def save_morph_data(self, morph_stats_filename):
if not os.path.exists(morph_stats_filename):
# load a neuron from an SWC file
nrn = nm.load_neuron(self.morph_file)
morph_stats = {}
morph_stats['cell_id'] = self.cell_id
morph_stats['soma_suface'] = nm.get('soma_surface_areas', nrn)[0]
morph_stats['soma_radius'] = np.mean(nm.get('soma_radii', nrn))
# Morph stats
for nrn_type_ in NEURITES:
morph_stats['length' + '.' +
str(nrn_type_).split('.')[1]] = np.sum(
nm.get('segment_lengths',
nrn,
neurite_type=nrn_type_))
morph_stats['area' + '.' + str(nrn_type_).split('.')[1]] = sum(
mm.segment_area(s) for s in nm.iter_segments(
nrn, neurite_filter=tree_type_checker(nrn_type_)))
morph_stats[
'volume' + '.' + str(nrn_type_).split('.')[1]] = sum(
mm.segment_volume(s) for s in nm.iter_segments(
nrn, neurite_filter=tree_type_checker(nrn_type_)))
morph_stats['taper_rate' + '.' + str(nrn_type_).split('.')[1]] = \
np.mean([mm.segment_taper_rate(s) for s in nm.iter_segments(
nrn, neurite_filter=tree_type_checker(nrn_type_))])
utility.save_json(morph_stats_filename, morph_stats)
def neurite_centre_of_mass(neurite):
'''Calculate and return centre of mass of a neurite.'''
centre_of_mass = np.zeros(3)
total_volume = 0
seg_vol = np.array(map(mm.segment_volume, nm.iter_segments(neurite)))
seg_centre_of_mass = np.array(map(segment_centre_of_mass, nm.iter_segments(neurite)))
# multiply array of scalars with array of arrays
# http://stackoverflow.com/questions/5795700/multiply-numpy-array-of-scalars-by-array-of-vectors
seg_centre_of_mass = seg_centre_of_mass * seg_vol[:, np.newaxis]
centre_of_mass = np.sum(seg_centre_of_mass, axis=0)
total_volume = np.sum(seg_vol)
return centre_of_mass / total_volume
def neurite_centre_of_mass(neurite):
"""Calculate and return centre of mass of a neurite."""
centre_of_mass = np.zeros(3)
total_volume = 0
seg_vol = np.array(map(mm.segment_volume, nm.iter_segments(neurite)))
seg_centre_of_mass = np.array(map(segment_centre_of_mass, nm.iter_segments(neurite)))
# multiply array of scalars with array of arrays
# http://stackoverflow.com/questions/5795700/multiply-numpy-array-of-scalars-by-array-of-vectors
seg_centre_of_mass = seg_centre_of_mass * seg_vol[:, np.newaxis]
centre_of_mass = np.sum(seg_centre_of_mass, axis=0)
total_volume = np.sum(seg_vol)
return centre_of_mass / total_volume
def radius_of_gyration(neurite):
"""Calculate and return radius of gyration of a given neurite."""
centre_mass = neurite_centre_of_mass(neurite)
sum_sqr_distance = 0
N = 0
dist_sqr = [distance_sqr(centre_mass, s) for s in nm.iter_segments(neurite)]
sum_sqr_distance = np.sum(dist_sqr)
N = len(dist_sqr)
return np.sqrt(sum_sqr_distance / N)
def radius_of_gyration(neurite):
'''Calculate and return radius of gyration of a given neurite.'''
centre_mass = neurite_centre_of_mass(neurite)
sum_sqr_distance = 0
N = 0
dist_sqr = [distance_sqr(centre_mass, s) for s in nm.iter_segments(neurite)]
sum_sqr_distance = np.sum(dist_sqr)
N = len(dist_sqr)
return np.sqrt(sum_sqr_distance / N)
def calculate_and_plot_end_to_end_distance(neurite):
'''Calculate and plot the end-to-end distance vs the number of segments for
an increasingly larger part of a given neurite.
Note that the plots are not very meaningful for bifurcating trees.'''
def _dist(seg):
'''Distance between segmenr end and trunk'''
return morphmath.point_dist(seg[1], neurite.root_node.points[0])
end_to_end_distance = [_dist(s) for s in nm.iter_segments(neurite)]
make_end_to_end_distance_plot(np.arange(len(end_to_end_distance)) + 1,
end_to_end_distance, neurite.type)
def calculate_and_plot_end_to_end_distance(neurite):
"""Calculate and plot the end-to-end distance vs the number of segments for
an increasingly larger part of a given neurite.
Note that the plots are not very meaningful for bifurcating trees."""
def _dist(seg):
"""Distance between segmenr end and trunk."""
return morphmath.point_dist(seg[1], neurite.root_node.points[0])
end_to_end_distance = [_dist(s) for s in nm.iter_segments(neurite)]
make_end_to_end_distance_plot(np.arange(len(end_to_end_distance)) + 1,
end_to_end_distance, neurite.type)
def _make_trace(neuron,
plane,
prefix='',
opacity=1.,
visible=True,
style=None,
line_width=2):
'''Create the trace to be plotted'''
names = defaultdict(int)
lines = list()
for neurite in iter_neurites(neuron):
names[neurite.type] += 1
coords = dict(x=list(), y=list(), z=list())
colors = list()
try:
default_color = style[neurite]['color']
except KeyError:
default_color = TREE_COLOR.get(neurite.root_node.type, 'black')
for section in iter_sections(neurite):
segs = [(s[0][COLS.XYZ], s[1][COLS.XYZ])
for s in iter_segments(section)]
section_style = style.get(section, {
'range': slice(0, len(segs)),
'color': default_color
})
range_ = section_style['range']
colors += list(repeat(default_color, 3 * range_.start))
colors += list(
repeat(section_style['color'],
3 * (range_.stop - range_.start)))
colors += list(repeat(default_color,
3 * (len(segs) - range_.stop)))
for i, coord in enumerate('xyz'):
coords[coord] += list(
chain.from_iterable(
(p1[i], p2[i], None) for p1, p2 in segs) if coord in
plane else chain.from_iterable((0, 0, None) for _ in segs))
lines.append(
go.Scatter3d(name=_neurite_name(neurite, prefix, names),
showlegend=False,
visible=visible,
opacity=opacity,
line=dict(color=colors, width=line_width),
mode='lines',
**coords))
return lines
def _make_trace2d(neuron,
plane,
prefix='',
opacity=1.,
visible=True,
style=None,
line_width=2):
'''Create the trace to be plotted'''
names = defaultdict(int)
lines = list()
for neurite in iter_neurites(neuron):
names[neurite.type] += 1
try:
neurite_color = style[neurite]['color']
except KeyError:
neurite_color = TREE_COLOR.get(neurite.root_node.type, 'black')
name = _neurite_name(neurite, prefix, names)
for section in iter_sections(neurite):
segs = [(s[0][COLS.XYZ], s[1][COLS.XYZ])
for s in iter_segments(section)]
try:
colors = style[section]['color']
except KeyError:
colors = neurite_color
coords = dict()
for i, coord in enumerate('xyz'):
coords[coord] = list(
chain.from_iterable(
(p1[i], p2[i], None) for p1, p2 in segs))
coords = dict(x=coords[plane[0]], y=coords[plane[1]])
lines.append(
go.Scattergl(name=name,
visible=visible,
opacity=opacity,
showlegend=False,
line=dict(color=colors, width=line_width),
mode='lines',
**coords))
return lines
def _make_trace(neuron, plane):
"""Create the trace to be plotted."""
for neurite in iter_neurites(neuron):
segments = list(iter_segments(neurite))
segs = [(s[0][COLS.XYZ], s[1][COLS.XYZ]) for s in segments]
coords = dict(
x=list(chain.from_iterable(
(p1[0], p2[0], None) for p1, p2 in segs)),
y=list(chain.from_iterable(
(p1[1], p2[1], None) for p1, p2 in segs)),
z=list(chain.from_iterable(
(p1[2], p2[2], None) for p1, p2 in segs)))
color = TREE_COLOR.get(neurite.root_node.type, 'black')
if plane.lower() == '3d':
plot_fun = go.Scatter3d
else:
plot_fun = go.Scatter
coords = dict(x=coords[plane[0]], y=coords[plane[1]])
yield plot_fun(line=dict(color=color, width=2), mode='lines', **coords)
def _make_trace(neuron, plane):
'''Create the trace to be plotted'''
for neurite in iter_neurites(neuron):
segments = list(iter_segments(neurite))
segs = [(s[0][COLS.XYZ], s[1][COLS.XYZ]) for s in segments]
coords = dict(x=list(chain.from_iterable((p1[0], p2[0], None) for p1, p2 in segs)),
y=list(chain.from_iterable((p1[1], p2[1], None) for p1, p2 in segs)),
z=list(chain.from_iterable((p1[2], p2[2], None) for p1, p2 in segs)))
color = TREE_COLOR.get(neurite.root_node.type, 'black')
if plane.lower() == '3d':
plot_fun = go.Scatter3d
else:
plot_fun = go.Scatter
coords = dict(x=coords[plane[0]], y=coords[plane[1]])
yield plot_fun(
line=dict(color=color, width=2),
mode='lines',
**coords
)
# any function that takes a segment or section.
# Get of all neurites in cell by iterating over sections,
# and summing the section lengths
def sec_len(sec):
"""Return the length of a section."""
return mm.section_length(sec.points)
print('Total neurite length (sections):',
sum(sec_len(s) for s in nm.iter_sections(nrn)))
# Get length of all neurites in cell by iterating over segments,
# and summing the segment lengths.
# This should yield the same result as iterating over sections.
print('Total neurite length (segments):',
sum(mm.segment_length(s) for s in nm.iter_segments(nrn)))
# get volume of all neurites in cell by summing over segment
# volumes
print('Total neurite volume:',
sum(mm.segment_volume(s) for s in nm.iter_segments(nrn)))
# get area of all neurites in cell by summing over segment
# areas
print('Total neurite surface area:',
sum(mm.segment_area(s) for s in nm.iter_segments(nrn)))
# get total number of neurite points in cell.
def n_points(sec):
"""number of points in a section."""
n = len(sec.points)
# any function that takes a segment or section.
# Get of all neurites in cell by iterating over sections,
# and summing the section lengths
def sec_len(sec):
'''Return the length of a section'''
return mm.section_length(sec.points)
print('Total neurite length (sections):',
sum(sec_len(s) for s in nm.iter_sections(nrn)))
# Get length of all neurites in cell by iterating over segments,
# and summing the segment lengths.
# This should yield the same result as iterating over sections.
print('Total neurite length (segments):',
sum(mm.segment_length(s) for s in nm.iter_segments(nrn)))
# get volume of all neurites in cell by summing over segment
# volumes
print('Total neurite volume:',
sum(mm.segment_volume(s) for s in nm.iter_segments(nrn)))
# get area of all neurites in cell by summing over segment
# areas
print('Total neurite surface area:',
sum(mm.segment_area(s) for s in nm.iter_segments(nrn)))
# get total number of neurite points in cell.
def n_points(sec):
'''number of points in a section'''
n = len(sec.points)
