def get_granules_below(p, glomid):
bnd_up = misc.Ellipsoid(params.bulbCenter, params.granAxisUp)
bnd_dw = misc.Ellipsoid(params.bulbCenter, params.granAxisDw)
p_up = bnd_up.project(p)
p_dw = bnd_dw.project(p) #params.glomRealCoords[glomid])
def get_neighbors(q):
neighpt = []
for dx, dy, dz in _gran_voxel:
neighpt.append((q[0] + dx, q[1] + dy, q[2] + dz))
return neighpt
def get_p(x):
d = params.gran_voxel
return (int((p_dw[0] + x * (p_up[0] - p_dw[0])) / d) * d,
int((p_dw[1] + x * (p_up[1] - p_dw[1])) / d) * d,
int((p_dw[2] + x * (p_up[2] - p_dw[2])) / d) * d)
pts = set()
nmoves = 1 + int(misc.distance(p_up, p_dw) / params.gran_voxel)
x = 0.0
while x < 1:
pts.update(get_neighbors(get_p(x)))
x += 1.0 / nmoves
return pts
def connect_to_granule(ci, rng, gconnected):
up = misc.Ellipsoid(params.bulbCenter, params.granAxisUp)
dw = misc.Ellipsoid(params.bulbCenter, params.granAxisDw)
gvoxels = list(get_granules_below(ci[-1], mgid2glom(ci[0])))
def inside_boundary(p):
return up.normalRadius(p) < 1 and dw.normalRadius(p) >= 1
def is_proper_type(cgid, gpos):
gtype = pos2type[gpos]
if ismitral(cgid):
return gtype == 0 or gtype == 1
elif ismtufted(cgid):
return gtype == 1 or gtype == 2
return False
while True:
# cannot connect
if len(gvoxels) == 0:
break
index = int(rng.discunif(0, len(gvoxels) - 1))
gpos = gvoxels[index]
# the voxel is a granule
if inside_boundary(gpos) and gpos not in gconnected and is_proper_type(
ci[0], gpos):
return granules.pos2ggid[gpos], 0, rng.uniform(0, 1), gpos
del gvoxels[index]
return None
def gc_is_superficial(ggid):
p = granules.ggid2pos[ggid]
# it fix the granule cells type
up = misc.Ellipsoid(params.bulbCenter, params.granAxisUp)
dw = misc.Ellipsoid(params.bulbCenter, params.granAxisDw)
return (dw.normalRadius(p) - 1) / (dw.normalRadius(up.project(p)) -
1) > 0.5
def initgranules():
global Ngranule
global ngranule
ggid2pos.clear()
pos2ggid.clear()
eup = misc.Ellipsoid(params.bulbCenter, params.somaAxis[0])
edw = misc.Ellipsoid(params.bulbCenter, params.granAxisInf)
for index in range(params.Nx_granule * params.Ny_granule *
params.Nz_granule):
pos = [0.] * 3
pos[0] = (
(index % (params.Nx_granule * params.Ny_granule)) %
params.Nx_granule) * params.grid_dim + params.granule_origin[0]
pos[1] = int(
(index % (params.Nx_granule * params.Ny_granule)) /
params.Nx_granule) * params.grid_dim + params.granule_origin[1]
pos[2] = int(index / (params.Nx_granule * params.Ny_granule)
) * params.grid_dim + params.granule_origin[2]
if eup.normalRadius(pos) < 1. and edw.normalRadius(pos) > 1.:
pos = tuple(pos)
ggid = len(ggid2pos) + params.gid_granule_begin
ggid2pos.update({ggid: pos})
pos2ggid.update({pos: ggid})
Ngranule = len(ggid2pos)
ngranule = Ngranule
def gpo(ggid): import granules import misc import params p=granules.ggid2pos[ggid] pj=misc.Ellipsoid(params.bulbCenter,params.somaAxis[0]).project(p) u=misc.versor(p,params.bulbCenter) return list(p),u,list(pj)
def init():
from math import exp
# it fix the granule cells type
up = misc.Ellipsoid(params.bulbCenter, params.granAxisUp)
dw = misc.Ellipsoid(params.bulbCenter, params.granAxisDw)
for p, ggid in granules.pos2ggid.items():
rng_type = params.ranstream(ggid, params.stream_granule_type)
if rng_type.uniform(0, 1) < params.gc_type3_prob:
# if False:
gtype = 1
else:
prob = (dw.normalRadius(p) - 1) / (dw.normalRadius(up.project(p)) -
1)
#if rng_type.uniform(0, 1) > prob:
if prob <= 0.5:
# if not gc_is_superficial(ggid):
gtype = 0 # right type for mitral only
else:
gtype = 2 # right type for mid. tufted only
pos2type.update({p: gtype})
# initialize the voxel grid to connect segment to granule cells
d = params.gran_voxel
ndepth = int(round(params.gran_connect_radius / d))
old_moves = set([(0, 0, 0)])
for idepth in range(ndepth):
new_moves = set()
for m in old_moves:
for dx in range(-d, d + 1, d):
for dy in range(-d, d + 1, d):
for dz in range(-d, d + 1, d):
p = (m[0] + dx, m[1] + dy, m[2] + dz)
new_moves.add(p)
_gran_voxel.add(p)
old_moves = new_moves
def _select(self):
SceneObject._select(self)
# add apical
if self.__apic == None:
if self.gctype == 1:
axis = bulbdef.mid_tufted_dw
else:
axis = bulbdef.bulb_axis
self.__apic = graphmeat.get_line(self.pos, \
misc.Ellipsoid(bulbdef.bulb_center, axis).project(self.pos)
)
self.__apic.property.color = self.selcolor
def _select(self):
self.__soma = graphmeat.get_sphere(self.pos,
bulbdef.gran_voxel / 2.0, 10)
self.__soma.property.color = self.selcolor
# add apical
if self.__apic == None:
if self.gctype == 1:
axis = bulbdef.mid_tufted_dw
else:
axis = bulbdef.bulb_axis
self.__apic = graphmeat.get_line(self.pos, \
misc.Ellipsoid(bulbdef.bulb_center, axis).project(self.pos)
)
self.__apic.property.color = self.selcolor