ITK/Examples/ImageProcessing/RelabelComponentImageFilter

Description

Relabel the components (blobs) in an image such that consecutive labels are used. This example creates a black image with one rectangle consisting of pixels with value 100 and a second rectangle consisting of pixels with value 200. There are three resulting components (the background and the two rectangles). The relabel filter labels these three components 0, 1, and 2.

Displayed Output

The original image and an intensity scaled version of the relabeled image.

RelabelComponentImageFilter.cxx

<source lang="cpp">

1. include "itkImage.h"
2. include "itkImageFileReader.h"
3. include "itkCustomColormapFunction.h"
4. include "itkScalarToRGBColormapImageFilter.h"
5. include "itkRGBPixel.h"
6. include "itkMersenneTwisterRandomVariateGenerator.h"

1. include "itkRelabelComponentImageFilter.h"

1. include "QuickView.h"

typedef itk::RGBPixel<unsigned char> RGBPixelType; typedef itk::Image<RGBPixelType, 2> RGBImageType; typedef itk::Image<unsigned char, 2> ImageType; typedef itk::Function::CustomColormapFunction<

 ImageType::PixelType, RGBImageType::PixelType> ColormapType;

static void CreateImage(

 ImageType::Pointer image);

static void CreateRandomColormap(\

 unsigned int size, ColormapType::Pointer colormap);

int main(int, char *[]) {

 ImageType::Pointer image = ImageType::New();

 CreateImage(image);
 
 typedef itk::RelabelComponentImageFilter<ImageType, ImageType> FilterType;
 FilterType::Pointer relabelFilter =
   FilterType::New();
 relabelFilter->SetInput(image);

 typedef itk::ScalarToRGBColormapImageFilter<ImageType, RGBImageType> ColormapFilterType;
 ColormapFilterType::Pointer colormapFilter1 =
   ColormapFilterType::New();

 ColormapType::Pointer largeColormap
   = ColormapType::New();
 CreateRandomColormap(255, largeColormap);

 colormapFilter1->SetInput (image);
 colormapFilter1->SetColormap(largeColormap);

 ColormapFilterType::Pointer colormapFilter2 =
  ColormapFilterType::New();
 colormapFilter2->SetInput (relabelFilter->GetOutput());
 colormapFilter2->SetColormap(largeColormap);

 QuickView viewer;
 viewer.AddRGBImage(
   colormapFilter1->GetOutput(),
   true,
   "Original");

 viewer.AddRGBImage(
   colormapFilter2->GetOutput(),
   true,
   "Relabeled");

 viewer.Visualize();

 return EXIT_SUCCESS;

}

void CreateImage(ImageType::Pointer image) {

 // Create an image with 2 connected components
 ImageType::RegionType region;
 ImageType::IndexType start;
 start[0] = 0;
 start[1] = 0;

 ImageType::SizeType size;
 size[0] = 200;
 size[1] = 300;

 region.SetSize(size);
 region.SetIndex(start);

 image->SetRegions(region);
 image->Allocate();

 itk::ImageRegionIterator<ImageType> imageIterator(image,region);

 while(!imageIterator.IsAtEnd())
   {
   if(imageIterator.GetIndex()[0] > 100 &&
     imageIterator.GetIndex()[0] < 150 &&
     imageIterator.GetIndex()[1] > 100 &&
     imageIterator.GetIndex()[1] < 150)
     {
     imageIterator.Set(200);
     }
   else if(imageIterator.GetIndex()[0] > 50 &&
     imageIterator.GetIndex()[0] < 70 &&
     imageIterator.GetIndex()[1] > 50 &&
     imageIterator.GetIndex()[1] < 70)
     {
     imageIterator.Set(100);
     }
   else
     {
     imageIterator.Set(0);
     }

   ++imageIterator;
 }

}

void CreateRandomColormap(unsigned int size, ColormapType::Pointer colormap) {

 ColormapType::ChannelType redChannel;
 ColormapType::ChannelType greenChannel;
 ColormapType::ChannelType blueChannel;
 itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer random =
   itk::Statistics::MersenneTwisterRandomVariateGenerator::New();

 random->SetSeed ( 8775070 );
 for (unsigned int i = 0; i < size; ++i)
   {
   redChannel.push_back(static_cast<ColormapType::RealType>
                        (random->GetUniformVariate(.3, 1.0)));
   greenChannel.push_back(static_cast<ColormapType::RealType>
                          (random->GetUniformVariate(.3, 1.0)));
   blueChannel.push_back(static_cast<ColormapType::RealType>
                         (random->GetUniformVariate(.3, 1.0)));
   }
 colormap->SetRedChannel(redChannel);
 colormap->SetGreenChannel(greenChannel);
 colormap->SetBlueChannel(blueChannel);

} </source>

CMakeLists.txt

<syntaxhighlight lang="cmake"> cmake_minimum_required(VERSION 3.9.5)

project(RelabelComponentImageFilter)

find_package(ITK REQUIRED) include(${ITK_USE_FILE}) if (ITKVtkGlue_LOADED)

 find_package(VTK REQUIRED)
 include(${VTK_USE_FILE})

else()

 find_package(ItkVtkGlue REQUIRED)
 include(${ItkVtkGlue_USE_FILE})
 set(Glue ItkVtkGlue)

endif()

add_executable(RelabelComponentImageFilter MACOSX_BUNDLE RelabelComponentImageFilter.cxx) target_link_libraries(RelabelComponentImageFilter

 ${Glue}  ${VTK_LIBRARIES} ${ITK_LIBRARIES})

</syntaxhighlight>

Download and Build RelabelComponentImageFilter

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

cd RelabelComponentImageFilter/build 

• If ITK is installed:

cmake ..

• If ITK is not installed but compiled on your system, you will need to specify the path to your ITK build:

cmake -DITK_DIR:PATH=/home/me/itk_build ..

Build the project,

make

and run it:

./RelabelComponentImageFilter

WINDOWS USERS PLEASE NOTE: Be sure to add the VTK and ITK bin directories to your path. This will resolve the VTK and ITK dll's at run time.

Building All of the Examples

Many of the examples in the ITK Wiki Examples Collection require VTK. You can build all of the the examples by following these instructions. If you are a new VTK user, you may want to try the Superbuild which will build a proper ITK and VTK.

ItkVtkGlue

ITK >= 4

For examples that use QuickView (which depends on VTK), you must have built ITK with Module_ITKVtkGlue=ON.

ITK < 4

Some of the ITK Examples require VTK to display the images. If you download the entire ITK Wiki Examples Collection, the ItkVtkGlue directory will be included and configured. If you wish to just build a few examples, then you will need to download ItkVtkGlue and build it. When you run cmake it will ask you to specify the location of the ItkVtkGlue binary directory.