def __init__(self, *args):
QtGui.QMainWindow.__init__(self, *args)
self.squid_setup = SquidSetup()
self._plotdt = SquidGui.defaults['plotdt']
self._plot_dict = defaultdict(list)
self.setWindowTitle('Squid Axon simulation')
self.setDockNestingEnabled(True)
self._createRunControl()
self.addDockWidget(QtCore.Qt.LeftDockWidgetArea, self._runControlDock)
self._runControlDock.setFeatures(
QtGui.QDockWidget.AllDockWidgetFeatures)
self._createChannelControl()
self._channelCtrlBox.setWindowTitle('Channel properties')
self._channelControlDock.setFeatures(
QtGui.QDockWidget.AllDockWidgetFeatures)
self.addDockWidget(QtCore.Qt.LeftDockWidgetArea,
self._channelControlDock)
self._createElectronicsControl()
self._electronicsDock.setFeatures(
QtGui.QDockWidget.AllDockWidgetFeatures)
self._electronicsDock.setWindowTitle('Electronics')
self.addDockWidget(QtCore.Qt.LeftDockWidgetArea, self._electronicsDock)
self._createPlotWidget()
self.setCentralWidget(self._plotWidget)
self._createStatePlotWidget()
self._createHelpMessage()
self._helpWindow.setVisible(False)
self._statePlotWidget.setWindowFlags(QtCore.Qt.Window)
self._statePlotWidget.setWindowTitle('State plot')
self._initActions()
self._createRunToolBar()
self._createPlotToolBar()
def __init__(self, *args):
QMainWindow.__init__(self, *args)
self.squid_setup = SquidSetup()
self._plotdt = SquidGui.defaults['plotdt']
self._plot_dict = defaultdict(list)
self.setWindowTitle('Squid Axon simulation')
self.setDockNestingEnabled(True)
self._createRunControl()
self.addDockWidget(QtCore.Qt.LeftDockWidgetArea, self._runControlDock)
self._runControlDock.setFeatures(QDockWidget.AllDockWidgetFeatures)
self._createChannelControl()
self._channelCtrlBox.setWindowTitle('Channel properties')
self._channelControlDock.setFeatures(QDockWidget.AllDockWidgetFeatures)
self.addDockWidget(QtCore.Qt.LeftDockWidgetArea, self._channelControlDock)
self._createElectronicsControl()
self._electronicsDock.setFeatures(QDockWidget.AllDockWidgetFeatures)
self._electronicsDock.setWindowTitle('Electronics')
self.addDockWidget(QtCore.Qt.LeftDockWidgetArea, self._electronicsDock)
self._createPlotWidget()
self.setCentralWidget(self._plotWidget)
self._createStatePlotWidget()
self._createHelpMessage()
self._helpWindow.setVisible(False)
self._statePlotWidget.setWindowFlags(QtCore.Qt.Window)
self._statePlotWidget.setWindowTitle('State plot')
self._initActions()
self._createRunToolBar()
self._createPlotToolBar()
class SquidGui( QMainWindow ):
defaults = {}
defaults.update(SquidAxon.defaults)
defaults.update(ClampCircuit.defaults)
defaults.update({'runtime': 50.0,
'simdt': 0.01,
'plotdt': 0.1,
'vclamp.holdingV': 0.0,
'vclamp.holdingT': 10.0,
'vclamp.prepulseV': 0.0,
'vclamp.prepulseT': 0.0,
'vclamp.clampV': 50.0,
'vclamp.clampT': 20.0,
'iclamp.baseI': 0.0,
'iclamp.firstI': 0.1,
'iclamp.firstT': 40.0,
'iclamp.firstD': 5.0,
'iclamp.secondI': 0.0,
'iclamp.secondT': 0.0,
'iclamp.secondD': 0.0
})
def __init__(self, *args):
QMainWindow.__init__(self, *args)
self.squid_setup = SquidSetup()
self._plotdt = SquidGui.defaults['plotdt']
self._plot_dict = defaultdict(list)
self.setWindowTitle('Squid Axon simulation')
self.setDockNestingEnabled(True)
self._createRunControl()
self.addDockWidget(QtCore.Qt.LeftDockWidgetArea, self._runControlDock)
self._runControlDock.setFeatures(QDockWidget.AllDockWidgetFeatures)
self._createChannelControl()
self._channelCtrlBox.setWindowTitle('Channel properties')
self._channelControlDock.setFeatures(QDockWidget.AllDockWidgetFeatures)
self.addDockWidget(QtCore.Qt.LeftDockWidgetArea, self._channelControlDock)
self._createElectronicsControl()
self._electronicsDock.setFeatures(QDockWidget.AllDockWidgetFeatures)
self._electronicsDock.setWindowTitle('Electronics')
self.addDockWidget(QtCore.Qt.LeftDockWidgetArea, self._electronicsDock)
self._createPlotWidget()
self.setCentralWidget(self._plotWidget)
self._createStatePlotWidget()
self._createHelpMessage()
self._helpWindow.setVisible(False)
self._statePlotWidget.setWindowFlags(QtCore.Qt.Window)
self._statePlotWidget.setWindowTitle('State plot')
self._initActions()
self._createRunToolBar()
self._createPlotToolBar()
def getFloatInput(self, widget, name):
try:
return float(str(widget.text()))
except ValueError:
QMessageBox.critical(self, 'Invalid input', 'Please enter a valid number for {}'.format(name))
raise
def _createPlotWidget(self):
self._plotWidget = QWidget()
self._plotFigure = Figure()
self._plotCanvas = FigureCanvas(self._plotFigure)
self._plotCanvas.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
self._plotCanvas.updateGeometry()
self._plotCanvas.setParent(self._plotWidget)
self._plotCanvas.mpl_connect('scroll_event', self._onScroll)
self._plotFigure.set_canvas(self._plotCanvas)
# Vm and command voltage go in the same subplot
self._vm_axes = self._plotFigure.add_subplot(2,2,1, title='Membrane potential')
self._vm_axes.set_ylim(-20.0, 120.0)
# Channel conductances go to the same subplot
self._g_axes = self._plotFigure.add_subplot(2,2,2, title='Channel conductance')
self._g_axes.set_ylim(0.0, 0.5)
# Injection current for Vclamp/Iclamp go to the same subplot
self._im_axes = self._plotFigure.add_subplot(2,2,3, title='Injection current')
self._im_axes.set_ylim(-0.5, 0.5)
# Channel currents go to the same subplot
self._i_axes = self._plotFigure.add_subplot(2,2,4, title='Channel current')
self._i_axes.set_ylim(-10, 10)
for axis in self._plotFigure.axes:
axis.set_autoscale_on(False)
layout = QVBoxLayout()
layout.addWidget(self._plotCanvas)
self._plotNavigator = NavigationToolbar(self._plotCanvas, self._plotWidget)
layout.addWidget(self._plotNavigator)
self._plotWidget.setLayout(layout)
def _createStatePlotWidget(self):
self._statePlotWidget = QWidget()
self._statePlotFigure = Figure()
self._statePlotCanvas = FigureCanvas(self._statePlotFigure)
self._statePlotCanvas.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
self._statePlotCanvas.updateGeometry()
self._statePlotCanvas.setParent(self._statePlotWidget)
self._statePlotFigure.set_canvas(self._statePlotCanvas)
self._statePlotFigure.subplots_adjust(hspace=0.5)
self._statePlotAxes = self._statePlotFigure.add_subplot(2,1,1, title='State plot')
self._state_plot, = self._statePlotAxes.plot([], [], label='state')
self._activationParamAxes = self._statePlotFigure.add_subplot(2,1,2, title='H-H activation parameters vs time')
self._activationParamAxes.set_xlabel('Time (ms)')
#for axis in self._plotFigure.axes:
# axis.autoscale(False)
self._stateplot_xvar_label = QLabel('Variable on X-axis')
self._stateplot_xvar_combo = QComboBox()
self._stateplot_xvar_combo.addItems(['V', 'm', 'n', 'h'])
self._stateplot_xvar_combo.setCurrentText('V')
self._stateplot_xvar_combo.setEditable(False)
self._stateplot_xvar_combo.currentIndexChanged[str].connect( self._statePlotXSlot )
self._stateplot_yvar_label = QLabel('Variable on Y-axis')
self._stateplot_yvar_combo = QComboBox()
self._stateplot_yvar_combo.addItems(['V', 'm', 'n', 'h'])
self._stateplot_yvar_combo.setCurrentIndex(2)
self._stateplot_yvar_combo.setEditable(False)
self._stateplot_yvar_combo.currentIndexChanged[str].connect(self._statePlotYSlot)
self._statePlotNavigator = NavigationToolbar(self._statePlotCanvas, self._statePlotWidget)
frame = QFrame()
frame.setFrameStyle(QFrame.StyledPanel + QFrame.Raised)
layout = QHBoxLayout()
layout.addWidget(self._stateplot_xvar_label)
layout.addWidget(self._stateplot_xvar_combo)
layout.addWidget(self._stateplot_yvar_label)
layout.addWidget(self._stateplot_yvar_combo)
frame.setLayout(layout)
self._closeStatePlotAction = QAction('Close', self)
self._closeStatePlotAction.triggered.connect(self._statePlotWidget.close)
self._closeStatePlotButton = QToolButton()
self._closeStatePlotButton.setDefaultAction(self._closeStatePlotAction)
layout = QVBoxLayout()
layout.addWidget(frame)
layout.addWidget(self._statePlotCanvas)
layout.addWidget(self._statePlotNavigator)
layout.addWidget(self._closeStatePlotButton)
self._statePlotWidget.setLayout(layout)
# Setting the close event so that when the help window is
# closed the ``State plot`` button becomes unchecked
self._statePlotWidget.closeEvent = lambda event: self._showStatePlotAction.setChecked(False)
def _createRunControl(self):
self._runControlBox = QGroupBox(self)
self._runControlBox.setSizePolicy(QSizePolicy.Preferred, QSizePolicy.Preferred)
self._runTimeLabel = QLabel("Run time (ms)", self._runControlBox)
self._simTimeStepLabel = QLabel("Simulation time step (ms)", self._runControlBox)
self._runTimeEdit = QLineEdit('%g' % (SquidGui.defaults['runtime']), self._runControlBox)
set_default_line_edit_size(self._runTimeEdit)
self._simTimeStepEdit = QLineEdit('%g' % (SquidGui.defaults['simdt']), self._runControlBox)
set_default_line_edit_size(self._simTimeStepEdit)
layout = QGridLayout()
layout.addWidget(self._runTimeLabel, 0, 0)
layout.addWidget(self._runTimeEdit, 0, 1)
layout.addWidget(self._simTimeStepLabel, 1, 0)
layout.addWidget(self._simTimeStepEdit, 1, 1)
layout.setColumnStretch(2, 1.0)
layout.setRowStretch(2, 1.0)
self._runControlBox.setLayout(layout)
self._runControlDock = QDockWidget('Simulation', self)
self._runControlDock.setWidget(self._runControlBox)
def _createChannelControl(self):
self._channelControlDock = QDockWidget('Channels', self)
self._channelCtrlBox = QGroupBox(self)
self._naConductanceToggle = QCheckBox('Block Na+ channel', self._channelCtrlBox)
self._naConductanceToggle.setToolTip('<html>%s</html>' % (tooltip_NaChan))
self._kConductanceToggle = QCheckBox('Block K+ channel', self._channelCtrlBox)
self._kConductanceToggle.setToolTip('<html>%s</html>' % (tooltip_KChan))
self._kOutLabel = QLabel('[K+]out (mM)', self._channelCtrlBox)
self._kOutEdit = QLineEdit('%g' % (self.squid_setup.squid_axon.K_out),
self._channelCtrlBox)
self._kOutLabel.setToolTip('<html>%s</html>' % (tooltip_Nernst))
self._kOutEdit.setToolTip('<html>%s</html>' % (tooltip_Nernst))
set_default_line_edit_size(self._kOutEdit)
self._naOutLabel = QLabel('[Na+]out (mM)', self._channelCtrlBox)
self._naOutEdit = QLineEdit('%g' % (self.squid_setup.squid_axon.Na_out),
self._channelCtrlBox)
self._naOutLabel.setToolTip('<html>%s</html>' % (tooltip_Nernst))
self._naOutEdit.setToolTip('<html>%s</html>' % (tooltip_Nernst))
set_default_line_edit_size(self._naOutEdit)
self._kInLabel = QLabel('[K+]in (mM)', self._channelCtrlBox)
self._kInEdit = QLineEdit('%g' % (self.squid_setup.squid_axon.K_in),
self._channelCtrlBox)
self._kInEdit.setToolTip(tooltip_Nernst)
self._naInLabel = QLabel('[Na+]in (mM)', self._channelCtrlBox)
self._naInEdit = QLineEdit('%g' % (self.squid_setup.squid_axon.Na_in),
self._channelCtrlBox)
self._naInEdit.setToolTip('<html>%s</html>' % (tooltip_Nernst))
self._temperatureLabel = QLabel('Temperature (C)', self._channelCtrlBox)
self._temperatureEdit = QLineEdit('%g' % (self.defaults['temperature'] - CELSIUS_TO_KELVIN),
self._channelCtrlBox)
self._temperatureEdit.setToolTip('<html>%s</html>' % (tooltip_Nernst))
set_default_line_edit_size(self._temperatureEdit)
for child in self._channelCtrlBox.children():
if isinstance(child, QLineEdit):
set_default_line_edit_size(child)
layout = QGridLayout(self._channelCtrlBox)
layout.addWidget(self._naConductanceToggle, 0, 0)
layout.addWidget(self._kConductanceToggle, 1, 0)
layout.addWidget(self._naOutLabel, 2, 0)
layout.addWidget(self._naOutEdit, 2, 1)
layout.addWidget(self._naInLabel, 3, 0)
layout.addWidget(self._naInEdit, 3, 1)
layout.addWidget(self._kOutLabel, 4, 0)
layout.addWidget(self._kOutEdit, 4, 1)
layout.addWidget(self._kInLabel, 5, 0)
layout.addWidget(self._kInEdit, 5, 1)
layout.addWidget(self._temperatureLabel, 6, 0)
layout.addWidget(self._temperatureEdit, 6, 1)
layout.setRowStretch(7, 1.0)
self._channelCtrlBox.setLayout(layout)
self._channelControlDock.setWidget(self._channelCtrlBox)
return self._channelCtrlBox
def __get_stateplot_data(self, name):
data = []
if name == 'V':
data = self.squid_setup.vm_table.vector
elif name == 'm':
data = self.squid_setup.m_table.vector
elif name == 'h':
data = self.squid_setup.h_table.vector
elif name == 'n':
data = self.squid_setup.n_table.vector
else:
raise ValueError('Unrecognized selection: %s' % name )
return numpy.asarray(data)
def _statePlotYSlot(self, selectedItem):
ydata = self.__get_stateplot_data(str(selectedItem))
self._state_plot.set_ydata(ydata)
self._statePlotAxes.set_ylabel(selectedItem)
if str(selectedItem) == 'V':
self._statePlotAxes.set_ylim(-20, 120)
else:
self._statePlotAxes.set_ylim(0, 1)
self._statePlotCanvas.draw()
def _statePlotXSlot(self, selectedItem):
xdata = self.__get_stateplot_data(str(selectedItem))
self._state_plot.set_xdata(xdata)
self._statePlotAxes.set_xlabel(selectedItem)
if str(selectedItem) == 'V':
self._statePlotAxes.set_xlim(-20, 120)
else:
self._statePlotAxes.set_xlim(0, 1)
self._statePlotCanvas.draw()
def _createElectronicsControl(self):
"""Creates a tabbed widget of voltage clamp and current clamp controls"""
self._electronicsTab = QTabWidget(self)
self._electronicsTab.addTab(self._getIClampCtrlBox(), 'Current clamp')
self._electronicsTab.addTab(self._getVClampCtrlBox(), 'Voltage clamp')
self._electronicsDock = QDockWidget(self)
self._electronicsDock.setWidget(self._electronicsTab)
def _getVClampCtrlBox(self):
vClampPanel = QGroupBox(self)
self._vClampCtrlBox = vClampPanel
self._holdingVLabel = QLabel("Holding Voltage (mV)", vClampPanel)
self._holdingVEdit = QLineEdit('%g' % (SquidGui.defaults['vclamp.holdingV']), vClampPanel)
self._holdingTimeLabel = QLabel("Holding Time (ms)", vClampPanel)
self._holdingTimeEdit = QLineEdit('%g' % (SquidGui.defaults['vclamp.holdingT']), vClampPanel)
self._prePulseVLabel = QLabel("Pre-pulse Voltage (mV)", vClampPanel)
self._prePulseVEdit = QLineEdit('%g' % (SquidGui.defaults['vclamp.prepulseV']), vClampPanel)
self._prePulseTimeLabel = QLabel("Pre-pulse Time (ms)", vClampPanel)
self._prePulseTimeEdit = QLineEdit('%g' % (SquidGui.defaults['vclamp.prepulseT']), vClampPanel)
self._clampVLabel = QLabel("Clamp Voltage (mV)", vClampPanel)
self._clampVEdit = QLineEdit('%g' % (SquidGui.defaults['vclamp.clampV']), vClampPanel)
self._clampTimeLabel = QLabel("Clamp Time (ms)", vClampPanel)
self._clampTimeEdit = QLineEdit('%g' % (SquidGui.defaults['vclamp.clampT']), vClampPanel)
for child in vClampPanel.children():
if isinstance(child, QLineEdit):
set_default_line_edit_size(child)
layout = QGridLayout(vClampPanel)
layout.addWidget(self._holdingVLabel, 0, 0)
layout.addWidget(self._holdingVEdit, 0, 1)
layout.addWidget(self._holdingTimeLabel, 1, 0)
layout.addWidget(self._holdingTimeEdit, 1, 1)
layout.addWidget(self._prePulseVLabel, 2, 0)
layout.addWidget(self._prePulseVEdit, 2, 1)
layout.addWidget(self._prePulseTimeLabel,3,0)
layout.addWidget(self._prePulseTimeEdit, 3, 1)
layout.addWidget(self._clampVLabel, 4, 0)
layout.addWidget(self._clampVEdit, 4, 1)
layout.addWidget(self._clampTimeLabel, 5, 0)
layout.addWidget(self._clampTimeEdit, 5, 1)
layout.setRowStretch(6, 1.0)
vClampPanel.setLayout(layout)
return self._vClampCtrlBox
def _getIClampCtrlBox(self):
iClampPanel = QGroupBox(self)
self._iClampCtrlBox = iClampPanel
self._baseCurrentLabel = QLabel("Base Current Level (uA)",iClampPanel)
self._baseCurrentEdit = QLineEdit('%g' % (SquidGui.defaults['iclamp.baseI']),iClampPanel)
self._firstPulseLabel = QLabel("First Pulse Current (uA)", iClampPanel)
self._firstPulseEdit = QLineEdit('%g' % (SquidGui.defaults['iclamp.firstI']), iClampPanel)
self._firstDelayLabel = QLabel("First Onset Delay (ms)", iClampPanel)
self._firstDelayEdit = QLineEdit('%g' % (SquidGui.defaults['iclamp.firstD']),iClampPanel)
self._firstPulseWidthLabel = QLabel("First Pulse Width (ms)", iClampPanel)
self._firstPulseWidthEdit = QLineEdit('%g' % (SquidGui.defaults['iclamp.firstT']), iClampPanel)
self._secondPulseLabel = QLabel("Second Pulse Current (uA)", iClampPanel)
self._secondPulseEdit = QLineEdit('%g' % (SquidGui.defaults['iclamp.secondI']), iClampPanel)
self._secondDelayLabel = QLabel("Second Onset Delay (ms)", iClampPanel)
self._secondDelayEdit = QLineEdit('%g' % (SquidGui.defaults['iclamp.secondD']),iClampPanel)
self._secondPulseWidthLabel = QLabel("Second Pulse Width (ms)", iClampPanel)
self._secondPulseWidthEdit = QLineEdit('%g' % (SquidGui.defaults['iclamp.secondT']), iClampPanel)
self._pulseMode = QComboBox(iClampPanel)
self._pulseMode.addItem("Single Pulse")
self._pulseMode.addItem("Pulse Train")
for child in iClampPanel.children():
if isinstance(child, QLineEdit):
set_default_line_edit_size(child)
layout = QGridLayout(iClampPanel)
layout.addWidget(self._baseCurrentLabel, 0, 0)
layout.addWidget(self._baseCurrentEdit, 0, 1)
layout.addWidget(self._firstPulseLabel, 1, 0)
layout.addWidget(self._firstPulseEdit, 1, 1)
layout.addWidget(self._firstDelayLabel, 2, 0)
layout.addWidget(self._firstDelayEdit, 2, 1)
layout.addWidget(self._firstPulseWidthLabel, 3, 0)
layout.addWidget(self._firstPulseWidthEdit, 3, 1)
layout.addWidget(self._secondPulseLabel, 4, 0)
layout.addWidget(self._secondPulseEdit, 4, 1)
layout.addWidget(self._secondDelayLabel, 5, 0)
layout.addWidget(self._secondDelayEdit, 5, 1)
layout.addWidget(self._secondPulseWidthLabel, 6, 0)
layout.addWidget(self._secondPulseWidthEdit, 6, 1)
layout.addWidget(self._pulseMode, 7, 0, 1, 2)
layout.setRowStretch(8, 1.0)
# layout.setSizeConstraint(QLayout.SetFixedSize)
iClampPanel.setLayout(layout)
return self._iClampCtrlBox
def _overlayPlots(self, overlay):
if not overlay:
for axis in (self._plotFigure.axes + self._statePlotFigure.axes):
title = axis.get_title()
axis.clear()
axis.set_title(title)
suffix = ''
else:
suffix = '_%d' % (len(self._plot_dict['vm']))
self._vm_axes.set_xlim(0.0, self._runtime)
self._g_axes.set_xlim(0.0, self._runtime)
self._im_axes.set_xlim(0.0, self._runtime)
self._i_axes.set_xlim(0.0, self._runtime)
self._vm_plot, = self._vm_axes.plot([], [], label='Vm%s'%(suffix))
self._plot_dict['vm'].append(self._vm_plot)
self._command_plot, = self._vm_axes.plot([], [], label='command%s'%(suffix))
self._plot_dict['command'].append(self._command_plot)
# Channel conductances go to the same subplot
self._gna_plot, = self._g_axes.plot([], [], label='Na%s'%(suffix))
self._plot_dict['gna'].append(self._gna_plot)
self._gk_plot, = self._g_axes.plot([], [], label='K%s'%(suffix))
self._plot_dict['gk'].append(self._gk_plot)
# Injection current for Vclamp/Iclamp go to the same subplot
self._iclamp_plot, = self._im_axes.plot([], [], label='Iclamp%s'%(suffix))
self._vclamp_plot, = self._im_axes.plot([], [], label='Vclamp%s'%(suffix))
self._plot_dict['iclamp'].append(self._iclamp_plot)
self._plot_dict['vclamp'].append(self._vclamp_plot)
# Channel currents go to the same subplot
self._ina_plot, = self._i_axes.plot([], [], label='Na%s'%(suffix))
self._plot_dict['ina'].append(self._ina_plot)
self._ik_plot, = self._i_axes.plot([], [], label='K%s'%(suffix))
self._plot_dict['ik'].append(self._ik_plot)
# self._i_axes.legend()
# State plots
self._state_plot, = self._statePlotAxes.plot([], [], label='state%s'%(suffix))
self._plot_dict['state'].append(self._state_plot)
self._m_plot, = self._activationParamAxes.plot([],[], label='m%s'%(suffix))
self._h_plot, = self._activationParamAxes.plot([], [], label='h%s'%(suffix))
self._n_plot, = self._activationParamAxes.plot([], [], label='n%s'%(suffix))
self._plot_dict['m'].append(self._m_plot)
self._plot_dict['h'].append(self._h_plot)
self._plot_dict['n'].append(self._n_plot)
if self._showLegendAction.isChecked():
for axis in (self._plotFigure.axes + self._statePlotFigure.axes):
axis.legend()
def _updateAllPlots(self):
self._updatePlots()
self._updateStatePlot()
def _updatePlots(self):
if len(self.squid_setup.vm_table.vector) <= 0:
return
vm = numpy.asarray(self.squid_setup.vm_table.vector)
cmd = numpy.asarray(self.squid_setup.cmd_table.vector)
ik = numpy.asarray(self.squid_setup.ik_table.vector)
ina = numpy.asarray(self.squid_setup.ina_table.vector)
iclamp = numpy.asarray(self.squid_setup.iclamp_table.vector)
vclamp = numpy.asarray(self.squid_setup.vclamp_table.vector)
gk = numpy.asarray(self.squid_setup.gk_table.vector)
gna = numpy.asarray(self.squid_setup.gna_table.vector)
time_series = numpy.linspace(0, self._plotdt * len(vm), len(vm))
self._vm_plot.set_data(time_series, vm)
time_series = numpy.linspace(0, self._plotdt * len(cmd), len(cmd))
self._command_plot.set_data(time_series, cmd)
time_series = numpy.linspace(0, self._plotdt * len(ik), len(ik))
self._ik_plot.set_data(time_series, ik)
time_series = numpy.linspace(0, self._plotdt * len(ina), len(ina))
self._ina_plot.set_data(time_series, ina)
time_series = numpy.linspace(0, self._plotdt * len(iclamp), len(iclamp))
self._iclamp_plot.set_data(time_series, iclamp)
time_series = numpy.linspace(0, self._plotdt * len(vclamp), len(vclamp))
self._vclamp_plot.set_data(time_series, vclamp)
time_series = numpy.linspace(0, self._plotdt * len(gk), len(gk))
self._gk_plot.set_data(time_series, gk)
time_series = numpy.linspace(0, self._plotdt * len(gna), len(gna))
self._gna_plot.set_data(time_series, gna)
# self._vm_axes.margins(y=0.1)
# self._g_axes.margin(y=0.1)
# self._im_axes.margins(y=0.1)
# self._i_axes.margins(y=0.1)
if self._autoscaleAction.isChecked():
for axis in self._plotFigure.axes:
axis.relim()
axis.margins(0.1, 0.1)
axis.autoscale_view(tight=True)
else:
self._vm_axes.set_ylim(-20.0, 120.0)
self._g_axes.set_ylim(0.0, 0.5)
self._im_axes.set_ylim(-0.5, 0.5)
self._i_axes.set_ylim(-10, 10)
self._vm_axes.set_xlim(0.0, time_series[-1])
self._g_axes.set_xlim(0.0, time_series[-1])
self._im_axes.set_xlim(0.0, time_series[-1])
self._i_axes.set_xlim(0.0, time_series[-1])
self._plotCanvas.draw()
def _updateStatePlot(self):
if len(self.squid_setup.vm_table.vector) <= 0:
return
sx = str(self._stateplot_xvar_combo.currentText())
sy = str(self._stateplot_yvar_combo.currentText())
xdata = self.__get_stateplot_data(sx)
ydata = self.__get_stateplot_data(sy)
minlen = min(len(xdata), len(ydata))
self._state_plot.set_data(xdata[:minlen], ydata[:minlen])
self._statePlotAxes.set_xlabel(sx)
self._statePlotAxes.set_ylabel(sy)
if sx == 'V':
self._statePlotAxes.set_xlim(-20, 120)
else:
self._statePlotAxes.set_xlim(0, 1)
if sy == 'V':
self._statePlotAxes.set_ylim(-20, 120)
else:
self._statePlotAxes.set_ylim(0, 1)
self._activationParamAxes.set_xlim(0, self._runtime)
m = self.__get_stateplot_data('m')
n = self.__get_stateplot_data('n')
h = self.__get_stateplot_data('h')
time_series = numpy.linspace(0, self._plotdt*len(m), len(m))
self._m_plot.set_data(time_series, m)
time_series = numpy.linspace(0, self._plotdt*len(h), len(h))
self._h_plot.set_data(time_series, h)
time_series = numpy.linspace(0, self._plotdt*len(n), len(n))
self._n_plot.set_data(time_series, n)
if self._autoscaleAction.isChecked():
for axis in self._statePlotFigure.axes:
axis.relim()
axis.set_autoscale_on(True)
axis.autoscale_view(True)
self._statePlotCanvas.draw()
def _runSlot(self):
if moose.isRunning():
print('Stopping simulation in progress ...')
moose.stop()
self._runtime = self.getFloatInput(self._runTimeEdit, self._runTimeLabel.text())
self._overlayPlots(self._overlayAction.isChecked())
self._simdt = self.getFloatInput(self._simTimeStepEdit, self._simTimeStepLabel.text())
clampMode = None
singlePulse = True
if self._electronicsTab.currentWidget() == self._vClampCtrlBox:
clampMode = 'vclamp'
baseLevel = self.getFloatInput(self._holdingVEdit, self._holdingVLabel.text())
firstDelay = self.getFloatInput(self._holdingTimeEdit, self._holdingTimeLabel.text())
firstWidth = self.getFloatInput(self._prePulseTimeEdit, self._prePulseTimeLabel.text())
firstLevel = self.getFloatInput(self._prePulseVEdit, self._prePulseVLabel.text())
secondDelay = firstWidth
secondWidth = self.getFloatInput(self._clampTimeEdit, self._clampTimeLabel.text())
secondLevel = self.getFloatInput(self._clampVEdit, self._clampVLabel.text())
if not self._autoscaleAction.isChecked():
self._im_axes.set_ylim(-10.0, 10.0)
else:
clampMode = 'iclamp'
baseLevel = self.getFloatInput(self._baseCurrentEdit, self._baseCurrentLabel.text())
firstDelay = self.getFloatInput(self._firstDelayEdit, self._firstDelayLabel.text())
firstWidth = self.getFloatInput(self._firstPulseWidthEdit, self._firstPulseWidthLabel.text())
firstLevel = self.getFloatInput(self._firstPulseEdit, self._firstPulseLabel.text())
secondDelay = self.getFloatInput(self._secondDelayEdit, self._secondDelayLabel.text())
secondLevel = self.getFloatInput(self._secondPulseEdit, self._secondPulseLabel.text())
secondWidth = self.getFloatInput(self._secondPulseWidthEdit, self._secondPulseWidthLabel.text())
singlePulse = (self._pulseMode.currentIndex() == 0)
if not self._autoscaleAction.isChecked():
self._im_axes.set_ylim(-0.4, 0.4)
self.squid_setup.clamp_ckt.configure_pulses(baseLevel=baseLevel,
firstDelay=firstDelay,
firstWidth=firstWidth,
firstLevel=firstLevel,
secondDelay=secondDelay,
secondWidth=secondWidth,
secondLevel=secondLevel,
singlePulse=singlePulse)
if self._kConductanceToggle.isChecked():
self.squid_setup.squid_axon.specific_gK = 0.0
else:
self.squid_setup.squid_axon.specific_gK = SquidAxon.defaults['specific_gK']
if self._naConductanceToggle.isChecked():
self.squid_setup.squid_axon.specific_gNa = 0.0
else:
self.squid_setup.squid_axon.specific_gNa = SquidAxon.defaults['specific_gNa']
self.squid_setup.squid_axon.celsius = self.getFloatInput(self._temperatureEdit, self._temperatureLabel.text())
self.squid_setup.squid_axon.K_out = self.getFloatInput(self._kOutEdit, self._kOutLabel.text())
self.squid_setup.squid_axon.Na_out = self.getFloatInput(self._naOutEdit, self._naOutLabel.text())
self.squid_setup.squid_axon.K_in = self.getFloatInput(self._kInEdit, self._kInLabel.text())
self.squid_setup.squid_axon.Na_in = self.getFloatInput(self._naInEdit, self._naInLabel.text())
self.squid_setup.squid_axon.updateEk()
self.squid_setup.schedule(self._simdt, self._plotdt, clampMode)
# The following line is for use with Qthread
self.squid_setup.run(self._runtime)
self._updateAllPlots()
def _toggleDocking(self, on):
self._channelControlDock.setFloating(on)
self._electronicsDock.setFloating(on)
self._runControlDock.setFloating(on)
def _restoreDocks(self):
self._channelControlDock.setVisible(True)
self._electronicsDock.setVisible(True)
self._runControlDock.setVisible(True)
def _initActions(self):
self._runAction = QAction(self.tr('Run'), self)
self._runAction.setShortcut(self.tr('F5'))
self._runAction.setToolTip('Run simulation (F5)')
self._runAction.triggered.connect( self._runSlot)
self._resetToDefaultsAction = QAction(self.tr('Restore defaults'), self)
self._resetToDefaultsAction.setToolTip('Reset all settings to their default values')
self._resetToDefaultsAction.triggered.connect( self._useDefaults)
self._showLegendAction = QAction(self.tr('Display legend'), self)
self._showLegendAction.setCheckable(True)
self._showLegendAction.toggled.connect(self._showLegend)
self._showStatePlotAction = QAction(self.tr('State plot'), self)
self._showStatePlotAction.setCheckable(True)
self._showStatePlotAction.setChecked(False)
self._showStatePlotAction.toggled.connect(self._statePlotWidget.setVisible)
self._autoscaleAction = QAction(self.tr('Auto-scale plots'), self)
self._autoscaleAction.setCheckable(True)
self._autoscaleAction.setChecked(False)
self._autoscaleAction.toggled.connect(self._autoscale)
self._overlayAction = QAction('Overlay plots', self)
self._overlayAction.setCheckable(True)
self._overlayAction.setChecked(False)
self._dockAction = QAction('Undock all', self)
self._dockAction.setCheckable(True)
self._dockAction.setChecked(False)
# self._dockAction.toggle.connect( self._toggleDocking)
self._restoreDocksAction = QAction('Show all', self)
self._restoreDocksAction.triggered.connect( self._restoreDocks)
self._quitAction = QAction(self.tr('&Quit'), self)
self._quitAction.setShortcut(self.tr('Ctrl+Q'))
self._quitAction.triggered.connect(qApp.closeAllWindows)
def _createRunToolBar(self):
self._simToolBar = self.addToolBar(self.tr('Simulation control'))
self._simToolBar.addAction(self._quitAction)
self._simToolBar.addAction(self._runAction)
self._simToolBar.addAction(self._resetToDefaultsAction)
self._simToolBar.addAction(self._dockAction)
self._simToolBar.addAction(self._restoreDocksAction)
def _createPlotToolBar(self):
self._plotToolBar = self.addToolBar(self.tr('Plotting control'))
self._plotToolBar.addAction(self._showLegendAction)
self._plotToolBar.addAction(self._autoscaleAction)
self._plotToolBar.addAction(self._overlayAction)
self._plotToolBar.addAction(self._showStatePlotAction)
self._plotToolBar.addAction(self._helpAction)
self._plotToolBar.addAction(self._helpBiophysicsAction)
def _showLegend(self, on):
if on:
for axis in (self._plotFigure.axes + self._statePlotFigure.axes):
axis.legend().set_visible(True)
else:
for axis in (self._plotFigure.axes + self._statePlotFigure.axes):
axis.legend().set_visible(False)
self._plotCanvas.draw()
self._statePlotCanvas.draw()
def _autoscale(self, on):
if on:
for axis in (self._plotFigure.axes + self._statePlotFigure.axes):
axis.relim()
axis.set_autoscale_on(True)
axis.autoscale_view(True)
else:
for axis in self._plotFigure.axes:
axis.set_autoscale_on(False)
self._vm_axes.set_ylim(-20.0, 120.0)
self._g_axes.set_ylim(0.0, 0.5)
self._im_axes.set_ylim(-0.5, 0.5)
self._i_axes.set_ylim(-10, 10)
self._plotCanvas.draw()
self._statePlotCanvas.draw()
def _useDefaults(self):
self._runTimeEdit.setText('%g' % (self.defaults['runtime']))
self._simTimeStepEdit.setText('%g' % (self.defaults['simdt']))
self._overlayAction.setChecked(False)
self._naConductanceToggle.setChecked(False)
self._kConductanceToggle.setChecked(False)
self._kOutEdit.setText('%g' % (SquidGui.defaults['K_out']))
self._naOutEdit.setText('%g' % (SquidGui.defaults['Na_out']))
self._kInEdit.setText('%g' % (SquidGui.defaults['K_in']))
self._naInEdit.setText('%g' % (SquidGui.defaults['Na_in']))
self._temperatureEdit.setText('%g' % (SquidGui.defaults['temperature'] - CELSIUS_TO_KELVIN))
self._holdingVEdit.setText('%g' % (SquidGui.defaults['vclamp.holdingV']))
self._holdingTimeEdit.setText('%g' % (SquidGui.defaults['vclamp.holdingT']))
self._prePulseVEdit.setText('%g' % (SquidGui.defaults['vclamp.prepulseV']))
self._prePulseTimeEdit.setText('%g' % (SquidGui.defaults['vclamp.prepulseT']))
self._clampVEdit.setText('%g' % (SquidGui.defaults['vclamp.clampV']))
self._clampTimeEdit.setText('%g' % (SquidGui.defaults['vclamp.clampT']))
self._baseCurrentEdit.setText('%g' % (SquidGui.defaults['iclamp.baseI']))
self._firstPulseEdit.setText('%g' % (SquidGui.defaults['iclamp.firstI']))
self._firstDelayEdit.setText('%g' % (SquidGui.defaults['iclamp.firstD']))
self._firstPulseWidthEdit.setText('%g' % (SquidGui.defaults['iclamp.firstT']))
self._secondPulseEdit.setText('%g' % (SquidGui.defaults['iclamp.secondI']))
self._secondDelayEdit.setText('%g' % (SquidGui.defaults['iclamp.secondD']))
self._secondPulseWidthEdit.setText('%g' % (SquidGui.defaults['iclamp.secondT']))
self._pulseMode.setCurrentIndex(0)
def _onScroll(self, event):
if event.inaxes is None:
return
axes = event.inaxes
zoom = 0.0
if event.button == 'up':
zoom = -1.0
elif event.button == 'down':
zoom = 1.0
if zoom != 0.0:
self._plotNavigator.push_current()
axes.get_xaxis().zoom(zoom)
axes.get_yaxis().zoom(zoom)
self._plotCanvas.draw()
def closeEvent(self, event):
qApp.closeAllWindows()
def _showBioPhysicsHelp(self):
self._createHelpMessage()
self._helpMessageText.setText('<html><p>%s</p><p>%s</p><p>%s</p><p>%s</p><p>%s</p></html>' %
(tooltip_Nernst,
tooltip_Erest,
tooltip_KChan,
tooltip_NaChan,
tooltip_Im))
self._helpWindow.setVisible(True)
def _showRunningHelp(self):
self._createHelpMessage()
self._helpMessageText.setSource(QtCore.QUrl(self._helpBaseURL))
self._helpWindow.setVisible(True)
def _createHelpMessage(self):
if hasattr(self, '_helpWindow'):
return
self._helpWindow = QWidget()
self._helpWindow.setWindowFlags(QtCore.Qt.Window)
layout = QVBoxLayout()
self._helpWindow.setLayout(layout)
self._helpMessageArea = QScrollArea()
self._helpMessageText = QTextBrowser()
self._helpMessageText.setOpenExternalLinks(True)
self._helpMessageArea.setWidget(self._helpMessageText)
layout.addWidget(self._helpMessageText)
self._squidGuiPath = os.path.dirname(os.path.abspath(__file__))
self._helpBaseURL = os.path.join(self._squidGuiPath,'help.html')
self._helpMessageText.setSource(QtCore.QUrl(self._helpBaseURL))
self._helpMessageText.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
self._helpMessageArea.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
self._helpMessageText.setMinimumSize(800, 600)
self._closeHelpAction = QAction('Close', self)
self._closeHelpAction.triggered.connect(self._helpWindow.close)
# Setting the close event so that the ``Help`` button is
# unchecked when the help window is closed
self._helpWindow.closeEvent = lambda event: self._helpAction.setChecked(False)
self._helpTOCAction = QAction('Help running demo', self)
self._helpTOCAction.triggered.connect( self._jumpToHelpTOC)
# This panel is for putting two buttons using horizontal
# layout
panel = QFrame()
panel.setFrameStyle(QFrame.StyledPanel + QFrame.Raised)
layout.addWidget(panel)
layout = QHBoxLayout()
panel.setLayout(layout)
self._helpAction = QAction('Help running', self)
self._helpAction.triggered.connect(self._showRunningHelp)
self._helpBiophysicsAction = QAction('Help biophysics', self)
self._helpBiophysicsAction.triggered.connect(self._showBioPhysicsHelp)
self._helpTOCButton = QToolButton()
self._helpTOCButton.setDefaultAction(self._helpTOCAction)
self._helpBiophysicsButton = QToolButton()
self._helpBiophysicsButton.setDefaultAction(self._helpBiophysicsAction)
layout.addWidget(self._helpTOCButton)
layout.addWidget(self._helpBiophysicsButton)
self._closeHelpButton = QToolButton()
self._closeHelpButton.setDefaultAction(self._closeHelpAction)
layout.addWidget(self._closeHelpButton)
def _jumpToHelpTOC(self):
self._helpMessageText.setSource(QtCore.QUrl(self._helpBaseURL))
class SquidGui(QtGui.QMainWindow):
defaults = {}
defaults.update(SquidAxon.defaults)
defaults.update(ClampCircuit.defaults)
defaults.update({
'runtime': 50.0,
'simdt': 0.01,
'plotdt': 0.1,
'vclamp.holdingV': 0.0,
'vclamp.holdingT': 10.0,
'vclamp.prepulseV': 0.0,
'vclamp.prepulseT': 0.0,
'vclamp.clampV': 50.0,
'vclamp.clampT': 20.0,
'iclamp.baseI': 0.0,
'iclamp.firstI': 0.1,
'iclamp.firstT': 40.0,
'iclamp.firstD': 5.0,
'iclamp.secondI': 0.0,
'iclamp.secondT': 0.0,
'iclamp.secondD': 0.0
})
def __init__(self, *args):
QtGui.QMainWindow.__init__(self, *args)
self.squid_setup = SquidSetup()
self._plotdt = SquidGui.defaults['plotdt']
self._plot_dict = defaultdict(list)
self.setWindowTitle('Squid Axon simulation')
self.setDockNestingEnabled(True)
self._createRunControl()
self.addDockWidget(QtCore.Qt.LeftDockWidgetArea, self._runControlDock)
self._runControlDock.setFeatures(
QtGui.QDockWidget.AllDockWidgetFeatures)
self._createChannelControl()
self._channelCtrlBox.setWindowTitle('Channel properties')
self._channelControlDock.setFeatures(
QtGui.QDockWidget.AllDockWidgetFeatures)
self.addDockWidget(QtCore.Qt.LeftDockWidgetArea,
self._channelControlDock)
self._createElectronicsControl()
self._electronicsDock.setFeatures(
QtGui.QDockWidget.AllDockWidgetFeatures)
self._electronicsDock.setWindowTitle('Electronics')
self.addDockWidget(QtCore.Qt.LeftDockWidgetArea, self._electronicsDock)
self._createPlotWidget()
self.setCentralWidget(self._plotWidget)
self._createStatePlotWidget()
self._createHelpMessage()
self._helpWindow.setVisible(False)
self._statePlotWidget.setWindowFlags(QtCore.Qt.Window)
self._statePlotWidget.setWindowTitle('State plot')
self._initActions()
self._createRunToolBar()
self._createPlotToolBar()
def _createPlotWidget(self):
self._plotWidget = QtGui.QWidget()
self._plotFigure = Figure()
self._plotCanvas = FigureCanvas(self._plotFigure)
self._plotCanvas.setSizePolicy(QtGui.QSizePolicy.Expanding,
QtGui.QSizePolicy.Expanding)
self._plotCanvas.updateGeometry()
self._plotCanvas.setParent(self._plotWidget)
self._plotCanvas.mpl_connect('scroll_event', self._onScroll)
self._plotFigure.set_canvas(self._plotCanvas)
# Vm and command voltage go in the same subplot
self._vm_axes = self._plotFigure.add_subplot(
2, 2, 1, title='Membrane potential')
self._vm_axes.set_ylim(-20.0, 120.0)
# Channel conductances go to the same subplot
self._g_axes = self._plotFigure.add_subplot(
2, 2, 2, title='Channel conductance')
self._g_axes.set_ylim(0.0, 0.5)
# Injection current for Vclamp/Iclamp go to the same subplot
self._im_axes = self._plotFigure.add_subplot(2,
2,
3,
title='Injection current')
self._im_axes.set_ylim(-0.5, 0.5)
# Channel currents go to the same subplot
self._i_axes = self._plotFigure.add_subplot(2,
2,
4,
title='Channel current')
self._i_axes.set_ylim(-10, 10)
for axis in self._plotFigure.axes:
axis.set_autoscale_on(False)
layout = QtGui.QVBoxLayout()
layout.addWidget(self._plotCanvas)
self._plotNavigator = NavigationToolbar(self._plotCanvas,
self._plotWidget)
layout.addWidget(self._plotNavigator)
self._plotWidget.setLayout(layout)
def _createStatePlotWidget(self):
self._statePlotWidget = QtGui.QWidget()
self._statePlotFigure = Figure()
self._statePlotCanvas = FigureCanvas(self._statePlotFigure)
self._statePlotCanvas.setSizePolicy(QtGui.QSizePolicy.Expanding,
QtGui.QSizePolicy.Expanding)
self._statePlotCanvas.updateGeometry()
self._statePlotCanvas.setParent(self._statePlotWidget)
self._statePlotFigure.set_canvas(self._statePlotCanvas)
self._statePlotFigure.subplots_adjust(hspace=0.5)
self._statePlotAxes = self._statePlotFigure.add_subplot(
2, 1, 1, title='State plot')
self._state_plot, = self._statePlotAxes.plot([], [], label='state')
self._activationParamAxes = self._statePlotFigure.add_subplot(
2, 1, 2, title='H-H activation parameters vs time')
self._activationParamAxes.set_xlabel('Time (ms)')
#for axis in self._plotFigure.axes:
# axis.autoscale(False)
self._stateplot_xvar_label = QtGui.QLabel('Variable on X-axis')
self._stateplot_xvar_combo = QtGui.QComboBox()
self._stateplot_xvar_combo.addItems(['V', 'm', 'n', 'h'])
self._stateplot_xvar_combo.setCurrentIndex(0)
self._stateplot_xvar_combo.setEditable(False)
self.connect(self._stateplot_xvar_combo,
QtCore.SIGNAL('currentIndexChanged(const QString&)'),
self._statePlotXSlot)
self._stateplot_yvar_label = QtGui.QLabel('Variable on Y-axis')
self._stateplot_yvar_combo = QtGui.QComboBox()
self._stateplot_yvar_combo.addItems(['V', 'm', 'n', 'h'])
self._stateplot_yvar_combo.setCurrentIndex(2)
self._stateplot_yvar_combo.setEditable(False)
self.connect(self._stateplot_yvar_combo,
QtCore.SIGNAL('currentIndexChanged(const QString&)'),
self._statePlotYSlot)
self._statePlotNavigator = NavigationToolbar(self._statePlotCanvas,
self._statePlotWidget)
frame = QtGui.QFrame()
frame.setFrameStyle(QtGui.QFrame.StyledPanel + QtGui.QFrame.Raised)
layout = QtGui.QHBoxLayout()
layout.addWidget(self._stateplot_xvar_label)
layout.addWidget(self._stateplot_xvar_combo)
layout.addWidget(self._stateplot_yvar_label)
layout.addWidget(self._stateplot_yvar_combo)
frame.setLayout(layout)
self._closeStatePlotAction = QtGui.QAction('Close', self)
self.connect(self._closeStatePlotAction, QtCore.SIGNAL('triggered()'),
self._statePlotWidget.close)
self._closeStatePlotButton = QtGui.QToolButton()
self._closeStatePlotButton.setDefaultAction(self._closeStatePlotAction)
layout = QtGui.QVBoxLayout()
layout.addWidget(frame)
layout.addWidget(self._statePlotCanvas)
layout.addWidget(self._statePlotNavigator)
layout.addWidget(self._closeStatePlotButton)
self._statePlotWidget.setLayout(layout)
# Setting the close event so that when the help window is
# closed the ``State plot`` button becomes unchecked
self._statePlotWidget.closeEvent = lambda event: self._showStatePlotAction.setChecked(
False)
def _createRunControl(self):
self._runControlBox = QtGui.QGroupBox(self)
self._runControlBox.setSizePolicy(QtGui.QSizePolicy.Preferred,
QtGui.QSizePolicy.Preferred)
self._runTimeLabel = QtGui.QLabel("Run time (ms)", self._runControlBox)
self._simTimeStepLabel = QtGui.QLabel("Simulation time step (ms)",
self._runControlBox)
self._runTimeEdit = QtGui.QLineEdit(
'%g' % (SquidGui.defaults['runtime']), self._runControlBox)
set_default_line_edit_size(self._runTimeEdit)
self._simTimeStepEdit = QtGui.QLineEdit(
'%g' % (SquidGui.defaults['simdt']), self._runControlBox)
set_default_line_edit_size(self._simTimeStepEdit)
layout = QtGui.QGridLayout()
layout.addWidget(self._runTimeLabel, 0, 0)
layout.addWidget(self._runTimeEdit, 0, 1)
layout.addWidget(self._simTimeStepLabel, 1, 0)
layout.addWidget(self._simTimeStepEdit, 1, 1)
layout.setColumnStretch(2, 1.0)
layout.setRowStretch(2, 1.0)
self._runControlBox.setLayout(layout)
self._runControlDock = QtGui.QDockWidget('Simulation', self)
self._runControlDock.setWidget(self._runControlBox)
def _createChannelControl(self):
self._channelControlDock = QtGui.QDockWidget('Channels', self)
self._channelCtrlBox = QtGui.QGroupBox(self)
self._naConductanceToggle = QtGui.QCheckBox('Block Na+ channel',
self._channelCtrlBox)
self._naConductanceToggle.setToolTip('<html>%s</html>' %
(tooltip_NaChan))
self._kConductanceToggle = QtGui.QCheckBox('Block K+ channel',
self._channelCtrlBox)
self._kConductanceToggle.setToolTip('<html>%s</html>' %
(tooltip_KChan))
self._kOutLabel = QtGui.QLabel('[K+]out (mM)', self._channelCtrlBox)
self._kOutEdit = QtGui.QLineEdit(
'%g' % (self.squid_setup.squid_axon.K_out), self._channelCtrlBox)
self._kOutLabel.setToolTip('<html>%s</html>' % (tooltip_Nernst))
self._kOutEdit.setToolTip('<html>%s</html>' % (tooltip_Nernst))
set_default_line_edit_size(self._kOutEdit)
self._naOutLabel = QtGui.QLabel('[Na+]out (mM)', self._channelCtrlBox)
self._naOutEdit = QtGui.QLineEdit(
'%g' % (self.squid_setup.squid_axon.Na_out), self._channelCtrlBox)
self._naOutLabel.setToolTip('<html>%s</html>' % (tooltip_Nernst))
self._naOutEdit.setToolTip('<html>%s</html>' % (tooltip_Nernst))
set_default_line_edit_size(self._naOutEdit)
self._kInLabel = QtGui.QLabel('[K+]in (mM)', self._channelCtrlBox)
self._kInEdit = QtGui.QLabel('%g' % (self.squid_setup.squid_axon.K_in),
self._channelCtrlBox)
self._kInEdit.setToolTip(tooltip_Nernst)
self._naInLabel = QtGui.QLabel('[Na+]in (mM)', self._channelCtrlBox)
self._naInEdit = QtGui.QLabel(
'%g' % (self.squid_setup.squid_axon.Na_in), self._channelCtrlBox)
self._naInEdit.setToolTip('<html>%s</html>' % (tooltip_Nernst))
self._temperatureLabel = QtGui.QLabel('Temperature (C)',
self._channelCtrlBox)
self._temperatureEdit = QtGui.QLineEdit(
'%g' % (self.defaults['temperature'] - CELSIUS_TO_KELVIN),
self._channelCtrlBox)
self._temperatureEdit.setToolTip('<html>%s</html>' % (tooltip_Nernst))
set_default_line_edit_size(self._temperatureEdit)
for child in self._channelCtrlBox.children():
if isinstance(child, QtGui.QLineEdit):
set_default_line_edit_size(child)
layout = QtGui.QGridLayout(self._channelCtrlBox)
layout.addWidget(self._naConductanceToggle, 0, 0)
layout.addWidget(self._kConductanceToggle, 1, 0)
layout.addWidget(self._naOutLabel, 2, 0)
layout.addWidget(self._naOutEdit, 2, 1)
layout.addWidget(self._naInLabel, 3, 0)
layout.addWidget(self._naInEdit, 3, 1)
layout.addWidget(self._kOutLabel, 4, 0)
layout.addWidget(self._kOutEdit, 4, 1)
layout.addWidget(self._kInLabel, 5, 0)
layout.addWidget(self._kInEdit, 5, 1)
layout.addWidget(self._temperatureLabel, 6, 0)
layout.addWidget(self._temperatureEdit, 6, 1)
layout.setRowStretch(7, 1.0)
self._channelCtrlBox.setLayout(layout)
self._channelControlDock.setWidget(self._channelCtrlBox)
return self._channelCtrlBox
def __get_stateplot_data(self, name):
data = []
if name == 'V':
data = self.squid_setup.vm_table.vector
elif name == 'm':
data = self.squid_setup.m_table.vector
elif name == 'h':
data = self.squid_setup.h_table.vector
elif name == 'n':
data = self.squid_setup.n_table.vector
else:
raise ValueError('Unrecognized selection: %s' % (name))
return numpy.asarray(data)
def _statePlotYSlot(self, selectedItem):
ydata = self.__get_stateplot_data(str(selectedItem))
self._state_plot.set_ydata(ydata)
self._statePlotAxes.set_ylabel(selectedItem)
if str(selectedItem) == 'V':
self._statePlotAxes.set_ylim(-20, 120)
else:
self._statePlotAxes.set_ylim(0, 1)
self._statePlotCanvas.draw()
def _statePlotXSlot(self, selectedItem):
xdata = self.__get_stateplot_data(str(selectedItem))
self._state_plot.set_xdata(xdata)
self._statePlotAxes.set_xlabel(selectedItem)
if str(selectedItem) == 'V':
self._statePlotAxes.set_xlim(-20, 120)
else:
self._statePlotAxes.set_xlim(0, 1)
self._statePlotCanvas.draw()
def _createElectronicsControl(self):
"""Creates a tabbed widget of voltage clamp and current clamp controls"""
self._electronicsTab = QtGui.QTabWidget(self)
self._electronicsTab.addTab(self._getIClampCtrlBox(), 'Current clamp')
self._electronicsTab.addTab(self._getVClampCtrlBox(), 'Voltage clamp')
self._electronicsDock = QtGui.QDockWidget(self)
self._electronicsDock.setWidget(self._electronicsTab)
def _getVClampCtrlBox(self):
vClampPanel = QtGui.QGroupBox(self)
self._vClampCtrlBox = vClampPanel
self._holdingVLabel = QtGui.QLabel("Holding Voltage (mV)", vClampPanel)
self._holdingVEdit = QtGui.QLineEdit(
'%g' % (SquidGui.defaults['vclamp.holdingV']), vClampPanel)
self._holdingTimeLabel = QtGui.QLabel("Holding Time (ms)", vClampPanel)
self._holdingTimeEdit = QtGui.QLineEdit(
'%g' % (SquidGui.defaults['vclamp.holdingT']), vClampPanel)
self._prePulseVLabel = QtGui.QLabel("Pre-pulse Voltage (mV)",
vClampPanel)
self._prePulseVEdit = QtGui.QLineEdit(
'%g' % (SquidGui.defaults['vclamp.prepulseV']), vClampPanel)
self._prePulseTimeLabel = QtGui.QLabel("Pre-pulse Time (ms)",
vClampPanel)
self._prePulseTimeEdit = QtGui.QLineEdit(
'%g' % (SquidGui.defaults['vclamp.prepulseT']), vClampPanel)
self._clampVLabel = QtGui.QLabel("Clamp Voltage (mV)", vClampPanel)
self._clampVEdit = QtGui.QLineEdit(
'%g' % (SquidGui.defaults['vclamp.clampV']), vClampPanel)
self._clampTimeLabel = QtGui.QLabel("Clamp Time (ms)", vClampPanel)
self._clampTimeEdit = QtGui.QLineEdit(
'%g' % (SquidGui.defaults['vclamp.clampT']), vClampPanel)
for child in vClampPanel.children():
if isinstance(child, QtGui.QLineEdit):
set_default_line_edit_size(child)
layout = QtGui.QGridLayout(vClampPanel)
layout.addWidget(self._holdingVLabel, 0, 0)
layout.addWidget(self._holdingVEdit, 0, 1)
layout.addWidget(self._holdingTimeLabel, 1, 0)
layout.addWidget(self._holdingTimeEdit, 1, 1)
layout.addWidget(self._prePulseVLabel, 2, 0)
layout.addWidget(self._prePulseVEdit, 2, 1)
layout.addWidget(self._prePulseTimeLabel, 3, 0)
layout.addWidget(self._prePulseTimeEdit, 3, 1)
layout.addWidget(self._clampVLabel, 4, 0)
layout.addWidget(self._clampVEdit, 4, 1)
layout.addWidget(self._clampTimeLabel, 5, 0)
layout.addWidget(self._clampTimeEdit, 5, 1)
layout.setRowStretch(6, 1.0)
vClampPanel.setLayout(layout)
return self._vClampCtrlBox
def _getIClampCtrlBox(self):
iClampPanel = QtGui.QGroupBox(self)
self._iClampCtrlBox = iClampPanel
self._baseCurrentLabel = QtGui.QLabel("Base Current Level (uA)",
iClampPanel)
self._baseCurrentEdit = QtGui.QLineEdit(
'%g' % (SquidGui.defaults['iclamp.baseI']), iClampPanel)
self._firstPulseLabel = QtGui.QLabel("First Pulse Current (uA)",
iClampPanel)
self._firstPulseEdit = QtGui.QLineEdit(
'%g' % (SquidGui.defaults['iclamp.firstI']), iClampPanel)
self._firstDelayLabel = QtGui.QLabel("First Onset Delay (ms)",
iClampPanel)
self._firstDelayEdit = QtGui.QLineEdit(
'%g' % (SquidGui.defaults['iclamp.firstD']), iClampPanel)
self._firstPulseWidthLabel = QtGui.QLabel("First Pulse Width (ms)",
iClampPanel)
self._firstPulseWidthEdit = QtGui.QLineEdit(
'%g' % (SquidGui.defaults['iclamp.firstT']), iClampPanel)
self._secondPulseLabel = QtGui.QLabel("Second Pulse Current (uA)",
iClampPanel)
self._secondPulseEdit = QtGui.QLineEdit(
'%g' % (SquidGui.defaults['iclamp.secondI']), iClampPanel)
self._secondDelayLabel = QtGui.QLabel("Second Onset Delay (ms)",
iClampPanel)
self._secondDelayEdit = QtGui.QLineEdit(
'%g' % (SquidGui.defaults['iclamp.secondD']), iClampPanel)
self._secondPulseWidthLabel = QtGui.QLabel("Second Pulse Width (ms)",
iClampPanel)
self._secondPulseWidthEdit = QtGui.QLineEdit(
'%g' % (SquidGui.defaults['iclamp.secondT']), iClampPanel)
self._pulseMode = QtGui.QComboBox(iClampPanel)
self._pulseMode.addItem("Single Pulse")
self._pulseMode.addItem("Pulse Train")
for child in iClampPanel.children():
if isinstance(child, QtGui.QLineEdit):
set_default_line_edit_size(child)
layout = QtGui.QGridLayout(iClampPanel)
layout.addWidget(self._baseCurrentLabel, 0, 0)
layout.addWidget(self._baseCurrentEdit, 0, 1)
layout.addWidget(self._firstPulseLabel, 1, 0)
layout.addWidget(self._firstPulseEdit, 1, 1)
layout.addWidget(self._firstDelayLabel, 2, 0)
layout.addWidget(self._firstDelayEdit, 2, 1)
layout.addWidget(self._firstPulseWidthLabel, 3, 0)
layout.addWidget(self._firstPulseWidthEdit, 3, 1)
layout.addWidget(self._secondPulseLabel, 4, 0)
layout.addWidget(self._secondPulseEdit, 4, 1)
layout.addWidget(self._secondDelayLabel, 5, 0)
layout.addWidget(self._secondDelayEdit, 5, 1)
layout.addWidget(self._secondPulseWidthLabel, 6, 0)
layout.addWidget(self._secondPulseWidthEdit, 6, 1)
layout.addWidget(self._pulseMode, 7, 0, 1, 2)
layout.setRowStretch(8, 1.0)
# layout.setSizeConstraint(QtGui.QLayout.SetFixedSize)
iClampPanel.setLayout(layout)
return self._iClampCtrlBox
def _overlayPlots(self, overlay):
if not overlay:
for axis in (self._plotFigure.axes + self._statePlotFigure.axes):
title = axis.get_title()
axis.clear()
axis.set_title(title)
suffix = ''
else:
suffix = '_%d' % (len(self._plot_dict['vm']))
self._vm_axes.set_xlim(0.0, self._runtime)
self._g_axes.set_xlim(0.0, self._runtime)
self._im_axes.set_xlim(0.0, self._runtime)
self._i_axes.set_xlim(0.0, self._runtime)
self._vm_plot, = self._vm_axes.plot([], [], label='Vm%s' % (suffix))
self._plot_dict['vm'].append(self._vm_plot)
self._command_plot, = self._vm_axes.plot([], [],
label='command%s' % (suffix))
self._plot_dict['command'].append(self._command_plot)
# Channel conductances go to the same subplot
self._gna_plot, = self._g_axes.plot([], [], label='Na%s' % (suffix))
self._plot_dict['gna'].append(self._gna_plot)
self._gk_plot, = self._g_axes.plot([], [], label='K%s' % (suffix))
self._plot_dict['gk'].append(self._gk_plot)
# Injection current for Vclamp/Iclamp go to the same subplot
self._iclamp_plot, = self._im_axes.plot([], [],
label='Iclamp%s' % (suffix))
self._vclamp_plot, = self._im_axes.plot([], [],
label='Vclamp%s' % (suffix))
self._plot_dict['iclamp'].append(self._iclamp_plot)
self._plot_dict['vclamp'].append(self._vclamp_plot)
# Channel currents go to the same subplot
self._ina_plot, = self._i_axes.plot([], [], label='Na%s' % (suffix))
self._plot_dict['ina'].append(self._ina_plot)
self._ik_plot, = self._i_axes.plot([], [], label='K%s' % (suffix))
self._plot_dict['ik'].append(self._ik_plot)
# self._i_axes.legend()
# State plots
self._state_plot, = self._statePlotAxes.plot([], [],
label='state%s' %
(suffix))
self._plot_dict['state'].append(self._state_plot)
self._m_plot, = self._activationParamAxes.plot([], [],
label='m%s' % (suffix))
self._h_plot, = self._activationParamAxes.plot([], [],
label='h%s' % (suffix))
self._n_plot, = self._activationParamAxes.plot([], [],
label='n%s' % (suffix))
self._plot_dict['m'].append(self._m_plot)
self._plot_dict['h'].append(self._h_plot)
self._plot_dict['n'].append(self._n_plot)
if self._showLegendAction.isChecked():
for axis in (self._plotFigure.axes + self._statePlotFigure.axes):
axis.legend()
def _updateAllPlots(self):
self._updatePlots()
self._updateStatePlot()
def _updatePlots(self):
if len(self.squid_setup.vm_table.vector) <= 0:
return
vm = numpy.asarray(self.squid_setup.vm_table.vector)
cmd = numpy.asarray(self.squid_setup.cmd_table.vector)
ik = numpy.asarray(self.squid_setup.ik_table.vector)
ina = numpy.asarray(self.squid_setup.ina_table.vector)
iclamp = numpy.asarray(self.squid_setup.iclamp_table.vector)
vclamp = numpy.asarray(self.squid_setup.vclamp_table.vector)
gk = numpy.asarray(self.squid_setup.gk_table.vector)
gna = numpy.asarray(self.squid_setup.gna_table.vector)
time_series = numpy.linspace(0, self._plotdt * len(vm), len(vm))
self._vm_plot.set_data(time_series, vm)
time_series = numpy.linspace(0, self._plotdt * len(cmd), len(cmd))
self._command_plot.set_data(time_series, cmd)
time_series = numpy.linspace(0, self._plotdt * len(ik), len(ik))
self._ik_plot.set_data(time_series, ik)
time_series = numpy.linspace(0, self._plotdt * len(ina), len(ina))
self._ina_plot.set_data(time_series, ina)
time_series = numpy.linspace(0, self._plotdt * len(iclamp),
len(iclamp))
self._iclamp_plot.set_data(time_series, iclamp)
time_series = numpy.linspace(0, self._plotdt * len(vclamp),
len(vclamp))
self._vclamp_plot.set_data(time_series, vclamp)
time_series = numpy.linspace(0, self._plotdt * len(gk), len(gk))
self._gk_plot.set_data(time_series, gk)
time_series = numpy.linspace(0, self._plotdt * len(gna), len(gna))
self._gna_plot.set_data(time_series, gna)
if self._autoscaleAction.isChecked():
for axis in self._plotFigure.axes:
axis.relim()
axis.set_autoscale_on(True)
else:
self._vm_axes.set_ylim(-20.0, 120.0)
self._g_axes.set_ylim(0.0, 0.5)
self._im_axes.set_ylim(-0.5, 0.5)
self._i_axes.set_ylim(-10, 10)
self._vm_axes.set_xlim(0.0, time_series[-1])
self._g_axes.set_xlim(0.0, time_series[-1])
self._im_axes.set_xlim(0.0, time_series[-1])
self._i_axes.set_xlim(0.0, time_series[-1])
self._plotCanvas.draw()
def _updateStatePlot(self):
if len(self.squid_setup.vm_table.vector) <= 0:
return
sx = str(self._stateplot_xvar_combo.currentText())
sy = str(self._stateplot_yvar_combo.currentText())
xdata = self.__get_stateplot_data(sx)
ydata = self.__get_stateplot_data(sy)
minlen = min(len(xdata), len(ydata))
self._state_plot.set_data(xdata[:minlen], ydata[:minlen])
self._statePlotAxes.set_xlabel(sx)
self._statePlotAxes.set_ylabel(sy)
if sx == 'V':
self._statePlotAxes.set_xlim(-20, 120)
else:
self._statePlotAxes.set_xlim(0, 1)
if sy == 'V':
self._statePlotAxes.set_ylim(-20, 120)
else:
self._statePlotAxes.set_ylim(0, 1)
self._activationParamAxes.set_xlim(0, self._runtime)
m = self.__get_stateplot_data('m')
n = self.__get_stateplot_data('n')
h = self.__get_stateplot_data('h')
time_series = numpy.linspace(0, self._plotdt * len(m), len(m))
self._m_plot.set_data(time_series, m)
time_series = numpy.linspace(0, self._plotdt * len(h), len(h))
self._h_plot.set_data(time_series, h)
time_series = numpy.linspace(0, self._plotdt * len(n), len(n))
self._n_plot.set_data(time_series, n)
if self._autoscaleAction.isChecked():
for axis in self._statePlotFigure.axes:
axis.relim()
axis.set_autoscale_on(True)
self._statePlotCanvas.draw()
def _runSlot(self):
if moose.isRunning():
print 'Stopping simulation in progress ...'
moose.stop()
self._runtime = float(str(self._runTimeEdit.text()))
self._overlayPlots(self._overlayAction.isChecked())
self._simdt = float(str(self._simTimeStepEdit.text()))
clampMode = None
singlePulse = True
if self._electronicsTab.currentWidget() == self._vClampCtrlBox:
clampMode = 'vclamp'
baseLevel = float(str(self._holdingVEdit.text()))
firstDelay = float(str(self._holdingTimeEdit.text()))
firstWidth = float(str(self._prePulseTimeEdit.text()))
firstLevel = float(str(self._prePulseVEdit.text()))
secondDelay = firstWidth
secondWidth = float(str(self._clampTimeEdit.text()))
secondLevel = float(str(self._clampVEdit.text()))
self._im_axes.set_ylim(-10.0, 10.0)
else:
clampMode = 'iclamp'
baseLevel = float(str(self._baseCurrentEdit.text()))
firstDelay = float(str(self._firstDelayEdit.text()))
firstWidth = float(str(self._firstPulseWidthEdit.text()))
firstLevel = float(str(self._firstPulseEdit.text()))
secondDelay = float(str(self._secondDelayEdit.text()))
secondLevel = float(str(self._secondPulseEdit.text()))
secondWidth = float(str(self._secondPulseWidthEdit.text()))
singlePulse = (self._pulseMode.currentIndex() == 0)
self._im_axes.set_ylim(-0.4, 0.4)
self.squid_setup.clamp_ckt.configure_pulses(baseLevel=baseLevel,
firstDelay=firstDelay,
firstWidth=firstWidth,
firstLevel=firstLevel,
secondDelay=secondDelay,
secondWidth=secondWidth,
secondLevel=secondLevel,
singlePulse=singlePulse)
if self._kConductanceToggle.isChecked():
self.squid_setup.squid_axon.specific_gK = 0.0
else:
self.squid_setup.squid_axon.specific_gK = SquidAxon.defaults[
'specific_gK']
if self._naConductanceToggle.isChecked():
self.squid_setup.squid_axon.specific_gNa = 0.0
else:
self.squid_setup.squid_axon.specific_gNa = SquidAxon.defaults[
'specific_gNa']
self.squid_setup.squid_axon.celsius = float(
str(self._temperatureEdit.text()))
self.squid_setup.squid_axon.K_out = float(str(self._kOutEdit.text()))
self.squid_setup.squid_axon.Na_out = float(str(self._naOutEdit.text()))
self.squid_setup.squid_axon.updateEk()
self.squid_setup.schedule(self._simdt, self._plotdt, clampMode)
# The following line is for use with Qthread
self.squid_setup.run(self._runtime)
self._updateAllPlots()
def _toggleDocking(self, on):
self._channelControlDock.setFloating(on)
self._electronicsDock.setFloating(on)
self._runControlDock.setFloating(on)
def _restoreDocks(self):
self._channelControlDock.setVisible(True)
self._electronicsDock.setVisible(True)
self._runControlDock.setVisible(True)
def _initActions(self):
self._runAction = QtGui.QAction(self.tr('Run'), self)
self._runAction.setShortcut(self.tr('F5'))
self._runAction.setToolTip('Run simulation (F5)')
self.connect(self._runAction, QtCore.SIGNAL('triggered()'),
self._runSlot)
self._resetToDefaultsAction = QtGui.QAction(
self.tr('Restore defaults'), self)
self._resetToDefaultsAction.setToolTip(
'Reset all settings to their default values')
self.connect(self._resetToDefaultsAction, QtCore.SIGNAL('triggered()'),
self._useDefaults)
self._showLegendAction = QtGui.QAction(self.tr('Display legend'), self)
self._showLegendAction.setCheckable(True)
self.connect(self._showLegendAction, QtCore.SIGNAL('toggled(bool)'),
self._showLegend)
self._showStatePlotAction = QtGui.QAction(self.tr('State plot'), self)
self._showStatePlotAction.setCheckable(True)
self._showStatePlotAction.setChecked(False)
self.connect(self._showStatePlotAction, QtCore.SIGNAL('toggled(bool)'),
self._statePlotWidget.setVisible)
self._autoscaleAction = QtGui.QAction(self.tr('Auto-scale plots'),
self)
self._autoscaleAction.setCheckable(True)
self._autoscaleAction.setChecked(False)
self.connect(self._autoscaleAction, QtCore.SIGNAL('toggled(bool)'),
self._autoscale)
self._overlayAction = QtGui.QAction('Overlay plots', self)
self._overlayAction.setCheckable(True)
self._overlayAction.setChecked(False)
self._dockAction = QtGui.QAction('Undock all', self)
self._dockAction.setCheckable(True)
self._dockAction.setChecked(False)
self.connect(self._dockAction, QtCore.SIGNAL('toggled(bool)'),
self._toggleDocking)
self._restoreDocksAction = QtGui.QAction('Show all', self)
self.connect(self._restoreDocksAction, QtCore.SIGNAL('triggered()'),
self._restoreDocks)
self._quitAction = QtGui.QAction(self.tr('&Quit'), self)
self._quitAction.setShortcut(self.tr('Ctrl+Q'))
self.connect(self._quitAction, QtCore.SIGNAL('triggered()'),
QtGui.qApp.closeAllWindows)
def _createRunToolBar(self):
self._simToolBar = self.addToolBar(self.tr('Simulation control'))
self._simToolBar.addAction(self._quitAction)
self._simToolBar.addAction(self._runAction)
self._simToolBar.addAction(self._resetToDefaultsAction)
self._simToolBar.addAction(self._dockAction)
self._simToolBar.addAction(self._restoreDocksAction)
def _createPlotToolBar(self):
self._plotToolBar = self.addToolBar(self.tr('Plotting control'))
self._plotToolBar.addAction(self._showLegendAction)
self._plotToolBar.addAction(self._autoscaleAction)
self._plotToolBar.addAction(self._overlayAction)
self._plotToolBar.addAction(self._showStatePlotAction)
self._plotToolBar.addAction(self._helpAction)
self._plotToolBar.addAction(self._helpBiophysicsAction)
def _showLegend(self, on):
if on:
for axis in (self._plotFigure.axes + self._statePlotFigure.axes):
axis.legend().set_visible(True)
else:
for axis in (self._plotFigure.axes + self._statePlotFigure.axes):
axis.legend().set_visible(False)
self._plotCanvas.draw()
self._statePlotCanvas.draw()
def _autoscale(self, on):
if on:
for axis in (self._plotFigure.axes + self._statePlotFigure.axes):
axis.relim()
axis.set_autoscale_on(True)
else:
for axis in self._plotFigure.axes:
axis.set_autoscale_on(False)
self._vm_axes.set_ylim(-20.0, 120.0)
self._g_axes.set_ylim(0.0, 0.5)
self._im_axes.set_ylim(-0.5, 0.5)
self._i_axes.set_ylim(-10, 10)
self._plotCanvas.draw()
self._statePlotCanvas.draw()
def _useDefaults(self):
self._runTimeEdit.setText('%g' % (self.defaults['runtime']))
self._simTimeStepEdit.setText('%g' % (self.defaults['simdt']))
self._overlayAction.setChecked(False)
self._naConductanceToggle.setChecked(False)
self._kConductanceToggle.setChecked(False)
self._kOutEdit.setText('%g' % (SquidGui.defaults['K_out']))
self._naOutEdit.setText('%g' % (SquidGui.defaults['Na_out']))
self._temperatureEdit.setText(
'%g' % (SquidGui.defaults['temperature'] - CELSIUS_TO_KELVIN))
self._holdingVEdit.setText('%g' %
(SquidGui.defaults['vclamp.holdingV']))
self._holdingTimeEdit.setText('%g' %
(SquidGui.defaults['vclamp.holdingT']))
self._prePulseVEdit.setText('%g' %
(SquidGui.defaults['vclamp.prepulseV']))
self._prePulseTimeEdit.setText('%g' %
(SquidGui.defaults['vclamp.prepulseT']))
self._clampVEdit.setText('%g' % (SquidGui.defaults['vclamp.clampV']))
self._clampTimeEdit.setText('%g' %
(SquidGui.defaults['vclamp.clampT']))
self._baseCurrentEdit.setText('%g' %
(SquidGui.defaults['iclamp.baseI']))
self._firstPulseEdit.setText('%g' %
(SquidGui.defaults['iclamp.firstI']))
self._firstDelayEdit.setText('%g' %
(SquidGui.defaults['iclamp.firstD']))
self._firstPulseWidthEdit.setText('%g' %
(SquidGui.defaults['iclamp.firstT']))
self._secondPulseEdit.setText('%g' %
(SquidGui.defaults['iclamp.secondI']))
self._secondDelayEdit.setText('%g' %
(SquidGui.defaults['iclamp.secondD']))
self._secondPulseWidthEdit.setText(
'%g' % (SquidGui.defaults['iclamp.secondT']))
self._pulseMode.setCurrentIndex(0)
def _onScroll(self, event):
if event.inaxes is None:
return
axes = event.inaxes
zoom = 0.0
if event.button == 'up':
zoom = -1.0
elif event.button == 'down':
zoom = 1.0
if zoom != 0.0:
self._plotNavigator.push_current()
axes.get_xaxis().zoom(zoom)
axes.get_yaxis().zoom(zoom)
self._plotCanvas.draw()
def closeEvent(self, event):
QtGui.qApp.closeAllWindows()
def _showBioPhysicsHelp(self):
print '11111'
self._createHelpMessage()
self._helpMessageText.setText(
'<html><p>%s</p><p>%s</p><p>%s</p><p>%s</p><p>%s</p></html>' %
(tooltip_Nernst, tooltip_Erest, tooltip_KChan, tooltip_NaChan,
tooltip_Im))
self._helpWindow.setVisible(True)
def _showRunningHelp(self):
self._createHelpMessage()
self._helpMessageText.setSource(QtCore.QUrl(self._helpBaseURL))
self._helpWindow.setVisible(True)
def _createHelpMessage(self):
if hasattr(self, '_helpWindow'):
return
self._helpWindow = QtGui.QWidget()
self._helpWindow.setWindowFlags(QtCore.Qt.Window)
layout = QtGui.QVBoxLayout()
self._helpWindow.setLayout(layout)
self._helpMessageArea = QtGui.QScrollArea()
self._helpMessageText = QtGui.QTextBrowser()
self._helpMessageText.setOpenExternalLinks(True)
self._helpMessageArea.setWidget(self._helpMessageText)
layout.addWidget(self._helpMessageText)
self._squidGuiPath = os.path.dirname(os.path.abspath(__file__))
self._helpBaseURL = os.path.join(self._squidGuiPath, 'help.html')
self._helpMessageText.setSource(QtCore.QUrl(self._helpBaseURL))
self._helpMessageText.setSizePolicy(QtGui.QSizePolicy.Expanding,
QtGui.QSizePolicy.Expanding)
self._helpMessageArea.setSizePolicy(QtGui.QSizePolicy.Expanding,
QtGui.QSizePolicy.Expanding)
self._helpMessageText.setMinimumSize(800, 600)
self._closeHelpAction = QtGui.QAction('Close', self)
self.connect(self._closeHelpAction, QtCore.SIGNAL('triggered()'),
self._helpWindow.close)
# Setting the close event so that the ``Help`` button is
# unchecked when the help window is closed
self._helpWindow.closeEvent = lambda event: self._helpAction.setChecked(
False)
self._helpTOCAction = QtGui.QAction('Help running demo', self)
self.connect(self._helpTOCAction, QtCore.SIGNAL('triggered()'),
self._jumpToHelpTOC)
# This panel is for putting two buttons using horizontal
# layout
panel = QtGui.QFrame()
panel.setFrameStyle(QtGui.QFrame.StyledPanel + QtGui.QFrame.Raised)
layout.addWidget(panel)
layout = QtGui.QHBoxLayout()
panel.setLayout(layout)
self._helpAction = QtGui.QAction('Help running', self)
self.connect(self._helpAction, QtCore.SIGNAL('triggered()'),
self._showRunningHelp)
self._helpBiophysicsAction = QtGui.QAction('Help biophysics', self)
self.connect(self._helpBiophysicsAction, QtCore.SIGNAL('triggered()'),
self._showBioPhysicsHelp)
self._helpTOCButton = QtGui.QToolButton()
self._helpTOCButton.setDefaultAction(self._helpTOCAction)
self._helpBiophysicsButton = QtGui.QToolButton()
self._helpBiophysicsButton.setDefaultAction(self._helpBiophysicsAction)
layout.addWidget(self._helpTOCButton)
layout.addWidget(self._helpBiophysicsButton)
self._closeHelpButton = QtGui.QToolButton()
self._closeHelpButton.setDefaultAction(self._closeHelpAction)
layout.addWidget(self._closeHelpButton)
def _jumpToHelpTOC(self):
self._helpMessageText.setSource(QtCore.QUrl(self._helpBaseURL))
