def test4():
from neuron import h, gui
# distance between circles as function of surface distance for
# inner and outemost layers. Also length of cells.
g1 = h.Graph()
#for j, layer in enumerate([0, nlayer-1]):
for j, layer in enumerate(range(nlayer)):
p0 = xyz(layer, 0, 0)
d_surf = [
distance(xyz(layer, i, 0), p0) for i in range(1, ncircle[layer])
]
d_circle = [
distance(xyz(layer, i, 0), xyz(layer, i - 1, 0))
for i in range(1, ncircle[layer])
]
print(d_circle, d_surf)
h.Vector(d_circle).line(g1, h.Vector(d_surf), j + 1, 2)
return g1
def test2(layer, circle, ipt):
print(layer, circle, ipt)
print("npts ", npts[ilayer][circle], npts[ilayer][circle + 1])
a = overlap((layer, circle, ipt), layer, circle + 1)
print(a)
for x in a:
b = overlap((layer, circle + 1, x[0]), layer, circle)
print(b)
print("length d_angle of circle ", circle,
distance(xyz(layer, circle, 0), xyz(layer, circle, 1)),
ipt2angle(1, layer, circle))
print("length d_angle of circle ", circle + 1,
distance(xyz(layer, circle + 1, 0), xyz(layer, circle + 1, 1)),
ipt2angle(1, layer, circle + 1))
for i, y in enumerate([a, b]):
c = circle + (1 - i)
for x in y:
print([layer, c, x[0]], xyz(layer, c, x[0]))
print()
def test5(): #pt2circle
from neuron import h, gui
o0 = paraboloid[0]
n = 4
o1 = paraboloid[n]
d = distance(o1[0][0], o0[0][0])
g = h.Graph()
for p in o1:
g.mark(p[0][0], p[0][2], "|", 10, 1, 1)
for o in o0:
p = o[0]
p1 = addmul(p, d, normgrad(p))
i = pt2circle(n, p1)
g.mark(p1[0], p1[2], "|", 10, 2, 1)
g.mark(o1[i][0][0], o1[i][0][2], "|", 10, 3, 1)
d1 = distance(p1, o1[i][0])
if i < len(o1) - 1:
zi = o1[i][0][2]
z = p1[2]
zip = o1[i + 1][0][2]
print("zi=%g z=%g zip=%g" % (zi, z, zip))
assert (zi <= z + 1e-9 and z <= zip + 1e-9)
return g
def gaps_for_gid(gid):
if not gid_is_simulated(gid):
return None
o = gid2org(gid)
ilayer, icircle, ipt = o
pinfo = paraboloid[ilayer][icircle]
rf = pinfo[2] # RegionFace
a = ipt2angle(1, ilayer, icircle)
afirst = a * ipt
alast = a * (ipt + 1)
gs = []
#circum coordinate, end to end
if icircle < ncircle[ilayer] - 1:
npt = npts[ilayer][icircle]
area = area_circum(ilayer, icircle)
for jpt in [ipt - 1, ipt + 1]:
g2 = org2gid(ilayer, icircle, jpt)
if g2 > gid:
#dens_ipt = ipt if jpt < ipt else jpt%npts[ilayer][icircle]
#g = conductance_density_circum(ilayer, icircle, dens_ipt)
if gid_is_simulated(g2):
gs.append(set_gap(gid, g2, area)) #abscond(area, g)))
# between layers
if icircle < ncircle[ilayer] - 1:
pinfo1 = paraboloid[ilayer][icircle + 1]
for jlayer in [ilayer - 1, ilayer + 1]:
if jlayer >= 0 and jlayer < nlayer:
# usually 2, sometimes 1, and rarely 3, circles in jlayer overlap icircle
# n = int(param.layer_thickness/param.cell_diameter)
n = 1
#jcircle, b = rf.p0b if jlayer < ilayer else rf.p1b
p0, plast, (jcircle,
b) = (pinfo[0], pinfo1[0],
rf.p0b) if jlayer < ilayer else (pinfo[1],
pinfo1[1],
rf.p1b)
for p1 in b + [plast]:
jpt, angles = angle_overlap(o, jlayer, jcircle)
a0 = afirst
for a1 in angles + [alast]:
area = side_area(p0, p1, a1 - a0)
if area > 1e-9: # ignore very small areas
g2 = org2gid(jlayer, jcircle, jpt)
if g2 > gid:
#dens_layer, dens_circle, dens_ipt = (ilayer, icircle, ipt) if jlayer < ilayer else (jlayer, jcircle, jpt)
#g = conductance_density_layer(dens_layer, dens_circle, dens_ipt)
if gid_is_simulated(
g2) and jcircle < ncircle[jlayer] - 1:
gs.append(set_gap(
gid, g2, area)) #abscond(area, g)))
jpt += 1
a0 = a1
jcircle += 1
p0 = p1
# between circles in same layer
jlayer = ilayer
for jcircle in [icircle - 1, icircle + 1]:
if jcircle >= 0 and jcircle < ncircle[jlayer]:
# how many cells between icircle and jcircle
d = distance(xyz(ilayer, icircle, 0), xyz(jlayer, jcircle, 0))
n = int(d / param.cell_diameter)
jpt, angles = angle_overlap(o, jlayer, jcircle)
a0 = afirst
pinfo1 = paraboloid[ilayer][jcircle]
p0, p1, dens_circle, dens_ipt = (pinfo[0], pinfo[1], icircle,
ipt) if jcircle < icircle else (
pinfo1[0], pinfo1[1], jcircle,
jpt)
for a1 in angles + [alast]:
area = side_area(p0, p1, a1 - a0)
if area > 1e-9:
g2 = org2gid(jlayer, jcircle, jpt)
if g2 > gid:
#dens_circle, dens_ipt = (icircle, ipt) if jcircle < icircle else (jcircle, jpt)
#g = conductance_density_parabola(ilayer, dens_circle, dens_ipt)
if gid_is_simulated(
g2) and jcircle < ncircle[jlayer] - 1:
gs.append(set_gap(gid, g2,
area)) #abscond(area, g)))
jpt += 1
a0 = a1
return gs
def area3pt(pts): d = [distance(pts[i], pts[(i+1)%3]) for i in range(3)] return accurate_triangle_area(*d)
def end_area(pts): d = [distance(pts[i], pts[(i+1)%4]) for i in range(4)] x = distance(pts[0], pts[2]) return accurate_triangle_area(d[0], d[1], x) + accurate_triangle_area(x, d[2], d[3])