"""
test_mechanisms.py
This program displays the results of inserting NEURON mechaanisms from .mod files
into a point cell to voltage steps in voltage clamp.
This code is primarily for visual verification of model function.
Usage: python test_mechanisms.py <mechname>
Available mechanisms::
CaPCalyx bkpkj hcno hcnobo hpkj
ihpyr ihsgcApical ihsgcBasalMiddle ihvcn jsrna
ka kcnq kdpyr kht kif
kis klt kpkj kpkj2 kpkjslow
kpksk leak lkpkj na naRsg
nacn nacncoop nap napyr nav11
Note: only modfiles that implement voltage-dependent ion channel models make sense to run
with this routine. the list "nottestablemechs" in the file defines mechanisms provided
with cnmodel that cannot be run with this program.
"""
import neuron as h
import gc
import numpy as np
#import scipy as sp
import cnmodel.util
import pyqtgraph as pg
import pyqtgraph.exporters
from pyqtgraph.Qt import QtCore, QtGui
import cnmodel.util.pynrnutilities as Util
nottestablemechs = ['cadyn', 'ca_ion', 'cadiff', 'cadifpmp', 'Mechanism',
'capmp', 'capump', 'cl_ion', 'extracellular', 'fastpas',
'k_ion', 'KIR', 'hh', 'na_ion', 'narsg', 'pas', 'cap'] # cap uses "pcabar"
[docs]class ChannelKinetics():
def __init__(self, args, export=False):
modfile = []
if isinstance(args, list):
for arg in args:
modfile.append(arg) # must be string, not list...
else:
modfile.append(args) # 'CaPCalyx'
print 'modfile: ', modfile
colors = ['b', 'r', 'g', 'y', 'c', 'm', 'w']
if len(modfile) > len(colors):
print 'Too many modfiles... keep it simple!'
exit()
# if isinstance(args, list) and len(args) > 1:
# modfile2 = args[1]
doKinetics = False
self.app = pg.mkQApp()
self.win = pg.GraphicsWindow()
self.win.setWindowTitle('VC Plots')
self.win.resize(600,800)
# cw = QtGui.QWidget()
# self.win.setCentralWidget(cw)
# self.gridLayout = QtGui.QGridLayout()
# cw.setLayout(self.gridLayout)
# self.gridLayout.setContentsMargins(9, 9, 4, 4)
# self.gridLayout.setSpacing(1)
self.p1 = self.win.addPlot(title="I (VC)")
# self.gridLayout.addWidget(self.p1, 0, 0, 1, 1)
self.p2 = self.win.addPlot(title="I_ss, I_max")
# self.gridLayout.addWidget(self.p2, 0, 1, 1, 1)
self.win.nextRow()
self.p3 = self.win.addPlot(title="V command")
# self.gridLayout.addWidget(self.p3, 1, 0, 1, 1)
self.p5 = self.win.addPlot(title="I_min")
# self.gridLayout.addWidget(self.p5, 1, 1, 1, 1)
self.win.show()
QtGui.QApplication.processEvents()
#
# self.tdur is a table of durations for the pulse and post-pulse for each channel type (best to highlight features
# on appropriate time scales)
#
self.tdur = {'CaPCalyx': [20., 10.],
'nav11': [10., 5.], 'jsrna': [10., 5.], 'ichanWT2005': [10., 5.],
'nacn': [10., 5.], 'nacncoop': [10., 5.],
'kht':[200., 20.], 'klt': [200., 20.], 'ka': [25., 5.],
'hcno': [1000., 200.], 'ih': [1000., 200.], 'ihvcn': [1000., 200.],'hcnobo': [1000., 200.],
'ihsgcBasalMiddle': [1000., 200.], 'ihsgcApical': [1000., 200.],
'kif': [100., 100.], 'kis': [100., 10.], 'napyr': [10, 5.], 'ihpyr': [1000., 200.],
'kdpyr': [200., 20.], 'kcnq': [200, 20], 'nap': [200., 100.],
}
for i, mfile in enumerate(modfile):
self.run(modfile=mfile, color=colors[i], export=export)
s=''
#self.win.setWindowTitle('VC Plots: ' + [s+sn+'; ' for sn in modfile])
gc.collect()
if doKinetics:
self.win2 = pg.GraphicsWindow(title='KineticPlots')
self.win2.resize(800, 600)
self.kp1 = self.win.addPlot(title="htau")
self.computeKinetics('nav11')
#self.win.show()
[docs] def run(self, modfile='CaPCalyx', color='r', export=False):
if isinstance(modfile, list):
modfile = modfile[0]
if modfile in self.tdur:
tstep = self.tdur[modfile]
else:
tstep = [200., 50.]
tdelay = 5.0
Channel = cnmodel.util.Mechanism(modfile)
leak = cnmodel.util.Mechanism('leak')
Channel.set_parameters({'gbar': 1})
leak.set_parameters({'gbar': 1e-12})
# if modfile == 'nacncoop':
# self.soma().nacncoop.p = 0.
# self.soma().nacncoop.KJ = 0.
# # Channel.set_parameters({'p': 0., 'KJ': 000.})
self.soma = cnmodel.util.Section(L=10, diam=10, mechanisms=[Channel, leak])
if modfile == 'bkpjk':
ca_init = 100e-6
self.soma().cai = ca_init
else:
ca_init = 70e-6
if modfile == 'nacncoop':
self.soma().nacncoop.p = 0.1
self.soma().nacncoop.KJ = 1000.
# Channel.set_parameters({'p': 0., 'KJ': 000.})
h.celsius = 37. # set the temperature.
self.vec={}
for var in ['time', 'V', 'IChan', 'Vcmd']:
self.vec[var] = h.Vector()
h.dt = 0.025
v_init = -65.
clampV = v_init
self.vcPost = h.SEClamp(0.5, sec=self.soma)
self.vcPost.dur1 = tdelay
self.vcPost.amp1 = clampV
self.vcPost.dur2 = tstep[0]
self.vcPost.amp2 = clampV-0.0 # just a tiny step to keep the system honest
self.vcPost.dur3 = tstep[1]
self.vcPost.amp3 = clampV
self.vcPost.rs = 1e-9
print "soma: ", self.soma,
print ' vcpost sec: ', self.vcPost.Section()
if modfile[0:2] == 'ih':
stimamp = np.linspace(-140, -40, num=21, endpoint=True)
else:
stimamp = np.linspace(-100, 60, num=35, endpoint=True)
self.ivss = np.zeros((2, stimamp.shape[0]))
self.ivmin = np.zeros((2, stimamp.shape[0]))
self.ivmax = np.zeros((2, stimamp.shape[0]))
print('I range = %6.1f-%6.1f, T = %4.1f' % (np.min(stimamp), np.max(stimamp), h.celsius))
for i, V in enumerate(stimamp):
stim={}
stim['NP'] = 1
stim['Sfreq'] = 1 # stimulus frequency
stim['delay'] = 5
stim['dur'] = 100
stim['amp'] = V
stim['PT'] = 0.0
self.vcPost.amp2 = V
self.vec['IChan'].record(self.vcPost._ref_i, sec=self.soma)
self.vec['V'].record(self.soma()._ref_v, sec=self.soma)
self.vec['time'].record(h._ref_t)
# print
h.tstop = self.vcPost.dur1+self.vcPost.dur2+self.vcPost.dur3
h.finitialize(v_init)
h.run()
self.t = np.array(self.vec['time'])
self.ichan = np.array(self.vec['IChan'])
self.v = np.array(self.vec['V'])
self.p1.plot(self.t, self.ichan, pen=pg.mkPen((i, len(stimamp)*1.5)))
self.p3.plot(self.t, self.v, pen=pg.mkPen((i, len(stimamp)*1.5)))
(self.ivss[1, i], r2) = Util.measure('mean', self.t, self.ichan, tdelay+tstep[0]-10., tdelay+tstep[0])
(self.ivmin[1, i], r2) = Util.measure('min', self.t, self.ichan, tdelay+0.1, tdelay+tstep[0]/5.0)
(self.ivmax[1, i], r2) = Util.measure('max', self.t, self.ichan, tdelay+0.1, tdelay+tstep[0]/5.0)
self.ivss[0,i] = V
self.ivmin[0,i] = V
self.ivmax[0,i] = V
self.p2.plot(self.ivss[0,:], self.ivss[1,:], symbol='o', symbolSize=4.0, pen=pg.mkPen(color))
self.p2.plot(self.ivmax[0,:], self.ivmax[1,:], symbol='t', symbolSize=4.0, pen=pg.mkPen(color))
self.p5.plot(self.ivmin[0,:], self.ivmin[1,:], symbol='s', symbolSize=4.0, pen=pg.mkPen(color))
print export
if export:
exporter = pg.exporters.MatplotlibExporter(self.p1)
print 'exporting: ' + '%s_traces.svg' % modfile
exporter.export(fileName='%s_traces.pdf' % modfile)
exporter = pg.exporters.MatplotlibExporter(self.p3)
exporter.export('%s_command.pdf' % modfile)
exporter = pg.exporters.MatplotlibExporter(self.p2)
exporter.export('%s_IV.pdf' % modfile)
[docs] def computeKinetics(self, ch):
pass
[docs]def getmechs():
mechs = []
for n in dir(nrn):
o = getattr(nrn, n)
if str(o) == str(nrn.Mechanism):
mechs.append(n)
return mechs
if __name__ == "__main__":
mechs = getmechs()
if len(sys.argv) < 2:
print "\n\nUsage: python test_mechanisms.py <mechname>"
print " Available mechanisms:"
linelen = 0
for i, n in enumerate(mechs):
if n in nottestablemechs: # 'Mechanism':
continue
print "%20s" % n,
linelen += 20
if linelen > 80:
print ""
linelen = 0
sys.exit(1)
if sys.argv[1:] in nottestablemechs:
exit()
export = False
if len(sys.argv) > 2:
if sys.argv[2] == 'export':
export = True
if sys.argv[1] == 'all':
for n in mechs:
if n in nottestablemechs:
print('Skipping %s' % n)
continue
else:
ck = ChannelKinetics(n)
else:
ck = ChannelKinetics(sys.argv[1], export=export)
if sys.flags.interactive == 0:
pg.QtGui.QApplication.exec_()