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GenerateModelsFromLabels

vtk-examples/Cxx/Medical/GenerateModelsFromLabels

Description

This example uses vtkDiscreteFlyingEdges3D or vtkDiscreteMarchingCubes to create vtkPolyData models from a 3D volume that contains discrete labels. These volumes are normally the output of a segmentation algorithm. The polydata for each label will be output into a separate file.

You can load these files into ParaView, where they will appear as a series of time steps. You can then single step through displaying the polydate from each file making up the series.

If you want to see the segmentation results as cube models, see the example GenerateCubesFromLabels

The input volume must be in MetaIO format.

Once you generate the models, you can view them with Paraview

Note

This original source code for this example is here.

Other languages

See (Python)

Question

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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 <vtkGeometryFilter.h>
#include <vtkImageAccumulate.h>
#include <vtkMaskFields.h>
#include <vtkMetaImageReader.h>
#include <vtkNew.h>
#include <vtkThreshold.h>
#include <vtkVersion.h>
#include <vtkWindowedSincPolyDataFilter.h>
#include <vtkXMLPolyDataWriter.h>

// vtkDiscreteFlyingEdges3D was introduced in VTK >= 8.2
#if VTK_MAJOR_VERSION >= 9 || (VTK_MAJOR_VERSION >= 8 && VTK_MINOR_VERSION >= 2)
#define USE_FLYING_EDGES
#else
#undef USE_FLYING_EDGES
#endif
//#undef USE_FLYING_EDGES

#ifdef USE_FLYING_EDGES
#include <vtkDiscreteFlyingEdges3D.h>
#else
#include <vtkDiscreteMarchingCubes.h>
#endif

#include <sstream>
#include <vtkImageData.h>
#include <vtkPointData.h>
#include <vtkUnstructuredGrid.h>

int main(int argc, char* argv[])
{
  if (argc < 4)
  {
    std::cout
        << "Usage: " << argv[0]
        << " InputVolume StartLabel EndLabel  e.g. Frog/frogtissue.mhd 1 29"
        << std::endl;
    return EXIT_FAILURE;
  }

  // Create all of the classes we will need
  vtkNew<vtkMetaImageReader> reader;
  vtkNew<vtkImageAccumulate> histogram;
#ifdef USE_FLYING_EDGES
  vtkNew<vtkDiscreteFlyingEdges3D> discreteCubes;
#else
  vtkNew<vtkDiscreteMarchingCubes> discreteCubes;
#endif
  vtkNew<vtkWindowedSincPolyDataFilter> smoother;
  vtkNew<vtkThreshold> selector;
  vtkNew<vtkMaskFields> scalarsOff;
  vtkNew<vtkGeometryFilter> geometry;
  vtkNew<vtkXMLPolyDataWriter> writer;

  // 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());
#ifdef USE_FLYING_EDGES
  selector->SetInputArrayToProcess(0, 0, 0,
                                   vtkDataObject::FIELD_ASSOCIATION_POINTS,
                                   vtkDataSetAttributes::SCALARS);
#else
  selector->SetInputArrayToProcess(0, 0, 0,
                                   vtkDataObject::FIELD_ASSOCIATION_CELLS,
                                   vtkDataSetAttributes::SCALARS);
#endif

  // 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->SetLowerThreshold(i);
    selector->SetUpperThreshold(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 3.3 FATAL_ERROR)

project(GenerateModelsFromLabels)

find_package(VTK COMPONENTS 
  vtkCommonCore
  vtkCommonDataModel
  vtkFiltersCore
  vtkFiltersGeneral
  vtkFiltersGeometry
  vtkIOImage
  vtkIOXML
  vtkImagingStatistics
  QUIET
)

if (NOT VTK_FOUND)
  message("Skipping GenerateModelsFromLabels: ${VTK_NOT_FOUND_MESSAGE}")
  return ()
endif()
message (STATUS "VTK_VERSION: ${VTK_VERSION}")
if (VTK_VERSION VERSION_LESS "8.90.0")
  # old system
  include(${VTK_USE_FILE})
  add_executable(GenerateModelsFromLabels MACOSX_BUNDLE GenerateModelsFromLabels.cxx )
  target_link_libraries(GenerateModelsFromLabels PRIVATE ${VTK_LIBRARIES})
else ()
  # include all components
  add_executable(GenerateModelsFromLabels MACOSX_BUNDLE GenerateModelsFromLabels.cxx )
  target_link_libraries(GenerateModelsFromLabels PRIVATE ${VTK_LIBRARIES})
  # vtk_module_autoinit is needed
  vtk_module_autoinit(
    TARGETS GenerateModelsFromLabels
    MODULES ${VTK_LIBRARIES}
    )
endif ()

Download and Build GenerateModelsFromLabels

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

Be sure to add the VTK bin directory to your path. This will resolve the VTK dll's at run time.