CLDicom2Nrrd.cpp

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/*============================================================================

The Medical Imaging Interaction Toolkit (MITK)

Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.

Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.

============================================================================*/

#include "mitkProperties.h"

#include "mitkCommandLineParser.h"
#include "mitkIOUtil.h"

#include <itksys/SystemTools.hxx>

#include "mitkPreferenceListReaderOptionsFunctor.h"


int main(int argc, char* argv[])
{
  mitkCommandLineParser parser;

  parser.setTitle("Dicom Loader");
  parser.setCategory("Preprocessing Tools");
  parser.setDescription("");
  parser.setContributor("German Cancer Research Center (DKFZ)");

  parser.setArgumentPrefix("--","-");
  // Add command line argument names
  parser.addArgument("help", "h",mitkCommandLineParser::Bool, "Help:", "Show this help text");
  parser.addArgument("input", "i", mitkCommandLineParser::Directory, "Input folder:", "Input folder",us::Any(),false, false, false, mitkCommandLineParser::Input);
  parser.addArgument("output", "o", mitkCommandLineParser::File, "Output file:", "Output file", us::Any(), false, false, false, mitkCommandLineParser::Output);
  parser.addArgument("reader", "r", mitkCommandLineParser::String, "Reader Name", "Reader Name", us::Any());


  std::map<std::string, us::Any> 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<std::string>(parsedArgs["input"]);
  std::string outFileName = us::any_cast<std::string>(parsedArgs["output"]);

  mitk::PreferenceListReaderOptionsFunctor::ListType preference = {};
  if (parsedArgs.count("reader"))
  {
    preference.push_back(us::any_cast<std::string>(parsedArgs["reader"]));
  }
  mitk::PreferenceListReaderOptionsFunctor::ListType emptyList = {};
  mitk::IOUtil::LoadInfo info(inputFolder);
  mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor(preference, emptyList);
  functor(info);

  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, &functor);

  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);
    ++count;
  }

  return EXIT_SUCCESS;
}