X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDicomDir.cxx;h=6f80dfce2b7d19b98e1c92d63edf93ca73365ad9;hb=8cdbf11a3b1f8427281f31a9fd2a70aa66d620fa;hp=23f33438381c7bcaba3c3defa3d39e2095ff7e62;hpb=e785350bf905bcac85e241f9cf9f07d03eae345d;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index 23f33438..6f80dfce 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -1,58 +1,141 @@ // gdcmDicomDir.cxx //----------------------------------------------------------------------------- -#include "gdcmDicomDir.h" -#include "gdcmStudy.h" -#include "gdcmSerie.h" -#include "gdcmImage.h" -#include "gdcmDirList.h" -#include "gdcmUtil.h" - #include #include - #include #include + +#ifdef _MSC_VER + #include +#else + #include +#endif + +#include "gdcmDicomDir.h" +#include "gdcmDicomDirStudy.h" +#include "gdcmDicomDirSerie.h" +#include "gdcmDicomDirImage.h" +#include "gdcmDirList.h" +#include "gdcmUtil.h" +#include "gdcmDebug.h" +#include "gdcmGlobal.h" + //----------------------------------------------------------------------------- // For full DICOMDIR description, see: // PS 3.3-2003, pages 731-750 //----------------------------------------------------------------------------- + + // Constructor / Destructor -/* - * \ingroup gdcmDicomDir - * \brief Constructor - * @param Filename - * @param exception_on_error + +/** + * \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 + * @param exception_on_error whether we want to throw an exception or not */ gdcmDicomDir::gdcmDicomDir(const char *FileName, bool parseDir, bool exception_on_error): - gdcmParser(FileName,exception_on_error,true) + gdcmParser(FileName,exception_on_error,true) // true : enable SeQuences { + // que l'on ai passe un root directory ou un DICOMDIR + // et quelle que soit la valeur de parseDir, + // on a lance gdcmParser + + 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; +// gdcmParser already executed +// if user passed a root directory, sure we didn't get anything + if( GetListEntry().begin()==GetListEntry().end() ) { + // if parseDir == false, it should be tagged as an error dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : entry list empty"); + if(strlen(FileName)==1 && FileName[0]=='.') { // user passed '.' as Name + // we get current directory name + char* dummy= new char[1000]; + getcwd(dummy, (size_t)1000); + SetFileName(dummy); // will be converted into a string + delete[] dummy; // no longer needed + } + if(parseDir) { - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : Parse directory and create the DicomDir"); + dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : Parse directory" + " and create the DicomDir"); ParseDirectory(); } } - else + else { CreateDicomDir(); + CheckBoundaries(); // to maintain consistency between + // home-made gdcmDicomDir + // and the ones comming from a DICOMDIR file + } +} + +/** + * \ingroup gdcmDicomDir + * \brief Constructor : creates an empty gdcmDicomDir + * @param exception_on_error whether we want to throw an exception or not + */ +gdcmDicomDir::gdcmDicomDir(bool exception_on_error): + gdcmParser(exception_on_error) +{ + startMethod= NULL; + progressMethod= NULL; + endMethod= NULL; + startMethodArgDelete= NULL; + progressMethodArgDelete=NULL; + endMethodArgDelete= NULL; + startArg= NULL; + progressArg= NULL; + endArg= NULL; + + progress=0.0; + abort=false; + std::string pathBidon = ""; // Sorry, NULL not allowed ... + SetElement(pathBidon, GDCM_DICOMDIR_META, NULL); // Set the META elements + + AddDicomDirMetaToEnd(listEntries.begin(),--listEntries.end()); } -/* + +/** * \ingroup gdcmDicomDir * \brief Canonical destructor */ gdcmDicomDir::~gdcmDicomDir() { + SetStartMethod(NULL); + SetProgressMethod(NULL); + SetEndMethod(NULL); + if(metaElems) delete metaElems; - for(ListPatient::iterator cc=patients.begin();cc!=patients.end();++cc) + for(ListDicomDirPatient::iterator cc=patients.begin();cc!=patients.end();++cc) { delete *cc; } @@ -60,7 +143,7 @@ gdcmDicomDir::~gdcmDicomDir() //----------------------------------------------------------------------------- // Print -/* +/** * \ingroup gdcmDicomDir * \brief Canonical Printer */ @@ -70,25 +153,149 @@ void gdcmDicomDir::Print(std::ostream &os) { metaElems->SetPrintLevel(printLevel); metaElems->Print(os); - } - - for(ListPatient::iterator cc=patients.begin();cc!=patients.end();++cc) + } + for(ListDicomDirPatient::iterator cc=patients.begin();cc!=patients.end();++cc) { (*cc)->SetPrintLevel(printLevel); - (*cc)->Print(os); + (*cc)->Print(os); } } //----------------------------------------------------------------------------- // Public +/** + * \ingroup gdcmDicomDir + * \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 gdcmParser is the one of a reasonable DicomDir, + * false otherwise. + */ +bool gdcmDicomDir::IsReadable(void) +{ + if(!gdcmParser::IsReadable()) + return(false); + if(!metaElems) + return(false); + if(patients.size()<=0) + return(false); + + return(true); +} + +/** + * \ingroup gdcmDicomDir + * \brief fills the whole structure, starting from a root Directory + */ +void gdcmDicomDir::ParseDirectory(void) +{ + CreateDicomDirChainedList(GetFileName()); + CreateDicomDir(); +} + +/** + * \ingroup gdcmDicomDir + * \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) +{ + if((startArg)&&(startMethodArgDelete)) + startMethodArgDelete(startArg); + + 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) +{ + startMethodArgDelete=method; +} + +/** + * \ingroup gdcmDicomDir + * \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) +{ + if((progressArg)&&(progressMethodArgDelete)) + progressMethodArgDelete(progressArg); + + 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) +{ + 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) +{ + if((endArg)&&(endMethodArgDelete)) + endMethodArgDelete(endArg); + + 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 + * @param method Method to call to delete the argument + */ +void gdcmDicomDir::SetEndMethodArgDelete(gdcmMethod *method) +{ + endMethodArgDelete=method; +} + /** * \ingroup gdcmDicomDir * \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 gdcmDicomDir::Write(std::string fileName) { FILE * fp1; @@ -100,39 +307,83 @@ bool gdcmDicomDir::Write(std::string fileName) return(false); } - char * filePreamble; - filePreamble=(char*)calloc(128,1); + char * filePreamble = new char[128]; fwrite(filePreamble,128,1,fp1); fwrite("DICM",4,1,fp1); - free(filePreamble); - - WriteEntries(fp1,DICOMDIR); + delete[] filePreamble; + UpdateDirectoryRecordSequenceLength(); + WriteEntries(fp1); fclose(fp1); - return true; } -/* - * \ingroup gdcmDicomDir - * \brief fills whole the structure +/** + * \brief Writes in a file using the tree-like structure. + * @param _fp already open file pointer */ -void gdcmDicomDir::ParseDirectory(void) -{ - NewDicomDir(GetPath()); - CreateDicomDir(); -} +void gdcmDicomDir::WriteEntries(FILE *_fp) +{ + /// \todo (?) tester les echecs en ecriture + /// (apres chaque fwrite, dans le WriteEntry) + + 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, ExplicitVR); + } + + itPatient = GetDicomDirPatients().begin(); + while ( itPatient != GetDicomDirPatients().end() ) { + for(i=(*itPatient)->debut();i!=(*itPatient)->fin();++i) { + WriteEntry(*i,_fp, ExplicitVR); + } + itStudy = ((*itPatient)->GetDicomDirStudies()).begin(); + while (itStudy != (*itPatient)->GetDicomDirStudies().end() ) { + for(i=(*itStudy)->debut();i!=(*itStudy)->fin();++i) { + WriteEntry(*i,_fp, ExplicitVR); + } + itSerie = ((*itStudy)->GetDicomDirSeries()).begin(); + while (itSerie != (*itStudy)->GetDicomDirSeries().end() ) { + for(i=(*itSerie)->debut();i!=(*itSerie)->fin();++i) { + WriteEntry(*i,_fp, ExplicitVR); + } + itImage = ((*itSerie)->GetDicomDirImages()).begin(); + while (itImage != (*itSerie)->GetDicomDirImages().end() ) { + for(i=(*itImage)->debut();i!=(*itImage)->fin();++i) { + WriteEntry(*i,_fp, ExplicitVR); + } + ++itImage; + } + ++itSerie; + } + ++itStudy; + } + ++itPatient; + } +} + //----------------------------------------------------------------------------- // Protected -/* + +/** * \ingroup gdcmDicomDir - * \brief create a gdcmDicomDir from a root Directory - * @param path entry point of the stree-like structure + * \brief create a gdcmHeader-like chained list from a root Directory + * @param path entry point of the tree-like structure */ -void gdcmDicomDir::NewDicomDir(std::string path) +void gdcmDicomDir::CreateDicomDirChainedList(std::string path) { - gdcmDirList fileList(path,1); + CallStartMethod(); + + gdcmDirList fileList(path,1); // gets recursively the file list + unsigned int count=0; ListHeader list; gdcmHeader *header; @@ -140,59 +391,184 @@ void gdcmDicomDir::NewDicomDir(std::string path) patients.clear(); for(gdcmDirList::iterator it=fileList.begin(); - it!=fileList.end(); ++it) + it!=fileList.end(); + ++it) { - std::cout<<*it<c_str()); if(header->IsReadable()) - list.push_back(header); + list.push_back(header); // adds the file header to the chained list 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); + + CallEndMethod(); } -/* +/** * \ingroup gdcmDicomDir - * \brief Get the DicomDir path - * @param + * \brief modifies the limits of a gdcmObject, created from a DICOMDIR file */ -std::string gdcmDicomDir::GetPath(void) -{ - std::string path=GetFileName(); - int pos1=path.rfind("/"); - int pos2=path.rfind("\\"); - if(pos1>pos2) - path.resize(pos1); - else - path.resize(pos2); +void gdcmDicomDir::CheckBoundaries() +{ + ListDicomDirPatient::iterator itPatient; + ListDicomDirStudy::iterator itStudy; + ListDicomDirSerie::iterator itSerie; + ListDicomDirImage::iterator itImage; + ListTag::iterator i,j; + + GetDicomDirMeta()->ResetBoundaries(0); + + itPatient = GetDicomDirPatients().begin(); + while ( itPatient != GetDicomDirPatients().end() ) { + (*itPatient)->ResetBoundaries(1); + itStudy = ((*itPatient)->GetDicomDirStudies()).begin(); + while (itStudy != (*itPatient)->GetDicomDirStudies().end() ) { + (*itStudy)->ResetBoundaries(1); + itSerie = ((*itStudy)->GetDicomDirSeries()).begin(); + while (itSerie != (*itStudy)->GetDicomDirSeries().end() ) { + (*itSerie)->ResetBoundaries(1); + itImage = ((*itSerie)->GetDicomDirImages()).begin(); + while (itImage != (*itSerie)->GetDicomDirImages().end() ) { + (*itImage)->ResetBoundaries(1); + ++itImage; + } + ++itSerie; + } + ++itStudy; + } + ++itPatient; + } +} + + +/** + * \ingroup gdcmDicomDir + * \brief adds a new Patient to a partially created DICOMDIR + */ +gdcmDicomDirPatient * gdcmDicomDir::NewPatient(void) { + std::list elemList; + std::list::iterator it; + guint16 tmpGr,tmpEl; + gdcmDictEntry *dictEntry; + gdcmHeaderEntry *entry; + + elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirPatientElements(); + std::list::iterator debInsertion, finInsertion, i,j; + + debInsertion = metaElems->fin(); + ++debInsertion; + finInsertion=debInsertion; + + // for all the DicomDirPatient Elements + for(it=elemList.begin();it!=elemList.end();++it) + { + tmpGr=it->group; + tmpEl=it->elem; + dictEntry=GetPubDict()->GetDictEntryByNumber(tmpGr,tmpEl); + entry=new gdcmHeaderEntry(dictEntry); + entry->SetOffset(0); // just to avoid missprinting + entry->SetValue(it->value); - return(path); + 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()); + } + + tagHT.insert( PairHT(entry->GetKey(),entry) ); // add in the (multimap) H Table + listEntries.insert(debInsertion ,entry); // en tete de liste des Patients + ++finInsertion; + } + + i=metaElems->fin(); + i++; + + gdcmDicomDirPatient *p = new gdcmDicomDirPatient(i, --debInsertion, + &tagHT, &listEntries); + patients.push_front(p); + return p; +} + +/** + * \ingroup gdcmDicomDir + * \brief CallStartMethod + */ +void gdcmDicomDir::CallStartMethod(void) +{ + progress=0.0f; + abort=false; + if(startMethod) + startMethod(startArg); +} +/** + * \ingroup gdcmDicomDir + * \brief CallProgressMethod + */ +void gdcmDicomDir::CallProgressMethod(void) +{ + if(progressMethod) + progressMethod(progressArg); +} +/** + * \ingroup gdcmDicomDir + * \brief CallEndMethod + */ +void gdcmDicomDir::CallEndMethod(void) +{ + progress=1.0f; + if(endMethod) + endMethod(endArg); } //----------------------------------------------------------------------------- // Private -/* +/** * \ingroup gdcmDicomDir * \brief create a 'gdcmDicomDir' from a DICOMDIR gdcmHeader */ void gdcmDicomDir::CreateDicomDir() { - // The list is parsed. When a tag is found : + // 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 - - gdcmDicomDirType type=gdcmDicomDir::GDCM_META; + gdcmDicomDirType type=gdcmDicomDir::GDCM_DICOMDIR_META; ListTag::iterator begin; - ListTag::iterator end; + ListTag::iterator end, end2; begin=listEntries.begin(); end=begin; @@ -201,53 +577,47 @@ void gdcmDicomDir::CreateDicomDir() std::string v=(*i)->GetValue(); if(v=="PATIENT ") { - end=i; - AddObjectToEnd(type,begin,end); - - type=gdcmDicomDir::GDCM_PATIENT; + end=end2=i; + AddObjectToEnd(type,begin,--end2); + type=gdcmDicomDir::GDCM_DICOMDIR_PATIENT; begin=end; } if(v=="STUDY ") { - end=i; - AddObjectToEnd(type,begin,end); - - type=gdcmDicomDir::GDCM_STUDY; + end=end2=i; + AddObjectToEnd(type,begin,--end2); + type=gdcmDicomDir::GDCM_DICOMDIR_STUDY; begin=end; } if(v=="SERIES") { - end=i; - AddObjectToEnd(type,begin,end); - - type=gdcmDicomDir::GDCM_SERIE; + end=end2=i; + AddObjectToEnd(type,begin,--end2); + type=gdcmDicomDir::GDCM_DICOMDIR_SERIE; begin=end; } if(v=="IMAGE ") { - end=i; - AddObjectToEnd(type,begin,end); - - type=gdcmDicomDir::GDCM_IMAGE; + end=end2=i; + AddObjectToEnd(type,begin,--end2); + type=gdcmDicomDir::GDCM_DICOMDIR_IMAGE; begin=end; } } + end=end2=listEntries.end(); if(begin!=end) - { - end=GetListEntry().end(); - AddObjectToEnd(type,begin,end); - } + AddObjectToEnd(type,begin,--end2); } -/* +/** * \ingroup gdcmDicomDir - * \brief + * \brief AddObjectToEnd * @param type - * @param begin - * @param end + * @param begin iterator on the first HeaderEntry within the chained List + * @param end iterator on the last HeaderEntry within the chained List */ void gdcmDicomDir::AddObjectToEnd(gdcmDicomDirType type,ListTag::iterator begin,ListTag::iterator end) { @@ -256,171 +626,175 @@ void gdcmDicomDir::AddObjectToEnd(gdcmDicomDirType type,ListTag::iterator begin, switch(type) { - case gdcmDicomDir::GDCM_META: - AddMetaToEnd(begin,end); + case gdcmDicomDir::GDCM_DICOMDIR_META: + AddDicomDirMetaToEnd(begin,end); break; - case gdcmDicomDir::GDCM_PATIENT: - AddPatientToEnd(begin,end); + case gdcmDicomDir::GDCM_DICOMDIR_PATIENT: + AddDicomDirPatientToEnd(begin,end); break; - case gdcmDicomDir::GDCM_STUDY: - AddStudyToEnd(begin,end); + case gdcmDicomDir::GDCM_DICOMDIR_STUDY: + AddDicomDirStudyToEnd(begin,end); break; - case gdcmDicomDir::GDCM_SERIE: - AddSerieToEnd(begin,end); + case gdcmDicomDir::GDCM_DICOMDIR_SERIE: + AddDicomDirSerieToEnd(begin,end); break; - case gdcmDicomDir::GDCM_IMAGE: - AddImageToEnd(begin,end); + case gdcmDicomDir::GDCM_DICOMDIR_IMAGE: + AddDicomDirImageToEnd(begin,end); break; + case gdcmDicomDir::GDCM_DICOMDIR_NONE: + AddDicomDirImageToEnd(begin,end); //FIXME + break; } } -/* +/** * \ingroup gdcmDicomDir * \brief Well ... Not realy to end, there is only one occurence - * @param begin - * @param end + * @param begin iterator on the first HeaderEntry within the chained List + * @param end iterator on the last HeaderEntry within the chained List */ -void gdcmDicomDir::AddMetaToEnd(ListTag::iterator begin,ListTag::iterator end) +void gdcmDicomDir::AddDicomDirMetaToEnd(ListTag::iterator begin,ListTag::iterator end) { if(metaElems) delete metaElems; - metaElems = new gdcmMeta(begin,end); + metaElems = new gdcmDicomDirMeta(begin,end,&tagHT,&listEntries); } -/* +/** * \ingroup gdcmDicomDir - * \brief - * @param begin - * @param end + * \brief AddDicomDirPatientToEnd + * @param begin iterator on the first HeaderEntry within the chained List + * @param end iterator on the last HeaderEntry within the chained List */ -void gdcmDicomDir::AddPatientToEnd(ListTag::iterator begin,ListTag::iterator end) +void gdcmDicomDir::AddDicomDirPatientToEnd(ListTag::iterator begin,ListTag::iterator end) { - patients.push_back(new gdcmPatient(begin,end)); + patients.push_back(new gdcmDicomDirPatient(begin,end,&tagHT, &listEntries)); } -/* +/** * \ingroup gdcmDicomDir - * \brief - * @param begin - * @param end + * \brief AddDicomDirStudyToEnd + * @param begin iterator on the first HeaderEntry within the chained List + * @param end iterator on the last HeaderEntry within the chained List */ - void gdcmDicomDir::AddStudyToEnd(ListTag::iterator begin,ListTag::iterator end) + void gdcmDicomDir::AddDicomDirStudyToEnd(ListTag::iterator begin,ListTag::iterator end) { if(patients.size()>0) { - ListPatient::iterator itp=patients.end(); + ListDicomDirPatient::iterator itp=patients.end(); itp--; - (*itp)->AddStudy(new gdcmStudy(begin,end)); + (*itp)->AddDicomDirStudy(new gdcmDicomDirStudy(begin,end,&tagHT, &listEntries)); } } -/* +/** * \ingroup gdcmDicomDir - * \brief - * @param begin - * @param end + * \brief AddDicomDirSerieToEnd + * @param begin iterator on the first HeaderEntry within the chained List + * @param end iterator on the last HeaderEntry within the chained List */ -void gdcmDicomDir::AddSerieToEnd(ListTag::iterator begin,ListTag::iterator end) +void gdcmDicomDir::AddDicomDirSerieToEnd(ListTag::iterator begin,ListTag::iterator end) { if(patients.size()>0) { - ListPatient::iterator itp=patients.end(); + ListDicomDirPatient::iterator itp=patients.end(); itp--; - if((*itp)->GetStudies().size()>0) + if((*itp)->GetDicomDirStudies().size()>0) { - ListStudy::iterator itst=(*itp)->GetStudies().end(); + ListDicomDirStudy::iterator itst=(*itp)->GetDicomDirStudies().end(); itst--; - (*itst)->AddSerie(new gdcmSerie(begin,end)); + (*itst)->AddDicomDirSerie(new gdcmDicomDirSerie(begin,end,&tagHT, &listEntries)); } } } -/* +/** * \ingroup gdcmDicomDir - * @param begin - * @param end - * @param + * \brief AddDicomDirImageToEnd + * @param begin iterator on the first HeaderEntry within the chained List + * @param end iterator on the last HeaderEntry within the chained List */ - void gdcmDicomDir::AddImageToEnd(ListTag::iterator begin,ListTag::iterator end) + void gdcmDicomDir::AddDicomDirImageToEnd(ListTag::iterator begin,ListTag::iterator end) { if(patients.size()>0) { - ListPatient::iterator itp=patients.end(); + ListDicomDirPatient::iterator itp=patients.end(); itp--; - if((*itp)->GetStudies().size()>0) + if((*itp)->GetDicomDirStudies().size()>0) { - ListStudy::iterator itst=(*itp)->GetStudies().end(); + ListDicomDirStudy::iterator itst=(*itp)->GetDicomDirStudies().end(); itst--; - if((*itst)->GetSeries().size()>0) + if((*itst)->GetDicomDirSeries().size()>0) { - ListSerie::iterator its=(*itst)->GetSeries().end(); + ListDicomDirSerie::iterator its=(*itst)->GetDicomDirSeries().end(); its--; - (*its)->AddImage(new gdcmImage(begin,end)); + (*its)->AddDicomDirImage(new gdcmDicomDirImage(begin,end,&tagHT, &listEntries)); } } } } -/* +/** * \ingroup gdcmDicomDir - * \brief - * @param path - * @param list + * \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,ListHeader &list) +void gdcmDicomDir::SetElements(std::string &path, ListHeader &list) { - std::string patPrevName="", patPrevID=""; + std::string patPrevName="", patPrevID=""; std::string studPrevInstanceUID="", studPrevID=""; - std::string serPrevInstanceUID="", serPrevID=""; + std::string serPrevInstanceUID="", serPrevID=""; - std::string patCurName, patCurID; + std::string patCurName, patCurID; std::string studCurInstanceUID, studCurID; - std::string serCurInstanceUID, serCurID; + std::string serCurInstanceUID, serCurID; - SetElement(path,GDCM_NONE,NULL); + SetElement(path,GDCM_DICOMDIR_META,NULL); ListTag::iterator debPat=listEntries.begin(); for(ListHeader::iterator it=list.begin();it!=list.end();++it) { // get the current file characteristics - patCurName=(*it)->GetEntryByNumber(0x0010,0x0010); - patCurID=(*it)->GetEntryByNumber(0x0010,0x0011); + 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); + studCurID= (*it)->GetEntryByNumber(0x0020,0x0010); + serCurInstanceUID= (*it)->GetEntryByNumber(0x0020,0x000e); + serCurID= (*it)->GetEntryByNumber(0x0020,0x0011); if(patCurName!=patPrevName || patCurID!=patPrevID) - SetElement(path,GDCM_PATIENT,*it); + SetElement(path,GDCM_DICOMDIR_PATIENT,*it); // if new Study Deal with 'STUDY' Elements if(studCurInstanceUID!=studPrevInstanceUID || studCurID!=studPrevID) - SetElement(path,GDCM_STUDY,*it); + SetElement(path,GDCM_DICOMDIR_STUDY,*it); // if new Serie Deal with 'SERIE' Elements if(serCurInstanceUID!=serPrevInstanceUID || serCurID!=serPrevID) - SetElement(path,GDCM_SERIE,*it); + SetElement(path,GDCM_DICOMDIR_SERIE,*it); // Always Deal with 'IMAGE' Elements - SetElement(path,GDCM_IMAGE,*it); + SetElement(path,GDCM_DICOMDIR_IMAGE,*it); - patPrevName=patCurName; - patPrevID=patCurID; + patPrevName= patCurName; + patPrevID= patCurID; studPrevInstanceUID=studCurInstanceUID; - studPrevID=studCurID; - serPrevInstanceUID=serCurInstanceUID; - serPrevID=serCurID; + studPrevID= studCurID; + serPrevInstanceUID= serCurInstanceUID; + serPrevID= serCurID; } } -/* +/** * \ingroup gdcmDicomDir - * \brief - * @param path - * @param type - * @param header + * \brief adds to the HTable and at the end of the Chained List + * the gdcmEntries (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, GDCM_DICOMDIR_STUDY, GDCM_DICOMDIR_SERIE ...) + * @param header gdcmHeader of the current file */ void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type,gdcmHeader *header) { @@ -433,20 +807,20 @@ void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type,gdcmHeader switch(type) { - case GDCM_PATIENT: - elemList=gdcmGlobal::GetDicomDirElements()->GetPatientElements(); + case GDCM_DICOMDIR_PATIENT: + elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirPatientElements(); break; - case GDCM_STUDY: - elemList=gdcmGlobal::GetDicomDirElements()->GetStudyElements(); + case GDCM_DICOMDIR_STUDY: + elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirStudyElements(); break; - case GDCM_SERIE: - elemList=gdcmGlobal::GetDicomDirElements()->GetSerieElements(); + case GDCM_DICOMDIR_SERIE: + elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirSerieElements(); break; - case GDCM_IMAGE: - elemList=gdcmGlobal::GetDicomDirElements()->GetImageElements(); + case GDCM_DICOMDIR_IMAGE: + elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirImageElements(); break; - case GDCM_NONE: - elemList=gdcmGlobal::GetDicomDirElements()->GetMetaElements(); + case GDCM_DICOMDIR_META: + elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirMetaElements(); break; default: return; @@ -456,7 +830,6 @@ void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type,gdcmHeader { tmpGr=it->group; tmpEl=it->elem; - dictEntry=GetPubDict()->GetDictEntryByNumber(tmpGr,tmpEl); entry=new gdcmHeaderEntry(dictEntry); entry->SetOffset(0); // just to avoid missprinting @@ -468,10 +841,10 @@ void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type,gdcmHeader if(val==GDCM_UNFOUND) { - if((tmpGr==0x0004) &&(tmpEl==0x1130) ) - { - // TODO force the *end* File Name(remove path) - val=path; + if((tmpGr==0x0004) &&(tmpEl==0x1130) ) // File-set ID + { + // force to the *end* File Name + val=GetName(path); } else if( (tmpGr==0x0004) && (tmpEl==0x1500) ) // Only used for image { @@ -480,19 +853,30 @@ void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type,gdcmHeader dbg.Verbose(0, "gdcmDicomDir::SetElement : the base path of file name is incorrect"); val=header->GetFileName(); } - else - val=&(header->GetFileName()[path.length()]); + else { + val=&(header->GetFileName().c_str()[path.length()]); + } } else { val=it->value; } + } + else + { + if (header->GetEntryLengthByNumber(tmpGr,tmpEl)== 0) + val=it->value; } + entry->SetValue(val); if(dictEntry) { - if( (dictEntry->GetVR()=="UL") || (dictEntry->GetVR()=="SL") ) + if(dictEntry->GetGroup()==0xfffe) + { + entry->SetLength(entry->GetValue().length()); + } + else if( (dictEntry->GetVR()=="UL") || (dictEntry->GetVR()=="SL") ) { entry->SetLength(4); } @@ -509,14 +893,47 @@ void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type,gdcmHeader entry->SetLength(entry->GetValue().length()); } } - - listEntries.push_back(entry); + //AddHeaderEntry(entry); // both in H Table and in chained list + tagHT.insert( PairHT( entry->GetKey(),entry) ); + listEntries.push_back(entry); + //wasUpdated = 1; // is private } } - +/** + * \ingroup gdcmDicomDir + * \brief compares two dgcmHeaders + */ bool gdcmDicomDir::HeaderLessThan(gdcmHeader *header1,gdcmHeader *header2) { return(*header1<*header2); } +/** + * \ingroup gdcmDicomDir + * \brief Sets the accurate value for the (0x0004,0x1220) element of a DICOMDIR + */ + +void gdcmDicomDir::UpdateDirectoryRecordSequenceLength() { + 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. + } + } + //bool res=SetEntryLengthByNumber(offset, 0x0004, 0x1220); // Hope there is no dupps. + SetEntryLengthByNumber(offset, 0x0004, 0x1220); // Hope there is no dupps. + return; +} + //-----------------------------------------------------------------------------