/usr/share/pyshared/brian/compartments.py is in python-brian 1.4.1-2.
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# Copyright ENS, INRIA, CNRS
# Contributors: Romain Brette (brette@di.ens.fr) and Dan Goodman (goodman@di.ens.fr)
#
# Brian is a computer program whose purpose is to simulate models
# of biological neural networks.
#
# This software is governed by the CeCILL license under French law and
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# modify and/ or redistribute the software under the terms of the CeCILL
# license as circulated by CEA, CNRS and INRIA at the following URL
# "http://www.cecill.info".
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#
'''
Compartmental models for Brian.
'''
from equations import *
from membrane_equations import *
from units import check_units, ohm
#TODO: add MembraneEquation
class Compartments(Equations):
"""
Creates a compartmental model from a dictionary
of MembraneEquation objects. Compartments are initially unconnected.
Caution: the original objects are modified.
"""
def __init__(self, comps):
Equations.__init__(self, '')
for name, eqs in comps.iteritems():
name = str(name)
# Change variable names
vars = eqs._units.keys()
for var in vars:
eqs.substitute(var, var + '_' + name)
self += eqs
@check_units(Ra=ohm)
def connect(self, a, b, Ra):
"""
Connects compartment a to compartment b with axial resistance Ra.
"""
a, b = str(a), str(b)
# Axial current from a to b
Ia_name = 'Ia_' + a + '_' + b
self += Equations('Ia=(va-vb)*invRa : amp', Ia=Ia_name, invRa=1. / Ra, va='vm_' + a, vb='vm_' + b)
# Add the current to both compartments
self._string['__membrane_Im_' + a] += '-' + Ia_name
self._string['__membrane_Im_' + b] += '+' + Ia_name
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