dtmri_view.cpp

this a image processing program

/*-------------------------------------------------------------------------------

  File        : dtmri_view.cpp

  Description : A viewer of Diffusion-Tensor MRI volumes (medical imaging).

  Copyright  : David Tschumperle - http://www.greyc.ensicaen.fr/~dtschump/

  This software is governed by the CeCILL-C license under French law and
  abiding by the rules of distribution of free software.  You can  use,
  modify and/ or redistribute the software under the terms of the CeCILL-C
  license as circulated by CEA, CNRS and INRIA at the following URL
  "http://www.cecill.info".

  As a counterpart to the access to the source code and  rights to copy,
  modify and redistribute granted by the license, users are provided only
  with a limited warranty  and the software's author,  the holder of the
  economic rights,  and the successive licensors  have only  limited
  liability.

  In this respect, the user's attention is drawn to the risks associated
  with loading,  using,  modifying and/or developing or reproducing the
  software by the user in light of its specific status of free software,
  that may mean  that it is complicated to manipulate,  and  that  also
  therefore means  that it is reserved for developers  and  experienced
  professionals having in-depth computer knowledge. Users are therefore
  encouraged to load and test the software's suitability as regards their
  requirements in conditions enabling the security of their systems and/or
  data to be ensured and,  more generally, to use and operate it in the
  same conditions as regards security.

  The fact that you are presently reading this means that you have had
  knowledge of the CeCILL-C license and that you accept its terms.

  ------------------------------------------------------------------------------*/

#include "../CImg.h"
using namespace cimg_library;
// The undef below is necessary when using a non-standard compiler.
#ifdef cimg_use_visualcpp6
#define std
#endif

// Compute fractional anisotropy (FA) of a tensor
//-------------------------------------------
template<typename T> float get_FA(const T& val1, const T& val2, const T& val3) {
  const float
    l1 = val1>0?val1:0, l2 = val2>0?val2:0, l3 = val3>0?val3:0,
    lm = (l1+l2+l3)/3,
    tr2 = 2*( l1*l1 + l2*l2 + l3*l3 ),
    ll1 = l1-lm,
    ll2 = l2-lm,
    ll3 = l3-lm;
  if (tr2>0) return (float)std::sqrt( 3*(ll1*ll1 + ll2*ll2 + ll3*ll3)/tr2 );
  return 0;
}

// Insert an ellipsoid in a CImg 3D scene
//----------------------------------------
template<typename t,typename tp,typename tf,typename tc>
void insert_ellipsoid(const CImg<t>& tensor,const float X,const float Y,const float Z,const float tfact,
		      const float vx, const float vy, const float vz,
		      CImgList<tp>& points, CImgList<tf>& faces, CImgList<tc>& colors,
		      const unsigned int res1 = 20, const unsigned int res2 = 20) {

  // Compute eigen elements
  const float l1 = tensor[0], l2 = tensor[1], l3 = tensor[2], fa = get_FA(l1,l2,l3);

  CImg<> vec = CImg<>::matrix(tensor[3],tensor[6],tensor[9],
			      tensor[4],tensor[7],tensor[10],
			      tensor[5],tensor[8],tensor[11]);
  const int
    r = (int)cimg::min(30+1.5f*cimg::abs(255*fa*tensor[3]),255.0f),
    g = (int)cimg::min(30+1.5f*cimg::abs(255*fa*tensor[4]),255.0f),
    b = (int)cimg::min(30+1.5f*cimg::abs(255*fa*tensor[5]),255.0f);

  // Define mesh points
  const unsigned int N0 = points.size;
  for (unsigned int v=1; v<res2; v++)
    for (unsigned int u=0; u<res1; u++) {
      const float
	alpha = (float)(u*2*cimg::PI/res1),
	beta = (float)(-cimg::PI/2 + v*cimg::PI/res2),
	x = (float)(tfact*l1*std::cos(beta)*std::cos(alpha)),
	y = (float)(tfact*l2*std::cos(beta)*std::sin(alpha)),
	z = (float)(tfact*l3*std::sin(beta));
      points.insert((CImg<tp>::vector(X,Y,Z)+vec*CImg<tp>::vector(x,y,z)).mul(CImg<tp>::vector(vx,vy,vz)));
    }
  const unsigned int N1 = points.size;
  points.insert((CImg<tp>::vector(X,Y,Z)+vec*CImg<tp>::vector(0,0,-l3*tfact)));
  points.insert((CImg<tp>::vector(X,Y,Z)+vec*CImg<tp>::vector(0,0,l3*tfact)));
  points[points.size-2](0)*=vx; points[points.size-2](1)*=vy;  points[points.size-2](2)*=vz;
  points[points.size-1](0)*=vx; points[points.size-1](1)*=vy;  points[points.size-1](2)*=vz;

  // Define mesh triangles
  for (unsigned int vv=0; vv<res2-2; vv++)
    for (unsigned int uu=0; uu<res1; uu++) {
      const int nv = (vv+1)%(res2-1), nu = (uu+1)%res1;
      faces.insert(CImg<tf>::vector(N0+res1*vv+nu,N0+res1*nv+uu,N0+res1*vv+uu));
      faces.insert(CImg<tf>::vector(N0+res1*vv+nu,N0+res1*nv+nu,N0+res1*nv+uu));
      colors.insert(CImg<tc>::vector(r,g,b));
      colors.insert(CImg<tc>::vector(r,g,b));
    }
  for (unsigned int uu=0; uu<res1; uu++) {
    const int nu = (uu+1)%res1;
    faces.insert(CImg<tf>::vector(N0+nu,N0+uu,N1));
    faces.insert(CImg<tf>::vector(N0+res1*(res2-2)+nu, N1+1,N0+res1*(res2-2)+uu));
    colors.insert(CImg<tc>::vector(r,g,b));
    colors.insert(CImg<tc>::vector(r,g,b));
  }
}

// Insert a fiber in a CImg 3D scene
//-----------------------------------
template<typename T,typename te,typename tp, typename tf, typename tc>
void insert_fiber(const CImg<T>& fiber, const CImg<te>& eigen, const CImg<tc>& palette,
		  const int xm, const int ym, const int zm,
		  const float vx, const float vy, const float vz,
		  CImgList<tp>& points, CImgList<tf>& primitives, CImgList<tc>& colors) {
  const int N0 = points.size;
  float x0 = fiber(0,0), y0 = fiber(0,1), z0 = fiber(0,2), fa0 = eigen.linear_pix3d(x0,y0,z0,12);
  points.insert(CImg<>::vector(vx*(x0-xm),vy*(y0-ym),vz*(z0-zm)));
  for (unsigned int l=1; l<fiber.width; l++) {
    float x1 = fiber(l,0), y1 = fiber(l,1), z1 = fiber(l,2), fa1 = eigen.linear_pix3d(x1,y1,z1,12);
    points.insert(CImg<tp>::vector(vx*(x1-xm),vy*(y1-ym),vz*(z1-zm)));
    primitives.insert(CImg<tf>::vector(N0+l-1,N0+l));
    const unsigned char
      icol = (unsigned char)(fa0*255),
      r = palette(icol,0),
      g = palette(icol,1),
      b = palette(icol,2);
    colors.insert(CImg<unsigned char>::vector(r,g,b));
    x0=x1; y0=y1; z0=z1; fa0=fa1;
  }
}

// Compute fiber tracking using 4th-order Runge Kutta integration
//-----------------------------------------------------------------
template<typename T>
CImg<> get_fibertrack(CImg<T>& eigen,
		      const int X0, const int Y0, const int Z0, const float lmax=100,
		      const float dl = 0.1f, const float FAmin=0.7f, const float cmin=0.5f) {

#define align_eigen(i,j,k) \
      { T &u = eigen(i,j,k,3), &v = eigen(i,j,k,4), &w = eigen(i,j,k,5); \
        if (u*cu+v*cv+w*cw<0) { u=-u; v=-v; w=-w; }}

  CImgList<> resf;

  // Forward tracking
  float normU = 0, normpU = 0, l = 0, X = (float)X0, Y = (float)Y0, Z = (float)Z0;
  T
    pu = eigen(X0,Y0,Z0,3),
    pv = eigen(X0,Y0,Z0,4),
    pw = eigen(X0,Y0,Z0,5);
  normpU = (float)std::sqrt(pu*pu+pv*pv+pw*pw);
  bool stopflag = false;

  while (!stopflag) {
    if (X<0 || X>eigen.dimx()-1 || Y<0 || Y>eigen.dimy()-1 || Z<0 || Z>eigen.dimz()-1 ||
	eigen((int)X,(int)Y,(int)Z,12)<FAmin || l>lmax) stopflag = true;
    else {
      resf.insert(CImg<>::vector(X,Y,Z));

      const int
	cx = (int)X, px = (cx-1<0)?0:cx-1, nx = (cx+1>=eigen.dimx())?eigen.dimx()-1:cx+1,
	cy = (int)Y, py = (cy-1<0)?0:cy-1, ny = (cy+1>=eigen.dimy())?eigen.dimy()-1:cy+1,
	cz = (int)Z, pz = (cz-1<0)?0:cz-1, nz = (cz+1>=eigen.dimz())?eigen.dimz()-1:cz+1;
      const T cu = eigen(cx,cy,cz,3), cv = eigen(cx,cy,cz,4), cw = eigen(cx,cy,cz,5);

      align_eigen(px,py,pz); align_eigen(cx,py,pz); align_eigen(nx,py,pz);
      align_eigen(px,cy,pz); align_eigen(cx,cy,pz); align_eigen(nx,cy,pz);
      align_eigen(px,ny,pz); align_eigen(cx,ny,pz); align_eigen(nx,ny,pz);
      align_eigen(px,py,cz); align_eigen(cx,py,cz); align_eigen(nx,py,cz);
      align_eigen(px,cy,cz);                        align_eigen(nx,cy,cz);
      align_eigen(px,ny,cz); align_eigen(cx,ny,cz); align_eigen(nx,ny,cz);
      align_eigen(px,py,nz); align_eigen(cx,py,nz); align_eigen(nx,py,nz);
      align_eigen(px,cy,nz); align_eigen(cx,cy,nz); align_eigen(nx,cy,nz);
      align_eigen(px,ny,nz); align_eigen(cx,ny,nz); align_eigen(nx,ny,nz);

      const T
	u0 = 0.5f*dl*eigen.linear_pix3d(X,Y,Z,3),
	v0 = 0.5f*dl*eigen.linear_pix3d(X,Y,Z,4),
	w0 = 0.5f*dl*eigen.linear_pix3d(X,Y,Z,5),
	u1 = 0.5f*dl*eigen.linear_pix3d(X+u0,Y+v0,Z+w0,3),
	v1 = 0.5f*dl*eigen.linear_pix3d(X+u0,Y+v0,Z+w0,4),
	w1 = 0.5f*dl*eigen.linear_pix3d(X+u0,Y+v0,Z+w0,5),
	u2 = 0.5f*dl*eigen.linear_pix3d(X+u1,Y+v1,Z+w1,3),
	v2 = 0.5f*dl*eigen.linear_pix3d(X+u1,Y+v1,Z+w1,4),
	w2 = 0.5f*dl*eigen.linear_pix3d(X+u1,Y+v1,Z+w1,5),
	u3 = 0.5f*dl*eigen.linear_pix3d(X+u2,Y+v2,Z+w2,3),
	v3 = 0.5f*dl*eigen.linear_pix3d(X+u2,Y+v2,Z+w2,4),
	w3 = 0.5f*dl*eigen.linear_pix3d(X+u2,Y+v2,Z+w2,5);
      T
	u = u0/3 + 2*u1/3 + 2*u2/3 + u3/3,
	v = v0/3 + 2*v1/3 + 2*v2/3 + v3/3,
	w = w0/3 + 2*w1/3 + 2*w2/3 + w3/3;
      if (u*pu+v*pv+w*pw<0) { u=-u; v=-v; w=-w; }
      normU = (float)std::sqrt(u*u+v*v+w*w);
      const float scal = (u*pu+v*pv+w*pw)/(normU*normpU);
      if (scal<cmin) stopflag=true;

      X+=(pu=u); Y+=(pv=v); Z+=(pw=w);
      normpU = normU;
      l+=dl;
    }
  }

  // Backward tracking
  l = dl; X = (float)X0; Y = (float)Y0; Z = (float)Z0;
  pu = eigen(X0,Y0,Z0,3);
  pv = eigen(X0,Y0,Z0,4);
  pw = eigen(X0,Y0,Z0,5);
  normpU = (float)std::sqrt(pu*pu+pv*pv+pw*pw);
  stopflag = false;

  while (!stopflag) {
    if (X<0 || X>eigen.dimx()-1 || Y<0 || Y>eigen.dimy()-1 || Z<0 || Z>eigen.dimz()-1 ||
	eigen((int)X,(int)Y,(int)Z,12)<FAmin || l>lmax) stopflag = true;
    else {

      const int
	cx = (int)X, px = (cx-1<0)?0:cx-1, nx = (cx+1>=eigen.dimx())?eigen.dimx()-1:cx+1,
	cy = (int)Y, py = (cy-1<0)?0:cy-1, ny = (cy+1>=eigen.dimy())?eigen.dimy()-1:cy+1,
	cz = (int)Z, pz = (cz-1<0)?0:cz-1, nz = (cz+1>=eigen.dimz())?eigen.dimz()-1:cz+1;
      const T cu = eigen(cx,cy,cz,3), cv = eigen(cx,cy,cz,4), cw = eigen(cx,cy,cz,5);

      align_eigen(px,py,pz); align_eigen(cx,py,pz); align_eigen(nx,py,pz);
      align_eigen(px,cy,pz); align_eigen(cx,cy,pz); align_eigen(nx,cy,pz);
      align_eigen(px,ny,pz); align_eigen(cx,ny,pz); align_eigen(nx,ny,pz);
      align_eigen(px,py,cz); align_eigen(cx,py,cz); align_eigen(nx,py,cz);
      align_eigen(px,cy,cz);                        align_eigen(nx,cy,cz);
      align_eigen(px,ny,cz); align_eigen(cx,ny,cz); align_eigen(nx,ny,cz);
      align_eigen(px,py,nz); align_eigen(cx,py,nz); align_eigen(nx,py,nz);
      align_eigen(px,cy,nz); align_eigen(cx,cy,nz); align_eigen(nx,cy,nz);
      align_eigen(px,ny,nz); align_eigen(cx,ny,nz); align_eigen(nx,ny,nz);

      const T
	u0 = 0.5f*dl*eigen.linear_pix3d(X,Y,Z,3),
	v0 = 0.5f*dl*eigen.linear_pix3d(X,Y,Z,4),
	w0 = 0.5f*dl*eigen.linear_pix3d(X,Y,Z,5),
	u1 = 0.5f*dl*eigen.linear_pix3d(X+u0,Y+v0,Z+w0,3),
	v1 = 0.5f*dl*eigen.linear_pix3d(X+u0,Y+v0,Z+w0,4),
	w1 = 0.5f*dl*eigen.linear_pix3d(X+u0,Y+v0,Z+w0,5),
	u2 = 0.5f*dl*eigen.linear_pix3d(X+u1,Y+v1,Z+w1,3),
	v2 = 0.5f*dl*eigen.linear_pix3d(X+u1,Y+v1,Z+w1,4),
	w2 = 0.5f*dl*eigen.linear_pix3d(X+u1,Y+v1,Z+w1,5),
	u3 = 0.5f*dl*eigen.linear_pix3d(X+u2,Y+v2,Z+w2,3),
	v3 = 0.5f*dl*eigen.linear_pix3d(X+u2,Y+v2,Z+w2,4),
	w3 = 0.5f*dl*eigen.linear_pix3d(X+u2,Y+v2,Z+w2,5);
      T
	u = u0/3 + 2*u1/3 + 2*u2/3 + u3/3,
	v = v0/3 + 2*v1/3 + 2*v2/3 + v3/3,
	w = w0/3 + 2*w1/3 + 2*w2/3 + w3/3;
      if (u*pu+v*pv+w*pw<0) { u=-u; v=-v; w=-w; }
      normU = (float)std::sqrt(u*u+v*v+w*w);
      const float scal = (u*pu+v*pv+w*pw)/(normU*normpU);
      if (scal<cmin) stopflag=true;

      X-=(pu=u); Y-=(pv=v); Z-=(pw=w);
      normpU=normU;
      l+=dl;

      resf.insert(CImg<>::vector(X,Y,Z),0);
    }
  }

  return resf.get_append('x');
}

// Main procedure
//----------------
int main(int argc,char **argv) {

  // Read and init data
  //--------------------
  cimg_usage("A viewer of Diffusion-Tensor MRI volumes.");