TableNode* addNewDeclTable(char isparam, TableNode* symbol, Node* ast,Table* table) {
TableNode* temp;
listID* aux;
checkIfExists(ast->id->id,table);
temp = (TableNode*) calloc(sizeof(TableNode),1);
assert(temp != NULL);
symbol->next = temp;
symbol = temp;
symbol->n_type = TABLE_DECL;
symbol->type = ast->type;
symbol->id = ast->id;
symbol->isParam = isparam;
//If more than a id has been if() declared in the same line
if(symbol->id->next != NULL) {
aux = symbol->id->next;
while(aux != NULL) {
checkIfExists(aux->id,table);
temp = (TableNode*) calloc(sizeof(TableNode),1);
assert(temp!=NULL);
symbol->next = temp;
symbol = temp;
symbol->n_type = TABLE_DECL;
symbol->type = ast->type;
symbol->id = aux;
aux = aux->next;
}
}
return temp;
}
Table* createSymbols(Node* ast) {
Table* mainTable = NULL;
Table* currentTable = NULL;
Table* tempTable = NULL;
TableNode* temp = NULL;
TableNode * symbol = NULL;
TableNode* auxiliar = NULL;
Node* aux;
if(ast != NULL && ast->n_type == NODE_PROGRAM) {
if(mainTable == NULL){
//Create the table
mainTable = (Table*) calloc(sizeof(Table),1);
assert(mainTable != NULL);
//Create the TableNode and add it to the table
temp = (TableNode*) calloc(sizeof(TableNode),1);
assert(temp != NULL);
temp->n_type = TABLE_CLASS;
temp->id = ast->id;
mainTable->table = temp;
currentTable = mainTable;
symbol = temp;
}
else {
assert(mainTable != NULL);
}
ast = ast->next;
}
while(ast != NULL) {
if( ast->n_type == NODE_VARDECL) {
symbol = addNewDeclTable(0, symbol,ast, mainTable);
ast = ast->next;
}
else if( ast->n_type == NODE_METHODDECL) {
//Create a local table
tempTable = (Table*) calloc(sizeof(Table),1);
assert(tempTable!=NULL);
//Link it to the old table
currentTable->next = tempTable;
currentTable = tempTable;
checkIfExists(ast->id->id,mainTable);
//Add the MethodDecl to the old table (it must be the mainTable??)
temp = (TableNode*) calloc(sizeof(TableNode),1);
assert(temp!=NULL);
symbol->next = temp;
symbol = temp;
symbol->n_type = TABLE_METHOD;
symbol->type = ast->type;
symbol->id = ast->id;
auxiliar = temp;
//Create the first and the second symbol of the new table
temp = (TableNode*) calloc(sizeof(TableNode),1);
assert(temp!=NULL);
currentTable->table = temp;
symbol = temp;
symbol->n_type = TABLE_METHOD;
symbol->type = ast->type;
symbol->id = ast->id;
//add the params of the method to the method decl
if(ast->n1->n1 != NULL) {
aux = ast->n1->n1;
while(aux != NULL) {
symbol = addNewDeclTable(1,symbol,aux, currentTable);
aux = aux->next;
}
}
//Add the decls of the method to the method decl
if(ast->n2->n1!=NULL) {
aux = ast->n2->n1;
while(aux != NULL) {
symbol = addNewDeclTable(0,symbol,aux, currentTable);
aux = aux->next;
}
}
symbol = auxiliar;
ast = ast->next;
}
}
return mainTable;
}
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 );
}
