diff --git a/apps/VoxelizerTool/VoxelizerToolHelper.cpp b/apps/VoxelizerTool/VoxelizerToolHelper.cpp index 5d2dd70..f270d09 100644 --- a/apps/VoxelizerTool/VoxelizerToolHelper.cpp +++ b/apps/VoxelizerTool/VoxelizerToolHelper.cpp @@ -1,238 +1,238 @@ // ----------------------------------------------------------------------- // RTToolbox - DKFZ radiotherapy quantitative evaluation library // // Copyright (c) German Cancer Research Center (DKFZ), // Software development for Integrated Diagnostics and Therapy (SIDT). // ALL RIGHTS RESERVED. // See rttbCopyright.txt or // http://www.dkfz.de/en/sidt/projects/rttb/copyright.html // // This software is distributed WITHOUT ANY WARRANTY; without even // the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR // PURPOSE. See the above copyright notices for more information. // //------------------------------------------------------------------------ /*! // @file // @version $Revision: 1127 $ (last changed revision) // @date $Date: 2015-10-01 13:33:33 +0200 (Do, 01 Okt 2015) $ (last change date) // @author $Author: hentsch $ (last changed by) */ #include #include "rttbBoostMaskAccessor.h" #include "itkMacro.h" #include "VoxelizerToolHelper.h" #include "VoxelizerToolApplicationData.h" #include "rttbITKImageMaskAccessorConverter.h" #include "rttbImageWriter.h" #include "itkBinaryThresholdImageFilter.h" #include "itkAddImageFilter.h" #include #include #include #include "rttbDicomFileStructureSetGenerator.h" void rttb::apps::voxelizerTool::removeSpecialCharacters(std::string& label) { //Replace / to avoid problems with directories (struct "Magen/DD" --> Magen/DD.mhd), delete trailing . to avoid filenames with two trailing points (Niere re. --> Niere re..mhd) while (label.find("/") != std::string::npos) { label.replace(label.find("/"), 1, "_"); } if (*label.rbegin() == '.') { label.replace(label.size() - 1, 1, ""); } } std::string rttb::apps::voxelizerTool::getFilenameWithoutEnding(const std::string& outfilename) { boost::filesystem::path p(outfilename); return p.replace_extension("").string(); } std::string rttb::apps::voxelizerTool::getFileEnding(const std::string& outfilename) { boost::filesystem::path p(outfilename); return p.extension().string(); } rttb::core::MaskAccessorInterface::MaskAccessorPointer rttb::apps::voxelizerTool::createMask( rttb::core::DoseAccessorInterface::DoseAccessorPointer doseAccessorPtr, rttb::core::Structure::StructTypePointer structurePtr, bool strict) { rttb::core::MaskAccessorInterface::MaskAccessorPointer maskAccessorPtr; if (doseAccessorPtr != nullptr && structurePtr != nullptr) { maskAccessorPtr = boost::make_shared (structurePtr, doseAccessorPtr->getGeometricInfo(), strict); maskAccessorPtr->updateMask(); } return maskAccessorPtr; } -void rttb::apps::voxelizerTool::writeMaskToFile(std::vector& maskVector, +void rttb::apps::voxelizerTool::writeMaskToFile(std::vector maskVector, const std::string& outputFileName, bool voxelization) { if (!maskVector.empty()) { io::itk::ITKImageMaskAccessor::ITKMaskImageType::ConstPointer itkImage; if (maskVector.size() > 1) { itkImage = addMultipleStructsToImage(maskVector); } else { io::itk::ITKImageMaskAccessorConverter maskAccessorConverter(maskVector.at(0)); maskAccessorConverter.process(); itkImage = maskAccessorConverter.getITKImage(); } if (voxelization) { itkImage = applyThresholdFilter(itkImage); } io::itk::ImageWriter writer(outputFileName, itkImage); writer.writeFile(); } } rttb::io::itk::ITKImageMaskAccessor::ITKMaskImageType::ConstPointer rttb::apps::voxelizerTool::addMultipleStructsToImage( - std::vector& maskVector) + std::vector maskVector) { std::vector listOfITKImages; for (const auto & i : maskVector) { io::itk::ITKImageMaskAccessorConverter maskAccessorConverter(i); maskAccessorConverter.process(); listOfITKImages.push_back(maskAccessorConverter.getITKImage()); } itk::AddImageFilter , itk::Image>::Pointer addFilter = itk::AddImageFilter , itk::Image>::New(); io::itk::ITKImageMaskAccessor::ITKMaskImageType::Pointer filterResult; for (int k = 1; k < listOfITKImages.size(); k++) { if (k == 1) { addFilter->SetInput1(listOfITKImages.at(0)); } else { addFilter->SetInput1(filterResult); } addFilter->SetInput2(listOfITKImages.at(k)); addFilter->Update(); filterResult = addFilter->GetOutput(); } io::itk::ITKImageMaskAccessor::ITKMaskImageType::ConstPointer filterResultConst(filterResult); return filterResultConst; } rttb::io::itk::ITKImageMaskAccessor::ITKMaskImageType::ConstPointer rttb::apps::voxelizerTool::applyThresholdFilter( - io::itk::ITKImageMaskAccessor::ITKMaskImageType::ConstPointer& itkImage) + io::itk::ITKImageMaskAccessor::ITKMaskImageType::ConstPointer itkImage) { itk::BinaryThresholdImageFilter< itk::Image, itk::Image >::Pointer filter = itk::BinaryThresholdImageFilter< itk::Image, itk::Image >::New(); filter->SetInput(itkImage); filter->SetLowerThreshold(0.5); filter->SetUpperThreshold(1.0); filter->SetInsideValue(1.0); filter->Update(); return filter->GetOutput(); } void rttb::apps::voxelizerTool::writeITKImageToFile(io::itk::ITKImageMaskAccessor::ITKMaskImageType::ConstPointer& itkImage, const std::string& outputfilename, bool useCompression) { itk::ImageFileWriter< itk::Image >::Pointer writer = itk::ImageFileWriter< itk::Image >::New(); writer->SetFileName(outputfilename); writer->SetUseCompression(useCompression); writer->SetInput(itkImage); writer->Update(); } void rttb::apps::voxelizerTool::processData(rttb::apps::voxelizerTool::ApplicationData& appData) { if (appData._struct->getNumberOfStructures()>0) { std::vector maskVector; if (appData._addStructures) { for (size_t i=0; igetNumberOfStructures(); i++ ) { std::cout << "creating mask #" << i << "..."; maskVector.push_back(createMask(appData._dose, appData._struct->getStructure(i), !appData._noStrictVoxelization)); std::cout << "done" << std::endl; } std::cout << "writing mask to file..."; writeMaskToFile(maskVector, appData._outputFilename, appData._binaryVoxelization); std::cout << "done" << std::endl; } else { //default behavior: read only first struct that matches the regex unsigned int maxIterationCount = 1; //only if specified: read all structs that matches the regex if (appData._multipleStructs) { maxIterationCount = appData._struct->getNumberOfStructures(); } for (size_t i = 0; igetStructure(i), !appData._noStrictVoxelization); std::cout << "done" << std::endl; std::string labelOfInterest = appData._struct->getStructure(i)->getLabel(); removeSpecialCharacters(labelOfInterest); std::string outputName = appData._outputFilename; if (appData._multipleStructs) { std::string fileName = getFilenameWithoutEnding( appData._outputFilename); std::string fileEnding = getFileEnding(appData._outputFilename); outputName = fileName + "_" + labelOfInterest + fileEnding; } std::vector currenMaskVector{ currentMask }; writeMaskToFile(currenMaskVector, outputName, appData._binaryVoxelization); } } } else { std::cout << "No struct found" << std::endl; } } \ No newline at end of file diff --git a/apps/VoxelizerTool/VoxelizerToolHelper.h b/apps/VoxelizerTool/VoxelizerToolHelper.h index c349de9..63dfd8e 100644 --- a/apps/VoxelizerTool/VoxelizerToolHelper.h +++ b/apps/VoxelizerTool/VoxelizerToolHelper.h @@ -1,71 +1,71 @@ // ----------------------------------------------------------------------- // RTToolbox - DKFZ radiotherapy quantitative evaluation library // // Copyright (c) German Cancer Research Center (DKFZ), // Software development for Integrated Diagnostics and Therapy (SIDT). // ALL RIGHTS RESERVED. // See rttbCopyright.txt or // http://www.dkfz.de/en/sidt/projects/rttb/copyright.html // // This software is distributed WITHOUT ANY WARRANTY; without even // the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR // PURPOSE. See the above copyright notices for more information. // //------------------------------------------------------------------------ /*! // @file // @version $Revision: 1127 $ (last changed revision) // @date $Date: 2015-10-01 13:33:33 +0200 (Do, 01 Okt 2015) $ (last change date) // @author $Author: hentsch $ (last changed by) */ #include #include #include "rttbStructure.h" #include "rttbMaskAccessorInterface.h" #include "rttbITKImageMaskAccessor.h" #include "rttbDoseAccessorInterface.h" namespace rttb { namespace apps { namespace voxelizerTool { class ApplicationData; void processData(ApplicationData& appData); /**@brief Search the label with the position from index @return a label from the list as string */ void removeSpecialCharacters(std::string& label); /**@brief create a mask with _rtStructureSet and _doseAccessor object. @return a mask object */ core::MaskAccessorInterface::MaskAccessorPointer createMask( core::DoseAccessorInterface::DoseAccessorPointer doseAccessorPtr, rttb::core::Structure::StructTypePointer structurePtr, bool strict); /**@brief write the mask into the outputfile @param Outputfilename */ - void writeMaskToFile(std::vector& maskVector, + void writeMaskToFile(std::vector maskVector, const std::string& outputFileName, bool voxelization); io::itk::ITKImageMaskAccessor::ITKMaskImageType::ConstPointer addMultipleStructsToImage( - std::vector& maskVector); + std::vector maskVector); io::itk::ITKImageMaskAccessor::ITKMaskImageType::ConstPointer applyThresholdFilter( - io::itk::ITKImageMaskAccessor::ITKMaskImageType::ConstPointer& itkImage); + io::itk::ITKImageMaskAccessor::ITKMaskImageType::ConstPointer itkImage); void writeITKImageToFile(io::itk::ITKImageMaskAccessor::ITKMaskImageType::ConstPointer& itkImage, const std::string& outputfilename, bool useCompression); std::string getFilenameWithoutEnding(const std::string& outfilename); std::string getFileEnding(const std::string& outfilename); } } } \ No newline at end of file