Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Remove the points added oustide of a mask. Fix the related tests. #1666

Merged
merged 2 commits into from Feb 8, 2019
Merged

Remove the points added oustide of a mask. Fix the related tests. #1666

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
6b8eb80
Remove the points added oustide of a mask. Fix the related tests.
Nov 2, 2018
1bb4a56
Merge branch 'master' of https://github.com/nipy/dipy into localtrack…
Feb 7, 2019
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Jump to
Jump to file
Failed to load files.
Diff view
Diff view
6 changes: 2 additions & 4 deletions dipy/tracking/local/localtrack.pyx
View file
Open in desktop
Expand Up @@ -185,10 +185,8 @@ cdef int _local_tracker(DirectionGetter dg,
if tissue_class[0] == TRACKPOINT:
continue
elif (tissue_class[0] == ENDPOINT or
tissue_class[0] == INVALIDPOINT):
i += 1
break
elif tissue_class[0] == OUTSIDEIMAGE:
tissue_class[0] == INVALIDPOINT or
tissue_class[0] == OUTSIDEIMAGE):
break
else:
# maximum length of streamline has been reached, return everything
Expand Down
62 changes: 27 additions & 35 deletions dipy/tracking/local/tests/test_tracking.py
View file
Open in desktop
Expand Up @@ -75,26 +75,26 @@ def test_stop_conditions():
# Check that the first streamline stops at 0 and 3 (ENDPOINT)
y = 0
sl = next(streamlines_not_all)
npt.assert_equal(sl[0], [0, y, 0])
npt.assert_equal(sl[-1], [0, y, 3])
npt.assert_equal(len(sl), 4)
npt.assert_equal(sl[0], [0, y, 1])
npt.assert_equal(sl[-1], [0, y, 2])
npt.assert_equal(len(sl), 2)

sl = next(streamlines_all)
npt.assert_equal(sl[0], [0, y, 0])
npt.assert_equal(sl[-1], [0, y, 3])
npt.assert_equal(len(sl), 4)
npt.assert_equal(sl[0], [0, y, 1])
npt.assert_equal(sl[-1], [0, y, 2])
npt.assert_equal(len(sl), 2)

# Check that the first streamline stops at 0 and 4 (ENDPOINT)
y = 1
sl = next(streamlines_not_all)
npt.assert_equal(sl[0], [0, y, 0])
npt.assert_equal(sl[-1], [0, y, 4])
npt.assert_equal(len(sl), 5)
npt.assert_equal(sl[0], [0, y, 1])
npt.assert_equal(sl[-1], [0, y, 3])
npt.assert_equal(len(sl), 3)

sl = next(streamlines_all)
npt.assert_equal(sl[0], [0, y, 0])
npt.assert_equal(sl[-1], [0, y, 4])
npt.assert_equal(len(sl), 5)
npt.assert_equal(sl[0], [0, y, 1])
npt.assert_equal(sl[-1], [0, y, 3])
npt.assert_equal(len(sl), 3)

# This streamline should be the same as above. This row does not have
# ENDPOINTs, but the streamline should stop at the edge and not include
Expand Down Expand Up @@ -128,16 +128,16 @@ def test_stop_conditions():
# The streamline stops at 0 (INVALIDPOINT) and 4 (ENDPOINT)
y = 4
sl = next(streamlines_all)
npt.assert_equal(sl[0], [0, y, 0])
npt.assert_equal(sl[-1], [0, y, 4])
npt.assert_equal(len(sl), 5)
npt.assert_equal(sl[0], [0, y, 1])
npt.assert_equal(sl[-1], [0, y, 3])
npt.assert_equal(len(sl), 3)

# The streamline stops at 0 (INVALIDPOINT) and 4 (INVALIDPOINT)
y = 5
sl = next(streamlines_all)
npt.assert_equal(sl[0], [0, y, 0])
npt.assert_equal(sl[-1], [0, y, 3])
npt.assert_equal(len(sl), 4)
npt.assert_equal(sl[0], [0, y, 1])
npt.assert_equal(sl[-1], [0, y, 2])
npt.assert_equal(len(sl), 2)

# The last streamline should contain only one point, the seed point,
# because no valid inital direction was returned.
Expand Down Expand Up @@ -184,8 +184,7 @@ def test_probabilistic_odf_weighted_tracker():
[2., 1., 0.],
[2., 2., 0.],
[2., 3., 0.],
[2., 4., 0.],
[2., 5., 0.]]),
[2., 4., 0.]]),
np.array([[0., 1., 0.],
[1., 1., 0.],
[2., 1., 0.],
Expand Down Expand Up @@ -227,7 +226,7 @@ def allclose(x, y):
streamlines = LocalTracking(dg, tc, seeds, np.eye(4), 0.2, max_cross=1,
return_all=True)
streamlines = Streamlines(streamlines)
npt.assert_(len(streamlines[0]) == 3) # INVALIDPOINT
npt.assert_(len(streamlines[0]) == 1) # INVALIDPOINT
npt.assert_(len(streamlines[1]) == 1) # OUTSIDEIMAGE

# Test that all points are within the image volume
Expand Down Expand Up @@ -431,8 +430,7 @@ def test_maximum_deterministic_tracker():
[2., 1., 0.],
[2., 2., 0.],
[2., 3., 0.],
[2., 4., 0.],
[2., 5., 0.]]),
[2., 4., 0.]]),
np.array([[0., 1., 0.],
[1., 1., 0.],
[2., 1., 0.],
Expand Down Expand Up @@ -518,8 +516,7 @@ def test_bootstap_peak_tracker():
[2., 1., 0.],
[3., 1., 0.],
[4., 1., 0.]]),
np.array([[2., 5., 0.],
[2., 4., 0.],
np.array([[2., 4., 0.],
[2., 3., 0.],
[2., 2., 0.],
[2., 1., 0.],
Expand Down Expand Up @@ -575,8 +572,7 @@ def test_closest_peak_tracker():
[2., 1., 0.],
[2., 2., 0.],
[2., 3., 0.],
[2., 4., 0.],
[2., 5., 0.]])]
[2., 4., 0.]])]

def allclose(x, y):
return x.shape == y.shape and np.allclose(x, y)
Expand Down Expand Up @@ -674,17 +670,13 @@ def test_affine_transformations():
seeds = [np.array([1., 1., 0.]),
np.array([2., 4., 0.])]

expected = [np.array([[0., 1., 0.],
[1., 1., 0.],
[2., 1., 0.],
[3., 1., 0.],
[4., 1., 0.]]),
np.array([[2., 0., 0.],
expected = [np.array([[1., 1., 0.],
[2., 1., 0.],
[3., 1., 0.]]),
np.array([[2., 1., 0.],
[2., 2., 0.],
[2., 3., 0.],
[2., 4., 0.],
[2., 5., 0.]])]
[2., 4., 0.]])]

mask = (simple_image > 0).astype(float)
tc = BinaryTissueClassifier(mask)
Expand Down