def test_angle_between_vectors():
angle1 = mm.angle_between_vectors((1, 0), (0, 1))
assert angle1 == np.pi/2
angle1 = mm.angle_between_vectors((1, 0), (1, 0))
assert angle1 == 0.0
angle1 = mm.angle_between_vectors((1, 0), (-1, 0))
assert angle1 == np.pi
def test_angle_between_vectors():
angle1 = mm.angle_between_vectors((1, 0), (0, 1))
nt.assert_equal(angle1, np.pi/2)
angle1 = mm.angle_between_vectors((1, 0), (1, 0))
nt.assert_equal(angle1, 0.0)
angle1 = mm.angle_between_vectors((1, 0), (-1, 0))
nt.assert_equal(angle1, np.pi)
def trunk_angles(nrn, neurite_type=NeuriteType.all):
"""Calculates the angles between all the trunks of the neuron.
The angles are defined on the x-y plane and the trees
are sorted from the y axis and anticlock-wise.
"""
vectors = trunk_vectors(nrn, neurite_type=neurite_type)
# In order to avoid the failure of the process in case the neurite_type does not exist
if not vectors.size:
return []
def _sort_angle(p1, p2):
"""Angle between p1-p2 to sort vectors."""
ang1 = np.arctan2(*p1[::-1])
ang2 = np.arctan2(*p2[::-1])
return (ang1 - ang2)
# Sorting angles according to x-y plane
order = np.argsort(
np.array([
_sort_angle(i / np.linalg.norm(i), [0, 1]) for i in vectors[:, 0:2]
]))
ordered_vectors = vectors[order][:, [COLS.X, COLS.Y]]
return [
morphmath.angle_between_vectors(ordered_vectors[i],
ordered_vectors[i - 1])
for i, _ in enumerate(ordered_vectors)
]
def align(section, direction):
"""Rotate a section (and all its descendents) so its initial segment is along ``direction``."""
section_dir = section.points[1] - section.points[0]
alpha = angle_between_vectors(section_dir, direction)
if alpha < 1e-8:
return
if abs(alpha - np.pi) < 1e-8:
axis = np.cross(section_dir, [1, 0, 0])
# Case where X axis and section_dir are colinear
if np.linalg.norm(axis) < 1e-8:
axis = np.cross(section_dir, [0, 1, 0])
else:
axis = np.cross(section_dir, direction)
axis /= np.linalg.norm(axis)
matrix = Rotation.from_rotvec(alpha * axis).as_matrix()
rotate(section, matrix, origin=section.points[0])