Merge pull request #397 from AurelienJaquier/stochastic-mech-features

Stochastic mech features

Author: wvangeit

bluepyopt/ephys/mechanisms.py

@@ -123,18 +123,19 @@ def instantiate_determinism(self, deterministic, icell, isec, sim):
                 (self.suffix),
                 1 if deterministic else 0)
 
-            if not deterministic:
-                # Set the seeds
-                short_secname = sim.neuron.h.secname(sec=isec).split('.')[-1]
-                for iseg in isec:
-                    seg_name = '%s.%.19g' % (short_secname, iseg.x)
-                    getattr(sim.neuron.h,
-                            "setdata_%s" % self.suffix)(iseg.x, sec=isec)
-                    seed_id1 = icell.gid
-                    seed_id2 = self.hash_py(seg_name)
-                    getattr(
-                        sim.neuron.h,
-                        "setRNG_%s" % self.suffix)(seed_id1, seed_id2)
+            # Set the seeds even when deterministic,
+            # that way neuron's psection does not crash
+            # when encountering a stoch mech var that is not set (e.g. rng)
+            short_secname = sim.neuron.h.secname(sec=isec).split('.')[-1]
+            for iseg in isec:
+                seg_name = '%s.%.19g' % (short_secname, iseg.x)
+                getattr(sim.neuron.h,
+                        "setdata_%s" % self.suffix)(iseg.x, sec=isec)
+                seed_id1 = icell.gid
+                seed_id2 = self.hash_py(seg_name)
+                getattr(
+                    sim.neuron.h,
+                    "setRNG_%s" % self.suffix)(seed_id1, seed_id2)
         else:
             if not deterministic:
                 # can't do this for non-Stoch channels

bluepyopt/ephys/protocols.py

@@ -134,7 +134,8 @@ def __init__(
             name=None,
             stimuli=None,
             recordings=None,
-            cvode_active=None):
+            cvode_active=None,
+            deterministic=False):
         """Constructor
 
         Args:
@@ -143,12 +144,15 @@ def __init__(
             recordings (list of Recordings): Recording objects used in the
                 protocol
             cvode_active (bool): whether to use variable time step
+            deterministic (bool): whether to force all mechanism
+                to be deterministic
         """
 
         super(SweepProtocol, self).__init__(name)
         self.stimuli = stimuli
         self.recordings = recordings
         self.cvode_active = cvode_active
+        self.deterministic = deterministic
 
     @property
     def total_duration(self):
@@ -161,6 +165,26 @@ def subprotocols(self):
 
         return collections.OrderedDict({self.name: self})
 
+    def adjust_stochasticity(func):
+        """Decorator method to adjust the stochasticity of the mechanisms"""
+        def inner(self, cell_model, param_values, **kwargs):
+            """Inner function"""
+            previous_stoch_state = []
+            if self.deterministic:
+                for mech in cell_model.mechanisms:
+                    previous_stoch_state.append(mech.deterministic)
+                    mech.deterministic = True
+
+            responses = func(self, cell_model, param_values, **kwargs)
+
+            if self.deterministic:
+                for i, mech in enumerate(cell_model.mechanisms):
+                    mech.deterministic = previous_stoch_state[i]
+
+            return responses
+
+        return inner
+
     def _run_func(self, cell_model, param_values, sim=None):
         """Run protocols"""
 
@@ -198,6 +222,7 @@ def _run_func(self, cell_model, param_values, sim=None):
                 "".join(
                     traceback.format_exception(*sys.exc_info())))
 
+    @adjust_stochasticity
     def run(
             self,
             cell_model,
@@ -295,7 +320,8 @@ def __init__(
             step_stimulus=None,
             holding_stimulus=None,
             recordings=None,
-            cvode_active=None):
+            cvode_active=None,
+            deterministic=False):
         """Constructor
 
         Args:
@@ -304,6 +330,8 @@ def __init__(
             recordings (list of Recordings): Recording objects used in the
                 protocol
             cvode_active (bool): whether to use variable time step
+            deterministic (bool): whether to force all mechanism
+                to be deterministic
         """
 
         super(StepProtocol, self).__init__(