Exemple #1
0
def runColumnSimulation(simConfig="TempSimConfig",
                        simDuration=100,
                        simDt=0.025,
                        neuroConstructSeed=1234,
                        simulatorSeed=1234,
                        simulators=["NEURON"],
                        simRefPrefix="Net_",
                        suggestedRemoteRunTime=120,
                        defaultSynapticDelay=0.05,
                        mpiConf=MpiSettings.LOCAL_SERIAL,
                        scaleCortex=0.1,
                        scaleThalamus=0,
                        gabaScaling=1,
                        l4ssAmpaScaling=1,
                        l5PyrGapScaling=1,
                        inNrtTcrNmdaScaling=1,
                        pyrSsNmdaScaling=1,
                        deepBiasCurrent=-1,
                        maxElecLenFRB=0.01,
                        maxElecLenRS=0.01,
                        maxElecLenIN=0.01,
                        maxElecLenSS=0.01,
                        somaNseg=-1,
                        varTimestepNeuron=False,
                        verbose=True,
                        runInBackground=False):

    print "Running new column simulation..."

    ############################################

    # Full column populations

    numFRB = 50  #   full model: 50
    numRS = 1000  #   full model: 1000
    numSupBask = 90  #   full model: 90
    numSupAxAx = 90  #   full model: 90
    numSupLTS = 90  #   full model: 90
    numL4SpinStell = 240  #   full model: 240
    numL5TuftIB = 800  #   full model: 800
    numL5TuftRS = 200  #   full model: 200
    numDeepBask = 100  #   full model: 100
    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)

    while File("%s/simulations/%s_N" %
               (project.getProjectMainDirectory().getCanonicalPath(),
                simRef)).exists():
        simRef = "%s%i" % (simRefPrefix, index)
        index = index + 1

    project.simulationParameters.setReference(simRef)

    ### Change num in each cell group

    numFRB = int(scaleCortex * numFRB)
    numRS = int(scaleCortex * numRS)
    numSupBask = int(scaleCortex * numSupBask)
    numSupAxAx = int(scaleCortex * numSupAxAx)
    numSupLTS = int(scaleCortex * numSupLTS)
    numL4SpinStell = int(scaleCortex * numL4SpinStell)
    numL5TuftIB = int(scaleCortex * numL5TuftIB)
    numL5TuftRS = int(scaleCortex * numL5TuftRS)
    numDeepBask = int(scaleCortex * numDeepBask)
    numDeepAxAx = int(scaleCortex * numDeepAxAx)
    numDeepLTS = int(scaleCortex * numDeepLTS)
    numL6NonTuftRS = int(scaleCortex * numL6NonTuftRS)

    numTCR = int(scaleThalamus * numTCR)
    numnRT = int(scaleThalamus * numnRT)

    project.cellGroupsInfo.getCellPackingAdapter(
        "CG3D_L23PyrFRB").setMaxNumberCells(
            numFRB)  # Note only works if RandomCellPackingAdapter
    project.cellGroupsInfo.getCellPackingAdapter(
        "CG3D_L23PyrRS").setMaxNumberCells(numRS)
    project.cellGroupsInfo.getCellPackingAdapter(
        "CG3D_SupBask").setMaxNumberCells(numSupBask)
    project.cellGroupsInfo.getCellPackingAdapter(
        "CG3D_SupAxAx").setMaxNumberCells(numSupAxAx)
    project.cellGroupsInfo.getCellPackingAdapter(
        "CG3D_SupLTS").setMaxNumberCells(numSupLTS)
    project.cellGroupsInfo.getCellPackingAdapter(
        "CG3D_L4SpinStell").setMaxNumberCells(numL4SpinStell)
    project.cellGroupsInfo.getCellPackingAdapter(
        "CG3D_L5TuftIB").setMaxNumberCells(numL5TuftIB)
    project.cellGroupsInfo.getCellPackingAdapter(
        "CG3D_L5TuftRS").setMaxNumberCells(numL5TuftRS)
    project.cellGroupsInfo.getCellPackingAdapter(
        "CG3D_DeepBask").setMaxNumberCells(numDeepBask)
    project.cellGroupsInfo.getCellPackingAdapter(
        "CG3D_DeepAxAx").setMaxNumberCells(numDeepAxAx)
    project.cellGroupsInfo.getCellPackingAdapter(
        "CG3D_DeepLTS").setMaxNumberCells(numDeepLTS)
    project.cellGroupsInfo.getCellPackingAdapter(
        "CG3D_L6NonTuftRS").setMaxNumberCells(numL6NonTuftRS)
    project.cellGroupsInfo.getCellPackingAdapter("CG3D_TCR").setMaxNumberCells(
        numTCR)
    project.cellGroupsInfo.getCellPackingAdapter("CG3D_nRT").setMaxNumberCells(
        numnRT)

    ### Change weights in synapses/gap junctions

    for netConnName in simConfig.getNetConns():

        if gabaScaling != 1:

            SimulationsInfo.addExtraSimProperty("gabaWeightScaling",
                                                str(gabaScaling))
            synList = project.morphNetworkConnectionsInfo.getSynapseList(
                netConnName)

            for index in range(0, len(synList)):
                synName = project.morphNetworkConnectionsInfo.getSynapseList(
                    netConnName).get(index).getSynapseType()
                if synName.count("GABAA") > 0:
                    print "Changing synaptic weight for syn %s in net conn %s by factor %f" % (
                        synName, netConnName, gabaScaling)

                    project.morphNetworkConnectionsInfo.getSynapseList(
                        netConnName).get(index).setWeightsGenerator(
                            NumberGenerator(gabaScaling))

        if l4ssAmpaScaling != 1:

            SimulationsInfo.addExtraSimProperty("l4ssAmpaScaling",
                                                str(l4ssAmpaScaling))
            synList = project.morphNetworkConnectionsInfo.getSynapseList(
                netConnName)

            for index in range(0, len(synList)):
                synName = project.morphNetworkConnectionsInfo.getSynapseList(
                    netConnName).get(index).getSynapseType()
                if synName.count("Syn_AMPA_L4SS_L4SS") > 0:
                    print "Changing synaptic weight for syn %s in net conn %s by factor %f" % (
                        synName, netConnName, l4ssAmpaScaling)

                    project.morphNetworkConnectionsInfo.getSynapseList(
                        netConnName).get(index).setWeightsGenerator(
                            NumberGenerator(l4ssAmpaScaling))

        if l5PyrGapScaling != 1:

            SimulationsInfo.addExtraSimProperty("l5PyrGapScaling",
                                                str(l5PyrGapScaling))
            synList = project.morphNetworkConnectionsInfo.getSynapseList(
                netConnName)

            for index in range(0, len(synList)):
                synName = project.morphNetworkConnectionsInfo.getSynapseList(
                    netConnName).get(index).getSynapseType()
                tgtCG = project.morphNetworkConnectionsInfo.getTargetCellGroup(
                    netConnName)
                if synName.count("Syn_Elect_DeepPyr_DeepPyr"
                                 ) > 0 and tgtCG.count("CG3D_L5") > 0:
                    print "Changing synaptic weight for syn %s in net conn %s by factor %f" % (
                        synName, netConnName, l5PyrGapScaling)

                    project.morphNetworkConnectionsInfo.getSynapseList(
                        netConnName).get(index).setWeightsGenerator(
                            NumberGenerator(l5PyrGapScaling))

        if inNrtTcrNmdaScaling != 1:

            SimulationsInfo.addExtraSimProperty("inNrtTcrNmdaScaling",
                                                str(inNrtTcrNmdaScaling))
            synList = project.morphNetworkConnectionsInfo.getSynapseList(
                netConnName)

            for index in range(0, len(synList)):
                synName = project.morphNetworkConnectionsInfo.getSynapseList(
                    netConnName).get(index).getSynapseType()
                if synName.count("NMDA") > 0 and (
                        synName.endswith("_IN") > 0
                        or synName.endswith("_DeepIN") > 0
                        or synName.endswith("_SupIN") > 0
                        or synName.endswith("_SupFS") > 0
                        or synName.endswith("_DeepFS") > 0
                        or synName.endswith("_SupLTS") > 0
                        or synName.endswith("_DeepLTS") > 0
                        or synName.endswith("_nRT") > 0
                        or synName.endswith("_TCR") > 0):

                    print "Changing synaptic weight for syn %s in net conn %s by factor %f" % (
                        synName, netConnName, inNrtTcrNmdaScaling)

                    project.morphNetworkConnectionsInfo.getSynapseList(
                        netConnName).get(index).setWeightsGenerator(
                            NumberGenerator(inNrtTcrNmdaScaling))

        if pyrSsNmdaScaling != 1:

            SimulationsInfo.addExtraSimProperty("pyrSsNmdaScaling",
                                                str(pyrSsNmdaScaling))
            synList = project.morphNetworkConnectionsInfo.getSynapseList(
                netConnName)

            for index in range(0, len(synList)):
                synName = project.morphNetworkConnectionsInfo.getSynapseList(
                    netConnName).get(index).getSynapseType()
                if synName.count("NMDA") > 0 and (
                        synName.endswith("_SupPyr") > 0
                        or synName.endswith("_DeepPyr") > 0
                        or synName.endswith("_L4SS") > 0
                        or synName.endswith("_L5Pyr") > 0
                        or synName.endswith("_L5RS") > 0
                        or synName.endswith("_L5IB") > 0
                        or synName.endswith("_L6NT") > 0
                        or synName.endswith("_Pyr") > 0):

                    print "Changing synaptic weight for syn %s in net conn %s by factor %f" % (
                        synName, netConnName, pyrSsNmdaScaling)

                    project.morphNetworkConnectionsInfo.getSynapseList(
                        netConnName).get(index).setWeightsGenerator(
                            NumberGenerator(pyrSsNmdaScaling))

    ### Change bias currents

    for inputName in simConfig.getInputs():

        stim = project.elecInputInfo.getStim(inputName)

        if deepBiasCurrent >= 0:

            if stim.getElectricalInput().TYPE == "IClamp" and (
                    stim.getCellGroup() == "CG3D_L5TuftIB"
                    or stim.getCellGroup() == "CG3D_L5TuftRS"
                    or stim.getCellGroup() == "CG3D_L6NonTuftRS"):

                print "Changing offset current in %s to %f" % (
                    stim.getCellGroup(), deepBiasCurrent)

                stim.setAmp(NumberGenerator(deepBiasCurrent))
                project.elecInputInfo.updateStim(stim)

    ### Change spatial discretisation of some cells. This will impact accuracy & simulation speed

    if maxElecLenFRB > 0:
        frbCell = project.cellManager.getCell("L23PyrFRB_varInit")
        info = CellTopologyHelper.recompartmentaliseCell(
            frbCell, maxElecLenFRB, project)
        print "Recompartmentalised FRB cell: " + info
        if somaNseg > 0:
            frbCell.getSegmentWithId(
                0).getSection().setNumberInternalDivisions(somaNseg)

    if maxElecLenRS > 0:
        rsCell = project.cellManager.getCell("L23PyrRS")
        info = CellTopologyHelper.recompartmentaliseCell(
            rsCell, maxElecLenRS, project)
        print "Recompartmentalised RS cell: " + info
        if somaNseg > 0:
            rsCell.getSegmentWithId(0).getSection().setNumberInternalDivisions(
                somaNseg)

    if maxElecLenIN > 0:
        inCells = [
            "SupBasket", "SupAxAx", "SupLTSInter", "DeepBasket", "DeepAxAx",
            "DeepLTSInter"
        ]

        for inCellName in inCells:
            inCell = project.cellManager.getCell(inCellName)
            info = CellTopologyHelper.recompartmentaliseCell(
                inCell, maxElecLenIN, project)
            print "Recompartmentalised " + inCellName + " cell: " + info
            if somaNseg > 0:
                inCell.getSegmentWithId(
                    0).getSection().setNumberInternalDivisions(somaNseg)

    ### Change parallel configuration

    mpiSettings = MpiSettings()
    simConfig.setMpiConf(mpiSettings.getMpiConfiguration(mpiConf))
    print "Parallel configuration: " + str(simConfig.getMpiConf())

    if suggestedRemoteRunTime > 0:
        project.neuronFileManager.setSuggestedRemoteRunTime(
            suggestedRemoteRunTime)
        project.genesisFileManager.setSuggestedRemoteRunTime(
            suggestedRemoteRunTime)

    ### Change synaptic delay associated with each net conn

    for netConnName in simConfig.getNetConns():
        if netConnName.count("gap") == 0:
            print "Changing synaptic delay in %s to %f" % (
                netConnName, defaultSynapticDelay)
            delayGen = NumberGenerator(defaultSynapticDelay)
            for synProps in project.morphNetworkConnectionsInfo.getSynapseList(
                    netConnName):
                synProps.setDelayGenerator(delayGen)

    # defaultSynapticDelay will be recorded in simulation.props and listed in SimulationBrowser GUI
    SimulationsInfo.addExtraSimProperty("defaultSynapticDelay",
                                        str(defaultSynapticDelay))

    ### Generate network structure in neuroConstruct

    pm.doGenerate(simConfig.getName(), neuroConstructSeed)

    while pm.isGenerating():
        print "Waiting for the project to be generated with Simulation Configuration: " + str(
            simConfig)
        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())

    if simulators.count("NEURON") > 0:

        simRefN = simRef + "_N"
        project.simulationParameters.setReference(simRefN)

        nc.generateAndRunNeuron(project,
                                pm,
                                simConfig,
                                simRefN,
                                simulatorSeed,
                                verbose=verbose,
                                runInBackground=runInBackground,
                                varTimestep=varTimestepNeuron)

        sleep(2)  # wait a while before running GENESIS...

    if simulators.count("GENESIS") > 0:

        simRefG = simRef + "_G"
        project.simulationParameters.setReference(simRefG)

        nc.generateAndRunGenesis(project,
                                 pm,
                                 simConfig,
                                 simRefG,
                                 simulatorSeed,
                                 verbose=verbose,
                                 runInBackground=runInBackground)

        sleep(2)  # wait a while before running MOOSE...

    if simulators.count("MOOSE") > 0:

        simRefM = simRef + "_M"
        project.simulationParameters.setReference(simRefM)

        nc.generateAndRunMoose(project,
                               pm,
                               simConfig,
                               simRefM,
                               simulatorSeed,
                               verbose=verbose,
                               runInBackground=runInBackground)

        sleep(2)  # wait a while before running GENESIS...

    print "Finished running all sims, shutting down..."

    stop = datetime.datetime.now()
    print
    print "Started: %s, finished: %s" % (start.strftime("%Y-%m-%d %H:%M"),
                                         stop.strftime("%Y-%m-%d %H:%M"))
    print
                            simulatorSeed,
                            verbose=verbose,
                            runInBackground=runInBackground,
                            varTimestep=varTimestepNeuron)
        
    sleep(2) # wait a while before running GENESIS...
    
if simulators.count("GENESIS")>0:
    
    simRefG = simRef+"_G"
    project.simulationParameters.setReference(simRefG)

    nc.generateAndRunGenesis(project,
                            pm,
                            simConfig,
                            simRefG,
                            simulatorSeed,
                            verbose=verbose,
                            runInBackground=runInBackground)
                            
    sleep(2) # wait a while before running MOOSE...


if simulators.count("MOOSE")>0:

    simRefM = simRef+"_M"
    project.simulationParameters.setReference(simRefM)

    nc.generateAndRunMoose(project,
                            pm,
                            simConfig,
Exemple #3
0
                            runInBackground=runInBackground,
                            saveAsHdf5 = saveAsHdf5,
                            varTimestep=varTimestepNeuron,
                            runMode = runMode)

    sleep(2) # wait a while before running GENESIS...

if simulators.count("GENESIS")>0:

    simRefG = simRef+"_G"
    project.simulationParameters.setReference(simRefG)

    nc.generateAndRunGenesis(project,
                            pm,
                            simConfig,
                            simRefG,
                            simulatorSeed,
                            verbose=verbose,
                            runInBackground=runInBackground)

    sleep(2) # wait a while before running MOOSE...


if simulators.count("MOOSE")>0:

    simRefM = simRef+"_M"
    project.simulationParameters.setReference(simRefM)

    nc.generateAndRunMoose(project,
                            pm,
                            simConfig,
def runColumnSimulation(simConfig=    			"TempSimConfig",
		        simDuration = 			100,
			simDt = 			0.025, 
			neuroConstructSeed = 		1234,
			simulatorSeed = 		1234,
			simulators = 			["NEURON"],
			simRefPrefix =          	"Net_",
			suggestedRemoteRunTime = 	120,
			defaultSynapticDelay =  	0.05,
			mpiConf = 			MpiSettings.LOCAL_SERIAL,
			scaleCortex = 			0.1,
			scaleThalamus = 		0,
			gabaScaling = 			1,
			l4ssAmpaScaling = 		1,
			l5PyrGapScaling = 		1,
			inNrtTcrNmdaScaling = 		1,
			pyrSsNmdaScaling = 		1,
			deepBiasCurrent = 		-1,
			maxElecLenFRB = 		0.01,
			maxElecLenRS =          	0.01,
			maxElecLenIN =         		0.01,
			maxElecLenSS =         		0.01,
			somaNseg =              	-1,
			varTimestepNeuron =     	False,
			verbose =               	True,
			runInBackground = 		False):
			  
    print "Running new column simulation..."

    ############################################

    # Full column populations

    numFRB =                50       #   full model: 50
    numRS =                 1000     #   full model: 1000
    numSupBask =            90       #   full model: 90
    numSupAxAx =            90       #   full model: 90
    numSupLTS =             90       #   full model: 90
    numL4SpinStell =        240      #   full model: 240
    numL5TuftIB =           800      #   full model: 800
    numL5TuftRS =           200      #   full model: 200
    numDeepBask =           100      #   full model: 100
    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)


    while File( "%s/simulations/%s_N"%(project.getProjectMainDirectory().getCanonicalPath(), simRef)).exists():
	simRef = "%s%i"%(simRefPrefix,index)
	index = index+1

    project.simulationParameters.setReference(simRef)


    ### Change num in each cell group

    numFRB = int(scaleCortex * numFRB)
    numRS = int(scaleCortex * numRS)
    numSupBask = int(scaleCortex * numSupBask)
    numSupAxAx = int(scaleCortex * numSupAxAx)
    numSupLTS = int(scaleCortex * numSupLTS)
    numL4SpinStell = int(scaleCortex * numL4SpinStell)
    numL5TuftIB = int(scaleCortex * numL5TuftIB)
    numL5TuftRS = int(scaleCortex * numL5TuftRS)
    numDeepBask = int(scaleCortex * numDeepBask)
    numDeepAxAx = int(scaleCortex * numDeepAxAx)
    numDeepLTS = int(scaleCortex * numDeepLTS)
    numL6NonTuftRS = int(scaleCortex * numL6NonTuftRS)

    numTCR = int(scaleThalamus * numTCR)
    numnRT = int(scaleThalamus * numnRT)

    project.cellGroupsInfo.getCellPackingAdapter("CG3D_L23PyrFRB").setMaxNumberCells(numFRB) # Note only works if RandomCellPackingAdapter
    project.cellGroupsInfo.getCellPackingAdapter("CG3D_L23PyrRS").setMaxNumberCells(numRS)
    project.cellGroupsInfo.getCellPackingAdapter("CG3D_SupBask").setMaxNumberCells(numSupBask)
    project.cellGroupsInfo.getCellPackingAdapter("CG3D_SupAxAx").setMaxNumberCells(numSupAxAx)
    project.cellGroupsInfo.getCellPackingAdapter("CG3D_SupLTS").setMaxNumberCells(numSupLTS)
    project.cellGroupsInfo.getCellPackingAdapter("CG3D_L4SpinStell").setMaxNumberCells(numL4SpinStell)
    project.cellGroupsInfo.getCellPackingAdapter("CG3D_L5TuftIB").setMaxNumberCells(numL5TuftIB)
    project.cellGroupsInfo.getCellPackingAdapter("CG3D_L5TuftRS").setMaxNumberCells(numL5TuftRS)
    project.cellGroupsInfo.getCellPackingAdapter("CG3D_DeepBask").setMaxNumberCells(numDeepBask)
    project.cellGroupsInfo.getCellPackingAdapter("CG3D_DeepAxAx").setMaxNumberCells(numDeepAxAx)
    project.cellGroupsInfo.getCellPackingAdapter("CG3D_DeepLTS").setMaxNumberCells(numDeepLTS)
    project.cellGroupsInfo.getCellPackingAdapter("CG3D_L6NonTuftRS").setMaxNumberCells(numL6NonTuftRS)
    project.cellGroupsInfo.getCellPackingAdapter("CG3D_TCR").setMaxNumberCells(numTCR)
    project.cellGroupsInfo.getCellPackingAdapter("CG3D_nRT").setMaxNumberCells(numnRT)



    ### Change weights in synapses/gap junctions

    for netConnName in simConfig.getNetConns():

	if gabaScaling != 1:

	    SimulationsInfo.addExtraSimProperty("gabaWeightScaling", str(gabaScaling))
	    synList = project.morphNetworkConnectionsInfo.getSynapseList(netConnName)
	    
	    for index in range(0, len(synList)):
		synName = project.morphNetworkConnectionsInfo.getSynapseList(netConnName).get(index).getSynapseType()
		if synName.count("GABAA")>0:
		    print "Changing synaptic weight for syn %s in net conn %s by factor %f"%(synName, netConnName, gabaScaling)
		
		    project.morphNetworkConnectionsInfo.getSynapseList(netConnName).get(index).setWeightsGenerator(NumberGenerator(gabaScaling))
		    
	if l4ssAmpaScaling !=1:
	  
	    SimulationsInfo.addExtraSimProperty("l4ssAmpaScaling", str(l4ssAmpaScaling))
	    synList = project.morphNetworkConnectionsInfo.getSynapseList(netConnName)
	    
	    for index in range(0, len(synList)):
		synName = project.morphNetworkConnectionsInfo.getSynapseList(netConnName).get(index).getSynapseType()
		if synName.count("Syn_AMPA_L4SS_L4SS")>0:
		    print "Changing synaptic weight for syn %s in net conn %s by factor %f"%(synName, netConnName, l4ssAmpaScaling)
		
		    project.morphNetworkConnectionsInfo.getSynapseList(netConnName).get(index).setWeightsGenerator(NumberGenerator(l4ssAmpaScaling))
		    
	if l5PyrGapScaling !=1:
	  
	    SimulationsInfo.addExtraSimProperty("l5PyrGapScaling", str(l5PyrGapScaling))
	    synList = project.morphNetworkConnectionsInfo.getSynapseList(netConnName)
	    
	    for index in range(0, len(synList)):
		synName = project.morphNetworkConnectionsInfo.getSynapseList(netConnName).get(index).getSynapseType()
		tgtCG = project.morphNetworkConnectionsInfo.getTargetCellGroup(netConnName)
		if synName.count("Syn_Elect_DeepPyr_DeepPyr")>0 and tgtCG.count("CG3D_L5")>0:
		    print "Changing synaptic weight for syn %s in net conn %s by factor %f"%(synName, netConnName, l5PyrGapScaling)
		
		    project.morphNetworkConnectionsInfo.getSynapseList(netConnName).get(index).setWeightsGenerator(NumberGenerator(l5PyrGapScaling))
		    
	if inNrtTcrNmdaScaling !=1:
	  
	    SimulationsInfo.addExtraSimProperty("inNrtTcrNmdaScaling", str(inNrtTcrNmdaScaling))
	    synList = project.morphNetworkConnectionsInfo.getSynapseList(netConnName)
	    
	    for index in range(0, len(synList)):
		synName = project.morphNetworkConnectionsInfo.getSynapseList(netConnName).get(index).getSynapseType()
		if synName.count("NMDA")>0 and (synName.endswith("_IN")>0 or 
						synName.endswith("_DeepIN")>0 or 
						synName.endswith("_SupIN")>0 or 
						synName.endswith("_SupFS")>0 or 
						synName.endswith("_DeepFS")>0 or 
						synName.endswith("_SupLTS")>0 or 
						synName.endswith("_DeepLTS")>0 or 
						synName.endswith("_nRT")>0 or 
						synName.endswith("_TCR")>0):
						  
		    print "Changing synaptic weight for syn %s in net conn %s by factor %f"%(synName, netConnName, inNrtTcrNmdaScaling)
		
		    project.morphNetworkConnectionsInfo.getSynapseList(netConnName).get(index).setWeightsGenerator(NumberGenerator(inNrtTcrNmdaScaling))
	  
	if pyrSsNmdaScaling !=1:
	  
	    SimulationsInfo.addExtraSimProperty("pyrSsNmdaScaling", str(pyrSsNmdaScaling))
	    synList = project.morphNetworkConnectionsInfo.getSynapseList(netConnName)
	    
	    for index in range(0, len(synList)):
		synName = project.morphNetworkConnectionsInfo.getSynapseList(netConnName).get(index).getSynapseType()
		if synName.count("NMDA")>0 and (synName.endswith("_SupPyr")>0 or
						synName.endswith("_DeepPyr")>0 or
						synName.endswith("_L4SS")>0 or
						synName.endswith("_L5Pyr")>0 or
						synName.endswith("_L5RS")>0 or
						synName.endswith("_L5IB")>0 or
						synName.endswith("_L6NT")>0 or
						synName.endswith("_Pyr")>0):
						  
		    print "Changing synaptic weight for syn %s in net conn %s by factor %f"%(synName, netConnName, pyrSsNmdaScaling)
		
		    project.morphNetworkConnectionsInfo.getSynapseList(netConnName).get(index).setWeightsGenerator(NumberGenerator(pyrSsNmdaScaling))


    ### Change bias currents

    for inputName in simConfig.getInputs():
      
	stim = project.elecInputInfo.getStim(inputName)
      
	if deepBiasCurrent >= 0:
	    
	    if stim.getElectricalInput().TYPE == "IClamp" and (stim.getCellGroup()=="CG3D_L5TuftIB" or stim.getCellGroup()=="CG3D_L5TuftRS" or stim.getCellGroup()=="CG3D_L6NonTuftRS"):
	    
	      print "Changing offset current in %s to %f"%(stim.getCellGroup(), deepBiasCurrent)
	      
	      stim.setAmp(NumberGenerator(deepBiasCurrent))
	      project.elecInputInfo.updateStim(stim)
	  


    ### Change spatial discretisation of some cells. This will impact accuracy & simulation speed

    if maxElecLenFRB > 0:
	frbCell = project.cellManager.getCell("L23PyrFRB_varInit")
	info = CellTopologyHelper.recompartmentaliseCell(frbCell, maxElecLenFRB, project)
	print "Recompartmentalised FRB cell: "+info
	if somaNseg > 0:
	    frbCell.getSegmentWithId(0).getSection().setNumberInternalDivisions(somaNseg)

    if maxElecLenRS > 0:
	rsCell = project.cellManager.getCell("L23PyrRS")
	info = CellTopologyHelper.recompartmentaliseCell(rsCell, maxElecLenRS, project)
	print "Recompartmentalised RS cell: "+info
	if somaNseg > 0:
	    rsCell.getSegmentWithId(0).getSection().setNumberInternalDivisions(somaNseg)

    if maxElecLenIN > 0:
	inCells = ["SupBasket", "SupAxAx","SupLTSInter","DeepBasket", "DeepAxAx","DeepLTSInter"]

	for inCellName in inCells:
	    inCell = project.cellManager.getCell(inCellName)
	    info = CellTopologyHelper.recompartmentaliseCell(inCell, maxElecLenIN, project)
	    print "Recompartmentalised "+inCellName+" cell: "+info
	    if somaNseg > 0:
		inCell.getSegmentWithId(0).getSection().setNumberInternalDivisions(somaNseg)


    ### Change parallel configuration

    mpiSettings = MpiSettings()
    simConfig.setMpiConf(mpiSettings.getMpiConfiguration(mpiConf))
    print "Parallel configuration: "+ str(simConfig.getMpiConf())

    if suggestedRemoteRunTime > 0:
	project.neuronFileManager.setSuggestedRemoteRunTime(suggestedRemoteRunTime)
	project.genesisFileManager.setSuggestedRemoteRunTime(suggestedRemoteRunTime)


    ### Change synaptic delay associated with each net conn

    for netConnName in simConfig.getNetConns():
	if netConnName.count("gap")==0:
	    print "Changing synaptic delay in %s to %f"%(netConnName, defaultSynapticDelay)
	    delayGen = NumberGenerator(defaultSynapticDelay)
	    for synProps in project.morphNetworkConnectionsInfo.getSynapseList(netConnName):
		synProps.setDelayGenerator(delayGen)

    # defaultSynapticDelay will be recorded in simulation.props and listed in SimulationBrowser GUI
    SimulationsInfo.addExtraSimProperty("defaultSynapticDelay", str(defaultSynapticDelay))


    ### Generate network structure in neuroConstruct

    pm.doGenerate(simConfig.getName(), neuroConstructSeed)

    while pm.isGenerating():
	    print "Waiting for the project to be generated with Simulation Configuration: "+str(simConfig)
	    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())


    if simulators.count("NEURON")>0:
	
	simRefN = simRef+"_N"
	project.simulationParameters.setReference(simRefN)

	nc.generateAndRunNeuron(project,
				pm,
				simConfig,
				simRefN,
				simulatorSeed,
				verbose=verbose,
				runInBackground=runInBackground,
				varTimestep=varTimestepNeuron)
	    
	sleep(2) # wait a while before running GENESIS...
	
    if simulators.count("GENESIS")>0:
	
	simRefG = simRef+"_G"
	project.simulationParameters.setReference(simRefG)

	nc.generateAndRunGenesis(project,
				pm,
				simConfig,
				simRefG,
				simulatorSeed,
				verbose=verbose,
				runInBackground=runInBackground)
				
	sleep(2) # wait a while before running MOOSE...


    if simulators.count("MOOSE")>0:

	simRefM = simRef+"_M"
	project.simulationParameters.setReference(simRefM)

	nc.generateAndRunMoose(project,
				pm,
				simConfig,
				simRefM,
				simulatorSeed,
				verbose=verbose,
				runInBackground=runInBackground)
				
	sleep(2) # wait a while before running GENESIS...


    print "Finished running all sims, shutting down..."


    stop = datetime.datetime.now()
    print
    print "Started: %s, finished: %s" % (start.strftime("%Y-%m-%d %H:%M"),stop.strftime("%Y-%m-%d %H:%M"))
    print
Exemple #5
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        if "_SI" in sim:
            simRef = simRef+"_SI"
            units = UnitConverter.GENESIS_SI_UNITS
        if "_PHYS" in sim:
            simRef = simRef+"_PHYS"
            units = UnitConverter.GENESIS_PHYSIOLOGICAL_UNITS

        project.simulationParameters.setReference(simRef)

        if runSims:
            nc.generateAndRunGenesis(project,
                             pm,
                             simConfig,
                             simRef,
                             simulatorSeed,
                             verbose=verbose,
                             quitAfterRun=runInBackground,
                             runInBackground=runInBackground,
                             units=units,
                             symmetricComps=False)

        allRunningSims.append(simRef)

        time.sleep(2) # wait a while before running GENESISsym...
        
    doCheckNumberSims()

    if simulators.count("GENESISsym")>0:

        simRef = simRefPrefix+"_Gs"+recompSuffix
        project.simulationParameters.setReference(simRef)