CTK/Libs/DICOM/Core/ctkDICOMIndexer.cpp

/*=========================================================================

  Library:   CTK

  Copyright (c) Kitware Inc. 
  All rights reserved.
  Distributed under a BSD License. See LICENSE.txt file.

  This software is distributed "AS IS" WITHOUT ANY WARRANTY; without even
  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
  See the above copyright notice for more information.

=========================================================================*/

// Qt includes
#include <QSqlQuery>
#include <QSqlRecord>
#include <QVariant>
#include <QDate>
#include <QStringList>
#include <QSet>
#include <QFile>
#include <QDirIterator>
#include <QFileInfo>
#include <QDebug>

// ctkDICOM includes
#include "ctkDICOMIndexer.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 */

#define MITK_ERROR std::cout
#define MITK_INFO std::cout

//------------------------------------------------------------------------------
class ctkDICOMIndexerPrivate: public ctkPrivate<ctkDICOMIndexer>
{
public:
  ctkDICOMIndexerPrivate();
  ~ctkDICOMIndexerPrivate();

};

//------------------------------------------------------------------------------
// ctkDICOMIndexerPrivate methods

//------------------------------------------------------------------------------
ctkDICOMIndexerPrivate::ctkDICOMIndexerPrivate()
{
}

//------------------------------------------------------------------------------
ctkDICOMIndexerPrivate::~ctkDICOMIndexerPrivate()
{
}

//------------------------------------------------------------------------------
// ctkDICOMIndexer methods

//------------------------------------------------------------------------------
ctkDICOMIndexer::ctkDICOMIndexer()
{
}

//------------------------------------------------------------------------------
ctkDICOMIndexer::~ctkDICOMIndexer()
{
}

//------------------------------------------------------------------------------
void ctkDICOMIndexer::addDirectory(QSqlDatabase database, const QString& directoryName,const QString& destinationDirectoryName)
{
  QSqlDatabase db = database;
  const std::string src_directory(directoryName.toStdString());

  OFList<OFString> originalDcmtkFileNames;
  OFList<OFString> dcmtkFileNames;
  OFStandard::searchDirectoryRecursively(src_directory.c_str(), originalDcmtkFileNames, NULL, NULL);

  // 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;

  OFListIterator(OFString) iter = dcmtkFileNames.begin();
  OFListIterator(OFString) last = dcmtkFileNames.end();

  if(iter == last) return;

  QSqlQuery query(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);
    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;

    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;

    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 (!fileformat.getDataset()->findAndGetOFString(DCM_PatientsName, patientsName).good())
    {
      MITK_ERROR << "Could not read DCM_PatientsName from " << filename;
      continue;
    }

    if (!fileformat.getDataset()->findAndGetOFString(DCM_StudyInstanceUID, studyInstanceUID).good())
    {
      MITK_ERROR << "Could not read DCM_StudyInstanceUID from " << filename;
      continue;
    }

    if (!fileformat.getDataset()->findAndGetOFString(DCM_SeriesInstanceUID, seriesInstanceUID).good())
    {
      MITK_ERROR << "Could not read DCM_SeriesInstanceUID from " << filename;
      continue;
    }
    if (!fileformat.getDataset()->findAndGetOFString(DCM_InstanceNumber, instanceNumber).good())
    {
      MITK_ERROR << "Could not read DCM_InstanceNumber from " << filename;
      continue;
    }


    fileformat.getDataset()->findAndGetOFString(DCM_PatientID, patientID);
    fileformat.getDataset()->findAndGetOFString(DCM_PatientsBirthDate, patientsBirthDate);
    fileformat.getDataset()->findAndGetOFString(DCM_PatientsBirthTime, patientsBirthTime);
    fileformat.getDataset()->findAndGetOFString(DCM_PatientsSex, patientsSex);
    fileformat.getDataset()->findAndGetOFString(DCM_PatientsAge, patientsAge);
    fileformat.getDataset()->findAndGetOFString(DCM_PatientComments, patientComments);
    fileformat.getDataset()->findAndGetOFString(DCM_StudyID, studyID);
    fileformat.getDataset()->findAndGetOFString(DCM_StudyDate, studyDate);
    fileformat.getDataset()->findAndGetOFString(DCM_StudyTime, studyTime);
    fileformat.getDataset()->findAndGetOFString(DCM_AccessionNumber, accessionNumber);
    fileformat.getDataset()->findAndGetOFString(DCM_ModalitiesInStudy, modalitiesInStudy);
    fileformat.getDataset()->findAndGetOFString(DCM_InstitutionName, institutionName);
    fileformat.getDataset()->findAndGetOFString(DCM_PerformingPhysiciansName, performingPhysiciansName);
    fileformat.getDataset()->findAndGetOFString(DCM_ReferringPhysiciansName, referringPhysician);
    fileformat.getDataset()->findAndGetOFString(DCM_StudyDescription, studyDescription);

    fileformat.getDataset()->findAndGetOFString(DCM_SeriesDate, seriesDate);
    fileformat.getDataset()->findAndGetOFString(DCM_SeriesTime, seriesTime);
    fileformat.getDataset()->findAndGetOFString(DCM_SeriesDescription, seriesDescription);
    fileformat.getDataset()->findAndGetOFString(DCM_BodyPartExamined, bodyPartExamined);
    fileformat.getDataset()->findAndGetOFString(DCM_FrameOfReferenceUID, frameOfReferenceUID);
    fileformat.getDataset()->findAndGetOFString(DCM_ContrastBolusAgent, contrastAgent);
    fileformat.getDataset()->findAndGetOFString(DCM_ScanningSequence, scanningSequence);

    fileformat.getDataset()->findAndGetSint32(DCM_SeriesNumber, seriesNumber);
    fileformat.getDataset()->findAndGetSint32(DCM_AcquisitionNumber, acquisitionNumber);
    fileformat.getDataset()->findAndGetSint32(DCM_EchoNumbers, echoNumber);
    fileformat.getDataset()->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);
      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);
      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);
      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 << "','" << (int) seriesNumber << "','"
          << QDate::fromString(seriesDate.c_str(), "yyyyMMdd").toString("yyyy-MM-dd").toStdString() << "','"
          << seriesTime << "','" << seriesDescription << "','" << bodyPartExamined << "','"
          << frameOfReferenceUID << "','" << (int) acquisitionNumber << "','" << contrastAgent << "','"
          << scanningSequence << "','" << (int) echoNumber << "','" << (int) temporalPosition << "')";

        query.exec(query_string.str().c_str());
      }
    }

    lastSeriesInstanceUID = seriesInstanceUID;


    //----------------------------------
    //Move file to destination directory
    //----------------------------------

    if (!destinationDirectoryName.isEmpty())
      {
      QFile currentFile( qfilename );
      QDir destinationDir(destinationDirectoryName);

      QString uniqueDirName = QString(studyInstanceUID.c_str()) + "/" + seriesInstanceUID.c_str();
      qDebug() << "MKPath: " << uniqueDirName;
      destinationDir.mkpath(uniqueDirName);
      QString destFileName = destinationDir.absolutePath().append("/").append(instanceNumber.c_str());
      qDebug() << "Copy: " << qfilename << " -> " << destFileName;
      currentFile.copy(destFileName);
      //for testing only: copy file instead of moving
      //currentFile.copyTo(destDirectoryPath.str());
    }
    // */
    //------------------------
    //Add Filename to Database
    //------------------------

//    std::stringstream relativeFilePath;
//    relativeFilePath << seriesInstanceUID.c_str() << "/" << currentFilePath.getFileName();

    QSqlQuery check_exists_query(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 Filename = '" << filename << "'";
    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('"
        << /*relativeFilePath.str()*/ filename << "','" << seriesInstanceUID << "','" << QDateTime::currentDateTime().toString(Qt::ISODate).toStdString() << "')";

      query.exec(query_string.str().c_str());
    }
  }

  // db.commit();
  // db.close();

}

//------------------------------------------------------------------------------
void ctkDICOMIndexer::refreshDatabase(QSqlDatabase database, const QString& directoryName)
{
  /// get all filenames from the database
  QSqlQuery allFilesQuery(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());
    }
}