def __init__(self, pts, master=True):
self.master = master
diam = p.cell_diameter
self.pts = pts
self.sections = {}
self.sl = h.SectionList()
for pt in pts:
gid = org2gid(*pt)
sec = h.Section(name=str(gid))
sec.pt3dclear()
#draw the line a little shorter so we can see the junctions
p1 = xyz(*pt)
p2 = xyz(pt[0], pt[1], pt[2] + 1)
dp = (p2[0] - p1[0], p2[1] - p1[1], p2[2] - p1[2])
x, y, z = p1[0] + .05 * dp[0], p1[1] + .05 * dp[1], p1[
2] + .05 * dp[2]
sec.pt3dadd(x, y, z, diam - 1)
x, y, z = p2[0] - .05 * dp[0], p2[1] - .05 * dp[1], p2[
2] - .05 * dp[2]
sec.pt3dadd(x, y, z, diam - 1)
self.sections[sec] = gid
self.sl.append(sec=sec)
self.sh = h.Shape(self.sl)
self.sh.menu_tool("print info", self.callback)
if not master:
for sec in self.sections:
self.sh.color(gid2org(self.sections[sec])[0] + 1, sec=sec)
def write_connection_file(outlayer, confile):
"""
column 1: id of the first cell
column 2: id of the second cell
column 3: area of the connection between the two cells
column 4: meang of the connection between the two cells
"""
# have to generate gap junctions associated with outlayer
layer_gids = set()
gaps = []
# all the layer gids
for icircle in range(cellorg.ncircle[outlayer]):
for ipt in range(cellorg.npts[outlayer][icircle]):
gid = cellorg.org2gid(outlayer, icircle, ipt)
layer_gids.add(gid)
timeit("determined set of gids in layer (%d)"%(len(layer_gids),))
# all the gaps with both sides in the layer
for gid in layer_gids:
gs = mkgap.gaps_for_gid(gid)
for gap in gs:
if gap.gid1 in layer_gids and gap.gid2 in layer_gids:
gaps.append(gap)
timeit("determined gaps with both sides in layer (%d)"%(len(gaps),))
cf = open(confile, "w")
for gap in gaps:
cf.write("%d %d %g %d %g\n" % (gap.gid1, gap.gid2, gap.area, is_purkinje_gap(gap.gid1, gap.gid2), conductance(gap)))
cf.close()
def test2():
pts = []
for ilayer in range(1):
for icircle in range(ncircle[ilayer]):
for ipt in range(0, npts[ilayer][icircle], 5):
if gid_is_simulated(org2gid(ilayer, icircle, ipt)):
pts.append((ilayer, icircle, ipt))
return View(pts)
def write_morphfile(outlayer, morphfile):
mf = open(morphfile, "w")
for icircle in range(cellorg.ncircle[outlayer]):
for ipt in range(cellorg.npts[outlayer][icircle]):
x,y,z = xyz(outlayer, icircle, ipt)
gid = cellorg.org2gid(outlayer, icircle, ipt)
assert (gid not in gid2orgmap)
gid2orgmap[gid] = (outlayer, icircle, ipt)
mf.write("%d %g %g %g\n"%(gid, x, y, z))
mf.close()
def vertstim():
from cellorg import nlayer, ncircle, npts, org2gid
r = []
ilayer = 0
for icircle in range(ncircle[ilayer]):
for ipt in range(2):
r.append(org2gid(ilayer, icircle, ipt))
if rank == 0:
print("vertstim (%d [0:%d] [0,1])" % (ilayer, ncircle[ilayer]))
r = h.Vector(r)
return r
def circlestim():
#return vertstim()
from cellorg import nlayer, ncircle, npts, org2gid
r = []
ilayer = 0
for icircle in range(ncircle[ilayer])[-2:]:
npt = npts[ilayer][icircle]
for ipt in range(npt):
r.append(org2gid(ilayer, icircle, ipt))
if rank == 0:
print("circlestim (%d %d [0:%d])" % (ilayer, icircle, npt))
r = h.Vector(r)
return r
def neighborhood(ilayer, icircle, ipt):
global focusedview
x, y, z = xyz(ilayer, icircle, ipt)
gid = org2gid(ilayer, icircle, ipt)
angle = ipt2angle(ipt, ilayer, icircle)
pts = []
for jlayer in range(nlayer):
for jcircle in range(max([icircle - 5, 0]),
min([icircle + 1 + 5, ncircle[jlayer]])):
npt = npts[jlayer][jcircle]
n = min([int(npts[jlayer][jcircle] / 2), 5])
kpt = angle2ipt(angle, jlayer, jcircle)
for jpt in [i % npt for i in range(kpt - n, kpt + 1 + n)]:
pts.append((jlayer, jcircle, jpt))
focusedview = View(pts, master=False)
def test1(ilayer, icircle, ipt):
print(gaps_for_gid(org2gid(ilayer, icircle, ipt)))
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