X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDicomDir.cxx;h=3959a469bd712cfb07f1f7faa73e5f814cd56ec3;hb=ab62b1a706df8e2ab1fbf26fa5037d6c22293655;hp=34ceb7dc6da8e8dac47d84ccc7b4ac6fbc80aff9;hpb=55d77e0913ff360d639af1841c70d14dc8687584;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index 34ceb7dc..3959a469 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -1,104 +1,131 @@ -// gdcmDicomDir.cxx -//----------------------------------------------------------------------------- +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmDicomDir.cxx,v $ + Language: C++ + Date: $Date: 2004/08/02 16:42:14 $ + Version: $Revision: 1.63 $ + + 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(); + + std::string pathBidon = "Bidon"; // Sorry, NULL not allowed ... + SetElement(pathBidon, GDCM_DICOMDIR_META, NULL); // Set the META elements + AddDicomDirMeta(); +} + +/** + * \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; + // 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(); -// Si on passe un root directory, on est assuré de n'avoir rien ramené + // gdcmDocument already executed + // if user passed a root directory, sure we didn't get anything - if( GetListEntry().begin()==GetListEntry().end() ) + if ( TagHT.begin() == TagHT.end() ) { - // 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 ( fileName.size() == 1 && fileName[0] == '.' ) + { + // user passed '.' as Name + // we get current directory name + char* dummy = new char[1000]; + getcwd(dummy, (size_t)1000); + std::cout << "Directory to parse : [" << dummy << "]" << std::endl; + SetFileName( dummy ); // will be converted into a string + delete[] dummy; // no longer needed + } - if(parseDir) + 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 + { + /// \todo if parseDir == false, it should be tagged as an error + // NON ! il suffit d'appeler ParseDirectory() + // apres le constructeur + } } 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 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() @@ -107,10 +134,14 @@ gdcmDicomDir::~gdcmDicomDir() SetProgressMethod(NULL); SetEndMethod(NULL); - if(metaElems) + 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; } @@ -118,133 +149,174 @@ gdcmDicomDir::~gdcmDicomDir() //----------------------------------------------------------------------------- // 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 +325,7 @@ void gdcmDicomDir::SetEndMethod(gdcmMethod *method,void *arg,gdcmMethod *argDele */ void gdcmDicomDir::SetEndMethodArgDelete(gdcmMethod *method) { - endMethodArgDelete=method; + endMethodArgDelete = method; } /** @@ -268,43 +340,38 @@ void gdcmDicomDir::SetEndMethodArgDelete(gdcmMethod *method) * @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) + FILE * 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); - //UpdateDirectoryRecordSequenceLength(); // a reecrire en utilisant - // la structure arborescente JPR - WriteDicomDirEntries(fp1); - - fclose(fp1); + delete[] filePreamble; + UpdateDirectoryRecordSequenceLength(); + WriteEntries(fp1); + fclose( fp1 ); 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 + * \brief Writes in a file using the tree-like structure. * @param _fp already open file pointer */ -void gdcmDicomDir::WriteDicomDirEntries(FILE *_fp) +void gdcmDicomDir::WriteEntries(FILE *) //_fp { - // TODO (?) tester les echecs en ecriture - // (apres chaque fwrite, dans le WriteEntry) + /// \todo (?) tester les echecs en ecriture + /// (apres chaque fwrite, dans le WriteEntry) + + +/* TODO : to go on compiling gdcmDicomDirMeta *ptrMeta; ListDicomDirPatient::iterator itPatient; @@ -315,200 +382,357 @@ void gdcmDicomDir::WriteDicomDirEntries(FILE *_fp) ptrMeta= GetDicomDirMeta(); for(i=ptrMeta->debut();i!=ptrMeta->fin();++i) { - WriteEntry(*i,_fp,DICOMDIR); + WriteEntry(*i,_fp, gdcmExplicitVR); } itPatient = GetDicomDirPatients().begin(); while ( itPatient != GetDicomDirPatients().end() ) { for(i=(*itPatient)->debut();i!=(*itPatient)->fin();++i) { - WriteEntry(*i,_fp,DICOMDIR); + WriteEntry(*i,_fp, gdcmExplicitVR); } - itStudy = ((*itPatient)->GetDicomDirStudies()).begin(); - while (itStudy != (*itPatient)->GetDicomDirStudies().end() ) { + itStudy = ((*itPatient)->GetDicomDirStudies()).begin(); + while (itStudy != (*itPatient)->GetDicomDirStudies().end() ) { for(i=(*itStudy)->debut();i!=(*itStudy)->fin();++i) { - WriteEntry(*i,_fp,DICOMDIR); + WriteEntry(*i,_fp, gdcmExplicitVR); } itSerie = ((*itStudy)->GetDicomDirSeries()).begin(); while (itSerie != (*itStudy)->GetDicomDirSeries().end() ) { for(i=(*itSerie)->debut();i!=(*itSerie)->fin();++i) { - WriteEntry(*i,_fp,DICOMDIR); + WriteEntry(*i,_fp, gdcmExplicitVR); } itImage = ((*itSerie)->GetDicomDirImages()).begin(); while (itImage != (*itSerie)->GetDicomDirImages().end() ) { for(i=(*itImage)->debut();i!=(*itImage)->fin();++i) { - WriteEntry(*i,_fp,DICOMDIR); + WriteEntry(*i,_fp, gdcmExplicitVR); } - ++itImage; - } - ++itSerie; + ++itImage; + } + ++itSerie; } - ++itStudy; + ++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::sort(list.begin(), list.end(), gdcmDicomDir::HeaderLessThan ); - std::string tmp=fileList.GetDirName(); + 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; + + /// \todo FIXME : Heuuuuu ! Il prend les Entries du Document deja parse, + /// il ne fabrique rien ! + +gdcmDicomDirMeta * gdcmDicomDir::NewMeta() +{ + gdcmDicomDirMeta *m = new gdcmDicomDirMeta( &TagHT ); + for ( TagDocEntryHT::iterator cc = TagHT.begin(); + cc != TagHT.end(); ++cc) + { + m->AddDocEntry( cc->second ); + } + 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; - - - debInsertion = metaElems->fin(); - ++debInsertion; - finInsertion=debInsertion; + gdcmValEntry *entry; - // for all the DicomDirPatient Elements - for(it=elemList.begin();it!=elemList.end();++it) + std::list elemList; + elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirPatientElements(); +// Looks nice, but gdcmDicomDir IS NOT a gdcmObject ... +// gdcmDicomDirPatient *p = new gdcmDicomDirPatient(ptagHT); +// FillObject(elemList); +// patients.push_front( p ); +// return p; +/// \todo TODO : find a trick to use FillObject !!! + + 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 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") ) - { - entry->SetLength(4); - } - else if( (dictEntry->GetVR()=="US") || (dictEntry->GetVR()=="SS") ) - { - entry->SetLength(2); - } - else if(dictEntry->GetVR()=="SQ") - { - entry->SetLength(0xffffffff); - } + 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()); - } - - 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() ); + } + s->AddDocEntry( entry ); } - i=metaElems->fin(); - i++; + gdcmDicomDirPatient *p = new gdcmDicomDirPatient(s, &TagHT); + patients.push_front( p ); - gdcmDicomDirPatient *p = new gdcmDicomDirPatient(i, --debInsertion, - &tagHT, &listEntries); - patients.push_front(p); return p; } -/* - * \ingroup gdcmDicomDir - * \brief Get the DicomDir path +/** + * \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 */ -std::string gdcmDicomDir::GetPath(void) +void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type, + gdcmDocument *header) { - std::string path=GetFileName(); + std::list elemList; + std::list::iterator it; + uint16_t tmpGr, tmpEl; + gdcmDictEntry *dictEntry; + gdcmValEntry *entry; + std::string val; + //gdcmObject *o; + switch( type ) + { + case GDCM_DICOMDIR_IMAGE: + elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirImageElements(); + break; - int pos1=path.rfind("/"); - int pos2=path.rfind("\\"); - if(pos1>pos2) - path.resize(pos1); - else - path.resize(pos2); + case GDCM_DICOMDIR_SERIE: + elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirSerieElements(); + break; + + 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; + } + + 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 - return(path); + 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; + } + } + + entry->SetValue( val ); + + 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" ) + { + entry->SetLength(2); + } + else if( dictEntry->GetVR() == "SQ" ) + { + entry->SetLength( 0xffffffff ); + } + else + { + entry->SetLength( entry->GetValue().length() ); + } + } + std::cout << " was TagHT[entry->GetKey()] = entry " << std::endl; + if ( type == GDCM_DICOMDIR_META ) { + std::cout << " special Treatment for GDCM_DICOMDIR_META" << std::endl; + + } + //TagHT[entry->GetKey()] = entry; // FIXME : use a SEQUENCE ! + } } -/* - * \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 +746,301 @@ 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 ); + //AddObjectToEnd(type,*i); + type = gdcmDicomDir::GDCM_DICOMDIR_PATIENT; } - - if(v=="IMAGE ") + else if( v == "STUDY " ) { - end=end2=i; - AddObjectToEnd(type,begin,--end2); - type=gdcmDicomDir::GDCM_DICOMDIR_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=end2=listEntries.end(); - if(begin!=end) - AddObjectToEnd(type,begin,--end2); } -/* + +/** * \ingroup gdcmDicomDir * \brief AddObjectToEnd * @param type - * @param begin - * @param end + * @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_DICOMDIR_META: - AddDicomDirMetaToEnd(begin,end); + AddDicomDirMeta(); break; case gdcmDicomDir::GDCM_DICOMDIR_PATIENT: - AddDicomDirPatientToEnd(begin,end); + AddDicomDirPatientToEnd(s); break; case gdcmDicomDir::GDCM_DICOMDIR_STUDY: - AddDicomDirStudyToEnd(begin,end); + AddDicomDirStudyToEnd(s); break; case gdcmDicomDir::GDCM_DICOMDIR_SERIE: - AddDicomDirSerieToEnd(begin,end); + AddDicomDirSerieToEnd(s); break; case gdcmDicomDir::GDCM_DICOMDIR_IMAGE: - AddDicomDirImageToEnd(begin,end); + AddDicomDirImageToEnd(s); + break; + case gdcmDicomDir::GDCM_DICOMDIR_NONE: + AddDicomDirImageToEnd(s); //FIXME 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) + +/** + * \ingroup gdcmDicomDir + * \brief Well ... there is only one occurence + */ +void gdcmDicomDir::AddDicomDirMeta() { - if(metaElems) + 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); + 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 - } + 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); -} - - -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; +/// \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; +/// } //-----------------------------------------------------------------------------