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ES-DE/external/CImg/examples/dtmri_view3d.cpp

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Squashed 'external/CImg/' content from commit c0becdf8 git-subtree-dir: external/CImg git-subtree-split: c0becdf881b0f3e2445975cac01c2422170d1fd9
2021-06-07 20:08:20 +00:00
/*
#
# 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 Tschumperlé
# ( 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> sel = coloredFA.get_select(disp,2,XYZ);
int xm, ym, zm, xM, yM, zM;
if (!disp.key()) { xm = sel[0]; ym = sel[1]; zm = sel[2]; xM = sel[3]; yM = sel[4]; zM = sel[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> sel = coloredFA.get_select(disp,2,XYZ);
const unsigned int N = fibers.size();
for (int z = sel[2]; z<=sel[5]; ++z)
for (int y = sel[1]; y<=sel[4]; ++y)
for (int x = sel[0]; x<=sel[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> sel = coloredFA.get_select(disp,2,XYZ);
std::fprintf(stderr," Select ending region."); std::fflush(stderr);
const CImg<int> nsel = coloredFA.get_select(disp,2,XYZ);
const unsigned int N = fibers.size();
// Track from start to end
for (int z = sel[2]; z<=sel[5]; ++z)
for (int y = sel[1]; y<=sel[4]; ++y)
for (int x = sel[0]; x<=sel[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>=nsel[0] && fx<=nsel[3] &&
fy>=nsel[1] && fy<=nsel[4] &&
fz>=nsel[2] && fz<=nsel[5]) valid_fiber = true;
}
if (valid_fiber) fibers.insert(fiber);
}
}
// Track from end to start
for (int z = nsel[2]; z<=nsel[5]; ++z)
for (int y = nsel[1]; y<=nsel[4]; ++y)
for (int x = nsel[0]; x<=nsel[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>=sel[0] && fx<=sel[3] &&
fy>=sel[1] && fy<=sel[4] &&
fz>=sel[2] && fz<=sel[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;
}
Reference in a new issue Copy permalink