void mitk::DCUtilities::EnsureUCharImageInDC(mitk::DataCollection::Pointer dc, std::string name, std::string origin) { typedef itk::Image<unsigned char, 3> FeatureImage; typedef itk::Image<unsigned char, 3> LabelImage; mitk::DataCollectionImageIterator<unsigned char , 3> iter( dc, origin); while (!iter.IsAtEnd()) { ++iter; } if (dc->HasElement(origin)) { LabelImage::Pointer originImage = dynamic_cast<LabelImage*>(dc->GetData(origin).GetPointer()); // = dynamic_cast<LabelImage*>(dc->GetItkImage<LabelImage>(origin).GetPointer()); if (!dc->HasElement(name) && originImage.IsNotNull()) { MITK_INFO << "New unsigned char image necessary"; FeatureImage::Pointer image = FeatureImage::New(); image->SetRegions(originImage->GetLargestPossibleRegion()); image->SetSpacing(originImage->GetSpacing()); image->SetOrigin(originImage->GetOrigin()); image->SetDirection(originImage->GetDirection()); image->Allocate(); image->FillBuffer(0); dc->AddData(dynamic_cast<itk::DataObject*>(image.GetPointer()),name,""); } } for (std::size_t i = 0; i < dc->Size();++i) { mitk::DataCollection* newCol = dynamic_cast<mitk::DataCollection*>(dc->GetData(i).GetPointer()); if (newCol != 0) { EnsureUCharImageInDC(newCol, name, origin); } } }
static void EnsureDataImageInCollection(mitk::DataCollection::Pointer collection, std::string origin, std::string target) { typedef itk::Image<double, 3> FeatureImage; if (collection->HasElement(origin)) { mitk::Image::Pointer originImage = dynamic_cast<mitk::Image*>(collection->GetMitkImage(origin).GetPointer()); FeatureImage::Pointer itkOriginImage = FeatureImage::New(); mitk::CastToItkImage(originImage,itkOriginImage); if (!collection->HasElement(target) && itkOriginImage.IsNotNull()) { FeatureImage::Pointer image = FeatureImage::New(); image->SetRegions(itkOriginImage->GetLargestPossibleRegion()); image->SetSpacing(itkOriginImage->GetSpacing()); image->SetOrigin(itkOriginImage->GetOrigin()); image->SetDirection(itkOriginImage->GetDirection()); image->Allocate(); collection->AddData(dynamic_cast<itk::DataObject*>(image.GetPointer()),target,""); } } for (std::size_t i = 0; i < collection->Size();++i) { mitk::DataCollection* newCol = dynamic_cast<mitk::DataCollection*>(collection->GetData(i).GetPointer()); if (newCol != 0) { EnsureDataImageInCollection(newCol, origin, target); } } }
int main(int argc, char *argv[]) { mitkCommandLineParser parser; parser.setTitle("Mri Normalization"); parser.setCategory("Preprocessing Tools"); parser.setDescription( "Normalizes an MRI volume between medians of two given masks (e.g. ventricles and brain matter)"); parser.setContributor("MBI"); parser.setArgumentPrefix("--", "-"); // Add command line argument names parser.addArgument("input", "i", mitkCommandLineParser::Image, "input image", "", us::Any(), false, false, false, mitkCommandLineParser::Input); parser.addArgument("output", "o", mitkCommandLineParser::File, "output image", "", us::Any(), false, false, false, mitkCommandLineParser::Output); parser.addArgument( "maxMask", "m", mitkCommandLineParser::Image, "mask of which median is set as maximal value (1)", "", us::Any(), false, false, false, mitkCommandLineParser::Input); parser.addArgument( "minMask", "l", mitkCommandLineParser::Image, "mask of which median is set as minimal value (0)", "", us::Any(), false, false, false, mitkCommandLineParser::Input); parser.addArgument( "excludeMask", "e", mitkCommandLineParser::Image, "region which is exluded from the other two", "", us::Any(), false, false, false, mitkCommandLineParser::Input); map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv); // Show a help message if (parsedArgs.size() == 0 || parsedArgs.count("help") || parsedArgs.count("h")) { std::cout << parser.helpText(); return EXIT_SUCCESS; } std::string outFile = us::any_cast<string>(parsedArgs["output"]); mitk::Image::Pointer inputFile = mitk::IOUtil::Load<mitk::Image>(us::any_cast<string>(parsedArgs["input"])); mitk::Image::Pointer maxMask = mitk::IOUtil::Load<mitk::Image>(us::any_cast<string>(parsedArgs["maxMask"])); mitk::Image::Pointer minMask = mitk::IOUtil::Load<mitk::Image>(us::any_cast<string>(parsedArgs["minMask"])); mitk::Image::Pointer excludeMask = mitk::IOUtil::Load<mitk::Image>(us::any_cast<string>(parsedArgs["excludeMask"])); SeedImage::Pointer itkMaxImage = SeedImage::New(); SeedImage::Pointer itkMinImage = SeedImage::New(); SeedImage::Pointer itkExcludeImage = SeedImage::New(); FeatureImage::Pointer itkInputImage = FeatureImage::New(); mitk::CastToItkImage(inputFile, itkInputImage); mitk::CastToItkImage(maxMask, itkMaxImage); mitk::CastToItkImage(minMask, itkMinImage); mitk::CastToItkImage(excludeMask, itkExcludeImage); std::vector<mitk::ScalarType> medianMin; std::vector<mitk::ScalarType> medianMax; itk::ImageRegionIterator<FeatureImage> inputIt(itkInputImage, itkInputImage->GetLargestPossibleRegion()); itk::ImageRegionIterator<SeedImage> excludeIt(itkExcludeImage, itkExcludeImage->GetLargestPossibleRegion()); itk::ImageRegionIterator<SeedImage> minIt(itkMinImage, itkMinImage->GetLargestPossibleRegion()); itk::ImageRegionIterator<SeedImage> maxIt(itkMaxImage, itkMaxImage->GetLargestPossibleRegion()); while (!inputIt.IsAtEnd()) { if (excludeIt.Get() == 0) { if (minIt.Get() != 0) medianMin.push_back(inputIt.Get()); if (maxIt.Get() != 0) medianMax.push_back(inputIt.Get()); } ++inputIt; ++excludeIt; ++minIt; ++maxIt; } std::sort(medianMax.begin(), medianMax.end()); std::sort(medianMin.begin(), medianMin.end()); mitk::ScalarType minVal = medianMin.at(medianMin.size() / 2); mitk::ScalarType maxVal = medianMax.at(medianMax.size() / 2); inputIt.GoToBegin(); // Create mapping while (!inputIt.IsAtEnd()) { inputIt.Set(1.0 * (inputIt.Get() - minVal) / (maxVal - minVal)); ++inputIt; } mitk::Image::Pointer mitkResult = mitk::Image::New(); mitkResult = mitk::GrabItkImageMemory(itkInputImage); mitk::IOUtil::Save(mitkResult, outFile); return EXIT_SUCCESS; }
int main(int argc, char *argv[]) { mitkCommandLineParser parser; parser.setTitle("Mri Normalization"); parser.setCategory("Preprocessing Tools"); parser.setDescription("Normalizes an MRI volume based on regions determined by Otsu."); parser.setContributor("MBI"); parser.setArgumentPrefix("--", "-"); // Add command line argument names parser.addArgument("input", "i", mitkCommandLineParser::InputImage, "input image", "input image"); parser.addArgument("output", "o", mitkCommandLineParser::OutputFile, "output image", "output image"); parser.addArgument("bins", "b", mitkCommandLineParser::Int, "number of regions (bins)", "number of regions (bins)"); parser.addArgument( "minBin", "l", mitkCommandLineParser::Int, "bin of which median is set to 0", "bin of which median is set to 0"); parser.addArgument( "maxBin", "h", mitkCommandLineParser::Int, "bin of which median is set to 1", "bin of which median is set to 1"); map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv); // Show a help message if (parsedArgs.size() == 0 || parsedArgs.count("help") || parsedArgs.count("h")) { std::cout << parser.helpText(); return EXIT_SUCCESS; } std::string outFile = us::any_cast<string>(parsedArgs["output"]); mitk::Image::Pointer inputFile = mitk::IOUtil::Load<mitk::Image>(us::any_cast<string>(parsedArgs["input"])); int numberOfThresholds = us::any_cast<int>(parsedArgs["bins"]); int minBin = us::any_cast<int>(parsedArgs["minBin"]); int maxBin = us::any_cast<int>(parsedArgs["maxBin"]); FeatureImage::Pointer itkInputImage = FeatureImage::New(); mitk::CastToItkImage(inputFile, itkInputImage); typedef itk::OtsuMultipleThresholdsImageFilter<FeatureImage, FeatureImage> FilterType; FilterType::Pointer otsuFilter = FilterType::New(); otsuFilter->SetInput(itkInputImage); otsuFilter->SetNumberOfThresholds(numberOfThresholds - 1); otsuFilter->Update(); FeatureImage::Pointer itkLabelImage = otsuFilter->GetOutput(); std::vector<mitk::ScalarType> medianMin; std::vector<mitk::ScalarType> medianMax; itk::ImageRegionIterator<FeatureImage> inputIt(itkInputImage, itkInputImage->GetLargestPossibleRegion()); itk::ImageRegionIterator<FeatureImage> labelIt(itkLabelImage, itkLabelImage->GetLargestPossibleRegion()); while (!inputIt.IsAtEnd()) { if (labelIt.Get() == minBin) { medianMin.push_back(inputIt.Get()); } else if (labelIt.Get() == maxBin) { medianMax.push_back(inputIt.Get()); } ++inputIt; ++labelIt; } std::sort(medianMax.begin(), medianMax.end()); std::sort(medianMin.begin(), medianMin.end()); mitk::ScalarType minVal = medianMin.at(medianMin.size() / 2); mitk::ScalarType maxVal = medianMax.at(medianMax.size() / 2); inputIt.GoToBegin(); // labelIt.GoToBegin(); // Create mapping while (!inputIt.IsAtEnd()) { inputIt.Set(1.0 * (inputIt.Get() - minVal) / (maxVal - minVal)); // inputIt.Set(labelIt.Get()); ++inputIt; //++labelIt; } mitk::Image::Pointer mitkResult = mitk::Image::New(); mitkResult = mitk::GrabItkImageMemory(itkInputImage); mitk::IOUtil::Save(mitkResult, outFile); return EXIT_SUCCESS; }