1 /*=========================================================================
4 Module: $RCSfile: gdcmDicomDir.cxx,v $
6 Date: $Date: 2005/02/07 14:48:34 $
7 Version: $Revision: 1.130 $
9 Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
10 l'Image). All rights reserved. See Doc/License.txt or
11 http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
13 This software is distributed WITHOUT ANY WARRANTY; without even
14 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 PURPOSE. See the above copyright notices for more information.
17 =========================================================================*/
19 //-----------------------------------------------------------------------------
20 // For full DICOMDIR description, see:
21 // PS 3.3-2003, pages 731-750
22 //-----------------------------------------------------------------------------
23 #include "gdcmDicomDir.h"
24 #include "gdcmDicomDirStudy.h"
25 #include "gdcmDicomDirSerie.h"
26 #include "gdcmDicomDirImage.h"
27 #include "gdcmDicomDirPatient.h"
28 #include "gdcmDicomDirMeta.h"
29 #include "gdcmDicomDirElement.h"
30 #include "gdcmDirList.h"
32 #include "gdcmDebug.h"
33 #include "gdcmGlobal.h"
35 #include "gdcmSeqEntry.h"
36 #include "gdcmSQItem.h"
37 #include "gdcmValEntry.h"
42 #include <sys/types.h>
45 # define getcwd _getcwd
48 #if defined(_MSC_VER) || defined(__BORLANDC__)
53 // ----------------------------------------------------------------------------
54 // Note for future developpers
55 // ----------------------------------------------------------------------------
57 // Dicom PS 3.3 describes the relationship between Directory Records, as follow
59 // Directory Record Type Directory Record Types which may be included
60 // in the next lower-èlevel directory Entity
62 // (Root directory Entity) PATIENT
66 // STUDY SERIES, VISIT, RESULTS, STUDY COMPONENT
68 // SERIES IMAGE, OVERLAYS, MODALITY LUT, VOI LUT,
69 // CURVE, STORED PRINT, RT DOSE, RT STRUCTURE SET
70 // RT PLAN, RT TREAT RECORD, PRESENTATION, WAVEFORM,
71 // SR DOCUMENT, KEY OBJECT DOC, SPECTROSCOPY,
72 // RAW DATA, REGISTRATION, FIDUCIAL
92 // ----------------------
93 // The current gdcm version only deals with :
95 // (Root directory Entity) PATIENT
101 // DicomDir::CreateDicomDir will have to be completed
102 // Treelike structure management will have to be upgraded
103 // ----------------------------------------------------------------------------
107 //-----------------------------------------------------------------------------
108 // Constructor / Destructor
110 * \brief Constructor : creates an empty DicomDir
115 Initialize(); // sets all private fields to NULL
120 * \brief Constructor Parses recursively the directory and creates the DicomDir
121 * or uses an already built DICOMDIR, depending on 'parseDir' value.
122 * @param fileName name
123 * - of the root directory (parseDir = true)
124 * - of the DICOMDIR (parseDir = false)
125 * @param parseDir boolean
126 * - true if user passed an entry point
127 * and wants to explore recursively the directories
128 * - false if user passed an already built DICOMDIR file
129 * and wants to use it
131 DicomDir::DicomDir(std::string const &fileName, bool parseDir ):
134 // At this step, Document constructor is already executed,
135 // whatever user passed (a root directory or a DICOMDIR)
136 // and whatever the value of parseDir was.
137 // (nothing is cheked in Document constructor, to avoid overhead)
139 Initialize(); // sets all private fields to NULL
141 // if user passed a root directory, sure we didn't get anything
143 if ( GetFirstEntry() == 0 ) // when user passed a Directory to parse
146 gdcmWarningMacro( "Entry HT empty for file: "<<fileName);
148 // Only if user passed a root directory
149 // ------------------------------------
150 if ( fileName == "." )
152 // user passed '.' as Name
153 // we get current directory name
155 getcwd(dummy, (size_t)1000);
156 SetFileName( dummy ); // will be converted into a string
159 if ( parseDir ) // user asked for a recursive parsing of a root directory
163 gdcmWarningMacro( "Parse directory and create the DicomDir");
168 /// \todo if parseDir == false, it should be tagged as an error
169 // NO ! user may just call ParseDirectory() *after* constructor
172 // Only if user passed a DICOMDIR
173 // ------------------------------
176 // Directory record sequence
177 DocEntry *e = GetDocEntry(0x0004, 0x1220);
180 gdcmWarningMacro( "NO 'Directory record sequence' (0x0004,0x1220)"
181 << " in file " << fileName);
182 /// \todo FIXME : what do we do when the parsed file IS NOT a
191 * \brief Canonical destructor
193 DicomDir::~DicomDir()
195 SetStartMethod(NULL);
196 SetProgressMethod(NULL);
206 //-----------------------------------------------------------------------------
209 * \brief This predicate, based on hopefully reasonable heuristics,
210 * decides whether or not the current document was properly parsed
211 * and contains the mandatory information for being considered as
212 * a well formed and usable DicomDir.
213 * @return true when Document is the one of a reasonable DicomDir,
216 bool DicomDir::IsReadable()
218 if( Filetype == Unknown)
220 gdcmWarningMacro( "Wrong filetype");
225 gdcmWarningMacro( "Meta Elements missing in DicomDir");
228 if( Patients.size() <= 0 )
230 gdcmWarningMacro( "NO Patient in DicomDir");
238 * \brief adds *the* Meta to a partially created DICOMDIR
240 DicomDirMeta *DicomDir::NewMeta()
245 DocEntry *entry = GetFirstEntry();
248 MetaElems = new DicomDirMeta(true);
250 entry = GetFirstEntry();
253 if( dynamic_cast<SeqEntry *>(entry) )
256 RemoveEntryNoDestroy(entry);
257 MetaElems->AddEntry(entry);
259 entry = GetFirstEntry();
262 else // after root directory parsing
264 MetaElems = new DicomDirMeta(false);
266 MetaElems->SetSQItemNumber(0); // To avoid further missprinting
271 * \brief adds a new Patient (with the basic elements) to a partially created
274 DicomDirPatient *DicomDir::NewPatient()
276 DicomDirPatient *p = new DicomDirPatient();
277 AddPatientToEnd( p );
282 * \brief Remove all Patients
284 void DicomDir::ClearPatient()
286 for(ListDicomDirPatient::iterator cc = Patients.begin();
296 * \brief Get the first entry while visiting the DicomDirPatients
297 * \return The first DicomDirPatient if found, otherwhise NULL
299 DicomDirPatient *DicomDir::GetFirstPatient()
301 ItPatient = Patients.begin();
302 if ( ItPatient != Patients.end() )
308 * \brief Get the next entry while visiting the DicomDirPatients
309 * \note : meaningfull only if GetFirstEntry already called
310 * \return The next DicomDirPatient if found, otherwhise NULL
312 DicomDirPatient *DicomDir::GetNextPatient()
314 gdcmAssertMacro (ItPatient != Patients.end());
317 if ( ItPatient != Patients.end() )
323 * \brief fills the whole structure, starting from a root Directory
325 void DicomDir::ParseDirectory()
327 CreateDicomDirChainedList( GetFileName() );
332 * \brief Set the start method to call when the parsing of the
334 * @param method Method to call
335 * @param arg Argument to pass to the method
336 * @param argDelete Argument
337 * \warning In python : the arg parameter isn't considered
339 void DicomDir::SetStartMethod( DicomDir::Method *method, void *arg,
340 DicomDir::Method *argDelete )
342 if( StartArg && StartMethodArgDelete )
344 StartMethodArgDelete( StartArg );
347 StartMethod = method;
349 StartMethodArgDelete = argDelete;
353 * \brief Set the progress method to call when the parsing of the
355 * @param method Method to call
356 * @param arg Argument to pass to the method
357 * @param argDelete Argument
358 * \warning In python : the arg parameter isn't considered
360 void DicomDir::SetProgressMethod( DicomDir::Method *method, void *arg,
361 DicomDir::Method *argDelete )
363 if( ProgressArg && ProgressMethodArgDelete )
365 ProgressMethodArgDelete( ProgressArg );
368 ProgressMethod = method;
370 ProgressMethodArgDelete = argDelete;
374 * \brief Set the end method to call when the parsing of the directory ends
375 * @param method Method to call
376 * @param arg Argument to pass to the method
377 * @param argDelete Argument
378 * \warning In python : the arg parameter isn't considered
380 void DicomDir::SetEndMethod( DicomDir::Method *method, void *arg,
381 DicomDir::Method *argDelete )
383 if( EndArg && EndMethodArgDelete )
385 EndMethodArgDelete( EndArg );
390 EndMethodArgDelete = argDelete;
394 * \brief Set the method to delete the argument
395 * The argument is destroyed when the method is changed or when the
397 * @param method Method to call to delete the argument
399 void DicomDir::SetStartMethodArgDelete( DicomDir::Method *method )
401 StartMethodArgDelete = method;
405 * \brief Set the method to delete the argument
406 * The argument is destroyed when the method is changed or when the
408 * @param method Method to call to delete the argument
410 void DicomDir::SetProgressMethodArgDelete( DicomDir::Method *method )
412 ProgressMethodArgDelete = method;
416 * \brief Set the method to delete the argument
417 * The argument is destroyed when the method is changed or when
418 * the class is destroyed
419 * @param method Method to call to delete the argument
421 void DicomDir::SetEndMethodArgDelete( DicomDir::Method *method )
423 EndMethodArgDelete = method;
427 * \brief writes on disc a DICOMDIR
428 * \ warning does NOT add the missing elements in the header :
429 * it's up to the user doing it !
430 * \todo : to be re-written using the DICOMDIR tree-like structure
431 * *not* the chained list
432 * (does NOT exist if the DICOMDIR is user-forged !)
433 * @param fileName file to be written to
434 * @return false only when fail to open
437 bool DicomDir::WriteDicomDir(std::string const &fileName)
440 uint16_t sq[4] = { 0x0004, 0x1220, 0xffff, 0xffff };
441 uint16_t sqt[4]= { 0xfffe, 0xe0dd, 0xffff, 0xffff };
443 std::ofstream *fp = new std::ofstream(fileName.c_str(),
444 std::ios::out | std::ios::binary);
447 gdcmWarningMacro("Failed to open(write) File: " << fileName.c_str());
451 char filePreamble[128];
452 memset(filePreamble, 0, 128);
453 fp->write(filePreamble, 128); //FIXME
454 binary_write( *fp, "DICM");
456 DicomDirMeta *ptrMeta = GetMeta();
457 ptrMeta->WriteContent(fp, ExplicitVR);
459 // force writing 0004|1220 [SQ ], that CANNOT exist within DicomDirMeta
462 binary_write(*fp, sq[i]);
465 for(ListDicomDirPatient::iterator cc = Patients.begin();
466 cc != Patients.end();
469 (*cc)->WriteContent( fp, ExplicitVR );
472 // force writing Sequence Delimitation Item
475 binary_write(*fp, sqt[i]); // fffe e0dd ffff ffff
484 //-----------------------------------------------------------------------------
487 * \brief create a Document-like chained list from a root Directory
488 * @param path entry point of the tree-like structure
490 void DicomDir::CreateDicomDirChainedList(std::string const &path)
493 DirList dirList(path,1); // gets recursively the file list
494 unsigned int count = 0;
498 DirListType fileList = dirList.GetFilenames();
500 for( DirListType::iterator it = fileList.begin();
501 it != fileList.end();
504 Progress = (float)(count+1)/(float)fileList.size();
505 CallProgressMethod();
511 header = new File( it->c_str() );
514 gdcmWarningMacro( "Failure in new gdcm::File " << it->c_str() );
518 if( header->IsReadable() )
520 // Add the file to the chained list:
521 list.push_back(header);
522 gdcmWarningMacro( "Readable " << it->c_str() );
530 // sorts Patient/Study/Serie/
531 std::sort(list.begin(), list.end(), DicomDir::HeaderLessThan );
533 std::string tmp = dirList.GetDirName();
534 //for each File of the chained list, add/update the Patient/Study/Serie/Image info
535 SetElements(tmp, list);
538 for(VectDocument::iterator itDoc=list.begin();
542 delete dynamic_cast<File *>(*itDoc);
547 * \brief CallStartMethod
549 void DicomDir::CallStartMethod()
555 StartMethod( StartArg );
560 * \brief CallProgressMethod
562 void DicomDir::CallProgressMethod()
566 ProgressMethod( ProgressArg );
571 * \brief CallEndMethod
573 void DicomDir::CallEndMethod()
582 //-----------------------------------------------------------------------------
585 * \brief Sets all fields to NULL
587 void DicomDir::Initialize()
590 ProgressMethod = NULL;
592 StartMethodArgDelete = NULL;
593 ProgressMethodArgDelete = NULL;
594 EndMethodArgDelete = NULL;
606 * \brief create a 'DicomDir' from a DICOMDIR Header
608 void DicomDir::CreateDicomDir()
610 // The SeqEntries of "Directory Record Sequence" are parsed.
611 // When a DicomDir tag ("PATIENT", "STUDY", "SERIE", "IMAGE") is found :
612 // 1 - we save the beginning iterator
613 // 2 - we continue to parse
614 // 3 - we find an other tag
615 // + we create the object for the precedent tag
618 // Directory record sequence
619 DocEntry *e = GetDocEntry(0x0004, 0x1220);
622 gdcmWarningMacro( "No Directory Record Sequence (0004,1220) found");
623 /// \todo FIXME: what to do when the parsed file IS NOT a DICOMDIR file ?
627 SeqEntry *s = dynamic_cast<SeqEntry *>(e);
630 gdcmWarningMacro( "Element (0004,1220) is not a Sequence ?!?");
640 SQItem *tmpSI=s->GetFirstSQItem();
643 d = tmpSI->GetDocEntry(0x0004, 0x1430); // Directory Record Type
644 if ( ValEntry* valEntry = dynamic_cast<ValEntry *>(d) )
646 v = valEntry->GetValue();
650 gdcmWarningMacro( "Not a ValEntry.");
654 if( v == "PATIENT " )
656 si = new DicomDirPatient(true);
657 if( !AddPatientToEnd( static_cast<DicomDirPatient *>(si)) )
661 gdcmErrorMacro( "Add PatientToEnd failed");
664 else if( v == "STUDY " )
666 si = new DicomDirStudy(true);
667 if( !AddStudyToEnd( static_cast<DicomDirStudy *>(si)) )
671 gdcmErrorMacro( "Add AddStudyToEnd failed");
674 else if( v == "SERIES" )
676 si = new DicomDirSerie(true);
677 if( !AddSerieToEnd( static_cast<DicomDirSerie *>(si)) )
681 gdcmErrorMacro( "Add AddSerieToEnd failed");
684 else if( v == "IMAGE " )
686 si = new DicomDirImage(true);
687 if( !AddImageToEnd( static_cast<DicomDirImage *>(si)) )
691 gdcmErrorMacro( "Add AddImageToEnd failed");
696 // It was not a 'PATIENT', nor a 'STUDY', nor a 'SERIE',
697 // neither an 'IMAGE' SQItem. Skip to next item.
701 MoveSQItem(si,tmpSI);
703 tmpSI=s->GetNextSQItem();
709 * \brief AddPatientToEnd
710 * @param dd SQ Item to enqueue to the DicomPatient chained List
712 bool DicomDir::AddPatientToEnd(DicomDirPatient *dd)
714 Patients.push_back(dd);
719 * \brief AddStudyToEnd
720 * @param dd SQ Item to enqueue to the DicomDirStudy chained List
722 bool DicomDir::AddStudyToEnd(DicomDirStudy *dd)
724 if( Patients.size() > 0 )
726 ListDicomDirPatient::iterator itp = Patients.end();
728 (*itp)->AddStudy(dd);
735 * \brief AddSerieToEnd
736 * @param dd SQ Item to enqueue to the DicomDirSerie chained List
738 bool DicomDir::AddSerieToEnd(DicomDirSerie *dd)
740 if( Patients.size() > 0 )
742 ListDicomDirPatient::iterator itp = Patients.end();
745 DicomDirStudy *study = (*itp)->GetLastStudy();
756 * \brief AddImageToEnd
757 * @param dd SQ Item to enqueue to the DicomDirImage chained List
759 bool DicomDir::AddImageToEnd(DicomDirImage *dd)
761 if( Patients.size() > 0 )
763 ListDicomDirPatient::iterator itp = Patients.end();
766 DicomDirStudy *study = (*itp)->GetLastStudy();
769 DicomDirSerie *serie = study->GetLastSerie();
781 * \brief for each Header of the chained list,
782 * add/update the Patient/Study/Serie/Image info
783 * @param path path of the root directory
784 * @param list chained list of Headers
786 void DicomDir::SetElements(std::string const &path, VectDocument const &list)
791 std::string patPrevName = "", patPrevID = "";
792 std::string studPrevInstanceUID = "", studPrevID = "";
793 std::string serPrevInstanceUID = "", serPrevID = "";
795 std::string patCurName, patCurID;
796 std::string studCurInstanceUID, studCurID;
797 std::string serCurInstanceUID, serCurID;
800 for( VectDocument::const_iterator it = list.begin();
804 // get the current file characteristics
805 patCurName = (*it)->GetEntryValue(0x0010,0x0010);
806 patCurID = (*it)->GetEntryValue(0x0010,0x0011);
807 studCurInstanceUID = (*it)->GetEntryValue(0x0020,0x000d);
808 studCurID = (*it)->GetEntryValue(0x0020,0x0010);
809 serCurInstanceUID = (*it)->GetEntryValue(0x0020,0x000e);
810 serCurID = (*it)->GetEntryValue(0x0020,0x0011);
812 if( patCurName != patPrevName || patCurID != patPrevID || first )
814 SetElement(path, GDCM_DICOMDIR_PATIENT, *it);
818 // if new Study Deal with 'STUDY' Elements
819 if( studCurInstanceUID != studPrevInstanceUID || studCurID != studPrevID
822 SetElement(path, GDCM_DICOMDIR_STUDY, *it);
826 // if new Serie Deal with 'SERIE' Elements
827 if( serCurInstanceUID != serPrevInstanceUID || serCurID != serPrevID
830 SetElement(path, GDCM_DICOMDIR_SERIE, *it);
834 // Always Deal with 'IMAGE' Elements
835 SetElement(path, GDCM_DICOMDIR_IMAGE, *it);
837 patPrevName = patCurName;
838 patPrevID = patCurID;
839 studPrevInstanceUID = studCurInstanceUID;
840 studPrevID = studCurID;
841 serPrevInstanceUID = serCurInstanceUID;
842 serPrevID = serCurID;
848 * \brief adds to the HTable
849 * the Entries (Dicom Elements) corresponding to the given type
850 * @param path full path file name (only used when type = GDCM_DICOMDIR_IMAGE
851 * @param type DicomDirObject type to create (GDCM_DICOMDIR_PATIENT,
852 * GDCM_DICOMDIR_STUDY, GDCM_DICOMDIR_SERIE ...)
853 * @param header Header of the current file
855 void DicomDir::SetElement(std::string const &path, DicomDirType type,
858 ListDicomDirElem elemList; //FIXME this is going to be a by copy operation
859 ListDicomDirElem::const_iterator it;
860 uint16_t tmpGr, tmpEl;
861 DictEntry *dictEntry;
868 case GDCM_DICOMDIR_IMAGE:
869 elemList = Global::GetDicomDirElements()->GetDicomDirImageElements();
870 si = new DicomDirImage(true);
871 if( !AddImageToEnd(static_cast<DicomDirImage *>(si)) )
874 gdcmErrorMacro( "Add ImageToEnd failed");
877 case GDCM_DICOMDIR_SERIE:
878 elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements();
879 si = new DicomDirSerie(true);
880 if( !AddSerieToEnd(static_cast<DicomDirSerie *>(si)) )
883 gdcmErrorMacro( "Add SerieToEnd failed");
886 case GDCM_DICOMDIR_STUDY:
887 elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements();
888 si = new DicomDirStudy(true);
889 if( !AddStudyToEnd(static_cast<DicomDirStudy *>(si)) )
892 gdcmErrorMacro( "Add StudyToEnd failed");
895 case GDCM_DICOMDIR_PATIENT:
896 elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements();
897 si = new DicomDirPatient(true);
898 if( !AddPatientToEnd(static_cast<DicomDirPatient *>(si)) )
901 gdcmErrorMacro( "Add PatientToEnd failed");
904 case GDCM_DICOMDIR_META:
905 elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements();
906 si = new DicomDirMeta(true);
910 gdcmErrorMacro( "MetaElements already exist, they will be destroyed");
912 MetaElems = static_cast<DicomDirMeta *>(si);
917 // removed all the seems-to-be-useless stuff about Referenced Image Sequence
918 // to avoid further troubles
919 // imageElem 0008 1140 "" // Referenced Image Sequence
920 // imageElem fffe e000 "" // 'no length' item : length to be set to 0xffffffff later
921 // imageElem 0008 1150 "" // Referenced SOP Class UID : to be set/forged later
922 // imageElem 0008 1155 "" // Referenced SOP Instance UID : to be set/forged later
923 // imageElem fffe e00d "" // Item delimitation : length to be set to ZERO later
925 // FIXME : troubles found when it's a SeqEntry
927 // for all the relevant elements found in their own spot of the DicomDir.dic
928 for( it = elemList.begin(); it != elemList.end(); ++it)
932 dictEntry = GetPubDict()->GetEntry(tmpGr, tmpEl);
934 entry = new ValEntry( dictEntry ); // Be sure it's never a BinEntry !
936 entry->SetOffset(0); // just to avoid further missprinting
940 // NULL when we Build Up (ex nihilo) a DICOMDIR
941 // or when we add the META elems
942 val = header->GetEntryValue(tmpGr, tmpEl);
949 if( val == GDCM_UNFOUND)
951 if( tmpGr == 0x0004 && tmpEl == 0x1130 ) // File-set ID
953 // force to the *end* File Name
954 val = Util::GetName( path );
956 else if( tmpGr == 0x0004 && tmpEl == 0x1500 ) // Only used for image
958 if( header->GetFileName().substr(0, path.length()) != path )
960 gdcmWarningMacro( "The base path of file name is incorrect");
961 val = header->GetFileName();
965 val = &(header->GetFileName().c_str()[path.length()]);
975 if ( header->GetEntryLength(tmpGr,tmpEl) == 0 )
979 entry->SetValue( val ); // troubles expected when vr=SQ ...
981 if ( type == GDCM_DICOMDIR_META ) // fusible : should never print !
983 gdcmWarningMacro("GDCM_DICOMDIR_META ?!? should never print that");
990 * \brief Move the content of the source SQItem to the destination SQItem
991 * Only DocEntry's are moved
992 * @param dst destination SQItem
993 * @param src source SQItem
995 void DicomDir::MoveSQItem(DocEntrySet *dst,DocEntrySet *src)
999 entry = src->GetFirstEntry();
1002 src->RemoveEntryNoDestroy(entry);
1003 dst->AddEntry(entry);
1004 // we destroyed -> the current iterator is not longer valid
1005 entry = src->GetFirstEntry();
1010 * \brief compares two files
1012 bool DicomDir::HeaderLessThan(Document *header1, Document *header2)
1014 return *header1 < *header2;
1017 //-----------------------------------------------------------------------------
1020 * \brief Canonical Printer
1021 * @param os ostream we want to print in
1022 * @param indent Indentation string to be prepended during printing
1024 void DicomDir::Print(std::ostream &os, std::string const & )
1028 MetaElems->SetPrintLevel(PrintLevel);
1029 MetaElems->Print(os);
1031 for(ListDicomDirPatient::iterator cc = Patients.begin();
1032 cc != Patients.end();
1035 (*cc)->SetPrintLevel(PrintLevel);
1040 //-----------------------------------------------------------------------------
1041 } // end namespace gdcm