Squashed 'third_party/cimg/' content from commit 4b66369
Change-Id: I7454d9107a08dba899fd4659731733049165ae0a
git-subtree-dir: third_party/cimg
git-subtree-split: 4b66369ab4e34a46119d6c43e9adce061bb40f4b
diff --git a/examples/dtmri_view3d.cpp b/examples/dtmri_view3d.cpp
new file mode 100644
index 0000000..e0420955
--- /dev/null
+++ b/examples/dtmri_view3d.cpp
@@ -0,0 +1,562 @@
+/*
+ #
+ # File : dtmri_view3d.cpp
+ # ( C++ source file )
+ #
+ # Description : A viewer of Diffusion-Tensor MRI volumes (medical imaging).
+ # This file is a part of the CImg Library project.
+ # ( http://cimg.eu )
+ #
+ # Copyright : David Tschumperle
+ # ( http://tschumperle.users.greyc.fr/ )
+ #
+ # License : CeCILL v2.0
+ # ( http://www.cecill.info/licences/Licence_CeCILL_V2-en.html )
+ #
+ # This software is governed by the CeCILL 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
+ # 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 license and that you accept its terms.
+ #
+*/
+
+#include "CImg.h"
+using namespace cimg_library;
+#undef min
+#undef max
+
+// 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
+ 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)std::min(30 + 1.5f*cimg::abs(255*fa*tensor[3]),255.0f),
+ g = (int)std::min(30 + 1.5f*cimg::abs(255*fa*tensor[4]),255.0f),
+ b = (int)std::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((tc)r,(tc)g,(tc)b));
+ colors.insert(CImg<tc>::vector((tc)r,(tc)g,(tc)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((tc)r,(tc)g,(tc)b));
+ colors.insert(CImg<tc>::vector((tc)r,(tc)g,(tc)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_atXYZ(x0,y0,z0,12);
+ points.insert(CImg<>::vector(vx*(x0 -xm),vy*(y0 - ym),vz*(z0 - zm)));
+ for (int l = 1; l<fiber.width(); ++l) {
+ float x1 = fiber(l,0), y1 = fiber(l,1), z1 = fiber(l,2), fa1 = eigen.linear_atXYZ(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.width() - 1 || Y<0 || Y>eigen.height() - 1 || Z<0 || Z>eigen.depth() - 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.width())?eigen.width() - 1:cx + 1,
+ cy = (int)Y, py = (cy - 1<0)?0:cy - 1, ny = (cy + 1>=eigen.height())?eigen.height() - 1:cy + 1,
+ cz = (int)Z, pz = (cz - 1<0)?0:cz - 1, nz = (cz + 1>=eigen.depth())?eigen.depth() - 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_atXYZ(X,Y,Z,3),
+ v0 = 0.5f*dl*eigen.linear_atXYZ(X,Y,Z,4),
+ w0 = 0.5f*dl*eigen.linear_atXYZ(X,Y,Z,5),
+ u1 = 0.5f*dl*eigen.linear_atXYZ(X + u0,Y + v0,Z + w0,3),
+ v1 = 0.5f*dl*eigen.linear_atXYZ(X + u0,Y + v0,Z + w0,4),
+ w1 = 0.5f*dl*eigen.linear_atXYZ(X + u0,Y + v0,Z + w0,5),
+ u2 = 0.5f*dl*eigen.linear_atXYZ(X + u1,Y + v1,Z + w1,3),
+ v2 = 0.5f*dl*eigen.linear_atXYZ(X + u1,Y + v1,Z + w1,4),
+ w2 = 0.5f*dl*eigen.linear_atXYZ(X + u1,Y + v1,Z + w1,5),
+ u3 = 0.5f*dl*eigen.linear_atXYZ(X + u2,Y + v2,Z + w2,3),
+ v3 = 0.5f*dl*eigen.linear_atXYZ(X + u2,Y + v2,Z + w2,4),
+ w3 = 0.5f*dl*eigen.linear_atXYZ(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.width() - 1 || Y<0 || Y>eigen.height() - 1 || Z<0 || Z>eigen.depth() - 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.width())?eigen.width() - 1:cx + 1,
+ cy = (int)Y, py = (cy - 1<0)?0:cy - 1, ny = (cy + 1>=eigen.height())?eigen.height() - 1:cy + 1,
+ cz = (int)Z, pz = (cz - 1<0)?0:cz - 1, nz = (cz + 1>=eigen.depth())?eigen.depth() - 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_atXYZ(X,Y,Z,3),
+ v0 = 0.5f*dl*eigen.linear_atXYZ(X,Y,Z,4),
+ w0 = 0.5f*dl*eigen.linear_atXYZ(X,Y,Z,5),
+ u1 = 0.5f*dl*eigen.linear_atXYZ(X + u0,Y + v0,Z + w0,3),
+ v1 = 0.5f*dl*eigen.linear_atXYZ(X + u0,Y + v0,Z + w0,4),
+ w1 = 0.5f*dl*eigen.linear_atXYZ(X + u0,Y + v0,Z + w0,5),
+ u2 = 0.5f*dl*eigen.linear_atXYZ(X + u1,Y + v1,Z + w1,3),
+ v2 = 0.5f*dl*eigen.linear_atXYZ(X + u1,Y + v1,Z + w1,4),
+ w2 = 0.5f*dl*eigen.linear_atXYZ(X + u1,Y + v1,Z + w1,5),
+ u3 = 0.5f*dl*eigen.linear_atXYZ(X + u2,Y + v2,Z + w2,3),
+ v3 = 0.5f*dl*eigen.linear_atXYZ(X + u2,Y + v2,Z + w2,4),
+ w3 = 0.5f*dl*eigen.linear_atXYZ(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>'x';
+}
+
+// Main procedure
+//----------------
+int main(int argc,char **argv) {
+
+ // Read and init data
+ //--------------------
+ cimg_usage("A viewer of Diffusion-Tensor MRI volumes.");
+ const char *file_i = cimg_option("-i",(char*)0,"Input : Filename of tensor field (volume wxhxdx6)");
+ const char* vsize = cimg_option("-vsize","1x1x1","Input : Voxel aspect");
+ const bool normalize = cimg_option("-normalize",true,"Input : Enable tensor normalization");
+ const char *file_f = cimg_option("-f",(char*)0,"Input : Input fibers\n");
+ const float dl = cimg_option("-dl",0.5f,"Fiber computation : Integration step");
+ const float famin = cimg_option("-famin",0.3f,"Fiber computation : Fractional Anisotropy threshold");
+ const float cmin = cimg_option("-cmin",0.2f,"Fiber computation : Curvature threshold");
+ const float lmin = cimg_option("-lmin",10.0f,"Fiber computation : Minimum length\n");
+ const float lmax = cimg_option("-lmax",1000.0f,"Fiber computation : Maximum length\n");
+ const float tfact = cimg_option("-tfact",1.2f,"Display : Tensor size factor");
+ const char *bgcolor = cimg_option("-bg","0,0,0","Display : Background color");
+ unsigned int bgr = 0, bgg = 0, bgb = 0;
+ std::sscanf(bgcolor,"%u%*c%u%*c%u",&bgr,&bgg,&bgb);
+
+ CImg<> tensors;
+ if (file_i) {
+ std::fprintf(stderr,"\n- Loading tensors '%s'",cimg::basename(file_i));
+ tensors.load(file_i);
+ } else {
+ // Create a synthetic tensor field here
+ std::fprintf(stderr,"\n- No input files : Creating a synthetic tensor field");
+ tensors.assign(32,32,32,6);
+ cimg_forXYZ(tensors,x,y,z) {
+ const float
+ u = x - tensors.width()/2.0f,
+ v = y - tensors.height()/2.0f,
+ w = z - tensors.depth()/2.0f,
+ norm = (float)std::sqrt(1e-5f + u*u + v*v + w*w),
+ nu = u/norm, nv = v/norm, nw = w/norm;
+ const CImg<>
+ dir1 = CImg<>::vector(nu,nv,nw),
+ dir2 = CImg<>::vector(-nv,nu,nw),
+ dir3 = CImg<>::vector(nw*(nv - nu),-nw*(nu + nv),nu*nu + nv*nv);
+ tensors.set_tensor_at(2.0*dir1*dir1.get_transpose() +
+ 1.0*dir2*dir2.get_transpose() +
+ 0.7*dir3*dir3.get_transpose(),
+ x,y,z);
+ }
+ }
+ float voxw = 1, voxh = 1, voxd = 1;
+ std::sscanf(vsize,"%f%*c%f%*c%f",&voxw,&voxh,&voxd);
+
+ std::fprintf(stderr," : %ux%ux%u image, voxsize=%gx%gx%g.",
+ tensors.width(),tensors.height(),tensors.depth(),
+ voxw,voxh,voxd);
+
+ CImgList<> fibers;
+ if (file_f) {
+ std::fprintf(stderr,"\n- Loading fibers '%s'.",cimg::basename(file_f));
+ fibers.load(file_f);
+ }
+
+ const CImg<unsigned char> fiber_palette =
+ CImg<>(2,1,1,3).fill(200,255,0,255,0,200).RGBtoHSV().resize(256,1,1,3,3).HSVtoRGB();
+
+ // Compute eigen elements
+ //------------------------
+ std::fprintf(stderr,"\n- Compute eigen elements.");
+ CImg<unsigned char> coloredFA(tensors.width(),tensors.height(),tensors.depth(),3);
+ CImg<> eigen(tensors.width(),tensors.height(),tensors.depth(),13);
+ CImg<> val,vec;
+ float eigmax = 0;
+ cimg_forXYZ(tensors,x,y,z) {
+ tensors.get_tensor_at(x,y,z).symmetric_eigen(val,vec);
+ eigen(x,y,z,0) = val[0]; eigen(x,y,z,1) = val[1]; eigen(x,y,z,2) = val[2];
+ if (val[0]<0) val[0] = 0;
+ if (val[1]<0) val[1] = 0;
+ if (val[2]<0) val[2] = 0;
+ if (val[0]>eigmax) eigmax = val[0];
+ eigen(x,y,z,3) = vec(0,0); eigen(x,y,z,4) = vec(0,1); eigen(x,y,z,5) = vec(0,2);
+ eigen(x,y,z,6) = vec(1,0); eigen(x,y,z,7) = vec(1,1); eigen(x,y,z,8) = vec(1,2);
+ eigen(x,y,z,9) = vec(2,0); eigen(x,y,z,10) = vec(2,1); eigen(x,y,z,11) = vec(2,2);
+ const float fa = get_FA(val[0],val[1],val[2]);
+ eigen(x,y,z,12) = fa;
+ const int
+ r = (int)std::min(255.0f,1.5f*cimg::abs(255*fa*vec(0,0))),
+ g = (int)std::min(255.0f,1.5f*cimg::abs(255*fa*vec(0,1))),
+ b = (int)std::min(255.0f,1.5f*cimg::abs(255*fa*vec(0,2)));
+ coloredFA(x,y,z,0) = (unsigned char)r;
+ coloredFA(x,y,z,1) = (unsigned char)g;
+ coloredFA(x,y,z,2) = (unsigned char)b;
+ }
+ tensors.assign();
+ std::fprintf(stderr,"\n- Maximum diffusivity = %g, Maximum FA = %g",eigmax,eigen.get_shared_channel(12).max());
+ if (normalize) {
+ std::fprintf(stderr,"\n- Normalize tensors.");
+ eigen.get_shared_channels(0,2)/=eigmax;
+ }
+
+ // Init display and begin user interaction
+ //-----------------------------------------
+ std::fprintf(stderr,"\n- Open user window.");
+ CImgDisplay disp(256,256,"DTMRI Viewer",0);
+ CImgDisplay disp3d(800,600,"3D Local View",0,false,true);
+ unsigned int XYZ[3];
+ XYZ[0] = eigen.width()/2; XYZ[1] = eigen.height()/2; XYZ[2] = eigen.depth()/2;
+
+ while (!disp.is_closed() && !disp.is_keyQ() && !disp.is_keyESC()) {
+ const CImg<int> s = coloredFA.get_select(disp,2,XYZ);
+ if (!disp.is_closed()) switch (disp.key()) {
+
+ // Open 3D visualization window
+ //-----------------------------
+ case cimg::keyA :
+ case 0 : {
+ const unsigned char white[] = { 255 };
+ disp3d.display(CImg<unsigned char>(disp3d.width(),disp3d.height(),1,1,0).
+ draw_text(10,10,"Please wait...",white)).show();
+ int xm,ym,zm,xM,yM,zM;
+ if (!disp.key()) { xm = s[0]; ym = s[1]; zm = s[2]; xM = s[3]; yM = s[4]; zM = s[5]; }
+ else { xm = ym = zm = 0; xM = eigen.width() - 1; yM = eigen.height() - 1; zM = eigen.height() - 1; }
+ const CImg<> img = eigen.get_crop(xm,ym,zm,xM,yM,zM);
+ CImgList<> points;
+ CImgList<unsigned int> primitives;
+ CImgList<unsigned char> colors;
+
+ // Add ellipsoids to the 3D scene
+ int X = img.width()/2, Y = img.height()/2, Z = img.depth()/2;
+ cimg_forXY(img,x,y)
+ insert_ellipsoid(img.get_vector_at(x,y,Z),(float)x,(float)y,(float)Z,
+ tfact,voxw,voxh,voxd,points,primitives,colors,10,6);
+ cimg_forXZ(img,x,z)
+ insert_ellipsoid(img.get_vector_at(x,Y,z),(float)x,(float)Y,(float)z,
+ tfact,voxw,voxh,voxd,points,primitives,colors,10,6);
+ cimg_forYZ(img,y,z)
+ insert_ellipsoid(img.get_vector_at(X,y,z),(float)X,(float)y,(float)z,
+ tfact,voxw,voxh,voxd,points,primitives,colors,10,6);
+
+ // Add computed fibers to the 3D scene
+ const CImg<> veigen = eigen.get_crop(xm,ym,zm,xM,yM,zM);
+ cimglist_for(fibers,l) {
+ const CImg<>& fiber = fibers[l];
+ if (fiber.width()) insert_fiber(fiber,eigen,fiber_palette,
+ xm,ym,zm,voxw,voxh,voxd,
+ points,primitives,colors);
+ }
+
+ // Display 3D object
+ CImg<unsigned char> visu = CImg<unsigned char>(3,disp3d.width(),disp3d.height(),1,0).
+ fill((unsigned char)bgr,(unsigned char)bgg,(unsigned char)bgb).
+ permute_axes("yzcx");
+ bool stopflag = false;
+ while (!disp3d.is_closed() && !stopflag) {
+ const CImg<> pts = points>'x';
+ visu.display_object3d(disp3d,pts,primitives,colors,true,4,-1,false,800,0.05f,1.0f);
+ disp3d.close();
+ switch (disp3d.key()) {
+ case cimg::keyM : { // Create movie
+ std::fprintf(stderr,"\n- Movie mode.\n");
+ const unsigned int N = 256;
+ CImg<> cpts(pts);
+ const CImg<> x = pts.get_shared_row(0), y = pts.get_shared_row(1), z = pts.get_shared_row(2);
+ float
+ xm, xM = x.max_min(xm),
+ ym, yM = y.max_min(ym),
+ zm, zM = z.max_min(zm),
+ ratio = 2.0f*std::min(visu.width(),visu.height())/(3.0f*cimg::max(xM - xm,yM - ym,zM - zm)),
+ dx = 0.5f*(xM + xm), dy = 0.5f*(yM + ym), dz = 0.5f*(zM +zm);
+ cimg_forX(pts,l) {
+ cpts(l,0) = (pts(l,0) - dx)*ratio;
+ cpts(l,1) = (pts(l,1) - dy)*ratio;
+ cpts(l,2) = (pts(l,2) - dz)*ratio;
+ }
+
+ for (unsigned int i=0; i<N; i++) {
+ std::fprintf(stderr,"\r- Frame %u/%u.",i,N);
+ const float alpha = (float)(i*360/N);
+ const CImg<> rpts = CImg<>::rotation_matrix(0,1,0,alpha)*CImg<>::rotation_matrix(1,0,0,75)*cpts;
+ visu.fill(0).draw_object3d(visu.width()/2.0f,visu.height()/2.0f,-500.0f,rpts,primitives,colors,
+ 4,false,800.0f,visu.width()/2.0f,visu.height()/2.0f,-800.0f,0.05f,1.0f).
+ display(disp3d);
+ visu.save("frame.png",i);
+ }
+ visu.fill(0);
+ } break;
+ default: stopflag = true;
+ }
+ }
+ if (disp3d.is_fullscreen()) disp3d.toggle_fullscreen().resize(800,600).close();
+ } break;
+
+ // Compute region statistics
+ //---------------------------
+ case cimg::keyR : {
+ std::fprintf(stderr,"\n- Statistics computation. Select region."); std::fflush(stderr);
+ const CImg<int> s = coloredFA.get_select(disp,2,XYZ);
+ int xm, ym, zm, xM, yM, zM;
+ if (!disp.key()) { xm = s[0]; ym = s[1]; zm = s[2]; xM = s[3]; yM = s[4]; zM = s[5]; }
+ else { xm = ym = zm = 0; xM = eigen.width() - 1; yM = eigen.height() - 1; zM = eigen.height() - 1; }
+ const CImg<> img = eigen.get_crop(xm,ym,zm,xM,yM,zM);
+ std::fprintf(stderr,"\n- Mean diffusivity = %g, Mean FA = %g\n",
+ eigen.get_shared_channel(0).mean(),
+ eigen.get_shared_channel(12).mean());
+ } break;
+
+ // Track fiber bundle (single region)
+ //----------------------------------
+ case cimg::keyF : {
+ std::fprintf(stderr,"\n- Tracking mode (single region). Select starting region.\n"); std::fflush(stderr);
+ const CImg<int> s = coloredFA.get_select(disp,2,XYZ);
+ const unsigned int N = fibers.size();
+ for (int z=s[2]; z<=s[5]; z++)
+ for (int y=s[1]; y<=s[4]; y++)
+ for (int x=s[0]; x<=s[3]; x++) {
+ const CImg<> fiber = get_fibertrack(eigen,x,y,z,lmax,dl,famin,cmin);
+ if (fiber.width()>lmin) {
+ std::fprintf(stderr,"\rFiber %u : Starting from (%d,%d,%d)\t\t",fibers.size(),x,y,z);
+ fibers.insert(fiber);
+ }
+ }
+ std::fprintf(stderr,"\n- %u fiber(s) added (total %u).",fibers.size() - N,fibers.size());
+ } break;
+
+ // Track fiber bundle (double regions)
+ //------------------------------------
+ case cimg::keyG : {
+ std::fprintf(stderr,"\n- Tracking mode (double region). Select starting region."); std::fflush(stderr);
+ const CImg<int> s = coloredFA.get_select(disp,2,XYZ);
+ std::fprintf(stderr," Select ending region."); std::fflush(stderr);
+ const CImg<int> ns = coloredFA.get_select(disp,2,XYZ);
+ const unsigned int N = fibers.size();
+
+ // Track from start to end
+ for (int z = s[2]; z<=s[5]; ++z)
+ for (int y = s[1]; y<=s[4]; ++y)
+ for (int x = s[0]; x<=s[3]; ++x) {
+ const CImg<> fiber = get_fibertrack(eigen,x,y,z,lmax,dl,famin,cmin);
+ if (fiber.width()>lmin) {
+ bool valid_fiber = false;
+ cimg_forX(fiber,k) {
+ const int fx = (int)fiber(k,0), fy = (int)fiber(k,1), fz = (int)fiber(k,2);
+ if (fx>=ns[0] && fx<=ns[3] &&
+ fy>=ns[1] && fy<=ns[4] &&
+ fz>=ns[2] && fz<=ns[5]) valid_fiber = true;
+ }
+ if (valid_fiber) fibers.insert(fiber);
+ }
+ }
+
+ // Track from end to start
+ for (int z = ns[2]; z<=ns[5]; ++z)
+ for (int y = ns[1]; y<=ns[4]; ++y)
+ for (int x = ns[0]; x<=ns[3]; ++x) {
+ const CImg<> fiber = get_fibertrack(eigen,x,y,z,lmax,dl,famin,cmin);
+ if (fiber.width()>lmin) {
+ bool valid_fiber = false;
+ cimg_forX(fiber,k) {
+ const int fx = (int)fiber(k,0), fy = (int)fiber(k,1), fz = (int)fiber(k,2);
+ if (fx>=s[0] && fx<=s[3] &&
+ fy>=s[1] && fy<=s[4] &&
+ fz>=s[2] && fz<=s[5]) valid_fiber = true;
+ }
+ if (valid_fiber) {
+ std::fprintf(stderr,"\rFiber %u : Starting from (%d,%d,%d)\t\t",fibers.size(),x,y,z);
+ fibers.insert(fiber);
+ }
+ }
+ }
+
+ std::fprintf(stderr," %u fiber(s) added (total %u).",fibers.size() - N,fibers.size());
+ } break;
+
+ // Clear fiber bundle
+ //-------------------
+ case cimg::keyC : {
+ std::fprintf(stderr,"\n- Fibers removed.");
+ fibers.assign();
+ } break;
+
+ // Save fibers
+ //-------------
+ case cimg::keyS : {
+ fibers.save("fibers.cimg");
+ std::fprintf(stderr,"\n- Fibers saved.");
+ } break;
+
+ }
+ }
+
+ std::fprintf(stderr,"\n- Exit.\n\n\n");
+ return 0;
+}