def test_legacy_runs_without_errors(self):
import random
# The old compartment based system should still run without errors
v = len(Branch.vectors)
root = Branch(*(np.ones(v) for i in range(v)))
branches = [root]
for _ in range(20):
branch = Branch(*(np.ones(v) for i in range(v)))
branch.label(random.choice(["A", "B", "C"]))
random.choice(branches).attach_child(branch)
branches.append(branch)
m = Morphology([root])
# Call all of the legacy functions
m.update_compartment_tree()
m.voxelize(1)
# Too complex to give correct input and already covered by other tests
# m.create_compartment_map()
m.get_bounding_box()
m.get_search_radius()
m.get_compartment_network()
m.get_compartment_positions()
m.get_compartment_positions(labels=["A"])
m.get_plot_range()
m.get_compartment_tree()
m.get_compartment_tree(labels=["B"])
m.get_compartment_submask(["C"])
m.get_compartments()
m.get_compartments(labels=["A"])
m.get_branches()
m.get_branches(labels=["B"])
def test_point_labels(self):
v = len(Branch.vectors)
branch = Branch(*(np.ones(v) for i in range(v)))
branch.label_points("A", [False, True] + [False] * (v - 2))
self.assertEqual([], branch._full_labels)
self.assertEqual([[], ["A"]] + [[]] * (v - 2),
list(map(list, branch.label_walk())))
def test_branch_nargs(self):
v = len(Branch.vectors)
Branch(*(np.ones(i) for i in range(v)))
with self.assertRaises(TypeError):
Branch(*(np.ones(i) for i in range(v - 1)))
with self.assertRaises(TypeError):
Branch(*(np.ones(i) for i in range(v + 1)))
def test_full_labels(self):
v = len(Branch.vectors)
branch = Branch(*(np.ones(v) for i in range(v)))
branch.label("A", "B", "C")
self.assertEqual(["A", "B", "C"], branch._full_labels)
self.assertEqual(["A", "B", "C"], list(next(branch.label_walk())))
self.assertTrue(
all(["A", "B", "C"] == list(l) for l in branch.label_walk()))
def test_rotate(self):
root = Branch(
np.array([0.0, 1.0, 2.0]),
np.array([0.0, 0.0, 0.0]),
np.array([0.0, 0.0, 0.0]),
np.array([1.0, 1.0, 1.0]),
)
m = Morphology([root])
v0 = [1.0, 0.0, 0.0]
v = [0.0, 1.0, 0.0]
# Store pre rotation checks
x0 = m.compartments[0].end.copy()
# Rotate
m.rotate(v0, v)
s = m.compartments[0].start
# Verify rotations
self.assertEqualPoints(s, [0.0, 0.0, 0.0], "Rotation moved the origin!")
self.assertEqualPoints(m.compartments[0].end, [0.0, 1.0, 0.0], v0=v0, v=v, x0=x0)
def test_properties(self):
branch = Branch(
np.array([0, 1, 2]),
np.array([0, 1, 2]),
np.array([0, 1, 2]),
np.array([0, 1, 2]),
)
self.assertEqual(3, branch.size, "Incorrect branch size")
comps = branch.to_compartments()
self.assertTrue(np.array_equal(comps[0].midpoint, [0.5, 0.5, 0.5]))
self.assertEqual(comps[0].spherical, np.sqrt(3) / 2)
self.assertTrue(branch.terminal)
branch.attach_child(
Branch(*(np.ones(0) for i in range(len(Branch.vectors)))))
self.assertFalse(branch.terminal)
def test_mr_labels(self):
v = len(Branch.vectors)
branch = Branch(*(np.ones(v) for i in range(v)))
branch.label_points("A", [False, True] + [False] * (v - 2))
branch.label("B")
m = Morphology([branch])
mr = bsb.output.MorphologyRepository("tmp.h5")
mr.get_handle("w")
mr.save_morphology("test", m)
m_loaded = mr.get_morphology("test")
branch_loaded = m_loaded.roots[0]
self.assertEqual(["B"], branch_loaded._full_labels)
self.assertEqual(
[["B"], ["B", "A"]] + [["B"]] * (v - 2),
list(map(list, branch_loaded.label_walk())),
)
def test_branch_attachment(self):
v = len(Branch.vectors)
branch_A = Branch(*(np.ones(v) for i in range(v)))
branch_B = Branch(*(np.ones(v) for i in range(v)))
branch_C = Branch(*(np.ones(v) for i in range(v)))
branch_D = Branch(*(np.ones(v) for i in range(v)))
branch_A.attach_child(branch_B)
branch_A.attach_child(branch_C)
branch_B.attach_child(branch_D)
self.assertEqual([branch_B, branch_C], branch_A._children)
self.assertFalse(branch_A.terminal)
self.assertFalse(branch_B.terminal)
self.assertTrue(branch_C.terminal)
self.assertTrue(branch_D.terminal)
branch_A.detach_child(branch_C)
self.assertIsNone(branch_C._parent)
with self.assertRaises(ValueError):
branch_A.detach_child(branch_D)
self.assertEqual(branch_B, branch_D._parent)