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 "Number of cells generated: " + str(project.generatedCellPositions.getNumberInAllCellGroups())
print "Number of network connections generated: " + str(project.generatedNetworkConnections.getNumAllSynConns())
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
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)):
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
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)
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..."
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()
numFRB = 3
numRS = 3
numLTS = 0
numBask = 0
numAxAx = 0
numFRB = 6
numRS = 20
numLTS = 10
numBask = 10
numAxAx = 10
'''
numPyr = 1152
fractFRB = 0.05
SimulationsInfo.addExtraSimProperty("fractFRB", str(fractFRB))
numFRB = int(fractFRB*numPyr)
numRS = numPyr - numFRB
numLTS = 96
numBask = 96
numAxAx = 96
# Maximum electronic length of compartments (adjusts nseg etc.)
maxElecLenFRB = -1 # 0.01 will give ~700, -1 will leave as is
maxElecLenRS = -1 # 0.01 will give ~700, -1 will leave as is
maxElecLenLTS = -1 # 0.01 will give ~570, -1 will leave as is
maxElecLenAxAx = -1 # 0.01 will give ~570, -1 will leave as is
maxElecLenBask = -1 # 0.01 will give ~570, -1 will leave as is
somaNseg = -1 # 12
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)
