#ifndef _HPP_CONNECTION
#define _HPP_CONNECTION

#include "simelement.hpp"


    
    
// forward declaration
class layer;
class learning;

struct Synapse
{
    Synapse(int snr, int tnr, float w, int d): Weight(w), SourceNr(snr), TargetNr(tnr), Delay(d) {};
    float Weight;
    int SourceNr;
    int TargetNr;
    int Delay;
};

struct SourceTargetDim
{
    SourceTargetDim()
        : NSource(0), NSx(0), NSy(0), NTarget(0), NTx(0), NTy(0)
    {}
    SourceTargetDim(int _NSource, int _NSx, int _NSy, int _NTarget, int _NTx, int _NTy)
        : NSource(_NSource), NSx(_NSx), NSy(_NSy), NTarget(_NTarget), NTx(_NTx), NTy(_NTy)
    {}
    std::string stringify()
    {
        std::stringstream o;
        o << NSource << " " << NSx << " " << NSy << " " << NTarget << " " << NTx << " " << NTy;
        return o.str();
    }
    int NSource;
    int NSx;
    int NSy;
    int NTarget;
    int NTx;
    int NTy;
};

/** like SourceTargetDim plus one new item: ArrayOrderXFast
 */
struct SourceTargetDim1
{
    SourceTargetDim1()
        : NSource(0), NSx(0), NSy(0), NTarget(0), NTx(0), NTy(0)
    {}
    SourceTargetDim1(int _NSource, int _NSx, int _NSy, int _NTarget, int _NTx, int _NTy)
        : NSource(_NSource), NSx(_NSx), NSy(_NSy), NTarget(_NTarget), NTx(_NTx), NTy(_NTy)
    {}
    std::string stringify()
    {
        std::stringstream o;
        o << NSource << " " << NSx << " " << NSy << " " << NTarget << " " << NTx << " " << NTy << " " << ArrayOrderXFast;
        return o.str();
    }
    int NSource;
    int NSx;
    int NSy;
    int NTarget;
    int NTx;
    int NTy;
    int ArrayOrderXFast;
};


/*! \brief Klasse Connection
 *         abstrakte Basis-Klasse für connection und VecConnection
 *
 *  Detailed description starts here.
 */
class Connection : public SimElement
{
protected:
    layer  *TargetLayer,  *SourceLayer;
    float *InputPointer;
    std::string WeightFileName;
    float connectivity;
    float Strength;
    float InitialWeight; // for rewiring
    bool AutoSave;
    bool learn;
    bool RewireOn;
    float RewireMaxConnectivity;
    float RewireNNewConnections;
    float RewireThreshold;
    clock_t cpu_start, cpu_end;
    double cpu_time_used;
public:
    Connection();
    Connection(layer*, layer*, csimInputChannel _InputChannel=csimInputChannel_AMPA, bool _nonself=true);
    ~Connection();
    virtual int Save()=0;
    virtual int Save(int nr)=0;
    virtual int Save(const string&)=0;
    virtual bool Learning();
    virtual int SetLearn(bool) =0;
    virtual int DeleteLowWeights(float threshold) =0;
    virtual int SetAllWeights(float WeightValue) {};
    virtual int MultiplyAllTargetWeights(float Factor) {cout << "not implemented\n";};
    // BEGIN used by TomWaitsQt
    virtual float GetSourceWeights(int CurSource, vector<Synapse>& SynList, int &MaxDelay)=0;
    virtual float GetTargetWeights(int CurTarget, vector<Synapse>& SynList, int &MaxDelay)=0;
    virtual float GetMaxWeight()=0;
    virtual int GetMaxDelay()=0;
    virtual float GetMinWeight(){return 0;};
    virtual int GetMinDelay(){return 0;};
    virtual long calcMemoryConsumption(){return 0;};
    // END used by TomWaitsQt
    
    virtual bool CheckHeaderConsistency();
    int SetRewiring(float threshold, float maxCon, int NNewCon=1, float _InitialWeight=-1);
    void SetRewiringOff();
    int SetAutoSave(bool);
    void SetNonSelf(bool);
//      virtual int WriteSimInfo(fstream &fw) =0;
//      virtual int WriteSimInfo(fstream &fw, const string &ChildInfo) =0;
    layer* GetTargetLayer();
    int GetNTarget() {return nt;};
    int GetNSource() {return ns;};
    void GetSourceTargetDim(unsigned int& snx, unsigned int& sny, unsigned int& tnx, unsigned int& tny)
    {snx=SourceNx;sny=SourceNy;tnx=TargetNx;tny=TargetNy;};
    SourceTargetDim GetSourceTargetDim()
    {
        return SourceTargetDim(ns, SourceNx, SourceNy, nt, TargetNx, TargetNy);
    }
    
    
    bool NonSelf;
    csimInputChannel InputChannel;
    T_Delays Dmax;  // global maximum delay
    T_Delays maximumDelay;  // maximum delay of current delay distribution
    T_Delays minimumDelay;  // minimum delay of current delay distribution
    T_Delays DelayDiff;
    bool ArrayOrderXFast;
protected:
    int ns,nt;
    int SourceNx, SourceNy, TargetNx, TargetNy;
    float maxWeight;
};


/*! \brief Klasse connection
 *         "alte" connection-Klasse, benutzt selbst generierte, mehrdimensionale c-Arrays
 *
 *  Detailed description starts here.
 */
class connection : public Connection
{
protected:
    learning* learnobj;
    int SetupPresynapticInfo_old();
    int SetupPresynapticInfo();
    int DeletePresynapticInfo();
    int CheckPresynapticInfo_old();
    int SetMinMaxDelay(float _MaxDelay, float _MinDelay);
    virtual int InitializeDynamicalArrays(
                                           const int _N, const int _M, const int Dmax);
    int DeleteDynamicalArrays();
    int Observe_s, Observe_m;
public:
    connection(layer*, layer*, csimInputChannel _InputChannel=csimInputChannel_AMPA, bool _nonself=true);
    connection();
    ~connection();
    virtual int Save();
    virtual int Save(int nr);
    virtual int Save(const string&);
    float GetSourceWeights(int CurSource, vector<Synapse>& SynList, int &MaxDelay);
    float GetTargetWeights(int CurTarget, vector<Synapse>& SynList, int &MaxDelay);
    float GetMaxWeight();
    int GetMaxDelay();
    
    virtual bool CheckHeaderConsistency();
    int Load();
    int Load(const char* FileName);
    int Load(const char* FileName, const char* DirName);
    int ConnectMatrix(const vector<vector<float> > &WeightMatrix,
                       float MaxDelay =20, float MinDelay=0);
    int ConnectRandom(float _connectivity,
                      float _InitialWeights,
                      float _maxDelay=20,
                      float minDelay=0,
                      bool RandomDelays=true);
    int ConnectRandom2(float _Connectivity,
                       float _InitialWeights,
                       float _maxDelay=20,
                       float minDelay=0,
                       bool RandomDelays=true);
    int ConnectRandom2(int NIncommingConnections,
                       float _InitialWeights,
                       float _maxDelay=20,
                       float minDelay=0,
                       bool RandomDelays=true);
    int ConnectPartialRandom(float _connectivity, float InitialWeights,
                             int MaxTarget, int MaxSource, float =20, float =0);
    int ConnectDirectional(float, float);
    int ConnectGaussianProb(float Sigma, float MaxWeight,
                            float MaxDelay =20, float MinDelay=0,
                            float MinConDistance=0, float MaxConnectivity=1, bool Cyclic=false);
    int ConnectGaussian(float Sigma,
                        float MaxWeight,
                        float MaxDelay =20,
                        float MinDelay=0,
                        bool Cyclic=false);
    int ConnectGaussianColumnwise(float Sigma,
                                  float MaxWeight,
                                  int dimx,
                                  int dimy,
                                  bool Cyclic=false,
                                  bool Shifted=true,
                                  float MaxDelay =20,
                                  float MinDelay=0,
                                  bool divergent=true,
                                  bool notstraight=true);
    int ConnectIdenticalGaussian(float Sigma,
                                 float MaxWeight,
                                 float MaxDelay =20,
                                 float MinDelay=0,
                                 float mpx=0.5,
                                 float mpy=0.5);
    int ConnectProfile(DistanceProfile* profile,
                       float MaxWeight,
                       float MaxDelay =20,
                       float MinDelay=0,
                       bool Cyclic=false);
    int ConnectCircular(float PreConnectivity,
                        float MaxWeight,
                        float MaxDelay =20,
                        float MinDelay=0);
    int ConnectCircularPre(float Connectivity,
                           float MaxWeight,
                           float MaxDelay =20,
                           float MinDelay=0);
    int ConnectFull(float MaxWeight,
                    float MaxDelay =20,
                    float MinDelay =0,
                    bool RandomWeights=false);
    int ConnectFullColumnwise(float MaxWeight,
                              int dimx,
                              int dimy,
                              int sourcedimx,
                              int sourcedimy,
                              float MaxDelay =20,
                              float MinDelay =0,
                              bool divergentrow=false,
                              float sigma_divrow=0.1,
                              bool Cyclic=false,
                              bool convergent=false);
    
    int ConnectGradientFields(float MaxWeight=1,
                              float xslope=0.5,
                              float yslope=0.5,
                              int dimx=50,
                              int dimy=50,
                              int sourcedimx=50,
                              int sourcedimy=50,
                              float MaxDelay =20,
                              float MinDelay =0);
    int ConnectSelf(float MaxWeight,
                    float MaxDelay =20,
                    float MinDelay =0);
    int ConnectPartial(int maxTarget,
                       float MaxWeight,
                       float MaxDelay =20,
                       float MinDelay =0);
    int CheckPresynapticInfo();
    int CheckConnection();
    int DeleteWeight(int SourceNr, int ConnectionNr);
    int DeleteWeightCorrectPreInfo(int SourceNr, int ConnectionNr, int SupposedDelay=-1);  // not tested
    int SetSystematicWeights();  // for test purpose only
    int CheckSystematicWeights();  // for test purpose only
    virtual int DeleteLowWeights(float threshold);
    int InsertNewWeight(int SourceNr, int TargetNr, float InitialWeight=0, int delay=1);
    int SetNewWeights(int NNewTargets, int NMaxTargets);
    int SetNewWeights2(int NNewTargets, int NMaxTargets);
    int Rewire(float minWeight, float maxConnectivity);
    int Print();
    int SetWeights(vector<vector<float> >& );
    int SetupDelays(float MaxDelay,float MinDelay=0);
    int SetupDelays();
    int SetupRandomDelays(float MaxDelay, float minDelay=0);
    int SetupRandomDelays();
    virtual int proceede(int =0);
    virtual int prepare(int =0);
    virtual void SetName(const char*);
    int SetFileName(char*);
    virtual int SetLearn(bool);
    int SetLearnObj(learning*);
    int ObserveSynapse(int SourceNumber=0, int MNumber=0, char* RecName="synapse.txt");
    int ObserveSynapsePrePost(int SourceNumber=0, int TargetNumber=0, char* RecName="synapse.txt");
    virtual int StartBinRec(int PostsynNum);
    ConnectionInfo GetConnectionInfo();
    virtual int WriteSimInfo(fstream &fw);
    virtual int WriteSimInfo(fstream &fw, const string &ChildInfo);
    
    int M,maxN_pre;
    
  /// limitation: all presynaptic neurons have the same number of target neurons (M!) ??
  /// not true!! --> no delay, no cry!!
    
    int *N_post;   // number of synapses per presynaptic neuron;
    int **post;     // 2D-Array with indices of target neurons. TargetNr=post[SourceNr][index]
    float **s;  // 2D-Array with weight strenghes. weight=s[SourceNr][index]
    float **sd;
    short **delays_length;
    short ***delays;
    int *N_pre;
    int **I_pre, **D_pre;
    int **m_pre; // presynaptic connection index m in s[i][m] array
    pfloat **s_pre, **sd_pre;
};

/*! \brief Klasse DepressiveConnection
 *         "alte" connection-Klasse, benutzt selbst generierte, mehrdimensionale c-Arrays
 *
 * Depressive Synapses 
 *      Tsodyks M, Pawelzik K, Markram H. 
 *      Neural networks with dynamic synapses. 
 *      Neural Comput. 1998 May 15;10(4):821-35. 
 */

class DepressiveConnection : public connection
{
protected:
     float U_se_fac;  // (proportion of transmitter per spike)     
     float U_SE;
     float TauRec;  //recovery dynamics
     float **efficacy;     // for every synapse
     int **LastEpsp;     // for every synapse
public:
     DepressiveConnection(
      layer*, layer*, csimInputChannel =csimInputChannel_AMPA, 
      float _TauRec=20, float U_se=0.2);
     ~DepressiveConnection();
/*      boost::multi_array<float,2> efficacy; */
/*      boost::multi_array<int,2> LastEpsp; */
     virtual int proceede(int =0);
     virtual int prepare(int =0);
     virtual int reset(int t);
     virtual int InitializeDynamicalArrays(
      const int _N, const int _M, const int Dmax);
     virtual int WriteSimInfo(fstream &fw);
};


/*! \brief Klasse Facilitatory Synapses
 *   Tsodyks M, Pawelzik K, Markram H. 
 *
 * Tsodyks M, Pawelzik K, Markram H. 
 * Neural networks with dynamic synapses. 
 * Neural Comput. 1998 May 15;10(4):821-35.
 *
 * could be made faster if only one U_SE value per presynaptic neuron
 * instead one per synapse
 */
class FacilitativeConnection : public DepressiveConnection
{
protected: 
     float **U_SEvalue;
     float UseTauDec, UseInc, UseConst;
public: 
     FacilitativeConnection(
      layer*, layer*, csimInputChannel =csimInputChannel_AMPA, 
      float _TauRec=20, float U_se=0.2, float _TauFac=20, float _UseInc=0.01);
     ~FacilitativeConnection();
     virtual int proceede(int =0);
     virtual int reset(int t);
     virtual int StartBinRec(int PostsynNum);
     virtual int InitializeDynamicalArrays(
      const int _N, const int _M, const int Dmax);
}; 

class PspConnection : public connection
{
protected:
     float *PspTemplate;
     float **Psp;
     int PspDuration;
     int PspArrayPointer;
public:
     PspConnection(layer*, layer*, csimInputChannel InputChannel = csimInputChannel_AMPA, bool _nonself=true);
     ~PspConnection();
/*      ~PspConnection(); */
/*      virtual int proceede(int =0); */
/*      virtual int prepare(int =0);      */
};


#endif /*_HPP_CONNECTION */