Example #1
0
//------------------------------------------------------------------------------
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();
    }
}
Example #2
0
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();
      }
    }
}