Moved ctkDICOMDatabase::insert to private class, simplified store code

Libs/DICOM/Core/ctkDICOMDatabase.cpp

@@ -80,6 +80,11 @@ public:
   bool loggedExec(QSqlQuery& query);
   bool loggedExec(QSqlQuery& query, const QString& queryString);
 
+  // dataset must be set always
+  // filePath has to be set if this is an import of an actual file
+  void insert ( const ctkDICOMDataset& ctkDataset, const QString& filePath, bool storeFile = true, bool generateThumbnail = true);
+
+
   /// Name of the database file (i.e. for SQLITE the sqlite file)
   QString      DatabaseFileName;
   QString      LastError;
@@ -449,10 +454,47 @@ void ctkDICOMDatabase::insert( DcmDataset *dataset, bool storeFile, bool generat
   ctkDataset.InitializeFromDataset(dataset);
   this->insert(ctkDataset,storeFile,generateThumbnail);
 }
-
 void ctkDICOMDatabase::insert( const ctkDICOMDataset& ctkDataset, bool storeFile, bool generateThumbnail)
 {
   Q_D(ctkDICOMDatabase);
+  d->insert(ctkDataset, QString(), storeFile, generateThumbnail);
+}
+
+
+//------------------------------------------------------------------------------
+void ctkDICOMDatabase::insert ( const QString& filePath, bool storeFile, bool generateThumbnail, bool createHierarchy, const QString& destinationDirectoryName)
+{
+  Q_D(ctkDICOMDatabase);
+
+  /// 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);
+  }
+}
+
+//------------------------------------------------------------------------------
+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:
@@ -462,7 +504,7 @@ void ctkDICOMDatabase::insert( const ctkDICOMDataset& ctkDataset, bool storeFile
 
   QString sopInstanceUID ( ctkDataset.GetElementAsString(DCM_SOPInstanceUID) );
 
-  QSqlQuery fileExists ( d->Database );
+  QSqlQuery fileExists ( Database );
   fileExists.prepare("SELECT InsertTimestamp,Filename FROM Images WHERE SOPInstanceUID == ?");
   fileExists.bindValue(0,sopInstanceUID);
   fileExists.exec();
@@ -515,25 +557,37 @@ void ctkDICOMDatabase::insert( const ctkDICOMDataset& ctkDataset, bool storeFile
   // TODO: if we are called from insert(file) we
   // have to do something else
   // 
-  QString filename;
-  if ( storeFile && !this->isInMemory() )
+  QString filename = filePath;
+  if ( storeFile && !q->isInMemory() )
   {
-
-    QString destinationDirectoryName = databaseDirectory() + "/dicom/";
+    // QString studySeriesDirectory = studyInstanceUID + "/" + seriesInstanceUID;
+    QString destinationDirectoryName = q->databaseDirectory() + "/dicom/";
     QDir destinationDir(destinationDirectoryName);
-    QString studySeriesDirectory = studyInstanceUID + "/" + seriesInstanceUID;
-    destinationDir.mkpath(studySeriesDirectory);
+    filename = destinationDirectoryName + q->pathForDataset(ctkDataset);
+    destinationDir.mkpath(QFileInfo(q->pathForDataset(ctkDataset)).dir().canonicalPath());
 
-    filename = databaseDirectory() + "/dicom/" + pathForDataset(ctkDataset);
-    logger.debug ( "Saving file: " + filename );
-    if ( !ctkDataset.SaveToFile( filename) )
+    if(filePath.isEmpty())
     {
-      logger.error ( "Error saving file: " + filename );
-      return;
+      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(d->Database);
+  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;
@@ -541,7 +595,7 @@ void ctkDICOMDatabase::insert( const ctkDICOMDataset& ctkDataset, bool storeFile
   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( d->lastPatientID != patientID || d->lastPatientsBirthDate != patientsBirthDate || d->lastPatientsName != patientsName )
+    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.
@@ -552,7 +606,7 @@ void ctkDICOMDatabase::insert( const ctkDICOMDataset& ctkDataset, bool storeFile
       checkPatientExistsQuery.prepare ( "SELECT * FROM Patients WHERE PatientID = ? AND PatientsName = ?" );
       checkPatientExistsQuery.bindValue ( 0, patientID );
       checkPatientExistsQuery.bindValue ( 1, patientsName );
-      d->loggedExec(checkPatientExistsQuery);
+      loggedExec(checkPatientExistsQuery);
 
       if (checkPatientExistsQuery.next())
       {
@@ -562,7 +616,7 @@ void ctkDICOMDatabase::insert( const ctkDICOMDataset& ctkDataset, bool storeFile
       else
       {
         // Insert it
-        QSqlQuery insertPatientStatement ( d->Database );
+        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 );
@@ -572,29 +626,29 @@ void ctkDICOMDatabase::insert( const ctkDICOMDataset& ctkDataset, bool storeFile
         // 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 );
-        d->loggedExec(insertPatientStatement);
+        loggedExec(insertPatientStatement);
         dbPatientID = insertPatientStatement.lastInsertId().toInt();
         logger.debug ( "New patient inserted: " + QString().setNum ( dbPatientID ) );
 
       }
       /// keep this for the next image
-      d->lastPatientUID = dbPatientID;
-      d->lastPatientID = patientID;
-      d->lastPatientsBirthDate = patientsBirthDate;
-      d->lastPatientsName = patientsName;
+      lastPatientUID = dbPatientID;
+      lastPatientID = patientID;
+      lastPatientsBirthDate = patientsBirthDate;
+      lastPatientsName = patientsName;
     }
 
     // Patient is in now. Let's continue with the study
 
-    if ( studyInstanceUID != "" && d->lastStudyInstanceUID != studyInstanceUID ) 
+    if ( studyInstanceUID != "" && lastStudyInstanceUID != studyInstanceUID )
     {
-      QSqlQuery checkStudyExistsQuery (d->Database);
+      QSqlQuery checkStudyExistsQuery (Database);
       checkStudyExistsQuery.prepare ( "SELECT * FROM Studies WHERE StudyInstanceUID = ?" );
       checkStudyExistsQuery.bindValue ( 0, studyInstanceUID );
       checkStudyExistsQuery.exec();
       if(!checkStudyExistsQuery.next())
       {
-        QSqlQuery insertStudyStatement ( d->Database );
+        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 );
@@ -613,22 +667,22 @@ void ctkDICOMDatabase::insert( const ctkDICOMDataset& ctkDataset, bool storeFile
         }
         else
         {
-          d->lastStudyInstanceUID = studyInstanceUID;
+          lastStudyInstanceUID = studyInstanceUID;
         }
 
       }
     }
 
-    if ( seriesInstanceUID != "" && seriesInstanceUID != d->lastSeriesInstanceUID )
+    if ( seriesInstanceUID != "" && seriesInstanceUID != lastSeriesInstanceUID )
     {
-      QSqlQuery checkSeriesExistsQuery (d->Database);
+      QSqlQuery checkSeriesExistsQuery (Database);
       checkSeriesExistsQuery.prepare ( "SELECT * FROM Series WHERE SeriesInstanceUID = ?" );
       checkSeriesExistsQuery.bindValue ( 0, seriesInstanceUID );
       logger.warn ( "Statement: " + checkSeriesExistsQuery.lastQuery() );
-      d->loggedExec(checkSeriesExistsQuery);
+      loggedExec(checkSeriesExistsQuery);
       if(!checkSeriesExistsQuery.next())
       {
-        QSqlQuery insertSeriesStatement ( d->Database );
+        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 );
@@ -646,11 +700,11 @@ void ctkDICOMDatabase::insert( const ctkDICOMDataset& ctkDataset, bool storeFile
         if ( !insertSeriesStatement.exec() )
         {
           logger.error ( "Error executing statament: " + insertSeriesStatement.lastQuery() + " Error: " + insertSeriesStatement.lastError().text() );
-          d->lastSeriesInstanceUID = "";
+          lastSeriesInstanceUID = "";
         }
         else
         {
-          d->lastSeriesInstanceUID = seriesInstanceUID;
+          lastSeriesInstanceUID = seriesInstanceUID;
         }
 
       }
@@ -659,13 +713,13 @@ void ctkDICOMDatabase::insert( const ctkDICOMDataset& ctkDataset, bool storeFile
     //
     if ( !filename.isEmpty() )
     {
-      QSqlQuery checkImageExistsQuery (d->Database);
+      QSqlQuery checkImageExistsQuery (Database);
       checkImageExistsQuery.prepare ( "SELECT * FROM Images WHERE Filename = ?" );
       checkImageExistsQuery.bindValue ( 0, filename );
       checkImageExistsQuery.exec();
       if(!checkImageExistsQuery.next())
       {
-        QSqlQuery insertImageStatement ( d->Database );
+        QSqlQuery insertImageStatement ( Database );
         insertImageStatement.prepare ( "INSERT INTO Images ( 'SOPInstanceUID', 'Filename', 'SeriesInstanceUID', 'InsertTimestamp' ) VALUES ( ?, ?, ?, ? )" );
         insertImageStatement.bindValue ( 0, sopInstanceUID );
         insertImageStatement.bindValue ( 1, filename );
@@ -705,61 +759,31 @@ void ctkDICOMDatabase::insert( const ctkDICOMDataset& ctkDataset, bool storeFile
 */
 
     if(generateThumbnail){
-      if(d->thumbnailGenerator)
+      if(thumbnailGenerator)
       {
         QString studySeriesDirectory = studyInstanceUID + "/" + seriesInstanceUID;
         //Create thumbnail here
-        QString thumbnailPath = databaseDirectory() +
-          "/thumbs/" + this->pathForDataset(ctkDataset) + ".png";
+        QString thumbnailPath = q->databaseDirectory() +
+          "/thumbs/" + q->pathForDataset(ctkDataset) + ".png";
         //studyInstanceUID + "/" +
         //seriesInstanceUID + "/" +
         //sopInstanceUID + ".png";
         QFileInfo thumbnailInfo(thumbnailPath);
         if(!(thumbnailInfo.exists() && (thumbnailInfo.lastModified() > QFileInfo(filename).lastModified()))){
-          QDir(databaseDirectory() + "/thumbs/").mkpath(studySeriesDirectory);
+          QDir(q->databaseDirectory() + "/thumbs/").mkpath(studySeriesDirectory);
           DicomImage dcmImage(QDir::toNativeSeparators(filename).toAscii());
-          d->thumbnailGenerator->generateThumbnail(&dcmImage, thumbnailPath);
+          thumbnailGenerator->generateThumbnail(&dcmImage, thumbnailPath);
         }
       }
     }
 
-    if (isInMemory())
+    if (q->isInMemory())
     {
-      emit databaseChanged();
+      emit q->databaseChanged();
     }
   }
 }
 
-
-//------------------------------------------------------------------------------
-void ctkDICOMDatabase::insert ( const QString& filePath, bool storeFile, bool generateThumbnail, bool createHierarchy, const QString& 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() )
-  {
-    this->insert( ctkDataset, storeFile, generateThumbnail );
-  }
-  else
-  {
-    logger.warn(QString("Could not read DICOM file:") + filePath);
-  }
-}
-
 bool ctkDICOMDatabase::fileExistsAndUpToDate(const QString& filePath)
 {
   Q_D(ctkDICOMDatabase);