1 /*=========================================================================
4 Module: $RCSfile: gdcmDicomDir.cxx,v $
6 Date: $Date: 2004/11/30 17:04:01 $
7 Version: $Revision: 1.83 $
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 #include "gdcmDicomDir.h"
20 #include "gdcmDicomDirStudy.h"
21 #include "gdcmDicomDirSerie.h"
22 #include "gdcmDicomDirImage.h"
23 #include "gdcmDirList.h"
25 #include "gdcmDebug.h"
26 #include "gdcmGlobal.h"
27 #include "gdcmHeader.h"
28 #include "gdcmSeqEntry.h"
29 #include "gdcmSQItem.h"
30 #include "gdcmValEntry.h"
35 #include <sys/types.h>
38 #define getcwd _getcwd
41 #if defined( _MSC_VER) || defined(__BORLANDC__)
50 //-----------------------------------------------------------------------------
51 // For full DICOMDIR description, see:
52 // PS 3.3-2003, pages 731-750
53 //-----------------------------------------------------------------------------
54 // Constructor / Destructor
58 * \brief Constructor : creates an empty DicomDir
63 Initialize(); // sets all private fields to NULL
64 std::string pathBidon = "Bidon"; // Sorry, NULL not allowed ...
65 MetaElems = NewMeta();
69 * \brief Constructor Parses recursively the directory and creates the DicomDir
70 * or uses an already built DICOMDIR, depending on 'parseDir' value.
71 * @param fileName name
72 * - of the root directory (parseDir = true)
73 * - of the DICOMDIR (parseDir = false)
74 * @param parseDir boolean
75 * - true if user passed an entry point
76 * and wants to explore recursively the directories
77 * - false if user passed an already built DICOMDIR file
80 DicomDir::DicomDir(std::string const & fileName, bool parseDir ):
83 // Whatever user passed (a root directory or a DICOMDIR)
84 // and whatever the value of parseDir was,
85 // Document is already executed
86 Initialize(); // sets all private fields to NULL
88 // if user passed a root directory, sure we didn't get anything
90 if ( TagHT.begin() == TagHT.end() ) // when user passed a Directory to parse
92 dbg.Verbose(0, "DicomDir::DicomDir : entry HT empty");
94 if ( fileName.size() == 1 && fileName[0] == '.' )
96 // user passed '.' as Name
97 // we get current directory name
99 getcwd(dummy, (size_t)1000);
100 SetFileName( dummy ); // will be converted into a string
103 if ( parseDir ) // user asked for a recursive parsing of a root directory
105 MetaElems = NewMeta();
107 dbg.Verbose(0, "DicomDir::DicomDir : Parse directory"
108 " and create the DicomDir");
113 /// \todo if parseDir == false, it should be tagged as an error
114 // NON ! il suffit d'appeler ParseDirectory()
115 // apres le constructeur
118 else // Only if user passed a DICOMDIR
120 // Directory record sequence
121 DocEntry *e = GetDocEntryByNumber(0x0004, 0x1220);
124 dbg.Verbose(0, "DicomDir::DicomDir : NO Directory record"
125 " sequence (0x0004,0x1220)");
126 /// \todo FIXME : what do we do when the parsed file IS NOT a
135 * \brief Canonical destructor
137 DicomDir::~DicomDir()
139 SetStartMethod(NULL);
140 SetProgressMethod(NULL);
144 for(ListDicomDirPatient::iterator cc = Patients.begin();
156 //-----------------------------------------------------------------------------
159 * \brief Canonical Printer
161 void DicomDir::Print(std::ostream &os)
165 MetaElems->SetPrintLevel(PrintLevel);
166 MetaElems->Print(os);
168 for(ListDicomDirPatient::iterator cc = Patients.begin();
169 cc != Patients.end();
172 (*cc)->SetPrintLevel( PrintLevel );
177 //-----------------------------------------------------------------------------
180 * \brief This predicate, based on hopefully reasonable heuristics,
181 * decides whether or not the current header was properly parsed
182 * and contains the mandatory information for being considered as
183 * a well formed and usable DicomDir.
184 * @return true when Document is the one of a reasonable DicomDir,
187 bool DicomDir::IsReadable()
189 if( !Document::IsReadable() )
197 if( Patients.size() <= 0 )
206 * \brief Sets all fields to NULL
209 void DicomDir::Initialize()
212 ProgressMethod = NULL;
214 StartMethodArgDelete = NULL;
215 ProgressMethodArgDelete = NULL;
216 EndMethodArgDelete = NULL;
230 * \brief fills the whole structure, starting from a root Directory
232 void DicomDir::ParseDirectory()
234 CreateDicomDirChainedList( GetFileName() );
240 * \brief Set the start method to call when the parsing of the
242 * @param method Method to call
243 * @param arg Argument to pass to the method
244 * @param argDelete Argument
245 * \warning In python : the arg parameter isn't considered
247 void DicomDir::SetStartMethod( DicomDir::Method* method, void* arg,
248 DicomDir::Method* argDelete )
250 if( StartArg && StartMethodArgDelete )
252 StartMethodArgDelete( StartArg );
255 StartMethod = method;
257 StartMethodArgDelete = argDelete;
262 * \brief Set the method to delete the argument
263 * The argument is destroyed when the method is changed or when the
265 * @param method Method to call to delete the argument
267 void DicomDir::SetStartMethodArgDelete( DicomDir::Method* method )
269 StartMethodArgDelete = method;
274 * \brief Set the progress method to call when the parsing of the
276 * @param method Method to call
277 * @param arg Argument to pass to the method
278 * @param argDelete Argument
279 * \warning In python : the arg parameter isn't considered
281 void DicomDir::SetProgressMethod( DicomDir::Method* method, void* arg,
282 DicomDir::Method* argDelete )
284 if( ProgressArg && ProgressMethodArgDelete )
286 ProgressMethodArgDelete( ProgressArg );
289 ProgressMethod = method;
291 ProgressMethodArgDelete = argDelete;
296 * \brief Set the method to delete the argument
297 * The argument is destroyed when the method is changed or when the
299 * @param method Method to call to delete the argument
301 void DicomDir::SetProgressMethodArgDelete( DicomDir::Method* method )
303 ProgressMethodArgDelete = method;
308 * \brief Set the end method to call when the parsing of the directory ends
309 * @param method Method to call
310 * @param arg Argument to pass to the method
311 * @param argDelete Argument
312 * \warning In python : the arg parameter isn't considered
314 void DicomDir::SetEndMethod( DicomDir::Method* method, void* arg,
315 DicomDir::Method* argDelete )
317 if( EndArg && EndMethodArgDelete )
319 EndMethodArgDelete( EndArg );
324 EndMethodArgDelete = argDelete;
329 * \brief Set the method to delete the argument
330 * The argument is destroyed when the method is changed or when
331 * the class is destroyed
332 * @param method Method to call to delete the argument
334 void DicomDir::SetEndMethodArgDelete( DicomDir::Method* method )
336 EndMethodArgDelete = method;
341 * \brief writes on disc a DICOMDIR
342 * \ warning does NOT add the missing elements in the header :
343 * it's up to the user doing it !
344 * \todo : to be re-written using the DICOMDIR tree-like structure
345 * *not* the chained list
346 * (does NOT exist if the DICOMDIR is user-forged !)
347 * @param fileName file to be written to
348 * @return false only when fail to open
351 bool DicomDir::WriteDicomDir(std::string const& fileName)
354 uint16_t sq[4] = { 0x0004, 0x1220, 0xffff, 0xffff };
355 uint16_t sqt[4]= { 0xfffe, 0xe0dd, 0xffff, 0xffff };
357 std::ofstream* fp = new std::ofstream(fileName.c_str(),
358 std::ios::out | std::ios::binary);
361 dbg.Verbose(2, "Failed to open(write) File: ", fileName.c_str());
365 char filePreamble[128];
366 memset(filePreamble, 0, 128);
367 fp->write(filePreamble, 128); //FIXME
368 binary_write( *fp, "DICM");
370 DicomDirMeta *ptrMeta = GetDicomDirMeta();
371 ptrMeta->WriteContent(fp, ExplicitVR);
373 // force writing 0004|1220 [SQ ], that CANNOT exist within DicomDirMeta
376 binary_write(*fp, sq[i]);
379 for(ListDicomDirPatient::iterator cc = Patients.begin();
380 cc != Patients.end();
383 (*cc)->WriteContent( fp, ExplicitVR );
386 // force writing Sequence Delimitation Item
389 binary_write(*fp, sqt[i]); // fffe e0dd ffff ffff
396 //-----------------------------------------------------------------------------
401 * \brief create a Document-like chained list from a root Directory
402 * @param path entry point of the tree-like structure
404 void DicomDir::CreateDicomDirChainedList(std::string const & path)
407 DirList fileList(path,1); // gets recursively the file list
408 unsigned int count = 0;
412 for( DirList::iterator it = fileList.begin();
413 it != fileList.end();
416 Progress = (float)(count+1)/(float)fileList.size();
417 CallProgressMethod();
423 header = new Header( it->c_str() );
427 "DicomDir::CreateDicomDirChainedList: "
428 "failure in new Header ",
432 if( header->IsReadable() )
434 // Add the file header to the chained list:
435 list.push_back(header);
437 "DicomDir::CreateDicomDirChainedList: readable ",
447 // sorts Patient/Study/Serie/
448 std::sort(list.begin(), list.end(), DicomDir::HeaderLessThan );
450 std::string tmp = fileList.GetDirName();
451 //for each Header of the chained list, add/update the Patient/Study/Serie/Image info
452 SetElements(tmp, list);
458 * \brief adds *the* Meta to a partially created DICOMDIR
461 DicomDirMeta * DicomDir::NewMeta()
463 DicomDirMeta *m = new DicomDirMeta( &TagHT );
465 if ( TagHT.begin() != TagHT.end() ) // after Document Parsing
467 TagDocEntryHT::iterator lastOneButSequence = TagHT.end();
468 lastOneButSequence --;
469 // ALL the 'out of Sequence' Tags belong to Meta Elems
470 // (we skip 0004|1220 [Directory record sequence] )
471 for ( TagDocEntryHT::iterator cc = TagHT.begin();
472 cc != lastOneButSequence;
475 m->AddDocEntry( cc->second );
478 else // after root directory parsing
480 ListDicomDirMetaElem const & elemList =
481 Global::GetDicomDirElements()->GetDicomDirMetaElements();
482 m->FillObject(elemList);
484 m->SetSQItemNumber(0); // To avoid further missprinting
489 * \brief adds a new Patient (with the basic elements) to a partially created DICOMDIR
491 DicomDirPatient * DicomDir::NewPatient()
493 ListDicomDirPatientElem::const_iterator it;
494 uint16_t tmpGr,tmpEl;
495 DictEntry *dictEntry;
498 ListDicomDirPatientElem const & elemList =
499 Global::GetDicomDirElements()->GetDicomDirPatientElements();
500 SQItem *s = new SQItem(0);
502 // for all the DicomDirPatient Elements
503 for( it = elemList.begin(); it != elemList.end(); ++it )
507 dictEntry = GetPubDict()->GetDictEntryByNumber(tmpGr, tmpEl);
508 entry = new ValEntry( dictEntry );
509 entry->SetOffset(0); // just to avoid further missprinting
510 entry->SetValue( it->Value );
512 // dealing with value length ...
514 if( dictEntry->GetGroup() == 0xfffe)
516 entry->SetLength(entry->GetValue().length());
518 else if( dictEntry->GetVR() == "UL" || dictEntry->GetVR() == "SL" )
520 entry->SetLength( 4 );
522 else if( dictEntry->GetVR() == "US" || dictEntry->GetVR() == "SS" )
526 else if( dictEntry->GetVR() == "SQ" )
528 entry->SetLength( 0xffffffff );
532 entry->SetLength( entry->GetValue().length() );
534 s->AddDocEntry( entry );
537 DicomDirPatient *p = new DicomDirPatient(s, &TagHT);
538 Patients.push_front( p );
544 * \brief adds to the HTable
545 * the Entries (Dicom Elements) corresponding to the given type
546 * @param path full path file name (only used when type = GDCM_DICOMDIR_IMAGE
547 * @param type DicomDirObject type to create (GDCM_DICOMDIR_PATIENT,
548 * GDCM_DICOMDIR_STUDY, GDCM_DICOMDIR_SERIE ...)
549 * @param header Header of the current file
551 void DicomDir::SetElement(std::string const & path, DicomDirType type,
554 ListDicomDirElem elemList; //FIXME this is going to be a by copy operation
555 ListDicomDirElem::const_iterator it;
556 uint16_t tmpGr, tmpEl;
557 DictEntry *dictEntry;
560 SQItem *si = new SQItem(0); // all the items will be at level 1
564 case GDCM_DICOMDIR_IMAGE:
565 elemList = Global::GetDicomDirElements()->GetDicomDirImageElements();
568 case GDCM_DICOMDIR_SERIE:
569 elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements();
572 case GDCM_DICOMDIR_STUDY:
573 elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements();
576 case GDCM_DICOMDIR_PATIENT:
577 elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements();
580 case GDCM_DICOMDIR_META:
581 elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements();
587 // removed all the seems-to-be-useless stuff about Referenced Image Sequence
588 // to avoid further troubles
589 // imageElem 0008 1140 "" // Referenced Image Sequence
590 // imageElem fffe e000 "" // 'no length' item : length to be set to 0xffffffff later
591 // imageElem 0008 1150 "" // Referenced SOP Class UID : to be set/forged later
592 // imageElem 0008 1155 "" // Referenced SOP Instance UID : to be set/forged later
593 // imageElem fffe e00d "" // Item delimitation : length to be set to ZERO later
594 // for all the relevant elements found in their own spot of the DicomDir.dic
595 // FIXME : troubles found when it's a SeqEntry
597 for( it = elemList.begin(); it != elemList.end(); ++it)
601 dictEntry = GetPubDict()->GetDictEntryByNumber(tmpGr, tmpEl);
603 entry = new ValEntry( dictEntry ); // Be sure it's never a BinEntry !
605 entry->SetOffset(0); // just to avoid further missprinting
606 entry->SetLength(0); // just to avoid further missprinting
610 // NULL when we Build Up (ex nihilo) a DICOMDIR
611 // or when we add the META elems
612 val = header->GetEntryByNumber(tmpGr, tmpEl);
619 if( val == GDCM_UNFOUND)
621 if( tmpGr == 0x0004 && tmpEl == 0x1130 ) // File-set ID
623 // force to the *end* File Name
624 val = Util::GetName( path );
626 else if( tmpGr == 0x0004 && tmpEl == 0x1500 ) // Only used for image
628 if( header->GetFileName().substr(0, path.length()) != path )
630 dbg.Verbose(0, "DicomDir::SetElement : the base path"
631 " of file name is incorrect");
632 val = header->GetFileName();
636 val = &(header->GetFileName().c_str()[path.length()]);
646 if ( header->GetEntryLengthByNumber(tmpGr,tmpEl) == 0 )
650 // GDCM_UNFOUND or not !
652 entry->SetValue( val ); // troubles expected when vr=SQ ...
656 if( dictEntry->GetGroup() == 0xfffe )
658 entry->SetLength( entry->GetValue().length() ); // FIXME
660 else if( dictEntry->GetVR() == "UL" || dictEntry->GetVR() == "SL" )
664 else if( dictEntry->GetVR() == "US" || dictEntry->GetVR() == "SS" )
668 else if( dictEntry->GetVR() == "SQ" )
670 entry->SetLength( 0xffffffff );
674 entry->SetLength( entry->GetValue().length() );
678 if ( type == GDCM_DICOMDIR_META ) // fusible : should never print !
680 std::cout << "GDCM_DICOMDIR_META ?!? should never print that"
687 case GDCM_DICOMDIR_IMAGE:
688 AddDicomDirImageToEnd(si);
691 case GDCM_DICOMDIR_SERIE:
692 AddDicomDirSerieToEnd(si);
695 case GDCM_DICOMDIR_STUDY:
696 AddDicomDirStudyToEnd(si);
699 case GDCM_DICOMDIR_PATIENT:
700 AddDicomDirPatientToEnd(si);
706 //int count=1; // find a trick to increment
707 //s->AddEntry(si, count); // Seg Faults
711 //-----------------------------------------------------------------------------
713 * \brief CallStartMethod
715 void DicomDir::CallStartMethod()
721 StartMethod( StartArg );
725 //-----------------------------------------------------------------------------
728 * \brief CallProgressMethod
730 void DicomDir::CallProgressMethod()
734 ProgressMethod( ProgressArg );
738 //-----------------------------------------------------------------------------
741 * \brief CallEndMethod
743 void DicomDir::CallEndMethod()
752 //-----------------------------------------------------------------------------
756 * \brief create a 'DicomDir' from a DICOMDIR Header
758 void DicomDir::CreateDicomDir()
760 // The list is parsed.
761 // When a DicomDir tag ("PATIENT", "STUDY", "SERIE", "IMAGE") is found :
762 // 1 - we save the beginning iterator
763 // 2 - we continue to parse
764 // 3 - we find an other tag
765 // + we create the object for the precedent tag
768 // Directory record sequence
769 DocEntry *e = GetDocEntryByNumber(0x0004, 0x1220);
772 dbg.Verbose(0, "DicomDir::DicomDir : NO Directory record"
773 " sequence (0x0004,0x1220)");
774 /// \todo FIXME: what to do when the parsed file IS NOT a DICOMDIR file ?
778 SeqEntry* s = dynamic_cast<SeqEntry*>(e);
781 dbg.Verbose(0, "DicomDir::CreateDicomDir: no SeqEntry present");
782 // useless : (0x0004,0x1220) IS a Sequence !
786 DicomDirType type; // = DicomDir::GDCM_DICOMDIR_META;
787 MetaElems = NewMeta();
789 ListSQItem listItems = s->GetSQItems();
793 for( ListSQItem::iterator i = listItems.begin();
794 i !=listItems.end(); ++i )
796 d = (*i)->GetDocEntryByNumber(0x0004, 0x1430); // Directory Record Type
797 if ( ValEntry* valEntry = dynamic_cast< ValEntry* >(d) )
799 v = valEntry->GetValue();
803 dbg.Verbose(0, "DicomDir::CreateDicomDir: not a ValEntry.");
807 if( v == "PATIENT " )
809 AddDicomDirPatientToEnd( *i );
810 type = DicomDir::GDCM_DICOMDIR_PATIENT;
812 else if( v == "STUDY " )
814 AddDicomDirStudyToEnd( *i );
815 type = DicomDir::GDCM_DICOMDIR_STUDY;
817 else if( v == "SERIES" )
819 AddDicomDirSerieToEnd( *i );
820 type = DicomDir::GDCM_DICOMDIR_SERIE;
822 else if( v == "IMAGE " )
824 AddDicomDirImageToEnd( *i );
825 type = DicomDir::GDCM_DICOMDIR_IMAGE;
829 // It was not a 'PATIENT', nor a 'STUDY', nor a 'SERIE',
830 // neither an 'IMAGE' SQItem. Skip to next item.
838 * \brief Well ... there is only one occurence
840 void DicomDir::AddDicomDirMeta()
846 MetaElems = new DicomDirMeta( &TagHT );
851 * \brief AddDicomDirPatientToEnd
852 * @param s SQ Item to enqueue to the DicomPatient chained List
854 void DicomDir::AddDicomDirPatientToEnd(SQItem *s)
856 Patients.push_back(new DicomDirPatient(s, &TagHT));
861 * \brief AddDicomDirStudyToEnd
862 * @param s SQ Item to enqueue to the DicomDirStudy chained List
864 void DicomDir::AddDicomDirStudyToEnd(SQItem *s)
866 if( Patients.size() > 0 )
868 ListDicomDirPatient::iterator itp = Patients.end();
870 (*itp)->AddDicomDirStudy(new DicomDirStudy(s, &TagHT));
876 * \brief AddDicomDirSerieToEnd
877 * @param s SQ Item to enqueue to the DicomDirSerie chained List
879 void DicomDir::AddDicomDirSerieToEnd(SQItem *s)
881 if( Patients.size() > 0 )
883 ListDicomDirPatient::iterator itp = Patients.end();
886 if( (*itp)->GetDicomDirStudies().size() > 0 )
888 ListDicomDirStudy::const_iterator itst =
889 (*itp)->GetDicomDirStudies().end();
891 (*itst)->AddDicomDirSerie(new DicomDirSerie(s, &TagHT));
898 * \brief AddDicomDirImageToEnd
899 * @param s SQ Item to enqueue to the DicomDirImage chained List
901 void DicomDir::AddDicomDirImageToEnd(SQItem *s)
903 if( Patients.size() > 0 )
905 ListDicomDirPatient::iterator itp = Patients.end();
908 if( (*itp)->GetDicomDirStudies().size() > 0 )
910 ListDicomDirStudy::const_iterator itst =
911 (*itp)->GetDicomDirStudies().end();
914 if( (*itst)->GetDicomDirSeries().size() > 0 )
916 ListDicomDirSerie::const_iterator its = (*itst)->GetDicomDirSeries().end();
918 (*its)->AddDicomDirImage(new DicomDirImage(s, &TagHT));
926 * \brief for each Header of the chained list, add/update the Patient/Study/Serie/Image info
927 * @param path path of the root directory
928 * @param list chained list of Headers
930 void DicomDir::SetElements(std::string const & path, VectDocument const &list)
935 std::string patPrevName = "", patPrevID = "";
936 std::string studPrevInstanceUID = "", studPrevID = "";
937 std::string serPrevInstanceUID = "", serPrevID = "";
939 std::string patCurName, patCurID;
940 std::string studCurInstanceUID, studCurID;
941 std::string serCurInstanceUID, serCurID;
943 for( VectDocument::const_iterator it = list.begin();
944 it != list.end(); ++it )
946 // get the current file characteristics
947 patCurName = (*it)->GetEntryByNumber(0x0010,0x0010);
948 patCurID = (*it)->GetEntryByNumber(0x0010,0x0011);
949 studCurInstanceUID = (*it)->GetEntryByNumber(0x0020,0x000d);
950 studCurID = (*it)->GetEntryByNumber(0x0020,0x0010);
951 serCurInstanceUID = (*it)->GetEntryByNumber(0x0020,0x000e);
952 serCurID = (*it)->GetEntryByNumber(0x0020,0x0011);
954 if( patCurName != patPrevName || patCurID != patPrevID)
956 SetElement(path, GDCM_DICOMDIR_PATIENT, *it);
959 // if new Study Deal with 'STUDY' Elements
960 if( studCurInstanceUID != studPrevInstanceUID || studCurID != studPrevID )
962 SetElement(path, GDCM_DICOMDIR_STUDY, *it);
965 // if new Serie Deal with 'SERIE' Elements
966 if( serCurInstanceUID != serPrevInstanceUID || serCurID != serPrevID )
968 SetElement(path, GDCM_DICOMDIR_SERIE, *it);
971 // Always Deal with 'IMAGE' Elements
972 SetElement(path, GDCM_DICOMDIR_IMAGE, *it);
974 patPrevName = patCurName;
975 patPrevID = patCurID;
976 studPrevInstanceUID = studCurInstanceUID;
977 studPrevID = studCurID;
978 serPrevInstanceUID = serCurInstanceUID;
979 serPrevID = serCurID;
985 * \brief compares two dgcmHeaders
987 bool DicomDir::HeaderLessThan(Document *header1, Document *header2)
989 return *header1 < *header2;
991 } // end namespace gdcm
993 //-----------------------------------------------------------------------------