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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
# abiding by the rules of distribution of free software. You can use,
# 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".
#
# As a counterpart to the access to the source code and rights to copy,
# modify and redistribute granted by the license, users are provided only
# with a limited warranty and the software's author, the holder of the
# economic rights, and the successive licensors have only limited
# liability.
#
# In this respect, the user's attention is drawn to the risks associated
# with loading, using, modifying and/or developing or reproducing the
# software by the user in light of its specific status of free software,
# that may mean that it is complicated to manipulate, and that also
# therefore means that it is reserved for developers and experienced
# professionals having in-depth computer knowledge. Users are therefore
# encouraged to load and test the software's suitability as regards their
# requirements in conditions enabling the security of their systems and/or
# data to be ensured and, more generally, to use and operate it in the
# same conditions as regards security.
#
# The fact that you are presently reading this means that you have had
# knowledge of the CeCILL license and that you accept its terms.
# ----------------------------------------------------------------------------------
#
'''
Membrane equations for Brian models.
'''
__all__ = ['Current', 'IonicCurrent', 'InjectedCurrent', 'MembraneEquation']
from equations import *
from units import have_same_dimensions, get_unit, second, volt, amp
from warnings import warn
class Current(Equations):
'''
A set of equations defining a current.
current_name is the name of the variable that must be added as a membrane current
to the membrane equation.
'''
def __init__(self, expr='', current_name=None, level=0, surfacic=False, **kwd):
Equations.__init__(self, expr, level=level + 1, **kwd)
if surfacic: # A surfacic current is multiplied by membrane area in a MembraneEquation
self._prefix = '__scurrent_'
else:
self._prefix = '__current_'
# Find which variable is the current
if current_name: # Explicitly given
self.set_current_name(current_name)
elif expr != '': # Guess
if len(self._units) == 2: # only one variable (the other one is t)
# Only 1 variable: it's the current
correct_names = [name for name in self._units.keys() if name != 't']
if len(correct_names) != 1:
raise NameError, "The equations do not include time (variable t)"
name, = correct_names
self.set_current_name(name)
else:
# Look for variables with dimensions of current: won't work with units off!
current_names = [name for name, unit in self._units.iteritems()\
if have_same_dimensions(unit, amp)]
if len(current_names) == 1: # only one current
self.set_current_name(current_names[0])
else:
warn("The current variable could not be found!")
def set_current_name(self, name):
if name != 't':
if name is None:
name = unique_id()
current_name = self._prefix + name
self.add_eq(current_name, name, self._units[name]) # not an alias because read-only
def __iadd__(self, other):
# Adding a MembraneEquation
if isinstance(other, MembraneEquation):
return other.__iadd__(self)
else:
return Equations.__iadd__(self, other)
class IonicCurrent(Current):
'''
A ionic current; current direction is defined from intracellular
to extracellular.
'''
def set_current_name(self, name):
if name != 't':
if name is None:
name = unique_id()
current_name = self._prefix + name
self.add_eq(current_name, '-' + name, self._units[name])
InjectedCurrent = Current
class MembraneEquation(Equations):
'''
A membrane equation, defined by a capacitance C and a sum of currents.
Ex:
eq=MembraneEquation(200*pF)
eq=MembraneEquation(200*pF,vm='V')
No more than one membrane equation allowed per system of equations.
'''
def __init__(self, C=None, **kwd):
if C is not None:
expr = '''
dvm/dt=__membrane_Im/C : volt
__membrane_Im=0*unit : unit
'''
Equations.__init__(self, expr, C=C, unit=get_unit(C * volt / second), **kwd)
else:
Equations.__init__(self)
def __iadd__(self, other):
Equations.__iadd__(self, other)
self.set_membrane_current()
return self
def set_membrane_current(self):
current_vars = [name for name in self._eq_names if name.startswith('__current_')] # point current
scurrent_vars = [name for name in self._eq_names if name.startswith('__scurrent_')] # surfacic current
if scurrent_vars != []:
if current_vars != []:
self._string['__membrane_Im'] = '+'.join(current_vars) + '+__area*(' + '+'.join(scurrent_vars) + ')'
else:
self._string['__membrane_Im'] = '__area*(' + '+'.join(scurrent_vars) + ')'
self._namespace[name]['__area'] = self.area
elif current_vars != []:
self._string['__membrane_Im'] = '+'.join(current_vars)
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