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;
}
