CTK/Libs/DICOM/Core/ctkDICOMIndexer.cpp

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

  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 <QSqlError>
#include <QVariant>
#include <QDate>
#include <QStringList>
#include <QSet>
#include <QFile>
#include <QDirIterator>
#include <QFileInfo>
#include <QDebug>
#include <QPixmap>

// ctkDICOM includes
#include "ctkLogger.h"
#include "ctkDICOMIndexer.h"
#include "ctkDICOMIndexer_p.h"
#include "ctkDICOMDatabase.h"

// DCMTK includes
#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 <dcmtk/dcmimgle/dcmimage.h>  /* for class DicomImage */
#include <dcmtk/dcmimage/diregist.h>  /* include support for color images */


//------------------------------------------------------------------------------
static ctkLogger logger("org.commontk.dicom.DICOMIndexer" );
//------------------------------------------------------------------------------


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

//------------------------------------------------------------------------------
ctkDICOMIndexerPrivate::ctkDICOMIndexerPrivate(ctkDICOMIndexer& o) : q_ptr(&o), Canceled(false)
{
  Q_Q(ctkDICOMIndexer);
}

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

//------------------------------------------------------------------------------

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

//------------------------------------------------------------------------------
ctkDICOMIndexer::ctkDICOMIndexer(QObject *parent):d_ptr(new ctkDICOMIndexerPrivate(*this))
{
  Q_UNUSED(parent);
}

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

//------------------------------------------------------------------------------
void ctkDICOMIndexer::addFile(ctkDICOMDatabase& database,
                                   const QString filePath,
                                   const QString& destinationDirectoryName)
{
  std::cout << filePath.toStdString();
  if (!destinationDirectoryName.isEmpty())
  {
    logger.warn("Ignoring destinationDirectoryName parameter, just taking it as indication we should copy!");
  }

  emit indexingFilePath(filePath);

  database.insert(filePath, !destinationDirectoryName.isEmpty(), true);
}

//------------------------------------------------------------------------------
void ctkDICOMIndexer::addDirectory(ctkDICOMDatabase& ctkDICOMDatabase,
                                   const QString& directoryName,
                                   const QString& destinationDirectoryName)
{
  Q_D(ctkDICOMIndexer);

  QStringList listOfFiles;
  QDir directory(directoryName);

  if(directory.exists("DICOMDIR"))
  {
    addDicomdir(ctkDICOMDatabase,directoryName,destinationDirectoryName);
  }
  else
  {
    QDirIterator it(directoryName,QDir::Files,QDirIterator::Subdirectories);
    while(it.hasNext())
    {
      listOfFiles << it.next();
    }
    emit foundFilesToIndex(listOfFiles.count());
    addListOfFiles(ctkDICOMDatabase,listOfFiles,destinationDirectoryName);
  }
}

//------------------------------------------------------------------------------
void ctkDICOMIndexer::addListOfFiles(ctkDICOMDatabase& ctkDICOMDatabase,
                                     const QStringList& listOfFiles,
                                     const QString& destinationDirectoryName)
{
  Q_D(ctkDICOMIndexer);
  d->Canceled = false;
  int CurrentFileIndex = 0;
  foreach(QString filePath, listOfFiles)
  {
    int percent = ( 100 * CurrentFileIndex ) / listOfFiles.size();
    emit this->progress(percent);
    this->addFile(ctkDICOMDatabase, filePath, destinationDirectoryName);
    CurrentFileIndex++;

    if( d->Canceled )
      {
      break;
      }
  }
  emit this->indexingComplete();
}

//------------------------------------------------------------------------------
void ctkDICOMIndexer::addDicomdir(ctkDICOMDatabase& ctkDICOMDatabase,
                 const QString& directoryName,
                 const QString& destinationDirectoryName
                 )
{
  Q_D(ctkDICOMIndexer);

  //Initialize dicomdir with directory path
  QString dcmFilePath = directoryName;
  dcmFilePath.append("/DICOMDIR");
  DcmDicomDir* dicomDir = new DcmDicomDir(dcmFilePath.toStdString().c_str());

  //Values to store records data at the moment only uid needed
  OFString patientsName, studyInstanceUID, seriesInstanceUID, sopInstanceUID, referencedFileName ;

  //Variables for progress operations
  QString instanceFilePath;
  QStringList listOfInstances;

  DcmDirectoryRecord* rootRecord = &(dicomDir->getRootRecord());
  DcmDirectoryRecord* patientRecord = NULL;
  DcmDirectoryRecord* studyRecord = NULL;
  DcmDirectoryRecord* seriesRecord = NULL;
  DcmDirectoryRecord* fileRecord = NULL;

  /*Iterate over all records in dicomdir and setup path to the dataset of the filerecord
  then insert. the filerecord into the database.
  If any UID is missing the record and all of it's subelements won't be added to the database*/
  if(rootRecord != NULL)
  {
    while (((patientRecord = rootRecord->nextSub(patientRecord)) != NULL)
      &&(patientRecord->findAndGetOFString(DCM_PatientName, patientsName).good()))
    {
      logger.debug( "Reading new Patients:" );
      logger.debug( "Patient's Name: " + QString(patientsName.c_str()) );

      while (((studyRecord = patientRecord->nextSub(studyRecord)) != NULL)
        && (studyRecord->findAndGetOFString(DCM_StudyInstanceUID, studyInstanceUID).good()))
      {
        logger.debug( "Reading new Studys:" );
        logger.debug( "Studies Name: " + QString(studyInstanceUID.c_str()) );

        while (((seriesRecord = studyRecord->nextSub(seriesRecord)) != NULL)
          &&(seriesRecord->findAndGetOFString(DCM_SeriesInstanceUID, seriesInstanceUID).good()))
        {
          logger.debug( "Reading new Series:" );
          logger.debug( "Series Instance Name: " + QString(seriesInstanceUID.c_str()) );

          while (((fileRecord = seriesRecord->nextSub(fileRecord)) != NULL)
            &&(fileRecord->findAndGetOFStringArray(DCM_ReferencedSOPInstanceUIDInFile, sopInstanceUID).good())
            &&(fileRecord->findAndGetOFStringArray(DCM_ReferencedFileID,referencedFileName).good()))
          {

            //Get the filepath of the instance and insert it into a list
            instanceFilePath = directoryName;
            instanceFilePath.append("/");
            instanceFilePath.append(QString( referencedFileName.c_str() ));
            instanceFilePath.replace("\\","/");
            listOfInstances << instanceFilePath;
          }
        }
      }
    }
    emit foundFilesToIndex(listOfInstances.count());
    addListOfFiles(ctkDICOMDatabase,listOfInstances,destinationDirectoryName);
  }
}

//------------------------------------------------------------------------------
void ctkDICOMIndexer::refreshDatabase(ctkDICOMDatabase& dicomDatabase, const QString& directoryName)
{
  Q_UNUSED(dicomDatabase);
  Q_UNUSED(directoryName);
  /*
   * Probably this should go to the database class as well
   * Or we have to extend the interface to make possible what we do here
   * without using SQL directly

  /// get all filenames from the database
  QSqlQuery allFilesQuery(dicomDatabase.database());
  QStringList databaseFileNames;
  QStringList filesToRemove;
  this->loggedExec(allFilesQuery, "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());
    }

  // TODO: it looks like this function was never finished...
  //
  // I guess the next step is to remove all filesToRemove from the database
  // and also to add filesystemFiles into the database tables
  */
  }

//----------------------------------------------------------------------------
void ctkDICOMIndexer::cancel()
{
  Q_D(ctkDICOMIndexer);
  d->Canceled = true;
}