/*  tbss_skeleton.cc

    Stephen Smith, FMRIB Analysis Group

    Copyright (C) 2005-2008 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
    
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    University").
    
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    makes clear that no condition is made or to be implied, nor is any
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// {{{ includes and options

#define _GNU_SOURCE 1
#define POSIX_SOURCE 1

#include "newimage/newimageall.h"
#include "miscmaths/miscmaths.h"
#include "utils/options.h"

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

string title="tbss_skeleton (Version 1.03)\nCopyright(c) 2005-2007, University of Oxford (Stephen Smith)";
string examples="tbss_skeleton -i <inputimage> -o <skeleton>\ntbss_skeleton -i <inputimage> -p <skel_thresh> <distancemap> <search_rule_mask> <4Ddata> <projected_4Ddata> [-a <alt_4D>] [-s <alt_skeleton>]}";

Option<string> inname(string("-i,--in"), string(""),
		  string("input image"),
		  true, requires_argument);
Option<string> outname(string("-o,--out"), string(""),
		  string("output image"),
		  false, requires_argument);
Option<string> projectargs(string("-p"), "",
			   string("~<skel_thresh> <distancemap> <search_rule_mask> <4Ddata> <projected_4Ddata>"), false, requires_5_arguments);
Option<string> alt4Dname(string("-a"), string(""),
		  string("alternative 4Ddata (e.g. L1)"),
		  false, requires_argument);
Option<string> altskelname(string("-s"), string(""),
		  string("alternative skeleton"),
		  false, requires_argument);
Option<bool> help(string("-h,--help"), false,
		  string("display this message"),
		  false, no_argument);
Option<bool> debugging(string("-d,--debug"), false, 
		     string("switch on debugging image outputs"), 
		     false, no_argument);
Option<string> debugging2(string("-D,--debug2"), string(""),
		  string("~<skelpoints>\tde-project <skelpoints> points on skeleton back to all_FA space"),
		  false, requires_argument);

int nonoptarg;

// }}}

#define SEARCHSIGMA 10 /* length in linear voxel dimensions */
#define MAXSEARCHLENGTH (3*SEARCHSIGMA)

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

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

  try {
    options.add(inname);
    options.add(outname);
    options.add(projectargs);
    options.add(alt4Dname);
    options.add(altskelname);
    options.add(help);
    options.add(debugging);
    options.add(debugging2);

    nonoptarg = options.parse_command_line(argc, argv);

    // line below stops the program if the help was requested or 
    //  a compulsory option was not set
    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;
  } 

// }}}

  volume<float> im;
  read_volume(im,inname.value());

  // {{{ estimate perp from CofG and curvature, and store this in X,Y,Z

volume<short> X(im.xsize(),im.ysize(),im.zsize()),
  Y(im.xsize(),im.ysize(),im.zsize()),
  Z(im.xsize(),im.ysize(),im.zsize());

X=0; Y=0; Z=0;

for(int z=1;z<im.zsize()-1;z++) for(int y=1;y<im.ysize()-1;y++) for(int x=1;x<im.xsize()-1;x++)
  {
    float theval = im(x,y,z);

    if ( theval != 0 )
      {
	float CofGx=0, CofGy=0, CofGz=0, Sum=0, CofGl;
	int xxx=0, yyy=0, zzz=0;

	for(int zz=-1; zz<=1; zz++) for(int yy=-1; yy<=1; yy++) for(int xx=-1; xx<=1; xx++)
	  {
	    float val = im(x+xx,y+yy,z+zz);
	    Sum   += val;
	    CofGx += xx * val;  CofGy += yy * val;  CofGz += zz * val;
	  }	      
	      
	CofGx /= Sum;  CofGy /= Sum;  CofGz /= Sum;
	CofGl = sqrt(CofGx*CofGx+CofGy*CofGy+CofGz*CofGz);
	      
	if (CofGl > .1)  /* is CofG far enough away from centre voxel? */
	  {
	    // if (CofGl > 1.4) cout << CofGx << " " << CofGy << " " << CofGz << " " << Sum << endl;
	    xxx = MISCMATHS::Max( MISCMATHS::Min( round(CofGx/CofGl) , 1 ) , -1);
	    yyy = MISCMATHS::Max( MISCMATHS::Min( round(CofGy/CofGl) , 1 ) , -1);
	    zzz = MISCMATHS::Max( MISCMATHS::Min( round(CofGz/CofGl) , 1 ) , -1);
	  }
	else
	  // {{{ find direction of max curvature

	{
	  float maxcost=0, centreval=2*theval;

	  for(int zz=0; zz<=1; zz++) /* note - starts at zero as we're only searching half the voxels */
	    for(int yy=-1; yy<=1; yy++)
	      for(int xx=-1; xx<=1; xx++)
		if ( (zz==1) || (yy==1) || ((yy==0)&&(xx==1)) ) /* only search half the voxels */
		  {
		    float weighting = pow( (float)(xx*xx+yy*yy+zz*zz) , -0.7 ); /* power is arbitrary: maybe test other functions here */
		    float cost = weighting * ( centreval 
					       - (float)im(x+xx,y+yy,z+zz)
					       - (float)im(x-xx,y-yy,z-zz) );

		    if (cost>maxcost)
		      {
			maxcost=cost;
			xxx=xx;
			yyy=yy;
			zzz=zz;
		      }
		  }
	}

// }}}
							   
	  X(x,y,z)=xxx;
	  Y(x,y,z)=yyy;
	  Z(x,y,z)=zzz;
      }

  }

// {{{ save perp image

if (debugging.set())
  {
    volume4D<float>tmpim(im.xsize(),im.ysize(),im.zsize(),3);
    copybasicproperties(im,tmpim);
    tmpim=0;
    
    for(int z=0;z<im.zsize();z++) for(int y=0;y<im.ysize();y++) for(int x=0;x<im.xsize();x++)
      {
	float tmpX=X(x,y,z), tmpY=Y(x,y,z), tmpZ=Z(x,y,z),
	  tmpf=sqrt(tmpX*tmpX+tmpY*tmpY+tmpZ*tmpZ);

	if (tmpf>0)
	  {
	    tmpim(x,y,z,0)=tmpX/tmpf;
	    tmpim(x,y,z,1)=tmpY/tmpf;
	    tmpim(x,y,z,2)=tmpZ/tmpf;
	  }
      }
    
    save_volume4D(tmpim,inname.value()+"_flow");
  }

// }}}

// }}}
  // {{{ smooth X,Y,Z and store in XX,YY,ZZ

volume<short> XX(im.xsize(),im.ysize(),im.zsize()),
  YY(im.xsize(),im.ysize(),im.zsize()),
  ZZ(im.xsize(),im.ysize(),im.zsize());

XX=0; YY=0; ZZ=0;

for(int z=1;z<im.zsize()-1;z++) for(int y=1;y<im.ysize()-1;y++) for(int x=1;x<im.xsize()-1;x++)
  {
    int* localsum = new int[27];
    int localmax=0, xxx, yyy, zzz;

    for(int zz=0; zz<27; zz++) localsum[zz]=0;

    for(int zz=-1; zz<=1; zz++) for(int yy=-1; yy<=1; yy++) for(int xx=-1; xx<=1; xx++)
      {
	xxx = X(x+xx,y+yy,z+zz);
	yyy = Y(x+xx,y+yy,z+zz);
	zzz = Z(x+xx,y+yy,z+zz);
	// cout << xxx << " " << yyy << " " << zzz << " " << (1+zzz)*9+(1+yyy)*3+1+xxx << endl;
	localsum[(1+zzz)*9+(1+yyy)*3+1+xxx]++;
	localsum[(1-zzz)*9+(1-yyy)*3+1-xxx]++;
      }
    
    for(int zz=-1; zz<=1; zz++) for(int yy=-1; yy<=1; yy++) for(int xx=-1; xx<=1; xx++)
      {
	if (localsum[(1+zz)*9+(1+yy)*3+1+xx]>localmax)
	  {
	    localmax=localsum[(1+zz)*9+(1+yy)*3+1+xx];
	    XX(x,y,z)=xx;
	    YY(x,y,z)=yy;
	    ZZ(x,y,z)=zz;
	  }
      }

    delete localsum;
  }

X.destroy();
Y.destroy();
Z.destroy();

// {{{ save perp image

if (debugging.set())
  {
    volume4D<float>tmpim(im.xsize(),im.ysize(),im.zsize(),3);
    copybasicproperties(im,tmpim);
    tmpim=0;
    
    for(int z=0;z<im.zsize();z++) for(int y=0;y<im.ysize();y++) for(int x=0;x<im.xsize();x++)
      {
	float tmpX=XX(x,y,z), tmpY=YY(x,y,z), tmpZ=ZZ(x,y,z),
	  tmpf=sqrt(tmpX*tmpX+tmpY*tmpY+tmpZ*tmpZ);

	if (tmpf>0)
	  {
	    tmpim(x,y,z,0)=tmpX/tmpf;
	    tmpim(x,y,z,1)=tmpY/tmpf;
	    tmpim(x,y,z,2)=tmpZ/tmpf;
	  }
      }
    
    save_volume4D(tmpim,inname.value()+"_flowsmooth");
  }

// }}}

// }}}
  // {{{ do non-max-suppression in the direction of perp and save to file

volume<float> tmpim(im);
tmpim=0;

for(int z=1;z<im.zsize()-1;z++) for(int y=1;y<im.ysize()-1;y++) for(int x=1;x<im.xsize()-1;x++)
  {
    float theval = im(x,y,z);
    int xxx=XX(x,y,z);
    int yyy=YY(x,y,z);
    int zzz=ZZ(x,y,z);
    
    if ( ( (xxx!=0) || (yyy!=0) || (zzz!=0) ) &&
	 ( theval >= im(x+xxx,y+yyy,z+zzz) ) &&
	 ( theval >  im(x-xxx,y-yyy,z-zzz) ) &&
	 ( theval >= im(x+2*xxx,y+2*yyy,z+2*zzz) ) &&
	 ( theval >  im(x-2*xxx,y-2*yyy,z-2*zzz) ) )
      tmpim(x,y,z) = theval;
  }

if (outname.set())
  save_volume(tmpim,outname.value());

// }}}

  if (projectargs.set())
    // {{{ do search in the direction of perp

{
  float origthresh = atof(projectargs.value(0).c_str());

  volume<float> distancemap;
  read_volume(distancemap,projectargs.value(1));

  volume<int> lowercingulum;
  read_volume(lowercingulum,projectargs.value(2));

  volume4D<float> data_4d;
  read_volume4D(data_4d,projectargs.value(3));

  volume4D<float> alt_data_4d;
  if (alt4Dname.set())
    read_volume4D(alt_data_4d,alt4Dname.value());

  if (altskelname.set())
    read_volume(tmpim,altskelname.value());

  volume4D<float> data_4d_projected(data_4d);
  data_4d_projected=0;

  // {{{ debugging

  volume4D<short> tmpimFLOWx, tmpimFLOWy, tmpimFLOWz;
  if (debugging.set())
    {
      tmpimFLOWx.reinitialize(im.xsize(),im.ysize(),im.zsize(),data_4d.tsize());
      tmpimFLOWy.reinitialize(im.xsize(),im.ysize(),im.zsize(),data_4d.tsize());
      tmpimFLOWz.reinitialize(im.xsize(),im.ysize(),im.zsize(),data_4d.tsize());
      copybasicproperties(im,tmpimFLOWx);
      copybasicproperties(im,tmpimFLOWy);
      copybasicproperties(im,tmpimFLOWz);
      tmpimFLOWx=0;
      tmpimFLOWy=0;
      tmpimFLOWz=0;
    }

  volume<float> debug2in;
  volume4D<float> debug2out;
  if (debugging2.set())
    {
      read_volume(debug2in,debugging2.value());
      debug2out.reinitialize(im.xsize(),im.ysize(),im.zsize(),data_4d.tsize());
      copybasicproperties(im,debug2out);
      debug2out=0;
    }

// }}}

  for(int T=0;T<data_4d.tsize();T++) for(int z=1;z<im.zsize()-1;z++) for(int y=1;y<im.ysize()-1;y++) for(int x=1;x<im.xsize()-1;x++)
    if (tmpim(x,y,z) > origthresh)
      {
	int xxx=XX(x,y,z), yyy=YY(x,y,z), zzz=ZZ(x,y,z);
	short maxvalX=0, maxvalY=0, maxvalZ=0;
	float maxval=data_4d(x,y,z,T), maxval_weighted=maxval,
	  exponentfactor = -0.5 * (xxx*xxx+yyy*yyy+zzz*zzz) / (float)(SEARCHSIGMA*SEARCHSIGMA);
	if (alt4Dname.set()) maxval=alt_data_4d(x,y,z,T);

	if (lowercingulum(x,y,z) == 0)
	  // {{{ search perp to sheet

{
  for(int iters=0;iters<2;iters++)
    {
      float distance=0;

      for(int d=1;d<MAXSEARCHLENGTH;d++)
	{
	  int D=d;
	  if (iters==1) D=-d;
		    
	  if (distancemap(x+xxx*D,y+yyy*D,z+zzz*D)>=distance)
	    {
	      float distanceweight = exp(d * d * exponentfactor);
	      distance=distancemap(x+xxx*D,y+yyy*D,z+zzz*D);
	      if (distanceweight * data_4d(x+xxx*D,y+yyy*D,z+zzz*D,T)>maxval_weighted)
		{
		  maxval=data_4d(x+xxx*D,y+yyy*D,z+zzz*D,T);
		  maxval_weighted=maxval*distanceweight;
		  maxvalX=xxx*D;
		  maxvalY=yyy*D;
		  maxvalZ=zzz*D;
		  if (alt4Dname.set()) maxval=alt_data_4d(x+xxx*D,y+yyy*D,z+zzz*D,T);
		}
	    }
	  else
	    d=MAXSEARCHLENGTH;
	}
    }
}

// }}}
	else
	  // {{{ search all around tube

{
  for(int yyy=-MAXSEARCHLENGTH; yyy<=MAXSEARCHLENGTH; yyy++) for(int xxx=-MAXSEARCHLENGTH; xxx<=MAXSEARCHLENGTH; xxx++) 
    {
      float distanceweight = exp(-0.5 * (xxx*xxx+yyy*yyy) / (float)(SEARCHSIGMA*SEARCHSIGMA) );

      float r=sqrt((float)(xxx*xxx+yyy*yyy));

      if (r>0)
	{
	  int allok=1;
	  
	  for(float rr=1; rr<=r+0.1; rr++) /* search outwards from centre to current voxel - test that distancemap always increasing */
	    {
	      int xxx1=round(rr*xxx/r);
	      int yyy1=round(rr*yyy/r);
	      int xxx2=round((rr+1)*xxx/r);
	      int yyy2=round((rr+1)*yyy/r);
	      if ( distancemap(x+xxx1,y+yyy1,z) > distancemap(x+xxx2,y+yyy2,z) )
		allok=0;
	    }

	  if ( allok &&
	       ( distanceweight * data_4d(x+xxx,y+yyy,z,T) > maxval_weighted ) )
	    {
	      maxval=data_4d(x+xxx,y+yyy,z,T);
	      maxval_weighted=maxval*distanceweight;
	      maxvalX=xxx;
	      maxvalY=yyy;
	      maxvalZ=0;
	      if (alt4Dname.set()) maxval=alt_data_4d(x+xxx,y+yyy,z,T);
	    }
	}
    }

}

// }}}
	
	  data_4d_projected(x,y,z,T)=maxval; /* output maxsearch data */

	  // {{{ debugging search

	  if (debugging.set())
	    {
	      tmpimFLOWx(x,y,z,T)=maxvalX;
	      tmpimFLOWy(x,y,z,T)=maxvalY;
	      tmpimFLOWz(x,y,z,T)=maxvalZ;
	    }

	  if (debugging2.set())
	    if (debug2in(x,y,z)>0)
	      debug2out(x+maxvalX,y+maxvalY,z+maxvalZ,T)=debug2in(x,y,z);

// }}}
      }

  data_4d.destroy();
  alt_data_4d.destroy();
  save_volume4D(data_4d_projected,projectargs.value(4));

  // {{{ debugging search

  if (debugging.set())
    {
      save_volume4D(tmpimFLOWx,projectargs.value(4)+"_search_X");
      save_volume4D(tmpimFLOWy,projectargs.value(4)+"_search_Y");
      save_volume4D(tmpimFLOWz,projectargs.value(4)+"_search_Z");
    }

  if (debugging2.set())
    save_volume4D(debug2out,projectargs.value(4)+"_deprojected");

// }}}
}

// }}}
}