from growdef import *
from struct import unpack
class CellReader:
def __init__(self, filename):
self.__fi = open(filename, 'rb')
self.__cell_offset = [None]*unpack('>I', self.__fi.read(4))[0]
for i in range(len(self.__cell_offset)):
self.__cell_offset[i] = unpack('>I', self.__fi.read(4))[0]
dataoffset = self.__fi.tell()
for i in range(len(self.__cell_offset)):
self.__cell_offset[i] += dataoffset
def close(self):
self.__fi.close()
def __readsections(self, sections):
nsec = unpack('>H', self.__fi.read(2))[0]
for isec in range(nsec):
sec = Section()
npt = unpack('>I', self.__fi.read(4))[0]
for ipt in range(npt):
sec.points.append(unpack('>ffff', self.__fi.read(16)))
sections.append(sec)
def __connect(self, cell):
def get_section(sectype, isec):
if sectype == 0:
return cell.soma[isec]
elif sectype == 1:
return cell.apic[isec]
elif sectype == 2:
return cell.tuft[isec]
elif sectype == 3:
return cell.dend[isec]
return None
nconn = unpack('>I', self.__fi.read(4))[0]
for i in range(nconn):
sectype1 = unpack('>B', self.__fi.read(1))[0]
isec1 = unpack('>H', self.__fi.read(2))[0]
sectype2 = unpack('>B', self.__fi.read(1))[0]
isec2 = unpack('>H', self.__fi.read(2))[0]
sec1 = get_section(sectype1, isec1)
sec2 = get_section(sectype2, isec2)
sec1.parent = sec2
sec2.children.append(sec1)
def readcell(self, gid):
cell = Neuron()
self.__fi.seek(self.__cell_offset[gid])
self.__readsections(cell.soma)
self.__readsections(cell.apic)
self.__readsections(cell.tuft)
self.__readsections(cell.dend)
self.__connect(cell)
return cell
if __name__ == '__main__':
cr = CellReader('../bulbvis/mccells.car')
hist = [0]*int(1040/40)
import misc
for i in range(635, 1904):
try:
cell = cr.readcell(i)
center = misc.centroid(cell.soma[0].points)
for dnd in cell.dend:
for p in dnd.points:
d = misc.distance(p, center)
hist[int(d/40)] += 1.
except:
break
s = 0.
for x in hist:
s += x
for i in range(len(hist)):
hist[i] /= s
with open('../sholl.txt', 'w') as fo:
for i in range(len(hist)):
fo.write('%d %g\n'%(i*40,hist[i]))
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