def __init__(self):
# set up simulation in remote process
self.dt = 25*us
self.proc = mp.QtProcess(debug=False)
ndemo = self.proc._import('neurodemo')
self.sim = ndemo.Sim(temp=6.3, dt=self.dt)
self.sim._setProxyOptions(deferGetattr=True)
self.neuron = ndemo.Section(name='soma')
self.sim.add(self.neuron)
self.hhna = self.neuron.add(ndemo.HHNa())
self.leak = self.neuron.add(ndemo.Leak())
self.hhk = self.neuron.add(ndemo.HHK())
self.dexh = self.neuron.add(ndemo.IH())
self.dexh.enabled = False
self.clamp = self.neuron.add(ndemo.PatchClamp(mode='ic'))
#cmd = np.zeros(int(1/self.dt))
#cmd[int(0.4/self.dt):int(0.8/self.dt)] = 200e-12
#self.clamp.set_command(cmd, dt=self.dt)
mechanisms = [self.clamp, self.hhna, self.leak, self.hhk, self.dexh]
# loop to run the simulation indefinitely
self.runner = ndemo.SimRunner(self.sim)
#self.runner.add_request('soma.Vm')
self.runner.add_request('t')
self.runner.new_result.connect(mp.proxy(self.new_result, autoProxy=False, callSync='off'))
# set up GUI
QtGui.QWidget.__init__(self)
self.fullscreen_widget = None
self.resize(1024, 768)
self.layout = QtGui.QGridLayout()
self.layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(self.layout)
self.splitter = QtGui.QSplitter(QtCore.Qt.Horizontal)
self.layout.addWidget(self.splitter, 0, 0)
self.ptree = pt.ParameterTree(showHeader=False)
self.splitter.addWidget(self.ptree)
self.plot_splitter = QtGui.QSplitter(QtCore.Qt.Vertical)
self.splitter.addWidget(self.plot_splitter)
self.neuronview = NeuronView(self.neuron, mechanisms)
self.plot_splitter.addWidget(self.neuronview)
#self.vm_plot = ScrollingPlot(dt=self.dt, npts=int(1.0/self.dt),
#parent=self, labels={'left': ('Membrane Potential', 'V'),
#'bottom': ('Time', 's')})
#self.vm_plot.setYRange(-90*mV, 50*mV)
#self.vm_plot.setXRange(-1000*ms, 0*ms)
#self.vm_plot.addLine(y=self.neuron.ek)
#self.vm_plot.addLine(y=self.neuron.ena)
#self.plot_splitter.addWidget(self.vm_plot)
self.channel_plots = {}
self.channel_params = [
ChannelParameter(self.leak),
ChannelParameter(self.hhna),
ChannelParameter(self.hhk),
ChannelParameter(self.dexh),
]
for ch in self.channel_params:
ch.plots_changed.connect(self.plots_changed)
self.clamp_param = ClampParameter(self.clamp, self)
self.clamp_param.plots_changed.connect(self.plots_changed)
self.vm_plot = self.add_plot('soma.V', 'Membrane Potential', 'V')
self.splitter.setSizes([350, 650])
self.show()
self.params = pt.Parameter.create(name='params', type='group', children=[
dict(name='Preset', type='list', values=['', 'Passive Membrane', 'Action Potential']),
dict(name='Run', type='bool', value=True),
dict(name='Speed', type='float', value=0.3, limits=[0, 10], step=1, dec=True),
dict(name='Temp', type='float', value=self.sim.temp, suffix='C', step=1.0),
dict(name='Capacitance', type='float', value=self.neuron.cap, suffix='F', siPrefix=True, dec=True),
dict(name='Cell Schematic', type='bool', value=True, children=[
dict(name='Show Circuit', type='bool', value=False),
]),
self.clamp_param,
dict(name='Ion Channels', type='group', children=self.channel_params),
])
self.ptree.setParameters(self.params)
self.params.sigTreeStateChanged.connect(self.params_changed)
self.start()
self.clamp_param['Plot Current'] = True
self.plot_splitter.setSizes([300, 500, 200])
self.pause_shortcut = QtGui.QShortcut(QtGui.QKeySequence('Space'), self)
self.pause_shortcut.activated.connect(self.pause)
self.slow_shortcut = QtGui.QShortcut(QtGui.QKeySequence('-'), self)
self.slow_shortcut.activated.connect(self.slower)
self.fast_shortcut = QtGui.QShortcut(QtGui.QKeySequence('='), self)
self.fast_shortcut.activated.connect(self.faster)
self.fullscreen_shortcut = QtGui.QShortcut(QtGui.QKeySequence('F11'), self)
self.fullscreen_shortcut.activated.connect(self.fullscreen)
self.fullscreen_shortcut.setContext(QtCore.Qt.ApplicationShortcut)
class DemoWindow(QtGui.QWidget):
def __init__(self):
# set up simulation in remote process
self.dt = 25*us
self.proc = mp.QtProcess(debug=False)
ndemo = self.proc._import('neurodemo')
self.sim = ndemo.Sim(temp=6.3, dt=self.dt)
self.sim._setProxyOptions(deferGetattr=True)
self.neuron = ndemo.Section(name='soma')
self.sim.add(self.neuron)
self.hhna = self.neuron.add(ndemo.HHNa())
self.leak = self.neuron.add(ndemo.Leak())
self.hhk = self.neuron.add(ndemo.HHK())
self.dexh = self.neuron.add(ndemo.IH())
self.dexh.enabled = False
self.clamp = self.neuron.add(ndemo.PatchClamp(mode='ic'))
#cmd = np.zeros(int(1/self.dt))
#cmd[int(0.4/self.dt):int(0.8/self.dt)] = 200e-12
#self.clamp.set_command(cmd, dt=self.dt)
mechanisms = [self.clamp, self.hhna, self.leak, self.hhk, self.dexh]
# loop to run the simulation indefinitely
self.runner = ndemo.SimRunner(self.sim)
#self.runner.add_request('soma.Vm')
self.runner.add_request('t')
self.runner.new_result.connect(mp.proxy(self.new_result, autoProxy=False, callSync='off'))
# set up GUI
QtGui.QWidget.__init__(self)
self.fullscreen_widget = None
self.resize(1024, 768)
self.layout = QtGui.QGridLayout()
self.layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(self.layout)
self.splitter = QtGui.QSplitter(QtCore.Qt.Horizontal)
self.layout.addWidget(self.splitter, 0, 0)
self.ptree = pt.ParameterTree(showHeader=False)
self.splitter.addWidget(self.ptree)
self.plot_splitter = QtGui.QSplitter(QtCore.Qt.Vertical)
self.splitter.addWidget(self.plot_splitter)
self.neuronview = NeuronView(self.neuron, mechanisms)
self.plot_splitter.addWidget(self.neuronview)
#self.vm_plot = ScrollingPlot(dt=self.dt, npts=int(1.0/self.dt),
#parent=self, labels={'left': ('Membrane Potential', 'V'),
#'bottom': ('Time', 's')})
#self.vm_plot.setYRange(-90*mV, 50*mV)
#self.vm_plot.setXRange(-1000*ms, 0*ms)
#self.vm_plot.addLine(y=self.neuron.ek)
#self.vm_plot.addLine(y=self.neuron.ena)
#self.plot_splitter.addWidget(self.vm_plot)
self.channel_plots = {}
self.channel_params = [
ChannelParameter(self.leak),
ChannelParameter(self.hhna),
ChannelParameter(self.hhk),
ChannelParameter(self.dexh),
]
for ch in self.channel_params:
ch.plots_changed.connect(self.plots_changed)
self.clamp_param = ClampParameter(self.clamp, self)
self.clamp_param.plots_changed.connect(self.plots_changed)
self.vm_plot = self.add_plot('soma.V', 'Membrane Potential', 'V')
self.splitter.setSizes([350, 650])
self.show()
self.params = pt.Parameter.create(name='params', type='group', children=[
dict(name='Preset', type='list', values=['', 'Passive Membrane', 'Action Potential']),
dict(name='Run', type='bool', value=True),
dict(name='Speed', type='float', value=0.3, limits=[0, 10], step=1, dec=True),
dict(name='Temp', type='float', value=self.sim.temp, suffix='C', step=1.0),
dict(name='Capacitance', type='float', value=self.neuron.cap, suffix='F', siPrefix=True, dec=True),
dict(name='Cell Schematic', type='bool', value=True, children=[
dict(name='Show Circuit', type='bool', value=False),
]),
self.clamp_param,
dict(name='Ion Channels', type='group', children=self.channel_params),
])
self.ptree.setParameters(self.params)
self.params.sigTreeStateChanged.connect(self.params_changed)
self.start()
self.clamp_param['Plot Current'] = True
self.plot_splitter.setSizes([300, 500, 200])
self.pause_shortcut = QtGui.QShortcut(QtGui.QKeySequence('Space'), self)
self.pause_shortcut.activated.connect(self.pause)
self.slow_shortcut = QtGui.QShortcut(QtGui.QKeySequence('-'), self)
self.slow_shortcut.activated.connect(self.slower)
self.fast_shortcut = QtGui.QShortcut(QtGui.QKeySequence('='), self)
self.fast_shortcut.activated.connect(self.faster)
self.fullscreen_shortcut = QtGui.QShortcut(QtGui.QKeySequence('F11'), self)
self.fullscreen_shortcut.activated.connect(self.fullscreen)
self.fullscreen_shortcut.setContext(QtCore.Qt.ApplicationShortcut)
def params_changed(self, root, changes):
for param, change, val in changes:
if change != 'value':
continue
if param is self.params.child('Run'):
if val:
self.start()
else:
self.stop()
elif param is self.params.child('Speed'):
self.runner.set_speed(val)
elif param is self.params.child('Temp'):
self.sim.temp = val
elif param is self.params.child('Capacitance'):
self.neuron.cap = val
elif param is self.params.child('Preset'):
self.load_preset(val)
elif param is self.params.child('Cell Schematic'):
self.neuronview.setVisible(val)
elif param is self.params.child('Cell Schematic', 'Show Circuit'):
self.neuronview.show_circuit(val)
def plots_changed(self, param, channel, name, plot):
key = channel.name + '.' + name
if plot:
self.add_plot(key, param.name(), name)
else:
self.remove_plot(key)
def add_plot(self, key, pname, name):
# decide on y range, label, and units for new plot
yranges = {
'V': (-100*mV, 50*mV),
'I': (-1*nA, 1*nA),
'G': (0, 100*nS),
'OP': (0, 1),
'm': (0, 1),
'h': (0, 1),
'n': (0, 1),
}
color = {'I': 'c', 'G': 'y', 'OP': 'g', 'V': 'w'}.get(name, 0.7)
units = {'I': 'A', 'G': 'S', 'V': 'V'}
label = pname + ' ' + name
if name in units:
label = (label, units[name])
# create new plot
plt = ScrollingPlot(dt=self.dt, npts=int(1.0 / self.dt),
labels={'left': label}, pen=color)
if hasattr(self, 'vm_plot'):
plt.setXLink(self.vm_plot)
else:
plt.setXRange(-1, 0)
plt.setYRange(*yranges.get(name, (0, 1)))
# register this plot for later..
self.channel_plots[key] = plt
self.runner.add_request(key)
# add new plot to splitter and resize all accordingly
sizes = self.plot_splitter.sizes()
self.plot_splitter.addWidget(plt)
size = self.plot_splitter.height() / (len(sizes) + 1.)
r = len(sizes) / (len(sizes)+1)
sizes = [s * r for s in sizes] + [size]
self.plot_splitter.setSizes(sizes)
# Ask sequence plotter to update as well
self.clamp_param.add_plot(key, label)
return plt
def remove_plot(self, key):
plt = self.channel_plots.pop(key)
self.runner.remove_request(key)
self.clamp_param.remove_plot(key)
plt.setParent(None)
plt.close()
def start(self):
self.runner.start(blocksize=100)
def stop(self):
self.runner.stop()
def pause(self):
self.params['Run'] = not self.params['Run']
def slower(self):
self.params['Speed'] *= 0.5
def faster(self):
self.params['Speed'] = min(self.params['Speed'] * 2.0, 10)
def fullscreen(self):
if self.fullscreen_widget is None:
w = QtGui.QApplication.focusWidget()
ind = self.plot_splitter.indexOf(w)
if ind < 0:
return
self.fs_widget_index = ind
w.setParent(None)
w.showFullScreen()
self.fullscreen_widget = w
else:
self.fullscreen_widget.showNormal()
self.plot_splitter.insertWidget(self.fs_widget_index, self.fullscreen_widget)
self.fullscreen_widget = None
def new_result(self, final_state, result):
for k, plt in self.channel_plots.items():
if k not in result:
continue
plt.append(result[k][1:])
# Let the clamp decide which triggered regions of the data to extract
# for pulse plots
self.clamp_param.new_result(result)
# update the schematic
self.neuronview.update_state(final_state)
def load_preset(self, preset):
if preset == 'Passive Membrane':
self.params['Temp'] = 6.3
self.params['Speed'] = 0.05
self.params['Patch Clamp', 'Plot Current'] = False
self.params['Patch Clamp', 'Plot Voltage'] = False
chans = self.params.child('Ion Channels')
chans['soma.Ileak'] = True
chans['soma.Ileak', 'Erev'] = 0
chans['soma.INa'] = False
chans['soma.IK'] = False
chans['soma.IH'] = False
elif preset == 'Action Potential':
self.params['Temp'] = 6.3
self.params['Speed'] = 0.05
chans = self.params.child('Ion Channels')
chans['soma.Ileak'] = True
chans['soma.Ileak', 'Erev'] = -55*mV
chans['soma.INa'] = True
chans['soma.IK'] = True
chans['soma.IH'] = False
self.params['Preset'] = ''
def closeEvent(self, ev):
self.runner.stop()
self.proc.close()
QtGui.QApplication.instance().quit()