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)