/*========================================================================= Program: gdcm Module: $RCSfile: gdcmDicomDir.cxx,v $ Language: C++ Date: $Date: 2005/01/16 04:50:41 $ Version: $Revision: 1.102 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "gdcmDicomDir.h" #include "gdcmDicomDirStudy.h" #include "gdcmDicomDirSerie.h" #include "gdcmDicomDirImage.h" #include "gdcmDicomDirPatient.h" #include "gdcmDicomDirMeta.h" #include "gdcmDicomDirElement.h" #include "gdcmDirList.h" #include "gdcmUtil.h" #include "gdcmDebug.h" #include "gdcmGlobal.h" #include "gdcmHeader.h" #include "gdcmSeqEntry.h" #include "gdcmSQItem.h" #include "gdcmValEntry.h" #include #include #include #include #ifdef _MSC_VER # define getcwd _getcwd #endif #if defined(_MSC_VER) || defined(__BORLANDC__) # include #else # include #endif namespace gdcm { //----------------------------------------------------------------------------- // For full DICOMDIR description, see: // PS 3.3-2003, pages 731-750 //----------------------------------------------------------------------------- // Constructor / Destructor /** * \ingroup DicomDir * \brief Constructor : creates an empty DicomDir */ DicomDir::DicomDir() :Document( ) { Initialize(); // sets all private fields to NULL MetaElems = NewMeta(); } /** * \brief Constructor Parses recursively the directory and creates the DicomDir * or uses an already built DICOMDIR, depending on 'parseDir' value. * @param fileName name * - of the root directory (parseDir = true) * - of the DICOMDIR (parseDir = false) * @param parseDir boolean * - true if user passed an entry point * and wants to explore recursively the directories * - false if user passed an already built DICOMDIR file * and wants to use it */ DicomDir::DicomDir(std::string const &fileName, bool parseDir ): Document( fileName ) { // At this step, Document constructor is already executed, // whatever user passed (a root directory or a DICOMDIR) // and whatever the value of parseDir was. // (nothing is cheked in Document constructor, to avoid overhead) Initialize(); // sets all private fields to NULL // if user passed a root directory, sure we didn't get anything if ( TagHT.begin() == TagHT.end() ) // when user passed a Directory to parse { if (!parseDir) gdcmVerboseMacro( "Entry HT empty for file: "<SetPrintLevel(PrintLevel); MetaElems->Print(os); } for(ListDicomDirPatient::iterator cc = Patients.begin(); cc != Patients.end(); ++cc) { (*cc)->SetPrintLevel(PrintLevel); (*cc)->Print(os); } } //----------------------------------------------------------------------------- // Public /** * \brief This predicate, based on hopefully reasonable heuristics, * decides whether or not the current header was properly parsed * and contains the mandatory information for being considered as * a well formed and usable DicomDir. * @return true when Document is the one of a reasonable DicomDir, * false otherwise. */ bool DicomDir::IsReadable() { if( Filetype == Unknown) { gdcmVerboseMacro( "Wrong filetype"); return false; } if( !MetaElems ) { gdcmVerboseMacro( "Meta Elements missing in DicomDir"); return false; } if( Patients.size() <= 0 ) { gdcmVerboseMacro( "NO Patient in DicomDir"); return false; } return true; } /** * \brief Sets all fields to NULL */ void DicomDir::Initialize() { StartMethod = NULL; ProgressMethod = NULL; EndMethod = NULL; StartMethodArgDelete = NULL; ProgressMethodArgDelete = NULL; EndMethodArgDelete = NULL; StartArg = NULL; ProgressArg = NULL; EndArg = NULL; Progress = 0.0; Abort = false; MetaElems = NULL; } /** * \ingroup DicomDir * \brief fills the whole structure, starting from a root Directory */ void DicomDir::ParseDirectory() { CreateDicomDirChainedList( GetFileName() ); CreateDicomDir(); } /** * \ingroup DicomDir * \brief Set the start method to call when the parsing of the * directory starts. * @param method Method to call * @param arg Argument to pass to the method * @param argDelete Argument * \warning In python : the arg parameter isn't considered */ void DicomDir::SetStartMethod( DicomDir::Method *method, void *arg, DicomDir::Method *argDelete ) { if( StartArg && StartMethodArgDelete ) { StartMethodArgDelete( StartArg ); } StartMethod = method; StartArg = arg; StartMethodArgDelete = argDelete; } /** * \ingroup DicomDir * \brief Set the method to delete the argument * The argument is destroyed when the method is changed or when the * class is destroyed * @param method Method to call to delete the argument */ void DicomDir::SetStartMethodArgDelete( DicomDir::Method *method ) { StartMethodArgDelete = method; } /** * \ingroup DicomDir * \brief Set the progress method to call when the parsing of the * directory progress * @param method Method to call * @param arg Argument to pass to the method * @param argDelete Argument * \warning In python : the arg parameter isn't considered */ void DicomDir::SetProgressMethod( DicomDir::Method *method, void *arg, DicomDir::Method *argDelete ) { if( ProgressArg && ProgressMethodArgDelete ) { ProgressMethodArgDelete( ProgressArg ); } ProgressMethod = method; ProgressArg = arg; ProgressMethodArgDelete = argDelete; } /** * \ingroup DicomDir * \brief Set the method to delete the argument * The argument is destroyed when the method is changed or when the * class is destroyed * @param method Method to call to delete the argument */ void DicomDir::SetProgressMethodArgDelete( DicomDir::Method *method ) { ProgressMethodArgDelete = method; } /** * \ingroup DicomDir * \brief Set the end method to call when the parsing of the directory ends * @param method Method to call * @param arg Argument to pass to the method * @param argDelete Argument * \warning In python : the arg parameter isn't considered */ void DicomDir::SetEndMethod( DicomDir::Method *method, void *arg, DicomDir::Method *argDelete ) { if( EndArg && EndMethodArgDelete ) { EndMethodArgDelete( EndArg ); } EndMethod = method; EndArg = arg; EndMethodArgDelete = argDelete; } /** * \ingroup DicomDir * \brief Set the method to delete the argument * The argument is destroyed when the method is changed or when * the class is destroyed * @param method Method to call to delete the argument */ void DicomDir::SetEndMethodArgDelete( DicomDir::Method *method ) { EndMethodArgDelete = method; } /** * \ingroup DicomDir * \brief writes on disc a DICOMDIR * \ warning does NOT add the missing elements in the header : * it's up to the user doing it ! * \todo : to be re-written using the DICOMDIR tree-like structure * *not* the chained list * (does NOT exist if the DICOMDIR is user-forged !) * @param fileName file to be written to * @return false only when fail to open */ bool DicomDir::WriteDicomDir(std::string const &fileName) { int i; uint16_t sq[4] = { 0x0004, 0x1220, 0xffff, 0xffff }; uint16_t sqt[4]= { 0xfffe, 0xe0dd, 0xffff, 0xffff }; std::ofstream *fp = new std::ofstream(fileName.c_str(), std::ios::out | std::ios::binary); if( !fp ) { gdcmVerboseMacro("Failed to open(write) File: " << fileName.c_str()); return false; } char filePreamble[128]; memset(filePreamble, 0, 128); fp->write(filePreamble, 128); //FIXME binary_write( *fp, "DICM"); DicomDirMeta *ptrMeta = GetDicomDirMeta(); ptrMeta->WriteContent(fp, ExplicitVR); // force writing 0004|1220 [SQ ], that CANNOT exist within DicomDirMeta for(i=0;i<4;++i) { binary_write(*fp, sq[i]); } for(ListDicomDirPatient::iterator cc = Patients.begin(); cc != Patients.end(); ++cc ) { (*cc)->WriteContent( fp, ExplicitVR ); } // force writing Sequence Delimitation Item for(i=0;i<4;++i) { binary_write(*fp, sqt[i]); // fffe e0dd ffff ffff } fp->close(); delete fp; return true; } //----------------------------------------------------------------------------- // Protected /** * \ingroup DicomDir * \brief create a Document-like chained list from a root Directory * @param path entry point of the tree-like structure */ void DicomDir::CreateDicomDirChainedList(std::string const & path) { CallStartMethod(); DirList dirList(path,1); // gets recursively the file list unsigned int count = 0; VectDocument list; Header *header; DirListType fileList = dirList.GetFilenames(); for( DirListType::iterator it = fileList.begin(); it != fileList.end(); ++it ) { Progress = (float)(count+1)/(float)fileList.size(); CallProgressMethod(); if( Abort ) { break; } header = new Header( it->c_str() ); if( !header ) { gdcmVerboseMacro( "Failure in new Header " << it->c_str() ); continue; } if( header->IsReadable() ) { // Add the file header to the chained list: list.push_back(header); gdcmVerboseMacro( "Readable " << it->c_str() ); } else { delete header; } count++; } // sorts Patient/Study/Serie/ std::sort(list.begin(), list.end(), DicomDir::HeaderLessThan ); std::string tmp = dirList.GetDirName(); //for each Header of the chained list, add/update the Patient/Study/Serie/Image info SetElements(tmp, list); CallEndMethod(); for(VectDocument::iterator itDoc=list.begin(); itDoc!=list.end(); ++itDoc) { delete dynamic_cast
(*itDoc); } } /** * \ingroup DicomDir * \brief adds *the* Meta to a partially created DICOMDIR */ DicomDirMeta * DicomDir::NewMeta() { DicomDirMeta *m = new DicomDirMeta(); if ( TagHT.begin() != TagHT.end() ) // after Document Parsing { TagDocEntryHT::iterator lastOneButSequence = TagHT.end(); lastOneButSequence --; // ALL the 'out of Sequence' Tags belong to Meta Elems // (we skip 0004|1220 [Directory record sequence] ) for ( TagDocEntryHT::iterator cc = TagHT.begin(); cc != lastOneButSequence; ++cc) { m->AddEntry( cc->second ); } } else // after root directory parsing { ListDicomDirMetaElem const &elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements(); m->FillObject(elemList); } m->SetSQItemNumber(0); // To avoid further missprinting return m; } /** * \brief adds a new Patient (with the basic elements) to a partially created DICOMDIR */ DicomDirPatient *DicomDir::NewPatient() { ListDicomDirPatientElem::const_iterator it; uint16_t tmpGr,tmpEl; DictEntry *dictEntry; ValEntry *entry; ListDicomDirPatientElem const & elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements(); DicomDirPatient *p = new DicomDirPatient(); // for all the DicomDirPatient Elements for( it = elemList.begin(); it != elemList.end(); ++it ) { tmpGr = it->Group; tmpEl = it->Elem; dictEntry = GetPubDict()->GetDictEntry(tmpGr, tmpEl); entry = new ValEntry( dictEntry ); entry->SetOffset(0); // just to avoid further missprinting entry->SetValue( it->Value ); p->AddEntry( entry ); } Patients.push_front( p ); return p; } /** * \brief adds to the HTable * the Entries (Dicom Elements) corresponding to the given type * @param path full path file name (only used when type = GDCM_DICOMDIR_IMAGE * @param type DicomDirObject type to create (GDCM_DICOMDIR_PATIENT, * GDCM_DICOMDIR_STUDY, GDCM_DICOMDIR_SERIE ...) * @param header Header of the current file */ void DicomDir::SetElement(std::string const &path, DicomDirType type, Document *header) { ListDicomDirElem elemList; //FIXME this is going to be a by copy operation ListDicomDirElem::const_iterator it; uint16_t tmpGr, tmpEl; DictEntry *dictEntry; ValEntry *entry; std::string val; SQItem *si; switch( type ) { case GDCM_DICOMDIR_IMAGE: elemList = Global::GetDicomDirElements()->GetDicomDirImageElements(); si = new DicomDirImage(); if( !AddDicomDirImageToEnd(static_cast(si)) ) { gdcmVerboseMacro( "Add DicomDirImageToEnd failed"); } break; case GDCM_DICOMDIR_SERIE: elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements(); si = new DicomDirSerie(); if( !AddDicomDirSerieToEnd(static_cast(si)) ) { gdcmVerboseMacro( "Add DicomDirSerieToEnd failed"); } break; case GDCM_DICOMDIR_STUDY: elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements(); si = new DicomDirStudy(); if( !AddDicomDirStudyToEnd(static_cast(si)) ) { gdcmVerboseMacro( "Add DicomDirStudyToEnd failed"); } break; case GDCM_DICOMDIR_PATIENT: elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements(); si = new DicomDirPatient(); if( !AddDicomDirPatientToEnd(static_cast(si)) ) { gdcmVerboseMacro( "Add DicomDirPatientToEnd failed"); } break; case GDCM_DICOMDIR_META: elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements(); si = new DicomDirMeta(); if( MetaElems ) { gdcmVerboseMacro( "MetaElements already exist, they will be destroyed"); delete MetaElems; } MetaElems = static_cast(si); break; default: return; } // removed all the seems-to-be-useless stuff about Referenced Image Sequence // to avoid further troubles // imageElem 0008 1140 "" // Referenced Image Sequence // imageElem fffe e000 "" // 'no length' item : length to be set to 0xffffffff later // imageElem 0008 1150 "" // Referenced SOP Class UID : to be set/forged later // imageElem 0008 1155 "" // Referenced SOP Instance UID : to be set/forged later // imageElem fffe e00d "" // Item delimitation : length to be set to ZERO later // for all the relevant elements found in their own spot of the DicomDir.dic // FIXME : troubles found when it's a SeqEntry for( it = elemList.begin(); it != elemList.end(); ++it) { tmpGr = it->Group; tmpEl = it->Elem; dictEntry = GetPubDict()->GetDictEntry(tmpGr, tmpEl); entry = new ValEntry( dictEntry ); // Be sure it's never a BinEntry ! entry->SetOffset(0); // just to avoid further missprinting if( header ) { // NULL when we Build Up (ex nihilo) a DICOMDIR // or when we add the META elems val = header->GetEntry(tmpGr, tmpEl); } else { val = GDCM_UNFOUND; } if( val == GDCM_UNFOUND) { if( tmpGr == 0x0004 && tmpEl == 0x1130 ) // File-set ID { // force to the *end* File Name val = Util::GetName( path ); } else if( tmpGr == 0x0004 && tmpEl == 0x1500 ) // Only used for image { if( header->GetFileName().substr(0, path.length()) != path ) { gdcmVerboseMacro( "The base path of file name is incorrect"); val = header->GetFileName(); } else { val = &(header->GetFileName().c_str()[path.length()]); } } else { val = it->Value; } } else { if ( header->GetEntryLength(tmpGr,tmpEl) == 0 ) val = it->Value; } entry->SetValue( val ); // troubles expected when vr=SQ ... if ( type == GDCM_DICOMDIR_META ) // fusible : should never print ! { std::cout << "GDCM_DICOMDIR_META ?!? should never print that" << std::endl; } si->AddEntry(entry); } } //----------------------------------------------------------------------------- /** * \brief CallStartMethod */ void DicomDir::CallStartMethod() { Progress = 0.0f; Abort = false; if( StartMethod ) { StartMethod( StartArg ); } } //----------------------------------------------------------------------------- /** * \ingroup DicomDir * \brief CallProgressMethod */ void DicomDir::CallProgressMethod() { if( ProgressMethod ) { ProgressMethod( ProgressArg ); } } //----------------------------------------------------------------------------- /** * \ingroup DicomDir * \brief CallEndMethod */ void DicomDir::CallEndMethod() { Progress = 1.0f; if( EndMethod ) { EndMethod( EndArg ); } } //----------------------------------------------------------------------------- // Private /** * \ingroup DicomDir * \brief create a 'DicomDir' from a DICOMDIR Header */ void DicomDir::CreateDicomDir() { // The list is parsed. // When a DicomDir tag ("PATIENT", "STUDY", "SERIE", "IMAGE") is found : // 1 - we save the beginning iterator // 2 - we continue to parse // 3 - we find an other tag // + we create the object for the precedent tag // + loop to 1 - // Directory record sequence DocEntry *e = GetDocEntry(0x0004, 0x1220); if ( !e ) { gdcmVerboseMacro( "NO Directory record sequence (0x0004,0x1220)"); /// \todo FIXME: what to do when the parsed file IS NOT a DICOMDIR file ? return; } SeqEntry *s = dynamic_cast(e); if ( !s ) { gdcmVerboseMacro( "No SeqEntry present"); // useless : (0x0004,0x1220) IS a Sequence ! return; } MetaElems = NewMeta(); ListSQItem listItems = s->GetSQItems(); DocEntry *d; std::string v; SQItem *si; for( ListSQItem::iterator i = listItems.begin(); i !=listItems.end(); ++i ) { d = (*i)->GetDocEntry(0x0004, 0x1430); // Directory Record Type if ( ValEntry* valEntry = dynamic_cast(d) ) { v = valEntry->GetValue(); } else { gdcmVerboseMacro( "Not a ValEntry."); continue; } if( v == "PATIENT " ) { si = new DicomDirPatient(); AddDicomDirPatientToEnd( static_cast(si) ); } else if( v == "STUDY " ) { si = new DicomDirStudy(); AddDicomDirStudyToEnd( static_cast(si) ); } else if( v == "SERIES" ) { si = new DicomDirSerie(); AddDicomDirSerieToEnd( static_cast(si) ); } else if( v == "IMAGE " ) { si = new DicomDirImage(); AddDicomDirImageToEnd( static_cast(si) ); } else { // It was not a 'PATIENT', nor a 'STUDY', nor a 'SERIE', // neither an 'IMAGE' SQItem. Skip to next item. continue; } MoveSQItem(si,*i); } TagHT.clear(); } /** * \ingroup DicomDir * \brief Well ... there is only one occurence */ bool DicomDir::AddDicomDirMeta() { if( MetaElems ) { delete MetaElems; } MetaElems = new DicomDirMeta(); return true; } /** * \ingroup DicomDir * \brief AddDicomDirPatientToEnd * @param dd SQ Item to enqueue to the DicomPatient chained List */ bool DicomDir::AddDicomDirPatientToEnd(DicomDirPatient *dd) { Patients.push_back(dd); return true; } /** * \ingroup DicomDir * \brief AddDicomDirStudyToEnd * @param dd SQ Item to enqueue to the DicomDirStudy chained List */ bool DicomDir::AddDicomDirStudyToEnd(DicomDirStudy *dd) { if( Patients.size() > 0 ) { ListDicomDirPatient::iterator itp = Patients.end(); itp--; (*itp)->AddDicomDirStudy(dd); return true; } return false; } /** * \ingroup DicomDir * \brief AddDicomDirSerieToEnd * @param dd SQ Item to enqueue to the DicomDirSerie chained List */ bool DicomDir::AddDicomDirSerieToEnd(DicomDirSerie *dd) { if( Patients.size() > 0 ) { ListDicomDirPatient::iterator itp = Patients.end(); itp--; if( (*itp)->GetDicomDirStudies().size() > 0 ) { ListDicomDirStudy::const_iterator itst = (*itp)->GetDicomDirStudies().end(); itst--; (*itst)->AddDicomDirSerie(dd); return true; } } return false; } /** * \ingroup DicomDir * \brief AddDicomDirImageToEnd * @param dd SQ Item to enqueue to the DicomDirImage chained List */ bool DicomDir::AddDicomDirImageToEnd(DicomDirImage *dd) { if( Patients.size() > 0 ) { ListDicomDirPatient::iterator itp = Patients.end(); itp--; if( (*itp)->GetDicomDirStudies().size() > 0 ) { ListDicomDirStudy::const_iterator itst = (*itp)->GetDicomDirStudies().end(); itst--; if( (*itst)->GetDicomDirSeries().size() > 0 ) { ListDicomDirSerie::const_iterator its = (*itst)->GetDicomDirSeries().end(); its--; (*its)->AddDicomDirImage(dd); return true; } } } return false; } /** * \ingroup DicomDir * \brief for each Header of the chained list, add/update the Patient/Study/Serie/Image info * @param path path of the root directory * @param list chained list of Headers */ void DicomDir::SetElements(std::string const & path, VectDocument const &list) { TagHT.clear(); Patients.clear(); std::string patPrevName = "", patPrevID = ""; std::string studPrevInstanceUID = "", studPrevID = ""; std::string serPrevInstanceUID = "", serPrevID = ""; std::string patCurName, patCurID; std::string studCurInstanceUID, studCurID; std::string serCurInstanceUID, serCurID; bool first = true; for( VectDocument::const_iterator it = list.begin(); it != list.end(); ++it ) { // get the current file characteristics patCurName = (*it)->GetEntry(0x0010,0x0010); patCurID = (*it)->GetEntry(0x0010,0x0011); studCurInstanceUID = (*it)->GetEntry(0x0020,0x000d); studCurID = (*it)->GetEntry(0x0020,0x0010); serCurInstanceUID = (*it)->GetEntry(0x0020,0x000e); serCurID = (*it)->GetEntry(0x0020,0x0011); if( patCurName != patPrevName || patCurID != patPrevID || first ) { SetElement(path, GDCM_DICOMDIR_PATIENT, *it); first = true; } // if new Study Deal with 'STUDY' Elements if( studCurInstanceUID != studPrevInstanceUID || studCurID != studPrevID || first ) { SetElement(path, GDCM_DICOMDIR_STUDY, *it); first = true; } // if new Serie Deal with 'SERIE' Elements if( serCurInstanceUID != serPrevInstanceUID || serCurID != serPrevID || first ) { SetElement(path, GDCM_DICOMDIR_SERIE, *it); first = true; } // Always Deal with 'IMAGE' Elements SetElement(path, GDCM_DICOMDIR_IMAGE, *it); patPrevName = patCurName; patPrevID = patCurID; studPrevInstanceUID = studCurInstanceUID; studPrevID = studCurID; serPrevInstanceUID = serCurInstanceUID; serPrevID = serCurID; first = false; } } /** * \ingroup DicomDir * \brief Move the content of the src SQItem to the dst SQItem * Only DocEntry's are moved * */ void DicomDir::MoveSQItem(SQItem *dst,SQItem *src) { DocEntry *entry; src->Initialize(); entry = src->GetNextEntry(); while(entry) { src->RemoveEntryNoDestroy(entry); dst->AddEntry(entry); src->Initialize(); entry = src->GetNextEntry(); } } /** * \ingroup DicomDir * \brief compares two dgcmHeaders */ bool DicomDir::HeaderLessThan(Document *header1, Document *header2) { return *header1 < *header2; } } // end namespace gdcm //-----------------------------------------------------------------------------