def test_add_inplace_assembly(self, sim=sim):
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_conductance_based(self):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(6, sim.IF_cond_alpha())
p3 = sim.Population(3, sim.IF_curr_exp())
a1 = sim.Assembly(p1, p2)
a2 = sim.Assembly(p1, p3)
self.assertTrue(a1.conductance_based)
self.assertFalse(a2.conductance_based)
def test__homogeneous_synapses(self):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(6, sim.IF_cond_alpha())
p3 = sim.Population(3, sim.IF_curr_exp())
a1 = sim.Assembly(p1, p2)
a2 = sim.Assembly(p1, p3)
self.assertTrue(a1._homogeneous_synapses)
self.assertFalse(a2._homogeneous_synapses)
def test__add__assembly(self, sim=sim):
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_first_and_last_id(self, sim=sim):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(6, sim.IF_cond_alpha())
p3 = sim.Population(3, sim.IF_curr_exp())
a = sim.Assembly(p3, p1, p2)
self.assertEqual(a.first_id, p1[0])
self.assertEqual(a.last_id, p3[-1])
def test_initialize(self, sim=sim):
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_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__population(self, sim=sim):
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_getitem_int(self, sim=sim):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(6, sim.IF_cond_alpha())
p3 = sim.Population(3, sim.IF_curr_exp())
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_all_iterator(self, sim=sim):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(6, sim.IF_cond_alpha())
p3 = sim.Population(3, sim.IF_curr_exp())
a = sim.Assembly(p1, p2, p3)
assert hasattr(a.all(), "next") or hasattr(a.all(), "__next__") # 2nd form is for Py3
ids = list(a.all())
self.assertEqual(ids, p1.all_cells.tolist() + p2.all_cells.tolist() + p3.all_cells.tolist())
def test_get_population(self, sim=sim):
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_get_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.get_data = Mock()
a.get_v()
a.get_data.assert_called_with('v', True)
def test_id_to_index(self, sim=sim):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(6, sim.IF_cond_alpha())
p3 = sim.Population(3, sim.IF_curr_exp())
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_getSpikes(self, sim=sim):
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_get_gsyn(self, sim=sim):
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_print_v(self, sim=sim):
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_sample(self, sim=sim):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(6, sim.IF_cond_alpha())
p3 = sim.Population(3, sim.IF_curr_exp())
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_print_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.write_data = Mock()
a.print_gsyn("foo.txt")
a.write_data.assert_called_with('foo.txt', ['gsyn_exc', 'gsyn_inh'],
True)
def test_local_cells(self, sim=sim):
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, sim=sim):
# 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_mask_local(self, sim=sim):
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_getitem_slice(self, sim=sim):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(6, sim.IF_cond_alpha())
p3 = sim.Population(3, sim.IF_curr_exp())
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, sim=sim):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(6, sim.IF_cond_alpha())
p3 = sim.Population(3, sim.IF_curr_exp())
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, sim=sim):
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([[0, 0, 1, 2],
[1, 3, 4, 5],
[2, 6, 7, 8],
[3, 9, 10, 11]]))
self.assertEqual(output_file.write.call_args[0][1], {'assembly': a.label})
def test_get_data_with_gather(self, sim=sim):
t1 = 12.3
t2 = 13.4
t3 = 14.5
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(6, sim.IF_cond_alpha())
p3 = sim.Population(3, sim.EIF_cond_exp_isfa_ista())
a = sim.Assembly(p3, p1, p2)
a.record('v')
sim.run(t1)
# what if we call p.record between two run statements?
# would be nice to get an AnalogSignal with a non-zero t_start
# but then need to make sure we get the right initial value
sim.run(t2)
sim.reset()
a.record('spikes')
p3.record('w')
sim.run(t3)
data = a.get_data(gather=True)
self.assertEqual(len(data.segments), 2)
seg0 = data.segments[0]
self.assertEqual(len(seg0.analogsignals), 1)
v = seg0.filter(name='v')[0]
self.assertEqual(v.name, 'v')
num_points = int(round((t1 + t2) / sim.get_time_step())) + 1
self.assertEqual(v.shape, (num_points, a.size))
self.assertEqual(v.t_start, 0.0 * pq.ms)
self.assertEqual(v.units, pq.mV)
self.assertEqual(v.sampling_period, 0.1 * pq.ms)
self.assertEqual(len(seg0.spiketrains), 0)
seg1 = data.segments[1]
self.assertEqual(len(seg1.analogsignals), 2)
w = seg1.filter(name='w')[0]
self.assertEqual(w.name, 'w')
num_points = int(round(t3 / sim.get_time_step())) + 1
self.assertEqual(w.shape, (num_points, p3.size))
self.assertEqual(v.t_start, 0.0)
self.assertEqual(len(seg1.spiketrains), a.size)
def test_local_cells(self, sim=sim):
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.local_cells, numpy.append(p1.local_cells, p2.local_cells))
def test__len__(self, sim=sim):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(11, sim.IF_cond_exp())
a = sim.Assembly(p1, p2, label="test")
self.assertEqual(len(a), len(p1) + len(p2))
def test_size_property(self, sim=sim):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(11, sim.IF_cond_exp())
a = sim.Assembly(p1, p2, label="test")
self.assertEqual(a.size, p1.size + p2.size)
def test_create_with_two_populations(self, sim=sim):
p1 = sim.Population(11, sim.IF_cond_exp())
p2 = sim.Population(11, sim.IF_cond_exp())
a = sim.Assembly(p1, p2, label="test")
self.assertEqual(a.populations, [p1, p2])
self.assertEqual(a.label, "test")
def test_create_with_one_population(self, sim=sim):
p = sim.Population(11, sim.IF_cond_exp())
a = sim.Assembly(p)
self.assertEqual(a.populations, [p])
self.assertIsInstance(a.label, basestring)
