def ivwrap (func, label=''): wrapper = h.VBox() wrapper.intercept(1) func() wrapper.intercept(0) wrapper.map(label) return wrapper
def __init__ (self, type, li) :
self.izhtype = type
vbox, hbox, hbox1 = h.VBox(), h.HBox(), h.HBox()
self.vbox = vbox
lil = len(li)
self.cols, self.rows = {20:(4,5), 8:(4,2), 9:(3,3)}[lil]
self.label=h.ref('================================================================================')
vbox.intercept(1)
h.xpanel("")
h.xvarlabel(self.label)
if newmodel(self.izhtype):
h.xlabel("V' = (k*(V-vr)*(V-vt) - u + Iin)/C if (V>vpeak) V=c [reset]")
h.xlabel("u' = a*(b*(V-vr) - u) if (V>vpeak) u=u+d")
else:
h.xlabel("v' = 0.04*v*v + f*v + g - u + Iin; if (v>thresh) v=c [reset]")
h.xlabel("u' = a*(b*v - u); if (v>thresh) u=u+d")
h.xpanel()
hbox1.intercept(1)
h.xpanel(""); h.xbutton("RUN",h.run); h.xpanel()
self.xvalue('I0','I0')
self.xvalue('I1','I1')
self.xvalue('T1','T1')
hbox1.intercept(0); hbox1.map("")
hbox.intercept(1)
for ii,(k,v) in enumerate(li.iteritems()):
if ii%self.rows==0: h.xpanel("")
h.xbutton(k, (lambda f, arg1, arg2: lambda: f(arg1,arg2))(p, k, v)) # alternative is to use functools.partial
if ii%self.rows==self.rows-1: h.xpanel()
hbox.intercept(0); hbox.map("")
vbox.intercept(0); vbox.map("Spike patterns")
self.label[0]=""
def paramPanel(self):
self.box = h.VBox()
self.box.intercept(1)
h.xpanel('')
h.xlabel('Likelihood numerical parameters')
h.xlabel(' Measurement noise')
c = self.Eve.Obs.C
for o in c:
h.xvalue('sigma: ' + o.hpt.s(), (o, 'sigma'), 1)
h.xlabel(' Process noise')
h.xvalue('Injection interval', (self, 'inj_invl'), 1,
self.inj_invl_changed)
s = h.Vector()
cvodewrap.states(s)
sref = h.ref('')
for i in range(len(s)):
cvodewrap.statename(i, sref, 1)
h.xvalue('Diffusion Coeff[%d,%d]: ' % (i, i) + sref[0],
(self.processNoise[i], 'x'), 1, (self.fillPB, i))
h.xcheckbox('Fox & Lu Diffusion (for Hodgkin-Huxley)?', (self, 'hhB'),
self.hhBButton)
h.xvalue(' Fox & Lu: Number Na Channels', (self, 'nNa'), 1,
self.hhBButton)
h.xvalue(' Fox & Lu: Number K Channels', (self, 'nK'), 1,
self.hhBButton)
h.xlabel(' Initial Uncertainty')
for i in range(len(s)):
print i
cvodewrap.statename(i, sref, 1)
h.xvalue('Initial Stand Dev[%d]: ' % i + sref[0],
(self.Sdiag[i], 'x'), 1, (self.fillS, i))
h.xbutton('Show state funnels', self.show_state_funnels)
h.xpanel()
self.box.intercept(0)
self.box.map('Likelihood parameters')
def show_synapses_PP_LTP(self):
"""Shows a box containing the model shape plot with marked recording sites and synapses."""
# build dummy current clamps and demarcate locations
dum_CC = [
h.IClamp(self.CA1.lm_medium1(0.1)),
h.IClamp(self.CA1.radTdist2(0.1))
]
for cc in dum_CC:
cc.dur = 0
cc.amp = 0
self.vBoxShape = h.VBox()
self.vBoxShape.intercept(True)
self.shplot = h.Shape()
for sec in self.synapses:
for syn in self.synapses[sec]:
if syn.type == 'AMPA':
self.shplot.point_mark(syn.synapse, 1, 'O', 6)
self.shplot.point_mark(dum_CC[0], 2, 'O', 12)
self.shplot.point_mark(dum_CC[1], 3, 'O', 12)
self.shplot.label("Large circles: recording sites")
self.shplot.label("Black: Synapses")
self.shplot.exec_menu("Whole Scene")
self.shplot.flush()
self.vBoxShape.intercept(0)
self.vBoxShape.map("Spatial distribution of point processes", 1200, 0,
500, 900)
self.shplot.exec_menu("View = plot")
self.shplot.exec_menu("Show Diam")
def show_nrnshape():
global shapebox
h.load_file("shapebox.hoc")
if shapebox:
shapebox.unmap()
shapebox = None
shapebox = h.VBox()
shapebox.intercept(True)
h.makeMenuExplore()
shapebox.intercept(False)
shapebox.map("NEURON ShapeName", 100, 500, -1, -1)
def bld(x, y):
global g, tt, ttstr, grp, sgrp, pras
tt = 0.0
ttstr = h.ref('tt=0.000000000')
v = h.VBox()
v.intercept(1)
g = h.Graph()
g.size(0, x, 0, y)
h.xpanel("", 1)
h.xvarlabel(ttstr)
h.xvalue("group", (this_module, "grp"), 1, ttcallback)
h.xslider((this_module, "sgrp"), 0, 100, ttscallback)
h.xpanel()
v.intercept(0)
v.map("wave front", 100, 100, 700, 500)
return v
from neuron import h
a = h.Vector([1])
b = h.Vector([2])
s = h.Section(name='section1')
ell = h.List('Vector')
ell.browser()
h.xpanel('mywindow', 4, h.ref(5))
myvbox = h.VBox('Neuron')
print('myvbox.ismapped() =', myvbox.ismapped())
print('mapping...')
myvbox.map()
print('myvbox.ismapped() =', myvbox.ismapped())
h('preference = boolean_dialog("Do you prefer HOC or Python", "Python", "HOC")'
)
print('h.preference =', h.preference)
# create a current clamp and add it to the cell
cell.ic = h.IClamp(cell.soma(0.5))
cell.ic.dur = 3 # ms
cell.ic.amp = 1.5 # nA
# setup graphs needed by both simulations
concentration_graph = h.Graph(False)
concentration_graph.size(0, 3000, 4, 4.4)
voltage_graph = h.Graph(False)
voltage_graph.size(0, 3000, -90, 60)
h.graphList[0].append(voltage_graph)
h.graphList[1].append(concentration_graph)
# pop up the run control
h.nrncontrolmenu()
# call the funciton which actually sets up the specific simulation
simulation(cell, voltage_graph, concentration_graph)
if __name__ == '__main__':
# display a control panel to allow users to choose a simulation
sim_control = h.VBox()
sim_control.intercept(True)
h.xpanel('')
h.xlabel('Choose a simulation to run')
h.xbutton('Fig 3A', lambda: do_sim(fig3a, sim_control))
h.xbutton('Fig 6B', lambda: do_sim(fig6b, sim_control))
h.xpanel()
sim_control.intercept(False)
sim_control.map('Choose simulation', 100, 100, 200, 100)
