Fixes #497: tweaks phase for NEST ACSource (#502)

* Fixes #497: tweaks phase for NEST ACSource

* Updates test for #497

* Updates test for #497: Excludes simulators as current recording not available in master

* Updates comment and minor change in test for #497

* Updates comment for #497

* Updates NEST phase fix and test for #497

* Updates NEST phase fix, restricts to ACSource

pyNN/nest/standardmodels/electrodes.py

@@ -27,6 +27,7 @@ class NestCurrentSource(StandardCurrentSource):
     def __init__(self, **parameters):
         self._device = nest.Create(self.nest_name)
         self.cell_list = []
+        self.phase_given = 0.0  # required for PR #502
         parameter_space = ParameterSpace(self.default_parameters,
                                          self.get_schema(),
                                          shape=(1,))
@@ -57,6 +58,17 @@ def _delay_correction(self, value):
             corrected = max(corrected, 0.0)
         return corrected
 
+    def _phase_correction(self, start, freq, phase):
+        """
+        Fixes #497 (PR #502)
+        Tweaks the value of phase supplied to NEST ACSource
+        so as to remain consistent with other simulators
+        """
+        phase_fix = ( (phase*numpy.pi/180) - (2*numpy.pi*freq*start/1000)) * 180/numpy.pi
+        phase_fix.shape = (1)
+        phase_fix = phase_fix.evaluate()[0]
+        nest.SetStatus(self._device, {'phase': phase_fix})
+
     def set_native_parameters(self, parameters):
         parameters.evaluate(simplify=True)
         for key, value in parameters.items():
@@ -74,6 +86,14 @@ def set_native_parameters(self, parameters):
                                               'amplitude_times': times})
             elif key in ("start", "stop"):
                 nest.SetStatus(self._device, {key: self._delay_correction(value)})
+                if key == "start" and type(self).__name__ == "ACSource":
+                    self._phase_correction(self.start, self.frequency, self.phase_given)
+            elif key == "frequency":
+                nest.SetStatus(self._device, {key: value})
+                self._phase_correction(self.start, self.frequency, self.phase_given)
+            elif key == "phase":
+                self.phase_given = value
+                self._phase_correction(self.start, self.frequency, self.phase_given)
             elif not key == "amplitude_times":
                 nest.SetStatus(self._device, {key: value})
 

test/system/scenarios/test_electrodes.py

@@ -368,6 +368,64 @@ def issue487(sim):
     assert_true (numpy.isclose(v_step_2_arr[0:int(step_2.times[0]/dt)], v_rest).all())
 
 
+@register(exclude=["brian", "neuron", "nest"])
+def issue497(sim):
+    """
+    This is a test to check that the specified phase for the ACSource is valid
+    at the specified start time (and not, for example, at t=0 as NEST currently does)
+
+    NOTE: This test is currently excluded for all the simulators as the final
+    current recording implementation is currently unavailable on 'master'.
+
+    Approach:
+    > Two signals with different initial specified phases
+    > 'start' of one signal updated on the fly
+    > 'frequency' of other signal updated on the fly
+    > Test to ensure that initial specified phases applicable at t = start
+    """
+    sim_dt = 0.1
+    sim.setup(min_delay=1.0, timestep = sim_dt)
+
+    start1 = 5.0
+    freq1 = 100.0
+    phase1 = 0.0
+    start2 = 5.0
+    freq2 = 100.0
+    phase2 = 90.0
+    amplitude = 1.0
+
+    cells = sim.Population(2, sim.IF_curr_exp(v_thresh=-55.0, tau_refrac=5.0))
+
+    acsource1 = sim.ACSource(start=start1, stop=20.0, amplitude=amplitude, offset=0.0,
+                        frequency=freq1, phase=phase1)
+    cells[0].inject(acsource1)
+    acsource1.record()
+    acsource2 = sim.ACSource(start=start2, stop=20.0, amplitude=amplitude, offset=0.0,
+                        frequency=freq2, phase=phase2)
+    cells[1].inject(acsource2)
+    acsource2.record()
+
+    # cannot directly assign/read from electrode variables, as each
+    # simulator currently returns parameters in different units (see #452)
+    start1 = 10.0
+    acsource1.start = start1
+    freq2 = 20.0
+    acsource2.frequency = freq2
+
+    cells.record('v')
+    sim.run(25.0)
+    vm = cells.get_data().segments[0].filter(name="v")[0]
+    sim.end()
+    i_t_ac1, i_amp_ac1 = acsource1.get_data()
+    i_t_ac2, i_amp_ac2 = acsource2.get_data()
+
+    # verify that acsource1 has value at t = start as 0 and as non-zero at next dt
+    assert_true (abs(i_amp_ac1[int(start1/sim_dt)]) < 1e-9)
+    assert_true (abs(i_amp_ac1[int(start1/sim_dt)+1]) > 1e-9)
+    # verify that acsources has value at t = start as 'amplitude'
+    assert_true (abs(i_amp_ac2[int(start2/sim_dt)]-amplitude) < 1e-9)
+
+
 if __name__ == '__main__':
     from pyNN.utility import get_simulator
     sim, args = get_simulator()
@@ -381,3 +439,4 @@ def issue487(sim):
     issue451(sim)
     issue483(sim)
     issue487(sim)
+    issue497(sim)