//-----------------------------------------------------------------------------
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();
}
}
//------------------------------------------------------------------------------
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);
}
}
//-----------------------------------------------------------------------------
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 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 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];
}
//------------------------------------------------------------------------------
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 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 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 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 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();
}
}
}