X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDicomDir.cxx;h=b8501864e7d4907f7125c4d1cbfe911fe34aafcf;hb=14900333988858a95935ec735224433cf308c21c;hp=92cdc6f8702234cf7474e1132bf527ec82ede3d0;hpb=e503428831ed53cbd0d206d87ac25bac3254af2b;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index 92cdc6f8..b8501864 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -1,64 +1,167 @@ -// gdcmDicomDir.cxx -//----------------------------------------------------------------------------- -#include "gdcmDicomDir.h" -#include "gdcmStudy.h" -#include "gdcmSerie.h" -#include "gdcmImage.h" -#include "gdcmDirList.h" -#include "gdcmUtil.h" +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmDicomDir.cxx,v $ + Language: C++ + Date: $Date: 2004/07/17 22:36:55 $ + Version: $Revision: 1.56 $ + + 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. + + 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 #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" +#include "gdcmHeader.h" +#include "gdcmSeqEntry.h" +#include "gdcmSQItem.h" +#include "gdcmValEntry.h" + +//----------------------------------------------------------------------------- +// For full DICOMDIR description, see: +// PS 3.3-2003, pages 731-750 //----------------------------------------------------------------------------- // Constructor / Destructor -/* - * \ingroup gdcmDicomDir - * \brief - * @param Filename - * @param exception_on_error + +void gdcmDicomDir::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 = (gdcmDicomDirMeta *)0; +} + + +/** + * \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, +gdcmDicomDir::gdcmDicomDir(std::string const & fileName, bool parseDir, bool exception_on_error): - gdcmParser(FileName,exception_on_error,true) + gdcmDocument( fileName, exception_on_error, true) // true : enable SeQuences { - if( GetListEntry().begin()==GetListEntry().end() ) + // que l'on ai passe un root directory ou un DICOMDIR + // et quelle que soit la valeur de parseDir, + // on a deja lance gdcmDocument + Initialize(); + + // gdcmDocument already executed + // if user passed a root directory, sure we didn't get anything + + if( GetEntry().begin() == GetEntry().end() ) { - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : entry list empty"); + dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : entry HT empty"); - if(parseDir) + if( fileName.size() == 1 && fileName[0] == '.' ) { - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : Parse directory and create the DicomDir"); + // 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"); ParseDirectory(); } + else + { + /// \todo if parseDir == false, it should be tagged as an error + } } else + { + // Directory record sequence + gdcmDocEntry *e = GetDocEntryByNumber(0x0004, 0x1220); + if ( !e ) + { + dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : NO Directory record" + " sequence (0x0004,0x1220)"); + /// \todo FIXME : what do we do when the parsed file IS NOT a + /// DICOMDIR file ? + } CreateDicomDir(); + } } -/* +/** * \ingroup gdcmDicomDir - * \brief - * @param exception_on_error + * \brief Constructor : creates an empty gdcmDicomDir + * @param exception_on_error whether we want to throw an exception or not */ -/*gdcmDicomDir::gdcmDicomDir(ListTag *l, - bool exception_on_error): - gdcmParser(exception_on_error ) -{ - listEntries=*l; - CreateDicomDir(); -}*/ +gdcmDicomDir::gdcmDicomDir(bool exception_on_error): + gdcmDocument( exception_on_error ) +{ + Initialize(); -/* - * \ingroup gdcmDicomDir + std::string pathBidon = "Bidon"; // Sorry, NULL not allowed ... + SetElement(pathBidon, GDCM_DICOMDIR_META, NULL); // Set the META elements + AddDicomDirMeta(); +} + +/** * \brief Canonical destructor */ gdcmDicomDir::~gdcmDicomDir() { - for(ListPatient::iterator cc=patients.begin();cc!=patients.end();++cc) + SetStartMethod(NULL); + SetProgressMethod(NULL); + SetEndMethod(NULL); + + if( metaElems ) + { + delete metaElems; + } + + for(ListDicomDirPatient::iterator cc = patients.begin(); + cc!= patients.end(); + ++cc) { delete *cc; } @@ -66,422 +169,856 @@ gdcmDicomDir::~gdcmDicomDir() //----------------------------------------------------------------------------- // Print +/** + * \brief Canonical Printer + */ void gdcmDicomDir::Print(std::ostream &os) { - for(ListPatient::iterator cc=patients.begin();cc!=patients.end();++cc) + if(metaElems) { - (*cc)->SetPrintLevel(printLevel); - (*cc)->Print(os); + metaElems->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 gdcmDocument is the one of a reasonable DicomDir, + * false otherwise. + */ +bool gdcmDicomDir::IsReadable() +{ + if( !gdcmDocument::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() +{ + 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 ! + * 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 + * @return false only when fail to open */ -bool gdcmDicomDir::Write(std::string fileName) + +bool gdcmDicomDir::Write(std::string const & fileName) { FILE * fp1; - fp1=fopen(fileName.c_str(),"wb"); - if(fp1==NULL) + fp1 = fopen(fileName.c_str(), "wb"); + if( !fp1 ) { - printf("Failed to open(write) File [%s] \n",fileName.c_str()); - return(false); + printf("Failed to open(write) File [%s] \n", fileName.c_str()); + 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); - - fclose(fp1); + delete[] filePreamble; + UpdateDirectoryRecordSequenceLength(); + WriteEntries(fp1); + fclose( fp1 ); return true; } -void gdcmDicomDir::ParseDirectory(void) -{ - NewDicomDir(GetPath()); - CreateDicomDir(); -} +/** + * \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 - * @param + * \brief create a gdcmDocument-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 const & path) { - gdcmDirList fileList(path,1); - ListHeader list; + CallStartMethod(); + gdcmDirList fileList(path,1); // gets recursively the file list + unsigned int count = 0; + VectDocument list; gdcmHeader *header; - listEntries.clear(); + tagHT.clear(); patients.clear(); - for(gdcmDirList::iterator it=fileList.begin(); - it!=fileList.end(); ++it) + for( gdcmDirList::iterator it = fileList.begin(); + it != fileList.end(); + ++it ) { - header=new gdcmHeader(it->c_str()); - if(header->IsReadable()) - list.push_back(header); + progress = (float)(count+1)/(float)fileList.size(); + CallProgressMethod(); + if( abort ) + { + break; + } + + header = new gdcmHeader(it->c_str(),false,true); + if(!header) { + std::cout << "echec new Header " << it->c_str() << std::endl; // JPR + } + if(header->IsReadable()) { + list.push_back(header); // adds the file header to the chained list + std::cout << "readable : " <c_str() << std::endl; // JPR + } else + { delete header; - } + } + count++; - std::sort(list.begin(),list.end(),gdcmDicomDir::HeaderLessThan); + } + // sorts Patient/Study/Serie/ + std::sort(list.begin(), list.end(), gdcmDicomDir::HeaderLessThan ); - SetElements(path,list); + 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 dicom dir path - * @param + * \brief adds *the* Meta to a partially created DICOMDIR */ -std::string gdcmDicomDir::GetPath(void) + + /// \todo FIXME : Heuuuuu ! Il prend les Entries du Document deja parse, + /// il ne fabrique rien ! + +gdcmDicomDirMeta * gdcmDicomDir::NewMeta() { - std::string path=GetFileName(); + gdcmDicomDirMeta *m = new gdcmDicomDirMeta( &tagHT ); + for ( TagDocEntryHT::iterator cc = tagHT.begin(); + cc != tagHT.end(); ++cc) + { + m->AddDocEntry( cc->second ); + } + return m; +} - int pos1=path.rfind("/"); - int pos2=path.rfind("\\"); - if(pos1>pos2) - path.resize(pos1); - else - path.resize(pos2); - return(path); +/** + * \brief adds a new Patient (with the basic elements) to a partially created DICOMDIR + */ +gdcmDicomDirPatient * gdcmDicomDir::NewPatient() +{ + std::list::iterator it; + uint16_t tmpGr,tmpEl; + gdcmDictEntry *dictEntry; + gdcmValEntry *entry; + + gdcmSQItem *s = new gdcmSQItem(0); + + std::list elemList = + gdcmGlobal::GetDicomDirElements()->GetDicomDirPatientElements(); + + /// \todo TODO : use FillObject !!! + + // 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 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 ); + } + + gdcmDicomDirPatient *p = new gdcmDicomDirPatient(s, &tagHT); + patients.push_front( p ); + + return p; +} + +/** + * \brief adds to the HTable + * 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, + gdcmDocument *header) +{ + std::list elemList; + std::list::iterator it; + uint16_t tmpGr, tmpEl; + gdcmDictEntry *dictEntry; + gdcmValEntry *entry; + std::string val; + + switch( type ) + { + case GDCM_DICOMDIR_PATIENT: + elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirPatientElements(); + break; + case GDCM_DICOMDIR_STUDY: + elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirStudyElements(); + break; + case GDCM_DICOMDIR_SERIE: + elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirSerieElements(); + break; + case GDCM_DICOMDIR_IMAGE: + elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirImageElements(); + break; + case GDCM_DICOMDIR_META: + elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirMetaElements(); + break; + default: + return; + } + + 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->SetOffset(0); // just to avoid further missprinting + + if( header ) + { + val = header->GetEntryByNumber(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 = GetName( path ); + } + else if( tmpGr == 0x0004 && tmpEl == 0x1500 ) // Only used for image + { + if( header->GetFileName().substr(0, path.length()) != path ) + { + dbg.Verbose(0, "gdcmDicomDir::SetElement : 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->GetEntryLengthByNumber(tmpGr,tmpEl) == 0 ) + { + val = it->value; + } + } + + entry->SetValue( val ); + + if( dictEntry ) + { + 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() ); + } + } + //AddDocEntry(entry); // both in H Table and in chained list + tagHT[entry->GetKey()] = entry; // FIXME : use a SEQUENCE ! + } +} + +/** + * \brief CallStartMethod + */ +void gdcmDicomDir::CallStartMethod() +{ + progress = 0.0f; + abort = false; + if( startMethod ) + { + startMethod( startArg ); + } +} + +/** + * \ingroup gdcmDicomDir + * \brief CallProgressMethod + */ +void gdcmDicomDir::CallProgressMethod() +{ + if( progressMethod ) + { + progressMethod( progressArg ); + } +} + +/** + * \ingroup gdcmDicomDir + * \brief CallEndMethod + */ +void gdcmDicomDir::CallEndMethod() +{ + progress = 1.0f; + if( endMethod ) + { + endMethod( endArg ); + } } //----------------------------------------------------------------------------- // Private -/* +/** * \ingroup gdcmDicomDir - * \brief - * @param + * \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_NONE; - ListTag::iterator begin; - ListTag::iterator end; + gdcmDicomDirType type = gdcmDicomDir::GDCM_DICOMDIR_META; + + // Directory record sequence + gdcmDocEntry *e = GetDocEntryByNumber(0x0004, 0x1220); + if ( !e ) + { + dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : NO Directory record" + " sequence (0x0004,0x1220)"); + /// \todo FIXME: what to do when the parsed file IS NOT a DICOMDIR file ? + return; + } + + gdcmSeqEntry* s = dynamic_cast(e); + if ( !s ) + { + dbg.Verbose(0, "gdcmDicomDir::CreateDicomDir: no SeqEntry present"); + return; + } - begin=listEntries.begin(); - end=begin; - for(ListTag::iterator i=listEntries.begin();i !=listEntries.end();++i) + ListSQItem listItems = s->GetSQItems(); + gdcmDicomDirMeta *m = new gdcmDicomDirMeta(&tagHT); + (void)m; //?? + + gdcmDocEntry * d; + std::string v; + for( ListSQItem::iterator i = listItems.begin(); + i !=listItems.end(); ++i ) { - std::string v=(*i)->GetValue(); - if(v=="PATIENT ") + d = (*i)->GetDocEntryByNumber(0x0004, 0x1430); // Directory Record Type + if ( gdcmValEntry* ValEntry = dynamic_cast< gdcmValEntry* >(d) ) { - end=i; - AddObjectToEnd(type,begin,end); - - type=gdcmDicomDir::GDCM_PATIENT; - begin=end; - } - - if(v=="STUDY ") + v = ValEntry->GetValue(); + } + else { - end=i; - AddObjectToEnd(type,begin,end); - - type=gdcmDicomDir::GDCM_STUDY; - begin=end; + dbg.Verbose(0, "gdcmDicomDir::CreateDicomDir: not a ValEntry."); + continue; } - if(v=="SERIES") + if( v == "PATIENT " ) { - end=i; - AddObjectToEnd(type,begin,end); - - type=gdcmDicomDir::GDCM_SERIE; - begin=end; + AddDicomDirPatientToEnd( *i ); + //AddObjectToEnd(type,*i); + type = gdcmDicomDir::GDCM_DICOMDIR_PATIENT; } - - if(v=="IMAGE ") + else if( v == "STUDY " ) { - end=i; - AddObjectToEnd(type,begin,end); - - type=gdcmDicomDir::GDCM_IMAGE; - begin=end; + AddDicomDirStudyToEnd( *i ); + // AddObjectToEnd(type,*i); + type = gdcmDicomDir::GDCM_DICOMDIR_STUDY; + } + else if( v == "SERIES" ) + { + AddDicomDirSerieToEnd( *i ); + // AddObjectToEnd(type,*i); + type = gdcmDicomDir::GDCM_DICOMDIR_SERIE; + } + else if( v == "IMAGE " ) + { + AddDicomDirImageToEnd( *i ); + // AddObjectToEnd(type,*i); + type = gdcmDicomDir::GDCM_DICOMDIR_IMAGE; + } + else + { + // It was not a 'PATIENT', nor a 'STUDY', nor a 'SERIE', + // neither an 'IMAGE' SQItem. Skip to next item. + continue; } } - - end=GetListEntry().end(); - AddObjectToEnd(type,begin,end); } -/* + +/** * \ingroup gdcmDicomDir - * \brief - * @param + * \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 */ -void gdcmDicomDir::AddObjectToEnd(gdcmDicomDirType type,ListTag::iterator begin,ListTag::iterator end) + +// now useless ? + +/*void gdcmDicomDir::AddObjectToEnd(gdcmDicomDirType type,gdcmSQItem *s) { - if(begin==end) + if(s==NULL) // ?? return; switch(type) { - case gdcmDicomDir::GDCM_PATIENT: - AddPatientToEnd(begin,end); + 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_STUDY: - AddStudyToEnd(begin,end); + case gdcmDicomDir::GDCM_DICOMDIR_SERIE: + AddDicomDirSerieToEnd(s); break; - case gdcmDicomDir::GDCM_SERIE: - AddSerieToEnd(begin,end); + case gdcmDicomDir::GDCM_DICOMDIR_IMAGE: + AddDicomDirImageToEnd(s); break; - case gdcmDicomDir::GDCM_IMAGE: - AddImageToEnd(begin,end); + case gdcmDicomDir::GDCM_DICOMDIR_NONE: + AddDicomDirImageToEnd(s); //FIXME break; } } -/* +*/ + +/** + * \ingroup gdcmDicomDir + * \brief Well ... there is only one occurence + */ +void gdcmDicomDir::AddDicomDirMeta() +{ + if( metaElems ) + { + delete metaElems; + } + metaElems = new gdcmDicomDirMeta( &tagHT ); +} + +/** * \ingroup gdcmDicomDir - * \brief - * @param + * \brief AddDicomDirPatientToEnd + * @param s SQ Item to enqueue to the DicomPatient chained List */ -void gdcmDicomDir::AddPatientToEnd(ListTag::iterator begin,ListTag::iterator end) +void gdcmDicomDir::AddDicomDirPatientToEnd(gdcmSQItem *s) { - patients.push_back(new gdcmPatient(begin,end)); + patients.push_back(new gdcmDicomDirPatient(s, &tagHT)); } -/* +/** * \ingroup gdcmDicomDir - * \brief - * @param + * \brief AddDicomDirStudyToEnd + * @param s SQ Item to enqueue to the DicomDirStudy chained List */ - void gdcmDicomDir::AddStudyToEnd(ListTag::iterator begin,ListTag::iterator end) + void gdcmDicomDir::AddDicomDirStudyToEnd(gdcmSQItem *s) { - if(patients.size()>0) + 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(s, &tagHT)); } } -/* + +/** * \ingroup gdcmDicomDir - * \brief - * @param + * \brief AddDicomDirSerieToEnd + * @param s SQ Item to enqueue to the DicomDirSerie chained List */ -void gdcmDicomDir::AddSerieToEnd(ListTag::iterator begin,ListTag::iterator end) +void gdcmDicomDir::AddDicomDirSerieToEnd(gdcmSQItem *s) { - if(patients.size()>0) + 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(s, &tagHT)); } } } -/* +/** * \ingroup gdcmDicomDir - * \brief - * @param + * \brief AddDicomDirImageToEnd + * @param s SQ Item to enqueue to the DicomDirImage chained List */ - void gdcmDicomDir::AddImageToEnd(ListTag::iterator begin,ListTag::iterator end) + void gdcmDicomDir::AddDicomDirImageToEnd(gdcmSQItem *s) { - if(patients.size()>0) + 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(s, &tagHT)); } } } } -/* +/** * \ingroup gdcmDicomDir - * \brief - * @param + * \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, VectDocument &list) { - std::string patPrevName="", patPrevID=""; - std::string studPrevInstanceUID="", studPrevID=""; - std::string serPrevInstanceUID="", serPrevID=""; + std::string patPrevName = "", patPrevID = ""; + std::string studPrevInstanceUID = "", studPrevID = ""; + 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) + for( VectDocument::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); + 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_PATIENT,*it); + if( patCurName != patPrevName || patCurID != patPrevID) + { + SetElement(path, GDCM_DICOMDIR_PATIENT, *it); + } // if new Study Deal with 'STUDY' Elements - if(studCurInstanceUID!=studPrevInstanceUID || studCurID!=studPrevID) - SetElement(path,GDCM_STUDY,*it); + if( studCurInstanceUID != studPrevInstanceUID || studCurID != studPrevID ) + { + SetElement(path, GDCM_DICOMDIR_STUDY, *it); + } // if new Serie Deal with 'SERIE' Elements - if(serCurInstanceUID!=serPrevInstanceUID || serCurID!=serPrevID) + 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); - - 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; } } -/* +/** * \ingroup gdcmDicomDir - * \brief - * @param + * \brief compares two dgcmHeaders */ -void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type,gdcmHeader *header) +bool gdcmDicomDir::HeaderLessThan(gdcmDocument *header1, gdcmDocument *header2) { - std::list elemList; - std::list::iterator it; - guint16 tmpGr, tmpEl; - gdcmDictEntry *dictEntry; - gdcmHeaderEntry *entry; - std::string val; - - switch(type) - { - case GDCM_PATIENT: - elemList=gdcmGlobal::GetDicomDirElements()->GetPatientElements(); - break; - case GDCM_STUDY: - elemList=gdcmGlobal::GetDicomDirElements()->GetStudyElements(); - break; - case GDCM_SERIE: - elemList=gdcmGlobal::GetDicomDirElements()->GetSerieElements(); - break; - case GDCM_IMAGE: - elemList=gdcmGlobal::GetDicomDirElements()->GetImageElements(); - break; - case GDCM_NONE: - elemList=gdcmGlobal::GetDicomDirElements()->GetMetaElements(); - break; - default: - return; - } - - 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 - - if(header) - val=header->GetEntryByNumber(tmpGr,tmpEl); - else - val=GDCM_UNFOUND; - - if(val==GDCM_UNFOUND) - { - if((tmpGr==0x0004) &&(tmpEl==0x1130) ) - { - // TODO force the *end* File Name(remove path) - val=path; - } - else if( (tmpGr==0x0004) && (tmpEl==0x1500) ) // Only used for image - { - if(header->GetFileName().substr(0,path.length())!=path) - { - dbg.Verbose(0, "gdcmDicomDir::SetElement : the base path of file name is incorrect"); - val=header->GetFileName(); - } - else - val=&(header->GetFileName()[path.length()]); - } - else - { - val=it->value; - } - } - entry->SetValue(val); - - if(dictEntry) - { - 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()); - } - } - - listEntries.push_back(entry); - } + return *header1 < *header2; } -bool gdcmDicomDir::HeaderLessThan(gdcmHeader *header1,gdcmHeader *header2) +/** + * \brief Sets the accurate value for the (0x0004,0x1220) element of a DICOMDIR + */ +void gdcmDicomDir::UpdateDirectoryRecordSequenceLength() { - return(*header1<*header2); + +/// \todo FIXME : to go on compiling +/// +/// to be re written ! +/// int offset = 0; +/// ListTag::iterator it; +/// uint16_t 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; +/// } //-----------------------------------------------------------------------------