- args_info_clitkGammaIndex args_info;
-
- if (cmdline_parser_clitkGammaIndex(argc, argv, &args_info) != 0)
- exit(1);
-
- if (!args_info.absolute_dose_margin_given && !args_info.relative_dose_margin_given) {
- std::cerr << "Specify either relative or absolute dose margin" << endl;
- exit(1);
- }
-
- bool verbose = args_info.verbose_flag;
-
- std::string reference_filename(args_info.reference_arg);
- std::string target_filename(args_info.target_arg);
- std::string gamma_filename(args_info.output_arg);
- double space_margin = args_info.spatial_margin_arg;
- double dose_rel_margin = args_info.relative_dose_margin_arg;
- double dose_margin = args_info.absolute_dose_margin_arg;
- bool use_dose_margin = args_info.absolute_dose_margin_given;
-
- if (verbose) {
- cout << "reference_filename=" << reference_filename << endl;
- cout << "target_filename=" << target_filename << endl;
- cout << "gamma_filename=" << gamma_filename << endl;
- cout << "space_margin=" << space_margin << endl;
- if (use_dose_margin) cout << "dose_margin=" << dose_margin << endl;
- else cout << "dose_rel_margin=" << dose_rel_margin << endl;
- }
-
- // load reference
- vtkImageData *reference = loadImage(reference_filename);
- assert2D(reference);
-
- // intensity normalisation
- if (!use_dose_margin) {
- dose_margin = getMaximum(reference)*dose_rel_margin;
- if (verbose) cout << "dose_margin=" << dose_margin << endl;
- }
-
- // build surface
- vtkPolyData *data = buildPlane(reference,space_margin,dose_margin);
- reference->Delete();
-
- vtkAbstractCellLocator *locator = vtkCellLocator::New();
- locator->SetDataSet(data);
- data->Delete();
- locator->CacheCellBoundsOn();
- locator->AutomaticOn();
- locator->BuildLocator();
-
- // load target
- vtkImageData *target = loadImage(target_filename);
- assert2D(target);
-
- // allocate output
- vtkImageData *output = vtkImageData::New();
- output->SetExtent(target->GetWholeExtent());
- output->SetOrigin(target->GetOrigin());
- output->SetSpacing(target->GetSpacing());
- output->SetScalarTypeToFloat();
- output->AllocateScalars();
-
- // fill output
- unsigned long total = 0;
- unsigned long over_one = 0;
- for (int kk=0; kk<target->GetNumberOfPoints(); kk++) {
- double *point = target->GetPoint(kk);
- double value = target->GetPointData()->GetScalars()->GetTuple1(kk);
- assert(value>=0);
- assert(point[2]==0);
- point[2] = value;
-
- point[0] /= space_margin;
- point[1] /= space_margin;
- point[2] /= dose_margin;
-
- double closest_point[3] = {0,0,0};
- vtkIdType cell_id = 0;
- int foo = 0;
- double squared_distance = 0;
-
- locator->FindClosestPoint(point,closest_point,cell_id,foo,squared_distance);
-
- double distance = sqrt(squared_distance);
- output->GetPointData()->GetScalars()->SetTuple1(kk,distance);
-
- if (value>1) over_one++;
- total++;
-
- }
-
- if (verbose) {
- cout << "total=" << total << endl;
- cout << "over_one=" << over_one << endl;
- cout << "ratio=" << static_cast<float>(over_one)/total << endl;
- }
-
- locator->Delete();
- target->Delete();
-
- saveImage(output,gamma_filename);
- output->Delete();
-
- return 0;
+ clitk::RegisterClitkFactories();
+
+ args_info_clitkGammaIndex args_info;
+
+ if (cmdline_parser_clitkGammaIndex(argc, argv, &args_info) != 0)
+ exit(1);
+
+ if (!args_info.absolute_dose_margin_given && !args_info.relative_dose_margin_given) {
+ std::cerr << "Specify either relative or absolute dose margin" << endl;
+ exit(1);
+ }
+
+ bool verbose = args_info.verbose_flag;
+
+ std::string reference_filename(args_info.reference_arg);
+ std::string target_filename(args_info.target_arg);
+ std::string gamma_filename(args_info.output_arg);
+ double space_margin = args_info.spatial_margin_arg;
+ double dose_rel_margin = args_info.relative_dose_margin_arg;
+ double dose_margin = args_info.absolute_dose_margin_arg;
+ bool use_dose_margin = args_info.absolute_dose_margin_given;
+
+ if (verbose) {
+ cout << "reference_filename=" << reference_filename << endl;
+ cout << "target_filename=" << target_filename << endl;
+ cout << "gamma_filename=" << gamma_filename << endl;
+ cout << "space_margin=" << space_margin << endl;
+ if (use_dose_margin) cout << "dose_margin=" << dose_margin << endl;
+ else cout << "dose_rel_margin=" << dose_rel_margin << endl;
+ }
+
+ // load reference
+ vtkImageData* reference = loadImage(reference_filename);
+ assert(reference);
+
+ // translate target with arguments values
+ // reference is translated instead of target so that the output space stay the same as target
+ {
+ double reference_origin[3];
+ reference->GetOrigin(reference_origin);
+ reference_origin[0] -= args_info.translation_x_arg;
+ reference_origin[1] -= args_info.translation_y_arg;
+ reference_origin[2] -= args_info.translation_z_arg;
+ reference->SetOrigin(reference_origin);
+ }
+
+ // intensity normalisation
+ if (!use_dose_margin) {
+ dose_margin = getMaximum(reference)*dose_rel_margin;
+ if (verbose) cout << "dose_margin=" << dose_margin << endl;
+ }
+
+ // build surface
+ vtkPolyData *data = buildPlane(reference,space_margin,dose_margin);
+ reference->Delete();
+
+ vtkAbstractCellLocator *locator = vtkCellLocator::New();
+ locator->SetDataSet(data);
+ data->Delete();
+ locator->CacheCellBoundsOn();
+ locator->AutomaticOn();
+ locator->BuildLocator();
+
+ // load target
+ vtkImageData* target = loadImage(target_filename);
+ assert(target);
+
+
+ // allocate output
+ OutputImageType::Pointer output = OutputImageType::New();
+ {
+ OutputImageType::SizeType::SizeValueType output_array_size[2];
+ output_array_size[0] = target->GetDimensions()[0];
+ output_array_size[1] = target->GetDimensions()[1];
+ OutputImageType::SizeType output_size;
+ output_size.SetSize(output_array_size);
+ output->SetRegions(OutputImageType::RegionType(output_size));
+ output->SetOrigin(target->GetOrigin());
+ output->SetSpacing(target->GetSpacing());
+ output->Allocate();
+ }
+
+ // fill output
+ unsigned long kk = 0;
+ unsigned long over_one = 0;
+ OutputImageIterator iter(output,output->GetLargestPossibleRegion());
+ iter.GoToBegin();
+ while (!iter.IsAtEnd()) {
+ double *point = target->GetPoint(kk);
+ double value = target->GetPointData()->GetScalars()->GetTuple1(kk);
+ assert(value>=0);
+ assert(point[2]==0);
+ point[2] = value;
+
+ point[0] /= space_margin;
+ point[1] /= space_margin;
+ point[2] /= dose_margin;
+
+ double closest_point[3] = {0,0,0};
+ vtkIdType cell_id = 0;
+ int foo = 0;
+ double squared_distance = 0;
+
+ locator->FindClosestPoint(point,closest_point,cell_id,foo,squared_distance);
+ double distance = sqrt(squared_distance);
+ iter.Set(distance);
+
+ if (distance>1) over_one++;
+ kk++;
+ ++iter;
+ }
+
+ if (verbose) {
+ cout << "total=" << kk << endl;
+ cout << "over_one=" << over_one << endl;
+ cout << "ratio=" << static_cast<float>(over_one)/kk << endl;
+ }
+
+ locator->Delete();
+ target->Delete();
+
+ saveImage(output,gamma_filename);
+
+ return 0;