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Added path length properties to Morphology and Branch (#680)
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* added euclidian dists

* shuffled some names around

* fixed property

* fixed expected/actual, added `Morphology.path_length` test

---------

Co-authored-by: Robin De Schepper <robin.deschepper93@gmail.com>
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@igorcantele @Helveg
igorcantele and Helveg committed Apr 4, 2023
1 parent 63f0954 commit c7a8441
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Showing 2 changed files with 49 additions and 42 deletions.
23 changes: 15 additions & 8 deletions bsb/morphologies/__init__.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -391,6 +391,14 @@ def branch_adjacency(self):
idmap = {b: n for n, b in enumerate(self.branches)}
return {n: list(map(idmap.get, b.children)) for n, b in enumerate(self.branches)}

@property
def path_length(self):
"""
Return the total path length as the sum of the euclidian distances between
consecutive points.
"""
return sum(b.path_length for b in self.branches)

def subtree(self, labels=None):
return SubTree(self.get_branches(labels))

Expand Down Expand Up @@ -1203,14 +1211,6 @@ def euclidean_dist(self):
except IndexError:
raise EmptyBranchError("Empty branch has no Euclidean distance") from None

@property
def path_dist(self):
"""
Return the path distance from the start to the terminal point of this branch,
computed as the sum of Euclidean segments between consecutive branch points.
"""
return np.sum(np.sqrt(np.sum(self.point_vectors**2, axis=1)))

@property
def max_displacement(self):
"""
Expand All @@ -1226,6 +1226,13 @@ def max_displacement(self):
"Impossible to compute max_displacement in branches with 0 or 1 points."
) from None

@property
def path_length(self):
"""
Return the sum of the euclidean distances between the points on the branch.
"""
return np.sum(np.sqrt(np.sum(self.point_vectors**2, axis=1)))

@property
def fractal_dim(self):
"""
Expand Down
68 changes: 34 additions & 34 deletions tests/test_morphologies.py
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Original file line number Diff line number Diff line change
Expand Up @@ -664,75 +664,75 @@ def test_short_branch(self):
getattr(self.bzero1, attr)

def test_zero_len(self):
for attr in ("euclidean_dist", "path_dist"):
for attr in ("euclidean_dist", "path_length"):
with self.subTest(attr=attr):
self.assertEqual(getattr(self.b1, attr), 0)
self.assertEqual(getattr(self.bzero1, attr), 0)
self.assertEqual(getattr(self.bzero_r1, attr), 0)
self.assertEqual(getattr(self.bzero2, attr), 0)
self.assertEqual(getattr(self.bzero_r2, attr), 0)
self.assertEqual(getattr(self.bzero10, attr), 0)
self.assertEqual(getattr(self.bzero_r10, attr), 0)
self.assertEqual(0, getattr(self.b1, attr))
self.assertEqual(0, getattr(self.bzero1, attr))
self.assertEqual(0, getattr(self.bzero_r1, attr))
self.assertEqual(0, getattr(self.bzero2, attr))
self.assertEqual(0, getattr(self.bzero_r2, attr))
self.assertEqual(0, getattr(self.bzero10, attr))
self.assertEqual(0, getattr(self.bzero_r10, attr))

def test_known_len(self):
self.assertClose(self.b3.path_dist, 12)
self.assertClose(self.b3.euclidean_dist, 6)
self.assertClose(12, self.b3.path_length)
self.assertClose(12, Morphology([self.b3]).path_length)
self.assertClose(6, self.b3.euclidean_dist)

def test_adjacency(self):
known_adj = {0: [1, 2], 1: [], 2: [3, 4, 5], 3: [], 4: [], 5: []}
self.assertEqual(len(self.branches[0].children), 2)
self.assertEqual(len(self.branches[2].children), 3)
self.assertEqual(2, len(self.branches[0].children))
self.assertEqual(3, len(self.branches[2].children))
self.assertDictEqual(known_adj, self.adjacency)

def test_start_end(self):
self.assertClose(self.branches[0].start, [0.0, 1.0, 0.0])
self.assertClose(self.branches[0].end, [0.0, 1.0, 0.0])
self.assertClose(self.branches[1].start, [0.0, 1.0, 0.0])
self.assertClose(self.branches[1].end, [-5.0, np.exp(5), 0.0])
self.assertClose(self.branches[2].start, [0.0, 1.0, 0.0])
self.assertClose(self.branches[2].end, [0.0, 11.0, 0.0])
self.assertClose(self.branches[3].start, [0.0, 11.0, 0.0])
self.assertClose([0.0, 1.0, 0.0], self.branches[0].start)
self.assertClose([0.0, 1.0, 0.0], self.branches[0].end)
self.assertClose([0.0, 1.0, 0.0], self.branches[1].start)
self.assertClose([-5.0, np.exp(5), 0.0], self.branches[1].end)
self.assertClose([0.0, 1.0, 0.0], self.branches[2].start)
self.assertClose([0.0, 11.0, 0.0], self.branches[2].end)
self.assertClose([0.0, 11.0, 0.0], self.branches[3].start)
self.assertClose(
self.branches[3].end,
[0.0 + 10 * np.cos(np.pi / 2), 11.0 + 10 * np.sin(np.pi / 2), 0.0],
self.branches[3].end,
)
self.assertClose(self.branches[4].start, [0.0, 11.0, 0.0])
self.assertClose([0.0, 11.0, 0.0], self.branches[4].start)
self.assertClose(
self.branches[4].end,
[0.0 + 10 * np.cos(np.pi / 3), 11.0 + 10 * np.sin(np.pi / 3), 0.0],
self.branches[4].end,
)
self.assertClose(self.branches[5].start, [0.0, 11.0, 0.0])
self.assertClose([0.0, 11.0, 0.0], self.branches[5].start)
self.assertClose(
self.branches[5].end,
[
0.0 + 10 * np.cos((2 / 3) * np.pi),
11.0 + 10 * np.sin((2 / 3) * np.pi),
0.0,
],
self.branches[5].end,
)

def test_vectors(self):
self.assertClose(self.branches[2].versor, [0.0, 1.0, 0.0])
self.assertClose(self.branches[2].vector, [0.0, 10.0, 0.0])
self.assertClose(self.branches[3].versor, [0, 1.0, 0.0])
self.assertClose(self.branches[3].vector, [0, 10.0, 0.0])
self.assertClose([0.0, 1.0, 0.0], self.branches[2].versor)
self.assertClose([0.0, 10.0, 0.0], self.branches[2].vector)
self.assertClose([0, 1.0, 0.0], self.branches[3].versor)
self.assertClose([0, 10.0, 0.0], self.branches[3].vector)
self.assertClose(
self.branches[4].versor, [np.cos(np.pi / 3), np.sin(np.pi / 3), 0.0]
[np.cos(np.pi / 3), np.sin(np.pi / 3), 0.0], self.branches[4].versor
)
self.assertClose(
self.branches[5].versor,
[np.cos((2 / 3) * np.pi), np.sin((2 / 3) * np.pi), 0.0],
self.branches[5].versor,
)
pass

def test_displacement(self):
self.assertClose(self.branches[2].max_displacement, 5.0)
self.assertClose(5.0, self.branches[2].max_displacement)
for b in self.branches[3:]:
self.assertClose(b.max_displacement, 0, atol=1e-06)
self.assertClose(0, b.max_displacement, atol=1e-06)

def test_fractal_dim(self):
for b in self.branches[3:]:
self.assertClose(b.fractal_dim, 1.0)
self.assertClose(1.0, b.fractal_dim)


class TestSwcFiles(NumpyTestCase, unittest.TestCase):
Expand Down

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