gdcmdicomdir.cxx

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/*=========================================================================
  
  Program:   gdcm
  Module:    $RCSfile: gdcmDicomDir.cxx,v $
  Language:  C++
  Date:      $Date: 2008-05-26 00:47:50 $
  Version:   $Revision: 1.13 $
  
  Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
  l'Image). All rights reserved. See Doc/License.txt or
  http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
  
     This software is distributed WITHOUT ANY WARRANTY; without even
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
     PURPOSE.  See the above copyright notices for more information.
  
=========================================================================*/

//-----------------------------------------------------------------------------
//  For full DICOMDIR description, see:
//  PS 3.3-2003, pages 731-750
//-----------------------------------------------------------------------------
#include "gdcmDicomDir.h"
#include "gdcmDicomDirObject.h"
#include "gdcmDicomDirStudy.h"
#include "gdcmDicomDirSerie.h"
#include "gdcmDicomDirVisit.h"
#include "gdcmDicomDirImage.h"
#include "gdcmDicomDirPatient.h"
#include "gdcmDicomDirMeta.h"
#include "gdcmDicomDirElement.h"
#include "gdcmDirList.h"
#include "gdcmUtil.h"
#include "gdcmDebug.h"
#include "gdcmGlobal.h"
#include "gdcmFile.h"
#include "gdcmSeqEntry.h"
#include "gdcmSQItem.h"
#include "gdcmValEntry.h"

#include <fstream>
#include <string>
#include <algorithm>
#include <sys/types.h>

#ifdef _MSC_VER
#   define getcwd _getcwd
#endif

#if defined(_MSC_VER) || defined(__BORLANDC__)
#   include <direct.h>
#else
#   include <unistd.h>
#endif

#if defined(__BORLANDC__)
   #include <mem.h> // for memset
#endif

// ----------------------------------------------------------------------------
//         Note for future developpers
// ----------------------------------------------------------------------------
//
//  Dicom PS 3.3 describes the relationship between Directory Records, as follow
//    (see also PS 4.3, 2004, page 50 for Entity-Relationship model)
//
//  Directory Record Type      Directory Record Types which may be included
//                                in the next lower-level directory Entity
//
// (Root directory Entity)     PATIENT, TOPIC, PRIVATE
//
// PATIENT                     STUDY, PRIVATE
//
// STUDY                       SERIES, VISIT, RESULTS, STUDY COMPONENT, PRIVATE
//
// SERIES                      IMAGE, OVERLAYS, MODALITY LUT, VOI LUT,
//                             CURVE, STORED PRINT, RT DOSE, RT STRUCTURE SET
//                             RT PLAN, RT TREAT RECORD, PRESENTATION, WAVEFORM,
//                             SR DOCUMENT, KEY OBJECT DOC, SPECTROSCOPY,
//                             RAW DATA, REGISTRATION, FIDUCIAL, PRIVATE,
//                             ENCAP DOC
// IMAGE
// OVERLAY
// MODALITY LUT
// VOI LUT
// CURVE
// STORED PRINT
// RT DOSE
// RT STRUCTURE SET
// RT PLAN
// RT TREAT RECORD
// PRESENTATION
// WAVEFORM
// SR DOCUMENT
// KEY OBJECT DOC
// SPECTROSCOPY
// RAW DATA
// REGISTRATION
// FIDUCIAL
// PRIVATE
// ENCAP DOC
// 
// ----------------------
// The current gdcm version only deals with :
//
// (Root directory Entity)     PATIENT
// PATIENT                     STUDY
// STUDY                       SERIES
// STUDY                       VISIT 
// SERIES                      IMAGE
// IMAGE                       /
//
// DicomDir::CreateDicomDir will have to be completed
// Treelike structure management will have to be upgraded
// ----------------------------------------------------------------------------
    
namespace gdcm 
{
//-----------------------------------------------------------------------------
// Constructor / Destructor
/**
 * \brief   Constructor : creates an empty DicomDir
 */
DicomDir::DicomDir()
         :Document( )
{
   Initialize();  // sets all private fields to NULL
   ParseDir = false;
   NewMeta();
}

#ifndef GDCM_LEGACY_REMOVE
/**
 * \brief Constructor Parses recursively the directory and creates the DicomDir
 *        or uses an already built DICOMDIR, depending on 'parseDir' value.
 * @param fileName  name 
 *                      - of the root directory (parseDir = true)
 *                      - of the DICOMDIR       (parseDir = false)
 * @param parseDir boolean
 *                      - true if user passed an entry point 
 *                        and wants to explore recursively the directories
 *                      - false if user passed an already built DICOMDIR file
 *                        and wants to use it 
 * @deprecated use : new DicomDir() + [ SetLoadMode(lm) + ] SetDirectoryName(name)
 *              or : new DicomDir() + SetFileName(name)
 */
DicomDir::DicomDir(std::string const &fileName, bool parseDir )
{
   // At this step, Document constructor is already executed,
   // whatever user passed (either a root directory or a DICOMDIR)
   // and whatever the value of parseDir was.
   // (nothing is cheked in Document constructor, to avoid overhead)

   ParseDir = parseDir;
   SetLoadMode (LD_ALL); // concerns only dicom files
   SetFileName( fileName );
   Load( );
}
#endif

/**
 * \brief  Canonical destructor 
 */
DicomDir::~DicomDir() 
{
   SetStartMethod(NULL,NULL,NULL);
   SetProgressMethod(NULL,NULL,NULL);
   SetEndMethod(NULL,NULL,NULL);

   ClearPatient();
   if ( MetaElems )
   {
      delete MetaElems;
   }
}

//-----------------------------------------------------------------------------
// Public

/**
 * \brief   Loader. use SetFileName(fn) 
 *                  or SetLoadMode(lm) + SetDirectoryName(dn)  before !  
 * @return false if file cannot be open or no swap info was found,
 *         or no tag was found.
 */
bool DicomDir::Load( ) 
{
   // We should clean out anything that already exists.
   Initialize();  // sets all private fields to NULL

   if (!ParseDir)
   {
      if ( ! this->Document::Load( ) )
         return false;
   }
   return DoTheLoadingJob( );   
}

#ifndef GDCM_LEGACY_REMOVE
/**
 * \brief   Loader. (DEPRECATED : kept not to break the API)
 * @param   fileName file to be open for parsing
 * @return false if file cannot be open or no swap info was found,
 *         or no tag was found.
 * @deprecated use SetFileName(n) + Load() instead
 */
bool DicomDir::Load(std::string const &fileName ) 
{
   // We should clean out anything that already exists.
   Initialize();  // sets all private fields to NULL

   SetFileName( fileName );
   if (!ParseDir)
   {
      if ( ! this->Document::Load( ) )
         return false;
   }
   return DoTheLoadingJob( );
}

/// DEPRECATED : use SetDirectoryName(dname) instead
/**
 * \brief   Loader. (DEPRECATED : kept not to break the API)
 * @param   paseDir Parse Dir
 * @deprecated use SetDirectoryName(dname) instead
 */
void DicomDir::SetParseDir(bool parseDir)
{
   ParseDir = parseDir;
}
#endif

/**
 * \brief   Does the Loading Job (internal use only)
 * @return false if file cannot be open or no swap info was found,
 *         or no tag was found.
 */
bool DicomDir::DoTheLoadingJob( ) 
{
   // We should clean out anything that already exists.
   Initialize();  // sets all private fields to NULL

   if (!ParseDir)
   {
   // Only if user passed a DICOMDIR
   // ------------------------------
      Fp = 0;
      if ( !OpenFile() )
      {
         return false;
      }
      if (!Document::Load() )
      {
         return false;
      }

      if ( GetFirstEntry() == 0 ) // when user passed a Directory to parse
      {
         gdcmWarningMacro( "Entry HT empty for file: "<< GetFileName());
         return false;
      }
      // Directory record sequence
      DocEntry *e = GetDocEntry(0x0004, 0x1220);
      if ( !e )
      {
         gdcmWarningMacro( "NO 'Directory record sequence' (0x0004,0x1220)"
                          << " in file " << GetFileName());
         return false;
      }
      else
         CreateDicomDir();
   }
   else
   {
   // Only if user passed a root directory
   // ------------------------------------
      if ( GetFileName() == "." )
      {
         // user passed '.' as Name
         // we get current directory name
         char buf[2048];
         const char *cwd = getcwd(buf, 2048);
         if( cwd )
         {
            SetFileName( buf ); // will be converted into a string
         }
         else
         {
            gdcmErrorMacro( "Path was too long to fit on 2048 bytes" );
         }
      }
      NewMeta();
      gdcmDebugMacro( "Parse directory and create the DicomDir : " 
                         << GetFileName() );
      ParseDirectory();
   }
   return true;
}

/**
 * \brief  This predicate, based on hopefully reasonable heuristics,
 *         decides whether or not the current document was properly parsed
 *         and contains the mandatory information for being considered as
 *         a well formed and usable DicomDir.
 * @return true when Document is the one of a reasonable DicomDir,
 *         false otherwise. 
 */
bool DicomDir::IsReadable()
{
   if ( Filetype == Unknown )
   {
      gdcmErrorMacro( "Wrong filetype for " << GetFileName());
      return false;
   }
   if ( !MetaElems )
   {
      gdcmWarningMacro( "Meta Elements missing in DicomDir");
      return false;
   }
   if ( Patients.size() <= 0 )
   {
      gdcmWarningMacro( "NO Patient in DicomDir");
      return false;
   }

   return true;
}

/**
 * \brief   adds *the* Meta to a partially created DICOMDIR
 */  
DicomDirMeta *DicomDir::NewMeta()
{
   if ( MetaElems )
      delete MetaElems;

   DocEntry *entry = GetFirstEntry();
   if ( entry )
   { 
      MetaElems = new DicomDirMeta(true); // true = empty

      entry = GetFirstEntry();
      while( entry )
      {
         if ( dynamic_cast<SeqEntry *>(entry) )
            break;

         RemoveEntryNoDestroy(entry);
         MetaElems->AddEntry(entry);

         entry = GetFirstEntry();
      }
   }
   else  // after root directory parsing
   {
      MetaElems = new DicomDirMeta(false); // false = not empty
   }
   MetaElems->SetSQItemNumber(0); // To avoid further missprinting
   return MetaElems;  
}

/**
 * \brief   adds a new Patient (with the basic elements) to a partially created
 *          DICOMDIR
 */
DicomDirPatient *DicomDir::NewPatient()
{
   DicomDirPatient *p = new DicomDirPatient();
   AddPatientToEnd( p );
   return p;
}

/**
 * \brief   Remove all Patients
 */
void DicomDir::ClearPatient()
{
   for(ListDicomDirPatient::iterator cc = Patients.begin();
                                     cc!= Patients.end();
                                   ++cc)
   {
      delete *cc;
   }
   Patients.clear();
}

/**
 * \brief   Get the first entry while visiting the DicomDirPatients
 * \return  The first DicomDirPatient if found, otherwhise NULL
 */ 
DicomDirPatient *DicomDir::GetFirstPatient()
{
   ItPatient = Patients.begin();
   if ( ItPatient != Patients.end() )
      return *ItPatient;
   return NULL;
}

/**
 * \brief   Get the next entry while visiting the DicomDirPatients
 * \note : meaningfull only if GetFirstEntry already called
 * \return  The next DicomDirPatient if found, otherwhise NULL
 */
DicomDirPatient *DicomDir::GetNextPatient()
{
   gdcmAssertMacro (ItPatient != Patients.end());

   ++ItPatient;
   if ( ItPatient != Patients.end() )
      return *ItPatient;