/*  Copyright (C) 2004 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")
    
    The Software remains the property of the University of Oxford ("the
    University").
    
    The Software is distributed "AS IS" under this Licence solely for
    non-commercial use in the hope that it will be useful, but in order
    that the University as a charitable foundation protects its assets for
    the benefit of its educational and research purposes, the University
    makes clear that no condition is made or to be implied, nor is any
    warranty given or to be implied, as to the accuracy of the Software,
    or that it will be suitable for any particular purpose or for use
    under any specific conditions. Furthermore, the University disclaims
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    further disclaims any liability for the outcomes arising from using
    the Software.
    
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    You are not permitted under this Licence to use this Software
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    by or on behalf of Licensee to third parties or (2) use of the
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#ifndef EXPOSE_TREACHEROUS
#define EXPOSE_TREACHEROUS
#endif

#include "miscmaths/miscmaths.h"
#include "miscmaths/SpMat.h"
#include "streamlines.h"


using namespace MISCMATHS;

void read_file_names(const string& filename,vector<string>& filelist){
  ifstream fs(filename.c_str());
  string tmp;
  if(fs){
    fs>>tmp;
    do{
      filelist.push_back(tmp);
      fs>>tmp;
    }while(!fs.eof());
    }
  else{
    cerr<<filename<<" does not exist"<<endl;
    exit(0);
  }
}

int main(int argc, char** argv){

  if(argc<2){
    cout<<"fdt_matrix_merge <matlist> <outfile> [-omatrix4]"<<endl;
    exit(1);
  }

  vector<string> filelist;
  read_file_names(argv[1],filelist);
  bool domat4 = false;

  if( argc>3 ){ if( string(argv[3])=="-omatrix4"){ domat4=true; } }

  cout<<"merge "<<filelist.size()<<" files"<<endl<<endl;
  if( !domat4 ){
    SpMat<float> omat(filelist[0]);
    SpMat<float>* tmpmat;
    for(unsigned int i=1;i<filelist.size();i++){
      cout<<filelist[i]<<endl;
      cout<<"...load new file"<<endl;
      tmpmat = new SpMat<float>(filelist[i]);
      omat += *tmpmat;
      delete(tmpmat);
   }
    cout<<"save"<<endl;
    omat.Print(argv[2]);
  }
  else{
    cout<<"Matrix4 merge"<<endl;
    string file1=filelist[0]+"1.mtx";
    ifstream fs1(file1.c_str());
    if (!fs1) { 
      cerr << "Could not open file " << file1 << " for reading" << endl;
      return -1;
    }
    int nrows, ncols;
    fs1 >> nrows;
    fs1 >> ncols;
    fs1.close();
    SpMat_HCP omat(nrows,ncols,filelist[0]);
    SpMat_HCP* tmpmat;
      
    //int testcol=15442, testrow=135590;
    for(unsigned int i=1;i<filelist.size();i++){
      cout<<filelist[i]<<endl;
      cout<<"...loading new file"<<endl;
      tmpmat = new SpMat_HCP(nrows,ncols,filelist[i]);
      cout<<"...increment"<<endl;
      //tmpmat->Print(testrow,testcol);
      omat += (*tmpmat);
      //omat.Print(testrow,testcol);
      delete(tmpmat);
    }
    cout<<"save"<<endl;
    omat.SaveTrajFile(argv[2]);
  }
  return 0;
}
