/*  new_invwarp.cc

    Jesper Andersson, FMRIB Image Analysis Group

    Copyright (C) 2010 University of Oxford  */

/*  Part of FSL - FMRIB's Software Library
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#include "utils/options.h"
#include "miscmaths/miscmaths.h"
#include "warpfns/warpfns.h"
#include "warpfns/fnirt_file_reader.h"
#include "warpfns/fnirt_file_writer.h"
#include "tetrahedron.h"
#include "dilator.h"

#define _GNU_SOURCE 1
#define POSIX_SOURCE 1

using namespace std;
using namespace Utilities;
using namespace NEWMAT;
using namespace MISCMATHS;
using namespace NEWIMAGE;

// COMMAND LINE OPTIONS

string title="new_invwarp\nCopyright(c) 2010, University of Oxford (Jesper Andersson)";
string examples="invwarp -w warpvol -o invwarpvol -r refvol";

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> debug(string("--debug"), false,
		  string("turn on debugging output"),
		  false, no_argument);
Option<bool> abswarp(string("--abs"), false,
		  string("use absolute warp convention (default): x' = w(x)"),
		  false, no_argument);
Option<bool> relwarp(string("--rel"), false,
		  string("use relative warp convention: x' = x + w(x)"),
		  false, no_argument);
Option<bool> nojaccon(string("--noconstraint"), false,
		  string("do not apply the Jacobian constraint"),
		  false, no_argument);
Option<float> jmin(string("--jmin"), 0.01,
			string("minimum acceptable Jacobian value for constraint (default 0.01)"),
			false, requires_argument);
Option<float> jmax(string("--jmax"), 100.0,
			string("maximum acceptable Jacobian value for constraint (default 100.0)"),
			false, requires_argument);
Option<string> refvolname(string("-r,--ref"), string(""),
		       string("filename for new reference image, i.e., what was originally the input image (determines inverse warpvol's FOV and pixdims)"),
		       true, requires_argument);
Option<string> outname(string("-o,--out"), string(""),
		       string("filename for output (inverse warped) image"),
		       true, requires_argument);
Option<string> warpname(string("-w,--warp"), string(""),
			string("filename for warp/shiftmap transform (volume)"),
			true, requires_argument);
Option<string> extrapolation(string("-e,--extrap"), string("affine"),
			     string("Extrapolation method to use outside FOV [affine | fancy], default affine"),
			     true, requires_argument);

int new_invwarp()
{
  // Read warps
  // N.B. that latest version of FnirtFileReader
  // will separate Affine and non-linear component
  // even for files that aren't fnirt coefficient
  // files. This makes it easier to write code where
  // one truly does not need to care about where the
  // files come from,
  if (verbose.value()) cout << "Reading input files" << endl;
  AbsOrRelWarps      spec_wt=UnknownWarps;        // Specified warp convention
  if (abswarp.value()) spec_wt = AbsoluteWarps;
  else if (relwarp.value()) spec_wt = RelativeWarps;
  FnirtFileReader    fnirtfile(warpname.value(),spec_wt,verbose.set());
  boost::shared_ptr<volume4D<float> > warpvol(new volume4D<float>);
  *warpvol = fnirtfile.FieldAsNewimageVolume4D();
  NEWMAT::Matrix aff = fnirtfile.AffineMat();

  // Read reference volume and set size of invwarp
  volume4D<float>    invwarp;
  read_volume4D(invwarp,refvolname.value());
  while (invwarp.tsize()<3) { invwarp.addvolume(invwarp[0]); }
  while (invwarp.tsize()>3) { invwarp.deletevolume(invwarp.maxt()); }
  // inwarp.tsize() == 3 here
  invwarp=0.0f;
  invwarp.setDisplayMaximumMinimum(0,0);
  const volume<float>& ref=invwarp[0];   // To make subsequent code easier to understand (I hope)

  // Create mm->mm transformation matrix for
  // use within tetrahedron and for use as
  // initial guess.
  NEWMAT::Matrix B = warpvol->sampling_mat().i()*aff*ref.sampling_mat();      // For initial guess
  double b11, b12, b13, b14;
  double b21, b22, b23, b24;
  double b31, b32, b33, b34;
  b11=B(1,1); b12=B(1,2); b13=B(1,3); b14=B(1,4);
  b21=B(2,1); b22=B(2,2); b23=B(2,3); b24=B(2,4);
  b31=B(3,1); b32=B(3,2); b33=B(3,3); b34=B(3,4);

  // Rescale displacement fields mm->voxels_in_ref_space
  (*warpvol)[0] /= ref.xdim();
  (*warpvol)[1] /= ref.ydim();
  (*warpvol)[2] /= ref.zdim();

  // Do the inversion
  if (verbose.value()) {
    cout << "Inverting field" << endl;
  }
  NEWMAT::Matrix iB = B.i();
  Tetrahedron  tet(0,0,0,warpvol,iB); // The guy doing the work
  tet.SetIgnoreFOV();
  bool found_it = false;
  for (int k=0; k<invwarp.zsize(); k++) {
    if (verbose.value()) { cout << "\b\b\b\b\b\b\b\b\b\b" << "Slice: " << k+1; cout.flush(); }
    for (int j=0; j<invwarp.ysize(); j++) {
      for (int i=0; i<invwarp.xsize(); i++) {
        double ox, oy, oz;
        double ax = b11*i+b12*j+b13*k+b14;
        double ay = b21*i+b22*j+b23*k+b24;
        double az = b31*i+b32*j+b33*k+b34;
        if (!i || !found_it) {
	  tet.SetFirstPoint(int(ax),int(ay),int(az));
	}
        if (tet.FindPoint(double(i),double(j),double(k),ox,oy,oz)) {
          invwarp(i,j,k,0) = ox-ax; 
          invwarp(i,j,k,1) = oy-ay;
          invwarp(i,j,k,2) = oz-az;
          found_it = true;
	}
        else { // Indicates singularity.
          invwarp(i,j,k,0) = -999; // NaN
          invwarp(i,j,k,1) = -999; // NaN
          invwarp(i,j,k,2) = -999; // NaN
          found_it = false;
        }
      }
    }
  }
  if (verbose.value()) cout << endl;

  // Perform dilations to replace NaNs
  // with average of non-NaN neighbours.
  if (verbose.value()) cout << "Fudging values at edge of FOV" << endl;
  for (int i=0; i<3; i++) {
    Dilator dil(invwarp[i]);
    unsigned int n = dil.Dilate();
    while (n) {
      n = dil.Dilate();
    }
    invwarp[i] = dil.Get();
  }

  // Convert back to mm
  std::vector<double> vxs = fnirtfile.VoxelSize();
  invwarp[0] *= vxs[0]; invwarp[1] *= vxs[1]; invwarp[2] *= vxs[2];

  // Add affine component back in
  NEWMAT::Matrix M = ref.sampling_mat();
  double m11, m12, m13, m14;
  double m21, m22, m23, m24;
  double m31, m32, m33, m34;
  m11=M(1,1); m12=M(1,2); m13=M(1,3); m14=M(1,4);
  m21=M(2,1); m22=M(2,2); m23=M(2,3); m24=M(2,4);
  m31=M(3,1); m32=M(3,2); m33=M(3,3); m34=M(3,4);
  NEWMAT::Matrix A = aff;
  double a11, a12, a13, a14;
  double a21, a22, a23, a24;
  double a31, a32, a33, a34;
  a11=A(1,1); a12=A(1,2); a13=A(1,3); a14=A(1,4);
  a21=A(2,1); a22=A(2,2); a23=A(2,3); a24=A(2,4);
  a31=A(3,1); a32=A(3,2); a33=A(3,3); a34=A(3,4);
  for (int k=0; k<invwarp.zsize(); k++) {
    for (int j=0; j<invwarp.ysize(); j++) {
      for (int i=0; i<invwarp.xsize(); i++) {
        double mmx = m11*i+m12*j+m13*k+m14;
        double mmy = m21*i+m22*j+m23*k+m24;
        double mmz = m31*i+m32*j+m33*k+m34;
        double ax = a11*mmx+a12*mmy+a13*mmz+a14;
        double ay = a21*mmx+a22*mmy+a23*mmz+a24;
        double az = a31*mmx+a32*mmy+a33*mmz+a34;
        invwarp(i,j,k,0) += ax-mmx; 
        invwarp(i,j,k,1) += ay-mmy;
        invwarp(i,j,k,2) += az-mmz;
      }
    }
  }

  // Constrain range of Jacobians of inverse field
  if (!nojaccon.value()) {
    if (verbose.value()) cout << "Constraining range of Jacobians in inverse field" << endl;
    convertwarp_rel2abs(invwarp);
    constrain_topology(invwarp,jmin.value(),jmax.value());
    convertwarp_abs2rel(invwarp);
  }
  
  // Save inverse. I save it as a "fnirt field", which is different
  // from "old" invwarp. The advantage is that now the field is 
  // "in the system" and we can make assumptions about it.
  if (verbose.value()) cout << "Saving inverted field" << endl;
  FnirtFileWriter(outname.value(),ref,invwarp);
 
  return(EXIT_SUCCESS); 
}

//@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
//
// The main pretty much just does some argument checking and then
// calls the new_invwarp function that does the job.
//
//@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@

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

  Tracer tr("main");

  OptionParser options(title, examples);

  try {
    options.add(warpname);
    options.add(outname);
    options.add(refvolname);
    options.add(relwarp);
    options.add(abswarp);
    options.add(nojaccon);
    options.add(jmin);
    options.add(jmax);
    options.add(debug);
    options.add(verbose);
    options.add(help);
    
    int nparsed = options.parse_command_line(argc, argv);
    if (nparsed < argc) {
      for (; nparsed<argc; nparsed++) {
        cerr << "Unknown input: " << argv[nparsed] << endl;
      }
      exit(EXIT_FAILURE);
    }

    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;
  } 

  if (abswarp.value() && relwarp.value()) {
    cerr << "--abs and --rel flags cannot both be set" << endl;
    exit(EXIT_FAILURE);
  }

  volume4D<float>   warpvol;
  try {
    read_volume4D_hdr_only(warpvol,warpname.value());
  }
  catch(...) {
    cerr << "invwarp: Problem reading warp-file " << warpname.value() << endl;
    exit(EXIT_FAILURE);
  }
  if ((warpvol.intent_code()==FSL_CUBIC_SPLINE_COEFFICIENTS || 
       warpvol.intent_code()==FSL_QUADRATIC_SPLINE_COEFFICIENTS || 
       warpvol.intent_code()==FSL_DCT_COEFFICIENTS ||
       warpvol.intent_code()==FSL_FNIRT_DISPLACEMENT_FIELD) &&
      (abswarp.value() || relwarp.value())) {
    cout << "--abs and --rel flags ignored when reading fnirt coefficient files" << endl;
  }

  return new_invwarp();
}