VoxelsOnBoundary

VTKExamples/Cxx/ImageData/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 FullHead.mhd which references FullHead.raw.gz.

Question

If you have a simple question about this example contact us at VTKExamplesProject If your question is more complex and may require extended discussion, please use the VTK Discourse Forum

Code

VoxelsOnBoundary.cxx

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

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


int main (int argc, char *argv[])
{
  auto reader =
    vtkSmartPointer<vtkMetaImageReader>::New();
  reader->SetFileName (argv[1]);
  reader->Update();

  auto shrink =
    vtkSmartPointer<vtkImageShrink3D>::New();
  shrink->SetShrinkFactors(4, 4, 4);
  shrink->SetInputConnection(reader->GetOutputPort());
  shrink->Update();

  // Create a PointSet from the ImageData
  auto imageDataToPointSet =
    vtkSmartPointer<vtkImageDataToPointSet>::New();
  imageDataToPointSet->SetInputConnection(reader->GetOutputPort());
  imageDataToPointSet->SetInputConnection(shrink->GetOutputPort());
  imageDataToPointSet->Update();

  // Extract voxels on the border between the inside and outside.
  auto threshold =
    vtkSmartPointer<vtkMultiThreshold>::New();
  // 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
  auto colors =
    vtkSmartPointer<vtkNamedColors>::New();
  //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");

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

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

  auto insideActor =
    vtkSmartPointer<vtkActor>::New();
  insideActor->SetMapper(insideMapper);
  insideActor->GetProperty()->SetDiffuseColor(insideColor.GetData());
  insideActor->GetProperty()->SetSpecular(.6);
  insideActor->GetProperty()->SetSpecularPower(30);
  insideActor->GetProperty()->EdgeVisibilityOn();

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

  auto borderActor =
    vtkSmartPointer<vtkActor>::New();
  borderActor->SetMapper(borderMapper);
  borderActor->GetProperty()->SetDiffuseColor(borderColor.GetData());
  borderActor->GetProperty()->SetSpecular(.6);
  borderActor->GetProperty()->SetSpecularPower(30);
  borderActor->GetProperty()->EdgeVisibilityOn();

  auto renderer =
    vtkSmartPointer<vtkRenderer>::New();
  auto renderWindow =
    vtkSmartPointer<vtkRenderWindow>::New();
  renderWindow->AddRenderer(renderer);
  renderWindow->SetSize(640, 480);

  auto renderWindowInteractor =
    vtkSmartPointer<vtkRenderWindowInteractor>::New();
  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 3.3 FATAL_ERROR)

project(VoxelsOnBoundary)

find_package(VTK COMPONENTS 
  vtkCommonColor
  vtkCommonCore
  vtkCommonDataModel
  vtkFiltersGeneral
  vtkIOImage
  vtkImagingCore
  vtkInteractionStyle
  vtkRenderingContextOpenGL2
  vtkRenderingCore
  vtkRenderingFreeType
  vtkRenderingGL2PSOpenGL2
  vtkRenderingOpenGL2 QUIET)
if (NOT VTK_FOUND)
  message("Skipping VoxelsOnBoundary: ${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(VoxelsOnBoundary MACOSX_BUNDLE VoxelsOnBoundary.cxx )
  target_link_libraries(VoxelsOnBoundary PRIVATE ${VTK_LIBRARIES})
else ()
  # include all components
  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}
    )
endif () 

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.