/*  b0sim.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
    
    
    LICENCE
    
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    Oxford (the "Software")
    
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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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    under any specific conditions. Furthermore, the University disclaims
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// Simulator for static B0 - made specifically for HBM2004

#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;

// The two strings below specify the title and example usage that is
//  printed out as the help or usage message

string title="b0sim \nCopyright(c) 2003, University of Oxford (Mark Jenkinson)";
string examples="b0sim [options] -i <input model> -b <b0 input> -o <output>";


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("-d,--debug"), false,
		  string("turn debugging outputs (files) on"),
		  false, no_argument);
Option<bool> zerogradients(string("--zerogradients"), false,
		  string("use mean b0 in each voxel but have zero b0 gradients"),
		  false, no_argument);
Option<string> inname(string("-i,--in"), string(""),
		  string("input filename for object model"),
		  true, requires_argument);
Option<string> b0name(string("-b,--b0"), string(""),
		  string("filename for object b0 (in Tesla)"),
		  false, requires_argument);
Option<string> outname(string("-o,--out"), string(""),
		  string("filename for output image (complex)"),
		  true, requires_argument);
int nonoptarg;

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

// Local functions

int calc_gradients(const volume<double>& im, volume<double>& gx, 
		   volume<double>& gy, volume<double>& gz)
{
  // Input image, im, must be in uT : output gradients in uT/mm
  // NB: sets all gradients at the edge of the volume to zero for
  //     simplicity, as normally just need to know inside the brain
  //     which doesn't extend this far!
  gx = im*0;
  gy = gx;
  gz = gx;
  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++) {
	gx(x,y,z) = 1*(im(x+1,y+1,z+1) + im(x+1,y-1,z+1) + im(x+1,y-1,z-1)
		       + im(x+1,y+1,z-1) - im(x-1,y+1,z+1)
		       - im(x-1,y-1,z+1) - im(x-1,y-1,z-1) - im(x-1,y+1,z-1))
	  + 6*(im(x+1,y,z+1) + im(x+1,y,z-1) + im(x+1,y+1,z) + im(x+1,y-1,z)
	       - im(x-1,y,z+1) - im(x-1,y,z-1) - im(x-1,y+1,z) - im(x-1,y-1,z))
	  + 36*(im(x+1,y,z) - im(x-1,y,z));
	gy(x,y,z) = 1*(im(x+1,y+1,z+1) + im(x-1,y+1,z+1) + im(x-1,y+1,z-1)
		       + im(x+1,y+1,z-1) - im(x+1,y-1,z+1)
		       - im(x-1,y-1,z+1) - im(x-1,y-1,z-1) - im(x+1,y-1,z-1))
	  + 6*(im(x,y+1,z+1) + im(x,y+1,z-1) + im(x+1,y+1,z) + im(x-1,y+1,z)
	       - im(x,y-1,z+1) - im(x,y-1,z-1) - im(x+1,y-1,z) - im(x-1,y-1,z))
	  + 36*(im(x,y+1,z) - im(x,y-1,z));
	gz(x,y,z) = 1*(im(x+1,y+1,z+1) + im(x-1,y+1,z+1) + im(x-1,y-1,z+1)
		       + im(x+1,y-1,z+1) - im(x+1,y+1,z-1)
		       - im(x-1,y+1,z-1) - im(x-1,y-1,z-1) - im(x+1,y-1,z-1))
	  + 6*(im(x,y+1,z+1) + im(x,y-1,z+1) + im(x+1,y,z+1) + im(x-1,y,z+1)
	       - im(x,y+1,z-1) - im(x,y-1,z-1) - im(x+1,y,z-1) - im(x-1,y,z-1))
	  + 36*(im(x,y,z+1) - im(x,y,z-1));
      }
    }
  }
  // compensate for weightings and that grad = dI / dx, and dx = 2 here
  double scalefac = 1.0/(2*(4*1 + 4*6 + 1*36));
  gx *= scalefac/im.xdim();  // in uT/mm
  gy *= scalefac/im.ydim();
  gz *= scalefac/im.zdim();
  return 0;
}


int do_work(int argc, char* argv[]) 
{
  // Simulates an EPI image based on rho from brainweb_t2 and b0
  // inhomogeneity from input file
  
  if (debug.value()) cout << "Debugging on" << endl;
  
  string fname=fslbasename(outname.value());

  // random scanner and physics parameters
  double gmax = 35;  // max grad strength of 10 mT/m = uT/mm
  double gammabar = 42.6;  // MHz/T = kHz/mT
  // NB: gammabar * field in mT/m = kHz/m = Hz/mm
  double te = 40*1e-3;  // in sec
  
  // read input object model
  volume<double> rho, b0, gx, gy, gz;
  read_volume(rho,inname.value());
  int inx=rho.xsize();
  int iny=rho.ysize();
  int inz=rho.zsize();
  double lx=rho.xdim(), ly=rho.ydim(), lz=rho.zdim(); // input voxel dims in mm
  double x0=MISCMATHS::round(inx/2)*lx; // centre of input image in mm
  double y0=MISCMATHS::round(iny/2)*ly;
  double z0=MISCMATHS::round(inz/2)*lz;
  volume<double> xpos(inx,iny,1), ypos(inx,iny,1);  // both in mm
  xpos = rho*0.0;
  ypos = xpos;
  for (int x=0; x<inx; x++) {
    for (int y=0; y<iny; y++) {
      xpos(x,y,0)=(x+1)*lx - x0;  // for consistency with matlab
      ypos(x,y,0)=(y+1)*ly - y0;
    }
  }
  // read in b0 inhomogeneity
  if (b0name.set()) {
    read_volume(b0,b0name.value());
    b0=b0*1e6;  // must be in uT (so that gammabar*b0 is in Hz)
  } else {
    b0=rho*0;
  }
  if (verbose.value()) cout << "Calculating b0 gradients" << endl;
  if (zerogradients.value()) {
    gx=b0*0.0f;
    gy=b0*0.0f;
    gz=b0*0.0f;
  } else {
    calc_gradients(b0,gx,gy,gz);
    if (debug.value()) save_volume(gx,fname+"debug_gx");
    if (debug.value()) save_volume(gy,fname+"debug_gy");
    if (debug.value()) save_volume(gz,fname+"debug_gz");
  }

  // EPI params
  //int nx=64, ny=64, nz=25;
  int nx=64, ny=64, nz=1;
  double dx=4.0, dy=4.0, dz=6.0; // output voxel dims in mm
  
  // set up k-space
  double dkx=1/(nx*dx); // in mm^-1
  double dky=1/(ny*dy);
  
  ColumnVector kx1(nx), ky1(nx);
  for (int m=1, n=(-nx/2); n<=(nx-1)/2; m++, n++) {
    kx1(m)=n;
  }
  for (int m=1, n=(-ny/2); n<=(ny-1)/2; m++, n++) {
    ky1(m)=n;
  }
  ColumnVector kx(nx*ny), ky(nx*ny);
  for (int n=1; n<=ny/2; n++) {
    for (int m=1; m<=nx; m++) {
      kx((2*n-2)*nx + m)=kx1(m);
      kx((2*n-1)*nx + m)=kx1(nx + 1 - m);
      ky((2*n-2)*nx + m)=ky1(2*n-1);
      ky((2*n-1)*nx + m)=ky1(2*n);
    }
  }
  kx=kx*dkx;
  ky=ky*dky;
  
  // set up timing
  double dt = dkx/(gammabar*gmax); // in sec
  double t0 = te - ((ny/2)*(nx-1) + nx/2)*dt;
  ColumnVector t(nx*ny);
  for (int n=0; n<(nx*ny); n++) { t(n+1)=t0 + dt*n; }

  if (debug.value()) write_ascii_matrix(t,fname+"debug_t");
  if (debug.value()) write_ascii_matrix(kx,fname+"debug_kx");
  if (debug.value()) write_ascii_matrix(ky,fname+"debug_ky");
  
  // setup final image
  volume<float> dummy(nx,ny,nz);
  dummy.setdims(dx,dy,dz);
  dummy = 0;
  complexvolume finalimage(dummy,dummy);

  // calculate signal s(t)
  
  Matrix sig(2,nx*ny);
  double twopi = 2.0*M_PI;
  for (int oz=0; oz<nz; oz++) { // slice number of output
    sig = 0;
    int zstart, zend;
    // the mess below just tries to set middle of output = middle of input
    zstart = MISCMATHS::round(dz/lz)*MISCMATHS::round(oz - MISCMATHS::round(nz/2)) + MISCMATHS::round(inz/2) - MISCMATHS::round((dz-lz)/(2*lz));
    zend = zstart + MISCMATHS::round(dz/lz) - 1;
    if (zstart<0) zstart=0;
    if (zend>=inz) zend=inz-1;
    if ( (zstart>=inz) || (zend<0) ) {
      zstart=1; zend=0;  // do not want the following loop to run!
    } else if (verbose.value()) { 
      cout << "Output slice " << oz << " ;  input slice range : ";
    }
    for (int z=zstart; z<=zend; z++) {  // slice number of input
      if (verbose.value()) { 
	if (z==zend) cout << z << endl; 
	else { cout <<  z << " , "; cout.flush(); }
      }
      double zpos=lz*(z+1)-z0;   // NB z+1 for MATLAB equivalence
      for (int m=1; m<=nx*ny; m++) { // time point index
	double gbart = gammabar*t(m);
	for (int y=0; y<iny; y++) {
	  for (int x=0; x<inx; x++) {
	    if (rho(x,y,z)>0) {
	      double kxx=kx(m) + gbart*gx(x,y,z);
	      double kyy=ky(m) + gbart*gy(x,y,z);
	      double kzz=gbart*gz(x,y,z);
	      double phi = twopi*(gbart*b0(x,y,z) + kx(m)*xpos(x,y,0) + 
				  ky(m)*ypos(x,y,0));   
	      double term = rho(x,y,z)*MISCMATHS::Sinc(lx*kxx)*
		MISCMATHS::Sinc(ly*kyy)*MISCMATHS::Sinc(lz*kzz);
	      sig(1,m) += cos(phi)*term;
	      sig(2,m) += sin(phi)*term;
	    }
	  }
	}
      }
    }
    sig *= (lx*ly*lz);
    
    if (debug.value()) write_ascii_matrix(sig,fname+"debug_signal");
    
    // reconstruct slice
    volume<float> dummy(nx,ny,1);
    dummy = 0.0;
    complexvolume kslice(dummy,dummy);
    for (int n=1; n<=(ny/2); n++) {
      int tidx = (n-1)*2*nx + 1;
      for (int m=1; m<=nx; m++) {
	kslice.re(m-1,2*n-2,0) = (double) sig(1,tidx + m - 1);
	kslice.im(m-1,2*n-2,0) = (double) sig(2,tidx + m - 1);
	kslice.re(m-1,2*n-1,0) = (double) sig(1,tidx+2*nx-m);
	kslice.im(m-1,2*n-1,0) = (double) sig(2,tidx+2*nx-m);
      }
    }
  
    if (debug.value()) save_complexvolume(kslice,fname+"debug_kspace");
    fft2(kslice);
    fftshift(kslice);
    // copy transformed slice into final image
    for (int oy=0; oy<ny; oy++) {
      for (int ox=0; ox<nx; ox++) {
	finalimage.re(ox,oy,oz)=kslice.re(ox,oy,0);
	finalimage.im(ox,oy,oz)=kslice.im(ox,oy,0);
      }
    }
  }

  if (debug.value()) print_volume_info(finalimage.re(),"finalimage.re()");
  if (debug.value()) print_volume_info(finalimage.im(),"finalimage.im()");
  save_complexvolume(finalimage,fname);
  
  return 0;
}



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

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

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

  try {
    // must include all wanted options here (the order determines how
    //  the help message is printed)
    options.add(inname);
    options.add(b0name);
    options.add(outname);
    options.add(zerogradients);
    options.add(verbose);
    options.add(help);
    options.add(debug);
    
    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);
}