def test_read_transformation_matrix_from_gifti_metadata():
file_path = get_data_file(TEST_MODIF_SUBJECT, TEST_SURFACE_FOLDER,
"lh.pial.gii")
surface_io = IOUtils.surface_io_factory(file_path)
surf = surface_io.read(file_path, False)
matrix = surface_io.read_transformation_matrix_from_metadata(
surf.get_main_metadata())
assert matrix == [[-1, 0, 0, 0], [0, 0, 1, 0], [0, -1, 0, 0], [0, 0, 0, 1]]
def test_read_transformation_matrix_from_gifti_metadata():
file_path = get_data_file(
TEST_MODIF_SUBJECT, TEST_SURFACE_FOLDER, "lh.pial.gii")
surface_io = IOUtils.surface_io_factory(file_path)
surf = surface_io.read(file_path, False)
matrix = surface_io.read_transformation_matrix_from_metadata(
surf.get_main_metadata())
assert matrix == [[-1, 0, 0, 0], [0, 0, 1, 0], [0, -1, 0, 0], [0, 0, 0, 1]]
def test_write_transformation_matrix_fs_metadata():
file_path = get_data_file(TEST_FS_SUBJECT, TEST_SURFACE_FOLDER, "lh.pial")
surface_io = IOUtils.surface_io_factory(file_path)
surf = surface_io.read(file_path, False)
surface_io.write_transformation_matrix(surf.get_main_metadata())
matrix = surface_io.read_transformation_matrix_from_metadata(
surf.get_main_metadata())
assert matrix.tolist() == [[1.0, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0],
[0.0, 0.0, 1.0, 0.0], [0.0, 0.0, 0.0, 1.0]]
def test_write_transformation_matrix_fs_metadata():
file_path = get_data_file(TEST_FS_SUBJECT, TEST_SURFACE_FOLDER, "lh.pial")
surface_io = IOUtils.surface_io_factory(file_path)
surf = surface_io.read(file_path, False)
surface_io.write_transformation_matrix(surf.get_main_metadata())
matrix = surface_io.read_transformation_matrix_from_metadata(
surf.get_main_metadata())
assert matrix.tolist() == [[1.0, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0], [
0.0, 0.0, 1.0, 0.0], [0.0, 0.0, 0.0, 1.0]]
if __name__ == "__main__":
args = parse_arguments()
surface_path = os.path.expandvars(args.surface_path)
output_path = os.path.expandvars(args.output_path)
logger = get_logger(__name__)
image_processor = ImageProcessor(snapshots_directory=os.environ[SNAPSHOTS_DIRECTORY_ENVIRON_VAR],
snapshot_count=int(os.environ.get(SNAPSHOT_NUMBER_ENVIRON_VAR, 0)))
generic_io = GenericIO()
logger.info("The surface transformation process has began")
surface_io = IOUtils.surface_io_factory(surface_path)
surface = surface_io.read(surface_path, False)
if len(args.matrix_paths) is not 0:
transformation_matrices = []
for transform_matrix_path in args.matrix_paths:
transformation_matrices.append(
numpy.array(generic_io.read_transformation_matrix(os.path.expandvars(transform_matrix_path))))
for i in range(len(surface.vertices)):
for j in range(len(transformation_matrices)):
if len(transformation_matrices[j]) > 3:
vertex_coords = numpy.array(
[surface.vertices[i][0], surface.vertices[i][1], surface.vertices[i][2], 1])
else:
if __name__ == "__main__":
args = parse_arguments()
surface_path = os.path.expandvars(args.surface_path)
output_path = os.path.expandvars(args.output_path)
logger = get_logger(__name__)
image_processor = ImageProcessor(
snapshots_directory=os.environ[SNAPSHOTS_DIRECTORY_ENVIRON_VAR],
snapshot_count=int(os.environ.get(SNAPSHOT_NUMBER_ENVIRON_VAR, 0)))
generic_io = GenericIO()
logger.info("The surface transformation process has began")
surface_io = IOUtils.surface_io_factory(surface_path)
surface = surface_io.read(surface_path, False)
if len(args.matrix_paths) is not 0:
transformation_matrices = []
for transform_matrix_path in args.matrix_paths:
transformation_matrices.append(
numpy.array(
generic_io.read_transformation_matrix(
os.path.expandvars(transform_matrix_path))))
for i in range(len(surface.vertices)):
for j in range(len(transformation_matrices)):
if len(transformation_matrices[j]) > 3:
vertex_coords = numpy.array([
