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DynClmpComposite.py
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DynClmpComposite.py
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from traits.api import HasTraits, Instance, Int, Float, Array, on_trait_change, Button
from traitsui.api import View, Group, Item
from enable.api import ColorTrait
from enable.component_editor import ComponentEditor
from chaco.api import marker_trait, Plot, ArrayPlotData, VPlotContainer
from numpy import linspace, sin
import pdb
import numpy as np
import sys
class HHCurrentTraits(HasTraits):
plots = Instance(VPlotContainer)
# write_button = Instance(Button)
write_button = Button()
ErevCur1 = Float(20)
GmaxCur1 = Float(0.05)
MvhalfCur1 = Float(50)
MKCur1 = Float(-80)
MssminCur1 = Float(0)
Mdenom_expCur1 = Float(1)
MpCur1 = Float(1)
NvhalfCur1 = Float(25)
NKCur1 = Float(10)
NssminCur1 = Float(0)
Ndenom_expCur1 = Float(1)
NpCur1 = Float(1)
HvhalfCur1 = Float(-80)
HKCur1 = Float(10)
HssminCur1 = Float(0)
Hdenom_expCur1 = Float(1)
HpCur1 = Float(0)
ErevCur2 = Float(20)
GmaxCur2 = Float(0.08)
MvhalfCur2 = Float(-45)
MKCur2 = Float(-5)
MssminCur2 = Float(0)
Mdenom_expCur2 = Float(1)
MpCur2 = Float(1)
NvhalfCur2 = Float(25)
NKCur2 = Float(10)
NssminCur2 = Float(0)
Ndenom_expCur2 = Float(1)
NpCur2 = Float(1)
HvhalfCur2 = Float(-80)
HKCur2 = Float(10)
HssminCur2 = Float(0)
Hdenom_expCur2 = Float(1)
HpCur2 = Float(0)
traits_view = View(
Group(
Item('plots', editor=ComponentEditor(), show_label=False),
Group(
Group(
Group(
Item('MvhalfCur1'),
Item('MKCur1'),
Item('MssminCur1'),
Item('Mdenom_expCur1'),
Item('MpCur1'),
orientation = "vertical"),
Group(
Item('NvhalfCur1'),
Item('NKCur1'),
Item('NssminCur1'),
Item('Ndenom_expCur1'),
Item('NpCur1'),
orientation = "vertical"),
Group(
Item('HvhalfCur1'),
Item('HKCur1'),
Item('HssminCur1'),
Item('Hdenom_expCur1'),
Item('HpCur1'),
orientation = "vertical"),
Group(
Item('GmaxCur1'),
Item('ErevCur1'),
orientation = "vertical")),
Group(
Group(
Item('MvhalfCur2'),
Item('MKCur2'),
Item('MssminCur2'),
Item('Mdenom_expCur2'),
Item('MpCur2'),
orientation = "vertical"),
Group(
Item('NvhalfCur2'),
Item('NKCur2'),
Item('NssminCur2'),
Item('Ndenom_expCur2'),
Item('NpCur2'),
orientation = "vertical"),
Group(
Item('HvhalfCur2'),
Item('HKCur2'),
Item('HssminCur2'),
Item('Hdenom_expCur2'),
Item('HpCur2'),
orientation = "vertical"),
Group(
Item('GmaxCur2'),
Item('ErevCur2'),
orientation = "vertical")),
Item('write_button'),
orientation = "horizontal"),
orientation = "horizontal"))
def __init__(self, ExprmntVm=None, ExprmntnA=None):
super(HHCurrentTraits, self).__init__()
# gates
self.vm = linspace(-120,65,1000)
((MCur1,NCur1,HCur1),(MCur2,NCur2,HCur2)) = self.__gates()
self.Cur1gatedata = ArrayPlotData(x=self.vm, M=MCur1, N=NCur1, H=HCur1)
self.Cur2gatedata = ArrayPlotData(x=self.vm, M=MCur2, N=NCur2, H=HCur2)
Cur1gatesplot = Plot(self.Cur1gatedata)
Cur1gatesplot.plot(("x", "M"), type = "line", color = "blue")
Cur1gatesplot.plot(("x", "N"), type = "line", color = "green")
Cur1gatesplot.plot(("x", "H"), type = "line", color = "red")
Cur2gatesplot = Plot(self.Cur2gatedata)
Cur2gatesplot.plot(("x", "M"), type = "line", color = "blue")
Cur2gatesplot.plot(("x", "N"), type = "line", color = "green")
Cur2gatesplot.plot(("x", "H"), type = "line", color = "red")
(Cur1,Cur2) = self.__iv()
self.ivdata = ArrayPlotData(x=self.vm, nA1=Cur1, nA2=Cur2, combin=Cur1+Cur2)
ivplot = Plot(self.ivdata)
ivplot.plot(("x", "nA1"), type = "line", color = "blue")
ivplot.plot(("x", "nA2"), type = "line", color = "green")
ivplot.plot(("x", "combin"), type = "line", color = "black")
if ExprmntVm is not None:
self.ivdata.set_data('ExptVm',ExprmntVm)
self.ivdata.set_data('ExptnA',ExprmntnA)
ivplot.plot(("ExptVm", "ExptnA"),
type = "scatter", color = "red", marker_size = 5)
self.plots = VPlotContainer(ivplot, Cur2gatesplot, Cur1gatesplot)
self.plots.spacing = 0
ivplot.padding_top = 0
Cur1gatesplot.padding_bottom = 0
Cur2gatesplot.padding_top = 0
self.write_button = Button(label="Print_Pars")
def __gates(self):
MCur1 = (1-self.MssminCur1)/(1 + np.exp((self.vm - self.MvhalfCur1)/self.MKCur1))**self.Mdenom_expCur1 + self.MssminCur1
NCur1 = (1-self.NssminCur1)/(1 + np.exp((self.vm - self.NvhalfCur1)/self.NKCur1))**self.Ndenom_expCur1 + self.NssminCur1
HCur1 = (1-self.HssminCur1)/(1 + np.exp((self.vm - self.HvhalfCur1)/self.HKCur1))**self.Hdenom_expCur1 + self.HssminCur1
MCur2 = (1-self.MssminCur2)/(1 + np.exp((self.vm - self.MvhalfCur2)/self.MKCur2))**self.Mdenom_expCur2 + self.MssminCur2
NCur2 = (1-self.NssminCur2)/(1 + np.exp((self.vm - self.NvhalfCur2)/self.NKCur2))**self.Ndenom_expCur2 + self.NssminCur2
HCur2 = (1-self.HssminCur2)/(1 + np.exp((self.vm - self.HvhalfCur2)/self.HKCur2))**self.Hdenom_expCur2 + self.HssminCur2
if self.MpCur1==0:
MCur1 = np.repeat(0,len(self.vm))
if self.NpCur1==0:
NCur1 = np.repeat(0,len(self.vm))
if self.HpCur1==0:
HCur1 = np.repeat(0,len(self.vm))
if self.MpCur2==0:
MCur2 = np.repeat(0,len(self.vm))
if self.NpCur2==0:
NCur2 = np.repeat(0,len(self.vm))
if self.HpCur2==0:
HCur2 = np.repeat(0,len(self.vm))
return ((MCur1,NCur1,HCur1),(MCur2, NCur2, HCur2))
def __iv(self):
((MCur1,NCur1,HCur1),(MCur2,NCur2,HCur2)) = self.__gates()
Cur1 = (MCur1**self.MpCur1 * NCur1**self.NpCur1 * HCur1**self.HpCur1)*self.GmaxCur1*(self.vm - self.ErevCur1)
Cur2 = (MCur2**self.MpCur2 * NCur2**self.NpCur2 * HCur2**self.HpCur2)*self.GmaxCur2*(self.vm - self.ErevCur2)
return (Cur1,Cur2)
# '+' matches all traits on the object
@on_trait_change('+')
def _calc_current(self):
((MCur1,NCur1,HCur1),(MCur2,NCur2,HCur2)) = self.__gates()
(Cur1, Cur2) = self.__iv()
comb = Cur1 + Cur2
self.Cur1gatedata.set_data("M", MCur1)
self.Cur1gatedata.set_data("N", NCur1)
self.Cur1gatedata.set_data("H", HCur1)
self.Cur2gatedata.set_data("M", MCur2)
self.Cur2gatedata.set_data("N", NCur2)
self.Cur2gatedata.set_data("H", HCur2)
self.ivdata.set_data("nA1", Cur1)
self.ivdata.set_data("nA2", Cur2)
self.ivdata.set_data("combin", comb)
def _write_button_fired(self):
with open('pars.txt', 'wt') as sys.stdout: self.print_traits()
def main(atf_path):
''' pass in the full path of an ATF file with the difference current IV'''
from atf_reader import ATFreader
atf = ATFreader(atf_path)
mV = atf.read_data()[:,0]
nA = atf.read_data()[:,1]
HHCurrentTraits(ExprmntVm = mV, ExprmntnA = nA).configure_traits()
if __name__ == "__main__":
''' pass in the full path of an ATF file with the difference current IV'''
import sys
if len(sys.argv)<2:
print("need name of axon text file")
raise ValueError
main(sys.argv[1])