def cut(self, w, pos, dep):
def set_cut_1(act, grw):
from math import sqrt
for i in range(1, len(grw.points)):
p = grw.points[i]
d = plane_dist(p, w, pos)
if d <= dep and act[i - 1].property.opacity == 1:
op = 1.
else:
op = 0.
act[i - 1].property.opacity = op
def set_cut_2(acts, grws):
for i in range(len(acts)):
set_cut_1(acts[i], grws[i])
from misc import centroid, mean
if plane_dist(centroid(self.mitral.soma.points), w, pos) <= dep:
self.soma.property.opacity = 1.
else:
self.soma.property.opacity = 0.
set_cut_1(self.apic, self.mitral.apic)
set_cut_2(self.tuft, self.mitral.tuft)
set_cut_2(self.dend, self.mitral.dend)
self.__cutted = (tuple(w), tuple(pos), dep)
def drawsoma():
pts = self.mitral.soma.points
center = misc.centroid(pts)
# calc. soma radius
radius = 0.
for p in pts:
radius += misc.distance(p, center)
radius /= len(pts)
radius *= cone_factor
# versor
u = tuple(
misc.versor(self.mitral.apic.points[0],
self.mitral.apic.points[1]))
src = tvtk.ConeSource(center=tuple(center[0:3]),
radius=radius,
height=radius,
direction=u,
resolution=20)
mapper = tvtk.PolyDataMapper(input=src.output)
actor = tvtk.Actor(mapper=mapper)
fig.scene.add_actor(actor)
actor.property.color = self.soma_color
return actor
def realSoma(i, p):
soma1 = copy.deepcopy(__somar[i])
# translation vector calculation
vec = centroid(soma1)
for j in range(3):
vec[j] = p[j] - vec[j]
# translate
for x in soma1:
for j in range(3):
x[j] += vec[j]
return soma1
def fill_soma(sections, elements, cellid):
points = []
for sec in sections:
points += sec.points
center = misc.centroid(points)[:3]
radius = 0.0
for p in sec.points:
radius += misc.distance(p[:3], center)
radius /= len(points)
verse = misc.versor(bulbdef.bulb_center, center)
o = Soma(center, radius, verse)
o.gids.append(cellid)
elements.objs.append(o)
def drawsoma():
pts = self.mitral.soma.points
center = misc.centroid(pts)
# calc. soma radius
radius = 0.
for p in pts:
radius += misc.distance(p, center)
radius /= len(pts)
radius *= cone_factor
# versor
u = tuple(misc.versor(self.mitral.apic.points[0], self.mitral.apic.points[1]))
src = tvtk.ConeSource(center=tuple(center[0:3]), radius=radius, height=radius, direction=u, resolution=20)
mapper = tvtk.PolyDataMapper(input=src.output)
actor = tvtk.Actor(mapper=mapper)
fig.scene.add_actor(actor)
actor.property.color = self.soma_color
return actor
self.__readsections(cell.soma)
self.__readsections(cell.apic)
self.__readsections(cell.tuft)
self.__readsections(cell.dend)
self.__connect(cell)
return cell
if __name__ == '__main__':
cr = CellReader('../bulbvis/mccells.car')
hist = [0] * int(1040 / 40)
import misc
for i in range(635, 1904):
try:
cell = cr.readcell(i)
center = misc.centroid(cell.soma[0].points)
for dnd in cell.dend:
for p in dnd.points:
d = misc.distance(p, center)
hist[int(d / 40)] += 1.
except:
break
s = 0.
for x in hist:
s += x
for i in range(len(hist)):
hist[i] /= s
with open('../sholl.txt', 'w') as fo:
for i in range(len(hist)):
fo.write('%d %g\n' % (i * 40, hist[i]))
