X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDicomDir.cxx;h=1c205cb948b077e5556ed7f7147b6b8caa18273b;hb=3e82e8b67eddf5d4b95b6aa2a2e2615aced4c452;hp=7fbc137c187952a3e690a05ee07aa930f246ef4d;hpb=513f52eb83d002f898a8f0995e8525b269d9d225;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index 7fbc137c..1c205cb9 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -3,12 +3,12 @@ Program: gdcm Module: $RCSfile: gdcmDicomDir.cxx,v $ Language: C++ - Date: $Date: 2004/06/23 13:02:36 $ - Version: $Revision: 1.52 $ + Date: $Date: 2005/02/02 10:02:16 $ + Version: $Revision: 1.126 $ 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.htm for details. + 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 @@ -16,59 +16,59 @@ =========================================================================*/ -#include -#include -#include -#include - -#ifdef _MSC_VER - #include -#else - #include -#endif - +//----------------------------------------------------------------------------- +// For full DICOMDIR description, see: +// PS 3.3-2003, pages 731-750 +//----------------------------------------------------------------------------- #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 "gdcmFile.h" #include "gdcmSeqEntry.h" #include "gdcmSQItem.h" #include "gdcmValEntry.h" -//----------------------------------------------------------------------------- -// For full DICOMDIR description, see: -// PS 3.3-2003, pages 731-750 -//----------------------------------------------------------------------------- -// Constructor / Destructor +#include +#include +#include +#include -void gdcmDicomDir::Initialize(void) -{ - startMethod = NULL; - progressMethod = NULL; - endMethod = NULL; - startMethodArgDelete = NULL; - progressMethodArgDelete = NULL; - endMethodArgDelete = NULL; - startArg = NULL; - progressArg = NULL; - endArg = NULL; +#ifdef _MSC_VER +# define getcwd _getcwd +#endif - progress = 0.0; - abort = false; +#if defined(_MSC_VER) || defined(__BORLANDC__) +# include +#else +# include +#endif - metaElems = (gdcmDicomDirMeta *)0; +namespace gdcm +{ +//----------------------------------------------------------------------------- +// Constructor / Destructor +/** + * \brief Constructor : creates an empty DicomDir + */ +DicomDir::DicomDir() + :Document( ) +{ + Initialize(); // sets all private fields to NULL + NewMeta(); } - /** * \brief Constructor Parses recursively the directory and creates the DicomDir * or uses an already built DICOMDIR, depending on 'parseDir' value. - * @param FileName name + * @param fileName name * - of the root directory (parseDir = true) * - of the DICOMDIR (parseDir = false) * @param parseDir boolean @@ -76,109 +76,79 @@ void gdcmDicomDir::Initialize(void) * and wants to explore recursively the directories * - false if user passed an already built DICOMDIR file * and wants to use it - * @param exception_on_error whether we want to throw an exception or not */ -gdcmDicomDir::gdcmDicomDir(const char *FileName, bool parseDir, - bool exception_on_error): - gdcmDocument(FileName,exception_on_error,true) // true : enable SeQuences +DicomDir::DicomDir(std::string const &fileName, bool parseDir ): + Document( fileName ) { - // que l'on ai passe un root directory ou un DICOMDIR - // et quelle que soit la valeur de parseDir, - // on a lance gdcmDocument - Initialize(); + // 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 - // gdcmDocument already executed // if user passed a root directory, sure we didn't get anything - if( GetEntry().begin() == GetEntry().end() ) + if ( GetFirstEntry() == 0 ) // when user passed a Directory to parse { - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : entry HT empty"); + 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); + delete MetaElems; } } @@ -186,127 +156,166 @@ void gdcmDicomDir::Print(std::ostream &os) // Public /** * \brief This predicate, based on hopefully reasonable heuristics, - * decides whether or not the current header was properly parsed + * decides whether or not the current document was properly parsed * and contains the mandatory information for being considered as * a well formed and usable DicomDir. - * @return true when gdcmDocument is the one of a reasonable DicomDir, + * @return true when Document is the one of a reasonable DicomDir, * false otherwise. */ -bool gdcmDicomDir::IsReadable(void) +bool DicomDir::IsReadable() { - if(!gdcmDocument::IsReadable()) - return(false); - if(!metaElems) - return(false); - if(patients.size()<=0) - return(false); + 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); + return true; } /** - * \ingroup gdcmDicomDir * \brief fills the whole structure, starting from a root Directory */ -void gdcmDicomDir::ParseDirectory(void) +void DicomDir::ParseDirectory() { - CreateDicomDirChainedList(GetFileName()); + CreateDicomDirChainedList( GetFileName() ); CreateDicomDir(); } /** - * \ingroup gdcmDicomDir - * \brief Set the start method to call when the parsing of the directory starts + * \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 gdcmDicomDir::SetStartMethod(gdcmMethod *method,void *arg,gdcmMethod *argDelete) +void DicomDir::SetStartMethod( DicomDir::Method *method, void *arg, + DicomDir::Method *argDelete ) { - if((startArg)&&(startMethodArgDelete)) - startMethodArgDelete(startArg); + if( StartArg && StartMethodArgDelete ) + { + StartMethodArgDelete( StartArg ); + } - startMethod=method; - startArg=arg; - startMethodArgDelete=argDelete; + StartMethod = method; + StartArg = arg; + StartMethodArgDelete = argDelete; } /** - * \ingroup gdcmDicomDir * \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 gdcmDicomDir::SetStartMethodArgDelete(gdcmMethod *method) +void DicomDir::SetStartMethodArgDelete( DicomDir::Method *method ) { - startMethodArgDelete=method; + StartMethodArgDelete = method; } /** - * \ingroup gdcmDicomDir - * \brief Set the progress method to call when the parsing of the directory progress + * \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 gdcmDicomDir::SetProgressMethod(gdcmMethod *method,void *arg,gdcmMethod *argDelete) +void DicomDir::SetProgressMethod( DicomDir::Method *method, void *arg, + DicomDir::Method *argDelete ) { - if((progressArg)&&(progressMethodArgDelete)) - progressMethodArgDelete(progressArg); + if( ProgressArg && ProgressMethodArgDelete ) + { + ProgressMethodArgDelete( ProgressArg ); + } - progressMethod=method; - progressArg=arg; - progressMethodArgDelete=argDelete; + ProgressMethod = method; + ProgressArg = arg; + ProgressMethodArgDelete = argDelete; } /** - * \ingroup gdcmDicomDir * \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 gdcmDicomDir::SetProgressMethodArgDelete(gdcmMethod *method) +void DicomDir::SetProgressMethodArgDelete( DicomDir::Method *method ) { - progressMethodArgDelete=method; + ProgressMethodArgDelete = method; } /** - * \ingroup gdcmDicomDir * \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 gdcmDicomDir::SetEndMethod(gdcmMethod *method, void *arg, gdcmMethod *argDelete) +void DicomDir::SetEndMethod( DicomDir::Method *method, void *arg, + DicomDir::Method *argDelete ) { - if((endArg)&&(endMethodArgDelete)) - endMethodArgDelete(endArg); + if( EndArg && EndMethodArgDelete ) + { + EndMethodArgDelete( EndArg ); + } - endMethod=method; - endArg=arg; - endMethodArgDelete=argDelete; + EndMethod = method; + EndArg = arg; + EndMethodArgDelete = argDelete; } /** - * \ingroup gdcmDicomDir * \brief Set the method to delete the argument - * The argument is destroyed when the method is changed or when the class - * is destroyed + * 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 gdcmDicomDir::SetEndMethodArgDelete(gdcmMethod *method) +void DicomDir::SetEndMethodArgDelete( DicomDir::Method *method ) +{ + EndMethodArgDelete = method; +} + +/** + * \brief Get the first entry while visiting the DicomDirPatients + * \return The first DicomDirPatient if found, otherwhise NULL + */ +DicomDirPatient *DicomDir::GetFirstPatient() +{ + ItPatient = Patients.begin(); + if ( ItPatient != Patients.end() ) + return *ItPatient; + return NULL; +} + +/** + * \brief Get the next entry while visiting the DicomDirPatients + * \note : meaningfull only if GetFirstEntry already called + * \return The next DicomDirPatient if found, otherwhise NULL + */ +DicomDirPatient *DicomDir::GetNextPatient() { - endMethodArgDelete=method; + gdcmAssertMacro (ItPatient != Patients.end()); + + ++ItPatient; + if ( ItPatient != Patients.end() ) + return *ItPatient; + return NULL; } /** - * \ingroup gdcmDicomDir - * \brief writes on disc a 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 @@ -316,357 +325,380 @@ void gdcmDicomDir::SetEndMethodArgDelete(gdcmMethod *method) * @return false only when fail to open */ -bool gdcmDicomDir::Write(std::string fileName) -{ - FILE * fp1; +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; + } - fp1=fopen(fileName.c_str(),"wb"); - if(fp1==NULL) + char filePreamble[128]; + memset(filePreamble, 0, 128); + fp->write(filePreamble, 128); //FIXME + binary_write( *fp, "DICM"); + + DicomDirMeta *ptrMeta = GetMeta(); + ptrMeta->WriteContent(fp, ExplicitVR); + + // force writing 0004|1220 [SQ ], that CANNOT exist within DicomDirMeta + for(i=0;i<4;++i) { - printf("Failed to open(write) File [%s] \n",fileName.c_str()); - return(false); + 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 } - char * filePreamble = new char[128]; - fwrite(filePreamble,128,1,fp1); - fwrite("DICM",4,1,fp1); - delete[] filePreamble; - UpdateDirectoryRecordSequenceLength(); - WriteEntries(fp1); + fp->close(); + delete fp; - fclose(fp1); return true; } -/** - * \brief Writes in a file using the tree-like structure. - * @param _fp already open file pointer - */ - -void gdcmDicomDir::WriteEntries(FILE *) //_fp -{ - /// \todo (?) tester les echecs en ecriture - /// (apres chaque fwrite, dans le WriteEntry) - - -/* TODO : to go on compiling - - gdcmDicomDirMeta *ptrMeta; - ListDicomDirPatient::iterator itPatient; - ListDicomDirStudy::iterator itStudy; - ListDicomDirSerie::iterator itSerie; - ListDicomDirImage::iterator itImage; - ListTag::iterator i; - - ptrMeta= GetDicomDirMeta(); - for(i=ptrMeta->debut();i!=ptrMeta->fin();++i) { - WriteEntry(*i,_fp, gdcmExplicitVR); - } - - itPatient = GetDicomDirPatients().begin(); - while ( itPatient != GetDicomDirPatients().end() ) { - for(i=(*itPatient)->debut();i!=(*itPatient)->fin();++i) { - WriteEntry(*i,_fp, gdcmExplicitVR); - } - itStudy = ((*itPatient)->GetDicomDirStudies()).begin(); - while (itStudy != (*itPatient)->GetDicomDirStudies().end() ) { - for(i=(*itStudy)->debut();i!=(*itStudy)->fin();++i) { - WriteEntry(*i,_fp, gdcmExplicitVR); - } - itSerie = ((*itStudy)->GetDicomDirSeries()).begin(); - while (itSerie != (*itStudy)->GetDicomDirSeries().end() ) { - for(i=(*itSerie)->debut();i!=(*itSerie)->fin();++i) { - WriteEntry(*i,_fp, gdcmExplicitVR); - } - itImage = ((*itSerie)->GetDicomDirImages()).begin(); - while (itImage != (*itSerie)->GetDicomDirImages().end() ) { - for(i=(*itImage)->debut();i!=(*itImage)->fin();++i) { - WriteEntry(*i,_fp, gdcmExplicitVR); - } - ++itImage; - } - ++itSerie; - } - ++itStudy; - } - ++itPatient; - } - */ -} - //----------------------------------------------------------------------------- // Protected - /** - * \ingroup gdcmDicomDir - * \brief create a gdcmDocument-like chained list from a root Directory + * \brief create a Document-like chained list from a root Directory * @param path entry point of the tree-like structure */ -void gdcmDicomDir::CreateDicomDirChainedList(std::string path) +void DicomDir::CreateDicomDirChainedList(std::string const &path) { CallStartMethod(); - - gdcmDirList fileList(path,1); // gets recursively the file list - unsigned int count=0; + DirList dirList(path,1); // gets recursively the file list + unsigned int count = 0; VectDocument list; - gdcmHeader *header; + File *header; - tagHT.clear(); - patients.clear(); + DirListType fileList = dirList.GetFilenames(); - for(gdcmDirList::iterator it=fileList.begin(); - it!=fileList.end(); - ++it) + for( DirListType::iterator it = fileList.begin(); + it != fileList.end(); + ++it ) { - progress=(float)(count+1)/(float)fileList.size(); + Progress = (float)(count+1)/(float)fileList.size(); CallProgressMethod(); - if(abort) + if( Abort ) + { break; + } - header=new gdcmHeader(it->c_str()); - if(header->IsReadable()) - list.push_back(header); // adds the file header to the chained list - else - delete header; - - count++; + header = new File( it->c_str() ); + if( !header ) + { + gdcmVerboseMacro( "Failure in new gdcm::File " << it->c_str() ); + continue; + } + + if( header->IsReadable() ) + { + // Add the file 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(),gdcmDicomDir::HeaderLessThan); - - std::string tmp=fileList.GetDirName(); - - //for each Header of the chained list, add/update the Patient/Study/Serie/Image info - SetElements(tmp,list); - + std::sort(list.begin(), list.end(), DicomDir::HeaderLessThan ); + + std::string tmp = dirList.GetDirName(); + //for each File 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 gdcmDicomDir * \brief adds *the* Meta to a partially created DICOMDIR - */ - - // FIXME : Heuuuuu ! Il prend les Entries du Document deja parse, - // il ne fabrique rien ! - -gdcmDicomDirMeta * gdcmDicomDir::NewMeta(void) { - gdcmDicomDirMeta *m = new gdcmDicomDirMeta(&tagHT); - for (TagDocEntryHT::iterator cc = tagHT.begin();cc != tagHT.end();++cc) { - m->AddDocEntry(cc->second); + */ +DicomDirMeta *DicomDir::NewMeta() +{ + if( MetaElems ) + delete MetaElems; + + DocEntry *entry = GetFirstEntry(); + if( entry ) + { + MetaElems = new DicomDirMeta(true); + + entry = GetFirstEntry(); + while( entry ) + { + if( dynamic_cast(entry) ) + break; + + RemoveEntryNoDestroy(entry); + MetaElems->AddEntry(entry); + + entry = GetFirstEntry(); + } + } + else // after root directory parsing + { + MetaElems = new DicomDirMeta(false); } - return m; + MetaElems->SetSQItemNumber(0); // To avoid further missprinting + return MetaElems; } - /** - * \ingroup gdcmDicomDir - * \brief adds a new Patient (with the basic elements) to a partially created DICOMDIR + * \brief adds a new Patient (with the basic elements) to a partially created + * DICOMDIR */ -gdcmDicomDirPatient * gdcmDicomDir::NewPatient(void) { - std::list elemList; - std::list::iterator it; - guint16 tmpGr,tmpEl; - gdcmDictEntry *dictEntry; - gdcmValEntry *entry; - - gdcmSQItem *s = new gdcmSQItem(0); - - elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirPatientElements(); - - // TODO : use FillObject !!! +DicomDirPatient *DicomDir::NewPatient() +{ + DicomDirPatient *p = new DicomDirPatient(); + AddPatientToEnd( p ); + return p; +} - // for all the DicomDirPatient Elements - - for(it=elemList.begin();it!=elemList.end();++it) +/** + * \brief Remove all Patients + */ +void DicomDir::ClearPatient() +{ + for(ListDicomDirPatient::iterator cc = Patients.begin(); + cc!= Patients.end(); + ++cc) { - tmpGr=it->group; - tmpEl=it->elem; - dictEntry=GetPubDict()->GetDictEntryByNumber(tmpGr,tmpEl); - entry=new gdcmValEntry(dictEntry); - entry->SetOffset(0); // just to avoid further missprinting - entry->SetValue(it->value); - - // dealing with value length ... - - if(dictEntry->GetGroup()==0xfffe) - { - entry->SetLength(entry->GetValue().length()); - } - else if( (dictEntry->GetVR()=="UL") || (dictEntry->GetVR()=="SL") ) - { - entry->SetLength(4); - } - else if( (dictEntry->GetVR()=="US") || (dictEntry->GetVR()=="SS") ) - { - entry->SetLength(2); - } - else if(dictEntry->GetVR()=="SQ") - { - entry->SetLength(0xffffffff); - } - else - { - entry->SetLength(entry->GetValue().length()); - } - s->AddDocEntry(entry); + delete *cc; } - - gdcmDicomDirPatient *p = new gdcmDicomDirPatient(s, &tagHT); - patients.push_front(p); - return p; + Patients.clear(); } /** * \brief adds to the HTable - * the gdcmEntries (Dicom Elements) corresponding to the given type + * the Entries (Dicom Elements) corresponding to the given type * @param path full path file name (only used when type = GDCM_DICOMDIR_IMAGE - * @param type gdcmObject type to create (GDCM_DICOMDIR_PATIENT, + * @param type DicomDirObject type to create (GDCM_DICOMDIR_PATIENT, * GDCM_DICOMDIR_STUDY, GDCM_DICOMDIR_SERIE ...) - * @param header gdcmHeader of the current file + * @param header Header of the current file */ -void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type, - gdcmDocument *header) -{ - std::list elemList; - std::list::iterator it; - guint16 tmpGr, tmpEl; - gdcmDictEntry *dictEntry; - gdcmValEntry *entry; +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_PATIENT: - elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirPatientElements(); - break; - case GDCM_DICOMDIR_STUDY: - elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirStudyElements(); + switch( type ) + { + case GDCM_DICOMDIR_IMAGE: + elemList = Global::GetDicomDirElements()->GetDicomDirImageElements(); + si = new DicomDirImage(true); + if( !AddImageToEnd(static_cast(si)) ) + { + delete si; + gdcmErrorMacro( "Add ImageToEnd failed"); + } break; case GDCM_DICOMDIR_SERIE: - elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirSerieElements(); + elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements(); + si = new DicomDirSerie(true); + if( !AddSerieToEnd(static_cast(si)) ) + { + delete si; + gdcmErrorMacro( "Add SerieToEnd failed"); + } break; - case GDCM_DICOMDIR_IMAGE: - elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirImageElements(); + case GDCM_DICOMDIR_STUDY: + elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements(); + si = new DicomDirStudy(true); + if( !AddStudyToEnd(static_cast(si)) ) + { + delete si; + gdcmErrorMacro( "Add StudyToEnd failed"); + } + break; + case GDCM_DICOMDIR_PATIENT: + elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements(); + si = new DicomDirPatient(true); + if( !AddPatientToEnd(static_cast(si)) ) + { + delete si; + gdcmErrorMacro( "Add PatientToEnd failed"); + } break; case GDCM_DICOMDIR_META: - elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirMetaElements(); + elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements(); + si = new DicomDirMeta(true); + if( MetaElems ) + { + delete MetaElems; + gdcmErrorMacro( "MetaElements already exist, they will be destroyed"); + } + 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()->GetEntry(tmpGr, tmpEl); - for(it=elemList.begin();it!=elemList.end();++it) { - tmpGr=it->group; - tmpEl=it->elem; - dictEntry=GetPubDict()->GetDictEntryByNumber(tmpGr,tmpEl); - entry=new gdcmValEntry(dictEntry); // Be sure it's never a BinEntry ! + entry = new ValEntry( dictEntry ); // Be sure it's never a BinEntry ! entry->SetOffset(0); // just to avoid further missprinting - if(header) - val=header->GetEntryByNumber(tmpGr,tmpEl); + if( header ) + { + // NULL when we Build Up (ex nihilo) a DICOMDIR + // or when we add the META elems + val = header->GetEntryValue(tmpGr, tmpEl); + } else - val=GDCM_UNFOUND; + { + val = GDCM_UNFOUND; + } - if(val==GDCM_UNFOUND) + if( val == GDCM_UNFOUND) { - if((tmpGr==0x0004) &&(tmpEl==0x1130) ) // File-set ID + if( tmpGr == 0x0004 && tmpEl == 0x1130 ) // File-set ID { // force to the *end* File Name - val=GetName(path); + val = Util::GetName( path ); } - else if( (tmpGr==0x0004) && (tmpEl==0x1500) ) // Only used for image + else if( tmpGr == 0x0004 && tmpEl == 0x1500 ) // Only used for image { - if(header->GetFileName().substr(0,path.length())!=path) + if( header->GetFileName().substr(0, path.length()) != path ) { - dbg.Verbose(0, "gdcmDicomDir::SetElement : the base path" - " of file name is incorrect"); - val=header->GetFileName(); + gdcmVerboseMacro( "The base path of file name is incorrect"); + val = header->GetFileName(); } else { - val=&(header->GetFileName().c_str()[path.length()]); - } + val = &(header->GetFileName().c_str()[path.length()]); + } } else { - val=it->value; + val = it->Value; } - } + } else { - if (header->GetEntryLengthByNumber(tmpGr,tmpEl)== 0) - val=it->value; + if ( header->GetEntryLength(tmpGr,tmpEl) == 0 ) + val = it->Value; } - - entry->SetValue(val); - if(dictEntry) + entry->SetValue( val ); // troubles expected when vr=SQ ... + + if ( type == GDCM_DICOMDIR_META ) // fusible : should never print ! { - if(dictEntry->GetGroup()==0xfffe) { - entry->SetLength(entry->GetValue().length()); + gdcmVerboseMacro("GDCM_DICOMDIR_META ?!? should never print that"); } - else if( (dictEntry->GetVR()=="UL") || (dictEntry->GetVR()=="SL") ) - { - entry->SetLength(4); - } - else if( (dictEntry->GetVR()=="US") || (dictEntry->GetVR()=="SS") ) - { - entry->SetLength(2); - } - else if(dictEntry->GetVR()=="SQ") - { - entry->SetLength(0xffffffff); - } - else - { - entry->SetLength(entry->GetValue().length()); - } - } - //AddDocEntry(entry); // both in H Table and in chained list - tagHT[entry->GetKey()] = entry; // FIXME : use a SEQUENCE ! - } + si->AddEntry(entry); + } } /** * \brief CallStartMethod */ -void gdcmDicomDir::CallStartMethod(void) +void DicomDir::CallStartMethod() { - progress=0.0f; - abort=false; - if(startMethod) - startMethod(startArg); + Progress = 0.0f; + Abort = false; + if( StartMethod ) + { + StartMethod( StartArg ); + } } + /** - * \ingroup gdcmDicomDir * \brief CallProgressMethod */ -void gdcmDicomDir::CallProgressMethod(void) +void DicomDir::CallProgressMethod() { - if(progressMethod) - progressMethod(progressArg); + if( ProgressMethod ) + { + ProgressMethod( ProgressArg ); + } } + /** - * \ingroup gdcmDicomDir * \brief CallEndMethod */ -void gdcmDicomDir::CallEndMethod(void) +void DicomDir::CallEndMethod() { - progress=1.0f; - if(endMethod) - endMethod(endArg); + Progress = 1.0f; + if( EndMethod ) + { + EndMethod( EndArg ); + } } //----------------------------------------------------------------------------- // Private /** - * \ingroup gdcmDicomDir - * \brief create a 'gdcmDicomDir' from a DICOMDIR gdcmHeader + * \brief Sets all fields to NULL */ -void gdcmDicomDir::CreateDicomDir() +void DicomDir::Initialize() { - // The list is parsed. + 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; +} + +/** + * \brief create a 'DicomDir' from a DICOMDIR Header + */ +void DicomDir::CreateDicomDir() +{ + // The SeqEntries of "Directory Record Sequence" are parsed. // When a DicomDir tag ("PATIENT", "STUDY", "SERIE", "IMAGE") is found : // 1 - we save the beginning iterator // 2 - we continue to parse @@ -674,293 +706,284 @@ void gdcmDicomDir::CreateDicomDir() // + we create the object for the precedent tag // + loop to 1 - - gdcmDicomDirType type=gdcmDicomDir::GDCM_DICOMDIR_META; - // Directory record sequence - gdcmDocEntry *e = GetDocEntryByNumber(0x0004, 0x1220); - if (e==NULL) + DocEntry *e = GetDocEntry(0x0004, 0x1220); + if ( !e ) { - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : NO Directory record" - " sequence (0x0004,0x1220)"); + gdcmVerboseMacro( "No Directory Record Sequence (0004,1220) found"); /// \todo FIXME: what to do when the parsed file IS NOT a DICOMDIR file ? return; } - gdcmSeqEntry* s = dynamic_cast(e); - if (!s) + SeqEntry *s = dynamic_cast(e); + if ( !s ) { - dbg.Verbose(0, "gdcmDicomDir::CreateDicomDir: no SeqEntry present"); + gdcmVerboseMacro( "Element (0004,1220) is not a Sequence ?!?"); return; } - ListSQItem listItems = s->GetSQItems(); - gdcmDicomDirMeta *m = new gdcmDicomDirMeta(&tagHT); - (void)m; //?? + NewMeta(); - gdcmDocEntry * d; + DocEntry *d; std::string v; - for(ListSQItem::iterator i=listItems.begin(); i !=listItems.end();++i) - { - d=(*i)->GetDocEntryByNumber(0x0004, 0x1430); // Directory Record Type - if (gdcmValEntry* ValEntry = dynamic_cast< gdcmValEntry* >(d) ) + SQItem *si; + + SQItem *tmpSI=s->GetFirstSQItem(); + while(tmpSI) + { + d = tmpSI->GetDocEntry(0x0004, 0x1430); // Directory Record Type + if ( ValEntry* valEntry = dynamic_cast(d) ) { - v = ValEntry->GetValue(); + v = valEntry->GetValue(); } - else + else { - dbg.Verbose(0, "gdcmDicomDir::CreateDicomDir: not a ValEntry."); + gdcmVerboseMacro( "Not a ValEntry."); continue; - } - - if(v=="PATIENT ") - { - AddDicomDirPatientToEnd(*i); - //AddObjectToEnd(type,*i); - type=gdcmDicomDir::GDCM_DICOMDIR_PATIENT; } - else if(v=="STUDY ") + if( v == "PATIENT " ) { - AddDicomDirStudyToEnd(*i); - // AddObjectToEnd(type,*i); - type=gdcmDicomDir::GDCM_DICOMDIR_STUDY; + si = new DicomDirPatient(true); + if( !AddPatientToEnd( static_cast(si)) ) + { + delete si; + si = NULL; + gdcmErrorMacro( "Add PatientToEnd failed"); + } } - - else if(v=="SERIES") + else if( v == "STUDY " ) { - AddDicomDirSerieToEnd(*i); - // AddObjectToEnd(type,*i); - type=gdcmDicomDir::GDCM_DICOMDIR_SERIE; + si = new DicomDirStudy(true); + if( !AddStudyToEnd( static_cast(si)) ) + { + delete si; + si = NULL; + gdcmErrorMacro( "Add AddStudyToEnd failed"); + } } - - else if(v=="IMAGE ") + else if( v == "SERIES" ) { - AddDicomDirImageToEnd(*i); - // AddObjectToEnd(type,*i); - type=gdcmDicomDir::GDCM_DICOMDIR_IMAGE; + si = new DicomDirSerie(true); + if( !AddSerieToEnd( static_cast(si)) ) + { + delete si; + si = NULL; + gdcmErrorMacro( "Add AddSerieToEnd failed"); + } + } + else if( v == "IMAGE " ) + { + si = new DicomDirImage(true); + if( !AddImageToEnd( static_cast(si)) ) + { + delete si; + si = NULL; + gdcmErrorMacro( "Add AddImageToEnd failed"); + } } - else + { // It was not a 'PATIENT', nor a 'STUDY', nor a 'SERIE', // neither an 'IMAGE' SQItem. Skip to next item. continue; - } -} -/** - * \ingroup gdcmDicomDir - * \brief AddObjectToEnd - * @param type - * @param begin iterator on the first DocEntry within the chained List - * @param end iterator on the last DocEntry within the chained List - */ - -// now useless ? - -/*void gdcmDicomDir::AddObjectToEnd(gdcmDicomDirType type,gdcmSQItem *s) -{ - if(s==NULL) // ?? - return; + } + if( si ) + MoveSQItem(si,tmpSI); - switch(type) - { - case gdcmDicomDir::GDCM_DICOMDIR_META: - AddDicomDirMeta(); - break; - case gdcmDicomDir::GDCM_DICOMDIR_PATIENT: - AddDicomDirPatientToEnd(s); - break; - case gdcmDicomDir::GDCM_DICOMDIR_STUDY: - AddDicomDirStudyToEnd(s); - break; - case gdcmDicomDir::GDCM_DICOMDIR_SERIE: - AddDicomDirSerieToEnd(s); - break; - case gdcmDicomDir::GDCM_DICOMDIR_IMAGE: - AddDicomDirImageToEnd(s); - break; - case gdcmDicomDir::GDCM_DICOMDIR_NONE: - AddDicomDirImageToEnd(s); //FIXME - break; + tmpSI=s->GetNextSQItem(); } -} - -*/ - -/** - * \ingroup gdcmDicomDir - * \brief Well ... there is only one occurence -*/ -void gdcmDicomDir::AddDicomDirMeta() -{ - if(metaElems) - delete metaElems; - metaElems = new gdcmDicomDirMeta(&tagHT); + ClearEntry(); } /** - * \ingroup gdcmDicomDir - * \brief AddDicomDirPatientToEnd - * @param s SQ Item to enqueue to the DicomPatient chained List -*/ -void gdcmDicomDir::AddDicomDirPatientToEnd(gdcmSQItem *s) + * \brief AddPatientToEnd + * @param dd SQ Item to enqueue to the DicomPatient chained List + */ +bool DicomDir::AddPatientToEnd(DicomDirPatient *dd) { - patients.push_back(new gdcmDicomDirPatient(s, &tagHT)); + Patients.push_back(dd); + return true; } /** - * \ingroup gdcmDicomDir - * \brief AddDicomDirStudyToEnd - * @param s SQ Item to enqueue to the DicomDirStudy chained List + * \brief AddStudyToEnd + * @param dd SQ Item to enqueue to the DicomDirStudy chained List */ - void gdcmDicomDir::AddDicomDirStudyToEnd(gdcmSQItem *s) +bool DicomDir::AddStudyToEnd(DicomDirStudy *dd) { - if(patients.size()>0) + if( Patients.size() > 0 ) { - ListDicomDirPatient::iterator itp=patients.end(); + ListDicomDirPatient::iterator itp = Patients.end(); itp--; - (*itp)->AddDicomDirStudy(new gdcmDicomDirStudy(s, &tagHT)); + (*itp)->AddStudy(dd); + return true; } + return false; } + /** - * \ingroup gdcmDicomDir - * \brief AddDicomDirSerieToEnd - * @param s SQ Item to enqueue to the DicomDirSerie chained List + * \brief AddSerieToEnd + * @param dd SQ Item to enqueue to the DicomDirSerie chained List */ -void gdcmDicomDir::AddDicomDirSerieToEnd(gdcmSQItem *s) +bool DicomDir::AddSerieToEnd(DicomDirSerie *dd) { - if(patients.size()>0) + if( Patients.size() > 0 ) { - ListDicomDirPatient::iterator itp=patients.end(); + ListDicomDirPatient::iterator itp = Patients.end(); itp--; - if((*itp)->GetDicomDirStudies().size()>0) + DicomDirStudy *study = (*itp)->GetLastStudy(); + if( study ) { - ListDicomDirStudy::iterator itst=(*itp)->GetDicomDirStudies().end(); - itst--; - (*itst)->AddDicomDirSerie(new gdcmDicomDirSerie(s, &tagHT)); + study->AddSerie(dd); + return true; } } + return false; } /** - * \ingroup gdcmDicomDir - * \brief AddDicomDirImageToEnd - * @param s SQ Item to enqueue to the DicomDirImage chained List + * \brief AddImageToEnd + * @param dd SQ Item to enqueue to the DicomDirImage chained List */ - void gdcmDicomDir::AddDicomDirImageToEnd(gdcmSQItem *s) +bool DicomDir::AddImageToEnd(DicomDirImage *dd) { - if(patients.size()>0) + if( Patients.size() > 0 ) { - ListDicomDirPatient::iterator itp=patients.end(); + ListDicomDirPatient::iterator itp = Patients.end(); itp--; - if((*itp)->GetDicomDirStudies().size()>0) + DicomDirStudy *study = (*itp)->GetLastStudy(); + if( study ) { - ListDicomDirStudy::iterator itst=(*itp)->GetDicomDirStudies().end(); - itst--; - - if((*itst)->GetDicomDirSeries().size()>0) + DicomDirSerie *serie = study->GetLastSerie(); + if( serie ) { - ListDicomDirSerie::iterator its=(*itst)->GetDicomDirSeries().end(); - its--; - (*its)->AddDicomDirImage(new gdcmDicomDirImage(s, &tagHT)); + serie->AddImage(dd); + return true; } } } + return false; } /** - * \ingroup gdcmDicomDir - * \brief for each Header of the chained list, add/update the Patient/Study/Serie/Image info + * \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 gdcmDicomDir::SetElements(std::string &path, VectDocument &list) +void DicomDir::SetElements(std::string const & path, VectDocument const &list) { - std::string patPrevName="", patPrevID=""; - std::string studPrevInstanceUID="", studPrevID=""; - std::string serPrevInstanceUID="", serPrevID=""; + ClearEntry(); + ClearPatient(); + + std::string patPrevName = "", patPrevID = ""; + std::string studPrevInstanceUID = "", studPrevID = ""; + std::string serPrevInstanceUID = "", serPrevID = ""; std::string patCurName, patCurID; std::string studCurInstanceUID, studCurID; std::string serCurInstanceUID, serCurID; - SetElement(path,GDCM_DICOMDIR_META,NULL); - - for(VectDocument::iterator it=list.begin();it!=list.end();++it) + bool first = true; + for( VectDocument::const_iterator it = list.begin(); + it != list.end(); ++it ) { // get the current file characteristics - patCurName= (*it)->GetEntryByNumber(0x0010,0x0010); - patCurID= (*it)->GetEntryByNumber(0x0010,0x0011); - studCurInstanceUID=(*it)->GetEntryByNumber(0x0020,0x000d); - studCurID= (*it)->GetEntryByNumber(0x0020,0x0010); - serCurInstanceUID= (*it)->GetEntryByNumber(0x0020,0x000e); - serCurID= (*it)->GetEntryByNumber(0x0020,0x0011); - - if(patCurName!=patPrevName || patCurID!=patPrevID) - SetElement(path,GDCM_DICOMDIR_PATIENT,*it); + patCurName = (*it)->GetEntryValue(0x0010,0x0010); + patCurID = (*it)->GetEntryValue(0x0010,0x0011); + studCurInstanceUID = (*it)->GetEntryValue(0x0020,0x000d); + studCurID = (*it)->GetEntryValue(0x0020,0x0010); + serCurInstanceUID = (*it)->GetEntryValue(0x0020,0x000e); + serCurID = (*it)->GetEntryValue(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) - SetElement(path,GDCM_DICOMDIR_STUDY,*it); + 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) - SetElement(path,GDCM_DICOMDIR_SERIE,*it); + 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; + SetElement(path, GDCM_DICOMDIR_IMAGE, *it); + + patPrevName = patCurName; + patPrevID = patCurID; + studPrevInstanceUID = studCurInstanceUID; + studPrevID = studCurID; + serPrevInstanceUID = serCurInstanceUID; + serPrevID = serCurID; + first = false; } } /** - * \ingroup gdcmDicomDir - * \brief compares two dgcmHeaders + * \brief Move the content of the source SQItem to the destination SQItem + * Only DocEntry's are moved + * @param dst destination SQItem + * @param src source SQItem */ -bool gdcmDicomDir::HeaderLessThan(gdcmDocument *header1,gdcmDocument *header2) +void DicomDir::MoveSQItem(DocEntrySet *dst,DocEntrySet *src) { - return(*header1<*header2); + DocEntry *entry; + + entry = src->GetFirstEntry(); + while(entry) + { + src->RemoveEntryNoDestroy(entry); + dst->AddEntry(entry); + // we destroyed -> the current iterator is not longer valid + entry = src->GetFirstEntry(); + } } /** - * \ingroup gdcmDicomDir - * \brief Sets the accurate value for the (0x0004,0x1220) element of a DICOMDIR + * \brief compares two files */ +bool DicomDir::HeaderLessThan(Document *header1, Document *header2) +{ + return *header1 < *header2; +} -void gdcmDicomDir::UpdateDirectoryRecordSequenceLength() { - -// FIXME : to go on compiling - -// to be re written ! -/* - int offset = 0; - ListTag::iterator it; - guint16 gr, el; - std::string vr; - for(it=listEntries.begin();it!=listEntries.end();++it) { - gr = (*it)->GetGroup(); - el = (*it)->GetElement(); - vr = (*it)->GetVR(); - if (gr !=0xfffe) { - if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") ) { - offset += 4; // explicit VR AND OB, OW, SQ : 4 more bytes - } - offset += 2 + 2 + 4 + (*it)->GetLength(); - } else { - offset += 4; // delimiters don't have a value. - } +//----------------------------------------------------------------------------- +// Print +/** + * \brief Canonical Printer + * @param os ostream we want to print in + * @param indent Indentation string to be prepended during printing + */ +void DicomDir::Print(std::ostream &os, std::string const & ) +{ + if( MetaElems ) + { + MetaElems->SetPrintLevel(PrintLevel); + MetaElems->Print(os); } - //bool res=SetEntryLengthByNumber(offset, 0x0004, 0x1220); // Hope there is no dupps. - SetEntryLengthByNumber(offset, 0x0004, 0x1220); // Hope there is no dupps. - return; - */ + for(ListDicomDirPatient::iterator cc = Patients.begin(); + cc != Patients.end(); + ++cc) + { + (*cc)->SetPrintLevel(PrintLevel); + (*cc)->Print(os); + } } //----------------------------------------------------------------------------- +} // end namespace gdcm