1 /*=========================================================================
4 Module: $RCSfile: gdcmDicomDir.cxx,v $
6 Date: $Date: 2005/02/11 16:55:39 $
7 Version: $Revision: 1.132 $
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-level 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 // user may just call ParseDirectory() *after* constructor
171 // Only if user passed a DICOMDIR
172 // ------------------------------
175 // Directory record sequence
176 DocEntry *e = GetDocEntry(0x0004, 0x1220);
179 gdcmWarningMacro( "NO 'Directory record sequence' (0x0004,0x1220)"
180 << " in file " << fileName);
188 * \brief Canonical destructor
190 DicomDir::~DicomDir()
192 SetStartMethod(NULL);
193 SetProgressMethod(NULL);
203 //-----------------------------------------------------------------------------
206 * \brief This predicate, based on hopefully reasonable heuristics,
207 * decides whether or not the current document was properly parsed
208 * and contains the mandatory information for being considered as
209 * a well formed and usable DicomDir.
210 * @return true when Document is the one of a reasonable DicomDir,
213 bool DicomDir::IsReadable()
215 if( Filetype == Unknown)
217 gdcmWarningMacro( "Wrong filetype");
222 gdcmWarningMacro( "Meta Elements missing in DicomDir");
225 if( Patients.size() <= 0 )
227 gdcmWarningMacro( "NO Patient in DicomDir");
235 * \brief adds *the* Meta to a partially created DICOMDIR
237 DicomDirMeta *DicomDir::NewMeta()
242 DocEntry *entry = GetFirstEntry();
245 MetaElems = new DicomDirMeta(true);
247 entry = GetFirstEntry();
250 if( dynamic_cast<SeqEntry *>(entry) )
253 RemoveEntryNoDestroy(entry);
254 MetaElems->AddEntry(entry);
256 entry = GetFirstEntry();
259 else // after root directory parsing
261 MetaElems = new DicomDirMeta(false);
263 MetaElems->SetSQItemNumber(0); // To avoid further missprinting
268 * \brief adds a new Patient (with the basic elements) to a partially created
271 DicomDirPatient *DicomDir::NewPatient()
273 DicomDirPatient *p = new DicomDirPatient();
274 AddPatientToEnd( p );
279 * \brief Remove all Patients
281 void DicomDir::ClearPatient()
283 for(ListDicomDirPatient::iterator cc = Patients.begin();
293 * \brief Get the first entry while visiting the DicomDirPatients
294 * \return The first DicomDirPatient if found, otherwhise NULL
296 DicomDirPatient *DicomDir::GetFirstPatient()
298 ItPatient = Patients.begin();
299 if ( ItPatient != Patients.end() )
305 * \brief Get the next entry while visiting the DicomDirPatients
306 * \note : meaningfull only if GetFirstEntry already called
307 * \return The next DicomDirPatient if found, otherwhise NULL
309 DicomDirPatient *DicomDir::GetNextPatient()
311 gdcmAssertMacro (ItPatient != Patients.end());
314 if ( ItPatient != Patients.end() )
320 * \brief fills the whole structure, starting from a root Directory
322 void DicomDir::ParseDirectory()
324 CreateDicomDirChainedList( GetFileName() );
329 * \brief Set the start method to call when the parsing of the
331 * @param method Method to call
332 * @param arg Argument to pass to the method
333 * @param argDelete Argument
334 * \warning In python : the arg parameter isn't considered
336 void DicomDir::SetStartMethod( DicomDir::Method *method, void *arg,
337 DicomDir::Method *argDelete )
339 if( StartArg && StartMethodArgDelete )
341 StartMethodArgDelete( StartArg );
344 StartMethod = method;
346 StartMethodArgDelete = argDelete;
350 * \brief Set the progress method to call when the parsing of the
352 * @param method Method to call
353 * @param arg Argument to pass to the method
354 * @param argDelete Argument
355 * \warning In python : the arg parameter isn't considered
357 void DicomDir::SetProgressMethod( DicomDir::Method *method, void *arg,
358 DicomDir::Method *argDelete )
360 if( ProgressArg && ProgressMethodArgDelete )
362 ProgressMethodArgDelete( ProgressArg );
365 ProgressMethod = method;
367 ProgressMethodArgDelete = argDelete;
371 * \brief Set the end method to call when the parsing of the directory ends
372 * @param method Method to call
373 * @param arg Argument to pass to the method
374 * @param argDelete Argument
375 * \warning In python : the arg parameter isn't considered
377 void DicomDir::SetEndMethod( DicomDir::Method *method, void *arg,
378 DicomDir::Method *argDelete )
380 if( EndArg && EndMethodArgDelete )
382 EndMethodArgDelete( EndArg );
387 EndMethodArgDelete = argDelete;
391 * \brief Set the method to delete the argument
392 * The argument is destroyed when the method is changed or when the
394 * @param method Method to call to delete the argument
396 void DicomDir::SetStartMethodArgDelete( DicomDir::Method *method )
398 StartMethodArgDelete = method;
402 * \brief Set the method to delete the argument
403 * The argument is destroyed when the method is changed or when the
405 * @param method Method to call to delete the argument
407 void DicomDir::SetProgressMethodArgDelete( DicomDir::Method *method )
409 ProgressMethodArgDelete = method;
413 * \brief Set the method to delete the argument
414 * The argument is destroyed when the method is changed or when
415 * the class is destroyed
416 * @param method Method to call to delete the argument
418 void DicomDir::SetEndMethodArgDelete( DicomDir::Method *method )
420 EndMethodArgDelete = method;
424 * \brief writes on disc a DICOMDIR
425 * \ warning does NOT add the missing elements in the header :
426 * it's up to the user doing it !
427 * @param fileName file to be written to
428 * @return false only when fail to open
431 bool DicomDir::WriteDicomDir(std::string const &fileName)
434 uint16_t sq[4] = { 0x0004, 0x1220, 0xffff, 0xffff };
435 uint16_t sqt[4]= { 0xfffe, 0xe0dd, 0xffff, 0xffff };
437 std::ofstream *fp = new std::ofstream(fileName.c_str(),
438 std::ios::out | std::ios::binary);
441 gdcmWarningMacro("Failed to open(write) File: " << fileName.c_str());
445 char filePreamble[128];
446 memset(filePreamble, 0, 128);
447 fp->write(filePreamble, 128);
448 binary_write( *fp, "DICM");
450 DicomDirMeta *ptrMeta = GetMeta();
451 ptrMeta->WriteContent(fp, ExplicitVR);
453 // force writing 0004|1220 [SQ ], that CANNOT exist within DicomDirMeta
456 binary_write(*fp, sq[i]);
459 for(ListDicomDirPatient::iterator cc = Patients.begin();
460 cc != Patients.end();
463 (*cc)->WriteContent( fp, ExplicitVR );
466 // force writing Sequence Delimitation Item
469 binary_write(*fp, sqt[i]); // fffe e0dd ffff ffff
478 //-----------------------------------------------------------------------------
481 * \brief create a Document-like chained list from a root Directory
482 * @param path entry point of the tree-like structure
484 void DicomDir::CreateDicomDirChainedList(std::string const &path)
487 DirList dirList(path,1); // gets recursively the file list
488 unsigned int count = 0;
492 DirListType fileList = dirList.GetFilenames();
494 for( DirListType::iterator it = fileList.begin();
495 it != fileList.end();
498 Progress = (float)(count+1)/(float)fileList.size();
499 CallProgressMethod();
505 header = new File( it->c_str() );
508 gdcmWarningMacro( "Failure in new gdcm::File " << it->c_str() );
512 if( header->IsReadable() )
514 // Add the file to the chained list:
515 list.push_back(header);
516 gdcmWarningMacro( "Readable " << it->c_str() );
524 // sorts Patient/Study/Serie/
525 std::sort(list.begin(), list.end(), DicomDir::HeaderLessThan );
527 std::string tmp = dirList.GetDirName();
528 //for each File of the chained list, add/update the Patient/Study/Serie/Image info
529 SetElements(tmp, list);
532 for(VectDocument::iterator itDoc=list.begin();
536 delete dynamic_cast<File *>(*itDoc);
541 * \brief CallStartMethod
543 void DicomDir::CallStartMethod()
549 StartMethod( StartArg );
554 * \brief CallProgressMethod
556 void DicomDir::CallProgressMethod()
560 ProgressMethod( ProgressArg );
565 * \brief CallEndMethod
567 void DicomDir::CallEndMethod()
576 //-----------------------------------------------------------------------------
579 * \brief Sets all fields to NULL
581 void DicomDir::Initialize()
584 ProgressMethod = NULL;
586 StartMethodArgDelete = NULL;
587 ProgressMethodArgDelete = NULL;
588 EndMethodArgDelete = NULL;
600 * \brief create a 'DicomDir' from a DICOMDIR Header
602 void DicomDir::CreateDicomDir()
604 // The SeqEntries of "Directory Record Sequence" are parsed.
605 // When a DicomDir tag ("PATIENT", "STUDY", "SERIE", "IMAGE") is found :
606 // 1 - we save the beginning iterator
607 // 2 - we continue to parse
608 // 3 - we find an other tag
609 // + we create the object for the precedent tag
612 // Directory record sequence
613 DocEntry *e = GetDocEntry(0x0004, 0x1220);
616 gdcmWarningMacro( "No Directory Record Sequence (0004,1220) found");
620 SeqEntry *s = dynamic_cast<SeqEntry *>(e);
623 gdcmWarningMacro( "Element (0004,1220) is not a Sequence ?!?");
633 SQItem *tmpSI=s->GetFirstSQItem();
636 d = tmpSI->GetDocEntry(0x0004, 0x1430); // Directory Record Type
637 if ( ValEntry* valEntry = dynamic_cast<ValEntry *>(d) )
639 v = valEntry->GetValue();
643 gdcmWarningMacro( "Not a ValEntry.");
647 if( v == "PATIENT " )
649 si = new DicomDirPatient(true);
650 if( !AddPatientToEnd( static_cast<DicomDirPatient *>(si)) )
654 gdcmErrorMacro( "Add PatientToEnd failed");
657 else if( v == "STUDY " )
659 si = new DicomDirStudy(true);
660 if( !AddStudyToEnd( static_cast<DicomDirStudy *>(si)) )
664 gdcmErrorMacro( "Add AddStudyToEnd failed");
667 else if( v == "SERIES" )
669 si = new DicomDirSerie(true);
670 if( !AddSerieToEnd( static_cast<DicomDirSerie *>(si)) )
674 gdcmErrorMacro( "Add AddSerieToEnd failed");
677 else if( v == "IMAGE " )
679 si = new DicomDirImage(true);
680 if( !AddImageToEnd( static_cast<DicomDirImage *>(si)) )
684 gdcmErrorMacro( "Add AddImageToEnd failed");
689 // It was not a 'PATIENT', nor a 'STUDY', nor a 'SERIE',
690 // neither an 'IMAGE' SQItem. Skip to next item.
694 MoveSQItem(si,tmpSI);
696 tmpSI=s->GetNextSQItem();
702 * \brief AddPatientToEnd
703 * @param dd SQ Item to enqueue to the DicomPatient chained List
705 bool DicomDir::AddPatientToEnd(DicomDirPatient *dd)
707 Patients.push_back(dd);
712 * \brief AddStudyToEnd
713 * @param dd SQ Item to enqueue to the DicomDirStudy chained List
715 bool DicomDir::AddStudyToEnd(DicomDirStudy *dd)
717 if( Patients.size() > 0 )
719 ListDicomDirPatient::iterator itp = Patients.end();
721 (*itp)->AddStudy(dd);
728 * \brief AddSerieToEnd
729 * @param dd SQ Item to enqueue to the DicomDirSerie chained List
731 bool DicomDir::AddSerieToEnd(DicomDirSerie *dd)
733 if( Patients.size() > 0 )
735 ListDicomDirPatient::iterator itp = Patients.end();
738 DicomDirStudy *study = (*itp)->GetLastStudy();
749 * \brief AddImageToEnd
750 * @param dd SQ Item to enqueue to the DicomDirImage chained List
752 bool DicomDir::AddImageToEnd(DicomDirImage *dd)
754 if( Patients.size() > 0 )
756 ListDicomDirPatient::iterator itp = Patients.end();
759 DicomDirStudy *study = (*itp)->GetLastStudy();
762 DicomDirSerie *serie = study->GetLastSerie();
774 * \brief for each Header of the chained list,
775 * add/update the Patient/Study/Serie/Image info
776 * @param path path of the root directory
777 * @param list chained list of Headers
779 void DicomDir::SetElements(std::string const &path, VectDocument const &list)
784 std::string patPrevName = "", patPrevID = "";
785 std::string studPrevInstanceUID = "", studPrevID = "";
786 std::string serPrevInstanceUID = "", serPrevID = "";
788 std::string patCurName, patCurID;
789 std::string studCurInstanceUID, studCurID;
790 std::string serCurInstanceUID, serCurID;
793 for( VectDocument::const_iterator it = list.begin();
797 // get the current file characteristics
798 patCurName = (*it)->GetEntryValue(0x0010,0x0010);
799 patCurID = (*it)->GetEntryValue(0x0010,0x0011);
800 studCurInstanceUID = (*it)->GetEntryValue(0x0020,0x000d);
801 studCurID = (*it)->GetEntryValue(0x0020,0x0010);
802 serCurInstanceUID = (*it)->GetEntryValue(0x0020,0x000e);
803 serCurID = (*it)->GetEntryValue(0x0020,0x0011);
805 if( patCurName != patPrevName || patCurID != patPrevID || first )
807 SetElement(path, GDCM_DICOMDIR_PATIENT, *it);
811 // if new Study Deal with 'STUDY' Elements
812 if( studCurInstanceUID != studPrevInstanceUID || studCurID != studPrevID
815 SetElement(path, GDCM_DICOMDIR_STUDY, *it);
819 // if new Serie Deal with 'SERIE' Elements
820 if( serCurInstanceUID != serPrevInstanceUID || serCurID != serPrevID
823 SetElement(path, GDCM_DICOMDIR_SERIE, *it);
827 // Always Deal with 'IMAGE' Elements
828 SetElement(path, GDCM_DICOMDIR_IMAGE, *it);
830 patPrevName = patCurName;
831 patPrevID = patCurID;
832 studPrevInstanceUID = studCurInstanceUID;
833 studPrevID = studCurID;
834 serPrevInstanceUID = serCurInstanceUID;
835 serPrevID = serCurID;
841 * \brief adds to the HTable
842 * the Entries (Dicom Elements) corresponding to the given type
843 * @param path full path file name (only used when type = GDCM_DICOMDIR_IMAGE
844 * @param type DicomDirObject type to create (GDCM_DICOMDIR_PATIENT,
845 * GDCM_DICOMDIR_STUDY, GDCM_DICOMDIR_SERIE ...)
846 * @param header Header of the current file
848 void DicomDir::SetElement(std::string const &path, DicomDirType type,
851 ListDicomDirElem elemList;
852 ListDicomDirElem::const_iterator it;
853 uint16_t tmpGr, tmpEl;
854 DictEntry *dictEntry;
861 case GDCM_DICOMDIR_IMAGE:
862 elemList = Global::GetDicomDirElements()->GetDicomDirImageElements();
863 si = new DicomDirImage(true);
864 if( !AddImageToEnd(static_cast<DicomDirImage *>(si)) )
867 gdcmErrorMacro( "Add ImageToEnd failed");
870 case GDCM_DICOMDIR_SERIE:
871 elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements();
872 si = new DicomDirSerie(true);
873 if( !AddSerieToEnd(static_cast<DicomDirSerie *>(si)) )
876 gdcmErrorMacro( "Add SerieToEnd failed");
879 case GDCM_DICOMDIR_STUDY:
880 elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements();
881 si = new DicomDirStudy(true);
882 if( !AddStudyToEnd(static_cast<DicomDirStudy *>(si)) )
885 gdcmErrorMacro( "Add StudyToEnd failed");
888 case GDCM_DICOMDIR_PATIENT:
889 elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements();
890 si = new DicomDirPatient(true);
891 if( !AddPatientToEnd(static_cast<DicomDirPatient *>(si)) )
894 gdcmErrorMacro( "Add PatientToEnd failed");
897 case GDCM_DICOMDIR_META:
898 elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements();
899 si = new DicomDirMeta(true);
903 gdcmErrorMacro( "MetaElements already exist, they will be destroyed");
905 MetaElems = static_cast<DicomDirMeta *>(si);
910 // removed all the seems-to-be-useless stuff about Referenced Image Sequence
911 // to avoid further troubles
912 // imageElem 0008 1140 "" // Referenced Image Sequence
913 // imageElem fffe e000 "" // 'no length' item : length to be set to 0xffffffff later
914 // imageElem 0008 1150 "" // Referenced SOP Class UID : to be set/forged later
915 // imageElem 0008 1155 "" // Referenced SOP Instance UID : to be set/forged later
916 // imageElem fffe e00d "" // Item delimitation : length to be set to ZERO later
918 // FIXME : troubles found when it's a SeqEntry
920 // for all the relevant elements found in their own spot of the DicomDir.dic
921 for( it = elemList.begin(); it != elemList.end(); ++it)
925 dictEntry = GetPubDict()->GetEntry(tmpGr, tmpEl);
927 entry = new ValEntry( dictEntry ); // Be sure it's never a BinEntry !
929 entry->SetOffset(0); // just to avoid further missprinting
933 // NULL when we Build Up (ex nihilo) a DICOMDIR
934 // or when we add the META elems
935 val = header->GetEntryValue(tmpGr, tmpEl);
942 if( val == GDCM_UNFOUND)
944 if( tmpGr == 0x0004 && tmpEl == 0x1130 ) // File-set ID
946 // force to the *end* File Name
947 val = Util::GetName( path );
949 else if( tmpGr == 0x0004 && tmpEl == 0x1500 ) // Only used for image
951 if( header->GetFileName().substr(0, path.length()) != path )
953 gdcmWarningMacro( "The base path of file name is incorrect");
954 val = header->GetFileName();
958 val = &(header->GetFileName().c_str()[path.length()]);
968 if ( header->GetEntryLength(tmpGr,tmpEl) == 0 )
972 entry->SetValue( val ); // troubles expected when vr=SQ ...
974 if ( type == GDCM_DICOMDIR_META ) // fusible : should never print !
976 gdcmWarningMacro("GDCM_DICOMDIR_META ?!? should never print that");
983 * \brief Move the content of the source SQItem to the destination SQItem
984 * Only DocEntry's are moved
985 * @param dst destination SQItem
986 * @param src source SQItem
988 void DicomDir::MoveSQItem(DocEntrySet *dst,DocEntrySet *src)
992 entry = src->GetFirstEntry();
995 src->RemoveEntryNoDestroy(entry);
996 dst->AddEntry(entry);
997 // we destroyed -> the current iterator is not longer valid
998 entry = src->GetFirstEntry();
1003 * \brief compares two files
1005 bool DicomDir::HeaderLessThan(Document *header1, Document *header2)
1007 return *header1 < *header2;
1010 //-----------------------------------------------------------------------------
1013 * \brief Canonical Printer
1014 * @param os ostream we want to print in
1015 * @param indent Indentation string to be prepended during printing
1017 void DicomDir::Print(std::ostream &os, std::string const & )
1021 MetaElems->SetPrintLevel(PrintLevel);
1022 MetaElems->Print(os);
1024 for(ListDicomDirPatient::iterator cc = Patients.begin();
1025 cc != Patients.end();
1028 (*cc)->SetPrintLevel(PrintLevel);
1033 //-----------------------------------------------------------------------------
1034 } // end namespace gdcm