示例#1
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    def test_timestep_constant(self):
        rec = Record(self.soma(0.5))

        sim = Simulation(constant_timestep=True, dt=1)
        sim.run(100)
        r1 = rec.as_numpy('v')

        sim = Simulation(constant_timestep=False, dt=1)
        sim.run(100)
        r2 = rec.as_numpy('v')

        sim = Simulation(constant_timestep=False, dt=10)
        sim.run(100)
        r3 = rec.as_numpy('v')

        sim = Simulation(constant_timestep=False, dt=0.0001)
        sim.run(100)
        r4 = rec.as_numpy('v')

        sim.remove_immediate_from_neuron()
        rec.remove_immediate_from_neuron()

        self.assertEqual(101, r1.size)
        self.assertEqual(188, r2.size)
        self.assertEqual(180, r3.size)
        self.assertEqual(189, r4.size)
示例#2
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    def test_add_netcon_and_make_event_separately(self):
        g1 = self.cell.filter_synaptic_group(mod_name="Exp2Syn", tag="aa")
        nc = g1.add_netcon(source=None)

        exp2syn_rec = Record(g1['Exp2Syn'][0], variables='i')
        expsyn_rec = Record(g1['ExpSyn'][0], variables='i')

        sim = Simulation()
        sim.run(1)
        nc['Exp2Syn'][0].make_event(10)
        nc['ExpSyn'][0].make_event(20)
        sim.run(100)

        exp2syn_np = exp2syn_rec.as_numpy('i')
        stim_time_exp2syn = exp2syn_np.time[(exp2syn_np.records != 0).argmax()]
        expsyn_np = expsyn_rec.as_numpy('i')
        stim_time_expsyn = expsyn_np.time[(expsyn_np.records != 0).argmax()]

        self.assertEqual(12.05, round(stim_time_exp2syn, 4))
        self.assertEqual(22.025, round(stim_time_expsyn, 4))

        # Remove variables and clear NEURON
        nc['Exp2Syn'][0].remove_immediate_from_neuron()
        nc['ExpSyn'][0].remove_immediate_from_neuron()
        nc = {}
        g1.remove_immediate_from_neuron()
        exp2syn_rec.remove_immediate_from_neuron()
        expsyn_rec.remove_immediate_from_neuron()
        sim.remove_immediate_from_neuron()
示例#3
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    def test_iclamp_after_sim(self):
        """
        IClamp works in a regular way after simulation run. in this case (amplitude 3 pA)
        we have spike at the soma.

        However IClamp delay is in the absolute time.
        """
        # Record
        rec = Record(self.soma(0.5))

        # Run
        sim = Simulation(init_v=-70, warmup=20)
        sim.run(1)

        # IClamp to soma
        iclamp = IClamp(segment=self.soma(0.5))
        iclamp.stim(delay=25, dur=3, amp=3)

        sim.run(100)
        r = rec.as_numpy(variable="v")

        sim.remove_immediate_from_neuron()
        rec.remove_immediate_from_neuron()
        iclamp.remove_immediate_from_neuron()

        # Make assertions
        self.assertEqual(4051, r.size)
        self.assertEqual(34.3815, round(r.records.max(), 4))
        self.assertEqual(-75.3247, round(r.records.min(), 4))

        self.assertEqual(330, r.records.argmax())
        # time in ms of max mV value
        self.assertEqual(28, round(r.time[r.records.argmax()], 4))
示例#4
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    def test_netstim_after_sim(self):
        """
        NetStim created after simulation run has no effect, it won't go on this simulation at all.

        However NetStim start is in the absolute time.
        """
        # Record
        rec = Record(self.soma(0.5))
        # Run
        sim = Simulation(init_v=-70, warmup=20)
        sim.run(1)

        # Netstim to synapse
        stim = NetStimCell("stim").add_netstim(start=25, number=10, interval=2)
        self.cell.add_synapse(source=stim, netcon_weight=0.5, mod_name="ExpSyn", delay=1,
                              seg=self.apic1(0.5))
        sim.run(100)
        r = rec.as_numpy(variable="v")

        # Make assertions
        self.assertEqual(4051, r.size)
        self.assertEqual(-67.1917, round(r.records.max(), 4))
        self.assertEqual(-70.0, round(r.records.min(), 4))

        self.assertEqual(3, r.records.argmax())
        # time in ms of max mV value
        self.assertEqual(6, r.time[r.records.argmax()])

        stim.remove_immediate_from_neuron()
        sim.remove_immediate_from_neuron()
        rec.remove_immediate_from_neuron()
示例#5
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    def test_netcon_event_after_sim(self):
        syn = self.cell.add_synapse(source=None, netcon_weight=1.0, mod_name="ExpSyn", delay=1,
                                    seg=self.apic1(0.5))
        # Record
        rec = Record(self.soma(0.5))
        # Run
        sim = Simulation(init_v=-70, warmup=20)
        sim.run(1)

        syn.make_event(50)

        sim.run(100)
        r = rec.as_numpy(variable="v")

        syn.remove_immediate_from_neuron()
        sim.remove_immediate_from_neuron()
        rec.remove_immediate_from_neuron()

        # Make assertions
        self.assertEqual(4051, r.size)
        self.assertEqual(34.4582, round(r.records.max(), 4))
        self.assertEqual(-75.3478, round(r.records.min(), 4))

        self.assertEqual(2159, r.records.argmax())
        # time in ms of max mV value
        self.assertEqual(73.725, round(r.time[r.records.argmax()], 4))
示例#6
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    def test_netstim_before_sim(self):
        """
        NetStim run in a regular way before Simulation run, in this cale (netcon weight=1.0)
        we have spike of the soma.

        However NetStim start is in the absolute time.
        """
        # Netstim to synapse
        stim = NetStimCell("stim").add_netstim(start=25, number=10, interval=2)
        self.cell.add_synapse(source=stim, netcon_weight=1.0, mod_name="ExpSyn", delay=1,
                              seg=self.apic1(0.5))
        # Record
        rec = Record(self.soma(0.5))
        # Run
        sim = Simulation(init_v=-70, warmup=20)
        sim.run(1)

        sim.run(100)
        r = rec.as_numpy(variable="v")

        stim.remove_immediate_from_neuron()
        sim.remove_immediate_from_neuron()
        rec.remove_immediate_from_neuron()

        # Make assertions
        self.assertEqual(4051, r.size)
        self.assertEqual(34.5205, round(r.records.max(), 4))
        self.assertEqual(-75.3053, round(r.records.min(), 4))

        self.assertEqual(319, r.records.argmax())
        # time in ms of max mV value
        self.assertEqual(27.725, round(r.time[r.records.argmax()], 4))
示例#7
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    def test_warmup(self):
        rec = Record(self.soma(0.5))

        value_error = False
        try:
            sim = Simulation(warmup=-100)
            sim.run(100)
            r1 = rec.as_numpy('v')
        except ValueError:
            value_error = True
        self.assertTrue(value_error)

        sim = Simulation(warmup=100, dt=1)
        sim.run(100)
        r2 = rec.as_numpy('v')

        sim = Simulation(warmup=100, dt=1, warmup_dt=1)
        sim.run(100)
        r3 = rec.as_numpy('v')

        sim.remove_immediate_from_neuron()
        rec.remove_immediate_from_neuron()

        self.assertEqual(111, r2.size)
        self.assertEqual(201, r3.size)
    def setUpClass(cls):
        morpho_path = os.path.join(path, "..",
                                   "commons/morphologies/asc/cell2.asc")

        # Create cell
        cell = Cell(name="cell")
        cell.load_morpho(filepath=morpho_path)
        cell.insert("pas")
        cell.insert("hh")

        soma = cell.filter_secs("soma")
        dend = cell.filter_secs("apic[10]")
        syn = cell.add_synapse(source=None, mod_name="ExpSyn", seg=dend(0.5))

        # Prepare EPSP and AP (IClamp) protocols
        experiment = Experiment(iti=40)
        experiment.add_epsp(num=3,
                            synapse=syn,
                            init=20,
                            interval=20,
                            weight=0.02)
        experiment.add_iclamp(num=3,
                              segment=soma(0.5),
                              init=60,
                              interval=20,
                              dur=3,
                              amp=1.6)
        experiment.build()

        # Prepare plots
        rec = Record([soma(0.5), dend(0.5)], variables='v')

        # Run
        sim = Simulation(init_v=-70,
                         warmup=20,
                         with_neuron_gui=False,
                         constant_timestep=True)
        sim.run(runtime=100)

        cls.v_soma = rec.as_numpy('v', segment_name=soma(.5).name)
        cls.v_apic = rec.as_numpy('v', segment_name=dend(.5).name)

        syn.remove_immediate_from_neuron()
        soma.remove_immediate_from_neuron()
        dend.remove_immediate_from_neuron()
        rec.remove_immediate_from_neuron()
        experiment.remove_immediate_from_neuron()
        cell.remove_immediate_from_neuron()
        sim.remove_immediate_from_neuron()

        cls.sections_left = len(list(h.allsec()))
示例#9
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    def test_init_v(self):
        rec = Record(self.soma(0.5))

        sim = Simulation(init_v=-100)
        sim.run(100)
        r1 = rec.as_numpy('v')

        sim = Simulation(init_v=100)
        sim.run(100)
        r2 = rec.as_numpy('v')

        sim.remove_immediate_from_neuron()
        rec.remove_immediate_from_neuron()

        self.assertEqual(-100, r1.records[0])
        self.assertEqual(100, r2.records[0])
示例#10
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    def test_dt(self):
        rec = Record(self.soma(0.5))

        sim = Simulation(dt=10)
        sim.run(100)
        r1 = rec.as_numpy('v')

        sim = Simulation(dt=0.01)
        sim.run(100)
        r2 = rec.as_numpy('v')

        sim.remove_immediate_from_neuron()
        rec.remove_immediate_from_neuron()

        self.assertEqual(11, r1.size)
        self.assertEqual(10001, r2.size)
示例#11
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    def test_stim_syns(self):
        gs = self.cell.filter_synaptic_group()

        gs0_exp2syn_rec = Record(gs[0]['Exp2Syn'][0], variables='i')
        gs0_expsyn_rec = Record(gs[0]['ExpSyn'][0], variables='i')

        gs1_exp2syn_rec = Record(gs[1]['Exp2Syn'][0], variables='i')
        gs1_expsyn_rec = Record(gs[1]['ExpSyn'][0], variables='i')

        sim = Simulation()
        sim.run(1)

        gs[0].make_event(10)
        gs[1].make_event(20)

        sim.run(100)

        # Test stim time of synaptic group 1
        gs0_exp2syn_np = gs0_exp2syn_rec.as_numpy('i')
        stim_time_gs0_exp2syn = gs0_exp2syn_np.time[(gs0_exp2syn_np.records != 0).argmax()]

        gs0_expsyn_np = gs0_expsyn_rec.as_numpy('i')
        stim_time_gs0_expsyn = gs0_expsyn_np.time[(gs0_expsyn_np.records != 0).argmax()]

        self.assertEqual(round(stim_time_gs0_exp2syn, 1), round(stim_time_gs0_expsyn, 1))

        # Test stim time of synaptic group 2
        gs1_exp2syn_np = gs1_exp2syn_rec.as_numpy('i')
        stim_time_gs1_exp2syn = gs1_exp2syn_np.time[(gs1_exp2syn_np.records != 0).argmax()]

        gs1_expsyn_np = gs1_expsyn_rec.as_numpy('i')
        stim_time_gs1_expsyn = gs1_expsyn_np.time[(gs1_expsyn_np.records != 0).argmax()]

        self.assertEqual(round(stim_time_gs1_exp2syn, 1), round(stim_time_gs1_expsyn, 1))

        # Test values of mV in soma
        self.assertEqual(31.3285, round(gs0_exp2syn_np.records.max(), 4))
        self.assertEqual(-61.309, round(gs0_exp2syn_np.records.min(), 4))

        # Remove variables and clear NEURON
        gs0_exp2syn_rec.remove_immediate_from_neuron()
        gs0_expsyn_rec.remove_immediate_from_neuron()
        gs1_exp2syn_rec.remove_immediate_from_neuron()
        gs1_expsyn_rec.remove_immediate_from_neuron()
        gs[0].remove_immediate_from_neuron()
        gs[1].remove_immediate_from_neuron()
        sim.remove_immediate_from_neuron()