int main (int argc, char *argv[])
{
    if(argc != 4)
    {
        std::cout << "Required arguments: InputFilename(ptx) NewRGB(mhd) OutputFilename(ptx)" << std::endl;
        return EXIT_FAILURE;
    }

    std::string inputFilename = argv[1];
    std::string newDepthImageFilename = argv[2];
    std::string outputFilename = argv[3];

    PTXImage ptxImage = PTXReader::Read(inputFilename);

    typedef itk::ImageFileReader<PTXImage::RGBVectorImageType> ImageReaderType;
    ImageReaderType::Pointer reader = ImageReaderType::New();
    reader->SetFileName(newDepthImageFilename);
    reader->Update();

    if(reader->GetOutput()->GetLargestPossibleRegion().GetSize() != ptxImage.GetSize())
    {
        std::cerr << "RGB image must be the same size as PTX image!" << std::endl;
        exit(-1);
    }

    ptxImage.ReplaceRGB(reader->GetOutput());

    ptxImage.WritePTX(outputFilename);

    return EXIT_SUCCESS;
}

// Run with: image.png image.mask 15 filled.png
int main(int argc, char *argv[])
{
  // Verify arguments
  if(argc != 5)
  {
    std::cerr << "Required arguments: image.png image.mask patchHalfWidth output.png" << std::endl;
    std::cerr << "Input arguments: ";
    for(int i = 1; i < argc; ++i)
    {
      std::cerr << argv[i] << " ";
    }
    return EXIT_FAILURE;
  }

  // Parse arguments
  std::string imageFilename = argv[1];
  std::string maskFilename = argv[2];

  std::stringstream ssPatchRadius;
  ssPatchRadius << argv[3];
  unsigned int patchHalfWidth = 0;
  ssPatchRadius >> patchHalfWidth;

  std::string outputFilename = argv[4];

  // Output arguments
  std::cout << "Reading image: " << imageFilename << std::endl;
  std::cout << "Reading mask: " << maskFilename << std::endl;
  std::cout << "Patch half width: " << patchHalfWidth << std::endl;
  std::cout << "Output: " << outputFilename << std::endl;

  typedef itk::Image<itk::CovariantVector<float, 3>, 2> ImageType;

  typedef  itk::ImageFileReader<ImageType> ImageReaderType;
  ImageReaderType::Pointer imageReader = ImageReaderType::New();
  imageReader->SetFileName(imageFilename);
  imageReader->Update();

  ImageType::Pointer image = ImageType::New();
  ITKHelpers::DeepCopy(imageReader->GetOutput(), image.GetPointer());

  Mask::Pointer mask = Mask::New();
  mask->Read(maskFilename);

  std::cout << "Mask size: " << mask->GetLargestPossibleRegion().GetSize() << std::endl;
  std::cout << "hole pixels: " << mask->CountHolePixels() << std::endl;
  std::cout << "valid pixels: " << mask->CountValidPixels() << std::endl;

  // Setup the GUI system
  QApplication app( argc, argv );
  // Without this, after we close the first dialog
  // (after the first iteration that is not accepted automatically), the event loop quits.
  app.setQuitOnLastWindowClosed(false);

  DummyPatchesDriver(image, mask, patchHalfWidth);

  return app.exec();
}

void QmitkDeformableRegistrationView::ApplyDeformationField()
{

  ImageReaderType::Pointer reader  = ImageReaderType::New();
  reader->SetFileName( m_Controls.m_QmitkBSplineRegistrationViewControls->m_Controls.m_DeformationField->text().toStdString() );
  reader->Update();

  DeformationFieldType::Pointer deformationField = reader->GetOutput();

  mitk::Image * mimage = dynamic_cast<mitk::Image*> (m_MovingNode->GetData());
  mitk::Image * fimage = dynamic_cast<mitk::Image*> (m_FixedNode->GetData());

  typedef itk::Image<float, 3> FloatImageType;

  FloatImageType::Pointer itkMovingImage = FloatImageType::New();
  FloatImageType::Pointer itkFixedImage = FloatImageType::New();
  mitk::CastToItkImage(mimage, itkMovingImage);
  mitk::CastToItkImage(fimage, itkFixedImage);

  typedef itk::WarpImageFilter<
                            FloatImageType,
                            FloatImageType,
                            DeformationFieldType  >     WarperType;

  typedef itk::LinearInterpolateImageFunction<
                                    FloatImageType,
                                    double          >  InterpolatorType;

  WarperType::Pointer warper = WarperType::New();
  InterpolatorType::Pointer interpolator = InterpolatorType::New();

  warper->SetInput( itkMovingImage );
  warper->SetInterpolator( interpolator );
  warper->SetOutputSpacing( itkFixedImage->GetSpacing() );
  warper->SetOutputOrigin( itkFixedImage->GetOrigin() );
  warper->SetOutputDirection (itkFixedImage->GetDirection() );
  warper->SetDisplacementField( deformationField );
  warper->Update();

  FloatImageType::Pointer outputImage = warper->GetOutput();
  mitk::Image::Pointer result = mitk::Image::New();

  mitk::CastToMitkImage(outputImage, result);

  // Create new DataNode
  mitk::DataNode::Pointer newNode = mitk::DataNode::New();
  newNode->SetData( result );
  newNode->SetProperty( "name", mitk::StringProperty::New("warped image") );

  // add the new datatree node to the datatree
  this->GetDefaultDataStorage()->Add(newNode);
  mitk::RenderingManager::GetInstance()->RequestUpdateAll();

  //Image::Pointer outputImage = this->GetOutput();
  //mitk::CastToMitkImage( warper->GetOutput(), outputImage );


}

int main(int argc, char*argv[])
{
  if(argc < 4)
  {
    std::cerr << "Required arguments: image mask output" << std::endl;
    return EXIT_FAILURE;
  }

  std::string imageFilename = argv[1];
  std::string maskFilename = argv[2];
  std::string outputFilename = argv[3];

  std::cout << "imageFilename: " << imageFilename << std::endl;
  std::cout << "maskFilename: " << maskFilename << std::endl;
  std::cout << "outputFilename: " << outputFilename << std::endl;

  typedef itk::ImageFileReader<ImageType> ImageReaderType;
  ImageReaderType::Pointer imageReader = ImageReaderType::New();
  imageReader->SetFileName(imageFilename);
  imageReader->Update();

  Mask::Pointer sourceMask = Mask::New();
  sourceMask->Read(maskFilename);

  Mask::Pointer targetMask = Mask::New();
  targetMask->SetRegions(sourceMask->GetLargestPossibleRegion());
  targetMask->Allocate();
  ITKHelpers::SetImageToConstant(targetMask.GetPointer(), HoleMaskPixelTypeEnum::VALID);

  typedef SSD<ImageType> DistanceFunctorType;
  DistanceFunctorType* patchDistanceFunctor = new DistanceFunctorType;
  patchDistanceFunctor->SetImage(imageReader->GetOutput());

  typedef Propagator<DistanceFunctorType> PropagatorType;
  PropagatorType* propagationFunctor = new PropagatorType;

  typedef RandomSearch<ImageType, DistanceFunctorType> RandomSearchType;
  RandomSearchType* randomSearchFunctor = new RandomSearchType;

  typedef PatchMatch<ImageType, PropagatorType, RandomSearchType> PatchMatchType;
  PatchMatchType patchMatch;
  patchMatch.SetImage(imageReader->GetOutput());
  patchMatch.SetPatchRadius(3);
  
  patchMatch.SetPropagationFunctor(propagationFunctor);
  patchMatch.SetRandomSearchFunctor(randomSearchFunctor);

  patchMatch.Compute();

  NNFieldType::Pointer output = patchMatch.GetNNField();
  PatchMatchHelpers::WriteNNField(output.GetPointer(), "nnfield.mha");

  return EXIT_SUCCESS;
}

void SuperPixelSegmentationGUI::OpenImage(const std::string& imageFileName)
{
  // Load and display image
  typedef itk::ImageFileReader<ImageType> ImageReaderType;
  ImageReaderType::Pointer imageReader = ImageReaderType::New();
  imageReader->SetFileName(imageFileName);
  imageReader->Update();

  Helpers::DeepCopy<ImageType>(imageReader->GetOutput(), this->Image);

  QImage qimageImage = HelpersQt::GetQImageRGBA<ImageType>(this->Image);
  this->ImagePixmapItem = this->Scene->addPixmap(QPixmap::fromImage(qimageImage));
  this->graphicsView->fitInView(this->ImagePixmapItem);
  Refresh();
}

int main(int argc, char *argv[])
{
  // Verify arguments
  if(argc != 5)
    {
    std::cerr << "Required arguments: image imageMask patchRadius output" << std::endl;
    return EXIT_FAILURE;
    }

  // Parse arguments
  std::string imageFilename = argv[1];
  std::string maskFilename = argv[2];

  std::stringstream ssPatchRadius;
  ssPatchRadius << argv[3];
  int patchRadius = 0;
  ssPatchRadius >> patchRadius;

  std::string outputFilename = argv[4];
  
  // Output arguments
  std::cout << "Reading image: " << imageFilename << std::endl;
  std::cout << "Reading mask: " << maskFilename << std::endl;
  std::cout << "Patch radius: " << patchRadius << std::endl;
  std::cout << "Output: " << outputFilename << std::endl;

  typedef  itk::ImageFileReader< FloatVectorImageType > ImageReaderType;
  ImageReaderType::Pointer imageReader = ImageReaderType::New();
  imageReader->SetFileName(imageFilename.c_str());
  imageReader->Update();

  typedef  itk::ImageFileReader< Mask  > MaskReaderType;
  MaskReaderType::Pointer maskReader = MaskReaderType::New();
  maskReader->SetFileName(maskFilename.c_str());
  maskReader->Update();

  CriminisiInpainting Inpainting;
  Inpainting.SetPatchRadius(patchRadius);
  Inpainting.SetDebug(false);
  Inpainting.SetImage(imageReader->GetOutput());
  Inpainting.SetMask(maskReader->GetOutput());
  Inpainting.Inpaint();

  Helpers::WriteImage<FloatVectorImageType>(Inpainting.GetResult(), outputFilename);

  return EXIT_SUCCESS;
}

void QmitkBSplineRegistrationView::PrintDeformationField()
{               
 
  ImageReaderType::Pointer reader  = ImageReaderType::New();
  reader->SetFileName(  m_Controls.m_DeformationField->text().toStdString()  );
  reader->Update();
      
  DeformationFieldType::Pointer deformationField = reader->GetOutput();
     

  typedef itk::ImageRegionIterator<DeformationFieldType> IteratorType;
  IteratorType deformIter(deformationField, deformationField->GetRequestedRegion());

  for(deformIter.GoToBegin(); !deformIter.IsAtEnd(); ++deformIter)
  {
    std::cout << deformIter.Get() << std::endl;
  }
}

BinaryImageType::Pointer readBinaryImage(const std::string& filename) {
    ImageReaderType::Pointer reader = ImageReaderType::New();
    reader->SetFileName(filename.c_str());
    reader->Update();

    // we make sure that the image really has value 0 and 1
    typedef itk::BinaryThresholdImageFilter<BinaryImageType, BinaryImageType> ThresholdFilterType;
    ThresholdFilterType::Pointer thresholdFilter = ThresholdFilterType::New();
    thresholdFilter->SetInsideValue(1);
    thresholdFilter->SetOutsideValue(0);
    thresholdFilter->SetLowerThreshold(1);
    thresholdFilter->SetUpperThreshold(255);
    thresholdFilter->SetInput(reader->GetOutput());
    thresholdFilter->Update();
    BinaryImageType::Pointer img = thresholdFilter->GetOutput();
    img->DisconnectPipeline();
    return img;
}

void Mask::ReadFromImage(const std::string& filename,
                         const HolePixelValueWrapper<TPixel>& holeValue,
                         const ValidPixelValueWrapper<TPixel>& validValue)
{
  std::cout << "Reading mask from image: " << filename << std::endl;

  // Ensure the input image can be interpreted as a mask.
  unsigned int numberOfComponents = GetNumberOfComponentsPerPixelInFile( filename );

  if(!(numberOfComponents == 1 || numberOfComponents == 3))
  {
    std::stringstream ss;
    ss << "Number of components for a mask must be 1 or 3! (" << filename
       << " is " << numberOfComponents << ")";
    throw std::runtime_error(ss.str());
  }

  // Read the image
  typedef int ReadPixelType;
  typedef itk::Image<ReadPixelType, 2> ImageType;
  typedef  itk::ImageFileReader<ImageType> ImageReaderType;
  ImageReaderType::Pointer imageReader = ImageReaderType::New();
  imageReader->SetFileName(filename);
  imageReader->Update();

  this->SetRegions(imageReader->GetOutput()->GetLargestPossibleRegion());
  this->Allocate();

  CreateHolesFromValue(imageReader->GetOutput(),
                       static_cast<ReadPixelType>(holeValue.Value));
  CreateValidPixelsFromValue(imageReader->GetOutput(),
                             static_cast<ReadPixelType>(validValue.Value));
}

int main(int argc, char*argv[])
{
  if(argc != 5)
    {
    std::cerr << "Required arguments: image mask kernelRadius output" << std::endl;
    return EXIT_FAILURE;
    }

  std::string imageFilename = argv[1];
  std::string maskFilename = argv[2];

  std::stringstream ssRadius;
  ssRadius << argv[3];
  unsigned int kernelRadius = 0;
  ssRadius >> kernelRadius;

  std::string outputFilename = argv[4];

  std::cout << "Reading image: " << imageFilename << std::endl;
  std::cout << "Reading mask: " << maskFilename << std::endl;
  std::cout << "Kernel radius: " << kernelRadius << std::endl;
  std::cout << "Output: " << outputFilename << std::endl;

  typedef itk::Image<float, 2> ImageType;

  typedef itk::ImageFileReader<ImageType> ImageReaderType;
  ImageReaderType::Pointer imageReader = ImageReaderType::New();
  imageReader->SetFileName(imageFilename.c_str());
  imageReader->Update();

  Mask::Pointer mask = Mask::New();
  mask->Read(maskFilename.c_str());

  MaskOperations::MedianFilterInHole(imageReader->GetOutput(), mask, kernelRadius);

  OutputHelpers::WriteImage(imageReader->GetOutput(), outputFilename);

  return EXIT_SUCCESS;
}

void ForegroundBackgroundSegmentMask::
ReadFromImage(const std::string& filename,
              const ForegroundPixelValueWrapper<TPixel>& foregroundValue,
              const BackgroundPixelValueWrapper<TPixel>& backgroundValue)
{
  std::cout << "Reading mask from image: " << filename << std::endl;

  // Ensure the input image can be interpreted as a mask.
  unsigned int numberOfComponents =
      ITKHelpers::GetNumberOfComponentsPerPixelInFile(filename);

  if(!(numberOfComponents == 1 || numberOfComponents == 3))
  {
    std::stringstream ss;
    ss << "Number of components for a mask must be 1 or 3! (" << filename
       << " is " << numberOfComponents << ")";
    throw std::runtime_error(ss.str());
  }

  // Read the image
  typedef int ReadPixelType;
  typedef itk::Image<ReadPixelType, 2> ImageType;
  typedef  itk::ImageFileReader<ImageType> ImageReaderType;
  ImageReaderType::Pointer imageReader = ImageReaderType::New();
  imageReader->SetFileName(filename);
  imageReader->Update();

  this->SetRegions(imageReader->GetOutput()->GetLargestPossibleRegion());
  this->Allocate();

  itk::ImageRegionConstIteratorWithIndex<ImageType>
      imageIterator(imageReader->GetOutput(),
                    imageReader->GetOutput()->GetLargestPossibleRegion());
  while(!imageIterator.IsAtEnd())
  {
    if(imageIterator.Get() == foregroundValue.Value)
    {
      this->SetPixel(imageIterator.GetIndex(),
                     ForegroundBackgroundSegmentMaskPixelTypeEnum::FOREGROUND);
    }
    else if(imageIterator.Get() == backgroundValue.Value)
    {
      this->SetPixel(imageIterator.GetIndex(),
                     ForegroundBackgroundSegmentMaskPixelTypeEnum::BACKGROUND);
    }
    else
    {
      std::cerr << "Warning: Pixels with value " << imageIterator.Get()
                << " found and is being ignored." << std::endl;
//      std::cerr << "Warning: Pixels with values other than the specified foreground "
//                   "and background values exist in the image and are being ignored." << std::endl;

    }
    ++imageIterator;
  }

}

int main(int argc, char*argv[])
{
  if(argc != 4)
    {
    std::cerr << "Required arguments: image mask output" << std::endl;
    return EXIT_FAILURE;
    }

  std::string imageFilename = argv[1];
  std::string maskFilename = argv[2];
  std::string outputFilename = argv[3];

  std::cout << "Reading image: " << imageFilename << std::endl;
  std::cout << "Reading mask: " << maskFilename << std::endl;
  std::cout << "Output: " << outputFilename << std::endl;

  //typedef itk::Image<float, 2> ImageType;

  //typedef itk::Image<itk::CovariantVector<unsigned char, 3>, 2> ImageType;
//   ImageType::PixelType color;
//   color[0] = 0;
//   color[1] = 255;
//   color[2] = 0;

  typedef itk::VectorImage<float, 2> ImageType;
  
//   ImageType::PixelType color;
//   color.SetRed(0);
//   color.SetGreen(255);
//   color.SetBlue(0);


  typedef itk::ImageFileReader<ImageType> ImageReaderType;
  ImageReaderType::Pointer imageReader = ImageReaderType::New();
  imageReader->SetFileName(imageFilename.c_str());
  imageReader->Update();

  ImageType::PixelType value(imageReader->GetOutput()->GetNumberOfComponentsPerPixel());
  value.Fill(0);
  
  Mask::Pointer mask = Mask::New();
  mask->Read(maskFilename.c_str());

  mask->ApplyToImage(imageReader->GetOutput(), value);

  OutputHelpers::WriteImage(imageReader->GetOutput(), outputFilename);

  return EXIT_SUCCESS;
}

void StrokeMask::
ReadFromImage(const std::string& filename,
              const TPixel& strokeValue)
{
  std::cout << "Reading stroke mask from image: " << filename << std::endl;

  // Ensure the input image can be interpreted as a mask.
  unsigned int numberOfComponents =
      ITKHelpers::GetNumberOfComponentsPerPixelInFile(filename);

  if(!(numberOfComponents == 1 || numberOfComponents == 3))
  {
    std::stringstream ss;
    ss << "Number of components for a mask must be 1 or 3! (" << filename
       << " is " << numberOfComponents << ")";
    throw std::runtime_error(ss.str());
  }

  // Read the image
  typedef int ReadPixelType;
  typedef itk::Image<ReadPixelType, 2> ImageType;
  typedef  itk::ImageFileReader<ImageType> ImageReaderType;
  ImageReaderType::Pointer imageReader = ImageReaderType::New();
  imageReader->SetFileName(filename);
  imageReader->Update();

  this->SetRegions(imageReader->GetOutput()->GetLargestPossibleRegion());
  this->Allocate();

  itk::ImageRegionConstIteratorWithIndex<ImageType>
      imageIterator(imageReader->GetOutput(),
                    imageReader->GetOutput()->GetLargestPossibleRegion());
  while(!imageIterator.IsAtEnd())
  {
    if(imageIterator.Get() == strokeValue)
    {
      this->SetPixel(imageIterator.GetIndex(),
                     StrokeMaskPixelTypeEnum::STROKE);
    }
    else
    {
      this->SetPixel(imageIterator.GetIndex(),
                     StrokeMaskPixelTypeEnum::NOTSTROKE);
    }
    ++imageIterator;
  }

}

int main(int argc, char *argv[])
{
  if(argc != 3)
    {
    std::cerr << "Required arguments: image mask" << std::endl;
    return EXIT_FAILURE;
    }
  std::string imageFilename = argv[1];
  std::string maskFilename = argv[2];
  std::cout << "Reading image: " << imageFilename << std::endl;
  std::cout << "Reading mask: " << maskFilename << std::endl;

  typedef itk::ImageFileReader<FloatVectorImageType> ImageReaderType;
  ImageReaderType::Pointer imageReader = ImageReaderType::New();
  imageReader->SetFileName(imageFilename.c_str());
  imageReader->Update();

  typedef itk::ImageFileReader<Mask> MaskReaderType;
  MaskReaderType::Pointer maskReader = MaskReaderType::New();
  maskReader->SetFileName(maskFilename.c_str());
  maskReader->Update();

  std::shared_ptr<SelfPatchCompare> patchCompare(new SelfPatchCompare);
  patchCompare->SetNumberOfComponentsPerPixel(imageReader->GetOutput()->GetNumberOfComponentsPerPixel());
  //patchCompare->FunctionsToCompute.push_back(boost::bind(&SelfPatchCompare::SetPatchAverageAbsoluteSourceDifference,patchCompare,_1));
  //patchCompare->FunctionsToCompute.push_back(boost::bind(&SelfPatchCompare::SetPatchColorDifference,patchCompare,_1));
  patchCompare->FunctionsToCompute.push_back(boost::bind(&SelfPatchCompare::SetPatchDepthDifference,patchCompare.get(),_1));
  //patchCompare->SetImage(imageReader->GetOutput());
  //patchCompare->SetMask(maskReader->GetOutput());

  PatchBasedInpainting inpainting;
  inpainting.SetMask(maskReader->GetOutput());
  inpainting.SetImage(imageReader->GetOutput());
  //inpainting.PatchSortFunction = &SortByDepthDifference;
  //inpainting.SetPatchCompare(patchCompare);
  inpainting.Initialize();
  inpainting.Iterate();

  CandidatePairs candidatePairs = inpainting.GetPotentialCandidatePairs()[0];
  //patchCompare->SetPairs(&candidatePairs);
  //patchCompare->ComputeAllSourceDifferences();
  WriteImageOfScores(candidatePairs, imageReader->GetOutput()->GetLargestPossibleRegion(), "ScoreImage_TargetPatch.mha");

  return EXIT_SUCCESS;
}

// Run with: Data/trashcan.mha Data/trashcan_mask.mha 15 filled.mha
int main(int argc, char *argv[])
{
  // Verify arguments
  if(argc != 6)
    {
    std::cerr << "Required arguments: image.mha imageMask.mha patchHalfWidth neighborhoodRadius output.mha" << std::endl;
    std::cerr << "Input arguments: ";
    for(int i = 1; i < argc; ++i)
      {
      std::cerr << argv[i] << " ";
      }
    return EXIT_FAILURE;
    }

  // Parse arguments
  std::string imageFileName = argv[1];
  std::string maskFileName = argv[2];

  std::stringstream ssPatchRadius;
  ssPatchRadius << argv[3];
  unsigned int patchHalfWidth = 0;
  ssPatchRadius >> patchHalfWidth;

  // The percent of the image size to use as the neighborhood (0 - 1)
  std::stringstream ssNeighborhoodPercent;
  ssNeighborhoodPercent << argv[4];
  float neighborhoodPercent = 0;
  ssNeighborhoodPercent >> neighborhoodPercent;

  std::string outputFileName = argv[5];

  // Output arguments
  std::cout << "Reading image: " << imageFileName << std::endl;
  std::cout << "Reading mask: " << maskFileName << std::endl;
  std::cout << "Patch half width: " << patchHalfWidth << std::endl;
  std::cout << "Neighborhood percent: " << neighborhoodPercent << std::endl;
  std::cout << "Output: " << outputFileName << std::endl;

  typedef itk::Image<itk::CovariantVector<int, 3>, 2> ImageType;

  typedef  itk::ImageFileReader<ImageType> ImageReaderType;
  ImageReaderType::Pointer imageReader = ImageReaderType::New();
  imageReader->SetFileName(imageFileName);
  imageReader->Update();

  ImageType::Pointer image = ImageType::New();
  ITKHelpers::DeepCopy(imageReader->GetOutput(), image.GetPointer());

  Mask::Pointer mask = Mask::New();
  mask->Read(maskFileName);

  std::cout << "hole pixels: " << mask->CountHolePixels() << std::endl;
  std::cout << "valid pixels: " << mask->CountValidPixels() << std::endl;

  typedef ImagePatchPixelDescriptor<ImageType> ImagePatchPixelDescriptorType;

  // Create the graph
  typedef boost::grid_graph<2> VertexListGraphType;
  boost::array<std::size_t, 2> graphSideLengths = { { imageReader->GetOutput()->GetLargestPossibleRegion().GetSize()[0],
                                                      imageReader->GetOutput()->GetLargestPossibleRegion().GetSize()[1] } };
//  VertexListGraphType graph(graphSideLengths);
  std::shared_ptr<VertexListGraphType> graph(new VertexListGraphType(graphSideLengths));
  typedef boost::graph_traits<VertexListGraphType>::vertex_descriptor VertexDescriptorType;


  //ImagePatchDescriptorMapType smallImagePatchDescriptorMap(num_vertices(graph), indexMap);

  // Create the patch inpainter. The inpainter needs to know the status of each pixel to determine if they should be inpainted.

  typedef PatchInpainter<ImageType> ImageInpainterType;
  std::shared_ptr<ImageInpainterType> imagePatchInpainter(new
      ImageInpainterType(patchHalfWidth, image, mask));

  // Create the priority function
   typedef PriorityRandom PriorityType;
   std::shared_ptr<PriorityType> priorityFunction(new PriorityType);
//  typedef PriorityCriminisi<ImageType> PriorityType;
//  std::shared_ptr<PriorityType> priorityFunction(new PriorityType(image, mask, patchHalfWidth));

  typedef IndirectPriorityQueue<VertexListGraphType> BoundaryNodeQueueType;
  std::shared_ptr<BoundaryNodeQueueType> boundaryNodeQueue(new BoundaryNodeQueueType(*graph));

  // Create the descriptor map. This is where the data for each pixel is stored.
  typedef boost::vector_property_map<ImagePatchPixelDescriptorType, BoundaryNodeQueueType::IndexMapType> ImagePatchDescriptorMapType;
//  ImagePatchDescriptorMapType imagePatchDescriptorMap(num_vertices(graph), indexMap);
  std::shared_ptr<ImagePatchDescriptorMapType> imagePatchDescriptorMap(new
      ImagePatchDescriptorMapType(num_vertices(*graph), *(boundaryNodeQueue->GetIndexMap())));

  // Create the descriptor visitor
  typedef ImagePatchDescriptorVisitor<VertexListGraphType, ImageType, ImagePatchDescriptorMapType>
          ImagePatchDescriptorVisitorType;
//  ImagePatchDescriptorVisitorType imagePatchDescriptorVisitor(image, mask, imagePatchDescriptorMap, patchHalfWidth);
  std::shared_ptr<ImagePatchDescriptorVisitorType> imagePatchDescriptorVisitor(new
      ImagePatchDescriptorVisitorType(image.GetPointer(), mask,
                                      imagePatchDescriptorMap, patchHalfWidth));
/*   ImagePatchDescriptorVisitor(TImage* const in_image, Mask* const in_mask,
  std::shared_ptr<TDescriptorMap> in_descriptorMap,
  const unsigned int in_half_width) : */
  typedef ImagePatchDifference<ImagePatchPixelDescriptorType, SumAbsolutePixelDifference<ImageType::PixelType> >
//.........这里部分代码省略.........

// Run with: Data/trashcan.mha Data/trashcan_mask.mha 15 filled.mha
int main(int argc, char *argv[])
{
  // Verify arguments
  if(argc != 5)
    {
    std::cerr << "Required arguments: image.mha imageMask.mha patchHalfWidth output.mha" << std::endl;
    std::cerr << "Input arguments: ";
    for(int i = 1; i < argc; ++i)
      {
      std::cerr << argv[i] << " ";
      }
    return EXIT_FAILURE;
    }

  // Setup the GUI system
  QApplication app( argc, argv );

  // Parse arguments
  std::string imageFilename = argv[1];
  std::string maskFilename = argv[2];

  std::stringstream ssPatchRadius;
  ssPatchRadius << argv[3];
  unsigned int patchHalfWidth = 0;
  ssPatchRadius >> patchHalfWidth;

  std::string outputFilename = argv[4];

  // Output arguments
  std::cout << "Reading image: " << imageFilename << std::endl;
  std::cout << "Reading mask: " << maskFilename << std::endl;
  std::cout << "Patch half width: " << patchHalfWidth << std::endl;
  std::cout << "Output: " << outputFilename << std::endl;

  typedef FloatVectorImageType ImageType;

  typedef  itk::ImageFileReader<ImageType> ImageReaderType;
  ImageReaderType::Pointer imageReader = ImageReaderType::New();
  imageReader->SetFileName(imageFilename);
  imageReader->Update();

  ImageType* image = imageReader->GetOutput();
  itk::ImageRegion<2> fullRegion = imageReader->GetOutput()->GetLargestPossibleRegion();

  Mask::Pointer mask = Mask::New();
  mask->Read(maskFilename);

  std::cout << "hole pixels: " << mask->CountHolePixels() << std::endl;
  std::cout << "valid pixels: " << mask->CountValidPixels() << std::endl;

  std::cout << "image has " << image->GetNumberOfComponentsPerPixel() << " components." << std::endl;

  typedef ImagePatchPixelDescriptor<ImageType> ImagePatchPixelDescriptorType;

  // Create the graph
  typedef boost::grid_graph<2> VertexListGraphType;
  boost::array<std::size_t, 2> graphSideLengths = { { fullRegion.GetSize()[0],
                                                      fullRegion.GetSize()[1] } };
  VertexListGraphType graph(graphSideLengths);
  typedef boost::graph_traits<VertexListGraphType>::vertex_descriptor VertexDescriptorType;

  // Get the index map
  typedef boost::property_map<VertexListGraphType, boost::vertex_index_t>::const_type IndexMapType;
  IndexMapType indexMap(get(boost::vertex_index, graph));

  // Create the priority map
  typedef boost::vector_property_map<float, IndexMapType> PriorityMapType;
  PriorityMapType priorityMap(num_vertices(graph), indexMap);

  // Create the boundary status map. A node is on the current boundary if this property is true.
  // This property helps the boundaryNodeQueue because we can mark here if a node has become no longer
  // part of the boundary, so when the queue is popped we can check this property to see if it should
  // actually be processed.
  typedef boost::vector_property_map<bool, IndexMapType> BoundaryStatusMapType;
  BoundaryStatusMapType boundaryStatusMap(num_vertices(graph), indexMap);

  // Create the descriptor map. This is where the data for each pixel is stored.
  typedef boost::vector_property_map<ImagePatchPixelDescriptorType, IndexMapType> ImagePatchDescriptorMapType;
  ImagePatchDescriptorMapType imagePatchDescriptorMap(num_vertices(graph), indexMap);

  //ImagePatchDescriptorMapType smallImagePatchDescriptorMap(num_vertices(graph), indexMap);

  // Create the patch inpainter. The inpainter needs to know the status of each
  // pixel to determine if they should be inpainted.
  typedef MaskImagePatchInpainter InpainterType;
  MaskImagePatchInpainter patchInpainter(patchHalfWidth, mask);

  // Create the priority function
//   typedef PriorityRandom PriorityType;
//   PriorityType priorityFunction;
  typedef PriorityOnionPeel PriorityType;
  PriorityType priorityFunction(mask, patchHalfWidth);

  // Create the boundary node queue. The priority of each node is used to order the queue.
  typedef boost::vector_property_map<std::size_t, IndexMapType> IndexInHeapMap;
  IndexInHeapMap index_in_heap(indexMap);

  // Create the priority compare functor (we want the highest priority nodes to be first in the queue)
  typedef std::greater<float> PriorityCompareType;
//.........这里部分代码省略.........

int main(int argc, char*argv[])
{
  if(argc != 6)
    {
    std::cerr << "Required arguments: image output R G B" << std::endl;
    return EXIT_FAILURE;
    }

  std::vector<int> values(3,0);
  std::stringstream ss;
  unsigned int counter = 0;
  for(int i = 3; i < argc; ++i)
  {
    ss << argv[i] << " ";
    counter++;
  }

  for(int i = 0; i < 3; ++i)
  {
    ss >> values[i];
  }

//   itk::RGBPixel<unsigned char> color;
//   color.SetRed(values[0]);
//   color.SetGreen(values[1]);
//   color.SetBlue(values[2]);
  Color color;
  color.r = values[0];
  color.g = values[1];
  color.b = values[2];

  std::string imageFilename = argv[1];
  std::string outputMaskFilename = argv[2];

  std::cout << "Reading image: " << imageFilename << std::endl;
  std::cout << "outputMaskFilename: " << outputMaskFilename << std::endl;

  std::cout << "Color: " << static_cast<int>(values[0]) << " " << static_cast<int>(values[1]) << " " << static_cast<int>(values[2]) << std::endl;

  //typedef itk::Image<float, 2> ImageType;

  typedef itk::Image<itk::CovariantVector<unsigned char, 3>, 2> ImageType;
  ImageType::PixelType pixelColor;
  pixelColor[0] = color.r;
  pixelColor[1] = color.g;
  pixelColor[2] = color.b;


  typedef itk::ImageFileReader<ImageType> ImageReaderType;
  ImageReaderType::Pointer imageReader = ImageReaderType::New();
  imageReader->SetFileName(imageFilename.c_str());
  imageReader->Update();

  Mask::Pointer mask = Mask::New();
  mask->SetRegions(imageReader->GetOutput()->GetLargestPossibleRegion());
  mask->Allocate();
  mask->CreateFromImage(imageReader->GetOutput(), pixelColor);

  OutputHelpers::WriteImage(mask.GetPointer(), outputMaskFilename);

  return EXIT_SUCCESS;
}

int main(int argc, char*argv[])
{
  // Parse the input
  if(argc < 6)
  {
    std::cerr << "Required arguments: image sourceMask.mask targetMask.mask patchRadius output" << std::endl;
    return EXIT_FAILURE;
  }

  std::stringstream ss;
  for(int i = 1; i < argc; ++i)
  {
    ss << argv[i] << " ";
  }

  std::string imageFilename;
  std::string sourceMaskFilename;
  std::string targetMaskFilename;
  unsigned int patchRadius;
  std::string outputFilename;

  ss >> imageFilename >> sourceMaskFilename >> targetMaskFilename >> patchRadius >> outputFilename;

  // Output the parsed values
  std::cout << "imageFilename: " << imageFilename << std::endl
            << "sourceMaskFilename: " << sourceMaskFilename << std::endl
            << "targetMaskFilename: " << targetMaskFilename << std::endl
            << "patchRadius: " << patchRadius << std::endl
            << "outputFilename: " << outputFilename << std::endl;

  typedef itk::Image<itk::CovariantVector<unsigned char, 3>, 2> ImageType;

  // Read the image and the masks
  typedef itk::ImageFileReader<ImageType> ImageReaderType;
  ImageReaderType::Pointer imageReader = ImageReaderType::New();
  imageReader->SetFileName(imageFilename);
  imageReader->Update();

  ImageType* image = imageReader->GetOutput();

  Mask::Pointer sourceMask = Mask::New();
  sourceMask->Read(sourceMaskFilename);

  Mask::Pointer targetMask = Mask::New();
  targetMask->Read(targetMaskFilename);

  // Poisson fill the input image in HSV space
  typedef itk::Image<itk::CovariantVector<float, 3>, 2> HSVImageType;
  HSVImageType::Pointer hsvImage = HSVImageType::New();
  ITKVTKHelpers::ConvertRGBtoHSV(image, hsvImage.GetPointer());

  ITKHelpers::WriteImage(image, "HSV.mha");

  typedef PoissonEditing<typename TypeTraits<HSVImageType::PixelType>::ComponentType> PoissonEditingType;

  typename PoissonEditingType::GuidanceFieldType::Pointer zeroGuidanceField =
            PoissonEditingType::GuidanceFieldType::New();
  zeroGuidanceField->SetRegions(hsvImage->GetLargestPossibleRegion());
  zeroGuidanceField->Allocate();
  typename PoissonEditingType::GuidanceFieldType::PixelType zeroPixel;
  zeroPixel.Fill(0);
  ITKHelpers::SetImageToConstant(zeroGuidanceField.GetPointer(), zeroPixel);

  PoissonEditingType::FillImage(hsvImage.GetPointer(), targetMask,
                                zeroGuidanceField.GetPointer(), hsvImage.GetPointer());

  ITKHelpers::WriteImage(image, "PoissonFilled_HSV.mha");

  ITKVTKHelpers::ConvertHSVtoRGB(hsvImage.GetPointer(), image);

  ITKHelpers::WriteRGBImage(image, "PoissonFilled_HSV.png");

  // PatchMatch requires that the target region be specified by valid pixels
  targetMask->InvertData();

  // Here, the source mask and target mask are the same, specifying the classicial
  // "use pixels outside the hole to fill the pixels inside the hole".
  // In an interactive algorith, the user could manually specify a source region,
  // improving the resulting inpainting.
  BDSInpaintingRings<ImageType> bdsInpainting;
  bdsInpainting.SetPatchRadius(patchRadius);
  bdsInpainting.SetImage(image);
  bdsInpainting.SetSourceMask(sourceMask);
  bdsInpainting.SetTargetMask(targetMask);

  bdsInpainting.SetIterations(1);
  //bdsInpainting.SetIterations(4);

  Compositor<ImageType, PixelCompositorAverage> compositor;
  bdsInpainting.Inpaint();

  ITKHelpers::WriteRGBImage(bdsInpainting.GetOutput(), outputFilename);

  return EXIT_SUCCESS;
}

int main(int argc, char* argv[])
{
  // Verify arguments
  if(argc < 5)
  {
    std::cout << "Usage: PatchImage repeatX repeatY outputImage" << std::endl;
    return EXIT_FAILURE;
  }

  // Parse arguments
  std::string patchImageFilename = argv[1];

  std::stringstream ssRepeatX;
  ssRepeatX << argv[2];
  unsigned int repeatX = 0;
  ssRepeatX >> repeatX;

  std::stringstream ssRepeatY;
  ssRepeatY << argv[3];
  unsigned int repeatY = 0;
  ssRepeatY >> repeatY;

  std::string outputFilename = argv[4];

  // Output arguments
  std::cout << &qu