def test_get_affine():
hdr = tv.empty_header()
# default header gives useless affine
yield assert_array_equal(tv.aff_from_hdr(hdr), np.diag([0, 0, 0, 1]))
hdr['voxel_size'] = 1
yield assert_array_equal(tv.aff_from_hdr(hdr), np.diag([0, 0, 0, 1]))
# DICOM direction cosines
hdr['image_orientation_patient'] = [1, 0, 0, 0, 1, 0]
yield assert_array_equal(tv.aff_from_hdr(hdr), np.diag([-1, -1, 1, 1]))
# RAS direction cosines
hdr['image_orientation_patient'] = [-1, 0, 0, 0, -1, 0]
yield assert_array_equal(tv.aff_from_hdr(hdr), np.eye(4))
# translations
hdr['origin'] = [1, 2, 3]
exp_aff = np.eye(4)
exp_aff[:3, 3] = [-1, -2, 3]
yield assert_array_equal(tv.aff_from_hdr(hdr), exp_aff)
# now use the easier vox_to_ras field
hdr = tv.empty_header()
aff = np.eye(4)
aff[:3, :] = np.arange(12).reshape(3, 4)
hdr['vox_to_ras'] = aff
yield assert_array_equal(tv.aff_from_hdr(hdr), aff)
# mappings work too
d = {
'version': 1,
'voxel_size': np.array([1, 2, 3]),
'image_orientation_patient': np.array([1, 0, 0, 0, 1, 0]),
'origin': np.array([10, 11, 12])
}
aff = tv.aff_from_hdr(d)
def test_get_affine():
hdr = tv.empty_header()
# default header gives useless affine
yield assert_array_equal(tv.aff_from_hdr(hdr),
np.diag([0,0,0,1]))
hdr['voxel_size'] = 1
yield assert_array_equal(tv.aff_from_hdr(hdr),
np.diag([0,0,0,1]))
# DICOM direction cosines
hdr['image_orientation_patient'] = [1,0,0,0,1,0]
yield assert_array_equal(tv.aff_from_hdr(hdr),
np.diag([-1,-1,1,1]))
# RAS direction cosines
hdr['image_orientation_patient'] = [-1,0,0,0,-1,0]
yield assert_array_equal(tv.aff_from_hdr(hdr),
np.eye(4))
# translations
hdr['origin'] = [1,2,3]
exp_aff = np.eye(4)
exp_aff[:3,3] = [-1,-2,3]
yield assert_array_equal(tv.aff_from_hdr(hdr),
exp_aff)
# now use the easier vox_to_ras field
hdr = tv.empty_header()
aff = np.eye(4)
aff[:3,:] = np.arange(12).reshape(3,4)
hdr['vox_to_ras'] = aff
yield assert_array_equal(tv.aff_from_hdr(hdr), aff)
# mappings work too
d = {'version': 1,
'voxel_size': np.array([1,2,3]),
'image_orientation_patient': np.array([1,0,0,0,1,0]),
'origin': np.array([10,11,12])}
aff = tv.aff_from_hdr(d)
def test_empty_header():
for endian in '<>':
hdr = tv.empty_header(endian)
yield assert_equal, hdr['id_string'], 'TRACK'
yield assert_equal, hdr['version'], 1
yield assert_equal, hdr['hdr_size'], 1000
hdr_endian = tv.endian_codes[tv.empty_header().dtype.byteorder]
yield assert_equal, hdr_endian, tv.native_code
def test_empty_header():
for endian in '<>':
hdr = tv.empty_header(endian)
yield assert_equal(hdr['id_string'], 'TRACK')
yield assert_equal(hdr['version'], 1)
yield assert_equal(hdr['hdr_size'], 1000)
yield assert_array_equal(
hdr['image_orientation_patient'],
[0,0,0,0,0,0])
hdr_endian = tv.endian_codes[tv.empty_header().dtype.byteorder]
yield assert_equal(hdr_endian, tv.native_code)
def test_empty_header():
for endian in '<>':
for version in (1, 2):
hdr = tv.empty_header(endian, version)
yield assert_equal(hdr['id_string'], 'TRACK')
yield assert_equal(hdr['version'], version)
yield assert_equal(hdr['hdr_size'], 1000)
yield assert_array_equal(hdr['image_orientation_patient'],
[0, 0, 0, 0, 0, 0])
hdr = tv.empty_header(version=2)
yield assert_array_equal(hdr['vox_to_ras'], np.zeros((4, 4)))
hdr_endian = tv.endian_codes[tv.empty_header().dtype.byteorder]
yield assert_equal(hdr_endian, tv.native_code)
def test_empty_header():
for endian in '<>':
for version in (1, 2):
hdr = tv.empty_header(endian, version)
yield assert_equal(hdr['id_string'], 'TRACK')
yield assert_equal(hdr['version'], version)
yield assert_equal(hdr['hdr_size'], 1000)
yield assert_array_equal(
hdr['image_orientation_patient'],
[0,0,0,0,0,0])
hdr = tv.empty_header(version=2)
yield assert_array_equal(hdr['vox_to_ras'], np.zeros((4,4)))
hdr_endian = tv.endian_codes[tv.empty_header().dtype.byteorder]
yield assert_equal(hdr_endian, tv.native_code)
def test_tv_class():
tvf = tv.TrackvisFile([])
yield assert_equal(tvf.streamlines, [])
yield assert_true(isinstance(tvf.header, np.ndarray))
yield assert_equal(tvf.endianness, tv.native_code)
yield assert_equal(tvf.filename, None)
out_f = StringIO()
tvf.to_file(out_f)
yield assert_equal(out_f.getvalue(), tv.empty_header().tostring())
out_f.truncate(0)
# Write something not-default
tvf = tv.TrackvisFile([], {'id_string': 'TRACKb'})
tvf.to_file(out_f)
# read it back
out_f.seek(0)
tvf_back = tv.TrackvisFile.from_file(out_f)
yield assert_equal(tvf_back.header['id_string'], 'TRACKb')
# check that we check input values
out_f.truncate(0)
yield assert_raises(tv.HeaderError, tv.TrackvisFile, [],
{'id_string': 'not OK'})
yield assert_raises(tv.HeaderError, tv.TrackvisFile, [], {'version': 3})
yield assert_raises(tv.HeaderError, tv.TrackvisFile, [], {'hdr_size': 0})
affine = np.diag([1, 2, 3, 1])
affine[:3, 3] = [10, 11, 12]
tvf.set_affine(affine)
yield assert_true(np.all(tvf.get_affine() == affine))
def test_write():
streams = []
out_f = StringIO()
tv.write(out_f, [], {})
yield assert_equal, out_f.getvalue(), tv.empty_header().tostring()
out_f.truncate(0)
# Write something not-default
tv.write(out_f, [], {'id_string':'TRACKb'})
# read it back
out_f.seek(0)
streams, hdr = tv.read(out_f)
yield assert_equal, hdr['id_string'], 'TRACKb'
# check that we can pass none for the header
out_f.truncate(0)
tv.write(out_f, [])
out_f.truncate(0)
tv.write(out_f, [], None)
# check that we check input values
out_f.truncate(0)
yield (assert_raises, tv.HeaderError,
tv.write, out_f, [],{'id_string':'not OK'})
yield (assert_raises, tv.HeaderError,
tv.write, out_f, [],{'version':2})
yield (assert_raises, tv.HeaderError,
tv.write, out_f, [],{'hdr_size':0})
def test_tv_class():
tvf = tv.TrackvisFile([])
yield assert_equal(tvf.streamlines, [])
yield assert_true(isinstance(tvf.header, np.ndarray))
yield assert_equal(tvf.endianness, tv.native_code)
yield assert_equal(tvf.filename, None)
out_f = StringIO()
tvf.to_file(out_f)
yield assert_equal(out_f.getvalue(), tv.empty_header().tostring())
out_f.truncate(0)
# Write something not-default
tvf = tv.TrackvisFile([], {'id_string':'TRACKb'})
tvf.to_file(out_f)
# read it back
out_f.seek(0)
tvf_back = tv.TrackvisFile.from_file(out_f)
yield assert_equal(tvf_back.header['id_string'], 'TRACKb')
# check that we check input values
out_f.truncate(0)
yield assert_raises(tv.HeaderError,
tv.TrackvisFile,
[],{'id_string':'not OK'})
yield assert_raises(tv.HeaderError,
tv.TrackvisFile,
[],{'version': 2})
yield assert_raises(tv.HeaderError,
tv.TrackvisFile,
[],{'hdr_size':0})
affine = np.diag([1,2,3,1])
affine[:3,3] = [10,11,12]
tvf.set_affine(affine)
yield assert_true(np.all(tvf.get_affine() == affine))
def test_write():
streams = []
out_f = StringIO()
tv.write(out_f, [], {})
yield assert_equal(out_f.getvalue(), tv.empty_header().tostring())
out_f.truncate(0)
# Write something not-default
tv.write(out_f, [], {'id_string': 'TRACKb'})
# read it back
out_f.seek(0)
streams, hdr = tv.read(out_f)
yield assert_equal(hdr['id_string'], 'TRACKb')
# check that we can pass none for the header
out_f.truncate(0)
tv.write(out_f, [])
out_f.truncate(0)
tv.write(out_f, [], None)
# check that we check input values
out_f.truncate(0)
yield assert_raises(tv.HeaderError, tv.write, out_f, [],
{'id_string': 'not OK'})
yield assert_raises(tv.HeaderError, tv.write, out_f, [], {'version': 3})
yield assert_raises(tv.HeaderError, tv.write, out_f, [], {'hdr_size': 0})
