def test_write_too_many_scalars_and_properties(self):
# TRK supports up to 10 data_per_point.
data_per_point = {}
for i in range(10):
data_per_point['#{0}'.format(i)] = DATA['fa']
tractogram = Tractogram(DATA['streamlines'],
data_per_point=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)
# More than 10 data_per_point should raise an error.
data_per_point['#{0}'.format(i+1)] = DATA['fa']
tractogram = Tractogram(DATA['streamlines'],
data_per_point=data_per_point,
affine_to_rasmm=np.eye(4))
trk = TrkFile(tractogram)
assert_raises(ValueError, trk.save, BytesIO())
# TRK supports up to 10 data_per_streamline.
data_per_streamline = {}
for i in range(10):
data_per_streamline['#{0}'.format(i)] = DATA['mean_torsion']
tractogram = Tractogram(DATA['streamlines'],
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)
# More than 10 data_per_streamline should raise an error.
data_per_streamline['#{0}'.format(i+1)] = DATA['mean_torsion']
tractogram = Tractogram(DATA['streamlines'],
data_per_streamline=data_per_streamline)
trk = TrkFile(tractogram)
assert_raises(ValueError, trk.save, BytesIO())
def test_load_write_file(self):
for fname in [DATA['empty_trk_fname'],
DATA['simple_trk_fname'],
DATA['complex_trk_fname']]:
for lazy_load in [False, True]:
trk = TrkFile.load(fname, lazy_load=lazy_load)
trk_file = BytesIO()
trk.save(trk_file)
new_trk = TrkFile.load(fname, lazy_load=False)
assert_tractogram_equal(new_trk.tractogram, trk.tractogram)
trk_file.seek(0, os.SEEK_SET)
def test_write_optional_header_fields(self):
# The TRK file format doesn't support additional header fields.
# If provided, they will be ignored.
tractogram = Tractogram(affine_to_rasmm=np.eye(4))
trk_file = BytesIO()
header = {'extra': 1234}
trk = TrkFile(tractogram, header)
trk.save(trk_file)
trk_file.seek(0, os.SEEK_SET)
new_trk = TrkFile.load(trk_file)
assert_true("extra" not in new_trk.header)
def test_header_read_restore(self):
# Test that reading a header restores the file position
trk_fname = DATA['simple_trk_fname']
bio = BytesIO()
bio.write(b'Along my very merry way')
hdr_pos = bio.tell()
hdr_from_fname = TrkFile._read_header(trk_fname)
with open(trk_fname, 'rb') as fobj:
bio.write(fobj.read())
bio.seek(hdr_pos)
# Check header is as expected
hdr_from_fname['_offset_data'] += hdr_pos # Correct for start position
assert_arr_dict_equal(TrkFile._read_header(bio), hdr_from_fname)
# Check fileobject file position has not changed
assert_equal(bio.tell(), hdr_pos)
def test_write_scalars_and_properties_name_too_long(self):
# TRK supports data_per_point name up to 20 characters.
# However, we reserve the last two characters to store
# the number of values associated to each data_per_point.
# So in reality we allow name of 18 characters, otherwise
# the name is truncated and warning is issue.
for nb_chars in range(22):
data_per_point = {'A'*nb_chars: DATA['colors']}
tractogram = Tractogram(DATA['streamlines'],
data_per_point=data_per_point,
affine_to_rasmm=np.eye(4))
trk = TrkFile(tractogram)
if nb_chars > 18:
assert_raises(ValueError, trk.save, BytesIO())
else:
trk.save(BytesIO())
data_per_point = {'A'*nb_chars: DATA['fa']}
tractogram = Tractogram(DATA['streamlines'],
data_per_point=data_per_point,
affine_to_rasmm=np.eye(4))
trk = TrkFile(tractogram)
if nb_chars > 20:
assert_raises(ValueError, trk.save, BytesIO())
else:
trk.save(BytesIO())
# TRK supports data_per_streamline name up to 20 characters.
# However, we reserve the last two characters to store
# the number of values associated to each data_per_streamline.
# So in reality we allow name of 18 characters, otherwise
# the name is truncated and warning is issue.
for nb_chars in range(22):
data_per_streamline = {'A'*nb_chars: DATA['mean_colors']}
tractogram = Tractogram(DATA['streamlines'],
data_per_streamline=data_per_streamline,
affine_to_rasmm=np.eye(4))
trk = TrkFile(tractogram)
if nb_chars > 18:
assert_raises(ValueError, trk.save, BytesIO())
else:
trk.save(BytesIO())
data_per_streamline = {'A'*nb_chars: DATA['mean_torsion']}
tractogram = Tractogram(DATA['streamlines'],
data_per_streamline=data_per_streamline,
affine_to_rasmm=np.eye(4))
trk = TrkFile(tractogram)
if nb_chars > 20:
assert_raises(ValueError, trk.save, BytesIO())
else:
trk.save(BytesIO())
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_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())
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_is_supported_detect_format():
# Test is_supported and detect_format functions
# Empty file/string
f = BytesIO()
assert_false(nib.streamlines.is_supported(f))
assert_false(nib.streamlines.is_supported(""))
assert_true(nib.streamlines.detect_format(f) is None)
assert_true(nib.streamlines.detect_format("") is None)
# Valid file without extension
for tfile_cls in nib.streamlines.FORMATS.values():
f = BytesIO()
f.write(tfile_cls.MAGIC_NUMBER)
f.seek(0, os.SEEK_SET)
assert_true(nib.streamlines.is_supported(f))
assert_true(nib.streamlines.detect_format(f) is tfile_cls)
# Wrong extension but right magic number
for tfile_cls in nib.streamlines.FORMATS.values():
with tempfile.TemporaryFile(mode="w+b", suffix=".txt") as f:
f.write(tfile_cls.MAGIC_NUMBER)
f.seek(0, os.SEEK_SET)
assert_true(nib.streamlines.is_supported(f))
assert_true(nib.streamlines.detect_format(f) is tfile_cls)
# Good extension but wrong magic number
for ext, tfile_cls in nib.streamlines.FORMATS.items():
with tempfile.TemporaryFile(mode="w+b", suffix=ext) as f:
f.write(b"pass")
f.seek(0, os.SEEK_SET)
assert_false(nib.streamlines.is_supported(f))
assert_true(nib.streamlines.detect_format(f) is None)
# Wrong extension, string only
f = "my_tractogram.asd"
assert_false(nib.streamlines.is_supported(f))
assert_true(nib.streamlines.detect_format(f) is None)
# Good extension, string only
for ext, tfile_cls in nib.streamlines.FORMATS.items():
f = "my_tractogram" + ext
assert_true(nib.streamlines.is_supported(f))
assert_equal(nib.streamlines.detect_format(f), tfile_cls)
# Extension should not be case-sensitive.
for ext, tfile_cls in nib.streamlines.FORMATS.items():
f = "my_tractogram" + ext.upper()
assert_true(nib.streamlines.detect_format(f) is tfile_cls)