def test_streamline_registration():
sl1 = [
np.array([[0, 0, 0], [0, 0, 0.5], [0, 0, 1], [0, 0, 1.5]]),
np.array([[0, 0, 0], [0, 0.5, 0.5], [0, 1, 1]])
]
affine = np.eye(4)
affine[:3, 3] = np.random.randn(3)
sl2 = list(transform_tracking_output(sl1, affine))
aligned, matrix = streamline_registration(sl2, sl1)
npt.assert_almost_equal(matrix, np.linalg.inv(affine))
npt.assert_almost_equal(aligned[0], sl1[0])
npt.assert_almost_equal(aligned[1], sl1[1])
# We assume the two tracks come from the same space, but it might have
# some affine associated with it:
base_aff = np.eye(4) * np.random.rand()
base_aff[:3, 3] = np.array([1, 2, 3])
base_aff[3, 3] = 1
with nbtmp.InTemporaryDirectory() as tmpdir:
for use_aff in [None, base_aff]:
fname1 = op.join(tmpdir, 'sl1.trk')
fname2 = op.join(tmpdir, 'sl2.trk')
if use_aff is not None:
img = nib.Nifti1Image(np.zeros((2, 2, 2)), use_aff)
# Move the streamlines to this other space, and report it:
tgm1 = StatefulTractogram(
transform_tracking_output(sl1, np.linalg.inv(use_aff)),
img, Space.VOX)
save_trk(tgm1, fname1, bbox_valid_check=False)
tgm2 = StatefulTractogram(
transform_tracking_output(sl2, np.linalg.inv(use_aff)),
img, Space.VOX)
save_trk(tgm2, fname2, bbox_valid_check=False)
else:
img = nib.Nifti1Image(np.zeros((2, 2, 2)), np.eye(4))
tgm1 = StatefulTractogram(sl1, img, Space.RASMM)
tgm2 = StatefulTractogram(sl2, img, Space.RASMM)
save_trk(tgm1, fname1, bbox_valid_check=False)
save_trk(tgm2, fname2, bbox_valid_check=False)
aligned, matrix = streamline_registration(fname2, fname1)
npt.assert_almost_equal(aligned[0], sl1[0], decimal=5)
npt.assert_almost_equal(aligned[1], sl1[1], decimal=5)
def test_streamline_registration():
sl1 = [
np.array([[0, 0, 0], [0, 0, 0.5], [0, 0, 1], [0, 0, 1.5]]),
np.array([[0, 0, 0], [0, 0.5, 0.5], [0, 1, 1]])
]
affine = np.eye(4)
affine[:3, 3] = np.random.randn(3)
sl2 = list(move_streamlines(sl1, affine))
aligned, matrix = streamline_registration(sl2, sl1)
npt.assert_almost_equal(matrix, np.linalg.inv(affine))
npt.assert_almost_equal(aligned[0], sl1[0])
npt.assert_almost_equal(aligned[1], sl1[1])
# We assume the two tracks come from the same space, but it might have
# some affine associated with it:
base_aff = np.eye(4) * np.random.rand()
base_aff[:3, 3] = np.array([1, 2, 3])
base_aff[3, 3] = 1
with nbtmp.InTemporaryDirectory() as tmpdir:
for use_aff in [None, base_aff]:
fname1 = op.join(tmpdir, 'sl1.trk')
fname2 = op.join(tmpdir, 'sl2.trk')
if use_aff is not None:
# Move the streamlines to this other space, and report it:
write_trk(fname1, move_streamlines(sl1,
np.linalg.inv(use_aff)),
use_aff)
write_trk(fname2, move_streamlines(sl2,
np.linalg.inv(use_aff)),
use_aff)
else:
write_trk(fname1, sl1)
write_trk(fname2, sl2)
aligned, matrix = streamline_registration(fname2, fname1)
npt.assert_almost_equal(aligned[0], sl1[0], decimal=5)
npt.assert_almost_equal(aligned[1], sl1[1], decimal=5)
def test_streamline_registration():
sl1 = [np.array([[0, 0, 0], [0, 0, 0.5], [0, 0, 1], [0, 0, 1.5]]),
np.array([[0, 0, 0], [0, 0.5, 0.5], [0, 1, 1]])]
affine = np.eye(4)
affine[:3, 3] = np.random.randn(3)
sl2 = list(move_streamlines(sl1, affine))
aligned, matrix = streamline_registration(sl2, sl1)
npt.assert_almost_equal(matrix, np.linalg.inv(affine))
npt.assert_almost_equal(aligned[0], sl1[0])
npt.assert_almost_equal(aligned[1], sl1[1])
# We assume the two tracks come from the same space, but it might have
# some affine associated with it:
base_aff = np.eye(4) * np.random.rand()
base_aff[:3, 3] = np.array([1, 2, 3])
base_aff[3, 3] = 1
with nbtmp.InTemporaryDirectory() as tmpdir:
for use_aff in [None, base_aff]:
fname1 = op.join(tmpdir, 'sl1.trk')
fname2 = op.join(tmpdir, 'sl2.trk')
if use_aff is not None:
# Move the streamlines to this other space, and report it:
write_trk(fname1,
move_streamlines(sl1, np.linalg.inv(use_aff)),
use_aff)
write_trk(fname2,
move_streamlines(sl2, np.linalg.inv(use_aff)),
use_aff)
else:
write_trk(fname1, sl1)
write_trk(fname2, sl2)
aligned, matrix = streamline_registration(fname2, fname1)
npt.assert_almost_equal(aligned[0], sl1[0], decimal=5)
npt.assert_almost_equal(aligned[1], sl1[1], decimal=5)