1 /*=========================================================================
4 Module: $RCSfile: gdcmDicomDir.cxx,v $
6 Date: $Date: 2005/03/09 19:29:38 $
7 Version: $Revision: 1.136 $
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
58 // (see also PS 4.3, 2004, page 50 for Entity-Relationship model)
60 // Directory Record Type Directory Record Types which may be included
61 // in the next lower-level directory Entity
63 // (Root directory Entity) PATIENT
67 // STUDY SERIES, VISIT, RESULTS, STUDY COMPONENT
69 // SERIES IMAGE, OVERLAYS, MODALITY LUT, VOI LUT,
70 // CURVE, STORED PRINT, RT DOSE, RT STRUCTURE SET
71 // RT PLAN, RT TREAT RECORD, PRESENTATION, WAVEFORM,
72 // SR DOCUMENT, KEY OBJECT DOC, SPECTROSCOPY,
73 // RAW DATA, REGISTRATION, FIDUCIAL
93 // ----------------------
94 // The current gdcm version only deals with :
96 // (Root directory Entity) PATIENT
102 // DicomDir::CreateDicomDir will have to be completed
103 // Treelike structure management will have to be upgraded
104 // ----------------------------------------------------------------------------
108 //-----------------------------------------------------------------------------
109 // Constructor / Destructor
111 * \brief Constructor : creates an empty DicomDir
116 Initialize(); // sets all private fields to NULL
121 * \brief Constructor Parses recursively the directory and creates the DicomDir
122 * or uses an already built DICOMDIR, depending on 'parseDir' value.
123 * @param fileName name
124 * - of the root directory (parseDir = true)
125 * - of the DICOMDIR (parseDir = false)
126 * @param parseDir boolean
127 * - true if user passed an entry point
128 * and wants to explore recursively the directories
129 * - false if user passed an already built DICOMDIR file
130 * and wants to use it
132 DicomDir::DicomDir(std::string const &fileName, bool parseDir ):
135 // At this step, Document constructor is already executed,
136 // whatever user passed (a root directory or a DICOMDIR)
137 // and whatever the value of parseDir was.
138 // (nothing is cheked in Document constructor, to avoid overhead)
140 Initialize(); // sets all private fields to NULL
142 // if user passed a root directory, sure we didn't get anything
144 if ( GetFirstEntry() == 0 ) // when user passed a Directory to parse
147 gdcmWarningMacro( "Entry HT empty for file: "<<fileName);
149 // Only if user passed a root directory
150 // ------------------------------------
151 if ( fileName == "." )
153 // user passed '.' as Name
154 // we get current directory name
156 getcwd(dummy, (size_t)1000);
157 SetFileName( dummy ); // will be converted into a string
160 if ( parseDir ) // user asked for a recursive parsing of a root directory
164 gdcmWarningMacro( "Parse directory and create the DicomDir");
170 // user may just call ParseDirectory() *after* constructor
174 // Only if user passed a DICOMDIR
175 // ------------------------------
178 // Directory record sequence
179 DocEntry *e = GetDocEntry(0x0004, 0x1220);
182 gdcmWarningMacro( "NO 'Directory record sequence' (0x0004,0x1220)"
183 << " in file " << fileName);
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 * @param fileName file to be written to
431 * @return false only when fail to open
434 bool DicomDir::WriteDicomDir(std::string const &fileName)
437 uint16_t sq[4] = { 0x0004, 0x1220, 0xffff, 0xffff };
438 uint16_t sqt[4]= { 0xfffe, 0xe0dd, 0xffff, 0xffff };
440 std::ofstream *fp = new std::ofstream(fileName.c_str(),
441 std::ios::out | std::ios::binary);
444 gdcmWarningMacro("Failed to open(write) File: " << fileName.c_str());
448 char filePreamble[128];
449 memset(filePreamble, 0, 128);
450 fp->write(filePreamble, 128);
451 binary_write( *fp, "DICM");
453 DicomDirMeta *ptrMeta = GetMeta();
454 ptrMeta->WriteContent(fp, ExplicitVR);
456 // force writing 0004|1220 [SQ ], that CANNOT exist within DicomDirMeta
459 binary_write(*fp, sq[i]);
462 for(ListDicomDirPatient::iterator cc = Patients.begin();
463 cc != Patients.end();
466 (*cc)->WriteContent( fp, ExplicitVR );
469 // force writing Sequence Delimitation Item
472 binary_write(*fp, sqt[i]); // fffe e0dd ffff ffff
482 * \brief Anonymize a DICOMDIR
486 bool DicomDir::AnonymizeDicomDir()
489 // Something clever to be found to forge the Patient names
490 std::ostringstream s;
492 for(ListDicomDirPatient::iterator cc = Patients.begin();
497 v = (*cc)->GetValEntry(0x0010, 0x0010) ; // Patient's Name
500 v->SetValue(s.str());
503 v = (*cc)->GetValEntry(0x0010, 0x0020) ; // Patient ID
509 v = (*cc)->GetValEntry(0x0010, 0x0030) ; // Patient's BirthDate
519 //-----------------------------------------------------------------------------
522 * \brief create a Document-like chained list from a root Directory
523 * @param path entry point of the tree-like structure
525 void DicomDir::CreateDicomDirChainedList(std::string const &path)
528 DirList dirList(path,1); // gets recursively the file list
529 unsigned int count = 0;
533 DirListType fileList = dirList.GetFilenames();
535 for( DirListType::iterator it = fileList.begin();
536 it != fileList.end();
539 Progress = (float)(count+1)/(float)fileList.size();
540 CallProgressMethod();
546 header = new File( it->c_str() );
549 gdcmWarningMacro( "Failure in new gdcm::File " << it->c_str() );
553 if( header->IsReadable() )
555 // Add the file to the chained list:
556 list.push_back(header);
557 gdcmWarningMacro( "Readable " << it->c_str() );
565 // sorts Patient/Study/Serie/
566 std::sort(list.begin(), list.end(), DicomDir::HeaderLessThan );
568 std::string tmp = dirList.GetDirName();
569 //for each File of the chained list, add/update the Patient/Study/Serie/Image info
570 SetElements(tmp, list);
573 for(VectDocument::iterator itDoc=list.begin();
577 delete dynamic_cast<File *>(*itDoc);
582 * \brief CallStartMethod
584 void DicomDir::CallStartMethod()
590 StartMethod( StartArg );
595 * \brief CallProgressMethod
597 void DicomDir::CallProgressMethod()
601 ProgressMethod( ProgressArg );
606 * \brief CallEndMethod
608 void DicomDir::CallEndMethod()
617 //-----------------------------------------------------------------------------
620 * \brief Sets all fields to NULL
622 void DicomDir::Initialize()
625 ProgressMethod = NULL;
627 StartMethodArgDelete = NULL;
628 ProgressMethodArgDelete = NULL;
629 EndMethodArgDelete = NULL;
641 * \brief create a 'DicomDir' from a DICOMDIR Header
643 void DicomDir::CreateDicomDir()
645 // The SeqEntries of "Directory Record Sequence" are parsed.
646 // When a DicomDir tag ("PATIENT", "STUDY", "SERIE", "IMAGE") is found :
647 // 1 - we save the beginning iterator
648 // 2 - we continue to parse
649 // 3 - we find an other tag
650 // + we create the object for the precedent tag
653 // Directory record sequence
654 DocEntry *e = GetDocEntry(0x0004, 0x1220);
657 gdcmWarningMacro( "No Directory Record Sequence (0004,1220) found");
661 SeqEntry *s = dynamic_cast<SeqEntry *>(e);
664 gdcmWarningMacro( "Element (0004,1220) is not a Sequence ?!?");
674 SQItem *tmpSI=s->GetFirstSQItem();
677 d = tmpSI->GetDocEntry(0x0004, 0x1430); // Directory Record Type
678 if ( ValEntry* valEntry = dynamic_cast<ValEntry *>(d) )
680 v = valEntry->GetValue();
684 gdcmWarningMacro( "(0004,1430) not a ValEntry ?!?");
688 if( v == "PATIENT " )
690 si = new DicomDirPatient(true);
691 if( !AddPatientToEnd( static_cast<DicomDirPatient *>(si)) )
695 gdcmErrorMacro( "Add PatientToEnd failed");
698 else if( v == "STUDY " )
700 si = new DicomDirStudy(true);
701 if( !AddStudyToEnd( static_cast<DicomDirStudy *>(si)) )
705 gdcmErrorMacro( "Add AddStudyToEnd failed");
708 else if( v == "SERIES" )
710 si = new DicomDirSerie(true);
711 if( !AddSerieToEnd( static_cast<DicomDirSerie *>(si)) )
715 gdcmErrorMacro( "Add AddSerieToEnd failed");
718 else if( v == "IMAGE " )
720 si = new DicomDirImage(true);
721 if( !AddImageToEnd( static_cast<DicomDirImage *>(si)) )
725 gdcmErrorMacro( "Add AddImageToEnd failed");
730 // It was not a 'PATIENT', nor a 'STUDY', nor a 'SERIE',
731 // neither an 'IMAGE' SQItem. Skip to next item.
735 MoveSQItem(si,tmpSI);
737 tmpSI=s->GetNextSQItem();
743 * \brief AddPatientToEnd
744 * @param dd SQ Item to enqueue to the DicomPatient chained List
746 bool DicomDir::AddPatientToEnd(DicomDirPatient *dd)
748 Patients.push_back(dd);
753 * \brief AddStudyToEnd
754 * @param dd SQ Item to enqueue to the DicomDirStudy chained List
756 bool DicomDir::AddStudyToEnd(DicomDirStudy *dd)
758 if( Patients.size() > 0 )
760 ListDicomDirPatient::iterator itp = Patients.end();
762 (*itp)->AddStudy(dd);
769 * \brief AddSerieToEnd
770 * @param dd SQ Item to enqueue to the DicomDirSerie chained List
772 bool DicomDir::AddSerieToEnd(DicomDirSerie *dd)
774 if( Patients.size() > 0 )
776 ListDicomDirPatient::iterator itp = Patients.end();
779 DicomDirStudy *study = (*itp)->GetLastStudy();
790 * \brief AddImageToEnd
791 * @param dd SQ Item to enqueue to the DicomDirImage chained List
793 bool DicomDir::AddImageToEnd(DicomDirImage *dd)
795 if( Patients.size() > 0 )
797 ListDicomDirPatient::iterator itp = Patients.end();
800 DicomDirStudy *study = (*itp)->GetLastStudy();
803 DicomDirSerie *serie = study->GetLastSerie();
815 * \brief for each Header of the chained list,
816 * add/update the Patient/Study/Serie/Image info
817 * @param path path of the root directory
818 * @param list chained list of Headers
820 void DicomDir::SetElements(std::string const &path, VectDocument const &list)
825 std::string patPrevName = "", patPrevID = "";
826 std::string studPrevInstanceUID = "", studPrevID = "";
827 std::string serPrevInstanceUID = "", serPrevID = "";
829 std::string patCurName, patCurID;
830 std::string studCurInstanceUID, studCurID;
831 std::string serCurInstanceUID, serCurID;
834 for( VectDocument::const_iterator it = list.begin();
838 // get the current file characteristics
839 patCurName = (*it)->GetEntryValue(0x0010,0x0010);
840 patCurID = (*it)->GetEntryValue(0x0010,0x0011);
841 studCurInstanceUID = (*it)->GetEntryValue(0x0020,0x000d);
842 studCurID = (*it)->GetEntryValue(0x0020,0x0010);
843 serCurInstanceUID = (*it)->GetEntryValue(0x0020,0x000e);
844 serCurID = (*it)->GetEntryValue(0x0020,0x0011);
846 if( patCurName != patPrevName || patCurID != patPrevID || first )
848 SetElement(path, GDCM_DICOMDIR_PATIENT, *it);
852 // if new Study Deal with 'STUDY' Elements
853 if( studCurInstanceUID != studPrevInstanceUID || studCurID != studPrevID
856 SetElement(path, GDCM_DICOMDIR_STUDY, *it);
860 // if new Serie Deal with 'SERIE' Elements
861 if( serCurInstanceUID != serPrevInstanceUID || serCurID != serPrevID
864 SetElement(path, GDCM_DICOMDIR_SERIE, *it);
867 // Always Deal with 'IMAGE' Elements
868 SetElement(path, GDCM_DICOMDIR_IMAGE, *it);
870 patPrevName = patCurName;
871 patPrevID = patCurID;
872 studPrevInstanceUID = studCurInstanceUID;
873 studPrevID = studCurID;
874 serPrevInstanceUID = serCurInstanceUID;
875 serPrevID = serCurID;
881 * \brief adds to the HTable
882 * the Entries (Dicom Elements) corresponding to the given type
883 * @param path full path file name (only used when type = GDCM_DICOMDIR_IMAGE
884 * @param type DicomDirObject type to create (GDCM_DICOMDIR_PATIENT,
885 * GDCM_DICOMDIR_STUDY, GDCM_DICOMDIR_SERIE ...)
886 * @param header Header of the current file
888 void DicomDir::SetElement(std::string const &path, DicomDirType type,
891 ListDicomDirElem elemList;
892 ListDicomDirElem::const_iterator it;
893 uint16_t tmpGr, tmpEl;
894 DictEntry *dictEntry;
901 case GDCM_DICOMDIR_IMAGE:
902 elemList = Global::GetDicomDirElements()->GetDicomDirImageElements();
903 si = new DicomDirImage(true);
904 if( !AddImageToEnd(static_cast<DicomDirImage *>(si)) )
907 gdcmErrorMacro( "Add ImageToEnd failed");
910 case GDCM_DICOMDIR_SERIE:
911 elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements();
912 si = new DicomDirSerie(true);
913 if( !AddSerieToEnd(static_cast<DicomDirSerie *>(si)) )
916 gdcmErrorMacro( "Add SerieToEnd failed");
919 case GDCM_DICOMDIR_STUDY:
920 elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements();
921 si = new DicomDirStudy(true);
922 if( !AddStudyToEnd(static_cast<DicomDirStudy *>(si)) )
925 gdcmErrorMacro( "Add StudyToEnd failed");
928 case GDCM_DICOMDIR_PATIENT:
929 elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements();
930 si = new DicomDirPatient(true);
931 if( !AddPatientToEnd(static_cast<DicomDirPatient *>(si)) )
934 gdcmErrorMacro( "Add PatientToEnd failed");
937 case GDCM_DICOMDIR_META:
938 elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements();
939 si = new DicomDirMeta(true);
943 gdcmErrorMacro( "MetaElements already exist, they will be destroyed");
945 MetaElems = static_cast<DicomDirMeta *>(si);
950 // removed all the seems-to-be-useless stuff about Referenced Image Sequence
951 // to avoid further troubles
952 // imageElem 0008 1140 "" // Referenced Image Sequence
953 // imageElem fffe e000 "" // 'no length' item : length to be set to 0xffffffff later
954 // imageElem 0008 1150 "" // Referenced SOP Class UID : to be set/forged later
955 // imageElem 0008 1155 "" // Referenced SOP Instance UID : to be set/forged later
956 // imageElem fffe e00d "" // Item delimitation : length to be set to ZERO later
958 // FIXME : troubles found when it's a SeqEntry
960 // for all the relevant elements found in their own spot of the DicomDir.dic
961 for( it = elemList.begin(); it != elemList.end(); ++it)
965 dictEntry = GetPubDict()->GetEntry(tmpGr, tmpEl);
967 entry = new ValEntry( dictEntry ); // Be sure it's never a BinEntry !
969 entry->SetOffset(0); // just to avoid further missprinting
973 // NULL when we Build Up (ex nihilo) a DICOMDIR
974 // or when we add the META elems
975 val = header->GetEntryValue(tmpGr, tmpEl);
982 if( val == GDCM_UNFOUND)
984 if( tmpGr == 0x0004 && tmpEl == 0x1130 ) // File-set ID
986 // force to the *end* File Name
987 val = Util::GetName( path );
989 else if( tmpGr == 0x0004 && tmpEl == 0x1500 ) // Only used for image
991 if( header->GetFileName().substr(0, path.length()) != path )
993 gdcmWarningMacro( "The base path of file name is incorrect");
994 val = header->GetFileName();
998 val = &(header->GetFileName().c_str()[path.length()]);
1008 if ( header->GetEntryLength(tmpGr,tmpEl) == 0 )
1012 entry->SetValue( val ); // troubles expected when vr=SQ ...
1014 if ( type == GDCM_DICOMDIR_META ) // fusible : should never print !
1016 gdcmWarningMacro("GDCM_DICOMDIR_META ?!? should never print that");
1018 si->AddEntry(entry);
1023 * \brief Move the content of the source SQItem to the destination SQItem
1024 * Only DocEntry's are moved
1025 * @param dst destination SQItem
1026 * @param src source SQItem
1028 void DicomDir::MoveSQItem(DocEntrySet *dst,DocEntrySet *src)
1032 entry = src->GetFirstEntry();
1035 src->RemoveEntryNoDestroy(entry);
1036 dst->AddEntry(entry);
1037 // we destroyed -> the current iterator is not longer valid
1038 entry = src->GetFirstEntry();
1043 * \brief compares two files
1045 bool DicomDir::HeaderLessThan(Document *header1, Document *header2)
1047 return *header1 < *header2;
1050 //-----------------------------------------------------------------------------
1053 * \brief Canonical Printer
1054 * @param os ostream we want to print in
1055 * @param indent Indentation string to be prepended during printing
1057 void DicomDir::Print(std::ostream &os, std::string const & )
1061 MetaElems->SetPrintLevel(PrintLevel);
1062 MetaElems->Print(os);
1064 for(ListDicomDirPatient::iterator cc = Patients.begin();
1065 cc != Patients.end();
1068 (*cc)->SetPrintLevel(PrintLevel);
1073 //-----------------------------------------------------------------------------
1074 } // end namespace gdcm