Convert Image With Labeled Regions to ShapeLabelMap

Synopsis

Convert an itk::Image consisting of labeled regions to a ShapeLabelMap.

Results

Output:

There are 2 objects.

Code

C++

#include "itkImage.h"
#include "itkImageFileWriter.h"
#include "itkLabelImageToShapeLabelMapFilter.h"
#include "itkConnectedComponentImageFilter.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 ConnectedComponentImageFilterType = itk::ConnectedComponentImageFilter<ImageType, ImageType>;
  ConnectedComponentImageFilterType::Pointer connectedComponentImageFilter = ConnectedComponentImageFilterType::New();
  connectedComponentImageFilter->SetInput(image);
  connectedComponentImageFilter->Update();

  using LabelImageToShapeLabelMapFilterType = itk::LabelImageToShapeLabelMapFilter<ImageType>;
  LabelImageToShapeLabelMapFilterType::Pointer labelImageToShapeLabelMapFilter =
    LabelImageToShapeLabelMapFilterType::New();
  labelImageToShapeLabelMapFilter->SetInput(connectedComponentImageFilter->GetOutput());
  labelImageToShapeLabelMapFilter->Update();

  // The output of this filter is an itk::LabelMap, which contains itk::LabelObject's
  std::cout << "There are " << labelImageToShapeLabelMapFilter->GetOutput()->GetNumberOfLabelObjects() << " objects."
            << std::endl;

  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;
  unsigned int        NumRows = 200;
  unsigned int        NumCols = 300;
  size[0] = NumRows;
  size[1] = NumCols;

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

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

  // Make a square
  for (unsigned int r = 20; r < 80; r++)
  {
    for (unsigned int c = 30; c < 100; c++)
    {
      ImageType::IndexType pixelIndex;
      pixelIndex[0] = r;
      pixelIndex[1] = c;

      image->SetPixel(pixelIndex, 255);
    }
  }

  // Make another square
  for (unsigned int r = 100; r < 130; r++)
  {
    for (unsigned int c = 115; c < 160; c++)
    {
      ImageType::IndexType pixelIndex;
      pixelIndex[0] = r;
      pixelIndex[1] = c;

      image->SetPixel(pixelIndex, 255);
    }
  }
}

Classes demonstrated

template<typename TInputImage, typename TOutputImage = LabelMap<ShapeLabelObject<typename TInputImage::PixelType, TInputImage::ImageDimension>>>
class LabelImageToShapeLabelMapFilter : public itk::ImageToImageFilter<TInputImage, TOutputImage>

Converts a label image to a label map and valuates the shape attributes.

A convenient class that converts a label image to a label map and valuates the shape attribute at once.

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

ShapeLabelObject, LabelShapeOpeningImageFilter, LabelStatisticsOpeningImageFilter

ITK Sphinx Examples:

• All ITK Sphinx Examples

• Shape Attributes For Binary Image

• Convert Image With Labeled Regions To ShapeLabelMap

See itk::LabelImageToShapeLabelMapFilter for additional documentation.