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SmoothDiscreteMarchingCubes

vtk-examples/Cxx/Modelling/SmoothDiscreteMarchingCubes

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. This example smooths the discrete models generated by vtkDiscreteMarchingCubes with vtkWindowedSincPolyDataFilter.

Seealso

DiscreteMarchingCubes produces rough models.

Other languages

See (Python)

Question

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

Code

SmoothDiscreteMarchingCubes.cxx

#include <vtkActor.h>
#include <vtkDiscreteMarchingCubes.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 <vtkWindowedSincPolyDataFilter.h>

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);

  vtkNew<vtkDiscreteMarchingCubes> discrete;
  discrete->SetInputData(blob);
  discrete->GenerateValues(n, 1, n);

  unsigned int smoothingIterations = 15;
  double passBand = 0.001;
  double featureAngle = 120.0;

  vtkNew<vtkWindowedSincPolyDataFilter> smoother;
  smoother->SetInputConnection(discrete->GetOutputPort());
  smoother->SetNumberOfIterations(smoothingIterations);
  smoother->BoundarySmoothingOff();
  smoother->FeatureEdgeSmoothingOff();
  smoother->SetFeatureAngle(featureAngle);
  smoother->SetPassBand(passBand);
  smoother->NonManifoldSmoothingOn();
  smoother->NormalizeCoordinatesOn();
  smoother->Update();

  vtkSmartPointer<vtkLookupTable> lut = MakeColors(n);

  vtkNew<vtkPolyDataMapper> mapper;
  mapper->SetInputConnection(smoother->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("SmoothDiscreteMarchingCubes");

  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;

  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(SmoothDiscreteMarchingCubes)

find_package(VTK COMPONENTS 
  vtkCommonColor
  vtkCommonCore
  vtkCommonDataModel
  vtkFiltersCore
  vtkFiltersGeneral
  vtkImagingCore
  vtkImagingHybrid
  vtkImagingMath
  vtkInteractionStyle
  vtkRenderingContextOpenGL2
  vtkRenderingCore
  vtkRenderingFreeType
  vtkRenderingGL2PSOpenGL2
  vtkRenderingOpenGL2
  QUIET
)

if (NOT VTK_FOUND)
  message("Skipping SmoothDiscreteMarchingCubes: ${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(SmoothDiscreteMarchingCubes MACOSX_BUNDLE SmoothDiscreteMarchingCubes.cxx )
  target_link_libraries(SmoothDiscreteMarchingCubes PRIVATE ${VTK_LIBRARIES})
else()
  # 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(SmoothDiscreteMarchingCubes MACOSX_BUNDLE SmoothDiscreteMarchingCubes.cxx )
  target_link_libraries(SmoothDiscreteMarchingCubes PRIVATE ${VTK_LIBRARIES})
  # vtk_module_autoinit is needed
  vtk_module_autoinit(
    TARGETS SmoothDiscreteMarchingCubes
    MODULES ${VTK_LIBRARIES}
    )
endif()

Download and Build SmoothDiscreteMarchingCubes

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

cd SmoothDiscreteMarchingCubes/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:

./SmoothDiscreteMarchingCubes

WINDOWS USERS

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