def test_NeuronCalibration(self):
with TemporaryDirectory() as tmp_dir:
backend = loadXMLBackend(tmp_dir)
nc0 = cal.NeuronCollection()
nc0.setSpeedup(int(1e4))
nc0.setStartingCycle(42)
tmp = cal.NeuronCalibration()
tmp.setDefaults()
nc0.insert(0, tmp)
self.assertLess(0, tmp.at(pyhalbe.HICANN.neuron_parameter.E_l).apply(0.5))
backend.store("fisch", cal.MetaData(), nc0)
nc1 = cal.NeuronCollection()
md = cal.MetaData()
backend.load("fisch", md, nc1)
self.assertEqual(int(1e4), nc1.getSpeedup())
self.assertEqual(42, nc0.getStartingCycle())
bio = cell.EIF_cond_exp_isfa_ista()
hwparam0 = nc0.applyNeuronCalibration(
bio, 0, cal.NeuronCalibrationParameters())
hwparam1 = nc1.applyNeuronCalibration(
bio, 0, cal.NeuronCalibrationParameters())
for idx in range(cal.HWNeuronParameter.size()):
self.assertEqual(hwparam0.getParam(idx), hwparam1.getParam(idx),
"HWNeuronParameter[{}]: {} != {}".format(
idx, hwparam0.getParam(idx), hwparam1.getParam(idx)))
def extract_bio_weight_range(src, speedup, cm_bio, bigcap, neuron_size):
"""
extract the biological range of synaptic weights in the hardware.
First, the hardware range of a single synapse is extracted from
the calibration of a synapse row, then these ranges are scaled back
to the biological domain considering the relevant settings (see below).
params:
src - calibdata for one synapse row of type
pycalibtic.SynapseRowCalibration
speedup - speedup factor of hardware emulation vs biological realtime
cm_bio - biological membrane capacitance in nF
bigcap - choose big (small) capacitance in hardware neuron if True (False)
neuron_size - number of hardware neurons forming one compound neuron
returns:
tuple(min weight, max weight) in microSiemens (PyNN unit for weights)
"""
hw_range = extract_hw_weight_range(src)
nc = cal.NeuronCalibration()
cm_hw = nc.big_cap if bigcap else nc.small_cap
cm_hw *= neuron_size
bio_range = []
nS_to_S = 1.e-9
nS_to_uS = 1.e-3
for val in hw_range:
bio_range.append(
nc.reverseScaleConductance(val * nS_to_S, speedup, cm_bio, cm_hw) *
nS_to_uS)
return bio_range
def test_ideal_calibration(self):
nc = cal.NeuronCalibration()
nc.setDefaults()
for dac in range(1024):
ideal_volt = float(dac)/nc.max_fg_value*nc.max_techn_volt
self.assertEqual(nc.ideal_volt_to_dac(ideal_volt), dac)
params = cal.NeuronCalibrationParameters()
params.alphaV = 10
params.shiftV = 1.2
pcp = cell.IF_cond_exp()
pcp.v_thresh = -50
pcp.v_rest = -60
pcp.e_rev_E = -70
pcp.e_rev_I = -80
pcp.tau_refrac = 10
pcp.tau_syn_E = 2
pcp.tau_syn_I = 2
hw_params = nc.applyNeuronCalibration(pcp, 10000, params)
# compare with scaling + ideal volt-to-dac or best-guess transformation
self.assertEqual(hw_params.getParam(pyhalbe.HICANN.neuron_parameter.names["V_t"]), 398)
self.assertEqual(hw_params.getParam(pyhalbe.HICANN.neuron_parameter.names["E_l"]), 341)
self.assertEqual(hw_params.getParam(pyhalbe.HICANN.neuron_parameter.names["E_synx"]), 291)
self.assertEqual(hw_params.getParam(pyhalbe.HICANN.neuron_parameter.names["E_syni"]), 227)
self.assertEqual(hw_params.getParam(pyhalbe.HICANN.neuron_parameter.names["I_pl"]), 17)
self.assertEqual(hw_params.getParam(pyhalbe.HICANN.neuron_parameter.names["V_convoffi"]), 1023)
self.assertEqual(hw_params.getParam(pyhalbe.HICANN.neuron_parameter.names["V_convoffx"]), 1023)
self.assertEqual(hw_params.getParam(pyhalbe.HICANN.neuron_parameter.names["I_convi"]), 1023)
self.assertEqual(hw_params.getParam(pyhalbe.HICANN.neuron_parameter.names["I_convx"]), 1023)
self.assertEqual(hw_params.getParam(pyhalbe.HICANN.neuron_parameter.names["I_intbbi"]), 511)
self.assertEqual(hw_params.getParam(pyhalbe.HICANN.neuron_parameter.names["I_intbbx"]), 511)
self.assertEqual(hw_params.getParam(pyhalbe.HICANN.neuron_parameter.names["V_syni"]), 511)
self.assertEqual(hw_params.getParam(pyhalbe.HICANN.neuron_parameter.names["V_synx"]), 511)
self.assertEqual(hw_params.getParam(pyhalbe.HICANN.neuron_parameter.names["I_spikeamp"]), 1023)
self.assertEqual(hw_params.getParam(pyhalbe.HICANN.neuron_parameter.names["V_syntci"]), 481)
self.assertEqual(hw_params.getParam(pyhalbe.HICANN.neuron_parameter.names["V_syntcx"]), 481)
def test_RegressionUpcast(self):
with TemporaryDirectory() as tmp_dir:
backend = loadXMLBackend(tmp_dir)
nc0 = cal.NeuronCollection()
tmp = cal.NeuronCalibration()
tmp.setDefaults()
nc0.insert(0, tmp)
backend.store("fisch", cal.MetaData(), nc0)
nc1 = cal.NeuronCollection()
md = cal.MetaData()
backend.load("fisch", md, nc1)
self.assertEqual(nc0.at(0).size(), nc1.at(0).size())
def print_default_bio_ranges():
nc = cal.NeuronCalibration()
nc.setDefaults()
nc_params = cal.NeuronCalibrationParameters()
cm_bio = 0.281 # nS, default ADEX membrane capacitance
#cm_bio = 10. # nS, default IF_cond_exp membrane capacitance
nc_params.bigcap = True
nc_params.alphaV = 5.
speedup = 10000.
bio_ranges = extract_bio_ranges(nc, nc_params.shiftV, nc_params.alphaV,
speedup, cm_bio, nc_params.bigcap)
print("Bio ranges for parameters")
print("speedup:", speedup)
print("shiftV:", nc_params.shiftV, "V")
print("alphaV:", nc_params.alphaV)
print("bigcap:", nc_params.bigcap)
print("cm_bio:", cm_bio, "nF")
#pprint.pprint(bio_ranges)
pprint_ranges_dict(bio_ranges)
def test_reverse_apply_reverse_domains(self):
nc = cal.NeuronCalibration()
nc.setDefaults()
for c in ["V_t", "E_l", "E_synx", "E_syni", "I_pl",
"I_gl_slow0_fast0_bigcap0", "V_syntcx", "V_syntcx"]:
calib = nc.at(cal.NeuronCalibrationParameters.Calibrations.calib.names[c])
reverse_domain = calib.getReverseDomainBoundaries()
at_lower_boundary = calib.reverseApply(reverse_domain.first)
at_upper_boundary = calib.reverseApply(reverse_domain.second)
below_boundary = calib.reverseApply(reverse_domain.first-1, cal.Transformation.CLIP)
above_boundary = calib.reverseApply(reverse_domain.second+1, cal.Transformation.CLIP)
self.assertEqual(at_lower_boundary, below_boundary)
self.assertEqual(at_upper_boundary, above_boundary)
def print_default_hw_ranges():
nc = cal.NeuronCalibration()
nc.setDefaults()
hw_ranges = extract_hw_ranges(nc)
print("DAC ranges:")
pprint.pprint(hw_ranges)
#!/usr/bin/env python import pycalibtic import pycellparameters from pyhalbe.HICANN import neuron_parameter, shared_parameter neuron_calib = pycalibtic.NeuronCalibration() neuron_calib.setDefaults() neuron_calib_params = pycalibtic.NeuronCalibrationParameters() neuron_calib_params.alphaV = 10 neuron_calib_params.shiftV = 1.2 bio_params = pycellparameters.EIF_cond_exp_isfa_ista() bio_params.tau_refrac = 1.00 bio_params.a = 2.5 bio_params.tau_m = 10.0 bio_params.e_rev_E = 0.0 bio_params.cm = 0.24 bio_params.delta_T = 1.2 bio_params.e_rev_I = -80.0 bio_params.v_thresh = -40.0 bio_params.b = 0.05 bio_params.tau_syn_E = 2 bio_params.v_spike = 0.0 bio_params.tau_syn_I = 2 bio_params.tau_w = 30.0 bio_params.v_rest = -60.0 speedup = 10000
"""
script to extract the domain values for the default calibration.
I.e. for each parameter, it extracts the range of biological parameters, that can be mapped to the voltage/current domain of the hardware.
"""
import pycalibtic as cal
import pyhalbe
import numpy as np
nrn_param = pyhalbe.HICANN.neuron_parameter
nc = cal.NeuronCalibration()
nc.setDefaults()
# remove domain!
for param in [
nrn_param.E_l, nrn_param.E_synx, nrn_param.E_syni, nrn_param.V_exp,
nrn_param.V_t, nrn_param.I_pl, nrn_param.I_radapt, nrn_param.V_syntcx,
nrn_param.V_syntci, nrn_param.I_gl, nrn_param.I_gladapt,
nrn_param.I_fire, nrn_param.I_rexp
]:
coeffs = nc.at(param).getData()
nc.reset(param, cal.Polynomial(coeffs))
min_current = 0.
max_current = 2500.
min_voltage = 0.
max_voltage = 1800.
min_current_tau = max_current * 1. / 1023
max_current_tau = max_current