//------------------------------------------------------------------------------
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 groupDicomFiles(const gdcm::Directory::FilenamesType &filenames,
SeriesTransform::Map &transforms)
{
// set up the dicom scanner
gdcm::Scanner scanner;
gdcm::Tag seriesNumberTag(0x0020,0x0011);
gdcm::Tag instanceTag(0x0020,0x0013);
gdcm::Tag numberOfImagesTag(0x0018,0x1090);
gdcm::Tag seriesDescription(0x0008,0x103e);
gdcm::Tag sliceThickness(0x0018,0x0050);
scanner.AddTag(seriesNumberTag);
scanner.AddTag(sliceThickness);
scanner.AddTag(seriesDescription);
scanner.AddTag(instanceTag);
scanner.AddTag(numberOfImagesTag);
scanner.Scan(filenames);
gdcm::Scanner::MappingType mapping = scanner.GetMappings();
for(unsigned int i = 0; i < filenames.size(); i++)
{
const char * fname = filenames[i].c_str();
// is the filename valid
if(mapping.count(fname) > 0)
{
if(mapping[fname].count(seriesNumberTag) > 0 &&
mapping[fname].count(instanceTag) > 0 &&
mapping[fname].count(numberOfImagesTag) > 0)
{
// extract the dicom header information
std::string seriesNumberStr, instanceNumberStr,
numberOfImagesStr, descriptionStr, thicknessStr;
seriesNumberStr = mapping[fname][seriesNumberTag];
instanceNumberStr = mapping[fname][instanceTag];
numberOfImagesStr = mapping[fname][numberOfImagesTag];
descriptionStr = mapping[fname][seriesDescription];
thicknessStr = mapping[fname][sliceThickness];
unsigned int seriesNum = QString::fromStdString(seriesNumberStr).toInt();
unsigned int instanceNum = QString::fromStdString(instanceNumberStr).toInt();
unsigned int numberOfImages = QString::fromStdString(numberOfImagesStr).toInt();
double thickness = QString::fromStdString(thicknessStr).toDouble();
descriptionStr = QString::fromStdString(descriptionStr).replace(" ","").toStdString();
if(transforms.count(seriesNum) == 0) continue;
// resize the image list if needed
if(transforms[seriesNum].imageFilenames.size() != numberOfImages)
{
transforms[seriesNum].imageFilenames.resize(numberOfImages);
}
// put the image file into the image list
transforms[seriesNum].description = descriptionStr;
transforms[seriesNum].sliceThickness = thickness;
transforms[seriesNum].imageFilenames[instanceNum-1] = fname;
}
}
}
}
