/*  distancemap.cc

    Mark Jenkinson, FMRIB Image Analysis Group

    Copyright (C) 2003 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/newimageall.h"
#include "miscmaths/miscmaths.h"

#define _GNU_SOURCE 1
#define POSIX_SOURCE 1

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

string title="distancemap (Version 2.0)\nCopyright(c) 2003-2008, University of Oxford (Mark Jenkinson)";
string examples="distancemap [options] -i <inputimage> -o <outputimage>";


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<bool> invertinput(string("--invert"), false,
		  string("invert input image"),
		  false, no_argument);
Option<string> inname(string("-i,--in"), string(""),
		  string("input image filename (calc distance to non-zero voxels)"),
		  true, requires_argument);
Option<string> outname(string("-o,--out"), string(""),
		  string("output image filename"),
		  true, requires_argument);
Option<string> maskname(string("-m,--mask"), string(""),
		  string("mask image filename (only calc values at these voxels)"),
		  false, requires_argument);
Option<string> valueimname(string("--interp"), string(""),
		  string("filename for values to interpolate (sparse sampling interpolation)"),
		  false, requires_argument);
Option<string> labelname(string("-l,--localmax"), string(""),
		  string("local maxima output image filename"),
		  false, requires_argument);
Option<string> segmentname(string("-s,--segment"), string(""),
		  string("segmented output image filename (unique value per segment is local maxima label)"),
		  false, requires_argument);
int nonoptarg;

////////////////////////////////////////////////////////////////////////////

// // Global variables (not options)

// find local maxima and returns volume with zero except at local max
volume<float> label_local_maxima(const volume<float>& vin, 
				  const volume<float>& mask) 
{
  int lmaxcount=0;
  volume<float> vout;
  vout = 0.0f*vin;
  bool usemask=true;
  if (mask.nvoxels()==0) usemask=false;
  for (int z=vin.minz(); z<=vin.maxz(); z++) {
    for (int y=vin.miny(); y<=vin.maxy(); y++) {
      for (int x=vin.minx(); x<=vin.maxx(); x++) {
	if ( (usemask && (mask(x,y,z)>0.5)) || (!usemask)) {
	  if (vin(x,y,z)>vin(x-1,y-1,z-1) &&
	     vin(x,y,z)>vin(x,  y-1,z-1) &&
	     vin(x,y,z)>vin(x+1,y-1,z-1) &&
	     vin(x,y,z)>vin(x-1,y,  z-1) &&
	     vin(x,y,z)>vin(x,  y,  z-1) &&
	     vin(x,y,z)>vin(x+1,y,  z-1) &&
	     vin(x,y,z)>vin(x-1,y+1,z-1) &&
	     vin(x,y,z)>vin(x,  y+1,z-1) &&
	     vin(x,y,z)>vin(x+1,y+1,z-1) &&
	     vin(x,y,z)>vin(x-1,y-1,z) &&
	     vin(x,y,z)>vin(x,  y-1,z) &&
	     vin(x,y,z)>vin(x+1,y-1,z) &&
	     vin(x,y,z)>vin(x-1,y,  z) &&
	     vin(x,y,z)>=vin(x+1,y,  z) &&
	     vin(x,y,z)>=vin(x-1,y+1,z) &&
	     vin(x,y,z)>=vin(x,  y+1,z) &&
	     vin(x,y,z)>=vin(x+1,y+1,z) &&
	     vin(x,y,z)>=vin(x-1,y-1,z+1) &&
	     vin(x,y,z)>=vin(x,  y-1,z+1) &&
	     vin(x,y,z)>=vin(x+1,y-1,z+1) &&
	     vin(x,y,z)>=vin(x-1,y,  z+1) &&
	     vin(x,y,z)>=vin(x,  y,  z+1) &&
	     vin(x,y,z)>=vin(x+1,y,  z+1) &&
	     vin(x,y,z)>=vin(x-1,y+1,z+1) &&
	     vin(x,y,z)>=vin(x,  y+1,z+1) &&
	     vin(x,y,z)>=vin(x+1,y+1,z+1) ) {
	    lmaxcount++;
	    vout(x,y,z)=lmaxcount;
	  }
	}
      }
    }
  }
  return vout;
}


// makes the minimum distance map for each voxel to the non-zero voxels
//  in the input image
int do_work(int argc, char* argv[]) 
{
  volume<float> vin, mask;
  volume4D<float> dmap, valim;

  read_volume(vin,inname.value());
  if (invertinput.value()) {
    vin = 1.0f - binarise(vin,0.5f);
  } else {
    vin.binarise(0.5f);
  }

  if (maskname.set()) {
    read_volume(mask,maskname.value());
  }

  if (valueimname.set()) {
    read_volume4D(valim,valueimname.value());
  }

  if (verbose.value()) { cout << "Creating distance map" << endl; }
  if (valueimname.set()) {
    dmap = sparseinterpolate(valim,vin);
  } else {
    if (maskname.set()) {
      dmap = distancemap(vin,mask);
    } else {
      dmap = distancemap(vin);
    }
  }
  save_volume4D(dmap,outname.value());

  if (labelname.set() || segmentname.set()) {
    if (verbose.value()) { cout << "Finding local max" << endl; }
    volume<float> label;
    label = label_local_maxima(dmap[0],mask);
    if (labelname.set()) { save_volume(label,labelname.value()); }
    if (segmentname.set()) {
      if (verbose.value()) { cout << "Segmenting wrt distance" << endl; }
      {
	volume4D<float> lab4;
	lab4=label;
	dmap = sparseinterpolate(lab4,vin,"nn");
      }
      save_volume4D(dmap,segmentname.value());
    }
  }
  return 0;
}
////////////////////////////////////////////////////////////////////////////

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

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

  try {
    options.add(inname);
    options.add(outname);
    options.add(maskname);
    options.add(labelname);
    options.add(segmentname);
    options.add(invertinput);
    options.add(valueimname);
    options.add(verbose);
    options.add(help);
    
    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;
  } 

  // Call the local functions

  return do_work(argc,argv);
}