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GenerateCubesFromLabels

vtk-examples/Cxx/Medical/GenerateCubesFromLabels


Description

Sometimes it is helpful to view the results of a segmentation without any post processing. This example converts the point data from a labeled volume into cell data. The surfaces are displayed as vtkPolydata. If you want to created smoothed polydata models from your segmented volumes, see the example GenerateModelsFromLabels. The input volume must be in MetaIO format.

 Usage: GenerateCubesFromLabels InputVolume.mhd 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.

Note

This original source code for this example is here.

Other languages

See (Python)

Question

If you have a question about this example, please use the VTK Discourse Forum

Code

GenerateCubesFromLabels.cxx

//
// GenerateCubesFromLabels
//   Usage: GenerateCubesFromLabels 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 <vtkCamera.h>
#include <vtkCellData.h>
#include <vtkGeometryFilter.h>
#include <vtkImageData.h>
#include <vtkImageWrapPad.h>
#include <vtkMetaImageReader.h>
#include <vtkNamedColors.h>
#include <vtkNew.h>
#include <vtkPointData.h>
#include <vtkPolyDataMapper.h>
#include <vtkRenderWindow.h>
#include <vtkRenderWindowInteractor.h>
#include <vtkRenderer.h>
#include <vtkThreshold.h>
#include <vtkTransform.h>
#include <vtkTransformFilter.h>

#include <iostream>

int main(int argc, char* argv[])
{
  vtkNew<vtkNamedColors> colors;

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

  // Define all of the variables
  unsigned int startLabel = atoi(argv[2]);
  unsigned int endLabel = atoi(argv[3]);

  // Generate cubes from labels.
  // 1) Read the meta file
  // 2) Convert point data to cell data
  // 3) Convert to geometry and display

  vtkNew<vtkMetaImageReader> reader;
  reader->SetFileName(argv[1]);
  reader->Update();

  // Pad the volume so that we can change the point data into cell.
  // data.
  int* extent = reader->GetOutput()->GetExtent();
  vtkNew<vtkImageWrapPad> pad;
  pad->SetInputConnection(reader->GetOutputPort());
  pad->SetOutputWholeExtent(extent[0], extent[1] + 1, extent[2], extent[3] + 1,
                            extent[4], extent[5] + 1);
  pad->Update();

  // Copy the scalar point data of the volume into the scalar cell data.
  pad->GetOutput()->GetCellData()->SetScalars(
      reader->GetOutput()->GetPointData()->GetScalars());

  vtkNew<vtkThreshold> selector;
  selector->SetInputArrayToProcess(0, 0, 0,
                                   vtkDataObject::FIELD_ASSOCIATION_CELLS,
                                   vtkDataSetAttributes::SCALARS);
  selector->SetInputConnection(pad->GetOutputPort());
  selector->SetLowerThreshold(startLabel);
  selector->SetUpperThreshold(endLabel);
  selector->Update();

  // Shift the geometry by 1/2.
  vtkNew<vtkTransform> transform;
  transform->Translate(-0.5, -0.5, -0.5);

  vtkNew<vtkTransformFilter> transformModel;
  transformModel->SetTransform(transform);
  transformModel->SetInputConnection(selector->GetOutputPort());

  vtkNew<vtkGeometryFilter> geometry;
  geometry->SetInputConnection(transformModel->GetOutputPort());

  vtkNew<vtkPolyDataMapper> mapper;
  mapper->SetInputConnection(geometry->GetOutputPort());
  mapper->SetScalarRange(startLabel, endLabel);
  mapper->SetScalarModeToUseCellData();
  mapper->SetColorModeToMapScalars();

  vtkNew<vtkActor> actor;
  actor->SetMapper(mapper);

  vtkNew<vtkRenderer> renderer;
  vtkNew<vtkRenderWindow> renderWindow;
  renderWindow->AddRenderer(renderer);
  renderWindow->SetSize(640, 480);
  renderWindow->SetWindowName("GenerateCubesFromLabels");

  vtkNew<vtkRenderWindowInteractor> renderWindowInteractor;
  renderWindowInteractor->SetRenderWindow(renderWindow);

  renderer->AddActor(actor);
  renderer->SetBackground(colors->GetColor3d("DarkSlateBlue").GetData());
  renderWindow->Render();

  auto camera = renderer->GetActiveCamera();
  camera->SetPosition(42.301174, 939.893457, -124.005030);
  camera->SetFocalPoint(224.697134, 221.301653, 146.823706);
  camera->SetViewUp(0.262286, -0.281321, -0.923073);
  camera->SetDistance(789.297581);
  camera->SetClippingRange(168.744328, 1509.660206);

  renderWindowInteractor->Start();
  return EXIT_SUCCESS;
}

CMakeLists.txt

cmake_minimum_required(VERSION 3.12 FATAL_ERROR)

project(GenerateCubesFromLabels)

find_package(VTK COMPONENTS 
  CommonColor
  CommonCore
  CommonDataModel
  CommonTransforms
  FiltersCore
  FiltersGeneral
  FiltersGeometry
  IOImage
  ImagingCore
  InteractionStyle
  RenderingContextOpenGL2
  RenderingCore
  RenderingFreeType
  RenderingGL2PSOpenGL2
  RenderingOpenGL2
)

if (NOT VTK_FOUND)
  message(FATAL_ERROR "GenerateCubesFromLabels: Unable to find the VTK build folder.")
endif()

# Prevent a "command line is too long" failure in Windows.
set(CMAKE_NINJA_FORCE_RESPONSE_FILE "ON" CACHE BOOL "Force Ninja to use response files.")
add_executable(GenerateCubesFromLabels MACOSX_BUNDLE GenerateCubesFromLabels.cxx )
  target_link_libraries(GenerateCubesFromLabels PRIVATE ${VTK_LIBRARIES}
)
# vtk_module_autoinit is needed
vtk_module_autoinit(
  TARGETS GenerateCubesFromLabels
  MODULES ${VTK_LIBRARIES}
)

Download and Build GenerateCubesFromLabels

Click here to download GenerateCubesFromLabels and its CMakeLists.txt file. Once the tarball GenerateCubesFromLabels.tar has been downloaded and extracted,

cd GenerateCubesFromLabels/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:

./GenerateCubesFromLabels

WINDOWS USERS

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