def nonzero_segment_lengths(neuron, threshold=0.0):
'''Check presence of neuron segments with length not above threshold
Arguments:
neuron: Neuron object whose segments will be tested
threshold: value above which a segment length is considered to be non-zero
Return: list of (first_id, second_id) of zero length segments
'''
l = [[s for s in val_iter(isegment(t)) if segment_length(s) <= threshold]
for t in neuron.neurites]
return [(i[0][COLS.ID], i[1][COLS.ID]) for i in chain(*l)]
def segment_centre_of_mass(seg):
'''Calculate and return centre of mass of a segment.
Calculated as centre of mass of conical frustum'''
h = morphmath.segment_length(seg)
r0 = seg[0][COLS.R]
r1 = seg[1][COLS.R]
num = r0 * r0 + 2 * r0 * r1 + 3 * r1 * r1
denom = 4 * (r0 * r0 + r0 * r1 + r1 * r1)
centre_of_mass_z_loc = num / denom
return seg[0][0:3] + (centre_of_mass_z_loc / h) * (seg[1][0:3] - seg[0][0:3])
def _generate_dendro(current_node, lines, colors, n, max_dims,
spacing, offsets, show_diameters=True):
'''Recursive function for dendrogram line computations
'''
start_x = _spacingx(current_node, max_dims, offsets, spacing)
radii = [0., 0.]
# store the parent radius in order to construct polygonal segments
# isntead of simple line segments
radii[0] = current_node.value[3] if show_diameters else 0.
for child in current_node.children:
# segment length
length = segment_length(list(val_iter((current_node, child))))
# extract the radius of the child node. Need both radius for
# realistic segment representation
radii[1] = child.value[3] if show_diameters else 0.
# number of leaves in child
terminations = n_terminations(child)
# horizontal spacing with respect to the number of
# terminations
new_offsets = (start_x + spacing[0] * terminations / 2.,
offsets[1] + spacing[1] * 2. + length)
# vertical segment
lines[n[0]] = _vertical_segment(offsets, new_offsets, spacing, radii)
# assign segment id to color array
colors[n[0]] = child.value[4]
n[0] += 1
if offsets[1] + spacing[1] * 2 + length > max_dims[1]:
max_dims[1] = offsets[1] + spacing[1] * 2. + length
# recursive call to self.
_generate_dendro(child, lines, colors, n, max_dims,
spacing, new_offsets, show_diameters=show_diameters)
# update the starting position for the next child
start_x += terminations * spacing[0]
# write the horizontal lines only for bifurcations, where the are actual horizontal lines
# and not zero ones
if offsets[0] != new_offsets[0]:
# horizontal segment
lines[n[0]] = _horizontal_segment(offsets, new_offsets, spacing, 0.)
colors[n[0]] = current_node.value[4]
n[0] += 1
def nonzero_segment_lengths(neuron, threshold=0.0):
'''Check presence of neuron segments with length not above threshold
Arguments:
neuron: Neuron object whose segments will be tested
threshold: value above which a segment length is considered to be non-zero
Return: list of (first_id, second_id) of zero length segments
'''
l = [[s for s in val_iter(isegment(t))
if segment_length(s) <= threshold]
for t in neuron.neurites]
return [(i[0][COLS.ID], i[1][COLS.ID]) for i in chain(*l)]
def segment_centre_of_mass(seg):
'''Calculate and return centre of mass of a segment.
Calculated as centre of mass of conical frustum'''
h = morphmath.segment_length(seg)
r0 = seg[0][COLS.R]
r1 = seg[1][COLS.R]
num = r0 * r0 + 2 * r0 * r1 + 3 * r1 * r1
denom = 4 * (r0 * r0 + r0 * r1 + r1 * r1)
centre_of_mass_z_loc = num / denom
return seg[0][0:3] + (centre_of_mass_z_loc / h) * (seg[1][0:3] -
seg[0][0:3])
def _generate_dendro(self, current_node, spacing, offsets):
'''Recursive function for dendrogram line computations
'''
max_dims = self._max_dims
start_x = _spacingx(current_node, max_dims, offsets[0], spacing[0])
radii = [0., 0.]
# store the parent radius in order to construct polygonal segments
# isntead of simple line segments
radii[0] = current_node.value[COLS.R] if self._show_diameters else 0.
for child in current_node.children:
# segment length
ln = segment_length((current_node.value, child.value))
# extract the radius of the child node. Need both radius for
# realistic segment representation
radii[1] = child.value[COLS.R] if self._show_diameters else 0.
# number of leaves in child
terminations = n_terminations(child)
# horizontal spacing with respect to the number of
# terminations
new_offsets = _update_offsets(start_x, spacing, terminations, offsets, ln)
# create and store vertical segment
self._rectangles[self._n] = _vertical_segment(offsets, new_offsets, spacing, radii)
# assign segment id to color array
# colors[n[0]] = child.value[4]
self._n += 1
if offsets[1] + spacing[1] * 2 + ln > max_dims[1]:
max_dims[1] = offsets[1] + spacing[1] * 2. + ln
self._max_dims = max_dims
# recursive call to self.
self._generate_dendro(child, spacing, new_offsets)
# update the starting position for the next child
start_x += terminations * spacing[0]
# write the horizontal lines only for bifurcations, where the are actual horizontal
# lines and not zero ones
if offsets[0] != new_offsets[0]:
# horizontal segment. Thickness is either 0 if show_diameters is false
# or 1. if show_diameters is true
self._rectangles[self._n] = _horizontal_segment(offsets, new_offsets, spacing, 0.)
self._n += 1
def test_segment_length():
nt.ok_(segment_length(((0,0,0), (0,0,42))) == 42)
nt.ok_(segment_length(((0,0,0), (0,42,0))) == 42)
nt.ok_(segment_length(((0,0,0), (42,0,0))) == 42)
def _generate_dendro(current_node,
lines,
colors,
n,
max_dims,
spacing,
offsets,
show_diameters=True):
'''Recursive function for dendrogram line computations
'''
start_x = _spacingx(current_node, max_dims, offsets, spacing)
radii = [0., 0.]
# store the parent radius in order to construct polygonal segments
# isntead of simple line segments
radii[0] = current_node.value[3] if show_diameters else 0.
for child in current_node.children:
# segment length
length = segment_length(list(val_iter((current_node, child))))
# extract the radius of the child node. Need both radius for
# realistic segment representation
radii[1] = child.value[3] if show_diameters else 0.
# number of leaves in child
terminations = n_terminations(child)
# horizontal spacing with respect to the number of
# terminations
new_offsets = (start_x + spacing[0] * terminations / 2.,
offsets[1] + spacing[1] * 2. + length)
# vertical segment
lines[n[0]] = _vertical_segment(offsets, new_offsets, spacing, radii)
# assign segment id to color array
colors[n[0]] = child.value[4]
n[0] += 1
if offsets[1] + spacing[1] * 2 + length > max_dims[1]:
max_dims[1] = offsets[1] + spacing[1] * 2. + length
# recursive call to self.
_generate_dendro(child,
lines,
colors,
n,
max_dims,
spacing,
new_offsets,
show_diameters=show_diameters)
# update the starting position for the next child
start_x += terminations * spacing[0]
# write the horizontal lines only for bifurcations, where the are actual horizontal lines
# and not zero ones
if offsets[0] != new_offsets[0]:
# horizontal segment
lines[n[0]] = _horizontal_segment(offsets, new_offsets, spacing,
0.)
colors[n[0]] = current_node.value[4]
n[0] += 1
