void GetImageStatisticsWithImageAndMaskNotConnected()
{
//create rules connection + add statistics to dataStorage
auto statisticsNode = mitk::CreateImageStatisticsNode(m_statisticsContainer, "testStatistics");
CreateNodeRelationImage(m_statisticsContainer.GetPointer(), m_image.GetPointer());
CreateNodeRelationMask(m_statisticsContainer.GetPointer(), m_mask.GetPointer());
auto standaloneDataStorage = mitk::StandaloneDataStorage::New();
standaloneDataStorage->Add(statisticsNode);
//rule: (image-->statistics, mask-->statistics), 1 connected image --> test return nullptr
mitk::ImageStatisticsContainer::ConstPointer statisticsWithImage;
CPPUNIT_ASSERT_NO_THROW(statisticsWithImage = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer()));
CPPUNIT_ASSERT_EQUAL(statisticsWithImage.IsNull(), true);
//rule: (image-->statistics, mask-->statistics), 1 unconnected image, 1 unconnected mask --> test return nullptr
mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageNotConnectedAndMaskNotConnected;
CPPUNIT_ASSERT_NO_THROW(statisticsWithImageNotConnectedAndMaskNotConnected = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image2.GetPointer(), m_mask2.GetPointer()));
CPPUNIT_ASSERT_EQUAL(statisticsWithImageNotConnectedAndMaskNotConnected.IsNull(), true);
//rule: (image-->statistics, mask-->statistics), 1 unconnected image, 1 connected mask --> test return nullptr
mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageAndMaskNotConnected;
CPPUNIT_ASSERT_NO_THROW(statisticsWithImageAndMaskNotConnected = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image2.GetPointer(), m_mask.GetPointer()));
CPPUNIT_ASSERT_EQUAL(statisticsWithImageAndMaskNotConnected.IsNull(), true);
//rule: (image-->statistics, mask-->statistics), 1 connected image, 1 unconnected planarFigure --> test return nullptr
mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageAndPlanarFigureNotConnected;
CPPUNIT_ASSERT_NO_THROW(statisticsWithImageAndPlanarFigureNotConnected = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer(), m_planarFigure.GetPointer()));
CPPUNIT_ASSERT_EQUAL(statisticsWithImageAndPlanarFigureNotConnected.IsNull(), true);
//rule: (image-->statistics, mask-->statistics), 1 unconnected image, 1 unconnected planarFigure --> test return nullptr
mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageNotConnectedAndPlanarFigureNotConnected;
CPPUNIT_ASSERT_NO_THROW(statisticsWithImageAndPlanarFigureNotConnected = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image2.GetPointer(), m_planarFigure.GetPointer()));
CPPUNIT_ASSERT_EQUAL(statisticsWithImageAndPlanarFigureNotConnected.IsNull(), true);
}
static bool CompareImages(mitk::Image::Pointer mitkImage, cv::Mat openCVImage)
{
float equal = true;
if ((mitkImage->GetDimension(0)!=openCVImage.cols)||(mitkImage->GetDimension(1)!=openCVImage.rows))
{
equal = false;
}
for (unsigned int i=0; i<openCVImage.cols; i++)
{
for (unsigned int j=0; j<openCVImage.rows; j++)
{
mitk::Index3D currentIndex;
currentIndex[0] = i;
currentIndex[1] = j;
currentIndex[2] = 0;
float mitkImageValue = mitkImage->GetPixelValueByIndex(currentIndex);
float openCVImageValue = openCVImage.at<float>(j,i);
if (!mitk::Equal(mitkImageValue,openCVImageValue))
{
equal = false;
}
}
}
return equal;
}
void mitk::SurfaceInterpolationController::SetCurrentInterpolationSession(mitk::Image::Pointer currentSegmentationImage)
{
if (currentSegmentationImage.GetPointer() == m_SelectedSegmentation)
return;
if (currentSegmentationImage.IsNull())
{
m_SelectedSegmentation = nullptr;
return;
}
m_SelectedSegmentation = currentSegmentationImage.GetPointer();
auto it = m_ListOfInterpolationSessions.find(currentSegmentationImage.GetPointer());
// If the session does not exist yet create a new ContourPositionPairList otherwise reinitialize the interpolation pipeline
if (it == m_ListOfInterpolationSessions.end())
{
ContourPositionInformationVec2D newList;
m_ListOfInterpolationSessions.insert(std::pair<mitk::Image*, ContourPositionInformationVec2D>(m_SelectedSegmentation, newList));
m_InterpolationResult = nullptr;
m_CurrentNumberOfReducedContours = 0;
itk::MemberCommand<SurfaceInterpolationController>::Pointer command = itk::MemberCommand<SurfaceInterpolationController>::New();
command->SetCallbackFunction(this, &SurfaceInterpolationController::OnSegmentationDeleted);
m_SegmentationObserverTags.insert( std::pair<mitk::Image*, unsigned long>( m_SelectedSegmentation, m_SelectedSegmentation->AddObserver( itk::DeleteEvent(), command ) ) );
}
this->ReinitializeInterpolation();
}
void mitk::MorphologicalOperations::FillHoles(mitk::Image::Pointer &image)
{
MITK_INFO << "Start FillHole...";
int timeSteps = static_cast<int>(image->GetTimeSteps());
if (timeSteps > 1)
{
mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New();
timeSelector->SetInput(image);
for (int t = 0; t < timeSteps; ++t)
{
MITK_INFO << " Processing time step " << t;
timeSelector->SetTimeNr(t);
timeSelector->Update();
mitk::Image::Pointer img3D = timeSelector->GetOutput();
img3D->DisconnectPipeline();
AccessByItk_1(img3D, itkFillHoles, img3D);
mitk::ImageReadAccessor accessor(img3D);
image->SetVolume(accessor.GetData(), t);
}
}
else
{
AccessByItk_1(image, itkFillHoles, image);
}
MITK_INFO << "Finished FillHole";
}
static bool CompareImages(mitk::Image::Pointer mitkImage, cv::Mat openCVImage)
{
float equal = true;
if (static_cast<int>(mitkImage->GetDimension(0)) != openCVImage.cols || static_cast<int>(mitkImage->GetDimension(1)) != openCVImage.rows)
{
equal = false;
}
mitk::ImagePixelReadAccessor<float,2> imageAcces(mitkImage, mitkImage->GetSliceData(0));
for(int i=0; i<openCVImage.cols; i++)
{
for(int j=0; j<openCVImage.rows; j++)
{
itk::Index<2> currentIndex;
currentIndex[0] = i;
currentIndex[1] = j;
float mitkImageValue = imageAcces.GetPixelByIndex(currentIndex);
float openCVImageValue = openCVImage.at<float>(j,i);
if (!mitk::Equal(mitkImageValue,openCVImageValue))
{
equal = false;
}
}
}
return equal;
}
void mitk::USTelemedImageSource::GetNextRawImage( mitk::Image::Pointer& image)
{
if ( image.IsNull() ) { image = mitk::Image::New(); }
//get the actual resolution to check if it changed. We have to do this every time because the geometry takes a few frames to adapt
Usgfw2Lib::tagImageResolution resolutionInMetersActual;
m_ImageProperties->GetResolution(&resolutionInMetersActual, 0);
if (m_OldnXPelsPerUnit != resolutionInMetersActual.nXPelsPerUnit || m_OldnYPelsPerUnit != resolutionInMetersActual.nYPelsPerUnit)
{
//we can only update if the image exists and has a geometry
if (m_Image.IsNotNull() && m_Image->GetGeometry() != nullptr)
{
m_OldnXPelsPerUnit = resolutionInMetersActual.nXPelsPerUnit;
m_OldnYPelsPerUnit = resolutionInMetersActual.nYPelsPerUnit;
UpdateImageGeometry();
}
}
//now update image
if ( m_Image->IsInitialized() )
{
m_ImageMutex->Lock();
// copy contents of the given image into the member variable
image->Initialize(m_Image->GetPixelType(), m_Image->GetDimension(), m_Image->GetDimensions());
mitk::ImageReadAccessor inputReadAccessor(m_Image, m_Image->GetSliceData(0,0,0));
image->SetSlice(inputReadAccessor.GetData());
image->SetGeometry(m_Image->GetGeometry());
m_ImageMutex->Unlock();
}
}
/**
* @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 StartSimulation(FiberfoxParameters<double> parameters, FiberBundle::Pointer fiberBundle, mitk::Image::Pointer refImage, string message)
{
itk::TractsToDWIImageFilter< short >::Pointer tractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New();
tractsToDwiFilter->SetUseConstantRandSeed(true);
tractsToDwiFilter->SetParameters(parameters);
tractsToDwiFilter->SetFiberBundle(fiberBundle);
tractsToDwiFilter->Update();
mitk::Image::Pointer testImage = mitk::GrabItkImageMemory( tractsToDwiFilter->GetOutput() );
testImage->SetProperty( mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), mitk::GradientDirectionsProperty::New( parameters.m_SignalGen.GetGradientDirections() ) );
testImage->SetProperty( mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str(), mitk::FloatProperty::New( parameters.m_SignalGen.m_Bvalue ) );
mitk::DiffusionPropertyHelper propertyHelper( testImage );
propertyHelper.InitializeImage();
if (refImage.IsNotNull())
{
if( static_cast<mitk::GradientDirectionsProperty*>( refImage->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() )->GetGradientDirectionsContainer().IsNotNull() )
{
ItkDwiType::Pointer itkTestImagePointer = ItkDwiType::New();
mitk::CastToItkImage(testImage, itkTestImagePointer);
ItkDwiType::Pointer itkRefImagePointer = ItkDwiType::New();
mitk::CastToItkImage(refImage, itkRefImagePointer);
bool cond = CompareDwi(itkTestImagePointer, itkRefImagePointer);
if (!cond)
{
MITK_INFO << "Saving test and rference image to " << mitk::IOUtil::GetTempPath();
mitk::IOUtil::SaveBaseData(testImage, mitk::IOUtil::GetTempPath()+"testImage.dwi");
mitk::IOUtil::SaveBaseData(refImage, mitk::IOUtil::GetTempPath()+"refImage.dwi");
}
MITK_TEST_CONDITION_REQUIRED(cond, message);
}
}
}
void mitk::NonStaticArithmeticOperation::CallExecuteTwoImageFilter(mitk::Image::Pointer imageA, mitk::Image::Pointer imageB)
{
if (imageA->GetDimension() != imageB->GetDimension())
{
mitkThrow() << "Image have different dimensions. This is not supported by mitk::ArithmeticOperation";
}
switch (imageA->GetDimension())
{
case 1:
AccessTwoImagesFixedDimensionByItk(imageA, imageB, mitk::NonStaticArithmeticOperation::ExecuteTwoImageFilter, 1);
break;
case 2:
AccessTwoImagesFixedDimensionByItk(imageA, imageB, mitk::NonStaticArithmeticOperation::ExecuteTwoImageFilter, 2);
break;
case 3:
AccessTwoImagesFixedDimensionByItk(imageA, imageB, mitk::NonStaticArithmeticOperation::ExecuteTwoImageFilter, 3);
break;
case 4:
AccessTwoImagesFixedDimensionByItk(imageA, imageB, mitk::NonStaticArithmeticOperation::ExecuteTwoImageFilter, 4);
break;
default:
mitkThrow() << "Image Dimension of "<<imageA->GetDimension() << " is not supported";
break;
}
}
static bool CompareImages(mitk::Image::Pointer image1, mitk::Image::Pointer image2)
{
unsigned int dimX = image1->GetDimension(0);
unsigned int dimY = image1->GetDimension(1);
//make sure images have the same dimensions
if((dimX != image1->GetDimension(0)) || (dimY != image1->GetDimension(1)))
return false;
//compare all pixel values
for(unsigned int i = 0; i<dimX; i++)
{
for(unsigned int j = 0; j < dimY; j++)
{
mitk::Index3D idx;
idx[0] = i; idx[1] = j; idx[2] = 0;
if(!(mitk::Equal(image1->GetPixelValueByIndex(idx), image1->GetPixelValueByIndex(idx))))
{
return false;
}
}
}
//all pixels have identical values
return true;
}
void Init()
{
im1 = mitk::ImageGenerator::GenerateRandomImage<double>(2,2,2,1,2,2,2,1,0);
im2 = mitk::ImageGenerator::GenerateRandomImage<double>(3,3,3,1,3,3,3,3,2);
im3 = mitk::ImageGenerator::GenerateRandomImage<double>(4,4,4,1,4,4,4,5,4);
im4 = mitk::ImageGenerator::GenerateRandomImage<double>(5,5,5,1,5,5,5,7,6);
dataCol1 = mitk::DataCollection::New();
dataCol2 = mitk::DataCollection::New();
dataCol1->AddData(im1.GetPointer(),"T1");
dataCol1->AddData(im2.GetPointer(),"T2");
dataCol2->AddData(im3.GetPointer(),"T1");
dataCol2->AddData(im4.GetPointer(),"T2");
col1 = mitk::DataCollection::New();
col1->SetName("GnaBla");
col1->AddData(dataCol1.GetPointer(), "0001");
col1->AddData(dataCol2.GetPointer(), "0002");
m_Collection = mitk::DataCollection::New();
m_Collection->SetName("DummyCollection");
m_Collection->AddData(col1.GetPointer(), "C1");
}
bool mitkSegmentationInterpolationTestClass::LoadTestImages()
{
std::string filename1 = mitk::StandardFileLocations::GetInstance()->FindFile("interpolation_test_manual.pic.gz", "../mitk/Core/Testing/Data/");
if ( filename1.empty() )
{
filename1 = mitk::StandardFileLocations::GetInstance()->FindFile("interpolation_test_manual.pic.gz", "Testing/Data/");
}
std::cout << "Found test image (manual slices) in '" << filename1 << "'" << std::endl;
std::string filename2 = mitk::StandardFileLocations::GetInstance()->FindFile("interpolation_test_result.pic.gz", "../mitk/Core/Testing/Data/");
if ( filename2.empty() )
{
filename2 = mitk::StandardFileLocations::GetInstance()->FindFile("interpolation_test_result.pic.gz", "Testing/Data/");
}
std::cout << "Found test image (reference for interpolation) in '" << filename2 << "'" << std::endl;
if ( filename1.empty() || filename2.empty() )
{
return false;
}
else
{
m_ManualSlices = LoadImage( filename1 );
m_InterpolatedSlices = LoadImage( filename2 );
return ( m_ManualSlices.IsNotNull() && m_InterpolatedSlices.IsNotNull() );
}
return true;
}
Attributes::Attributes(mitk::Image::Pointer mitkImage)
{
log_trace(Log::New, this);
Pixel::ID pixelID;
Component::ID componentID;
unsigned int dimension;
log_info("pixelType: " << mitkImage->GetPixelType().GetPixelTypeAsString());
log_info("channels : " << mitkImage->GetPixelType().GetNumberOfComponents());
log_info("component: " << mitkImage->GetPixelType().GetComponentTypeAsString());
log_info("dimension: " << mitkImage->GetDimension());
switch (mitkImage->GetPixelType().GetPixelType())
{
case itk::ImageIOBase::SCALAR: pixelID = Pixel::ID::Scalar; break;
case itk::ImageIOBase::RGB: pixelID = Pixel::ID::Rgb; break;
case itk::ImageIOBase::RGBA: pixelID = Pixel::ID::Rgba; break;
default: pixelID = Pixel::ID::Scalar; break;
}
switch ((itk::ImageIOBase::IOComponentType) mitkImage->GetPixelType().GetComponentType())
{
case itk::ImageIOBase::UCHAR: componentID = Component::ID::UChar; break;
case itk::ImageIOBase::USHORT: componentID = Component::ID::UShort; break;
case itk::ImageIOBase::UINT: componentID = Component::ID::UInt; break;
case itk::ImageIOBase::CHAR: componentID = Component::ID::Char; break;
case itk::ImageIOBase::SHORT: componentID = Component::ID::Short; break;
case itk::ImageIOBase::INT: componentID = Component::ID::Int; break;
case itk::ImageIOBase::FLOAT: componentID = Component::ID::Float; break;
case itk::ImageIOBase::DOUBLE: componentID = Component::ID::Double; break;
default: componentID = Component::ID::Double; break;
}
if (mitkImage->GetPixelType().GetNumberOfComponents() == 1)
{
pixelID = Pixel::ID::Scalar;
}
if (mitkImage->GetPixelType().GetNumberOfComponents() == 3)
{
pixelID = Pixel::ID::Rgb;
}
if (mitkImage->GetPixelType().GetNumberOfComponents() == 4)
{
pixelID = Pixel::ID::Rgba;
}
dimension = mitkImage->GetDimension();
this->m_dimension = dimension;
this->m_pixelID = pixelID;
this->m_componentID = componentID;
}
void mitk::SurfaceInterpolationController::SetCurrentInterpolationSession(mitk::Image::Pointer currentSegmentationImage)
{
if (currentSegmentationImage.GetPointer() == m_SelectedSegmentation)
return;
m_ReduceFilter->Reset();
m_NormalsFilter->Reset();
m_InterpolateSurfaceFilter->Reset();
if (currentSegmentationImage.IsNull())
{
m_SelectedSegmentation = 0;
return;
}
ContourListMap::iterator it = m_ListOfInterpolationSessions.find(currentSegmentationImage.GetPointer());
m_SelectedSegmentation = currentSegmentationImage.GetPointer();
itk::ImageBase<3>::Pointer itkImage = itk::ImageBase<3>::New();
AccessFixedDimensionByItk_1( m_SelectedSegmentation, GetImageBase, 3, itkImage );
m_InterpolateSurfaceFilter->SetReferenceImage( itkImage.GetPointer() );
if (it == m_ListOfInterpolationSessions.end())
{
ContourPositionPairList newList;
m_ListOfInterpolationSessions.insert(std::pair<mitk::Image*, ContourPositionPairList>(m_SelectedSegmentation, newList));
m_InterpolationResult = 0;
m_CurrentNumberOfReducedContours = 0;
itk::MemberCommand<SurfaceInterpolationController>::Pointer command = itk::MemberCommand<SurfaceInterpolationController>::New();
command->SetCallbackFunction(this, &SurfaceInterpolationController::OnSegmentationDeleted);
m_SegmentationObserverTags.insert( std::pair<mitk::Image*, unsigned long>( m_SelectedSegmentation, m_SelectedSegmentation->AddObserver( itk::DeleteEvent(), command ) ) );
}
else
{
for (unsigned int i = 0; i < m_ListOfInterpolationSessions[m_SelectedSegmentation].size(); i++)
{
m_ReduceFilter->SetInput(i, m_ListOfInterpolationSessions[m_SelectedSegmentation].at(i).contour);
}
m_ReduceFilter->Update();
m_CurrentNumberOfReducedContours = m_ReduceFilter->GetNumberOfOutputs();
for (unsigned int i = 0; i < m_CurrentNumberOfReducedContours; i++)
{
m_NormalsFilter->SetInput(i, m_ReduceFilter->GetOutput(i));
m_InterpolateSurfaceFilter->SetInput(i, m_NormalsFilter->GetOutput(i));
}
}
Modified();
}
static void Paint(mitk::Image::Pointer image, itk::Index<3> index, unsigned int timeStep)
{
// As soon as the ImagePixelWriteAccessor object goes out of scope at the
// end of this function, the image will be unlocked again (RAII).
mitk::ImagePixelWriteAccessor<T> writeAccessor(image, image->GetVolumeData(timeStep));
writeAccessor.SetPixelByIndex(index, std::numeric_limits<T>::min());
// Don't forget to update the modified time stamp of the image. Otherwise,
// everything downstream wouldn't recognize that the image changed,
// including the rendering system.
image->Modified();
}
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 }};
}
/**
* @brief RemapIntoVectorImage Take a 3d+t image and reinterpret it as vector image
* @return vectoriamge
*/
mitk::DiffusionImageCreationFilter::VectorImageType::Pointer
mitk::DiffusionImageCreationFilter::RemapIntoVectorImage( mitk::Image::Pointer input)
{
typedef itk::Image<mitk::DiffusionPropertyHelper::DiffusionPixelType, 3> ImageVolumeType;
typedef itk::ComposeImageFilter< ImageVolumeType > ComposeFilterType;
ComposeFilterType::Pointer vec_composer = ComposeFilterType::New();
mitk::ImageTimeSelector::Pointer t_selector = mitk::ImageTimeSelector::New();
t_selector->SetInput( input );
for( unsigned int i=0; i< input->GetTimeSteps(); i++)
{
t_selector->SetTimeNr(i);
t_selector->Update();
ImageVolumeType::Pointer singleImageItk;
mitk::CastToItkImage( t_selector->GetOutput(), singleImageItk );
vec_composer->SetInput( i, singleImageItk );
}
try
{
vec_composer->Update();
}
catch( const itk::ExceptionObject& e)
{
MITK_ERROR << "Caught exception while updating compose filter: " << e.what();
}
mitk::DiffusionImageCreationFilter::VectorImageType::Pointer vector_image = vec_composer->GetOutput();
vector_image->GetPixelContainer()->ContainerManageMemoryOff();
return vector_image;
}
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 mitk::ToFVisualizationFilter::InitImage(mitk::Image::Pointer image)
{
unsigned int dimensions[2];
dimensions[0] = this->m_ImageWidth;
dimensions[1] = this->m_ImageHeight;
image->Initialize(mitk::PixelType(mitkIpPicUInt, 24, 3), 2, dimensions); //unsigned char RGB
}
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();
}
// Helper function to multiplex the actual Paint function call for different
// pixel types. As it's cumbersome and ugly, you may want to avoid such
// functions by using ITK for the actual painting and use the ITK access
// macros like we did for the AwesomeImageFilter.
static void Paint(mitk::Image::Pointer image, itk::Index<3> index, unsigned int timeStep)
{
switch (image->GetPixelType().GetComponentType())
{
case itk::ImageIOBase::CHAR:
Paint<char>(image, index, timeStep);
break;
case itk::ImageIOBase::UCHAR:
Paint<unsigned char>(image, index, timeStep);
break;
case itk::ImageIOBase::SHORT:
Paint<short>(image, index, timeStep);
break;
case itk::ImageIOBase::USHORT:
Paint<unsigned short>(image, index, timeStep);
break;
case itk::ImageIOBase::INT:
Paint<int>(image, index, timeStep);
break;
case itk::ImageIOBase::UINT:
Paint<unsigned int>(image, index, timeStep);
break;
default:
mitkThrow();
}
}
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
ResampleImage(itk::Image<TPixel, VImageDimension>* itkImage, float resolution, mitk::Image::Pointer& newImage)
{
typedef itk::Image<TPixel, VImageDimension> ImageType;
typedef itk::ResampleImageFilter<ImageType, ImageType> ResampleFilterType;
typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
auto spacing = itkImage->GetSpacing();
auto size = itkImage->GetLargestPossibleRegion().GetSize();
for (unsigned int i = 0; i < VImageDimension; ++i)
{
size[i] = size[i] / (1.0*resolution)*(1.0*spacing[i])+1.0;
}
spacing.Fill(resolution);
resampler->SetInput(itkImage);
resampler->SetSize(size);
resampler->SetOutputSpacing(spacing);
resampler->SetOutputOrigin(itkImage->GetOrigin());
resampler->SetOutputDirection(itkImage->GetDirection());
resampler->Update();
newImage->InitializeByItk(resampler->GetOutput());
mitk::GrabItkImageMemory(resampler->GetOutput(), newImage);
}
/**
* This test takes a generated gradient mitk image. Then an IGTL Message is produced
* using the ImageToIGTLMessageFilter. In the end it is tested, wether the image data in both images is equivalent.
*/
void Equal_ContentOfIGTLImageMessageAndMitkImage_True(unsigned int dim)
{
m_TestImage = mitk::ImageGenerator::GenerateGradientImage<unsigned char>(dim, dim, 1u);
m_ImageToIGTLMessageFilter->SetInput(m_TestImage);
m_ImageToIGTLMessageFilter->GenerateData();
mitk::IGTLMessage::Pointer resultMessage = m_ImageToIGTLMessageFilter->GetOutput();
CPPUNIT_ASSERT_MESSAGE("Output of ImageToIGTLMessageFilter was null", resultMessage != nullptr);
igtl::MessageBase::Pointer msgBase = resultMessage->GetMessage();
igtl::ImageMessage* igtlImageMessage = (igtl::ImageMessage*)(msgBase.GetPointer());
CPPUNIT_ASSERT_MESSAGE("Output of ImageToIGTLMessageFilter was not of type igtl::ImageMessage", igtlImageMessage != nullptr);
const void* outputBuffer = igtlImageMessage->GetScalarPointer();
CPPUNIT_ASSERT_MESSAGE("Output Buffer was null", outputBuffer != nullptr);
mitk::ImageReadAccessor readAccess(m_TestImage, m_TestImage->GetChannelData(0));
const void* inputBuffer = readAccess.GetData();
CPPUNIT_ASSERT_MESSAGE("Input Buffer was null", inputBuffer != nullptr);
CPPUNIT_ASSERT_MESSAGE("Images were not identical", memcmp(inputBuffer, outputBuffer, dim*dim) == 0);
}
static bool CompareImages(mitk::Image::Pointer image1, mitk::Image::Pointer image2)
{
//check if epsilon is exceeded
unsigned int sliceDimension = image1->GetDimension(0)*image1->GetDimension(1);
bool picturesEqual = true;
float* floatArray1 = (float*)image1->GetSliceData(0, 0, 0)->GetData();
float* floatArray2 = (float*)image2->GetSliceData(0, 0, 0)->GetData();
for(unsigned int i = 0; i < sliceDimension; i++)
{
if(!(mitk::Equal(floatArray1[i], floatArray2[i])))
{
picturesEqual = false;
}
}
return picturesEqual;
}
bool mitkSegmentationInterpolationTestClass::ClearSegmentation()
{
int* p = (int*)m_Image->GetData(); // pointer to pixel data
int size = dim[0]*dim[1]*dim[2];
for(int i=0; i<size; ++i, ++p) *p=0; // fill image with zeros
return true;
}
void GetImageStatisticsWithImageConnected()
{
//create rules connection
auto statisticsNode = mitk::CreateImageStatisticsNode(m_statisticsContainer, "testStatistics");
CreateNodeRelationImage(m_statisticsContainer.GetPointer(), m_image.GetPointer());
auto standaloneDataStorage = mitk::StandaloneDataStorage::New();
standaloneDataStorage->Add(statisticsNode);
//rule: (image-->statistics), 1 connected image --> test return image statistics
mitk::ImageStatisticsContainer::ConstPointer statisticsWithImage;
CPPUNIT_ASSERT_NO_THROW(statisticsWithImage = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer()));
CPPUNIT_ASSERT_EQUAL(statisticsWithImage->GetUID(), m_statisticsContainer->GetUID());
//new rule: (image2-->statistics2 AND mask --> statistics2)
CreateNodeRelationImage(m_statisticsContainer2.GetPointer(), m_image2.GetPointer());
CreateNodeRelationMask(m_statisticsContainer2.GetPointer(), m_mask.GetPointer());
auto statisticsNode2 = mitk::CreateImageStatisticsNode(m_statisticsContainer2, "testStatistics2");
standaloneDataStorage->Add(statisticsNode2);
//--> test return (still) image statistics (!= statistics2)
mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageAgain;
CPPUNIT_ASSERT_NO_THROW(statisticsWithImageAgain = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer()));
CPPUNIT_ASSERT_EQUAL(statisticsWithImageAgain->GetUID(), m_statisticsContainer->GetUID());
CPPUNIT_ASSERT_EQUAL(statisticsWithImageAgain->GetUID() != m_statisticsContainer2->GetUID(), true);
//--> test return image statistics 2
CPPUNIT_ASSERT_NO_THROW(statisticsWithImageAgain = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image2.GetPointer(), m_mask.GetPointer()));
CPPUNIT_ASSERT_EQUAL(statisticsWithImageAgain->GetUID(), m_statisticsContainer2->GetUID());
CPPUNIT_ASSERT_EQUAL(statisticsWithImageAgain->GetUID() != m_statisticsContainer->GetUID(), true);
//add another newer statistic: should return this newer one
auto statisticsContainerNew = mitk::ImageStatisticsContainer::New();
CreateNodeRelationImage(statisticsContainerNew.GetPointer(), m_image.GetPointer());
auto statisticsNodeNew = mitk::CreateImageStatisticsNode(statisticsContainerNew, "testStatisticsNew");
standaloneDataStorage->Add(statisticsNodeNew);
statisticsContainerNew->Modified();
mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageNew;
CPPUNIT_ASSERT_NO_THROW(statisticsWithImageNew = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer()));
CPPUNIT_ASSERT_EQUAL(statisticsWithImageNew->GetUID(), statisticsContainerNew->GetUID());
CPPUNIT_ASSERT_EQUAL(statisticsWithImageNew->GetUID() != m_statisticsContainer->GetUID(), true);
}
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 ToFOpenCVImageGrabber::MapScalars( mitk::Image::Pointer mitkImage, IplImage* openCVImage)
{
unsigned int numOfPixel = m_ImageGrabber->GetCaptureWidth()*m_ImageGrabber->GetCaptureHeight();
float* floatData = (float*)mitkImage->GetSliceData(0, 0, 0)->GetData();
vtkSmartPointer<vtkColorTransferFunction> colorTransferFunction = vtkColorTransferFunction::New();
vtkSmartPointer<vtkFloatArray> floatArrayInt;
floatArrayInt = vtkFloatArray::New();
floatArrayInt->Initialize();
floatArrayInt->SetArray(floatData, numOfPixel, 0);
mitk::ScalarType min = mitkImage->GetScalarValueMin();
mitk::ScalarType max = mitkImage->GetScalarValueMaxNoRecompute();
MITK_INFO<<"Minimum: "<<min;
MITK_INFO<<"Maximum: "<<max;
colorTransferFunction->RemoveAllPoints();
colorTransferFunction->AddRGBPoint(min, 0, 0, 0);
colorTransferFunction->AddRGBPoint(max, 1, 1, 1);
colorTransferFunction->SetColorSpaceToHSV();
//TODO other depth values
colorTransferFunction->MapScalarsThroughTable(floatArrayInt, (unsigned char*)openCVImage->imageData, VTK_LUMINANCE);
}
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();
}
