def test_popview_on_hicann(self, size):
pynn.setup(marocco=self.marocco)
neuron_size = 4
self.marocco.neuron_placement.default_neuron_size(neuron_size)
hicann = C.HICANNOnWafer(Enum(122))
hicann_1 = C.HICANNOnWafer(Enum(123))
hicann_2 = C.HICANNOnWafer(Enum(124))
hicann_3 = C.HICANNOnWafer(Enum(125))
pop = pynn.Population(size, pynn.IF_cond_exp, {})
pop_1 = pynn.Population(size, pynn.IF_cond_exp, {})
pop_view = pynn.PopulationView(pop,list(range(0,size,2)))
pop_view_1 = pynn.PopulationView(pop,list(range(1,size,2)))
pop_1_view = pynn.PopulationView(pop_1,list(range(1,size//2)))
pop_1_view_1 = pynn.PopulationView(pop_1,list(range(size-2,size//2,-1)))
pop_auto_placement = pynn.PopulationView(pop_1,[0,size//2,size-1])
self.marocco.manual_placement.on_hicann(pop_view, hicann)
self.marocco.manual_placement.on_hicann(pop_view_1, hicann_1)
self.marocco.manual_placement.on_hicann(pop_1_view, hicann_2)
self.marocco.manual_placement.on_hicann(pop_1_view_1, hicann_3)
if neuron_size * size//2 > C.NeuronOnHICANN.enum_type.size:
with self.assertRaises(RuntimeError):
pynn.run(0)
pynn.end()
return
pynn.run(0)
pynn.end()
results = self.load_results()
for nrn in pop_view:
placement_item, = results.placement.find(nrn)
logical_neuron = placement_item.logical_neuron()
for denmem in logical_neuron:
self.assertEqual(hicann, denmem.toHICANNOnWafer())
for nrn in pop_view_1:
placement_item, = results.placement.find(nrn)
logical_neuron = placement_item.logical_neuron()
for denmem in logical_neuron:
self.assertEqual(hicann_1, denmem.toHICANNOnWafer())
for nrn in pop_1_view:
placement_item, = results.placement.find(nrn)
logical_neuron = placement_item.logical_neuron()
for denmem in logical_neuron:
self.assertEqual(hicann_2, denmem.toHICANNOnWafer())
for nrn in pop_1_view_1:
placement_item, = results.placement.find(nrn)
logical_neuron = placement_item.logical_neuron()
for denmem in logical_neuron:
self.assertEqual(hicann_3, denmem.toHICANNOnWafer())
for nrn in pop_auto_placement:
placement_item, = results.placement.find(nrn)
logical_neuron = placement_item.logical_neuron()
for denmem in logical_neuron:
self.assertIsNotNone(denmem.toHICANNOnWafer())
def test_popview_on_neuron(self):
pynn.setup(marocco=self.marocco)
pop = pynn.Population(4, pynn.IF_cond_exp, {})
neuron_block = C.NeuronBlockOnWafer(C.NeuronBlockOnHICANN(3))
neuron_block_1 = C.NeuronBlockOnWafer(C.NeuronBlockOnHICANN(2))
logical_neuron = (LogicalNeuron.on(neuron_block)
.add(C.NeuronOnNeuronBlock(X(3), Y(0)), 2)
.add(C.NeuronOnNeuronBlock(X(3), Y(1)), 2)
.done())
logical_neuron_1 = (LogicalNeuron.on(neuron_block_1)
.add(C.NeuronOnNeuronBlock(X(4), Y(0)), 2)
.add(C.NeuronOnNeuronBlock(X(4), Y(1)), 2)
.done())
popview = pynn.PopulationView(pop,[0])
popview_1 = pynn.PopulationView(pop,[2])
popview_auto_placement= pynn.PopulationView(pop,[1,3])
self.marocco.manual_placement.on_neuron(popview, logical_neuron)
self.marocco.manual_placement.on_neuron(popview_1, logical_neuron_1)
pynn.run(0)
pynn.end()
results = self.load_results()
placement_item, = results.placement.find(popview[0])
self.assertEqual(logical_neuron, placement_item.logical_neuron())
placement_item, = results.placement.find(popview_1[0])
self.assertEqual(logical_neuron_1, placement_item.logical_neuron())
for nrn in popview_auto_placement:
placement_item, = results.placement.find(nrn)
self.assertIsNotNone(placement_item.logical_neuron())
def test_Constructor(self):
import numpy
import pymarocco
marocco = pymarocco.PyMarocco()
marocco.calib_backend = pymarocco.PyMarocco.CalibBackend.Default
pynn.setup(marocco=marocco)
N = 10
model = pynn.IF_cond_exp
selector = numpy.array(
[random.choice([True, False]) for x in range(0, N)])
pop = pynn.Population(N, model)
pv = pynn.PopulationView(pop, selector)
self.assertEqual(len(pv), len(numpy.where(selector == True)[0]))
# now a selection with wrong size is given
wrong_selector = numpy.array(
[random.choice([True, False]) for x in range(0, 2 * N)])
with self.assertRaises(RuntimeError):
pv = pynn.PopulationView(pop, wrong_selector)
pynn.run(100)
def test_same_popview_on_hicann(self, size):
pynn.setup(marocco=self.marocco)
neuron_size = 4
self.marocco.neuron_placement.default_neuron_size(neuron_size)
hicann = C.HICANNOnWafer(Enum(123))
hicann_1 = C.HICANNOnWafer(Enum(122))
pop = pynn.Population(size, pynn.IF_cond_exp, {})
pop_view = pynn.PopulationView(pop,[0])
pop_view_1 = pynn.PopulationView(pop,[0])
self.marocco.manual_placement.on_hicann(pop_view, hicann)
self.marocco.manual_placement.on_hicann(pop_view_1, hicann_1)
with self.assertRaises(RuntimeError):
pynn.run(0)
pynn.end()
def test_popview_external_source(self):
pynn.setup(marocco=self.marocco)
neuron_size = 4
self.marocco.neuron_placement.default_neuron_size(neuron_size)
size = 10
pop_ext = pynn.Population(size, pynn.SpikeSourcePoisson, {'rate':2})
pop_ext_1 = pynn.Population(size, pynn.SpikeSourcePoisson, {'rate':2})
pop = pynn.Population(size, pynn.IF_cond_exp, {})
connector = pynn.AllToAllConnector(weights=1)
projections = [
pynn.Projection(pop_ext, pop, connector, target='excitatory'),
pynn.Projection(pop_ext_1, pop, connector, target='excitatory'),
]
hicann = C.HICANNOnWafer(Enum(121))
hicann_1 = C.HICANNOnWafer(Enum(122))
pop_view = pynn.PopulationView(pop_ext,list(range(1,size,2)))
pop_view_1 = pynn.PopulationView(pop_ext,list(range(0,size,2)))
pop_1_view = pynn.PopulationView(pop_ext_1,list(range(1,size//2)))
pop_1_view_1 = pynn.PopulationView(pop_ext_1,list(range(size-2,size//2,-1)))
pop_1_auto_placement = pynn.PopulationView(pop_ext_1,[0,size//2,size-1])
self.marocco.manual_placement.on_hicann(pop_view, hicann)
self.marocco.manual_placement.on_hicann(pop_view_1, hicann_1)
self.marocco.manual_placement.on_hicann(pop_1_view, hicann)
self.marocco.manual_placement.on_hicann(pop_1_view_1, hicann_1)
pynn.run(0)
pynn.end()
results = self.load_results()
for nrn in pop_view:
placement_item, = results.placement.find(nrn)
self.assertEqual(hicann, placement_item.dnc_merger().toHICANNOnWafer())
for nrn in pop_view_1:
placement_item, = results.placement.find(nrn)
self.assertEqual(hicann_1, placement_item.dnc_merger().toHICANNOnWafer())
for nrn in pop_1_view:
placement_item, = results.placement.find(nrn)
self.assertEqual(hicann, placement_item.dnc_merger().toHICANNOnWafer())
for nrn in pop_1_view_1:
placement_item, = results.placement.find(nrn)
self.assertEqual(hicann_1, placement_item.dnc_merger().toHICANNOnWafer())
for nrn in pop_1_auto_placement:
placement_item, = results.placement.find(nrn)
self.assertIsNotNone(placement_item.dnc_merger().toHICANNOnWafer())
def test_population_view(self):
size = random.randint(1, 1000)
text = '%ds till the end' % size
celltype = pyhmf.IF_cond_exp
selector = numpy.array(
[random.choice([True, False]) for x in range(0, size)])
pop = pyhmf.Population(size, celltype, label=text)
pv = pyhmf.PopulationView(pop, selector)
size_selector = len(numpy.where(selector == True)[0])
pynn_text = 'view of \"%ds till the end\" containing %d' % (
size, size_selector)
self.assertEqual(size_selector, len(list(pv.__iter__())))
self.assertEqual(size_selector, len(list(pv.all())))
self.assertEqual(size_selector, len(pv))
self.assertEqual(size_selector, pv.size)
self.assertEqual(pynn_text, pv.label)
self.assertEqual(celltype, pv.celltype)
pv2_label = "test custom label"
pv2 = pyhmf.PopulationView(pop, selector, label=pv2_label)
self.assertEqual(pv2_label, pv2.label)
def test_popview_combinations(self, view_number):
# tests all possible combinations of mask lengths for different number of PopulationViews
import pylogging
from pymarocco import PyMarocco, Defects
from pymarocco.results import Marocco
pop_size = 5
hicanns = [C.HICANNOnWafer(Enum(180 + view)) for view in range(view_number)]
# generate possible mask lengths for Population Views
pool = tuple(i for i in range(1, pop_size - view_number + 2))
# generate all possible mask lengths for each PopulationView for a given total number of neurons
# [[lengths_of_Popviews],number_of_used_neurons]
view_lengths = [([], 0)]
for _ in range(view_number):
view_lengths = [(x+[y], csum+y) for x, csum in view_lengths for y in pool if csum <= pop_size - y]
neurons = list(range(pop_size))
for length in view_lengths:
marocco = PyMarocco()
marocco.backend = PyMarocco.Without
marocco.persist = "results.bin"
marocco.defects.backend = Defects.Backend.Without
neuron_size = 4
marocco.neuron_placement.default_neuron_size(neuron_size)
pynn.setup(marocco=marocco)
pop = pynn.Population(pop_size, pynn.IF_cond_exp, {})
pop_views = []
index = 0
for view in range(view_number):
# generate PopulationViews with all possible mask lengths
# no permutations of neurons are tested
pop_views.append(pynn.PopulationView(pop,neurons[index:index+length[0][view]]))
marocco.manual_placement.on_hicann(pop_views[view],hicanns[view])
index += length[0][view]
pynn.run(0)
pynn.end()
results = Marocco.from_file(marocco.persist)
for view in range(view_number):
for nrn in pop_views[view]:
placement_item, = results.placement.find(nrn)
logical_neuron = placement_item.logical_neuron()
for denmem in logical_neuron:
self.assertEqual(hicanns[view], denmem.toHICANNOnWafer())
marocco = PyMarocco()
marocco.calib_backend = PyMarocco.CalibBackend.Default
marocco.defects.backend = Defects.Backend.None
marocco.neuron_placement.skip_hicanns_without_neuron_blacklisting(False)
marocco.persist = "results.xml.gz"
pynn.setup(marocco=marocco)
# place the full population to a specific HICANN
pop = pynn.Population(1, pynn.IF_cond_exp)
marocco.manual_placement.on_hicann(pop, HICANNOnWafer(X(5), Y(5)), 4)
# place only parts of a population
pop2 = pynn.Population(3, pynn.IF_cond_exp)
marocco.manual_placement.on_hicann(pynn.PopulationView(pop2, [0]),
HICANNOnWafer(Enum(5)))
marocco.manual_placement.on_hicann(pynn.PopulationView(pop2, [1]),
HICANNOnWafer(Enum(1)))
# the third neuron will be automatically placed
pynn.run(10)
pynn.end()
results = Marocco.from_file(marocco.persist)
for denmem in get_denmems(pop, results):
print denmem
for denmem in get_denmems(pop2, results):
print denmem
for denmem in item.logical_neuron():
yield denmem
marocco = PyMarocco()
marocco.calib_backend = PyMarocco.CalibBackend.Default
marocco.defects.backend = Defects.Backend.None
marocco.neuron_placement.skip_hicanns_without_neuron_blacklisting(False)
marocco.persist = "results.xml.gz"
pynn.setup(marocco = marocco)
# place the full population to a specific HICANN
pop = pynn.Population(1, pynn.IF_cond_exp)
marocco.manual_placement.on_hicann(pop, C.HICANNOnWafer(C.X(5), C.Y(5)), 4)
# place only parts of a population
pop2 = pynn.Population(3, pynn.IF_cond_exp)
marocco.manual_placement.on_hicann(pynn.PopulationView(pop2, [0]), C.HICANNOnWafer(C.Enum(5)))
marocco.manual_placement.on_hicann(pynn.PopulationView(pop2, [1]), C.HICANNOnWafer(C.Enum(1)))
# the third neuron will be automatically placed
pynn.run(10)
pynn.end()
results = Marocco.from_file(marocco.persist)
for denmem in get_denmems(pop, results):
print denmem
for denmem in get_denmems(pop2, results):
print denmem
'cm': 0.2, # nF
'v_reset': -30, # mV
'v_rest': -20, # mV
'v_thresh': -16, # mV
'e_rev_I': -40, # mV
'e_rev_E': 0, # mV
'tau_m': 10, # ms
'tau_refrac': 1, # ms
'tau_syn_E': 5, # ms
'tau_syn_I': 5, # ms
}
population = pynn.Population(2, pynn.IF_cond_exp, neuron_parameters)
population.record()
neuron0 = pynn.PopulationView(population, [0])
neuron0.record_v()
neuron1 = pynn.PopulationView(population, [1])
neuron1.record_v()
stimulus_0 = pynn.Population(1, pynn.SpikeSourceArray, {"spike_times" : [10,50,55,60,65,105,110,115,120,125]}) # in ms
stimulus_1 = pynn.Population(1, pynn.SpikeSourceArray, {"spike_times" : [300,310,320,325,330,335,340,345]}) # in ms
marocco.manual_placement.on_hicann(stimulus_1, C.HICANNOnWafer(C.Enum(98)))
pynn.Projection(stimulus_0, neuron0, pynn.AllToAllConnector(weights=0.005), target="excitatory") # weight in uS
pynn.Projection(stimulus_0, neuron1, pynn.AllToAllConnector(weights=0.005), target="excitatory") # weight in uS
pynn.Projection(stimulus_1, neuron0, pynn.AllToAllConnector(weights=0.1), target="excitatory") # weight in uS
pynn.Projection(stimulus_1, neuron1, pynn.AllToAllConnector(weights=0.1), target="excitatory") # weight in uS