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))
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 == ""):
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)
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: "
