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)
simManager.runMultipleSims(simConfigs = simConfigs,
simDt = simDt,
simulators = simulators,
runInBackground = runInBackground,
varTimestepNeuron = varTimestepNeuron,
varTimestepTolerance = varTimestepTolerance,
mpiConfig = mpiConfig,
suggestedRemoteRunTime = suggestedRemoteRunTime)
simManager.reloadSims(plotVoltageOnly = plotVoltageOnly,
plotSims = plotSims,
analyseSims = analyseSims)
report= ""
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell13-TCR-FigA7-600"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.TCRFigA7_600.mep')['TCRFigA7_600']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGTCR_0': mep_from_nml2}
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
return report
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)
simManager.runMultipleSims(simConfigs = simConfigs,
simDt = simDt,
simulators = simulators,
runInBackground = runInBackground,
varTimestepNeuron = varTimestepNeuron,
varTimestepTolerance = varTimestepTolerance,
mpiConfig = mpiConfig,
suggestedRemoteRunTime = suggestedRemoteRunTime)
simManager.reloadSims(plotVoltageOnly = plotVoltageOnly,
plotSims = plotSims,
analyseSims = analyseSims)
report= ""
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.supaxax.mep')['SupAxAx']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGsupaxax_0': mep_from_nml2}
spikeTimeAccuracy = 0.711 # ms # could be more accurate with var time step in nrn, but need to compare these to jNeuroML_NEURON
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,
spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+"\n"
return report
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)
simManager.runMultipleSims(simConfigs=simConfigs,
simDt=simDt,
simulators=simulators,
runInBackground=runInBackground,
varTimestepNeuron=varTimestepNeuron,
varTimestepTolerance=varTimestepTolerance,
mpiConfig=mpiConfig,
suggestedRemoteRunTime=suggestedRemoteRunTime)
simManager.reloadSims(plotVoltageOnly=plotVoltageOnly,
plotSims=plotSims,
analyseSims=analyseSims)
report = ""
mep_from_nml2 = nc.loadMepFile(
'../../NeuroML2/test/.test.supaxax.mep')['SupAxAx']
for value in range(0, len(mep_from_nml2)):
mep_from_nml2[value] = 1000 * mep_from_nml2[value]
spikeTimesToCheck = {'CGsupaxax_0': mep_from_nml2}
spikeTimeAccuracy = 0.711 # ms # could be more accurate with var time step in nrn, but need to compare these to jNeuroML_NEURON
report2 = simManager.checkSims(spikeTimesToCheck=spikeTimesToCheck,
spikeTimeAccuracy=spikeTimeAccuracy)
print report2
report = report + report2 + "\n"
return report
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)
simManager.runMultipleSims(simConfigs=simConfigs,
simDt=simDt,
simulators=simulators,
runInBackground=runInBackground,
varTimestepNeuron=varTimestepNeuron,
varTimestepTolerance=varTimestepTolerance,
mpiConfig=mpiConfig,
suggestedRemoteRunTime=suggestedRemoteRunTime)
simManager.reloadSims(plotVoltageOnly=plotVoltageOnly,
plotSims=plotSims,
analyseSims=analyseSims)
report = ""
if simDt == 0.005:
if "Default Simulation Configuration" in simConfigs:
# These were discovered using analyseSims = True above.
# They need to hold for all simulators
spikeTimesToCheck = {
'CG_CML_0':
nc.loadMepFile('.testNoTable0005.mep')['Current clamp']
}
spikeTimeAccuracy = 0.0751 # could be more accurate with var time step in nrn, but need to compare these to jNeuroML_NEURON
report0 = simManager.checkSims(spikeTimesToCheck=spikeTimesToCheck,
spikeTimeAccuracy=spikeTimeAccuracy)
print report0
report = report + report0 + "\n"
if "Cell7-tuftIB-FigA4-1300" in simConfigs:
print(
"Tests for default project simulation for %s with 0.005 dt in NEURON"
% ("Cell7-tuftIB-FigA4-1300"))
spikeTimesToCheck = {
'CGtuftIB_0':
nc.loadMepFile('.test.tuftIBFigA4_1300_0005NoTable.mep')
['FigA4']
}
spikeTimeAccuracy = 0 # # could be more accurate with var time step in nrn, but need to compare these to jNeuroML_NEURON
report2 = simManager.checkSims(
spikeTimesToCheck=spikeTimesToCheck,
spikeTimeAccuracy=spikeTimeAccuracy)
print report2
report = report + report2 + '\n'
if "Cell7-tuftIB-FigA4-1500" in simConfigs:
print(
"Tests for default project simulation for %s with 0.01 dt in NEURON"
% ("Cell7-tuftIB-FigA4-1500"))
spikeTimesToCheck = {
'CGtuftIB_0':
nc.loadMepFile('.test.tuftIBFigA4_1500_0005NoTable.mep')
['tuftIBFigA4_1500']
}
spikeTimeAccuracy = 0
report2 = simManager.checkSims(
spikeTimesToCheck=spikeTimesToCheck,
spikeTimeAccuracy=spikeTimeAccuracy)
print report2
report = report + report2 + '\n'
######## added by Rokas Stanislovas : tests for all figures with 0.01 dt and default project spatial discretization in NEURON
if "NEURON" == simulators[0]:
if simDt == 0.01:
if "Cell1-supppyrRS-FigA1RS" in simConfigs:
print(
"Tests for default project simulation for %s with 0.01 dt in NEURON"
% ("Cell1-supppyrRS-FigA1RS"))
spikeTimesToCheck = {
'CGsuppyrRS_0':
nc.loadMepFile('.test.FigA1RSNoTable.mep')['FigA1RS']
}
spikeTimeAccuracy = 0
report2 = simManager.checkSims(
spikeTimesToCheck=spikeTimesToCheck,
spikeTimeAccuracy=spikeTimeAccuracy)
print report2
report = report + report2 + '\n'
if "Default Simulation Configuration" in simConfigs:
# These were discovered using analyseSims = True above.
# They need to hold for all simulators
spikeTimesToCheck = {
'CG_CML_0':
nc.loadMepFile('.testNoTable.mep')['Current clamp']
}
spikeTimeAccuracy = 0.0751 # could be more accurate with var time step in nrn, but need to compare these to jNeuroML_NEURON
report0 = simManager.checkSims(
spikeTimesToCheck=spikeTimesToCheck,
spikeTimeAccuracy=spikeTimeAccuracy)
print report0
report = report + report0 + "\n"
return report
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)
simManager.runMultipleSims(simConfigs = simConfigs,
simDt = simDt,
simulators = simulators,
runInBackground = runInBackground,
varTimestepNeuron = varTimestepNeuron,
varTimestepTolerance = varTimestepTolerance,
mpiConfig = mpiConfig,
suggestedRemoteRunTime = suggestedRemoteRunTime)
simManager.reloadSims(plotVoltageOnly = plotVoltageOnly,
plotSims = plotSims,
analyseSims = analyseSims)
report= ""
if simDt==0.005:
if "Default Simulation Configuration" in simConfigs:
# These were discovered using analyseSims = True above.
# They need to hold for all simulators
mep_from_nml2=nc.loadMepFile('../generatedNeuroML2/.test.mep')['Current clamp']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CG_CML_0': mep_from_nml2}
spikeTimeAccuracy = 0.0751 # could be more accurate with var time step in nrn, but need to compare these to jNeuroML_NEURON
report0 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,
spikeTimeAccuracy = spikeTimeAccuracy)
print report0
report = report + report0+"\n"
if "Cell2-suppyrFRB-FigA1FRB" in simConfigs:
# These were discovered using analyseSims = True above.
# They need to hold for all simulators
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.l23frb.mep')['L23FRB']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGsuppyrFRB_0': mep_from_nml2}
spikeTimeAccuracy = 2.32 # # could be more accurate with var time step in nrn, but need to compare these to jNeuroML_NEURON
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,
spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell4-supaxax-FigA2a" in simConfigs:
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.supaxax.mep')['SupAxAx']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGsupaxax_0': mep_from_nml2}
spikeTimeAccuracy = 0.711 # ms # could be more accurate with var time step in nrn, but need to compare these to jNeuroML_NEURON
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,
spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+"\n"
if "Cell14-nRT-FigA8-00" in simConfigs:
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.nrt.mep')['nRT']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGnRT_0': mep_from_nml2}
spikeTimeAccuracy = 0.271 # ms # could be more accurate with var time step in nrn, but need to compare these to jNeuroML_NEURON
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,
spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+"\n"
###### the .mep tests below are NEURON specific - not tested on other simulators; added by Rokas Stanislovas GSoC 2016 project Cortical Networks
if "NEURON"==simulators[0]:
if "Cell1-supppyrRS-FigA1RS" in simConfigs:
print("Tests for default project simulation for %s with 0.005 dt in NEURON"%("Cell1-supppyrRS-FigA1RS"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.FigA1RS0005.mep')['FigA1RS']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGsuppyrRS_0': mep_from_nml2 }
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell2-suppyrFRB-FigA1FRB" in simConfigs:
print("Tests for default project simulation for %s with 0.005 dt in NEURON"%("Cell2-suppyrFRB-FigA1FRB"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.FigA1FRB0005.mep')['FigA1FRB']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGsuppyrFRB_0': mep_from_nml2 }
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,
spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
###########################
if "NEURON"==simulators[0]:
if simDt==0.01:
if "Cell1-supppyrRS-FigA1RS" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell1-supppyrRS-FigA1RS"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.FigA1RS.mep')['FigA1RS']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGsuppyrRS_0': mep_from_nml2}
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell2-suppyrFRB-FigA1FRB" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell2-suppyrFRB-FigA1FRB"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.FigA1FRB.mep')['FigA1FRB']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGsuppyrFRB_0': mep_from_nml2}
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell3-supbask-FigA2a" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell3-supbask-FigA2a"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.supbaskFigA2a.mep')['supbaskFigA2a']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGsupbask_0': mep_from_nml2}
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell4-supaxax-FigA2a" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell4-supaxax-FigA2a"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.supaxaxFigA2a.mep')['supaxaxFigA2a']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGsupaxax_0': mep_from_nml2}
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell5-supLTS-FigA2b" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell5-supLTS-FigA2b"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.supLTSFigA2b.mep')['supLTSFigA2b']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGsupLTS_0': mep_from_nml2}
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell6-spinstell-FigA3-333" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell6-spinstell-FigA3-333"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.spinstellFigA3_333.mep')['spinstellFigA3_333']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGspinstell_0': mep_from_nml2 }
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell7-tuftIB-FigA4-1300" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell7-tuftIB-FigA4-1300"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.tuftIBFigA4_1300.mep')['tuftIBFigA4_1300']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGtuftIB_0': mep_from_nml2}
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell7-tuftIB-FigA4-1500" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell7-tuftIB-FigA4-1500"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.tuftIBFigA4_1500.mep')['tuftIBFigA4_1500']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGtuftIB_0': mep_from_nml2}
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell8-tuftRS-Fig5A-1400" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell8-tuftRS-Fig5A-1400"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.tuftRSFig5A_1400.mep')['tuftRSFig5A_1400']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGtuftRS_0': mep_from_nml2}
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell9-nontuftRS-FigA6-1000" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell9-nontuftRS-FigA6-1000"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.nontuftRSFigA6_1000.mep')['nontuftRSFigA6_1000']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGnontuftRS_0': mep_from_nml2}
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell12-deepLTS-FigA2b" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell12-deepLTS-FigA2b"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.deepLTSFigA2b.mep')['deepLTSFigA2b']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGdeepLTS_0': mep_from_nml2}
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell13-TCR-FigA7-600" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell13-TCR-FigA7-600"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.TCRFigA7_600.mep')['TCRFigA7_600']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGTCR_0': mep_from_nml2}
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell14-nRT-FigA8-00" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell14-nRT-FigA8-00"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.nRTFigA8_00.mep')['nRTFigA8_00']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGnRT_0': mep_from_nml2}
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell1-supppyrRS-10ms" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell1-supppyrRS-10ms"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.suppyrRS10ms.mep')['suppyrRS10ms']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGsuppyrRS_0': mep_from_nml2 }
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell2-suppyrFRB-10ms" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell2-suppyrFRB-10ms"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.suppyrFRB10ms.mep')['suppyrFRB10ms']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGsuppyrFRB_0': mep_from_nml2 }
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell3-supbask-10ms" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell3-supbask-10ms"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.supbask10ms.mep')['supbask10ms']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGsupbask_0': mep_from_nml2 }
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell4-supaxax-10ms" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell4-supaxax-10ms"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.supaxax10ms.mep')['supaxax10ms']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGsupaxax_0': mep_from_nml2 }
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell5-supLTS-10ms" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell5-supLTS-10ms"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.supLTS10ms.mep')['supLTS10ms']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGsupLTS_0': mep_from_nml2 }
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell6-spinstell-10ms" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell6-spinstell-10ms"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.spinstell10ms.mep')['spinstell10ms']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGspinstell_0': mep_from_nml2}
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell7-tuftIB-10ms" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell7-tuftIB-10ms"))
mep_from_nml2= nc.loadMepFile('../../NeuroML2/test/.test.tuftIB10ms.mep')['tuftIB10ms']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGtuftIB_0': mep_from_nml2}
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell8-tuftRS-10ms" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell8-tuftRS-10ms"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.tuftRS10ms.mep')['tuftRS10ms']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGtuftRS_0': mep_from_nml2}
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell9-nontuftRS-10ms" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell9-nontuftRS-10ms"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.nontuftRS10ms.mep')['nontuftRS10ms']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGnontuftRS_0': mep_from_nml2}
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell10-deepbask-10ms" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell10-deepbask-10ms"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.deepbask10ms.mep')['deepbask10ms']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGdeepbask_0': mep_from_nml2}
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell11-deepaxax-10ms" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell11-deepaxax-10ms"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.deepaxax10ms.mep')['deepaxax10ms']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGdeepaxax_0': mep_from_nml2}
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell12-deepLTS-10ms" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell12-deepLTS-10ms"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.deepLTS10ms.mep')['deepLTS10ms']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGdeepLTS_0': mep_from_nml2}
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell13-TCR-10ms" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell13-TCR-10ms"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.TCR10ms.mep')['TCR10ms']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGTCR_0': mep_from_nml2 }
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell14-nRT-10ms" in simConfigs:
print("Tests for default project simulation for %s with 0.01 dt in NEURON"%("Cell14-nRT-10ms"))
mep_from_nml2=nc.loadMepFile('../../NeuroML2/test/.test.nRT10ms.mep')['nRT10ms']
for value in range(0,len(mep_from_nml2)):
mep_from_nml2[value]=1000*mep_from_nml2[value]
spikeTimesToCheck = {'CGnRT_min75init_0': mep_from_nml2}
spikeTimeAccuracy = 0.00000001
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
return report
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)
simManager.runMultipleSims(simConfigs = simConfigs,
simDt = simDt,
simulators = simulators,
runInBackground = runInBackground,
varTimestepNeuron = varTimestepNeuron,
varTimestepTolerance = varTimestepTolerance,
mpiConfig = mpiConfig,
suggestedRemoteRunTime = suggestedRemoteRunTime)
simManager.reloadSims(plotVoltageOnly = plotVoltageOnly,
plotSims = plotSims,
analyseSims = analyseSims)
report= ""
if "Default Simulation Configuration" in simConfigs:
# These were discovered using analyseSims = True above.
# They need to hold for all simulators
spikeTimesToCheck = {'CG_CML_0': nc.loadMepFile('.test.mep')['Current clamp']}
spikeTimeAccuracy = 0.0751 # could be more accurate with var time step in nrn, but need to compare these to jNeuroML_NEURON
report0 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,
spikeTimeAccuracy = spikeTimeAccuracy)
print report0
report = report + report0+"\n"
if "Cell2-suppyrFRB-FigA1FRB" in simConfigs:
# These were discovered using analyseSims = True above.
# They need to hold for all simulators
spikeTimesToCheck = {'CGsuppyrFRB_0': nc.loadMepFile('.test.l23frb.mep')['L23FRB']}
spikeTimeAccuracy = 2.32 # # could be more accurate with var time step in nrn, but need to compare these to jNeuroML_NEURON
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,
spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+ '\n'
if "Cell4-supaxax-FigA2a" in simConfigs:
spikeTimesToCheck = {'CGsupaxax_0': nc.loadMepFile('.test.supaxax.mep')['SupAxAx']}
spikeTimeAccuracy = 0.711 # ms # could be more accurate with var time step in nrn, but need to compare these to jNeuroML_NEURON
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,
spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+"\n"
if "Cell14-nRT-FigA8-00" in simConfigs:
spikeTimesToCheck = {'CGnRT_0': nc.loadMepFile('.test.nrt.mep')['nRT']}
spikeTimeAccuracy = 0.271 # ms # could be more accurate with var time step in nrn, but need to compare these to jNeuroML_NEURON
report2 = simManager.checkSims(spikeTimesToCheck = spikeTimesToCheck,
spikeTimeAccuracy = spikeTimeAccuracy)
print report2
report = report + report2+"\n"
return report
varTimestepNeuron = False
varTimestepTolerance = 0.00001
analyseSims = True
plotSims = True
plotVoltageOnly = True
simAllPrefix = "" # Adds a prefix to simulation reference
runInBackground = True #(mpiConf == MpiSettings.LOCAL_SERIAL)
suggestedRemoteRunTime = 233
verbose = True
spike_times = nc.loadMepFile('../generatedNeuroML2/.test.mep', scale=1000)
#############################################
def testAll(argv=None):
if argv is None:
argv = sys.argv
print "Loading project from " + projFile.getCanonicalPath()
simManager = nc.SimulationManager(projFile,
numConcurrentSims=2,
verbose=verbose)
simManager.runMultipleSims(simConfigs=simConfigs,
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)
simManager.runMultipleSims(
simConfigs=simConfigs,
simDt=simDt,
simulators=simulators,
runInBackground=runInBackground,
varTimestepNeuron=varTimestepNeuron,
varTimestepTolerance=varTimestepTolerance,
mpiConfig=mpiConfig,
suggestedRemoteRunTime=suggestedRemoteRunTime,
)
simManager.reloadSims(plotVoltageOnly=plotVoltageOnly, plotSims=plotSims, analyseSims=analyseSims)
report = ""
if simDt == 0.005:
if "Default Simulation Configuration" in simConfigs:
# These were discovered using analyseSims = True above.
# They need to hold for all simulators
spikeTimesToCheck = {"CG_CML_0": nc.loadMepFile(".testNoTable0005.mep")["Current clamp"]}
spikeTimeAccuracy = (
0.0751
) # could be more accurate with var time step in nrn, but need to compare these to jNeuroML_NEURON
report0 = simManager.checkSims(spikeTimesToCheck=spikeTimesToCheck, spikeTimeAccuracy=spikeTimeAccuracy)
print report0
report = report + report0 + "\n"
if "Cell7-tuftIB-FigA4-1300" in simConfigs:
print (
"Tests for default project simulation for %s with 0.005 dt in NEURON" % ("Cell7-tuftIB-FigA4-1300")
)
spikeTimesToCheck = {"CGtuftIB_0": nc.loadMepFile(".test.tuftIBFigA4_1300_0005NoTable.mep")["FigA4"]}
spikeTimeAccuracy = (
0
) # # could be more accurate with var time step in nrn, but need to compare these to jNeuroML_NEURON
report2 = simManager.checkSims(spikeTimesToCheck=spikeTimesToCheck, spikeTimeAccuracy=spikeTimeAccuracy)
print report2
report = report + report2 + "\n"
if "Cell7-tuftIB-FigA4-1500" in simConfigs:
print (
"Tests for default project simulation for %s with 0.01 dt in NEURON" % ("Cell7-tuftIB-FigA4-1500")
)
spikeTimesToCheck = {
"CGtuftIB_0": nc.loadMepFile(".test.tuftIBFigA4_1500_0005NoTable.mep")["tuftIBFigA4_1500"]
}
spikeTimeAccuracy = 0
report2 = simManager.checkSims(spikeTimesToCheck=spikeTimesToCheck, spikeTimeAccuracy=spikeTimeAccuracy)
print report2
report = report + report2 + "\n"
######## added by Rokas Stanislovas : tests for all figures with 0.01 dt and default project spatial discretization in NEURON
if "NEURON" == simulators[0]:
if simDt == 0.01:
if "Cell1-supppyrRS-FigA1RS" in simConfigs:
print (
"Tests for default project simulation for %s with 0.01 dt in NEURON" % ("Cell1-supppyrRS-FigA1RS")
)
spikeTimesToCheck = {"CGsuppyrRS_0": nc.loadMepFile(".test.FigA1RSNoTable.mep")["FigA1RS"]}
spikeTimeAccuracy = 0
report2 = simManager.checkSims(spikeTimesToCheck=spikeTimesToCheck, spikeTimeAccuracy=spikeTimeAccuracy)
print report2
report = report + report2 + "\n"
if "Default Simulation Configuration" in simConfigs:
# These were discovered using analyseSims = True above.
# They need to hold for all simulators
spikeTimesToCheck = {"CG_CML_0": nc.loadMepFile(".testNoTable.mep")["Current clamp"]}
spikeTimeAccuracy = (
0.0751
) # could be more accurate with var time step in nrn, but need to compare these to jNeuroML_NEURON
report0 = simManager.checkSims(spikeTimesToCheck=spikeTimesToCheck, spikeTimeAccuracy=spikeTimeAccuracy)
print report0
report = report + report0 + "\n"
return report
varTimestepTolerance = 0.00001
analyseSims = True
plotSims = True
plotVoltageOnly = True
simAllPrefix = "" # Adds a prefix to simulation reference
runInBackground = True #(mpiConf == MpiSettings.LOCAL_SERIAL)
suggestedRemoteRunTime = 233
verbose = True
spike_times = nc.loadMepFile('../generatedNeuroML2/.test.mep',scale=1000)
#############################################
def testAll(argv=None):
if argv is None:
argv = sys.argv
print "Loading project from "+ projFile.getCanonicalPath()
simManager = nc.SimulationManager(projFile,
numConcurrentSims = 2,
verbose = verbose)