void medAbstractDatabaseImporter::importFile ( void )
{
QMutexLocker locker ( &d->mutex );
/* The idea of this algorithm can be summarized in 3 steps:
* 1. Get a list of all the files that will (try to) be imported or indexed
* 2. Filter files that cannot be read, or won't be possible to write afterwards, or are already in the db
* 3. Fill files metadata, write them to the db, and populate db tables
*
* note that depending on the input files, they might be aggregated by volume
*/
// 1) Obtain a list of all the files that are going to be processed
// this flattens the tree structure (if the input is a directory)
// and puts all the files in one single list
QStringList fileList = getAllFilesToBeProcessed ( d->file );
// Files that pass the filters named above are grouped
// by volume in this map and will be written in the db after.
// the key will be the name of the aggregated file with the volume
QMap<QString, QStringList> imagesGroupedByVolume;
QMap<QString, QString> imagesGroupedByPatient;
QMap<QString, QString> imagesGroupedBySeriesId;
int currentFileNumber = 0; // this variable will be used only for calculating progress
// if importing, and depending on the input files, they might be aggregated
// that is: files corresponding to the same volume will be written
// in a single output meta file (e.g. .mha)
// this map is used to store a unique id per volume and its volume number
QMap<QString, int> volumeUniqueIdToVolumeNumber;
int volumeNumber = 1;
// 2) Select (by filtering) files to be imported
//
// In this first loop we read the headers of all the images to be imported
// and check if we don't have any problem in reading the file, the header
// or in selecting a proper format to store the new file afterwards
// new files ARE NOT written in medInria database yet, but are stored in a map for writing in a posterior step
QString tmpPatientId;
QString currentPatientId = "";
QString patientID;
QString tmpSeriesUid;
QString currentSeriesUid = "-1";
QString currentSeriesId = "";
bool atLeastOneImportSucceeded = false;
foreach ( QString file, fileList )
{
if ( d->isCancelled ) // check if user cancelled the process
break;
emit progress ( this, ( ( qreal ) currentFileNumber/ ( qreal ) fileList.count() ) * 50.0 ); //TODO: reading and filtering represents 50% of the importing process?
currentFileNumber++;
QFileInfo fileInfo ( file );
if (fileInfo.size() != 0)
{
dtkSmartPointer<medAbstractData> medData;
// 2.1) Try reading file information, just the header not the whole file
bool readOnlyImageInformation = true;
medData = tryReadImages ( QStringList ( fileInfo.filePath() ), readOnlyImageInformation );
if ( !medData )
{
qWarning() << "Reader was unable to read: " << fileInfo.filePath();
continue;
}
// 2.2) Fill missing metadata
populateMissingMetadata ( medData, medMetaDataKeys::SeriesID.getFirstValue(medData));
QString patientName = medMetaDataKeys::PatientName.getFirstValue(medData).simplified();
QString birthDate = medMetaDataKeys::BirthDate.getFirstValue(medData);
tmpPatientId = patientName + birthDate;
if(tmpPatientId != currentPatientId)
{
currentPatientId = tmpPatientId;
patientID = getPatientID(patientName, birthDate);
}
medData->setMetaData ( medMetaDataKeys::PatientID.key(), QStringList() << patientID );
tmpSeriesUid = medMetaDataKeys::SeriesDicomID.getFirstValue(medData);
if (tmpSeriesUid != currentSeriesUid)
{
currentSeriesUid = tmpSeriesUid;
currentSeriesId = medMetaDataKeys::SeriesID.getFirstValue(medData);
}
else
medData->setMetaData ( medMetaDataKeys::SeriesID.key(), QStringList() << currentSeriesId );
// 2.3) Generate an unique id for each volume
// all images of the same volume should share the same id
QString volumeId = generateUniqueVolumeId ( medData );
// check whether the image belongs to a new volume
if ( !volumeUniqueIdToVolumeNumber.contains ( volumeId ) )
{
volumeUniqueIdToVolumeNumber[volumeId] = volumeNumber;
volumeNumber++;
}
// 2.3) a) Determine future file name and path based on patient/study/series/image
// i.e.: where we will write the imported image
QString imageFileName = determineFutureImageFileName ( medData, volumeUniqueIdToVolumeNumber[volumeId] );
#ifdef Q_OS_WIN32
if ( (medStorage::dataLocation() + "/" + imageFileName).length() > 255 )
{
emit showError ( tr ( "Your database path is too long" ), 5000 );
emit dataImported(medDataIndex(), d->uuid);
emit failure ( this );
return;
}
#endif
// 2.3) b) Find the proper extension according to the type of the data
// i.e.: in which format we will write the file in our database
QString futureExtension = determineFutureImageExtensionByDataType ( medData );
// we care whether we can write the image or not if we are importing
if (!d->indexWithoutImporting && futureExtension.isEmpty()) {
emit showError(tr("Could not save file due to unhandled data type: ") + medData->identifier(), 5000);
continue;
}
imageFileName = imageFileName + futureExtension;
// 2.3) c) Add the image to a map for writing them all in medInria's database in a posterior step
// First check if patient/study/series/image path already exists in the database
// Should we emit a message otherwise ??? TO
if ( !checkIfExists ( medData, fileInfo.fileName() ) )
{
imagesGroupedByVolume[imageFileName] << fileInfo.filePath();
imagesGroupedByPatient[imageFileName] = patientID;
imagesGroupedBySeriesId[imageFileName] = currentSeriesId;
}
}
else
{
QString error = QString(tr("Could not read empty file: ") + fileInfo.completeBaseName());
qWarning() << __FUNCTION__ << error;
emit showError(error, 5000);
}
}
// some checks to see if the user cancelled or something failed
if ( d->isCancelled )
{
emit showError (tr ( "User cancelled import process" ), 5000 );
emit dataImported(medDataIndex(), d->uuid);
emit cancelled ( this );
return;
}
// from now on the process cannot be cancelled
emit disableCancel ( this );
// 3) Re-read selected files and re-populate them with missing metadata
// then write them to medInria db and populate db tables
QMap<QString, QStringList>::const_iterator it = imagesGroupedByVolume.begin();
QMap<QString, QString>::const_iterator itPat = imagesGroupedByPatient.begin();
QMap<QString, QString>::const_iterator itSer = imagesGroupedBySeriesId.begin();
// 3.1) first check is after the filtering we have something to import
// maybe we had problems with all the files, or they were already in the database
if ( it == imagesGroupedByVolume.end() )
{
// TODO we know if it's either one or the other error, we can make this error better...
emit showError (tr ( "No compatible image found or all of them had been already imported." ), 5000 );
emit dataImported(medDataIndex(), d->uuid);
emit failure ( this );
return;
}
else
qDebug() << "Chosen directory contains " << imagesGroupedByVolume.size() << " files";
int imagesCount = imagesGroupedByVolume.count(); // used only to calculate progress
int currentImageIndex = 0; // used only to calculate progress
medDataIndex index; //stores the last volume's index to be emitted on success
// final loop: re-read, re-populate and write to db
for ( ; it != imagesGroupedByVolume.end(); it++ )
{
emit progress ( this, ( ( qreal ) currentImageIndex/ ( qreal ) imagesCount ) * 50.0 + 50.0 ); // 50? I do not think that reading all the headers is half the job...
currentImageIndex++;
QString aggregatedFileName = it.key(); // note that this file might be aggregating more than one input files
QStringList filesPaths = it.value(); // input files being aggregated, might be only one or many
patientID = itPat.value();
QString seriesID = itSer.value();
//qDebug() << currentImageIndex << ": " << aggregatedFileName << "with " << filesPaths.size() << " files";
dtkSmartPointer<medAbstractData> imagemedData;
QFileInfo imagefileInfo ( filesPaths[0] );
// 3.2) Try to read the whole image, not just the header
bool readOnlyImageInformation = false;
imagemedData = tryReadImages ( filesPaths, readOnlyImageInformation );
if ( imagemedData )
{
// 3.3) a) re-populate missing metadata
// if there is no SeriesDescription, we use the tag Series Instance UID (specific and required)
populateMissingMetadata ( imagemedData, medMetaDataKeys::SeriesDicomID.getFirstValue(imagemedData));
imagemedData->setMetaData ( medMetaDataKeys::PatientID.key(), QStringList() << patientID );
imagemedData->setMetaData ( medMetaDataKeys::SeriesID.key(), QStringList() << seriesID );
// 3.3) b) now we are able to add some more metadata
addAdditionalMetaData ( imagemedData, aggregatedFileName, filesPaths );
}
else
{
qWarning() << "Could not repopulate data!";
emit showError (tr ( "Could not read data: " ) + filesPaths[0], 5000 );
emit dataImported(medDataIndex(), d->uuid);
emit failure(this);
return;
}
if ( !d->indexWithoutImporting )
{
// create location to store file
QFileInfo fileInfo ( medStorage::dataLocation() + aggregatedFileName );
if ( !fileInfo.dir().exists() && !medStorage::mkpath ( fileInfo.dir().path() ) )
{
qDebug() << "Cannot create directory: " << fileInfo.dir().path();
continue;
}
// now writing file
bool writeSuccess = tryWriteImage ( fileInfo.filePath(), imagemedData );
if ( !writeSuccess )
{
emit showError (tr ( "Could not save data file: " ) + filesPaths[0], 5000 );
continue;
}
}
atLeastOneImportSucceeded = true;
// and finally we populate the database
QFileInfo aggregatedFileNameFileInfo ( aggregatedFileName );
QString pathToStoreThumbnails = aggregatedFileNameFileInfo.dir().path() + "/" + aggregatedFileNameFileInfo.completeBaseName() + "/";
index = this->populateDatabaseAndGenerateThumbnails ( imagemedData, pathToStoreThumbnails );
if(!d->uuid.isNull())
{
emit dataImported(index, d->uuid);
}
else
{
emit dataImported(index);
}
itPat++;
itSer++;
} // end of the final loop
if ( ! atLeastOneImportSucceeded) {
emit progress ( this,100 );
emit dataImported(medDataIndex(), d->uuid);
emit failure(this);
return;
}
d->index = index;
emit progress ( this,100 );
emit success ( this );
}
void medAbstractDatabaseImporter::importData()
{
QMutexLocker locker ( &d->mutex );
if ( !d->data )
{
emit failure ( this );
emit dataImported(medDataIndex(), d->uuid);
return;
}
populateMissingMetadata(d->data, "EmptySeries");
if ( !d->data->hasMetaData ( medMetaDataKeys::FilePaths.key() ) )
d->data->addMetaData ( medMetaDataKeys::FilePaths.key(), QStringList() << "data created internally" );
// Information about the app and version of the application
QString attachedInfoApp = QString("generated with " +
QString(PROJECT_NAME) +
" " +
QString(MEDINRIA_VERSION));
d->data->setMetaData(medMetaDataKeys::Description.key(), attachedInfoApp);
QString size ="";
if ( medAbstractImageData *imagedata = dynamic_cast<medAbstractImageData*> ( d->data.data()) )
size = QString::number ( imagedata->zDimension() );
d->data->setMetaData ( medMetaDataKeys::Size.key(), size );
QString patientName = medMetaDataKeys::PatientName.getFirstValue(d->data).simplified();
QString birthDate = medMetaDataKeys::BirthDate.getFirstValue(d->data);
QString seriesId = medMetaDataKeys::SeriesID.getFirstValue(d->data);
QString patientId = getPatientID(patientName, birthDate);
d->data->setMetaData ( medMetaDataKeys::PatientID.key(), QStringList() << patientId );
bool writeSuccess = true;
QString thumb_dir;
if ( !d->indexWithoutImporting )
{
QString subDirName = "/" + patientId;
QString imageFileNameBase = subDirName + "/" + seriesId;
QDir dir ( medStorage::dataLocation() + subDirName );
if ( !dir.exists() )
{
if ( !medStorage::mkpath ( medStorage::dataLocation() + subDirName ) )
{
qWarning() << "Unable to create directory for images";
emit failure ( this );
emit dataImported(medDataIndex(), d->uuid);
return ;
}
}
QString extension = determineFutureImageExtensionByDataType ( d->data );
QString imageFileName = imageFileNameBase + extension;
// writing file
writeSuccess = tryWriteImage ( medStorage::dataLocation()+imageFileName, d->data );
if ( !writeSuccess )
{
// when creating empty patients or studies, we need to continue to populate the database
qWarning() << "Unable to write image " + imageFileName;
qWarning() << "Either there is nothing to write or a problem occured when writing.";
}
else
{
d->data->setMetaData ( "FileName", imageFileName );
}
QFileInfo seriesInfo ( imageFileName );
thumb_dir = seriesInfo.dir().path() + "/" + seriesInfo.completeBaseName() + "/";
}
// Now, populate the database
medDataIndex index = this->populateDatabaseAndGenerateThumbnails ( d->data, thumb_dir );
emit progress(this, 100);
emit success(this);
if (d->uuid == "")
emit dataImported(index);
else
emit dataImported(index,d->uuid);
}
int PET::write( int options ) {
int sl, fr;
ofstream outfile;
char outbuff[100];
string patid( getPatientID() );
string outname( getPatientID() );
string patname( _prefix );
cout << "PET::write(): " << _numFrame << " frames of " << _numSlice << " slices." << endl;
if ( options & OPT_VOLU ) {
// Using one output file.
// string outname( _prefix + "." );
// string outname( + "." );
outname.append( "." );
outname.append( (options & OPT_ANAL) ? "img" : "raw");
outfile.open( outname.c_str(), ios::binary );
if ( !outfile.is_open() )
error( "Cannot open output file", outname );
// Write the Analyze header if required.
if ( options & OPT_ANAL )
analyze->writePET( this, outname, options, 0 );
}
// Run through each frame and write to disk.
std::transform(patname.begin(), patname.end(), patname.begin(),
(int(*)(int)) toupper);
for ( fr = 0; fr < _numFrame; fr++ ) {
if ( !( options & OPT_VOLU )) {
// New output file per frame if not writing to one file.
// Changed this 4/2/07 ahc. Can't remember why I was using patid
// rather than abbreviated name for Analyze files.
// sprintf( outbuff, "%s_%02d.%s",
// patid.c_str(), fr, (options & OPT_ANAL) ? "img" : "raw" );
sprintf( outbuff, "%s_%02d.%s",
patname.c_str(), fr, (options & OPT_ANAL) ? "img" : "raw" );
outfile.open( outbuff, ios::binary );
if ( !outfile.is_open() )
error( "Cannot open output file", outbuff );
// Write the Analyze header if required.
if ( options & OPT_ANAL )
analyze->writePET( this, outbuff, options, fr );
}
// Call virtual fn. for specific PET slices.
for ( int sl = 0; sl < _numSlice; sl++ ) {
writeSliceData( fr, sl, outfile, options );
}
if ( !( options & OPT_VOLU ))
outfile.close();
cout << ((fr + 1) % 10) << flush;
}
cout << endl;
if ( outfile.is_open() )
outfile.close();
return 0;
}
