def test_load_file_with_wrong_information(self):
trk_file = open(DATA['simple_trk_fname'], 'rb').read()
# Simulate a TRK file where `count` was not provided.
count = np.array(0, dtype="int32").tostring()
new_trk_file = trk_file[:1000-12] + count + trk_file[1000-8:]
trk = TrkFile.load(BytesIO(new_trk_file), lazy_load=False)
assert_tractogram_equal(trk.tractogram, DATA['simple_tractogram'])
# Simulate a TRK where `vox_to_ras` is not recorded (i.e. all zeros).
vox_to_ras = np.zeros((4, 4), dtype=np.float32).tostring()
new_trk_file = trk_file[:440] + vox_to_ras + trk_file[440+64:]
with clear_and_catch_warnings(record=True, modules=[trk_module]) as w:
trk = TrkFile.load(BytesIO(new_trk_file))
assert_equal(len(w), 1)
assert_true(issubclass(w[0].category, HeaderWarning))
assert_true("identity" in str(w[0].message))
assert_array_equal(trk.affine, np.eye(4))
# Simulate a TRK where `vox_to_ras` is invalid.
vox_to_ras = np.zeros((4, 4), dtype=np.float32)
vox_to_ras[3, 3] = 1
vox_to_ras = vox_to_ras.tostring()
new_trk_file = trk_file[:440] + vox_to_ras + trk_file[440+64:]
with clear_and_catch_warnings(record=True, modules=[trk_module]) as w:
assert_raises(HeaderError, TrkFile.load, BytesIO(new_trk_file))
# Simulate a TRK file where `voxel_order` was not provided.
voxel_order = np.zeros(1, dtype="|S3").tostring()
new_trk_file = trk_file[:948] + voxel_order + trk_file[948+3:]
with clear_and_catch_warnings(record=True, modules=[trk_module]) as w:
TrkFile.load(BytesIO(new_trk_file))
assert_equal(len(w), 1)
assert_true(issubclass(w[0].category, HeaderWarning))
assert_true("LPS" in str(w[0].message))
# Simulate a TRK file with an unsupported version.
version = np.int32(123).tostring()
new_trk_file = trk_file[:992] + version + trk_file[992+4:]
assert_raises(HeaderError, TrkFile.load, BytesIO(new_trk_file))
# Simulate a TRK file with a wrong hdr_size.
hdr_size = np.int32(1234).tostring()
new_trk_file = trk_file[:996] + hdr_size + trk_file[996+4:]
assert_raises(HeaderError, TrkFile.load, BytesIO(new_trk_file))
# Simulate a TRK file with a wrong scalar_name.
trk_file = open(DATA['complex_trk_fname'], 'rb').read()
noise = np.int32(42).tostring()
new_trk_file = trk_file[:47] + noise + trk_file[47+4:]
assert_raises(HeaderError, TrkFile.load, BytesIO(new_trk_file))
# Simulate a TRK file with a wrong property_name.
noise = np.int32(42).tostring()
new_trk_file = trk_file[:254] + noise + trk_file[254+4:]
assert_raises(HeaderError, TrkFile.load, BytesIO(new_trk_file))
def test_metadata():
# Test deprecation
with clear_and_catch_warnings() as w:
warnings.filterwarnings('once', category=DeprecationWarning)
assert_equal(len(GiftiDataArray().get_metadata()), 0)
# Test deprecation
with clear_and_catch_warnings() as w:
warnings.filterwarnings('once', category=DeprecationWarning)
assert_equal(len(GiftiMetaData().get_metadata()), 0)
def test_metadata():
# Test deprecation
with clear_and_catch_warnings() as w:
warnings.filterwarnings('once', category=DeprecationWarning)
assert_equal(len(GiftiDataArray().get_metadata()), 0)
# Test deprecation
with clear_and_catch_warnings() as w:
warnings.filterwarnings('once', category=DeprecationWarning)
assert_equal(len(GiftiMetaData().get_metadata()), 0)
def test_to_xml_open_close_deprecations():
# Smoke test on deprecated functions
da = GiftiDataArray(np.ones((1,)), 'triangle')
with clear_and_catch_warnings() as w:
warnings.filterwarnings('always', category=DeprecationWarning)
assert_true(isinstance(da.to_xml_open(), string_types))
assert_equal(len(w), 1)
with clear_and_catch_warnings() as w:
warnings.filterwarnings('once', category=DeprecationWarning)
assert_true(isinstance(da.to_xml_close(), string_types))
assert_equal(len(w), 1)
def test_to_xml_open_close_deprecations():
# Smoke test on deprecated functions
da = GiftiDataArray(np.ones((1, )), 'triangle')
with clear_and_catch_warnings() as w:
warnings.filterwarnings('always', category=DeprecationWarning)
assert_true(isinstance(da.to_xml_open(), str))
assert_equal(len(w), 1)
with clear_and_catch_warnings() as w:
warnings.filterwarnings('once', category=DeprecationWarning)
assert_true(isinstance(da.to_xml_close(), str))
assert_equal(len(w), 1)
def test_load_file_with_wrong_information(self):
tck_file = open(DATA['simple_tck_fname'], 'rb').read()
# Simulate a TCK file where `datatype` has not the right endianness.
new_tck_file = tck_file.replace(asbytes("Float32LE"),
asbytes("Float32BE"))
assert_raises(DataError, TckFile.load, BytesIO(new_tck_file))
# Simulate a TCK file with unsupported `datatype`.
new_tck_file = tck_file.replace(asbytes("Float32LE"),
asbytes("int32"))
assert_raises(HeaderError, TckFile.load, BytesIO(new_tck_file))
# Simulate a TCK file with no `datatype` field.
new_tck_file = tck_file.replace(b"datatype: Float32LE\n", b"")
# Need to adjust data offset.
new_tck_file = new_tck_file.replace(b"file: . 67\n", b"file: . 47\n")
with clear_and_catch_warnings(record=True, modules=[tck_module]) as w:
tck = TckFile.load(BytesIO(new_tck_file))
assert_equal(len(w), 1)
assert_true(issubclass(w[0].category, HeaderWarning))
assert_true("Missing 'datatype'" in str(w[0].message))
assert_array_equal(tck.header['datatype'], "Float32LE")
# Simulate a TCK file with no `file` field.
new_tck_file = tck_file.replace(b"\nfile: . 67", b"")
with clear_and_catch_warnings(record=True, modules=[tck_module]) as w:
tck = TckFile.load(BytesIO(new_tck_file))
assert_equal(len(w), 1)
assert_true(issubclass(w[0].category, HeaderWarning))
assert_true("Missing 'file'" in str(w[0].message))
assert_array_equal(tck.header['file'], ". 56")
# Simulate a TCK file with `file` field pointing to another file.
new_tck_file = tck_file.replace(b"file: . 67\n",
b"file: dummy.mat 75\n")
assert_raises(HeaderError, TckFile.load, BytesIO(new_tck_file))
# Simulate a TCK file which is missing a streamline delimiter.
eos = TckFile.FIBER_DELIMITER.tostring()
eof = TckFile.EOF_DELIMITER.tostring()
new_tck_file = tck_file[:-(len(eos) + len(eof))] + tck_file[-len(eof):]
# Force TCK loading to use buffering.
buffer_size = 1. / 1024**2 # 1 bytes
hdr = TckFile._read_header(BytesIO(new_tck_file))
tck_reader = TckFile._read(BytesIO(new_tck_file), hdr, buffer_size)
assert_raises(DataError, list, tck_reader)
# Simulate a TCK file which is missing the end-of-file delimiter.
new_tck_file = tck_file[:-len(eof)]
assert_raises(DataError, TckFile.load, BytesIO(new_tck_file))
def test_load_file_with_wrong_information(self):
# Simulate a TRK file where `count` was not provided.
trk_struct, trk_bytes = self.trk_with_bytes()
trk_struct[Field.NB_STREAMLINES] = 0
trk = TrkFile.load(BytesIO(trk_bytes), lazy_load=False)
assert_tractogram_equal(trk.tractogram, DATA['simple_tractogram'])
# Simulate a TRK where `vox_to_ras` is not recorded (i.e. all zeros).
trk_struct, trk_bytes = self.trk_with_bytes()
trk_struct[Field.VOXEL_TO_RASMM] = np.zeros((4, 4))
with clear_and_catch_warnings(record=True, modules=[trk_module]) as w:
trk = TrkFile.load(BytesIO(trk_bytes))
assert_equal(len(w), 1)
assert_true(issubclass(w[0].category, HeaderWarning))
assert_true("identity" in str(w[0].message))
assert_array_equal(trk.affine, np.eye(4))
# Simulate a TRK where `vox_to_ras` is invalid.
trk_struct, trk_bytes = self.trk_with_bytes()
trk_struct[Field.VOXEL_TO_RASMM] = np.diag([0, 0, 0, 1])
with clear_and_catch_warnings(record=True, modules=[trk_module]) as w:
assert_raises(HeaderError, TrkFile.load, BytesIO(trk_bytes))
# Simulate a TRK file where `voxel_order` was not provided.
trk_struct, trk_bytes = self.trk_with_bytes()
trk_struct[Field.VOXEL_ORDER] = b''
with clear_and_catch_warnings(record=True, modules=[trk_module]) as w:
TrkFile.load(BytesIO(trk_bytes))
assert_equal(len(w), 1)
assert_true(issubclass(w[0].category, HeaderWarning))
assert_true("LPS" in str(w[0].message))
# Simulate a TRK file with an unsupported version.
trk_struct, trk_bytes = self.trk_with_bytes()
trk_struct['version'] = 123
assert_raises(HeaderError, TrkFile.load, BytesIO(trk_bytes))
# Simulate a TRK file with a wrong hdr_size.
trk_struct, trk_bytes = self.trk_with_bytes()
trk_struct['hdr_size'] = 1234
assert_raises(HeaderError, TrkFile.load, BytesIO(trk_bytes))
# Simulate a TRK file with a wrong scalar_name.
trk_struct, trk_bytes = self.trk_with_bytes('complex_trk_fname')
trk_struct['scalar_name'][0, 0] = b'colors\x003\x004'
assert_raises(HeaderError, TrkFile.load, BytesIO(trk_bytes))
# Simulate a TRK file with a wrong property_name.
trk_struct, trk_bytes = self.trk_with_bytes('complex_trk_fname')
trk_struct['property_name'][0, 0] = b'colors\x003\x004'
assert_raises(HeaderError, TrkFile.load, BytesIO(trk_bytes))
def test_gifti_label_rgba():
rgba = np.random.rand(4)
kwargs = dict(zip(['red', 'green', 'blue', 'alpha'], rgba))
gl1 = GiftiLabel(**kwargs)
assert_array_equal(rgba, gl1.rgba)
gl1.red = 2 * gl1.red
assert_false(np.allclose(rgba, gl1.rgba)) # don't just store the list!
gl2 = GiftiLabel()
gl2.rgba = rgba
assert_array_equal(rgba, gl2.rgba)
gl2.blue = 2 * gl2.blue
assert_false(np.allclose(rgba, gl2.rgba)) # don't just store the list!
def assign_rgba(gl, val):
gl.rgba = val
gl3 = GiftiLabel(**kwargs)
assert_raises(ValueError, assign_rgba, gl3, rgba[:2])
assert_raises(ValueError, assign_rgba, gl3, rgba.tolist() + rgba.tolist())
# Test deprecation
with clear_and_catch_warnings() as w:
warnings.filterwarnings('once', category=DeprecationWarning)
assert_equal(kwargs['red'], gl3.get_rgba()[0])
assert_equal(len(w), 1)
# Test default value
gl4 = GiftiLabel()
assert_equal(len(gl4.rgba), 4)
assert_true(np.all([elem is None for elem in gl4.rgba]))
def test_gifti_label_rgba():
rgba = np.random.rand(4)
kwargs = dict(zip(['red', 'green', 'blue', 'alpha'], rgba))
gl1 = GiftiLabel(**kwargs)
assert_array_equal(rgba, gl1.rgba)
gl1.red = 2 * gl1.red
assert_false(np.allclose(rgba, gl1.rgba)) # don't just store the list!
gl2 = GiftiLabel()
gl2.rgba = rgba
assert_array_equal(rgba, gl2.rgba)
gl2.blue = 2 * gl2.blue
assert_false(np.allclose(rgba, gl2.rgba)) # don't just store the list!
def assign_rgba(gl, val):
gl.rgba = val
gl3 = GiftiLabel(**kwargs)
assert_raises(ValueError, assign_rgba, gl3, rgba[:2])
assert_raises(ValueError, assign_rgba, gl3, rgba.tolist() + rgba.tolist())
# Test deprecation
with clear_and_catch_warnings() as w:
warnings.filterwarnings('once', category=DeprecationWarning)
assert_equal(kwargs['red'], gl3.get_rgba()[0])
assert_equal(len(w), 1)
# Test default value
gl4 = GiftiLabel()
assert_equal(len(gl4.rgba), 4)
assert_true(np.all([elem is None for elem in gl4.rgba]))
def test_save_complex_file(self):
complex_tractogram = Tractogram(DATA['streamlines'],
DATA['data_per_streamline'],
DATA['data_per_point'],
affine_to_rasmm=np.eye(4))
for ext, cls in nib.streamlines.FORMATS.items():
with InTemporaryDirectory():
filename = 'streamlines' + ext
with clear_and_catch_warnings(record=True,
modules=[trk]) as w:
nib.streamlines.save(complex_tractogram, filename)
# If streamlines format does not support saving data
# per point or data per streamline, a warning message
# should be issued.
if not (cls.SUPPORTS_DATA_PER_POINT and
cls.SUPPORTS_DATA_PER_STREAMLINE):
assert_equal(len(w), 1)
assert_true(issubclass(w[0].category, Warning))
tractogram = Tractogram(DATA['streamlines'],
affine_to_rasmm=np.eye(4))
if cls.SUPPORTS_DATA_PER_POINT:
tractogram.data_per_point = DATA['data_per_point']
if cls.SUPPORTS_DATA_PER_STREAMLINE:
data = DATA['data_per_streamline']
tractogram.data_per_streamline = data
tfile = nib.streamlines.load(filename, lazy_load=False)
assert_tractogram_equal(tfile.tractogram, tractogram)
def test_save_complex_file(self):
complex_tractogram = Tractogram(DATA['streamlines'],
DATA['data_per_streamline'],
DATA['data_per_point'],
affine_to_rasmm=np.eye(4))
for ext, cls in nib.streamlines.FORMATS.items():
with InTemporaryDirectory():
filename = 'streamlines' + ext
with clear_and_catch_warnings(record=True, modules=[trk]) as w:
nib.streamlines.save(complex_tractogram, filename)
# If streamlines format does not support saving data
# per point or data per streamline, a warning message
# should be issued.
if not (cls.SUPPORTS_DATA_PER_POINT
and cls.SUPPORTS_DATA_PER_STREAMLINE):
assert_equal(len(w), 1)
assert_true(issubclass(w[0].category, Warning))
tractogram = Tractogram(DATA['streamlines'],
affine_to_rasmm=np.eye(4))
if cls.SUPPORTS_DATA_PER_POINT:
tractogram.data_per_point = DATA['data_per_point']
if cls.SUPPORTS_DATA_PER_STREAMLINE:
data = DATA['data_per_streamline']
tractogram.data_per_streamline = data
tfile = nib.streamlines.load(filename, lazy_load=False)
assert_tractogram_equal(tfile.tractogram, tractogram)
def test_save_tractogram_file(self):
tractogram = Tractogram(DATA['streamlines'], affine_to_rasmm=np.eye(4))
trk_file = trk.TrkFile(tractogram)
# No need for keyword arguments.
assert_raises(ValueError,
nib.streamlines.save,
trk_file,
"dummy.trk",
header={})
# Wrong extension.
with clear_and_catch_warnings(record=True,
modules=[nib.streamlines]) as w:
trk_file = trk.TrkFile(tractogram)
assert_raises(ValueError,
nib.streamlines.save,
trk_file,
"dummy.tck",
header={})
assert_equal(len(w), 1)
assert_true(issubclass(w[0].category, ExtensionWarning))
assert_true("extension" in str(w[0].message))
with InTemporaryDirectory():
nib.streamlines.save(trk_file, "dummy.trk")
tfile = nib.streamlines.load("dummy.trk", lazy_load=False)
assert_tractogram_equal(tfile.tractogram, tractogram)
def test_deprecations():
with clear_and_catch_warnings(modules=[imageclasses]) as w:
warnings.filterwarnings('always', category=DeprecationWarning)
nifti_single = class_map['nifti_single']
assert nifti_single['class'] == Nifti1Image
assert len(w) == 1
nifti_ext = ext_map['.nii']
assert nifti_ext == 'nifti_single'
assert len(w) == 2
def test_deprecations():
with clear_and_catch_warnings(modules=[imageclasses]) as w:
warnings.filterwarnings('always', category=DeprecationWarning)
nifti_single = class_map['nifti_single']
assert_equal(nifti_single['class'], Nifti1Image)
assert_equal(len(w), 1)
nifti_ext = ext_map['.nii']
assert_equal(nifti_ext, 'nifti_single')
assert_equal(len(w), 2)
def test_deprecations():
with clear_and_catch_warnings(modules=[imageclasses]) as w:
warnings.filterwarnings('always', category=DeprecationWarning)
nifti_single = class_map['nifti_single']
assert_equal(nifti_single['class'], Nifti1Image)
assert_equal(len(w), 1)
nifti_ext = ext_map['.nii']
assert_equal(nifti_ext, 'nifti_single')
assert_equal(len(w), 2)
def test_metadata():
nvpair = GiftiNVPairs('key', 'value')
da = GiftiMetaData(nvpair=nvpair)
assert_equal(da.data[0].name, 'key')
assert_equal(da.data[0].value, 'value')
# Test deprecation
with clear_and_catch_warnings() as w:
warnings.filterwarnings('always', category=DeprecationWarning)
assert_equal(len(GiftiDataArray().get_metadata()), 0)
assert_equal(len(w), 1)
def test_read_deprecated():
with clear_and_catch_warnings() as w:
warnings.simplefilter('always', DeprecationWarning)
from nibabel.gifti.giftiio import read, write
img = read(DATA_FILE1)
assert_equal(len(w), 1)
with InTemporaryDirectory():
write(img, 'test.gii')
assert_equal(len(w), 2)
def test_read_deprecated():
with clear_and_catch_warnings() as w:
warnings.simplefilter('always', DeprecationWarning)
from nibabel.gifti.giftiio import read, write
img = read(DATA_FILE1)
assert_equal(len(w), 1)
with InTemporaryDirectory():
write(img, 'test.gii')
assert_equal(len(w), 2)
def test_metadata():
nvpair = GiftiNVPairs('key', 'value')
da = GiftiMetaData(nvpair=nvpair)
assert_equal(da.data[0].name, 'key')
assert_equal(da.data[0].value, 'value')
# Test deprecation
with clear_and_catch_warnings() as w:
warnings.filterwarnings('always', category=DeprecationWarning)
assert_equal(len(GiftiDataArray().get_metadata()), 0)
assert_equal(len(w), 1)
def test_num_dim_deprecation():
da = GiftiDataArray(np.ones((2, 3, 4)))
# num_dim is property, set automatically from len(da.dims)
assert_equal(da.num_dim, 3)
with clear_and_catch_warnings() as w:
warnings.filterwarnings('always', category=DeprecationWarning)
# OK setting num_dim to correct value, but raises DeprecationWarning
da.num_dim = 3
assert_equal(len(w), 1)
# Any other value gives a ValueError
assert_raises(ValueError, setattr, da, 'num_dim', 4)
def test_num_dim_deprecation():
da = GiftiDataArray(np.ones((2, 3, 4)))
# num_dim is property, set automatically from len(da.dims)
assert_equal(da.num_dim, 3)
with clear_and_catch_warnings() as w:
warnings.filterwarnings('always', category=DeprecationWarning)
# OK setting num_dim to correct value, but raises DeprecationWarning
da.num_dim = 3
assert_equal(len(w), 1)
# Any other value gives a ValueError
assert_raises(ValueError, setattr, da, 'num_dim', 4)
def test_dataarray():
for dt_code in data_type_codes.value_set():
data_type = data_type_codes.type[dt_code]
if data_type is np.void: # not supported
continue
arr = np.zeros((10, 3), dtype=data_type)
da = GiftiDataArray.from_array(arr, 'triangle')
assert_equal(da.datatype, data_type_codes[arr.dtype])
bs_arr = arr.byteswap().newbyteorder()
da = GiftiDataArray.from_array(bs_arr, 'triangle')
assert_equal(da.datatype, data_type_codes[arr.dtype])
# Smoke test on deprecated functions
da = GiftiDataArray.from_array(np.ones((1,)), 'triangle')
with clear_and_catch_warnings() as w:
warnings.filterwarnings('always', category=DeprecationWarning)
assert_true(isinstance(da.to_xml_open(), string_types))
assert_equal(len(w), 1)
with clear_and_catch_warnings() as w:
warnings.filterwarnings('once', category=DeprecationWarning)
assert_true(isinstance(da.to_xml_close(), string_types))
assert_equal(len(w), 1)
def test_dataarray():
for dt_code in data_type_codes.value_set():
data_type = data_type_codes.type[dt_code]
if data_type is np.void: # not supported
continue
arr = np.zeros((10, 3), dtype=data_type)
da = GiftiDataArray.from_array(arr, 'triangle')
assert_equal(da.datatype, data_type_codes[arr.dtype])
bs_arr = arr.byteswap().newbyteorder()
da = GiftiDataArray.from_array(bs_arr, 'triangle')
assert_equal(da.datatype, data_type_codes[arr.dtype])
# Smoke test on deprecated functions
da = GiftiDataArray.from_array(np.ones((1, )), 'triangle')
with clear_and_catch_warnings() as w:
warnings.filterwarnings('always', category=DeprecationWarning)
assert_true(isinstance(da.to_xml_open(), string_types))
assert_equal(len(w), 1)
with clear_and_catch_warnings() as w:
warnings.filterwarnings('once', category=DeprecationWarning)
assert_true(isinstance(da.to_xml_close(), string_types))
assert_equal(len(w), 1)
def test_dataarray_from_array():
with clear_and_catch_warnings() as w:
warnings.filterwarnings('always', category=DeprecationWarning)
da = GiftiDataArray.from_array(np.ones((3, 4)))
assert_equal(len(w), 1)
for dt_code in data_type_codes.value_set():
data_type = data_type_codes.type[dt_code]
if data_type is np.void: # not supported
continue
arr = np.zeros((10, 3), dtype=data_type)
da = GiftiDataArray.from_array(arr, 'triangle')
assert_equal(da.datatype, data_type_codes[arr.dtype])
bs_arr = arr.byteswap().newbyteorder()
da = GiftiDataArray.from_array(bs_arr, 'triangle')
assert_equal(da.datatype, data_type_codes[arr.dtype])
def test_lazy_tractogram_len(self):
modules = [module_tractogram] # Modules for which to catch warnings.
with clear_and_catch_warnings(record=True, modules=modules) as w:
warnings.simplefilter("always") # Always trigger warnings.
# Calling `len` will create new generators each time.
tractogram = LazyTractogram(DATA['streamlines_func'])
assert_true(tractogram._nb_streamlines is None)
# This should produce a warning message.
assert_equal(len(tractogram), len(DATA['streamlines']))
assert_equal(tractogram._nb_streamlines, len(DATA['streamlines']))
assert_equal(len(w), 1)
tractogram = LazyTractogram(DATA['streamlines_func'])
# New instances should still produce a warning message.
assert_equal(len(tractogram), len(DATA['streamlines']))
assert_equal(len(w), 2)
assert_true(issubclass(w[-1].category, Warning))
# Calling again 'len' again should *not* produce a warning.
assert_equal(len(tractogram), len(DATA['streamlines']))
assert_equal(len(w), 2)
with clear_and_catch_warnings(record=True, modules=modules) as w:
# Once we iterated through the tractogram, we know the length.
tractogram = LazyTractogram(DATA['streamlines_func'])
assert_true(tractogram._nb_streamlines is None)
[t for t in tractogram] # Force iteration through tractogram.
assert_equal(tractogram._nb_streamlines, len(DATA['streamlines']))
# This should *not* produce a warning.
assert_equal(len(tractogram), len(DATA['streamlines']))
assert_equal(len(w), 0)
def test_dataarray_from_array():
with clear_and_catch_warnings() as w:
warnings.filterwarnings('always', category=DeprecationWarning)
da = GiftiDataArray.from_array(np.ones((3, 4)))
assert_equal(len(w), 1)
for dt_code in data_type_codes.value_set():
data_type = data_type_codes.type[dt_code]
if data_type is np.void: # not supported
continue
arr = np.zeros((10, 3), dtype=data_type)
da = GiftiDataArray.from_array(arr, 'triangle')
assert_equal(da.datatype, data_type_codes[arr.dtype])
bs_arr = arr.byteswap().newbyteorder()
da = GiftiDataArray.from_array(bs_arr, 'triangle')
assert_equal(da.datatype, data_type_codes[arr.dtype])
def test_lazy_tractogram_len(self):
modules = [module_tractogram] # Modules for which to catch warnings.
with clear_and_catch_warnings(record=True, modules=modules) as w:
warnings.simplefilter("always") # Always trigger warnings.
# Calling `len` will create new generators each time.
tractogram = LazyTractogram(DATA['streamlines_func'])
assert_true(tractogram._nb_streamlines is None)
# This should produce a warning message.
assert_equal(len(tractogram), len(DATA['streamlines']))
assert_equal(tractogram._nb_streamlines, len(DATA['streamlines']))
assert_equal(len(w), 1)
tractogram = LazyTractogram(DATA['streamlines_func'])
# New instances should still produce a warning message.
assert_equal(len(tractogram), len(DATA['streamlines']))
assert_equal(len(w), 2)
assert_true(issubclass(w[-1].category, Warning))
# Calling again 'len' again should *not* produce a warning.
assert_equal(len(tractogram), len(DATA['streamlines']))
assert_equal(len(w), 2)
with clear_and_catch_warnings(record=True, modules=modules) as w:
# Once we iterated through the tractogram, we know the length.
tractogram = LazyTractogram(DATA['streamlines_func'])
assert_true(tractogram._nb_streamlines is None)
[t for t in tractogram] # Force iteration through tractogram.
assert_equal(tractogram._nb_streamlines, len(DATA['streamlines']))
# This should *not* produce a warning.
assert_equal(len(tractogram), len(DATA['streamlines']))
assert_equal(len(w), 0)
def test_load_trk_version_1(self):
# Simulate and test a TRK (version 1).
# First check that setting the RAS affine works in version 2.
trk_struct, trk_bytes = self.trk_with_bytes()
trk_struct[Field.VOXEL_TO_RASMM] = np.diag([2, 3, 4, 1])
trk = TrkFile.load(BytesIO(trk_bytes))
assert_array_equal(trk.affine, np.diag([2, 3, 4, 1]))
# Next check that affine assumed identity if version 1.
trk_struct['version'] = 1
with clear_and_catch_warnings(record=True, modules=[trk_module]) as w:
trk = TrkFile.load(BytesIO(trk_bytes))
assert_equal(len(w), 1)
assert_true(issubclass(w[0].category, HeaderWarning))
assert_true("identity" in str(w[0].message))
assert_array_equal(trk.affine, np.eye(4))
assert_array_equal(trk.header['version'], 1)
def validate_filenames(self, imaker, params):
# Validate the filename, file_map interface
if not self.can_save:
raise unittest.SkipTest
img = imaker()
img.set_data_dtype(np.float32) # to avoid rounding in load / save
# Make sure the object does not have a file_map
img.file_map = None
# The bytesio_round_trip helper tests bytesio load / save via file_map
rt_img = bytesio_round_trip(img)
assert_array_equal(img.shape, rt_img.shape)
assert_almost_equal(img.get_fdata(), rt_img.get_fdata())
assert_almost_equal(np.asanyarray(img.dataobj),
np.asanyarray(rt_img.dataobj))
# Give the image a file map
klass = type(img)
rt_img.file_map = bytesio_filemap(klass)
# This object can now be saved and loaded from its own file_map
rt_img.to_file_map()
rt_rt_img = klass.from_file_map(rt_img.file_map)
assert_almost_equal(img.get_fdata(), rt_rt_img.get_fdata())
assert_almost_equal(np.asanyarray(img.dataobj),
np.asanyarray(rt_img.dataobj))
# get_ / set_ filename
fname = 'an_image' + self.standard_extension
for path in (fname, pathlib.Path(fname)):
img.set_filename(path)
assert img.get_filename() == str(path)
assert img.file_map['image'].filename == str(path)
# to_ / from_ filename
fname = 'another_image' + self.standard_extension
for path in (fname, pathlib.Path(fname)):
with InTemporaryDirectory():
# Validate that saving or loading a file doesn't use deprecated methods internally
with clear_and_catch_warnings() as w:
warnings.filterwarnings('error',
category=DeprecationWarning,
module=r"nibabel.*")
img.to_filename(path)
rt_img = img.__class__.from_filename(path)
assert_array_equal(img.shape, rt_img.shape)
assert_almost_equal(img.get_fdata(), rt_img.get_fdata())
assert_almost_equal(np.asanyarray(img.dataobj),
np.asanyarray(rt_img.dataobj))
del rt_img # to allow windows to delete the directory
def test_labeltable():
img = GiftiImage()
assert_equal(len(img.labeltable.labels), 0)
new_table = GiftiLabelTable()
new_table.labels += ['test', 'me']
img.labeltable = new_table
assert_equal(len(img.labeltable.labels), 2)
# Test deprecations
with clear_and_catch_warnings() as w:
warnings.filterwarnings('always', category=DeprecationWarning)
newer_table = GiftiLabelTable()
newer_table.labels += ['test', 'me', 'again']
img.set_labeltable(newer_table)
assert_equal(len(w), 1)
assert_equal(len(img.get_labeltable().labels), 3)
assert_equal(len(w), 2)
def test_labeltable():
img = GiftiImage()
assert_equal(len(img.labeltable.labels), 0)
new_table = GiftiLabelTable()
new_table.labels += ['test', 'me']
img.labeltable = new_table
assert_equal(len(img.labeltable.labels), 2)
# Test deprecations
with clear_and_catch_warnings() as w:
warnings.filterwarnings('always', category=DeprecationWarning)
newer_table = GiftiLabelTable()
newer_table.labels += ['test', 'me', 'again']
img.set_labeltable(newer_table)
assert_equal(len(w), 1)
assert_equal(len(img.get_labeltable().labels), 3)
assert_equal(len(w), 2)
def test_wrong_shape():
scalar_map = create_scalar_map((0, ))
brain_model_map = create_geometry_map((1, ))
matrix = ci.Cifti2Matrix()
matrix.append(scalar_map)
matrix.append(brain_model_map)
hdr = ci.Cifti2Header(matrix)
# correct shape is (2, 10)
for data in (
np.random.randn(1, 11),
np.random.randn(2, 10, 1),
np.random.randn(1, 2, 10),
np.random.randn(3, 10),
np.random.randn(2, 9),
):
with clear_and_catch_warnings():
with error_warnings():
assert_raises(UserWarning, ci.Cifti2Image, data, hdr)
with suppress_warnings():
img = ci.Cifti2Image(data, hdr)
assert_raises(ValueError, img.to_file_map)
def test_save_tractogram_file(self):
tractogram = Tractogram(DATA['streamlines'],
affine_to_rasmm=np.eye(4))
trk_file = trk.TrkFile(tractogram)
# No need for keyword arguments.
assert_raises(ValueError, nib.streamlines.save,
trk_file, "dummy.trk", header={})
# Wrong extension.
with clear_and_catch_warnings(record=True,
modules=[nib.streamlines]) as w:
trk_file = trk.TrkFile(tractogram)
assert_raises(ValueError, nib.streamlines.save,
trk_file, "dummy.tck", header={})
assert_equal(len(w), 1)
assert_true(issubclass(w[0].category, ExtensionWarning))
assert_true("extension" in str(w[0].message))
with InTemporaryDirectory():
nib.streamlines.save(trk_file, "dummy.trk")
tfile = nib.streamlines.load("dummy.trk", lazy_load=False)
assert_tractogram_equal(tfile.tractogram, tractogram)
def test_data_tag_deprecated():
with clear_and_catch_warnings() as w:
warnings.filterwarnings('once', category=DeprecationWarning)
data_tag(np.array([]), 'ASCII', '%i', 1)
assert_equal(len(w), 1)
def setUp(self):
with clear_and_catch_warnings() as w:
warnings.simplefilter('always', DeprecationWarning)
assert_equal(len(w), 1)
def test_load_file_with_wrong_information(self):
# Simulate a TRK file where `voxel_order` is lowercase.
trk_struct1, trk_bytes1 = self.trk_with_bytes()
trk_struct1[Field.VOXEL_ORDER] = b'LAS'
trk1 = TrkFile.load(BytesIO(trk_bytes1))
trk_struct2, trk_bytes2 = self.trk_with_bytes()
trk_struct2[Field.VOXEL_ORDER] = b'las'
trk2 = TrkFile.load(BytesIO(trk_bytes2))
trk1_aff2rasmm = get_affine_trackvis_to_rasmm(trk1.header)
trk2_aff2rasmm = get_affine_trackvis_to_rasmm(trk2.header)
assert_array_equal(trk1_aff2rasmm,trk2_aff2rasmm)
# Simulate a TRK file where `count` was not provided.
trk_struct, trk_bytes = self.trk_with_bytes()
trk_struct[Field.NB_STREAMLINES] = 0
trk = TrkFile.load(BytesIO(trk_bytes), lazy_load=False)
assert_tractogram_equal(trk.tractogram, DATA['simple_tractogram'])
# Simulate a TRK where `vox_to_ras` is not recorded (i.e. all zeros).
trk_struct, trk_bytes = self.trk_with_bytes()
trk_struct[Field.VOXEL_TO_RASMM] = np.zeros((4, 4))
with clear_and_catch_warnings(record=True, modules=[trk_module]) as w:
trk = TrkFile.load(BytesIO(trk_bytes))
assert_equal(len(w), 1)
assert_true(issubclass(w[0].category, HeaderWarning))
assert_true("identity" in str(w[0].message))
assert_array_equal(trk.affine, np.eye(4))
# Simulate a TRK where `vox_to_ras` is invalid.
trk_struct, trk_bytes = self.trk_with_bytes()
trk_struct[Field.VOXEL_TO_RASMM] = np.diag([0, 0, 0, 1])
with clear_and_catch_warnings(record=True, modules=[trk_module]) as w:
assert_raises(HeaderError, TrkFile.load, BytesIO(trk_bytes))
# Simulate a TRK file where `voxel_order` was not provided.
trk_struct, trk_bytes = self.trk_with_bytes()
trk_struct[Field.VOXEL_ORDER] = b''
with clear_and_catch_warnings(record=True, modules=[trk_module]) as w:
TrkFile.load(BytesIO(trk_bytes))
assert_equal(len(w), 1)
assert_true(issubclass(w[0].category, HeaderWarning))
assert_true("LPS" in str(w[0].message))
# Simulate a TRK file with an unsupported version.
trk_struct, trk_bytes = self.trk_with_bytes()
trk_struct['version'] = 123
assert_raises(HeaderError, TrkFile.load, BytesIO(trk_bytes))
# Simulate a TRK file with a wrong hdr_size.
trk_struct, trk_bytes = self.trk_with_bytes()
trk_struct['hdr_size'] = 1234
assert_raises(HeaderError, TrkFile.load, BytesIO(trk_bytes))
# Simulate a TRK file with a wrong scalar_name.
trk_struct, trk_bytes = self.trk_with_bytes('complex_trk_fname')
trk_struct['scalar_name'][0, 0] = b'colors\x003\x004'
assert_raises(HeaderError, TrkFile.load, BytesIO(trk_bytes))
# Simulate a TRK file with a wrong property_name.
trk_struct, trk_bytes = self.trk_with_bytes('complex_trk_fname')
trk_struct['property_name'][0, 0] = b'colors\x003\x004'
assert_raises(HeaderError, TrkFile.load, BytesIO(trk_bytes))
def test_data_tag_deprecated():
with clear_and_catch_warnings() as w:
warnings.filterwarnings('once', category=DeprecationWarning)
data_tag(np.array([]), 'ASCII', '%i', 1)
assert_equal(len(w), 1)
def setUp(self):
with clear_and_catch_warnings() as w:
warnings.simplefilter('always', DeprecationWarning)
assert_equal(len(w), 1)
