//------------------------------------------------------------------------------
void ctkDICOMDatabase::insert ( const QString& filePath, bool storeFile, bool generateThumbnail, bool createHierarchy, const QString& destinationDirectoryName)
{
Q_D(ctkDICOMDatabase);
Q_UNUSED(createHierarchy);
Q_UNUSED(destinationDirectoryName);
/// first we check if the file is already in the database
if (fileExistsAndUpToDate(filePath))
{
logger.debug( "File " + filePath + " already added.");
return;
}
logger.debug( "Processing " + filePath );
std::string filename = filePath.toStdString();
DcmFileFormat fileformat;
ctkDICOMDataset ctkDataset;
ctkDataset.InitializeFromFile(filePath);
if ( ctkDataset.IsInitialized() )
{
d->insert( ctkDataset, filePath, storeFile, generateThumbnail );
}
else
{
logger.warn(QString("Could not read DICOM file:") + filePath);
}
}
//------------------------------------------------------------------------------
bool ctkDICOMRetrievePrivate::initializeSCU( const QString& studyInstanceUID,
const QString& seriesInstanceUID,
const RetrieveType retrieveType,
DcmDataset *retrieveParameters)
{
if ( !this->Database )
{
logger.error ( "No Database for retrieve transaction" );
return false;
}
// If we like to query another server than before, be sure to disconnect first
if (this->SCU.isConnected() && this->ConnectionParamsChanged)
{
this->SCU.closeAssociation(DCMSCU_RELEASE_ASSOCIATION);
}
// Connect to server if not already connected
if (!this->SCU.isConnected())
{
// Check and initialize networking parameters in DCMTK
if ( !this->SCU.initNetwork().good() )
{
logger.error ( "Error initializing the network" );
return false;
}
// Negotiate (i.e. start the) association
logger.debug ( "Negotiating Association" );
if ( !this->SCU.negotiateAssociation().good() )
{
logger.error ( "Error negotiating association" );
return false;;
}
}
this->ConnectionParamsChanged = false;
// Setup query about what to be received from the PACS
logger.debug ( "Setting Retrieve Parameters" );
if ( retrieveType == RetrieveSeries )
{
retrieveParameters->putAndInsertString ( DCM_QueryRetrieveLevel, "SERIES" );
retrieveParameters->putAndInsertString ( DCM_SeriesInstanceUID,
seriesInstanceUID.toStdString().c_str() );
// Always required to send all highler level unique keys, so add study here (we are in Study Root)
retrieveParameters->putAndInsertString ( DCM_StudyInstanceUID,
studyInstanceUID.toStdString().c_str() ); //TODO
}
else
{
retrieveParameters->putAndInsertString ( DCM_QueryRetrieveLevel, "STUDY" );
retrieveParameters->putAndInsertString ( DCM_StudyInstanceUID,
studyInstanceUID.toStdString().c_str() );
}
return true;
}
// --------------------------------------------------------------------------
void ctkWorkflowGroupBox::updateGroupBox(ctkWorkflowStep* currentStep)
{
Q_D(ctkWorkflowGroupBox);
d->StepShownPreviously = d->StepShownCurrently;
d->StepShownCurrently = currentStep;
if (currentStep)
{
this->setTitle(currentStep->name());
this->setSubTitle(currentStep->description());
this->setErrorText(currentStep->statusText());
// don't show textual elements if they are empty
d->SubTitleTextBrowser->setVisible(!this->subTitle().isEmpty());
d->PreTextBrowser->setVisible(!this->preText().isEmpty());
d->PostTextBrowser->setVisible(!this->postText().isEmpty());
d->ErrorTextBrowser->setVisible(!this->errorText().isEmpty());
}
// disable/hide the previously shown step
if (ctkWorkflowWidgetStep* prevStep = dynamic_cast<ctkWorkflowWidgetStep*>(d->StepShownPreviously))
{
logger.debug(QString("updateClientArea - hiding %1").arg(prevStep->name()));
if (QWidget* stepArea = prevStep->stepArea())
{
stepArea->setEnabled(false);
if (d->HideWidgetsOfNonCurrentSteps)
{
stepArea->hide();
}
}
}
ctkWorkflowWidgetStep* currentWidgetStep = dynamic_cast<ctkWorkflowWidgetStep*>(currentStep);
// show/enable the current step
if (currentWidgetStep)
{
currentWidgetStep->showUserInterface();
if (QWidget* stepArea = currentWidgetStep->stepArea())
{
// add the step's client area to the widget if we haven't before
if (!this->isAncestorOf(stepArea))
{
d->ClientAreaLayout->addWidget(stepArea);
}
stepArea->setEnabled(true);
stepArea->show();
}
}
}
//------------------------------------------------------------------------------
void ctkDICOMDatabasePrivate::registerCompressionLibraries(){
logger.debug("Register compression libraries");
// 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();
}
//------------------------------------------------------------------------------
bool ctkDICOMDatabasePrivate::loggedExec(QSqlQuery& query, const QString& queryString)
{
bool success;
if (queryString.compare(""))
{
success = query.exec(queryString);
}
else
{
success = query.exec();
}
if (!success)
{
QSqlError sqlError = query.lastError();
logger.debug( "SQL failed\n Bad SQL: " + query.lastQuery());
logger.debug( "Error text: " + sqlError.text());
}
else
{
logger.debug( "SQL worked!\n SQL: " + query.lastQuery());
}
return (success);
}
// -------------------------------------------------------------------------
void ctkDICOMDatasetView::displayImage(int imageIndex){
Q_D(ctkDICOMDatasetView);
if(d->CurrentImageIndex.isValid())
{
QModelIndex seriesIndex = d->CurrentImageIndex.parent();
ctkDICOMModel* model = const_cast<ctkDICOMModel*>(qobject_cast<const ctkDICOMModel*>(seriesIndex.model()));
if(model)
{
if(imageIndex >= 0 && imageIndex < model->rowCount(seriesIndex))
{
this->onModelSelected(model->index(imageIndex, 0, seriesIndex));
}
else
{
logger.debug("out of index");
}
}
}
}
//----------------------------------------------------------------------------
void ctkDICOMThumbnailListWidgetPrivate
::addThumbnailWidget(const QModelIndex& imageIndex,
const QModelIndex& sourceIndex, const QString &text)
{
ctkDICOMModel* model = const_cast<ctkDICOMModel*>(
qobject_cast<const ctkDICOMModel*>(imageIndex.model()));
if(!model)
{
return;
}
QModelIndex seriesIndex = imageIndex.parent();
QModelIndex studyIndex = seriesIndex.parent();
QString thumbnailPath = this->DatabaseDirectory +
"/thumbs/" + model->data(studyIndex ,ctkDICOMModel::UIDRole).toString() + "/" +
model->data(seriesIndex ,ctkDICOMModel::UIDRole).toString() + "/" +
model->data(imageIndex, ctkDICOMModel::UIDRole).toString() + ".png";
if(!QFileInfo(thumbnailPath).exists())
{
return;
}
ctkThumbnailLabel* widget = new ctkThumbnailLabel(this->ScrollAreaContentWidget);
QString widgetLabel = text;
widget->setText( widgetLabel );
QPixmap pix(thumbnailPath);
logger.debug("Setting pixmap to " + thumbnailPath);
if(this->ThumbnailSize.isValid())
{
widget->setFixedSize(this->ThumbnailSize);
}
widget->setPixmap(pix);
QVariant var;
var.setValue(QPersistentModelIndex(sourceIndex));
widget->setProperty("sourceIndex", var);
this->addThumbnail(widget);
}
//----------------------------------------------------------------------------
void ctkDICOMThumbnailListWidgetPrivate
::addSeriesThumbnails(const QModelIndex &index)
{
QModelIndex studyIndex = index.parent();
QModelIndex seriesIndex = index;
ctkDICOMModel* model = const_cast<ctkDICOMModel*>(qobject_cast<const ctkDICOMModel*>(index.model()));
if (!model)
{
return;
}
model->fetchMore(seriesIndex);
const int imageCount = model->rowCount(seriesIndex);
logger.debug(QString("Thumbs: %1").arg(imageCount));
for (int i = 0 ; i < imageCount ; i++ )
{
QModelIndex imageIndex = seriesIndex.child(i,0);
this->addThumbnailWidget(imageIndex, imageIndex, QString("Image %1").arg(i));
}
}
//------------------------------------------------------------------------------
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();
}
}
//------------------------------------------------------------------------------
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;
}
bool ctkDICOMDatabase::removeSeries(const QString& seriesInstanceUID)
{
Q_D(ctkDICOMDatabase);
// get all images from series
QSqlQuery fileExists ( d->Database );
fileExists.prepare("SELECT Filename, SOPInstanceUID, StudyInstanceUID FROM Images,Series WHERE Series.SeriesInstanceUID = Images.SeriesInstanceUID AND Images.SeriesInstanceUID = :seriesID");
fileExists.bindValue(":seriesID",seriesInstanceUID);
bool success = fileExists.exec();
if (!success)
{
logger.error("SQLITE ERROR: " + fileExists.lastError().driverText());
return false;
}
QList< QPair<QString,QString> > removeList;
while ( fileExists.next() )
{
QString dbFilePath = fileExists.value(fileExists.record().indexOf("Filename")).toString();
QString sopInstanceUID = fileExists.value(fileExists.record().indexOf("SOPInstanceUID")).toString();
QString studyInstanceUID = fileExists.value(fileExists.record().indexOf("StudyInstanceUID")).toString();
QString internalFilePath = studyInstanceUID + "/" + seriesInstanceUID + "/" + sopInstanceUID;
removeList << qMakePair(dbFilePath,internalFilePath);
}
QSqlQuery fileRemove ( d->Database );
fileRemove.prepare("DELETE FROM Images WHERE SeriesInstanceUID == :seriesID");
fileRemove.bindValue(":seriesID",seriesInstanceUID);
logger.debug("SQLITE: removing seriesInstanceUID " + seriesInstanceUID);
success = fileRemove.exec();
if (!success)
{
logger.error("SQLITE ERROR: could not remove seriesInstanceUID " + seriesInstanceUID);
logger.error("SQLITE ERROR: " + fileRemove.lastError().driverText());
}
QPair<QString,QString> fileToRemove;
foreach (fileToRemove, removeList)
{
QString dbFilePath = fileToRemove.first;
QString thumbnailToRemove = databaseDirectory() + "/thumbs/" + fileToRemove.second + ".png";
// check that the file is below our internal storage
if (dbFilePath.startsWith( databaseDirectory() + "/dicom/"))
{
if (!dbFilePath.endsWith(fileToRemove.second))
{
logger.error("Database inconsistency detected during delete!");
continue;
}
if (QFile( dbFilePath ).remove())
{
logger.debug("Removed file " + dbFilePath );
}
else
{
logger.warn("Failed to remove file " + dbFilePath );
}
}
if (QFile( thumbnailToRemove ).remove())
{
logger.debug("Removed thumbnail " + thumbnailToRemove);
}
else
{
logger.warn("Failed to remove thumbnail " + thumbnailToRemove);
}
}
//------------------------------------------------------------------------------
void ctkDICOMDatabasePrivate::insert( const ctkDICOMDataset& ctkDataset, const QString& filePath, bool storeFile, bool generateThumbnail)
{
Q_Q(ctkDICOMDatabase);
// Check to see if the file has already been loaded
// TODO:
// It could make sense to actually remove the dataset and re-add it. This needs the remove
// method we still have to write.
//
QString sopInstanceUID ( ctkDataset.GetElementAsString(DCM_SOPInstanceUID) );
QSqlQuery fileExists ( Database );
fileExists.prepare("SELECT InsertTimestamp,Filename FROM Images WHERE SOPInstanceUID == :sopInstanceUID");
fileExists.bindValue(":sopInstanceUID",sopInstanceUID);
bool success = fileExists.exec();
if (!success)
{
logger.error("SQLITE ERROR: " + fileExists.lastError().driverText());
return;
}
qDebug() << "filename is: " << fileExists.value(1).toString();
qDebug() << "modified date is: " << QFileInfo(fileExists.value(1).toString()).lastModified();
qDebug() << "db mod date is: " << QDateTime::fromString(fileExists.value(0).toString(),Qt::ISODate);
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;
}
//If the following fields can not be evaluated, cancel evaluation of the DICOM file
QString patientsName(ctkDataset.GetElementAsString(DCM_PatientName) );
QString studyInstanceUID(ctkDataset.GetElementAsString(DCM_StudyInstanceUID) );
QString seriesInstanceUID(ctkDataset.GetElementAsString(DCM_SeriesInstanceUID) );
QString patientID(ctkDataset.GetElementAsString(DCM_PatientID) );
if ( patientsName.isEmpty() && !patientID.isEmpty() )
{ // Use patient id as name if name is empty - can happen on anonymized datasets
// see: http://www.na-mic.org/Bug/view.php?id=1643
patientsName = patientID;
}
if ( patientsName.isEmpty() || studyInstanceUID.isEmpty() || patientID.isEmpty() )
{
logger.error("Dataset is missing necessary information!");
return;
}
QString patientsBirthDate(ctkDataset.GetElementAsString(DCM_PatientBirthDate) );
QString patientsBirthTime(ctkDataset.GetElementAsString(DCM_PatientBirthTime) );
QString patientsSex(ctkDataset.GetElementAsString(DCM_PatientSex) );
QString patientsAge(ctkDataset.GetElementAsString(DCM_PatientAge) );
QString patientComments(ctkDataset.GetElementAsString(DCM_PatientComments) );
QString studyID(ctkDataset.GetElementAsString(DCM_StudyID) );
QString studyDate(ctkDataset.GetElementAsString(DCM_StudyDate) );
QString studyTime(ctkDataset.GetElementAsString(DCM_StudyTime) );
QString accessionNumber(ctkDataset.GetElementAsString(DCM_AccessionNumber) );
QString modalitiesInStudy(ctkDataset.GetElementAsString(DCM_ModalitiesInStudy) );
QString institutionName(ctkDataset.GetElementAsString(DCM_InstitutionName) );
QString performingPhysiciansName(ctkDataset.GetElementAsString(DCM_PerformingPhysicianName) );
QString referringPhysician(ctkDataset.GetElementAsString(DCM_ReferringPhysicianName) );
QString studyDescription(ctkDataset.GetElementAsString(DCM_StudyDescription) );
QString seriesDate(ctkDataset.GetElementAsString(DCM_SeriesDate) );
QString seriesTime(ctkDataset.GetElementAsString(DCM_SeriesTime) );
QString seriesDescription(ctkDataset.GetElementAsString(DCM_SeriesDescription) );
QString bodyPartExamined(ctkDataset.GetElementAsString(DCM_BodyPartExamined) );
QString frameOfReferenceUID(ctkDataset.GetElementAsString(DCM_FrameOfReferenceUID) );
QString contrastAgent(ctkDataset.GetElementAsString(DCM_ContrastBolusAgent) );
QString scanningSequence(ctkDataset.GetElementAsString(DCM_ScanningSequence) );
long seriesNumber(ctkDataset.GetElementAsInteger(DCM_SeriesNumber) );
long acquisitionNumber(ctkDataset.GetElementAsInteger(DCM_AcquisitionNumber) );
long echoNumber(ctkDataset.GetElementAsInteger(DCM_EchoNumbers) );
long temporalPosition(ctkDataset.GetElementAsInteger(DCM_TemporalPositionIdentifier) );
// store the file if the database is not in memomry
// TODO: if we are called from insert(file) we
// have to do something else
//
QString filename = filePath;
if ( storeFile && !q->isInMemory() && !seriesInstanceUID.isEmpty() )
{
// QString studySeriesDirectory = studyInstanceUID + "/" + seriesInstanceUID;
QString destinationDirectoryName = q->databaseDirectory() + "/dicom/";
QDir destinationDir(destinationDirectoryName);
filename = destinationDirectoryName +
studyInstanceUID + "/" +
seriesInstanceUID + "/" +
sopInstanceUID;
destinationDir.mkpath(studyInstanceUID + "/" +
seriesInstanceUID);
if(filePath.isEmpty())
{
logger.debug ( "Saving file: " + filename );
if ( !ctkDataset.SaveToFile( filename) )
{
logger.error ( "Error saving file: " + filename );
return;
}
}
else
{
// we're inserting an existing file
QFile currentFile( filePath );
currentFile.copy(filename);
logger.debug( "Copy file from: " + filePath );
logger.debug( "Copy file to : " + filename );
}
}
QSqlQuery checkPatientExistsQuery(Database);
//The dbPatientID is a unique number within the database,
//generated by the sqlite autoincrement
//The patientID is the (non-unique) DICOM patient id
int dbPatientID = -1;
if ( patientID != "" && patientsName != "" )
{
//Speed up: Check if patient is the same as in last file;
// very probable, as all images belonging to a study have the same patient
if ( lastPatientID != patientID
|| lastPatientsBirthDate != patientsBirthDate
|| lastPatientsName != patientsName )
{
// Ok, something is different from last insert, let's insert him if he's not
// already in the db.
//
// Check if patient is already present in the db
// TODO: maybe add birthdate check for extra safety
checkPatientExistsQuery.prepare ( "SELECT * FROM Patients WHERE PatientID = ? AND PatientsName = ?" );
checkPatientExistsQuery.bindValue ( 0, patientID );
checkPatientExistsQuery.bindValue ( 1, patientsName );
loggedExec(checkPatientExistsQuery);
if (checkPatientExistsQuery.next())
{
// we found him
dbPatientID = checkPatientExistsQuery.value(checkPatientExistsQuery.record().indexOf("UID")).toInt();
}
else
{
// Insert it
QSqlQuery insertPatientStatement ( Database );
insertPatientStatement.prepare ( "INSERT INTO Patients ('UID', 'PatientsName', 'PatientID', 'PatientsBirthDate', 'PatientsBirthTime', 'PatientsSex', 'PatientsAge', 'PatientsComments' ) values ( NULL, ?, ?, ?, ?, ?, ?, ? )" );
insertPatientStatement.bindValue ( 0, patientsName );
insertPatientStatement.bindValue ( 1, patientID );
insertPatientStatement.bindValue ( 2, patientsBirthDate );
insertPatientStatement.bindValue ( 3, patientsBirthTime );
insertPatientStatement.bindValue ( 4, patientsSex );
// TODO: shift patient's age to study,
// since this is not a patient level attribute in images
// insertPatientStatement.bindValue ( 5, patientsAge );
insertPatientStatement.bindValue ( 6, patientComments );
loggedExec(insertPatientStatement);
dbPatientID = insertPatientStatement.lastInsertId().toInt();
logger.debug ( "New patient inserted: " + QString().setNum ( dbPatientID ) );
}
/// keep this for the next image
lastPatientUID = dbPatientID;
lastPatientID = patientID;
lastPatientsBirthDate = patientsBirthDate;
lastPatientsName = patientsName;
}
// Patient is in now. Let's continue with the study
if ( studyInstanceUID != "" && lastStudyInstanceUID != studyInstanceUID )
{
QSqlQuery checkStudyExistsQuery (Database);
checkStudyExistsQuery.prepare ( "SELECT * FROM Studies WHERE StudyInstanceUID = ?" );
checkStudyExistsQuery.bindValue ( 0, studyInstanceUID );
checkStudyExistsQuery.exec();
if(!checkStudyExistsQuery.next())
{
QSqlQuery insertStudyStatement ( Database );
insertStudyStatement.prepare ( "INSERT INTO Studies ( 'StudyInstanceUID', 'PatientsUID', 'StudyID', 'StudyDate', 'StudyTime', 'AccessionNumber', 'ModalitiesInStudy', 'InstitutionName', 'ReferringPhysician', 'PerformingPhysiciansName', 'StudyDescription' ) VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? )" );
insertStudyStatement.bindValue ( 0, studyInstanceUID );
insertStudyStatement.bindValue ( 1, dbPatientID );
insertStudyStatement.bindValue ( 2, studyID );
insertStudyStatement.bindValue ( 3, QDate::fromString ( studyDate, "yyyyMMdd" ) );
insertStudyStatement.bindValue ( 4, studyTime );
insertStudyStatement.bindValue ( 5, accessionNumber );
insertStudyStatement.bindValue ( 6, modalitiesInStudy );
insertStudyStatement.bindValue ( 7, institutionName );
insertStudyStatement.bindValue ( 8, referringPhysician );
insertStudyStatement.bindValue ( 9, performingPhysiciansName );
insertStudyStatement.bindValue ( 10, studyDescription );
if ( !insertStudyStatement.exec() )
{
logger.error ( "Error executing statament: " + insertStudyStatement.lastQuery() + " Error: " + insertStudyStatement.lastError().text() );
}
else
{
lastStudyInstanceUID = studyInstanceUID;
}
}
}
if ( seriesInstanceUID != "" && seriesInstanceUID != lastSeriesInstanceUID )
{
QSqlQuery checkSeriesExistsQuery (Database);
checkSeriesExistsQuery.prepare ( "SELECT * FROM Series WHERE SeriesInstanceUID = ?" );
checkSeriesExistsQuery.bindValue ( 0, seriesInstanceUID );
logger.warn ( "Statement: " + checkSeriesExistsQuery.lastQuery() );
loggedExec(checkSeriesExistsQuery);
if(!checkSeriesExistsQuery.next())
{
QSqlQuery insertSeriesStatement ( Database );
insertSeriesStatement.prepare ( "INSERT INTO Series ( 'SeriesInstanceUID', 'StudyInstanceUID', 'SeriesNumber', 'SeriesDate', 'SeriesTime', 'SeriesDescription', 'BodyPartExamined', 'FrameOfReferenceUID', 'AcquisitionNumber', 'ContrastAgent', 'ScanningSequence', 'EchoNumber', 'TemporalPosition' ) VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? )" );
insertSeriesStatement.bindValue ( 0, seriesInstanceUID );
insertSeriesStatement.bindValue ( 1, studyInstanceUID );
insertSeriesStatement.bindValue ( 2, static_cast<int>(seriesNumber) );
insertSeriesStatement.bindValue ( 3, seriesDate );
insertSeriesStatement.bindValue ( 4, QDate::fromString ( seriesTime, "yyyyMMdd" ) );
insertSeriesStatement.bindValue ( 5, seriesDescription );
insertSeriesStatement.bindValue ( 6, bodyPartExamined );
insertSeriesStatement.bindValue ( 7, frameOfReferenceUID );
insertSeriesStatement.bindValue ( 8, static_cast<int>(acquisitionNumber) );
insertSeriesStatement.bindValue ( 9, contrastAgent );
insertSeriesStatement.bindValue ( 10, scanningSequence );
insertSeriesStatement.bindValue ( 11, static_cast<int>(echoNumber) );
insertSeriesStatement.bindValue ( 12, static_cast<int>(temporalPosition) );
if ( !insertSeriesStatement.exec() )
{
logger.error ( "Error executing statament: "
+ insertSeriesStatement.lastQuery()
+ " Error: " + insertSeriesStatement.lastError().text() );
lastSeriesInstanceUID = "";
}
else
{
lastSeriesInstanceUID = seriesInstanceUID;
}
}
}
// TODO: what to do with imported files
//
if ( !filename.isEmpty() && !seriesInstanceUID.isEmpty() )
{
QSqlQuery checkImageExistsQuery (Database);
checkImageExistsQuery.prepare ( "SELECT * FROM Images WHERE Filename = ?" );
checkImageExistsQuery.bindValue ( 0, filename );
checkImageExistsQuery.exec();
if(!checkImageExistsQuery.next())
{
QSqlQuery insertImageStatement ( Database );
insertImageStatement.prepare ( "INSERT INTO Images ( 'SOPInstanceUID', 'Filename', 'SeriesInstanceUID', 'InsertTimestamp' ) VALUES ( ?, ?, ?, ? )" );
insertImageStatement.bindValue ( 0, sopInstanceUID );
insertImageStatement.bindValue ( 1, filename );
insertImageStatement.bindValue ( 2, seriesInstanceUID );
insertImageStatement.bindValue ( 3, QDateTime::currentDateTime() );
insertImageStatement.exec();
}
}
if( generateThumbnail && thumbnailGenerator && !seriesInstanceUID.isEmpty() )
{
QString studySeriesDirectory = studyInstanceUID + "/" + seriesInstanceUID;
//Create thumbnail here
QString thumbnailPath = q->databaseDirectory() +
"/thumbs/" + studyInstanceUID + "/" + seriesInstanceUID
+ "/" + sopInstanceUID + ".png";
QFileInfo thumbnailInfo(thumbnailPath);
if( !(thumbnailInfo.exists()
&& (thumbnailInfo.lastModified() > QFileInfo(filename).lastModified())))
{
QDir(q->databaseDirectory() + "/thumbs/").mkpath(studySeriesDirectory);
DicomImage dcmImage(QDir::toNativeSeparators(filename).toAscii());
thumbnailGenerator->generateThumbnail(&dcmImage, thumbnailPath);
}
}
if (q->isInMemory())
{
emit q->databaseChanged();
}
}
}
void ctkDICOMIndexerBase::insert ( DcmDataset *dataset, QString filename ) {
CTK_D(ctkDICOMIndexerBase);
// Check to see if the file has already been loaded
QSqlQuery fileExists ( d->db );
fileExists.prepare("SELECT InsertTimestamp FROM Images WHERE Filename == ?");
fileExists.bindValue(0,filename);
fileExists.exec();
if ( fileExists.next() && QFileInfo(filename).lastModified() < QDateTime::fromString(fileExists.value(0).toString(),Qt::ISODate) )
{
logger.debug ( "File " + filename + " 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_PatientsName, patientsName);
dataset->findAndGetOFString(DCM_StudyInstanceUID, studyInstanceUID);
dataset->findAndGetOFString(DCM_SeriesInstanceUID, seriesInstanceUID);
dataset->findAndGetOFString(DCM_PatientID, patientID);
dataset->findAndGetOFString(DCM_PatientsBirthDate, patientsBirthDate);
dataset->findAndGetOFString(DCM_PatientsBirthTime, patientsBirthTime);
dataset->findAndGetOFString(DCM_PatientsSex, patientsSex);
dataset->findAndGetOFString(DCM_PatientsAge, 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_PerformingPhysiciansName, performingPhysiciansName);
dataset->findAndGetOFString(DCM_ReferringPhysiciansName, 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);
QSqlQuery check_exists_query(d->db);
//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->db );
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() ) );
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->db );
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->db );
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->db );
statement.prepare ( "INSERT INTO Images ( 'Filename', 'SeriesInstanceUID', 'InsertTimestamp' ) VALUES ( ?, ?, ? )" );
statement.bindValue ( 0, filename );
statement.bindValue ( 1, QString ( seriesInstanceUID.c_str() ) );
statement.bindValue ( 2, QDateTime::currentDateTime() );
statement.exec();
}
}
}
//------------------------------------------------------------------------------
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;
}
