예제 #1
0
void TestExtractChannels()
{
  typedef itk::VectorImage<float, 2> VectorImageType;
  VectorImageType::Pointer image = VectorImageType::New();

  itk::Index<2> corner = {{0,0}};
  itk::Size<2> size = {{100,100}};
  itk::ImageRegion<2> region(corner, size);

  image->SetRegions(region);
  image->SetNumberOfComponentsPerPixel(3);
  image->Allocate();

  // Extract the first two channels
  std::vector<unsigned int> channels;
  channels.push_back(0);
  channels.push_back(1);

  typedef itk::VectorImage<float, 2> FloatScalarImageType;
  FloatScalarImageType::Pointer floatScalarImage = FloatScalarImageType::New();
  ITKHelpers::ExtractChannels(image.GetPointer(), channels, floatScalarImage.GetPointer());

  typedef itk::VectorImage<unsigned char, 2> UnsignedCharScalarImageType;
  UnsignedCharScalarImageType::Pointer unsignedCharScalarImage = UnsignedCharScalarImageType::New();
  ITKHelpers::ExtractChannels(image.GetPointer(), channels, unsignedCharScalarImage.GetPointer());
}
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;
}
void Difference::CreateDepthImage(FloatScalarImageType::Pointer image)
{
  image->SetRegions(this->Image->GetLargestPossibleRegion());
  image->Allocate();
  image->FillBuffer(0);
  
  itk::ImageRegionIterator<ImageType> fullImageIterator(this->Image, this->Image->GetLargestPossibleRegion());
  itk::ImageRegionIterator<FloatScalarImageType> rgbImageIterator(image, image->GetLargestPossibleRegion());
  
  while(!fullImageIterator.IsAtEnd())
    {
    ImageType::PixelType fullPixel = fullImageIterator.Get();
  
    float depthPixel = fullPixel[3];
  
    rgbImageIterator.Set(depthPixel);
    ++fullImageIterator;
    ++rgbImageIterator;
    }
}
예제 #4
0
void TestExtractChannel()
{
  typedef itk::VectorImage<float, 2> VectorImageType;
  VectorImageType::Pointer image = VectorImageType::New();

  itk::Index<2> corner = {{0,0}};
  itk::Size<2> size = {{100,100}};
  itk::ImageRegion<2> region(corner, size);

  image->SetRegions(region);
  image->SetNumberOfComponentsPerPixel(2);
  image->Allocate();

  typedef itk::Image<float, 2> FloatScalarImageType;
  FloatScalarImageType::Pointer floatScalarImage = FloatScalarImageType::New();
  ITKHelpers::ExtractChannel(image.GetPointer(), 0, floatScalarImage.GetPointer());

  typedef itk::Image<unsigned char, 2> UnsignedCharScalarImageType;
  UnsignedCharScalarImageType::Pointer unsignedCharScalarImage = UnsignedCharScalarImageType::New();
  ITKHelpers::ExtractChannel(image.GetPointer(), 0, unsignedCharScalarImage.GetPointer());
}
예제 #5
0
void ComputeColorIsophotesInRegion(const TVectorImageType* const image, const Mask* const mask,
                                   const itk::ImageRegion<2>& region , TIsophoteImageType* const isophotes)
{
  /*
   * 'isophotes' must already be initialized to the right size and allocated.
   */
  
  //EnterFunction("ComputeIsophotes()");
  RGBImageType::Pointer rgbImage = RGBImageType::New();
  ITKHelpers::VectorImageToRGBImage(image, rgbImage);

  //HelpersOutput::WriteImageConditional<RGBImageType>(rgbImage, "Debug/Initialize.rgb.mha", this->DebugImages);

  typedef itk::RGBToLuminanceImageFilter< RGBImageType, FloatScalarImageType > LuminanceFilterType;
  LuminanceFilterType::Pointer luminanceFilter = LuminanceFilterType::New();
  luminanceFilter->SetInput(rgbImage);
  luminanceFilter->Update();

  FloatScalarImageType::Pointer luminanceImage = FloatScalarImageType::New();
  ITKHelpers::DeepCopy(luminanceFilter->GetOutput(), luminanceImage.GetPointer());

  FloatScalarImageType::Pointer blurredLuminance = FloatScalarImageType::New();
  // Blur with a Gaussian kernel. From TestIsophotes.cpp, it actually seems like not blurring,
  // but using a masked sobel operator produces the most reliable isophotes.
  unsigned int kernelRadius = 0;
  MaskOperations::MaskedBlur(luminanceFilter->GetOutput(), mask,
                             kernelRadius, blurredLuminance.GetPointer());

  //HelpersOutput::WriteImageConditional(blurredLuminance,
  //                                  "Debug/Initialize.blurredLuminance.mha", true);

  //ITKHelpers::InitializeImage(isophotes, image->GetLargestPossibleRegion());
  Isophotes::ComputeMaskedIsophotesInRegion(blurredLuminance.GetPointer(), mask, region, isophotes);

//   if(this->DebugImages)
//     {
//     HelpersOutput::Write2DVectorImage(this->IsophoteImage, "Debug/Initialize.IsophoteImage.mha");
//     }
  //LeaveFunction("ComputeIsophotes()");
}
예제 #6
0
void FullPatchScalarComparison()
{
  std::cout << "FullPatchScalarComparison()" << std::endl;
  FloatScalarImageType::Pointer scalarImage = FloatScalarImageType::New();
  Testing::GetBlankImage<FloatScalarImageType>(scalarImage);

  // Make the left half of the image 0, and the right half 5
  itk::ImageRegionIterator<FloatScalarImageType> imageIterator(scalarImage, scalarImage->GetLargestPossibleRegion());

  while(!imageIterator.IsAtEnd())
    {
    if(imageIterator.GetIndex()[0] < static_cast<int>(scalarImage->GetLargestPossibleRegion().GetSize()[0]/2))
      {
      imageIterator.Set(0);
      }
    else
      {
      imageIterator.Set(5);
      }

    ++imageIterator;
    }

  itk::Size<2> patchSize;
  patchSize.Fill(10);

  std::cout << "Full patch different test." << std::endl;
  // Full patch is different
  {
  itk::Index<2> sourceCorner;
  sourceCorner.Fill(0);
  itk::ImageRegion<2> sourceRegion(sourceCorner, patchSize);
  ImagePatchPixelDescriptor<FloatScalarImageType> sourcePatch(scalarImage, sourceRegion, true);

  itk::Index<2> targetCorner;
  targetCorner.Fill(scalarImage->GetLargestPossibleRegion().GetSize()[0]/2 + 4); // No magic about 4, just want a patch on the right side of the image
  itk::ImageRegion<2> targetRegion(targetCorner, patchSize);
  ImagePatchPixelDescriptor<FloatScalarImageType> targetPatch(scalarImage, targetRegion, true);
  std::cout << "targetPatch: " << targetPatch << std::endl;

  PatchPair<FloatScalarImageType> patchPair(&sourcePatch, targetPatch);
  PatchDifferencePixelWiseSum<FloatScalarImageType, PixelDifference> scalar_patchDifferencePixelWiseSum;
  scalar_patchDifferencePixelWiseSum.SetImage(scalarImage);
  float difference = scalar_patchDifferencePixelWiseSum.Difference(patchPair);

  std::cout << "Number of pixels: " << targetPatch.GetRegion().GetNumberOfPixels() << std::endl;

  float correctDifference = targetPatch.GetRegion().GetNumberOfPixels() * 5;

  if(difference != correctDifference)
    {
    std::stringstream ss;
    ss << "Difference " << difference << " does not match correctDifference " << correctDifference;
    throw std::runtime_error(ss.str());
    }
  }

  std::cout << "Identical patch test." << std::endl;
  // Patches are identical
  {
  itk::Index<2> sourceCorner;
  sourceCorner.Fill(0);
  itk::ImageRegion<2> sourceRegion(sourceCorner, patchSize);
  ImagePatchPixelDescriptor<FloatScalarImageType> sourcePatch(scalarImage, sourceRegion, true);

  itk::Index<2> targetCorner;
  targetCorner.Fill(10); // No magic about 10, just want a patch not at (0,0) but still fully on the left side of the image
  itk::ImageRegion<2> targetRegion(targetCorner, patchSize);
  ImagePatchPixelDescriptor<FloatScalarImageType> targetPatch(scalarImage, targetRegion, true);

  PatchPair<FloatScalarImageType> patchPair(&sourcePatch, targetPatch);
  PatchDifferencePixelWiseSum<FloatScalarImageType, PixelDifference> scalar_patchDifferencePixelWiseSum;
  scalar_patchDifferencePixelWiseSum.SetImage(scalarImage);
  float difference = scalar_patchDifferencePixelWiseSum.Difference(patchPair);

  float correctDifference = 0;
  if(difference != correctDifference)
    {
    std::stringstream ss;
    ss << "Difference " << difference << " does not match correctDifference " << correctDifference;
    throw std::runtime_error(ss.str());
    }
  }
}
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();

  std::cout << "Read image " << imageReader->GetOutput()->GetLargestPossibleRegion() << std::endl;

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

  std::cout << "Read mask " << maskReader->GetOutput()->GetLargestPossibleRegion() << std::endl;

  // Prepare image
  RGBImageType::Pointer rgbImage = RGBImageType::New();
  // Helpers::VectorImageToRGBImage(imageReader->GetOutput(), rgbImage);
  // TODO: Update this call to new API
  //maskReader->GetOutput()->ApplyToImage(rgbImage.GetPointer(), Qt::black);
  OutputHelpers::WriteImage<RGBImageType>(rgbImage, "Test/TestIsophotes.rgb.mha");

  typedef itk::RGBToLuminanceImageFilter< RGBImageType, FloatScalarImageType > LuminanceFilterType;
  LuminanceFilterType::Pointer luminanceFilter = LuminanceFilterType::New();
  luminanceFilter->SetInput(rgbImage);
  luminanceFilter->Update();

  OutputHelpers::WriteImage<FloatScalarImageType>(luminanceFilter->GetOutput(), "Test/Luminance.mha");

//   PatchBasedInpainting inpainting;
//   inpainting.SetDebugImages(true);
//   inpainting.SetMask(maskReader->GetOutput());
//   inpainting.SetImage(imageReader->GetOutput());
  //Helpers::Write2DVectorImage(inpainting.GetIsophoteImage(), "Test/TestIsophotes.isophotes.mha");
  //inpainting.FindBoundary();

  // After blurVariance == 4, you cannot tell the difference in the output.
  for(unsigned int blurVariance = 0; blurVariance < 5; ++blurVariance)
    {
    std::string fileNumber = Helpers::ZeroPad(blurVariance, 2);

    FloatScalarImageType::Pointer blurredLuminance = FloatScalarImageType::New();

    // Blur with a Gaussian kernel
    MaskOperations::MaskedBlur(luminanceFilter->GetOutput(), maskReader->GetOutput(),
                               blurVariance, blurredLuminance.GetPointer());
    std::stringstream ssBlurredLuminance;
    ssBlurredLuminance << "Test/BlurredLuminance_" << fileNumber << ".mha";
    OutputHelpers::WriteImage(blurredLuminance.GetPointer(), ssBlurredLuminance.str());

    //Helpers::WriteImage<FloatScalarImageType>(blurredLuminance, "Test/TestIsophotes.blurred.mha");
    FloatVector2ImageType::Pointer gradient = FloatVector2ImageType::New();
    Derivatives::MaskedGradient(blurredLuminance.GetPointer(), maskReader->GetOutput(), gradient.GetPointer());

    // Boundary gradient
    typedef itk::MaskImageFilter< FloatVector2ImageType, UnsignedCharScalarImageType, FloatVector2ImageType > MaskFilterType;
    MaskFilterType::Pointer maskFilter = MaskFilterType::New();
    maskFilter->SetInput(gradient);
    //maskFilter->SetMaskImage(inpainting.GetBoundaryImage());
    maskFilter->Update();

    vtkSmartPointer<vtkPolyData> boundaryGradient = vtkSmartPointer<vtkPolyData>::New();
    // TODO: Convert this call to new API
    //Helpers::ConvertNonZeroPixelsToVectors(maskFilter->GetOutput(), boundaryGradient);
    std::stringstream ssPolyData;
    ssPolyData << "Test/BoundaryGradient_" << fileNumber << ".vtp";
    OutputHelpers::WritePolyData(boundaryGradient, ssPolyData.str());
    }

  return EXIT_SUCCESS;
}
void LidarSegmentationWidget::GenerateNeighborSinks()
{
  Mask::Pointer sourcesImage = Mask::New();
  sourcesImage->SetRegions(this->ImageRegion);
  ITKHelpers::IndicesToBinaryImage(this->Sources, sourcesImage);
  ITKHelpers::WriteImage(sourcesImage.GetPointer(), "sourcesImage.png");
  
  // Dilate the mask
  std::cout << "Dilating mask..." << std::endl;
  typedef itk::BinaryBallStructuringElement<Mask::PixelType, 2> StructuringElementType;
  StructuringElementType structuringElement;
  structuringElement.SetRadius(1);
  structuringElement.CreateStructuringElement();

  typedef itk::BinaryDilateImageFilter<Mask, Mask, StructuringElementType> BinaryDilateImageFilterType;

  BinaryDilateImageFilterType::Pointer dilateFilter = BinaryDilateImageFilterType::New();
  dilateFilter->SetInput(sourcesImage);
  dilateFilter->SetKernel(structuringElement);
  dilateFilter->Update();

  // Binary XOR the images to get the difference image
  //std::cout << "XORing masks..." << std::endl;
  typedef itk::XorImageFilter<Mask> XorImageFilterType;

  XorImageFilterType::Pointer xorFilter = XorImageFilterType::New();
  xorFilter->SetInput1(dilateFilter->GetOutput());
  xorFilter->SetInput2(sourcesImage);
  xorFilter->Update();

  ITKHelpers::WriteImage(xorFilter->GetOutput(), "boundaryOfSegmentation.png");
  
  // Iterate over the border pixels. If the closest pixel in the original segmentation has
  // a depth greater than a threshold, mark it as a new sink. Else, do not.
  std::cout << "Determining which boundary pixels should be declared background..." << std::endl;
  //std::cout << "There should be " << Helpers::CountNonZeroPixels(xorFilter->GetOutput())
  //          << " considered." << std::endl;
  typedef std::vector<itk::Index<2> > VectorOfPixelsType;
  VectorOfPixelsType newSinks;

  typedef itk::VectorIndexSelectionCastImageFilter<ImageType, FloatScalarImageType> IndexSelectionType;
  IndexSelectionType::Pointer indexSelectionFilter = IndexSelectionType::New();
  indexSelectionFilter->SetIndex(3);
  indexSelectionFilter->SetInput(this->Image);
  indexSelectionFilter->Update();
  
  FloatScalarImageType::Pointer depthImage = indexSelectionFilter->GetOutput();

  //float sameObjectThreshold = 0.1f;

  VectorOfPixelsType consideredPixels;

  itk::ImageRegionIterator<Mask> imageIterator(xorFilter->GetOutput(),
                                               xorFilter->GetOutput()->GetLargestPossibleRegion());
  while(!imageIterator.IsAtEnd())
    {
    if(imageIterator.Get()) // If the current pixel is in question
      {
      consideredPixels.push_back(imageIterator.GetIndex());
      }
    ++imageIterator;
    }

  std::cout << "There are " << consideredPixels.size() << " potential new sink pixels." << std::endl;
  
  for(VectorOfPixelsType::const_iterator iter = consideredPixels.begin(); iter != consideredPixels.end(); ++iter)
    {
    //std::cout << "Considering pixel " << consideredCounter << " (index "
    //          << imageIterator.GetIndex() << ")" << std::endl;
    ImageType::PixelType currentPixel = this->Image->GetPixel(*iter);

    unsigned int radius = this->txtBackgroundCheckRadius->text().toUInt();
    ImageType::RegionType desiredRegion = ITKHelpers::GetRegionInRadiusAroundPixel(*iter, radius);
    //std::cout << "desiredRegion: " << desiredRegion << std::endl;
    
    itk::ImageRegionIterator<Mask> sourcesImageIterator(sourcesImage, desiredRegion);
    
    std::vector<float> nonForegroundDepths;
    std::vector<float> foregroundDepths;
    while(!sourcesImageIterator.IsAtEnd())
      {
      if(sourcesImageIterator.Get())
        {
        foregroundDepths.push_back(depthImage->GetPixel(sourcesImageIterator.GetIndex()));
        }
      else
        {
        nonForegroundDepths.push_back(depthImage->GetPixel(sourcesImageIterator.GetIndex()));
        }
      ++sourcesImageIterator;
      }

    if(nonForegroundDepths.size() < 1)
    {
    }
    
    float nonForegroundMedian = Helpers::VectorMedian(nonForegroundDepths);
    float foregroundMedian = Helpers::VectorMedian(foregroundDepths);

    float difference = fabs(foregroundMedian - nonForegroundMedian);

    if(difference > this->txtBackgroundThreshold->text().toFloat())
      {
      //std::cout << "Difference was " << difference << " so this is a sink pixel." << std::endl;
      newSinks.push_back(*iter);
      }
    else
      {
      //std::cout << "Difference was " << difference << " so this is NOT a sink pixel." << std::endl;
      }
    } // end loop over considered pixels
  
  unsigned char blue[3] = {0, 0, 255};
//   ImageType::PixelType blue(3);
//   blue[0] = 0;
//   blue[1] = 0;
//   blue[2] = 255;
  
  ITKVTKHelpers::SetPixels(this->SourceSinkImageData.GetPointer(), consideredPixels, blue);
  this->SourceSinkImageData->Modified();
  this->Refresh();
  
  // Save the new sink pixels for inspection
  UnsignedCharScalarImageType::Pointer newSinksImage = UnsignedCharScalarImageType::New();
  newSinksImage->SetRegions(this->Image->GetLargestPossibleRegion());
  newSinksImage->Allocate();

  ITKHelpers::IndicesToBinaryImage(newSinks, newSinksImage);
  ITKHelpers::WriteImage(newSinksImage.GetPointer(), "newSinks.png");

  //std::cout << "Out of " << consideredCounter << " pixels considered, "
  //          << backgroundCounter << " were declared background." << std::endl;
  // Set the new sinks
  std::cout << "Setting " << newSinks.size() << " new sinks." << std::endl;

  // Modify the list of sinks so it can be retrieved by the MainWindow after the segmentation is finished
  this->Sinks.insert(this->Sinks.end(), newSinks.begin(), newSinks.end());

  UpdateSelections();
}
예제 #9
0
bool TestExtractChannel()
{
  // VectorImage
  {
  typedef itk::VectorImage<float, 2> VectorImageType;
  VectorImageType::Pointer image = VectorImageType::New();

  itk::Index<2> corner = {{0,0}};
  itk::Size<2> size = {{100,100}};
  itk::ImageRegion<2> region(corner, size);

  image->SetRegions(region);
  image->SetNumberOfComponentsPerPixel(2);
  image->Allocate();

  typedef itk::Image<float, 2> FloatScalarImageType;
  FloatScalarImageType::Pointer floatScalarImage = FloatScalarImageType::New();
  ITKHelpers::ExtractChannel(image.GetPointer(), 0, floatScalarImage.GetPointer());

  typedef itk::Image<unsigned char, 2> UnsignedCharScalarImageType;
  UnsignedCharScalarImageType::Pointer unsignedCharScalarImage = UnsignedCharScalarImageType::New();
  ITKHelpers::ExtractChannel(image.GetPointer(), 0, unsignedCharScalarImage.GetPointer());
  }

  // VectorImage different output type
  {
  typedef itk::VectorImage<float, 2> VectorImageType;
  VectorImageType::Pointer image = VectorImageType::New();

  itk::Index<2> corner = {{0,0}};
  itk::Size<2> size = {{100,100}};
  itk::ImageRegion<2> region(corner, size);

  image->SetRegions(region);
  image->SetNumberOfComponentsPerPixel(2);
  image->Allocate();

  typedef itk::Image<unsigned char, 2> UnsignedCharScalarImageType;
  UnsignedCharScalarImageType::Pointer unsignedCharScalarImage = UnsignedCharScalarImageType::New();
  ITKHelpers::ExtractChannel(image.GetPointer(), 0, unsignedCharScalarImage.GetPointer());
  }

  // Scalar Image
  {
  typedef itk::Image<float, 2> VectorImageType;
  VectorImageType::Pointer image = VectorImageType::New();

  itk::Index<2> corner = {{0,0}};
  itk::Size<2> size = {{100,100}};
  itk::ImageRegion<2> region(corner, size);

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

  typedef itk::Image<float, 2> FloatScalarImageType;
  FloatScalarImageType::Pointer floatScalarImage = FloatScalarImageType::New();
  ITKHelpers::ExtractChannel(image.GetPointer(), 0, floatScalarImage.GetPointer());

  typedef itk::Image<unsigned char, 2> UnsignedCharScalarImageType;
  UnsignedCharScalarImageType::Pointer unsignedCharScalarImage = UnsignedCharScalarImageType::New();
  ITKHelpers::ExtractChannel(image.GetPointer(), 0, unsignedCharScalarImage.GetPointer());
  }

  // Image<CovariantVector>
  {
  typedef itk::Image<itk::CovariantVector<float, 3>, 2> VectorImageType;
  VectorImageType::Pointer image = VectorImageType::New();

  itk::Index<2> corner = {{0,0}};
  itk::Size<2> size = {{100,100}};
  itk::ImageRegion<2> region(corner, size);

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

  typedef itk::Image<float, 2> FloatScalarImageType;
  FloatScalarImageType::Pointer floatScalarImage = FloatScalarImageType::New();
  ITKHelpers::ExtractChannel(image.GetPointer(), 0, floatScalarImage.GetPointer());
  }

  // Image<Vector>
  {
  typedef itk::Image<itk::Vector<float, 3>, 2> VectorImageType;
  VectorImageType::Pointer image = VectorImageType::New();

  itk::Index<2> corner = {{0,0}};
  itk::Size<2> size = {{100,100}};
  itk::ImageRegion<2> region(corner, size);

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

  typedef itk::Image<float, 2> FloatScalarImageType;
  FloatScalarImageType::Pointer floatScalarImage = FloatScalarImageType::New();
  ITKHelpers::ExtractChannel(image.GetPointer(), 0, floatScalarImage.GetPointer());
  }

  return true;
}