void _volume2Sample(svm_model *model, volume<float> &volSample, volume<float> &mask, int sampleSize, float minValue, svm_node * &sample) { sample=(struct svm_node *) malloc((sampleSize+1)*sizeof(struct svm_node)); int i=0; for(int z=0; z < volSample.zsize();z++) for(int y=0; y < volSample.ysize();y++) for(int x=0; x < volSample.xsize();x++) if (mask.value(x,y,z) > minValue) { sample[i].index = (i+1); sample[i].value = volSample.value(x,y,z); i++; } sample[i].index = -1; }
// calculates the mean for each roi void RoiMeanCalculation::calculateMeans(volume<float> &actualvolume) { if (means.size()) { for (int i = 0; i < means.size(); i++) means[i] = 0; for (int z = 0; z < reference.zsize(); z++) for (int y = 0; y < reference.ysize(); y++) for (int x = 0; x < reference.xsize(); x++) { float value = reference.value(x, y, z); if (value != 0) { int idx = mapping[value]; if (idx >= -1) means[idx] += actualvolume.value(x, y, z); } } for (int i = 0; i < means.size(); i++) { if (counts[i]) means[i] = means[i] / (float)counts[i]; } } }
// transforms a 4D Volume in a SVM samples file, based on a mask void saveSVMFile(volume4D <float> &volSamples, volume<float> &mask, const char *outputFileName, float minValue, vector <int > &indexes, vector <int> &classes) { FILE *f; f = fopen(outputFileName, "wt+"); if (f != NULL) { int i, t; for (int h = 0; h < indexes.size(); h++) { // picking the right indexes t = indexes[h] - 1; i = 0; // saving the class value. Remember indexes size is different from classes. classes has the same sime of the number of volumes fprintf(f, "%d ", classes[t]); for (int z = 0; z < mask.zsize(); z++) for (int y = 0; y < mask.ysize(); y++) for (int x = 0; x < mask.xsize(); x++) if (mask.value(x, y, z) > minValue) { i++; // writing each voxel value in svm format fprintf(f, "%d:%f ", i, volSamples.value(x, y, z, t)); } fprintf(f, "\n"); } fclose(f); } }
// returns in `output` the best voxels of `region` void RegionExtraction::regionBestVoxels(RoiMeanCalculation &reference, volume<float>&values, volume<float>&output, int region, int regionSize, float percentage) { vector<roiPoint> roi; roi.resize(regionSize); greaterRoiPoint greaterFirst; int index=0; // Filter the voxels of the region `region` for(int z=0;z<values.zsize();z++) for(int y=0;y<values.ysize();y++) for(int x=0;x<values.xsize();x++) { // get the voxel intensity in reference int voxelRegion = (int) reference.voxelValues(x,y,z); // if is the chosen region, records the voxel values (T values or other voxel value) if (region == voxelRegion) { roi[index].value = values.value(x,y,z); roi[index].roiValue = region; roi[index].x=x; roi[index].y=y; roi[index].z=z; index++; } else values.value(x,y,z)=(float)0.0; } // sorts the vector of values in descending order std::sort(roi.begin(), roi.end(), greaterFirst); // calculates the cut Index. Remember the voxels descending order int cutIndex = (int) (roi.size() * percentage + 0.5); // recording the result in `output` for (int j=0; j<=cutIndex;j++) { output.value(roi[j].x, roi[j].y, roi[j].z) = roi[j].roiValue; } }
// transforms an array in a volume void array2Volume(const char *maskFile, float minValue, vector <double> &weightVector, volume<float> &weightVolume) { volume<float> mask; if (maskFile != NULL) { string Maskfile = maskFile; read_volume(mask, Maskfile); } weightVolume.reinitialize(mask.xsize(), mask.ysize(), mask.zsize(), 0, true); weightVolume.copyproperties(mask); int i = 0; for(int z=0;z < mask.zsize();z++) for(int y=0;y < mask.ysize();y++) for(int x=0;x < mask.xsize();x++) if (mask.value(x,y,z) > minValue) { weightVolume.value(x,y,z) = (float) weightVector[i]; i++; } else weightVolume.value(x,y,z) = (float) 0.0; }
volume<float> inside_mesh(const volume<float> & image, const Mesh& m) { volume<float> res = image; int xsize = image.xsize(); int ysize = image.ysize(); int zsize = image.zsize(); volume<short> inside = make_mask_from_mesh(image, m); for (int k=0; k<zsize; k++) for (int j=0; j<ysize; j++) for (int i=0; i<xsize; i++) res.value(i, j, k) = (1-inside.value(i, j, k)) * image.value(i, j, k); return res; }
double step_of_computation(const volume<float> & image, Mesh & m, const double bet_main_parameter, const int pass, const double increase_smoothing, const int iteration_number, double & l, const double t2, const double tm, const double t, const double E,const double F, const double zcog, const double radius, const double local_th=0., const int d1=7, const int d2=3){ double xdim = image.xdim(); double ydim = image.ydim(); double zdim = image.zdim(); if (iteration_number==50 || iteration_number%100 == 0 ) { l = 0; int counter = 0; for (vector<Mpoint*>::iterator i = m._points.begin(); i!=m._points.end(); i++ ) { counter++; l += (*i)->medium_distance_of_neighbours(); } l/=counter; } for (vector<Mpoint*>::iterator i = m._points.begin(); i!=m._points.end(); i++) { Vec sn, st, u1, u2, u3, u; double f2, f3=0; Vec n = (*i)->local_normal(); Vec dv = (*i)->difference_vector(); double tmp = dv|n; sn = n * tmp; st = dv - sn; u1 = st*.5; double rinv = (2 * fabs(sn|n))/(l*l); f2 = (1+tanh(F*(rinv - E)))*0.5; if (pass > 0) if (tmp > 0) { f2*=increase_smoothing; f2 = Min(f2, 1.); } u2 = f2 * sn; //main term of bet { double local_t = bet_main_parameter; if (local_th != 0.0) { local_t = Min(1., Max(0., bet_main_parameter + local_th*((*i)->get_coord().Z - zcog)/radius)); } double Imin = tm; double Imax = t; Pt p = (*i)->get_coord() + (-1)*n; double iv = p.X/xdim + .5, jv = p.Y/ydim +.5, kv = p.Z/zdim +.5; if (image.in_bounds((int)iv,(int) jv,(int) kv)) { double im=image.value((int)iv,(int)jv,(int)kv); Imin = Min(Imin, im); Imax = Max(Imax,im); double nxv=n.X/xdim, nyv=n.Y/ydim, nzv=n.Z/zdim; int i2=(int)(iv-(d1-1)*nxv), j2 =(int) (jv-(d1-1)*nyv), k2 =(int)(kv-(d1-1)*nzv); if (image.in_bounds(i2, j2, k2)) { im=image.value(i2,j2,k2); Imin = Min(Imin, im); for (int gi=2; gi<d1; gi++) { // the following is a quick calc of Pt p = (*i)->get_coord() + (-gi)*n; iv-=nxv; jv-=nyv; kv-=nzv; im = image.value((int) (iv), (int) (jv), (int) (kv)); Imin = Min(Imin, im); if (gi<d2) Imax = Max(Imax,im); } Imin = Max (t2, Imin); Imax = Min (tm, Imax); const double tl = (Imax - t2) * local_t + t2; if (Imax - t2 > 0) f3=2*(Imin - tl)/(Imax - t2); else f3=(Imin - tl)*2; } } } f3 *= (normal_max_update_fraction * lambda_fit * l); u3 = f3 * n; u = u1 + u2 + u3; //cout<<"l "<<l<<"u1 "<<((u1*n).norm())<<"u2 "<<(u2|n)<<"u3 "<<(u3|n)<<endl; (*i)->_update_coord = (*i)->get_coord() + u; } m.update(); return (0); }
bet_parameters adjust_initial_mesh(const volume<float> & image, Mesh& m, const double & rad = 0., const double xpara=0., const double ypara=0., const double zpara=0.) { bet_parameters bp; double xdim = image.xdim(); double ydim = image.ydim(); double zdim = image.zdim(); double t2, t98, t; //computing t2 && t98 // cout<<"computing robust min && max begins"<<endl; bp.min = image.min(); bp.max = image.max(); t2 = image.robustmin(); t98 = image.robustmax(); //t2=32.; //t98=16121.; // cout<<"computing robust min && max ends"<<endl; t = t2 + .1*(t98 - t2); bp.t98 = t98; bp.t2 = t2; bp.t = t; // cout<<"t2 "<<t2<<" t98 "<<t98<<" t "<<t<<endl; // cout<<"computing center && radius begins"<<endl; //finds the COG Pt center(0, 0, 0); double counter = 0; if (xpara == 0. & ypara==0. & zpara==0.) { double tmp = t - t2; for (int k=0; k<image.zsize(); k++) for (int j=0; j<image.ysize(); j++) for (int i=0; i<image.xsize(); i++) { double c = image(i, j, k ) - t2; if (c > tmp) { c = min(c, t98 - t2); counter+=c; center += Pt(c*i*xdim, c*j*ydim, c*k*zdim); } } center=Pt(center.X/counter, center.Y/counter, center.Z/counter); //cout<<counter<<endl; // cout<<"cog "<<center.X<<" "<<center.Y<<" "<<center.Z<<endl; } else center=Pt(xpara, ypara, zpara); bp.cog = center; if (rad == 0.) { double radius=0; counter=0; double scale=xdim*ydim*zdim; for (int k=0; k<image.zsize(); k++) for (int j=0; j<image.ysize(); j++) for (int i=0; i<image.xsize(); i++) { double c = image(i, j, k); if (c > t) { counter+=1; } } radius = pow (.75 * counter*scale/M_PI, 1.0/3.0); // cout<<radius<<endl; bp.radius = radius; } else (bp.radius = rad); m.translation(center.X, center.Y, center.Z); m.rescale (bp.radius/2, center); // cout<<"computing center && radius ends"<<endl; //computing tm // cout<<"computing tm begins"<<endl; vector<double> vm; for (int k=0; k<image.zsize(); k++) for (int j=0; j<image.ysize(); j++) for (int i=0; i<image.xsize(); i++) { double d = image.value(i, j, k); Pt p(i*xdim, j*ydim, k*zdim); if (d > t2 && d < t98 && ((p - center)|(p - center)) < bp.radius * bp.radius) vm.push_back(d); } int med = (int) floor(vm.size()/2.); // cout<<"before sort"<<endl; nth_element(vm.begin(), vm.begin() + med - 1, vm.end()); //partial_sort(vm.begin(), vm.begin() + med + 1, vm.end()); //double tm = vm[med]; double tm=(*max_element(vm.begin(), vm.begin() + med)); // cout<<"tm "<<tm<<endl; bp.tm = tm; // cout<<"computing tm ends"<<endl; return bp; }