def make_fF_Curve(self,
projFile,
simulator,
simConfig,
nTrains,
simDuration,
analyseStartTime, analyseStopTime,
analyseThreshold,
maxNumSimultaneousSims = 4):
# Load neuroConstruct project
print "Loading project from file: " + projFile.getAbsolutePath()+", exists: "+ str(projFile.exists())
pm = ProjectManager()
self.myProject = pm.loadProject(projFile)
self.simulator = simulator
simConfig = self.myProject.simConfigInfo.getSimConfig(simConfig)
simConfig.setSimDuration(simDuration)
pm.doGenerate(simConfig.getName(), self.neuroConstructSeed)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: "+str(simConfig)
time.sleep(2)
numGenerated = self.myProject.generatedCellPositions.getNumberInAllCellGroups()
print "Number of cells generated: " + str(numGenerated)
simReferences = {}
if numGenerated > 0:
print "Generating scripts for simulator: %s..."%simulator
if simulator == 'NEURON':
self.myProject.neuronFileManager.setQuitAfterRun(1) # Remove this line to leave the NEURON sim windows open after finishing
self.myProject.neuronSettings.setCopySimFiles(1) # 1 copies hoc/mod files to PySim_0 etc. and will allow multiple sims to run at once
self.myProject.neuronSettings.setGraphicsMode(0) # 0 hides graphs during execution
if simulator == 'GENESIS':
self.myProject.genesisFileManager.setQuitAfterRun(1) # Remove this line to leave the NEURON sim windows open after finishing
self.myProject.genesisSettings.setCopySimFiles(1) # 1 copies hoc/mod files to PySim_0 etc. and will allow multiple sims to run at once
self.myProject.genesisSettings.setGraphicsMode(0) # 0 hides graphs during execution
currentTrain = 0
ADD_TO_START_FINITIALIZE = self.myProject.neuronSettings.getNativeBlock(NativeCodeLocation.START_FINITIALIZE)
ADD_TO_RECORD_I = self.myProject.neuronSettings.getNativeBlock(NativeCodeLocation.AFTER_SIMULATION)
while currentTrain <= nTrains:
while (len(self.simsRunning)>=maxNumSimultaneousSims):
print "Sims currently running: "+str(self.simsRunning)
print "Waiting..."
time.sleep(3) # wait a while...
self.updateSimsRunning()
simRef = "PySim_"+str(currentTrain)
print "Going to run simulation: "+simRef
######## Adjusting the amplitude of the Voltage clamp ###############
TEXT_BEFORE_CREATION = """objref vector, gTrainFile\n""" + "objectvar clamp\n"
### TEXT_BEFORE_INIT = "GranuleCell_mod_tonic[0].Soma {\n" + "clampobj = new VClamp(0.5)\n" + "clampobj.dur[0] = " + str(stimDur) + "\n" + "clampobj.amp[0] = " + str(stimAmp) + "\n" + "}\n" # This should do the trick
TEXT_START_FINITIALIZE = "\n" + "gTrainFile = new File() \n" + "vector = new Vector(100000) \n" + "access GranuleCell_mod_tonic[0].Soma \n" + "clamp = new SEClamp(0.5) \n" + "clamp.amp1 = 0 \n" + "clamp.dur1 = 1e9 \n" + """gTrainFile.ropen("E:/neuroConstruct/models/Dan_GranCell/gTrains_nS/gAMPA_""" + str(currentTrain) + """.txt") \n""" + "vector.scanf(gTrainFile) \n" + "gTrainFile.close \n" + "for i = 0, vector.size() -1 { \n" + " if (vector.x[i] <= 0) { \n" + " vector.x[i] = 1e-20 \n" + " } \n" + " } \n" + "for i = 0, vector.size() -1 { \n" + " vector.x[i] = ( 1 / vector.x[i] ) * 1000 \n" + " } \n" + "vector.play(&clamp.rs, 0.03) \n" # This
TEXT_START_FINITIALIZE = TEXT_START_FINITIALIZE + ADD_TO_START_FINITIALIZE
TEXT_TO_RECORD_I = """// currently not used \n"""
TEXT_TO_RECORD_I = TEXT_TO_RECORD_I + ADD_TO_RECORD_I
self.myProject.neuronSettings.setNativeBlock(NativeCodeLocation.BEFORE_CELL_CREATION, TEXT_BEFORE_CREATION)
self.myProject.neuronSettings.setNativeBlock(NativeCodeLocation.START_FINITIALIZE, TEXT_START_FINITIALIZE)
self.myProject.neuronSettings.setNativeBlock(NativeCodeLocation.AFTER_SIMULATION, TEXT_TO_RECORD_I)
print "Next Train: "+ str(currentTrain)
self.myProject.simulationParameters.setReference(simRef)
if simulator == "NEURON":
self.myProject.neuronFileManager.generateTheNeuronFiles(simConfig,
None,
NeuronFileManager.RUN_HOC,
self.simulatorSeed)
print "Generated NEURON files for: "+simRef
compileProcess = ProcessManager(self.myProject.neuronFileManager.getMainHocFile())
compileSuccess = compileProcess.compileFileWithNeuron(0,0)
print "Compiled NEURON files for: "+simRef
if compileSuccess:
pm.doRunNeuron(simConfig)
print "Set running simulation: "+simRef
self.simsRunning.append(simRef)
if simulator == "GENESIS":
compartmentalisation = GenesisCompartmentalisation()
self.myProject.genesisFileManager.generateTheGenesisFiles(simConfig,
None,
compartmentalisation,
self.simulatorSeed)
print "Generated GENESIS files for: "+simRef
pm.doRunGenesis(simConfig)
print "Set running simulation: "+simRef
self.simsRunning.append(simRef)
time.sleep(1) # Wait for sim to be kicked off
simReferences[simRef] = currentTrain
currentTrain = currentTrain + 1
print
print "Finished running "+str(len(simReferences))+" simulations for project "+ projFile.getAbsolutePath()
print "These can be loaded and replayed in the previous simulation browser in the GUI"
print
while (len(self.simsRunning)>0):
print "Sims currently running: "+str(self.simsRunning)
print "Waiting..."
time.sleep(4) # wait a while...
self.updateSimsRunning()
#simReferences = {'PySim_0.3':0.3,'PySim_0.4':0.4,'PySim_0.5':0.5}
plotFrameFf = PlotManager.getPlotterFrame("F-f curve from project: "+str(self.myProject.getProjectFile())+" on "+simulator , 1, 1)
plotFrameVolts = PlotManager.getPlotterFrame("VoltageTraces from project: "+str(self.myProject.getProjectFile())+" on "+simulator , 1, 1)
plotFrameFf.setViewMode(PlotCanvas.INCLUDE_ORIGIN_VIEW)
info = "F-f curve for Simulation Configuration: "+str(simConfig)
dataSet = DataSet(info, info, "Hz", "Hz", "Input_Freq", "Output_Freq")
dataSet.setGraphFormat(PlotCanvas.USE_CIRCLES_FOR_PLOT)
simList = simReferences.keys()
simList.sort()
traininfos = open("E:/neuroConstruct/models/Dan_GranCell/gAMPA_traininfo.txt")
train_info_list = traininfos.readlines()
currentTrain = 0
for sim in simList:
simDir = File(projFile.getParentFile(), "E:/neuroConstruct/models/Dan_GranCell/simulations/"+sim)
print
print "--- Reloading data from simulation in directory: %s"%simDir.getCanonicalPath()
try:
simData = SimulationData(simDir)
simData.initialise()
print "Data loaded: "
print simData.getAllLoadedDataStores()
times = simData.getAllTimes()
cellSegmentRef = simConfig.getCellGroups().get(0)+"_0"
volts = simData.getVoltageAtAllTimes(cellSegmentRef)
time.sleep(2)
traceInfo = "Voltage at: %s in simulation: %s"%(cellSegmentRef, sim)
dataSetV = DataSet(traceInfo, traceInfo, "ms", "mV", "Time", "Membrane Potential")
Spike_List = []
Spike_List.append(0.00)
for i in range(len(times)):
dataSetV.addPoint(times[i], volts[i])
for i in range(len(times)):
if (volts[i] > 0.0):
if (times[i] - Spike_List[len(Spike_List)-1] > 0.50):
Spike_List.append(times[i])
Spike_List.remove(0.00)
plotFrameVolts.addDataSet(dataSetV)
spikeTimes = SpikeAnalyser.getSpikeTimes(volts, times, analyseThreshold, analyseStartTime, analyseStopTime)
currentTrain_Freq = float(train_info_list[currentTrain-1])
print "Number of spikes in sim %s: %i"%(sim, len(spikeTimes))
avgFreq = 0
if len(Spike_List)>0:
avgFreq = 1000.0 / ((Spike_List[len(Spike_List)-1] - Spike_List[0]) / (len(Spike_List) -1))
dataSet.addPoint(currentTrain_Freq,avgFreq)
currentTrain = currentTrain + 1
except:
print "Error analysing simulation data from: %s"%simDir.getCanonicalPath()
print sys.exc_info()[0]
plotFrameFf.addDataSet(dataSet)
def testAll(argv=None):
if argv is None:
argv = sys.argv
print "Loading project from "+ projFile.getCanonicalPath()
simManager = nc.SimulationManager(projFile,
numConcurrentSims = numConcurrentSims,
verbose = verbose)
### Change num in each cell group
simManager.project.cellGroupsInfo.getCellPackingAdapter("lg1").setMaxNumberCells(numCells1)
simManager.project.cellGroupsInfo.getCellPackingAdapter("lg2").setMaxNumberCells(numCells2)
allSims = simManager.runMultipleSims(simConfigs = simConfigs,
simDt = simDt,
simDuration = simDuration,
simulators = simulators,
runInBackground = runInBackground,
varTimestepNeuron = varTimestepNeuron,
mpiConfigs = mpiConfigs,
suggestedRemoteRunTime = suggestedRemoteRunTime,
simRefGlobalPrefix = simAllPrefix,
runSims = runSims,
maxElecLens = multipleRuns,
saveAsHdf5 = saveAsHdf5,
saveOnlySpikes = saveOnlySpikes,
runMode = runMode)
while (len(simManager.allRunningSims)>0):
print "Waiting for the following sims to finish: "+str(simManager.allRunningSims)
time.sleep(5) # wait a while...
simManager.updateSimsRunning()
times = []
procNums = []
for sim in allSims:
simDir = File(projFile.getParentFile(), "/simulations/"+sim)
try:
simData = SimulationData(simDir)
simData.initialise()
simTime = simData.getSimulationProperties().getProperty("RealSimulationTime")
print "Simulation: %s took %s seconds"%(sim, simTime)
times.append(float(simTime))
paraConfig = simData.getSimulationProperties().getProperty("Parallel configuration")
print paraConfig
numProc = int(paraConfig[max(paraConfig.find(" host, ")+7, paraConfig.find(" hosts, ")+8):paraConfig.find(" processor")])
procNums.append(numProc)
except:
print "Error analysing simulation data from: %s"%simDir.getCanonicalPath()
print sys.exc_info()
print times
print procNums
'''
import matplotlib.pyplot as plt
lines = plt.loglog(times, procNums, 'r:')
plt.ylabel('Simulation time')
plt.xlabel('Number of processors')
plt.show()'''
from ucl.physiol.neuroconstruct.gui.plotter import PlotManager
from ucl.physiol.neuroconstruct.gui.plotter import PlotCanvas
from ucl.physiol.neuroconstruct.dataset import DataSet
plotFrame = PlotManager.getPlotterFrame("Time for simulation run on different numbers of processors", 0, 1)
plotFrame.setViewMode(PlotCanvas.INCLUDE_ORIGIN_VIEW)
info = "Simulation times for: "+str(procNums)
dataSet = DataSet(info, info, "#", "s", "Number of processors", "Simulation time")
dataSet.setGraphFormat(PlotCanvas.USE_CIRCLES_FOR_PLOT)
for i in range(len(times)):
#dataSet.addPoint(procNums[i],times[i]*procNums[i])
dataSet.addPoint(procNums[i],times[i])
plotFrame.addDataSet(dataSet)
analyseStopTime = 600
analyseThreshold = -20 # mV
spikeTimes_nC = SpikeAnalyser.getSpikeTimes(voltages_nC, times_nC, analyseThreshold, analyseStartTime, analyseStopTime)
print "neuroConcsturct spike times:"
print spikeTimes_nC
spikeTimes_original = SpikeAnalyser.getSpikeTimes(voltages_original, times_original, analyseThreshold, analyseStartTime, analyseStopTime)
print "modelDB spike times:"
print spikeTimes_original
plotFrame = PlotManager.getPlotterFrame("test model: "+str(myProject.getProjectFile()) , 1, 1)
plotFrame.setViewMode(PlotCanvas.INCLUDE_ORIGIN_VIEW)
info = "modelDB vs nC: "+str(simConfig)
dataSet_nC = DataSet(info, info, "ms", "nC", "time", "nC")
dataSet_nC.setGraphFormat(PlotCanvas.USE_CIRCLES_FOR_PLOT)
for t1 in spikeTimes_nC:
dataSet_nC.addPoint(t1,1)
dataSet_original = DataSet(info, info, "ms", "modelDB", "time", "modelDB")
dataSet_original.setGraphFormat(PlotCanvas.USE_CIRCLES_FOR_PLOT)
for t2 in spikeTimes_original:
dataSet_original.addPoint(t2,1)
plotFrame.addDataSet(dataSet_nC)
plotFrame.addDataSet(dataSet_original)
test = 0
if len(spikeTimes_nC) == len(spikeTimes_original):
test = 1
def testAll(argv=None):
if argv is None:
argv = sys.argv
print "Loading project from "+ projFile.getCanonicalPath()
simManager = nc.SimulationManager(projFile,
numConcurrentSims = numConcurrentSims,
verbose = verbose)
### Change num in each cell group
densityGrC = 1.90e6
densityMF = 6.6e5
densityGoC = 4607
totDens = densityGrC + densityMF + densityGoC
numMF = int(targetNum * densityMF/totDens)
numGoC = int(targetNum * densityGoC/totDens)
numGrC = targetNum - numMF - numGoC
vol = targetNum/(totDens*1e-9)
height = 150
side = math.sqrt(vol/height)
info = "Number in %fx%fx%i box (vol: %f mm^3): GrC: %i, MF: %i, GoC: %i, Total: %i"%(side, side, height, vol*1e-9,numGrC, numMF,numGoC, (numGrC +numMF +numGoC))
print info
SimulationsInfo.addExtraSimProperty("summary", info)
region3D = simManager.project.regionsInfo.getRegionObject("TestGranCellVolume")
region3D.setParameter(region3D.WIDTH_PARAM, side)
region3D.setParameter(region3D.HEIGHT_PARAM, height)
region3D.setParameter(region3D.DEPTH_PARAM, side)
simManager.project.cellGroupsInfo.getCellPackingAdapter("TestScalingGrC").setMaxNumberCells(numGrC)
simManager.project.cellGroupsInfo.getCellPackingAdapter("TestScalingGoC").setMaxNumberCells(numGoC)
simManager.project.cellGroupsInfo.getCellPackingAdapter("TestScalingMF").setMaxNumberCells(numMF)
######simManager.project.cellGroupsInfo.getCellPackingAdapter("lg2").setMaxNumberCells(numCells2)
allSims = simManager.runMultipleSims(simConfigs = simConfigs,
simDt = simDt,
simDuration = simDuration,
simulators = simulators,
runInBackground = runInBackground,
varTimestepNeuron = varTimestepNeuron,
mpiConfigs = mpiConfigs,
suggestedRemoteRunTime = suggestedRemoteRunTime,
simRefGlobalPrefix = simAllPrefix,
runSims = runSims,
maxElecLens = multipleRuns,
saveAsHdf5 = saveAsHdf5,
saveOnlySpikes = saveOnlySpikes,
runMode = runMode)
while (len(simManager.allRunningSims)>0):
print "Waiting for the following sims to finish: "+str(simManager.allRunningSims)
time.sleep(5) # wait a while...
simManager.updateSimsRunning()
times = []
procNums = []
for sim in allSims:
simDir = File(projFile.getParentFile(), "/simulations/"+sim)
try:
simData = SimulationData(simDir)
simData.initialise()
simTime = simData.getSimulationProperties().getProperty("RealSimulationTime")
print "Simulation: %s took %s seconds"%(sim, simTime)
times.append(float(simTime))
paraConfig = simData.getSimulationProperties().getProperty("Parallel configuration")
print paraConfig
numProc = int(paraConfig[max(paraConfig.find(" host, ")+7, paraConfig.find(" hosts, ")+8):paraConfig.find(" processor")])
procNums.append(numProc)
except:
print "Error analysing simulation data from: %s"%simDir.getCanonicalPath()
print sys.exc_info()
print times
print procNums
'''
import matplotlib.pyplot as plt
lines = plt.loglog(times, procNums, 'r:')
plt.ylabel('Simulation time')
plt.xlabel('Number of processors')
plt.show()'''
from ucl.physiol.neuroconstruct.gui.plotter import PlotManager
from ucl.physiol.neuroconstruct.gui.plotter import PlotCanvas
from ucl.physiol.neuroconstruct.dataset import DataSet
plotFrame = PlotManager.getPlotterFrame("Time for simulation run on different numbers of processors", 0, 1)
plotFrame.setViewMode(PlotCanvas.INCLUDE_ORIGIN_VIEW)
info = "Simulation times for: "+str(procNums)
dataSet = DataSet(info, info, "#", "s", "Number of processors", "Simulation time")
dataSet.setGraphFormat(PlotCanvas.USE_CIRCLES_FOR_PLOT)
for i in range(len(times)):
dataSet.addPoint(procNums[i],times[i]*procNums[i])
#dataSet.addPoint(procNums[i],times[i])
plotFrame.addDataSet(dataSet)
volts, times, analyseThreshold, analyseStartTime,
analyseStopTime)
#print "Spike times in %s for sim %s: %s"%(cellSegmentRef, simRef, str(spikeTimes))
if totNumSpikes < 0: totNumSpikes = len(spikeTimes)
for spikeIndex in range(max(totNumSpikes - numSpikes, 0),
totNumSpikes):
spikeTimeTrace = "Times_" + sim + "_" + simConfigName + "_" + str(
spikeIndex)
if not allSpikeTimeDataSets.has_key(spikeTimeTrace):
ds = DataSet(spikeTimeTrace, spikeTimeTrace, "",
"ms", "Number of compartments",
"Spike time")
allSpikeTimeDataSets[spikeTimeTrace] = ds
spikeTrace = allSpikeTimeDataSets[spikeTimeTrace]
print "Adding point to " + spikeTimeTrace
#pointNum = spikeTrace.addPoint(1/maxElecLen, spikeTimes[-1])
##pointNum = spikeTrace.addPoint(1/maxElecLen, spikeTimes[spikeIndex])
morphProp = simData.getSimulationProperties(
).getProperty("Morph summary nRT")
comps = morphProp.split(":")[-1]
pointNum = spikeTrace.addPoint(float(comps),
spikeTimes[spikeIndex])
#spikeTrace.setCommentOnPoint(pointNum, "Point for electrotonic len: "+str(maxElecLen))
def generateF_ICurve(self,
projFile,
simulator,
simConfig,
preStimAmp, preStimDel, preStimDur,
stimAmpLow, stimAmpInc, stimAmpHigh,
stimDel, stimDur,
simDuration,
analyseStartTime, analyseStopTime,
analyseThreshold,
maxNumSimultaneousSims = 4):
# Load neuroConstruct project
print "Loading project from file: " + projFile.getAbsolutePath()+", exists: "+ str(projFile.exists())
pm = ProjectManager()
self.myProject = pm.loadProject(projFile)
self.simulator = simulator
simConfig = self.myProject.simConfigInfo.getSimConfig(simConfig)
simConfig.setSimDuration(simDuration)
pm.doGenerate(simConfig.getName(), self.neuroConstructSeed)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: "+str(simConfig)
time.sleep(2)
numGenerated = self.myProject.generatedCellPositions.getNumberInAllCellGroups()
print "Number of cells generated: " + str(numGenerated)
simReferences = {}
if numGenerated > 0:
print "Generating scripts for simulator: %s..."%simulator
if simulator == 'NEURON':
self.myProject.neuronFileManager.setQuitAfterRun(1) # Remove this line to leave the NEURON sim windows open after finishing
self.myProject.neuronSettings.setCopySimFiles(1) # 1 copies hoc/mod files to PySim_0 etc. and will allow multiple sims to run at once
self.myProject.neuronSettings.setGraphicsMode(0) # 0 hides graphs during execution
if simulator == 'GENESIS':
self.myProject.genesisFileManager.setQuitAfterRun(1) # Remove this line to leave the NEURON sim windows open after finishing
self.myProject.genesisSettings.setCopySimFiles(1) # 1 copies hoc/mod files to PySim_0 etc. and will allow multiple sims to run at once
self.myProject.genesisSettings.setGraphicsMode(0) # 0 hides graphs during execution
stimAmp = stimAmpLow
while stimAmp <= stimAmpHigh:
while (len(self.simsRunning)>=maxNumSimultaneousSims):
print "Sims currently running: "+str(self.simsRunning)
print "Waiting..."
time.sleep(3) # wait a while...
self.updateSimsRunning()
simRef = "PySim_"+str(float(stimAmp))
print "Going to run simulation: "+simRef
######## Adjusting the amplitude of the current clamp ###############
# preStim = self.myProject.elecInputInfo.getStim(simConfig.getInputs().get(0))
preStim = self.myProject.elecInputInfo.getStim("Input_3")
preStim.setAmp(NumberGenerator(preStimAmp))
preStim.setDel(NumberGenerator(preStimDel))
preStim.setDur(NumberGenerator(preStimDur))
self.myProject.elecInputInfo.updateStim(preStim)
# stim = self.myProject.elecInputInfo.getStim(simConfig.getInputs().get(1))
stim = self.myProject.elecInputInfo.getStim("Input_4")
stim.setAmp(NumberGenerator(stimAmp))
stim.setDel(NumberGenerator(stimDel))
stim.setDur(NumberGenerator(stimDur))
self.myProject.elecInputInfo.updateStim(stim)
print "Next stim: "+ str(stim)
self.myProject.simulationParameters.setReference(simRef)
if simulator == "NEURON":
self.myProject.neuronFileManager.generateTheNeuronFiles(simConfig,
None,
NeuronFileManager.RUN_HOC,
self.simulatorSeed)
print "Generated NEURON files for: "+simRef
compileProcess = ProcessManager(self.myProject.neuronFileManager.getMainHocFile())
compileSuccess = compileProcess.compileFileWithNeuron(0,0)
print "Compiled NEURON files for: "+simRef
if compileSuccess:
pm.doRunNeuron(simConfig)
print "Set running simulation: "+simRef
self.simsRunning.append(simRef)
if simulator == "GENESIS":
compartmentalisation = GenesisCompartmentalisation()
self.myProject.genesisFileManager.generateTheGenesisFiles(simConfig,
None,
compartmentalisation,
self.simulatorSeed)
print "Generated GENESIS files for: "+simRef
pm.doRunGenesis(simConfig)
print "Set running simulation: "+simRef
self.simsRunning.append(simRef)
time.sleep(1) # Wait for sim to be kicked off
simReferences[simRef] = stimAmp
stimAmp = stimAmp +stimAmpInc
print
print "Finished running "+str(len(simReferences))+" simulations for project "+ projFile.getAbsolutePath()
print "These can be loaded and replayed in the previous simulation browser in the GUI"
print
while (len(self.simsRunning)>0):
print "Sims currently running: "+str(self.simsRunning)
print "Waiting..."
time.sleep(4) # wait a while...
self.updateSimsRunning()
#simReferences = {'PySim_0.3':0.3,'PySim_0.4':0.4,'PySim_0.5':0.5}
plotFrameFI = PlotManager.getPlotterFrame("F-I curve from project: "+str(self.myProject.getProjectFile())+" on "+simulator , 1, 1)
plotFrameVolts = PlotManager.getPlotterFrame("VoltageTraces from project: "+str(self.myProject.getProjectFile())+" on "+simulator , 1, 1)
plotFrameFI.setViewMode(PlotCanvas.INCLUDE_ORIGIN_VIEW)
info = "F-I curve for Simulation Configuration: "+str(simConfig)
dataSet = DataSet(info, info, "nA", "Hz", "Current injected", "Firing frequency")
dataSet.setGraphFormat(PlotCanvas.USE_CIRCLES_FOR_PLOT)
simList = simReferences.keys()
simList.sort()
for sim in simList:
simDir = File(projFile.getParentFile(), "/neuroConstruct/models/Dan_GranCell/simulations/"+sim)
print
print "--- Reloading data from simulation in directory: %s"%simDir.getCanonicalPath()
try:
simData = SimulationData(simDir)
simData.initialise()
print "Data loaded: "
print simData.getAllLoadedDataStores()
times = simData.getAllTimes()
cellSegmentRef = simConfig.getCellGroups().get(0)+"_0"
volts = simData.getVoltageAtAllTimes(cellSegmentRef)
traceInfo = "Voltage at: %s in simulation: %s"%(cellSegmentRef, sim)
dataSetV = DataSet(traceInfo, traceInfo, "mV", "ms", "Membrane potential", "Time")
for i in range(len(times)):
dataSetV.addPoint(times[i], volts[i])
plotFrameVolts.addDataSet(dataSetV)
spikeTimes = SpikeAnalyser.getSpikeTimes(volts, times, analyseThreshold, analyseStartTime, analyseStopTime)
stimAmp = simReferences[sim]
print "Number of spikes at %f nA in sim %s: %i"%(stimAmp, sim, len(spikeTimes))
avgFreq = 0
if len(spikeTimes)>1:
avgFreq = len(spikeTimes)/ ((analyseStopTime - analyseStartTime)/1000.0)
dataSet.addPoint(stimAmp,avgFreq)
except:
print "Error analysing simulation data from: %s"%simDir.getCanonicalPath()
print sys.exc_info()[0]
plotFrameFI.addDataSet(dataSet)
analyseStartTime = 0
analyseStopTime = 2000
analyseThreshold = -20 # mV
spikeTimes = SpikeAnalyser.getSpikeTimes(volts, times, analyseThreshold, analyseStartTime, analyseStopTime)
#print "Spike times in %s for sim %s: %s"%(cellSegmentRef, simRef, str(spikeTimes))
if totNumSpikes <0: totNumSpikes = len(spikeTimes)
for spikeIndex in range(max(totNumSpikes-numSpikes, 0), totNumSpikes):
spikeTimeTrace = "Times_"+sim+"_"+simConfigName+"_"+str(spikeIndex)
if not allSpikeTimeDataSets.has_key(spikeTimeTrace):
ds = DataSet(spikeTimeTrace, spikeTimeTrace, "", "ms", "Number of compartments", "Spike time")
allSpikeTimeDataSets[spikeTimeTrace] = ds
spikeTrace = allSpikeTimeDataSets[spikeTimeTrace]
print "Adding point to "+spikeTimeTrace
#pointNum = spikeTrace.addPoint(1/maxElecLen, spikeTimes[-1])
##pointNum = spikeTrace.addPoint(1/maxElecLen, spikeTimes[spikeIndex])
morphProp = simData.getSimulationProperties().getProperty("Morph summary nRT")
comps = morphProp.split(":")[-1]
pointNum = spikeTrace.addPoint(float(comps), spikeTimes[spikeIndex])
#spikeTrace.setCommentOnPoint(pointNum, "Point for electrotonic len: "+str(maxElecLen))
spikeTrace.setCommentOnPoint(pointNum, morphProp)
try:
simData = SimulationData(simDir)
simData.initialise()
print("Data loaded: ")
print(simData.getAllLoadedDataStores())
times = simData.getAllTimes()
# simConfig was just grabbed for use here, it was CGspinstell_0
cellSegmentRef = simConfig.getCellGroups().get(0)+"_0"
volts = simData.getVoltageAtAllTimes(cellSegmentRef)
traceInfo = "Voltage at: %s in simulation: %s"%(cellSegmentRef, sim)
dataSetV = DataSet(traceInfo, traceInfo, "ms", "mV", "Time", "Membrane potential")
for i in range(len(times)):
dataSetV.addPoint(times[i], volts[i])
if plotAllTraces:
plotFrameAlltraces.addDataSet(dataSetV)
# needs adjusting for a comprehensive maxx maxy minx miny
plotFrameAlltraces.setMaxMinScaleValues(dataSetV.getMaxX()[0],dataSetV.getMinX()[0],dataSetV.getMaxY()[1],dataSetV.getMinY()[1])
if (curveType == "F-I") :
print "F-I analisys..."
# initialize the dataSet for the graph
if (dataSet == "") :
dataSet = DataSet("info 1", "info 2", "nA", "Hz", "Current injected", "Firing frequency")
dataSet.setGraphFormat(PlotCanvas.USE_CIRCLES_FOR_PLOT)
spikeTimes = SpikeAnalyser.getSpikeTimes(volts, times, analyseThreshold, analyseStartTime, analyseStopTime)
except:
print "Error analysing simulation data from: %s"%simRef
print exc_info()
num_peaks = 1e9
for ds in peaks_wave.values():
if ds.getNumberPoints() < num_peaks:
num_peaks = ds.getNumberPoints()
info = "Averaged peak trace"
avg = DataSet(info, info, "Time", "Peak", "ms", "")
avg.setGraphFormat(PlotCanvas.USE_THICK_LINES_FOR_PLOT)
for i in xrange(num_peaks):
tot_val = 0
for ds in peaks_wave.values():
tot_val += ds.getPoint(i)[1]
avg.addPoint(i, tot_val/len(peaks_wave))
plotFrame2.addDataSet(avg)
plotFrame.setVisible(True)
plotFrame2.setVisible(True)
innerRadius = outerRadius
def generateV_ICurve(self,
projFile,
simulator,
simConfig,
stimAmpLow, stimAmpInc, stimAmpHigh,
stimDur,
simDuration,
maxNumSimultaneousSims = 4):
# Load neuroConstruct project
print "Loading project from file: " + projFile.getAbsolutePath()+", exists: "+ str(projFile.exists())
pm = ProjectManager()
self.myProject = pm.loadProject(projFile)
self.simulator = simulator
simConfig = self.myProject.simConfigInfo.getSimConfig(simConfig)
simConfig.setSimDuration(simDuration)
pm.doGenerate(simConfig.getName(), self.neuroConstructSeed)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: "+str(simConfig)
time.sleep(2)
numGenerated = self.myProject.generatedCellPositions.getNumberInAllCellGroups()
print "Number of cells generated: " + str(numGenerated)
simReferences = {}
if numGenerated > 0:
print "Generating scripts for simulator: %s..."%simulator
if simulator == 'NEURON':
self.myProject.neuronFileManager.setQuitAfterRun(1) # Remove this line to leave the NEURON sim windows open after finishing
self.myProject.neuronSettings.setCopySimFiles(1) # 1 copies hoc/mod files to PySim_0 etc. and will allow multiple sims to run at once
self.myProject.neuronSettings.setGraphicsMode(0) # 0 hides graphs during execution
if simulator == 'GENESIS':
self.myProject.genesisFileManager.setQuitAfterRun(1) # Remove this line to leave the NEURON sim windows open after finishing
self.myProject.genesisSettings.setCopySimFiles(1) # 1 copies hoc/mod files to PySim_0 etc. and will allow multiple sims to run at once
self.myProject.genesisSettings.setGraphicsMode(0) # 0 hides graphs during execution
stimAmp = stimAmpLow
ADD_TO_BEFORE_INIT = self.myProject.neuronSettings.getNativeBlock(NativeCodeLocation.BEFORE_INITIAL)
ADD_TO_RECORD_I = self.myProject.neuronSettings.getNativeBlock(NativeCodeLocation.AFTER_SIMULATION)
ADD_TO_START_FINITIALIZE = self.myProject.neuronSettings.getNativeBlock(NativeCodeLocation.START_FINITIALIZE)
while stimAmp <= stimAmpHigh:
while (len(self.simsRunning)>=maxNumSimultaneousSims):
print "Sims currently running: "+str(self.simsRunning)
print "Waiting..."
time.sleep(3) # wait a while...
self.updateSimsRunning()
simRef = "PySim_"+str(float(stimAmp))
print "Going to run simulation: "+simRef
######## Adjusting the amplitude of the Voltage clamp ###############
TEXT_BEFORE_CREATION = "objref clampobj" + "\n" + "objref record_current" + "\n" + "objref data_save" + "\n"
# TEXT_BEFORE_INIT = "GranuleCell_mod_tonic[0].Soma {\n" + "clampobj = new SEClamp(0.5)\n" + "clampobj.dur1 = 150.0" + "\n" + "clampobj.amp1 = -100.0" + "\n" + "clampobj.dur2 = " + str(stimDur) + "\n" + "clampobj.amp2 = " + str(stimAmp) + "\n" + "clampobj.dur3 = 150.0" + "\n" + "clampobj.amp3 = -100.0" + "\n" + "clampobj.rs = 0.00001\n " + "}\n" # This should do the trick
# TEXT_BEFORE_INIT = TEXT_BEFORE_INIT + ADD_TO_BEFORE_INIT
TEXT_START_FINITIALIZE = "GranuleCell_mod_tonic[0].Soma {\n" + "clampobj = new SEClamp(0.5)\n" + "clampobj.dur1 = 150.0" + "\n" + "clampobj.amp1 = -100.0" + "\n" + "clampobj.dur2 = " + str(stimDur) + "\n" + "clampobj.amp2 = " + str(stimAmp) + "\n" + "clampobj.dur3 = 150.0" + "\n" + "clampobj.amp3 = -40.0" + "\n" + "clampobj.rs = 0.00001\n" + "record_current = new Vector()" + "\n" + "record_current.record(&clampobj.i)" + "\n" + "}\n" #This should do the trick
TEXT_START_FINITIALIZE = TEXT_START_FINITIALIZE + ADD_TO_START_FINITIALIZE
TEXT_TO_RECORD_I = """data_save = new File() \n""" + """strdef filename \n""" + """sprint(filename, """" + self.myProject.getProjectMainDirectory().getAbsolutePath() + """/simulations/current%.3f.txt", clampobj.amp2) \n""" + """data_save.wopen(filename) \n""" + """record_current.printf(data_save) \n""" + """data_save.close() \n"""
TEXT_TO_RECORD_I = TEXT_TO_RECORD_I + ADD_TO_RECORD_I
self.myProject.neuronSettings.setNativeBlock(NativeCodeLocation.BEFORE_CELL_CREATION, TEXT_BEFORE_CREATION)
# self.myProject.neuronSettings.setNativeBlock(NativeCodeLocation.BEFORE_INITIAL, TEXT_BEFORE_INIT)
self.myProject.neuronSettings.setNativeBlock(NativeCodeLocation.START_FINITIALIZE, TEXT_START_FINITIALIZE)
self.myProject.neuronSettings.setNativeBlock(NativeCodeLocation.AFTER_SIMULATION, TEXT_TO_RECORD_I)
print "Next stim: "+ str(stimAmp)
self.myProject.simulationParameters.setReference(simRef)
if simulator == "NEURON":
self.myProject.neuronFileManager.generateTheNeuronFiles(simConfig,
None,
NeuronFileManager.RUN_HOC,
self.simulatorSeed)
print "Generated NEURON files for: "+simRef
compileProcess = ProcessManager(self.myProject.neuronFileManager.getMainHocFile())
compileSuccess = compileProcess.compileFileWithNeuron(0,0)
print "Compiled NEURON files for: "+simRef
if compileSuccess:
pm.doRunNeuron(simConfig)
print "Set running simulation: "+simRef
self.simsRunning.append(simRef)
if simulator == "GENESIS":
compartmentalisation = GenesisCompartmentalisation()
self.myProject.genesisFileManager.generateTheGenesisFiles(simConfig,
None,
compartmentalisation,
self.simulatorSeed)
print "Generated GENESIS files for: "+simRef
pm.doRunGenesis(simConfig)
print "Set running simulation: "+simRef
self.simsRunning.append(simRef)
time.sleep(1) # Wait for sim to be kicked off
simReferences[simRef] = stimAmp
stimAmp = stimAmp +stimAmpInc
print
print "Finished running "+str(len(simReferences))+" simulations for project "+ projFile.getAbsolutePath()
print "These can be loaded and replayed in the previous simulation browser in the GUI"
print
while (len(self.simsRunning)>0):
print "Sims currently running: "+str(self.simsRunning)
print "Waiting..."
time.sleep(4) # wait a while...
self.updateSimsRunning()
#simReferences = {'PySim_0.3':0.3,'PySim_0.4':0.4,'PySim_0.5':0.5}
plotFrameVI = PlotManager.getPlotterFrame("V-I curve from project: "+str(self.myProject.getProjectFile())+" on "+simulator , 1, 1)
plotFrameVI.setViewMode(PlotCanvas.INCLUDE_ORIGIN_VIEW)
info = "V-I curve for Simulation Configuration: "+str(simConfig)
dataSet = DataSet(info, info, "mV", "nA", "Voltage", "Current")
dataSet.setGraphFormat(PlotCanvas.USE_CIRCLES_FOR_PLOT)
simList = simReferences.keys()
simList.sort()
for sim in simList:
simDir = File(projFile.getParentFile(), "/neuroConstruct/models/Dan_GranCell/simulations/"+sim)
print
print "--- Reloading data from simulation in directory: %s"%simDir.getCanonicalPath()
try:
simData = SimulationData(simDir)
simData.initialise()
print "Data loaded: "
print simData.getAllLoadedDataStores()
times = simData.getAllTimes()
cellSegmentRef = simConfig.getCellGroups().get(0)+"_0"
cfilename = "E:/neuroConstruct/models/Dan_GranCell/simulations/" + sim + "/current.txt"
trace = "E:/neuroConstruct/models/Dan_GranCell/simulations/" + sim + ".txt"
# cFILE = open(cfilename, "r")
strom = 0.0
volts = simData.getVoltageAtAllTimes(cellSegmentRef)
traceInfo = "Voltage at: %s in simulation: %s"%(cellSegmentRef, sim)
stimAmp = simReferences[sim]
print "Current at %f mV in sim %s: %f"%(stimAmp, sim, float(strom))
dataSet.addPoint(stimAmp,float(strom))
except:
print "Error analysing simulation data from: %s"%simDir.getCanonicalPath()
print sys.exc_info()[0]
plotFrameVI.addDataSet(dataSet)
def testAll(argv=None):
if argv is None:
argv = sys.argv
print "Loading project from " + projFile.getCanonicalPath()
simManager = nc.SimulationManager(projFile,
numConcurrentSims=numConcurrentSims,
verbose=verbose)
allSims = simManager.runMultipleSims(
simConfigs=simConfigs,
simDt=simDt,
simDuration=simDuration,
simulators=simulators,
runInBackground=runInBackground,
varTimestepNeuron=varTimestepNeuron,
mpiConfigs=mpiConfigs,
suggestedRemoteRunTime=suggestedRemoteRunTime,
simRefGlobalPrefix=simAllPrefix,
runSims=runSims,
maxElecLens=multipleRuns,
saveAsHdf5=saveAsHdf5,
saveOnlySpikes=saveOnlySpikes)
while (len(simManager.allRunningSims) > 0):
print "Waiting for the following sims to finish: " + str(
simManager.allRunningSims)
time.sleep(5) # wait a while...
simManager.updateSimsRunning()
times = []
procNums = []
for sim in allSims:
simDir = File(projFile.getParentFile(), "/simulations/" + sim)
try:
simData = SimulationData(simDir)
simData.initialise()
simTime = simData.getSimulationProperties().getProperty(
"RealSimulationTime")
print "Simulation: %s took %s seconds" % (sim, simTime)
times.append(float(simTime))
paraConfig = simData.getSimulationProperties().getProperty(
"Parallel configuration")
print paraConfig
numProc = int(paraConfig[max(
paraConfig.find(" host, ") + 7,
paraConfig.find(" hosts, ") +
8):paraConfig.find(" processor")])
procNums.append(numProc)
except:
print "Error analysing simulation data from: %s" % simDir.getCanonicalPath(
)
print sys.exc_info()
print times
print procNums
'''
import matplotlib.pyplot as plt
lines = plt.loglog(times, procNums, 'r:')
plt.ylabel('Simulation time')
plt.xlabel('Number of processors')
plt.show()'''
from ucl.physiol.neuroconstruct.gui.plotter import PlotManager
from ucl.physiol.neuroconstruct.gui.plotter import PlotCanvas
from ucl.physiol.neuroconstruct.dataset import DataSet
plotFrame = PlotManager.getPlotterFrame(
"Time for simulation run on different numbers of processors", 0, 1)
plotFrame.setViewMode(PlotCanvas.INCLUDE_ORIGIN_VIEW)
info = "Simulation times for: " + str(procNums)
dataSet = DataSet(info, info, "#", "s", "Number of processors",
"Simulation time")
dataSet.setGraphFormat(PlotCanvas.USE_CIRCLES_FOR_PLOT)
for i in range(len(times)):
dataSet.addPoint(procNums[i], times[i] * procNums[i])
plotFrame.addDataSet(dataSet)
try:
simData = SimulationData(simDir)
simData.initialise()
print("Data loaded: ")
print(simData.getAllLoadedDataStores())
times = simData.getAllTimes()
# simConfig was just grabbed for use here, it was CGspinstell_0
cellSegmentRef = simConfig.getCellGroups().get(0) + "_0"
volts = simData.getVoltageAtAllTimes(cellSegmentRef)
traceInfo = "Voltage at: %s in simulation: %s" % (cellSegmentRef, sim)
dataSetV = DataSet(traceInfo, traceInfo, "ms", "mV", "Time",
"Membrane potential")
for i in range(len(times)):
dataSetV.addPoint(times[i], volts[i])
if plotAllTraces:
plotFrameAlltraces.addDataSet(dataSetV)
# needs adjusting for a comprehensive maxx maxy minx miny
plotFrameAlltraces.setMaxMinScaleValues(dataSetV.getMaxX()[0],
dataSetV.getMinX()[0],
dataSetV.getMaxY()[1],
dataSetV.getMinY()[1])
if (curveType == "F-I"):
print "F-I analisys..."
# initialize the dataSet for the graph
if (dataSet == ""):
time.sleep(1) # Wait for sim to be kicked off
print
print "Finished running "+str(numSimulationsToRun)+" simulations for project "+ projFile.getAbsolutePath()
print "These can be loaded and replayed in the previous simulation browser in the GUI"
print
######## Generating a current versus firing rate plot #######
plotFrameFI = PlotManager.getPlotterFrame("F-I curve from project: "+str(myProject.getProjectFile()) , 1, 1)
plotFrameFI.setViewMode(PlotCanvas.INCLUDE_ORIGIN_VIEW)
info = "F-I curve for Simulation Configuration: "+str(simConfig)
dataSet = DataSet(info, info, "nA", "Hz", "Current injected", "Firing frequency")
dataSet.setGraphFormat(PlotCanvas.USE_CIRCLES_FOR_PLOT)
simList = simReferences.keys()
simList.sort()
for sim in simList:
simDir = File(projFile.getParentFile(), "/simulations/"+sim)
print
print "--- Reloading data from simulation in directory: %s"%simDir.getCanonicalPath()
try:
simData = SimulationData(simDir)
simData.initialise()
print "Data loaded: "
print simData.getAllLoadedDataStores()
print "Finished running " + str(
numSimulationsToRun
) + " simulations for project " + projFile.getAbsolutePath()
print "These can be loaded and replayed in the previous simulation browser in the GUI"
print
######## Generating a current versus firing rate plot #######
plotFrameFI = PlotManager.getPlotterFrame(
"F-I curve from project: " + str(myProject.getProjectFile()), 1, 1)
plotFrameFI.setViewMode(PlotCanvas.INCLUDE_ORIGIN_VIEW)
info = "F-I curve for Simulation Configuration: " + str(simConfig)
dataSet = DataSet(info, info, "nA", "Hz", "Current injected",
"Firing frequency")
dataSet.setGraphFormat(PlotCanvas.USE_CIRCLES_FOR_PLOT)
simList = simReferences.keys()
simList.sort()
for sim in simList:
simDir = File(projFile.getParentFile(), "/simulations/" + sim)
print
print "--- Reloading data from simulation in directory: %s" % simDir.getCanonicalPath(
)
try:
simData = SimulationData(simDir)
simData.initialise()
print "Data loaded: "
