def samefile(path, path2):
"""Test whether two pathnames reference the same actual file"""
path = _tostr(path, "samefile")
path2 = _tostr(path2, "samefile")
f = File(path)
f2 = File(path2)
return f.getCanonicalPath() == f2.getCanonicalPath()
def downloadRemoteScanFile(Framework):
remoteScanFileLocation = Framework.getProperty(InventoryUtils.STATE_PROPERTY_REMOTE_SCAN_FILE_LOCATION)
# download scanner log file before downloading scan file
downloadScanLogFile(Framework)
if remoteScanFileLocation is None:
logger.debug("No scan file to downloaded from current execution")
return None
logger.debug("About to download scan file from current execution:", remoteScanFileLocation)
extension = InventoryUtils.getFileExtension(remoteScanFileLocation)
localScanFileName = InventoryUtils.generateScanFileName(Framework, extension)
# folder for scan files
localScanFileFolderPath = (
CollectorsParameters.PROBE_MGR_INVENTORY_XMLENRICHER_FILES_FOLDER + XmlEnricherConstants.INCOMING_FOLDER_NAME
)
downloadedScanFilesDir = File(localScanFileFolderPath)
downloadedScanFilesDir.mkdirs()
# this scan file will be created after downloading from remote machine
targetScanFile = File(downloadedScanFilesDir, localScanFileName)
# get file to the local machine
logger.debug("Scan file to be downloaded to location:", targetScanFile.getCanonicalPath())
if not InventoryUtils.copyRemoteFileToLocal(Framework, remoteScanFileLocation, targetScanFile.getCanonicalPath()):
return None
return targetScanFile
def removeLocalScanLog(Framework):
localScanLogName = InventoryUtils.generateScanLogName(Framework)
localScanLogFolderPath = CollectorsParameters.PROBE_MGR_INVENTORY_XMLENRICHER_FILES_FOLDER + XmlEnricherConstants.LOGS_FOLDER_NAME + CollectorsParameters.FILE_SEPARATOR
localScanLogFile = File(localScanLogFolderPath, localScanLogName)
try:
# if the local scan log exists, delete it before next steps
if localScanLogFile.exists():
logger.debug("local scan log file found, just delete it: ", localScanLogFile.getCanonicalPath())
if not localScanLogFile.delete():
logger.warn("delete scan log file failed, ensure the there's permission and it's not locked:", localScanLogFile.getCanonicalPath())
except:
logger.warn("delete scan log file failed: ", localScanLogFile.getCanonicalPath())
Framework.setStepExecutionStatus(WorkflowStepStatus.SUCCESS)
def useTempScanFile(Framework):
tempScanFilePath = Framework.getProperty(InventoryUtils.STATE_PROPERTY_TEMP_SCAN_FILE)
if tempScanFilePath is None:
logger.debug("No scan file found from previous scanner execution")
return None
logger.debug("Using scan file from previous execution:", tempScanFilePath)
extension = InventoryUtils.getFileExtension(tempScanFilePath)
localScanFileName = InventoryUtils.generateScanFileName(Framework, extension)
# folder for scan files
localScanFileFolderPath = (
CollectorsParameters.PROBE_MGR_INVENTORY_XMLENRICHER_FILES_FOLDER + XmlEnricherConstants.INCOMING_FOLDER_NAME
)
downloadedScanFilesDir = File(localScanFileFolderPath)
downloadedScanFilesDir.mkdirs()
# this scan file will be created after downloading from remote machine
targetScanFile = File(downloadedScanFilesDir, localScanFileName)
logger.debug("Scan file from previous execution will be moved to ", targetScanFile.getCanonicalPath())
tempScanFile = File(tempScanFilePath)
if not tempScanFile.renameTo(targetScanFile):
return None
return targetScanFile
def get_path_with_real_case(filename):
from java.io import File # noqa
f = File(filename)
ret = f.getCanonicalPath()
if IS_PY2 and not isinstance(ret, str):
return ret.encode(getfilesystemencoding())
return ret
def test_image_example_dir_iteration(self):
f = File(str(inspect.getfile( inspect.currentframe() )))
example_dir = File(File(f.getParentFile().getParentFile().getParentFile(),"character_examples"),"A")
image_example_dir = ImageExampleDir(example_dir.getCanonicalPath())
for label, image in image_example_dir:
if label != "A":
raise "The label of the examples in this dir should be A"
def lstat(path):
"""lstat(path) -> stat result
Like stat(path), but do not follow symbolic links.
"""
abs_path = sys.getPath(path)
try:
return stat_result.from_jnastat(_posix.lstat(abs_path))
except NotImplementedError:
pass
except:
raise
f = File(sys.getPath(path))
# XXX: jna-posix implements similar link detection in
# JavaFileStat.calculateSymlink, fallback to that instead when not
# native
abs_parent = f.getAbsoluteFile().getParentFile()
if not abs_parent:
# root isn't a link
return stat(path)
can_parent = abs_parent.getCanonicalFile()
if can_parent.getAbsolutePath() == abs_parent.getAbsolutePath():
# The parent directory's absolute path is canonical..
if f.getAbsolutePath() != f.getCanonicalPath():
# but the file's absolute and canonical paths differ (a
# link)
return stat_result((_stat.S_IFLNK, 0, 0, 0, 0, 0, 0, 0, 0, 0))
# The parent directory's path is not canonical (one of the parent
# directories is a symlink). Build a new path with the parent's
# canonical path and compare the files
f = File(_path.join(can_parent.getAbsolutePath(), f.getName()))
if f.getAbsolutePath() != f.getCanonicalPath():
return stat_result((_stat.S_IFLNK, 0, 0, 0, 0, 0, 0, 0, 0, 0))
# Not a link, only now can we determine if it exists (because
# File.exists() returns False for dead links)
if not f.exists():
raise OSError(errno.ENOENT, strerror(errno.ENOENT), path)
return stat(path)
def loaddata():
filepath = File(pyplugin.dataFolder, "config")
months = {0: 0, 1: 1, 2: 2, 3: 2, 4: 3, 5: 0, 6: 0}
if filepath.exists():
for line in open(filepath.getCanonicalPath()):
data = line.strip().split(':')
try:
if int(data[0]) in months:
months[int(data[0])] = int(data[1])
except:
logs.info("error in configfile")
return months
def checkScanFileExistance(Framework):
# this step is always finished with success since we DON'T require scan file from previous execution, just nice to have
Framework.setStepExecutionStatus(WorkflowStepStatus.SUCCESS)
DownloadScanFileBeforeExecution = Boolean.parseBoolean(Framework.getParameter('DownloadScanFileBeforeExecution'))
if DownloadScanFileBeforeExecution:
try:
client = Framework.getConnectedClient()
options = LockUtils.getClientOptionsMap(client)
previousExecutionStarted = options.get(InventoryUtils.STATE_PROPERTY_EXECUTION_STARTED)
if (previousExecutionStarted is None) or (len(previousExecutionStarted.strip()) == 0):
logger.debug('Previous execution timestamp no found, continuing with workflow')
return
remoteScanFileLocation = options.get(InventoryUtils.AGENT_OPTION_DISCOVERY_SCANFILENAME)
if not InventoryUtils.isPathValid(remoteScanFileLocation):
logger.debug('No scan file path found on remote machine, continuing with workflow')
return
lastSuccessExecuton = Framework.getState().getJobLastSuccessfulRun()
logger.debug('Last success execution ' + str(lastSuccessExecuton))
logger.debug('Remote scan file execution ' + str(previousExecutionStarted))
if long(lastSuccessExecuton) > long(previousExecutionStarted):
logger.debug('Scan file on probe side is newer than on remote machine, skipping downloading')
return
logger.debug('Last success execution ' + str(lastSuccessExecuton) + ' older than scan file on remote machine ' + str(remoteScanFileLocation) + '. Going to download scan file:' + str(remoteScanFileLocation))
tempScanFileFolder = CollectorsParameters.PROBE_MGR_TEMPDOWNLOAD + Framework.getDiscoveryJobId() + CollectorsParameters.FILE_SEPARATOR
File(tempScanFileFolder).mkdirs()
extension = InventoryUtils.getFileExtension(remoteScanFileLocation)
tempScanFileName = InventoryUtils.generateScanFileName(Framework, extension)
tempScanFile = File(tempScanFileFolder, tempScanFileName)
tempScanFilePath = tempScanFile.getCanonicalPath()
logger.debug('Try to download scan file to the:', tempScanFilePath)
if not InventoryUtils.copyRemoteFileToLocal(Framework, remoteScanFileLocation, tempScanFilePath, 0):
logger.debug('Failed to download scan file before current execution')
Framework.setProperty(InventoryUtils.STATE_PROPERTY_TEMP_SCAN_FILE, tempScanFilePath)
except:
reason = str(sys.exc_info()[1])
logger.debug('Failed to check/download scan file from previous execution. Reason:', reason)
else:
logger.debug('Even not checking whether scan file exists on remote machine or not.')
def getLocalScanLogFileLocation(Framework):
localScanLogName = InventoryUtils.generateScanLogName(Framework)
# folder for scan files
localScanLogFolder = (
CollectorsParameters.PROBE_MGR_INVENTORY_XMLENRICHER_FILES_FOLDER + XmlEnricherConstants.LOGS_FOLDER_NAME
)
downloadedScanLogDir = File(localScanLogFolder)
downloadedScanLogDir.mkdirs()
# this scan log file will be created after downloading from remote machine
targetScanFile = File(downloadedScanLogDir, localScanLogName)
localScanLogLocation = targetScanFile.getCanonicalPath()
return localScanLogLocation
def RunConfigs(projString,simConfigs,simDt,argv=None):
projFile = File(os.getcwd(), projString)
if argv is None:
argv = sys.argv
print "Loading project from "+ projFile.getCanonicalPath()
simManager = nc.SimulationManager(projFile,
numConcurrentSims = numConcurrentSims,
verbose = verbose)
simManager.runMultipleSims(simConfigs = simConfigs,
simDt = simDt,
simulators = simulators,
runInBackground = runInBackground,
varTimestepNeuron = varTimestepNeuron,
varTimestepTolerance = varTimestepTolerance,
mpiConfig = mpiConfig,
suggestedRemoteRunTime = suggestedRemoteRunTime)
def downloadLogsIfNeeded(Framework):
platform = Framework.getProperty(InventoryUtils.STATE_PROPERTY_PLATFORM)
logger.debug('Checking if to print install/uninstall logs')
downloadMigrateLog = Framework.getProperty(AgentUtils.DOWNLOAD_MIGRATE_LOG_FILE)
downloadInstallLog = Framework.getProperty(AgentUtils.DOWNLOAD_INSTALL_LOG_FILE)
downloadUnInstallLog = Framework.getProperty(AgentUtils.DOWNLOAD_UNINSTALL_LOG_FILE)
if not downloadMigrateLog and not downloadInstallLog and not downloadUnInstallLog:
logger.debug('Migrate/Install/UnInstall log should not be downloaded')
return
try:
logger.debug('Releasing old connection')
InventoryUtils.releaseConnection(Framework)
logger.debug('Preparing framework for new connection')
AgentUtils.prepareFrameworkForShellOrAgentConnect(Framework)
except:
errorMessage = str(sys.exc_info()[1])
logger.debugException('Failed to initialize connection for downloading agent log files' + errorMessage)
return
if downloadMigrateLog:
# If need to download migrate log, we need to connect to DDMi agent as well
Framework.setProperty(InventoryUtils.STATE_PROPERTY_IS_MIGRATE, str('true'))
if not InventoryUtils.ensureConnection(Framework):
logger.debug('Failed to connect to the remote machine, no logs available')
else:
ip_address = Framework.getTriggerCIData('ip_address')
localInstallFile = None
localUnInstallFile = None
try:
try:
agentsConfigFile = Framework.getConfigFile(CollectorsConstants.AGENTSSBYPLATFORM_FILE_NAME)
BASEDIR = Framework.getProperty(InventoryUtils.STATE_PROPERTY_RESOLVED_BASEDIR)
architecture = Framework.getProperty(InventoryUtils.STATE_PROPERTY_ARCHITECTURE)
agentPlatformConfig = agentsConfigFile.getPlatformConfiguration(platform, architecture)
ip_address_str = str(ip_address)
if (ip_address_str.find(':') <> -1):
ip_address_str = ip_address_str.replace(':','-')
if downloadMigrateLog:
logger.debug('Download the migrate log')
installLogFile = agentPlatformConfig.getUpgradeLogFile()
localInstallFile = File(AGENTS_LOGS_TEMP_DIR_FILE, ip_address_str + '-' + installLogFile)
getLogFileContent(Framework, localInstallFile, str(BASEDIR) + installLogFile)
if downloadInstallLog:
logger.debug('Download the install/update log')
if AgentUtils.isUpgradeByUDAgent(Framework):
installLogFile = agentPlatformConfig.getUpgradeLogFile()
else:
installLogFile = agentPlatformConfig.getInstallLogFile()
localInstallFile = File(AGENTS_LOGS_TEMP_DIR_FILE, ip_address_str + '-' + installLogFile)
getLogFileContent(Framework, localInstallFile, str(BASEDIR) + installLogFile)
if downloadUnInstallLog:
logger.debug('Download the uninstall log')
unInstallLogFile = agentPlatformConfig.getUnInstallLogFile()
localUnInstallFile = File(AGENTS_LOGS_TEMP_DIR_FILE, ip_address_str + '-' + unInstallLogFile)
getLogFileContent(Framework, localUnInstallFile, str(BASEDIR) + unInstallLogFile)
except:
errorMessage = str(sys.exc_info()[1])
logger.debugException(errorMessage)
Framework.reportError(inventoryerrorcodes.INVENTORY_DISCOVERY_FAILED_EXECUTE_STEP, ['FinalizeAndReleaseResources', errorMessage])
finally:
try:
if localInstallFile and not localInstallFile.delete():
logger.debug('File was not deleted:' + localInstallFile.getCanonicalPath())
except:
logger.debugException('Failed to delete ' + localInstallFile.getCanonicalPath())
try:
logger.debug('Going to delete file ' + localInstallFile.getCanonicalPath())
if localUnInstallFile and not localUnInstallFile.delete():
logger.debug('File was not deleted:' + localUnInstallFile.getCanonicalPath())
except:
logger.debugException('Failed to delete ' + localUnInstallFile.getCanonicalPath())
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)
saveDataAsHdf5 = False
varTimestepNeuron = False
verbose = True
runInBackground= False
suggestedRemoteRunTime = 120
#######################################
### Load neuroConstruct project
print "Loading project from "+ projFile.getCanonicalPath()
pm = ProjectManager()
project = pm.loadProject(projFile)
### Set duration & timestep & simulation configuration
project.simulationParameters.setDt(simDt)
simConfig = project.simConfigInfo.getSimConfig(simConfig)
simConfig.setSimDuration(simDuration)
if saveDataAsHdf5:
project.neuronSettings.setDataSaveFormat(NeuronSettings.DataSaveFormat.HDF5_NC)
def samefile(path, path2):
"""Test whether two pathnames reference the same actual file"""
f = File(path)
f2 = File(path2)
return f.getCanonicalPath() == f2.getCanonicalPath()
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)
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("ExcCells").setMaxNumberCells(numExcCells)
simManager.project.cellGroupsInfo.getCellPackingAdapter("INCells").setMaxNumberCells(numINCells)
### Change weights in synapses/gap junctions
simConfig = simManager.project.simConfigInfo.getSimConfig(simConfigName)
for netConnName in simConfig.getNetConns():
print "Changing synaptic delay in %s to %f"%(netConnName, defaultSynapticDelay)
delayGen = NumberGenerator(defaultSynapticDelay)
for synProps in simManager.project.morphNetworkConnectionsInfo.getSynapseList(netConnName):
synProps.setDelayGenerator(delayGen)
# defaultSynapticDelay will be recorded in simulation.props and listed in SimulationBrowser GUI
SimulationsInfo.addExtraSimProperty("defaultSynapticDelay", str(defaultSynapticDelay))
allSims = simManager.runMultipleSims(simConfigs = [simConfigName],
simDt = simDt,
simDuration = simDuration,
simulators = simulators,
runInBackground = runInBackground,
varTimestepNeuron = varTimestepNeuron,
mpiConfigs = mpiConfigs,
suggestedRemoteRunTime = suggestedRemoteRunTime,
simRefGlobalPrefix = simAllPrefix,
runSims = runSims,
neuroConstructSeed = neuroConstructSeed,
simulatorSeed = simulatorSeed)
while (len(simManager.allRunningSims)>0):
print "Waiting for the following sims to finish: "+str(simManager.allRunningSims)
time.sleep(5) # wait a while...
simManager.updateSimsRunning()
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)
except:
print "Error analysing simulation data from: %s"%simDir.getCanonicalPath()
if mpiConfigs == [MpiSettings.LOCAL_SERIAL] or mpiConfigs == [MpiSettings.MATLEM_1PROC]:
simManager.reloadSims(plotVoltageOnly = True,
plotSims = plotSims,
analyseSims = analyseSims)
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)
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)
pm = simManager.projectManager
project = simManager.project
pm.doGenerate(simConfigs[0], neuroConstructSeed)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: "+str(simConfigs[0])
sleep(2)
print "Generated %i cells in %i cell groups" % (project.generatedCellPositions.getNumberInAllCellGroups(), project.generatedCellPositions.getNumberNonEmptyCellGroups())
print "Generated %i instances in %i network connections" % (project.generatedNetworkConnections.getNumAllSynConns(), project.generatedNetworkConnections.getNumNonEmptyNetConns())
print "Generated %i instances in %i elect inputs" % (project.generatedElecInputs.getNumberSingleInputs(), project.generatedElecInputs.getNonEmptyInputRefs().size())
fileX = File( "%s/savedNetworks/Net_%s.nml"%(project.getProjectMainDirectory().getCanonicalPath(), targetNum))
print "Saving XML net to %s"%fileX.getCanonicalPath()
pm.saveNetworkStructureXML(project, fileX, 0, 0, simConfigs[0], "Physiological Units")
fileH = File( "%s/savedNetworks/Net_%s.h5"%(project.getProjectMainDirectory().getCanonicalPath(), targetNum))
print "Saving HDF5 net to %s"%fileH.getCanonicalPath()
pm.saveNetworkStructureHDF5(project, fileH, simConfigs[0], "Physiological Units")
print "Finished running all sims, shutting down..."
numTCR = 100 # full model: 100
numnRT = 100 # full model: 100
#######################################
### Load neuroConstruct project
import datetime
start = datetime.datetime.now()
print "Loading project %s from at %s " % (projFile.getCanonicalPath(),start.strftime("%Y-%m-%d %H:%M"))
pm = ProjectManager()
project = pm.loadProject(projFile)
### Set duration & timestep & simulation configuration
project.simulationParameters.setDt(simDt)
simConfig = project.simConfigInfo.getSimConfig(simConfig)
simConfig.setSimDuration(simDuration)
### Set simulation reference
index = 0
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
for conf in confs.keys():
numb = conf
mpiConfigs = [confs[conf]]
perProc = 5000
targetNum = perProc*numb
simAllPrefix = "NZ_%i_%i_"%(perProc, numb) # Adds a prefix to simulation reference
print "Simulation pref: "+simAllPrefix
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)
if wait:
while (len(simManager.allRunningSims)>0):
print "Waiting for the following sims to finish: "+str(simManager.allRunningSims)
time.sleep(30) # 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()
# Load an existing neuroConstruct project
projFile = File("TestPython/TestPython.neuro.xml")
print "Loading project from file: " + projFile.getAbsolutePath()+", exists: "+ str(projFile.exists())
pm = ProjectManager()
myProject = pm.loadProject(projFile)
print "Loaded project: " + myProject.getProjectName()
morphDir = File("../nCexamples/Ex3_Morphology/importedMorphologies/")
morphmlFile = File(morphDir, "SimplePurkinjeCell.morph.xml")
print "Going to load morphology from: " + morphmlFile.getCanonicalPath()
converter = MorphMLConverter()
cell = converter.loadFromMorphologyFile(morphmlFile, "NewCell")
print "Loaded cell: " + cell.getInstanceName() + " with " + str(cell.getAllSegments().size()) +" segments"
myProject.cellManager.addCellType(cell) # Actually add it to the project
myProject.cellGroupsInfo.setCellType("SampleCellGroup", cell.getInstanceName()) # Set the type of an existing cell group to this
# Now the project can be generated as in Ex5_MultiSimGenerate.py
# * OR *
varTimestepNeuron = False
verbose = True
runInBackground= False
suggestedRemoteRunTime = 120
#######################################
### Load neuroConstruct project
print "Loading project from "+ projFile.getCanonicalPath()
pm = ProjectManager()
project = pm.loadProject(projFile)
### Set duration & timestep & simulation configuration
project.simulationParameters.setDt(simDt)
simConfig = project.simConfigInfo.getSimConfig(simConfig)
simConfig.setSimDuration(simDuration)
if saveDataAsHdf5:
project.neuronSettings.setDataSaveFormat(NeuronSettings.DataSaveFormat.HDF5_NC)
numTCR = 100 # full model: 100
numnRT = 100 # full model: 100
#######################################
### Load neuroConstruct project
import datetime
start = datetime.datetime.now()
print "Loading project %s from at %s " % (projFile.getCanonicalPath(),start.strftime("%Y-%m-%d %H:%M"))
pm = ProjectManager()
project = pm.loadProject(projFile)
### Set duration & timestep & simulation configuration
project.simulationParameters.setDt(simDt)
simConfig = project.simConfigInfo.getSimConfig(simConfig)
simConfig.setSimDuration(simDuration)
### Set simulation reference
index = 0
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()
times = simData.getAllTimes()
cellSegmentRef = simConfig.getCellGroups().get(0) + "_0"
volts = simData.getVoltageAtAllTimes(cellSegmentRef)
print "Got " + str(
len(volts)) + " data points on cell seg ref: " + cellSegmentRef
analyseStartTime = 100 # So it's firing at a steady rate...
analyseStopTime = simConfig.getSimDuration()
analyseThreshold = -20 # mV
numDeepAxAx = 100 # full model: 100
numDeepLTS = 100 # full model: 100
numL6NonTuftRS = 500 # full model: 500
numTCR = 100 # full model: 100
numnRT = 100 # full model: 100
#######################################
### Load neuroConstruct project
import datetime
start = datetime.datetime.now()
print "Loading project %s from at %s " % (projFile.getCanonicalPath(),
start.strftime("%Y-%m-%d %H:%M"))
pm = ProjectManager()
project = pm.loadProject(projFile)
### Set duration & timestep & simulation configuration
project.simulationParameters.setDt(simDt)
simConfig = project.simConfigInfo.getSimConfig(simConfig)
simConfig.setSimDuration(simDuration)
### Set simulation reference
index = 0
simRef = "%s%i" % (simRefPrefix, index)
maxElecLens = [0.025, 0.01, 0.0075, 0.005, 0.0025, 0.001, 0.00075, 0.0005, 0.00025, 0.0001]
maxElecLens = [0.025, 0.01, 0.0075, 0.005, 0.0025]
#maxElecLens = [.025, 0.01, 0.005, 0.0025]
#maxElecLens = [0.01, 0.005, 0.0025, 0.001]
#simAllPrefix = ""
simAllPrefix = "Lodt_"
simAllPrefix = "Looodt_"
numSpikes = 3
verbose = True
#############################################
print "Loading project from "+ projFile.getCanonicalPath()
pm = ProjectManager()
project = pm.loadProject(projFile)
allFinishedSims = []
plotVoltageOnly = True
plotSomaOnly = True
plotSims = False
allSpikeTimeDataSets = {}
for simConfigName in simConfigs:
def get_path_with_real_case(filename):
from java.io import File # noqa
f = File(filename)
ret = f.getCanonicalPath()
return ret
simDuration = 200 # ms
simDt = 0.01 # ms
neuroConstructSeed = 1234
simulatorSeed = 1111
simRefPrefix = "SB_"
defaultSynapticDelay = 0.2 # ms
runInBackground = True
#######################################
# Load neuroConstruct project
print "Loading project from "+ projFile.getCanonicalPath()
pm = ProjectManager()
myProject = pm.loadProject(projFile)
myProject.simulationParameters.setDt(simDt)
index = 0
while File( "%s/simulations/%s%i"%(myProject.getProjectMainDirectory().getCanonicalPath(), simRefPrefix,index)).exists():
index = index+1
simRef = "%s%i"%(simRefPrefix,index)
myProject.simulationParameters.setReference(simRef)
def reloadSims(waitForSimsToFinish):
print "Trying to reload sims: "+str(allFinishedSims)
plottedSims = []
for simRef in allFinishedSims:
simDir = File(projFile.getParentFile(), "/simulations/"+simRef)
timeFile = File(simDir, "time.dat")
timeFile2 = File(simDir,"time.txt") # for PSICS...
if timeFile.exists() or timeFile2.exists():
if verbose: print "--- Reloading data from simulation in directory: %s"%simDir.getCanonicalPath()
time.sleep(1) # wait a while...
try:
simData = SimulationData(simDir)
simData.initialise()
times = simData.getAllTimes()
if analyseSims:
'''
volts = simData.getVoltageAtAllTimes(cellSegmentRef)
if verbose: print "Got "+str(len(volts))+" data points on cell seg ref: "+cellSegmentRef
analyseStartTime = 0
analyseStopTime = simConfig.getSimDuration()
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 plotSims:
simConfigName = simData.getSimulationProperties().getProperty("Sim Config")
if simConfigName.find('(')>=0:
simConfigName = simConfigName[0:simConfigName.find('(')]
for dataStore in simData.getAllLoadedDataStores():
ds = simData.getDataSet(dataStore.getCellSegRef(), dataStore.getVariable(), False)
if not plotVoltageOnly or dataStore.getVariable() == SimPlot.VOLTAGE:
plotFrame = PlotManager.getPlotterFrame("Behaviour of "+dataStore.getVariable() \
+" on: %s for sim config: %s"%(str(simulators), simConfigName))
plotFrame.addDataSet(ds)
plottedSims.append(simRef)
except:
print "Error analysing simulation data from: %s"%simDir.getCanonicalPath()
print sys.exc_info()
for simRef in plottedSims:
allFinishedSims.remove(simRef)
if waitForSimsToFinish and len(allRunningSims)>0:
if verbose: print "Waiting for sims: %s to finish..."%str(allRunningSims)
time.sleep(2) # wait a while...
updateSimsRunning()
reloadSims(True)
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 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)
simRef = "Sim_2296"
#################################################
from ucl.physiol.neuroconstruct.project import ProjectManager
print 'Loading project file: ', projFile.getAbsolutePath()
pm = ProjectManager()
project = pm.loadProject(projFile)
print 'Successfully loaded project: ', project.getProjectName()
simDir = File(projFile.getParentFile(), "/simulations/"+simRef)
print
print "--- Reloading data from simulation in directory: %s"%simDir.getCanonicalPath()
plotFrame = PlotManager.getPlotterFrame("All voltage traces from simulation: "+simRef, False)
try:
simData = SimulationData(simDir)
simData.initialise()
volt_traces = simData.getCellSegRefs(True)
for trace in volt_traces:
ds = simData.getDataSet(trace, SimPlot.VOLTAGE, False)
plotFrame.addDataSet(ds)
except:
print "Error analysing simulation data from: %s"%simDir.getCanonicalPath()
print exc_info()
def get_example_image(self):
f = File(str(inspect.getfile( inspect.currentframe() )))
example_dir = File(File(f.getParentFile().getParentFile().getParentFile(),"character_examples"),"A")
image_example_dir = ImageExampleDir(example_dir.getCanonicalPath())
label, image = image_example_dir.__iter__().next()
return image
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)
