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Changes to fix issue #361: matrix sizing in tracking.utils.connectivity_matrix #362

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merged 3 commits into from May 6, 2014
Merged

Changes to fix issue #361: matrix sizing in tracking.utils.connectivity_matrix #362

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Changes to fix issue #361: matrix sizing in dipy.tracking.utils.conne…
AndrewLawrence May 6, 2014
d12834c
Update test_utils.py
AndrewLawrence May 6, 2014
5df339b
tidying code.
AndrewLawrence May 6, 2014
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2 changes: 1 addition & 1 deletion dipy/tracking/_utils.py
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Expand Up @@ -210,7 +210,7 @@ def connectivity_matrix(streamlines, label_volume, voxel_size=None,
endlabels = label_volume[i, j, k]
if symmetric:
endlabels.sort(0)
mx = endlabels.max() + 1
mx = label_volume.max() + 1
matrix = ndbincount(endlabels, shape=(mx, mx))
if symmetric:
matrix = np.maximum(matrix, matrix.T)
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16 changes: 16 additions & 0 deletions dipy/tracking/tests/test_utils.py
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Expand Up @@ -410,3 +410,19 @@ def test_seeds_from_mask():
in_444 = ((seeds > 3.5) & (seeds < 4.5)).all(1)
assert_equal(in_444.sum(), 3 * 4 * 5)


def test_connectivity_matrix_shape():

# Labels: z-planes have labels 0,1,2
labels = np.zeros((3,3,3))
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You can pass the dtype to zeros right here so you don't have to cast to int later, ie labels = np.zeros((3, 3, 3), dtype=int).

labels[:,:,1] = 1
labels[:,:,2] = 2
# Streamline set, only moves between first two z-planes.
streamlines = [np.array([[0., 0., 0.],
[0., 0., 0.5],
[0., 0., 1.]]),
np.array([[0., 1., 1.],
[0., 1., 0.5],
[0., 1., 0.]])]
matrix = connectivity_matrix(streamlines,labels.astype('int'),affine=np.eye(4))
assert_equal(matrix.shape,(3,3))