Пример #1
0
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()
Пример #2
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')
Пример #3
0
 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)
Пример #4
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
Пример #5
0
    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()
Пример #6
0
 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)
Пример #7
0
 def xpvalue (self,name,ptr,runner=pr):
   "Doesn't work currently"
   h.xpanel("")
   h.xpvalue(name,ptr,1,runner)
   h.xpanel()
Пример #8
0
 def xvalue (self,name,var,obj=py,runner=pr):
   h.xpanel("")
   h.xvalue(name,(obj, var),0,runner)
   h.xpanel()
Пример #9
0
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()
Пример #10
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 def panel(self):
     h.xpanel("Variable or Fixed step")
     h.xcheckbox('use_fixed_step', (self, 'use_fixed_step'))
     h.xpanel()
Пример #11
0
def make_Vpanel():                    # make panel
    h.xpanel("Brette-Gerstner network")
    h.xbutton("Run simulation", "py.run_sim(1)")
    h.xpanel()
Пример #12
0
        # 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))
Пример #13
0
 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")
Пример #14
0
  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()
Пример #15
0
    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
Пример #16
0
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)

Пример #17
0
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)
Пример #18
0
def xspikeres():
    h.xpanel("Spike results")
    h.xbutton("Write out", "spikeout()")
    h.xbutton("Plot", "spikeplot()")
    h.xpanel()
Пример #19
0
 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]=""
Пример #20
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")
Пример #21
0
    # 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)