1 /*=========================================================================
4 Module: $RCSfile: gdcmDicomDir.cxx,v $
6 Date: $Date: 2004/11/03 20:52:13 $
7 Version: $Revision: 1.77 $
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>
45 //-----------------------------------------------------------------------------
46 // For full DICOMDIR description, see:
47 // PS 3.3-2003, pages 731-750
48 //-----------------------------------------------------------------------------
49 // Constructor / Destructor
53 * \brief Constructor : creates an empty DicomDir
58 Initialize(); // sets all private fields to NULL
59 std::string pathBidon = "Bidon"; // Sorry, NULL not allowed ...
60 MetaElems = NewMeta();
64 * \brief Constructor Parses recursively the directory and creates the DicomDir
65 * or uses an already built DICOMDIR, depending on 'parseDir' value.
66 * @param fileName name
67 * - of the root directory (parseDir = true)
68 * - of the DICOMDIR (parseDir = false)
69 * @param parseDir boolean
70 * - true if user passed an entry point
71 * and wants to explore recursively the directories
72 * - false if user passed an already built DICOMDIR file
75 DicomDir::DicomDir(std::string const & fileName, bool parseDir ):
78 // Whatever user passed (a root directory or a DICOMDIR)
79 // and whatever the value of parseDir was,
80 // Document is already executed
81 Initialize(); // sets all private fields to NULL
83 // if user passed a root directory, sure we didn't get anything
85 if ( TagHT.begin() == TagHT.end() ) // when user passed a Directory to parse
87 dbg.Verbose(0, "DicomDir::DicomDir : entry HT empty");
89 if ( fileName.size() == 1 && fileName[0] == '.' )
91 // user passed '.' as Name
92 // we get current directory name
94 getcwd(dummy, (size_t)1000);
95 SetFileName( dummy ); // will be converted into a string
98 if ( parseDir ) // user asked for a recursive parsing of a root directory
100 MetaElems = NewMeta();
102 dbg.Verbose(0, "DicomDir::DicomDir : Parse directory"
103 " and create the DicomDir");
108 /// \todo if parseDir == false, it should be tagged as an error
109 // NON ! il suffit d'appeler ParseDirectory()
110 // apres le constructeur
113 else // Only if user passed a DICOMDIR
115 // Directory record sequence
116 DocEntry *e = GetDocEntryByNumber(0x0004, 0x1220);
119 dbg.Verbose(0, "DicomDir::DicomDir : NO Directory record"
120 " sequence (0x0004,0x1220)");
121 /// \todo FIXME : what do we do when the parsed file IS NOT a
129 * \brief Canonical destructor
131 DicomDir::~DicomDir()
133 SetStartMethod(NULL);
134 SetProgressMethod(NULL);
136 for(ListDicomDirPatient::iterator cc = Patients.begin();
148 //-----------------------------------------------------------------------------
151 * \brief Canonical Printer
153 void DicomDir::Print(std::ostream &os)
157 MetaElems->SetPrintLevel(PrintLevel);
158 MetaElems->Print(os);
160 for(ListDicomDirPatient::iterator cc = Patients.begin();
161 cc != Patients.end();
164 (*cc)->SetPrintLevel( PrintLevel );
169 //-----------------------------------------------------------------------------
172 * \brief This predicate, based on hopefully reasonable heuristics,
173 * decides whether or not the current header was properly parsed
174 * and contains the mandatory information for being considered as
175 * a well formed and usable DicomDir.
176 * @return true when Document is the one of a reasonable DicomDir,
179 bool DicomDir::IsReadable()
181 if( !Document::IsReadable() )
189 if( Patients.size() <= 0 )
198 * \brief Sets all fields to NULL
201 void DicomDir::Initialize()
204 ProgressMethod = NULL;
206 StartMethodArgDelete = NULL;
207 ProgressMethodArgDelete = NULL;
208 EndMethodArgDelete = NULL;
222 * \brief fills the whole structure, starting from a root Directory
224 void DicomDir::ParseDirectory()
226 CreateDicomDirChainedList( GetFileName() );
232 * \brief Set the start method to call when the parsing of the directory starts
233 * @param method Method to call
234 * @param arg Argument to pass to the method
235 * @param argDelete Argument
236 * \warning In python : the arg parameter isn't considered
238 void DicomDir::SetStartMethod(Method* method, void* arg,
241 if( StartArg && StartMethodArgDelete )
243 StartMethodArgDelete( StartArg );
246 StartMethod = method;
248 StartMethodArgDelete = argDelete;
253 * \brief Set the method to delete the argument
254 * The argument is destroyed when the method is changed or when the
256 * @param method Method to call to delete the argument
258 void DicomDir::SetStartMethodArgDelete(Method* method)
260 StartMethodArgDelete = method;
265 * \brief Set the progress method to call when the parsing of the directory progress
266 * @param method Method to call
267 * @param arg Argument to pass to the method
268 * @param argDelete Argument
269 * \warning In python : the arg parameter isn't considered
271 void DicomDir::SetProgressMethod(Method* method, void* arg,
274 if( ProgressArg && ProgressMethodArgDelete )
276 ProgressMethodArgDelete( ProgressArg );
279 ProgressMethod = method;
281 ProgressMethodArgDelete = argDelete;
286 * \brief Set the method to delete the argument
287 * The argument is destroyed when the method is changed or when the
289 * @param method Method to call to delete the argument
291 void DicomDir::SetProgressMethodArgDelete(Method* method)
293 ProgressMethodArgDelete = method;
298 * \brief Set the end method to call when the parsing of the directory ends
299 * @param method Method to call
300 * @param arg Argument to pass to the method
301 * @param argDelete Argument
302 * \warning In python : the arg parameter isn't considered
304 void DicomDir::SetEndMethod(Method* method, void* arg,
307 if( EndArg && EndMethodArgDelete )
309 EndMethodArgDelete( EndArg );
314 EndMethodArgDelete = argDelete;
319 * \brief Set the method to delete the argument
320 * The argument is destroyed when the method is changed or when the class
322 * @param method Method to call to delete the argument
324 void DicomDir::SetEndMethodArgDelete(Method* method)
326 EndMethodArgDelete = method;
331 * \brief writes on disc a DICOMDIR
332 * \ warning does NOT add the missing elements in the header :
333 * it's up to the user doing it !
334 * \todo : to be re-written using the DICOMDIR tree-like structure
335 * *not* the chained list
336 * (does NOT exist if the DICOMDIR is user-forged !)
337 * @param fileName file to be written to
338 * @return false only when fail to open
341 bool DicomDir::WriteDicomDir(std::string const& fileName)
344 uint16_t sq[4] = { 0x0004, 0x1220, 0xffff, 0xffff };
345 uint16_t sqt[4]= { 0xfffe, 0xe0dd, 0xffff, 0xffff };
347 std::ofstream* fp = new std::ofstream(fileName.c_str(),
348 std::ios::out | std::ios::binary);
351 dbg.Verbose(2, "Failed to open(write) File: ", fileName.c_str());
355 char filePreamble[128];
356 memset(filePreamble, 0, 128);
357 fp->write(filePreamble, 128); //FIXME
358 binary_write( *fp, "DICM");
360 DicomDirMeta *ptrMeta = GetDicomDirMeta();
361 ptrMeta->Write(fp, ExplicitVR);
363 // force writing 0004|1220 [SQ ], that CANNOT exist within DicomDirMeta
366 binary_write(*fp, sq[i]);
369 for(ListDicomDirPatient::iterator cc = Patients.begin();
370 cc != Patients.end();
373 (*cc)->Write( fp, ExplicitVR );
376 // force writing Sequence Delimitation Item
379 binary_write(*fp, sqt[i]); // fffe e0dd ffff ffff
386 //-----------------------------------------------------------------------------
391 * \brief create a Document-like chained list from a root Directory
392 * @param path entry point of the tree-like structure
394 void DicomDir::CreateDicomDirChainedList(std::string const & path)
397 DirList fileList(path,1); // gets recursively the file list
398 unsigned int count = 0;
405 for( DirList::iterator it = fileList.begin();
406 it != fileList.end();
409 Progress = (float)(count+1)/(float)fileList.size();
410 CallProgressMethod();
416 header = new Header( it->c_str() );
420 "DicomDir::CreateDicomDirChainedList: "
421 "failure in new Header ",
425 if( header->IsReadable() )
427 // Add the file header to the chained list:
428 list.push_back(header);
430 "DicomDir::CreateDicomDirChainedList: readable ",
440 // sorts Patient/Study/Serie/
441 std::sort(list.begin(), list.end(), DicomDir::HeaderLessThan );
443 std::string tmp = fileList.GetDirName();
444 //for each Header of the chained list, add/update the Patient/Study/Serie/Image info
445 SetElements(tmp, list);
451 * \brief adds *the* Meta to a partially created DICOMDIR
454 DicomDirMeta * DicomDir::NewMeta()
456 DicomDirMeta *m = new DicomDirMeta( &TagHT );
458 if ( TagHT.begin() != TagHT.end() ) // after Document Parsing
460 TagDocEntryHT::iterator lastOneButSequence = TagHT.end();
461 lastOneButSequence --;
462 // ALL the 'out of Sequence' Tags belong to Meta Elems
463 // (we skip 0004|1220 [Directory record sequence] )
464 for ( TagDocEntryHT::iterator cc = TagHT.begin();
465 cc != lastOneButSequence;
468 m->AddDocEntry( cc->second );
471 else // after root directory parsing
473 ListDicomDirMetaElem const & elemList =
474 Global::GetDicomDirElements()->GetDicomDirMetaElements();
475 m->FillObject(elemList);
477 m->SetSQItemNumber(0); // To avoid further missprinting
482 * \brief adds a new Patient (with the basic elements) to a partially created DICOMDIR
484 DicomDirPatient * DicomDir::NewPatient()
486 ListDicomDirPatientElem::const_iterator it;
487 uint16_t tmpGr,tmpEl;
488 DictEntry *dictEntry;
491 ListDicomDirPatientElem const & elemList =
492 Global::GetDicomDirElements()->GetDicomDirPatientElements();
493 SQItem *s = new SQItem(0);
495 // for all the DicomDirPatient Elements
496 for( it = elemList.begin(); it != elemList.end(); ++it )
500 dictEntry = GetPubDict()->GetDictEntryByNumber(tmpGr, tmpEl);
501 entry = new ValEntry( dictEntry );
502 entry->SetOffset(0); // just to avoid further missprinting
503 entry->SetValue( it->Value );
505 // dealing with value length ...
507 if( dictEntry->GetGroup() == 0xfffe)
509 entry->SetLength(entry->GetValue().length());
511 else if( dictEntry->GetVR() == "UL" || dictEntry->GetVR() == "SL" )
513 entry->SetLength( 4 );
515 else if( dictEntry->GetVR() == "US" || dictEntry->GetVR() == "SS" )
519 else if( dictEntry->GetVR() == "SQ" )
521 entry->SetLength( 0xffffffff );
525 entry->SetLength( entry->GetValue().length() );
527 s->AddDocEntry( entry );
530 DicomDirPatient *p = new DicomDirPatient(s, &TagHT);
531 Patients.push_front( p );
537 * \brief adds to the HTable
538 * the Entries (Dicom Elements) corresponding to the given type
539 * @param path full path file name (only used when type = GDCM_DICOMDIR_IMAGE
540 * @param type DicomDirObject type to create (GDCM_DICOMDIR_PATIENT,
541 * GDCM_DICOMDIR_STUDY, GDCM_DICOMDIR_SERIE ...)
542 * @param header Header of the current file
544 void DicomDir::SetElement(std::string const & path, DicomDirType type,
547 ListDicomDirElem elemList; //FIXME this is going to be a by copy operation
548 ListDicomDirElem::const_iterator it;
549 uint16_t tmpGr, tmpEl;
550 DictEntry *dictEntry;
553 SQItem *si = new SQItem(0); // all the items will be at level 1
556 case GDCM_DICOMDIR_IMAGE:
557 elemList = Global::GetDicomDirElements()->GetDicomDirImageElements();
560 case GDCM_DICOMDIR_SERIE:
561 elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements();
564 case GDCM_DICOMDIR_STUDY:
565 elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements();
568 case GDCM_DICOMDIR_PATIENT:
569 elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements();
572 case GDCM_DICOMDIR_META:
573 elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements();
579 // removed all the seems-to-be-useless stuff about Referenced Image Sequence
580 // to avoid further troubles
581 // imageElem 0008 1140 "" // Referenced Image Sequence
582 // imageElem fffe e000 "" // 'no length' item : length to be set to 0xffffffff later
583 // imageElem 0008 1150 "" // Referenced SOP Class UID : to be set/forged later
584 // imageElem 0008 1155 "" // Referenced SOP Instance UID : to be set/forged later
585 // imageElem fffe e00d "" // Item delimitation : length to be set to ZERO later
586 // for all the relevant elements found in their own spot of the DicomDir.dic
587 // FIXME : troubles found when it's a SeqEntry
589 for( it = elemList.begin(); it != elemList.end(); ++it)
593 dictEntry = GetPubDict()->GetDictEntryByNumber(tmpGr, tmpEl);
595 entry = new ValEntry( dictEntry ); // Be sure it's never a BinEntry !
597 entry->SetOffset(0); // just to avoid further missprinting
598 entry->SetLength(0); // just to avoid further missprinting
602 // NULL when we Build Up (ex nihilo) a DICOMDIR
603 // or when we add the META elems
604 val = header->GetEntryByNumber(tmpGr, tmpEl);
611 if( val == GDCM_UNFOUND)
613 if( tmpGr == 0x0004 && tmpEl == 0x1130 ) // File-set ID
615 // force to the *end* File Name
616 val = Util::GetName( path );
618 else if( tmpGr == 0x0004 && tmpEl == 0x1500 ) // Only used for image
620 if( header->GetFileName().substr(0, path.length()) != path )
622 dbg.Verbose(0, "DicomDir::SetElement : the base path"
623 " of file name is incorrect");
624 val = header->GetFileName();
628 val = &(header->GetFileName().c_str()[path.length()]);
638 if ( header->GetEntryLengthByNumber(tmpGr,tmpEl) == 0 )
642 // GDCM_UNFOUND or not !
644 entry->SetValue( val ); // troubles expected when vr=SQ ...
648 if( dictEntry->GetGroup() == 0xfffe )
650 entry->SetLength( entry->GetValue().length() ); // FIXME
652 else if( dictEntry->GetVR() == "UL" || dictEntry->GetVR() == "SL" )
656 else if( dictEntry->GetVR() == "US" || dictEntry->GetVR() == "SS" )
660 else if( dictEntry->GetVR() == "SQ" )
662 entry->SetLength( 0xffffffff );
666 entry->SetLength( entry->GetValue().length() );
670 if ( type == GDCM_DICOMDIR_META ) // fusible : should never print !
672 std::cout << "GDCM_DICOMDIR_META ?!? should never print that"
679 case GDCM_DICOMDIR_IMAGE:
680 AddDicomDirImageToEnd(si);
683 case GDCM_DICOMDIR_SERIE:
684 AddDicomDirSerieToEnd(si);
687 case GDCM_DICOMDIR_STUDY:
688 AddDicomDirStudyToEnd(si);
691 case GDCM_DICOMDIR_PATIENT:
692 AddDicomDirPatientToEnd(si);
698 //int count=1; // find a trick to increment
699 //s->AddEntry(si, count); // Seg Faults
703 //-----------------------------------------------------------------------------
705 * \brief CallStartMethod
707 void DicomDir::CallStartMethod()
713 StartMethod( StartArg );
717 //-----------------------------------------------------------------------------
720 * \brief CallProgressMethod
722 void DicomDir::CallProgressMethod()
726 ProgressMethod( ProgressArg );
730 //-----------------------------------------------------------------------------
733 * \brief CallEndMethod
735 void DicomDir::CallEndMethod()
744 //-----------------------------------------------------------------------------
748 * \brief create a 'DicomDir' from a DICOMDIR Header
750 void DicomDir::CreateDicomDir()
752 // The list is parsed.
753 // When a DicomDir tag ("PATIENT", "STUDY", "SERIE", "IMAGE") is found :
754 // 1 - we save the beginning iterator
755 // 2 - we continue to parse
756 // 3 - we find an other tag
757 // + we create the object for the precedent tag
760 // Directory record sequence
761 DocEntry *e = GetDocEntryByNumber(0x0004, 0x1220);
764 dbg.Verbose(0, "DicomDir::DicomDir : NO Directory record"
765 " sequence (0x0004,0x1220)");
766 /// \todo FIXME: what to do when the parsed file IS NOT a DICOMDIR file ?
770 SeqEntry* s = dynamic_cast<SeqEntry*>(e);
773 dbg.Verbose(0, "DicomDir::CreateDicomDir: no SeqEntry present");
774 // useless : (0x0004,0x1220) IS a Sequence !
778 DicomDirType type = DicomDir::GDCM_DICOMDIR_META;
779 MetaElems = NewMeta();
781 ListSQItem listItems = s->GetSQItems();
785 for( ListSQItem::iterator i = listItems.begin();
786 i !=listItems.end(); ++i )
788 d = (*i)->GetDocEntryByNumber(0x0004, 0x1430); // Directory Record Type
789 if ( ValEntry* valEntry = dynamic_cast< ValEntry* >(d) )
791 v = valEntry->GetValue();
795 dbg.Verbose(0, "DicomDir::CreateDicomDir: not a ValEntry.");
799 if( v == "PATIENT " )
801 AddDicomDirPatientToEnd( *i );
802 type = DicomDir::GDCM_DICOMDIR_PATIENT;
804 else if( v == "STUDY " )
806 AddDicomDirStudyToEnd( *i );
807 type = DicomDir::GDCM_DICOMDIR_STUDY;
809 else if( v == "SERIES" )
811 AddDicomDirSerieToEnd( *i );
812 type = DicomDir::GDCM_DICOMDIR_SERIE;
814 else if( v == "IMAGE " )
816 AddDicomDirImageToEnd( *i );
817 type = DicomDir::GDCM_DICOMDIR_IMAGE;
821 // It was not a 'PATIENT', nor a 'STUDY', nor a 'SERIE',
822 // neither an 'IMAGE' SQItem. Skip to next item.
830 * \brief Well ... there is only one occurence
832 void DicomDir::AddDicomDirMeta()
838 MetaElems = new DicomDirMeta( &TagHT );
843 * \brief AddDicomDirPatientToEnd
844 * @param s SQ Item to enqueue to the DicomPatient chained List
846 void DicomDir::AddDicomDirPatientToEnd(SQItem *s)
848 Patients.push_back(new DicomDirPatient(s, &TagHT));
853 * \brief AddDicomDirStudyToEnd
854 * @param s SQ Item to enqueue to the DicomDirStudy chained List
856 void DicomDir::AddDicomDirStudyToEnd(SQItem *s)
858 if( Patients.size() > 0 )
860 ListDicomDirPatient::iterator itp = Patients.end();
862 (*itp)->AddDicomDirStudy(new DicomDirStudy(s, &TagHT));
868 * \brief AddDicomDirSerieToEnd
869 * @param s SQ Item to enqueue to the DicomDirSerie chained List
871 void DicomDir::AddDicomDirSerieToEnd(SQItem *s)
873 if( Patients.size() > 0 )
875 ListDicomDirPatient::iterator itp = Patients.end();
878 if( (*itp)->GetDicomDirStudies().size() > 0 )
880 ListDicomDirStudy::const_iterator itst =
881 (*itp)->GetDicomDirStudies().end();
883 (*itst)->AddDicomDirSerie(new DicomDirSerie(s, &TagHT));
890 * \brief AddDicomDirImageToEnd
891 * @param s SQ Item to enqueue to the DicomDirImage chained List
893 void DicomDir::AddDicomDirImageToEnd(SQItem *s)
895 if( Patients.size() > 0 )
897 ListDicomDirPatient::iterator itp = Patients.end();
900 if( (*itp)->GetDicomDirStudies().size() > 0 )
902 ListDicomDirStudy::const_iterator itst =
903 (*itp)->GetDicomDirStudies().end();
906 if( (*itst)->GetDicomDirSeries().size() > 0 )
908 ListDicomDirSerie::const_iterator its = (*itst)->GetDicomDirSeries().end();
910 (*its)->AddDicomDirImage(new DicomDirImage(s, &TagHT));
918 * \brief for each Header of the chained list, add/update the Patient/Study/Serie/Image info
919 * @param path path of the root directory
920 * @param list chained list of Headers
922 void DicomDir::SetElements(std::string const & path, VectDocument const &list)
924 std::string patPrevName = "", patPrevID = "";
925 std::string studPrevInstanceUID = "", studPrevID = "";
926 std::string serPrevInstanceUID = "", serPrevID = "";
928 std::string patCurName, patCurID;
929 std::string studCurInstanceUID, studCurID;
930 std::string serCurInstanceUID, serCurID;
932 for( VectDocument::const_iterator it = list.begin();
933 it != list.end(); ++it )
935 // get the current file characteristics
936 patCurName = (*it)->GetEntryByNumber(0x0010,0x0010);
937 patCurID = (*it)->GetEntryByNumber(0x0010,0x0011);
938 studCurInstanceUID = (*it)->GetEntryByNumber(0x0020,0x000d);
939 studCurID = (*it)->GetEntryByNumber(0x0020,0x0010);
940 serCurInstanceUID = (*it)->GetEntryByNumber(0x0020,0x000e);
941 serCurID = (*it)->GetEntryByNumber(0x0020,0x0011);
943 if( patCurName != patPrevName || patCurID != patPrevID)
945 SetElement(path, GDCM_DICOMDIR_PATIENT, *it);
948 // if new Study Deal with 'STUDY' Elements
949 if( studCurInstanceUID != studPrevInstanceUID || studCurID != studPrevID )
951 SetElement(path, GDCM_DICOMDIR_STUDY, *it);
954 // if new Serie Deal with 'SERIE' Elements
955 if( serCurInstanceUID != serPrevInstanceUID || serCurID != serPrevID )
957 SetElement(path, GDCM_DICOMDIR_SERIE, *it);
960 // Always Deal with 'IMAGE' Elements
961 SetElement(path, GDCM_DICOMDIR_IMAGE, *it);
963 patPrevName = patCurName;
964 patPrevID = patCurID;
965 studPrevInstanceUID = studCurInstanceUID;
966 studPrevID = studCurID;
967 serPrevInstanceUID = serCurInstanceUID;
968 serPrevID = serCurID;
974 * \brief compares two dgcmHeaders
976 bool DicomDir::HeaderLessThan(Document *header1, Document *header2)
978 return *header1 < *header2;
980 } // end namespace gdcm
982 //-----------------------------------------------------------------------------