ObjSim/src/libcsim.hpp

/*Copyright (C) 2005, 2006, 2007, 2008 Frank Michler, Philipps-University Marburg, Germany

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
*/

#ifndef _H_LIBCSIM
#define _H_LIBCSIM

#include "libvector.h"
#include <vector>
#include <cassert>
#include "anyoption.h"
#include <time.h>
#include <sys/stat.h>

#include <math.h>
#include <stdio.h>
#include <stdlib.h> 

#include <iostream>
#include <sstream>
#include <string>
#include <stdexcept>
#include <fstream>
#include <map>
#include "lut.hpp"

#include "typedefs.hpp"
#include "stringutils.h"


//#include <idlrpc/idl_rpc.h>

using namespace std;

inline string AddSpaces(const string &st)
{
     string Spaces = "     ";
     string out=st;
     string::size_type i;
     out.replace(0,0,Spaces);
     i=0;
     i = out.find("\n", i+1);
     while (i != string::npos) {
	  if (i+1 < out.size()) out.replace(i+1, 0, Spaces);	  
	  i = out.find("\n", i+1);
     }
     return out;
}



#define getrandom(max1) ((rand()%(int)((max1)))) // random integer between 0 and max-1

#define ExpDec(t) (LutExpDec(int(t)))
const int NLutExpDec=100000;
const float TauLut=NLutExpDec/10;
static LUT_function<0, NLutExpDec> LutExpDec(exp,-1./(TauLut));


//define lookup table for NMDA current
inline double NmdaCurrent(double Voltage)
{
     // from Deco&Rolls 2005
     // (they cite Jahr and Stevens 1990).
     return -0.327*Voltage/(1+exp(-0.062*Voltage)/3.57);
}
const int NLutNmda=10000;
const float NmdaV0=-200;
const float NmdaV1=50;
const float NmdaVRange=NmdaV1-NmdaV0;
const float NmdaVToIntFactor=NLutNmda/NmdaVRange;
const float NmdaIntToVFactor=NmdaVRange/NLutNmda;
//!static LUT_function<int(NmdaV0*NmdaVToIntFactor), int(NmdaV1*NmdaVToIntFactor)> 
static LUT_function<-8000, 2000> LutNmdaCurrent(NmdaCurrent,0.0250000);
// FixMe clean up this, converted const expressions into literals after 
// transition to debian etch g++ 4.1.2

#define INmda(v) (LutNmdaCurrent(int(NmdaVToIntFactor*v)))

double gauss(double x, double sigma=1, double x0=0);

int fexist(const char *filename );
int FileSize(const char *filename );

// alpha function: f(t) = t*exp(-t/tau)/(tau/e)
inline float* AlphaFktLut(
     int &N, float TauPeak=10, float Amp=1, float BaseLine=0, float dt=0.25)
{
     float Bound = 10*TauPeak;
     N = int(Bound/dt);
     float* Lut = new float [N];
     float Em1 = exp(-1.0); //  1/e
     for (int n=0;n<N;++n) {
	  Lut[n] = BaseLine + Amp*n*dt*exp(-n*dt/TauPeak)/(TauPeak*Em1);
     }     
     return Lut;
}

// exp decay function
inline float* ExpDecayLut(
     int &N, float TauDecay=10, float Amp=1, float BaseLine=0, float dt=0.25, float BoundFkt=5)
{
     float Bound = BoundFkt*TauDecay;
     N = int(Bound/dt);
     float* Lut = new float [N];
     for (int n=0;n<N;++n) {
	  Lut[n] = BaseLine + Amp*exp(-n*dt/TauDecay);
     }     
     return Lut;
}



inline const char* testfunction()
{
     return "Hallo Welt\n";
}


inline vector<vector2d> Rectangle(float x0, float x1, float y0, float y1, int N)
{
     vector<vector2d> tmp;
     if (N>=4)
     {
	  float circumference =2*(x1+y1-x0-y0);
 	  float corners [4] = {0, x1-x0, circumference/2, circumference-(y1-y0)};
//	  float corners[4] = {3,3,3,3};
	  float CurMP=0;
	  float StepSize=circumference/(N);
	  while ((circumference-CurMP)>(StepSize/2))
	  {	  
	       cout << "CurMP=" << CurMP << " circ=" << circumference << "diff=" << circumference-CurMP << "\n";
	       if (CurMP< corners[1]) tmp.push_back(vector2d(x0 + CurMP, y0));
	       else if (CurMP<corners[2]) tmp.push_back(vector2d(x1, y0+CurMP-(corners[1])));
	       else  if (CurMP<corners[3]) tmp.push_back(vector2d(x1- (CurMP - corners[2]), y1));
	       else tmp.push_back(vector2d(x0, y0+(circumference-CurMP)));
	       CurMP += StepSize;
	  }	  	 	  
     }
     return tmp;
}






typedef  float* pfloat;

template<class T> 
T** NewArray2d(T** &temp, int a, int b) 
{
     temp = new T*[a];
     for (int i=0; i<a;++i) temp[i] = new T[b];
}

template<class T>
int DeleteArray2d(T** &ArrayPointer, int a)
{
     int i;
     for (i=0; i<a;++i) delete []ArrayPointer[i];
     delete []ArrayPointer;
     return 0;
}

template<class T> 
T*** NewArray3d(T*** &temp, int a, int b, int c) 
{
     temp = new T**[a];
     for (int i=0; i<a;++i) 
     {
	  temp[i] = new T*[b];
	  for (int j=0;j<b;++j) temp[i][j] = new T[c];
     }
}

template<class T>
int DeleteArray3d(T*** &ArrayPointer, int a, int b)
{
     int i,j;
     for (i=0;i<a;++i) 
     {
	  for (j=0;j<b;++j) delete [] ArrayPointer[i][j];
	  delete [] ArrayPointer[i];
     }
     delete []ArrayPointer;
	return 0;
}

enum LookUpType {loNONE, loEXP, loNMDA};

class LookUpTable
{
protected:
     float xRange0, xRange1, RDiff;
     int LBound, UBound;
     float IndexFactor;
public:
     float* tmpvalue;
     float* value;
     int N;
     LookUpTable();
     ~LookUpTable();
     void InitExp(int N, float Tau, float v0=1, float Range0=0, float Range1=0);
     float GetValue(int index);
     double GetValue(double X);
     void Reset();
};


class Recorder
{
     FILE* fs;
     string FileName;
public:     
     Recorder(char* ="data.txt");
     ~Recorder();
     int record(float, float);
     int record(float, float, float);
};

typedef struct _BinRecHeader
{
     char finfo[7];     // "BinRec" + \0
     char version[5];    // "0.05" + \0
     int N, M, ValueSize, FrameSize;  
     float dt;
} BinRecHeader;

enum ParaType {
    PARA_U_SE,
    PARA_TAU_REC,
};

class BinRecorder
{
     FILE* fs;
     string FileName;
     string BaseFileName;
     string SimTag;
     float** PBuffer;
     float* RecBuffer;
     float* RecBuffPointer;
     float* RecBuffMax;
     int N, M;
     int MacroTimeStep;
     BinRecHeader Header;
public:
     BinRecorder(int _MacroTimeStep, int _N, int _M, float** _PBuffer, float _dt=0.25, const char* ="data.bin");
     ~BinRecorder();
     int record();
     int restart();
     int restart(string _SimTag);
     int WriteToFile();
};

class DistanceProfile
{
protected:
     int N;
     float* profile;
     float* xscale;
public:
     DistanceProfile(int N);
     DistanceProfile(int N, float Sigma1, float Sigma2);
     DistanceProfile(const vector<float> &Profile);
     ~DistanceProfile();
     float GetValue(float dist);
     float GetMaxConDistance(float minweight);
     void print();
};

class CircleDistanceProfile: public DistanceProfile
{
public:
     CircleDistanceProfile(int N, float Radius, bool invers=false);
};


enum DirType {CSIM_left=-1, CSIM_right=1};

/** @brief input channels
*/
enum csimInputChannel {
     csimInputChannel_AMPA,       //!< AMPA: fast excitatory
     csimInputChannel_GABAa,      //!< GABAa: fast inhibitory
     //! NMDA_AMPA: combined NMDA and AMPA input, NMDA is long lasting excitatory
     csimInputChannel_NMDA_AMPA,  
     csimInputChannel_GABAb,      //!< GABAb: long lasting inhibitory
     csimInputChannel_AMPA2,      //!< 
     csimInputChannel_Linking,    //!<
     csimInputChannel_Endu,       //!<
     csimInputChannel_EnduLinking,//!<
     csimInputChannel_Membrane,   //!< inject current directly to membrand potential
};

class layer; // forward declaration
class Connection; //! forward declaration
class connection; //! forward declaration --> loeschen geht noch nicht??
class AbstractNormalize; //! forward declaration
class learning;  // forward declaration for learning pointer in class connection
class veclearning;  // forward declaration for learning pointer in class connection
class input;

//! structure for transfering connection parameters to learning object
typedef struct {
     int Dmax; 
     int maximumDelay;
     float MaxWeight;
     layer *TargetLayer, *SourceLayer;
     short** delays_length;
     short*** delays;
     int M;
     int **post;
     int **I_pre, **D_pre;
     int **m_pre;
     float  **WeightPointer;
     float **WeightDerivativePointer;
     int maxN_pre;
     int *N_pre;     
     pfloat **s_pre, **sd_pre;
} ConnectionInfo;

//! structure for transfering connection parameters to learning object
typedef struct {
     int Dmax; 
     int maximumDelay;
     float MaxWeight;
     layer *TargetLayer, *SourceLayer;
     vector<float>* PSynWeights;
     vector<T_NNeurons>* PSynSourceNr;
     vector<T_NNeurons>* PSynTargetNr;
     vector<T_Delays>* PSynDelays;
     vector<vector<T_NSynapses> >* PPreSynNr;
     vector<vector<vector<T_NSynapses> > >* Pdelays;
} VecConnectionInfo;

/////////////////////////////////////////

class ParameterSet
{
public:
    // virtual destructor needed to make class polymorphic and use dynamic_cast
    virtual ~ParameterSet(){}  
};

template<class T1, class T2>
class TwoParameters: public ParameterSet
{
public:
    TwoParameters(T1 Val1, T2 Val2): first(Val1), second(Val2) {}
    T1 first;
    T2 second;
};

class Changable
{
public:
    virtual void changeParameter(ParameterSet* Paras)=0;
};


/////////////////////////////////

class SimpleTextProgressBar
{
     float Status;     // 0<=status<=Final
     float StepSize;     
     int Final;
public:
     SimpleTextProgressBar(int MaxSteps=10);
     int Next(int StepNr);
     int Reset(int MaxSteps);
};



//////////////////////
// forward declaration
class AnyOptionWrapper;

//StandardOptions
class CSimStandardOptions
{
private:
     AnyOptionWrapper *myAnyWrap;     
public:
     CSimStandardOptions(AnyOptionWrapper* _opt);     
     int NTrials;
     int NSteps;
     int TestNSteps;
     string DataDirectory;
     bool LoadWeights;
     bool SimFinishButton;
     float InputStrength;
     bool SaveInitialWeights;
};





/////////////////

/*********IDLrpc******************/

/* class IDLrpc */
/* { */
/* public: */
/*      IDLrpc(); */
/*      ~IDLrpc(); */
/* }; */





////////////////////
#endif /*_H_LIBCSIM */