VoxelsOnBoundary
vtk-examples/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 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 <vtkImageData.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 <vtkPointSet.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[])
{
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 3.3 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.