def test_load_write_LPS_file(self):
# Load the RAS and LPS version of the standard.
trk_RAS = TrkFile.load(DATA['standard_trk_fname'], lazy_load=False)
trk_LPS = TrkFile.load(DATA['standard_LPS_trk_fname'], lazy_load=False)
assert_tractogram_equal(trk_LPS.tractogram, trk_RAS.tractogram)
# Write back the standard.
trk_file = BytesIO()
trk = TrkFile(trk_LPS.tractogram, trk_LPS.header)
trk.save(trk_file)
trk_file.seek(0, os.SEEK_SET)
new_trk = TrkFile.load(trk_file)
assert_arr_dict_equal(new_trk.header, trk.header)
assert_tractogram_equal(new_trk.tractogram, trk.tractogram)
new_trk_orig = TrkFile.load(DATA['standard_LPS_trk_fname'])
assert_tractogram_equal(new_trk.tractogram, new_trk_orig.tractogram)
trk_file.seek(0, os.SEEK_SET)
assert_equal(trk_file.read(),
open(DATA['standard_LPS_trk_fname'], 'rb').read())
# Test writing a file where the header is missing the
# Field.VOXEL_ORDER.
trk_file = BytesIO()
# For TRK file format, the default voxel order is LPS.
header = copy.deepcopy(trk_LPS.header)
header[Field.VOXEL_ORDER] = b""
trk = TrkFile(trk_LPS.tractogram, header)
trk.save(trk_file)
trk_file.seek(0, os.SEEK_SET)
new_trk = TrkFile.load(trk_file)
assert_arr_dict_equal(new_trk.header, trk_LPS.header)
assert_tractogram_equal(new_trk.tractogram, trk.tractogram)
new_trk_orig = TrkFile.load(DATA['standard_LPS_trk_fname'])
assert_tractogram_equal(new_trk.tractogram, new_trk_orig.tractogram)
trk_file.seek(0, os.SEEK_SET)
assert_equal(trk_file.read(),
open(DATA['standard_LPS_trk_fname'], 'rb').read())
def test_write_complex_file(self):
# With scalars
tractogram = Tractogram(DATA['streamlines'],
data_per_point=DATA['data_per_point'],
affine_to_rasmm=np.eye(4))
trk_file = BytesIO()
trk = TrkFile(tractogram)
trk.save(trk_file)
trk_file.seek(0, os.SEEK_SET)
new_trk = TrkFile.load(trk_file, lazy_load=False)
assert_tractogram_equal(new_trk.tractogram, tractogram)
# With properties
data_per_streamline = DATA['data_per_streamline']
tractogram = Tractogram(DATA['streamlines'],
data_per_streamline=data_per_streamline,
affine_to_rasmm=np.eye(4))
trk = TrkFile(tractogram)
trk_file = BytesIO()
trk.save(trk_file)
trk_file.seek(0, os.SEEK_SET)
new_trk = TrkFile.load(trk_file, lazy_load=False)
assert_tractogram_equal(new_trk.tractogram, tractogram)
# With scalars and properties
data_per_streamline = DATA['data_per_streamline']
tractogram = Tractogram(DATA['streamlines'],
data_per_point=DATA['data_per_point'],
data_per_streamline=data_per_streamline,
affine_to_rasmm=np.eye(4))
trk_file = BytesIO()
trk = TrkFile(tractogram)
trk.save(trk_file)
trk_file.seek(0, os.SEEK_SET)
new_trk = TrkFile.load(trk_file, lazy_load=False)
assert_tractogram_equal(new_trk.tractogram, tractogram)
new_trk_orig = TrkFile.load(DATA['complex_trk_fname'])
assert_tractogram_equal(new_trk.tractogram, new_trk_orig.tractogram)
trk_file.seek(0, os.SEEK_SET)
assert_equal(trk_file.read(),
open(DATA['complex_trk_fname'], 'rb').read())
def test_write_empty_file(self):
tractogram = Tractogram(affine_to_rasmm=np.eye(4))
trk_file = BytesIO()
trk = TrkFile(tractogram)
trk.save(trk_file)
trk_file.seek(0, os.SEEK_SET)
new_trk = TrkFile.load(trk_file)
assert_tractogram_equal(new_trk.tractogram, tractogram)
new_trk_orig = TrkFile.load(DATA['empty_trk_fname'])
assert_tractogram_equal(new_trk.tractogram, new_trk_orig.tractogram)
trk_file.seek(0, os.SEEK_SET)
assert_equal(trk_file.read(),
open(DATA['empty_trk_fname'], 'rb').read())
