def test_interval_lengths():
assert_array_almost_equal(mm.interval_lengths([[0, 0, 0], [1, 1, 0], [2, 11, 0]]),
[1.414214, 10.049876])
assert_array_almost_equal(mm.interval_lengths([[0, 0, 0], [1, 1, 0], [2, 11, 0]],
prepend_zero=True),
[0, 1.414214, 10.049876])
def _sec_taper_rate(sec):
"""Taper rate from fit along a section."""
path_distances = np.cumsum(
interval_lengths(sec.points, prepend_zero=True))
return np.polynomial.polynomial.polyfit(path_distances,
2 * sec.points[:, COLS.R],
1)[1]
def __init__(self, neurom_section):
"""Dendrogram for NeuroM section tree.
Args:
neurom_section (Neurite|Neuron|Section): tree to build dendrogram for.
"""
if isinstance(neurom_section, Neuron):
self.neurite_type = NeuriteType.soma
self.height = 1
self.width = 1
self.coords = self.get_coords(
np.array([0, self.height]),
np.array([.5 * self.width, .5 * self.width]))
self.children = [
Dendrogram(neurite.root_node)
for neurite in neurom_section.neurites
]
else:
if isinstance(neurom_section, Neurite):
neurom_section = neurom_section.root_node
lengths = interval_lengths(neurom_section.points,
prepend_zero=True)
radii = neurom_section.points[:, COLS.R]
self.neurite_type = neurom_section.type
self.height = np.sum(lengths)
self.width = 2 * np.max(radii)
self.coords = Dendrogram.get_coords(lengths, radii)
self.children = [
Dendrogram(child) for child in neurom_section.children
]
def segment_lengths(section):
'''Returns the list of segment lengths within the section'''
return interval_lengths(section.points)
def _unravel_section_path_length(sec, window_half_length, soma,
legacy_behavior):
'''Unravel a section using path length as window_half_length'''
unraveled_points = sec.points
n_points = len(sec.points)
if legacy_behavior and sec.is_root and len(soma.points) > 1:
unraveled_points = np.vstack((soma.points[0], unraveled_points))
# ensure the first point is the parent's last point
if not sec.is_root:
unraveled_points[0] = sec.parent.points[-1]
for window_center in range(1, n_points):
# find how many segement on the left and right to be close to window_half_length
intervals = interval_lengths(sec.points)
_l_left = np.cumsum(intervals[window_center::-1])
_l_right = np.cumsum(intervals[min(n_points - 2, window_center):])
window_start = np.argmin(abs(_l_left - window_half_length))
window_end = np.argmin(abs(_l_right - window_half_length))
# if we are near the first point of the section we increase window from the right/left
# the 0.9 is only to not do that to often
_left_length = _l_left[window_start]
if _left_length < 0.9 * window_half_length:
window_end = np.argmin(
abs(_l_right - (2 * window_half_length - _left_length)))
_right_length = _l_right[window_end]
if _right_length < 0.9 * window_half_length:
window_start = np.argmin(
abs(_l_left - (2 * window_half_length - _right_length)))
# center bounds to windows center
window_start = window_center - window_start
window_end = window_center + window_end
# if windows as 0 width, extend by one segment on each side if possible
if window_start == window_end:
window_start = max(0, window_start - 1)
window_end = min(n_points, window_end + 1)
direction = _get_principal_direction(
sec.points[window_start:window_end])
original_segment = sec.points[window_center] - sec.points[window_center
- 1]
# make it span length the same as the original segment within the window
direction *= np.linalg.norm(original_segment)
# point it in the same direction as the window
window_direction = sec.points[window_end -
1] - sec.points[window_start]
scalar_product = np.dot(window_direction, direction)
direction *= np.sign(scalar_product or 1.)
# update the unravel points
unraveled_points[window_center] = unraveled_points[window_center -
1] + direction
sec.points = unraveled_points
if legacy_behavior and sec.is_root and len(soma.points) > 1:
sec.diameters = np.hstack((soma.diameters[0], sec.diameters))
def _sec_taper_rate(sec):
'''Taper rate from fit along a section'''
distances = interval_lengths(sec.points, prepend_zero=True)
return np.polynomial.polynomial.polyfit(distances,
2 * sec.points[:, COLS.R],
1)[1]
def segment_lengths(section, prepend_zero=False):
"""Returns the list of segment lengths within the section."""
return interval_lengths(section.points, prepend_zero=prepend_zero)