def BKchan_proto(chanparams,
VDIVS=3000,
VMIN=-100e-3,
VMAX=50e-3,
CAMIN=0,
CAMAX=1,
CADIVS=5000):
ZFbyRT = 2 * 96520 / (8.3134 * (23 + 273.15))
v_array = np.linspace(VMIN, VMAX, VDIVS)
ca_array = np.linspace(CAMIN, CAMAX, CADIVS)
#set up the two dimensional gating matrix:
gatingMatrix = []
for i, pars in enumerate(chanparams.Xparam):
Vdepgating = pars.K * np.exp(pars.delta * ZFbyRT * v_array)
#These assignments are specific to the BK channel, calculate 2D array of gating values
if i == 0:
#This is the forward rate constant for a two state channel
gatingMatrix.append(
pars.alphabeta * ca_array[None, :] /
(ca_array[None, :] + pars.K * Vdepgating[:, None]))
else:
#this is backward rate constant for a two state channel
gatingMatrix.append(
pars.alphabeta /
(1 + ca_array[None, :] / pars.K * Vdepgating[:, None]))
#adding forward rate to backward rate gives “alpha+beta” which = 1/tau
gatingMatrix[i] += gatingMatrix[0]
chan = moose.HHChannel2D(
'/library/' +
chanparams.name) # two dimensional tabulated channel gating
chan.Xpower = chanparams.Xpow
chan.Ek = chanparams.Erev
chan.Xindex = "VOLT_C1_INDEX" # critical for correctly using voltage and calcium
xGate = moose.HHGate2D(chan.path + '/gateX')
xGate.xminA = xGate.xminB = VMIN
xGate.xmaxA = xGate.xmaxB = VMAX
xGate.xdivsA = xGate.xdivsB = VDIVS
xGate.yminA = xGate.yminB = CAMIN
xGate.ymaxA = xGate.ymaxB = CAMAX
xGate.ydivsA = xGate.ydivsB = CADIVS
xGate.tableA = gatingMatrix[
0] # assign gatingMatrix to tables, [0] is forw rate = ss/tau
xGate.tableB = gatingMatrix[1] #[1] is 1/tau
return chan
def BKchan_proto(model, chanpath, params):
ZFbyRT= 2 * constants.Faraday / (constants.R * constants.celsius_to_kelvin(model.Temp))
v_array = np.linspace(model.VMIN, model.VMAX, model.VDIVS)
ca_array = np.linspace(model.CAMIN, model.CAMAX, model.CADIVS)
if model.VDIVS<=5 and model.CADIVS<=5:
log.info("{}, {}", v_array, ca_array)
gatingMatrix = []
for i,pars in enumerate(params.X):
Vdepgating=pars.K*np.exp(pars.delta*ZFbyRT*v_array)
if i == 0:
gatingMatrix.append(pars.alphabeta*ca_array[None,:]/(ca_array[None,:]+pars.K*Vdepgating[:,None]))
#table.tableVector2D=gatingMatrix
else:
gatingMatrix.append(pars.alphabeta/(1+ca_array[None,:]/pars.K*Vdepgating[:,None]))
gatingMatrix[i] += gatingMatrix[0]
#table.tableVector2D=gatingMatrix
chan = moose.HHChannel2D(chanpath)
chan.Xpower = params.channel.Xpow
chan.Ek=params.channel.Erev
chan.Xindex="VOLT_C1_INDEX"
xGate = moose.HHGate2D(chan.path + '/gateX')
xGate.xminA=xGate.xminB=model.VMIN
xGate.xmaxA=xGate.xmaxB=model.VMAX
xGate.xdivsA=xGate.xdivsB=model.VDIVS
xGate.yminA=xGate.yminB=model.CAMIN
xGate.ymaxA=xGate.ymaxB=model.CAMAX
xGate.ydivsA=xGate.ydivsB=model.CADIVS
xGate.tableA=gatingMatrix[0]
xGate.tableB=gatingMatrix[1]
if log.isEnabledFor(logging.INFO):
log.info("{}", chan.path)
for ii in np.arange(0, model.VDIVS,1000):
log.info("V={}", model.VMIN+ii*(model.VMAX-model.VMIN)/(model.VDIVS-1))
for jj in np.arange(0,model.CADIVS,1000):
log.info(" Ca={} A,B={},{}",
model.CAMIN+jj*(model.CAMAX-model.CAMIN)/(model.CADIVS-1),
xGate.tableA[ii][jj], xGate.tableB[ii][jj])
return chan
def readChannelML(self, channelElement, params={}, units="SI units"):
"""Loads a single channel
"""
# I first calculate all functions assuming a consistent system of units.
# While filling in the A and B tables, I just convert to SI. Also
# convert gmax and Erev.
if 'Physiological Units' in units:
# see pg 219 (sec 13.2) of Book of Genesis
Vfactor = 1e-3 # V from mV
Tfactor = 1e-3 # s from ms
Gfactor = 1e1 # S/m^2 from mS/cm^2
concfactor = 1e6 # Mol = mol/m^-3 from mol/cm^-3
elif 'SI Units' in units:
Vfactor = 1.0
Tfactor = 1.0
Gfactor = 1.0
concfactor = 1.0
else:
debug.printDebug("ERR",
"wrong units %s. Existing... " % units,
frame=inspect.currentframe())
raise UserWarning, "Unknown units"
# creates /library in MOOSE tree; elif present, wraps
channel_name = channelElement.attrib['name']
if utils.neuroml_debug:
msg = "Loading channel {} into {} ".format(channel_name,
self.libraryPath)
debug.printDebug("INFO", msg)
IVrelation = channelElement.find('./{' + self.cml +
'}current_voltage_relation')
concdep = IVrelation.find('./{' + self.cml + '}conc_dependence')
cPath = os.path.join(self.libraryPath, channel_name)
if concdep is None:
channel = moose.HHChannel(cPath)
else:
channel = moose.HHChannel2D(cPath)
if IVrelation.attrib['cond_law'] == "ohmic":
channel.Gbar = float(IVrelation.attrib['default_gmax']) * Gfactor
channel.Ek = float(IVrelation.attrib['default_erev']) * Vfactor
channelIon = moose.Mstring(channel.path + '/ion')
channelIon.value = IVrelation.attrib['ion']
if concdep is not None:
channelIonDependency = moose.Mstring(channel.path +
'/ionDependency')
channelIonDependency.value = concdep.attrib['ion']
nernstnote = IVrelation.find('./{' + utils.meta_ns + '}notes')
if nernstnote is not None:
# the text in nernstnote is "Nernst,Cout=<float>,z=<int>"
nernst_params = string.split(nernstnote.text, ',')
if nernst_params[0] == 'Nernst':
nernstMstring = moose.Mstring(channel.path + '/nernst_str')
nernstMstring.value = str(
float(string.split(nernst_params[1], '=')[1]) *
concfactor) + ',' + str(
int(string.split(nernst_params[2], '=')[1]))
gates = IVrelation.findall('./{' + self.cml + '}gate')
if len(gates) > 3:
msg = "Sorry! Maximum x, y, and z (three) gates are possible in\
MOOSE/Genesis"
debug.printDebug("ERR", msg, frame=inspect.currentframe())
raise UserWarning, "Bad value or parameter"
# These are the names that MOOSE uses to create gates.
gate_full_name = ['gateX', 'gateY', 'gateZ']
# if impl_prefs tag is present change VMIN, VMAX and NDIVS
impl_prefs = channelElement.find('./{' + self.cml + '}impl_prefs')
if impl_prefs is not None:
table_settings = impl_prefs.find('./{' + self.cml +
'}table_settings')
# some problem here... disable
VMIN_here = float(table_settings.attrib['min_v'])
VMAX_here = float(table_settings.attrib['max_v'])
NDIVS_here = int(table_settings.attrib['table_divisions'])
dv_here = (VMAX_here - VMIN_here) / NDIVS_here
else:
# default VMIN, VMAX and dv are in SI convert them to current
# calculation units used by channel definition while loading into
# tables, convert them back to SI
VMIN_here = utils.VMIN / Vfactor
VMAX_here = utils.VMAX / Vfactor
NDIVS_here = utils.NDIVS
dv_here = utils.dv / Vfactor
offset = IVrelation.find('./{' + self.cml + '}offset')
if offset is None:
vNegOffset = 0.0
else:
vNegOffset = float(offset.attrib['value'])
self.parameters = []
for parameter in channelElement.findall('.//{' + self.cml +
'}parameter'):
self.parameters.append(
(parameter.attrib['name'], float(parameter.attrib['value'])))
for num, gate in enumerate(gates):
# if no q10settings tag, the q10factor remains 1.0 if present but no
# gate attribute, then set q10factor if there is a gate attribute,
# then set it only if gate attrib matches gate name
self.q10factor = 1.0
self.gate_name = gate.attrib['name']
q10sets = IVrelation.findall('./{' + self.cml + '}q10_settings')
for q10settings in q10sets:
# self.temperature from neuro.utils
if 'gate' in list(q10settings.attrib.keys()):
if q10settings.attrib['gate'] == self.gate_name:
self.setQ10(q10settings)
break
else:
self.setQ10(q10settings)
# HHChannel2D crashing on setting Xpower! temperamental! If you
# print something before, it gives cannot creategate from copied
# channel, else crashes Setting power first. This is necessary
# because it also initializes the gate's internal data structures as
# a side effect. Alternatively, gates can be initialized explicitly
# by calling HHChannel.createGate().
gate_power = float(gate.get('instances'))
if num == 0:
channel.Xpower = gate_power
if concdep is not None: channel.Xindex = "VOLT_C1_INDEX"
elif num == 1:
channel.Ypower = gate_power
if concdep is not None: channel.Yindex = "VOLT_C1_INDEX"
elif num == 2:
channel.Zpower = gate_power
if concdep is not None: channel.Zindex = "VOLT_C1_INDEX"
## Getting handle to gate using the gate's path.
gate_path = os.path.join(channel.path, gate_full_name[num])
if concdep is None:
moosegate = moose.HHGate(gate_path)
# set SI values inside MOOSE
moosegate.min = VMIN_here * Vfactor
moosegate.max = VMAX_here * Vfactor
moosegate.divs = NDIVS_here
## V.IMP to get smooth curves, else even with 3000 divisions
## there are sudden transitions.
moosegate.useInterpolation = True
else:
moosegate = moose.HHGate2D(gate_path)
# If alpha and beta functions exist, make them here
for transition in gate.findall('./{' + self.cml + '}transition'):
# make python functions with names of transitions...
fn_name = transition.attrib['name']
# I assume that transitions if present are called alpha and beta
# for forwand backward transitions...
if fn_name in ['alpha', 'beta']:
self.make_cml_function(transition, fn_name, concdep)
else:
debug.printDebug(
"ERROR", "Unsupported transition {0}".format(fn_name))
sys.exit()
time_course = gate.find('./{' + self.cml + '}time_course')
# tau is divided by self.q10factor in make_function() thus, it gets
# divided irrespective of <time_course> tag present or not.
if time_course is not None:
self.make_cml_function(time_course, 'tau', concdep)
steady_state = gate.find('./{' + self.cml + '}steady_state')
if steady_state is not None:
self.make_cml_function(steady_state, 'inf', concdep)
if concdep is None:
ca_name = '' # no Ca dependence
else:
# Ca dependence
ca_name = ',' + concdep.attrib['variable_name']
# Create tau() and inf() if not present, from alpha() and beta()
for fn_element, fn_name, fn_expr in [
(time_course, 'tau', "1/(alpha+beta)"),
(steady_state, 'inf', "alpha/(alpha+beta)")
]:
# put in args for alpha and beta, could be v and Ca dep.
expr_string = self.replace(fn_expr, 'alpha',
'self.alpha(v' + ca_name + ')')
expr_string = self.replace(expr_string, 'beta',
'self.beta(v' + ca_name + ')')
# if time_course/steady_state are not present, then alpha annd
# beta transition elements should be present, and fns created.
if fn_element is None:
self.make_function(fn_name,
'generic',
expr_string=expr_string,
concdep=concdep)
# non Ca dependent channel
if concdep is None:
# while calculating, use the units used in xml defn, while
# filling in table, I convert to SI units.
v0 = VMIN_here - vNegOffset
n_entries = NDIVS_here + 1
tableA = [0.0] * n_entries
tableB = [0.0] * n_entries
for i in range(n_entries):
v = v0 + (i * dv_here)
inf = self.inf(v)
tau = self.tau(v)
# convert to SI before writing to table
# qfactor is already in inf and tau
tableA[i] = (inf / tau) / Tfactor
tableB[i] = (1.0 / tau) / Tfactor
moosegate.tableA = tableA
moosegate.tableB = tableB
## Ca dependent channel
else:
# UNITS: while calculating, use the units used in xml defn,
# while filling in table, I convert to SI units. Note here Ca
# units do not enter, but units of CaMIN, CaMAX and ca_conc in
# fn expr should match.
v = VMIN_here - vNegOffset
CaMIN = float(concdep.attrib['min_conc'])
CaMAX = float(concdep.attrib['max_conc'])
CaNDIVS = 100
dCa = (CaMAX - CaMIN) / CaNDIVS
# CAREFUL!: tableA = [[0.0]*(CaNDIVS+1)]*(NDIVS_here+1) will not
# work! * does a shallow copy, same list will get repeated 200
# times! Thus setting tableA[35][1] = 5.0 will set all rows,
# 1st col to 5.0!!!!
tableA = [[0.0] * (CaNDIVS + 1) for i in range(NDIVS_here + 1)]
tableB = [[0.0] * (CaNDIVS + 1) for i in range(NDIVS_here + 1)]
for i in range(NDIVS_here + 1):
Ca = CaMIN
for j in range(CaNDIVS + 1):
inf = self.inf(v, Ca)
tau = self.tau(v, Ca)
# convert to SI (Tfactor) before writing to table
# qfactor is already in inf and tau
tableA[i][j] = (inf / tau) / Tfactor
tableB[i][j] = (1.0 / tau) / Tfactor
Ca += dCa
v += dv_here
# Presently HHGate2D doesn't allow the setting of tables as 2D
# vectors directly
#moosegate.tableA = tableA #moosegate.tableB = tableB
# Instead, I wrap the interpol2D objects inside HHGate2D and set
# the tables
moosegate_tableA = moose.Interpol2D(moosegate.path + '/tableA')
# set SI values inside MOOSE
moosegate_tableA.xmin = VMIN_here * Vfactor
moosegate_tableA.xmax = VMAX_here * Vfactor
moosegate_tableA.xdivs = NDIVS_here
#moosegate_tableA.dx = dv_here*Vfactor
moosegate_tableA.ymin = CaMIN * concfactor
moosegate_tableA.ymax = CaMAX * concfactor
moosegate_tableA.ydivs = CaNDIVS
#moosegate_tableA.dy = dCa*concfactor
moosegate_tableA.tableVector2D = tableA
moosegate_tableB = moose.Interpol2D(moosegate.path + '/tableB')
## set SI values inside MOOSE
moosegate_tableB.xmin = VMIN_here * Vfactor
moosegate_tableB.xmax = VMAX_here * Vfactor
moosegate_tableB.xdivs = NDIVS_here
#moosegate_tableB.dx = dv_here*Vfactor
moosegate_tableB.ymin = CaMIN * concfactor
moosegate_tableB.ymax = CaMAX * concfactor
moosegate_tableB.ydivs = CaNDIVS
#moosegate_tableB.dy = dCa*concfactor
moosegate_tableB.tableVector2D = tableB
def readChannelML(self, channelElement, params={}, units="SI units"):
## I first calculate all functions assuming a consistent system of units.
## While filling in the A and B tables, I just convert to SI.
## Also convert gmax and Erev.
if 'Physiological Units' in units: # see pg 219 (sec 13.2) of Book of Genesis
Vfactor = 1e-3 # V from mV
Tfactor = 1e-3 # s from ms
Gfactor = 1e1 # S/m^2 from mS/cm^2
concfactor = 1e6 # Mol = mol/m^-3 from mol/cm^-3
elif 'SI Units' in units:
Vfactor = 1.0
Tfactor = 1.0
Gfactor = 1.0
concfactor = 1.0
else:
raise RuntimeError("Wrong units %s. Existing" % units)
if not moose.exists('/library'):
moose.Neutral('/library')
channel_name = channelElement.attrib['name']
if utils.neuroml_debug:
pu.info("Loading channel %s into /library" % channel_name)
IVrelation = channelElement.find('./{' + self.cml +
'}current_voltage_relation')
intfire = IVrelation.find('./{' + self.cml + '}integrate_and_fire')
if intfire is not None:
## Below params need to be set while making an LIF compartment
moosechannel = moose.Neutral('/library/' + channel_name)
moosechannelval = moose.Mstring(moosechannel.path + '/vReset')
moosechannelval.value = str(
float(intfire.attrib['v_reset']) * Vfactor)
moosechannelval = moose.Mstring(moosechannel.path + '/thresh')
moosechannelval.value = str(
float(intfire.attrib['threshold']) * Vfactor)
moosechannelval = moose.Mstring(moosechannel.path + '/refracT')
moosechannelval.value = str(
float(intfire.attrib['t_refrac']) * Tfactor)
## refracG is currently not supported by moose.LIF
## Confirm if g_refrac is a conductance density or not?
## assuming g_refrac is a conductance density below
moosechannelval = moose.Mstring(moosechannel.path + '/refracG')
moosechannelval.value = str(
float(intfire.attrib['g_refrac']) * Gfactor)
## create an Mstring saying this is an integrate_and_fire mechanism
moosechannelval = moose.Mstring(moosechannel.path +
'/integrate_and_fire')
moosechannelval.value = 'True'
return
concdep = IVrelation.find('./{' + self.cml + '}conc_dependence')
if concdep is None:
moosechannel = moose.HHChannel('/library/' + channel_name)
else:
moosechannel = moose.HHChannel2D('/library/' + channel_name)
if IVrelation.attrib['cond_law'] == "ohmic":
moosechannel.Gbar = float(
IVrelation.attrib['default_gmax']) * Gfactor
moosechannel.Ek = float(
IVrelation.attrib['default_erev']) * Vfactor
moosechannelIon = moose.Mstring(moosechannel.path + '/ion')
moosechannelIon.value = IVrelation.attrib['ion']
if concdep is not None:
moosechannelIonDependency = moose.Mstring(moosechannel.path +
'/ionDependency')
moosechannelIonDependency.value = concdep.attrib['ion']
nernstnote = IVrelation.find('./{' + utils.meta_ns + '}notes')
if nernstnote is not None:
## the text in nernstnote is "Nernst,Cout=<float>,z=<int>"
nernst_params = nernstnote.text.split(',')
if nernst_params[0] == 'Nernst':
nernstMstring = moose.Mstring(moosechannel.path +
'/nernst_str')
nernstMstring.value = str( float(nernst_params[1].split('=')[1]) * concfactor ) + \
',' + str( int(nernst_params[2].split('=')[1]) )
gates = IVrelation.findall('./{' + self.cml + '}gate')
if len(gates) > 3:
pu.fatal(
"Sorry! Maximum x, y, and z (three) gates are possible in MOOSE/Genesis"
)
sys.exit()
gate_full_name = [
'gateX', 'gateY', 'gateZ'
] # These are the names that MOOSE uses to create gates.
## if impl_prefs tag is present change VMIN, VMAX and NDIVS
impl_prefs = channelElement.find('./{' + self.cml + '}impl_prefs')
if impl_prefs is not None:
table_settings = impl_prefs.find('./{' + self.cml +
'}table_settings')
## some problem here... disable
VMIN_here = float(table_settings.attrib['min_v'])
VMAX_here = float(table_settings.attrib['max_v'])
NDIVS_here = int(table_settings.attrib['table_divisions'])
dv_here = (VMAX_here - VMIN_here) / NDIVS_here
else:
## default VMIN, VMAX and dv are in SI
## convert them to current calculation units used by channel definition
## while loading into tables, convert them back to SI
VMIN_here = utils.VMIN / Vfactor
VMAX_here = utils.VMAX / Vfactor
NDIVS_here = utils.NDIVS
dv_here = utils.dv / Vfactor
offset = IVrelation.find('./{' + self.cml + '}offset')
if offset is None: vNegOffset = 0.0
else: vNegOffset = float(offset.attrib['value'])
self.parameters = []
for parameter in channelElement.findall('.//{' + self.cml +
'}parameter'):
self.parameters.append(
(parameter.attrib['name'], float(parameter.attrib['value'])))
for num, gate in enumerate(gates):
# if no q10settings tag, the q10factor remains 1.0
# if present but no gate attribute, then set q10factor
# if there is a gate attribute, then set it only if gate attrib matches gate name
self.q10factor = 1.0
self.gate_name = gate.attrib['name']
for q10settings in IVrelation.findall('./{' + self.cml +
'}q10_settings'):
## self.temperature from neuro.utils
if 'gate' in q10settings.attrib:
if q10settings.attrib['gate'] == self.gate_name:
self.setQ10(q10settings)
break
else:
self.setQ10(q10settings)
############### HHChannel2D crashing on setting Xpower!
#### temperamental! If you print something before, it gives cannot creategate from copied channel, else crashes
## Setting power first. This is necessary because it also
## initializes the gate's internal data structures as a side
## effect. Alternatively, gates can be initialized explicitly
## by calling HHChannel.createGate().
gate_power = float(gate.get('instances'))
if num == 0:
moosechannel.Xpower = gate_power
if concdep is not None: moosechannel.Xindex = "VOLT_C1_INDEX"
elif num == 1:
moosechannel.Ypower = gate_power
if concdep is not None: moosechannel.Yindex = "VOLT_C1_INDEX"
elif num == 2:
moosechannel.Zpower = gate_power
if concdep is not None: moosechannel.Zindex = "VOLT_C1_INDEX"
## Getting handle to gate using the gate's path.
gate_path = moosechannel.path + '/' + gate_full_name[num]
if concdep is None:
if not moose.exists(gate_path):
moosegate = moose.HHGate(gate_path)
else:
moosegate = moose.element(gate_path)
## set SI values inside MOOSE
moosegate.min = VMIN_here * Vfactor
moosegate.max = VMAX_here * Vfactor
moosegate.divs = NDIVS_here
## V.IMP to get smooth curves, else even with 3000 divisions
## there are sudden transitions.
moosegate.useInterpolation = True
else:
moosegate = moose.HHGate2D(gate_path)
##### If alpha and beta functions exist, make them here
for transition in gate.findall('./{' + self.cml + '}transition'):
## make python functions with names of transitions...
fn_name = transition.attrib['name']
## I assume that transitions if present are called alpha and beta
## for forward and backward transitions...
if fn_name in ['alpha', 'beta']:
self.make_cml_function(transition, fn_name, concdep)
else:
pu.fatal("Unsupported transition %s" % fn_name)
sys.exit()
time_course = gate.find('./{' + self.cml + '}time_course')
## tau is divided by self.q10factor in make_function()
## thus, it gets divided irrespective of <time_course> tag present or not.
if time_course is not None:
self.make_cml_function(time_course, 'tau', concdep)
steady_state = gate.find('./{' + self.cml + '}steady_state')
if steady_state is not None:
self.make_cml_function(steady_state, 'inf', concdep)
if concdep is None: ca_name = '' # no Ca dependence
else:
ca_name = ',' + concdep.attrib[
'variable_name'] # Ca dependence
## Create tau() and inf() if not present, from alpha() and beta()
for fn_element,fn_name,fn_expr in [(time_course,'tau',"1/(alpha+beta)"),\
(steady_state,'inf',"alpha/(alpha+beta)")]:
## put in args for alpha and beta, could be v and Ca dep.
expr_string = fn_expr.replace('alpha',
'self.alpha(v' + ca_name + ')')
expr_string = expr_string.replace(
'beta', 'self.beta(v' + ca_name + ')')
## if time_course/steady_state are not present,
## then alpha annd beta transition elements should be present, and fns created.
if fn_element is None:
self.make_function(fn_name,
'generic',
expr_string=expr_string,
concdep=concdep)
## non Ca dependent channel
if concdep is None:
## while calculating, use the units used in xml defn,
## while filling in table, I convert to SI units.
v0 = VMIN_here - vNegOffset
n_entries = NDIVS_here + 1
tableA = [0.0] * n_entries
tableB = [0.0] * n_entries
for i in range(n_entries):
v = v0 + i * dv_here
inf = self.inf(v)
tau = self.tau(v)
## convert to SI before writing to table
## qfactor is already in inf and tau
tableA[i] = inf / tau / Tfactor
tableB[i] = 1.0 / tau / Tfactor
moosegate.tableA = tableA
moosegate.tableB = tableB
## Ca dependent channel
else:
## UNITS: while calculating, use the units used in xml defn,
## while filling in table, I convert to SI units.
## Note here Ca units do not enter, but
## units of CaMIN, CaMAX and ca_conc in fn expr should match.
v = VMIN_here - vNegOffset
CaMIN = float(concdep.attrib['min_conc'])
CaMAX = float(concdep.attrib['max_conc'])
CaNDIVS = 100
dCa = (CaMAX - CaMIN) / CaNDIVS
## CAREFUL!: tableA = [[0.0]*(CaNDIVS+1)]*(NDIVS_here+1) will not work!
## * does a shallow copy, same list will get repeated 200 times!
## Thus setting tableA[35][1] = 5.0 will set all rows, 1st col to 5.0!!!!
tableA = [[0.0] * (CaNDIVS + 1) for i in range(NDIVS_here + 1)]
tableB = [[0.0] * (CaNDIVS + 1) for i in range(NDIVS_here + 1)]
for i in range(NDIVS_here + 1):
Ca = CaMIN
for j in range(CaNDIVS + 1):
inf = self.inf(v, Ca)
tau = self.tau(v, Ca)
## convert to SI (Tfactor) before writing to table
## qfactor is already in inf and tau
tableA[i][j] = inf / tau / Tfactor
tableB[i][j] = 1.0 / tau / Tfactor
Ca += dCa
v += dv_here
## Presently HHGate2D doesn't allow the setting of tables as 2D vectors directly
moosegate.tableA = tableA
moosegate.tableB = tableB
## set SI values inside MOOSE
moosegate.xminA = VMIN_here * Vfactor
moosegate.xmaxA = VMAX_here * Vfactor
moosegate.xdivsA = NDIVS_here
#moosegate.dxA = dv_here*Vfactor
moosegate.yminA = CaMIN * concfactor
moosegate.ymaxA = CaMAX * concfactor
moosegate.ydivsA = CaNDIVS
#moosegate.dyB = dCa*concfactor
## set SI values inside MOOSE
moosegate.xminB = VMIN_here * Vfactor
moosegate.xmaxB = VMAX_here * Vfactor
moosegate.xdivsB = NDIVS_here
#moosegate.dxB = dv_here*Vfactor
moosegate.yminB = CaMIN * concfactor
moosegate.ymaxB = CaMAX * concfactor
moosegate.ydivsB = CaNDIVS