totalSimDur = simDuration + simSettleTime
net.run(totalSimDur, report='text')
simT, memV = dlint2.getMemVTrace()
spikeTimes = dlint2.getSpikes()
fig, axs = plt.subplots(nrows=2, figsize=(10, 6.25), sharex='col')
axs[0].plot(simT / units.ms, memV / units.mV)
spikesY = memV.min() + 1.05 * (memV.max() - memV.min())
axs[0].plot(spikeTimes / units.ms, [spikesY / units.mV] * spikeTimes.shape[0],
'k^')
axs[0].set_ylabel('DLInt1 \nmemV (mV)')
axs[0].set_xlim([simSettleTime / units.ms - 50, totalSimDur / units.ms + 50])
sineInput = getSineInput(simSettleTime=simSettleTime,
simDur=simDuration,
simStepSize=simStepSize,
sinPulseDurs=inputPars['sinPulseDurs'],
sinPulseStarts=inputPars['sinPulseStarts'],
freq=265 * units.Hz)
axs[1].plot(simT / units.ms, sineInput, 'r-', label='Vibration Input')
axs[1].plot(JO.spikeTimes / units.ms,
[sineInput.max() * 1.05] * len(JO.spikeTimes),
'k^',
label='JO Spikes')
axs[1].legend(loc='upper right')
axs[1].set_xlabel('time (ms)')
axs[1].set_ylabel('Vibration \nInput/JO\n Spikes')
fig.tight_layout()
fig.canvas.draw()
# plt.show()
fig.savefig(os.path.join(opDir, 'Traces.png'), dpi=150)
def runJODLInt1DLInt2(simStepSize: Quantity, simDuration: Quantity, simSettleTime: Quantity,
inputParsName: str, showBefore: Quantity, showAfter: Quantity,
DLInt1ModelProps: str, DLInt2ModelProps: str,
DLInt1SynapsePropsE: str, DLInt1SynapsePropsI: str,
DLInt2SynapseProps: str, DLInt1DLInt2SynProps: str,
askReplace=True):
sns.set(style="whitegrid", rc=mplPars)
DLInt1SynapseProps = "".join((DLInt1SynapsePropsE, DLInt1SynapsePropsI))
opDir = os.path.join(homeFolder, DLInt1ModelProps + DLInt2ModelProps,
DLInt1SynapseProps + DLInt2SynapseProps + DLInt1DLInt2SynProps,
inputParsName)
opFile = os.path.join(opDir, 'Traces.png')
OPNixFile = os.path.join(opDir, 'SimResults.h5')
if askReplace:
if os.path.isfile(opFile):
ch = input('Results already exist at {}. Delete?(y/n):'.format(opFile))
if ch == 'y':
os.remove(opFile)
if os.path.isfile(OPNixFile):
os.remove(OPNixFile)
else:
sys.exit('User Abort!')
elif not os.path.isdir(opDir):
os.makedirs(opDir)
else:
if os.path.isfile(opFile):
os.remove(opFile)
if os.path.isfile(OPNixFile):
os.remove(OPNixFile)
elif not os.path.isdir(opDir):
os.makedirs(opDir)
inputPars = getattr(inputParsList, inputParsName)
net = Network()
JO = JOSpikes265(nOutputs=1, simSettleTime=simSettleTime, **inputPars)
net.add(JO.JOSGG)
DLInt1PropsDict = getattr(AdExpPars, DLInt1ModelProps)
dlint1 = VSNeuron(**AdExp, inits=DLInt1PropsDict, name='dlint1')
dlint1.recordSpikes()
dlint1.recordMembraneV()
if DLInt1SynapsePropsE:
dlint1.addSynapse(synName="ExiJO", sourceNG=JO.JOSGG, **exp2Syn,
synParsInits=getattr(synapsePropsList, DLInt1SynapsePropsE),
synStateInits=exp2SynStateInits,
sourceInd=0, destInd=0
)
if DLInt1SynapsePropsI:
dlint1.addSynapse(synName="InhJO", sourceNG=JO.JOSGG, **exp2Syn,
synParsInits=getattr(synapsePropsList, DLInt1SynapsePropsI),
synStateInits=exp2SynStateInits,
sourceInd=0, destInd=0
)
dlint1.addToNetwork(net)
DLInt2PropsDict = getattr(AdExpPars, DLInt2ModelProps)
dlint2 = VSNeuron(**AdExp, inits=DLInt2PropsDict, name='dlint2')
dlint2.recordMembraneV()
dlint2.recordSpikes()
if DLInt2SynapseProps:
dlint2.addSynapse(synName="JOExi", sourceNG=JO.JOSGG, **exp2Syn,
synParsInits=getattr(synapsePropsList, DLInt2SynapseProps),
synStateInits=exp2SynStateInits,
sourceInd=0, destInd=0
)
if DLInt1DLInt2SynProps:
dlint2.addSynapse(synName="DLInt1", sourceNG=dlint1.ng, **exp2Syn,
synParsInits=getattr(synapsePropsList, DLInt1DLInt2SynProps),
synStateInits=exp2SynStateInits,
sourceInd=0, destInd=0
)
dlint2.addToNetwork(net)
defaultclock.dt = simStepSize
totalSimDur = simDuration + simSettleTime
net.run(totalSimDur, report='text')
simT, DLInt1_memV = dlint1.getMemVTrace()
DLInt1_spikeTimes = dlint1.getSpikes()
fig, axs = plt.subplots(nrows=3, figsize=(10, 6.25), sharex='col')
axs[0].plot(simT / units.ms, DLInt1_memV / units.mV)
spikesY = DLInt1_memV.min() + 1.05 * (DLInt1_memV.max() - DLInt1_memV.min())
axs[0].plot(DLInt1_spikeTimes / units.ms, [spikesY / units.mV] * DLInt1_spikeTimes.shape[0], 'k^')
axs[0].set_ylabel('DLInt1 \nmemV (mV)')
axs[0].set_xlim([(simSettleTime - showBefore) / units.ms,
(totalSimDur + showAfter) / units.ms])
simT, DLInt2_memV = dlint2.getMemVTrace()
DLInt2_spikeTimes = dlint2.getSpikes()
axs[1].plot(simT / units.ms, DLInt2_memV / units.mV)
spikesY = DLInt2_memV.min() + 1.05 * (DLInt2_memV.max() - DLInt2_memV.min())
axs[1].plot(DLInt2_spikeTimes / units.ms, [spikesY / units.mV] * DLInt2_spikeTimes.shape[0], 'k^')
axs[1].set_ylabel('DLInt2 \nmemV (mV)')
sineInput = getSineInput(simDur=simDuration, simStepSize=simStepSize,
sinPulseDurs=inputPars['sinPulseDurs'],
sinPulseStarts=inputPars['sinPulseStarts'],
freq=265 * units.Hz, simSettleTime=simSettleTime)
axs[2].plot(simT / units.ms, sineInput, 'r-', label='Vibration Input')
axs[2].plot(JO.spikeTimes / units.ms, [sineInput.max() * 1.05] * len(JO.spikeTimes), 'k^',
label='JO Spikes')
axs[2].legend(loc='upper right')
axs[2].set_xlabel('time (ms)')
axs[2].set_ylabel('Vibration \nInput/JO\n Spikes')
fig.tight_layout()
fig.canvas.draw()
fig.savefig(opFile, dpi=150)
plt.close(fig.number)
del fig
dlint1MemVAS = AnalogSignal(signal=DLInt1_memV /units.mV,
sampling_period=(simStepSize / units.ms) * qu.ms,
t_start=0 * qu.mV,
units="mV",
name="DLInt1 MemV")
dlint2MemVAS = AnalogSignal(signal=DLInt2_memV / units.mV,
sampling_period=(simStepSize / units.ms) * qu.ms,
t_start=0 * qu.mV,
units="mV",
name="DLInt2 MemV")
inputAS = AnalogSignal(signal=sineInput,
sampling_period=(simStepSize / units.ms) * qu.ms,
t_start=0 * qu.mV,
units="um",
name="Input Vibration Signal")
dlint1SpikesQU = (DLInt1_spikeTimes / units.ms) * qu.ms
dlint2SpikesQU = (DLInt2_spikeTimes / units.ms) * qu.ms
joSpikesQU = (JO.spikeTimes / units.ms) * qu.ms
nixFile = nixio.File.open(OPNixFile, mode=nixio.FileMode.ReadWrite)
neuronModels = nixFile.create_section("Neuron Models", "Model Parameters")
DLInt1PropsSec = neuronModels.create_section("DL-Int-1", "AdExp")
for propName, propVal in DLInt1PropsDict.items():
addBrianQuantity2Section(DLInt1PropsSec, propName, propVal)
DLInt2PropsSec = neuronModels.create_section("DL-Int-2", "AdExp")
for propName, propVal in DLInt2PropsDict.items():
addBrianQuantity2Section(DLInt2PropsSec, propName, propVal)
inputSec = nixFile.create_section("Input Parameters", "Sinusoidal Pulses")
for parName, parVal in inputPars.items():
addBrianQuantity2Section(inputSec, parName, parVal)
addBrianQuantity2Section(inputSec, "simSettleTime", simSettleTime)
brianSimSettingsSec = nixFile.create_section("Simulation Parameters", "Brian Simulation")
addBrianQuantity2Section(brianSimSettingsSec, "simStepSize", simStepSize)
addBrianQuantity2Section(brianSimSettingsSec, "totalSimDuration", totalSimDur)
brianSimSettingsSec.create_property("method", nixio.Value("euler"))
synPropsSec = nixFile.create_section("Synapse Models", "Model Parameters")
if DLInt1SynapsePropsE:
JODLInt1SynESec = synPropsSec.create_section("JODLInt1Exi", "DoubleExpSyn")
JODLInt1SynEDict = getattr(synapsePropsList, DLInt1SynapsePropsE)
for propName, propVal in JODLInt1SynEDict.items():
addBrianQuantity2Section(JODLInt1SynESec, propName, propVal)
JODLInt1SynESec.create_property("PreSynaptic Neuron", nixio.Value("JO"))
JODLInt1SynESec.create_property("PostSynaptic Neuron", nixio.Value("DLInt1"))
if DLInt1SynapsePropsI:
JODLInt1SynISec = synPropsSec.create_section("JODLInt1Inh", "DoubleExpSyn")
JODLInt1SynIDict = getattr(synapsePropsList, DLInt1SynapsePropsI)
for propName, propVal in JODLInt1SynIDict.items():
addBrianQuantity2Section(JODLInt1SynISec, propName, propVal)
JODLInt1SynISec.create_property("PreSynaptic Neuron", nixio.Value("JO"))
JODLInt1SynISec.create_property("PostSynaptic Neuron", nixio.Value("DLInt1"))
if DLInt2SynapseProps:
JODLInt2SynESec = synPropsSec.create_section("JODLInt2Exi", "DoubleExpSyn")
JODLInt2SynEDict = getattr(synapsePropsList, DLInt2SynapseProps)
for propName, propVal in JODLInt2SynEDict.items():
addBrianQuantity2Section(JODLInt2SynESec, propName, propVal)
JODLInt2SynESec.create_property("PreSynaptic Neuron", nixio.Value("JO"))
JODLInt2SynESec.create_property("PostSynaptic Neuron", nixio.Value("DLInt2"))
if DLInt1DLInt2SynProps:
DLInt1DLInt2SynSec = synPropsSec.create_section("DLInt1DLInt2Inh", "DoubleExpSyn")
DLInt1DLInt2SynDict = getattr(synapsePropsList, DLInt1DLInt2SynProps)
for propName, propVal in DLInt1DLInt2SynDict.items():
addBrianQuantity2Section(DLInt1DLInt2SynSec, propName, propVal)
DLInt1DLInt2SynSec.create_property("PreSynaptic Neuron", nixio.Value("DLInt1"))
DLInt1DLInt2SynSec.create_property("PostSynaptic Neuron", nixio.Value("DLInt2"))
blk = nixFile.create_block("Simulation Traces", "Brian Output")
DLInt1DA = addAnalogSignal2Block(blk, dlint1MemVAS)
DLInt2DA = addAnalogSignal2Block(blk, dlint2MemVAS)
inputDA = addAnalogSignal2Block(blk, inputAS)
addMultiTag("DLInt1 Spikes", type="Spikes", positions=dlint1SpikesQU,
blk=blk, refs=[DLInt1DA])
addMultiTag("DLInt2 Spikes", type="Spikes", positions=dlint2SpikesQU,
blk=blk, refs=[DLInt2DA])
addMultiTag("JO Spikes", type="Spikes", positions=joSpikesQU,
blk=blk, refs=[inputDA])
nixFile.close()