def get_below(p):
def get_nears(q):
npt = []
for dx, dy, dz in moves:
npt.append((q[0] + dx, q[1] + dy, q[2] + dz))
return npt
def get_p(x, u):
dim = params.grid_dim
o = params.granule_origin
q = ()
for i in range(3):
q += (int(round((p[i] + x * u[i] - o[i]) / dim) * dim + o[i]), )
return q
# scroll the line from points to the center
u = misc.versor(params.bulbCenter, p)
L = misc.distance(p, params.bulbCenter)
dx = L / params.grid_dim
nnpts = set()
x = 0.
while x <= L:
q = get_p(x, u)
if q not in nnpts:
nnpts.update(get_nears(q))
x += dx
return nnpts
def Bifurcate(self):
r = self.r[self.extr_type]
_extrLs = []
if self.extr_type == Extreme.APICAL:
if distance(self.sec.points[-1][:3], self.glomPos) != GLOM_RADIUS:
pos = getP(
distance(self.sec.points[-1][:3], self.glomPos) -
GLOM_RADIUS, versor(self.glomPos, self.sec.points[-1][:3]),
self.sec.points[-1][:3])
stretchSection(self.sec.points, pos)
# orientation respect glomerulus
gl_phi, gl_theta = Spherical.to(self.glomPos,
self.sec.points[-1][:3])[1:]
# make tuft
TUFTS = int(r.discunif(self.cfg.N_MIN_TUFT, self.cfg.N_MAX_TUFT))
for i in range(TUFTS):
sec = Section()
sec.connect(self.nrn.apic[0])
self.nrn.tuft.append(sec)
extr = Extreme()
extr.sec = sec
extr.phi, extr.theta = i * 2 * pi / TUFTS * (
1 + 0.75 * r.uniform(-0.5 / TUFTS, 0.5 / TUFTS)), pi / 4
extr.basePhi, extr.baseTheta = self.basePhi, self.baseTheta
extr.limit = r.uniform(self.cfg.TUFT_MIN_LEN,
self.cfg.TUFT_MAX_LEN)
extr.extr_type = Extreme.TUFT
extr.glomPos = self.glomPos
extr.cfg = self.cfg
extr.r = self.r
extr.nrn = self.nrn
_extrLs.append(extr)
elif self.extr_type == Extreme.DENDRITE:
def get_phi():
phi = r.negexp(self.cfg.BIFURC_PHI_MU)
while phi < self.cfg.BIFURC_PHI_MIN or phi > self.cfg.BIFURC_PHI_MAX:
phi = r.repick()
return phi
for i in range(2):
sec, extr = mkDendrite(self.cfg, self.r, self.nrn,
self.depth + 1, self.sec)
self.nrn.dend.append(sec)
extr.phi = self.phi + ((-1)**i) * get_phi()
extr.theta = self.theta
extr.dist = self.dist
extr.basePhi = self.basePhi
extr.baseTheta = self.baseTheta
_extrLs.append(extr)
return _extrLs
def get_below(p):
def get_nears(q):
npt = []
for dx, dy, dz in moves:
npt.append((q[0]+dx, q[1]+dy, q[2]+dz))
return npt
def get_p(x, u):
dim = params.grid_dim
o = params.granule_origin
q = ()
for i in range(3):
q += (int(round((p[i] + x * u[i] - o[i])/dim)*dim+o[i]),)
return q
# scroll the line from points to the center
u = misc.versor(params.bulbCenter, p)
L = misc.distance(p, params.bulbCenter)
dx = L / params.grid_dim
nnpts = set()
x = 0.
while x <= L:
q = get_p(x, u)
if q not in nnpts:
nnpts.update(get_nears(q))
x += dx
return nnpts
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 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 bias():
_phi, _theta = convert_direction(self.phi, self.theta,
self.basePhi, self.baseTheta)
p = Spherical.xyz(self.cfg.GRW_WALK_LEN, _phi, _theta,
self.sec.points[-1][:3])
dglom = distance(p, self.glomPos)
if dglom > GLOM_RADIUS * 0.9:
_phi, _theta = Spherical.to(
getP(dglom - GLOM_RADIUS * 0.9,
versor(self.glomPos, p), p),
self.sec.points[-1][:3])[1:]
self.phi, self.theta = convert_direction(
_phi, _theta, self.basePhi, self.baseTheta, True)
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 EllipsoidPression(p, axis, up, k):
e = Ellipsoid(bulbCenter, axis)
h = e.normalRadius(p)
q = None
_lamb, _phi = e.toElliptical(p)[1:]
F = h * k
q = [
-F * sin(_lamb) * cos(_phi) + p[0],
-F * cos(_lamb) * cos(_phi) + p[1], -F * sin(_phi) + p[2]
]
vNew = versor(q, self.sec.points[-1][:3])
_p = getP(self.cfg.GRW_WALK_LEN, vNew, self.sec.points[-1][:3])
_phi, _theta = Spherical.to(_p, self.sec.points[-1][:3])[1:]
return _p, _phi, _theta
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 granule_voxels(p1, p2):
u = misc.versor(p2, p1)
def nears(q):
nn = []
for dx, dy, dz in moves:
nn.append((q[0] + dx, q[1] + dy, q[2] + dz))
return nn
def pt(x):
p = ( p1[0] + x * u[0], p1[1] + x * u[1], p1[2] + x * u[2])
p = ( int(round((p[0] - params.granule_origin[0]) / params.grid_dim)) * params.grid_dim + params.granule_origin[0], \
int(round((p[1] - params.granule_origin[1]) / params.grid_dim)) * params.grid_dim + params.granule_origin[1], \
int(round((p[2] - params.granule_origin[2]) / params.grid_dim)) * params.grid_dim + params.granule_origin[2])
return p
L = misc.distance(p1, p2)
dx = L / params.grid_dim
visited = set()
x = 0.
while x <= L:
visited.add(pt(x))
x += dx
nnpts = set() # near points
for q in visited:
nnpts.update(nears(q))
# return ggids
ggids = set()
for q in nnpts:
if pos2gid.has_key(q):
ggids.add(pos2gid[q])
return list(ggids)
def granule_voxels(p1, p2):
u = misc.versor(p2, p1)
def nears(q):
nn = []
for dx, dy, dz in moves:
nn.append((q[0] + dx, q[1] + dy, q[2] + dz))
return nn
def pt(x):
p = (p1[0] + x * u[0], p1[1] + x * u[1], p1[2] + x * u[2])
p = ( int(round((p[0] - params.granule_origin[0]) / params.grid_dim)) * params.grid_dim + params.granule_origin[0], \
int(round((p[1] - params.granule_origin[1]) / params.grid_dim)) * params.grid_dim + params.granule_origin[1], \
int(round((p[2] - params.granule_origin[2]) / params.grid_dim)) * params.grid_dim + params.granule_origin[2])
return p
L = misc.distance(p1, p2)
dx = L / params.grid_dim
visited = set()
x = 0.
while x <= L:
visited.add(pt(x))
x += dx
nnpts = set() # near points
for q in visited:
nnpts.update(nears(q))
# return ggids
ggids = set()
for q in nnpts:
if pos2gid.has_key(q):
ggids.add(pos2gid[q])
return list(ggids)
def granule_position_orientation(gid):
from misc import versor, ellipseLineIntersec as eli
pos = list(ggid2pos[gid])
u = versor(pos, params.bulbCenter)
proj = eli(u, pos, params.bulbCenter, params.somaAxis[1])
return pos, u, proj
def granule_position_orientation(gid):
from misc import versor, ellipseLineIntersec as eli
pos = list(ggid2pos[gid])
u = versor(pos, params.bulbCenter)
proj = eli(u, pos, params.bulbCenter, params.somaAxis[1])
return pos, u, proj
