VoxelsOnBoundary

Description¶

This example uses vtkMultiThreshold to extract voxels that are inside an isosurface and on the boundary of the isosurface. The result is a vtkUnstructuredGrid for each set of voxels. Before processing, vtkImageShrink3D reduces the resolution by a factor of 4.

Compare these results with

usage

VoxelsOnBoundary FullHead.mhd

Info

Compare these results with MedicalDemo1 that extracts the surface using vtkMarchingCubes to extract an interpolated isosurface.

Info

The example uses src/Testing/Data/FullHead.mhd which references src/Testing/Data/FullHead.raw.gz.

Question

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

Code¶

VoxelsOnBoundary.cxx

#include <vtkActor.h>
#include <vtkCamera.h>
#include <vtkDataSetMapper.h>
#include <vtkImageDataToPointSet.h>
#include <vtkImageShrink3D.h>
#include <vtkMetaImageReader.h>
#include <vtkMultiBlockDataSet.h>
#include <vtkMultiThreshold.h>
#include <vtkNamedColors.h>
#include <vtkNew.h>
#include <vtkPlane.h>
#include <vtkProperty.h>
#include <vtkRenderWindow.h>
#include <vtkRenderWindowInteractor.h>
#include <vtkRenderer.h>
#include <vtkUnstructuredGrid.h>

#include <iostream>
#include <string>
#include <vector>

int main(int argc, char* argv[])
{
  if (argc < 2)
  {
    cout << "Usage: " << argv[0] << " file.mhd e.g. FullHead.mhd" << endl;
    return EXIT_FAILURE;
  }

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

  vtkNew<vtkImageShrink3D> shrink;
  shrink->SetShrinkFactors(4, 4, 4);
  shrink->SetInputConnection(reader->GetOutputPort());
  shrink->Update();

  // Create a PointSet from the ImageData
  vtkNew<vtkImageDataToPointSet> imageDataToPointSet;
  imageDataToPointSet->SetInputConnection(reader->GetOutputPort());
  imageDataToPointSet->SetInputConnection(shrink->GetOutputPort());
  imageDataToPointSet->Update();

  // Extract voxels on the border between the inside and outside.
  vtkNew<vtkMultiThreshold> threshold;
  // Inside points have one or more points above the isosurface
  int insideId = threshold->AddIntervalSet(
      501, 20000, vtkMultiThreshold::CLOSED, vtkMultiThreshold::CLOSED,
      vtkDataObject::FIELD_ASSOCIATION_POINTS, "ImageScalars", 0, 0);
  // Border points have points that straddle the boundary
  int borderId = threshold->AddIntervalSet(
      499.9999, 501.0000, vtkMultiThreshold::OPEN, vtkMultiThreshold::OPEN,
      vtkDataObject::FIELD_ASSOCIATION_POINTS, "ImageScalars", 0, 0);

  threshold->SetInputData(imageDataToPointSet->GetOutput());

  // Select the intervals to be output
  threshold->OutputSet(insideId);
  threshold->OutputSet(borderId);
  threshold->Update();

  // Visualize
  vtkNew<vtkNamedColors> colors;
  // vtkColor3d outsideColor    = colors->GetColor3d("Crimson");
  vtkColor3d insideColor = colors->GetColor3d("Banana");
  vtkColor3d borderColor = colors->GetColor3d("Mint");
  // vtkColor3d surfaceColor    = colors->GetColor3d("Peacock");
  vtkColor3d backgroundColor = colors->GetColor3d("Silver");

  vtkNew<vtkPlane> plane;
  plane->SetOrigin(dynamic_cast<vtkUnstructuredGrid*>(
                       vtkMultiBlockDataSet::SafeDownCast(
                           threshold->GetOutput()->GetBlock(insideId))
                           ->GetBlock(0))
                       ->GetCenter());
  plane->SetNormal(1.0, -1.0, -1.0);

  // Inside
  vtkNew<vtkDataSetMapper> insideMapper;
  insideMapper->SetInputData(dynamic_cast<vtkUnstructuredGrid*>(
      vtkMultiBlockDataSet::SafeDownCast(
          threshold->GetOutput()->GetBlock(insideId))
          ->GetBlock(0)));
  insideMapper->ScalarVisibilityOff();

  vtkNew<vtkActor> insideActor;
  insideActor->SetMapper(insideMapper);
  insideActor->GetProperty()->SetDiffuseColor(insideColor.GetData());
  insideActor->GetProperty()->SetSpecular(.6);
  insideActor->GetProperty()->SetSpecularPower(30);
  insideActor->GetProperty()->EdgeVisibilityOn();

  // Border
  vtkNew<vtkDataSetMapper> borderMapper;
  borderMapper->SetInputData(dynamic_cast<vtkUnstructuredGrid*>(
      vtkMultiBlockDataSet::SafeDownCast(
          threshold->GetOutput()->GetBlock(borderId))
          ->GetBlock(0)));
  borderMapper->ScalarVisibilityOff();

  vtkNew<vtkActor> borderActor;
  borderActor->SetMapper(borderMapper);
  borderActor->GetProperty()->SetDiffuseColor(borderColor.GetData());
  borderActor->GetProperty()->SetSpecular(.6);
  borderActor->GetProperty()->SetSpecularPower(30);
  borderActor->GetProperty()->EdgeVisibilityOn();

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

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

  renderer->SetBackground(backgroundColor.GetData());
  renderer->UseHiddenLineRemovalOn();

  renderer->AddActor(insideActor);
  renderer->AddActor(borderActor);

  renderWindow->SetWindowName("CellsOnBoundary");
  renderWindow->Render();

  // Setup a good view
  renderer->GetActiveCamera()->SetViewUp(0, 0, -1);
  renderer->GetActiveCamera()->SetPosition(0, -1, 0);
  renderer->GetActiveCamera()->SetFocalPoint(0, 0, 0);
  renderer->GetActiveCamera()->Azimuth(30.0);
  renderer->GetActiveCamera()->Elevation(30.0);
  renderer->ResetCamera();
  renderer->GetActiveCamera()->Dolly(1.5);

  renderWindowInteractor->Start();

  return EXIT_SUCCESS;
}

CMakeLists.txt¶

cmake_minimum_required(VERSION 3.12 FATAL_ERROR)

project(VoxelsOnBoundary)

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

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

Download and Build VoxelsOnBoundary¶

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

cd VoxelsOnBoundary/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:

./VoxelsOnBoundary

WINDOWS USERS

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