diff --git a/Modules/Classification/CLMiniApps/CLDicom2Nrrd.cpp b/Modules/Classification/CLMiniApps/CLDicom2Nrrd.cpp index 0332c5f98b..72d79ca344 100644 --- a/Modules/Classification/CLMiniApps/CLDicom2Nrrd.cpp +++ b/Modules/Classification/CLMiniApps/CLDicom2Nrrd.cpp @@ -1,87 +1,107 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkDicomSeriesReader.h" #include "mitkProperties.h" #include "mitkCommandLineParser.h" #include "mitkIOUtil.h" int main(int argc, char* argv[]) { mitkCommandLineParser parser; parser.setTitle("Dicom Loader"); parser.setCategory("Preprocessing Tools"); parser.setDescription(""); parser.setContributor("MBI"); parser.setArgumentPrefix("--","-"); // Add command line argument names parser.addArgument("help", "h",mitkCommandLineParser::Bool, "Help:", "Show this help text"); parser.addArgument("input", "i", mitkCommandLineParser::InputDirectory, "Input folder:", "Input folder",us::Any(),false); parser.addArgument("output", "o", mitkCommandLineParser::OutputFile, "Output file:", "Output file",us::Any(),false); std::map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; // Show a help message if ( parsedArgs.count("help") || parsedArgs.count("h")) { std::cout << parser.helpText(); return EXIT_SUCCESS; } std::string inputFolder = us::any_cast(parsedArgs["input"]); std::string outFileName = us::any_cast(parsedArgs["output"]); + + /* //check if DICOMTags have been set as property for mitk::Image mitk::DicomSeriesReader::FileNamesGrouping seriesInFiles = mitk::DicomSeriesReader::GetSeries( inputFolder, true ); std::list images; std::map fileMap; // TODO sort series UIDs, implementation of map iterator might differ on different platforms (or verify this is a standard topic??) for (mitk::DicomSeriesReader::FileNamesGrouping::const_iterator seriesIter = seriesInFiles.begin(); seriesIter != seriesInFiles.end(); ++seriesIter) { mitk::DicomSeriesReader::StringContainer files = seriesIter->second.GetFilenames(); mitk::DataNode::Pointer node = mitk::DicomSeriesReader::LoadDicomSeries( files ); if (node.IsNotNull()) { mitk::Image::Pointer image = dynamic_cast( node->GetData() ); images.push_back( image ); fileMap.insert( std::pair(image,files)); } } + */ + std::string extension = itksys::SystemTools::GetFilenameExtension(outFileName); + std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(outFileName); + std::string path = itksys::SystemTools::GetFilenamePath(outFileName); + + auto nodes = mitk::IOUtil::Load(inputFolder); + + unsigned count = 0; + for (auto node : nodes) + { + std::string writeName = path + "/" + filename + extension; + if (count > 0) + { + writeName = path + "/" + filename + "_" + std::to_string(count) + extension; + } + mitk::IOUtil::Save(node, writeName); + } + /* // WARN: EXPECT ONLY ONE ITEM PER FOLDER for ( std::list::const_iterator imageIter = images.begin(); imageIter != images.end(); ++imageIter ) { const mitk::Image::Pointer image = *imageIter; mitk::IOUtil::SaveImage(image,outFileName); - } + }*/ return EXIT_SUCCESS; }