Merge pull request #488 from appukuttan-shailesh/issue_487

Fixes issue #487: Updates _update_iclamp() for NEURON

pyNN/neuron/simulator.py

@@ -247,17 +247,17 @@ def _pre_run(self):
                     assert local_minimum_delay >= self.min_delay, \
                        "There are connections with delays (%g) shorter than the minimum delay (%g)" % (local_minimum_delay, self.min_delay)
 
-    def _update_current_sources(self):
+    def _update_current_sources(self, tstop):
         for source in self.current_sources:
             for iclamp in source._devices:
-                source._update_iclamp(iclamp)
+                source._update_iclamp(iclamp, tstop)
 
     def run(self, simtime):
         """Advance the simulation for a certain time."""
         self.run_until(self.tstop + simtime)
 
     def run_until(self, tstop):
-        self._update_current_sources()
+        self._update_current_sources(tstop)
         self._pre_run()
         self.tstop = tstop
         #logger.info("Running the simulation until %g ms" % tstop)

pyNN/neuron/standardmodels/electrodes.py

@@ -60,18 +60,28 @@ def _reset(self):
             self._times = None
             self._generate()
         for iclamp in self._h_iclamps.values():
-            self._update_iclamp(iclamp)
+            self._update_iclamp(iclamp, 0.0)    # send tstop = 0.0 on _reset()
 
-    def _update_iclamp(self, iclamp):
+    def _update_iclamp(self, iclamp, tstop):
         if not self._is_playable:
-            iclamp.delay = max(0, self.start - simulator.state.t)
+            iclamp.delay = self.start
             iclamp.dur = self.stop - self.start
             iclamp.amp = self.amplitude
 
         if self._is_playable:
             iclamp.delay = 0.0
             iclamp.dur = 1e12
             iclamp.amp = 0.0
+
+            # check exists only for StepCurrentSource (_is_playable = True, _is_computed = False)
+            # t_stop should be part of the time sequence to handle repeated runs
+            if not self._is_computed and tstop not in self._h_times.to_python():
+                ind = self._h_times.indwhere(">=", tstop)
+                if ind == -1:
+                    ind = self._h_times.size()
+                self._h_times.insrt(ind, tstop)
+                self._h_amplitudes.insrt(ind, self._h_amplitudes.x[int(ind)-1])
+
             self._h_amplitudes.play(iclamp._ref_amp, self._h_times)
 
     def set_native_parameters(self, parameters):

test/system/scenarios/test_electrodes.py

@@ -1,6 +1,6 @@
 
 
-from nose.tools import assert_equal, assert_true
+from nose.tools import assert_equal, assert_true, assert_false
 from numpy.testing import assert_array_equal
 import quantities as pq
 import numpy
@@ -311,6 +311,51 @@ def issue483(sim):
     assert (len(v) == (int(simtime/dt) + 1))
 
 
+@register()
+def issue487(sim):
+    """
+    Test to ensure that DCSource and StepCurrentSource work properly
+    for repeated runs. Problem existed under pyNN.neuron.
+    Three sub-tests performed:
+    1) DCSource active across two runs
+    2) StepCurrentSource active across two runs
+    3) DCSource active only during second run (earlier resulted in no current input)
+    """
+    dt = 0.1
+    sim.setup(timestep=dt, min_delay=dt)
+
+    v_rest = -60.0
+    cells = sim.Population(3, sim.IF_curr_exp(v_thresh=-55.0, tau_refrac=5.0, v_rest=v_rest))
+    cells.initialize(v=v_rest)
+    cells.record('v')
+
+    dcsource = sim.DCSource(amplitude=0.15, start=25.0, stop=115.0)
+    cells[0].inject(dcsource)
+
+    step = sim.StepCurrentSource(times=[25.0, 75.0, 115.0], amplitudes=[0.05, 0.10, 0.20])
+    cells[1].inject(step)
+
+    dcsource_2 = sim.DCSource(amplitude=0.15, start=115.0, stop=145.0)
+    cells[2].inject(dcsource_2)
+
+    simtime = 100.0
+    sim.run(simtime)
+    sim.run(simtime)
+
+    v = cells.get_data().segments[0].filter(name="v")[0]
+    sim.end()
+    v_dc = v[:, 0]
+    v_step = v[:, 1]
+    v_dc_2 = v[:, 2]
+
+    # check that membrane potential does not fall after end of first run
+    assert_true (v_dc[int(simtime/dt)] < v_dc[int(simtime/dt)+1])
+    assert_true (v_step[int(simtime/dt)] < v_step[int(simtime/dt)+1])
+    # check that membrane potential of cell undergoes a change
+    v_dc_2_arr = numpy.squeeze(numpy.array(v_dc_2))
+    assert_false (numpy.isclose(v_dc_2_arr, v_rest).all())
+
+
 if __name__ == '__main__':
     from pyNN.utility import get_simulator
     sim, args = get_simulator()
@@ -323,3 +368,4 @@ def issue483(sim):
     issue445(sim)
     issue451(sim)
     issue483(sim)
+    issue487(sim)