Merge pull request #157 from lungd/pass_dt_to_c302nrnsimulation

Pass dt to C302NRNSimulation

Author: skhayrulin

inc/owSignalSimulator.h

@@ -53,7 +53,7 @@
 
 class SignalSimulator: public owINeuronSimulator{
 public:
-  SignalSimulator(const std::string & simFileName = "main_sim", const std::string & simClassName = "MuscleSimulation");
+  SignalSimulator(const std::string & simFileName = "main_sim", const std::string & simClassName = "MuscleSimulation", float timeStep=0.005);
   std::vector<float> run();
   ~SignalSimulator();
 };

main_sim.py

@@ -120,6 +120,9 @@ def __init__(self,increment=1.0):
         self.increment = increment
         self.step = 0
 
+    def set_timestep(self, dt):
+        pass
+
     def run(self, skip_to_time=0, do_plot = True):
         self.contraction_array =  parallel_waves(step = self.step)
         self.step += self.increment
@@ -147,15 +150,25 @@ class C302NRNSimulation():
     def __init__(self, tstop=100, dt=0.005, activity_file=None, verbose=True):
 
         #from LEMS_c302_C1_Full_nrn import NeuronSimulation
-        from LEMS_c302_nrn import NeuronSimulation
+        #from LEMS_c302_nrn import NeuronSimulation
 
-        import neuron
-        self.h = neuron.h
+        #import neuron
+        #self.h = neuron.h
 
+        self.tstop = tstop
         self.verbose = verbose
 
-        self.ns = NeuronSimulation(tstop, dt)
-        print_("Initialised C302NRNSimulation of length %s ms and dt = %s ms..."%(tstop,dt))
+        #self.ns = NeuronSimulation(tstop, dt)
+        #print_("Initialised C302NRNSimulation of length %s ms and dt = %s ms..."%(tstop,dt))
+
+    def set_timestep(self, dt):
+        dt = float('{:0.1e}'.format(dt)) * 1000.0 # memory issue fix
+        from LEMS_c302_nrn import NeuronSimulation
+        import neuron
+        self.h = neuron.h
+        
+        self.ns = NeuronSimulation(self.tstop, dt)
+        print_("Initialised C302NRNSimulation of length %s ms and dt = %s ms..."%(self.tstop,dt))
 
 
     def save_results(self):

src/owConfigProperty.cpp

@@ -147,9 +147,9 @@ owConfigProperty::owConfigProperty(int argc, char **argv)
       }
 
       if (simName.compare("") == 0)
-        simulation = new SignalSimulator("main_sim", pythonClass);
+        simulation = new SignalSimulator("main_sim", pythonClass, this->timeStep);
       else
-        simulation = new SignalSimulator(simName, pythonClass);
+        simulation = new SignalSimulator(simName, pythonClass, this->timeStep);
     } else {
       simulation =
           new owNeuronSimulator(1, this->timeStep, nrnSimulationFileName);

src/owSignalSimulator.cpp

@@ -46,7 +46,8 @@
 #include "owSignalSimulator.h"
 
 SignalSimulator::SignalSimulator(const std::string &simFileName,
-                                 const std::string &simClassName) {
+                                 const std::string &simClassName,
+                                 float timeStep) {
 
   // char pyClass[] = "SiberneticNEURONWrapper";
   // char pyClass[] = "C302Simulation";
@@ -81,6 +82,14 @@ SignalSimulator::SignalSimulator(const std::string &simFileName,
     pInstance = PyObject_CallObject(pClass, nullptr);
     if (PyErr_Occurred())
       PyErr_Print();
+    PyObject *dt = Py_BuildValue("f", timeStep); // Create tuple of arguments for initialization
+    PyObject *pFuncName = Py_BuildValue("s", "set_timestep");
+    //pInstance = PyObject_CallMethod(pInstance, "set_timestep", "(f)", timeStep);
+    PyObject_CallMethodObjArgs(pInstance, pFuncName, dt, nullptr);
+    if (PyErr_Occurred())
+      PyErr_Print();
+    Py_DECREF(dt);
+    Py_DECREF(pFuncName);
     std::cout << "Python muscle signal generator class: " << simClassName
               << " loaded!" << std::endl;
   } else {