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); }