Fixed changes accidentially overwritten during adaption to latest DCMTK.

Libs/DICOM/Core/ctkDICOMIndexer.cpp

@@ -1,484 +1,486 @@
-/*=========================================================================
-
-  Library:   CTK
-
-  Copyright (c) Kitware Inc.
-
-  Licensed under the Apache License, Version 2.0 (the "License");
-  you may not use this file except in compliance with the License.
-  You may obtain a copy of the License at
-
-      http://www.apache.org/licenses/LICENSE-2.0.txt
-
-  Unless required by applicable law or agreed to in writing, software
-  distributed under the License is distributed on an "AS IS" BASIS,
-  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-  See the License for the specific language governing permissions and
-  limitations under the License.
-
-=========================================================================*/
-
-// Qt includes
-#include <QSqlQuery>
-#include <QSqlRecord>
-#include <QVariant>
-#include <QDate>
-#include <QStringList>
-#include <QSet>
-#include <QFile>
-#include <QDirIterator>
-#include <QFileInfo>
-#include <QDebug>
-#include <QPixmap>
-
-
-// ctkDICOM includes
-#include "ctkDICOMIndexer.h"
-#include "ctkDICOMAbstractThumbnailGenerator.h"
-
-// DCMTK includes
-#ifndef WIN32
-  #define HAVE_CONFIG_H
-#endif
-#include <dcmtk/dcmdata/dcfilefo.h>
-#include <dcmtk/dcmdata/dcfilefo.h>
-#include <dcmtk/dcmdata/dcdeftag.h>
-#include <dcmtk/dcmdata/dcdatset.h>
-#include <dcmtk/ofstd/ofcond.h>
-#include <dcmtk/ofstd/ofstring.h>
-#include <dcmtk/ofstd/ofstd.h>        /* for class OFStandard */
-#include <dcmtk/dcmdata/dcddirif.h>   /* for class DicomDirInterface */
-#include "dcmimage.h"
-
-#define MITK_ERROR std::cout
-#define MITK_INFO std::cout
-
-//------------------------------------------------------------------------------
-class ctkDICOMIndexerPrivate
-{
-public:
-  ctkDICOMIndexerPrivate();
-  ~ctkDICOMIndexerPrivate();
-
-  ctkDICOMAbstractThumbnailGenerator* thumbnailGenerator;
-};
-
-//------------------------------------------------------------------------------
-// ctkDICOMIndexerPrivate methods
-
-//------------------------------------------------------------------------------
-ctkDICOMIndexerPrivate::ctkDICOMIndexerPrivate()
-{
-    this->thumbnailGenerator = NULL;
-}
-
-//------------------------------------------------------------------------------
-ctkDICOMIndexerPrivate::~ctkDICOMIndexerPrivate()
-{
-}
-
-//------------------------------------------------------------------------------
-
-//------------------------------------------------------------------------------
-// ctkDICOMIndexer methods
-
-//------------------------------------------------------------------------------
-ctkDICOMIndexer::ctkDICOMIndexer():d_ptr(new ctkDICOMIndexerPrivate)
-{
-}
-
-//------------------------------------------------------------------------------
-ctkDICOMIndexer::~ctkDICOMIndexer()
-{
-}
-
-//------------------------------------------------------------------------------
-void ctkDICOMIndexer::addDirectory(const QString& directoryName,
-                                   bool createHierarchy,
-                                   bool createThumbnails)
-{
-  Q_D(ctkDICOMIndexer);
-
-  QSqlDatabase db = database.database();
-  const std::string src_directory(directoryName.toStdString());
-
-  OFList<OFString> originalDcmtkFileNames;
-  OFList<OFString> dcmtkFileNames;
-  OFStandard::searchDirectoryRecursively( QDir::toNativeSeparators(src_directory.c_str()).toAscii().data(), originalDcmtkFileNames, "", "");
-
-  // hack to reverse list of filenames (not neccessary when image loading works correctly)
-  for ( OFListIterator(OFString) iter = originalDcmtkFileNames.begin(); iter != originalDcmtkFileNames.end(); ++iter )
-  {
-    dcmtkFileNames.push_front( *iter );
-  }
-
-  DcmFileFormat fileformat;
-  DcmDataset *dataset;
-
-  OFListIterator(OFString) iter = dcmtkFileNames.begin();
-  OFListIterator(OFString) last = dcmtkFileNames.end();
-
-  if(iter == last) return;
-
-  QSqlQuery query(database.database());
-
-
-  /// these are for optimizing the import of image sequences
-  /// since most information are identical for all slices
-  OFString lastPatientID = "";
-  OFString lastPatientsName = "";
-  OFString lastPatientsBirthDate = "";
-  OFString lastStudyInstanceUID = "";
-  OFString lastSeriesInstanceUID = "";
-  int lastPatientUID = -1;
-
-  /* iterate over all input filenames */
-  while (iter != last)
-  {
-    std::string filename((*iter).c_str());
-    QString qfilename(filename.c_str());
-    /// first we check if the file is already in the database
-    QSqlQuery fileExists(database.database());
-    fileExists.prepare("SELECT InsertTimestamp FROM Images WHERE Filename == ?");
-    fileExists.bindValue(0,qfilename);
-    fileExists.exec();
-    if (
-      fileExists.next() &&
-      QFileInfo(qfilename).lastModified() < QDateTime::fromString(fileExists.value(0).toString(),Qt::ISODate)
-      )
-      {
-      MITK_INFO << "File " << filename << " already added.";
-      continue;
-      }
-
-    MITK_INFO << filename << "\n";
-    OFCondition status = fileformat.loadFile(filename.c_str());
-    ++iter;
-
-    dataset = fileformat.getDataset();
-
-    if (!status.good())
-    {
-      MITK_ERROR << "Could not load " << filename << "\nDCMTK says: " << status.text();
-      continue;
-    }
-
-    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, sopInstanceUID ;
-
-    Sint32 seriesNumber = 0, acquisitionNumber = 0, echoNumber = 0, temporalPosition = 0;
-
-    //The patient UID is a unique number within the database, generated by the sqlite autoincrement
-    int patientUID = -1;
-
-    //If the following fields can not be evaluated, cancel evaluation of the DICOM file
-    if (!dataset->findAndGetOFString(DCM_PatientName, patientsName).good())
-    {
-      MITK_ERROR << "Could not read DCM_PatientName from " << filename;
-      continue;
-    }
-
-    if (!dataset->findAndGetOFString(DCM_StudyInstanceUID, studyInstanceUID).good())
-    {
-      MITK_ERROR << "Could not read DCM_StudyInstanceUID from " << filename;
-      continue;
-    }
-
-    if (!dataset->findAndGetOFString(DCM_SeriesInstanceUID, seriesInstanceUID).good())
-    {
-      MITK_ERROR << "Could not read DCM_SeriesInstanceUID from " << filename;
-      continue;
-    }
-
-    if (!dataset->findAndGetOFString(DCM_SOPInstanceUID, sopInstanceUID).good())
-    {
-      MITK_ERROR << "Could not read DCM_SOPInstanceUID from " << filename;
-      continue;
-    }
-
-    if (!dataset->findAndGetOFString(DCM_InstanceNumber, instanceNumber).good())
-    {
-      MITK_ERROR << "Could not read DCM_InstanceNumber from " << filename;
-      continue;
-    }
-
-
-    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);
-
-    MITK_INFO << "Adding new items to database:";
-    MITK_INFO << "studyID: " << studyID;
-    MITK_INFO << "seriesInstanceUID: " << seriesInstanceUID;
-    MITK_INFO << "Patient's Name: " << patientsName;
-
-    //-----------------------
-    //Add Patient to Database
-    //-----------------------
-
-    //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
-    bool patientExists = false;
-    if(lastPatientID.compare(patientID) || lastPatientsBirthDate.compare(patientsBirthDate) || lastPatientsName.compare(patientsName))
-    {
-      //Check if patient is already present in the db
-      QSqlQuery check_exists_query(database.database());
-      std::stringstream check_exists_query_string;
-      check_exists_query_string << "SELECT * FROM Patients WHERE PatientID = '" << patientID << "'";
-      check_exists_query.exec(check_exists_query_string.str().c_str());
-
-      /// we check only patients with the same PatientID
-      /// PatientID is not unique in DICOM, so we also compare Name and BirthDate
-      /// and assume this is sufficient
-      while (check_exists_query.next())
-      {
-        if (
-            check_exists_query.record().value("PatientsName").toString() == patientsName.c_str() &&
-            check_exists_query.record().value("PatientsBirthDate").toString() == patientsBirthDate.c_str()
-           )
-        {
-          /// found it
-          patientUID = check_exists_query.value(check_exists_query.record().indexOf("UID")).toInt();
-          break;
-        }
-      }
-
-      if(!patientExists)
-      {
-
-        std::stringstream query_string;
-
-        query_string << "INSERT INTO Patients VALUES( NULL,'"
-        << patientsName << "','"
-        << patientID << "','"
-        << patientsBirthDate << "','"
-        << patientsBirthTime << "','"
-        << patientsSex << "','"
-        << patientsAge << "','"
-        << patientComments << "')";
-
-        query.exec(query_string.str().c_str());
-
-        patientUID = query.lastInsertId().toInt();
-        MITK_INFO << "New patient inserted: " << patientUID << "\n";
-      }
-    }
-    else
-      {
-      patientUID = lastPatientUID;
-      }
-
-    /// keep this for the next image
-    lastPatientUID = patientUID;
-    lastPatientID = patientID;
-    lastPatientsBirthDate = patientsBirthDate;
-    lastPatientsName = patientsName;
-
-    //---------------------
-    //Add Study to Database
-    //---------------------
-
-    if(lastStudyInstanceUID.compare(studyInstanceUID))
-    {
-      QSqlQuery check_exists_query(database.database());
-      std::stringstream check_exists_query_string;
-      check_exists_query_string << "SELECT * FROM Studies WHERE StudyInstanceUID = '" << studyInstanceUID << "'";
-      check_exists_query.exec(check_exists_query_string.str().c_str());
-
-      if(!check_exists_query.next())
-      {
-
-        std::stringstream query_string;
-
-        query_string << "INSERT INTO Studies VALUES('"
-          << studyInstanceUID << "','"
-          << patientUID << "','"
-          << studyID << "','"
-          << QDate::fromString(studyDate.c_str(), "yyyyMMdd").toString("yyyy-MM-dd").toStdString() << "','"
-          << studyTime << "','"
-          << accessionNumber << "','"
-          << modalitiesInStudy << "','"
-          << institutionName << "','"
-          << referringPhysician << "','"
-          << performingPhysiciansName << "','"
-          << studyDescription << "')";
-
-        query.exec(query_string.str().c_str());
-      }
-    }
-
-    lastStudyInstanceUID = studyInstanceUID;
-
-    //----------------------
-    //Add Series to Database
-    //----------------------
-
-    if(lastSeriesInstanceUID.compare(seriesInstanceUID))
-    {
-
-      QSqlQuery check_exists_query(database.database());
-      std::stringstream check_exists_query_string;
-      check_exists_query_string << "SELECT * FROM Series WHERE SeriesInstanceUID = '" << seriesInstanceUID << "'";
-      check_exists_query.exec(check_exists_query_string.str().c_str());
-
-      if(!check_exists_query.next())
-      {
-
-        std::stringstream query_string;
-
-        query_string << "INSERT INTO Series VALUES('"
-          << seriesInstanceUID << "','"
-          << studyInstanceUID << "','"
-          << static_cast<int>(seriesNumber) << "','"
-          << QDate::fromString(seriesDate.c_str(), "yyyyMMdd").toString("yyyy-MM-dd").toStdString() << "','"
-          << seriesTime << "','"
-          << seriesDescription << "','"
-          << bodyPartExamined << "','"
-          << frameOfReferenceUID << "','"
-          << static_cast<int>(acquisitionNumber) << "','"
-          << contrastAgent << "','"
-          << scanningSequence << "','"
-          << static_cast<int>(echoNumber) << "','"
-          << static_cast<int>(temporalPosition) << "')";
-
-        query.exec(query_string.str().c_str());
-      }
-    }
-
-    lastSeriesInstanceUID = seriesInstanceUID;
-
-    QString studySeriesDirectory = QString(studyInstanceUID.c_str()) + "/" + seriesInstanceUID.c_str();
-
-    //----------------------------------
-    //Move file to destination directory
-    //----------------------------------
-
-    if (!destinationDirectoryName.isEmpty())
-      {
-      QFile currentFile( qfilename );
-      QDir destinationDir(destinationDirectoryName + "/dicom");
-      QString destFileName = sopInstanceUID.c_str();
-      if (createHierarchy)
-      {
-        destinationDir.mkpath(studySeriesDirectory);
-        destFileName.prepend( destinationDir.absolutePath() + "/"  + studySeriesDirectory + "/" );
-      }
-      currentFile.copy(destFileName);
-      qfilename = destFileName;
-    }
-
-    if (createThumbnails)
-    {
-        if(d->thumbnailGenerator){
-          QString thumbnailBaseDir =  database.databaseDirectory() + "/thumbs/";
-          QString thumbnailFilename = thumbnailBaseDir + "/" + database.pathForDataset(dataset) + ".png";
-          QFileInfo thumbnailInfo(thumbnailFilename);
-          if ( ! ( thumbnailInfo.exists() && thumbnailInfo.lastModified() < QFileInfo(qfilename).lastModified() ) )
-          {
-            QDir(thumbnailBaseDir).mkpath(studySeriesDirectory);
-            DicomImage dcmtkImage(qfilename.toAscii());
-            d->thumbnailGenerator->generateThumbnail(&dcmtkImage, thumbnailFilename);
-          }
-        }
-    }
-    //------------------------
-    //Add Filename to Database
-    //------------------------
-
-//    std::stringstream relativeFilePath;
-//    relativeFilePath << seriesInstanceUID.c_str() << "/" << currentFilePath.getFileName();
-
-    QSqlQuery check_exists_query(database.database());
-    std::stringstream check_exists_query_string;
-//    check_exists_query_string << "SELECT * FROM Images WHERE Filename = '" << relativeFilePath.str() << "'";
-    check_exists_query_string << "SELECT * FROM Images WHERE SOPInstanceUID = '" << sopInstanceUID << "'";
-    check_exists_query.exec(check_exists_query_string.str().c_str());
-
-    if(!check_exists_query.next())
-    {
-      std::stringstream query_string;
-
-      //To save absolute path: destDirectoryPath.str()
-      query_string << "INSERT INTO Images VALUES('"
-        << sopInstanceUID << "','" << qfilename.toStdString() << "','" << seriesInstanceUID << "','" << QDateTime::currentDateTime().toString(Qt::ISODate).toStdString() << "')";
-
-      query.exec(query_string.str().c_str());
-    }
-  }
-
-  // db.commit();
-  // db.close();
-
-}
-
-//------------------------------------------------------------------------------
-void ctkDICOMIndexer::refreshDatabase(ctkDICOMDatabase& database, const QString& directoryName)
-{
-  /// get all filenames from the database
-  QSqlQuery allFilesQuery(database.database());
-  QStringList databaseFileNames;
-  QStringList filesToRemove;
-  allFilesQuery.exec("SELECT Filename from Images;");
-
-  while (allFilesQuery.next())
-    {
-    QString fileName = allFilesQuery.value(0).toString();
-    databaseFileNames.append(fileName);
-    if (! QFile::exists(fileName) )
-      {
-      filesToRemove.append(fileName);
-      }
-    }
-
-  QSet<QString> filesytemFiles;
-  QDirIterator dirIt(directoryName);
-  while (dirIt.hasNext())
-    {
-    filesytemFiles.insert(dirIt.next());
-    }
-}
-
-//------------------------------------------------------------------------------
-void ctkDICOMIndexer::setThumbnailGenerator(ctkDICOMAbstractThumbnailGenerator *generator){
-    Q_D(ctkDICOMIndexer);
-    d->thumbnailGenerator = generator;
-}
-
-//------------------------------------------------------------------------------
-ctkDICOMAbstractThumbnailGenerator* ctkDICOMIndexer::thumbnailGenerator(){
-    Q_D(ctkDICOMIndexer);
-    return d->thumbnailGenerator;
-}
-
+/*=========================================================================
+
+  Library:   CTK
+
+  Copyright (c) Kitware Inc.
+
+  Licensed under the Apache License, Version 2.0 (the "License");
+  you may not use this file except in compliance with the License.
+  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0.txt
+
+  Unless required by applicable law or agreed to in writing, software
+  distributed under the License is distributed on an "AS IS" BASIS,
+  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+  See the License for the specific language governing permissions and
+  limitations under the License.
+
+=========================================================================*/
+
+// Qt includes
+#include <QSqlQuery>
+#include <QSqlRecord>
+#include <QVariant>
+#include <QDate>
+#include <QStringList>
+#include <QSet>
+#include <QFile>
+#include <QDirIterator>
+#include <QFileInfo>
+#include <QDebug>
+#include <QPixmap>
+
+
+// ctkDICOM includes
+#include "ctkDICOMIndexer.h"
+#include "ctkDICOMAbstractThumbnailGenerator.h"
+
+// DCMTK includes
+#ifndef WIN32
+  #define HAVE_CONFIG_H
+#endif
+#include <dcmtk/dcmdata/dcfilefo.h>
+#include <dcmtk/dcmdata/dcfilefo.h>
+#include <dcmtk/dcmdata/dcdeftag.h>
+#include <dcmtk/dcmdata/dcdatset.h>
+#include <dcmtk/ofstd/ofcond.h>
+#include <dcmtk/ofstd/ofstring.h>
+#include <dcmtk/ofstd/ofstd.h>        /* for class OFStandard */
+#include <dcmtk/dcmdata/dcddirif.h>   /* for class DicomDirInterface */
+#include "dcmimage.h"
+
+#define MITK_ERROR std::cout
+#define MITK_INFO std::cout
+
+//------------------------------------------------------------------------------
+class ctkDICOMIndexerPrivate
+{
+public:
+  ctkDICOMIndexerPrivate();
+  ~ctkDICOMIndexerPrivate();
+
+  ctkDICOMAbstractThumbnailGenerator* thumbnailGenerator;
+};
+
+//------------------------------------------------------------------------------
+// ctkDICOMIndexerPrivate methods
+
+//------------------------------------------------------------------------------
+ctkDICOMIndexerPrivate::ctkDICOMIndexerPrivate()
+{
+    this->thumbnailGenerator = NULL;
+}
+
+//------------------------------------------------------------------------------
+ctkDICOMIndexerPrivate::~ctkDICOMIndexerPrivate()
+{
+}
+
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
+// ctkDICOMIndexer methods
+
+//------------------------------------------------------------------------------
+ctkDICOMIndexer::ctkDICOMIndexer():d_ptr(new ctkDICOMIndexerPrivate)
+{
+}
+
+//------------------------------------------------------------------------------
+ctkDICOMIndexer::~ctkDICOMIndexer()
+{
+}
+
+//------------------------------------------------------------------------------
+void ctkDICOMIndexer::addDirectory(ctkDICOMDatabase& database, 
+                                   const QString& directoryName,
+                                   const QString& destinationDirectoryName,
+                                   bool createHierarchy,
+                                   bool createThumbnails)
+{
+  Q_D(ctkDICOMIndexer);
+
+  QSqlDatabase db = database.database();
+  const std::string src_directory(directoryName.toStdString());
+
+  OFList<OFString> originalDcmtkFileNames;
+  OFList<OFString> dcmtkFileNames;
+  OFStandard::searchDirectoryRecursively( QDir::toNativeSeparators(src_directory.c_str()).toAscii().data(), originalDcmtkFileNames, "", "");
+
+  // hack to reverse list of filenames (not neccessary when image loading works correctly)
+  for ( OFListIterator(OFString) iter = originalDcmtkFileNames.begin(); iter != originalDcmtkFileNames.end(); ++iter )
+  {
+    dcmtkFileNames.push_front( *iter );
+  }
+
+  DcmFileFormat fileformat;
+  DcmDataset *dataset;
+
+  OFListIterator(OFString) iter = dcmtkFileNames.begin();
+  OFListIterator(OFString) last = dcmtkFileNames.end();
+
+  if(iter == last) return;
+
+  QSqlQuery query(database.database());
+
+
+  /// these are for optimizing the import of image sequences
+  /// since most information are identical for all slices
+  OFString lastPatientID = "";
+  OFString lastPatientsName = "";
+  OFString lastPatientsBirthDate = "";
+  OFString lastStudyInstanceUID = "";
+  OFString lastSeriesInstanceUID = "";
+  int lastPatientUID = -1;
+
+  /* iterate over all input filenames */
+  while (iter != last)
+  {
+    std::string filename((*iter).c_str());
+    QString qfilename(filename.c_str());
+    /// first we check if the file is already in the database
+    QSqlQuery fileExists(database.database());
+    fileExists.prepare("SELECT InsertTimestamp FROM Images WHERE Filename == ?");
+    fileExists.bindValue(0,qfilename);
+    fileExists.exec();
+    if (
+      fileExists.next() &&
+      QFileInfo(qfilename).lastModified() < QDateTime::fromString(fileExists.value(0).toString(),Qt::ISODate)
+      )
+      {
+      MITK_INFO << "File " << filename << " already added.";
+      continue;
+      }
+
+    MITK_INFO << filename << "\n";
+    OFCondition status = fileformat.loadFile(filename.c_str());
+    ++iter;
+
+    dataset = fileformat.getDataset();
+
+    if (!status.good())
+    {
+      MITK_ERROR << "Could not load " << filename << "\nDCMTK says: " << status.text();
+      continue;
+    }
+
+    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, sopInstanceUID ;
+
+    Sint32 seriesNumber = 0, acquisitionNumber = 0, echoNumber = 0, temporalPosition = 0;
+
+    //The patient UID is a unique number within the database, generated by the sqlite autoincrement
+    int patientUID = -1;
+
+    //If the following fields can not be evaluated, cancel evaluation of the DICOM file
+    if (!dataset->findAndGetOFString(DCM_PatientName, patientsName).good())
+    {
+      MITK_ERROR << "Could not read DCM_PatientName from " << filename;
+      continue;
+    }
+
+    if (!dataset->findAndGetOFString(DCM_StudyInstanceUID, studyInstanceUID).good())
+    {
+      MITK_ERROR << "Could not read DCM_StudyInstanceUID from " << filename;
+      continue;
+    }
+
+    if (!dataset->findAndGetOFString(DCM_SeriesInstanceUID, seriesInstanceUID).good())
+    {
+      MITK_ERROR << "Could not read DCM_SeriesInstanceUID from " << filename;
+      continue;
+    }
+
+    if (!dataset->findAndGetOFString(DCM_SOPInstanceUID, sopInstanceUID).good())
+    {
+      MITK_ERROR << "Could not read DCM_SOPInstanceUID from " << filename;
+      continue;
+    }
+
+    if (!dataset->findAndGetOFString(DCM_InstanceNumber, instanceNumber).good())
+    {
+      MITK_ERROR << "Could not read DCM_InstanceNumber from " << filename;
+      continue;
+    }
+
+
+    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);
+
+    MITK_INFO << "Adding new items to database:";
+    MITK_INFO << "studyID: " << studyID;
+    MITK_INFO << "seriesInstanceUID: " << seriesInstanceUID;
+    MITK_INFO << "Patient's Name: " << patientsName;
+
+    //-----------------------
+    //Add Patient to Database
+    //-----------------------
+
+    //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
+    bool patientExists = false;
+    if(lastPatientID.compare(patientID) || lastPatientsBirthDate.compare(patientsBirthDate) || lastPatientsName.compare(patientsName))
+    {
+      //Check if patient is already present in the db
+      QSqlQuery check_exists_query(database.database());
+      std::stringstream check_exists_query_string;
+      check_exists_query_string << "SELECT * FROM Patients WHERE PatientID = '" << patientID << "'";
+      check_exists_query.exec(check_exists_query_string.str().c_str());
+
+      /// we check only patients with the same PatientID
+      /// PatientID is not unique in DICOM, so we also compare Name and BirthDate
+      /// and assume this is sufficient
+      while (check_exists_query.next())
+      {
+        if (
+            check_exists_query.record().value("PatientsName").toString() == patientsName.c_str() &&
+            check_exists_query.record().value("PatientsBirthDate").toString() == patientsBirthDate.c_str()
+           )
+        {
+          /// found it
+          patientUID = check_exists_query.value(check_exists_query.record().indexOf("UID")).toInt();
+          break;
+        }
+      }
+
+      if(!patientExists)
+      {
+
+        std::stringstream query_string;
+
+        query_string << "INSERT INTO Patients VALUES( NULL,'"
+        << patientsName << "','"
+        << patientID << "','"
+        << patientsBirthDate << "','"
+        << patientsBirthTime << "','"
+        << patientsSex << "','"
+        << patientsAge << "','"
+        << patientComments << "')";
+
+        query.exec(query_string.str().c_str());
+
+        patientUID = query.lastInsertId().toInt();
+        MITK_INFO << "New patient inserted: " << patientUID << "\n";
+      }
+    }
+    else
+      {
+      patientUID = lastPatientUID;
+      }
+
+    /// keep this for the next image
+    lastPatientUID = patientUID;
+    lastPatientID = patientID;
+    lastPatientsBirthDate = patientsBirthDate;
+    lastPatientsName = patientsName;
+
+    //---------------------
+    //Add Study to Database
+    //---------------------
+
+    if(lastStudyInstanceUID.compare(studyInstanceUID))
+    {
+      QSqlQuery check_exists_query(database.database());
+      std::stringstream check_exists_query_string;
+      check_exists_query_string << "SELECT * FROM Studies WHERE StudyInstanceUID = '" << studyInstanceUID << "'";
+      check_exists_query.exec(check_exists_query_string.str().c_str());
+
+      if(!check_exists_query.next())
+      {
+
+        std::stringstream query_string;
+
+        query_string << "INSERT INTO Studies VALUES('"
+          << studyInstanceUID << "','"
+          << patientUID << "','"
+          << studyID << "','"
+          << QDate::fromString(studyDate.c_str(), "yyyyMMdd").toString("yyyy-MM-dd").toStdString() << "','"
+          << studyTime << "','"
+          << accessionNumber << "','"
+          << modalitiesInStudy << "','"
+          << institutionName << "','"
+          << referringPhysician << "','"
+          << performingPhysiciansName << "','"
+          << studyDescription << "')";
+
+        query.exec(query_string.str().c_str());
+      }
+    }
+
+    lastStudyInstanceUID = studyInstanceUID;
+
+    //----------------------
+    //Add Series to Database
+    //----------------------
+
+    if(lastSeriesInstanceUID.compare(seriesInstanceUID))
+    {
+
+      QSqlQuery check_exists_query(database.database());
+      std::stringstream check_exists_query_string;
+      check_exists_query_string << "SELECT * FROM Series WHERE SeriesInstanceUID = '" << seriesInstanceUID << "'";
+      check_exists_query.exec(check_exists_query_string.str().c_str());
+
+      if(!check_exists_query.next())
+      {
+
+        std::stringstream query_string;
+
+        query_string << "INSERT INTO Series VALUES('"
+          << seriesInstanceUID << "','"
+          << studyInstanceUID << "','"
+          << static_cast<int>(seriesNumber) << "','"
+          << QDate::fromString(seriesDate.c_str(), "yyyyMMdd").toString("yyyy-MM-dd").toStdString() << "','"
+          << seriesTime << "','"
+          << seriesDescription << "','"
+          << bodyPartExamined << "','"
+          << frameOfReferenceUID << "','"
+          << static_cast<int>(acquisitionNumber) << "','"
+          << contrastAgent << "','"
+          << scanningSequence << "','"
+          << static_cast<int>(echoNumber) << "','"
+          << static_cast<int>(temporalPosition) << "')";
+
+        query.exec(query_string.str().c_str());
+      }
+    }
+
+    lastSeriesInstanceUID = seriesInstanceUID;
+
+    QString studySeriesDirectory = QString(studyInstanceUID.c_str()) + "/" + seriesInstanceUID.c_str();
+
+    //----------------------------------
+    //Move file to destination directory
+    //----------------------------------
+
+    if (!destinationDirectoryName.isEmpty())
+      {
+      QFile currentFile( qfilename );
+      QDir destinationDir(destinationDirectoryName + "/dicom");
+      QString destFileName = sopInstanceUID.c_str();
+      if (createHierarchy)
+      {
+        destinationDir.mkpath(studySeriesDirectory);
+        destFileName.prepend( destinationDir.absolutePath() + "/"  + studySeriesDirectory + "/" );
+      }
+      currentFile.copy(destFileName);
+      qfilename = destFileName;
+    }
+
+    if (createThumbnails)
+    {
+        if(d->thumbnailGenerator){
+          QString thumbnailBaseDir =  database.databaseDirectory() + "/thumbs/";
+          QString thumbnailFilename = thumbnailBaseDir + "/" + database.pathForDataset(dataset) + ".png";
+          QFileInfo thumbnailInfo(thumbnailFilename);
+          if ( ! ( thumbnailInfo.exists() && thumbnailInfo.lastModified() < QFileInfo(qfilename).lastModified() ) )
+          {
+            QDir(thumbnailBaseDir).mkpath(studySeriesDirectory);
+            DicomImage dcmtkImage(qfilename.toAscii());
+            d->thumbnailGenerator->generateThumbnail(&dcmtkImage, thumbnailFilename);
+          }
+        }
+    }
+    //------------------------
+    //Add Filename to Database
+    //------------------------
+
+//    std::stringstream relativeFilePath;
+//    relativeFilePath << seriesInstanceUID.c_str() << "/" << currentFilePath.getFileName();
+
+    QSqlQuery check_exists_query(database.database());
+    std::stringstream check_exists_query_string;
+//    check_exists_query_string << "SELECT * FROM Images WHERE Filename = '" << relativeFilePath.str() << "'";
+    check_exists_query_string << "SELECT * FROM Images WHERE SOPInstanceUID = '" << sopInstanceUID << "'";
+    check_exists_query.exec(check_exists_query_string.str().c_str());
+
+    if(!check_exists_query.next())
+    {
+      std::stringstream query_string;
+
+      //To save absolute path: destDirectoryPath.str()
+      query_string << "INSERT INTO Images VALUES('"
+        << sopInstanceUID << "','" << qfilename.toStdString() << "','" << seriesInstanceUID << "','" << QDateTime::currentDateTime().toString(Qt::ISODate).toStdString() << "')";
+
+      query.exec(query_string.str().c_str());
+    }
+  }
+
+  // db.commit();
+  // db.close();
+
+}
+
+//------------------------------------------------------------------------------
+void ctkDICOMIndexer::refreshDatabase(ctkDICOMDatabase& database, const QString& directoryName)
+{
+  /// get all filenames from the database
+  QSqlQuery allFilesQuery(database.database());
+  QStringList databaseFileNames;
+  QStringList filesToRemove;
+  allFilesQuery.exec("SELECT Filename from Images;");
+
+  while (allFilesQuery.next())
+    {
+    QString fileName = allFilesQuery.value(0).toString();
+    databaseFileNames.append(fileName);
+    if (! QFile::exists(fileName) )
+      {
+      filesToRemove.append(fileName);
+      }
+    }
+
+  QSet<QString> filesytemFiles;
+  QDirIterator dirIt(directoryName);
+  while (dirIt.hasNext())
+    {
+    filesytemFiles.insert(dirIt.next());
+    }
+}
+
+//------------------------------------------------------------------------------
+void ctkDICOMIndexer::setThumbnailGenerator(ctkDICOMAbstractThumbnailGenerator *generator){
+    Q_D(ctkDICOMIndexer);
+    d->thumbnailGenerator = generator;
+}
+
+//------------------------------------------------------------------------------
+ctkDICOMAbstractThumbnailGenerator* ctkDICOMIndexer::thumbnailGenerator(){
+    Q_D(ctkDICOMIndexer);
+    return d->thumbnailGenerator;
+}
+