/**
* @brief AddColouredOverlay - Overlays the rgbImage with an coloured overlay
*
* For all positions in overlayImage not zero, its value is multiplied the the colour value and added
* to the rgbImage.
*
* @param rgbImage - input rgbImage to which the coloured overlay is added
* @param overlayImage
* @param color
*/
void AddColouredOverlay(mitk::Image::Pointer rgbImage, mitk::Image::Pointer overlayImage, mitk::Color color)
{
unsigned int *dim = rgbImage->GetDimensions();
itk::Image<PixelType,3>::Pointer itkOverlayImage = itk::Image<PixelType,3>::New();
mitk::CastToItkImage(overlayImage.GetPointer(), itkOverlayImage);
mitk::ImagePixelWriteAccessor<RGBPixelType ,3> writeAcc(rgbImage);
itk::Index<3> idx;
itk::RGBPixel<PixelType> value;
unsigned short overlayVal=0;
// Fill rgb image with gray values
for (idx[2] =0; (unsigned int)idx[2] < dim[2]; idx[2]++)
{
for (idx[1] =0; (unsigned int)idx[1] < dim[1]; idx[1]++)
{
for (idx[0] =0; (unsigned int)idx[0] < dim[0]; idx[0]++)
{
overlayVal = 255*itkOverlayImage->GetPixel(idx);
value = writeAcc.GetPixelByIndex(idx);
value[0] = std::min( (int)(value[0] + overlayVal * color[0]),254*255);
value[1] = std::min((int)(value[1] + overlayVal * color[1]),254*255) ;
value[2] = std::min((int)(value[2] + overlayVal * color[2]),254*255);
writeAcc.SetPixelByIndex(idx, value);
}
}
}
}
void setUp() override
{
m_ReferenceImage = mitk::IOUtil::LoadImage(GetTestDataFilePath("Pic3D.nrrd"));
CPPUNIT_ASSERT_MESSAGE("Failed to load image for test: [Pic3D.nrrd]", m_ReferenceImage.IsNotNull());
m_InterpolationController = mitk::SegmentationInterpolationController::GetInstance();
// Create empty segmentation
// Surely there must be a better way to get an image with all zeros?
m_SegmentationImage = mitk::Image::New();
const mitk::PixelType pixelType(mitk::MakeScalarPixelType<mitk::Tool::DefaultSegmentationDataType>());
m_SegmentationImage->Initialize(pixelType, m_ReferenceImage->GetDimension(), m_ReferenceImage->GetDimensions());
m_SegmentationImage->SetClonedTimeGeometry(m_ReferenceImage->GetTimeGeometry());
unsigned int size = sizeof(mitk::Tool::DefaultSegmentationDataType);
for (unsigned int dim = 0; dim < m_SegmentationImage->GetDimension(); ++dim)
{
size *= m_SegmentationImage->GetDimension(dim);
}
mitk::ImageWriteAccessor imageAccessor(m_SegmentationImage);
memset(imageAccessor.GetData(), 0, size);
// Work in the center of the image (Pic3D)
m_CenterPoint = {{ 127, 127, 25 }};
}
void mitk::pa::SpectralUnmixingSO2::CheckPreConditions(mitk::Image::Pointer inputHbO2, mitk::Image::Pointer inputHb)
{
unsigned int xDimHb = inputHb->GetDimensions()[0];
unsigned int yDimHb = inputHb->GetDimensions()[1];
unsigned int zDimHb = inputHb->GetDimensions()[2];
unsigned int xDimHbO2 = inputHbO2->GetDimensions()[0];
unsigned int yDimHbO2 = inputHbO2->GetDimensions()[1];
unsigned int zDimHbO2 = inputHbO2->GetDimensions()[2];
if (xDimHb != xDimHbO2 || yDimHb != yDimHbO2 || zDimHb != zDimHbO2)
mitkThrow() << "DIMENTIONALITY ERROR!";
if (inputHbO2->GetPixelType() != mitk::MakeScalarPixelType<float>())
mitkThrow() << "PIXELTYPE ERROR! FLOAT REQUIRED";
if (inputHb->GetPixelType() != mitk::MakeScalarPixelType<float>())
mitkThrow() << "PIXELTYPE ERROR! FLOAT REQUIRED";
MITK_INFO(m_Verbose) << "CHECK PRECONDITIONS ...[DONE]";
}
mitk::pa::Volume::Volume(mitk::Image::Pointer image)
{
MITK_INFO << "Initialized by mitk::Image";
if (image.IsNull())
mitkThrow() << "You may not initialize a mitk::Volume with a null reference to an mitk image";
unsigned int* dimensions = image->GetDimensions();
m_YDim = dimensions[0];
m_XDim = dimensions[1];
m_ZDim = dimensions[2];
m_InternalMitkImage = image;
m_FastAccessDataPointer = GetData();
}
/**
* @brief ConvertToRGBImage converts a gray image to RGB by filling all three channels with the gray intensity
* @param grayImage
* @return
*/
mitk::Image::Pointer ConvertToRGBImage(mitk::Image::Pointer grayImage)
{
mitk::Image::Pointer rgbImage = mitk::Image::New();
unsigned int *dim = grayImage->GetDimensions();
rgbImage->Initialize(mitk::MakePixelType<PixelType, RGBPixelType,3>(),3,dim);
rgbImage->SetGeometry(grayImage->GetGeometry());
itk::Image<InputPixelType,3>::Pointer itkGrayImage = itk::Image<InputPixelType,3>::New();
mitk::CastToItkImage(grayImage, itkGrayImage);
mitk::ImagePixelWriteAccessor<RGBPixelType,3> writeAcc(rgbImage);
typedef itk::RescaleIntensityImageFilter< itk::Image<InputPixelType,3>, itk::Image<PixelType,3> > RescaleFilterType;
RescaleFilterType::Pointer rescaleFilter = RescaleFilterType::New();
rescaleFilter->SetInput(itkGrayImage);
rescaleFilter->SetOutputMinimum(0);
rescaleFilter->SetOutputMaximum(255*255);
rescaleFilter->Update();
itk::Index<3> idx;
RGBPixelType value;
// Fill rgb image with gray values
for (idx[2] =0; (unsigned int)idx[2] < dim[2]; idx[2]++)
{
for (idx[1] =0; (unsigned int)idx[1] < dim[1]; idx[1]++)
{
for (idx[0] =0; (unsigned int)idx[0] < dim[0]; idx[0]++)
{
value.Fill(rescaleFilter->GetOutput()->GetPixel(idx));
writeAcc.SetPixelByIndex(idx, value);
}
}
}
return rgbImage;
}