int main()
{
  FloatVectorImageType::Pointer image = FloatVectorImageType::New();
  Testing::GetBlankImage(image.GetPointer(), 4);

  Mask::Pointer mask = Mask::New();
  Testing::GetFullyValidMask(mask.GetPointer());

  UnsignedCharScalarImageType::Pointer manualPriorityImage = UnsignedCharScalarImageType::New();
  Testing::GetBlankImage(manualPriorityImage.GetPointer());

  unsigned int patchRadius = 5;
  typedef PriorityConfidence ConfidencePriorityType;
  ConfidencePriorityType priorityConfidence(mask, patchRadius);
  
  PriorityManual<itk::Index<2>, UnsignedCharScalarImageType, ConfidencePriorityType>
      priority(manualPriorityImage, &priorityConfidence);

  itk::Index<2> filledPixel = {{0,0}};
  priority.Update(filledPixel);
  priority.SetManualPriorityImage(manualPriorityImage);

  itk::Index<2> queryPixel = {{0,0}};
  priority.ComputePriority(queryPixel);

  return EXIT_SUCCESS;
}

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];

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

  typedef itk::Image<unsigned char, 2> ImageType;
  ImageType::Pointer image = ImageType::New();
  ITKHelpers::ReadImage(imageFilename, image.GetPointer());

  FastDigitalInpainting fastDigitalInpainting;
  fastDigitalInpainting.SetImage(image);
  fastDigitalInpainting.SetMask(mask);
  fastDigitalInpainting.SetNumberOfIterations(100);
  fastDigitalInpainting.Inpaint();

  ITKHelpers::WriteImage(fastDigitalInpainting.GetOutput(), outputFilename);
  return EXIT_SUCCESS;
}

void CriminisiInpainting::InitializeConfidence()
{

  // Clone the mask - we need to invert the mask to actually perform the masking, but we don't want to disturb the original mask
  Mask::Pointer maskClone = Mask::New();
  //Helpers::DeepCopy<Mask>(this->CurrentMask, maskClone);
  maskClone->DeepCopyFrom(this->CurrentMask);
  
  // Invert the mask
  typedef itk::InvertIntensityImageFilter <Mask> InvertIntensityImageFilterType;

  InvertIntensityImageFilterType::Pointer invertIntensityFilter = InvertIntensityImageFilterType::New();
  invertIntensityFilter->SetInput(maskClone);
  //invertIntensityFilter->InPlaceOn();
  invertIntensityFilter->Update();

  // Convert the inverted mask to floats and scale them to between 0 and 1
  // to serve as the initial confidence image
  typedef itk::RescaleIntensityImageFilter< Mask, FloatScalarImageType > RescaleFilterType;
  RescaleFilterType::Pointer rescaleFilter = RescaleFilterType::New();
  rescaleFilter->SetInput(invertIntensityFilter->GetOutput());
  rescaleFilter->SetOutputMinimum(0);
  rescaleFilter->SetOutputMaximum(1);
  rescaleFilter->Update();

  Helpers::DeepCopy<FloatScalarImageType>(rescaleFilter->GetOutput(), this->ConfidenceImage);
  //WriteImage<FloatImageType>(this->ConfidenceImage, "InitialConfidence.mhd");
}

void CriminisiInpainting::UpdateMask(const itk::Index<2> inputPixel)
{
  try
  {
    // Create a black patch
    Mask::Pointer blackPatch = Mask::New();
    //Helpers::CreateBlankPatch<UnsignedCharScalarImageType>(blackPatch, this->PatchRadius[0]);
    Helpers::CreateConstantPatch<Mask>(blackPatch, this->CurrentMask->GetValidValue(), this->PatchRadius[0]);
    itk::Index<2> pixel;
    pixel[0] = inputPixel[0] - blackPatch->GetLargestPossibleRegion().GetSize()[0]/2;
    pixel[1] = inputPixel[1] - blackPatch->GetLargestPossibleRegion().GetSize()[1]/2;

    // Paste it into the mask
    typedef itk::PasteImageFilter <Mask, Mask> PasteImageFilterType;
    PasteImageFilterType::Pointer pasteFilter = PasteImageFilterType::New();
    //pasteFilter->SetInput(0, this->CurrentMask);
    //pasteFilter->SetInput(1, blackPatch);
    pasteFilter->SetSourceImage(blackPatch);
    pasteFilter->SetDestinationImage(this->CurrentMask);
    pasteFilter->SetSourceRegion(blackPatch->GetLargestPossibleRegion());
    pasteFilter->SetDestinationIndex(pixel);
    pasteFilter->Update();

    // Not sure how Mask::DeepCopyFrom would work on the output of a filter, so do this manually.
    Helpers::DeepCopy<Mask>(pasteFilter->GetOutput(), this->CurrentMask);
    this->CurrentMask->SetHoleValue(this->OriginalMask->GetHoleValue());
    this->CurrentMask->SetValidValue(this->OriginalMask->GetValidValue());
  }
  catch( itk::ExceptionObject & err )
  {
    std::cerr << "ExceptionObject caught in UpdateMask!" << std::endl;
    std::cerr << err << std::endl;
    exit(-1);
  }
}

int main(int argc, char*argv[])
{
  if(argc != 3)
    {
    std::cerr << "Required arguments: mask output" << std::endl;
    return EXIT_FAILURE;
    }

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

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

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

  Mask::BoundaryImageType::Pointer boundaryImage = Mask::BoundaryImageType::New();
  boundaryImage->SetRegions(mask->GetLargestPossibleRegion());
  boundaryImage->Allocate();
  
//  mask->CreateBoundaryImage(boundaryImage.GetPointer(), mask->GetValidValue());
  mask->CreateBoundaryImage(boundaryImage.GetPointer(), Mask::VALID);
  
  ITKHelpers::WriteImage(boundaryImage.GetPointer(), outputFilename);

  return EXIT_SUCCESS;
}

int main()
{
  typedef itk::Image<itk::CovariantVector<float, 3>, 2> ImageType;
//  typedef FloatVectorImageType ImageType;
  ImageType::Pointer image = ImageType::New();
  Testing::GetBlankImage(image.GetPointer(), 4);

  Mask::Pointer mask = Mask::New();
  Testing::GetFullyValidMask(mask.GetPointer());

  unsigned int patchRadius = 5;
  PriorityCriminisi<ImageType> priority(image.GetPointer(), mask.GetPointer(),
                                                   patchRadius);

  itk::Index<2> sourcePixel;
  sourcePixel.Fill(0);

  itk::Index<2> targetPixel;
  targetPixel.Fill(1);

  priority.Update(sourcePixel, targetPixel);

  itk::Index<2> queryPixel = {{0,0}};
  priority.ComputePriority(queryPixel);

  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 Mask::CreateBoundaryImageInRegion(const itk::ImageRegion<2>& region, BoundaryImageType* const boundaryImage,
                                       const HoleMaskPixelTypeEnum& whichSideOfBoundary) const
{
  // Create a binary image of the mask
  unsigned char holeColor = 255;
  unsigned char validColor = 0;
  UnsignedCharImageType::Pointer fullBinaryImage = UnsignedCharImageType::New();
  CreateBinaryImageInRegion(region, fullBinaryImage, holeColor, validColor);

  // Extract the relevant region from the binary image
  UnsignedCharImageType::Pointer binaryImage = UnsignedCharImageType::New();
  binaryImage->SetRegions(region);
  binaryImage->Allocate();
  CopyRegion(fullBinaryImage.GetPointer(), binaryImage.GetPointer(), region, region);

  // Extract the relevant region from the mask
  Mask::Pointer extractedRegionMask = Mask::New();
  extractedRegionMask->SetRegions(region);
  extractedRegionMask->Allocate();
  CopyRegion(this, extractedRegionMask.GetPointer(), region, region);

  // Since the hole is white (we have specified this at the beginning of this function),
  // we want the foreground value of the contour filter to be black.
  // This means that the boundary will be detected in the black pixel region,
  // which is on the outside edge of the hole like we want. However,
  // The BinaryContourImageFilter will change all non-boundary pixels to the background color,
  // so the resulting output will be inverted - the boundary pixels will be black and the
  // non-boundary pixels will be white.

  // Find the boundary
  typedef itk::BinaryContourImageFilter<UnsignedCharImageType, UnsignedCharImageType> binaryContourImageFilterType;
  binaryContourImageFilterType::Pointer binaryContourFilter = binaryContourImageFilterType::New();
  binaryContourFilter->SetInput(binaryImage);
  binaryContourFilter->SetFullyConnected(true);

  if(whichSideOfBoundary == HoleMaskPixelTypeEnum::VALID)
  {
    // we want the boundary pixels to be in the valid region.
      binaryContourFilter->SetForegroundValue(validColor);
      binaryContourFilter->SetBackgroundValue(holeColor);
  }
  else if(whichSideOfBoundary == HoleMaskPixelTypeEnum::HOLE)
  {
    // we want the boundary pixels to be in the hole region.
      binaryContourFilter->SetForegroundValue(holeColor);
      binaryContourFilter->SetBackgroundValue(validColor);
  }
  else
  {
    throw std::runtime_error("An invalid side of the boundary was requested.");
  }

  binaryContourFilter->Update();

  DeepCopy(binaryContourFilter->GetOutput(), boundaryImage);
}

void Vector()
{
  typedef itk::Image<unsigned char, 2 >  ChannelType;
  const unsigned int NumberOfChannels = 3;
  typedef itk::Image<itk::CovariantVector<unsigned char, NumberOfChannels>, 2 >  ImageType;

  ImageType::Pointer image = ImageType::New();
  itk::Index<2> corner = {{0,0}};
  itk::Size<2> imageSize = {{500,500}};
  itk::ImageRegion<2> fullRegion(corner, imageSize);
  image->SetRegions(fullRegion);
  image->Allocate();

  for(unsigned int i = 0; i < NumberOfChannels; ++i)
  {
    itk::RandomImageSource<ChannelType>::Pointer randomImageSource =
      itk::RandomImageSource<ChannelType>::New();
    randomImageSource->SetNumberOfThreads(1); // to produce non-random results
    randomImageSource->SetSize(imageSize);
    randomImageSource->Update();

    ITKHelpers::SetChannel(image.GetPointer(), i, randomImageSource->GetOutput());
  }

  itk::Size<2> patchSize = {{21,21}};

  // There is nothing magic about these particular patches
  itk::Index<2> targetCorner = {{319, 302}};
  itk::ImageRegion<2> targetRegion(targetCorner, patchSize);

  itk::Index<2> sourceCorner = {{341, 300}};
  itk::ImageRegion<2> sourceRegion(sourceCorner, patchSize);

  Mask::Pointer mask = Mask::New();
  mask->SetRegions(fullRegion);
  mask->Allocate();
  ITKHelpers::SetImageToConstant(mask.GetPointer(), mask->GetValidValue());

  typedef SumSquaredPixelDifference<ImageType::PixelType> PixelDifferenceType;

  typedef ImagePatchPixelDescriptor<ImageType> PatchType;

  ImagePatchDifference<PatchType, PixelDifferenceType> imagePatchDifference;

  PatchType targetPatch(image, mask, targetRegion);
  PatchType sourcePatch(image, mask, sourceRegion);

  float difference = imagePatchDifference(targetPatch, sourcePatch);

  std::cout << "GMHDifference: " << difference << std::endl;

}

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 Mask::FindBoundary(UnsignedCharScalarImageType* boundaryImage) const
{
  // Compute the "outer" boundary of the region to fill. That is, we want the boundary pixels to be in the source region.

  //HelpersOutput::WriteImageConditional<Mask>(this->CurrentMask, "Debug/FindBoundary.CurrentMask.mha", this->DebugImages);
  //HelpersOutput::WriteImageConditional<Mask>(this->CurrentMask, "Debug/FindBoundary.CurrentMask.png", this->DebugImages);

  // Create a binary image (throw away the "dont use" pixels)
  Mask::Pointer holeOnly = Mask::New();
  holeOnly->DeepCopyFrom(this);

  itk::ImageRegionIterator<Mask> maskIterator(holeOnly, holeOnly->GetLargestPossibleRegion());
  // This should result in a white hole on a black background
  while(!maskIterator.IsAtEnd())
    {
    itk::Index<2> currentPixel = maskIterator.GetIndex();
    if(!holeOnly->IsHole(currentPixel))
      {
      holeOnly->SetPixel(currentPixel, holeOnly->GetValidValue());
      }
    ++maskIterator;
    }

  //HelpersOutput::WriteImageConditional<Mask>(holeOnly, "Debug/FindBoundary.HoleOnly.mha", this->DebugImages);
  //HelpersOutput::WriteImageConditional<Mask>(holeOnly, "Debug/FindBoundary.HoleOnly.png", this->DebugImages);

  // Since the hole is white, we want the foreground value of the contour filter to be black. This means that the boundary will
  // be detected in the black pixel region, which is on the outside edge of the hole like we want. However,
  // The BinaryContourImageFilter will change all non-boundary pixels to the background color, so the resulting output will be inverted -
  // the boundary pixels will be black and the non-boundary pixels will be white.

  // Find the boundary
  typedef itk::BinaryContourImageFilter <Mask, Mask> binaryContourImageFilterType;
  binaryContourImageFilterType::Pointer binaryContourFilter = binaryContourImageFilterType::New();
  binaryContourFilter->SetInput(holeOnly);
  binaryContourFilter->SetFullyConnected(true);
  binaryContourFilter->SetForegroundValue(holeOnly->GetValidValue());
  binaryContourFilter->SetBackgroundValue(holeOnly->GetHoleValue());
  binaryContourFilter->Update();

  //HelpersOutput::WriteImageConditional<Mask>(binaryContourFilter->GetOutput(), "Debug/FindBoundary.Boundary.mha", this->DebugImages);
  //HelpersOutput::WriteImageConditional<Mask>(binaryContourFilter->GetOutput(), "Debug/FindBoundary.Boundary.png", this->DebugImages);

  // Since we want to interpret non-zero pixels as boundary pixels, we must invert the image.
  typedef itk::InvertIntensityImageFilter <Mask> InvertIntensityImageFilterType;
  InvertIntensityImageFilterType::Pointer invertIntensityFilter = InvertIntensityImageFilterType::New();
  invertIntensityFilter->SetInput(binaryContourFilter->GetOutput());
  invertIntensityFilter->SetMaximum(255);
  invertIntensityFilter->Update();

  //this->BoundaryImage = binaryContourFilter->GetOutput();
  //this->BoundaryImage->Graft(binaryContourFilter->GetOutput());
  ITKHelpers::DeepCopy<UnsignedCharScalarImageType>(invertIntensityFilter->GetOutput(), boundaryImage);

  //HelpersOutput::WriteImageConditional<UnsignedCharScalarImageType>(this->BoundaryImage, "Debug/FindBoundary.BoundaryImage.mha", this->DebugImages);

}

static void CreateMask(Mask::Pointer mask)
{
  itk::Size<2> size;
  size.Fill(20);

  itk::Index<2> start;
  start.Fill(0);

  itk::ImageRegion<2> region(start,size);

  mask->SetRegions(region);
  mask->Allocate();
  mask->FillBuffer(mask->GetValidValue());

  itk::ImageRegionIterator<Mask> iterator(mask, mask->GetLargestPossibleRegion());

  while(!iterator.IsAtEnd())
    {
    if(iterator.GetIndex()[0] > 5 && iterator.GetIndex()[0] < 15 &&
       iterator.GetIndex()[1] > 5 && iterator.GetIndex()[1] < 15)
      {
      mask->SetPixel(iterator.GetIndex(), mask->GetHoleValue());
      }

    ++iterator;
    }
}

int main(int argc, char*argv[])
{
  Mask::Pointer mask = Mask::New();
  CreateMask(mask);

  OutputHelpers::WriteImage(mask.GetPointer(), "mask.png");
  
  UnsignedCharScalarImageType::Pointer image = UnsignedCharScalarImageType::New();
  CreateImage(image);
  OutputHelpers::WriteImage(image.GetPointer(), "image.png");
  
  FloatScalarImageType::Pointer output = FloatScalarImageType::New();
  MaskOperations::MaskedLaplacian(image.GetPointer(), mask.GetPointer(), output.GetPointer());

  OutputHelpers::WriteImage(output.GetPointer(), "laplacian.mha");

  return EXIT_SUCCESS;
}

int main()
{
  FloatVectorImageType::Pointer image = FloatVectorImageType::New();
  Testing::GetBlankImage(image.GetPointer(), 4);

  Mask::Pointer mask = Mask::New();
  Testing::GetFullyValidMask(mask.GetPointer());

  unsigned int patchRadius = 5;
  PriorityDepth<FloatVectorImageType> priority(image, mask, patchRadius);

  itk::Index<2> filledPixel = {{0,0}};
  priority.Update(filledPixel);

  itk::Index<2> queryPixel = {{0,0}};
  priority.ComputePriority(queryPixel);

  return EXIT_SUCCESS;
}

int main(int argc, char*argv[])
{
  if(argc != 2)
    {
    std::cerr << "Required arguments: mask" << std::endl;
    return EXIT_FAILURE;
    }

  std::string maskFilename = argv[1];

  std::cout << "Reading mask: " << maskFilename << std::endl;

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

  std::cout << "There are " << mask->CountBoundaryPixels() << " boundary pixels." << std::endl;

  return EXIT_SUCCESS;
}

void Scalar()
{
  typedef itk::Image< unsigned char, 2 >  ImageType;

  itk::Size<2> imageSize = {{500,500}};

  itk::RandomImageSource<ImageType>::Pointer randomImageSource =
    itk::RandomImageSource<ImageType>::New();
  randomImageSource->SetNumberOfThreads(1); // to produce non-random results
  randomImageSource->SetSize(imageSize);
  randomImageSource->Update();

  ImageType* image = randomImageSource->GetOutput();

  itk::Size<2> patchSize = {{21,21}};

  // There is nothing magic about these particular patches
  itk::Index<2> targetCorner = {{319, 302}};
  itk::ImageRegion<2> targetRegion(targetCorner, patchSize);

  itk::Index<2> sourceCorner = {{341, 300}};
  itk::ImageRegion<2> sourceRegion(sourceCorner, patchSize);

  Mask::Pointer mask = Mask::New();
  mask->SetRegions(randomImageSource->GetOutput()->GetLargestPossibleRegion());
  mask->Allocate();
  ITKHelpers::SetImageToConstant(mask.GetPointer(), mask->GetValidValue());

  typedef SumSquaredPixelDifference<ImageType::PixelType> PixelDifferenceType;

  typedef ImagePatchPixelDescriptor<ImageType> PatchType;

  ImagePatchDifference<PatchType, PixelDifferenceType> imagePatchDifference;

  PatchType targetPatch(image, mask, targetRegion);
  PatchType sourcePatch(image, mask, sourceRegion);

  float difference = imagePatchDifference(targetPatch, sourcePatch);

  std::cout << "Difference: " << difference << std::endl;

}

int main(int argc, char *argv[])
{
  Mask::Pointer mask = Mask::New();
  CreateMask(mask);

  itk::Index<2> queryPixel;
  queryPixel[0] = 5;
  queryPixel[1] = 5;

  FloatVector2Type direction;
  direction[0] = 1;
  direction[1] = 1;
  direction.Normalize();

  itk::Index<2> pixelAcross = mask->FindPixelAcrossHole(queryPixel, direction);

  std::cout << "Pixel across: " << pixelAcross << std::endl;

  //HelpersOutput::WriteImage<Mask>(blurredLuminance, "Test/TestIsophotes.blurred.mha");

  return EXIT_SUCCESS;
}

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;
}

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 LidarSegmentationWidget::on_btnErodeSources_clicked()
{
  Mask::Pointer sourcesImage = Mask::New();
  sourcesImage->SetRegions(this->ImageRegion);
  ITKHelpers::IndicesToBinaryImage(this->Sources, sourcesImage);

  typedef itk::BinaryBallStructuringElement<Mask::PixelType,2> StructuringElementType;
  StructuringElementType structuringElementBig;
  structuringElementBig.SetRadius(3);
  structuringElementBig.CreateStructuringElement();

  typedef itk::BinaryErodeImageFilter<Mask, Mask, StructuringElementType> BinaryErodeImageFilterType;

  BinaryErodeImageFilterType::Pointer erodeFilter = BinaryErodeImageFilterType::New();
  erodeFilter->SetInput(sourcesImage);
  erodeFilter->SetKernel(structuringElementBig);
  erodeFilter->Update();

  //this->Sources.clear();

  this->Sources = ITKHelpers::GetNonZeroPixels(erodeFilter->GetOutput());

  UpdateSelections();
}