def test_first_and_last_id(self):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(6, sim.IF_cond_exp())
p3 = sim.Population(3, sim.EIF_cond_exp_isfa_ista())
a = sim.Assembly(p3, p1, p2)
self.assertEqual(a.first_id, p1[0])
self.assertEqual(a.last_id, p3[-1])
def test___add__two(self):
# adding two population views should give an Assembly
pv1 = sim.Population(6, sim.IF_cond_exp())[2, 3, 5]
pv2 = sim.Population(17, sim.IF_cond_exp())[4, 2, 16]
assembly = pv1 + pv2
self.assertIsInstance(assembly, sim.Assembly)
self.assertEqual(assembly.populations, [pv1, pv2])
def test_positions_property(self):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(11, sim.IF_cond_exp())
a = sim.Assembly(p1, p2, label="test")
assert_array_equal(
a.positions, numpy.concatenate((p1.positions, p2.positions),
axis=1))
def test___add__two(self):
# adding two populations should give an Assembly
p1 = sim.Population(6, EIF_cond_exp_isfa_ista())
p2 = sim.Population(17, IF_cond_exp())
assembly = p1 + p2
self.assertIsInstance(assembly, sim.Assembly)
self.assertEqual(assembly.populations, [p1, p2])
def test_initialize(self):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(11, sim.IF_cond_exp())
a = sim.Assembly(p1, p2)
v_init = -54.3
a.initialize(v=v_init)
assert_array_equal(p2.initial_values['v'].evaluate(simplify=True), v_init)
def test_SpikeSourceArray(self):
spike_times = [50.]
p = sim.Population(3, sim.SpikeSourceArray(spike_times=spike_times))
p2 = sim.Population(3, sim.Hardware_IF_cond_exp())
syn = sim.StaticSynapse(weight=0.012)
con = sim.Projection(p,
p2,
connector=sim.OneToOneConnector(),
synapse_type=syn,
receptor_type='excitatory')
spike_times_g = p.get('spike_times')
p2.record('v')
sim.run(100.0)
weights = nan_to_num(con.get('weight', format="array"))
print weights
data = p2.get_data().segments[0]
vm = data.filter(name="v")[0]
print vm
Figure(
Panel(weights,
data_labels=["ext->cell"],
line_properties=[{
'xticks': True,
'yticks': True,
'cmap': 'Greys'
}]),
Panel(vm,
ylabel="Membrane potential (mV)",
data_labels=["excitatory", "excitatory"],
line_properties=[{
'xticks': True,
'yticks': True
}]),
).save("result")
def test__homogeneous_synapses(self):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(6, sim.IF_cond_exp())
p3 = sim.Population(3, sim.EIF_cond_exp_isfa_ista())
a1 = sim.Assembly(p1, p2)
a2 = sim.Assembly(p1, p3)
self.assertTrue(a1._homogeneous_synapses)
self.assertFalse(a2._homogeneous_synapses)
def test_getitem_int(self):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(6, sim.IF_cond_exp())
p3 = sim.Population(3, sim.EIF_cond_exp_isfa_ista())
a = sim.Assembly(p3, p1, p2)
self.assertEqual(a[0], p3[0])
self.assertEqual(a[3], p1[0])
self.assertEqual(a[14], p2[0])
def test_add_inplace_assembly(self):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(11, sim.IF_cond_exp())
p3 = sim.Population(11, sim.IF_cond_exp())
a1 = sim.Assembly(p1, p2)
a2 = sim.Assembly(p2, p3)
a1 += a2
self.assertEqual(a1.populations, [p1, p2, p3])
def test___add__three(self):
# adding three populations should give an Assembly
p1 = sim.Population(6, IF_cond_exp())
p2 = sim.Population(17, EIF_cond_exp_isfa_ista())
p3 = sim.Population(9, sim.SpikeSourceArray())
assembly = p1 + p2 + p3
self.assertIsInstance(assembly, sim.Assembly)
self.assertEqual(assembly.populations, [p1, p2, p3])
def test__add__assembly(self):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(11, sim.IF_cond_exp())
p3 = sim.Population(11, sim.IF_cond_exp())
a1 = sim.Assembly(p1, p2)
a2 = sim.Assembly(p2, p3)
a3 = a1 + a2
self.assertEqual(a3.populations, [p1, p2, p3]) # or do we want [p1, p2, p3]?
def test__add__population(self):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(11, sim.IF_cond_exp())
a1 = sim.Assembly(p1)
self.assertEqual(a1.populations, [p1])
a2 = a1 + p2
self.assertEqual(a1.populations, [p1])
self.assertEqual(a2.populations, [p1, p2])
def test_all_iterator(self):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(6, sim.IF_cond_exp())
p3 = sim.Population(3, sim.EIF_cond_exp_isfa_ista())
a = sim.Assembly(p1, p2, p3)
assert hasattr(a.all(), "next")
ids = list(a.all())
self.assertEqual(ids, p1.all_cells.tolist() + p2.all_cells.tolist() + p3.all_cells.tolist())
def test___add__three(self):
# adding three population views should give an Assembly
pv1 = sim.Population(6, sim.IF_cond_exp())[0:3]
pv2 = sim.Population(17, sim.IF_cond_exp())[1, 5, 14]
pv3 = sim.Population(9, sim.EIF_cond_exp_isfa_ista())[3:8]
assembly = pv1 + pv2 + pv3
self.assertIsInstance(assembly, sim.Assembly)
self.assertEqual(assembly.populations, [pv1, pv2, pv3])
def test_conductance_based(self):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(6, sim.IF_cond_exp())
p3 = sim.Population(3, sim.EIF_cond_exp_isfa_ista())
a1 = sim.Assembly(p1, p2)
a2 = sim.Assembly(p1, p3)
self.assertTrue(a1.conductance_based)
self.assertFalse(a2.conductance_based)
def runTest(self):
import numpy
import pyNN.hardware.brainscales as pynn
# set-up the simulator
pynn.setup(
timestep=0.1,
useSystemSim=True,
speedupFactor=8000,
ignoreDatabase=True,
ignoreHWParameterRanges=True,
hardware=pynn.hardwareSetup['one-hicann'],
)
# Set the neuron model class
neuron_model = pynn.IF_cond_exp # I&F
neuron_parameters = {
'cm': 0.281, # membrane capacitance nF
'e_rev_E': 0.0, # excitatory reversal potential in mV
'e_rev_I':
-50.0, # inhibitory reversal potential in mV (HIGHER THAN v_thresh)
'i_offset': 0.0, # offset current
'tau_m': 9.3667, # membrane time constant
'tau_refrac': 1.0, # absolute refractory period
'tau_syn_E': 5.0, # excitatory synaptic time constant
'tau_syn_I': 5.0, # inhibitory synaptic time constant
'v_reset': -70.6, # reset potential in mV
'v_rest': -70.6, # resting potential in mV
'v_thresh': -55., # spike initiaton threshold voltage in mV
}
# We create a Population with 1 neuron of our
N1 = pynn.Population(size=1,
cellclass=neuron_model,
cellparams=neuron_parameters)
spiketimes = numpy.arange(10., 60., 5.)
S1 = pynn.Population(1,
pynn.SpikeSourceArray,
cellparams={'spike_times': spiketimes})
pynn.Projection(S1,
N1,
pynn.AllToAllConnector(weights=0.010425507084882381),
target='excitatory') # max weight in hardware
# record the voltage of all neurons of the population
N1.record()
# run the simulation for 200 ms
pynn.run(80.)
spikes = N1.getSpikes()
pynn.end()
self.assertEqual(
spikes.shape, (3, 2),
"Number of spikes is not as expected") # should have 3 spikes!!
def test_print_v(self):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(11, sim.IF_cond_exp())
a = sim.Assembly(p1, p2, label="test")
a.record_v()
sim.run(10.0)
a.write_data = Mock()
a.print_v("foo.txt")
a.write_data.assert_called_with('foo.txt', 'v', True)
def test_get_gsyn(self):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(11, sim.IF_cond_exp())
a = sim.Assembly(p1, p2, label="test")
a.record_gsyn()
sim.run(10.0)
a.get_data = Mock()
a.get_gsyn()
a.get_data.assert_called_with(['gsyn_exc', 'gsyn_inh'], True)
def test_get_population(self):
p1 = sim.Population(11, sim.IF_cond_exp())
p1.label = "pop1"
p2 = sim.Population(11, sim.IF_cond_exp())
p2.label = "pop2"
a = sim.Assembly(p1, p2)
self.assertEqual(a.get_population("pop1"), p1)
self.assertEqual(a.get_population("pop2"), p2)
self.assertRaises(KeyError, a.get_population, "foo")
def test_getSpikes(self):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(11, sim.IF_cond_exp())
a = sim.Assembly(p1, p2, label="test")
a.record('spikes')
sim.run(10.0)
a.get_data = Mock()
a.getSpikes()
a.get_data.assert_called_with('spikes', True)
def test_id_to_index(self):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(6, sim.IF_cond_exp())
p3 = sim.Population(3, sim.EIF_cond_exp_isfa_ista())
a = sim.Assembly(p3, p1, p2)
self.assertEqual(a.id_to_index(p3[0]), 0)
self.assertEqual(a.id_to_index(p1[0]), 3)
self.assertEqual(a.id_to_index(p2[0]), 14)
assert_array_equal(a.id_to_index([p1[0], p2[0], p3[0]]), [3, 14, 0])
def test_local_cells(self):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(11, sim.IF_cond_exp())
p3 = sim.Population(11, sim.IF_cond_exp())
a = sim.Assembly(p1, p2, p3)
self.assertEqual(a.local_cells.size,
p1.local_cells.size + p2.local_cells.size + p3.local_cells.size)
self.assertEqual(a.local_cells[0], p1.local_cells[0])
self.assertEqual(a.local_cells[-1], p3.local_cells[-1])
assert_array_equal(a.local_cells, numpy.append(p1.local_cells, (p2.local_cells, p3.local_cells)))
def test_printSpikes(self):
# TODO: implement assert_deprecated
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(11, sim.IF_cond_exp())
a = sim.Assembly(p1, p2, label="test")
a.record('spikes')
sim.run(10.0)
a.write_data = Mock()
a.printSpikes("foo.txt")
a.write_data.assert_called_with('foo.txt', 'spikes', True)
def test_sample(self):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(6, sim.IF_cond_exp())
p3 = sim.Population(3, sim.EIF_cond_exp_isfa_ista())
a = sim.Assembly(p3, p1, p2)
a1 = a.sample(10, rng=MockRNG())
# MockRNG.permutation reverses the order
self.assertEqual(len(a1.populations), 2)
assert_array_equal(a1.populations[0].all_cells, p1[11:6:-1])
assert_array_equal(a1.populations[1].all_cells, p2[6::-1])
def test_mask_local(self):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(11, sim.IF_cond_exp())
p3 = sim.Population(11, sim.IF_cond_exp())
a = sim.Assembly(p1, p2, p3)
self.assertEqual(a._mask_local.size,
p1._mask_local.size + p2._mask_local.size + p3._mask_local.size)
self.assertEqual(a._mask_local[0], p1._mask_local[0])
self.assertEqual(a._mask_local[-1], p3._mask_local[-1])
assert_array_equal(a._mask_local, numpy.append(p1._mask_local, (p2._mask_local, p3._mask_local)))
assert_array_equal(a.local_cells, a.all_cells[a._mask_local])
def test_create_with_implicit_grid(self):
p = sim.Population((11,), IF_cond_exp())
self.assertEqual(p.size, 11)
self.assertIsInstance(p.structure, space.Line)
p = sim.Population((5, 6), IF_cond_exp())
self.assertEqual(p.size, 30)
self.assertIsInstance(p.structure, space.Grid2D)
p = sim.Population((2, 3, 4), IF_cond_exp())
self.assertEqual(p.size, 24)
self.assertIsInstance(p.structure, space.Grid3D)
self.assertRaises(Exception, sim.Population, (2, 3, 4, 5), IF_cond_exp())
def test_getitem_slice(self):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(6, sim.IF_cond_exp())
p3 = sim.Population(3, sim.EIF_cond_exp_isfa_ista())
a = sim.Assembly(p3, p1, p2)
a1 = a[0:3]
self.assertIsInstance(a1, sim.Assembly)
self.assertEqual(len(a1.populations), 1)
assert_array_equal(a1.populations[0].all_cells, p3[:].all_cells)
a2 = a[2:8]
self.assertEqual(len(a2.populations), 2)
assert_array_equal(a2.populations[0].all_cells, p3[2:].all_cells)
assert_array_equal(a2.populations[1].all_cells, p1[:5].all_cells)
def test_getitem_array(self):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(6, sim.IF_cond_exp())
p3 = sim.Population(3, sim.EIF_cond_exp_isfa_ista())
a = sim.Assembly(p3, p1, p2)
a1 = a[3, 5, 6, 10]
self.assertIsInstance(a1, sim.Assembly)
self.assertEqual(len(a1.populations), 1)
assert_array_equal(a1.populations[0].all_cells, [p1[0], p1[2], p1[3], p1[7]])
a2 = a[17, 2, 10, 11, 19]
self.assertEqual(len(a2.populations), 3)
assert_array_equal(a2.populations[0].all_cells, p3[2:].all_cells)
assert_array_equal(a2.populations[1].all_cells, p1[7:9].all_cells)
assert_array_equal(a2.populations[2].all_cells, p2[3, 5].all_cells)
def test_save_positions(self):
import os
p1 = sim.Population(2, sim.IF_cond_exp())
p2 = sim.Population(2, sim.IF_cond_exp())
p1.positions = numpy.arange(0, 6).reshape((2, 3)).T
p2.positions = numpy.arange(6, 12).reshape((2, 3)).T
a = sim.Assembly(p1, p2, label="test")
output_file = Mock()
a.save_positions(output_file)
assert_array_equal(
output_file.write.call_args[0][0],
numpy.array([[int(p1[0]), 0, 1, 2], [int(p1[1]), 3, 4, 5],
[int(p2[0]), 6, 7, 8], [int(p2[1]), 9, 10, 11]]))
self.assertEqual(output_file.write.call_args[0][1],
{'assembly': a.label})
def test_get_positions(self):
p = sim.Population(11, sim.IF_cond_exp())
ppos = numpy.random.uniform(size=(3, 11))
p._positions = ppos
pv = sim.PopulationView(parent=p, selector=slice(3, 9, 2))
assert_array_equal(pv.positions,
numpy.array([ppos[:, 3], ppos[:, 5], ppos[:, 7]]).T)