Color Labeled Regions in Image

Synopsis

Color labeled regions in an image.

Results

image.png

image.png

output.png

output.png

Code

C++

#include "itkBinaryImageToLabelMapFilter.h"
#include "itkImage.h"
#include "itkImageFileWriter.h"
#include "itkImageRegionIterator.h"
#include "itkLabelMapToLabelImageFilter.h"
#include "itkLabelMapOverlayImageFilter.h"
#include "itkRGBPixel.h"

using ImageType = itk::Image<unsigned char, 2>;
static void
CreateImage(ImageType::Pointer image);

int
main(int, char *[])
{
  ImageType::Pointer image = ImageType::New();
  CreateImage(image);

  using BinaryImageToLabelMapFilterType = itk::BinaryImageToLabelMapFilter<ImageType>;
  BinaryImageToLabelMapFilterType::Pointer binaryImageToLabelMapFilter = BinaryImageToLabelMapFilterType::New();
  binaryImageToLabelMapFilter->SetInput(image);
  binaryImageToLabelMapFilter->Update();

  using RGBPixelType = itk::RGBPixel<unsigned char>;
  using RGBImageType = itk::Image<RGBPixelType>;

  using LabelMapOverlayImageFilterType =
    itk::LabelMapOverlayImageFilter<BinaryImageToLabelMapFilterType::OutputImageType, ImageType, RGBImageType>;
  LabelMapOverlayImageFilterType::Pointer labelMapOverlayImageFilter = LabelMapOverlayImageFilterType::New();
  labelMapOverlayImageFilter->SetInput(binaryImageToLabelMapFilter->GetOutput());
  labelMapOverlayImageFilter->SetFeatureImage(image);
  labelMapOverlayImageFilter->SetOpacity(.5);
  labelMapOverlayImageFilter->Update();

  using WriterType = itk::ImageFileWriter<RGBImageType>;
  WriterType::Pointer writer = WriterType::New();
  writer->SetFileName("output.png");
  writer->SetInput(labelMapOverlayImageFilter->GetOutput());
  writer->Update();

  return EXIT_SUCCESS;
}

void
CreateImage(ImageType::Pointer image)
{
  // Create a black image with a white square
  ImageType::IndexType start;
  start.Fill(0);

  ImageType::SizeType size;
  size.Fill(100);

  ImageType::RegionType region;
  region.SetSize(size);
  region.SetIndex(start);
  image->SetRegions(region);
  image->Allocate();
  image->FillBuffer(0);

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

  // Make two squares
  while (!imageIterator.IsAtEnd())
  {
    if ((imageIterator.GetIndex()[0] > 5 && imageIterator.GetIndex()[0] < 20) &&
        (imageIterator.GetIndex()[1] > 5 && imageIterator.GetIndex()[1] < 20))
    {
      imageIterator.Set(255);
    }

    if ((imageIterator.GetIndex()[0] > 50 && imageIterator.GetIndex()[0] < 70) &&
        (imageIterator.GetIndex()[1] > 50 && imageIterator.GetIndex()[1] < 70))
    {
      imageIterator.Set(255);
    }
    ++imageIterator;
  }

  using WriterType = itk::ImageFileWriter<ImageType>;
  WriterType::Pointer writer = WriterType::New();
  writer->SetFileName("image.png");
  writer->SetInput(image);
  writer->Update();
}

Classes demonstrated

template<typename TLabelMap, typename TFeatureImage, typename TOutputImage = Image<RGBPixel<typename TFeatureImage::PixelType>, TFeatureImage::ImageDimension>>
class LabelMapOverlayImageFilter : public itk::LabelMapFilter<TLabelMap, TOutputImage>

Apply a colormap to a label map and superimpose it on an image.

Apply a colormap to a label map and put it on top of the feature image. The feature image is typically the image from which the labeling was produced. Use the SetInput function to set the LabelMap, and the SetFeatureImage function to set the feature image.

The set of colors is a good selection of distinct colors. The opacity of the label map can be defined by the user. A background label produce a gray pixel with the same intensity than the input one.

This implementation was taken from the Insight Journal paper:

https://www.insight-journal.org/browse/publication/176
Author

Gaetan Lehmann. Biologie du Developpement et de la Reproduction, INRA de Jouy-en-Josas, France.

See

LabelOverlayImageFilter, LabelOverlayFunctor

See

LabelMapToRGBImageFilter, LabelMapToBinaryImageFilter, LabelMapToLabelImageFilter

ITK Sphinx Examples:

See itk::LabelMapOverlayImageFilter for additional documentation.