//------------------------------------------------------------------------------
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);
}
}
//-----------------------------------------------------------------------------
void ctkVTKHistogram::setRange(qreal minRange, qreal maxRange)
{
Q_D(const ctkVTKHistogram);
if (d->DataArray.GetPointer() == 0)
{
//Q_ASSERT(d->DataArray.GetPointer());
logger.warn("no data array. range will be reset when setting array.");
minRange = 1.; // set incorrect values
maxRange = 0.;
return;
}
if (minRange >= maxRange)
{
//Q_ASSERT(d->DataArray.GetPointer());
logger.warn("minRange >= maxRange");
qreal pivot = minRange;
minRange = maxRange;
maxRange = pivot;
}
int numberOfBinsBefore = d->computeNumberOfBins();
d->Range[0] = minRange;
d->Range[1] = maxRange;
if (d->computeNumberOfBins() != numberOfBinsBefore)
{
this->build();
}
}
//------------------------------------------------------------------------------
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;
}
//------------------------------------------------------------------------------
bool ctkDICOMRetrieve::getStudy(const QString& studyInstanceUID)
{
if (studyInstanceUID.isEmpty())
{
logger.error("Cannot receive series: Study Instance UID empty.");
return false;
}
Q_D(ctkDICOMRetrieve);
logger.info ( "Starting getStudy" );
return d->get ( studyInstanceUID, "", ctkDICOMRetrievePrivate::RetrieveStudy );
}
//------------------------------------------------------------------------------
bool ctkDICOMRetrieve::getSeries(const QString& studyInstanceUID,
const QString& seriesInstanceUID)
{
if (studyInstanceUID.isEmpty() || seriesInstanceUID.isEmpty())
{
logger.error("Cannot receive series: Either Study or Series Instance UID empty.");
return false;
}
Q_D(ctkDICOMRetrieve);
logger.info ( "Starting getSeries" );
return d->get ( studyInstanceUID, seriesInstanceUID, ctkDICOMRetrievePrivate::RetrieveSeries );
}
//-----------------------------------------------------------------------------
void ctkVTKHistogram::resetRange()
{
Q_D(ctkVTKHistogram);
if (d->DataArray.GetPointer() == 0)
{
//Q_ASSERT(d->DataArray.GetPointer());
logger.warn("no dataArray");
d->Range[0] = 1.; // set incorrect values
d->Range[1] = 0.;
return;
}
if (d->DataArray->GetDataType() == VTK_CHAR ||
d->DataArray->GetDataType() == VTK_SIGNED_CHAR ||
d->DataArray->GetDataType() == VTK_UNSIGNED_CHAR)
{
d->Range[0] = d->DataArray->GetDataTypeMin();
d->Range[1] = d->DataArray->GetDataTypeMax();
}
else
{
d->DataArray->GetRange(d->Range, d->Component);
if (d->DataArray->GetDataType() == VTK_FLOAT ||
d->DataArray->GetDataType() == VTK_DOUBLE)
{
d->Range[1] += 0.01;
}
//else
// {
// this->Range[1] += 1;
// }
}
}
// --------------------------------------------------------------------------
void ctkWorkflowStep::validate(const QString& desiredBranchId)
{
Q_D(ctkWorkflowStep);
logger.info(QString("validate - validating the input from %1").arg(d->Name));
this->validationComplete(true, desiredBranchId);
}
//-----------------------------------------------------------------------------
QVariant ctkVTKColorTransferFunction::maxValue()const
{
Q_D(const ctkVTKColorTransferFunction);
if (d->ColorTransferFunction.GetPointer() == 0)
{
//Q_ASSERT(d->ColorTransferFunction.GetPointer());
logger.warn("no ColorTransferFunction");
return -1;
}
double rgb[3];
QColor minValue = QColor::fromRgbF(0.,0.,0.);
for (int i = 0; i < this->count(); ++i)
{
d->ColorTransferFunction->GetColor(i, rgb);
Q_ASSERT(rgb[0] >= 0. && rgb[0] <= 1. &&
rgb[1] >= 0. && rgb[1] <= 1. &&
rgb[2] >= 0. && rgb[2] <= 1.);
QColor color = QColor::fromRgbF(rgb[0], rgb[1], rgb[2]);
if ( qGray(color.red(), color.green(), color.blue()) >
qGray(minValue.red(), minValue.green(), minValue.blue()))
{
minValue = color;
}
}
return minValue;
}
//----------------------------------------------------------------------------
void ctkVTKSliceView::forceRender()
{
Q_D(ctkVTKSliceView);
if (!d->RenderEnabled || !this->isVisible())
{
return;
}
logger.trace("forceRender");
d->RenderWindow->Render();
d->RenderPending = false;
}
// --------------------------------------------------------------------------
void ctkWorkflowStep::setId(const QString& newId)
{
Q_D(ctkWorkflowStep);
if (d->Workflow && d->Workflow->hasStep(newId) && !this->id().isEmpty())
{
logger.error(QString("ctkWorkflowStep - Failed to change id from '%1' to '%2' - "
"Step already added to a workflow !").arg(this->id()).arg(newId));
return;
}
d->Id = newId;
}
// --------------------------------------------------------------------------
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();
}
//------------------------------------------------------------------------------
void ctkDICOMIndexer::addFile(ctkDICOMDatabase& database,
const QString filePath,
const QString& destinationDirectoryName)
{
std::cout << filePath.toStdString();
if (!destinationDirectoryName.isEmpty())
{
logger.warn("Ignoring destinationDirectoryName parameter, just taking it as indication we should copy!");
}
emit indexingFilePath(filePath);
database.insert(filePath, !destinationDirectoryName.isEmpty(), true);
}
//-----------------------------------------------------------------------------
void ctkVTKHistogram::range(qreal& minRange, qreal& maxRange)const
{
Q_D(const ctkVTKHistogram);
if (d->DataArray.GetPointer() == 0)
{
//Q_ASSERT(d->DataArray.GetPointer());
logger.warn("no dataArray");
minRange = 1.; // set incorrect values
maxRange = 0.;
return;
}
minRange = d->Range[0];
maxRange = d->Range[1];
}
//------------------------------------------------------------------------------
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 ctkWorkflowWidget::setWorkflow(ctkWorkflow* newWorkflow)
{
Q_D(ctkWorkflowWidget);
if (!newWorkflow)
{
logger.error(QString("setWorkflow - cannot set workflow to NULL"));
return;
}
if (d->Workflow)
{
QObject::disconnect(d->Workflow, SIGNAL(currentStepChanged(ctkWorkflowStep*)), this, SLOT(onCurrentStepChanged(ctkWorkflowStep)));
}
//----------------------------------------------------------------------------
void ctkVTKSliceView::scheduleRender()
{
Q_D(ctkVTKSliceView);
logger.trace("scheduleRender");
if (!d->RenderEnabled)
{
return;
}
if (!d->RenderPending)
{
d->RenderPending = true;
QTimer::singleShot(0, this, SLOT(forceRender()));
}
}
//-----------------------------------------------------------------------------
void ctkVTKColorTransferFunction::range(qreal& minRange, qreal& maxRange)const
{
Q_D(const ctkVTKColorTransferFunction);
if (d->ColorTransferFunction.GetPointer() == 0)
{
//Q_ASSERT(d->ColorTransferFunction.GetPointer());
logger.warn("no ColorTransferFunction");
minRange = 1.;
maxRange = 0.;
return;
}
double rangeValues[2];
d->ColorTransferFunction->GetRange(rangeValues);
minRange = rangeValues[0];
maxRange = rangeValues[1];
}
// --------------------------------------------------------------------------
void ctkWorkflowAbstractPagedWidget::associateStepWithPage(ctkWorkflowStep* step, int index)
{
Q_D(ctkWorkflowAbstractPagedWidget);
if (index < 0)
{
logger.error(QString("Cannot associate step with a page of index -1"));
return;
}
if (step)
{
d->StepToIndexMap[step] = index;
if (!d->IndexToGroupBoxMap.contains(index))
{
d->IndexToGroupBoxMap[index] = 0;
}
}
}
// -------------------------------------------------------------------------
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 ctkSettingsPanel::setSetting(const QString& key, const QVariant& newVal)
{
Q_D(ctkSettingsPanel);
QSettings* settings = d->settings(key);
if (!settings)
{
return;
}
QVariant oldVal = settings->value(key);
settings->setValue(key, newVal);
d->Properties[key].setValue(newVal);
if (settings->status() != QSettings::NoError)
{
logger.warn( QString("Error #%1 while writing setting \"%2\"")
.arg(static_cast<int>(settings->status()))
.arg(key));
}
if (oldVal != newVal)
{
emit settingChanged(key, newVal);
}
}
//----------------------------------------------------------------------------
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));
}
}
//------------------------------------------------------------------------------
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 ctkDICOMRetrieve::retrieveStudy( const QString& studyInstanceUID )
{
Q_D(ctkDICOMRetrieve);
logger.info ( "Starting retrieveStudy" );
return d->retrieve ( studyInstanceUID, ctkDICOMRetrievePrivate::RetrieveStudy );
}
//------------------------------------------------------------------------------
bool ctkDICOMRetrieve::retrieveSeries( const QString& seriesInstanceUID )
{
Q_D(ctkDICOMRetrieve);
logger.info ( "Starting retrieveSeries" );
return d->retrieve ( seriesInstanceUID, ctkDICOMRetrievePrivate::RetrieveSeries );
}
//------------------------------------------------------------------------------
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();
}
}
// -------------------------------------------------------------------------
void ctkDICOMDatasetView::addImage( DicomImage & dcmImage, bool defaultIntensity )
{
Q_D(ctkDICOMDatasetView);
QImage image;
// Check whether we have a valid image
EI_Status result = dcmImage.getStatus();
if (result != EIS_Normal)
{
logger.error(QString("Rendering of DICOM image failed for thumbnail failed: ") + DicomImage::getString(result));
return;
}
// Select first window defined in image. If none, compute min/max window as best guess.
// Only relevant for monochrome
if (d->AutoWindowLevel)
{
if (dcmImage.isMonochrome())
{
if (defaultIntensity && dcmImage.getWindowCount() > 0)
{
dcmImage.setWindow(0);
}
else
{
dcmImage.setMinMaxWindow(OFTrue /* ignore extreme values */);
dcmImage.getWindow(d->DicomIntensityLevel, d->DicomIntensityWindow);
}
}
}
else
{
dcmImage.setWindow(d->DicomIntensityLevel, d->DicomIntensityWindow);
}
/* get image extension and prepare image header */
const unsigned long width = dcmImage.getWidth();
const unsigned long height = dcmImage.getHeight();
unsigned long offset = 0;
unsigned long length = 0;
QString header;
if (dcmImage.isMonochrome())
{
// write PGM header (binary monochrome image format)
header = QString("P5 %1 %2 255\n").arg(width).arg(height);
offset = header.length();
length = width * height + offset;
}
else
{
// write PPM header (binary color image format)
header = QString("P6 %1 %2 255\n").arg(width).arg(height);
offset = header.length();
length = width * height * 3 /* RGB */ + offset;
}
/* create output buffer for DicomImage class */
QByteArray buffer;
/* copy header to output buffer and resize it for pixel data */
buffer.append(header);
buffer.resize(length);
/* render pixel data to buffer */
if (dcmImage.getOutputData(static_cast<void *>(buffer.data() + offset), length - offset, 8, 0))
{
if (!image.loadFromData( buffer ))
{
logger.error("QImage couldn't created");
}
}
this->addImage(image);
}
//------------------------------------------------------------------------------
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;
}
