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DiscreteMarchingCubes

Repository source: DiscreteMarchingCubes

Description

Creates surfaces from labeled data. Volume data does not always contain samples of continuous data. A volume may contain discrete integer values, often the result of segmentation. vtkDiscreteFlyingEdges3D or vtkDiscreteMarchingCubes create surfaces from these segmented volumes using a modified flying edges or marching cubes algorithm. The algorithm generates one or more models representing the boundaries between the specified label and the adjacent structures. One or more label values must be specified to generate the models. The boundary positions are always defined to be half-way between adjacent voxels.

Seealso

SmoothDiscreteMarchingCubes produces smooth models.

Other languages

See (Python)

Question

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

Code

DiscreteMarchingCubes.cxx

#include <vtkActor.h>
#include <vtkImageData.h>
#include <vtkImageMathematics.h>
#include <vtkImageThreshold.h>
#include <vtkLookupTable.h>
#include <vtkMinimalStandardRandomSequence.h>
#include <vtkNamedColors.h>
#include <vtkNew.h>
#include <vtkPolyDataMapper.h>
#include <vtkRenderWindow.h>
#include <vtkRenderWindowInteractor.h>
#include <vtkRenderer.h>
#include <vtkSampleFunction.h>
#include <vtkSmartPointer.h>
#include <vtkSphere.h>
#include <vtkVersion.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

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

namespace {
vtkSmartPointer<vtkLookupTable> MakeColors(unsigned int n);

vtkSmartPointer<vtkImageData> MakeBlob(int n, double radius);
} // namespace

int main(int /*argc*/, char* /* argv */[])
{
  int n = 20;
  double radius = 8;

  vtkSmartPointer<vtkImageData> blob = MakeBlob(n, radius);

#ifdef USE_FLYING_EDGES
  vtkNew<vtkDiscreteFlyingEdges3D> discrete;
#else
  vtkNew<vtkDiscreteMarchingCubes> discrete;
#endif
  discrete->SetInputData(blob);
  discrete->GenerateValues(n, 1, n);

  vtkSmartPointer<vtkLookupTable> lut = MakeColors(n);

  vtkNew<vtkPolyDataMapper> mapper;
  mapper->SetInputConnection(discrete->GetOutputPort());
  mapper->SetLookupTable(lut);
  mapper->SetScalarRange(0, lut->GetNumberOfColors());

  // Create the RenderWindow, Renderer and both Actors.
  //
  vtkNew<vtkRenderer> ren1;
  vtkNew<vtkRenderWindow> renWin;
  renWin->AddRenderer(ren1);
  renWin->SetWindowName("DiscreteMarchingCubes");

  vtkNew<vtkRenderWindowInteractor> iren;
  iren->SetRenderWindow(renWin);

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

  ren1->AddActor(actor);

  vtkNew<vtkNamedColors> colors;
  ren1->SetBackground(colors->GetColor3d("Burlywood").GetData());

  renWin->Render();

  iren->Start();

  return EXIT_SUCCESS;
}

namespace {
vtkSmartPointer<vtkImageData> MakeBlob(int n, double radius)
{
  vtkNew<vtkImageData> blobImage;

  double maxR = 50 - 2.0 * radius;
  vtkNew<vtkMinimalStandardRandomSequence> randomSequence;
  randomSequence->SetSeed(5071);
  for (int i = 0; i < n; ++i)
  {
    vtkNew<vtkSphere> sphere;
    sphere->SetRadius(radius);
    auto x = randomSequence->GetRangeValue(-maxR, maxR);
    randomSequence->Next();
    auto y = randomSequence->GetRangeValue(-maxR, maxR);
    randomSequence->Next();
    auto z = randomSequence->GetRangeValue(-maxR, maxR);
    randomSequence->Next();

    sphere->SetCenter(int(x), int(y), int(z));

    vtkNew<vtkSampleFunction> sampler;
    sampler->SetImplicitFunction(sphere);
    sampler->SetOutputScalarTypeToFloat();
    sampler->SetSampleDimensions(100, 100, 100);
    sampler->SetModelBounds(-50, 50, -50, 50, -50, 50);

    vtkNew<vtkImageThreshold> thres;
    thres->SetInputConnection(sampler->GetOutputPort());
    thres->ThresholdByLower(radius * radius);
    thres->ReplaceInOn();
    thres->ReplaceOutOn();
    thres->SetInValue(i + 1);
    thres->SetOutValue(0);
    thres->Update();
    if (i == 0)
    {
      blobImage->DeepCopy(thres->GetOutput());
    }

    vtkNew<vtkImageMathematics> maxValue;
    maxValue->SetInputData(0, blobImage);
    maxValue->SetInputData(1, thres->GetOutput());
    maxValue->SetOperationToMax();
    maxValue->Modified();
    maxValue->Update();

    blobImage->DeepCopy(maxValue->GetOutput());
  }
  return blobImage;
}

// Generate some random colors.
vtkSmartPointer<vtkLookupTable> MakeColors(unsigned int n)
{
  vtkNew<vtkLookupTable> lut;
  lut->SetNumberOfColors(n);
  lut->SetTableRange(0, n - 1);
  lut->SetScaleToLinear();
  lut->Build();
  lut->SetTableValue(0, 0, 0, 0, 1);

  vtkNew<vtkMinimalStandardRandomSequence> randomSequence;
  randomSequence->SetSeed(5071);
  for (int i = 1; i < static_cast<int>(n); ++i)
  {
    auto r = randomSequence->GetRangeValue(0.4, 1);
    randomSequence->Next();
    auto g = randomSequence->GetRangeValue(0.4, 1);
    randomSequence->Next();
    auto b = randomSequence->GetRangeValue(0.4, 1);
    randomSequence->Next();
    lut->SetTableValue(i, r, g, b, 1.0);
  }
  return lut;
}
} // namespace

CMakeLists.txt

cmake_minimum_required(VERSION 3.12 FATAL_ERROR)

project(DiscreteMarchingCubes)

find_package(VTK COMPONENTS 
  CommonColor
  CommonCore
  CommonDataModel
  FiltersGeneral
  ImagingCore
  ImagingHybrid
  ImagingMath
  InteractionStyle
  RenderingContextOpenGL2
  RenderingCore
  RenderingFreeType
  RenderingGL2PSOpenGL2
  RenderingOpenGL2
)

if (NOT VTK_FOUND)
  message(FATAL_ERROR "DiscreteMarchingCubes: 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(DiscreteMarchingCubes MACOSX_BUNDLE DiscreteMarchingCubes.cxx )
  target_link_libraries(DiscreteMarchingCubes PRIVATE ${VTK_LIBRARIES}
)
# vtk_module_autoinit is needed
vtk_module_autoinit(
  TARGETS DiscreteMarchingCubes
  MODULES ${VTK_LIBRARIES}
)

Download and Build DiscreteMarchingCubes

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

cd DiscreteMarchingCubes/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:

./DiscreteMarchingCubes

WINDOWS USERS

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