// 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);
}
}
FnirtFileWriter::FnirtFileWriter(const string& fname,
const volume<float>& fieldx,
const volume<float>& fieldy,
const volume<float>& fieldz)
{
volume<float> tmp(fieldx.xsize(),fieldx.ysize(),fieldx.zsize());
tmp.copyproperties(fieldx);
Matrix aff = IdentityMatrix(4);
common_field_construction(fname,tmp,fieldx,fieldy,fieldz,aff);
}
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;
}
//calculates the mask from the mesh by spreading an initial point outside the mesh, and stopping it when the mesh is reached.
volume<short> make_mask_from_mesh(const volume<float> & image, const Mesh& m)
{
// cout<<"make_mask_from_mesh begins"<<endl;
double xdim = (double) image.xdim();
double ydim = (double) image.ydim();
double zdim = (double) image.zdim();
volume<short> mask;
copyconvert(image,mask);
int xsize = mask.xsize();
int ysize = mask.ysize();
int zsize = mask.zsize();
mask = 1;
mask = draw_mesh(mask, m);
vector<Pt> current;
current.clear();
Pt c(0., 0., 0.);
for (vector<Mpoint *>::const_iterator it=m._points.begin(); it!=m._points.end(); it++)
c+=(*it)->get_coord();
c*=(1./m._points.size());
c.X/=xdim; c.Y/=ydim; c.Z/=zdim;
current.push_back(c);
while (!current.empty())
{
Pt pc = current.back();
int x, y, z;
x=(int) pc.X; y=(int) pc.Y; z=(int) pc.Z;
//current.remove(pc);
current.pop_back();
mask.value(x, y, z) = 0;
if (0<=x-1 && mask.value(x-1, y, z)==1) current.push_back(Pt(x-1, y, z));
if (0<=y-1 && mask.value(x, y-1, z)==1) current.push_back(Pt(x, y-1, z));
if (0<=z-1 && mask.value(x, y, z-1)==1) current.push_back(Pt(x, y, z-1));
if (xsize>x+1 && mask.value(x+1, y, z)==1) current.push_back(Pt(x+1, y, z));
if (ysize>y+1 && mask.value(x, y+1, z)==1) current.push_back(Pt(x, y+1, z));
if (zsize>z+1 && mask.value(x, y, z+1)==1) current.push_back(Pt(x, y, z+1));
}
// cout<<"make_mask_from_mesh ends"<<endl;
return mask;
}
// 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];
}
}
}
//extracts profiles in the area around the eyes
vector<double> t1only_special_extract(const volume<float> & t1, const Pt & point, const Vec & n) {
vector<double> resul;
resul.clear();
bool output = true;
const double INNER_DEPTH = 3;
const double OUTER_DEPTH = 100;
Profile pt1;
for (double d = -INNER_DEPTH; d < OUTER_DEPTH; d+=.5)
{
Pt c = point + d * n;
double tmp1 = t1.interpolate(c.X, c.Y, c.Z);
pt1.add (d, tmp1);
}
pt1.init_roi();
//outer skin
double outskin = pt1.last_point_over(pt1.end(), .2);
double check = pt1.last_point_over(outskin - 1.5, .2);
if (outskin - check > 2) output = false;
pt1.set_rroi(outskin);
double inskull = pt1.next_point_under(-INNER_DEPTH, .25);
if (inskull > 5) inskull = 0;
double outskull = pt1.next_point_over(inskull, .35);
resul.push_back(inskull);
resul.push_back(outskull);
resul.push_back(outskin);
return resul;
}
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;
}
void draw_segment(volume<short>& image, const Pt& p1, const Pt& p2)
{
double xdim = (double) image.xdim();
double ydim = (double) image.ydim();
double zdim = (double) image.zdim();
double mininc = min(xdim,min(ydim,zdim)) * .5;
Vec n = p1 - p2;
double d = n.norm();
n.normalize();
for (double i=0; i<=d; i+=mininc)
{
Pt p = p2 + i* n;
image((int) floor((p.X)/xdim +.5),(int) floor((p.Y)/ydim +.5),(int) floor((p.Z)/zdim +.5)) = 1;
}
}
void draw_mesh(volume<short>& image, const Mesh &m)
{
double xdim = (double) image.xdim();
double ydim = (double) image.ydim();
double zdim = (double) image.zdim();
double mininc = min(xdim,min(ydim,zdim)) * .5;
for (list<Triangle*>::const_iterator i = m._triangles.begin(); i!=m._triangles.end(); i++)
{
Vec n = (*(*i)->get_vertice(0) - *(*i)->get_vertice(1));
double d = n.norm();
n.normalize();
for (double j=0; j<=d; j+=mininc)
{
Pt p = (*i)->get_vertice(1)->get_coord() + j* n;
draw_segment(image, p, (*i)->get_vertice(2)->get_coord());
}
}
}
void check_integral(fields &f,
linear_integrand_data &d, const volume &v,
component cgrid)
{
double x1 = v.in_direction_min(d.dx);
double x2 = v.in_direction_max(d.dx);
double y1 = v.in_direction_min(d.dy);
double y2 = v.in_direction_max(d.dy);
double z1 = v.in_direction_min(d.dz);
double z2 = v.in_direction_max(d.dz);
master_printf("Check %d-dim. %s integral in %s cell with %s integrand...",
(x2 - x1 > 0) + (y2 - y1 > 0) + (z2 - z1 > 0),
component_name(cgrid),
v.dim == D3 ? "3d" : (v.dim == D2 ? "2d" :
(v.dim == Dcyl ? "cylindrical"
: "1d")),
(d.c == 1.0 && !d.axy && !d.ax && !d.ay && !d.az
&& !d.axy && !d.ayz && !d.axz) ? "unit" : "linear");
if (0)
master_printf("\n... grid_volume (%g,%g,%g) at (%g,%g,%g) with integral (%g, %g,%g,%g, %g,%g,%g, %g)...\n",
x2 - x1, y2 - y1, z2 - z1,
(x1+x2)/2, (y1+y2)/2, (z1+z2)/2,
d.c, d.ax,d.ay,d.az, d.axy,d.ayz,d.axz, d.axyz);
double sum = real(f.integrate(0, 0, linear_integrand, (void *) &d, v));
if (fabs(sum - correct_integral(v, d)) > 1e-9 * fabs(sum))
abort("FAILED: %0.16g instead of %0.16g\n",
(double) sum, correct_integral(v, d));
master_printf("...PASSED.\n");
}
volume<float> draw_mesh_bis(const volume<float>& image, const Mesh &m)
{
double xdim = (double) image.xdim();
double ydim = (double) image.ydim();
double zdim = (double) image.zdim();
double mininc = min(xdim,min(ydim,zdim)) * .5;
volume<float> res = image;
double max = image.max();
for (list<Triangle*>::const_iterator i = m._triangles.begin(); i!=m._triangles.end(); i++)
{
Vec n = (*(*i)->get_vertice(0) - *(*i)->get_vertice(1));
double d = n.norm();
n.normalize();
for (double j=0; j<=d; j+=mininc)
{
Pt p = (*i)->get_vertice(1)->get_coord() + j* n;
draw_segment_bis(res, p, (*i)->get_vertice(2)->get_coord(), max);
}
}
return res;
}
// 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;
}
void vega::data::hexagonal_prismatic_lattice::fill_volume_cell( volume& v, const prismatic_hexagon_node & node )
{
static const int hex_pixel_offset[8][2] = { {1, 0}, {2, 0}, {0, 1}, {1, 1}, {2, 1}, {3, 1}, {1, 2}, {2, 2}};
math::vector3d vertex = node.get_vertex();
for(size_t h=0;h<8;++h)
{
math::vector3d pixel;
int xx = (int)vertex.x + hex_pixel_offset[h][0];
int yy = (int)vertex.y + hex_pixel_offset[h][1];
int zz = (int)vertex.z;
if( xx >= 0 && yy >= 0 && zz >= 0 && xx < v.get_width() && yy < v.get_height() && zz < v.get_depth() )
{
#ifndef USE_COLOR_MAP
v.set_voxel(xx, yy, zz, (voxel)(node.density * 255.f));
#else
v.set_voxel(xx, yy, zz, (voxel)(node.color.A));
#endif
}
}
}
void basisfield::AsVolume(volume<float>& vol, FieldIndex fi)
{
if (int(FieldSz_x()) != vol.xsize() || int(FieldSz_y()) != vol.ysize() || int(FieldSz_z()) != vol.zsize()) {
throw BasisfieldException("basisfield::AsVolume:: Matrix size mismatch beween field and volume");
}
if (Vxs_x() != vol.xdim() || Vxs_y() != vol.ydim() || Vxs_z() != vol.zdim()) {
throw BasisfieldException("basisfield::AsVolume:: Voxel size mismatch beween field and volume");
}
if (!coef) {throw BasisfieldException("basisfield::AsVolume: Coefficients undefined");}
if (!UpToDate(fi)) {Update(fi);}
const boost::shared_ptr<NEWMAT::ColumnVector> tmptr = Get(fi);
int vindx=0;
for (unsigned int k=0; k<FieldSz_z(); k++) {
for (unsigned int j=0; j<FieldSz_y(); j++) {
for (unsigned int i=0; i<FieldSz_x(); i++) {
vol(i,j,k) = tmptr->element(vindx++);
}
}
}
}
void basisfield::Set(const volume<float>& pfield)
{
if (int(FieldSz_x()) != pfield.xsize() || int(FieldSz_y()) != pfield.ysize() || int(FieldSz_z()) != pfield.zsize()) {
throw BasisfieldException("basisfield::Set:: Matrix size mismatch beween basisfield class and supplied field");
}
if (Vxs_x() != pfield.xdim() || Vxs_y() != pfield.ydim() || Vxs_z() != pfield.zdim()) {
throw BasisfieldException("basisfield::Set:: Voxel size mismatch beween basisfield class and supplied field");
}
volume<float> volume_of_ones(pfield.xsize(),pfield.ysize(),pfield.zsize());
volume_of_ones.copyproperties(pfield);
volume_of_ones = 1.0;
double lambda = 0.001;
ColumnVector y = Jte(pfield,0);
boost::shared_ptr<MISCMATHS::BFMatrix> XtX = JtJ(volume_of_ones);
boost::shared_ptr<MISCMATHS::BFMatrix> BeEn = BendEnergyHess();
XtX->AddToMe(*BeEn,lambda);
ColumnVector coef_roof = XtX->SolveForx(y,SYM_POSDEF,1e-6,500);
SetCoef(coef_roof);
}
// 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;
}
}
static double correct_integral(const volume &v,
const linear_integrand_data &data)
{
direction x = data.dx, y = data.dy, z = data.dz;
double x1 = v.in_direction_min(x);
double x2 = v.in_direction_max(x);
double y1 = v.in_direction_min(y);
double y2 = v.in_direction_max(y);
double z1 = v.in_direction_min(z);
double z2 = v.in_direction_max(z);
return (data.c * integral1(x1,x2,x) * integral1(y1,y2,y) * integral1(z1,z2,z)
+ data.ax * integralx(x1,x2,x) * integral1(y1,y2,y) * integral1(z1,z2,z)
+ data.ay * integral1(x1,x2,x) * integralx(y1,y2,y) * integral1(z1,z2,z)
+ data.az * integral1(x1,x2,x) * integral1(y1,y2,y) * integralx(z1,z2,z)
+ data.axy * integralx(x1,x2,x) * integralx(y1,y2,y) * integral1(z1,z2,z)
+ data.ayz * integral1(x1,x2,x) * integralx(y1,y2,y) * integralx(z1,z2,z)
+ data.axz * integralx(x1,x2,x) * integral1(y1,y2,y) * integralx(z1,z2,z)
+ data.axyz * integralx(x1,x2,x) * integralx(y1,y2,y) * integralx(z1,z2,z)
);
}
vector<double> t1only_co_ext(const volume<float> & t1, const Pt & point, const Vec & n) {
vector<double> resul;
resul.clear();
bool output = true;
bool alloutput = true;
const double INNER_DEPTH = 3;
const double OUTER_DEPTH = 60;
Profile pt1;
for (double d = -INNER_DEPTH; d < OUTER_DEPTH; d+=.5)
{
Pt c = point + d * n;
double tmp1 = t1.interpolate(c.X, c.Y, c.Z);
pt1.add (d, tmp1);
}
pt1.init_roi();
//outer skin
double outskin = pt1.last_point_over(pt1.end(), .2);
double check = pt1.last_point_over(outskin - 1.5, .2);
if (outskin - check > 2) outskin = check;
const double OUTER_SKIN = outskin;
pt1.set_rroi(OUTER_SKIN);
double inskull = pt1.next_point_under(pt1.begin(), .25);
pt1.set_lroi(inskull);
if (alloutput)
{
//outer skull
//starting from the skin
double outskull2 = 0;
outskull2 = pt1.last_point_over(outskin, .75);
outskull2 = pt1.last_point_under(outskull2, .20);
//starting from the brain
double minabs = pt1.next_point_under(pt1.begin(), .30);
if (minabs == -500) output = false;
minabs = Max(minabs, -INNER_DEPTH);
double localminabs = minabs;//0
if (output)
{
bool stop = false;
const double lowthreshold = pt1.threshold(.15);
const double upthreshold = pt1.threshold(.60);
int test = 0;
for (vector<pro_pair>::const_iterator i = pt1.v.begin(); i != pt1.v.end(); i++)
{
if (!stop && (*i).abs>=minabs && i!=pt1.v.end() && i!=pt1.v.begin())
{
if ((*i).val>upthreshold) stop = true; //avoid climbing skin
if ((*i).val>lowthreshold) test++;
if ((*i).val<lowthreshold) test--;
if (test < 0) test=0;
if (test == 12) {stop = true;}
if ((*i).val<lowthreshold)
{
localminabs = (*i).abs;
}
}
}
}
double outskull = pt1.next_point_over(localminabs, .15);//.20
if (outskull2 - outskull < -2 || outskull2 - outskull >= 2) {output = false;}
if (outskin - outskull2 < 2) output = false;
if (output)
{
resul.push_back(inskull);
resul.push_back(outskull2);
resul.push_back(outskin);
}
else resul.push_back(outskin);
}
return resul;
}
//writes externall skull computed from image on output.
void t1only_write_ext_skull(volume<float> & output_inskull, volume<float> & output_outskull, volume<float> & output_outskin, const volume<float> & t1, const Mesh & m, const trMatrix & M) {
int glob_counter = 0;
int rem_counter = 0;
const double xdim = t1.xdim();
const double ydim = t1.ydim();
const double zdim = t1.zdim();
double imax = t1.max();
if (imax == 0) imax = 1;
volume<short> meshimage;
copyconvert(t1, meshimage);
meshimage = 0;
draw_mesh(meshimage, m);
for (vector<Mpoint*>::const_iterator i = m._points.begin(); i != m._points.end(); i++)
{
(*i)->data.clear();
double max_neighbour = 0;
const Vec normal = (*i)->local_normal();
const Vec n = Vec(normal.X/xdim, normal.Y/ydim, normal.Z/zdim);
for (list<Mpoint*>::const_iterator nei = (*i)->_neighbours.begin(); nei != (*i)->_neighbours.end(); nei++)
max_neighbour = Max(((**i) - (**nei)).norm(), max_neighbour);
max_neighbour = ceil((max_neighbour)/2);
const Pt mpoint((*i)->get_coord().X/xdim,(*i)->get_coord().Y/ydim,(*i)->get_coord().Z/zdim);
for (int ck = (int)floor(mpoint.Z - max_neighbour/zdim); ck <= (int)floor(mpoint.Z + max_neighbour/zdim); ck++)
for (int cj = (int)floor(mpoint.Y - max_neighbour/ydim); cj <= (int)floor(mpoint.Y + max_neighbour/ydim); cj++)
for (int ci = (int)floor(mpoint.X - max_neighbour/xdim); ci <= (int)floor(mpoint.X + max_neighbour/xdim); ci++)
{
bool compute = false;
const Pt point(ci, cj, ck);
const Pt realpoint(ci*xdim, cj*ydim, ck*zdim);
if (meshimage(ci, cj, ck) == 1)
{
double mindist = 10000;
for (list<Mpoint*>::const_iterator nei = (*i)->_neighbours.begin(); nei != (*i)->_neighbours.end(); nei++)
mindist = Min(((realpoint) - (**nei)).norm(), mindist);
if (mindist >= ((realpoint) - (**i)).norm()) compute = true;
}
if (compute)
{
glob_counter ++;
vector<double> val;
if (!special_case(realpoint, normal, M))
val = t1only_co_ext(t1, point, n);
else
{
val = t1only_special_extract(t1, point, n);
}
if (val.size() == 3)
{
Pt opoint(point.X, point.Y, point.Z);
Vec on(n.X, n.Y, n.Z);
Pt c0 = opoint + val[0]*on;
Pt c1 = opoint + val[1]*on;
Pt c2 = opoint + val[2]*on;
output_inskull((int)floor(c0.X + .5) + infxm,(int) floor(c0.Y + .5) + infym,(int) floor(c0.Z + .5) + infzm) +=1;
output_outskull((int)floor(c1.X + .5) + infxm,(int) floor(c1.Y + .5) + infym,(int) floor(c1.Z + .5) + infzm)+=1;
output_outskin((int)floor(c2.X + .5) + infxm,(int) floor(c2.Y + .5) + infym,(int) floor(c2.Z + .5) + infzm) +=1;
}
else {
rem_counter++;
if (val.size()==1)
{
Pt opoint(point.X, point.Y, point.Z);
Vec on(n.X, n.Y, n.Z);
Pt c0 = opoint + val[0]*on;
output_outskin((int)floor(c0.X + .5) + infxm,(int) floor(c0.Y + .5) + infym,(int) floor(c0.Z + .5) + infzm) +=1;
}
}
}
}
}
if (verbose.value())
{
cout<<" nb of profiles : "<<glob_counter<<endl;
cout<<" removed profiles : "<<100. * rem_counter/(double) glob_counter<<"%"<<endl;
}
}
double standard_step_of_computation(const volume<float> & image, Mesh & m, const int iteration_number, const double E,const double F, const float addsmooth, const float speed, const int nb_iter, const int id, const int od, const bool vol, const volume<short> & mask){
double xdim = image.xdim();
double ydim = image.ydim();
double zdim = image.zdim();
if (nb_iter % 50 == 0)
{
double l2 = 0;
int counter = 0;
for (vector<Mpoint*>::iterator i = m._points.begin(); i!=m._points.end(); i++ )
{
counter++;
l2 += (*i)->medium_distance_of_neighbours();
}
l = l2/counter;
}
if (nb_iter % 100 == 0)
{
for (vector<Mpoint*>::iterator i = m._points.begin(); i!=m._points.end(); i++)
{
Vec n = (*i)->local_normal();
Pt point = (*i)->get_coord();
Pt ipoint(point.X/xdim, point.Y/ydim, point.Z/zdim);
Vec in(n.X/xdim, n.Y/ydim, n.Z/zdim);
double max = 0;
Pt c_m1 = ipoint + (-1) * in;
double current = image.interpolate((c_m1.X),(c_m1.Y),(c_m1.Z));
for (double i2 = 1; i2 < 150; i2+=2)
{
if (max > .1) break;
Pt c_p = ipoint + i2 * in;
double tmpp = image.interpolate((c_p.X),(c_p.Y),(c_p.Z));
double tmp = (tmpp - current) * 100;
max = Max(max, tmp);
current = tmpp;
if (tmpp > .1) {max = 1; break;}
}
if (max < .1)
{
//There is a problem here for precision mode, since with the copy, no guarantee that data is non-zero size
//even if mesh.cpp operator = is modified to copy data, after retesselate "new" points will have zero size data member
if ( (*i)->data.size() ) (*i)->data.pop_back();
(*i)->data.push_back(1);
}
else
{
if ( (*i)->data.size() ) (*i)->data.pop_back();
(*i)->data.push_back(0);
}
}
}
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;
u2 = f2 * sn * addsmooth;
if ((*i)->data.back() == 0)
{
//main term of skull_extraction
{
Pt point = (*i)->get_coord();
Pt ipoint(point.X/xdim, point.Y/ydim, point.Z/zdim);
Vec in(n.X/xdim, n.Y/ydim, n.Z/zdim);
Pt c_m = ipoint + (-1.) * in;
Pt c_p = ipoint + 1. * in;
double tmp = image.interpolate((c_p.X ),( c_p.Y),(c_p.Z));
double gradient = tmp - image.interpolate((c_m.X),(c_m.Y), (c_m.Z));
double tmp2 = gradient*100;
f3 = max(-1., min(tmp2, 1.));
if (tmp2 >= 0 && tmp2 < .1 && tmp < .1 ) f3 = speed;
if (vol)
{
double tmpvol = mask.interpolate((ipoint.X ),(ipoint.Y),(ipoint.Z));
if (tmpvol > .0)
{
f3 = Max(Max(tmpvol*.5, .1), f3);
f2 = 0;
}
}
}
}
else
{
f3 = 0;
Pt point = (*i)->get_coord();
Pt ipoint(point.X/xdim, point.Y/ydim, point.Z/zdim);
double tmpvol = mask.interpolate((ipoint.X ),(ipoint.Y),(ipoint.Z));
if (tmpvol > .0)
{
f3 = Max(tmpvol*.5, .1);
f2 = 0;
}
}
u3 = .05 * f3 * n;
u = u1 + u2 + u3;
(*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;
}
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);
}
volume<float> find_skull (volume<float> & image, const Mesh & m, const double t2, double t, double t98)
{
const double skull_search = 30;
const double skull_start = -3;
volume<float> result = image;
result=0;
volume<short> volmesh;
copyconvert(image,volmesh);
int xsize = volmesh.xsize();
int ysize = volmesh.ysize();
int zsize = volmesh.zsize();
double xdim = volmesh.xdim();
double ydim = volmesh.ydim();
double zdim = volmesh.zdim();
double scale = Min(xdim, Min(ydim, zdim));
volmesh = 1;
volmesh = draw_mesh(volmesh, m);
image.setinterpolationmethod(trilinear);
for (vector<Mpoint*>::const_iterator i = m._points.begin(); i != m._points.end(); i++)
{
double max_neighbour = 0;
const Vec normal = (*i)->local_normal();
const Vec n = Vec(normal.X/xdim, normal.Y/ydim, normal.Z/zdim);
for (list<Mpoint*>::const_iterator nei = (*i)->_neighbours.begin(); nei != (*i)->_neighbours.end(); nei++)
max_neighbour = Max(((**i) - (**nei)).norm(), max_neighbour);
max_neighbour = ceil((max_neighbour)/2);
const Pt mpoint((*i)->get_coord().X/xdim,(*i)->get_coord().Y/ydim,(*i)->get_coord().Z/zdim);
for (int ck = (int)floor(mpoint.Z - max_neighbour/zdim); ck <= (int)floor(mpoint.Z + max_neighbour/zdim); ck++)
for (int cj = (int)floor(mpoint.Y - max_neighbour/ydim); cj <= (int)floor(mpoint.Y + max_neighbour/ydim); cj++)
for (int ci = (int)floor(mpoint.X - max_neighbour/xdim); ci <= (int)floor(mpoint.X + max_neighbour/xdim); ci++)
{
bool compute = false;
const Pt point(ci, cj, ck);
const Pt realpoint(ci*xdim, cj*ydim, ck*zdim);
if (volmesh(ci, cj, ck) == 0)
{
double mindist = 10000;
for (list<Mpoint*>::const_iterator nei = (*i)->_neighbours.begin(); nei != (*i)->_neighbours.end(); nei++)
mindist = Min(((realpoint) - (**nei)).norm(), mindist);
if (mindist >= ((realpoint) - (**i)).norm()) compute = true;
}
if (compute)
{
double maxval = t;
double minval = image.interpolate(point.X, point.Y, point.Z);
double d_max = 0;
for (double d=0; d<skull_search; d+=scale*.5)
{
Pt current = point + d * n;
double val = image.interpolate(current.X, current.Y, current.Z);
if (val>maxval)
{
maxval=val;
d_max=d;
}
if (val<minval)
minval=val;
}
if (maxval > t)
{
double d_min=skull_start;
double maxJ =-1000000;
double lastJ=-2000000;
for(double d=skull_start; d<d_max; d+=scale*0.5)
{
Pt current = point + d * n;
if (current.X >= 0 && current.Y >= 0 && current.Z >= 0 && current.X<xsize && current.Y<ysize && current.Z<zsize)
{
double tmpf = d/30 - image.interpolate(current.X, current.Y, current.Z) / (t98 - t2);
if (tmpf > maxJ)
{
maxJ=tmpf;
d_min = d;
}
lastJ=tmpf;
}
}
double maxgrad = 0;
double d_skull;
Pt current2 = point + d_min * n;
if (current2.X >= 0 && current2.Y >= 0 && current2.Z >= 0 && current2.X<xsize && current2.Y<ysize && current2.Z<zsize)
{
double val2 = image.interpolate(current2.X, current2.Y, current2.Z);
for(double d=d_min + scale; d<d_max; d+=0.5*scale)
{
Pt current = point + d * n;
if (current.X >= 0 && current.Y >= 0 && current.Z >= 0 && current.X<xsize && current.Y<ysize && current.Z<zsize)
{
double val = image.interpolate(current.X, current.Y, current.Z);
double grad = val - val2;
val2 = val;
if (grad > 0)
{
if (grad > maxgrad)
{
maxgrad=grad;
d_skull=d;
}
else d = d_max;
}
}
}
}
if (maxgrad > 0)
{
Pt current3 = point + d_skull * n;
if (current3.X >= 0 && current3.Y >= 0 && current3.Z >= 0 && current3.X<xsize && current3.Y<ysize && current3.Z<zsize)
result ((int)current3.X, (int)current3.Y, (int)current3.Z) = 100/*max*/;
}
}
}
}
}
return result;
}
void FnirtFileWriter::common_field_construction(const string& fname,
const volume<float>& ref,
const volume<float>& fieldx,
const volume<float>& fieldy,
const volume<float>& fieldz,
const Matrix& aff)
{
volume4D<float> fields(ref.xsize(),ref.ysize(),ref.zsize(),3);
fields.copyproperties(ref);
Matrix M;
bool add_affine = false;
if (add_affine = ((aff-IdentityMatrix(4)).MaximumAbsoluteValue() > 1e-6)) { // Add affine part to fields
M = (aff.i() - IdentityMatrix(4))*ref.sampling_mat();
}
if (samesize(ref,fieldx,true)) { // If ref is same size as the original field
fields[0] = fieldx; fields[1] = fieldy; fields[2] = fieldz;
fields.copyproperties(ref); // Put qform/sform and stuff back.
if (add_affine) {
ColumnVector xv(4), xo(4);
int zs = ref.zsize(), ys = ref.ysize(), xs = ref.xsize();
xv(4) = 1.0;
for (int z=0; z<zs; z++) {
xv(3) = double(z);
for (int y=0; y<ys; y++) {
xv(2) = double(y);
for (int x=0; x<xs; x++) {
xv(1) = double(x);
xo = M*xv;
fields(x,y,z,0) += xo(1);
fields(x,y,z,1) += xo(2);
fields(x,y,z,2) += xo(3);
}
}
}
}
}
else {
fieldx.setextrapolationmethod(extraslice);
fieldy.setextrapolationmethod(extraslice);
fieldz.setextrapolationmethod(extraslice);
Matrix R2F = fieldx.sampling_mat().i() * ref.sampling_mat();
ColumnVector xv(4), xo(4), xr(4);
int zs = ref.zsize(), ys = ref.ysize(), xs = ref.xsize();
xv(4) = 1.0;
for (int z=0; z<zs; z++) {
xv(3) = double(z);
for (int y=0; y<ys; y++) {
xv(2) = double(y);
for (int x=0; x<xs; x++) {
xv(1) = double(x);
xr = R2F*xv;
fields(x,y,z,0) = fieldx.interpolate(xr(1),xr(2),xr(3));
fields(x,y,z,1) = fieldy.interpolate(xr(1),xr(2),xr(3));
fields(x,y,z,2) = fieldz.interpolate(xr(1),xr(2),xr(3));
if (add_affine) {
xo = M*xv;
fields(x,y,z,0) += xo(1);
fields(x,y,z,1) += xo(2);
fields(x,y,z,2) += xo(3);
}
}
}
}
}
fields.set_intent(FSL_FNIRT_DISPLACEMENT_FIELD,fields.intent_param(0),fields.intent_param(1),fields.intent_param(2));
fields.setDisplayMaximum(0.0);
fields.setDisplayMinimum(0.0);
// Save resulting field
save_volume4D(fields,fname);
}
void volume::inset(double x_inset, double y_inset, double z_inset, volume& dst) const
{
dst = *this;
dst.inset(x_inset, y_inset, z_inset);
}
vega::data::hexagonal_prismatic_lattice::hexagonal_prismatic_lattice( const volume& v )
{
VEGA_LOG_FN;
// Lattice L = {Lx, Ly, Lz};
static const int Lx[3] = {2, -1, 0};
static const int Ly[3] = {0, 2, 0};
static const int Lz[3] = {0, 0, 1};
myWidth = v.get_width() / 2;
myHeight = v.get_height() / 2;
myDepth = v.get_depth();
assert(myWidth > 0 && myHeight > 0 && myDepth > 0);
myLatticeCells.reserve(myWidth * myHeight * myDepth);
for(uint16 k=0;k<myDepth;++k)
{
for(uint16 i=0;i<myHeight;++i)
{
for(uint16 j=0;j<myWidth;++j)
{
prismatic_hexagon_node cell;
cell.x = j;
cell.y = i + j/2 + j%2;
cell.z = k;
static const int hex_neighbor_offset[NEIGHBOR_COUNT][3] =
{
{1, 1, 0}, {0, 1, 0}, {-1, 0, 0}, {-1, -1, 0}, {0, -1, 0}, {1, 0, 0},
{0, 0,-1},
#if NEIGHBOR_COUNT==20
{1, 1,-1}, {0, 1,-1}, {-1, 0,-1}, {-1, -1,-1}, {0, -1,-1}, {1, 0,-1},
#endif
{0, 0, 1},
#if NEIGHBOR_COUNT==20
{1, 1, 1}, {0, 1, 1}, {-1, 0, 1}, {-1, -1, 1}, {0, -1, 1}, {1, 0, 1}
#endif
};
for(int h=0; h<NEIGHBOR_COUNT; ++h)
{
int hj = cell.x + hex_neighbor_offset[h][0];
int hi = cell.y + hex_neighbor_offset[h][1] - hj/2 - hj%2;
int hk = cell.z + hex_neighbor_offset[h][2];
if( hi >= 0 && hi < myHeight && hj >= 0 && hj < myWidth && hk >=0 && hk < myDepth )
cell.hex[h] = hk * myWidth * myHeight + hi * myWidth + hj;
else
cell.hex[h] = -1;
}
// the hexagon pixel offsets from the upper left corner
//
// x 1-2 o
// / \
// 3-4-5-6
// \ /
// o 7-8 o
//
static const int hex_pixel_offset[8][2] = { {1, 0}, {2, 0}, {0, 1}, {1, 1}, {2, 1}, {3, 1}, {1, 2}, {2, 2}};
math::vector3d vertex = cell.get_vertex();
#ifndef USE_COLOR_MAP
cell.density = 0.f;
#else
cell.color.RGBA = 0;
#endif
// compute average density
int k = 0;
for(size_t h=0;h<8;++h)
{
math::vector3d pixel;
int xx = (int)vertex.x + hex_pixel_offset[h][0];
int yy = (int)vertex.y + hex_pixel_offset[h][1];
int zz = (int)vertex.z;
if( xx >= 0 && yy >= 0 && zz >= 0 && xx < v.get_width() && yy < v.get_height() && zz < v.get_depth() )
{
#ifndef USE_COLOR_MAP
float vx = v.get_voxel(xx, yy, zz);
cell.density = (cell.density * k + vx) * (1.f/(++k));
#else
r8g8b8a8 vx = v.get_voxel_color(xx, yy, zz);
cell.color.A = (cell.color.A * k + vx.A) / ++k;
cell.color.R = (cell.color.R * k + vx.R) / ++k;
cell.color.G = (cell.color.G * k + vx.G) / ++k;
cell.color.B = (cell.color.B * k + vx.B) / ++k;
#endif
}
}
myLatticeCells.push_back(cell);
}
}
}
}
void reflect_z(volume &dst) const { dst = *this; dst.reflect_z(); }
/* default: simple numerical integration of surfaces/cubes, relative
tolerance 'tol'. This is superseded by the routines in the libctl
interface, which either use a semi-analytical average or can
use a proper adaptive cubature. */
void material_function::eff_chi1inv_row(component c, double chi1inv_row[3],
const volume &v,
double tol, int maxeval) {
field_type ft = type(c);
if (!maxeval) {
trivial:
chi1inv_row[0] = chi1inv_row[1] = chi1inv_row[2] = 0.0;
chi1inv_row[component_direction(c) % 3] = 1/chi1p1(ft,v.center());
return;
}
vec gradient(normal_vector(ft, v));
if (abs(gradient) < 1e-8) goto trivial;
double meps=1, minveps=1;
vec d = v.get_max_corner() - v.get_min_corner();
int ms = 10;
double old_meps=0, old_minveps=0;
int iter = 0;
switch(v.dim) {
case D3:
while ((fabs(meps - old_meps) > tol*fabs(old_meps)) && (fabs(minveps - old_minveps) > tol*fabs(old_minveps))) {
old_meps=meps;
old_minveps=minveps;
meps = minveps = 0;
for (int k=0; k < ms; k++)
for (int j=0; j < ms; j++)
for (int i=0; i < ms; i++) {
double ep = chi1p1(ft,v.get_min_corner() + vec(i*d.x()/ms, j*d.y()/ms, k*d.z()/ms));
if (ep < 0) goto trivial;
meps += ep;
minveps += 1/ep;
}
meps /= ms*ms*ms;
minveps /= ms*ms*ms;
ms *= 2;
if (maxeval && (iter += ms*ms*ms) >= maxeval) goto done;
}
break;
case D2:
while ((fabs(meps-old_meps) > tol*old_meps) && (fabs(minveps-old_minveps) > tol*old_minveps)) {
old_meps=meps;
old_minveps=minveps;
meps = minveps = 0;
for (int j=0; j < ms; j++)
for (int i=0; i < ms; i++) {
double ep = chi1p1(ft,v.get_min_corner() + vec(i*d.x()/ms, j*d.y()/ms));
if (ep < 0) goto trivial;
meps += ep;
minveps += 1/ep;
}
meps /= ms*ms;
minveps /= ms*ms;
ms *= 2;
if (maxeval && (iter += ms*ms) >= maxeval) goto done;
}
break;
case Dcyl:
while ((fabs(meps-old_meps) > tol*old_meps) && (fabs(minveps-old_minveps) > tol*old_minveps)) {
old_meps=meps;
old_minveps=minveps;
meps = minveps = 0;
double sumvol = 0;
for (int j=0; j < ms; j++)
for (int i=0; i < ms; i++) {
double r = v.get_min_corner().r() + i*d.r()/ms;
double ep = chi1p1(ft,v.get_min_corner() + veccyl(i*d.r()/ms, j*d.z()/ms));
if (ep < 0) goto trivial;
sumvol += r;
meps += ep * r;
minveps += r/ep;
}
meps /= sumvol;
minveps /= sumvol;
ms *= 2;
if (maxeval && (iter += ms*ms) >= maxeval) goto done;
}
break;
case D1:
while ((fabs(meps-old_meps) > tol*old_meps) && (fabs(minveps-old_minveps) > tol*old_minveps)) {
old_meps=meps;
old_minveps=minveps;
meps = minveps = 0;
for (int i=0; i < ms; i++) {
double ep = chi1p1(ft,v.get_min_corner() + vec(i*d.z()/ms));
if (ep < 0) {
meps = chi1p1(ft,v.center());
minveps = 1/meps;
goto done;
}
meps += ep;
minveps += 1/ep;
}
meps /= ms;
minveps /= ms;
ms *= 2;
if (maxeval && (iter += ms*ms) >= maxeval) goto done;
}
break;
}
done:
{
double n[3] = {0,0,0};
double nabsinv = 1.0/abs(gradient);
LOOP_OVER_DIRECTIONS(gradient.dim, k)
n[k%3] = gradient.in_direction(k) * nabsinv;
/* get rownum'th row of effective tensor
P * minveps + (I-P) * 1/meps = P * (minveps-1/meps) + I * 1/meps
where I is the identity and P is the projection matrix
P_{ij} = n[i] * n[j]. */
int rownum = component_direction(c) % 3;
for (int i=0; i<3; ++i)
chi1inv_row[i] = n[rownum] * n[i] * (minveps - 1/meps);
chi1inv_row[rownum] += 1/meps;
}
}
