DcmDirectoryRecord* DicomdirLoader::find_study(const std::string &studyinstanceuid, class DcmDicomDir &dir) {
DcmDirectoryRecord *patRec;
DcmDirectoryRecord *studyRec;
OFCondition ret;
DcmDirectoryRecord &root = dir.getRootRecord();
for ( patRec = root.nextSub(NULL); patRec != NULL; patRec = root.nextSub(patRec) ) {
if ( patRec->getRecordType() == ERT_Patient ) {
for ( studyRec = patRec->nextSub(NULL); studyRec; studyRec = patRec->nextSub(studyRec) ) {
if ( studyRec->getRecordType()==ERT_Study ) {
OFString uid;
if ( studyRec->findAndGetOFString(DCM_StudyInstanceUID, uid)==EC_Normal ) {
if ( studyinstanceuid == uid.c_str() )
return studyRec;
}
}
}
}
}
return NULL;
}
static void open_dicomdir_series_result(const Glib::ustring &dicomdir, DcmDirectoryRecord *patRec, DcmDirectoryRecord *studyRec, const sigc::slot< void, const Glib::RefPtr< ImagePool::Series >& >& resultslot) {
DcmDirectoryRecord *seriesRec;
DcmDirectoryRecord *sopRec;
assert(studyRec->getRecordType()==ERT_Study);
seriesRec = studyRec->nextSub(NULL);
while ( seriesRec ) {
DcmDataset series;
DcmElement *el;
if ( seriesRec->findAndCopyElement(DCM_SpecificCharacterSet, el) == ECC_Normal )
series.insert(el);
if ( seriesRec->findAndCopyElement(DCM_SeriesDescription, el) == ECC_Normal )
series.insert(el);
if ( seriesRec->findAndCopyElement(DCM_SeriesInstanceUID, el) == ECC_Normal )
series.insert(el);
if ( seriesRec->findAndCopyElement(DCM_Modality, el) == ECC_Normal )
series.insert(el);
if ( seriesRec->findAndCopyElement(DCM_SeriesDate, el) == ECC_Normal )
series.insert(el);
if ( seriesRec->findAndCopyElement(DCM_SeriesTime, el) == ECC_Normal )
series.insert(el);
if ( studyRec->findAndCopyElement(DCM_StudyDescription, el) == ECC_Normal )
series.insert(el);
if ( studyRec->findAndCopyElement(DCM_StationName, el) == ECC_Normal )
series.insert(el);
// Count Related SOP Instances
int nSop=0;
sopRec = seriesRec->nextSub(NULL);
while (sopRec) {
nSop++;
sopRec = seriesRec->nextSub(sopRec);
}
series.putAndInsertUint16(DCM_NumberOfSeriesRelatedInstances, nSop);
resultslot(create_query_series(&series));
seriesRec = studyRec->nextSub(seriesRec);
}
}
void open_dicomdir_series(const std::string& studyinstanceuid, const Glib::ustring& dicomdir, const sigc::slot< void, const Glib::RefPtr< ImagePool::Series >& >& resultslot) {
DcmDicomDir dir(dicomdir.c_str());
DcmDirectoryRecord *patRec;
DcmDirectoryRecord *studyRec;
DcmDirectoryRecord *seriesRec;
OFCondition ret;
if ( dir.error() != ECC_Normal ) {
std::cout << "DICOMDIR Error: " << ret.text() << std::endl;
return;
}
DcmDirectoryRecord &root = dir.getRootRecord();
for ( patRec = root.nextSub(NULL); patRec!=NULL; patRec = root.nextSub(patRec) ) {
switch ( patRec->getRecordType() ) {
case ERT_Patient:
for ( studyRec=patRec->nextSub(NULL); studyRec; studyRec = patRec->nextSub(studyRec) ) {
if ( studyRec->getRecordType()==ERT_Study ) {
OFString uid;
if ( studyRec->findAndGetOFString(DCM_StudyInstanceUID, uid)==ECC_Normal ) {
if ( studyinstanceuid == uid.c_str() ) {
open_dicomdir_series_result(dicomdir, patRec, studyRec, resultslot);
return;
}
}
}
}
break;
case ERT_HangingProtocol:
// FALLTHROUGH
case ERT_Private:
break;
default:
break;
}
}
std::cout << "WARNING: study[" << studyinstanceuid << "] not found in DICOMDIR\n";
}
/**
* Reads a dicomdir and signals every found study
*/
void open_dicomdir( const Glib::ustring &dicomdir, const sigc::slot< void, const Glib::RefPtr< ImagePool::Study >& >& resultslot) {
DcmDicomDir dir(dicomdir.c_str());
OFCondition ret;
if ( (ret=dir.error()) != ECC_Normal ) {
std::cout << "DICOMDIR Error: " << ret.text() << std::endl;
return;
}
DcmDirectoryRecord root = dir.getRootRecord();
DcmDirectoryRecord *rec = root.nextSub(NULL);
std::cout << "Reading DICOMDIR from [" << dicomdir << "]\n";
while ( rec != NULL ) {
switch ( rec->getRecordType() ) {
case ERT_Patient:
open_dicomdir_patient(dicomdir, rec, resultslot);
break;
case ERT_HangingProtocol:
// FALLTHROUGH
case ERT_Private:
break;
default:
std::cout << "WARNING: Bad DICOMDIR Record type[" << rec->getRecordType() << "] found\n";
}
rec = root.nextSub(rec);
}
/*
// Leggo il root record, � un paziente ?
{
case ERT_root = 0,
case ERT_Curve = 1,
case ERT_FilmBox = 2,
case ERT_FilmSession = 3,
case ERT_Image = 4,
case ERT_ImageBox = 5,
case ERT_Interpretation = 6,
ERT_ModalityLut = 7,
ERT_Mrdr = 8,
ERT_Overlay = 9,
ERT_Patient = 10,
ERT_PrintQueue = 11,
ERT_Private = 12,
ERT_Results = 13,
ERT_Series = 14,
ERT_Study = 15,
ERT_StudyComponent = 16,
ERT_Topic = 17,
ERT_Visit = 18,
ERT_VoiLut = 19,
ERT_StructReport = 20,
ERT_Presentation = 21,
ERT_Waveform = 22,
ERT_RTDose = 23,
ERT_RTStructureSet = 24,
ERT_RTPlan = 25,
ERT_RTTreatRecord = 26,
ERT_StoredPrint = 27,
ERT_KeyObjectDoc = 28,
ERT_Registration = 29,
ERT_Fiducial = 30,
ERT_RawData = 31,
ERT_Spectroscopy = 32,
ERT_EncapDoc = 33,
ERT_ValueMap = 34,
ERT_HangingProtocol = 35
*/
}
// Loads all dicom file in m_FileList
// Initializes m_Cache
// returns true if viewable files found, otherwise false
bool DicomdirLoader::scan_study(const std::string &studyinstanceuid, class DcmDirectoryRecord *studyRec, const Glib::ustring &dicomdir) {
DcmDirectoryRecord *seriesRec;
DcmDirectoryRecord *sopRec;
std::string path;
std::string file;
assert(studyRec->getRecordType()==ERT_Study);
path = Glib::path_get_dirname(dicomdir);
seriesRec = studyRec->nextSub(NULL);
while ( seriesRec ) {
OFString modality;
if ( seriesRec->findAndGetOFString(DCM_Modality, modality) == EC_Normal ) {
OFString seriesinstanceuid;
if ( seriesRec->findAndGetOFString(DCM_SeriesInstanceUID, seriesinstanceuid) != EC_Normal ) {
seriesRec = studyRec->nextSub(seriesRec);
continue;
}
if ( ImageModalities.find(modality.c_str()) != std::string::npos ) {
// Load Series...
OFString fileID;
int vm;
int i;
DcmElement *el;
for (sopRec = seriesRec->nextSub(NULL); sopRec; sopRec = seriesRec->nextSub(sopRec) ) {
switch ( sopRec->getRecordType() ) {
case ERT_Image:
case ERT_StoredPrint:
if ( sopRec->findAndGetElement(DCM_ReferencedFileID, el, true)!=EC_Normal ) {
sopRec = seriesRec->nextSub(sopRec);
continue;
}
vm = el->getVM();
file = "";
for ( i=0; i<vm; i++ ) {
el->getOFString(fileID, i);
file = file + "/" + fileID.c_str();
}
if ( file.size() > 0 ) {
std::cout << "Loading DICOMDIR file [" << path.c_str() << file.c_str() << "]" << std::endl;
m_filelist->push_back(path + file);
std::string SeriesUID = seriesinstanceuid.c_str();
m_cache[studyinstanceuid].m_instancecount++;
m_cache[studyinstanceuid].m_seriesuid.insert(SeriesUID);
m_cache[studyinstanceuid].m_seriescount = m_cache[studyinstanceuid].m_seriesuid.size();
}
break;
default:
break;
}
}
}
}
seriesRec = studyRec->nextSub(seriesRec);
}
return true;
}
//------------------------------------------------------------------------------
void ctkDICOMIndexer::addFromDICOMDIR(ctkDICOMDatabase& ctkDICOMDatabase,
const QString& directoryName,
const QString& destinationDirectoryName
)
{
logger.debug( "############## addFromDICOMDIR ####################" );
int fileNumber = 0;
std::string dcmFilePath = directoryName.toStdString() + "/DICOMDIR";
const char* dcmDirFilePath = dcmFilePath.c_str();
// currently it is not supported to have multiple
// parallel directory imports so the second call blocks
//
d->DirectoryImportWatcher.waitForFinished();
const std::string src_directory(directoryName.toStdString());
DcmDicomDir* dicomDir = new DcmDicomDir(dcmDirFilePath);
DcmDirectoryRecord* rootRecord = &(dicomDir->getRootRecord());
DcmDirectoryRecord* patientRecord = NULL;
DcmDirectoryRecord* studyRecord = NULL;
DcmDirectoryRecord* seriesRecord = NULL;
DcmDirectoryRecord* fileRecord = NULL;
QString finalFilePath=destinationDirectoryName + "/dicom";
////QDir destinationDir;
////QFile currentFile;
////Values to fill database
//OFString patientsName, patientID, patientsBirthDate, patientsBirthTime, patientsSex,
// patientComments, patientsAge;
//OFString studyInstanceUID, studyID, studyDate, studyTime,
// accessionNumber, modalitiesInStudy, institutionName, performingPhysiciansName, referringPhysician, studyDescription;
//OFString seriesInstanceUID, seriesDate, seriesTime,
// seriesDescription, bodyPartExamined, frameOfReferenceUID,
// contrastAgent, scanningSequence;
//OFString instanceNumber, sopInstanceUID, referencedFileName ;
//Sint32 seriesNumber = 0, acquisitionNumber = 0, echoNumber = 0, temporalPosition = 0;
////The patient UID is a unique number within the database, generated by the sqlite autoincrement
////Thus, this is _not_ the DICOM Patient ID.
////int patientUID(-1);
////int nrOfFiles(0);
if(rootRecord != NULL)
{
//DcmDataset *patientDataset;
while (((patientRecord = rootRecord->nextSub(patientRecord)) != NULL))
{
//if (patientRecord->findAndGetOFString(DCM_PatientName, patientsName).good()) {
// logger.debug( "Reading new Patients:" );
// logger.debug( "Patient's Name: " + QString(patientsName.c_str()) );
// patientDataset = new DcmDataset();
// patientRecord->findAndGetOFString(DCM_PatientID, patientID);
// patientRecord->findAndGetOFString(DCM_PatientBirthDate, patientsBirthDate);
// patientRecord->findAndGetOFString(DCM_PatientBirthTime, patientsBirthTime);
// patientRecord->findAndGetOFString(DCM_PatientSex, patientsSex);
// patientRecord->findAndGetOFString(DCM_PatientAge, patientsAge);
// patientRecord->findAndGetOFString(DCM_PatientComments, patientComments);
// patientDataset->putAndInsertOFStringArray(DCM_PatientName, patientsName);
// patientDataset->putAndInsertOFStringArray(DCM_PatientID, patientID);
// patientDataset->putAndInsertOFStringArray(DCM_PatientBirthDate, patientsBirthDate);
// patientDataset->putAndInsertOFStringArray(DCM_PatientBirthTime, patientsBirthTime);
// patientDataset->putAndInsertOFStringArray(DCM_PatientSex, patientsSex);
// patientDataset->putAndInsertOFStringArray(DCM_PatientAge, patientsAge);
// patientDataset->putAndInsertOFStringArray(DCM_PatientComments, patientComments);
//}
while (((studyRecord = patientRecord->nextSub(studyRecord)) != NULL))
{
//if (studyRecord->findAndGetOFString(DCM_StudyInstanceUID, studyInstanceUID).good()) {
// logger.debug( "Reading new Studys:" );
// logger.debug( "Studies Name: " + QString(studyInstanceUID.c_str()) );
// studyRecord->findAndGetOFString(DCM_StudyID, studyID);
// studyRecord->findAndGetOFString(DCM_StudyDate, studyDate);
// studyRecord->findAndGetOFString(DCM_StudyTime, studyTime);
// studyRecord->findAndGetOFString(DCM_AccessionNumber, accessionNumber);
// studyRecord->findAndGetOFString(DCM_ModalitiesInStudy, modalitiesInStudy);
// studyRecord->findAndGetOFString(DCM_InstitutionName, institutionName);
// studyRecord->findAndGetOFString(DCM_PerformingPhysicianName, performingPhysiciansName);
// studyRecord->findAndGetOFString(DCM_ReferringPhysicianName, referringPhysician);
// studyRecord->findAndGetOFString(DCM_StudyDescription, studyDescription);
// patientDataset->putAndInsertOFStringArray(DCM_StudyInstanceUID, studyInstanceUID);
// patientDataset->putAndInsertOFStringArray(DCM_StudyID, studyID);
// patientDataset->putAndInsertOFStringArray(DCM_StudyDate, studyDate);
// patientDataset->putAndInsertOFStringArray(DCM_StudyTime, studyTime);
// patientDataset->putAndInsertOFStringArray(DCM_AccessionNumber, accessionNumber);
// patientDataset->putAndInsertOFStringArray(DCM_ModalitiesInStudy, modalitiesInStudy);
// patientDataset->putAndInsertOFStringArray(DCM_InstitutionName, institutionName);
// patientDataset->putAndInsertOFStringArray(DCM_PerformingPhysicianName, performingPhysiciansName);
// patientDataset->putAndInsertOFStringArray(DCM_ReferringPhysicianName, referringPhysician);
// patientDataset->putAndInsertOFStringArray(DCM_StudyDescription, studyDescription);
while (((seriesRecord = studyRecord->nextSub(seriesRecord)) != NULL))
{
//if (seriesRecord->findAndGetOFString(DCM_SeriesInstanceUID, seriesInstanceUID).good()) {
// logger.debug( "Reading new Series:" );
// logger.debug( "Series Instance Name: " + QString(seriesInstanceUID.c_str()) );
// seriesRecord->findAndGetOFString(DCM_SeriesDate, seriesDate);
// seriesRecord->findAndGetOFString(DCM_SeriesTime, seriesTime);
// seriesRecord->findAndGetOFString(DCM_SeriesDescription, seriesDescription);
// seriesRecord->findAndGetOFString(DCM_BodyPartExamined, bodyPartExamined);
// seriesRecord->findAndGetOFString(DCM_FrameOfReferenceUID, frameOfReferenceUID);
// seriesRecord->findAndGetOFString(DCM_ContrastBolusAgent, contrastAgent);
// seriesRecord->findAndGetOFString(DCM_ScanningSequence, scanningSequence);
// seriesRecord->findAndGetSint32(DCM_SeriesNumber, seriesNumber);
// seriesRecord->findAndGetSint32(DCM_AcquisitionNumber, acquisitionNumber);
// seriesRecord->findAndGetSint32(DCM_EchoNumbers, echoNumber);
// seriesRecord->findAndGetSint32(DCM_TemporalPositionIdentifier, temporalPosition);
// patientDataset->putAndInsertOFStringArray(DCM_SeriesInstanceUID, seriesInstanceUID);
// patientDataset->putAndInsertOFStringArray(DCM_SeriesDate, seriesDate);
// patientDataset->putAndInsertOFStringArray(DCM_SeriesTime, seriesTime);
// patientDataset->putAndInsertOFStringArray(DCM_SeriesDescription, seriesDescription);
// patientDataset->putAndInsertOFStringArray(DCM_BodyPartExamined, bodyPartExamined);
// patientDataset->putAndInsertOFStringArray(DCM_FrameOfReferenceUID, frameOfReferenceUID);
// patientDataset->putAndInsertOFStringArray(DCM_ContrastBolusAgent, contrastAgent);
// patientDataset->putAndInsertOFStringArray(DCM_ScanningSequence, scanningSequence);
// patientDataset->putAndInsertSint16(DCM_SeriesNumber, seriesNumber);
// patientDataset->putAndInsertSint16(DCM_AcquisitionNumber, acquisitionNumber);
// patientDataset->putAndInsertSint16(DCM_EchoNumbers, echoNumber);
// patientDataset->putAndInsertSint16(DCM_TemporalPositionIdentifier, temporalPosition);
//}
while (((fileRecord = seriesRecord->nextSub(fileRecord)) != NULL))
{
//if (fileRecord->findAndGetOFStringArray(DCM_ReferencedSOPInstanceUIDInFile, sopInstanceUID).good()) {
// fileRecord->findAndGetOFString(DCM_ReferencedFileID,referencedFileName);
// patientDataset->putAndInsertOFStringArray(DCM_ReferencedSOPInstanceUIDInFile, sopInstanceUID);
// patientDataset->putAndInsertOFStringArray(DCM_ReferencedFileID, referencedFileName);
// const char* filename = fileRecord->getRecordsOriginFile();
// if(filename)
// {
// this->addFile();
// }
//}
emit indexingFileNumber(++fileNumber);
//TODO insert Record into Database Info: the database.insert() interface must change.
//it must be possible to add records and dataset
//suggestion: change the interface to dcmItem
}
}
}
}
emit foundFilesToIndex(fileNumber);
}
QString filePath((*iter).c_str());
d->FilesToIndex << filePath;
++iter;
}
