def createCentralWidget(self):
self._centralWidget = RunWidget.RunWidget(self.modelRoot)
self.plotWidgetContainer = PlotWidgetContainer(self.modelRoot)
self.geometry = neuroextractor.model(
moose.element(self.modelRoot + "/model"))
self.morphology = self.createMorphology(self.geometry)
self.morphology.set_compartment_order(
map(lambda x: x.path, self.compartmentOrder))
self.vms = np.empty(len(self.compartmentOrder),
dtype=np.float,
order='C')
self.ims = np.empty(len(self.compartmentOrder),
dtype=np.float,
order='C')
# self.visualizer.insertPlainText(pprint.pformat(self.geometry, indent = 4))
# self.visualizer = QTextEdit()#NeuroKitVisualizer(self.modelRoot)
self.visualizer = MorphologySimulator(self.morphology, 1000, 1000,
self.plugin)
# self.scheduler = self.getSchedulingDockWidget().widget()
# self._centralWidget.setChildWidget(self.scheduler, False, 0,0,1,-1)
self.visualizer.setGeometry(0, 0, 800, 600)
self.visualizer.show()
# self.visualizer.start()
self._centralWidget.setChildWidget(self.visualizer, False, 0, 0, -1, 1)
self._centralWidget.setChildWidget(self.plotWidgetContainer, False, 0,
1, -1, 1)
self._centralWidget.setPlotWidgetContainer(self.plotWidgetContainer)
# label = QLabel("Aviral Goel")
# self._centralWidget.setChildWidget(label, False, 0, 0)
# self._centralWidget.setWindowTitle("Aviral Goel")
# self.scheduler = self.getSchedulingDockWidget().widget()
# self.scheduler.runner.update.connect(self.kkitRunView.getCentralWidget().changeBgSize)
# self.scheduler.runner.resetAndRun.connect(self.kkitRunView.getCentralWidget().resetColor)
self.schedular = self.getSchedulingDockWidget().widget()
self.schedular.runner.simulationProgressed.connect(self.update)
self.schedular.runner.simulationReset.connect(self.reset)
self.schedular.preferences.getView().setCurrentIndex(1)
self.schedular.preferences.getView(
).electricalBaseColorDialog.colorSelected.connect(
lambda x: self.reset())
self.schedular.preferences.getView(
).electricalPeakColorDialog.colorSelected.connect(
lambda x: self.reset())
self.schedular.preferences.getView(
).electricalBackgroundColorDialog.colorSelected.connect(
lambda x: self.reset())
self.schedular.preferences.getView(
).electricalPeakMembraneVoltage.editingFinished.connect(self.reset)
self.schedular.preferences.getView(
).electricalBaseMembraneVoltage.editingFinished.connect(self.reset)
# print("getting central widget")
# self._centralWidget.show()
# print(self.schedular.runner._updateInterval)
self.reset()
return self._centralWidget
def createCentralWidget(self):
self._centralWidget = RunWidget.RunWidget(self.modelRoot)
self.plotWidgetContainer = PlotWidgetContainer(self.modelRoot)
self.geometry = neuroextractor.model(moose.element(self.modelRoot + "/model"))
self.morphology = self.createMorphology(self.geometry)
self.morphology.set_compartment_order(
map(lambda x : x.path, self.compartmentOrder)
)
self.vms = np.empty(len(self.compartmentOrder), dtype=np.float, order='C')
self.ims = np.empty(len(self.compartmentOrder), dtype=np.float, order='C')
# self.visualizer.insertPlainText(pprint.pformat(self.geometry, indent = 4))
# self.visualizer = QTextEdit()#NeuroKitVisualizer(self.modelRoot)
self.visualizer = MorphologySimulator(self.morphology, 1000, 1000, self.plugin)
# self.scheduler = self.getSchedulingDockWidget().widget()
# self._centralWidget.setChildWidget(self.scheduler, False, 0,0,1,-1)
self.visualizer.setGeometry( 0, 0, 800, 600 )
self.visualizer.show()
# self.visualizer.start()
self._centralWidget.setChildWidget(self.visualizer, False, 0, 0,-1,1)
self._centralWidget.setChildWidget(self.plotWidgetContainer, False, 0, 1,-1,1)
self._centralWidget.setPlotWidgetContainer(self.plotWidgetContainer)
# label = QLabel("Aviral Goel")
# self._centralWidget.setChildWidget(label, False, 0, 0)
# self._centralWidget.setWindowTitle("Aviral Goel")
# self.scheduler = self.getSchedulingDockWidget().widget()
# self.scheduler.runner.update.connect(self.kkitRunView.getCentralWidget().changeBgSize)
# self.scheduler.runner.resetAndRun.connect(self.kkitRunView.getCentralWidget().resetColor)
self.schedular = self.getSchedulingDockWidget().widget()
self.schedular.runner.simulationProgressed.connect(self.update)
self.schedular.runner.simulationReset.connect(self.reset)
self.schedular.preferences.getView().setCurrentIndex(1)
self.schedular.preferences.getView().electricalBaseColorDialog.colorSelected.connect(lambda x: self.reset())
self.schedular.preferences.getView().electricalPeakColorDialog.colorSelected.connect(lambda x: self.reset())
self.schedular.preferences.getView().electricalBackgroundColorDialog.colorSelected.connect(lambda x: self.reset())
self.schedular.preferences.getView().electricalPeakMembraneVoltage.editingFinished.connect(self.reset)
self.schedular.preferences.getView().electricalBaseMembraneVoltage.editingFinished.connect(self.reset)
# print("getting central widget")
# self._centralWidget.show()
# print(self.schedular.runner._updateInterval)
self.reset()
return self._centralWidget
class NeuroKitRunner(RunView):
def __init__(self, modelRoot, plugin,*args):
# super(NeuroKitRunner, self).__init__(self, moose.element(modelRoot), plugin, *args)
RunView.__init__(self, modelRoot, plugin, *args)
# RunBase.__init__(self, plugin)
self.modelRoot = modelRoot
self.plugin = plugin
# self.geometry = None
# self.morphology = None
self.schedular = self.getSchedulingDockWidget().widget()
def setBaseColor(self, color):
self.morphology.set_initial_color( color[0] / 255.0
, color[1] / 255.0
, color[2] / 255.0
, color[3] / 255.0
)
def setPeakColor(self, color):
self.morphology.set_final_color( color[0] / 255.0
, color[1] / 255.0
, color[2] / 255.0
, color[3] / 255.0
)
def setBackgroundColor(self, color):
self.visualizer.set_background_color( color[0] / 255.0
, color[1] / 255.0
, color[2] / 255.0
, color[3] / 255.0
)
def setBaseVm(self, vm):
self.morphology.set_base_membrane_voltage(vm)
def setPeakVm(self, vm):
self.morphology.set_peak_membrane_voltage(vm)
def createCentralWidget(self):
self._centralWidget = RunWidget.RunWidget(self.modelRoot)
self.plotWidgetContainer = PlotWidgetContainer(self.modelRoot)
self.geometry = neuroextractor.model(moose.element(self.modelRoot + "/model"))
self.morphology = self.createMorphology(self.geometry)
self.morphology.set_compartment_order(
map(lambda x : x.path, self.compartmentOrder)
)
self.vms = np.empty(len(self.compartmentOrder), dtype=np.float, order='C')
self.ims = np.empty(len(self.compartmentOrder), dtype=np.float, order='C')
# self.visualizer.insertPlainText(pprint.pformat(self.geometry, indent = 4))
# self.visualizer = QTextEdit()#NeuroKitVisualizer(self.modelRoot)
self.visualizer = MorphologySimulator(self.morphology, 1000, 1000, self.plugin)
# self.scheduler = self.getSchedulingDockWidget().widget()
# self._centralWidget.setChildWidget(self.scheduler, False, 0,0,1,-1)
self.visualizer.setGeometry( 0, 0, 800, 600 )
self.visualizer.show()
# self.visualizer.start()
self._centralWidget.setChildWidget(self.visualizer, False, 0, 0,-1,1)
self._centralWidget.setChildWidget(self.plotWidgetContainer, False, 0, 1,-1,1)
self._centralWidget.setPlotWidgetContainer(self.plotWidgetContainer)
# label = QLabel("Aviral Goel")
# self._centralWidget.setChildWidget(label, False, 0, 0)
# self._centralWidget.setWindowTitle("Aviral Goel")
# self.scheduler = self.getSchedulingDockWidget().widget()
# self.scheduler.runner.update.connect(self.kkitRunView.getCentralWidget().changeBgSize)
# self.scheduler.runner.resetAndRun.connect(self.kkitRunView.getCentralWidget().resetColor)
self.schedular = self.getSchedulingDockWidget().widget()
self.schedular.runner.simulationProgressed.connect(self.update)
self.schedular.runner.simulationReset.connect(self.reset)
self.schedular.preferences.getView().setCurrentIndex(1)
self.schedular.preferences.getView().electricalBaseColorDialog.colorSelected.connect(lambda x: self.reset())
self.schedular.preferences.getView().electricalPeakColorDialog.colorSelected.connect(lambda x: self.reset())
self.schedular.preferences.getView().electricalBackgroundColorDialog.colorSelected.connect(lambda x: self.reset())
self.schedular.preferences.getView().electricalPeakMembraneVoltage.editingFinished.connect(self.reset)
self.schedular.preferences.getView().electricalBaseMembraneVoltage.editingFinished.connect(self.reset)
# print("getting central widget")
# self._centralWidget.show()
# print(self.schedular.runner._updateInterval)
self.reset()
return self._centralWidget
def update(self, time):
# print("Update called => ", time)
# print("Update called")
# for neuron_id in self.geometry["neurons"]:
# neuron = self.geometry["neurons"][neuron_id]
# for compartment_id in neuron["compartments"]:
# voltage = neuron["compartments"][compartment_id]["object"].Vm
# print(compartment_id + " => " + str(voltage))
# self.visualizer.
self.updateVms()
# self.updateIms()
# self.visualizer.next()
# print(self.vms)
def updateVms(self):
for i in range(0, len(self.compartmentOrder)):
self.vms[i] = self.compartmentOrder[i].Vm
self.morphology.set_membrane_voltages(self.vms)
def updateIms(self):
for i in range(0, len(self.compartmentOrder)):
self.ims[i] = self.compartmentOrder[i].Im
def reset(self):
# print(" => reset called")
prefs = preferences.getElectricalPreferences()
self.setPeakColor(prefs["visualization"]["peak-color"])
self.setBaseColor(prefs["visualization"]["base-color"])
self.setBackgroundColor(prefs["visualization"]["background-color"])
self.setBaseVm(prefs["visualization"]["base-membrane-voltage"])
self.setPeakVm(prefs["visualization"]["peak-membrane-voltage"])
self.updateVms()
# self.visualizer.next()
# self.updateIms()
# self.ims[i] = self.compartmentOrder[i].Im
# print(self.vms)
# self.morphology.resetVms(self.vms)
# self.morphology.resetIms(self.ims)
def createMorphology(self, geometry):
# import json
# f = open("/home/aviral/purkinje.json", "w")
# f.write(json.dumps(geometry, indent=4))
# f.close()
# morphology = moogli.Morphology("morph")
# morphology.add_compartment( "a"
# , "b", 1.0, 1.0, 1.0, 1.0, 2.0, 2.0, 2.0, 2.0)
# morphology.add_compartment( "c"
# , "b"
# , 3.0, 3.0, 3.0, 3.0, 4.0, 4.0, 4.0, 4.0)
morphology = moogli.Morphology("morph", 1)
self.compartmentOrder = []
for neuron_id in geometry["neurons"]:
neuron = geometry["neurons"][neuron_id]
for compartment_id in neuron["compartments"]:
compartment = neuron["compartments"][compartment_id]
# print( compartment_id
# , neuron_id
# , compartment["proximal"]["x"]
# , compartment["proximal"]["y"]
# , compartment["proximal"]["z"]
# , compartment["diameter"]
# , compartment["distal"]["x"]
# , compartment["distal"]["y"]
# , compartment["distal"]["z"]
# , compartment["diameter"]
# )
self.compartmentOrder.append(compartment["object"])
morphology.add_compartment( compartment_id
, neuron_id
, compartment["proximal"]["x"] * 10000000
, compartment["proximal"]["y"] * 10000000
, compartment["proximal"]["z"] * 10000000
, compartment["diameter"] * 10000000
, compartment["distal"]["x"] * 10000000
, compartment["distal"]["y"] * 10000000
, compartment["distal"]["z"] * 10000000
, compartment["diameter"] * 10000000
)
return morphology
def getCentralWidget(self):
if self._centralWidget is None:
self.createCentralWidget()
# self._centralWidget.show()
return self._centralWidget
class NeuroKitRunner(RunView):
def __init__(self, modelRoot, plugin,*args):
# super(NeuroKitRunner, self).__init__(self, moose.element(modelRoot), plugin, *args)
RunView.__init__(self, modelRoot, plugin, *args)
# RunBase.__init__(self, plugin)
self.modelRoot = modelRoot
self.plugin = plugin
# self.geometry = None
# self.morphology = None
self.schedular = self.getSchedulingDockWidget().widget()
def setBaseColor(self, color):
self.morphology.set_initial_color( color[0] / 255.0
, color[1] / 255.0
, color[2] / 255.0
, color[3] / 255.0
)
def setPeakColor(self, color):
self.morphology.set_final_color( color[0] / 255.0
, color[1] / 255.0
, color[2] / 255.0
, color[3] / 255.0
)
def setBackgroundColor(self, color):
self.visualizer.set_background_color( color[0] / 255.0
, color[1] / 255.0
, color[2] / 255.0
, color[3] / 255.0
)
def setBaseVm(self, vm):
self.morphology.set_base_membrane_voltage(vm)
def setPeakVm(self, vm):
self.morphology.set_peak_membrane_voltage(vm)
def createCentralWidget(self):
self._centralWidget = RunWidget.RunWidget(self.modelRoot)
self.plotWidgetContainer = PlotWidgetContainer(self.modelRoot)
self.geometry = neuroextractor.model(moose.element(self.modelRoot + "/model"))
self.morphology = self.createMorphology(self.geometry)
self.morphology.set_compartment_order(
map(lambda x : x.path, self.compartmentOrder)
)
self.vms = np.empty(len(self.compartmentOrder), dtype=np.float, order='C')
self.ims = np.empty(len(self.compartmentOrder), dtype=np.float, order='C')
# self.visualizer.insertPlainText(pprint.pformat(self.geometry, indent = 4))
# self.visualizer = QTextEdit()#NeuroKitVisualizer(self.modelRoot)
self.visualizer = MorphologySimulator(self.morphology, 1000, 1000, self.plugin)
# self.scheduler = self.getSchedulingDockWidget().widget()
# self._centralWidget.setChildWidget(self.scheduler, False, 0,0,1,-1)
self.visualizer.setGeometry( 0, 0, 800, 600 )
self.visualizer.show()
# self.visualizer.start()
self._centralWidget.setChildWidget(self.visualizer, False, 0, 0,-1,1)
self._centralWidget.setChildWidget(self.plotWidgetContainer, False, 0, 1,-1,1)
self._centralWidget.setPlotWidgetContainer(self.plotWidgetContainer)
# label = QLabel("Aviral Goel")
# self._centralWidget.setChildWidget(label, False, 0, 0)
# self._centralWidget.setWindowTitle("Aviral Goel")
# self.scheduler = self.getSchedulingDockWidget().widget()
# self.scheduler.runner.update.connect(self.kkitRunView.getCentralWidget().changeBgSize)
# self.scheduler.runner.resetAndRun.connect(self.kkitRunView.getCentralWidget().resetColor)
self.schedular = self.getSchedulingDockWidget().widget()
self.schedular.runner.simulationProgressed.connect(self.update)
self.schedular.runner.simulationReset.connect(self.reset)
self.schedular.preferences.getView().setCurrentIndex(1)
self.schedular.preferences.getView().electricalBaseColorDialog.colorSelected.connect(lambda x: self.reset())
self.schedular.preferences.getView().electricalPeakColorDialog.colorSelected.connect(lambda x: self.reset())
self.schedular.preferences.getView().electricalBackgroundColorDialog.colorSelected.connect(lambda x: self.reset())
self.schedular.preferences.getView().electricalPeakMembraneVoltage.editingFinished.connect(self.reset)
self.schedular.preferences.getView().electricalBaseMembraneVoltage.editingFinished.connect(self.reset)
# print("getting central widget")
# self._centralWidget.show()
# print(self.schedular.runner._updateInterval)
self.reset()
return self._centralWidget
def update(self, time):
# print("Update called => ", time)
# print("Update called")
# for neuron_id in self.geometry["neurons"]:
# neuron = self.geometry["neurons"][neuron_id]
# for compartment_id in neuron["compartments"]:
# voltage = neuron["compartments"][compartment_id]["object"].Vm
# print(compartment_id + " => " + str(voltage))
# self.visualizer.
self.updateVms()
# self.updateIms()
# self.visualizer.next()
# print(self.vms)
def updateVms(self):
for i in range(0, len(self.compartmentOrder)):
self.vms[i] = self.compartmentOrder[i].Vm
self.morphology.set_membrane_voltages(self.vms)
def updateIms(self):
for i in range(0, len(self.compartmentOrder)):
self.ims[i] = self.compartmentOrder[i].Im
def reset(self):
# print(" => reset called")
prefs = preferences.getElectricalPreferences()
self.setPeakColor(prefs["visualization"]["peak-color"])
self.setBaseColor(prefs["visualization"]["base-color"])
self.setBackgroundColor(prefs["visualization"]["background-color"])
self.setBaseVm(prefs["visualization"]["base-membrane-voltage"])
self.setPeakVm(prefs["visualization"]["peak-membrane-voltage"])
self.updateVms()
# self.visualizer.next()
# self.updateIms()
# self.ims[i] = self.compartmentOrder[i].Im
# print(self.vms)
# self.morphology.resetVms(self.vms)
# self.morphology.resetIms(self.ims)
def createMorphology(self, geometry):
# import json
# f = open("/home/aviral/purkinje.json", "w")
# f.write(json.dumps(geometry, indent=4))
# f.close()
# morphology = moogli.Morphology("morph")
# morphology.add_compartment( "a"
# , "b", 1.0, 1.0, 1.0, 1.0, 2.0, 2.0, 2.0, 2.0)
# morphology.add_compartment( "c"
# , "b"
# , 3.0, 3.0, 3.0, 3.0, 4.0, 4.0, 4.0, 4.0)
morphology = moogli.Morphology("morph", 1)
self.compartmentOrder = []
for neuron_id in geometry["neurons"]:
neuron = geometry["neurons"][neuron_id]
for compartment_id in neuron["compartments"]:
compartment = neuron["compartments"][compartment_id]
# print( compartment_id
# , neuron_id
# , compartment["proximal"]["x"]
# , compartment["proximal"]["y"]
# , compartment["proximal"]["z"]
# , compartment["diameter"]
# , compartment["distal"]["x"]
# , compartment["distal"]["y"]
# , compartment["distal"]["z"]
# , compartment["diameter"]
# )
self.compartmentOrder.append(compartment["object"])
morphology.add_compartment( compartment_id
, neuron_id
, compartment["proximal"]["x"] * 10000000
, compartment["proximal"]["y"] * 10000000
, compartment["proximal"]["z"] * 10000000
, compartment["diameter"] * 10000000
, compartment["distal"]["x"] * 10000000
, compartment["distal"]["y"] * 10000000
, compartment["distal"]["z"] * 10000000
, compartment["diameter"] * 10000000
)
return morphology
def getCentralWidget(self):
if self._centralWidget is None:
self.createCentralWidget()
# self._centralWidget.show()
return self._centralWidget
