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)