owNeuronSimulator.cpp

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/*	owNeuronSimulator.cpp
 *	Implementation of owNeuronSimulator
 *  Created on: Jun 27, 2016
 *      Author: Sergey Khayrulin
 */
#include "owNeuronSimulator.h"
#include <stdexcept>

/** Constructor method for owNeuronSimulator.
 *
 *  @param muscleNumber
 *  Number of muscles in simulation
 *  @param time_step
 *  pass into NEURON for synchrony work
 *  @param simFileName
 *  File name with needed function default it's main.py
 *  from siberneti_NEURON and you don't need to change it actually
 *  You only need add path to sibenetic_NEURON folder into PYTHONPATH
 */
owNeuronSimulator::owNeuronSimulator(int muscleNumber, float timeStep,
                                     const std::string &modelFileName,
                                     const std::string &simFileName) {
  // Initialize the Python interpreter
  Py_Initialize();

  PyObject *pName;
  // Convert the file name to a Python string.
  pName = PyUnicode_FromString(simFileName.c_str());
  PyObject * temp_bytes = PyUnicode_AsEncodedString(pName, "UTF-8", "strict");
  const char * s = PyBytes_AS_STRING(temp_bytes);
  s = strdup(s);
  Py_DECREF(temp_bytes);

  printf("[debug] pName = \"%s\"\n", s);

  
  #if PY_MAJOR_VERSION == 3
    setlocale(LC_ALL, "en_US.utf8");
    char s2[10000];
    const wchar_t * s2_wide = Py_GetPath();
    std::wcstombs(s2, s2_wide, 10000);
  #else
    const char *s2 = Py_GetPath();
  #endif
  

  printf("[debug] PyPath = \"%s\"\n", s2);

  // Import the file as a Python module.
  pModule = PyImport_Import(pName);
  if (PyErr_Occurred())
    PyErr_Print();
  if (pModule == nullptr) {
    throw std::runtime_error("Module not loaded, have you set PYTHONPATH? If "
                             "yes just check have you added path to "
                             "sibenetic_NEURON");
  }
  PyObject *sectionNames = PyList_New(
      muscleNumber); // size should be equal to number of muscles in model
  for (int i = 0; i < muscleNumber; ++i)
    PyList_SetItem(sectionNames, i,
                   PyUnicode_FromString("SMDDR_mus")); // there you actually need
                                                      // put section names (from
                                                      // you'r .hoc file)
                                                      // file with NEURON model
  // from which you want read info about signal (Voltage)
  // Now it's hadrcoded for only one section SMDDR_mus it's a muscle section
  // from model file in sibernetic_NEURON you can find it in folder
  // (path/to/sibewnretic_NEURON/model/c.elegans/ria_.hoc)
  PyObject *dt = PyFloat_FromDouble(timeStep); // Create time step argument
  PyObject *fileName = PyUnicode_FromString(
      modelFileName.c_str()); // Create model file name argument
  PyObject *args = PyTuple_Pack(
      3, dt, fileName,
      sectionNames); // Create tuple of arguments for initialization
  PyObject *myFunction = PyObject_GetAttrString(pModule, (char *)"run_init");
  PyObject_CallObject(myFunction, args); // Run initialization method
  Py_DECREF(sectionNames);
  Py_DECREF(dt);
  Py_DECREF(fileName);
  Py_DECREF(args);
}

/** Run one step of NEURON simulation and read the data
 *  @return vector with neuron activity
 */
std::vector<float> owNeuronSimulator::run() {
  // Call a method
  PyObject *myFunction =
      PyObject_GetAttrString(pModule, (char *)"run_sim_one_step");
  pValue = PyObject_CallObject(myFunction, nullptr);
  // pValue = PyObject_CallMethod(nrn_sim, const_cast<char *>("one_step"),
  // nullptr);
  if (PyList_Check(pValue)) {
    std::vector<float> value_array;
    value_array = unpackPythonList(pValue);
    return value_array;

  } else {
    std::vector<float> single_element_array(0);
    single_element_array[0] = (float)PyFloat_AsDouble(pValue);
    return single_element_array;
  }
}

owNeuronSimulator::~owNeuronSimulator() {
  // TODO Auto-generated destructor stub
}