/*  fdt_matrix_split.cc

    Saad Jbabdi, FMRIB Image Analysis Group

    Copyright (C) 2010 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
    
    
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#include "utils/options.h"
#include "newimage/newimageio.h"
#include "miscmaths/miscmaths.h"
#include "miscmaths/SpMat.h"

using namespace Utilities;
using namespace NEWIMAGE;
using namespace MISCMATHS;

string title="Splits matrix3 output into seeds_to_target files";
string examples="fdt_matrix_split [options]";

Option<bool> verbose(string("-v,--verbose"),false,
		       string("switch on diagnostic messages"),
		       false,no_argument);
Option<bool> help(string("-h,--help"),false,
		       string("display this message"),
		       false,no_argument);
Option<string> ptxdir(string("-d,--ptxdir"),string(""),
		      string("probtrackx output directory"),
		      true,requires_argument);
Option<string> oBase(string("-o,--output"),string(""),
		       string("output basename (results will be <outbase>_<seed>_to_<target>)"),
		       true,requires_argument);
Option<string> seedsFileName(string("-s,--seeds"),string(""),
		       string("filename for ascii list of seeds"),
		       true,requires_argument);
Option<string> targetsFileName(string("-t,--targets"),string(""),
		       string("filename for ascii list of targets"),
		       true,requires_argument);
Option<string> refFileName(string("--refvol"),string(""),
			   string("reference volume (required if only using surfaces)"),
			   false,requires_argument);
Option<string> mask3FileName(string("-m,--mask3"),string(""),
		       string("filename for mask3 used in probtrackx"),
		       true,requires_argument);
Option<string> meshspace(string("--meshspace"),string("freesurfer"),
			  string("mesh space for surfaces. Either 'freesurfer' (default) or 'first' or 'caret'"),
			  false,requires_argument);


////////////////////////////////////////////////////////
void readMasks(vector<string>& masks, const string& filename){
  ifstream fs(filename.c_str());
  string tmp;
  if(fs){
    fs>>tmp;
    do{
      masks.push_back(tmp);
      fs>>tmp;
    }while(!fs.eof());
  }
  else{
    cerr<<filename<<" does not exist"<<endl;
    exit(1);
  }
}

void vol2vol(const volume<float>& mask,volume<float>& lu){
  lu.reinitialize(mask.xsize(),mask.ysize(),mask.zsize());
  lu=-1;
  int counter=0;
  for(int z=mask.minz();z<=mask.maxz();z++)
    for(int y=mask.miny();y<=mask.maxy();y++)
      for(int x=mask.minx();x<=mask.maxx();x++){
	if(mask(x,y,z)==0)continue;
	lu(x,y,z)=counter;
	counter++;
      }
}
void vol2mat(const volume<float>& mask,Matrix& coords,const volume<float>& lu,const volume<float>& mask3,const Matrix& xfm){
  int counter=0;
  ColumnVector seed_xyz(3),mask3_xyz(3),seed_dims(3),mask3_dims(3);
  seed_dims << mask.xdim() << mask.ydim() << mask.zdim();
  mask3_dims << mask3.xdim() << mask3.ydim() << mask3.zdim();
  for(int z=mask.minz();z<=mask.maxz();z++)
    for(int y=mask.miny();y<=mask.maxy();y++)
      for(int x=mask.minx();x<=mask.maxx();x++){
	if(mask(x,y,z)==0)continue;
	counter++;
      }
  coords.ReSize(counter,4);
  counter=0;
  int xx,yy,zz;
  for(int z=mask.minz();z<=mask.maxz();z++)
    for(int y=mask.miny();y<=mask.maxy();y++)
      for(int x=mask.minx();x<=mask.maxx();x++){
	if(mask(x,y,z)==0)continue;
	counter++;
	seed_xyz << x << y << z;
	mask3_xyz = vox_to_vox(seed_xyz,seed_dims,mask3_dims,xfm);	
	xx=(int)round(float(mask3_xyz(1)));
	yy=(int)round(float(mask3_xyz(2)));
	zz=(int)round(float(mask3_xyz(3)));
	if(mask3(xx,yy,zz)!=0)
	  coords(counter,1) = lu(xx,yy,zz);
	else
	  coords(counter,1) = -1; // seed voxel not found in mask3
	coords(counter,2) = x;
	coords(counter,3) = y;
	coords(counter,4) = z;
      }  
}

void getName(const string& istring,string& ostring){
  ostring=istring;
  int pos=istring.find("/",0);
  int lastpos=pos;
  while(pos>=0){
    lastpos=pos;
    pos=ostring.find("/",pos);
    ostring[pos]='_';
  }
  ostring=ostring.substr(lastpos+1,ostring.length()-lastpos-1);
}

int do_split_matrix(){
  if(verbose.value())
    cout<<"read all inputs"<<endl;
  
  SpMat<int> matrix3(ptxdir.value()+"/fdt_matrix3.dot");
  Matrix     coords3 = read_ascii_matrix(ptxdir.value()+"/coords_for_fdt_matrix3");

  Matrix seed2mask3 = IdentityMatrix(4);
  if(xfmFileName.value()!="")
    seed2mask3 = read_ascii_matrix(xfmFileName.value());
  

  CSV *mask3;
  {
    if(refFileName.value()!=0){
      volume<int> tmprefvol;
      read_volume(tmprefvol,refFileName.value());
      mask3 = new CSV(tmprefvol);
    }
    else{
      mask3 = new CSV();
    }
    mask3->load_rois(mask3FileName.value());
    mask3->set_convention(meshspace.value());
    if(mask3->nVols()==0 && refFileName.value()==""){
      cerr<<"Must provide a refvol for mask3 if only using surfaces"<<endl;
      exit(1);
    }
  }

  CSV *seeds,*targets;
  {
    if(refFileName.value()!=0){
      volume<int> tmprefvol;
      read_volume(tmprefvol,refFileName.value());
      seeds   = new CSV(tmprefvol);
      targets = new CSV(tmprefvol);
    }
    else{
      seeds   = new CSV();
      targets = new CSV();
    }
    seeds->load_rois(seedsFileName.value());
    targets->load_rois(seedsFileName.value());

    if(refFileName.value()==""){
      if(seeds->nVols()!=0){
	if(targets->nVols()==0)
	  targets->change_refvol(seeds->get_refvol());
      }
      else{
	if(targets->nVols()!=0)
	  seeds->change_refvol(targets->get_refvol());
	else{
	  cerr<<"Must provide a refvol for seeds/targets if only using surfaces"<<endl;
	  exit(1);
	}
      }
    }
    seeds->set_convention(meshspace.value());
    targets->set_convention(meshspace.value());
  }


  if(verbose.value())
    cout<<"split the matrix"<<endl;


  // iterate over seeds
  // iterate over targets
  // find coords for seed and target
  // find corresponding coords in matrix3? Argh, they must be in the same space! that's fine
  // and seed and target need to have correspondants in mask3 (when they are surfaces)
  // split the matrix
  
  vector<CSV*> out(targets->nRois());
  for(int i=0;i<targets->nRois();i++){
    out[i] = new CSV(seeds->get_refvol());
    out[i]->reset_values();
  }


  ColumnVector coords(3);vector<int> tlocs;int x,y,z;
  for(int si=0;si<seeds->nRois();si++){
    for(int st=0;st<targets->nRois();st++){
      string sname = seeds->get_name(si);
      string tname = targets->get_name(st);

      // argh! i need to loop through locations within that volume/surface, not all rois
      for(int sloc=1;sloc<=seeds->nLocs();sloc++){
	int isloc=intersectRoi(mask3,seeds,sloc);
	if(isloc<0)continue;
	tlocs.clear();
	for(int tloc=1;tloc<=targets->nLocs();tloc++){
	  int itloc = intersectRoi(mask3,targets,tloc);
	  if(iloc<0)continue;
	  tlocs.push_back(iloc);
	}
	// fill with matrix values! (remember the matrix is symmetric but only half filled)
	for(unsigned int i=0;i<tlocs.size();i++){
	  out->add_value(type,si,sloc,matrix3->Peek(isloc,tlocs[i]));
	  out->add_value(type,si,sloc,matrix3->Peek(tlocs[i],isloc));
	}
      }
    }

  }


  for(int i=0;i<targets->nRois();i++){
    tlocs.clear();
    for(int loc=1;loc<=targets->nLocs();loc++){
      if(targets->isVol(i)){
	coords = targets->get_loc_coords(loc);
	x=(int)round((float)coords(1));
	y=(int)round((float)coords(2));
	z=(int)round((float)coords(3));

	if(!mask3->isInRoi(x,y,z))continue;
	for(int j=0;j<mask3->nVols();j++)
	  tlocs.push_back(mask3->get_loc(j,x,y,z));

      }
      else{
      }
    }

  }
  
  copybasicproperties(mask3,tmpvol);
  string sname,tname;
  for(unsigned int i=0;i<seedCoords.size();i++){
    if(verbose.value())
      cout<<"Seed: "<<seedFiles[i]<<endl;
    getName(seedFiles[i],sname);
    for(unsigned int j=0;j<targetCoords.size();j++){
      if(verbose.value())
	cout<<"Target: "<<targetFiles[j]<<endl;
      getName(targetFiles[j],tname);

      tmpvol=0;
      for(int sr=1;sr<=seedCoords[i].Nrows();sr++){
	if(seedCoords[i](sr,1)==-1)continue;
	for(int tr=1;tr<=targetCoords[j].Nrows();tr++){
	  if(targetCoords[j](tr,1)==-1)continue;
	  int sc=(int)seedCoords  [i](sr,1)+1;
	  int tc=(int)targetCoords[j](tr,1)+1;
	  if(!isVol){
	    tmpvol((int)seedCoords[i](sr,2),
		   (int)seedCoords[i](sr,3),
		   (int)seedCoords[i](sr,4))+=matrix3->Peek(sc,tc);
	    tmpvol((int)seedCoords[i](sr,2),
		   (int)seedCoords[i](sr,3),
		   (int)seedCoords[i](sr,4))+=matrix3->Peek(tc,sc);
	  }
	  else{
	    tmpvol((int)seedCoords[i](sr,2),
		   (int)seedCoords[i](sr,3),
		   (int)seedCoords[i](sr,4))+=matrix3vol(tc-1,sc-1,0);	  
	  }
	}
      }
      // save
      tmpvol.setDisplayMaximumMinimum(tmpvol.max(),0);
      save_volume(tmpvol,oBase.value()+"_"+sname+"_to_"+tname);
    }
  }
  if(verbose.value())
    cout<<"Done!"<<endl;

  return 0;
}

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

  Tracer tr("main");
  OptionParser options(title,examples);

  try{
    options.add(verbose);
    options.add(help);
    options.add(matFileName);
    options.add(oBase);
    options.add(seedsFileName);
    options.add(targetsFileName);
    options.add(refFileName);
    options.add(mask3FileName);
    options.add(meshspace);

    options.parse_command_line(argc,argv);

    
    if ( (help.value()) || (!options.check_compulsory_arguments(true)) ){
      options.usage();
      exit(EXIT_FAILURE);
    }
    
  }
  catch(X_OptionError& e) {
    options.usage();
    cerr << endl << e.what() << endl;
    exit(EXIT_FAILURE);
  } 
  catch(std::exception &e) {
    cerr << e.what() << endl;
  } 
  
  return do_split_matrix();
  
  
}