def load_project(self, fname):
file = File(fname)
print 'Loading project file: ', file.getAbsolutePath()
pm = ProjectManager()
project = pm.loadProject(file)
print pm.status()
return project
def testAll(argv=None):
if argv is None:
argv = sys.argv
print "Loading project from " + projFile.getCanonicalPath()
projectManager = ProjectManager()
project = projectManager.loadProject(projFile)
assert (len(project.getProjectDescription()) > 0)
assert (len(project.cellManager.getAllCells()) >= 6)
#assert(project.proj3Dproperties.getDisplayOption() == Display3DProperties.DISPLAY_SOMA_SOLID_NEURITE_LINE)
assert (abs(project.simulationParameters.getDt() - 0.01) <= 1e-9)
assert (abs(project.simulationParameters.getTemperature() - 6.3) < 1e-6)
assert (not project.neuronSettings.isVarTimeStep())
assert (project.neuronSettings.getDataSaveFormat().equals(
NeuronSettings.DataSaveFormat.TEXT_NC))
assert (project.genesisSettings.isSymmetricCompartments())
assert (project.genesisSettings.isSIUnits())
defSimConfig = project.simConfigInfo.getSimConfig(
"Default Simulation Configuration")
assert (str(defSimConfig.getCellGroups()) == '[baskets, pyramidals]')
smallNetSimConfig = project.simConfigInfo.getSimConfig("SmallNetwork")
assert (smallNetSimConfig.getCellGroups().size() == 2)
assert (smallNetSimConfig.getNetConns().size() == 4)
assert (smallNetSimConfig.getInputs().size() == 1)
assert (project.cellGroupsInfo.getCellPackingAdapter(
"pyramidals_48").getMaxNumberCells() == 48)
assert (project.cellGroupsInfo.getCellPackingAdapter(
"baskets_12").getMaxNumberCells() == 12)
print "\n**************************************"
print " All tests passed!"
print "**************************************\n"
def testAll(argv=None):
if argv is None:
argv = sys.argv
print "Loading project from " + projFile.getCanonicalPath()
projectManager = ProjectManager()
project = projectManager.loadProject(projFile)
assert (len(project.getProjectDescription()) > 0)
assert (len(project.cellManager.getAllCells()) >= 7)
assert (len(project.cellGroupsInfo.getAllCellGroupNames()) >= 4)
assert (project.simulationParameters.getDt() - 0.0125 <= 1e-6)
assert (project.neuronSettings.isVarTimeStep())
assert (project.neuronSettings.getDataSaveFormat().equals(
NeuronSettings.DataSaveFormat.TEXT_NC))
assert (project.simulationParameters.getTemperature() == 34)
'''
sci = project.simConfigInfo
cgi = project.cellGroupsInfo
assert(cgi.getCellType("Channeltestgroup") == "Channeltest_Cell")
assert(cgi.getCellType("CMLtestGroup") == "CMLtest_Cell")
assert(cgi.getCellType("pyr_group") == "LarkumPyr")
assert(cgi.getCellType("pyrCML_group") == "LarkumPyr_NML")
arrayListsIdentical(sci.getSimConfig("Default Simulation Configuration").getCellGroups(), ["Channeltestgroup", "CMLtestGroup"])
arrayListsIdentical(sci.getSimConfig("test_IClamp").getCellGroups(), ["pyr_group", "pyrCML_group"])
arrayListsIdentical(sci.getSimConfig("background activity").getCellGroups(), ["pyr_group"])
'''
print "\n**************************************"
print " All tests passed!"
print "**************************************\n"
def testAll(argv=None):
if argv is None:
argv = sys.argv
print "Loading project from " + projFile.getCanonicalPath()
projectManager = ProjectManager()
project = projectManager.loadProject(projFile)
assert (len(project.getProjectDescription()) > 0)
assert (len(project.cellManager.getAllCells()) >= 1)
#assert(project.proj3Dproperties.getDisplayOption() == Display3DProperties.DISPLAY_SOMA_SOLID_NEURITE_LINE)
assert (abs(project.simulationParameters.getDt() - 0.02) <= 1e-9)
assert (abs(project.simulationParameters.getTemperature() - 6.3) < 1e-6)
assert (not project.neuronSettings.isVarTimeStep())
assert (project.neuronSettings.getDataSaveFormat().equals(
NeuronSettings.DataSaveFormat.TEXT_NC))
assert (project.genesisSettings.isSIUnits())
defSimConfig = project.simConfigInfo.getSimConfig(
"Default Simulation Configuration")
assert (str(defSimConfig.getCellGroups()) == '[SampleCellGroup]')
assert (defSimConfig.getCellGroups().size() == 1)
assert (defSimConfig.getInputs().size() == 1)
print "\n**************************************"
print " All tests passed!"
print "**************************************\n"
Vervaeke2012. """ import os import random import time from java.lang import System from java.io import File from java.util import ArrayList from ucl.physiol.neuroconstruct.project import ProjectManager from ucl.physiol.neuroconstruct.neuron import NeuronFileManager from ucl.physiol.neuroconstruct.nmodleditor.processes import ProcessManager from ucl.physiol.neuroconstruct.cell.utils import CellTopologyHelper timestamp = str(time.time()) pm = ProjectManager(None, None) project_path = '../GJGolgi_ReducedMorph.ncx' project_file = File(project_path) project = pm.loadProject(project_file) sim_config_name = 'dendritic_attenuation' sim_config = project.simConfigInfo.getSimConfig(sim_config_name) project.neuronSettings.setNoConsole() n_points = 18 detailed_distance_bounds = range(10.,190.,10.) rec_segs_reduced = [0,4,5,6] dendritic_group = 'apical_dend_2' # switch off Na channels (TTX)
from java.io import File
except ImportError:
print "Note: this file should be run using ..\\nC.bat -python XXX.py' or './nC.sh -python XXX.py'"
print "See http://www.neuroconstruct.org/docs/python.html for more details"
quit()
from ucl.physiol.neuroconstruct.project import ProjectManager
from ucl.physiol.neuroconstruct.cell.converters import MorphMLConverter
# 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(
"../osb/showcase/neuroConstructShowcase/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"
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
# Load an existing neuroConstruct project
projFile = File("../CElegans.ncx")
print "Loading project from file: " + projFile.getAbsolutePath()+", exists: "+ str(projFile.exists())
pm = ProjectManager()
project = pm.loadProject(projFile)
print "Loaded project: " + project.getProjectName()
defSimConfig = project.simConfigInfo.getDefaultSimConfig()
cellsOnlySimConfig = project.simConfigInfo.getSimConfig("CellsOnly")
pharyngealSimConfig = project.simConfigInfo.getSimConfig("PharyngealNeurons")
mdl08SimConfig = project.simConfigInfo.getSimConfig("MDL08Connections")
expectedNumberCells = 302
##########################
print "\n----- Test 1: Check number of cells in sim config "+defSimConfig.getName()+"..."
pm.doGenerate(defSimConfig.getName(), 1234)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: "+str(defSimConfig)
sleep(2)
numGenerated = project.generatedCellPositions.getNumberInAllCellGroups()
print "Number of cells generated: " + str(numGenerated)
assert numGenerated == expectedNumberCells
print "Correct number of cells generated!"
##########################
print "\n---- Test 2: number of cells in sim config "+cellsOnlySimConfig.getName()+"..."
pm.doGenerate(cellsOnlySimConfig.getName(), 1234)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: "+str(cellsOnlySimConfig)
sleep(2)
numGenerated = project.generatedCellPositions.getNumberInAllCellGroups()
print "Number of cells generated: " + str(numGenerated)
assert numGenerated == expectedNumberCells
print "Correct number of cells generated!"
##########################
filename = "../../CElegansNeuronTables.xls"
print "\n---- Test 3: confirm settings in project match those in "+filename+"..."
from xlrd import open_workbook
rb = open_workbook(filename)
print "Opened Excel file: "+ filename
confirmed = 0
prefix = "NCXLS_"
for row in range(1,rb.sheet_by_index(0).nrows):
pre = rb.sheet_by_index(0).cell(row,0).value
post = rb.sheet_by_index(0).cell(row,1).value
syntype = rb.sheet_by_index(0).cell(row,2).value
num = int(rb.sheet_by_index(0).cell(row,3).value)
synclass = rb.sheet_by_index(0).cell(row,4).value
#print "------------------------------------------\nConnection %i has %i from %s to %s (type: %s, synapse: %s)" %(row, num, pre, post, syntype, synclass)
netConnName = prefix+pre+"_"+post
if "GapJunction" in syntype:
netConnName = netConnName + "_GJ"
src = project.morphNetworkConnectionsInfo.getSourceCellGroup(netConnName)
tgt = project.morphNetworkConnectionsInfo.getTargetCellGroup(netConnName)
synlist = project.morphNetworkConnectionsInfo.getSynapseList(netConnName)
#print synlist
assert synclass == synlist[0].getSynapseType()
if '_GJ' in synclass and synclass != 'Generic_GJ':
print "Only allowed gap junction synapse is Generic_GJ, not "+synclass
assert synclass == 'Generic_GJ'
if not (src == pre and tgt == post):
print "------------------------------------------\nConnection %i has %i from %s to %s (type: %s, synapse: %s)" %(row, num, pre, post, syntype, synclass)
print "*** Couldn't find connection: %s, src: %s, tgt: %s"%(netConnName, src, tgt)
assert src == pre
assert tgt == post
if src == tgt:
print "------------------------------------------\nConnection %i has %i from %s to %s (type: %s, synapse: %s)" %(row, num, pre, post, syntype, synclass)
print "*** This connection is from: %s, src: %s, tgt: %s, synaptic connection on same cell!!"%(netConnName, src, tgt)
confirmed += 1
print "Confirmed %i connections in project match spreadsheet"%confirmed
havePrefix = 0
allNetConnNames = project.morphNetworkConnectionsInfo.getAllSimpleNetConnNames()
for name in allNetConnNames:
if name.startswith(prefix):
havePrefix +=1
print "Project contains %i Network connections starting with %s"%(havePrefix, prefix)
assert havePrefix == confirmed
##########################
print "\n---- Test 4: number of cells in sim config "+pharyngealSimConfig.getName()+"..."
pm.doGenerate(pharyngealSimConfig.getName(), 1234471)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: "+str(pharyngealSimConfig)
sleep(2)
numCells = project.generatedCellPositions.getNumberInAllCellGroups()
numConns = project.generatedNetworkConnections.getNumAllSynConns()
print "Number of cells: %i, number of connections: %i"%(numCells,numConns)
expectedCells = 20
expectedNetConns = 269
assert numCells == expectedCells
assert numConns == expectedNetConns
print "Correct number of cells & connections generated!"
##########################
print "\n---- Test 5: number of cells in sim config "+mdl08SimConfig.getName()+"..."
pm.doGenerate(mdl08SimConfig.getName(), 1234471)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: "+str(mdl08SimConfig)
sleep(2)
numCells = project.generatedCellPositions.getNumberInAllCellGroups()
numConns = project.generatedNetworkConnections.getNumAllSynConns()
print "Number of cells: %i, number of connections: %i"%(numCells,numConns)
expectedCells = 9
expectedNetConns = 21
assert numCells == expectedCells
assert numConns == expectedNetConns
print "Correct number of cells & connections generated!"
##########################
print "\n---- Test 6: General neuroConstruct project settings..."
assert(project.proj3Dproperties.getDisplayOption() == Display3DProperties.DISPLAY_SOMA_NEURITE_SOLID)
assert(abs(project.simulationParameters.getDt()-0.025)<=1e-9)
assert(not project.neuronSettings.isVarTimeStep())
assert(project.neuronSettings.getDataSaveFormat().equals(NeuronSettings.DataSaveFormat.TEXT_NC))
assert(abs(project.simulationParameters.getTemperature() - 20.0) < 1e-6)
##########################
print "\n------------------------------------------All tests completed!\n"
exit()
def SingleCellNML2generator(projString=" ",
ConfigDict={},
ElecLenList=[],
somaNseg=None,
savingDir=None):
projFile = File(os.getcwd(), projString)
pm = ProjectManager()
compSummary = {}
for config in ConfigDict.keys():
project = pm.loadProject(projFile)
nmlfm = NeuroMLFileManager(project)
compSummary[config] = {}
if " " in config:
configPath = config.replace(" ", "_")
else:
configPath = config
for maxElecLen in ElecLenList:
compSummary[config][str(maxElecLen)] = {}
cell = project.cellManager.getCell(ConfigDict[config])
if maxElecLen > 0:
info = CellTopologyHelper.recompartmentaliseCell(
cell, maxElecLen, project)
print "Recompartmentalising cell %s" % ConfigDict[config]
if somaNseg != None:
cell.getSegmentWithId(
0).getSection().setNumberInternalDivisions(somaNseg)
if savingDir != None:
cellpath = r'../../NeuroML2/%s/%s/%s_%f' % (
savingDir, configPath, configPath, maxElecLen)
else:
cellpath = r'../../NeuroML2/%s/%s_%f' % (
configPath, configPath, maxElecLen)
else:
if savingDir != None:
cellpath = r'../../NeuroML2/%s/%s/%s_default' % (
savingDir, configPath, configPath)
else:
cellpath = r'../../NeuroML2/%s/%s_default' % (configPath,
configPath)
summary = str(cell.getMorphSummary())
summary_string = summary.split("_")
for feature in summary_string:
feature_split = feature.split(":")
compSummary[config][str(maxElecLen)][
feature_split[0]] = feature_split[1]
# the format of summary : Segs:122_Secs:61_IntDivs:1458
print("Will be printing a cell morphology summary")
print compSummary[config][str(maxElecLen)]
######### it turns out that this does not save recompartmentalized cells - all saved cells have identical spatial discretization;
##### generateNeuroML2 receives the parent projFile but not the loaded project which is modified by the CellTopologyHelper.recompartmentaliseCell()
##################### neuroConstruct block #############################################################################
neuroConstructSeed = 1234
verbose = True
pm.doGenerate(config, neuroConstructSeed)
while pm.isGenerating():
if verbose:
print(
"Waiting for the project to be generated with Simulation Configuration: "
+ config)
time.sleep(5)
simConfig = project.simConfigInfo.getSimConfig(config)
seed = 1234
genDir = File(projFile.getParentFile(), "generatedNeuroML2")
nmlfm.generateNeuroMLFiles(
simConfig, NeuroMLConstants.NeuroMLVersion.getLatestVersion(),
LemsConstants.LemsOption.LEMS_WITHOUT_EXECUTE_MODEL,
OriginalCompartmentalisation(), seed, False, True, genDir,
"GENESIS Physiological Units", False)
########################################################################################################################
if not os.path.exists(cellpath):
print("Creating a new directory %s" % cellpath)
os.makedirs(cellpath)
else:
print("A directory %s already exists" % cellpath)
src_files = os.listdir("../generatedNeuroML2/")
for file_name in src_files:
full_file_name = os.path.join("../generatedNeuroML2/",
file_name)
if (os.path.isfile(full_file_name)):
print("Moving generated NeuroML2 to files to %s" %
cellpath)
shutil.copy(full_file_name, cellpath)
#with open("compSummary.json",'w') as fout:
#json.dump(compSummary, fout)
subprocess.call(["~/neuroConstruct/nC.sh -python RegenerateNml2.py -f"],
shell=True)
#subprocess.call(["cp compSummary.json ~/Thalamocortical/NeuroML2/"],shell=True)
quit()
def testAll(argv=None):
if argv is None:
argv = sys.argv
print "Loading project from " + projFile.getCanonicalPath()
projectManager = ProjectManager()
project = projectManager.loadProject(projFile)
assert (len(project.getProjectDescription()) > 0)
assert (len(project.cellManager.getAllCells()) >= 22)
assert (len(project.cellGroupsInfo.getAllCellGroupNames()) >= 36)
synSetupFile = open("netbuild/makeSyns.sh", 'r')
for line in synSetupFile:
line = line.strip()
if len(line) > 0 and not line.startswith("#"):
words = line.split()
if len(words) >= 6 and words[2].startswith("Syn_"):
synName = words[2]
syn_dir = "../cellMechanisms/%s" % synName
if os.path.isdir(syn_dir):
cm = project.cellMechanismInfo.getCellMechanism(synName)
print "Checked syn %s" % cm.getInstanceName()
else:
print("Problem finding directory: %s!! This is probably due to the synapses not having been generated \n"%syn_dir+ \
"from netbuild/makeSyns.sh (they need to be generated loacally; too many to commit to repository)")
netConnList = open("netbuild/netConnList", 'r')
for line in netConnList:
line = line.strip()
if len(line) > 0 and not line.startswith("#"):
#print "\n\n---- Deciphering line: "+ line
words = line.split()
source = words[0]
target = words[1]
syns = words[2].strip("[]").split(",")
netConnName = "NC3D_" + source[5:] + "_" + target[5:]
assert (source == project.morphNetworkConnectionsInfo.
getSourceCellGroup(netConnName))
assert (target == project.morphNetworkConnectionsInfo.
getTargetCellGroup(netConnName))
print "Checked %s" % netConnName
assert (project.proj3Dproperties.getDisplayOption() ==
Display3DProperties.DISPLAY_SOMA_SOLID_NEURITE_LINE)
assert (abs(project.simulationParameters.getDt() - 0.025) <= 1e-9)
assert (not project.neuronSettings.isVarTimeStep())
assert (project.neuronSettings.isForceCorrectInit())
assert (project.neuronSettings.getDataSaveFormat().equals(
NeuronSettings.DataSaveFormat.TEXT_NC))
assert (not project.genesisSettings.isSymmetricCompartments())
assert (project.genesisSettings.isPhysiologicalUnits())
print "\n**************************************"
print " All tests passed!"
print "**************************************\n"
