Esempio n. 1
0
void ReadMitkProjectImageAndMask(std::string input_file, mitk::Image::Pointer & raw_image, mitk::Image::Pointer & class_mask, mitk::Image::Pointer & brain_mask)
{
  auto so = mitk::IOUtil::Load(input_file);

  std::map<uint, uint> map;

  mitk::CLUtil::CountVoxel(dynamic_cast<mitk::Image *>(so[1].GetPointer()), map);

  raw_image = map.size() <= 7 ? dynamic_cast<mitk::Image *>(so[0].GetPointer()) : dynamic_cast<mitk::Image *>(so[1].GetPointer());
  class_mask = map.size() <= 7 ? dynamic_cast<mitk::Image *>(so[1].GetPointer()) : dynamic_cast<mitk::Image *>(so[0].GetPointer());

  std::map<uint, uint> merge_instructions;// = {{0,0},{1,1},{2,1},{3,1},{4,2},{5,3},{6,3}};
  merge_instructions[0] = 0;
  merge_instructions[1] = 1;
  merge_instructions[2] = 1;
  merge_instructions[3] = 1;
  merge_instructions[4] = 2;
  merge_instructions[5] = 3;
  merge_instructions[6] = 3;
  mitk::CLUtil::MergeLabels(class_mask, merge_instructions);

  brain_mask = class_mask->Clone();
  //merge_instructions = {{0,0},{1,1},{2,1},{3,1},{4,1},{5,1},{6,1}};
  merge_instructions[0] = 0;
  merge_instructions[1] = 1;
  merge_instructions[2] = 1;
  merge_instructions[3] = 1;
  merge_instructions[4] = 1;
  merge_instructions[5] = 1;
  merge_instructions[6] = 1;
  mitk::CLUtil::MergeLabels(brain_mask, merge_instructions);
}
void ConvertIplImageForthAndBack(mitk::Image::Pointer inputForIpl, std::string imageFileName)
{
  // now we convert it to OpenCV IplImage
  mitk::ImageToOpenCVImageFilter::Pointer toOCvConverter = mitk::ImageToOpenCVImageFilter::New();
  toOCvConverter->SetImage(inputForIpl);
  IplImage* iplTestImage = toOCvConverter->GetOpenCVImage();

  MITK_TEST_CONDITION_REQUIRED( iplTestImage != NULL, "Conversion to OpenCv IplImage successful!");

  mitk::OpenCVToMitkImageFilter::Pointer toMitkConverter = mitk::OpenCVToMitkImageFilter::New();
  toMitkConverter->SetOpenCVImage(iplTestImage);
  toMitkConverter->Update();

  // initialize the image with the input image, since we want to test equality and OpenCV does not feature geometries and spacing
  mitk::Image::Pointer result = inputForIpl->Clone();
  mitk::ImageReadAccessor resultAcc(toMitkConverter->GetOutput(), toMitkConverter->GetOutput()->GetSliceData());
  result->SetImportSlice(const_cast<void*>(resultAcc.GetData()));

  if( result->GetPixelType().GetNumberOfComponents() == 1 )
  {
    MITK_TEST_EQUAL( result, inputForIpl, "Testing equality of input and output image of IplImage conversion  for " << imageFileName );
  }
  else if( result->GetPixelType().GetNumberOfComponents() == 3 )
  {
    MITK_TEST_EQUAL( result, inputForIpl, "Testing equality of input and output image of cv::Mat conversion for " << imageFileName );
  }
  else
  {
    MITK_WARN << "Unhandled number of components used to test equality, please enhance test!";
  }
}
void QmitkImageStatisticsCalculationThread::Initialize( mitk::Image::Pointer image, mitk::Image::Pointer binaryImage, mitk::PlanarFigure::Pointer planarFig )
{
  // reset old values
  if( this->m_StatisticsImage.IsNotNull() )
    this->m_StatisticsImage = 0;

  if( this->m_BinaryMask.IsNotNull() )
    this->m_BinaryMask = 0;

  if( this->m_PlanarFigureMask.IsNotNull())
    this->m_PlanarFigureMask = 0;

  // set new values if passed in
  if(image.IsNotNull())
    this->m_StatisticsImage = image->Clone();
  if(binaryImage.IsNotNull())
    this->m_BinaryMask = binaryImage->Clone();
  if(planarFig.IsNotNull())
    this->m_PlanarFigureMask = planarFig->Clone();
}
void QmitkImageStatisticsCalculationThread::Initialize( mitk::Image::Pointer image, mitk::Image::Pointer binaryImage, mitk::PlanarFigure::Pointer planarFig )
{
  // reset old values
  if( this->m_StatisticsImage.IsNotNull() )
    this->m_StatisticsImage = 0;

  if( this->m_BinaryMask.IsNotNull() )
    this->m_BinaryMask = 0;

  if( this->m_PlanarFigureMask.IsNotNull())
    this->m_PlanarFigureMask = 0;

  // set new values if passed in
  if(image.IsNotNull())
    this->m_StatisticsImage = image->Clone();
  if(binaryImage.IsNotNull())
    this->m_BinaryMask = binaryImage->Clone();
  if(planarFig.IsNotNull())
    this->m_PlanarFigureMask = dynamic_cast<mitk::PlanarFigure*>(planarFig.GetPointer()); // once clone methods for planar figures are implemented, copy the data here!
}
void ConvertCVMatForthAndBack(mitk::Image::Pointer inputForCVMat, std::string imageFileName)
{
  // now we convert it to OpenCV IplImage
  mitk::ImageToOpenCVImageFilter::Pointer toOCvConverter = mitk::ImageToOpenCVImageFilter::New();
  toOCvConverter->SetImage(inputForCVMat);
  cv::Mat cvmatTestImage = toOCvConverter->GetOpenCVMat();

  MITK_TEST_CONDITION_REQUIRED( !cvmatTestImage.empty(), "Conversion to cv::Mat successful!");

  mitk::OpenCVToMitkImageFilter::Pointer toMitkConverter = mitk::OpenCVToMitkImageFilter::New();
  toMitkConverter->SetOpenCVMat(cvmatTestImage);
  toMitkConverter->Update();

  // initialize the image with the input image, since we want to test equality and OpenCV does not feature geometries and spacing
  mitk::Image::Pointer result = inputForCVMat->Clone();
  mitk::ImageReadAccessor resultAcc(toMitkConverter->GetOutput(), toMitkConverter->GetOutput()->GetSliceData());
  result->SetImportSlice(const_cast<void*>(resultAcc.GetData()));

  if( result->GetPixelType().GetNumberOfComponents() == 1 )
  {
    MITK_TEST_EQUAL( result, inputForCVMat, "Testing equality of input and output image of cv::Mat conversion for " << imageFileName );
  }
  else if( result->GetPixelType().GetNumberOfComponents() == 3 )
  {
    MITK_TEST_EQUAL( result, inputForCVMat, "Testing equality of input and output image of cv::Mat conversion for " << imageFileName );
  }
  else
  {
    MITK_WARN << "Unhandled number of components used to test equality, please enhance test!";
  }

  // change OpenCV image to test if the filter gets updated
  cv::Mat changedcvmatTestImage = cvmatTestImage.clone();
  changedcvmatTestImage.at<char>(0,0) = cvmatTestImage.at<char>(0,0) != 0 ? 0 : 1;

  toMitkConverter->SetOpenCVMat(changedcvmatTestImage);
  toMitkConverter->Update();

  MITK_TEST_NOT_EQUAL(toMitkConverter->GetOutput(), inputForCVMat, "Converted image must not be the same as before.");
}