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318 lines
10 KiB
318 lines
10 KiB
2 years ago
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"""
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test_mechanisms.py
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This program displays the results of inserting NEURON mechaanisms from .mod files
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into a point cell to voltage steps in voltage clamp.
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This code is primarily for visual verification of model function.
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Usage: python test_mechanisms.py <mechname>
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Available mechanisms::
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CaPCalyx bkpkj hcno hcnobo hpkj
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ihpyr ihsgcApical ihsgcBasalMiddle ihvcn jsrna
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ka kcnq kdpyr kht kif
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kis klt kpkj kpkj2 kpkjslow
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kpksk leak lkpkj na naRsg
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nacn nacncoop nap napyr nav11
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Note: only modfiles that implement voltage-dependent ion channel models make sense to run
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with this routine. the list "nottestablemechs" in the file defines mechanisms provided
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with cnmodel that cannot be run with this program.
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"""
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import sys
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from neuron import h
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from neuron import nrn
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import gc
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import numpy as np
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# import scipy as sp
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import cnmodel.util
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import pyqtgraph as pg
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import pyqtgraph.exporters
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from pyqtgraph.Qt import QtCore, QtGui
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import cnmodel.util.pynrnutilities as Util
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nottestablemechs = [
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"cadyn",
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"ca_ion",
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"cadiff",
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"cadifpmp",
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"Mechanism",
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"capmp",
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"capump",
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"cl_ion",
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"extracellular",
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"fastpas",
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"k_ion",
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"KIR",
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"hh",
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"na_ion",
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"narsg",
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"pas",
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"cap",
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] # cap uses "pcabar"
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class ChannelKinetics:
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def __init__(self, args, export=False):
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modfile = []
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if isinstance(args, list):
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for arg in args:
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modfile.append(arg) # must be string, not list...
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else:
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modfile.append(args) # 'CaPCalyx'
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print("modfile: ", modfile)
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colors = ["b", "r", "g", "y", "c", "m", "w"]
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if len(modfile) > len(colors):
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print("Too many modfiles... keep it simple!")
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exit()
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# if isinstance(args, list) and len(args) > 1:
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# modfile2 = args[1]
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doKinetics = False
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self.app = pg.mkQApp()
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self.win = pg.GraphicsWindow()
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self.win.setWindowTitle("VC Plots")
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self.win.resize(600, 800)
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# cw = QtGui.QWidget()
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# self.win.setCentralWidget(cw)
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# self.gridLayout = QtGui.QGridLayout()
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# cw.setLayout(self.gridLayout)
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# self.gridLayout.setContentsMargins(9, 9, 4, 4)
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# self.gridLayout.setSpacing(1)
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self.p1 = self.win.addPlot(title="I (VC)")
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# self.gridLayout.addWidget(self.p1, 0, 0, 1, 1)
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self.p2 = self.win.addPlot(title="I_ss, I_max")
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# self.gridLayout.addWidget(self.p2, 0, 1, 1, 1)
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self.win.nextRow()
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self.p3 = self.win.addPlot(title="V command")
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# self.gridLayout.addWidget(self.p3, 1, 0, 1, 1)
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self.p5 = self.win.addPlot(title="I_min")
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# self.gridLayout.addWidget(self.p5, 1, 1, 1, 1)
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self.win.show()
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QtGui.QApplication.processEvents()
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#
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# self.tdur is a table of durations for the pulse and post-pulse for each channel type (best to highlight features
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# on appropriate time scales)
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#
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self.tdur = {
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"CaPCalyx": [20.0, 10.0],
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"nav11": [10.0, 5.0],
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"jsrna": [10.0, 5.0],
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"ichanWT2005": [10.0, 5.0],
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"nacn": [10.0, 5.0],
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"nacncoop": [10.0, 5.0],
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"nabu": [10.0, 5.0],
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"kht": [200.0, 20.0],
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"klt": [200.0, 20.0],
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"ka": [25.0, 5.0],
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"hcno": [1000.0, 200.0],
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"ih": [1000.0, 200.0],
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"ihvcn": [1000.0, 200.0],
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"hcnobo": [1000.0, 200.0],
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"ihsgcBasalMiddle": [1000.0, 200.0],
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"ihsgcApical": [1000.0, 200.0],
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"kif": [100.0, 100.0],
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"kis": [100.0, 10.0],
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"napyr": [10, 5.0],
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"ihpyr": [1000.0, 200.0],
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"kdpyr": [200.0, 20.0],
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"kcnq": [200, 20],
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"nap": [200.0, 100.0],
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}
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for i, mfile in enumerate(modfile):
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self.run(modfile=mfile, color=colors[i], export=export)
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s = ""
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# self.win.setWindowTitle('VC Plots: ' + [s+sn+'; ' for sn in modfile])
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gc.collect()
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if doKinetics:
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self.win2 = pg.GraphicsWindow(title="KineticPlots")
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self.win2.resize(800, 600)
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self.kp1 = self.win.addPlot(title="htau")
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self.computeKinetics("nav11")
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# self.win.show()
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def run(self, modfile="CaPCalyx", color="r", export=False):
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if isinstance(modfile, list):
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modfile = modfile[0]
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if modfile in self.tdur:
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tstep = self.tdur[modfile]
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else:
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tstep = [200.0, 50.0]
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tdelay = 5.0
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Channel = cnmodel.util.Mechanism(modfile)
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leak = cnmodel.util.Mechanism("leak")
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Channel.set_parameters({"gbar": 1})
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leak.set_parameters({"gbar": 1e-12})
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# if modfile == 'nacncoop':
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# self.soma().nacncoop.p = 0.
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# self.soma().nacncoop.KJ = 0.
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# # Channel.set_parameters({'p': 0., 'KJ': 000.})
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self.soma = cnmodel.util.Section(L=10, diam=10, mechanisms=[Channel, leak])
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if modfile == "bkpjk":
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ca_init = 100e-6
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self.soma().cai = ca_init
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else:
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ca_init = 70e-6
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if modfile == "nacncoop":
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self.soma().nacncoop.p = 0.1
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self.soma().nacncoop.KJ = 1000.0
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# Channel.set_parameters({'p': 0., 'KJ': 000.})
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h.celsius = 37.0 # set the temperature.
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self.vec = {}
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for var in ["time", "V", "IChan", "Vcmd"]:
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self.vec[var] = h.Vector()
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h.dt = 0.025
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v_init = -65.0
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clampV = v_init
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self.vcPost = h.SEClamp(0.5, sec=self.soma)
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self.vcPost.dur1 = tdelay
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self.vcPost.amp1 = clampV
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self.vcPost.dur2 = tstep[0]
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self.vcPost.amp2 = clampV - 0.0 # just a tiny step to keep the system honest
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self.vcPost.dur3 = tstep[1]
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self.vcPost.amp3 = clampV
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self.vcPost.rs = 1e-9
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print("soma: ", self.soma, end=" ")
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# print(dir(self.vcPost))
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# print(' vcpost sec: ', self.vcPost.Section())
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if modfile[0:2] == "ih":
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stimamp = np.linspace(-140, -40, num=21, endpoint=True)
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else:
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stimamp = np.linspace(-100, 60, num=35, endpoint=True)
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self.ivss = np.zeros((2, stimamp.shape[0]))
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self.ivmin = np.zeros((2, stimamp.shape[0]))
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self.ivmax = np.zeros((2, stimamp.shape[0]))
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print(
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(
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"I range = %6.1f-%6.1f, T = %4.1f"
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% (np.min(stimamp), np.max(stimamp), h.celsius)
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)
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)
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for i, V in enumerate(stimamp):
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stim = {}
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stim["NP"] = 1
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stim["Sfreq"] = 1 # stimulus frequency
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stim["delay"] = 5
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stim["dur"] = 100
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stim["amp"] = V
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stim["PT"] = 0.0
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self.vcPost.amp2 = V
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self.vec["IChan"].record(self.vcPost._ref_i, sec=self.soma)
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self.vec["V"].record(self.soma()._ref_v, sec=self.soma)
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self.vec["time"].record(h._ref_t)
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# print
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h.tstop = self.vcPost.dur1 + self.vcPost.dur2 + self.vcPost.dur3
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h.finitialize(v_init)
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h.run()
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self.t = np.array(self.vec["time"])
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self.ichan = np.array(self.vec["IChan"])
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self.v = np.array(self.vec["V"])
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self.p1.plot(self.t, self.ichan, pen=pg.mkPen((i, len(stimamp) * 1.5)))
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self.p3.plot(self.t, self.v, pen=pg.mkPen((i, len(stimamp) * 1.5)))
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(self.ivss[1, i], r2) = Util.measure(
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"mean", self.t, self.ichan, tdelay + tstep[0] - 10.0, tdelay + tstep[0]
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)
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(self.ivmin[1, i], r2) = Util.measure(
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"min", self.t, self.ichan, tdelay + 0.1, tdelay + tstep[0] / 5.0
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)
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(self.ivmax[1, i], r2) = Util.measure(
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"max", self.t, self.ichan, tdelay + 0.1, tdelay + tstep[0] / 5.0
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)
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self.ivss[0, i] = V
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self.ivmin[0, i] = V
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self.ivmax[0, i] = V
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self.p2.plot(
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self.ivss[0, :],
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self.ivss[1, :],
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symbol="o",
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symbolSize=4.0,
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pen=pg.mkPen(color),
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)
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self.p2.plot(
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self.ivmax[0, :],
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self.ivmax[1, :],
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symbol="t",
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symbolSize=4.0,
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pen=pg.mkPen(color),
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)
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self.p5.plot(
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self.ivmin[0, :],
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self.ivmin[1, :],
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symbol="s",
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symbolSize=4.0,
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pen=pg.mkPen(color),
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)
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print(export)
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if export:
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exporter = pg.exporters.MatplotlibExporter(self.p1)
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print("exporting: " + "%s_traces.svg" % modfile)
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exporter.export(fileName="%s_traces.pdf" % modfile)
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exporter = pg.exporters.MatplotlibExporter(self.p3)
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exporter.export("%s_command.pdf" % modfile)
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exporter = pg.exporters.MatplotlibExporter(self.p2)
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exporter.export("%s_IV.pdf" % modfile)
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def computeKinetics(self, ch):
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pass
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def getmechs():
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mechs = []
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for n in dir(nrn):
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o = getattr(nrn, n)
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if str(o) == str(nrn.Mechanism):
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mechs.append(n)
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return mechs
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if __name__ == "__main__":
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mechs = getmechs()
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if len(sys.argv) < 2:
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print("\n\nUsage: python test_mechanisms.py <mechname>")
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print(" Available mechanisms:")
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linelen = 0
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for i, n in enumerate(mechs):
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if n in nottestablemechs: # 'Mechanism':
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continue
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print("%20s" % n, end=" ")
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linelen += 20
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if linelen > 80:
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print("")
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linelen = 0
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sys.exit(1)
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if sys.argv[1:] in nottestablemechs:
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exit()
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export = False
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if len(sys.argv) > 2:
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if sys.argv[2] == "export":
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export = True
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if sys.argv[1] == "all":
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for n in mechs:
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if n in nottestablemechs:
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print(("Skipping %s" % n))
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continue
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else:
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ck = ChannelKinetics(n)
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else:
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ck = ChannelKinetics(sys.argv[1], export=export)
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if sys.flags.interactive == 0:
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pg.QtGui.QApplication.exec_()
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