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,
// also register derived resources based on file patterns
// ------------------------------------------------------------------------------
// Create File list
FileListType movingImagesList = CreateFileList(inputPath, movingImgPattern);
// TODO Reactivate Resampling Feature
// mitk::Image::Pointer resampleImage = NULL;
// if (QFileInfo(resampleReference).isFile())
// {
// resampleImage = mitk::IOUtil::LoadImage(resampleReference.toStdString());
// }
for (unsigned int i =0; i < movingImagesList.size(); i++)
{
std::string fileMorphName = movingImagesList.at(i);
if (fileMorphName == referenceFileName)
{
// do not process reference image again
continue;
}
MITK_INFO << "Processing image " << fileMorphName;
// 1 Register morphological file to reference image
if (!itksys::SystemTools::FileExists(fileMorphName.c_str()))
{
MITK_WARN << "File does not exit. Skipping entry.";
continue;
}
// Origin of images is cancelled
// TODO make this optional!!
double transf[6];
double offset[3];
{
mitk::Image::Pointer movingImage = mitk::IOUtil::LoadImage(fileMorphName);
MITK_ERROR << "REF COUNT MOVING 0 " << movingImage->GetReferenceCount();
if (movingImage.IsNull())
MITK_ERROR << "Loaded moving image is NULL";
// Store transformation, apply it to morph file
MITK_INFO << "----------Registering moving image to reference----------";
MITK_ERROR << "REF COUNT MOVING 1 " << movingImage->GetReferenceCount();
//mitk::RegistrationWrapper::GetTransformation(refImage, movingImage, transf, offset, referenceMask);
MITK_ERROR << "REF COUNT MOVING 2 " << movingImage->GetReferenceCount();
mitk::RegistrationWrapper::ApplyTransformationToImage(movingImage, transf,offset, NULL); // , resampleImage
MITK_ERROR << "REF COUNT MOVING 3 " << movingImage->GetReferenceCount();
savePathAndFileName = GetSavePath(outputPath, fileMorphName);
std::string fileType = itksys::SystemTools::GetFilenameExtension(fileMorphName);
SaveImage(savePathAndFileName,movingImage,fileType );
}
if (!silent)
{
std::cout << "<filter-progress-text progress=\"" <<
(float)i / (float)movingImagesList.size()
<< "\" >.</filter-progress-text>";
}
// Now parse all derived resource and apply the above calculated transformation to them
// ------------------------------------------------------------------------------------
FileListType fList = CreateDerivedFileList(fileMorphName, movingImgPattern,derPatterns);
if (fList.size() > 0)
MITK_INFO << "----------DERIVED RESOURCES ---------";
for (unsigned int j=0; j < fList.size(); j++)
{
derivedResourceFilename = fList.at(j);
MITK_INFO << "----Processing derived resource " << derivedResourceFilename << " ...";
mitk::Image::Pointer derivedMovingResource = mitk::IOUtil::LoadImage(derivedResourceFilename);
// Apply transformation to derived resource, treat derived resource as binary
mitk::RegistrationWrapper::ApplyTransformationToImage(derivedMovingResource, transf,offset, NULL, true);
savePathAndFileName = GetSavePath(outputPath, derivedResourceFilename);
std::string fileType = itksys::SystemTools::GetFilenameExtension(derivedResourceFilename);
SaveImage(savePathAndFileName,derivedMovingResource,fileType );
}
}
if (!silent)
std::cout << "<filter-end/>";
return EXIT_SUCCESS;
}
int main( int argc, char* argv[] )
{
mitkCommandLineParser parser;
parser.setArgumentPrefix("--","-");
parser.setTitle("Folder Registration");
parser.setCategory("Preprocessing Tools");
parser.setDescription("For detail description see http://docs.mitk.org/nightly/DiffusionMiniApps.html");
parser.setContributor("MBI");
// Add command line argument names
parser.addArgument("help", "h",mitkCommandLineParser::Bool, "Help", "Show this help text");
//parser.addArgument("usemask", "u", QVariant::Bool, "Use segmentations (derived resources) to exclude areas from registration metrics");
parser.addArgument("input", "i", mitkCommandLineParser::InputDirectory, "Input:", "Input folder",us::Any(),false);
parser.addArgument("output", "o", mitkCommandLineParser::OutputDirectory, "Output:", "Output folder (ending with /)",us::Any(),false);
parser.addArgument("fixed", "f", mitkCommandLineParser::String, "Fixed images:", "Suffix for fixed image (if none is supplied first file matching moving pattern is chosen)",us::Any(),true);
parser.addArgument("moving", "m", mitkCommandLineParser::String, "Moving images:", "Suffix for moving images",us::Any(),false);
parser.addArgument("derived", "d", mitkCommandLineParser::String, "Derived resources:", "Derived resources suffixes (replaces suffix for moving images); comma separated",us::Any(),true);
parser.addArgument("silent", "s", mitkCommandLineParser::Bool, "Silent:", "No xml progress output.");
parser.addArgument("resample", "r", mitkCommandLineParser::String, "Resample (x,y,z)mm:", "Resample provide x,y,z spacing in mm (e.g. -r 1,1,3), is not applied to tensor data",us::Any());
parser.addArgument("binary", "b", mitkCommandLineParser::Bool, "Binary:", "Speficies that derived resource are binary (interpolation using nearest neighbor)",us::Any());
parser.addArgument("correct-origin", "c", mitkCommandLineParser::Bool, "Origin correction:", "Correct for large origin displacement. Use switch when you reveive: Joint PDF summed to zero ",us::Any());
parser.addArgument("sinc-int", "s", mitkCommandLineParser::Bool, "Windowed-sinc interpolation:", "Use windowed-sinc interpolation (3) instead of linear interpolation ",us::Any());
map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
// Handle special arguments
bool silent = false;
bool isBinary = false;
bool alignOrigin = false;
bool useLinearInterpol = true;
{
if (parsedArgs.size() == 0)
{
return EXIT_FAILURE;
}
if (parsedArgs.count("sinc-int"))
useLinearInterpol = false;
if (parsedArgs.count("silent"))
silent = true;
if (parsedArgs.count("binary"))
isBinary = true;
if (parsedArgs.count("correct-origin"))
alignOrigin = true;
// Show a help message
if ( parsedArgs.count("help") || parsedArgs.count("h"))
{
std::cout << parser.helpText();
return EXIT_SUCCESS;
}
}
std::string refPattern = "";
bool useFirstMoving = false;
std::string movingImgPattern = us::any_cast<string>(parsedArgs["moving"]);
if (parsedArgs.count("fixed"))
{
refPattern = us::any_cast<string>(parsedArgs["fixed"]);
}
else
{
useFirstMoving = true;
refPattern = movingImgPattern;
}
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);
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,
// also register derived resources based on file patterns
// ------------------------------------------------------------------------------
// Create File list
FileListType movingImagesList = CreateFileList(inputPath, movingImgPattern);
// TODO Reactivate Resampling Feature
// mitk::Image::Pointer resampleImage = NULL;
// if (QFileInfo(resampleReference).isFile())
// {
// resampleImage = mitk::IOUtil::LoadImage(resampleReference.toStdString());
// }
for (unsigned int i =0; i < movingImagesList.size(); i++)
{
std::string fileMorphName = movingImagesList.at(i);
if (fileMorphName == referenceFileName)
{
// do not process reference image again
continue;
}
MITK_INFO << "Processing image " << fileMorphName;
// 1 Register morphological file to reference image
if (!itksys::SystemTools::FileExists(fileMorphName.c_str()))
{
MITK_WARN << "File does not exit. Skipping entry.";
continue;
}
// Origin of images is cancelled
// TODO make this optional!!
double transf[6];
double offset[3];
{
std::string fileType = itksys::SystemTools::GetFilenameExtension(fileMorphName);
mitk::Image::Pointer movingImage = ExtractFirstTS(mitk::IOUtil::LoadImage(fileMorphName), fileType);
if (movingImage.IsNull())
MITK_ERROR << "Loaded moving image is NULL";
// Store transformation, apply it to morph file
MITK_INFO << "----------Registering moving image to reference----------";
mitk::RegistrationWrapper::GetTransformation(refImage, movingImage, transf, offset, alignOrigin, referenceMask);
mitk::RegistrationWrapper::ApplyTransformationToImage(movingImage, transf,offset, resampleReference); // , resampleImage
savePathAndFileName = GetSavePath(outputPath, fileMorphName);
if (fileType == ".dwi")
fileType = "dwi";
if (movingImage->GetData() == nullptr)
MITK_INFO <<"POST DATA is null";
mitk::IOUtil::Save(movingImage, savePathAndFileName);
}
if (!silent)
{
std::cout << "<filter-progress-text progress=\"" <<
(float)i / (float)movingImagesList.size()
<< "\" >.</filter-progress-text>";
}
// Now parse all derived resource and apply the above calculated transformation to them
// ------------------------------------------------------------------------------------
FileListType fList = CreateDerivedFileList(fileMorphName, movingImgPattern,derPatterns);
if (fList.size() > 0)
MITK_INFO << "----------DERIVED RESOURCES ---------";
for (unsigned int j=0; j < fList.size(); j++)
{
derivedResourceFilename = fList.at(j);
MITK_INFO << "----Processing derived resorce " << derivedResourceFilename << " ...";
std::string fileType = itksys::SystemTools::GetFilenameExtension(derivedResourceFilename);
mitk::Image::Pointer derivedMovingResource = ExtractFirstTS(mitk::IOUtil::LoadImage(derivedResourceFilename), fileType);
// Apply transformation to derived resource, treat derived resource as binary
mitk::RegistrationWrapper::ApplyTransformationToImage(derivedMovingResource, transf,offset, resampleReference,isBinary);
savePathAndFileName = GetSavePath(outputPath, derivedResourceFilename);
mitk::IOUtil::SaveImage(derivedMovingResource, savePathAndFileName);
}
}
if (!silent)
std::cout << "<filter-end/>";
return EXIT_SUCCESS;
}