/*  design.h

    Mark Woolrich, Tim Behrens and Matthew Webster - FMRIB Image Analysis Group

    Copyright (C) 2009 University of Oxford  */

/*  Part of FSL - FMRIB's Software Library
    http://www.fmrib.ox.ac.uk/fsl
    fsl@fmrib.ox.ac.uk
    
    Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
    Imaging of the Brain), Department of Clinical Neurology, Oxford
    University, Oxford, UK
    
    
    LICENCE
    
    FMRIB Software Library, Release 5.0 (c) 2012, The University of
    Oxford (the "Software")
    
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    University").
    
    The Software is distributed "AS IS" under this Licence solely for
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    makes clear that no condition is made or to be implied, nor is any
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#if !defined(design_h)
#define design_h
  
#include <string>
#include <iostream>
#include <fstream>
#include <vector>
#include "newmatap.h"
#include "newmatio.h"
#include "newimage/newimageall.h"

using namespace NEWIMAGE;
using namespace NEWMAT;
using namespace MISCMATHS;

namespace Gs{

  class Design
    {
    public:

      // constructor
      Design() :	
	nevs(0),
	ntpts(0),
	ngs(0),
	voxelwise_dm(false)
	{ 
	}

      // load design matrix in from file and set it up
      void setup(bool loadcontrasts = true);

      // getters
      const int getnevs() const { return nevs; }
      const int getntpts() const { return ntpts; }
      const int getngs() const { return ngs; }
      const int dof() const { return int(ols_dof(dm)); }
      void setvarcopedata(float val){varcopedata=val;}

     // returns full, global design matrix
      const Matrix& getdm() const { return dm; }
 
      // returns voxelwise design matrix with any voxelwise zero evs removed
      ReturnMatrix getdm(int x, int y, int z) const;

      // returns voxelwise design matrix for group g with any voxelwise zero evs removed
      ReturnMatrix getdm(int x, int y, int z, int g) const;

      const Matrix& getcovsplit() const { return covsplit; }
      
      ReturnMatrix gettcontrast(const int p_num) const { RowVector ret = tcontrasts.Row(p_num); ret.Release(); return ret; }

      const Matrix& getfcontrast(const int p_num) const { return fc[p_num-1]; }

      int getgroup(int t) const { return int(group_index(t)); } 
      int getglobalindex(int g, int within_t) const { return global_index[g-1][within_t-1]; } 
      int getindexingroup(int g, int global_t) const { return index_in_group[g-1][global_t-1]; } 

      int getntptsingroup(int g) const { return int(ntptsing(g)); }
      int getnevsingroup(int g) const { return int(nevsing(g)); }
 
      bool tcontrast_has_zeroevs(int x, int y, int z,const RowVector& tcontrast)
      {
// 	cout<< "evs_group" << evs_group<< endl;
// 	cout<< "tcontrast" << tcontrast<< endl;
	bool in=false;
	for(int e=1; e<=tcontrast.Ncols() && !in; e++)
	  {	    
	    in = (tcontrast(e)!=0 && zero_evs(x,y,z,e-1));
	  }
	return in;
      }

      bool is_group_in_tcontrast(int g, const RowVector& tcontrast)
      {
// 	cout<< "evs_group" << evs_group<< endl;
// 	cout<< "tcontrast" << tcontrast<< endl;
	bool in=false;
	for(int e=1; e<=tcontrast.Ncols() && !in; e++)
	  {	    
	    in = (tcontrast(e)!=0 && evs_group(e)==g);
	  }
	return in;
      }

     bool fcontrast_has_zeroevs(int x, int y, int z,const Matrix& fcontrast)
      {
	bool in=false;
	for(int f=1; f<=fcontrast.Nrows() && !in; f++)
	  {
	    for(int e=1; e<=fcontrast.Ncols() && !in; e++)
	      {	    
		in = (fcontrast(f,e)!=0 && zero_evs(x,y,z,e-1));
	      }	    	    
	  }
	return in;
      }

      bool is_group_in_fcontrast(int g, const Matrix& fcontrast)
      {
	bool in=false;
	for(int f=1; f<=fcontrast.Nrows() && !in; f++)
	  {
	    for(int e=1; e<=fcontrast.Ncols() && !in; e++)
	      {	    
		in = (fcontrast(f,e)!=0 && evs_group(e)==g);
	      }	    	    
	  }
	return in;
      }
      bool is_voxelwise_dm() const {return voxelwise_dm;}

      // indexed by ev number. Returns group that that ev belongs to
      int get_evs_group(int e, int x, int y, int z) {
	int ret = int(evs_group(e));
	if(zero_evs(x,y,z,e-1))
	  ret=-1;
	return ret;
      }

      int getnumfcontrasts() const { return numFcontrasts; }
      int getnumtcontrasts() const { return numTcontrasts; }
      //const Matrix& getfreduceddm(const int p_num) const { return reduceddms[p_num-1]; }
      
      const volume4D<float>& getcopedata() const {return copedata;}
      const volume4D<float>& getvarcopedata() const {return varcopedata;}
      const volume4D<float>& getdofvarcopedata() const {return dofvarcopedata;}
      const volume<float>& getsumdofvarcopedata() const {return sum_dofvarcopedata;}
      const volume<float>& getmask() const {return mask;}

      ReturnMatrix remove_zeroev_pes(int x, int y, int z, const ColumnVector& petmp);
      ReturnMatrix remove_zeroev_covpes(int x, int y, int z, const SymmetricMatrix& covpetmp);
      ReturnMatrix insert_zeroev_pemcmcsamples(int x, int y, int z, const Matrix& mcmcin);
      ReturnMatrix insert_zeroev_pes(int x, int y, int z, const ColumnVector& petmp);
      ReturnMatrix insert_zeroev_covpes(int x, int y, int z, const SymmetricMatrix& covpetmp);

      ReturnMatrix getcopedata(int x, int y, int z, int g);
      ReturnMatrix getvarcopedata(int x, int y, int z, int g);

    private:

      const Design& operator=(Design& par);     
      Design(Design& des) { operator=(des); }
      
      void setupfcontrasts();

      int nevs;
      int ntpts;
      int ngs;

      Matrix dm;
      Matrix covsplit;

      vector<volume4D<float> > voxelwise_evs;
      vector<int> voxelwise_ev_numbers;

      Matrix tcontrasts;
      Matrix fcontrasts;
      vector<Matrix> fc;

      //      vector<Matrix> reduceddms;

      ColumnVector group_index; // stores group for given global index
      vector<vector<int> > global_index; // stores global index for given group and within-group index

      ColumnVector ntptsing;
      ColumnVector nevsing;
      vector<vector<int> > index_in_group; // stores within-group index for given group and global index

      int numFcontrasts;
      int numTcontrasts;

      // indexed by ev number. Returns group that ev belongs to
      ColumnVector evs_group;

      bool voxelwise_dm;

      // inputs
      volume4D<float> copedata;
      volume4D<float> varcopedata;
      volume4D<float> dofvarcopedata;
      volume<float> sum_dofvarcopedata;
      volume<float> mask;

      volume4D<int> zero_evs;

    };
} 
#endif