+ typedef InternalIndexType SeedType;
+ SeedType trachea_centre, shape_centre, max_e_centre, prev_e_centre;
+ typedef std::list<SeedType> PointListType;
+ typedef std::list<PointListType> SequenceListType;
+ PointListType* current_sequence = NULL;
+ SequenceListType sequence_list;
+
+ prev_e_centre.Fill(0);
+ std::ostringstream file_name;
+ index[0] = index[1] = 0;
+ size[0] = size[1] = 512;
+ size[2] = 0;
+ while (nslices--) {
+ index[2] = start;
+ start += increment;
+
+ region.SetIndex(index);
+ region.SetSize(size);
+ slicer->SetExtractionRegion(region);
+ slicer->Update();
+ label_filter->SetInput(slicer->GetOutput());
+ label_filter->Update();
+
+ label_to_map_filter->SetInput(label_filter->GetOutput());
+ label_to_map_filter->Update();
+ typename LabelImageType::Pointer label_map = label_to_map_filter->GetOutput();
+
+ if (GetWriteStepFlag()) {
+ map_to_label_filter->SetInput(label_map);
+ writer->SetInput(map_to_label_filter->GetOutput());
+ file_name.str("");
+ file_name << "labels_";
+ file_name.width(3);
+ file_name.fill('0');
+ file_name << index[2] << ".mhd";
+ writer->SetFileName(file_name.str().c_str());
+ writer->Update();
+ }
+
+ typename ShapeLabelType::Pointer shape, max_e_shape;
+ double max_elongation = GetMaxElongation();
+ double max_size = size[0]*size[1]/128;
+ double max_e = 0;
+ int nshapes = 0;
+ unsigned int nlables = label_map->GetNumberOfLabelObjects();
+ for (unsigned int j = 0; j < nlables; j++) {
+ shape = label_map->GetNthLabelObject(j);
+ if (shape->Size() > 150 && shape->Size() <= max_size) {
+ double e = 1 - 1/shape->GetElongation();
+ //double area = 1 - r->Area() ;
+ if (e < max_elongation) {
+ nshapes++;
+ shape_centre[0] = (shape->GetCentroid()[0] - origin[0])/spacing[0];
+ shape_centre[1] = (shape->GetCentroid()[1] - origin[1])/spacing[1];
+ shape_centre[2] = index[2];
+ //double d = 1 - (shape_centre - image_centre).Magnitude()/max_dist;
+ double dx = shape_centre[0] - image_centre[0];
+ double d = 1 - dx*2/size[0];
+ e = e + d;
+ if (e > max_e)
+ {
+ max_e = e;
+ max_e_shape = shape;
+ max_e_centre = shape_centre;
+ }
+ }
+ }
+ }
+
+ if (nshapes > 0)
+ {
+ itk::Point<typename SeedType::IndexValueType, ImageType::ImageDimension> p1, p2;
+ p1[0] = max_e_centre[0];
+ p1[1] = max_e_centre[1];
+ p1[2] = max_e_centre[2];
+
+ p2[0] = prev_e_centre[0];
+ p2[1] = prev_e_centre[1];
+ p2[2] = prev_e_centre[2];
+
+ double mag = (p2 - p1).GetNorm();
+ if (GetVerboseRegionGrowingFlag()) {
+ cout.precision(3);
+ cout << index[2] << ": ";
+ cout << "region(" << max_e_centre[0] << ", " << max_e_centre[1] << ", " << max_e_centre[2] << "); ";
+ cout << "prev_region(" << prev_e_centre[0] << ", " << prev_e_centre[1] << ", " << prev_e_centre[2] << "); ";
+ cout << "mag(" << mag << "); " << endl;
+ }
+
+ if (mag > 5)
+ {
+ PointListType point_list;
+ point_list.push_back(max_e_centre);
+ sequence_list.push_back(point_list);
+ current_sequence = &sequence_list.back();
+ }
+ else if (current_sequence)
+ current_sequence->push_back(max_e_centre);
+
+ prev_e_centre= max_e_centre;
+ }
+ else {
+ if (GetVerboseRegionGrowingFlag()) {
+ cout << "No shapes found at slice " << index[2] << std::endl;
+ }
+ }
+ }
+
+ size_t longest = 0;
+ for (typename SequenceListType::iterator s = sequence_list.begin(); s != sequence_list.end(); s++)
+ {
+ if (s->size() > longest)
+ {
+ longest = s->size();
+ trachea_centre = s->front();
+ }
+ }
+
+ if (longest > 0) {
+ if (GetVerboseRegionGrowingFlag())
+ std::cout << "seed at: " << trachea_centre << std::endl;
+ m_Seeds.push_back(trachea_centre);
+ }
+ }
+
+ return (m_Seeds.size() != 0);
+}
+//--------------------------------------------------------------------
+