SphinxExamples/src/Segmentation/ConnectedComponents/LabelConnectComponentsInGrayscaleImage/Code.cxx

/*=========================================================================
 *
 *  Copyright NumFOCUS
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/
#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkLabelToRGBImageFilter.h"
#include "itkRelabelComponentImageFilter.h"
#include "itkLabelStatisticsImageFilter.h"
 
#include "itkScalarConnectedComponentImageFilter.h"
 
#include "itksys/SystemTools.hxx"
#include <sstream>
 
#ifdef ENABLE_QUICKVIEW
#  include "QuickView.h"
#endif
 
template <typename TImage>
static void
CreateImage(TImage * const image);
 
template <typename TImage, typename TLabelImage>
static void
SummarizeLabelStatistics(TImage * image, TLabelImage * labelImage);
 
int
main(int argc, char * argv[])
{
  constexpr unsigned int Dimension = 2;
  using PixelType = short;
  using ImageType = itk::Image<PixelType, Dimension>;
 
  using RGBPixelType = itk::RGBPixel<unsigned char>;
  using RGBImageType = itk::Image<RGBPixelType, Dimension>;
 
  using LabelPixelType = unsigned int;
  using LabelImageType = itk::Image<LabelPixelType, Dimension>;
 
  ImageType::Pointer image;
  PixelType          distanceThreshold = 4;
  if (argc < 2)
  {
    image = ImageType::New();
    CreateImage(image.GetPointer());
  }
  else
  {
    using ReaderType = itk::ImageFileReader<ImageType>;
    ReaderType::Pointer reader = ReaderType::New();
    reader->SetFileName(argv[1]);
    reader->Update();
 
    if (argc > 2)
    {
      distanceThreshold = static_cast<PixelType>(atoi(argv[2]));
    }
    image = reader->GetOutput();
  }
 
 
  using ConnectedComponentImageFilterType = itk::ScalarConnectedComponentImageFilter<ImageType, LabelImageType>;
 
  ConnectedComponentImageFilterType::Pointer connected = ConnectedComponentImageFilterType::New();
  connected->SetInput(image);
  connected->SetDistanceThreshold(distanceThreshold);
 
  using RelabelFilterType = itk::RelabelComponentImageFilter<LabelImageType, LabelImageType>;
  RelabelFilterType::Pointer        relabel = RelabelFilterType::New();
  RelabelFilterType::ObjectSizeType minSize = 20;
  if (argc > 3)
  {
    minSize = std::stoi(argv[3]);
  }
  relabel->SetInput(connected->GetOutput());
  relabel->SetMinimumObjectSize(minSize);
  relabel->Update();
 
  SummarizeLabelStatistics(image.GetPointer(), relabel->GetOutput());
 
  using RGBFilterType = itk::LabelToRGBImageFilter<LabelImageType, RGBImageType>;
  RGBFilterType::Pointer rgbFilter = RGBFilterType::New();
  rgbFilter->SetInput(relabel->GetOutput());
 
#ifdef ENABLE_QUICKVIEW
  QuickView viewer;
  viewer.AddImage(
    image.GetPointer(), true, argc > 1 ? itksys::SystemTools::GetFilenameName(argv[1]) : "Generated image");
 
  std::stringstream desc;
  desc << "Scalar Connected Components:\n# of Objects: " << relabel->GetNumberOfObjects() << " Threshold: "
       << itk::NumericTraits<ConnectedComponentImageFilterType::OutputPixelType>::PrintType(
            connected->GetDistanceThreshold())
       << " Min Size: " << relabel->GetMinimumObjectSize();
  viewer.AddRGBImage(rgbFilter->GetOutput(), true, desc.str());
 
  viewer.Visualize();
#endif
 
  return EXIT_SUCCESS;
}
 
template <typename TImage>
void
CreateImage(TImage * const image)
{
  // Create an image with 2 connected components
  typename TImage::IndexType start = { { 0, 0 } };
  start[0] = 0;
  start[1] = 0;
 
  typename TImage::SizeType size;
  unsigned int              NumRows = 200;
  unsigned int              NumCols = 300;
  size[0] = NumRows;
  size[1] = NumCols;
 
  typename TImage::RegionType region(start, size);
 
  image->SetRegions(region);
  image->Allocate();
 
  // Make a square
  for (typename TImage::IndexValueType r = 20; r < 80; r++)
  {
    for (typename TImage::IndexValueType c = 30; c < 100; c++)
    {
      typename TImage::IndexType pixelIndex = { { r, c } };
 
      image->SetPixel(pixelIndex, 255);
    }
  }
 
  // Make another square
  for (typename TImage::IndexValueType r = 100; r < 130; r++)
  {
    for (typename TImage::IndexValueType c = 115; c < 160; c++)
    {
      typename TImage::IndexType pixelIndex = { { r, c } };
 
      image->SetPixel(pixelIndex, 255);
    }
  }
}
 
template <typename TImage, typename TLabelImage>
void
SummarizeLabelStatistics(TImage * image, TLabelImage * labelImage)
{
  using LabelStatisticsImageFilterType = itk::LabelStatisticsImageFilter<TImage, TLabelImage>;
  typename LabelStatisticsImageFilterType::Pointer labelStatisticsImageFilter = LabelStatisticsImageFilterType::New();
  labelStatisticsImageFilter->SetLabelInput(labelImage);
  labelStatisticsImageFilter->SetInput(image);
  labelStatisticsImageFilter->UseHistogramsOn(); // needed to compute median
  labelStatisticsImageFilter->Update();
 
  std::cout << "Number of labels: " << labelStatisticsImageFilter->GetNumberOfLabels() << std::endl;
  std::cout << std::endl;
 
  using LabelPixelType = typename LabelStatisticsImageFilterType::LabelPixelType;
 
  for (auto vIt = labelStatisticsImageFilter->GetValidLabelValues().begin();
       vIt != labelStatisticsImageFilter->GetValidLabelValues().end();
       ++vIt)
  {
    if (labelStatisticsImageFilter->HasLabel(*vIt))
    {
      LabelPixelType labelValue = *vIt;
      std::cout << "Label: " << *vIt << std::endl;
      std::cout << "\tmin: " << labelStatisticsImageFilter->GetMinimum(labelValue) << std::endl;
      std::cout << "\tmax: " << labelStatisticsImageFilter->GetMaximum(labelValue) << std::endl;
      std::cout << "\tmedian: " << labelStatisticsImageFilter->GetMedian(labelValue) << std::endl;
      std::cout << "\tmean: " << labelStatisticsImageFilter->GetMean(labelValue) << std::endl;
      std::cout << "\tsigma: " << labelStatisticsImageFilter->GetSigma(labelValue) << std::endl;
      std::cout << "\tvariance: " << labelStatisticsImageFilter->GetVariance(labelValue) << std::endl;
      std::cout << "\tsum: " << labelStatisticsImageFilter->GetSum(labelValue) << std::endl;
      std::cout << "\tcount: " << labelStatisticsImageFilter->GetCount(labelValue) << std::endl;
      std::cout << "\tregion: " << labelStatisticsImageFilter->GetRegion(labelValue) << std::endl;
    }
  }
}