def chwin ():
"Launch windows from model list"
h.xpanel("Izhikevich models")
# outer lambda returns inner lambda so as to pass arg to winup() -- the innermost routine
for c in ch:
h.xbutton(c, (lambda f, arg1: lambda: f(arg1))(winup,c))
h.xpanel()
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 build(self):
self.box = h.HBox()
self.box.intercept(1)
self.box.ref(self)
h.xpanel("")
h.xbutton("Button 1", (self.bact, 1))
h.xbutton("Button 2", (self.bact, (2, )))
h.xbutton("Button 3", self.bact_noarg)
h.xbutton("Button 4", (self.bact_2arg, ("hello", 4)))
for i in range(3):
h.xradiobutton("Radio " + str(i), (self.bact, i))
h.xmenu("Menu")
for i in range(3):
h.xbutton("Item " + str(i), (self.bact, i))
for i in range(3):
h.xradiobutton("Radio " + str(i), (self.bact, i))
h.xcheckbox('checkbox', (self, 'cbstate'), self.cb)
h.xstatebutton('state', (self, 'sbut'), self.st)
h.xmenu()
h.xpanel()
self.g = h.Graph()
self.g.menu_tool('graph menu tool 1', self.gcb, (self.gsel, 1))
h.xpanel("")
h.xvalue("x", (self, "x"), 1, self.chgx)
h.xcheckbox('checkbox', (self, 'cbstate'), self.cb)
h.xstatebutton('state', (self, 'sbut'), self.st)
h.xlabel('fixed label')
h.xvarlabel((self, 'ss'))
h.xslider((self, 'x'), 0, 20, self.slide)
self.g.menu_tool('graph menu tool 2', self.gcb, (self.gsel, 2))
h.xpanel()
self.box.intercept(0)
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
def __init__(self, cell):
def show_val():
print("Spacer Ra of the model: {}".format(cell.spacer.Ra))
print(
'The starting point is {}, end point is {} with increasing steps of {}'
.format(min_current_var[0], max_current_var[0],
step_current_var[0]))
#Contorl Panel
sim_control = h.HBox()
sim_control.intercept(1)
h.nrncontrolmenu()
attach_current_clamp(cell)
h.xpanel('TEST')
h.xlabel('Choose a simulation to run')
h.xbutton('Spike Protocol', (spike_fig, cell))
h.xbutton('Rheobase Protocol', (fig_rheobase_check, cell))
h.xbutton('Multiple Rheobase Protocol',
(multiple_rheobase_plots_new, cell))
h.xbutton('Increasing Ra Protocol', (fig_ra_rheobase_spacerL, cell))
h.xbutton('Increasing spacer_gpas Protocol',
(fig_g_rheobase_spacerL, cell))
h.xbutton('Increasing cell c_m Protcol',
(fig_cm_rheobase_spacerL, cell))
h.xbutton('Combined Protocol Run', (Combined_Protocol, cell))
h.xpvalue('Rheobase protocol start', min_current_var, 1)
h.xpvalue('Rheobase protocol end', max_current_var, 1)
h.xpvalue('Rheobase step size', step_current_var, 1)
h.xbutton('show value', show_val)
# h.xvalue('enter value', (this_module, 'val'))
h.xpanel()
#Output panel
g = h.Graph()
g.addvar('soma(0.5).v', cell.soma(0.5)._ref_v)
g.addvar('AIS(0.5).v', cell.AIS(0.5)._ref_v)
g.size(0, 1000, -90, 90)
h.graphList[0].append(g)
h.MenuExplore()
sim_control.intercept(0)
sim_control.map()
input()
def build(self):
self.box = h.HBox()
self.box.intercept(1)
self.box.ref(self)
h.xpanel("")
h.xlabel('0<=')
h.xcheckbox('', (self, 'Vg'), self.button)
h.xcheckbox('', (self, 'mg'), self.button)
h.xcheckbox('', (self, 'ng'), self.button)
h.xcheckbox('', (self, 'hg'), self.button)
h.xcheckbox('', (self, 'Cag'), self.button)
h.xcheckbox('', (self, 'Og'), self.button)
h.xcheckbox('', (self, 'C1g'), self.button)
h.xcheckbox('', (self, 'C2g'), self.button)
h.xpanel()
h.xpanel("")
h.xlabel('<=1')
h.xcheckbox('V', (self, 'Vl'), self.button)
h.xcheckbox('m', (self, 'ml'), self.button)
h.xcheckbox('n', (self, 'nl'), self.button)
h.xcheckbox('h', (self, 'hl'), self.button)
h.xcheckbox('[Ca2+]', (self, 'Cal'), self.button)
h.xcheckbox('O', (self, 'Ol'), self.button)
h.xcheckbox('C1', (self, 'C1l'), self.button)
h.xcheckbox('C2', (self, 'C2l'), self.button)
h.xpanel()
h.xpanel("")
h.xlabel('S0')
h.xcheckbox('', (self, 'Vs0'), self.button)
h.xcheckbox('', (self, 'ms0'), self.button)
h.xcheckbox('', (self, 'ns0'), self.button)
h.xcheckbox('', (self, 'hs0'), self.button)
h.xcheckbox('', (self, 'Cas0'), self.button)
h.xcheckbox('', (self, 'Os0'), self.button)
h.xcheckbox('', (self, 'C1s0'), self.button)
h.xcheckbox('', (self, 'C2s0'), self.button)
h.xpanel()
h.xpanel("")
h.xlabel('S1')
h.xcheckbox('V', (self, 'Vs1'), self.button)
h.xcheckbox('m', (self, 'ms1'), self.button)
h.xcheckbox('n', (self, 'ns1'), self.button)
h.xcheckbox('h', (self, 'hs1'), self.button)
h.xcheckbox('[Ca2+]', (self, 'Cas1'), self.button)
h.xcheckbox('O', (self, 'Os1'), self.button)
h.xcheckbox('C1', (self, 'C1s1'), self.button)
h.xcheckbox('C2', (self, 'C2s1'), self.button)
h.xpanel()
h.xpanel("")
h.xbutton("Add S2", self.button)
h.xbutton("Remove Empty", self.button)
h.xbutton("Close", self.button)
h.xlabel('QP Solver:')
h.xstatebutton('cvxopt', (self, 'cvxopt_sel'), self.button)
h.xstatebutton('custom', (self, 'custom_sel'), self.button)
h.xpanel()
self.box.intercept(0)
def xpvalue (self,name,ptr,runner=pr):
"Doesn't work currently"
h.xpanel("")
h.xpvalue(name,ptr,1,runner)
h.xpanel()
def xvalue (self,name,var,obj=py,runner=pr):
h.xpanel("")
h.xvalue(name,(obj, var),0,runner)
h.xpanel()
from neuron import h
h('foo = 2')
h.variable_domain('foo', 1, 5)
h.units('foo', 'cm')
h.xpanel("test")
h.xvalue("foo", "foo", 1)
h.xpvalue("foo", h._ref_foo, 1)
h.xpanel()
def panel(self):
h.xpanel("Variable or Fixed step")
h.xcheckbox('use_fixed_step', (self, 'use_fixed_step'))
h.xpanel()
def make_Vpanel(): # make panel
h.xpanel("Brette-Gerstner network")
h.xbutton("Run simulation", "py.run_sim(1)")
h.xpanel()
# def on_button_press():
# print('you pressed the button')
<<<<<<< HEAD
def show_val():
print('The starting point is {}, end point is {} with increasing steps of {}'.format(min_current_var[0],max_current_var[0],step_current_var[0]))
=======
val = h.ref(42)
def show_val():
print('value is: %g' % val[0])
>>>>>>> faea529 (TEST)
#Contorl Panel
sim_control = h.HBox()
sim_control.intercept(1)
h.nrncontrolmenu()
attach_current_clamp(cell)
h.xpanel('TEST')
h.xlabel('Choose a simulation to run')
h.xbutton('Spike Protocol',(spike_fig, cell))
h.xbutton('Rheobase Protocol',(fig_rheobase_check, cell))
h.xbutton('Multiple Rheobase Protocol', (multiple_rheobase_plots_new, cell))
<<<<<<< HEAD
h.xbutton('Increasing Ra Protocol', (fig_ra_rheobase_spacerL, cell))
h.xbutton('Increasing spacer_gpas Protocol', (fig_g_rheobase_spacerL, cell))
h.xbutton('Increasing cell c_m Protcol', (fig_cm_rheobase_spacerL, cell))
h.xbutton('Combined Protocol Run', (temp_stack_ra_scatter, cell))
h.xpvalue('Rheobase protocol start', min_current_var, 1)
h.xpvalue('Rheobase protocol end', max_current_var, 1)
h.xpvalue('Rheobase step size', step_current_var, 1)
=======
h.xbutton('Fig 1', (fig1_rheobase_spacer_dend, cell))
h.xbutton('Fig 2', (fig2_rheobase_spacer_cm, cell))
def constraintsPanel(self):
self.box = h.HBox()
self.box.intercept(1)
self.box.ref(self)
s = h.Vector()
cvodewrap.states(s)
nstates = len(s)
sref = h.ref('')
h.xpanel("")
h.xlabel('0<=')
for i in range(nstates):
h.xcheckbox('', (self.geq0[i], 'x'), self.constraintsButton)
h.xpanel()
h.xpanel("")
h.xlabel('>=1')
for i in range(nstates):
cvodewrap.statename(i, sref, 1)
h.xcheckbox(sref[0], (self.leq1[i], 'x'), self.constraintsButton)
h.xpanel()
for j in range(self.nsums):
h.xpanel("")
h.xlabel("S%d" % j)
for i in range(nstates):
h.xcheckbox('', (self.sumto1[j][i], 'x'),
self.constraintsButton)
h.xpanel()
h.xpanel("")
h.xbutton("Add Sum-to-1", self.constraintsButton)
h.xbutton("Remove Empty", self.constraintsButton)
h.xbutton("Close", self.constraintsButton)
h.xlabel('QP Solver:')
h.xstatebutton('cvxopt', (self, 'cvxopt_sel'), self.constraintsButton)
h.xstatebutton('custom', (self, 'custom_sel'), self.constraintsButton)
h.xpanel()
self.box.intercept(0)
self.box.map("Constraints")
printf("enter %g %s %s\\n", $&1, $o2, $s3) \
$&1 = 2 \
$o2 = new List() \
$s3 = "goodbye" \
}''')
h('strdef hs')
h('objref ho')
h('hx = 0')
h.hs = 'hello'
h.hx = 1
h('change(&hx, ho, hs)')
print(h.hx, h.ho, h.hs)
h('load_file("nrngui.hoc")')
h('obfunc hocstring() { return new String($s1) }')
s = h.hocstring('hello world')
h.xpanel("test1")
h.xvarlabel(s.s)
h.xpanel()
h('strdef ss')
h('ss = "hello world"')
h.xpanel("test2")
h.xvarlabel(h.ss)
h.xpanel()
shapebox = None
shapebox = h.VBox()
shapebox.intercept(True)
h.makeMenuExplore()
shapebox.intercept(False)
shapebox.map("NEURON ShapeName", 100, 500, -1, -1)
def show(tdat):
global ig
cleanup()
ig = mkswc(tdat)
show_nrnshape()
if __name__ == "__main__":
ig = None
h.xpanel("Choose an swc example")
for i, dat in enumerate(tst_data):
s = str(i) + dat.split('\n')[1]
h.xradiobutton(s, (show, dat))
h.xpanel(80, 200)
tst_result=['''
soma[0] L=20
0 -10 0 0 20
1 0 0 0 20
2 10 0 0 20
dend[0] L=10 [0.0, 0.0, 0.0] parent soma[0](0.5)
0 0 10 0 2
1 0 20 0 2
dend[1] L=10 [0.0, 0.0, 0.0] parent soma[0](0.5)
0 0 -10 0 4
from neuron import h
h.load_file('stdrun.hoc')
soma = h.Section(name='soma')
seg = soma(0.5)
soma.insert('hh')
ic = h.IClamp(seg)
ic.amp = 40 # since by default a very large section
ic.delay = 1
ic.dur = 1
h.xpanel("neuron")
h.xlabel("voltage graph")
g = h.Graph()
g.addvar("v", "v(0.5)") #hoc string example
g.addvar("m", seg.hh._ref_m) #pointer example
#g.addvar("v", soma(0.5)._ref_v) #pointer
#g.addvar("v(0.5)") #no label (not yet)
h.xpanel()
h.finitialize(-65)
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)
def xspikeres():
h.xpanel("Spike results")
h.xbutton("Write out", "spikeout()")
h.xbutton("Plot", "spikeplot()")
h.xpanel()
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]=""
print("button test worked!")
print(thing1)
print(thing2)
return
is_checked2 = h.ref(0)
my_str = h.ref('yay!')
h("""
proc onpress() {
print "The HOC onpress function was called"
}
""")
h.xpanel("Hello world")
h.xlabel("Here is some text")
h.xvalue("h.t", "t")
h.xcheckbox("a checkbox", is_checked_ref, "onpress()")
h.xcheckbox("a checkbox", (is_checked, 'checked'), onpress)
h.xstatebutton("Toggle", is_checked2, onpress2)
hb = h.HBox()
hb.intercept(True)
h.xbutton("finitialize", "finitialize(-65)")
h.xbutton("run", "run()")
h.xbutton("test", (buttontest, ("hallo", "goodbye")))
hb.intercept(False)
hb.map()
h.xvarlabel(my_str)
#g = h.Graph()
#g.addvar("v", "seg.v")
# 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)
