X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDicomDir.cxx;h=e920abfe2464db1cd6dba1299aec3e3bfa574962;hb=8bf45262260369e9f9f773c5793acb4924639cc1;hp=34ceb7dc6da8e8dac47d84ccc7b4ac6fbc80aff9;hpb=55d77e0913ff360d639af1841c70d14dc8687584;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index 34ceb7dc..e920abfe 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -1,104 +1,129 @@ -// gdcmDicomDir.cxx -//----------------------------------------------------------------------------- +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmDicomDir.cxx,v $ + Language: C++ + Date: $Date: 2004/09/23 10:47:10 $ + Version: $Revision: 1.68 $ + + 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 + +#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 -#include - -#include -#include +#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 Constructor : Parses recursively the directory and creates the DicomDir - * \ or uses an already built DICOMDIR, depending on 'parseDir' value - * @param Name name of the root directory (parseDir = true) - * name of the DICOMDIR (parseDir = false) - * @param parseDir - true if user passed an entry point + * \brief Constructor : creates an empty gdcmDicomDir + */ +gdcmDicomDir::gdcmDicomDir() + :gdcmDocument( ) +{ + Initialize(); // sets all private fields to NULL + std::string pathBidon = "Bidon"; // Sorry, NULL not allowed ... + metaElems = NewMeta(); +} + +/** + * \brief Constructor Parses recursively the directory and creates the DicomDir + * or uses an already built DICOMDIR, depending on 'parseDir' value. + * @param fileName name + * - of the root directory (parseDir = true) + * - of the DICOMDIR (parseDir = false) + * @param parseDir boolean + * - true if user passed an entry point * and wants to explore recursively the directories - * - false if user passed an already built DICOMDIR file + * - 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 *Name, bool parseDir, - bool exception_on_error): - gdcmParser(Name,exception_on_error,true) // true : enable SeQuences +gdcmDicomDir::gdcmDicomDir(std::string const & fileName, bool parseDir ): + gdcmDocument( fileName ) { - // 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; + // Whatever user passed (a root directory or a DICOMDIR) + // and whatever the value of parseDir was, + // gdcmDocument is already executed + Initialize(); // sets all private fields to NULL -// Si on passe un root directory, on est assuré de n'avoir rien ramené + // if user passed a root directory, sure we didn't get anything - if( GetListEntry().begin()==GetListEntry().end() ) + if ( TagHT.begin() == TagHT.end() ) // when user passed a Directory to parse { - // Si, en plus, parseDir == false, ca devrait etre une erreur - 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 ) // user asked for a recursive parsing of a root directory + { + metaElems = NewMeta(); + + dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : Parse directory" + " and create the DicomDir"); ParseDirectory(); } + else + { + /// \todo if parseDir == false, it should be tagged as an error + // NON ! il suffit d'appeler ParseDirectory() + // apres le constructeur + } } - else + else // Only if user passed a DICOMDIR + { + // 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 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; - 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() @@ -106,145 +131,188 @@ gdcmDicomDir::~gdcmDicomDir() SetStartMethod(NULL); SetProgressMethod(NULL); SetEndMethod(NULL); - - if(metaElems) - delete metaElems; - - for(ListDicomDirPatient::iterator cc=patients.begin();cc!=patients.end();++cc) + for(ListDicomDirPatient::iterator cc = patients.begin(); + cc!= patients.end(); + ++cc) { delete *cc; } + if ( metaElems ) + { + delete metaElems; + } } //----------------------------------------------------------------------------- // Print -/* - * \ingroup gdcmDicomDir +/** * \brief Canonical Printer */ void gdcmDicomDir::Print(std::ostream &os) { if(metaElems) { - metaElems->SetPrintLevel(printLevel); + metaElems->SetPrintLevel(PrintLevel); metaElems->Print(os); } - for(ListDicomDirPatient::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)->SetPrintLevel( PrintLevel ); + (*cc)->Print( os ); } } //----------------------------------------------------------------------------- // Public -/* - * \ingroup gdcmDicomDir +/** * \brief This predicate, based on hopefully reasonable heuristics, - * decides whether or not the current gdcmParser was properly parsed + * 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, + * @return true when gdcmDocument is the one of a reasonable DicomDir, * false otherwise. */ -bool gdcmDicomDir::IsReadable(void) +bool gdcmDicomDir::IsReadable() +{ + if( !gdcmDocument::IsReadable() ) + { + return false; + } + if( !metaElems ) + { + return false; + } + if( patients.size() <= 0 ) + { + return false; + } + + return true; +} + +/** + * \brief Sets all fields to NULL + */ + +void gdcmDicomDir::Initialize() { - if(!gdcmParser::IsReadable()) - return(false); - if(!metaElems) - return(false); - if(patients.size()<=0) - return(false); - - return(true); + startMethod = NULL; + progressMethod = NULL; + endMethod = NULL; + startMethodArgDelete = NULL; + progressMethodArgDelete = NULL; + endMethodArgDelete = NULL; + startArg = NULL; + progressArg = NULL; + endArg = NULL; + + progress = 0.0; + abort = false; + + metaElems = 0; } -/* + +/** * \ingroup gdcmDicomDir - * \brief fills whole the structure + * \brief fills the whole structure, starting from a root Directory */ -void gdcmDicomDir::ParseDirectory(void) +void gdcmDicomDir::ParseDirectory() { - CreateDicomDirChainedList(GetPath()); + 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) +void gdcmDicomDir::SetStartMethod(gdcmMethod *method, void *arg, + gdcmMethod *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 + * 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; + 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) +void gdcmDicomDir::SetProgressMethod(gdcmMethod *method, void *arg, + gdcmMethod *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 + * 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; + 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 gdcmDicomDir::SetEndMethod(gdcmMethod *method, void *arg, + gdcmMethod *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 @@ -253,7 +321,7 @@ void gdcmDicomDir::SetEndMethod(gdcmMethod *method,void *arg,gdcmMethod *argDele */ void gdcmDicomDir::SetEndMethodArgDelete(gdcmMethod *method) { - endMethodArgDelete=method; + endMethodArgDelete = method; } /** @@ -268,247 +336,391 @@ void gdcmDicomDir::SetEndMethodArgDelete(gdcmMethod *method) * @return false only when fail to open */ -bool gdcmDicomDir::Write(std::string fileName) -{ - FILE * fp1; +bool gdcmDicomDir::WriteDicomDir(std::string const & fileName) +{ + uint16_t sq[4] = { 0x0004, 0x1220, 0xffff, 0xffff }; + uint16_t sqt[4]= { 0xfffe, 0xe0dd, 0xffff, 0xffff }; - fp1=fopen(fileName.c_str(),"wb"); - if(fp1==NULL) + FILE * fp = fopen(fileName.c_str(), "wb"); + if( !fp ) { - 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); - fwrite(filePreamble,128,1,fp1); - fwrite("DICM",4,1,fp1); - free(filePreamble); - //UpdateDirectoryRecordSequenceLength(); // a reecrire en utilisant - // la structure arborescente JPR - WriteDicomDirEntries(fp1); - - fclose(fp1); + uint8_t* filePreamble = new uint8_t[128]; + memset(filePreamble, 0, 128); + fwrite(filePreamble,128,1,fp); + fwrite("DICM",4,1,fp); + delete[] filePreamble; + + gdcmDicomDirMeta *ptrMeta = GetDicomDirMeta(); + ptrMeta->Write(fp, gdcmExplicitVR); + + // force writing 0004|1220 [SQ ], that CANNOT exist within gdcmDicomDirMeta + fwrite(&sq[0],8,1,fp); // 0004 1220 ffff ffff + + for(ListDicomDirPatient::iterator cc = patients.begin();cc!=patients.end();++cc) + { + (*cc)->Write( fp, gdcmExplicitVR ); + } + + // force writing Sequence Delimitation Item + fwrite(&sqt[0],8,1,fp); // fffe e0dd ffff ffff + fclose( fp ); return true; } -/** - * \ingroup gdcmParser - * \brief writes on disc according to the DICOMDIR format - * using the Chained List - * \todo a reecrire en utilisant la structure arborescente - * @param _fp already open file pointer - */ - -void gdcmDicomDir::WriteDicomDirEntries(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,DICOMDIR); - } - - itPatient = GetDicomDirPatients().begin(); - while ( itPatient != GetDicomDirPatients().end() ) { - for(i=(*itPatient)->debut();i!=(*itPatient)->fin();++i) { - WriteEntry(*i,_fp,DICOMDIR); - } - itStudy = ((*itPatient)->GetDicomDirStudies()).begin(); - while (itStudy != (*itPatient)->GetDicomDirStudies().end() ) { - for(i=(*itStudy)->debut();i!=(*itStudy)->fin();++i) { - WriteEntry(*i,_fp,DICOMDIR); - } - itSerie = ((*itStudy)->GetDicomDirSeries()).begin(); - while (itSerie != (*itStudy)->GetDicomDirSeries().end() ) { - for(i=(*itSerie)->debut();i!=(*itSerie)->fin();++i) { - WriteEntry(*i,_fp,DICOMDIR); - } - itImage = ((*itSerie)->GetDicomDirImages()).begin(); - while (itImage != (*itSerie)->GetDicomDirImages().end() ) { - for(i=(*itImage)->debut();i!=(*itImage)->fin();++i) { - WriteEntry(*i,_fp,DICOMDIR); - } - ++itImage; - } - ++itSerie; - } - ++itStudy; - } - ++itPatient; - } -} - //----------------------------------------------------------------------------- // Protected -/* +/** * \ingroup gdcmDicomDir - * \brief create a gdcmHeader-like chained list from a root Directory + * \brief create a gdcmDocument-like chained list from a root Directory * @param path entry point of the tree-like structure */ -void gdcmDicomDir::CreateDicomDirChainedList(std::string path) +void gdcmDicomDir::CreateDicomDirChainedList(std::string const & path) { CallStartMethod(); - gdcmDirList fileList(path,1); // gets recursively the file list - unsigned int count=0; - ListHeader 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 ) { - 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 gdcmHeader( it->c_str() ); + if( !header ) + { + dbg.Verbose( 1, + "gdcmDicomDir::CreateDicomDirChainedList: " + "failure in new Header ", + it->c_str() ); + } + + if( header->IsReadable() ) + { + // Add the file header to the chained list: + list.push_back(header); + dbg.Verbose( 1, + "gdcmDicomDir::CreateDicomDirChainedList: 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(); + 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); - + SetElements(tmp, list); CallEndMethod(); } -/* +/** * \ingroup gdcmDicomDir - * \brief adds a new Patient to a partially created DICOMDIR + * \brief adds *the* Meta to a partially created DICOMDIR */ -gdcmDicomDirPatient * gdcmDicomDir::NewPatient(void) { - std::list elemList; + +gdcmDicomDirMeta * gdcmDicomDir::NewMeta() +{ + gdcmDicomDirMeta *m = new gdcmDicomDirMeta( &TagHT ); + + if ( TagHT.begin() != TagHT.end() ) // after Document Parsing + { + TagDocEntryHT::iterator lastOneButSequence = TagHT.end(); + lastOneButSequence --; + // ALL the 'out of Sequence' Tags belong to Meta Elems + // (we skip 0004|1220 [Directory record sequence] ) + for ( TagDocEntryHT::iterator cc = TagHT.begin(); + cc != lastOneButSequence; + ++cc) + { + m->AddDocEntry( cc->second ); + } + } + else // after root directory parsing + { + std::list elemList; + elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirMetaElements(); + m->FillObject(elemList); + } + m->SetSQItemNumber(0); // To avoid further missprinting + return m; +} + +/** + * \brief adds a new Patient (with the basic elements) to a partially created DICOMDIR + */ +gdcmDicomDirPatient * gdcmDicomDir::NewPatient() +{ std::list::iterator it; - guint16 tmpGr,tmpEl; + uint16_t tmpGr,tmpEl; gdcmDictEntry *dictEntry; - gdcmHeaderEntry *entry; - - elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirPatientElements(); - std::list::iterator debInsertion, finInsertion, i,j; - + gdcmValEntry *entry; + + std::list elemList; + elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirPatientElements(); + gdcmSQItem *s = new gdcmSQItem(0); + + // 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 ... - debInsertion = metaElems->fin(); - ++debInsertion; - finInsertion=debInsertion; + 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 gdcmDicomDirObject 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; + gdcmSQItem *si = new gdcmSQItem(0); // all the items will be at level 1 + switch( type ) + { + case GDCM_DICOMDIR_IMAGE: + elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirImageElements(); + break; + + case GDCM_DICOMDIR_SERIE: + elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirSerieElements(); + break; - // for all the DicomDirPatient Elements - for(it=elemList.begin();it!=elemList.end();++it) + case GDCM_DICOMDIR_STUDY: + elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirStudyElements(); + break; + + case GDCM_DICOMDIR_PATIENT: + elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirPatientElements(); + break; + + case GDCM_DICOMDIR_META: + elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirMetaElements(); + 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()->GetDictEntryByNumber(tmpGr,tmpEl); - entry=new gdcmHeaderEntry(dictEntry); - entry->SetOffset(0); // just to avoid missprinting - entry->SetValue(it->value); - - if(dictEntry->GetGroup()==0xfffe) - { - entry->SetLength(entry->GetValue().length()); - } - else if( (dictEntry->GetVR()=="UL") || (dictEntry->GetVR()=="SL") ) + 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 + entry->SetLength(0); // just to avoid further missprinting + + if( header ) // NULL when we Build Up (ex nihilo) a DICOMDIR + // or when we add the META elems + val = header->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; + } + + // GDCM_UNFOUND or not ! + + entry->SetValue( val ); // troubles expected when vr=SQ ... + + if( dictEntry ) + { + if( dictEntry->GetGroup() == 0xfffe ) + { + entry->SetLength( entry->GetValue().length() ); // FIXME + } + else if( dictEntry->GetVR() == "UL" || dictEntry->GetVR() == "SL" ) { entry->SetLength(4); - } - else if( (dictEntry->GetVR()=="US") || (dictEntry->GetVR()=="SS") ) + } + else if( dictEntry->GetVR() == "US" || dictEntry->GetVR() == "SS" ) { entry->SetLength(2); - } - else if(dictEntry->GetVR()=="SQ") + } + else if( dictEntry->GetVR() == "SQ" ) { - entry->SetLength(0xffffffff); + entry->SetLength( 0xffffffff ); } - else + 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; + entry->SetLength( entry->GetValue().length() ); + } + } + + if ( type == GDCM_DICOMDIR_META ) // fusible : should never print ! + { + std::cout << "GDCM_DICOMDIR_META ?!? should never print that" + << std::endl; + } + si->AddEntry(entry); } + switch( type ) + { + case GDCM_DICOMDIR_IMAGE: + AddDicomDirImageToEnd(si); + break; - i=metaElems->fin(); - i++; + case GDCM_DICOMDIR_SERIE: + AddDicomDirSerieToEnd(si); + break; - gdcmDicomDirPatient *p = new gdcmDicomDirPatient(i, --debInsertion, - &tagHT, &listEntries); - patients.push_front(p); - return p; -} + case GDCM_DICOMDIR_STUDY: + AddDicomDirStudyToEnd(si); + break; -/* - * \ingroup gdcmDicomDir - * \brief Get the DicomDir path - */ -std::string gdcmDicomDir::GetPath(void) -{ - std::string path=GetFileName(); + case GDCM_DICOMDIR_PATIENT: + AddDicomDirPatientToEnd(si); + break; - int pos1=path.rfind("/"); - int pos2=path.rfind("\\"); - if(pos1>pos2) - path.resize(pos1); - else - path.resize(pos2); + default: + return; + } + //int count=1; // find a trick to increment + //s->AddEntry(si, count); // Seg Faults - return(path); } -/* - * \ingroup gdcmDicomDir + +/** * \brief CallStartMethod */ -void gdcmDicomDir::CallStartMethod(void) +void gdcmDicomDir::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 gdcmDicomDir::CallProgressMethod() { - if(progressMethod) - progressMethod(progressArg); + if( progressMethod ) + { + progressMethod( progressArg ); + } } -/* + +/** * \ingroup gdcmDicomDir * \brief CallEndMethod */ -void gdcmDicomDir::CallEndMethod(void) +void gdcmDicomDir::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 */ @@ -522,364 +734,223 @@ void gdcmDicomDir::CreateDicomDir() // + we create the object for the precedent tag // + loop to 1 - - gdcmDicomDirType type=gdcmDicomDir::GDCM_DICOMDIR_META; - ListTag::iterator begin; - ListTag::iterator end, end2; + // 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"); + // useless : (0x0004,0x1220) IS a Sequence ! + return; + } + + gdcmDicomDirType type = gdcmDicomDir::GDCM_DICOMDIR_META; + metaElems = NewMeta(); - begin=listEntries.begin(); - end=begin; - for(ListTag::iterator i=end;i !=listEntries.end();++i) + ListSQItem listItems = s->GetSQItems(); + + 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=end2=i; - AddObjectToEnd(type,begin,--end2); - type=gdcmDicomDir::GDCM_DICOMDIR_PATIENT; - begin=end; - } - - if(v=="STUDY ") + v = ValEntry->GetValue(); + } + else { - end=end2=i; - AddObjectToEnd(type,begin,--end2); - type=gdcmDicomDir::GDCM_DICOMDIR_STUDY; - begin=end; + dbg.Verbose(0, "gdcmDicomDir::CreateDicomDir: not a ValEntry."); + continue; } - if(v=="SERIES") + if( v == "PATIENT " ) { - end=end2=i; - AddObjectToEnd(type,begin,--end2); - type=gdcmDicomDir::GDCM_DICOMDIR_SERIE; - begin=end; + AddDicomDirPatientToEnd( *i ); + type = gdcmDicomDir::GDCM_DICOMDIR_PATIENT; } - - if(v=="IMAGE ") + else if( v == "STUDY " ) + { + AddDicomDirStudyToEnd( *i ); + type = gdcmDicomDir::GDCM_DICOMDIR_STUDY; + } + else if( v == "SERIES" ) { - end=end2=i; - AddObjectToEnd(type,begin,--end2); - type=gdcmDicomDir::GDCM_DICOMDIR_IMAGE; - begin=end; + AddDicomDirSerieToEnd( *i ); + type = gdcmDicomDir::GDCM_DICOMDIR_SERIE; + } + else if( v == "IMAGE " ) + { + AddDicomDirImageToEnd( *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=end2=listEntries.end(); - if(begin!=end) - AddObjectToEnd(type,begin,--end2); } -/* + +/** * \ingroup gdcmDicomDir - * \brief AddObjectToEnd - * @param type - * @param begin - * @param end + * \brief Well ... there is only one occurence */ -void gdcmDicomDir::AddObjectToEnd(gdcmDicomDirType type,ListTag::iterator begin,ListTag::iterator end) +void gdcmDicomDir::AddDicomDirMeta() { - if(begin==end) - return; - - switch(type) + if( metaElems ) { - case gdcmDicomDir::GDCM_DICOMDIR_META: - AddDicomDirMetaToEnd(begin,end); - break; - case gdcmDicomDir::GDCM_DICOMDIR_PATIENT: - AddDicomDirPatientToEnd(begin,end); - break; - case gdcmDicomDir::GDCM_DICOMDIR_STUDY: - AddDicomDirStudyToEnd(begin,end); - break; - case gdcmDicomDir::GDCM_DICOMDIR_SERIE: - AddDicomDirSerieToEnd(begin,end); - break; - case gdcmDicomDir::GDCM_DICOMDIR_IMAGE: - AddDicomDirImageToEnd(begin,end); - break; - } -} - -/* - * \ingroup gdcmDicomDir - * \brief Well ... Not realy to end, there is only one occurence - * @param begin - * @param end -*/ -void gdcmDicomDir::AddDicomDirMetaToEnd(ListTag::iterator begin,ListTag::iterator end) -{ - if(metaElems) delete metaElems; - metaElems = new gdcmDicomDirMeta(begin,end,&tagHT,&listEntries); + } + metaElems = new gdcmDicomDirMeta( &TagHT ); } -/* +/** * \ingroup gdcmDicomDir * \brief AddDicomDirPatientToEnd - * @param begin - * @param end -*/ -void gdcmDicomDir::AddDicomDirPatientToEnd(ListTag::iterator begin,ListTag::iterator end) + * @param s SQ Item to enqueue to the DicomPatient chained List + */ +void gdcmDicomDir::AddDicomDirPatientToEnd(gdcmSQItem *s) { - patients.push_back(new gdcmDicomDirPatient(begin,end,&tagHT, &listEntries)); + patients.push_back(new gdcmDicomDirPatient(s, &TagHT)); } -/* +/** * \ingroup gdcmDicomDir * \brief AddDicomDirStudyToEnd - * @param begin - * @param end + * @param s SQ Item to enqueue to the DicomDirStudy chained List */ - void gdcmDicomDir::AddDicomDirStudyToEnd(ListTag::iterator begin,ListTag::iterator end) + void gdcmDicomDir::AddDicomDirStudyToEnd(gdcmSQItem *s) { - if(patients.size()>0) + if( patients.size() > 0 ) { - ListDicomDirPatient::iterator itp=patients.end(); + ListDicomDirPatient::iterator itp = patients.end(); itp--; - (*itp)->AddDicomDirStudy(new gdcmDicomDirStudy(begin,end,&tagHT, &listEntries)); + (*itp)->AddDicomDirStudy(new gdcmDicomDirStudy(s, &TagHT)); } } -/* + +/** * \ingroup gdcmDicomDir * \brief AddDicomDirSerieToEnd - * @param begin - * @param end + * @param s SQ Item to enqueue to the DicomDirSerie chained List */ -void gdcmDicomDir::AddDicomDirSerieToEnd(ListTag::iterator begin,ListTag::iterator end) +void gdcmDicomDir::AddDicomDirSerieToEnd(gdcmSQItem *s) { - if(patients.size()>0) + if( patients.size() > 0 ) { - ListDicomDirPatient::iterator itp=patients.end(); + ListDicomDirPatient::iterator itp = patients.end(); itp--; - if((*itp)->GetDicomDirStudies().size()>0) + if( (*itp)->GetDicomDirStudies().size() > 0 ) { ListDicomDirStudy::iterator itst=(*itp)->GetDicomDirStudies().end(); itst--; - (*itst)->AddDicomDirSerie(new gdcmDicomDirSerie(begin,end,&tagHT, &listEntries)); + (*itst)->AddDicomDirSerie(new gdcmDicomDirSerie(s, &TagHT)); } } } -/* +/** * \ingroup gdcmDicomDir * \brief AddDicomDirImageToEnd - * @param begin - * @param end + * @param s SQ Item to enqueue to the DicomDirImage chained List */ - void gdcmDicomDir::AddDicomDirImageToEnd(ListTag::iterator begin,ListTag::iterator end) + void gdcmDicomDir::AddDicomDirImageToEnd(gdcmSQItem *s) { - if(patients.size()>0) + if( patients.size() > 0 ) { - ListDicomDirPatient::iterator itp=patients.end(); + ListDicomDirPatient::iterator itp = patients.end(); itp--; - if((*itp)->GetDicomDirStudies().size()>0) + if( (*itp)->GetDicomDirStudies().size() > 0 ) { - ListDicomDirStudy::iterator itst=(*itp)->GetDicomDirStudies().end(); + ListDicomDirStudy::iterator itst = (*itp)->GetDicomDirStudies().end(); itst--; - if((*itst)->GetDicomDirSeries().size()>0) + if( (*itst)->GetDicomDirSeries().size() > 0 ) { - ListDicomDirSerie::iterator its=(*itst)->GetDicomDirSeries().end(); + ListDicomDirSerie::iterator its = (*itst)->GetDicomDirSeries().end(); its--; - (*its)->AddDicomDirImage(new gdcmDicomDirImage(begin,end,&tagHT, &listEntries)); + (*its)->AddDicomDirImage(new gdcmDicomDirImage(s, &TagHT)); } } } } -/* +/** * \ingroup gdcmDicomDir * \brief for each Header of the chained list, add/update the Patient/Study/Serie/Image info - * @param path - * @param list + * @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 studCurInstanceUID, studCurID; std::string serCurInstanceUID, serCurID; - 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); - - if(patCurName!=patPrevName || patCurID!=patPrevID) - SetElement(path,GDCM_DICOMDIR_PATIENT,*it); + 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); + } // if new Study Deal with 'STUDY' Elements - if(studCurInstanceUID!=studPrevInstanceUID || studCurID!=studPrevID) - SetElement(path,GDCM_DICOMDIR_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) - SetElement(path,GDCM_DICOMDIR_SERIE,*it); + if( serCurInstanceUID != serPrevInstanceUID || serCurID != serPrevID ) + { + SetElement(path, GDCM_DICOMDIR_SERIE, *it); + } // 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; } } -/* +/** * \ingroup gdcmDicomDir - * \brief adds to the HTable and at the end of the Chained List - * the gdcmEntries (Dicom Elements) corresponding to the given type - * @param path file Path (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 + * \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_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 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; - } - } - else - { - if (header->GetEntryLengthByNumber(tmpGr,tmpEl)== 0) - val=it->value; - } - - entry->SetValue(val); - - if(dictEntry) - { - if(dictEntry->GetGroup()==0xfffe) - { - entry->SetLength(entry->GetValue().length()); //JPR - } - 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()); - } - } - //AddHeaderEntry(entry); // both in H Table and in chained list - tagHT.insert( PairHT( entry->GetKey(),entry) ); - listEntries.push_back(entry); - //wasUpdated = 1; // is private - } -} - -bool gdcmDicomDir::HeaderLessThan(gdcmHeader *header1,gdcmHeader *header2) -{ - return(*header1<*header2); -} - - - -void gdcmDicomDir::UpdateDirectoryRecordSequenceLength() { - int offset = 0; - ListTag::iterator it; - guint16 gr, el; - 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. - return; + return *header1 < *header2; } //-----------------------------------------------------------------------------