/*  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
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    that the University as a charitable foundation protects its assets for
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    makes clear that no condition is made or to be implied, nor is any
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    You are not permitted under this Licence to use this Software
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    of the source code or the Software into a product for sale or license
    by or on behalf of Licensee to third parties or (2) use of the
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#include <iostream>
#include <fstream>
#include <cmath>
#include "newimage/newimageall.h"
#include <vector>
#include <algorithm>

using namespace std;
using namespace NEWIMAGE;
using namespace NEWMAT;

  void spect_reord(SymmetricMatrix& A,ColumnVector& r,ColumnVector& y){
    SymmetricMatrix Q=-A;
      DiagonalMatrix t(Q.Nrows());
      t=0;
      DiagonalMatrix D;
      Matrix V;
      for(int i=1;i<=Q.Nrows();i++){
        float rowsum1=0, rowsum2=0;
        for(int j=1;j<=Q.Ncols();j++){
          if(i!=j) rowsum1+=Q(i,j);
          rowsum2+=A(i,j);
        }
          Q(i,i)=-rowsum1;
          t(i)=1/sqrt(rowsum2);
      }
      Q << t*Q*t;
      EigenValues(Q,D,V);
      vector<pair<float,int> > myvec;
      vector<pair<float,int> > myvec2;
      
      for(int i=1;i<=D.Nrows();i++){
	pair<float,int> mypair;
	mypair.first=D(i);
	mypair.second=i;
	myvec.push_back(mypair);
      }
      sort(myvec.begin(),myvec.end());
      int ind=myvec[1].second; // index for second eigenval
      
      ColumnVector v2scale(V.Nrows());
      for(int i=1;i<=V.Nrows();i++){
	v2scale(i)=V(i,ind); //second eigvec
      }
      v2scale=t*v2scale; //scale it
      
      
      for(int i=1;i<=D.Nrows();i++){
	pair<float,int> mypair;
	mypair.first=v2scale(i);
	mypair.second=i;
	myvec2.push_back(mypair);
      }
      //myvec2 contains scaled second eigenvector and index for sorting.
      
      
      sort(myvec2.begin(),myvec2.end());
      r.ReSize(D.Nrows());
      y.ReSize(D.Nrows());
      
      for(int i=1;i<=D.Nrows();i++){
	y(i)=myvec2[i-1].first;
	r(i)=myvec2[i-1].second;
      }
      
  } 


void rem_zrowcol(const Matrix& myOMmat,const Matrix& coordmat,const Matrix& tractcoordmat,const bool coordbool,const bool tractcoordbool,Matrix& newOMmat,Matrix& newcoordmat, Matrix& newtractcoordmat)
{
 
 vector<int> zerorows;
 vector<int> zerocols;
 int dimsum =0;



 cerr<< "Checking for all zero rows"<<endl;
 for(int i=1;i<=myOMmat.Nrows();i++){
   dimsum=0;
   for(int j=1;j<=myOMmat.Ncols();j++){
     dimsum+=(int)myOMmat(i,j);
   }
   if(dimsum==0){zerorows.push_back(i);}
 }



 cerr<< "Checking for all zero cols"<<endl;
 for(int j=1;j<=myOMmat.Ncols();j++){
   dimsum=0;
   for(int i=1;i<=myOMmat.Nrows();i++){
     dimsum+=(int)myOMmat(i,j);
   }
   if(dimsum==0){zerocols.push_back(j);}
 }


 newOMmat.ReSize(myOMmat.Nrows()-zerorows.size(),myOMmat.Ncols()-zerocols.size());
 if(coordbool){
   newcoordmat.ReSize(coordmat.Nrows()-zerorows.size(),3);
 }
 if(tractcoordbool){
   newtractcoordmat.ReSize(tractcoordmat.Nrows()-zerocols.size(),3);
 }

 int zrowcounter=0,zcolcounter=0,nzrowcounter=1,nzcolcounter=1;
 cerr<<"Forming New Matrix"<<endl;
 for(int j=1;j<=myOMmat.Ncols();j++){
   zrowcounter=0;
   nzrowcounter=1;

   if(zerocols.size()>0){ //Are there any Zero Columns
     if(zerocols[zcolcounter]!=j){  // Only add a col if it's not the next zcol
       for(int i=1;i<=myOMmat.Nrows();i++){
	 if(zerorows.size()>0){ //Are there any zero rows?
	   if(zerorows[zrowcounter]!=i){ //Only add a row if it's not the next zrow
	     newOMmat(nzrowcounter,nzcolcounter)=myOMmat(i,j);
	     nzrowcounter++;
	   }
	   else{zrowcounter++;}
	 }
	 else{newOMmat(nzrowcounter,nzcolcounter)=myOMmat(i,j);nzrowcounter++;}//No Zero Rows
       }
       nzcolcounter++;
     }
     else{zcolcounter++;} //move onto next z col
   }
   
   else{  //No zero Columns
     for(int i=1;i<=myOMmat.Nrows();i++){
       if(zerorows.size()>0){
	 if(zerorows[zrowcounter]!=i){ //Only add a row if it's not the next zrow
	   newOMmat(nzrowcounter,nzcolcounter)=myOMmat(i,j);
	   nzrowcounter++;
	 }
	 else{zrowcounter++;}
       }
       else{newOMmat(nzrowcounter,nzcolcounter)=myOMmat(i,j);nzrowcounter++;}
     }
     nzcolcounter++;
   }

}


 if(coordbool){
   cerr<<"Updating Seed Coordinates"<<endl;
   zrowcounter=0;nzrowcounter=1;
   if(zerorows.size()>0){//Are there any zero rows?
     for(int i=1;i<=coordmat.Nrows();i++){
       if(zerorows[zrowcounter]!=i){
	 newcoordmat(nzrowcounter,1)=coordmat(i,1);
	 newcoordmat(nzrowcounter,2)=coordmat(i,2);
	 newcoordmat(nzrowcounter,3)=coordmat(i,3);
	 nzrowcounter++;
       }
       else{zrowcounter++;}
     }
   } 
   else{//No zero Rows
     newcoordmat=coordmat;
   }
}

 if(tractcoordbool){
   cerr<<"Updating Tract Coordinates"<<endl;
   zcolcounter=0;nzcolcounter=1;
   if(zerocols.size()>0){//Are there any zero cols?
     for(int i=1;i<=tractcoordmat.Nrows();i++){
       if(zerocols[zcolcounter]!=i){
	 newtractcoordmat(nzcolcounter,1)=tractcoordmat(i,1);
	 newtractcoordmat(nzcolcounter,2)=tractcoordmat(i,2);
	 newtractcoordmat(nzcolcounter,3)=tractcoordmat(i,3);
	 nzcolcounter++;
       }
       else{zcolcounter++;}
     }
   }
   else{//No zero Cols 
     newtractcoordmat=tractcoordmat;
   }
 }

}









void rem_cols(Matrix& myOMmat,Matrix& tractcoordmat,const bool tractcoordbool,const vector<int>& excl_cols)
{
 

 Matrix newOMmat,newtractcoordmat;
 newOMmat.ReSize(myOMmat.Nrows(),myOMmat.Ncols()-excl_cols.size());

 if(tractcoordbool){
   newtractcoordmat.ReSize(tractcoordmat.Nrows()-excl_cols.size(),3);
 }

 int zrowcounter=0,zcolcounter=0,nzcolcounter=1,nzrowcounter=1;
 vector<int> zerorows;

 for(int j=1;j<=myOMmat.Ncols();j++){
   zrowcounter=0;
   nzrowcounter=1;   

   if(excl_cols.size()>0){ //Are there any excl Columns
     if(excl_cols[zcolcounter]!=j){  // Only add a col if it's not the next zcol
       for(int i=1;i<=myOMmat.Nrows();i++){
	 if(zerorows.size()>0){ //Are there any excl rows?
	   if(zerorows[zrowcounter]!=i){ //Only add a row if it's not the next zrow
	     newOMmat(nzrowcounter,nzcolcounter)=myOMmat(i,j);
	     nzrowcounter++;
	   }
	   else{zrowcounter++;}
	 }
	 else{newOMmat(nzrowcounter,nzcolcounter)=myOMmat(i,j);nzrowcounter++;}//No Zero Rows
       }
       nzcolcounter++;
     }
     else{zcolcounter++;} //move onto next z col
   }
   else{  //No zero Columns
     for(int i=1;i<=myOMmat.Nrows();i++){
       if(zerorows.size()>0){
	 if(zerorows[zrowcounter]!=i){ //Only add a row if it's not the next zrow
	   newOMmat(nzrowcounter,nzcolcounter)=myOMmat(i,j);
	   nzrowcounter++;
	 }
	 else{zrowcounter++;}
       }
       else{newOMmat(nzrowcounter,nzcolcounter)=myOMmat(i,j);nzrowcounter++;}
     }
     nzcolcounter++;
   }
}

 
 if(tractcoordbool){
   zcolcounter=0;nzcolcounter=1;
   if(excl_cols.size()>0){//Are there any zero cols?
     for(int i=1;i<=tractcoordmat.Nrows();i++){
       if(excl_cols[zcolcounter]!=i){
	 newtractcoordmat(nzcolcounter,1)=tractcoordmat(i,1);
	 newtractcoordmat(nzcolcounter,2)=tractcoordmat(i,2);
	 newtractcoordmat(nzcolcounter,3)=tractcoordmat(i,3);
	 nzcolcounter++;
       }
       else{zcolcounter++;}
     }
   }
   else{//No zero Cols 
     newtractcoordmat=tractcoordmat;
   }
 }

 myOMmat = newOMmat;
 tractcoordmat = newtractcoordmat;
  
}



int main ( int argc, char **argv ){
 if(argc<4){
    cerr<<"usage: reord_OM <matrix> <output base> <bin> [excl_mask]"<<endl;
    cerr<<" matrix in 2D analyze format"<<endl;
    cerr<<" bin=0 gives no binarising at all"<<endl;
    cerr<<" any other <bin> binarises above that number "<<endl;
    cerr<<""<<endl;
    cerr<<"Optional"<<endl;
    cerr<<" excl_mask - exclude contribution from "<<endl;
    cerr<<" voxels in this mask - this needs to be in the same low res"<<endl;
    cerr<<" space as the initial tract space analysis"<<endl;

    exit(0);
  }
 string ip=argv[1];
 make_basename(ip);

 ColumnVector y1,r1,y2,r2;
 volume<int> myOM;
 volume<int> coordvol;
 volume<int> tractcoordvol;
 bool coordbool=false,tractcoordbool=false;
 read_volume(myOM,ip);
 
 Matrix myOMmat(myOM.xsize(),myOM.ysize());
 Matrix mycoordmat,mytractcoordmat;
 Matrix newOMmat,newcoordmat,newtractcoordmat;

 for(int j=0;j<myOM.ysize();j++){
   for(int i=0;i<myOM.xsize();i++){
     if(atof(argv[3])==0)
       myOMmat(i+1,j+1)=float(myOM(i,j,0)); 
     else{
       if(myOM(i,j,0)>atof(argv[3])){
	 myOMmat(i+1,j+1)=1.0f;
       }
       else{
	 myOMmat(i+1,j+1)=0.0f;
       }
     }
   }
 }
 // write_ascii_matrix(newOMmat.t(),"preprecock");
 //Checking for and loading up Seed Coordinates

 string coordname="coords_for_"+ip;
 if(fsl_imageexists(coordname)){
   read_volume(coordvol,coordname);
   coordbool=true;
   mycoordmat.ReSize(coordvol.xsize(),coordvol.ysize());
   for(int j=0;j<coordvol.ysize();j++){
     for(int i=0;i<coordvol.xsize();i++){
       mycoordmat(i+1,j+1)=coordvol(i,j,0);
     }
   }
 }
 else{
   cerr<<"Seed Space Coordinate File Not present - Ignoring"<<endl;
 }

//Checking For and Loading Up Tract coordinates
 string trcoordname="tract_space_coords_for_"+ip;
 if(fsl_imageexists(trcoordname)){
   read_volume(tractcoordvol,trcoordname);
   tractcoordbool=true;
   mytractcoordmat.ReSize(tractcoordvol.xsize(),tractcoordvol.ysize());
   for(int j=0;j<tractcoordvol.ysize();j++){
     for(int i=0;i<tractcoordvol.xsize();i++){
       mytractcoordmat(i+1,j+1)=tractcoordvol(i,j,0);
     }
   }
 }
 else{
   cerr<<"Tract Space Coordinate File Not present - Ignoring"<<endl;
 }
 


 // If user specifies an exclusion mask in tract space. 
 // work out which columns in the matrix to remove 
 // This only works if there is a lookup matrix available


 if(argc==5){
   volume<int> lookup_tract;
   volume<int> excl;
   read_volume(lookup_tract,"lookup_tractspace_"+ip);
   string exname=argv[4];
   make_basename(exname);
   read_volume(excl,exname);
   if(!samesize(excl,lookup_tract)){
     cerr<<"Whoops - your exlusion mask does not appear to be in the same space as your original low resolution mask - sorry"<<endl;
     return(-1);
   }
   vector<int> excl_cols;
   for(int k=0;k<=excl.zsize();k++){
     for(int j=0;j<=excl.ysize();j++){
       for(int i=0;i<=excl.xsize();i++){
	 if(excl(i,j,k)==1){
	   if(lookup_tract(i,j,k)!=0){
	     
	     if(lookup_tract(i,j,k)<=mytractcoordmat.Nrows()){
	       excl_cols.push_back(lookup_tract(i,j,k)+1);
	     }
	     else{
	       cerr<<"Something a bit dodgy has happened here"<<endl;
	       cerr<<"Have you already run a reord_OM on this matrix"<<endl;
	       cerr<<"If so you can't use an exclusion mask as the"<<endl;
	       cerr<<"tractspace_lookup volume is not valid for this matrix"<<endl;
	     }
	     
	     
	   }
	 }
       }
     }
   }

   rem_cols(myOMmat,mytractcoordmat,tractcoordbool,excl_cols);
 }

 
 rem_zrowcol(myOMmat,mycoordmat,mytractcoordmat,coordbool,tractcoordbool,newOMmat,newcoordmat,newtractcoordmat);
//   cerr<<"NOW"<<endl;
//   cerr<<myOMmat.MaximumAbsoluteValue()<<endl;
//   cerr<<newOMmat.MaximumAbsoluteValue()<<endl;
 
//write_ascii_matrix("ncm",newcoordmat);
// write_ascii_matrix("nctm",newtractcoordmat);



 string base=argv[2];
 make_basename(base);
 volume<float> outCCvol(newOMmat.Nrows(),newOMmat.Nrows(),1);
 volume<int> outcoords(newcoordmat.Nrows(),3,1);

cerr<<"Starting first Reordering"<<endl;
 SymmetricMatrix CtCt;
 CtCt << corrcoef(newOMmat.t());
 CtCt << CtCt+1;

 spect_reord(CtCt,r1,y1);


 cerr<<"Permuting seed CC matrix"<<endl;
 for(int j=0;j<outCCvol.ysize();j++){
   for(int i=0;i<outCCvol.xsize();i++){
     outCCvol(i,j,0)=CtCt((int)r1(i+1),(int)r1(j+1));
   }
 }

 
  if(coordbool){
   cerr<<"Permuting Seed Coordinates"<<endl;
   for(int i=0;i<outcoords.xsize();i++){
     outcoords(i,0,0)=(int)newcoordmat(int(r1(i+1)),1);
     outcoords(i,1,0)=(int)newcoordmat(int(r1(i+1)),2);
     outcoords(i,2,0)=(int)newcoordmat(int(r1(i+1)),3);
   } 
 }
 
 write_ascii_matrix(r1,base+"r1");
 write_ascii_matrix(y1,base+"y1");
 save_volume(outCCvol,"reord_CC_"+base);
 save_volume(outcoords,"coords_for_reord_"+base);




 cerr<<"Starting Second Reordering"<<endl;
 SymmetricMatrix CC;
 CC << corrcoef(newOMmat);
 CC<<CC+1;
 spect_reord(CC,r2,y2);
 
 write_ascii_matrix(r2,base+"r2");
 write_ascii_matrix(y2,base+"y2");

 volume<int> outvol(newOMmat.Nrows(),newOMmat.Ncols(),1);
 volume<int> outtractcoords(newtractcoordmat.Nrows(),3,1);


 cerr<<"Permuting Matrix"<<endl;
 for(int j=0;j<outvol.ysize();j++){
   for(int i=0;i<outvol.xsize();i++){
     outvol(i,j,0)=(int)newOMmat((int)r1(i+1),(int)r2(j+1));
   }
 }

 if(tractcoordbool){
   cerr<<"Permuting Tract Coordinates"<<endl;
   for(int i=0;i<outtractcoords.xsize();i++){
     outtractcoords(i,0,0)=(int)newtractcoordmat(int(r2(i+1)),1);
     outtractcoords(i,1,0)=(int)newtractcoordmat(int(r2(i+1)),2);
     outtractcoords(i,2,0)=(int)newtractcoordmat(int(r2(i+1)),3);
   } 
 }
 save_volume(outvol,"reord_"+base);
 save_volume(outtractcoords,"tract_space_coords_for_reord_"+base);

 return 0;
}