def run(noNeurons):
runtime = 1000.0
import numpy as np
import pyNN.hardware.spikey as pynn
pynn.setup()
neurons = pynn.Population(noNeurons, pynn.IF_facets_hardware1)
neurons.record()
stim = pynn.Population(10, pynn.SpikeSourcePoisson, {
'rate': 20.0,
'duration': runtime
})
prj = pynn.Projection(stim, neurons, pynn.AllToAllConnector())
prj.setWeights(pynn.maxExcWeight())
pynn.run(runtime)
spikes = neurons.getSpikes([])
# for neuron in np.unique(spikes[:,0]):
# print 'neuron', int(neuron), 'has', len(spikes[spikes[:,0] ==
# neuron]), 'spikes'
noSpikes = len(spikes)
lost, sent = pynn.getInputSpikes()
pynn.end()
print 'no neurons / spikes in / lost / out:', noNeurons + 1, sent, lost, noSpikes
return noSpikes
def test():
'''mapping of bio index to hardware index should work for networks
where not all neurons are recorded'''
pynn.setup()
if mappingOffset > 0:
dummy = pynn.Population(mappingOffset, pynn.IF_facets_hardware1)
neuronList = []
for i in range(noNeurons):
neuronList.append(pynn.Population(1, pynn.IF_facets_hardware1))
neuronList[-1].record()
dummy = pynn.Population(1, pynn.IF_facets_hardware1)
stim = pynn.Population(1, pynn.SpikeSourcePoisson)
for neuron in neuronList:
pynn.Projection(stim, neuron,
pynn.AllToAllConnector(weights=pynn.minExcWeight()))
pynn.run(1000.0)
pynn.end()
f = open('spikeyconfig.out')
for line in f:
for i in range(mappingOffset + 2 * noNeurons):
if line.find('w ' + str(192 + i)) >= 0:
weight = int(line.split(' ')[256 + 2 - 1])
print 192 + i, weight
assert (weight == shouldPatternWeights[i]
), 'results do not fit expectation'
f.close()
def maxSpikesIn(runtime):
'''Maximum number of spikes that can be sent:
Should be limited by memory size on FPGA board (256MB => 256x1024x1024x8/32x3 approx. 200e6 spikes).'''
rate = 10.0
weight = 1.0
poissonParam = {'start': 0, 'duration': runtime, 'rate': rate}
pynn.setup()
stim = pynn.Population(256, pynn.SpikeSourcePoisson, poissonParam)
neuron = pynn.Population(192, pynn.IF_facets_hardware1)
prj = pynn.Projection(stim,
neuron,
pynn.AllToAllConnector(weights=pynn.minInhWeight() *
weight),
target='inhibitory')
neuron.record()
pynn.run(runtime)
spikes = neuron.getSpikes()
lost, sent = pynn.getInputSpikes()
print 'spikes in / out', sent, len(spikes)
pynn.end()
def test_poisson():
"""Test with Poisson source."""
import pyNN.hardware.spikey as pynn
duration = 1000.0 # ms
rate = 5000.0 # 1/s
poissonParam = {'start': 0, 'duration': duration, 'rate': rate}
limLost = 1.0 # %
pynn.setup()
stim = pynn.Population(1, pynn.SpikeSourcePoisson, poissonParam)
neuron = pynn.Population(1, pynn.IF_facets_hardware1)
pynn.Projection(stim,
neuron,
method=pynn.AllToAllConnector(weights=0),
target='inhibitory')
neuron.record()
pynn.run(duration)
lost, sent = pynn.getInputSpikes()
print 'Number of input spikes (lost, sent, %lost)', lost, sent, float(
lost) / sent * 1e2
assert float(lost) / sent * 1e2 < limLost, 'Too many spikes lost!'
pynn.end()
def test_spikey5_allneurons():
'''
Tests mapping and firing of all 384 neurons.
'''
runtime = 1000.0
stimRate = 10.0
weight = 7
pynn.setup()
neurons = pynn.Population(384, pynn.IF_facets_hardware1)
stim = pynn.Population(10, pynn.SpikeSourcePoisson, {
'start': 0,
'duration': runtime,
'rate': stimRate
})
prj = pynn.Projection(
stim,
neurons,
method=pynn.AllToAllConnector(weights=pynn.minExcWeight() * weight),
target='excitatory')
pynn.run(runtime)
spikes = neurons.getSpikes()
print 'spikes from', len(np.unique(spikes)), 'different neurons'
# TODO: check for spikes from all neurons
pynn.end()
def test_regular():
"""Maximum rate without packing:
Each second clock cycle a minimal loaded (filled with 1 spikes) spike packet."""
import numpy as np
import pyNN.hardware.spikey as pynn
import time
np.random.seed(int(time.time()))
lineDriverNo = np.random.random_integers(0, 255)
print 'Using line driver number', lineDriverNo
duration = 1000.0 # ms
h = 1e3 / 5000.0 # 0.2 ms
pynn.setup()
stim = pynn.Population(256, pynn.SpikeSourceArray)
stim[lineDriverNo].set_parameters(
spike_times=np.arange(0, duration + h / 2.0, h))
neuron = pynn.Population(1, pynn.IF_facets_hardware1)
pynn.Projection(stim,
neuron,
method=pynn.AllToAllConnector(weights=0),
target='inhibitory')
neuron.record()
pynn.run(duration)
lost, sent = pynn.getInputSpikes()
print 'Number of input spikes (lost, sent)', lost, sent
assert lost == 0, 'There should not be any spikes lost!'
pynn.end()
def test_regular_packed():
"""Maximum rate with packing:
Each clock cycle a full (filled with 3 spikes) spike packet."""
import numpy as np
import pyNN.hardware.spikey as pynn
duration = 1000.0 # ms
h = 1e3 / 5000.0 / 2.0 # 0.1 ms
spikeTimes = np.arange(0, duration + h / 2.0, h)
pynn.setup()
stim = pynn.Population(256, pynn.SpikeSourceArray)
# spikes have to be distributed over blocks of line drivers for efficient
# packing
stim[0].set_parameters(spike_times=spikeTimes)
stim[64].set_parameters(spike_times=spikeTimes)
stim[128].set_parameters(spike_times=spikeTimes)
neuron = pynn.Population(1, pynn.IF_facets_hardware1)
pynn.Projection(stim,
neuron,
method=pynn.AllToAllConnector(weights=0),
target='inhibitory')
neuron.record()
pynn.run(duration)
lost, sent = pynn.getInputSpikes()
print 'Number of input spikes (lost, sent)', lost, sent
assert lost == 0, 'There should not be any spikes lost!'
pynn.end()
def maxRuntime(runtime):
'''Maximum runtime:
Limited by wrap around of counter (after approx. 6600s).
Can be extended to infinitly long runtimes by considering wrap around.
Subtract/Add offset to in/out spike times for each wrap around.'''
rate = 1.0
weight = 1.0
poissonParam = {'start': 0, 'duration': runtime, 'rate': rate}
pynn.setup()
stim = pynn.Population(1, pynn.SpikeSourcePoisson, poissonParam)
neuron = pynn.Population(1, pynn.IF_facets_hardware1)
prj = pynn.Projection(stim,
neuron,
pynn.AllToAllConnector(weights=pynn.minInhWeight() *
weight),
target='inhibitory')
neuron.record()
pynn.run(runtime)
spikes = neuron.getSpikes()
lost, sent = pynn.getInputSpikes()
print 'spikes in / out', sent, len(spikes)
pynn.end()
def testRegularMaxPacked():
'''Maximum rate with packing:
Each clock cycle a full (filled with 3 spikes) spike packet.'''
import numpy as np
import pyNN.hardware.spikey as pynn
duration = 10000.0 # ms
h = 1e3 / 5000.0 / 2.0 # 10kHz for each of 3 sources = 30kHz
spikeTimes = np.arange(0, duration + h / 2.0, h)
pynn.setup()
stim = pynn.Population(256, pynn.SpikeSourceArray)
stim[0].set_parameters(spike_times=spikeTimes)
stim[63].set_parameters(spike_times=spikeTimes)
stim[127].set_parameters(spike_times=spikeTimes)
neuron = pynn.Population(1, pynn.IF_facets_hardware1)
pynn.Projection(stim,
neuron,
method=pynn.AllToAllConnector(weights=0),
target='inhibitory')
neuron.record()
pynn.run(duration)
print 'no out spikes:', len(neuron.getSpikes())
lost, sent = pynn.getInputSpikes()
print 'no in spikes (lost, sent)', lost, sent
assert lost == 0, 'there should not be any spikes lost!'
pynn.end()
def run(lowThreshold):
runtime = 1000.0
pynn.setup()
# set STDP params for low threshold -> fails when vcthigh-vctlow < 0.04
if lowThreshold:
pynn.hardware.hwa.setSTDPParams(0.0, default.tpcsec,
default.tpcorperiod, 1.0, 1.0, 1.0,
0.98, 2.5)
else:
pynn.hardware.hwa.setSTDPParams(0.0, default.tpcsec,
default.tpcorperiod, 1.0, 1.0, 1.0,
0.85, 2.5)
neuron = pynn.Population(1, pynn.IF_facets_hardware1)
spikeArray = pynn.Population(1, pynn.SpikeSourceArray)
stdp_model = pynn.STDPMechanism(
timing_dependence=pynn.SpikePairRule(),
weight_dependence=pynn.AdditiveWeightDependence())
prj = pynn.Projection(
spikeArray,
neuron,
method=pynn.AllToAllConnector(weights=pynn.minExcWeight() * 0),
target='excitatory',
synapse_dynamics=pynn.SynapseDynamics(slow=stdp_model))
pynn.run(runtime)
pynn.end()
def withDummyNeurons(mappingOffset, vrest):
pynn.setup()
if mappingOffset > 0:
pynn.Population(mappingOffset, pynn.IF_facets_hardware1)
pynn.Population(1, pynn.IF_facets_hardware1, vrest)
pynn.run(1000.0)
vout = copy.deepcopy(pynn.hardware.hwa.vouts[1, 2:4])
pynn.end()
return vout
def build(rateIn):
global neurons, stim
poissonParams = {'start': 0, 'duration': runtime, 'rate': rateIn}
stim = pynn.Population(32, pynn.SpikeSourcePoisson, poissonParams)
neurons = pynn.Population(numNeurons, pynn.IF_facets_hardware1)
pynn.Projection(stim,
neurons,
pynn.AllToAllConnector(weights=pynn.minExcWeight() *
5.0),
target='excitatory')
neurons.record()
def run_network(mappingOffset=0, neuronPermutation=[], noNeurons=-1):
pynn.setup(mappingOffset=mappingOffset,
neuronPermutation=neuronPermutation)
if noNeurons == -1:
noNeurons = 384
if pynn.getChipVersion() == 4:
noNeurons = 192
a = pynn.Population(noNeurons, pynn.IF_facets_hardware1)
b = pynn.Population(10, pynn.SpikeSourcePoisson)
prj = pynn.Projection(b, a, method=pynn.AllToAllConnector())
pynn.run(1.0)
def compareSpikesToMembrane(duration):
"""
Tests the precise timing of digital spikes and spikes extracted from the membrane potential.
The neuron is stimulated with Poisson spike sources.
"""
np.random.seed(int(time.time()))
neuronNo = np.random.random_integers(0, 191)
print 'Using neuron number', neuronNo
poissonParams = {'start': 100.0, 'duration': duration -
100.0, 'rate': 30.0} # offset of 100 ms to get all spikes
weightExc = 4 # digital hardware value
weightInh = 15 # digital hardware value
freqLimit = 1.0 # 1/s
meanLimit = 0.2 # ms
stdLimit = 0.2 # ms
import pyNN.hardware.spikey as pynn
pynn.setup(mappingOffset=neuronNo)
stimExc = pynn.Population(64, pynn.SpikeSourcePoisson, poissonParams)
stimInh = pynn.Population(192, pynn.SpikeSourcePoisson, poissonParams)
neuron = pynn.Population(1, pynn.IF_facets_hardware1)
prj = pynn.Projection(stimExc, neuron, pynn.AllToAllConnector(
weights=weightExc * pynn.minExcWeight()), target='excitatory')
prj = pynn.Projection(stimInh, neuron, pynn.AllToAllConnector(
weights=weightInh * pynn.minInhWeight()), target='inhibitory')
neuron.record()
pynn.record_v(neuron[0], '')
pynn.run(duration)
spikes = neuron.getSpikes()[:, 1]
membrane = pynn.membraneOutput
memTime = pynn.timeMembraneOutput
spikesMem, deriv, thresh = spikesFromMem(memTime, membrane)
pynn.end()
#plot(memTime, membrane, spikes, spikesMem, deriv, thresh)
print 'Spikes and spikes on membrane:', len(spikes), '/', len(spikesMem)
assert len(spikes) / duration * 1e3 >= freqLimit, 'Too less spikes.'
assert len(spikes) == len(spikesMem), 'Spikes do not match membrane.'
spikesDiff = spikesMem - spikes
spikesDiffMean = np.mean(spikesDiff)
spikesDiffStd = np.std(spikesDiff)
print 'Offset between spikes and membrane:', spikesDiffMean, '+-', spikesDiffStd
assert spikesDiffMean < meanLimit, 'Spike and membrane have too large offset.'
assert spikesDiffStd < stdLimit, 'Time axes of spikes and membrane are different.'
def withMappingOffset(mappingOffset, vrest):
pynn.setup(mappingOffset=mappingOffset)
pynn.Population(1, pynn.IF_facets_hardware1, vrest)
pynn.run(1000.0)
vout = copy.deepcopy(pynn.hardware.hwa.vouts[1, 2:4])
pynn.end()
return vout
def getMem(self, voltageRest, mappingOffset, calibOutputPins,
calibNeuronMems):
import pyNN.hardware.spikey as pynn
pynn.setup(useUsbAdc=True,
avoidSpikes=True,
mappingOffset=mappingOffset,
calibTauMem=False,
calibOutputPins=calibOutputPins,
calibNeuronMems=calibNeuronMems)
neuron = pynn.Population(1, pynn.IF_facets_hardware1,
self.neuronParams)
#neuronDummy = pynn.Population(1, pynn.IF_facets_hardware1, self.neuronParams)
neuron.set({'v_rest': voltageRest})
#neuronDummy.set({'v_rest': self.voltageRange[0]})
neuron.record()
pynn.record_v(neuron[0], '')
pynn.run(self.runtime)
mem = pynn.membraneOutput
spikes = neuron.getSpikes()
pynn.end()
self.assertTrue(
(float(len(spikes)) / self.runtime * 1e3) <= self.limFreq,
'there should not be any (too much) spikes')
return mem.mean()
def run(mappingOffset):
"""
Measures firing rate of one neuron (determined by mappingOffset) in dependence on value of g_leak.
If linear fit to these firing rates does not show a significantly large slope,
g_leak is assumed to be not set correctly.
"""
pynn.setup(mappingOffset=mappingOffset,
calibTauMem=False,
calibSynDrivers=False,
calibVthresh=False)
# set v_rest over v_reset to get neuron firing
neuron = pynn.Population(1, pynn.IF_facets_hardware1, {
'v_rest':
pynn.IF_facets_hardware1.default_parameters['v_thresh'] + 10.0
})
neuron.record()
rateList = []
for gLeak in gLeakRange:
neuron.set({'g_leak': gLeak / default.iLeak_base})
pynn.hardware.hwa._neuronsChanged = True
pynn.run(runtime)
rateList.append(
[gLeak, float(len(neuron.getSpikes())) / runtime * 1e3])
pynn.end()
rateList = np.array(rateList)
pol = np.polyfit(rateList[:, 0], rateList[:, 1], 1) # linear fit
print 'fitted polynom:', pol
assert pol[0] > slopeMin, 'rate does not change with g_leak'
def getMemLoop():
result = []
pynn.setup(useUsbAdc=True)
neuron = pynn.Population(noNeurons, pynn.IF_facets_hardware1)
for j in range(noNeurons):
if j % 2 == 0:
neuron[j].set_parameters(v_rest=vRestEven)
else:
neuron[j].set_parameters(v_rest=vRestOdd)
neuron.record()
for i in range(noNeurons):
pynn.record_v(neuron[i], '')
pynn.run(runtime)
mem = pynn.membraneOutput
spikes = neuron.getSpikes()
shutil.copy(spikeyconfigFilename,
spikeyconfigFilename + extListNo[i])
self.assertTrue(
(float(len(spikes)) / runtime * 1e3) <= limFreq,
'there should not be any (too much) spikes')
result.append([mem.mean(), mem.std()])
pynn.end()
return result
def maxSpikesOut(runtime):
'''Maximum number of spikes that can be received:
Should be limited by memory size on FPGA board (128MB approx. 100e6 spikes, other half for ADC).'''
neuronParams = {
'v_reset': -80.0, # mV
'e_rev_I': -80.0, # mV
'v_rest': -45.0, # mV / rest above threshold
'v_thresh': -55.0, # mV
'g_leak': 20.0, # nS / without Scherzer calib approx. tau_m = 2ms
}
pynn.setup()
neuron = pynn.Population(192, pynn.IF_facets_hardware1, neuronParams)
neuron.record()
pynn.run(runtime)
spikes = neuron.getSpikes()[:, 1]
lost, sent = pynn.getInputSpikes()
print 'spikes in / out', sent, len(spikes)
pynn.end()
def test_noSpikesBug():
import numpy as np
import pyNN.hardware.spikey as pynn
duration = 10 * 1000.0 # ms
neuronParams = {
'v_reset': -80.0, # mV
'e_rev_I': -80.0, # mV
'v_rest': -45.0, # mV / rest above threshold
'v_thresh': -55.0, # mV
'g_leak': 20.0, # nS / without Scherzer calib approx. tau_m = 2ms
}
noTrials = 100
failCount = 0
for i in range(noTrials):
pynn.setup()
neuron = pynn.Population(1, pynn.IF_facets_hardware1, neuronParams)
neuron.record()
pynn.run(duration)
spikes = neuron.getSpikes()[:, 1]
pynn.end() # comment this out and everything is fine
if len(spikes) == 0:
failCount += 1
assert failCount == 0, str(
float(failCount) / noTrials * 1e2) + ' % of runs did not have spikes'
def test_empty_exp():
"""
Initialize hardware and create one neuron.
"""
pynn.setup()
pynn.Population(1, pynn.IF_facets_hardware1)
pynn.run(1000.0)
pynn.end()
def emulation(doesWork):
numberSynapses = 10
runtime = 1000.0
weights = range(0, numberSynapses * numberSynapses)
pynn.setup()
pre = pynn.Population(numberSynapses, pynn.SpikeSourcePoisson)
post = pynn.Population(numberSynapses, pynn.IF_facets_hardware1)
if doesWork:
conn = pynn.Projection(pre, post, method=pynn.AllToAllConnector())
conn.setWeights(weights)
else:
conn = pynn.Projection(pre,
post,
method=pynn.AllToAllConnector(weights=weights))
pynn.run(runtime)
pynn.end()
def emulate():
# pynn.setup(useUsbAdc=True)
pynn.setup()
stimI = pynn.Population(40, pynn.SpikeSourcePoisson, {
'start': 0,
'duration': runtime,
'rate': rate
})
stimE = pynn.Population(20, pynn.SpikeSourcePoisson, {
'start': 0,
'duration': runtime,
'rate': rate
})
neuron = pynn.Population(192, pynn.IF_facets_hardware1)
prjI = pynn.Projection(stimI,
neuron,
pynn.AllToAllConnector(weights=weight *
pynn.minInhWeight()),
target='inhibitory')
prjE = pynn.Projection(stimE,
neuron,
pynn.AllToAllConnector(weights=weight *
pynn.minExcWeight()),
target='excitatory')
stimI.record()
stimE.record()
neuron.record()
pynn.record_v(neuron[0], '')
pynn.run(runtime)
spikesInI = stimI.getSpikes()
spikesInE = stimE.getSpikes()
spikes = neuron.getSpikes()
mem = pynn.membraneOutput
print 'spikes out', len(spikes)
print 'spikes in', len(spikesInI), len(spikesInE)
print 'mem data points', len(mem)
pynn.end()
def run(withSTDP):
runtime = 1000.0
pynn.setup()
stim = pynn.Population(1, pynn.SpikeSourcePoisson, {
'start': 0, 'duration': runtime, 'rate': 100.0})
neuron = pynn.Population(1, pynn.IF_facets_hardware1)
if withSTDP:
stdp_model = pynn.STDPMechanism(timing_dependence=pynn.SpikePairRule(),
weight_dependence=pynn.AdditiveWeightDependence())
pynn.Projection(stim, neuron,
method=pynn.AllToAllConnector(
weights=pynn.maxExcWeight()),
target='excitatory',
synapse_dynamics=pynn.SynapseDynamics(slow=stdp_model))
else:
pynn.Projection(stim, neuron,
method=pynn.AllToAllConnector(
weights=pynn.maxExcWeight()),
target='excitatory')
pynn.run(runtime)
pynn.end()
def emulation(seed, connType=0, returnValue=None):
numberNeurons = 192
noInputs = 15
pynn.setup()
rngPrj = pynn.random.NumpyRNG(seed=seed,
parallel_safe=True) # this may not work?!
neurons = pynn.Population(numberNeurons, pynn.IF_facets_hardware1)
connector = None
if connType == 0:
connector = pynn.FixedNumberPreConnector(noInputs,
weights=pynn.minExcWeight())
elif connType == 1:
connector = pynn.FixedNumberPostConnector(noInputs,
weights=pynn.minExcWeight())
elif connType == 2:
connector = pynn.FixedProbabilityConnector(float(noInputs) /
numberNeurons,
weights=pynn.minExcWeight())
else:
assert False, 'invalid connector type'
prj = pynn.Projection(neurons,
neurons,
method=connector,
target='inhibitory',
rng=rngPrj)
connList = []
for conn in prj.connections():
connList.append(conn)
assert len(connList) > 0, 'no connections'
assert len(connList) < numberNeurons * \
(numberNeurons - 1), 'all-to-all connection'
pynn.run(1.0)
pynn.end()
if returnValue != None:
returnValue = connList
else:
return connList
# define weights in digital hardware values
# --> these should be tuned first to obtain synfire chain behavior!
weightStimExcExc = 12 * pynn.minExcWeight() # 12
weightStimExcInh = 12 * pynn.minExcWeight() # 12
weightExcExc = 13 * pynn.minExcWeight() # 8
weightExcInh = 14 * pynn.minExcWeight() # 10
weightInhExc = 9 * pynn.minInhWeight() # 7
# kick starter input pulse(s)
#stimSpikes = np.array([100.0])
# to have several kick starter pulses, use (don't forget to reduce to first entry for closed chain):
stimSpikes = np.array([100.0, 200.0, 300.0])
stimExc = pynn.Population(popSize['exc'], pynn.SpikeSourceArray,
{'spike_times': stimSpikes})
# create neuron populations
popCollector = {'exc': [], 'inh': []}
for synType in ['exc', 'inh']:
for popIndex in range(noPops):
pop = pynn.Population(popSize[synType], pynn.IF_facets_hardware1,
neuronParams)
pop.record()
popCollector[synType].append(pop)
# connect stimulus
pynn.Projection(stimExc,
popCollector['exc'][0],
pynn.FixedProbabilityConnector(p_connect=probExcExc,
weights=weightStimExcExc),
def runTest(self):
import numpy as np
column = 4
row = 4
n = 20 # number of spike pairs
deltaTList = [-1.0, 1.0] # ms
deltaTLimit = 0.3 # allowed deviation
delay = 2.9 # ms (between stimulus and post)
# at beginning in ms (should be larger than max deltaT)
experimentOffset = 100.0
deltaTPairs = 100.0 # time between pre-post-pairs in ms
noStimulators = 3
weightStimulator = 15 # weight for stimulator neurons
weightMeasure = 0 # weight for measured neuron
procCorrOffset = 100.0 # time after experiment until correlations are processed in ms
for deltaT in deltaTList:
stimulus = np.arange(experimentOffset,
(n - 0.5) * deltaTPairs + experimentOffset,
deltaTPairs)
self.assertTrue(len(stimulus) == n)
stimulusMeasure = stimulus + delay - deltaT
import pyNN.hardware.spikey as pynn
import hwconfig_default_s1v2 as default
pynn.setup()
if column > 0:
pynn.Population(column, pynn.IF_facets_hardware1)
# stimulated neuron
neuron = pynn.Population(1, pynn.IF_facets_hardware1)
spikeSourceStim = None
spikeSourceMeasure = None
# stimulators above measured synapse
if row < noStimulators:
if row > 0:
dummy = pynn.Population(row, pynn.SpikeSourceArray)
spikeSourceMeasure = pynn.Population(
1, pynn.SpikeSourceArray, {'spike_times': stimulusMeasure})
spikeSourceStim = pynn.Population(noStimulators,
pynn.SpikeSourceArray,
{'spike_times': stimulus})
# stimulators below measured synapse
if row >= noStimulators:
if row > noStimulators:
dummy = pynn.Population(row - noStimulators,
pynn.SpikeSourceArray)
spikeSourceMeasure = pynn.Population(
1, pynn.SpikeSourceArray, {'spike_times': stimulusMeasure})
# connect and record
stdp_model = pynn.STDPMechanism(
timing_dependence=pynn.SpikePairRule(),
weight_dependence=pynn.AdditiveWeightDependence())
pynn.Projection(
spikeSourceStim,
neuron,
method=pynn.AllToAllConnector(weights=pynn.minExcWeight() *
weightStimulator),
target='excitatory')
prj = pynn.Projection(
spikeSourceMeasure,
neuron,
method=pynn.AllToAllConnector(weights=pynn.minExcWeight() *
weightMeasure),
target='excitatory',
synapse_dynamics=pynn.SynapseDynamics(slow=stdp_model))
neuron.record()
#######
# RUN #
#######
# correlation flags:
# 0: no weight change
# 1: causal weight change
# 2: anti-causal weight change
pynn.hardware.hwa.setLUT(
[1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[2, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
lastInputSpike = np.max(np.concatenate(
(stimulus, stimulusMeasure)))
runtime = lastInputSpike + procCorrOffset
pynn.hardware.hwa.autoSTDPFrequency = runtime
print 'runtime: ' + str(runtime) + '; last input spike: ' + str(
lastInputSpike) + '; STDP readout: ' + str(runtime)
pynn.run(runtime)
# get flag and spikes
corrFlag = (
np.array(prj.getWeightsHW(readHW=True, format='list')) /
pynn.minExcWeight())[0]
spikes = neuron.getSpikes()[:, 1]
print 'stimulus:', stimulus
print 'measure:', stimulusMeasure
print 'post:', spikes
self.assertTrue(
len(stimulusMeasure) == len(spikes), 'No proper spiking!')
print 'correlation flag: ' + str(corrFlag)
print 'deltaT (is / should / limit):', np.mean(
spikes - stimulusMeasure), '/', deltaT, '/', deltaTLimit
self.assertTrue(
abs(np.mean(spikes - stimulusMeasure) - deltaT) <= deltaTLimit,
'No precise spiking!')
if deltaT > 0: # causal
self.assertTrue(corrFlag == 1, 'Wrong correlation flag!')
else: # anti-causal
self.assertTrue(corrFlag == 2, 'Wrong correlation flag!')
pynn.end()
def runTest(self):
with_figure = False
import numpy
import pyNN.hardware.spikey as pynn
if with_figure:
import pylab
# some test parameters
neuron_param_even = {
'g_leak': 1.0, # nS
'tau_syn_E': 5.0, # ms
'tau_syn_I': 5.0, # ms
'v_reset': -100.0, # mV
'e_rev_I': -100.0, # mV,
'v_rest': -65.0, # mV
'v_thresh': -62.0 # mV
}
neuron_param_uneven = {
'g_leak': 1.0, # nS
'tau_syn_E': 5.0, # ms
'tau_syn_I': 5.0, # ms
'v_reset': -100.0, # mV
'e_rev_I': -100.0, # mV,
'v_rest': -65.0, # mV
'v_thresh': 0.0 # mV
}
stim_offset = 100.0 # ms
stim_isi = 500.0 # ms
stim_num = 10 # Number of external input spikes
stim_weight = 8.0 # in units of pyn.minExcWeight
stim_pop_size = 10 # size of stimulating population
duration = stim_offset + ((stim_num + 1) * stim_isi)
# neuron order: {0, 2, ..., 190, 1, 3, ..., 191, 192, 193, ... 343}
neuron_order = range(0, 191, 2) + range(1, 192, 2) + range(192, 384, 1)
if with_figure:
pynn.setup(neuronPermutation=neuron_order, useUsbAdc=True)
else:
pynn.setup(neuronPermutation=neuron_order)
# create the population with an even hardware neuron index
even_population = pynn.Population(96, pynn.IF_facets_hardware1,
neuron_param_even)
# create the population with an uneven hardware neuron index
uneven_population = pynn.Population(96, pynn.IF_facets_hardware1,
neuron_param_uneven)
if with_figure:
pynn.record_v(even_population[0], '')
# create the external stimulus
stim_times = numpy.arange(stim_offset, stim_num * stim_isi, stim_isi)
stim_pop = pynn.Population(stim_pop_size, pynn.SpikeSourceArray,
{'spike_times': stim_times})
# connect the external simulus
stim_con = pynn.AllToAllConnector(weights=stim_weight *
pynn.minExcWeight())
stim_prj_even = pynn.Projection(stim_pop, even_population, stim_con)
stim_prj_uneven = pynn.Projection(stim_pop, uneven_population,
stim_con)
# record spikes of all involved neurons
even_population.record()
uneven_population.record()
# run the emulation
pynn.run(duration)
# get the spike data
pre_swap_spikes_even = even_population.getSpikes()
pre_swap_spikes_uneven = uneven_population.getSpikes()
if with_figure:
plotVoltageAndSpikes(pylab, pynn.timeMembraneOutput,
pynn.membraneOutput, pre_swap_spikes_even,
pre_swap_spikes_uneven)
# swap the configurations
pynn.set(even_population[0], pynn.IF_facets_hardware1,
{'v_thresh': 0.0})
pynn.set(uneven_population[0], pynn.IF_facets_hardware1,
{'v_thresh': -62.0})
# run the emulation
pynn.run(duration)
# get the spike data
pst_swap_spikes_even = even_population.getSpikes()
pst_swap_spikes_uneven = uneven_population.getSpikes()
if with_figure:
plotVoltageAndSpikes(pylab, pynn.timeMembraneOutput,
pynn.membraneOutput, pst_swap_spikes_even,
pst_swap_spikes_uneven)
pre_spikes_count_even = float(len(pre_swap_spikes_even[:, 0]))
pre_spikes_count_uneven = float(len(pre_swap_spikes_uneven[:, 0]))
pst_spikes_count_even = float(len(pst_swap_spikes_even[:, 0]))
pst_spikes_count_uneven = float(len(pst_swap_spikes_uneven[:, 0]))
# let's see what we've got
assert (pre_spikes_count_even > 0)
assert (pst_spikes_count_uneven > 0)
assert (pre_spikes_count_uneven / pre_spikes_count_even < 0.01)
assert (pst_spikes_count_even / pst_spikes_count_uneven < 0.01)
assert (pre_spikes_count_uneven / pst_spikes_count_uneven < 0.01)
assert (pst_spikes_count_even / pre_spikes_count_even < 0.01)
def runTest(self):
with_figure = False
import numpy
import pyNN.hardware.spikey as pynn
if with_figure:
import pylab
# some test parameters
neuron_param = {
'g_leak': 1.0, # nS
'tau_syn_E': 5.0, # ms
'tau_syn_I': 5.0, # ms
'v_reset': -100.0, # mV
'e_rev_I': -100.0, # mV,
'v_rest': -65.0, # mV
'v_thresh': -62.0 # mV
}
stim_offset = 100.0 # ms
stim_isi = 500.0 # ms
stim_num = 10 # Number of external input spikes
stim_weight = 8.0 # in units of pyn.minExcWeight
stim_pop_size = 10 # size of stimulating population
duration = stim_offset + ((stim_num + 1) * stim_isi)
# neuron order: {0, 2, ..., 190, 1, 3, ..., 191, 192, 193, .., 383}
neuron_order = range(0, 191, 2) + range(1, 192, 2) + range(192, 384, 1)
if with_figure:
pynn.setup(neuronPermutation=neuron_order, useUsbAdc=True)
else:
pynn.setup(neuronPermutation=neuron_order)
# create first population with an even hardware neuron index
fst_population = pynn.Population(48, pynn.IF_facets_hardware1,
neuron_param)
# create second population with an even hardware neuron index
snd_population = pynn.Population(48, pynn.IF_facets_hardware1,
neuron_param)
if with_figure:
pynn.record_v(fst_population[0], '')
# create the external stimulus
stim_times = numpy.arange(stim_offset, stim_num * stim_isi, stim_isi)
stim_pop = pynn.Population(stim_pop_size, pynn.SpikeSourceArray,
{'spike_times': stim_times})
# connect the external simulus
stim_con = pynn.AllToAllConnector(weights=stim_weight *
pynn.minExcWeight())
stim_prj_fst = pynn.Projection(stim_pop, fst_population, stim_con)
stim_prj_snd = pynn.Projection(stim_pop, snd_population, stim_con)
# record spikes of all involved neurons
fst_population.record()
snd_population.record()
# run the emulation
pynn.run(duration)
# get the spike data
pre_change_spikes_fst = fst_population.getSpikes()
pre_change_spikes_snd = snd_population.getSpikes()
if with_figure:
plotVoltageAndSpikes(pylab,
pynn.timeMembraneOutput,
pynn.membraneOutput,
pre_change_spikes_fst,
pre_change_spikes_snd,
nrn_idx_lim=[0, 96])
# change the configuration for the first group
# desired behaviour: change the configuration for all even neurons
# "set" should be stronger than "previous setting in even/uneven group"
pynn.set(fst_population[0], pynn.IF_facets_hardware1,
{'v_thresh': 0.0})
# run the emulation
pynn.run(duration)
# get the spike data
lidx_change_spikes_fst = fst_population.getSpikes()
lidx_change_spikes_snd = snd_population.getSpikes()
if with_figure:
plotVoltageAndSpikes(pylab,
pynn.timeMembraneOutput,
pynn.membraneOutput,
lidx_change_spikes_fst,
lidx_change_spikes_snd,
nrn_idx_lim=[0, 96])
pre_spikes_count_fst = float(len(pre_change_spikes_fst[:, 0]))
pre_spikes_count_snd = float(len(pre_change_spikes_snd[:, 0]))
lidx_spikes_count_fst = float(len(lidx_change_spikes_fst[:, 0]))
lidx_spikes_count_snd = float(len(lidx_change_spikes_snd[:, 0]))
# let's see what we've got
assert (pre_spikes_count_fst > 0)
assert (pre_spikes_count_snd > 0)
assert (lidx_spikes_count_fst / pre_spikes_count_fst < 0.01)
assert (lidx_spikes_count_snd / pre_spikes_count_snd < 0.01)
# for plotting without X-server
import matplotlib as mpl
mpl.use('Agg')
import pyNN.hardware.spikey as pynn
import numpy as np
pynn.setup()
# set resting potential over spiking threshold
runtime = 1000.0 #ms
popSize = 192
weight = 7.0 * pynn.minExcWeight()
neuronParams = {'v_rest': -40.0}
neurons = pynn.Population(popSize, pynn.IF_facets_hardware1, neuronParams)
pynn.Projection(neurons,
neurons,
pynn.FixedNumberPreConnector(15, weights=weight),
target='inhibitory')
neurons.record()
pynn.run(runtime)
spikes = neurons.getSpikes()
pynn.end()
# visualize
print 'mean firing rate:', round(len(spikes) / runtime / popSize * 1000.0,
1), '1/s'