int main(int argc, char *argv[])
{
//print help
if( argc == 1 ) //argv[0]
{
PrintHelp(argv);
return 1;
}
if( argc == 2 ) //argv[0] -h
{
if( argv[1] == string("-h") || argv[1] == string("-H") || argv[1] == string("-help") )
{
PrintHelp(argv);
return 1;
}
else
{
cerr<< "For help: "<< argv[0] << " -h" <<endl;
return 0;
}
}
//tags used to name the converted 3d filename: PatientID_StudyID_StudyDate_Access#_Series#_SeriesDescription.mha
vector<string> tags;
tags.push_back("0010|0020");//patientID
tags.push_back("0020|0010");//studyID
tags.push_back("0008|0020");//studyDate
tags.push_back("0008|0050");//access#
tags.push_back("0020|0011");//series#
tags.push_back("0008|103e");//series description
//illegal filename chracters: \ / : * ? " < > | , which will be removed from tag value.
string illegalChars = "\\/:?\"<>|";
//accept output format, specified by -f
vector<string> acceptFormat;
acceptFormat.push_back("mha");
acceptFormat.push_back("nii");
acceptFormat.push_back("mhd");
acceptFormat.push_back("nrrd");
acceptFormat.push_back("hdr");
//timer start
const clock_t begin_time = clock();
//parse arguments
string dicomDirectory; // -i
string outputDirectory;// -o
bool write3D = false; //will be set to true, if outputDirectory is good
bool writeAllSeries = true; // default, if without -k
string outputFormat = "mha"; //default, if without -f
vector<string> seriesKeywords; //record series keywords specified by -f
string convertedList; //-l
bool writeConvertedList = false;
for (int ac = 1; ac < argc; ac++)
{
//-i
if( argv[ac] == string("-i") || argv[ac] == string("-I"))
{
if ( ++ac >= argc )
{
cerr<< "missing argument for -i" <<endl;
return 1;
}
dicomDirectory = argv[ac];
}
//-o
if( argv[ac] == string("-o") || argv[ac] == string("-O") )
{
if ( ++ac >= argc )
{
cerr<< "missing argument for -o" <<endl;
return 1;
}
outputDirectory = argv[ac];
}
//-f
if( argv[ac] == string("-f") || argv[ac] == string("-F") )
{
if ( ++ac >= argc )
{
cerr<< "missing argument for -f" <<endl;
return 1;
}
outputFormat = argv[ac];
transform(outputFormat.begin(), outputFormat.end(),outputFormat.begin(), tolower); //to lower case
}
//-k
if ( argv[ac] == string("-k") || argv[ac] == string("-K") )
{
if ( ++ac >= argc )
{
cerr<< "missing argument for -k" <<endl;
return 1;
}
//add elements after -f to vector serieskeywords
string seriesKeyword;
for( int i=ac; i<argc; i++ )
{
seriesKeyword=argv[i];
//push_back until next option
if( seriesKeyword == string("-l") || seriesKeyword == string("-i") || seriesKeyword == string("-o") || seriesKeyword == string("-f") )
{
break;
}
transform(seriesKeyword.begin(), seriesKeyword.end(), seriesKeyword.begin(), tolower);//to lower case
seriesKeyword = std::regex_replace(seriesKeyword, regex("^ +| +$|( ) +"), "$1");//remove leading,trailing and extra white space
seriesKeywords.push_back(seriesKeyword);
}
if( seriesKeywords.size() > 0 )
{
writeAllSeries = false;
}
}
//-l
if( argv[ac] == string("-l") || argv[ac] == string("-L") )
{
if ( ++ac >= argc )
{
cerr<< "missing argument for -l" <<endl;
return 1;
}
convertedList = argv[ac];
}
}
// Check if dicomDirectory is a directory and exist
bool exist = itksys::SystemTools::FileExists(dicomDirectory.c_str());
bool isDir = itksys::SystemTools::FileIsDirectory(dicomDirectory.c_str());
if ( !(exist && isDir) )
{
cerr << "ERROR: " << dicomDirectory << " does not exist or is no directory." << endl;
return 1;
}
//check if outputDirectory is good
if ( !(outputDirectory.empty()) )
{
//check if outputDirectory is a file
bool isFile = itksys::SystemTools::FileExists(outputDirectory.c_str(),true);
if ( isFile )
{
cerr << "ERROR: " << outputDirectory << " should be a directory!" << endl;
return 1;
}
// Check if outputDirectory exist
exist = itksys::SystemTools::FileExists( outputDirectory.c_str() );
if( !exist ) //create directory is not exist
{
try
{
itksys::SystemTools::MakeDirectory( outputDirectory.c_str() );
cout << outputDirectory << " created." << endl;
}
catch (itk::ExceptionObject &ex)
{
cout << ex << std::endl;
return 1;
}
}
//set write3D to ture when outputDirectory is good.
write3D = true;
}
//check if ouput format is accept
if ( !(find(acceptFormat.begin(), acceptFormat.end(), outputFormat) != acceptFormat.end()) )
{
cerr<< "accepted output formats:mha, nii, mhd, nrrd, hdr" <<endl;
return 1;
}
//open convertedList file specified by -l
ofstream convertedListFile;
if ( !convertedList.empty() )
{
convertedListFile.exceptions ( ofstream::failbit | ofstream::badbit );
try
{
convertedListFile.open( outputDirectory + string(PATH_SEP) + convertedList, ios::out | ios::app);
writeConvertedList = true;
}
catch (std::ofstream::failure e)
{
cerr << "Exception opening file."<<endl;
return 1;
}
}
cout<<"Analyzing "<<dicomDirectory<<endl;
//image type to read 2d dicom image, used to get the dicom tags of patientID,studyId,etc...
typedef itk::Image< signed short, 2 > ImageType2D;
typedef itk::ImageFileReader< ImageType2D > ReaderType2D;
ReaderType2D::Pointer reader2D = ReaderType2D::New();
//image type to write 3d mha image
typedef signed short PixelType;
const unsigned int Dimension = 3;
typedef itk::Image< PixelType, Dimension > ImageType;
typedef itk::ImageSeriesReader< ImageType > ReaderType;
typedef itk::GDCMSeriesFileNames NamesGeneratorType;
NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
ReaderType::Pointer reader = ReaderType::New();
typedef itk::GDCMImageIO ImageIOType;
ImageIOType::Pointer dicomIO = ImageIOType::New();
nameGenerator->SetRecursive(true);
nameGenerator->SetUseSeriesDetails(true);
nameGenerator->AddSeriesRestriction("0008|0021");
nameGenerator->SetDirectory(dicomDirectory);
//get all the series (by series UID) under the input folder
typedef std::vector< std::string > SeriesIdContainer;
const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
//get the correspondence between series UID and PatientID,studyId,studyDate,accessNumber,seriesNumber,seriesDescription
//key is series UID, vector<string> is PatientID,studyID,studyDate,accessNumber,seriesNumber,seriesDescription
map< string, vector<string> > seriesUidToOtherStuff;
seriesItr = seriesUID.begin();
while (seriesItr != seriesUID.end())
{
string seriesIdentifier = seriesItr->c_str();
//get file names belong to specific series
vector< string > fileNames = nameGenerator->GetFileNames(seriesIdentifier);
vector< string > otherStuff;
//read tags(PatientID StudyID StudyDate Access# Series# SeriesDescription) value from the first file of each series
if (!fileNames.empty())
{
reader2D->SetFileName(fileNames[0]);
reader2D->SetImageIO(dicomIO);
try
{
reader2D->UpdateLargestPossibleRegion(); //do not use reader->Update(),since image size is different across series.
}
catch (itk::ExceptionObject &ex)
{
cout << ex << endl;
return 1;
}
typedef itk::MetaDataDictionary DictionaryType;
const DictionaryType & dictionary = dicomIO->GetMetaDataDictionary();
typedef itk::MetaDataObject< std::string > MetaDataStringType;
DictionaryType::ConstIterator itr = dictionary.Begin();
DictionaryType::ConstIterator end = dictionary.End();
for (int i = 0; i < tags.size(); i++)
{
string entryId = tags[i];
DictionaryType::ConstIterator tagItr = dictionary.Find( entryId );
if( tagItr != end )
{
MetaDataStringType::ConstPointer entryvalue =dynamic_cast<const MetaDataStringType *>(tagItr->second.GetPointer() );
if( entryvalue )//entry found
{
string tagvalue = entryvalue->GetMetaDataObjectValue();
tagvalue = regex_replace(tagvalue, regex("^ +| +$|( ) +"), "$1");//remove leading,trailing and extra white space
otherStuff.push_back(tagvalue);
}
else
{
otherStuff.push_back("EntryNotFound");
}
}
}//end for
}//end if (!fileNames.empty())
seriesUidToOtherStuff[seriesIdentifier] = otherStuff;
seriesItr++;
}//end while
//list series number and description for each patient and access#
/*patientID, access#, series#, series descrition hierarchy:
patientid
access#
series#:series description
series#:series description
...
access#
series#:series description
series#:series description
...
patientid
...
...
*/
//create 2d vector for sorting
vector<string> vs;
vector< vector<string> > vvs;
for( map< string,vector<string> >::iterator ii=seriesUidToOtherStuff.begin(); ii!=seriesUidToOtherStuff.end(); ++ii)
{
vector<string> vsNew;
vs = (*ii).second;
vsNew.push_back(vs[0]);//patientID
vsNew.push_back(vs[3]);//access#
vsNew.push_back(vs[4]);//series#
vsNew.push_back(vs[5]);//series description
vvs.push_back(vsNew);
}
//sort: patientID and access# by string lexicographical order, series# by integer
sort(vvs.begin(),vvs.end(),comparator);
//print series number and description for each patient and access#
string patientID;
string accessNumber;
vector<string> patientIDVector;
vector<string> accessNumberVector;
if ( vvs.size()>0 )
{
cout <<dicomDirectory<<" contains the following DICOM Series:"<<endl;
for( int i = 0; i < vvs.size(); i++)
{
patientID = vvs[i][0];
accessNumber = vvs[i][1];
if (find(patientIDVector.begin(), patientIDVector.end(), patientID) == patientIDVector.end() ) // a new patientID
{
patientIDVector.push_back(patientID);
cout<<"patient ID: "<<patientID<<endl;
}
if (find(accessNumberVector.begin(), accessNumberVector.end(), accessNumber) == accessNumberVector.end() ) // a new accessNumber
{
accessNumberVector.push_back(accessNumber);
cout<<" "<<"access#: "<<accessNumber<<endl;
}
cout<<" "<<vvs[i][2]<<": "<<vvs[i][3]<<endl; //list series#:series description
}
}
else
{
cout << "The directory: "<<dicomDirectory<<" contains no DICOM Series! InputDirectory correct?"<<endl;
return 0;
}
//write 3D volume
if (write3D)
{
typedef std::vector< std::string > FileNamesContainer;
FileNamesContainer fileNames;
typedef itk::ImageFileWriter< ImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
string outFileName;
seriesItr = seriesUID.begin();
while (seriesItr != seriesUID.end())
{
string seriesIdentifier;
if (writeAllSeries) //without -k option
{
seriesIdentifier = seriesItr->c_str();
}
else //with -k option
{
//get sereisDescription according to seriesUID
string seriesDescription = seriesUidToOtherStuff[*seriesItr][5];
transform(seriesDescription.begin(), seriesDescription.end(), seriesDescription.begin(), tolower);//to lower case
//check if series Description contains the specified keyword (by -k)
for( int i = 0; i < seriesKeywords.size(); i++)
{
if (seriesDescription.find(seriesKeywords[i]) != string::npos)
{
seriesIdentifier = seriesItr->c_str();
}
}
}//end if (writeAllSeries)
if ( !seriesIdentifier.empty() )
{
//get file names belong to specific series
fileNames = nameGenerator->GetFileNames(seriesIdentifier);
reader->SetImageIO(dicomIO);
reader->SetFileNames(fileNames);
//get output file name:PatientID_StudyID_StudyDate_Access#_Series#_SeriesDescription
vector<string> vs = seriesUidToOtherStuff[seriesIdentifier];
string temp = vs[0]+"_"+vs[1]+"_"+vs[2]+"_"+vs[3]+"_"+vs[4]+"_"+vs[5];
string tempNew;
//remove illegal characters
for (string::iterator it = temp.begin(); it < temp.end(); ++it)
{
bool found = illegalChars.find(*it) != string::npos;
if(!found){
tempNew=tempNew+(*it);
}
}
//repace space with . . Many series descriptions come with spaces. But, filenames with spaces is not good.
replace( tempNew.begin(), tempNew.end(), ' ', '.');
//get full path file name
outFileName = outputDirectory + string(PATH_SEP) + tempNew + "."+outputFormat;
//write
writer->SetFileName(outFileName);
writer->UseCompressionOn();
writer->SetInput(reader->GetOutput());
cout << "Writing: " << outFileName << endl;
try
{
writer->Update();
}
catch (itk::ExceptionObject &ex)
{
cout << ex << std::endl;
continue;
}
//writing converted files full path to convertedList
if ( writeConvertedList )
{
try
{
convertedListFile << outFileName <<endl;
}
catch (std::ofstream::failure e)
{
cerr << "Exception writing file"<<endl;
}
}
}
seriesItr++;
}//end while
}//end if write3D
//close convertedList file
if (convertedListFile.is_open())
{
try
{
convertedListFile.close();
}
catch (std::ofstream::failure e)
{
cerr << "Exception closing file"<<endl;
}
}
//print elasped time
cout << "Elapsed time: "<<float( clock () - begin_time )/CLOCKS_PER_SEC<<" Seconds";
return 0;
}
void mitk::DiffusionImageNrrdWriterService::Write()
{
mitk::Image::ConstPointer input = dynamic_cast<const mitk::Image *>(this->GetInput());
VectorImageType::Pointer itkImg;
mitk::CastToItkImage(input,itkImg);
if (input.IsNull())
{
MITK_ERROR <<"Sorry, input to DiffusionImageNrrdWriterService is NULL!";
return;
}
if ( this->GetOutputLocation().empty() )
{
MITK_ERROR << "Sorry, filename has not been set!";
return ;
}
mitk::LocaleSwitch localeSwitch("C");
char keybuffer[512];
char valbuffer[512];
//itk::MetaDataDictionary dic = input->GetImage()->GetMetaDataDictionary();
vnl_matrix_fixed<double,3,3> measurementFrame = mitk::DiffusionPropertyHelper::GetMeasurementFrame(input);
if (measurementFrame(0,0) || measurementFrame(0,1) || measurementFrame(0,2) ||
measurementFrame(1,0) || measurementFrame(1,1) || measurementFrame(1,2) ||
measurementFrame(2,0) || measurementFrame(2,1) || measurementFrame(2,2))
{
sprintf( valbuffer, " (%lf,%lf,%lf) (%lf,%lf,%lf) (%lf,%lf,%lf)", measurementFrame(0,0), measurementFrame(0,1), measurementFrame(0,2), measurementFrame(1,0), measurementFrame(1,1), measurementFrame(1,2), measurementFrame(2,0), measurementFrame(2,1), measurementFrame(2,2));
itk::EncapsulateMetaData<std::string>(itkImg->GetMetaDataDictionary(),std::string("measurement frame"),std::string(valbuffer));
}
sprintf( valbuffer, "DWMRI");
itk::EncapsulateMetaData<std::string>(itkImg->GetMetaDataDictionary(),std::string("modality"),std::string(valbuffer));
if(mitk::DiffusionPropertyHelper::GetGradientContainer(input)->Size())
{
sprintf( valbuffer, "%1f", mitk::DiffusionPropertyHelper::GetReferenceBValue(input) );
itk::EncapsulateMetaData<std::string>(itkImg->GetMetaDataDictionary(),std::string("DWMRI_b-value"),std::string(valbuffer));
}
for(unsigned int i=0; i<mitk::DiffusionPropertyHelper::GetGradientContainer(input)->Size(); i++)
{
sprintf( keybuffer, "DWMRI_gradient_%04d", i );
/*if(itk::ExposeMetaData<std::string>(input->GetMetaDataDictionary(),
std::string(keybuffer),tmp))
continue;*/
sprintf( valbuffer, "%1f %1f %1f", mitk::DiffusionPropertyHelper::GetGradientContainer(input)->ElementAt(i).get(0),
mitk::DiffusionPropertyHelper::GetGradientContainer(input)->ElementAt(i).get(1), mitk::DiffusionPropertyHelper::GetGradientContainer(input)->ElementAt(i).get(2));
itk::EncapsulateMetaData<std::string>(itkImg->GetMetaDataDictionary(),std::string(keybuffer),std::string(valbuffer));
}
typedef itk::VectorImage<short,3> ImageType;
std::string ext = this->GetMimeType()->GetExtension(this->GetOutputLocation());
ext = itksys::SystemTools::LowerCase(ext);
// default extension is .dwi
if( ext == "")
{
ext = ".nrrd";
this->SetOutputLocation(this->GetOutputLocation() + ext);
}
if (ext == ".hdwi" || ext == ".nrrd" || ext == ".dwi")
{
MITK_INFO << "Extension " << ext;
itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
//io->SetNrrdVectorType( nrrdKindList );
io->SetFileType( itk::ImageIOBase::Binary );
io->UseCompressionOn();
typedef itk::ImageFileWriter<ImageType> WriterType;
WriterType::Pointer nrrdWriter = WriterType::New();
nrrdWriter->UseInputMetaDataDictionaryOn();
nrrdWriter->SetInput( itkImg );
nrrdWriter->SetImageIO(io);
nrrdWriter->SetFileName(this->GetOutputLocation());
nrrdWriter->UseCompressionOn();
nrrdWriter->SetImageIO(io);
try
{
nrrdWriter->Update();
}
catch (itk::ExceptionObject e)
{
std::cout << e << std::endl;
throw;
}
}
}