GenerateModelsFromLabels
VTKExamples/Cxx/Medical/GenerateModelsFromLabels
Description¶
This example creates polydata models from a 3D volume that contains discrete labels. These volume are normally the output of a segmentation algorithm. The polydata for each label will be output into a separate file. If you want to see the segmentation results as cube models, see the example cubes from labeled volume data. The input volume must be in MetaIO format.
Once you generate the models, you can view them with Paraview
Code¶
GenerateModelsFromLabels.cxx
// // GenerateModelsFromLabels // Usage: GenerateModelsFromLabels InputVolume Startlabel Endlabel // where // InputVolume is a meta file containing a 3 volume of // discrete labels. // StartLabel is the first label to be processed // EndLabel is the last label to be processed // NOTE: There can be gaps in the labeling. If a label does // not exist in the volume, it will be skipped. // // #include <vtkMetaImageReader.h> #include <vtkImageAccumulate.h> #include <vtkDiscreteMarchingCubes.h> #include <vtkWindowedSincPolyDataFilter.h> #include <vtkMaskFields.h> #include <vtkThreshold.h> #include <vtkGeometryFilter.h> #include <vtkXMLPolyDataWriter.h> #include <vtkSmartPointer.h> #include <vtkImageData.h> #include <vtkPointData.h> #include <vtkUnstructuredGrid.h> #include <sstream> int main (int argc, char *argv[]) { if (argc < 4) { std::cout << "Usage: " << argv[0] << " InputVolume StartLabel EndLabel" << std::endl; return EXIT_FAILURE; } // Create all of the classes we will need vtkSmartPointer<vtkMetaImageReader> reader = vtkSmartPointer<vtkMetaImageReader>::New(); vtkSmartPointer<vtkImageAccumulate> histogram = vtkSmartPointer<vtkImageAccumulate>::New(); vtkSmartPointer<vtkDiscreteMarchingCubes> discreteCubes = vtkSmartPointer<vtkDiscreteMarchingCubes>::New(); vtkSmartPointer<vtkWindowedSincPolyDataFilter> smoother = vtkSmartPointer<vtkWindowedSincPolyDataFilter>::New(); vtkSmartPointer<vtkThreshold> selector = vtkSmartPointer<vtkThreshold>::New(); vtkSmartPointer<vtkMaskFields> scalarsOff = vtkSmartPointer<vtkMaskFields>::New(); vtkSmartPointer<vtkGeometryFilter> geometry = vtkSmartPointer<vtkGeometryFilter>::New(); vtkSmartPointer<vtkXMLPolyDataWriter> writer = vtkSmartPointer<vtkXMLPolyDataWriter>::New(); // Define all of the variables unsigned int startLabel = atoi(argv[2]); unsigned int endLabel = atoi(argv[3]); std::string filePrefix = "Label"; unsigned int smoothingIterations = 15; double passBand = 0.001; double featureAngle = 120.0; // Generate models from labels // 1) Read the meta file // 2) Generate a histogram of the labels // 3) Generate models from the labeled volume // 4) Smooth the models // 5) Output each model into a separate file reader->SetFileName(argv[1]); histogram->SetInputConnection(reader->GetOutputPort()); histogram->SetComponentExtent(0, endLabel, 0, 0, 0, 0); histogram->SetComponentOrigin(0, 0, 0); histogram->SetComponentSpacing(1, 1, 1); histogram->Update(); discreteCubes->SetInputConnection(reader->GetOutputPort()); discreteCubes->GenerateValues( endLabel - startLabel + 1, startLabel, endLabel); smoother->SetInputConnection(discreteCubes->GetOutputPort()); smoother->SetNumberOfIterations(smoothingIterations); smoother->BoundarySmoothingOff(); smoother->FeatureEdgeSmoothingOff(); smoother->SetFeatureAngle(featureAngle); smoother->SetPassBand(passBand); smoother->NonManifoldSmoothingOn(); smoother->NormalizeCoordinatesOn(); smoother->Update(); selector->SetInputConnection(smoother->GetOutputPort()); selector->SetInputArrayToProcess(0, 0, 0, vtkDataObject::FIELD_ASSOCIATION_CELLS, vtkDataSetAttributes::SCALARS); // Strip the scalars from the output scalarsOff->SetInputConnection(selector->GetOutputPort()); scalarsOff->CopyAttributeOff(vtkMaskFields::POINT_DATA, vtkDataSetAttributes::SCALARS); scalarsOff->CopyAttributeOff(vtkMaskFields::CELL_DATA, vtkDataSetAttributes::SCALARS); geometry->SetInputConnection(scalarsOff->GetOutputPort()); writer->SetInputConnection(geometry->GetOutputPort()); for (unsigned int i = startLabel; i <= endLabel; i++) { // see if the label exists, if not skip it double frequency = histogram->GetOutput()->GetPointData()->GetScalars()->GetTuple1(i); if (frequency == 0.0) { continue; } // select the cells for a given label selector->ThresholdBetween(i, i); // output the polydata std::stringstream ss; ss << filePrefix << i << ".vtp"; std::cout << argv[0] << " writing " << ss.str() << std::endl; writer->SetFileName(ss.str().c_str()); writer->Write(); } return EXIT_SUCCESS; }
CMakeLists.txt¶
cmake_minimum_required(VERSION 2.8) PROJECT(GenerateModelsFromLabels) find_package(VTK REQUIRED) include(${VTK_USE_FILE}) add_executable(GenerateModelsFromLabels MACOSX_BUNDLE GenerateModelsFromLabels.cxx) target_link_libraries(GenerateModelsFromLabels ${VTK_LIBRARIES})
Download and Build GenerateModelsFromLabels¶
Danger
The generation of tar files has not been ported to the new VTKExamples. Some tarballs may be missing or out-of-date.
Click here to download GenerateModelsFromLabels and its CMakeLists.txt file. Once the tarball GenerateModelsFromLabels.tar has been downloaded and extracted,
cd GenerateModelsFromLabels/build
If VTK is installed:
cmake ..
If VTK is not installed but compiled on your system, you will need to specify the path to your VTK build:
cmake -DVTK_DIR:PATH=/home/me/vtk_build ..
Build the project:
make
and run it:
./GenerateModelsFromLabels
WINDOWS USERS PLEASE NOTE: Be sure to add the VTK bin directory to your path. This will resolve the VTK dll's at run time.