//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;
}
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;
}
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);
}
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);
}
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;
}
