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 Series::releaseResponses(OFList< QRResponse* > responses)
{
while (!responses.empty())
{
delete responses.front();
responses.pop_front();
}
}
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;
}
//------------------------------------------------------------------------------
void ctkDICOMIndexer::addDirectory(ctkDICOMDatabase& ctkDICOMDatabase,
const QString& directoryName,
const QString& destinationDirectoryName)
{
Q_D(ctkDICOMIndexer);
const std::string src_directory(directoryName.toStdString());
std::string dcmFilePath = directoryName.toStdString() + "/DICOMDIR";
const char* dcmDirFilePath = dcmFilePath.c_str();
//if(OFStandard::fileExists(dcmDirFilePath))
//{
// //this->addFromDICOMDIR(ctkDICOMDatabase, directoryName, destinationDirectoryName);
//}else{
OFList<OFString> originalDcmtkFileNames;
OFList<OFString> dcmtkFileNames;
OFStandard::searchDirectoryRecursively( QDir::toNativeSeparators(src_directory.c_str()).toAscii().data(), originalDcmtkFileNames, "", "");
int totalNumberOfFiles = originalDcmtkFileNames.size();
// hack to reverse list of filenames (not neccessary when image loading works correctly)
for ( OFListIterator(OFString) iter = originalDcmtkFileNames.begin(); iter != originalDcmtkFileNames.end(); ++iter )
{
dcmtkFileNames.push_front( *iter );
}
OFListIterator(OFString) iter = dcmtkFileNames.begin();
OFListIterator(OFString) last = dcmtkFileNames.end();
if(iter == last) return;
emit foundFilesToIndex(totalNumberOfFiles);
/* iterate over all input filenames */
int fileNumber = 0;
int currentProgress = -1;
d->Canceled = false;
while (iter != last)
{
if (d->Canceled)
{
break;
}
emit indexingFileNumber(++fileNumber);
int newProgress = ( fileNumber * 100 ) / totalNumberOfFiles;
if (newProgress != currentProgress)
{
currentProgress = newProgress;
emit progress( currentProgress );
}
QString filePath((*iter).c_str());
this->addFile(ctkDICOMDatabase, filePath, destinationDirectoryName);
++iter;
}
//}
}
//------------------------------------------------------------------------------
ctkDICOMRetrievePrivate::ctkDICOMRetrievePrivate(ctkDICOMRetrieve& obj)
: q_ptr(&obj)
{
this->Database = QSharedPointer<ctkDICOMDatabase> (0);
this->WasCanceled = false;
this->KeepAssociationOpen = true;
this->ConnectionParamsChanged = false;
this->LastRetrieveType = RetrieveNone;
// 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();
logger.info ( "Setting Transfer Syntaxes" );
OFList<OFString> transferSyntaxes;
transferSyntaxes.push_back ( UID_LittleEndianExplicitTransferSyntax );
transferSyntaxes.push_back ( UID_BigEndianExplicitTransferSyntax );
transferSyntaxes.push_back ( UID_LittleEndianImplicitTransferSyntax );
this->SCU.addPresentationContext (
UID_MOVEStudyRootQueryRetrieveInformationModel, transferSyntaxes );
this->SCU.addPresentationContext (
UID_GETStudyRootQueryRetrieveInformationModel, transferSyntaxes );
for (Uint16 i = 0; i < numberOfDcmLongSCUStorageSOPClassUIDs; i++)
{
this->SCU.addPresentationContext(dcmLongSCUStorageSOPClassUIDs[i],
transferSyntaxes, ASC_SC_ROLE_SCP);
}
}
//------------------------------------------------------------------------------
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;
}
Series::DicomSeriesContainer Series::toFwMedData(OFList< QRResponse* > responses)
{
DicomSeriesContainer seriesContainer;
OFIterator< QRResponse* > it;
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 data;
// Create series
::fwMedData::DicomSeries::sptr series = ::fwMedData::DicomSeries::New();
::fwMedData::Patient::sptr patient = ::fwMedData::Patient::New();
::fwMedData::Study::sptr study = ::fwMedData::Study::New();
::fwMedData::Equipment::sptr equipment = ::fwMedData::Equipment::New();
// Set informations to series
series->setPatient(patient);
series->setStudy(study);
series->setEquipment(equipment);
// ==================================
// Series
// ==================================
result = (*it)->m_dataset->findAndGetOFStringArray(DCM_SeriesInstanceUID, data);
series->setInstanceUID(data.c_str());
result = (*it)->m_dataset->findAndGetOFStringArray(DCM_Modality, data);
series->setModality(data.c_str());
result = (*it)->m_dataset->findAndGetOFStringArray(DCM_SeriesDate, data);
series->setDate(data.c_str());
result = (*it)->m_dataset->findAndGetOFStringArray(DCM_SeriesTime, data);
series->setTime(data.c_str());
result = (*it)->m_dataset->findAndGetOFStringArray(DCM_SeriesDescription, data);
series->setDescription(data.c_str());
result = (*it)->m_dataset->findAndGetOFStringArray(DCM_PerformingPhysicianName, data);
::fwMedData::DicomValuesType performingPhysiciansName;
performingPhysiciansName.push_back(data.c_str());
series->setPerformingPhysiciansName(performingPhysiciansName);
// ==================================
// Patient
// ==================================
result = (*it)->m_dataset->findAndGetOFStringArray(DCM_PatientName, data);
patient->setName(data.c_str());
result = (*it)->m_dataset->findAndGetOFStringArray(DCM_PatientID, data);
patient->setPatientId(data.c_str());
result = (*it)->m_dataset->findAndGetOFStringArray(DCM_PatientBirthDate, data);
patient->setBirthdate(data.c_str());
result = (*it)->m_dataset->findAndGetOFStringArray(DCM_PatientSex, data);
patient->setSex(data.c_str());
// ==================================
// Study
// ==================================
result = (*it)->m_dataset->findAndGetOFStringArray(DCM_StudyInstanceUID, data);
study->setInstanceUID(data.c_str());
result = (*it)->m_dataset->findAndGetOFStringArray(DCM_StudyDate, data);
study->setDate(data.c_str());
result = (*it)->m_dataset->findAndGetOFStringArray(DCM_StudyTime, data);
study->setTime(data.c_str());
result = (*it)->m_dataset->findAndGetOFStringArray(DCM_ReferringPhysicianName, data);
study->setReferringPhysicianName(data.c_str());
result = (*it)->m_dataset->findAndGetOFStringArray(DCM_StudyDescription, data);
study->setDescription(data.c_str());
result = (*it)->m_dataset->findAndGetOFStringArray(DCM_PatientAge, data);
study->setPatientAge(data.c_str());
// ==================================
// Equipment
// ==================================
(*it)->m_dataset->findAndGetOFStringArray(DCM_InstitutionName, data);
equipment->setInstitutionName(data.c_str());
// ==================================
// Number of instances
// ==================================
long int nbinstances;
(*it)->m_dataset->findAndGetLongInt(DCM_NumberOfSeriesRelatedInstances, nbinstances);
series->setNumberOfInstances(nbinstances);
// Add series to container
seriesContainer.push_back(series);
}
}
return seriesContainer;
}
//------------------------------------------------------------------------------
bool ctkDICOMRetrievePrivate::get ( const QString& studyInstanceUID,
const QString& seriesInstanceUID,
const RetrieveType retrieveType )
{
Q_Q(ctkDICOMRetrieve);
DcmDataset *retrieveParameters = new DcmDataset();
if (! this->initializeSCU(studyInstanceUID, seriesInstanceUID, retrieveType, retrieveParameters) )
{
delete retrieveParameters;
return false;
}
// Issue request
logger.debug ( "Sending Get Request" );
emit q->progress("Sending Get Request");
emit q->progress(0);
OFList<RetrieveResponse*> responses;
T_ASC_PresentationContextID presID = this->SCU.findPresentationContextID(
UID_GETStudyRootQueryRetrieveInformationModel,
"" /* don't care about transfer syntax */ );
if (presID == 0)
{
logger.error ( "GET Request failed: No valid Study Root GET Presentation Context available" );
if (!this->KeepAssociationOpen)
{
this->SCU.closeAssociation(DCMSCU_RELEASE_ASSOCIATION);
}
delete retrieveParameters;
return false;
}
emit q->progress("Found Presentation Context");
emit q->progress(1);
// do the actual move request
OFCondition status = this->SCU.sendCGETRequest (
presID, retrieveParameters, &responses );
emit q->progress("Sent Get Request");
emit q->progress(2);
// Close association if we do not want to explicitly keep it open
if (!this->KeepAssociationOpen)
{
this->SCU.closeAssociation(DCMSCU_RELEASE_ASSOCIATION);
}
// Free some (little) memory
delete retrieveParameters;
// If we do not receive a single response, something is fishy
if ( responses.begin() == responses.end() )
{
logger.error ( "No responses received at all! (at least one empty response always expected)" );
//throw std::runtime_error( std::string("No responses received from server!") );
emit q->progress("No Responses from Server!");
return false;
}
emit q->progress("Got Responses");
emit q->progress(3);
/* The server is permitted to acknowledge every image that was received, or
* to send a single move response.
* If there is only a single response, this can mean the following:
* 1) No images to transfer (Status Success and Number of Completed Subops = 0)
* 2) All images transferred (Status Success and Number of Completed Subops > 0)
* 3) Error code, i.e. no images transferred
* 4) Warning (one or more failures, i.e. some images transferred)
*/
if ( responses.size() == 1 )
{
RetrieveResponse* rsp = *responses.begin();
logger.debug ( "GET response receveid with status: " +
QString(DU_cmoveStatusString(rsp->m_status)) );
if ( (rsp->m_status == STATUS_Success)
|| (rsp->m_status == STATUS_GET_Warning_SubOperationsCompleteOneOrMoreFailures))
{
if (rsp->m_numberOfCompletedSubops == 0)
{
logger.error ( "No images transferred by PACS!" );
//throw std::runtime_error( std::string("No images transferred by PACS!") );
return false;
}
}
else
{
logger.error("GET request failed, server does report error");
QString statusDetail("No details");
if (rsp->m_statusDetail != NULL)
{
std::ostringstream out;
rsp->m_statusDetail->print(out);
statusDetail = "Status Detail: " + statusDetail.fromStdString(out.str());
}
statusDetail.prepend("GET request failed: ");
logger.error(statusDetail);
//throw std::runtime_error( statusDetail.toStdString() );
return false;
}
}
// Select the last GET response to output meaningful status information
OFIterator<RetrieveResponse*> it = responses.begin();
Uint32 numResults = responses.size();
for (Uint32 i = 1; i < numResults; i++)
{
it++;
}
logger.debug ( "GET responses report for study: " + studyInstanceUID +"\n"
+ QString::number(static_cast<unsigned int>((*it)->m_numberOfCompletedSubops))
+ " images transferred, and\n"
+ QString::number(static_cast<unsigned int>((*it)->m_numberOfWarningSubops))
+ " images transferred with warning, and\n"
+ QString::number(static_cast<unsigned int>((*it)->m_numberOfFailedSubops))
+ " images transfers failed");
emit q->progress("Finished Get");
emit q->progress(100);
return true;
}
void I2DOutputPlugSC::supportedSOPClassUIDs(OFList<OFString> suppSOPs)
{
suppSOPs.push_back(UID_SecondaryCaptureImageStorage);
}
