int main(int argc, char** argv)
{
// Check whether host and port are given
if (argc < 3)
{
print_usage();
return 2;
}
std::string host = argv[1];
unsigned int port = atoi(argv[2]);
std::string peerAET = "";
if (argc > 3)
{
peerAET = argv[3];
}
// Setup SCU
DcmSCU scu;
scu.setPeerHostName(host);
scu.setPeerPort(port);
OFString verificationSOP = UID_VerificationSOPClass;
OFList<OFString> ts;
ts.push_back(UID_LittleEndianExplicitTransferSyntax);
ts.push_back(UID_BigEndianExplicitTransferSyntax);
ts.push_back(UID_LittleEndianImplicitTransferSyntax);
scu.addPresentationContext(verificationSOP, ts);
if (peerAET != "")
{
scu.setPeerAETitle(peerAET);
}
OFCondition result = scu.initNetwork();
if (result.bad())
{
std::cerr << "Error setting up SCU: " << result.text() << "\n";
return 2;
}
// Negotiate association
result = scu.negotiateAssociation();
if (result.bad())
{
std::cerr << "Error negotiating association: " << result.text() << "\n";
return 2;
}
// Issue ECHO request and let scu find presentation context itself (0)
result = scu.sendECHORequest(0);
if (result.bad())
{
std::cerr << "Error issuing ECHO request or received rejecting response: " << result.text() << "\n";
return 2;
}
std::cout << "Successfully sent DICOM Echo to host " << argv[1] << " on port " << argv[2] << "\n";
return 0;
}
// Load our vtkImageData object from a list of DICOM image filenames...
// http://www.vtk.org/pipermail/vtkusers/2007-August/042635.html
void vtkDicom::load_dcmFiles(QStringList dcm_fileList) {
DcmFileFormat dcm;
std::string imgFname;
std::cout << "vtkdicom: Files/Images(?): " << dcm_fileList.size() << "\n";
for (int sei = 0; sei < dcm_fileList.size(); ++sei) {
imgFname = dcm_fileList.at(sei).toLocal8Bit().constData();
OFCondition status = dcm.loadFile(imgFname.c_str());
if (!status.good()) {
std::cout << " vtkdicom: Error: cannot read file (" << status.text() << ")" << "\n";
return;
}
if (sei == 0) {
OFString acquisitionNumber, instanceNumber, imagePositionPatient, patientsName;
DcmDataset *dcmDs = dcm.getDataset();
dcmDs->findAndGetOFStringArray(DCM_ImagePositionPatient, imagePositionPatient);
dcmDs->findAndGetOFString(DCM_AcquisitionNumber, acquisitionNumber);
dcmDs->findAndGetOFString(DCM_InstanceNumber, instanceNumber);
dcmDs->findAndGetOFString(DCM_PatientName, patientsName);
std::cout << "vtkdicom: I#, IPP: " << instanceNumber << " - " << imagePositionPatient << "\n";
}
dcm.loadAllDataIntoMemory();
const unsigned short* p = NULL;
dcm.getDataset()->findAndGetUint16Array(DCM_PixelData, p);
}
}
Series::InstanceUIDContainer Series::toSeriesInstanceUIDContainer(OFList< QRResponse* > responses)
{
InstanceUIDContainer instanceUIDContainer;
OFIterator< QRResponse* > it;
DcmDataset dataset;
OFCondition result;
// Every while loop run will get all image for a specific study
for (it = responses.begin(); it != responses.end(); ++it)
{
// Be sure we are not in the last response which does not have a dataset
if ((*it)->m_dataset != NULL)
{
OFString seriesInstanceUID;
result = (*it)->m_dataset->findAndGetOFStringArray(DCM_SeriesInstanceUID, seriesInstanceUID);
// Only try to get study if we actually have study instance uid, otherwise skip it
if (result.good())
{
instanceUIDContainer.push_back(seriesInstanceUID.c_str());
}
else
{
const std::string msg = "There is no \"SeriersInstanceUID\" tag in the selected series :"
+ std::string(result.text());
throw ::fwPacsIO::exceptions::TagMissing(msg);
}
}
}
return instanceUIDContainer;
}
void
LocalService::SolveFile(
const boost::filesystem::path & fileName, const boost::filesystem::path & path,
ResultSet &result)
{
OFString ofStr;
DcmFileFormat dfile;
OFCondition cond = dfile.loadFile( fileName.string().data());
if (! cond.good())
{
LOG( "Loading of " << fileName << " failed. (" << cond.text() << ")" );
return;
}
DcmDataset *dataSet = dfile.getDataset();
TableRow row;
SerieInfo serInfo;
// load data and check if it is already in tree
CheckDataSet( dataSet, serInfo, row, path.string());
// look if this row is already in resultSet
FoundStudiesSet::iterator found = m_alreadyFoundInRun.find(row.studyID);
// if not, add it
if( found == m_alreadyFoundInRun.end() )
{
m_alreadyFoundInRun.insert( FoundStudiesSet::value_type( row.studyID) );
result.push_back( row);
}
}
OFCondition Internals::findScp(T_ASC_Association * assoc,
T_DIMSE_Message * msg,
T_ASC_PresentationContextID presID,
IFindRequestHandler* findHandler,
IWorklistRequestHandler* worklistHandler,
const std::string& remoteIp,
const std::string& remoteAet,
const std::string& calledAet)
{
FindScpData data;
data.lastRequest_ = NULL;
data.findHandler_ = findHandler;
data.worklistHandler_ = worklistHandler;
data.remoteIp_ = &remoteIp;
data.remoteAet_ = &remoteAet;
data.calledAet_ = &calledAet;
OFCondition cond = DIMSE_findProvider(assoc, presID, &msg->msg.CFindRQ,
FindScpCallback, &data,
/*opt_blockMode*/ DIMSE_BLOCKING,
/*opt_dimse_timeout*/ 0);
// if some error occured, dump corresponding information and remove the outfile if necessary
if (cond.bad())
{
OFString temp_str;
LOG(ERROR) << "Find SCP Failed: " << cond.text();
}
return cond;
}
bool DicomdirLoader::load(const std::string &studyinstanceuid, const Glib::ustring &dicomdir) {
DcmDicomDir dir(dicomdir.c_str());
OFCondition ret;
if (busy() ) {
return false;
}
if ( (ret=dir.error()) != EC_Normal ) {
std::cout << "DicomdirLoader::load Error: " << ret.text() << std::endl;
return false;
}
// Open DICOMDIR and look for StudyInstanceUID
// Add all IMAGE record types to m_FileList and fill cache
// FileLoader::Start
DcmDirectoryRecord *studyRec = find_study(studyinstanceuid, dir);
if ( !studyRec ) {
std::cout << "DicomdirLoader::load Error: cannot find study" << std::endl;
return false;
}
m_filelist = new std::list< Glib::ustring >;
m_cache.clear();
if ( !scan_study(studyinstanceuid, studyRec, dicomdir) ) {
std::cout << "DicomdirLoader::load: no visible images" << std::endl;
return false;
}
FileLoader::start();
return true;
}
// Caller is responsible for deallocating returned object
AnnotationCollection* DcmModel::ReadAnnotationCollectionFromFile(const std::string& fileName){
DcmModelInternal dcmModelInternal(_uidPrefix);
AnnotationCollection* pCollection = NULL;
try
{
OFCondition ofCondition = dcmModelInternal.ReadDocFromFile(&pCollection, fileName);
if (!ofCondition.good())
{
if (pCollection){
delete pCollection;
pCollection = NULL;
}
std::string err = std::string("Failed to load SR from file <").append(fileName).append(">:");
err += ofCondition.text();
dcmModelInternal.printDebug(std::string(__FILE__).append(": ").append(err).c_str());
}
}
catch(const std::exception& ex)
{
std::string err = std::string("Error loading SR from file<").append(fileName).append(">:");
err += ex.what();
dcmModelInternal.printDebug(err.c_str());
}
return pCollection;
}
PACSRequestStatus::RetrieveRequestStatus RetrieveDICOMFilesFromPACS::retrieve(const QString &studyInstanceUID, const QString &seriesInstanceUID, const QString &sopInstanceUID)
{
T_ASC_PresentationContextID presentationContextID;
T_DIMSE_C_MoveRSP moveResponse;
DcmDataset *statusDetail = NULL;
m_pacsConnection = new PACSConnection(m_pacs);
PACSRequestStatus::RetrieveRequestStatus retrieveRequestStatus;
MoveSCPCallbackData moveSCPCallbackData;
DcmDataset *dcmDatasetToRetrieve = getDcmDatasetOfImagesToRetrieve(studyInstanceUID, seriesInstanceUID, sopInstanceUID);
m_numberOfImagesRetrieved = 0;
// TODO S'hauria de comprovar que es tracti d'un PACS amb el servei de retrieve configurat
if (!m_pacsConnection->connectToPACS(PACSConnection::RetrieveDICOMFiles))
{
ERROR_LOG("S'ha produit un error al intentar connectar al PACS per fer un retrieve. AE Title: " + m_pacs.getAETitle());
return PACSRequestStatus::RetrieveCanNotConnectToPACS;
}
// Which presentation context should be used, It's important that the connection has MoveStudyRoot level
T_ASC_Association *association = m_pacsConnection->getConnection();
presentationContextID = ASC_findAcceptedPresentationContextID(association, MoveAbstractSyntax);
if (presentationContextID == 0)
{
ERROR_LOG("No s'ha trobat cap presentation context valid");
return PACSRequestStatus::RetrieveFailureOrRefused;
}
moveSCPCallbackData.association = association;
moveSCPCallbackData.presentationContextId = presentationContextID;
moveSCPCallbackData.retrieveDICOMFilesFromPACS = this;
// Set the destination of the images to us
T_DIMSE_C_MoveRQ moveRequest = getConfiguredMoveRequest(association);
ASC_getAPTitles(association->params, moveRequest.MoveDestination, NULL, NULL);
OFCondition condition = DIMSE_moveUser(association, presentationContextID, &moveRequest, dcmDatasetToRetrieve, moveCallback, &moveSCPCallbackData,
DIMSE_BLOCKING, 0, m_pacsConnection->getNetwork(), subOperationCallback, this, &moveResponse, &statusDetail,
NULL /*responseIdentifiers*/);
if (condition.bad())
{
ERROR_LOG(QString("El metode descarrega no ha finalitzat correctament. Codi error: %1, descripcio error: %2").arg(condition.code())
.arg(condition.text()));
}
m_pacsConnection->disconnect();
retrieveRequestStatus = getDIMSEStatusCodeAsRetrieveRequestStatus(moveResponse.DimseStatus);
processServiceClassProviderResponseStatus(moveResponse.DimseStatus, statusDetail);
// Dump status detail information if there is some
if (statusDetail != NULL)
{
delete statusDetail;
}
delete dcmDatasetToRetrieve;
return retrieveRequestStatus;
}
OFCondition Internals::moveScp(T_ASC_Association * assoc,
T_DIMSE_Message * msg,
T_ASC_PresentationContextID presID,
IMoveRequestHandler& handler,
const std::string& remoteIp,
const std::string& remoteAet,
const std::string& calledAet)
{
MoveScpData data;
data.target_ = std::string(msg->msg.CMoveRQ.MoveDestination);
data.lastRequest_ = NULL;
data.handler_ = &handler;
data.remoteIp_ = &remoteIp;
data.remoteAet_ = &remoteAet;
data.calledAet_ = &calledAet;
OFCondition cond = DIMSE_moveProvider(assoc, presID, &msg->msg.CMoveRQ,
MoveScpCallback, &data,
/*opt_blockMode*/ DIMSE_BLOCKING,
/*opt_dimse_timeout*/ 0);
// if some error occured, dump corresponding information and remove the outfile if necessary
if (cond.bad())
{
OFString temp_str;
LOG(ERROR) << "Move SCP Failed: " << cond.text();
}
return cond;
}
OFCondition AssociationCleanup(T_ASC_Association *assoc)
{
OFString temp_str;
OFCondition cond = ASC_dropSCPAssociation(assoc);
if (cond.bad())
{
LOG(FATAL) << cond.text();
return cond;
}
cond = ASC_destroyAssociation(&assoc);
if (cond.bad())
{
LOG(FATAL) << cond.text();
return cond;
}
return cond;
}
void ctkDICOMDataset::Deserialize()
{
Q_D(ctkDICOMDataset);
// read attribute m_ctkDICOMDataset
// construct a DcmDataset from it
// calls InitializeData(DcmDataset*)
// this method can be called both from sub-classes when they get the InitializeData signal from the persistence framework
// and from EnsureDcmDataSetIsInitialized() when a GetElement.. or SetElement.. method is called.
if (d->m_DICOMDataSetInitialized) return; // only need to do this once
QString stringbuffer = this->GetStoredSerialization();
if ( stringbuffer.isEmpty() )
{
d->m_DICOMDataSetInitialized = true;
return; // TODO nicer: hold three states: newly created / loaded but not initialized / restored from DB
}
//std::cerr << "** " << (void*)this << " ctkDICOMDataset: Deserialize Dataset from string of size " << stringbuffer.size() << "\n" << stringbuffer.toStdString() << std::endl;
QByteArray qtArray = QByteArray::fromBase64( stringbuffer.toAscii() );
//std::cerr << "** " << (void*)this << " ctkDICOMDataset: Deserialize Dataset from byte array of size " << qtArray.size() << std::endl;
DcmInputBufferStream dcmbuffer;
dcmbuffer.setBuffer( qtArray.data(), qtArray.size() );
//std::cerr << "** Buffer state: " << dcmbuffer.status().code() << " " << dcmbuffer.good() << " " << dcmbuffer.eos() << " tell " << dcmbuffer.tell() << " avail " << dcmbuffer.avail() << std::endl;
DcmDataset dataset;
dataset.transferInit();
//std::cerr << "** Dataset state: " << dataset.transferState() << std::endl << std::endl;
OFCondition condition = dataset.read( dcmbuffer, EXS_LittleEndianImplicit );
dataset.transferEnd();
// do this in all cases, even when reading reported an error
this->InitializeFromDataset(&dataset);
if ( condition.bad() )
{
std::cerr << "** Condition code of Dataset::read() is "
<< condition.code() << std::endl;
std::cerr << "** Buffer state: " << dcmbuffer.status().code()
<< " " << dcmbuffer.good()
<< " " << dcmbuffer.eos()
<< " tell " << dcmbuffer.tell()
<< " avail " << dcmbuffer.avail() << std::endl;
std::cerr << "** Dataset state: "
<< static_cast<int>(dataset.transferState()) << std::endl;
std::cerr << "Could not DcmDataset::read(..): "
<< condition.text() << std::endl;
//throw std::invalid_argument( std::string("Could not DcmDataset::read(..): ") + condition.text() );
}
}
bool DicomSurfaceSegmentationLoad::_loadDataset()
{
bool success = false;
SmartPtr_DCMDataSet newDataset(new DcmDataset());
_datasetPointer = newDataset;
const OFCondition status = _datasetPointer->loadFile(_filename.c_str(), EXS_LittleEndianExplicit);
if(status.bad())
{
std::cerr << "Loading the dataset failed: " << status.text() << std::endl;
throw std::exception(status.text());
}
else
{
success = true;
}
return success;
}
Status ConvertDicomToLittleEndian::convert(QString inputFile, QString outputFile)
{
DcmFileFormat fileformat;
DcmDataset *dataset = fileformat.getDataset();
OFCondition error;
Status state;
// Transfer Syntax del fitxer d'entrada
E_TransferSyntax opt_ixfer = EXS_Unknown;
E_FileReadMode opt_readMode = ERM_autoDetect;
E_TransferSyntax opt_oxfer = EXS_LittleEndianExplicit;
QString descriptionError;
E_EncodingType opt_oenctype = EET_ExplicitLength;
E_GrpLenEncoding opt_oglenc = EGL_recalcGL;
E_PaddingEncoding opt_opadenc = EPD_noChange;
OFCmdUnsignedInt opt_filepad = 0;
OFCmdUnsignedInt opt_itempad = 0;
E_FileWriteMode writeMode = EWM_fileformat;
error = fileformat.loadFile(qPrintable(QDir::toNativeSeparators(inputFile)), opt_ixfer, EGL_noChange, DCM_MaxReadLength, opt_readMode);
if (error.bad())
{
ERROR_LOG(QString("No s'ha pogut obrir el fitxer a convertir LittleEndian %1, descripcio error: %2").arg(inputFile, error.text()));
return state.setStatus(error);
}
dataset->loadAllDataIntoMemory();
DcmXfer opt_oxferSyn(opt_oxfer);
dataset->chooseRepresentation(opt_oxfer, NULL);
if (!dataset->canWriteXfer(opt_oxfer))
{
descriptionError = "Error: no conversion to transfer syntax " + QString(opt_oxferSyn.getXferName()) + " possible";
state.setStatus(qPrintable(descriptionError), false, 1300);
ERROR_LOG(descriptionError);
return state;
}
error = fileformat.saveFile(qPrintable(QDir::toNativeSeparators(outputFile)), opt_oxfer, opt_oenctype, opt_oglenc, opt_opadenc,
OFstatic_cast(Uint32, opt_filepad), OFstatic_cast(Uint32, opt_itempad), writeMode);
if (!error.good())
{
ERROR_LOG(QString("S'ha produit un error al intentar gravar la imatge %1 convertida a LittleEndian al path %2, descripcio error: %3")
.arg(inputFile, outputFile, error.text()));
}
return state.setStatus(error);
}
OFCondition EchoScp( T_ASC_Association * assoc, T_DIMSE_Message * msg, T_ASC_PresentationContextID presID)
{
OFString temp_str;
LOG(INFO) << "Received Echo Request";
//LOG(DEBUG) << DIMSE_dumpMessage(temp_str, msg->msg.CEchoRQ, DIMSE_INCOMING, NULL, presID));
/* the echo succeeded !! */
OFCondition cond = DIMSE_sendEchoResponse(assoc, presID, &msg->msg.CEchoRQ, STATUS_Success, NULL);
if (cond.bad())
{
LOG(ERROR) << "Echo SCP Failed: " << cond.text();
}
return cond;
}
// print an error message to the console (stderr) that something went wrong with an attribute
static void printAttributeErrorMessage(const DcmTagKey &key,
const OFCondition &error,
const char *operation)
{
if (error.bad())
{
OFString str;
if (operation != NULL)
{
str = "cannot ";
str += operation;
str += " ";
}
LOG(ERROR) << error.text() << ": " << str << DcmTag(key).getTagName() << " " << key;
}
}
void vtkDicom::dumpDicomFile(std::string imgFname)
{
DcmFileFormat dfile;
OFCondition status = dfile.loadFile(imgFname.c_str());
if (status.good()) {
OFString acquisitionNumber, instanceNumber, imagePositionPatient, patientsName;
dfile.loadAllDataIntoMemory();
DcmDataset *dcmDs = dfile.getDataset();
dcmDs->findAndGetOFStringArray(DCM_ImagePositionPatient, imagePositionPatient);
dcmDs->findAndGetOFString(DCM_AcquisitionNumber, acquisitionNumber);
dcmDs->findAndGetOFString(DCM_InstanceNumber, instanceNumber);
dcmDs->findAndGetOFString(DCM_PatientName, patientsName);
std::cout << " " << instanceNumber << " - " << imagePositionPatient << "\n";
} else {
std::cout << " Error: cannot read file (" << status.text() << ")" << "\n";
}
}
void
LocalService::SolveFileGET( const boost::filesystem::path & fileName,
const std::string &patientID,
const std::string &studyID,
const std::string &serieID,
DicomObjSet &result,
const std::string &path)
{
OFString ofStr;
DcmFileFormat dfile;
OFCondition cond = dfile.loadFile( fileName.string().data());
if (! cond.good())
{
LOG( "Loading of " << fileName << " failed. (" << cond.text() << ")" );
return;
}
DcmDataset *dataSet = dfile.getDataset();
TableRow row;
SerieInfo serInfo;
// load data and check if it is already in tree
CheckDataSet( dataSet, serInfo, row, path);
// compare with wantend ones
if( row.patientID == patientID
&& row.studyID == studyID
&& serInfo.id == serieID)
{
// if it mathes, insert new image into result
DicomObj buddy;
result.push_back( buddy);
// copy dataset reference & init
DicomObj *newOne = &result.back();
newOne->Load( fileName.string() );
newOne->Init();
}
}
void ctkDICOMDataset::InitializeFromFile(const QString& filename,
const E_TransferSyntax readXfer,
const E_GrpLenEncoding groupLength,
const Uint32 maxReadLength,
const E_FileReadMode readMode)
{
DcmDataset *dataset;
DcmFileFormat fileformat;
OFCondition status = fileformat.loadFile(filename.toAscii().data(), readXfer, groupLength, maxReadLength, readMode);
dataset = fileformat.getAndRemoveDataset();
if (!status.good())
{
qDebug() << "Could not load " << filename << "\nDCMTK says: " << status.text();
delete dataset;
return;
}
InitializeFromDataset(dataset, true);
}
OFCondition Association::SendEchoRequest()
{
DIC_US status;
DcmDataset *statusDetail = NULL;
if (Stopped()) {
return DUL_NETWORKCLOSED;
}
OFCondition cond = DIMSE_echoUser(assoc, ++msgId, DIMSE_BLOCKING, 0, &status, &statusDetail);
if (cond.good()) {
LOG_DEBUG(ambitolog, "DIMSE ECHO completed. Status: " << DU_cstoreStatusString(status));
} else {
LOG_DEBUG(ambitolog, "DIMSE ECHO Failed: " << cond.text());
}
if (statusDetail != NULL) {
delete statusDetail;
}
return cond;
}
void DicomServer::Stop()
{
if (continue_)
{
continue_ = false;
if (pimpl_->thread_.joinable())
{
pimpl_->thread_.join();
}
pimpl_->workers_.reset(NULL);
/* drop the network, i.e. free memory of T_ASC_Network* structure. This call */
/* is the counterpart of ASC_initializeNetwork(...) which was called above. */
OFCondition cond = ASC_dropNetwork(&pimpl_->network_);
if (cond.bad())
{
LOG(ERROR) << "Error while dropping the network: " << cond.text();
}
}
}
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";
}
void ctkDICOMDataset::Serialize()
{
Q_D(ctkDICOMDataset);
EnsureDcmDataSetIsInitialized();
// store content of current DcmDataset (our parent) as QByteArray into m_ctkDICOMDataset
Uint32 buffersize = 1024*1024; // reserve 1MB
char* writebuffer = new char[buffersize];
// write into buffer
DcmOutputBufferStream dcmbuffer(writebuffer, buffersize);
d->m_DcmDataset->transferInit();
OFCondition condition = d->m_DcmDataset->write(dcmbuffer, EXS_LittleEndianImplicit, EET_UndefinedLength, NULL );
d->m_DcmDataset->transferEnd();
if ( condition.bad() )
{
std::cerr << "Could not DcmDataset::write(..): " << condition.text() << std::endl;
}
// get written contents of buffer
offile_off_t datasetsize = 0;
void* readbuffer = NULL;
dcmbuffer.flushBuffer(readbuffer, datasetsize);
//std::cerr << "** " << (void*)this << " ctkDICOMDataset: Serializing Dataset into " << datasetsize << " bytes" << std::endl;
// construct Qt type from that contents
QByteArray qtArray = QByteArray::fromRawData( static_cast<const char*>(readbuffer), datasetsize );
//std::cerr << "** Buffer size: " << qtArray.size() << std::endl;
QString stringbuffer = QString::fromAscii(qtArray.toBase64());
//std::cerr << "** String of size " << stringbuffer.size() << " looks like this:\n" << stringbuffer.toStdString() << std::endl << std::endl;
this->SetStoredSerialization( stringbuffer );
delete[] writebuffer;
}
bool IODicom<T>::GetAttributes(PGCore::MetaData<T>& oMetaDataObject, const std::string &iFilePath)
{
#ifdef _DEBUG
LOG0("{ IODicom::GetAttributes");
#endif
if (iFilePath.empty())
{
LOG0("IO/IODicom::GetAttributes Empty filename");
return false;
}
#ifdef _PG_GDDCM_
#else
OFCondition status = m_fileformat.loadFile(iFilePath.c_str());
if (!status.good())
{
LOG2("IO/IODicom::GetAttributes: Cannot read dicom file %s: (%s).", iFilePath.c_str(), status.text());
return false;
}
#ifdef _DEBUG
LOG2("\tIODicom::GetAttributes: Successfully read dicom file %s: (%s).", iFilePath.c_str(), status.text());
#endif
// read the meta file here
//LOG1("IO/IOBase::ReadMetaData: File: %s", iMetaFileName.c_str());
DcmDataset *dataset = m_fileformat.getDataset();
if (dataset==NULL)
{
return false;
}
// patient name
OFString patientsName;
bool res = dataset->findAndGetOFString(DCM_PatientsName, patientsName).good();
if (!res)
{
LOG0("IO/IODicom::Read: Cannot fetch patient name");
return false;
}
oMetaDataObject.SetPatientName(std::string(patientsName.c_str()));
#ifdef _DEBUG
LOG1("\tIODicom::Read: Successfully read PatientName: (%s).", patientsName.c_str());
#endif
// modality
OFString modalityStr;
res = dataset->findAndGetOFString(DCM_Modality, modalityStr).good();
if (!res)
{
LOG0("IO/IODicom::Read: Cannot fetch modality");
return false;
}
PGCore::ePGModality modality = PGCore::MetaData<T>::StrToModality(modalityStr.c_str());
oMetaDataObject.SetModality(modality);
#ifdef _DEBUG
LOG1("\tIODicom::Read: Successfully read Modality: (%s).", modalityStr.c_str());
#endif
// SOP Class UID
OFString sopClassUIDStr;
DcmMetaInfo *metaInfo = m_fileformat.getMetaInfo();
if (metaInfo)
{
metaInfo->findAndGetOFString(DCM_MediaStorageSOPClassUID, sopClassUIDStr);
PGCore::ePGSOPClass sopClass = PGCore::MetaData<T>::StrToSOPClass(sopClassUIDStr.c_str());
oMetaDataObject.SetSOPClass(sopClass);
// DCM_TransferSyntaxUID
OFString transferSyntaxStr;
res = metaInfo->findAndGetOFString(DCM_TransferSyntaxUID, transferSyntaxStr).good();
if (!res)
{
LOG0("IO/IODicom::Read:Warning: Cannot fetch TransferSyntaxUID");
} else
{
if (!strcmp(kPgTransferSyntaxUIDRawImplicitVRLittleEndian, transferSyntaxStr.c_str()))
{
oMetaDataObject.SetMSBFirst(0);
} else if (!strcmp(kPgTransferSyntaxUIDRawExplicitVRLittle, transferSyntaxStr.c_str()))
{
oMetaDataObject.SetMSBFirst(0);
} else if (!strcmp(kPgTransferSyntaxUIDRawExplicitVRLittle, transferSyntaxStr.c_str()))
{
oMetaDataObject.SetMSBFirst(1);
} else if (!strcmp(kPgTransferSyntaxUIDLossLessRLE, transferSyntaxStr.c_str()))
{
LOG0("IO/IODicom::Read: Cannot read RLE compressed images yet");
return false;
} else
{
std::string tstr(transferSyntaxStr.c_str());
std::string filterStr(kPgTransferSyntaxUIDJPEG);
PGCore::ToUpper(tstr);
PGCore::ToUpper(filterStr);
size_t found=tstr.find(filterStr);
bool isJPEG = (found!=string::npos);
if (isJPEG)
{
LOG0("IO/IODicom::Read: Cannot read JPEG images yet");
return false;
}
}
}
}
DcmItem *ditem = OFstatic_cast(DcmItem *, dataset);
if (!ditem)
{
LOG0("IO/IODicom::Read: Cannot fetch ditem");
return false;
}
// Samples Per Pixel
Uint16 samplesPerPixel = 0;
res = ditem->findAndGetUint16(DCM_SamplesPerPixel, samplesPerPixel).good();
if (!res)
{
LOG0("IO/IODicom::Read: Warning: Cannot fetch SamplesPerPixel");
} else if (samplesPerPixel > sizeof(T))
{
LOG2("IO/IODicom::Read: Cannot read SamplesPerPixel: %d, target resolution smaller: %d yet", samplesPerPixel, sizeof(T));
return false;
}
oMetaDataObject.SetSamplesPerPixel(samplesPerPixel);
// DCM_PhotometricInterpretation
OFString photoInterpretationStr;
res = metaInfo->findAndGetOFString(DCM_PhotometricInterpretation, photoInterpretationStr).good();
if (!res)
{
#ifdef _DEBUG
LOG0("IO/IODicom::Read:Warning Cannot fetch PhotometricInterpretation");
#endif
} else if (strcmp(kPgPhotometricRepresentationMChrome2, photoInterpretationStr.c_str()))
{
#ifdef _DEBUG
LOG1("IO/IODicom::Read: Cannot read PhotometricInterpretation %s", photoInterpretationStr.c_str());
#endif
return false;
}
// DCM_NumberOfFrames
long numFrames = 1;
res = dataset->findAndGetLongInt(DCM_NumberOfFrames, numFrames).good();
if (!res)
{
#ifdef _DEBUG
LOG0("IO/IODicom::Read: Warning: Cannot fetch NumberOfFrames");
#endif
oMetaDataObject.SetFrameCount(1);
} else
{
oMetaDataObject.SetFrameCount(numFrames);
}
// size
Uint16 imageRows = 0;
Uint16 imageColumns = 0;
res = ditem->findAndGetUint16(DCM_Rows, imageRows).good();
if (!res)
{
LOG0("IO/IODicom::Read: Cannot fetch rows");
return false;
}
res = ditem->findAndGetUint16(DCM_Columns, imageColumns).good();
if (!res)
{
LOG0("IO/IODicom::Read: Cannot fetch columns");
return false;
}
oMetaDataObject.SetSize(PGMath::Vector3D<int>(imageColumns, imageRows, 1));
#ifdef _DEBUG
LOG2("\tIODicom::Read: Size: Rows: %d, Columns: %d", imageRows, imageColumns);
#endif
// number of bits
Uint16 imageBitsAllocated = 0;
res = ditem->findAndGetUint16(DCM_BitsAllocated, imageBitsAllocated).good();
if (!res)
{
LOG0("IO/IODicom::Read: Cannot fetch bits allocated");
return false;
}
oMetaDataObject.SetNumberOfBits(imageBitsAllocated);
#ifdef _DEBUG
LOG1("\tIODicom::Read: bits allocated: %d", imageBitsAllocated);
#endif
// spacing
Float64 sx=1, sy=1;
DcmElement *elem = 0;
OFCondition cond = dataset->findAndGetElement(DCM_PixelSpacing, elem);
if(!cond.good())
{
LOG1("IO/IODicom::Read:Warning Cannot fetch pixel spacing (%s)", cond.text());
} else
{
cond = elem->getFloat64(sx, 0);
if(!cond.good())
{
LOG1("IO/IODicom::Read:Warning Cannot fetch pixel X spacing (%s)", cond.text());
}
cond = elem->getFloat64(sy, 1);
if(!cond.good())
{
LOG1("IO/IODicom::Read:Warning Cannot fetch pixel Y spacing (%s)", cond.text());
}
}
if (sx!=sy)
{
LOG2("IO/IODicom::Read:Warning: X/Y spacings (%3.2f, %3.2f) mismatch. Ignoring anisotrpy", sx, sy);
sy = sx;
}
#ifdef _DEBUG
LOG2("\tIODicom::Read: pixel X and Y spacings (%3.5f %3.5f)",sx, sy);
#endif
oMetaDataObject.SetSpacing(PGMath::Vector3D<float>(sx, sy, 1));
// STUDY UID
OFString studyUIDStr;
res = dataset->findAndGetOFString(DCM_StudyInstanceUID, studyUIDStr).good();
if (!res)
{
LOG0("IO/IODicom::Read:Warning Cannot fetch StudyUID");
} else
{
oMetaDataObject.SetStudyUID(std::string(studyUIDStr.c_str()));
}
// series UID
OFString seriesUIDStr;
res = dataset->findAndGetOFString(DCM_SeriesInstanceUID, seriesUIDStr).good();
if (!res)
{
LOG0("IO/IODicom::Read:Warning Cannot fetch seriesUID");
} else
{
oMetaDataObject.SetSeriesUID(std::string(seriesUIDStr.c_str()));
//LOG1("IO/IODicom::Read:seriesUID : %s", oMetaDataObject.GetSeriesUID().c_str());
}
// orientation
Float64 rowOr[3] = { 1.0f, 0.0f, 0.0f }, colOr[3] = { 0.0f, 1.0f, 0.0f };
std::vector<PGMath::Vector3D<float> > orXs;
std::vector<PGMath::Vector3D<float> > orYs;
cond = dataset->findAndGetElement(DCM_ImageOrientationPatient, elem);
if(!cond.good())
{
LOG1("IO/IODicom::Read:Warning Cannot fetch DCM_ImageOrientationPatient (%s)", cond.text());
} else
{
elem->getFloat64(rowOr[0], 0);
elem->getFloat64(rowOr[1], 1);
elem->getFloat64(rowOr[2], 2);
elem->getFloat64(colOr[0], 3);
elem->getFloat64(colOr[1], 4);
elem->getFloat64(colOr[2], 5);
}
orXs.push_back(PGMath::Vector3D<float>(rowOr[0], rowOr[1], rowOr[2]));
oMetaDataObject.SetImageOrientationsPatientX(orXs);
#ifdef _DEBUG
LOG3("\tIODicom::Read: Image Row vector orientation (%3.5f %3.5f %3.5f)", rowOr[0], rowOr[1], rowOr[2]);
#endif
orYs.push_back(PGMath::Vector3D<float>(colOr[0], colOr[1], colOr[2]));
oMetaDataObject.SetImageOrientationsPatientY(orYs);
#ifdef _DEBUG
LOG3("\tIODicom::Read: Image Col vector orientation (%3.5f %3.5f %3.5f)", colOr[0], colOr[1], colOr[2]);
#endif
// position
Float64 imgPos[3] = { 0.0f, 0.0f, 0.0f };
std::vector<PGMath::Vector3D<float> > positions;
cond = dataset->findAndGetElement(DCM_ImagePositionPatient, elem);
if(!cond.good())
{
LOG1("IO/IODicom::Read:Warning Cannot fetch DCM_ImagePositionPatient (%s)", cond.text());
} else
{
elem->getFloat64(imgPos[0], 0);
elem->getFloat64(imgPos[1], 1);
elem->getFloat64(imgPos[2], 2);
}
positions.push_back(PGMath::Vector3D<float>(imgPos[0], imgPos[1], imgPos[2]));
oMetaDataObject.SetImagePositionsPatient(positions);
#ifdef _DEBUG
LOG3("\tIODicom::Read: Image Position (%3.5f %3.5f %3.5f)", imgPos[0], imgPos[1], imgPos[2]);
#endif
// slope / intercept
if (modality==PGCore::kPGModalityCT || modality==PGCore::kPGModalityPT)
{
Float64 slope = -999.0f;
cond = dataset->findAndGetElement(DCM_RescaleSlope, elem);
if(!cond.good())
{
LOG1("IO/IODicom::Read:Warning Cannot fetch DCM_RescaleSlope (%s)", cond.text());
} else
{
cond = elem->getFloat64(slope, 0);
if(cond.good())
//if (dataset->findAndGetFloat64(DCM_RescaleIntercept, slope) == EC_Normal)
{
oMetaDataObject.SetSlope(slope);
//LOG1("IO/IODicom::Read: Cannot fetch pixel Y spacing (%s)", cond.text());
}
}
Float64 intercept = -999.0f;
//dataset->findAndGetFloat64(DCM_RescaleIntercept, intercept);
cond = dataset->findAndGetElement(DCM_RescaleIntercept, elem);
if(!cond.good())
{
LOG1("IO/IODicom::Read:Warning Cannot fetch DCM_RescaleIntercept (%s)", cond.text());
} else
{
cond = elem->getFloat64(intercept, 0);
if(cond.good())
//if (dataset->findAndGetFloat64(DCM_RescaleIntercept, intercept) == EC_Normal)
{
oMetaDataObject.SetIntercept(intercept);
}
}
}
/*
Uint16 imageBytesAllocated = 0;
Uint16 imagePlanarConfiguration = 0;
Uint16 imageSamplesPerPixel = 0;
Sint32 imageFrames = 1;
Uint16 imageBitsAllocated = 0;
if (result.good()) result = ditem->findAndGetUint16(DCM_BitsAllocated, imageBitsAllocated);
res = ditem->findAndGetUint16(DCM_SamplesPerPixel, imageSamplesPerPixel);
// slope / intercept
// high bit
// planar configuration
// endianness
oMetaData->SetMSBFirst(getValueI(iStr,std::string(kPGTagMSBFirst)));
*/
#endif
#ifdef _DEBUG
LOG0("} IODicom::GetAttributes");
#endif
return true;
}
//------------------------------------------------------------------------------
bool ctkDICOMRetrievePrivate::retrieve ( QString UID, RetrieveType retriveType ) {
if ( !this->RetrieveDatabase )
{
logger.error ( "Must have RetrieveDatabase for retrieve transaction" );
return false;
}
// Register the JPEG libraries in case we need them
// (registration only happens once, so it's okay to call repeatedly)
// register global JPEG decompression codecs
DJDecoderRegistration::registerCodecs();
// register global JPEG compression codecs
DJEncoderRegistration::registerCodecs();
// register RLE compression codec
DcmRLEEncoderRegistration::registerCodecs();
// register RLE decompression codec
DcmRLEDecoderRegistration::registerCodecs();
// Set the DCMTK log level
log4cplus::Logger rootLogger = log4cplus::Logger::getRoot();
rootLogger.setLogLevel(log4cplus::DEBUG_LOG_LEVEL);
// TODO: use this->SCU instead ?
DcmSCU scu;
scu.setAETitle ( OFString(this->CallingAETitle.toStdString().c_str()) );
scu.setPort ( this->CallingPort );
scu.setPeerAETitle ( OFString(this->CalledAETitle.toStdString().c_str()) );
scu.setPeerHostName ( OFString(this->Host.toStdString().c_str()) );
scu.setPeerPort ( this->CalledPort );
scu.setMoveDestinationAETitle ( OFString(this->MoveDestinationAETitle.toStdString().c_str()) );
logger.info ( "Setting Transfer Syntaxes" );
OFList<OFString> transferSyntaxes;
transferSyntaxes.push_back ( UID_LittleEndianExplicitTransferSyntax );
transferSyntaxes.push_back ( UID_BigEndianExplicitTransferSyntax );
transferSyntaxes.push_back ( UID_LittleEndianImplicitTransferSyntax );
scu.addPresentationContext ( UID_FINDStudyRootQueryRetrieveInformationModel, transferSyntaxes );
scu.addPresentationContext ( UID_MOVEStudyRootQueryRetrieveInformationModel, transferSyntaxes );
if ( !scu.initNetwork().good() )
{
logger.error ( "Error initializing the network" );
return false;
}
logger.debug ( "Negotiating Association" );
if ( !scu.negotiateAssociation().good() )
{
logger.error ( "Error negotiating association" );
return false;;
}
logger.debug ( "Setting Parameters" );
// Clear the query
unsigned long elements = this->parameters->card();
// Clean it out
for ( unsigned long i = 0; i < elements; i++ )
{
this->parameters->remove ( 0ul );
}
if ( retriveType == RetrieveSeries )
{
this->parameters->putAndInsertString ( DCM_QueryRetrieveLevel, "SERIES" );
this->parameters->putAndInsertString ( DCM_SeriesInstanceUID, UID.toStdString().c_str() );
}
else
{
this->parameters->putAndInsertString ( DCM_QueryRetrieveLevel, "STUDY" );
this->parameters->putAndInsertString ( DCM_StudyInstanceUID, UID.toStdString().c_str() );
}
logger.debug ( "Sending Move Request" );
MOVEResponses *responses = new MOVEResponses();
OFCondition status = scu.sendMOVERequest ( 0, this->parameters, responses );
if (!status.good())
{
logger.error ( "MOVE Request failed: " + QString ( status.text() ) );
return false;
}
logger.debug ( "Find succeded" );
logger.debug ( "Making Output Directory" );
QDir directory = QDir( RetrieveDatabase->databaseDirectory() );
if ( responses->begin() == responses->end() )
{
logger.error ( "No responses!" );
throw std::runtime_error( std::string("No responses!") );
}
// Write the responses out to disk
for ( OFListIterator(FINDResponse*) it = responses->begin(); it != responses->end(); it++ )
{
DcmDataset *dataset = (*it)->m_dataset;
if ( dataset != NULL )
{
logger.debug ( "Got a valid dataset" );
// Save in correct directory
E_TransferSyntax output_transfersyntax = dataset->getOriginalXfer();
dataset->chooseRepresentation( output_transfersyntax, NULL );
if ( !dataset->canWriteXfer( output_transfersyntax ) )
{
// Pick EXS_LittleEndianExplicit as our default
output_transfersyntax = EXS_LittleEndianExplicit;
}
DcmXfer opt_oxferSyn( output_transfersyntax );
if ( !dataset->chooseRepresentation( opt_oxferSyn.getXfer(), NULL ).bad() )
{
DcmFileFormat* fileformat = new DcmFileFormat ( dataset );
// Follow dcmdjpeg example
fileformat->loadAllDataIntoMemory();
OFString SOPInstanceUID;
dataset->findAndGetOFString ( DCM_SOPInstanceUID, SOPInstanceUID );
QFileInfo fi ( directory, QString ( SOPInstanceUID.c_str() ) );
logger.debug ( "Saving file: " + fi.absoluteFilePath() );
status = fileformat->saveFile ( fi.absoluteFilePath().toStdString().c_str(), opt_oxferSyn.getXfer() );
if ( !status.good() )
{
logger.error ( "Error saving file: " + fi.absoluteFilePath() + " Error is " + status.text() );
}
RetrieveDatabase->insert( dataset, true );
delete fileformat;
}
}
}
delete responses;
//if ( !scu.dropNetwork().good() )
//{
//logger.error ( "Error dropping the network" );
//return false;
//}
return true;
}
//------------------------------------------------------------------------------
void ctkDICOMDatabase::insert ( DcmDataset *dataset, bool storeFile, bool generateThumbnail)
{
Q_D(ctkDICOMDatabase);
if (!dataset)
{
return;
}
// Check to see if the file has already been loaded
OFString sopInstanceUID ;
dataset->findAndGetOFString(DCM_SOPInstanceUID, sopInstanceUID);
QSqlQuery fileExists ( d->Database );
fileExists.prepare("SELECT InsertTimestamp,Filename FROM Images WHERE SOPInstanceUID == ?");
fileExists.bindValue(0,QString(sopInstanceUID.c_str()));
fileExists.exec();
if ( fileExists.next() && QFileInfo(fileExists.value(1).toString()).lastModified() < QDateTime::fromString(fileExists.value(0).toString(),Qt::ISODate) )
{
logger.debug ( "File " + fileExists.value(1).toString() + " already added" );
return;
}
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;
Sint32 seriesNumber = 0, acquisitionNumber = 0, echoNumber = 0, temporalPosition = 0;
//If the following fields can not be evaluated, cancel evaluation of the DICOM file
dataset->findAndGetOFString(DCM_PatientName, patientsName);
dataset->findAndGetOFString(DCM_StudyInstanceUID, studyInstanceUID);
dataset->findAndGetOFString(DCM_SeriesInstanceUID, seriesInstanceUID);
dataset->findAndGetOFString(DCM_PatientID, patientID);
dataset->findAndGetOFString(DCM_PatientBirthDate, patientsBirthDate);
dataset->findAndGetOFString(DCM_PatientBirthTime, patientsBirthTime);
dataset->findAndGetOFString(DCM_PatientSex, patientsSex);
dataset->findAndGetOFString(DCM_PatientAge, patientsAge);
dataset->findAndGetOFString(DCM_PatientComments, patientComments);
dataset->findAndGetOFString(DCM_StudyID, studyID);
dataset->findAndGetOFString(DCM_StudyDate, studyDate);
dataset->findAndGetOFString(DCM_StudyTime, studyTime);
dataset->findAndGetOFString(DCM_AccessionNumber, accessionNumber);
dataset->findAndGetOFString(DCM_ModalitiesInStudy, modalitiesInStudy);
dataset->findAndGetOFString(DCM_InstitutionName, institutionName);
dataset->findAndGetOFString(DCM_PerformingPhysicianName, performingPhysiciansName);
dataset->findAndGetOFString(DCM_ReferringPhysicianName, referringPhysician);
dataset->findAndGetOFString(DCM_StudyDescription, studyDescription);
dataset->findAndGetOFString(DCM_SeriesDate, seriesDate);
dataset->findAndGetOFString(DCM_SeriesTime, seriesTime);
dataset->findAndGetOFString(DCM_SeriesDescription, seriesDescription);
dataset->findAndGetOFString(DCM_BodyPartExamined, bodyPartExamined);
dataset->findAndGetOFString(DCM_FrameOfReferenceUID, frameOfReferenceUID);
dataset->findAndGetOFString(DCM_ContrastBolusAgent, contrastAgent);
dataset->findAndGetOFString(DCM_ScanningSequence, scanningSequence);
dataset->findAndGetSint32(DCM_SeriesNumber, seriesNumber);
dataset->findAndGetSint32(DCM_AcquisitionNumber, acquisitionNumber);
dataset->findAndGetSint32(DCM_EchoNumbers, echoNumber);
dataset->findAndGetSint32(DCM_TemporalPositionIdentifier, temporalPosition);
// store the file if the database is not in memomry
QString filename;
if ( storeFile && !this->isInMemory() )
{
DcmFileFormat* fileformat = new DcmFileFormat ( dataset );
QString destinationDirectoryName = databaseDirectory() + "/dicom/";
QDir destinationDir(destinationDirectoryName);
QString studySeriesDirectory = QString(studyInstanceUID.c_str()) + "/" + seriesInstanceUID.c_str();
destinationDir.mkpath(studySeriesDirectory);
filename = databaseDirectory() + "/dicom/" + pathForDataset(dataset);
logger.debug ( "Saving file: " + filename );
OFCondition status = fileformat->saveFile ( filename.toAscii() );
if ( !status.good() )
{
logger.error ( "Error saving file: " + filename + "\nError is " + status.text() );
delete fileformat;
return;
}
delete fileformat;
}
QSqlQuery check_exists_query(d->Database);
//The patient UID is a unique number within the database, generated by the sqlite autoincrement
int patientUID = -1;
if ( patientID != "" && patientsName != "" )
{
//Check if patient is already present in the db
check_exists_query.prepare ( "SELECT * FROM Patients WHERE PatientID = ? AND PatientsName = ?" );
check_exists_query.bindValue ( 0, QString ( patientID.c_str() ) );
check_exists_query.bindValue ( 1, QString ( patientsName.c_str() ) );
check_exists_query.exec();
if (check_exists_query.next())
{
patientUID = check_exists_query.value(check_exists_query.record().indexOf("UID")).toInt();
}
else
{
// Insert it
QSqlQuery statement ( d->Database );
statement.prepare ( "INSERT INTO Patients ('UID', 'PatientsName', 'PatientID', 'PatientsBirthDate', 'PatientsBirthTime', 'PatientsSex', 'PatientsAge', 'PatientsComments' ) values ( NULL, ?, ?, ?, ?, ?, ?, ? )" );
statement.bindValue ( 0, QString ( patientsName.c_str() ) );
statement.bindValue ( 1, QString ( patientID.c_str() ) );
statement.bindValue ( 2, QString ( patientsBirthDate.c_str() ) );
statement.bindValue ( 3, QString ( patientsBirthTime.c_str() ) );
statement.bindValue ( 4, QString ( patientsSex.c_str() ) );
// TODO: shift patient's age to study, since this is not a patient level attribute in images
// statement.bindValue ( 5, QString ( patientsAge.c_str() ) );
statement.bindValue ( 6, QString ( patientComments.c_str() ) );
statement.exec ();
patientUID = statement.lastInsertId().toInt();
logger.debug ( "New patient inserted: " + QString().setNum ( patientUID ) );
}
}
if ( studyInstanceUID != "" )
{
check_exists_query.prepare ( "SELECT * FROM Studies WHERE StudyInstanceUID = ?" );
check_exists_query.bindValue ( 0, QString ( studyInstanceUID.c_str() ) );
check_exists_query.exec();
if(!check_exists_query.next())
{
QSqlQuery statement ( d->Database );
statement.prepare ( "INSERT INTO Studies ( 'StudyInstanceUID', 'PatientsUID', 'StudyID', 'StudyDate', 'StudyTime', 'AccessionNumber', 'ModalitiesInStudy', 'InstitutionName', 'ReferringPhysician', 'PerformingPhysiciansName', 'StudyDescription' ) VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? )" );
statement.bindValue ( 0, QString ( studyInstanceUID.c_str() ) );
statement.bindValue ( 1, patientUID );
statement.bindValue ( 2, QString ( studyID.c_str() ) );
statement.bindValue ( 3, QDate::fromString ( studyDate.c_str(), "yyyyMMdd" ) );
statement.bindValue ( 4, QString ( studyTime.c_str() ) );
statement.bindValue ( 5, QString ( accessionNumber.c_str() ) );
statement.bindValue ( 6, QString ( modalitiesInStudy.c_str() ) );
statement.bindValue ( 7, QString ( institutionName.c_str() ) );
statement.bindValue ( 8, QString ( referringPhysician.c_str() ) );
statement.bindValue ( 9, QString ( performingPhysiciansName.c_str() ) );
statement.bindValue ( 10, QString ( studyDescription.c_str() ) );
if ( !statement.exec() )
{
logger.error ( "Error executing statament: " + statement.lastQuery() + " Error: " + statement.lastError().text() );
}
}
}
if ( seriesInstanceUID != "" )
{
check_exists_query.prepare ( "SELECT * FROM Series WHERE SeriesInstanceUID = ?" );
check_exists_query.bindValue ( 0, QString ( seriesInstanceUID.c_str() ) );
logger.warn ( "Statement: " + check_exists_query.lastQuery() );
check_exists_query.exec();
if(!check_exists_query.next())
{
QSqlQuery statement ( d->Database );
statement.prepare ( "INSERT INTO Series ( 'SeriesInstanceUID', 'StudyInstanceUID', 'SeriesNumber', 'SeriesDate', 'SeriesTime', 'SeriesDescription', 'BodyPartExamined', 'FrameOfReferenceUID', 'AcquisitionNumber', 'ContrastAgent', 'ScanningSequence', 'EchoNumber', 'TemporalPosition' ) VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? )" );
statement.bindValue ( 0, QString ( seriesInstanceUID.c_str() ) );
statement.bindValue ( 1, QString ( studyInstanceUID.c_str() ) );
statement.bindValue ( 2, static_cast<int>(seriesNumber) );
statement.bindValue ( 3, QString ( seriesDate.c_str() ) );
statement.bindValue ( 4, QDate::fromString ( seriesTime.c_str(), "yyyyMMdd" ) );
statement.bindValue ( 5, QString ( seriesDescription.c_str() ) );
statement.bindValue ( 6, QString ( bodyPartExamined.c_str() ) );
statement.bindValue ( 7, QString ( frameOfReferenceUID.c_str() ) );
statement.bindValue ( 8, static_cast<int>(acquisitionNumber) );
statement.bindValue ( 9, QString ( contrastAgent.c_str() ) );
statement.bindValue ( 10, QString ( scanningSequence.c_str() ) );
statement.bindValue ( 11, static_cast<int>(echoNumber) );
statement.bindValue ( 12, static_cast<int>(temporalPosition) );
if ( !statement.exec() )
{
logger.error ( "Error executing statament: " + statement.lastQuery() + " Error: " + statement.lastError().text() );
}
}
}
if ( !filename.isEmpty() )
{
check_exists_query.prepare ( "SELECT * FROM Images WHERE Filename = ?" );
check_exists_query.bindValue ( 0, filename );
check_exists_query.exec();
if(!check_exists_query.next())
{
QSqlQuery statement ( d->Database );
statement.prepare ( "INSERT INTO Images ( 'SOPInstanceUID', 'Filename', 'SeriesInstanceUID', 'InsertTimestamp' ) VALUES ( ?, ?, ?, ? )" );
statement.bindValue ( 0, QString ( sopInstanceUID.c_str() ) );
statement.bindValue ( 1, filename );
statement.bindValue ( 2, QString ( seriesInstanceUID.c_str() ) );
statement.bindValue ( 3, QDateTime::currentDateTime() );
statement.exec();
}
}
if(generateThumbnail){
if(d->thumbnailGenerator){
QString studySeriesDirectory = QString(studyInstanceUID.c_str()) + "/" + QString(seriesInstanceUID.c_str());
//Create thumbnail here
QString thumbnailPath = databaseDirectory() +
"/thumbs/" + this->pathForDataset(dataset) + ".png";
//QString(studyInstanceUID.c_str()) + "/" +
//QString(seriesInstanceUID.c_str()) + "/" +
//QString(sopInstanceUID.c_str()) + ".png";
QFileInfo thumbnailInfo(thumbnailPath);
if(!(thumbnailInfo.exists() && (thumbnailInfo.lastModified() > QFileInfo(filename).lastModified()))){
QDir(databaseDirectory() + "/thumbs/").mkpath(studySeriesDirectory);
DicomImage dcmImage(QDir::toNativeSeparators(filename).toAscii());
d->thumbnailGenerator->generateThumbnail(&dcmImage, thumbnailPath);
}
}
}
if (isInMemory())
{
emit databaseChanged();
}
}
/* Helper function to write a DICOM file using C++ */
static int write_dcm_cpp(const char *path, const Image *const im,
const Dcm_meta *const meta, const float max_val) {
#define BUF_LEN 1024
char buf[BUF_LEN];
// Ensure the image is monochromatic
if (im->nc != 1) {
SIFT3D_ERR("write_dcm_cpp: image %s has %d channels. "
"Currently only signle-channel images are supported.\n",
path, im->nc);
return SIFT3D_FAILURE;
}
// If no metadata was provided, initialize default metadata
Dcm_meta meta_new;
set_meta_defaults(meta, &meta_new);
// Create a new fileformat object
DcmFileFormat fileFormat;
// Set the file type to derived
DcmDataset *const dataset = fileFormat.getDataset();
OFCondition status = dataset->putAndInsertString(DCM_ImageType,
"DERIVED");
if (status.bad()) {
std::cerr << "write_dcm_cpp: Failed to set the image type" <<
std::endl;
return SIFT3D_FAILURE;
}
// Set the class UID
dataset->putAndInsertString(DCM_SOPClassUID,
UID_CTImageStorage);
if (status.bad()) {
SIFT3D_ERR("write_dcm_cpp: Failed to set the SOPClassUID\n");
return SIFT3D_FAILURE;
}
// Set the photometric interpretation
const char *photoInterp;
if (im->nc == 1) {
photoInterp = "MONOCHROME2";
} else if (im->nc == 3) {
photoInterp = "RGB";
} else {
SIFT3D_ERR("write_dcm_cpp: failed to determine the "
"photometric representation for %d channels \n",
im->nc);
return SIFT3D_FAILURE;
}
dataset->putAndInsertString(DCM_PhotometricInterpretation,
photoInterp);
if (status.bad()) {
SIFT3D_ERR("write_dcm_cpp: Failed to set the photometric "
"interpretation \n");
return SIFT3D_FAILURE;
}
// Set the pixel representation to unsigned
dataset->putAndInsertUint16(DCM_PixelRepresentation, 0);
if (status.bad()) {
SIFT3D_ERR("write_dcm_cpp: Failed to set the pixel "
"representation \n");
return SIFT3D_FAILURE;
}
// Set the number of channels (Samples Per Pixel) and set the planar
// configuration to interlaced pixels
assert(SIFT3D_IM_GET_IDX(im, 0, 0, 0, 1) ==
SIFT3D_IM_GET_IDX(im, 0, 0, 0, 0) + 1);
snprintf(buf, BUF_LEN, "%d", im->nc);
dataset->putAndInsertString(DCM_SamplesPerPixel, buf);
dataset->putAndInsertString(DCM_PlanarConfiguration, "0");
// Set the bits allocated and stored, in big endian format
const unsigned int dcm_high_bit = dcm_bit_width - 1;
dataset->putAndInsertUint16(DCM_BitsAllocated, dcm_bit_width);
dataset->putAndInsertUint16(DCM_BitsStored, dcm_bit_width);
dataset->putAndInsertUint16(DCM_HighBit, dcm_high_bit);
if (status.bad()) {
SIFT3D_ERR("write_dcm_cpp: Failed to set the bit widths \n");
return SIFT3D_FAILURE;
}
// Set the patient name
status = dataset->putAndInsertString(DCM_PatientName,
meta_new.patient_name);
if (status.bad()) {
SIFT3D_ERR("write_dcm_cpp: Failed to set the patient name\n");
return SIFT3D_FAILURE;
}
// Set the patient ID
status = dataset->putAndInsertString(DCM_PatientID,
meta_new.patient_id);
if (status.bad()) {
SIFT3D_ERR("write_dcm_cpp: Failed to set the patient ID \n");
return SIFT3D_FAILURE;
}
// Set the study UID
status = dataset->putAndInsertString(DCM_StudyInstanceUID,
meta_new.study_uid);
if (status.bad()) {
SIFT3D_ERR("write_dcm_cpp: Failed to set the "
"StudyInstanceUID \n");
return SIFT3D_FAILURE;
}
// Set the series UID
status = dataset->putAndInsertString(DCM_SeriesInstanceUID,
meta_new.series_uid);
if (status.bad()) {
SIFT3D_ERR("write_dcm_cpp: Failed to set the "
"SeriesInstanceUID \n");
return SIFT3D_FAILURE;
}
// Set the series description
status = dataset->putAndInsertString(DCM_SeriesDescription,
meta_new.series_descrip);
if (status.bad()) {
SIFT3D_ERR("write_dcm_cpp: Failed to set the series "
"description \n");
return SIFT3D_FAILURE;
}
// Set the instance UID
status = dataset->putAndInsertString(DCM_SOPInstanceUID,
meta_new.instance_uid);
if (status.bad()) {
SIFT3D_ERR("write_dcm_cpp: failed to set the "
"SOPInstanceUID \n");
return SIFT3D_FAILURE;
}
// Set the dimensions
OFCondition xstatus = dataset->putAndInsertUint16(DCM_Rows, im->ny);
OFCondition ystatus = dataset->putAndInsertUint16(DCM_Columns, im->nx);
snprintf(buf, BUF_LEN, "%d", im->nz);
OFCondition zstatus = dataset->putAndInsertString(DCM_NumberOfFrames,
buf);
if (xstatus.bad() || ystatus.bad() || zstatus.bad()) {
SIFT3D_ERR("write_dcm_cpp: Failed to set the dimensions \n");
return SIFT3D_FAILURE;
}
// Set the instance number
snprintf(buf, BUF_LEN, "%u", meta_new.instance_num);
status = dataset->putAndInsertString(DCM_InstanceNumber, buf);
if (status.bad()) {
SIFT3D_ERR("write_dcm_cpp: Failed to set the instance "
"number \n");
return SIFT3D_FAILURE;
}
// Set the ImagePositionPatient vector
const double imPosX = static_cast<double>(im->nx - 1) * im->ux;
const double imPosY = static_cast<double>(im->ny - 1) * im->uy;
const double imPosZ = static_cast<double>(meta_new.instance_num) *
im->uz;
snprintf(buf, BUF_LEN, "%f\\%f\\%f", imPosX, imPosY, imPosZ);
status = dataset->putAndInsertString(DCM_ImagePositionPatient, buf);
if (status.bad()) {
SIFT3D_ERR("write_dcm_cpp: Failed to set the "
"ImagePositionPatient vector \n");
return SIFT3D_FAILURE;
}
// Set the slice location
snprintf(buf, BUF_LEN, "%f", imPosZ);
status = dataset->putAndInsertString(DCM_SliceLocation, buf);
if (status.bad()) {
SIFT3D_ERR("write_dcm_cpp: Failed to set the slice "
"location \n");
return SIFT3D_FAILURE;
}
// Set the pixel spacing
snprintf(buf, BUF_LEN, "%f\\%f", im->ux, im->uy);
status = dataset->putAndInsertString(DCM_PixelSpacing, buf);
if (status.bad()) {
SIFT3D_ERR("write_dcm_cpp: Failed to set the pixel "
"spacing \n");
return SIFT3D_FAILURE;
}
// Set the aspect ratio
snprintf(buf, BUF_LEN, "%f\\%f", im->ux, im->uy);
status = dataset->putAndInsertString(DCM_PixelAspectRatio, buf);
if (status.bad()) {
SIFT3D_ERR("write_dcm_cpp: Failed to set the pixel aspect "
"aspect ratio \n");
return SIFT3D_FAILURE;
}
// Set the slice thickness
snprintf(buf, BUF_LEN, "%f", im->uz);
status = dataset->putAndInsertString(DCM_SliceThickness, buf);
if (status.bad()) {
SIFT3D_ERR("write_dcm_cpp: Failed to set the slice "
"thickness \n");
return SIFT3D_FAILURE;
}
// Count the number of pixels in the image
unsigned long numPixels = im->dims[0];
for (int i = 1; i < IM_NDIMS; i++) {
numPixels *= im->dims[i];
}
// Get the image scaling factor
const float dcm_max_val = static_cast<float>(1 << dcm_bit_width) - 1.0f;
const float im_max = max_val < 0.0f ? im_max_abs(im) : max_val;
const float scale = im_max == 0.0f ? 1.0f : dcm_max_val / im_max;
// Render the data to an 8-bit unsigned integer array
assert(dcm_bit_width == 8);
assert(fabsf(dcm_max_val - 255.0f) < FLT_EPSILON);
uint8_t *pixelData = new uint8_t[numPixels];
int x, y, z, c;
SIFT3D_IM_LOOP_START_C(im, x, y, z, c)
const float vox = SIFT3D_IM_GET_VOX(im, x, y, z, c);
if (vox < 0.0f) {
SIFT3D_ERR("write_dcm_cpp: Image cannot be "
"negative \n");
return SIFT3D_FAILURE;
}
pixelData[c + x + y * im->nx + z * im->nx * im->ny] =
static_cast<uint8_t>(vox * scale);
SIFT3D_IM_LOOP_END_C
// Write the data
status = dataset->putAndInsertUint8Array(DCM_PixelData, pixelData,
numPixels);
delete[] pixelData;
if (status.bad()) {
SIFT3D_ERR("write_dcm_cpp: failed to set the pixel data \n");
return SIFT3D_FAILURE;
}
// Choose the encoding format
#if 0
DJEncoderRegistration::registerCodecs();
const E_TransferSyntax xfer = EXS_JPEGProcess14SV1TransferSyntax;
DJ_RPLossless rp_lossless;
status = dataset->chooseRepresentation(xfer, &rp_lossless);
#else
const E_TransferSyntax xfer = EXS_LittleEndianExplicit;
dataset->chooseRepresentation(xfer, NULL);
#endif
if (!dataset->canWriteXfer(xfer)) {
SIFT3D_ERR("write_dcm_cpp: Failed to choose the encoding "
"format \n");
return SIFT3D_FAILURE;
}
// Force the media storage UIDs to be re-generated by removing them
dataset->remove(DCM_MediaStorageSOPClassUID);
dataset->remove(DCM_MediaStorageSOPInstanceUID);
// Save the file
status = fileFormat.saveFile(path, xfer);
if (status.bad()) {
SIFT3D_ERR("write_dcm_cpp: failed to write file %s (%s) \n",
path, status.text());
return SIFT3D_FAILURE;
}
return SIFT3D_SUCCESS;
#undef BUF_LEN
}
/* Load the data from a DICOM file */
Dicom::Dicom(std::string path) : filename(path), valid(false) {
// Load the image as a DcmFileFormat
DcmFileFormat fileFormat;
OFCondition status = fileFormat.loadFile(path.c_str());
if (status.bad()) {
SIFT3D_ERR("Dicom.Dicom: failed to read DICOM file %s (%s)\n",
path.c_str(), status.text());
return;
}
// Get the dataset
DcmDataset *const data = fileFormat.getDataset();
// Get the series UID
const char *seriesUIDStr;
status = data->findAndGetString(DCM_SeriesInstanceUID, seriesUIDStr);
if (status.bad() || seriesUIDStr == NULL) {
SIFT3D_ERR("Dicom.Dicom: failed to get SeriesInstanceUID "
"from file %s (%s)\n", path.c_str(), status.text());
return;
}
seriesUID = std::string(seriesUIDStr);
#if 0
// Read the patient position
const char *patientPosStr;
status = data->findAndGetString(DCM_PatientPosition, patientPosStr);
if (status.bad() || patientPosStr == NULL) {
std::cerr << "Dicom.Dicom: failed to get PatientPosition " <<
"from file " << path << " (" << status.text() << ")" <<
std::endl;
return;
}
// Interpret the patient position to give the sign of the z axis
double zSign;
switch (patientPosStr[0]) {
case 'H':
zSign = -1.0;
break;
case 'F':
zSign = 1.0;
break;
default:
std::cerr << "Dicom.Dicom: unrecognized patient position: " <<
patientPosStr << std::endl;
return;
}
#else
//TODO: Is this needed?
const double zSign = 1.0;
#endif
// Read the image position patient vector
const char *imPosPatientStr;
status = data->findAndGetString(DCM_ImagePositionPatient,
imPosPatientStr);
if (status.bad() || imPosPatientStr == NULL) {
SIFT3D_ERR("Dicom.Dicom: failed to get ImagePositionPatient "
"from file %s (%s)\n", path.c_str(), status.text());
return;
}
// Parse the image position patient vector to get the z coordinate
double imPosZ;
if (sscanf(imPosPatientStr, "%*f\\%*f\\%lf", &imPosZ) != 1) {
SIFT3D_ERR("Dicom.Dicom: failed to parse "
"ImagePositionPatient tag %s from file %s\n",
imPosPatientStr, path.c_str());
return;
}
// Compute the z-location of the upper-left corner, in feet-first
// coordinates
z = zSign * imPosZ;
// Load the DicomImage object
DicomImage dicomImage(path.c_str());
if (dicomImage.getStatus() != EIS_Normal) {
SIFT3D_ERR("Dicom.Dicom: failed to open image %s (%s)\n",
path.c_str(),
DicomImage::getString(dicomImage.getStatus()));
return;
}
// Check for color images
if (!dicomImage.isMonochrome()) {
SIFT3D_ERR("Dicom.Dicom: reading of color DICOM images is "
"not supported at this time \n");
return;
}
nc = 1;
// Read the dimensions
nx = dicomImage.getWidth();
ny = dicomImage.getHeight();
nz = dicomImage.getFrameCount();
if (nx < 1 || ny < 1 || nz < 1) {
SIFT3D_ERR("Dicom.Dicom: invalid dimensions for file %s "
"(%d, %d, %d)\n", path.c_str(), nx, ny, nz);
return;
}
// Read the pixel spacing
const char *pixelSpacingStr;
status = data->findAndGetString(DCM_PixelSpacing, pixelSpacingStr);
if (status.bad()) {
SIFT3D_ERR("Dicom.Dicom: failed to get pixel spacing from "
"file %s (%s)\n", path.c_str(), status.text());
return;
}
if (sscanf(pixelSpacingStr, "%lf\\%lf", &ux, &uy) != 2) {
SIFT3D_ERR("Dicom.Dicom: unable to parse pixel spacing from "
"file %s \n", path.c_str());
return;
}
if (ux <= 0.0 || uy <= 0.0) {
SIFT3D_ERR("Dicom.Dicom: file %s has invalid pixel spacing "
"[%f, %f]\n", path.c_str(), ux, uy);
return;
}
// Read the slice thickness
Float64 sliceThickness;
status = data->findAndGetFloat64(DCM_SliceThickness, sliceThickness);
if (!status.good()) {
SIFT3D_ERR("Dicom.Dicom: failed to get slice thickness from "
"file %s (%s)\n", path.c_str(), status.text());
return;
}
// Convert to double
uz = sliceThickness;
if (uz <= 0.0) {
SIFT3D_ERR("Dicom.Dicom: file %s has invalid slice "
"thickness: %f \n", path.c_str(), uz);
return;
}
// Set the window
dicomImage.setMinMaxWindow();
valid = true;
}
CommandDispatcher* AcceptAssociation(const DicomServer& server, T_ASC_Network *net)
{
DcmAssociationConfiguration asccfg;
char buf[BUFSIZ];
T_ASC_Association *assoc;
OFCondition cond;
OFString sprofile;
OFString temp_str;
std::vector<const char*> knownAbstractSyntaxes;
// For C-STORE
if (server.HasStoreRequestHandlerFactory())
{
knownAbstractSyntaxes.push_back(UID_VerificationSOPClass);
}
// For C-FIND
if (server.HasFindRequestHandlerFactory())
{
knownAbstractSyntaxes.push_back(UID_FINDPatientRootQueryRetrieveInformationModel);
knownAbstractSyntaxes.push_back(UID_FINDStudyRootQueryRetrieveInformationModel);
}
// For C-MOVE
if (server.HasMoveRequestHandlerFactory())
{
knownAbstractSyntaxes.push_back(UID_MOVEStudyRootQueryRetrieveInformationModel);
}
const char* transferSyntaxes[] = { NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL };
int numTransferSyntaxes = 0;
cond = ASC_receiveAssociation(net, &assoc,
/*opt_maxPDU*/ ASC_DEFAULTMAXPDU,
NULL, NULL,
/*opt_secureConnection*/ OFFalse,
DUL_NOBLOCK, 1);
if (cond == DUL_NOASSOCIATIONREQUEST)
{
// Timeout
AssociationCleanup(assoc);
return NULL;
}
// if some kind of error occured, take care of it
if (cond.bad())
{
LOG(ERROR) << "Receiving Association failed: " << cond.text();
// no matter what kind of error occurred, we need to do a cleanup
AssociationCleanup(assoc);
return NULL;
}
LOG(INFO) << "Association Received";
transferSyntaxes[0] = UID_LittleEndianExplicitTransferSyntax;
transferSyntaxes[1] = UID_BigEndianExplicitTransferSyntax;
transferSyntaxes[2] = UID_LittleEndianImplicitTransferSyntax;
numTransferSyntaxes = 3;
/* accept the Verification SOP Class if presented */
cond = ASC_acceptContextsWithPreferredTransferSyntaxes( assoc->params, &knownAbstractSyntaxes[0], knownAbstractSyntaxes.size(), transferSyntaxes, numTransferSyntaxes);
if (cond.bad())
{
LOG(INFO) << cond.text();
AssociationCleanup(assoc);
return NULL;
}
/* the array of Storage SOP Class UIDs comes from dcuid.h */
cond = ASC_acceptContextsWithPreferredTransferSyntaxes( assoc->params, dcmAllStorageSOPClassUIDs, numberOfAllDcmStorageSOPClassUIDs, transferSyntaxes, numTransferSyntaxes);
if (cond.bad())
{
LOG(INFO) << cond.text();
AssociationCleanup(assoc);
return NULL;
}
/* set our app title */
ASC_setAPTitles(assoc->params, NULL, NULL, server.GetApplicationEntityTitle().c_str());
/* acknowledge or reject this association */
cond = ASC_getApplicationContextName(assoc->params, buf);
if ((cond.bad()) || strcmp(buf, UID_StandardApplicationContext) != 0)
{
/* reject: the application context name is not supported */
T_ASC_RejectParameters rej =
{
ASC_RESULT_REJECTEDPERMANENT,
ASC_SOURCE_SERVICEUSER,
ASC_REASON_SU_APPCONTEXTNAMENOTSUPPORTED
};
LOG(INFO) << "Association Rejected: Bad Application Context Name: " << buf;
cond = ASC_rejectAssociation(assoc, &rej);
if (cond.bad())
{
LOG(INFO) << cond.text();
}
AssociationCleanup(assoc);
return NULL;
}
/* check the AETs */
{
DIC_AE callingTitle_C;
DIC_AE calledTitle_C;
DIC_AE callingIP_C;
DIC_AE calledIP_C;
if (ASC_getAPTitles(assoc->params, callingTitle_C, calledTitle_C, NULL).bad() ||
ASC_getPresentationAddresses(assoc->params, callingIP_C, calledIP_C).bad())
{
T_ASC_RejectParameters rej =
{
ASC_RESULT_REJECTEDPERMANENT,
ASC_SOURCE_SERVICEUSER,
ASC_REASON_SU_NOREASON
};
ASC_rejectAssociation(assoc, &rej);
AssociationCleanup(assoc);
return NULL;
}
std::string callingIP(/*OFSTRING_GUARD*/(callingIP_C));
std::string callingTitle(/*OFSTRING_GUARD*/(callingTitle_C));
std::string calledTitle(/*OFSTRING_GUARD*/(calledTitle_C));
Toolbox::ToUpperCase(callingIP);
Toolbox::ToUpperCase(callingTitle);
Toolbox::ToUpperCase(calledTitle);
if (server.HasCalledApplicationEntityTitleCheck() &&
calledTitle != server.GetApplicationEntityTitle())
{
T_ASC_RejectParameters rej =
{
ASC_RESULT_REJECTEDPERMANENT,
ASC_SOURCE_SERVICEUSER,
ASC_REASON_SU_CALLEDAETITLENOTRECOGNIZED
};
ASC_rejectAssociation(assoc, &rej);
AssociationCleanup(assoc);
return NULL;
}
if (server.HasApplicationEntityFilter() &&
!server.GetApplicationEntityFilter().IsAllowed(callingIP, callingTitle))
{
T_ASC_RejectParameters rej =
{
ASC_RESULT_REJECTEDPERMANENT,
ASC_SOURCE_SERVICEUSER,
ASC_REASON_SU_CALLINGAETITLENOTRECOGNIZED
};
ASC_rejectAssociation(assoc, &rej);
AssociationCleanup(assoc);
return NULL;
}
}
if (opt_rejectWithoutImplementationUID && strlen(assoc->params->theirImplementationClassUID) == 0)
{
/* reject: the no implementation Class UID provided */
T_ASC_RejectParameters rej =
{
ASC_RESULT_REJECTEDPERMANENT,
ASC_SOURCE_SERVICEUSER,
ASC_REASON_SU_NOREASON
};
LOG(INFO) << "Association Rejected: No Implementation Class UID provided";
cond = ASC_rejectAssociation(assoc, &rej);
if (cond.bad())
{
LOG(INFO) << cond.text();
}
AssociationCleanup(assoc);
return NULL;
}
{
cond = ASC_acknowledgeAssociation(assoc);
if (cond.bad())
{
LOG(ERROR) << cond.text();
AssociationCleanup(assoc);
return NULL;
}
LOG(INFO) << "Association Acknowledged (Max Send PDV: " << assoc->sendPDVLength << ")";
if (ASC_countAcceptedPresentationContexts(assoc->params) == 0)
LOG(INFO) << " (but no valid presentation contexts)";
}
return new CommandDispatcher(server, assoc);
}
std::vector<itk::SmartPointer<mitk::BaseData> > mitk::FiberBundleDicomReader::Read()
{
std::vector<itk::SmartPointer<mitk::BaseData> > output_fibs;
try
{
const std::string& locale = "C";
const std::string& currLocale = setlocale( LC_ALL, nullptr );
setlocale(LC_ALL, locale.c_str());
std::string filename = this->GetInputLocation();
OFCondition result;
TrcTractographyResults *trc = nullptr;
result = TrcTractographyResults::loadFile(filename.c_str(), trc);
if (result.bad())
mitkThrow() << "Unable to load tractography dicom file: " << result.text();
OFString val = "-";
trc->getPatient().getPatientName(val);
MITK_INFO << "Patient Name: " << val; val = "-";
trc->getStudy().getStudyInstanceUID(val);
MITK_INFO << "Study : " << val; val = "-";
trc->getSeries().getSeriesInstanceUID(val);
MITK_INFO << "Series : " << val; val = "-";
trc->getSOPCommon().getSOPInstanceUID(val);
MITK_INFO << "Instance : " << val; val = "-";
MITK_INFO << "-------------------------------------------------------------------------";
size_t numTrackSets = trc->getNumberOfTrackSets();
OFVector<TrcTrackSet*>& sets = trc->getTrackSets();
for (size_t ts = 0; ts < numTrackSets; ts++)
{
size_t numTracks = sets[ts]->getNumberOfTracks();
MITK_INFO << " Track Set #" << ts << ": " << numTracks << " Tracks, "
<< sets[ts]->getNumberOfTrackSetStatistics() << " Track Set Statistics, "
<< sets[ts]->getNumberOfTrackStatistics() << " Track Statistics, "
<< sets[ts]->getNumberOfMeasurements() << " Measurements ";
vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
for (size_t t = 0; t < numTracks; t++)
{
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
TrcTrack* track = sets[ts]->getTracks()[t];
const Float32* vals = nullptr;
size_t numPoints = track->getTrackData(vals);
for (size_t v = 0; v < numPoints; ++v)
{
vtkIdType id = vtkNewPoints->InsertNextPoint(vals[v*3],vals[v*3+1],vals[v*3+2]);
container->GetPointIds()->InsertNextId(id);
}
vtkNewCells->InsertNextCell(container);
}
vtkSmartPointer<vtkPolyData> fiberPolyData = vtkSmartPointer<vtkPolyData>::New();
fiberPolyData->SetPoints(vtkNewPoints);
fiberPolyData->SetLines(vtkNewCells);
// // transform polydata from RAS (MRtrix) to LPS (MITK)
// mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New();
// vtkSmartPointer< vtkMatrix4x4 > matrix = vtkSmartPointer< vtkMatrix4x4 >::New();
// matrix->Identity();
// matrix->SetElement(0,0,-matrix->GetElement(0,0));
// matrix->SetElement(1,1,-matrix->GetElement(1,1));
// geometry->SetIndexToWorldTransformByVtkMatrix(matrix);
// vtkSmartPointer<vtkTransformPolyDataFilter> transformFilter = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
// transformFilter->SetInputData(fiberPolyData);
// transformFilter->SetTransform(geometry->GetVtkTransform());
// transformFilter->Update();
FiberBundle::Pointer fib = FiberBundle::New(fiberPolyData);
CodeSequenceMacro* algoCode = sets[ts]->getTrackingAlgorithmIdentification().at(0);
val = "-"; algoCode->getCodeValue(val);
fib->GetPropertyList()->SetStringProperty("DICOM.algo_code.value",val.c_str());
val = "-"; algoCode->getCodeMeaning(val);
fib->GetPropertyList()->SetStringProperty("DICOM.algo_code.meaning",val.c_str());
CodeSequenceMacro modelCode = sets[ts]->getDiffusionModelCode();
val = "-"; modelCode.getCodeValue(val);
fib->GetPropertyList()->SetStringProperty("DICOM.model_code.value",val.c_str());
val = "-"; modelCode.getCodeMeaning(val);
fib->GetPropertyList()->SetStringProperty("DICOM.model_code.meaning",val.c_str());
CodeWithModifiers anatomy = sets[ts]->getTrackSetAnatomy();
val = "-"; anatomy.getCodeValue(val);
fib->GetPropertyList()->SetStringProperty("DICOM.anatomy.value",val.c_str());
val = "-"; anatomy.getCodeMeaning(val);
fib->GetPropertyList()->SetStringProperty("DICOM.anatomy.meaning",val.c_str());
val = "-"; trc->getPatient().getPatientID(val);
fib->GetPropertyList()->SetStringProperty("DICOM.patient_id",val.c_str());
val = "-"; trc->getPatient().getPatientName(val);
fib->GetPropertyList()->SetStringProperty("DICOM.patient_name",val.c_str());
val = "-"; trc->getStudy().getStudyInstanceUID(val);
fib->GetPropertyList()->SetStringProperty("DICOM.study_instance_uid",val.c_str());
val = "-"; trc->getSeries().getSeriesInstanceUID(val);
fib->GetPropertyList()->SetStringProperty("DICOM.series_instance_uid",val.c_str());
val = "-"; trc->getSOPCommon().getSOPInstanceUID(val);
fib->GetPropertyList()->SetStringProperty("DICOM.sop_instance_uid",val.c_str());
val = "-"; trc->getSOPCommon().getSOPClassUID(val);
fib->GetPropertyList()->SetStringProperty("DICOM.sop_class_uid",val.c_str());
val = "-"; trc->getFrameOfReference().getFrameOfReferenceUID(val);
fib->GetPropertyList()->SetStringProperty("DICOM.frame_of_reference_uid",val.c_str());
output_fibs.push_back(fib.GetPointer());
MITK_INFO << "Fiber bundle read";
}
delete trc;
setlocale(LC_ALL, currLocale.c_str());
return output_fibs;
}
catch(...)
{
throw;
}
return output_fibs;
}
bool CommandDispatcher::Step()
/*
* This function receives DIMSE commmands over the network connection
* and handles these commands correspondingly. Note that in case of
* storscp only C-ECHO-RQ and C-STORE-RQ commands can be processed.
*/
{
bool finished = false;
// receive a DIMSE command over the network, with a timeout of 1 second
DcmDataset *statusDetail = NULL;
T_ASC_PresentationContextID presID = 0;
T_DIMSE_Message msg;
OFCondition cond = DIMSE_receiveCommand(assoc_, DIMSE_NONBLOCKING, 1, &presID, &msg, &statusDetail);
elapsedTimeSinceLastCommand_++;
// if the command which was received has extra status
// detail information, dump this information
if (statusDetail != NULL)
{
//LOG4CPP_WARN(Internals::GetLogger(), "Status Detail:" << OFendl << DcmObject::PrintHelper(*statusDetail));
delete statusDetail;
}
if (cond == DIMSE_OUTOFRESOURCES)
{
finished = true;
}
else if (cond == DIMSE_NODATAAVAILABLE)
{
// Timeout due to DIMSE_NONBLOCKING
if (clientTimeout_ != 0 &&
elapsedTimeSinceLastCommand_ >= clientTimeout_)
{
// This timeout is actually a client timeout
finished = true;
}
}
else if (cond == EC_Normal)
{
// Reset the client timeout counter
elapsedTimeSinceLastCommand_ = 0;
// in case we received a valid message, process this command
// note that storescp can only process a C-ECHO-RQ and a C-STORE-RQ
switch (msg.CommandField)
{
case DIMSE_C_ECHO_RQ:
// process C-ECHO-Request
cond = EchoScp(assoc_, &msg, presID);
break;
case DIMSE_C_STORE_RQ:
// process C-STORE-Request
if (server_.HasStoreRequestHandlerFactory())
{
std::auto_ptr<IStoreRequestHandler> handler
(server_.GetStoreRequestHandlerFactory().ConstructStoreRequestHandler());
cond = Internals::storeScp(assoc_, &msg, presID, *handler);
}
else
cond = DIMSE_BADCOMMANDTYPE; // Should never happen
break;
case DIMSE_C_MOVE_RQ:
// process C-MOVE-Request
if (server_.HasMoveRequestHandlerFactory())
{
std::auto_ptr<IMoveRequestHandler> handler
(server_.GetMoveRequestHandlerFactory().ConstructMoveRequestHandler());
cond = Internals::moveScp(assoc_, &msg, presID, *handler);
}
else
cond = DIMSE_BADCOMMANDTYPE; // Should never happen
break;
case DIMSE_C_FIND_RQ:
// process C-FIND-Request
if (server_.HasFindRequestHandlerFactory())
{
std::auto_ptr<IFindRequestHandler> handler
(server_.GetFindRequestHandlerFactory().ConstructFindRequestHandler());
cond = Internals::findScp(assoc_, &msg, presID, *handler);
}
else
cond = DIMSE_BADCOMMANDTYPE; // Should never happen
break;
default:
// we cannot handle this kind of message
cond = DIMSE_BADCOMMANDTYPE;
LOG(ERROR) << "cannot handle command: 0x" << std::hex << msg.CommandField;
break;
}
}
else
{
// Bad status, which indicates the closing of the connection by
// the peer or a network error
finished = true;
}
if (finished)
{
if (cond == DUL_PEERREQUESTEDRELEASE)
{
LOG(INFO) << "Association Release";
ASC_acknowledgeRelease(assoc_);
}
else if (cond == DUL_PEERABORTEDASSOCIATION)
{
LOG(INFO) << "Association Aborted";
}
else
{
OFString temp_str;
LOG(ERROR) << "DIMSE failure (aborting association): " << cond.text();
/* some kind of error so abort the association */
ASC_abortAssociation(assoc_);
}
}
return !finished;
}