www.neuron.yale.edu

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#!/usr/bin/env python
import neuron

class Cell:
    def __init__(self):
        self.soma = neuron.h.Section(name='soma', cell=self)
        self.soma.L = 30
        self.soma.diam = 30
        self.soma.nseg = 2
        self.dend = neuron.h.Section(name='dend', cell=self)
        self.dend.L = 1000
        self.dend.diam = 2
        self.dend.nseg = 20    
        self.dend.connect(self.soma, 1, 0)
    
        self.allseclist = self.create_seclist()
        
    def create_seclist(self):
        allseclist = neuron.h.SectionList()
        allseclist.append(self.soma)
        allseclist.append(self.dend)
        
        return allseclist

def print_secname(cell):
    for sec in cell.allseclist:
        print sec.name()

if __name__ == '__main__':    
    #this doesn't have an effect
    neuron.h('forall delete_section()')

    cell1 = Cell()
    
    print "this fails when using neuron.h.SectionList():"
    for sec in cell1.allseclist:
        print sec.name()

    print "same here:"
    print_secname(cell1)
    
    print "This is what I want to be in the allseclist:"
    print cell1.soma.name()
    print cell1.dend.name()
    
    print "presumably correct sections" 
    print neuron.h.topology()

Code: Select all

imt-iw23013124:markram ehagen$ ipython
Python 2.7.3 (default, Sep 18 2012, 12:03:14) 
Type "copyright", "credits" or "license" for more information.

IPython 0.13 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]: run seclistfail.py
NEURON -- VERSION 7.3 (736+:19ad148877ff+) 19ad148877ff
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2012
See http://www.neuron.yale.edu/credits.html

this fails when using neuron.h.SectionList():
<__main__.Cell instance at 0x110a3bfc8>.soma
<__main__.Cell instance at 0x110a3bfc8>.soma
same here:
<__main__.Cell instance at 0x110a3bfc8>.soma
<__main__.Cell instance at 0x110a3bfc8>.soma
This is what I want to be in the allseclist:
<__main__.Cell instance at 0x110a3bfc8>.soma
<__main__.Cell instance at 0x110a3bfc8>.dend
presumably correct sections

|--|       <__main__.Cell instance at 0x110a3bfc8>.soma(0-1)
    `-------------------|       <__main__.Cell instance at 0x110a3bfc8>.dend(0-1)

1.0

Code: Select all

>>> from neuron import h
>>> soma=h.Section(name='soma')
>>> dend=h.Section(name='dend')
>>> allsec = h.SectionList()
>>> allsec.append(sec=soma)
>>> allsec.append(sec=dend)
>>> for sec in allsec:
...   print h.secname()
... 
soma
dend