def reslice_image_set(in_files, image_shape, label_indices=None, crop=False):
if crop:
crop_slices = get_cropping_parameters([in_files])
else:
crop_slices = None
images = read_image_files(image_files=in_files,
image_shape=image_shape,
crop=crop_slices,
label_indices=label_indices)
return images
def reslice_image_set(in_files, image_shape, out_files=None, label_indices=None, crop=False):
if crop:
crop_slices = get_cropping_parameters([in_files])
else:
crop_slices = None
images = read_image_files(in_files, image_shape=image_shape, crop=crop_slices, label_indices=label_indices)
if out_files:
for image, out_file in zip(images, out_files):
image.to_filename(out_file)
return [os.path.abspath(out_file) for out_file in out_files]
else:
return images
def write_image_data_to_file(image_files,
data_storage,
truth_storage,
image_shape,
n_channels,
crop=None,
truth_dtype=np.uint8):
for set_of_files in image_files:
subject_data = read_image_files(set_of_files, image_shape, crop=crop)
data_storage.append(subject_data[:n_channels][np.newaxis])
truth_storage.append(
np.asarray(subject_data[n_channels][np.newaxis][np.newaxis],
dtype=truth_dtype))
return data_storage, truth_storage
def reslice_image_set(in_files,
image_shape,
out_files=None,
label_indices=None,
crop=False):
if crop:
crop_slices = get_cropping_parameters([in_files])
else:
crop_slices = None
images = read_image_files(in_files,
image_shape=image_shape,
crop=crop_slices,
label_indices=label_indices)
if out_files:
for image, out_file in zip(images, out_files):
image.to_filename(out_file)
#return [os.path.abspath(out_file) for out_file in out_files]
return [
os.path.join('/home/vjain/notebooks/3DUnetCNN/brats/', out_file)
for out_file in out_files
]
else:
return images