C++ FileListType类代码示例

/// Copy derived resources from first time step. Append _reg tag, but leave data untouched.
static void CopyResources(FileListType fileList, std::string outputPath)
{
  for (unsigned int j=0; j < fileList.size(); j++)
  {
    std::string derivedResourceFilename = fileList.at(j);
    std::string fileType = itksys::SystemTools::GetFilenameExtension(derivedResourceFilename);
    std::string fileStem = itksys::SystemTools::GetFilenameWithoutExtension(derivedResourceFilename);
    std::string savePathAndFileName = outputPath +fileStem + "_reg." + fileType;
    MITK_INFO << "Copy resource " << savePathAndFileName;
    mitk::Image::Pointer resImage = mitk::IOUtil::LoadImage(derivedResourceFilename);
    mitk::IOUtil::SaveImage(resImage, savePathAndFileName);
  }
}

/// Build a derived file name from moving images e.g. xxx_T2.nrrd becomes xxx_GTV.nrrd
static FileListType CreateDerivedFileList(std::string baseFN, std::string baseSuffix, std::vector<std::string> derivedPatterns)
{
  FileListType files;
  for (unsigned int i=0; i < derivedPatterns.size(); i++)
  {
    std::string derResourceSuffix =  derivedPatterns.at(i);
    std::string derivedResourceFilename = baseFN.substr(0,baseFN.length() -baseSuffix.length()) + derResourceSuffix;
    MITK_INFO <<" Looking for file: " << derivedResourceFilename;

    if (!itksys::SystemTools::FileExists(derivedResourceFilename.c_str()))
    {
      MITK_INFO << "CreateDerivedFileList: File does not exit. Skipping entry.";
      continue;
    }
    files.push_back(derivedResourceFilename);
  }
  return files;
}

/// Create list of all files in provided folder ending with same postfix
static FileListType CreateFileList(std::string folder , std::string postfix)
{
  itk::Directory::Pointer dir = itk::Directory::New();
  FileListType fileList;

  if( dir->Load(folder.c_str() ) )
  {
    int n = dir->GetNumberOfFiles();
    for(int r=0;r<n;r++)
    {
      std::string filename = dir->GetFile( r );
      if (filename == "." || filename == "..")
        continue;
      filename = folder + filename;
      if (!itksys::SystemTools::FileExists( filename.c_str()))
        continue;
      if (filename.substr(filename.length() -postfix.length() ) == postfix)
        fileList.push_back(filename);
    }
  }
  return fileList;
}

int BatchedFolderRegistration( int argc, char* argv[] )
{
  ctkCommandLineParser parser;
  parser.setArgumentPrefix("--","-");
  // Add command line argument names
  parser.addArgument("help", "h",ctkCommandLineParser::Bool, "Show this help text");
  parser.addArgument("xml", "x",ctkCommandLineParser::Bool, "Print a XML description of this modules command line interface");
  //parser.addArgument("usemask", "u", QVariant::Bool, "Use segmentations (derived resources) to exclude areas from registration metrics");
  parser.addArgument("input", "i", ctkCommandLineParser::String, "Input folder",us::Any(),false);
  parser.addArgument("output", "o", ctkCommandLineParser::String, "Output folder (ending with /)",us::Any(),false);
  parser.addArgument("fixed", "f", ctkCommandLineParser::String, "Suffix for fixed image",us::Any(),false);
  parser.addArgument("moving", "m", ctkCommandLineParser::String, "Suffix for moving images",us::Any(),false);
  parser.addArgument("derived", "d", ctkCommandLineParser::String, "Derived resources suffixes (replaces suffix for moving images); comma separated",us::Any(),true);
  parser.addArgument("silent", "s", ctkCommandLineParser::Bool, "No xml progress output.");
  // Feature currently disabled
  //parser.addArgument("resample", "r", QVariant::String, "Reference Image for resampling (optional), is not applied to tensor data");

  map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);

  // Handle special arguments
  bool silent = false;
  {
    if (parsedArgs.size() == 0)
    {
      MITK_ERROR << "Missig arguements" ;
      return EXIT_FAILURE;
    }

    if (parsedArgs.count("xml"))
    {
      MITK_ERROR << "This is to be handled by shell script";
      return EXIT_SUCCESS;
    }

    if (parsedArgs.count("silent"))
      silent = true;

    // Show a help message
    if ( parsedArgs.count("help") || parsedArgs.count("h"))
    {
      std::cout << parser.helpText();
      return EXIT_SUCCESS;
    }
  }
  std::string outputPath = us::any_cast<string>(parsedArgs["output"]);
  std::string refPattern = us::any_cast<string>(parsedArgs["fixed"]);
  std::string inputPath = us::any_cast<string>(parsedArgs["input"]);
  std::string movingImgPattern = us::any_cast<string>(parsedArgs["moving"]);
  //QString resampleReference = parsedArgs["resample"].toString();
  //bool maskTumor = parsedArgs["usemask"].toBool();

  // if derived sources pattern is provided, populate QStringList with possible filename postfixes
  std::vector<std::string> derPatterns;

  if (parsedArgs.count("derived") || parsedArgs.count("d") )
  {
    std::string arg =  us::any_cast<string>(parsedArgs["derived"]);
    derPatterns = split(arg ,',');
  }

  MITK_INFO << "Input Folder : " << inputPath;
  MITK_INFO << "Looking for reference image ...";
  FileListType referenceFileList = CreateFileList(inputPath,refPattern);

  if (referenceFileList.size() != 1)
  {
    MITK_ERROR << "None or more than one possible reference images (" << refPattern <<") found. Exiting." << referenceFileList.size();
    MITK_INFO  << "Choose a fixed arguement that is unique in the given folder!";
    return EXIT_FAILURE;
  }

  std::string referenceFileName = referenceFileList.at(0);

  MITK_INFO << "Loading Reference (fixed) image: " << referenceFileName;
  mitk::Image::Pointer refImage = mitk::IOUtil::LoadImage(referenceFileName);

  if (refImage.IsNull())
    MITK_ERROR << "Loaded fixed image is NULL";

  // Copy reference image to destination
  std::string savePathAndFileName = GetSavePath(outputPath, referenceFileName);
  mitk::IOUtil::SaveImage(refImage, savePathAndFileName);

  // Copy all derived resources also to output folder, adding _reg suffix
  referenceFileList = CreateDerivedFileList(referenceFileName, movingImgPattern,derPatterns);
  CopyResources(referenceFileList, outputPath);

  std::string derivedResourceFilename;
  mitk::Image::Pointer referenceMask = NULL; // union of all segmentations

  if (!silent)
  {
    // XML Output to report progress
    std::cout << "<filter-start>";
    std::cout << "<filter-name>Batched Registration</filter-name>";
    std::cout << "<filter-comment>Starting registration ... </filter-comment>";
    std::cout << "</filter-start>";
  }

  // Now iterate over all files and register them to the reference image,
//.........这里部分代码省略.........

//.........这里部分代码省略.........
  }

  std::string outputPath = us::any_cast<string>(parsedArgs["output"]);

  std::string inputPath = us::any_cast<string>(parsedArgs["input"]);
  //QString resampleReference = parsedArgs["resample"].toString();
  //bool maskTumor = parsedArgs["usemask"].toBool();

  // if derived sources pattern is provided, populate QStringList with possible filename postfixes
  std::vector<std::string> derPatterns;

  if (parsedArgs.count("derived") || parsedArgs.count("d") )
  {
    std::string arg =  us::any_cast<string>(parsedArgs["derived"]);
    derPatterns = split(arg ,',');
  }


  std::vector<std::string> spacings;
  float spacing[3];
  bool doResampling = false;
  if (parsedArgs.count("resample") || parsedArgs.count("d") )
  {
    std::string arg =  us::any_cast<string>(parsedArgs["resample"]);
    spacings = split(arg ,',');
    spacing[0] = atoi(spacings.at(0).c_str());
    spacing[1] = atoi(spacings.at(1).c_str());
    spacing[2] = atoi(spacings.at(2).c_str());
    doResampling = true;
  }

  MITK_INFO << "Input Folder : " << inputPath;
  MITK_INFO << "Looking for reference image ...";
  FileListType referenceFileList = CreateFileList(inputPath,refPattern);

  if ((!useFirstMoving && referenceFileList.size() != 1) || (useFirstMoving && referenceFileList.size() == 0))
  {
    MITK_ERROR << "None or more than one possible reference images (" << refPattern <<") found. Exiting." << referenceFileList.size();
    MITK_INFO  << "Choose a fixed arguement that is unique in the given folder!";
    return EXIT_FAILURE;
  }

  std::string referenceFileName = referenceFileList.at(0);

  MITK_INFO << "Loading Reference (fixed) image: " << referenceFileName;
  std::string fileType = itksys::SystemTools::GetFilenameExtension(referenceFileName);
  mitk::Image::Pointer refImage = ExtractFirstTS(mitk::IOUtil::LoadImage(referenceFileName), fileType);
  mitk::Image::Pointer resampleReference = NULL;
  if (doResampling)
  {
    refImage = ResampleBySpacing(refImage,spacing);
    resampleReference = refImage;
  }

  if (refImage.IsNull())
    MITK_ERROR << "Loaded fixed image is NULL";

  // Copy reference image to destination
  std::string savePathAndFileName = GetSavePath(outputPath, referenceFileName);

  mitk::IOUtil::SaveImage(refImage, savePathAndFileName);

  // Copy all derived resources also to output folder, adding _reg suffix
  referenceFileList = CreateDerivedFileList(referenceFileName, movingImgPattern,derPatterns);
  CopyResources(referenceFileList, outputPath);