void defiGroup::print(FILE* f) const {
int i;
fprintf(f, "Group '%s'\n", name());
if (hasRegionName()) {
fprintf(f, " region name '%s'\n", regionName());
}
if (hasRegionBox()) {
int size = numRects_;
int* xl = xl_;
int* yl = yl_;
int* xh = xh_;
int* yh = yh_;
for (i = 0; i < size; i++)
fprintf(f, " region box %d,%d %d,%d\n", xl[i], yl[i], xh[i], yh[i]);
}
if (hasMaxX()) {
fprintf(f, " max x %d\n", maxX());
}
if (hasMaxY()) {
fprintf(f, " max y %d\n", maxY());
}
if (hasPerim()) {
fprintf(f, " perim %d\n", perim());
}
}
/*!
* Initialize phi
*/
void ActiveContourSeed::initializePhi(int protobuf_idx, Protobuf *proto) {
// set resolution
phi_->setResolution(p_->res_x, p_->res_y, p_->res_z);
// initialize image
phi_->resize(_dimx_Rel, _dimy_Rel, _dimz_Rel);
// get cell centers, previous sparse segmentation from protobuf file
Array1D<int> xAbs(cb), yAbs(cb), zAbs(cb);
proto->getSparseSegmentationCoordinates("full", protobuf_idx, &xAbs, &yAbs,
&zAbs);
// if previous sparse segmentation is empty, then initialize phi from single point
if (xAbs.size() == 0) {
for (int x = 0; x < _dimx_Rel; x++) {
for (int y = 0; y < _dimy_Rel; y++) {
for (int z = 0; z < _dimz_Rel; z++) {
float xRadial = (float) (x - _hszX);
float yRadial = (float) (y - _hszY);
float zRadial = (float) (z - _hszZ);
(*phi_)(x, y, z) = sqrtf(
xRadial * xRadial + yRadial * yRadial + zRadial
* zRadial) - p_->r;
}
}
}
// otherwise, initialize phi using distance transform on previous segmentation
} else {
// get previous binary segmentation, store in phi
for (int p = 0; p < xAbs.size(); p++) {
int xRel, yRel, zRel;
absToRel(xRel, yRel, zRel, xAbs(p), yAbs(p), zAbs(p));
(*phi_)(xRel, yRel, zRel) = 1;
}
// get perimeter segmentation and store in phi. Store original segmentation in temp
Image3D<float> temp(*phi_);
perim(phi_, 1);
// calculate distance transform
bwdist(phi_);
// Make distances negative inside the segmentation
for (int x = 0; x < _dimx_Rel; x++) {
for (int y = 0; y < _dimy_Rel; y++) {
for (int z = 0; z < _dimz_Rel; z++) {
if (temp(x, y, z) > float(BWTHRESH)) {
(*phi_)(x, y, z) = -(*phi_)(x, y, z);
}
}
}
}
}
updateFullSeg(phi_);
}
void ActiveContourSeed::getSparseCoordinates_perim(Array1D<int> *xS,
Array1D<int> *yS, Array1D<int> *zS) {
// get binary segmentation
Image3D<float> bw(*phi_);
for (int x = 0; x < _dimx_Rel; x++) {
for (int y = 0; y < _dimy_Rel; y++) {
for (int z = 0; z < _dimz_Rel; z++) {
if (bw(x, y, z) <= 0) {
bw(x, y, z) = 1;
} else {
bw(x, y, z) = 0;
}
}
}
}
perim(&bw, 1);
// get sparse coordinates
getSparseCoordinates(xS, yS, zS, &bw);
}