Default behavior is for electrodes to input membrane current instead …

…of electrode current

neurodamus/core/stimuli.py

@@ -10,19 +10,21 @@
 
 class SignalSource:
 
-    def __init__(self, base_amp=0.0, *, delay=0, rng=None):
+    def __init__(self, base_amp=0.0, *, delay=0, rng=None, represents_physical_electrode=False):
         """
         Creates a new signal source, which can create composed signals
         Args:
             base_amp: The base (resting) amplitude of the signal (Default: 0)
             rng: The Random Number Generator. Used in the Noise functions
+            represents_physical_electrode: Whether the source represents a phsyical electrode or missing synaptic input
         """
         h = Neuron.h
         self.stim_vec = h.Vector()
         self.time_vec = h.Vector()
         self._cur_t = 0
         self._base_amp = base_amp
         self._rng = rng
+        self._represents_physical_electrode = represents_physical_electrode
         if delay > .0:
             self._add_point(base_amp)
             self._cur_t = delay
@@ -379,7 +381,13 @@ class _Clamp:
         def __init__(self, cell_section, position=0.5, clamp_container=None,
                      stim_vec_mode=True, time_vec=None, stim_vec=None,
                      **clamp_params):
-            self.clamp = Neuron.h.IClamp(position, sec=cell_section)
+
+            # Checks if new MembraneCurrentSource mechanism is available and if source does not represent physical electrode
+            if self._represents_physical_electrode == False and hasattr(Neuron.h, "MembraneCurrentSource"):
+                self.clamp = Neuron.h.MembraneCurrentSource(position, sec=cell_section)
+            else:
+                self.clamp = Neuron.h.IClamp(position, sec=cell_section)
+
             if stim_vec_mode:
                 assert time_vec is not None and stim_vec is not None
                 self.clamp.dur = time_vec[-1]
@@ -434,8 +442,8 @@ class _DynamicClamp:
         def __init__(self, cell_section, position=0.5, clamp_container=None,
                      stim_vec_mode=True, time_vec=None, stim_vec=None,
                      reversal=0.0, **clamp_params):
-            # Checks if new conductanceSource mechanism is available
-            if hasattr(Neuron.h, "conductanceSource"):
+            # Checks if new conductanceSource mechanism is available and if source does not represent physical electrode
+            if self._represents_physical_electrode == False and hasattr(Neuron.h, "conductanceSource"):
                 self.clamp = Neuron.h.conductanceSource(position, sec=cell_section)
             else:
                 self.clamp = Neuron.h.SEClamp(position, sec=cell_section)

neurodamus/stimulus_manager.py

@@ -86,6 +86,10 @@ def __init__(self, _target, stim_info: dict, _cell_manager):
         self.duration = float(stim_info["Duration"])  # duration [ms]
         self.delay = float(stim_info["Delay"])        # start time [ms]
 
+        if 'self.represents_physical_electrode' in stim_info.keys():
+            self.represents_physical_electrode = stim_info['represents_physical_electrode']
+        else:
+            self.represents_physical_electrode = False
 
 @StimulusManager.register_type
 class OrnsteinUhlenbeck(BaseStim):
@@ -123,7 +127,7 @@ def __init__(self, target, stim_info: dict, cell_manager):
 
                 rng = random.Random123(seed1, seed2, seed3(gid))  # setup RNG
                 ou_args = (self.tau, self.sigma, self.mean, self.duration)
-                ou_kwargs = {'dt': self.dt, 'delay': self.delay, 'rng': rng}
+                ou_kwargs = {'dt': self.dt, 'delay': self.delay, 'rng': rng, 'represents_physical_electrode':self.represents_physical_electrode}
                 # inject Ornstein-Uhlenbeck signal
                 if stim_info["Mode"] == "Conductance":
                     cs = ConductanceSource.ornstein_uhlenbeck(*ou_args, **ou_kwargs,
@@ -252,7 +256,7 @@ def __init__(self, target, stim_info: dict, cell_manager):
                 rng = random.Random123(seed1, seed2, seed3(gid))  # setup RNG
                 shotnoise_args = (self.tau_D, self.tau_R, self.rate,
                                   self.amp_mean, self.amp_var, self.duration)
-                shotnoise_kwargs = {'dt': self.dt, 'delay': self.delay, 'rng': rng}
+                shotnoise_kwargs = {'dt': self.dt, 'delay': self.delay, 'rng': rng, 'represents_physical_electrode':self.represents_physical_electrode}
                 # generate shot noise current source
                 if stim_info["Mode"] == "Conductance":
                     cs = ConductanceSource.shot_noise(*shotnoise_args, **shotnoise_kwargs,
@@ -455,7 +459,7 @@ def __init__(self, target, stim_info: dict, cell_manager):
 
                 # generate ramp current source
                 cs = CurrentSource.ramp(self.amp_start, self.amp_end, self.duration,
-                                        delay=self.delay)
+                                        delay=self.delay, represents_physical_electrode=self.represents_physical_electrode)
                 # attach current source to section
                 cs.attach_to(sc.sec, tpoint_list.x[sec_id])
                 self.stimList.append(cs)  # save CurrentSource
@@ -581,7 +585,7 @@ def __init__(self, target, stim_info: dict, cell_manager):
 
                 # generate noise current source
                 cs = CurrentSource.noise(self.mean, self.var, self.duration,
-                                         dt=self.dt, delay=self.delay, rng=rng)
+                                         dt=self.dt, delay=self.delay, rng=rng, represents_physical_electrode=self.represents_physical_electrode)
                 # attach current source to section
                 cs.attach_to(sc.sec, tpoint_list.x[sec_id])
                 self.stimList.append(cs)  # save CurrentSource
@@ -661,7 +665,7 @@ def __init__(self, target, stim_info: dict, cell_manager):
 
                 # generate pulse train current source
                 cs = CurrentSource.train(self.amp, self.freq, self.width,
-                                         self.duration, delay=self.delay)
+                                         self.duration, delay=self.delay,represents_physical_electrode=self.represents_physical_electrode)
                 # attach current source to section
                 cs.attach_to(sc.sec, tpoint_list.x[sec_id])
                 self.stimList.append(cs)  # save CurrentSource
@@ -697,7 +701,7 @@ def __init__(self, target, stim_info: dict, cell_manager):
 
                 # generate sinusoidal current source
                 cs = CurrentSource.sin(self.amp, self.duration, self.freq,
-                                       step=self.dt, delay=self.delay)
+                                       step=self.dt, delay=self.delay,represents_physical_electrode=self.represents_physical_electrode)
                 # attach current source to section
                 cs.attach_to(sc.sec, tpoint_list.x[sec_id])
                 self.stimList.append(cs)  # save CurrentSource
@@ -733,12 +737,9 @@ def __init__(self, target, stim_info: dict, cell_manager):
                 if not sc.exists():
                     continue
 
-                # If conductanceSource not available, insert standard SEClamp
-                if hasattr(Nd.h, "conductanceSource"):
-                    seclamp = Nd.h.conductanceSource(tpoint_list.x[sec_id], sec=sc.sec)
-                else:
-                    # create single electrode voltage clamp at location
-                    seclamp = Nd.h.SEClamp(tpoint_list.x[sec_id], sec=sc.sec)
+
+                # create single electrode voltage clamp at location
+                seclamp = Nd.h.SEClamp(tpoint_list.x[sec_id], sec=sc.sec)
 
                 seclamp.rs = self.rs
                 seclamp.dur1 = self.duration