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 mkcells(gidinfo):
timeit()
for gid in gidinfo:
x, y, z = gidinfo[gid]
cell = h.Cell()
gidinfo[gid] = CellInfo(cell)
# cell shape is actually an arc and area is fastidious with respect
# to all 6 sides. But length
# treated as line distance between org points (interior corners
# in circumferential direction. Set diam so area is correct including
# end areas.
cell.soma.pt3dclear()
cell.soma.pt3dadd(x, y, z, 1.)
ilayer, icircle, ipt = gid2org(gid)
x1, y1, z1 = xyz(ilayer, icircle, ipt + 1)
cell.soma.pt3dadd(x1, y1, z1, 1.)
length = cell.soma.L
area = sum(mkgap.cell_side_areas(gid))
diam = area / pi / length
cell.soma.diam = diam
assert (isclose(cell.soma(.5).area(), area, abs_tol=area * 1e-5))
cell.position(x, y, z)
pc.set_gid2node(gid, rank)
nc = cell.connect2target(None)
pc.cell(gid, nc)
x = pc.allreduce(len(gidinfo), 1)
pr("Global number of real cells is %d" % x)
timeit("mkcells")
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 movie(r, g1, g2):
tt = 0.0
c = 1.
for t, gid in r:
x, y, z = xyz(*gid2org(gid))
if t > tt:
time.sleep(0.1)
tt += 1.0
c = 1 + tt / 10.
#if int(tt)%50 == 0: g2.erase(); g1.erase()
g1.mark(x, z, "S", 10, c, 1)
g2.mark(y, z, "S", 10, c, 1)
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 cellcorners(ilayer, icircle, ipt):
c = Corners()
o0 = paraboloid[ilayer][icircle]
o1 = paraboloid[ilayer][icircle + 1]
a0 = ipt2angle(ipt, ilayer, icircle)
a1 = ipt2angle(ipt + 1, ilayer, icircle)
c.p000 = xyz(o0[0], a0)
c.p001 = xyz(o0[0], a1)
c.p100 = xyz(o0[1], a0)
c.p101 = xyz(o0[1], a1)
c.p010 = xyz(o1[0], a0)
c.p011 = xyz(o1[0], a1)
c.p110 = xyz(o1[1], a0)
c.p111 = xyz(o1[1], a1)
return c
def callback(self, type, x, y, keystate):
#info about nearest section to mouse
if type == 2:
s = self.sh
d = s.nearest(x, y)
arc = s.push_selected()
if arc >= 0:
s.select()
sec = h.cas()
gid = self.sections[sec]
ilayer, icircle, ipt = gid2org(gid)
x, y, z = xyz(ilayer, icircle, ipt)
print(
"gid %d id (%d, %d, %d) prox pt at (%g, %g, %g) length %g"
% (gid, ilayer, icircle, ipt, x, y, z, sec.L))
h.pop_section()
if self.master:
neighborhood(ilayer, icircle, ipt)
def cellconread():
timeit()
# new Heart-3D paraboloid organization
global ncon, ncell, connections
import cellorg, mkgap
from cellorg import sim_layers, sim_circles
ncell = cellorg.ngid
#old way iterating over all possible cells takes 5.4 seconds
for gid in range(rank, ncell, nhost):
ilayer, icircle, ipt = cellorg.gid2org(gid)
if icircle < cellorg.ncircle[ilayer] - 1:
if cellorg.is_simulated(ilayer, icircle, ipt):
xyz = cellorg.xyz(ilayer, icircle, ipt)
gidinfo[gid] = xyz
'''
#new way iterating only over cells that exist takes
import param as p
for ilayer in sim_layers:
for icircle in sim_circles[ilayer]:
i0 = cellorg.angle2ipt(p.simulation_angledeg[0]*2*pi/360, ilayer, icircle)
i1 = cellorg.angle2ipt(p.simulation_angledeg[1]*2*pi/360, ilayer, icircle)
for ipt in range(i0, i1+1):
if cellorg.is_simulated(ilayer, icircle, ipt):
gid = cellorg.org2gid(ilayer, icircle, ipt)
if gid%nhost == rank:
gidinfo[gid] = cellorg.xyz(ilayer, icircle, ipt)
'''
timeit("gidinfo setup")
for gid in gidinfo:
# because of floating round-off error which may or may not create
# a gap with area close to 0, guarantee gap pairs by only creating
# gaps where gid1 < gid2
mkgap.gaps_for_gid(gid)
n = int(pc.allreduce(n_triang_zero(), 1))
pr("accurate_triang_area calculation returned zero %d times" % n)
timeit("connections determined")
# for parallel, copy gid2 gaps to ranks that need them
mkgap.gaps_gid2_copy()
connections = mkgap.gaps
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