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WIP: Add functionality to clip streamlines between ROIs in orient_by_rois #1093

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WIP: Add functionality to clip streamlines between ROIs in orient_by_rois #1093

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c545c07
NF: Starting to work on functionality to clip streamlines between ROIs.
arokem Jul 1, 2016
b9e861f
Futz with the logic here.
arokem Jul 1, 2016
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47 changes: 31 additions & 16 deletions dipy/tracking/streamline.py
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Expand Up @@ -260,7 +260,7 @@ def select_by_rois(streamlines, rois, include, mode=None, affine=None,
yield sl


def _orient_generator(out, roi1, roi2):
def _orient_generator(out, roi1, roi2, clip=False):
"""
Helper function to `orient_by_rois`

Expand All @@ -273,12 +273,17 @@ def _orient_generator(out, roi1, roi2):
min1 = np.argmin(dist1, 0)
min2 = np.argmin(dist2, 0)
if min1[0] > min2[0]:
yield sl[::-1]
out = sl[::-1]
if clip:
out = out[min2:min1]
else:
yield sl
out = sl
if clip:
out = out[min1:min2]
yield out


def _orient_list(out, roi1, roi2):
def _orient_list(out, roi1, roi2, clip=False):
"""
Helper function to `orient_by_rois`

Expand All @@ -295,11 +300,17 @@ def _orient_list(out, roi1, roi2):
min2 = np.argmin(dist2, 0)
if min1[0] > min2[0]:
out[idx] = sl[::-1]
if clip:
out[idx] = out[idx][min2:min1]
else:
if clip:
out[idx] = out[idx][min1:min2]

return out


def orient_by_rois(streamlines, roi1, roi2, in_place=False,
as_generator=False, affine=None):
as_generator=False, affine=None, clip=False):
"""Orient a set of streamlines according to a pair of ROIs

Parameters
Expand All @@ -319,6 +330,8 @@ def orient_by_rois(streamlines, roi1, roi2, in_place=False,
Whether to return a generator as output. Default: False
affine : ndarray
Affine transformation from voxels to streamlines. Default: identity.
clip : bool
Whether to clip the streamlines between the ROIs

Returns
-------
Expand All @@ -328,20 +341,22 @@ def orient_by_rois(streamlines, roi1, roi2, in_place=False,

Examples
--------
>>> streamlines = [np.array([[0, 0., 0],
... [1, 0., 0.],
... [2, 0., 0.]]),
... np.array([[2, 0., 0.],
... [1, 0., 0],
... [0, 0, 0.]])]
>>> streamlines = [np.array([[0, 0, 0],
... [0.5, 0, 0],
... [1, 0, 0],
... [2, 0, 0]], dtype=float),
... np.array([[2, 0, 0],
... [1, 0, 0],
... [0, 0, 0]], dtype=float)]
>>> roi1 = np.zeros((4, 4, 4), dtype=bool)
>>> roi2 = np.zeros_like(roi1)
>>> roi1[0, 0, 0] = True
>>> roi2[1, 0, 0] = True
>>> orient_by_rois(streamlines, roi1, roi2)
[array([[ 0., 0., 0.],
[ 1., 0., 0.],
[ 2., 0., 0.]]), array([[ 0., 0., 0.],
[array([[ 0. , 0. , 0. ],
[ 0.5, 0. , 0. ],
[ 1. , 0. , 0. ],
[ 2. , 0. , 0. ]]), array([[ 0., 0., 0.],
[ 1., 0., 0.],
[ 2., 0., 0.]])]

Expand All @@ -360,7 +375,7 @@ def orient_by_rois(streamlines, roi1, roi2, in_place=False,
if in_place:
w_s = "Cannot return a generator when in_place is set to True"
raise ValueError(w_s)
return _orient_generator(streamlines, roi1, roi2)
return _orient_generator(streamlines, roi1, roi2, clip=clip)

# If it's a generator on input, we may as well generate it
# here and now:
Expand All @@ -373,7 +388,7 @@ def orient_by_rois(streamlines, roi1, roi2, in_place=False,
# Make a copy, so you don't change the output in place:
out = deepcopy(streamlines)

return _orient_list(out, roi1, roi2)
return _orient_list(out, roi1, roi2, clip=clip)


def _extract_vals(data, streamlines, affine=None, threedvec=False):
Expand Down
13 changes: 13 additions & 0 deletions dipy/tracking/tests/test_streamline.py
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Expand Up @@ -785,6 +785,7 @@ def test_select_by_rois():

def test_orient_by_rois():
streamlines = [np.array([[0, 0., 0],
[0.5, 0, 0],
[1, 0., 0.],
[2, 0., 0.]]),
np.array([[2, 0., 0.],
Expand Down Expand Up @@ -816,6 +817,18 @@ def test_orient_by_rois():
npt.assert_equal(new_streamlines, flipped_sl)
npt.assert_(new_streamlines is not streamlines)

# Clip to the ROIs:
new_streamlines = orient_by_rois(streamlines,
mask1_vol,
mask2_vol,
in_place=False,
affine=None,
as_generator=False,
clip=True)

expected = [streamlines[0][0:2], streamlines[1][::-1][0:1]]
npt.assert_equal(new_streamlines, expected)

# Test with affine:
x_flipped_sl = [s + affine[:3, 3] for s in flipped_sl]
new_streamlines = orient_by_rois(x_streamlines,
Expand Down