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 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 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_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 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 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_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_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 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 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 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 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 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 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 record_tau(self, neuronNr, iLeak, v_rest=None):
print 'now at neuron number', neuronNr
# linear dependency of simulation time on 1/iLeak
duration = 5.0*1000.0/float(iLeak)
duration = np.min([duration, 50000.0])
# initialize pyNN
mappingOffset = neuronNr
if self.chipVersion == 4:
mappingOffset = neuronNr - 192
p.setup(useUsbAdc=True, calibTauMem=False, calibVthresh=False, calibSynDrivers=False, calibIcb=False, mappingOffset=mappingOffset, workStationName=self.workstation)
# set g_leak such that iLeak is the desired value
iLeak_base = default.iLeak_base
g_leak = float(iLeak)/iLeak_base
# determine tau_mem, v_rest and v_reset all at once
trials = 0
params = deepcopy(self.neuronParams)
params['g_leak'] = g_leak
if v_rest != None:
params['v_rest'] = v_rest
neuron = p.Population(1, p.IF_facets_hardware1, params)
neuron.record()
p.record_v(neuron[0], '')
crossedTargetRate = False
while params['v_rest'] < self.maxVRest:
print 'now at trial', trials, '/ v_rest =', params['v_rest']
p.run(duration)
trace = p.membraneOutput
dig_spikes = neuron.getSpikes()[:,1]
memtime = p.timeMembraneOutput
timestep = memtime[1] - memtime[0]
# if neuron spikes with too low rate, try again with higher resting potential
if len(dig_spikes) < self.targetSpikes:
params['v_rest'] = params['v_rest'] + self.vRestStep
neuron.set(params)
print 'Neuron spiked with too low rate, trying again with parameters', params
trials += 1
else: # proper spiking
crossedTargetRate = True
break
if not crossedTargetRate:
utils.report('Could not find parameters for which neuron {0} spikes. Will return nan tau_mem'.format(neuronNr), self.reportFile)
return np.concatenate(([iLeak], [np.nan] * 6, [params['v_rest']]))
p.end()
# determine tau_mem from measurements
result = utils.fit_tau_mem(trace, memtime, dig_spikes, timestep=timestep, reportFile=self.reportFile)
if result == None: # fit failed
utils.report('Fit of membrane time constant for neuron {0} failed (iLeak = {1})'.format(neuronNr, iLeak), self.reportFile)
return np.concatenate(([iLeak], [np.nan] * 6, [params['v_rest']]))
return np.concatenate(([iLeak], result, [params['v_rest']]))
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 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 runClosed():
global neurons
rateOutList = []
for rate in rateRange:
pynn.setup()
build(rate)
pynn.run(runtime)
rateOutList.append(
len(neurons.getSpikes()) / runtime * 1e3 / numNeurons)
pynn.end()
return rateOutList
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 runLoop():
global neurons, stim
rateOutList = []
pynn.setup()
build(0)
for rate in rateRange:
poissonParams = {'start': 0, 'duration': runtime, 'rate': rate}
stim.set(poissonParams)
pynn.run(runtime)
rateOutList.append(
len(neurons.getSpikes()) / runtime * 1e3 / numNeurons)
pynn.end()
return rateOutList
def test_mappingOffset_and_Permutation_random():
# example with random neuron permutator
trials = 3
import time
seed = int(time.time())
print 'seed', seed
np.random.seed(seed)
pynn.setup()
chipVersion = pynn.getChipVersion()
pynn.end()
permutatorWorking = range(384)
if chipVersion == 4:
permutatorWorking = range(192, 384)
for i in range(trials):
np.random.shuffle(permutatorWorking)
mappingOffset = np.random.random_integers(0, 383)
permutator = copy.copy(permutatorWorking)
if chipVersion == 4:
mappingOffset = np.random.random_integers(0, 191)
permutator = copy.copy(permutatorWorking) + range(192)
run_network(mappingOffset=mappingOffset, neuronPermutation=permutator)
permutator = np.array(permutator)
should = np.concatenate(
(permutator[mappingOffset:384], permutator[0:mappingOffset]))
if chipVersion == 4:
should = np.concatenate((permutator[mappingOffset:192], permutator[
0:mappingOffset], np.ones(192, int) * -1))
assert np.array_equal(pynn.hardware.hwa.hardwareIndexMap, should)
neuronIndexMap = pynn.hardware.hwa.neuronIndexMap
noNeurons = 384
if chipVersion == 4:
noNeurons = 192
assert len(neuronIndexMap[
neuronIndexMap >= 0]) == noNeurons, 'number of hardware neuron IDs does not match'
assert len(neuronIndexMap[
neuronIndexMap >= 0]) == noNeurons, 'hardware neuron IDs not adjacent in map'
if chipVersion == 4:
noNeurons += 1 # +1 for "-1" entries
assert len(np.unique(neuronIndexMap)
) == noNeurons, 'not all hardware neuron IDs in map'
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
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 recordTauRef(self, neuronNr, icb):
# necessary hardware setup
p.setup(useUsbAdc=True, mappingOffset=neuronNr-192, calibTauMem=True, calibVthresh=False, calibSynDrivers=False, calibIcb=False, workStationName=self.workstation)
p.hardware.hwa.setIcb(icb)
# observed neuron
neuron = p.Population(1, p.IF_facets_hardware1, self.neuronParams)
# stimulating population
input = p.Population(self.inputParameters['numInputs'], p.SpikeSourceArray, self.inputParameters['inputSpikes'])
# connect input and neuron
conn = p.AllToAllConnector(allow_self_connections=False, weights=self.inputParameters['weight'])
proj = p.Projection(input, neuron, conn, synapse_dynamics=None, target='excitatory')
# record spikes and membrane potential
neuron.record()
p.record_v(neuron[0],'')
# run experiment
p.run(self.duration)
# evaluate results
spikesDig = neuron.getSpikes()[:,1]
membrane = p.membraneOutput
time = p.timeMembraneOutput
# clean up
p.end()
# determine sampling bins
timestep = time[1] - time[0]
# detect analog spikes
spikesAna, isiAna = utils.find_spikes(membrane, time, spikesDig, reportFile=self.reportFile)
# determine refractory period from measurement of analog spikes
tau_ref, tau_ref_err, doubles_spikes = utils.fit_tau_refrac(membrane, timestep, spikesAna, isiAna, noDigSpikes=len(spikesDig), reportFile=self.reportFile, debugPlot=self.debugPlot)
return tau_ref, tau_ref_err, doubles_spikes, spikesDig
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 emulate(self, driverIndexExc, driverIndexInh=None, drvirise=None, drvifallExc=None, drvifallInh=None, drvioutExc=None, drvioutInh=None, filename=None, calibSynDrivers=False):
'''Run emulations on hardware.'''
assert self.stimParams != None, 'specifiy stimulus first'
pynn.setup(calibTauMem=True,
calibSynDrivers=calibSynDrivers,
calibVthresh=False,
calibIcb=False,
workStationName=self.workstation,
writeConfigToFile=False)
#create neuron
self.neuronList.sort()
neuronCollector = []
currentIndex = 0
for neuronIndex in self.neuronList:
if neuronIndex > currentIndex: #insert dummy neurons if neuronList not continuous
dummyPopSize = neuronIndex - currentIndex
dummy = pynn.Population(dummyPopSize, pynn.IF_facets_hardware1, self.neuronParams)
currentIndex += dummyPopSize
self.logger.debug('inserted ' + str(dummyPopSize) + ' dummy neurons')
if neuronIndex == currentIndex:
neuron = pynn.Population(1, pynn.IF_facets_hardware1, self.neuronParams)
currentIndex += 1
neuron.record()
neuronCollector.append(neuron)
else:
raise Exception('Could not create all neurons')
#create input and connect to neuron
synDrivers = [[driverIndexExc, 'excitatory'], [driverIndexInh, 'inhibitory']]
synDrivers.sort()
currentIndex = 0
for synDriver in synDrivers:
toInsertIndex = synDriver[0]
targetType = synDriver[1]
if toInsertIndex == None:
self.logger.debug('skipping ' + targetType + ' stimulation')
continue
if toInsertIndex > currentIndex:
dummyPopSize = toInsertIndex - currentIndex
dummy = pynn.Population(dummyPopSize, pynn.SpikeSourcePoisson)
currentIndex += dummyPopSize
self.logger.debug('inserted ' + str(dummyPopSize) + ' dummy synapse drivers')
stim = pynn.Population(1, pynn.SpikeSourcePoisson, self.stimParams[targetType])
self.logger.debug('inserted 1 stimulus of type ' + targetType + ' with rate ' + str(self.stimParams[targetType]['rate']))
if targetType == 'excitatory':
hardwareWeightTemp = self.hardwareWeight * pynn.minExcWeight()
elif targetType == 'inhibitory':
hardwareWeightTemp = self.hardwareWeight * pynn.minInhWeight()
else:
raise Exception('Synapse type not supported!')
for neuron in neuronCollector:
pynn.Projection(stim, neuron, method=pynn.AllToAllConnector(weights=hardwareWeightTemp), target=targetType)
currentIndex += 1
#set custom parameters
if drvirise != None:
pynn.hardware.hwa.drvirise = drvirise
else:
pynn.hardware.hwa.drvirise = default.drvirise
if drvifallExc != None:
pynn.hardware.hwa.drvifall_base['exc'] = drvifallExc
else:
pynn.hardware.hwa.drvifall_base['exc'] = default.drvifall_base['exc']
if drvifallInh != None:
pynn.hardware.hwa.drvifall_base['inh'] = drvifallInh
else:
pynn.hardware.hwa.drvifall_base['inh'] = default.drvifall_base['inh']
if drvioutExc != None:
pynn.hardware.hwa.drviout_base['exc'] = drvioutExc
else:
pynn.hardware.hwa.drviout_base['exc'] = default.drviout_base['exc']
if drvioutInh != None:
pynn.hardware.hwa.drviout_base['inh'] = drvioutInh
else:
pynn.hardware.hwa.drviout_base['inh'] = default.drviout_base['inh']
#run
pynn.run(self.runtime)
#temperature = pynn.hardware.hwa.getTemperature()
#self.logger.debug('temperature ' + str(temperature) + ' degree Celsius')
#obtain firing rate
spikes = None
neuronCount = 0
for neuron in neuronCollector:
spikesNeuron = neuron.getSpikes()
neuronCount += neuron.size
if spikes == None:
spikes = spikesNeuron
else:
spikes = np.concatenate((spikes, spikesNeuron))
if len(spikes) > 0:
spikes = spikes[spikes[:,1] > self.cutfirst]
if len(spikes) > 0:
spikes = spikes[spikes[:,1] <= self.runtime]
if filename != None:
np.savetxt(os.path.join(self.folder, filename), spikes)
spikesPerNeuron = float(len(spikes)) / neuronCount
pynn.end()
rate = spikesPerNeuron * 1e3 / (self.runtime - self.cutfirst)
return rate
See also:
Pfeil et al. (2014).
The effect of heterogeneity on decorrelation mechanisms in spiking neural networks: a neuromorphic-hardware study.
arXiv:1411.7916 [q-bio.NC].
"""
# 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()
def calib(self):
self.result['datetime'] = dt.datetime.now()
self.result['temperature'] = 'TODO'
self.result['person'] = pwd.getpwuid(os.getuid()).pw_name
# one setup is necessary in order to determine spikey version
pynn.setup(workStationName=self.workstation, calibOutputPins=False, calibNeuronMems=False, calibTauMem=False, calibSynDrivers=False, calibVthresh=False, calibBioDynrange=False)
self.chipVersion = pynn.hardware.chipVersion()
for block in range(2):
if not self.chipVersion == 4 or block == 1:
for pin in range(4):
lower = -90.
upper = -40.
step = (upper - lower) / self.numVsteps
for vrest in numpy.arange(lower, upper+step/2., step):
pin_in = numpy.nan
pin_out = numpy.nan
for pinBlock in range(self.numPinBlocks):
neuron = block * 192 + pinBlock * 4 + pin
# necessary setup
mappingOffset = neuron
if self.chipVersion == 4:
mappingOffset = neuron % 192
pynn.setup(useUsbAdc=True, workStationName=self.workstation, mappingOffset=mappingOffset, rng_seeds=self.seeds, avoidSpikes=True, \
calibOutputPins=False, calibNeuronMems=False, calibTauMem=False, calibSynDrivers=False, calibVthresh=False)
self.neuronParams['v_rest'] = vrest
# set up network
n = pynn.create(pynn.IF_facets_hardware1,self.neuronParams,n=1)
pynn.record_v(n, '')
pynn.record(n, '')
#http://en.wikipedia.org/wiki/Algorithms_for_calculating_variance
traceSum = 0.0
traceSumSqr = 0.0
# execute the experiment in a loop
for i in range(self.numRuns):
pynn.run(self.duration, translateToBioVoltage=False)
if i==0:
pin_in = pynn.hardware.hwa.vouts[neuron/192,neuron%2 + 2]
else:
assert pin_in == pynn.hardware.hwa.vouts[neuron/192,neuron%2 + 2], 'vout should not differ'
mem = pynn.membraneOutput
memMean = mem.mean()
traceSum += memMean
traceSumSqr += numpy.power(memMean, 2)
noSpikes = len(pynn.spikeOutput[1])
if not float(noSpikes) / self.duration * 1e3 == 0:
self.noSpikesTotal += noSpikes
print 'there are', noSpikes, 'spikes on the membrane (most likely / hopefully ghost spikes)'
assert mem.std() < self.limMemStd, 'digital spikes and spikes on the membrane found!'
pin_out = traceSum / self.numRuns
pin_out_std = (traceSumSqr - (numpy.power(traceSum, 2) / self.numRuns)) / (self.numRuns - 1)
pynn.end()
print 'For neuron',neuron,'the written voltage',pin_in,'appeared on the scope as',pin_out,'/2'
#save raw data
newData = numpy.vstack((neuron, pin_in, pin_out, numpy.sqrt(pin_out_std))).T
if self.rawData == None:
self.rawData = newData
else:
self.rawData = numpy.vstack((self.rawData, newData))
def filter_and_fit(dataset):
#filter data
dataset = numpy.atleast_2d(dataset)
dataToFit = numpy.atleast_2d(dataset[dataset[:,1] >= self.voltageLimLow])
dataToFit = numpy.atleast_2d(dataToFit[dataToFit[:,1] <= self.voltageLimHigh])
noPins = len(numpy.unique(numpy.array(dataset[:,0] / 192, numpy.int) * 4 + dataset[:,0] % 4))
assert (len(dataset) - len(dataToFit)) % noPins == 0, 'discarding data failed'
print 'discarded', (len(dataset) - len(dataToFit)) / noPins, 'data points'
#fit polynomial
return numpy.polyfit(dataToFit[:,2], dataToFit[:,1], self.polyDegree)
for block in range(2):
if self.chipVersion == 4 and block == 0:
continue
for pin in range(4):
#data for output pin calibration
dataOnePin = self.rawData[numpy.array(self.rawData[:,0] / 192, numpy.int) * 4 + self.rawData[:,0] % 4 == block * 4 + pin]
#calculate mean over neurons with same pin
vouts = numpy.unique(dataOnePin[:,1])
mean = []
std = []
for vout in vouts:
mean.append(numpy.mean(dataOnePin[dataOnePin[:,1] == vout][:,2]))
std.append(numpy.std(dataOnePin[dataOnePin[:,1] == vout][:,2]))
dataOnePinMean = numpy.vstack((numpy.zeros_like(vouts), vouts, mean, std)).T
self.result['polyFitOutputPins']['pin' + str(block * 4 + pin)] = filter_and_fit(dataOnePinMean)
for pinBlock in range(self.numPinBlocks):
neuron = block * 192 + pinBlock * 4 + pin
#data for membrane calibration of single neurons
dataOneNeuron = self.rawData[self.rawData[:,0] == neuron]
self.result['polyFitNeuronMems']['neuron' + str(neuron).zfill(3)] = filter_and_fit(dataOneNeuron)
print 'total number of spikes', self.noSpikesTotal, 'in', len(numpy.unique(numpy.array(self.rawData[:,0] / 192, numpy.int) * 4 + self.rawData[:,0] % 4)) * (self.numVsteps + 1) * self.numPinBlocks * self.numRuns, 'runs'
return self.result, self.rawData
import pyNN.hardware.spikey as pynn
import numpy as np
import matplotlib.pyplot as plt
noStims = 64 # number of stimuli generated on the host computer
noNeurons = 32 # number of hardware neurons
noInputs = 16 # number for stimuli connected to each neuron
weight = 7.0 # synaptic weight in digital values
rateStim = 10.0 # rate of each stimulus in 1/s
runtime = 10 * 1000.0 # runtime in biological time domain in ms
gLeakList = np.arange(2,251,8) # hardware range with calibTauMem turned off: [2,250] micro siemens
resultCollector = []
pynn.setup(calibTauMem=False) #turn off calibration of membrane time constant tau_mem
#build network
stimuli = pynn.Population(noStims, pynn.SpikeSourcePoisson, {'start': 0, 'duration': runtime, 'rate': rateStim})
neurons = pynn.Population(noNeurons, pynn.IF_facets_hardware1)
pynn.Projection(stimuli, neurons, pynn.FixedNumberPreConnector(noInputs, weights=weight * pynn.minExcWeight()), target='excitatory')
neurons.record()
#sweep over g_leak values, emulate network and record spikes
for gLeakValue in gLeakList:
neurons.set({'g_leak': gLeakValue})
pynn.run(runtime)
resultCollector.append([gLeakValue, float(len(neurons.getSpikes())) / noNeurons / runtime * 1e3])
pynn.end()
#plot results
import pyNN.hardware.spikey as pynn
import numpy as np
runtime = 500.0 # ms
noPops = 15 # chain length #9
popSize = {'exc': 6, 'inh': 6} # size of each chain link #exc 10, inh 10
# connection probabilities
probExcExc = 1.0
probExcInh = 1.0
probInhExc = 1.0
# refractory period of neurons can be tuned for optimal synfire chain bahavior
neuronParams = {'tau_refrac': 10.0}
pynn.setup()
# 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])
# overwrite possibly existing data?
overwrite_data = True
if len(sys.argv) < 4:
raise Exception('provide arguments [station] [filename results] [filename raw data]')
workstation = sys.argv[1]
filenameResult = sys.argv[2]
filenameRawData = sys.argv[3]
# TODO: add report to JSON file for raw data; up to then store in same folder as raw data
filenameReport = os.path.join(os.path.splitext(filenameRawData)[0], 'report.dat')
import pyNN.hardware.spikey as pynn
pynn.setup(workStationName=workstation)
chipVersion = pynn.getChipVersion()
pynn.end()
if chipVersion == 4:
neuronIDs = range(192, 384)
##############################################################################################
# initiatlize calibrator object for given neurons and parameters
clb = calibrator.Calibrator_TauMem(neuronIDs=neuronIDs, workstation=workstation, numValues=numValues, iLeakRange=iLeakRange, filenameResult=filenameResult, filenameRawData=filenameRawData, overwrite_data=overwrite_data, chipVersion=chipVersion, reportFile=filenameReport)
startTime = time.time()
# run calibration
clb.calib()
# fit tau_mem vs iLeak
startTime = time.time()
if len(sys.argv) > 1:
workstation = sys.argv[1]
else:
workstation = None
if len(sys.argv) > 2:
filenameRawData = sys.argv[2]
else:
filenameRawData = './voutRaw.dat'
# necessary setup
pynn.setup(timestep=1.0, useUsbAdc=False, workStationName=workstation,
calibOutputPins=False, calibIcb=False, calibTauMem=False, calibSynDrivers=False, calibVthresh=False, rng_seeds=[1234])
####################################################################
# experiment parameters #
####################################################################
neuron = pynn.Population(1, pynn.IF_facets_hardware1)
neuron.record()
pynn.run(1000.0)
pynn.hardware.hwa.sp.autocalib(pynn.hardware.hwa.cfg, filenameRawData)
endTime = time.time()
print 'vouts calibration took', (endTime-startTime)/60.,'minutes'
print 'please commit results in "*/spikeyhal/spikeycalib.xml" (ignore the below warning that this file does not exist)'
noSpikePairs = 20 # number of spike pairs
timingPrePostPlastic = 1.0 # timing between pre- and postsynaptic spikes at plastic synapse in ms
intervalPairs = 100.0 # time interval between presynaptic spikes in ms
noStim = 3 # number of synapses to stimulate spiking of postsynaptic neuron
weightStim = 8.0 # weight of stimulating synapses
timingPrePostStim = 3.4 # timing between pre- and postsynaptic spikes of stimulating synapses in ms
spikePrecision = 0.3 # limit of precision of spiking in ms
stimulusOffset = 100.0 # offset from beginning and end of emulation in ms (should be larger than timingPrePostPlastic)
# prepare stimuli
stimulus = np.arange(stimulusOffset, (noSpikePairs - 0.5) * intervalPairs + stimulusOffset, intervalPairs)
stimulusPlastic = stimulus + timingPrePostStim - timingPrePostPlastic
assert len(stimulus) == noSpikePairs
pynn.setup(mappingOffset=column)
# create postsynaptic neuron
neuron = pynn.Population(1, pynn.IF_facets_hardware1)
spikeSourceStim = None
spikeSourcePlastic = None
# place stimulating synapses above plastic synapse
if row < noStim:
if row > 0:
dummy = pynn.Population(row, pynn.SpikeSourceArray)
spikeSourcePlastic = pynn.Population(1, pynn.SpikeSourceArray, {"spike_times": stimulusPlastic})
# create stimulating inputs
spikeSourceStim = pynn.Population(noStim, pynn.SpikeSourceArray, {"spike_times": stimulus})
# place stimulating synapses below plastic synapse
if row >= noStim:
# have to reduce the neuron count in the decision pop to fit in five digits,
#config['network']['num_dec_neurons'] = '6'
#config['network']['num_inh_dec_neurons'] = '6'
import neuclar.data.mnist as mnist
import neuclar.vrconvert as vrconvert
from timings import NeuclarTimings
start_time = time.time()
# doing the stuff
perm = numpy.random.permutation(192) + 192
perm = numpy.concatenate((perm, numpy.arange(192)))
setupargs = dict(writeConfigToFile=False, neuronPermutation=list(perm))
if not (workstation is None):
setupargs['workStationName'] = workstation
p.setup(**setupargs)
p.setup()
setup_time = time.time()
# load data
training_data, training_labels = mnist.get_training_data(digits, num_data_samples)
testing_data, testing_labels = mnist.get_training_data(digits, num_data_samples)
load_data_time = time.time()
# convert data with VRs
if retrain:
posfilename = "vrpos-{}-{}.npy".format("".join(['{}'.format(d) for d in digits]),
time.strftime("%Y-%m-%d-%H-%M-%S"))
lg.info("computing new VR positions, storing them to {}".format(posfilename))
vrs = vrconvert.NeuralGasSampler()
vrs.train_sampler(numpy.array(training_data, dtype=float), vrconvert.neural_gas_parameters)
#!/usr/bin/env python
import pyNN.hardware.spikey as pynn
import numpy as np
import matplotlib.pyplot as plt
weight = 7.0 # synaptic weight in digital values
runtime = 10 * 1000.0 # runtime in biological time domain in ms
durationInterval = 200.0 # interval between input spikes in ms
neuronIndex = 42 # choose neuron on chip in range(384)
synapseDriverIndex = 42 # choose synapse driver in range(256)
pynn.setup(mappingOffset=neuronIndex, calibSynDrivers=False) #turn off calibration of synapse line drivers
##build network
neurons = pynn.Population(1, pynn.IF_facets_hardware1)
pynn.record_v(neurons[0], '')
#allocate dummy synapse drivers sending no spikes
if synapseDriverIndex > 0:
stimuliDummy = pynn.Population(synapseDriverIndex, pynn.SpikeSourceArray, {'spike_times': []})
prj = pynn.Projection(stimuliDummy, neurons, pynn.AllToAllConnector(weights=0), target='excitatory')
#allocate synapse driver and configure spike times
stimProp = {'spike_times': np.arange(durationInterval, runtime - durationInterval, durationInterval)}
stimuli = pynn.Population(1, pynn.SpikeSourceArray, stimProp)
prj = pynn.Projection(stimuli, neurons, pynn.AllToAllConnector(weights=weight * pynn.minExcWeight()), target='excitatory')
#modify properties of synapse driver
print 'Range of calibration factors of drvifall for excitatory connections', prj.getDrvifallFactorsRange('exc')
prj.setDrvifallFactors([0.8])
#prj.setDrvioutFactors([1.0])