def get_input_files(input_files_listing, base_dir):
input_files = []
if input_files_listing:
for filename in input_files_listing:
try:
input_files.append(nifti_filepath_resolution(filename))
except ValueError:
input_files.append(
nifti_filepath_resolution(base_dir + '/' + filename))
return input_files
def run(self, args, extra_args):
mask = mdt.load_brain_mask(
nifti_filepath_resolution(os.path.realpath(args.mask)))
file_names = []
for file in args.input_files:
file_names.extend(glob.glob(file))
for file in file_names:
if args.overwrite:
mdt.apply_mask_to_file(file, mask)
else:
folder, basename, ext = split_image_path(
nifti_filepath_resolution(os.path.realpath(file)))
mdt.apply_mask_to_file(file,
mask,
output_fname=os.path.join(
folder, basename + '_masked' + ext))
def find_niftis(paths, recurse=True):
niftis = []
for path in paths:
if os.path.isdir(path):
if recurse:
niftis.extend(find_niftis(glob.glob(path + '/*.nii*'), recurse=False))
else:
try:
niftis.append(nifti_filepath_resolution(path))
except ValueError:
pass
return niftis
def load_nifti(nifti_volume):
"""Load and return a nifti file.
This will apply path resolution if a filename without extension is given. See the function
:func:`nifti_filepath_resolution` for details.
Args:
nifti_volume (string): The filename of the volume to use.
Returns:
:class:`nibabel.spatialimages.SpatialImage`
"""
path = nifti_filepath_resolution(nifti_volume)
return nib.load(path)
def run(self, args, extra_args):
for image in args.images:
image_path = os.path.realpath(image)
try:
image_path = nifti_filepath_resolution(image_path)
img = load_nifti(image_path)
header = img.get_header()
print('{}'.format(image))
self.print_info(header)
print('')
except ValueError:
warnings.warn('Could not load image "{}"'.format(image_path))
def _load_niftis(self):
niftis = []
for filename in self._input_filenames:
filename = nifti_filepath_resolution(filename)
_, basename, extension = split_image_path(filename)
if extension.endswith('gz'):
unzipped_nifti_path = os.path.join(self._tmp_dir,
basename + '.nii')
unzip_nifti(filename, unzipped_nifti_path)
self._files_to_remove.append(unzipped_nifti_path)
resolved_path = unzipped_nifti_path
else:
resolved_path = filename
niftis.append(load_nifti(resolved_path))
return niftis
def get_input_file(input_file, base_dir):
try:
return nifti_filepath_resolution(input_file)
except ValueError:
return nifti_filepath_resolution(base_dir + '/' + input_file)