def __init__(self, params, area):
"""
Default constructor.
:param parameters: the model parameters for the :class:`IonicCurrent`
:type parameters: dictionary
:param area: the cell area
:type area: string
"""
# Initialise attributes
IonicCurrent.__init__(self, params, area)
# self.tempK = "(" + params['temp'] + " + 273.15) * kelvin"
self.tau = params['tau']
self.caInf = params['caInf']
self.kUnit = params['kUnit']
self.kFaraday = params['kFaraday']
self.depth = params['depth']
# Store safe string representation of parameters
# self._tempK = utilities.getSafeStringParam(self.tempK)
self._tau = utilities.getSafeStringParam(self.tau)
self._caInf = utilities.getSafeStringParam(self.caInf)
self._kUnit = utilities.getSafeStringParam(self.kUnit)
self._kFaraday = utilities.getSafeStringParam(self.kFaraday)
self._depth = utilities.getSafeStringParam(self.depth)
def __init__(self, parameters):
"""
Default constructor.
:param area: the area of the soma of the neural cell
:type area: float
:param conductance: the conductance of the neural cell
:type conductance: float
"""
# Initialise attributes
self.parameters = parameters.values()[0]
self.name = parameters.keys()[0]
self.area = self.parameters['area']
self.conductance = self.parameters['conductance']
# Initialise list of defined currents - FG: fixes bug due to having an empty list of defined currents when including all the needed ones
if 'defined' not in self.parameters[
'currents']: # Keyword 'defined' doesn't exists
self.parameters['currents']['defined'] = []
elif self.parameters['currents'][
'defined'] is None: # List of 'defined' currents is undefined/empty
self.parameters['currents']['defined'] = []
# Check for parameters specified as include files
for f in self.parameters['currents'].get('included', []):
try:
with open(f) as curr:
# Load included currents from file
includes = yaml.load(curr)
# Add them the list of defined currents
self.parameters['currents'].get('defined',
[]).extend(includes)
except IOError:
raise IOError('Cannot load current parameter file named ' + f)
# Remove list of includesd currents from dict of currents
self.parameters['currents'].pop('included', [])
# Initialise ionic current factory
self.factory = icf.IonicCurrentFactory()
# Build current list
self.currents = []
for currentParams in self.parameters['currents'].get('defined', []):
tmpCurrent = self.factory.makeIonicCurrent(currentParams,
self.area)
self.currents.append(tmpCurrent)
# Store safe string representation of parameters
self._area = utilities.getSafeStringParam(self.area)
self._conductance = utilities.getSafeStringParam(
utilities.getSafeStringParam(self.conductance) + ' * ' +
self._area)
def __init__(self, params, area):
"""
Default constructor.
:param parameters: the model parameters for the :class:`IonicCurrent`
:type parameters: dictionary
:param area: the cell area
:type area: string
"""
# Initialise attributes
IonicCurrent.__init__(self, params, area)
self.beta = params['beta']
self.cac = params['cac']
self.tempAdj = "3.0 ** ((" + params['temp'] + " -22) / 10)"
# Store safe string representation of parameters
self._beta = utilities.getSafeStringParam(self.beta)
self._cac = utilities.getSafeStringParam(self.cac)
self._tempAdj = utilities.getSafeStringParam(self.tempAdj)
def __init__(self, params, area):
"""
Default constructor.
:param parameters: the model parameters for the :class:`IonicCurrent`
:type parameters: dictionary
:param area: the cell area
:type area: string
"""
# Initialise attributes
IonicCurrent.__init__(self, params, area)
self.tau = params['tau']
# Store safe string representation of parameters
self._tau = utilities.getSafeStringParam(self.tau)