists
# sct.check_file_exist(fname_label)
# apply transfo
sct.run('sct_apply_transfo -i '+fname_label+' -o '+path_out+folder_label+template_label_file[i] +' -d '+fname_src+' -w '+fname_transfo+' -x '+get_interp(template_label_file[i]), param.verbose)
# Copy list.txt
sct.run('cp '+path_label+folder_label+param.file_info_label+' '+path_out+folder_label, 0)