//------------------------------------------------------------------------------
void ctkDICOMDatabase::openDatabase(const QString databaseFile, const QString& connectionName )
{
Q_D(ctkDICOMDatabase);
d->DatabaseFileName = databaseFile;
d->Database = QSqlDatabase::addDatabase("QSQLITE", connectionName);
d->Database.setDatabaseName(databaseFile);
if ( ! (d->Database.open()) )
{
d->LastError = d->Database.lastError().text();
return;
}
if ( d->Database.tables().empty() )
{
if (!initializeDatabase())
{
d->LastError = QString("Unable to initialize DICOM database!");
return;
}
}
if (!isInMemory())
{
QFileSystemWatcher* watcher = new QFileSystemWatcher(QStringList(databaseFile),this);
connect(watcher, SIGNAL(fileChanged(QString)),this, SIGNAL (databaseChanged()) );
}
}
/**
* Sanity-check various pieces of the Ebwt
*/
void Ebwt::sanityCheckAll(int reverse) const {
const EbwtParams& eh = this->_eh;
assert(isInMemory());
// Check ftab
for(uint32_t i = 1; i < eh._ftabLen; i++) {
assert_geq(this->ftabHi(i), this->ftabLo(i-1));
assert_geq(this->ftabLo(i), this->ftabHi(i-1));
assert_leq(this->ftabHi(i), eh._bwtLen+1);
}
assert_eq(this->ftabHi(eh._ftabLen-1), eh._bwtLen);
// Check offs
int seenLen = (eh._bwtLen + 31) >> 5;
uint32_t *seen;
try {
seen = new uint32_t[seenLen]; // bitvector marking seen offsets
} catch(bad_alloc& e) {
cerr << "Out of memory allocating seen[] at " << __FILE__ << ":" << __LINE__ << endl;
throw e;
}
memset(seen, 0, 4 * seenLen);
uint32_t offsLen = eh._offsLen;
for(uint32_t i = 0; i < offsLen; i++) {
assert_lt(this->offs()[i], eh._bwtLen);
int w = this->offs()[i] >> 5;
int r = this->offs()[i] & 31;
assert_eq(0, (seen[w] >> r) & 1); // shouldn't have been seen before
seen[w] |= (1 << r);
}
delete[] seen;
// Check nPat
assert_gt(this->_nPat, 0);
// Check plen, flen
for(uint32_t i = 0; i < this->_nPat; i++) {
assert_geq(this->plen()[i], 0);
}
// Check rstarts
if(this->rstarts() != NULL) {
for(uint32_t i = 0; i < this->_nFrag-1; i++) {
assert_gt(this->rstarts()[(i+1)*3], this->rstarts()[i*3]);
if(reverse == REF_READ_REVERSE) {
assert(this->rstarts()[(i*3)+1] >= this->rstarts()[((i+1)*3)+1]);
} else {
assert(this->rstarts()[(i*3)+1] <= this->rstarts()[((i+1)*3)+1]);
}
}
}
// Check ebwt
sanityCheckUpToSide(eh._numSides);
VMSG_NL("Ebwt::sanityCheck passed");
}
/**
* Transform this Ebwt into the original string in linear time by using
* the LF mapping to walk backwards starting at the row correpsonding
* to the end of the string. The result is written to s. The Ebwt
* must be in memory.
*/
void Ebwt::restore(SString<char>& s) const {
assert(isInMemory());
s.resize(this->_eh._len);
uint32_t jumps = 0;
uint32_t i = this->_eh._len; // should point to final SA elt (starting with '$')
SideLocus l(i, this->_eh, this->ebwt());
while(i != _zOff) {
assert_lt(jumps, this->_eh._len);
//if(_verbose) cout << "restore: i: " << i << endl;
// Not a marked row; go back a char in the original string
uint32_t newi = mapLF(l ASSERT_ONLY(, false));
assert_neq(newi, i);
s[this->_eh._len - jumps - 1] = rowL(l);
i = newi;
l.initFromRow(i, this->_eh, this->ebwt());
jumps++;
}
assert_eq(jumps, this->_eh._len);
}
/**
* Check that the ebwt array is internally consistent up to (and not
* including) the given side index by re-counting the chars and
* comparing against the embedded occ[] arrays.
*/
void Ebwt::sanityCheckUpToSide(int upToSide) const {
assert(isInMemory());
uint32_t occ[] = {0, 0, 0, 0};
ASSERT_ONLY(uint32_t occ_save[] = {0, 0, 0, 0});
uint32_t cur = 0; // byte pointer
const EbwtParams& eh = this->_eh;
bool fw = false;
while(cur < (upToSide * eh._sideSz)) {
assert_leq(cur + eh._sideSz, eh._ebwtTotLen);
for(uint32_t i = 0; i < eh._sideBwtSz; i++) {
uint8_t by = this->ebwt()[cur + (fw ? i : eh._sideBwtSz-i-1)];
for(int j = 0; j < 4; j++) {
// Unpack from lowest to highest bit pair
int twoBit = unpack_2b_from_8b(by, fw ? j : 3-j);
occ[twoBit]++;
}
assert_eq(0, (occ[0] + occ[1] + occ[2] + occ[3]) % 4);
}
assert_eq(0, (occ[0] + occ[1] + occ[2] + occ[3]) % eh._sideBwtLen);
// Finished forward bucket; check saved [A], [C], [G] and [T]
// against the uint32_ts encoded here
ASSERT_ONLY(const uint32_t *u32ebwt = reinterpret_cast<const uint32_t*>(&ebwt()[cur + eh._sideBwtSz]));
ASSERT_ONLY(uint32_t as = u32ebwt[0]);
ASSERT_ONLY(uint32_t cs = u32ebwt[1]);
ASSERT_ONLY(uint32_t gs = u32ebwt[2]);
ASSERT_ONLY(uint32_t ts = u32ebwt[3]);
assert(as == occ_save[0] || as == occ_save[0]-1);
assert_eq(cs, occ_save[1]);
assert_eq(gs, occ_save[2]);
assert_eq(ts, occ_save[3]);
#ifndef NDEBUG
occ_save[0] = occ[0];
occ_save[1] = occ[1];
occ_save[2] = occ[2];
occ_save[3] = occ[3];
#endif
cur += eh._sideSz;
}
}
//------------------------------------------------------------------------------
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();
}
}
const Array<Vec3i>& indices (int submesh) const { FW_ASSERT(isInMemory()); return *m_submeshes[submesh].indices; }
Array<Vec3i>& mutableIndices (int submesh) { FW_ASSERT(isInMemory()); freeVBO(); return *m_submeshes[submesh].indices; }
U8* addVertices (const void* ptr, int num) { FW_ASSERT(isInMemory() && num >= 0); freeVBO(); m_numVertices += num; U8* slot = m_vertices.add(NULL, num * m_stride); if (ptr) memcpy(slot, ptr, num * m_stride); return slot; }
U8* mutableVertex (int idx) { FW_ASSERT(isInMemory() && idx >= 0 && idx < numVertices()); return getMutableVertexPtr(idx); }
const U8* vertex (int idx) const { FW_ASSERT(isInMemory() && idx >= 0 && idx < numVertices()); return getVertexPtr(idx); }
U8* getMutableVertexPtr (int idx = 0) { FW_ASSERT(isInMemory() && idx >= 0 && idx <= numVertices()); freeVBO(); return m_vertices.getPtr() + idx * m_stride; }
const U8* getVertexPtr (int idx = 0) const { FW_ASSERT(isInMemory() && idx >= 0 && idx <= numVertices()); return m_vertices.getPtr() + idx * m_stride; }