X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDicomDir.cxx;h=cc41e96dd951fbe7bb27058dcc6448bd4ef11642;hb=3842922fd2263cea5f679c9d283b3b4afead35d2;hp=b8501864e7d4907f7125c4d1cbfe911fe34aafcf;hpb=f24973b3daa0b2214838857d02bd61db6d4a0a40;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index b8501864..cc41e96d 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -3,12 +3,12 @@ Program: gdcm Module: $RCSfile: gdcmDicomDir.cxx,v $ Language: C++ - Date: $Date: 2004/07/17 22:36:55 $ - Version: $Revision: 1.56 $ + Date: $Date: 2005/01/19 08:57:14 $ + Version: $Revision: 1.106 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or - http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details. + http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR @@ -16,21 +16,13 @@ =========================================================================*/ -#include -#include -#include -#include - -#ifdef _MSC_VER - #include -#else - #include -#endif - #include "gdcmDicomDir.h" #include "gdcmDicomDirStudy.h" #include "gdcmDicomDirSerie.h" #include "gdcmDicomDirImage.h" +#include "gdcmDicomDirPatient.h" +#include "gdcmDicomDirMeta.h" +#include "gdcmDicomDirElement.h" #include "gdcmDirList.h" #include "gdcmUtil.h" #include "gdcmDebug.h" @@ -40,35 +32,44 @@ #include "gdcmSQItem.h" #include "gdcmValEntry.h" +#include +#include +#include +#include + +#ifdef _MSC_VER +# define getcwd _getcwd +#endif + +#if defined(_MSC_VER) || defined(__BORLANDC__) +# include +#else +# include +#endif + +namespace gdcm +{ + //----------------------------------------------------------------------------- // For full DICOMDIR description, see: // PS 3.3-2003, pages 731-750 //----------------------------------------------------------------------------- // Constructor / Destructor -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 : creates an empty DicomDir + */ +DicomDir::DicomDir() + :Document( ) +{ + Initialize(); // sets all private fields to NULL + 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 + * @param fileName name * - of the root directory (parseDir = true) * - of the DICOMDIR (parseDir = false) * @param parseDir boolean @@ -76,95 +77,84 @@ void gdcmDicomDir::Initialize() * 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(std::string const & fileName, bool parseDir, - bool exception_on_error): - gdcmDocument( fileName, exception_on_error, true) // true : enable SeQuences +DicomDir::DicomDir(std::string const &fileName, bool parseDir ): + Document( fileName ) { - // que l'on ai passe un root directory ou un DICOMDIR - // et quelle que soit la valeur de parseDir, - // on a deja lance gdcmDocument - Initialize(); + // At this step, Document constructor is already executed, + // whatever user passed (a root directory or a DICOMDIR) + // and whatever the value of parseDir was. + // (nothing is cheked in Document constructor, to avoid overhead) - // gdcmDocument already executed - // if user passed a root directory, sure we didn't get anything + Initialize(); // sets all private fields to NULL - if( GetEntry().begin() == GetEntry().end() ) + // if user passed a root directory, sure we didn't get anything + if ( TagHT.begin() == TagHT.end() ) // when user passed a Directory to parse { - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : entry HT empty"); + if (!parseDir) + gdcmVerboseMacro( "Entry HT empty for file: "<SetPrintLevel(printLevel); - metaElems->Print(os); + MetaElems->SetPrintLevel(PrintLevel); + MetaElems->Print(os); } - for(ListDicomDirPatient::iterator cc = patients.begin(); - cc != patients.end(); + for(ListDicomDirPatient::iterator cc = Patients.begin(); + cc != Patients.end(); ++cc) { - (*cc)->SetPrintLevel( printLevel ); - (*cc)->Print( os ); + (*cc)->SetPrintLevel(PrintLevel); + (*cc)->Print(os); } } @@ -195,21 +185,24 @@ void gdcmDicomDir::Print(std::ostream &os) * 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, + * @return true when Document is the one of a reasonable DicomDir, * false otherwise. */ -bool gdcmDicomDir::IsReadable() +bool DicomDir::IsReadable() { - if( !gdcmDocument::IsReadable() ) + if( Filetype == Unknown) { + gdcmVerboseMacro( "Wrong filetype"); return false; } - if( !metaElems ) + if( !MetaElems ) { + gdcmVerboseMacro( "Meta Elements missing in DicomDir"); return false; } - if( patients.size() <= 0 ) + if( Patients.size() <= 0 ) { + gdcmVerboseMacro( "NO Patient in DicomDir"); return false; } @@ -217,117 +210,134 @@ bool gdcmDicomDir::IsReadable() } /** - * \ingroup gdcmDicomDir + * \brief Sets all fields to NULL + */ + +void DicomDir::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 = NULL; +} + + +/** * \brief fills the whole structure, starting from a root Directory */ -void gdcmDicomDir::ParseDirectory() +void DicomDir::ParseDirectory() { CreateDicomDirChainedList( GetFileName() ); CreateDicomDir(); } /** - * \ingroup gdcmDicomDir - * \brief Set the start method to call when the parsing of the directory starts + * \brief Set the start method to call when the parsing of the + * directory starts. * @param method Method to call * @param arg Argument to pass to the method * @param argDelete Argument * \warning In python : the arg parameter isn't considered */ -void gdcmDicomDir::SetStartMethod(gdcmMethod *method, void *arg, - gdcmMethod *argDelete ) +void DicomDir::SetStartMethod( DicomDir::Method *method, void *arg, + DicomDir::Method *argDelete ) { - if( startArg && startMethodArgDelete ) + if( StartArg && StartMethodArgDelete ) { - startMethodArgDelete( startArg ); + StartMethodArgDelete( StartArg ); } - startMethod = method; - startArg = arg; - startMethodArgDelete = argDelete; + StartMethod = method; + StartArg = arg; + StartMethodArgDelete = argDelete; } /** - * \ingroup gdcmDicomDir * \brief Set the method to delete the argument * The argument is destroyed when the method is changed or when the * class is destroyed * @param method Method to call to delete the argument */ -void gdcmDicomDir::SetStartMethodArgDelete(gdcmMethod *method) +void DicomDir::SetStartMethodArgDelete( DicomDir::Method *method ) { - startMethodArgDelete = method; + StartMethodArgDelete = method; } /** - * \ingroup gdcmDicomDir - * \brief Set the progress method to call when the parsing of the directory progress + * \brief Set the progress method to call when the parsing of the + * directory progress * @param method Method to call * @param arg Argument to pass to the method * @param argDelete Argument * \warning In python : the arg parameter isn't considered */ -void gdcmDicomDir::SetProgressMethod(gdcmMethod *method, void *arg, - gdcmMethod *argDelete ) +void DicomDir::SetProgressMethod( DicomDir::Method *method, void *arg, + DicomDir::Method *argDelete ) { - if( progressArg && progressMethodArgDelete ) + if( ProgressArg && ProgressMethodArgDelete ) { - progressMethodArgDelete( progressArg ); + ProgressMethodArgDelete( ProgressArg ); } - progressMethod = method; - progressArg = arg; - progressMethodArgDelete = argDelete; + ProgressMethod = method; + ProgressArg = arg; + ProgressMethodArgDelete = argDelete; } /** - * \ingroup gdcmDicomDir * \brief Set the method to delete the argument * The argument is destroyed when the method is changed or when the * class is destroyed * @param method Method to call to delete the argument */ -void gdcmDicomDir::SetProgressMethodArgDelete(gdcmMethod *method) +void DicomDir::SetProgressMethodArgDelete( DicomDir::Method *method ) { - progressMethodArgDelete = method; + ProgressMethodArgDelete = method; } /** - * \ingroup gdcmDicomDir * \brief Set the end method to call when the parsing of the directory ends * @param method Method to call * @param arg Argument to pass to the method * @param argDelete Argument * \warning In python : the arg parameter isn't considered */ -void gdcmDicomDir::SetEndMethod(gdcmMethod *method, void *arg, - gdcmMethod *argDelete ) +void DicomDir::SetEndMethod( DicomDir::Method *method, void *arg, + DicomDir::Method *argDelete ) { - if( endArg && endMethodArgDelete ) + if( EndArg && EndMethodArgDelete ) { - endMethodArgDelete( endArg ); + EndMethodArgDelete( EndArg ); } - endMethod = method; - endArg = arg; - endMethodArgDelete = argDelete; + EndMethod = method; + EndArg = arg; + EndMethodArgDelete = argDelete; } /** - * \ingroup gdcmDicomDir * \brief Set the method to delete the argument - * The argument is destroyed when the method is changed or when the class - * is destroyed + * The argument is destroyed when the method is changed or when + * the class is destroyed * @param method Method to call to delete the argument */ -void gdcmDicomDir::SetEndMethodArgDelete(gdcmMethod *method) +void DicomDir::SetEndMethodArgDelete( DicomDir::Method *method ) { - endMethodArgDelete = method; + EndMethodArgDelete = method; } /** - * \ingroup gdcmDicomDir - * \brief writes on disc a DICOMDIR + * \brief writes on disc a DICOMDIR * \ warning does NOT add the missing elements in the header : * it's up to the user doing it ! * \todo : to be re-written using the DICOMDIR tree-like structure @@ -337,270 +347,270 @@ void gdcmDicomDir::SetEndMethodArgDelete(gdcmMethod *method) * @return false only when fail to open */ -bool gdcmDicomDir::Write(std::string const & fileName) -{ - FILE * fp1; - - fp1 = fopen(fileName.c_str(), "wb"); - if( !fp1 ) +bool DicomDir::WriteDicomDir(std::string const &fileName) +{ + int i; + uint16_t sq[4] = { 0x0004, 0x1220, 0xffff, 0xffff }; + uint16_t sqt[4]= { 0xfffe, 0xe0dd, 0xffff, 0xffff }; + + std::ofstream *fp = new std::ofstream(fileName.c_str(), + std::ios::out | std::ios::binary); + if( !fp ) { - printf("Failed to open(write) File [%s] \n", fileName.c_str()); + gdcmVerboseMacro("Failed to open(write) File: " << fileName.c_str()); return false; } - char * filePreamble = new char[128]; - fwrite(filePreamble,128,1,fp1); - fwrite("DICM",4,1,fp1); - delete[] filePreamble; - UpdateDirectoryRecordSequenceLength(); - WriteEntries(fp1); + char filePreamble[128]; + memset(filePreamble, 0, 128); + fp->write(filePreamble, 128); //FIXME + binary_write( *fp, "DICM"); + + DicomDirMeta *ptrMeta = GetDicomDirMeta(); + ptrMeta->WriteContent(fp, ExplicitVR); + + // force writing 0004|1220 [SQ ], that CANNOT exist within DicomDirMeta + for(i=0;i<4;++i) + { + binary_write(*fp, sq[i]); + } + + for(ListDicomDirPatient::iterator cc = Patients.begin(); + cc != Patients.end(); + ++cc ) + { + (*cc)->WriteContent( fp, ExplicitVR ); + } + + // force writing Sequence Delimitation Item + for(i=0;i<4;++i) + { + binary_write(*fp, sqt[i]); // fffe e0dd ffff ffff + } + + fp->close(); + delete fp; - fclose( fp1 ); return true; } -/** - * \brief Writes in a file using the tree-like structure. - * @param _fp already open file pointer - */ - -void gdcmDicomDir::WriteEntries(FILE *) //_fp -{ - /// \todo (?) tester les echecs en ecriture - /// (apres chaque fwrite, dans le WriteEntry) - - -/* TODO : to go on compiling - - gdcmDicomDirMeta *ptrMeta; - ListDicomDirPatient::iterator itPatient; - ListDicomDirStudy::iterator itStudy; - ListDicomDirSerie::iterator itSerie; - ListDicomDirImage::iterator itImage; - ListTag::iterator i; - - ptrMeta= GetDicomDirMeta(); - for(i=ptrMeta->debut();i!=ptrMeta->fin();++i) { - WriteEntry(*i,_fp, gdcmExplicitVR); - } - - itPatient = GetDicomDirPatients().begin(); - while ( itPatient != GetDicomDirPatients().end() ) { - for(i=(*itPatient)->debut();i!=(*itPatient)->fin();++i) { - WriteEntry(*i,_fp, gdcmExplicitVR); - } - itStudy = ((*itPatient)->GetDicomDirStudies()).begin(); - while (itStudy != (*itPatient)->GetDicomDirStudies().end() ) { - for(i=(*itStudy)->debut();i!=(*itStudy)->fin();++i) { - WriteEntry(*i,_fp, gdcmExplicitVR); - } - itSerie = ((*itStudy)->GetDicomDirSeries()).begin(); - while (itSerie != (*itStudy)->GetDicomDirSeries().end() ) { - for(i=(*itSerie)->debut();i!=(*itSerie)->fin();++i) { - WriteEntry(*i,_fp, gdcmExplicitVR); - } - itImage = ((*itSerie)->GetDicomDirImages()).begin(); - while (itImage != (*itSerie)->GetDicomDirImages().end() ) { - for(i=(*itImage)->debut();i!=(*itImage)->fin();++i) { - WriteEntry(*i,_fp, gdcmExplicitVR); - } - ++itImage; - } - ++itSerie; - } - ++itStudy; - } - ++itPatient; - } - */ -} - //----------------------------------------------------------------------------- // Protected /** - * \ingroup gdcmDicomDir - * \brief create a gdcmDocument-like chained list from a root Directory + * \brief create a Document-like chained list from a root Directory * @param path entry point of the tree-like structure */ -void gdcmDicomDir::CreateDicomDirChainedList(std::string const & path) +void DicomDir::CreateDicomDirChainedList(std::string const & path) { CallStartMethod(); - gdcmDirList fileList(path,1); // gets recursively the file list + DirList dirList(path,1); // gets recursively the file list unsigned int count = 0; VectDocument list; - gdcmHeader *header; + Header *header; - tagHT.clear(); - patients.clear(); + DirListType fileList = dirList.GetFilenames(); - for( gdcmDirList::iterator it = fileList.begin(); + for( DirListType::iterator it = fileList.begin(); it != fileList.end(); ++it ) { - progress = (float)(count+1)/(float)fileList.size(); + Progress = (float)(count+1)/(float)fileList.size(); CallProgressMethod(); - if( abort ) + if( Abort ) { break; } - header = new gdcmHeader(it->c_str(),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 + header = new Header( it->c_str() ); + if( !header ) { - delete header; + gdcmVerboseMacro( "Failure in new Header " << it->c_str() ); + continue; } - count++; - + + if( header->IsReadable() ) + { + // Add the file header to the chained list: + list.push_back(header); + gdcmVerboseMacro( "Readable " << it->c_str() ); + } + else + { + delete header; + } + count++; } // sorts Patient/Study/Serie/ - std::sort(list.begin(), list.end(), gdcmDicomDir::HeaderLessThan ); - - std::string tmp = fileList.GetDirName(); - + std::sort(list.begin(), list.end(), DicomDir::HeaderLessThan ); + + std::string tmp = dirList.GetDirName(); //for each Header of the chained list, add/update the Patient/Study/Serie/Image info SetElements(tmp, list); - CallEndMethod(); + + for(VectDocument::iterator itDoc=list.begin(); + itDoc!=list.end(); + ++itDoc) + { + delete dynamic_cast
(*itDoc); + } } /** - * \ingroup gdcmDicomDir * \brief adds *the* Meta to a partially created DICOMDIR */ - - /// \todo FIXME : Heuuuuu ! Il prend les Entries du Document deja parse, - /// il ne fabrique rien ! -gdcmDicomDirMeta * gdcmDicomDir::NewMeta() +DicomDirMeta * DicomDir::NewMeta() { - gdcmDicomDirMeta *m = new gdcmDicomDirMeta( &tagHT ); - for ( TagDocEntryHT::iterator cc = tagHT.begin(); - cc != tagHT.end(); ++cc) + DicomDirMeta *m = new DicomDirMeta(); + + 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->AddEntry( cc->second ); + } + } + else // after root directory parsing { - m->AddDocEntry( cc->second ); + ListDicomDirMetaElem const &elemList = + Global::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() +DicomDirPatient *DicomDir::NewPatient() { - std::list::iterator it; + ListDicomDirPatientElem::const_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 !!! + DictEntry *dictEntry; + ValEntry *entry; + + ListDicomDirPatientElem const & elemList = + Global::GetDicomDirElements()->GetDicomDirPatientElements(); + DicomDirPatient *p = new DicomDirPatient(); - // for all the DicomDirPatient Elements - + // 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 ); + tmpGr = it->Group; + tmpEl = it->Elem; + dictEntry = GetPubDict()->GetDictEntry(tmpGr, tmpEl); + entry = new ValEntry( dictEntry ); entry->SetOffset(0); // just to avoid further missprinting - entry->SetValue( it->value ); + 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 ); + p->AddEntry( entry ); } - gdcmDicomDirPatient *p = new gdcmDicomDirPatient(s, &tagHT); - patients.push_front( p ); + Patients.push_front( p ); - return p; + return p; } /** * \brief adds to the HTable - * the gdcmEntries (Dicom Elements) corresponding to the given type + * the Entries (Dicom Elements) corresponding to the given type * @param path full path file name (only used when type = GDCM_DICOMDIR_IMAGE - * @param type gdcmObject type to create (GDCM_DICOMDIR_PATIENT, + * @param type DicomDirObject type to create (GDCM_DICOMDIR_PATIENT, * GDCM_DICOMDIR_STUDY, GDCM_DICOMDIR_SERIE ...) - * @param header gdcmHeader of the current file + * @param header Header of the current file */ -void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type, - gdcmDocument *header) +void DicomDir::SetElement(std::string const &path, DicomDirType type, + Document *header) { - std::list elemList; - std::list::iterator it; + ListDicomDirElem elemList; //FIXME this is going to be a by copy operation + ListDicomDirElem::const_iterator it; uint16_t tmpGr, tmpEl; - gdcmDictEntry *dictEntry; - gdcmValEntry *entry; + DictEntry *dictEntry; + ValEntry *entry; std::string val; + SQItem *si; switch( type ) { - case GDCM_DICOMDIR_PATIENT: - elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirPatientElements(); - break; - case GDCM_DICOMDIR_STUDY: - elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirStudyElements(); + case GDCM_DICOMDIR_IMAGE: + elemList = Global::GetDicomDirElements()->GetDicomDirImageElements(); + si = new DicomDirImage(); + if( !AddDicomDirImageToEnd(static_cast(si)) ) + { + gdcmVerboseMacro( "Add DicomDirImageToEnd failed"); + } break; case GDCM_DICOMDIR_SERIE: - elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirSerieElements(); + elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements(); + si = new DicomDirSerie(); + if( !AddDicomDirSerieToEnd(static_cast(si)) ) + { + gdcmVerboseMacro( "Add DicomDirSerieToEnd failed"); + } break; - case GDCM_DICOMDIR_IMAGE: - elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirImageElements(); + case GDCM_DICOMDIR_STUDY: + elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements(); + si = new DicomDirStudy(); + if( !AddDicomDirStudyToEnd(static_cast(si)) ) + { + gdcmVerboseMacro( "Add DicomDirStudyToEnd failed"); + } + break; + case GDCM_DICOMDIR_PATIENT: + elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements(); + si = new DicomDirPatient(); + if( !AddDicomDirPatientToEnd(static_cast(si)) ) + { + gdcmVerboseMacro( "Add DicomDirPatientToEnd failed"); + } break; case GDCM_DICOMDIR_META: - elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirMetaElements(); + elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements(); + si = new DicomDirMeta(); + if( MetaElems ) + { + gdcmVerboseMacro( "MetaElements already exist, they will be destroyed"); + delete MetaElems; + } + MetaElems = static_cast(si); break; default: return; } + // removed all the seems-to-be-useless stuff about Referenced Image Sequence + // to avoid further troubles + // imageElem 0008 1140 "" // Referenced Image Sequence + // imageElem fffe e000 "" // 'no length' item : length to be set to 0xffffffff later + // imageElem 0008 1150 "" // Referenced SOP Class UID : to be set/forged later + // imageElem 0008 1155 "" // Referenced SOP Instance UID : to be set/forged later + // imageElem fffe e00d "" // Item delimitation : length to be set to ZERO later + // for all the relevant elements found in their own spot of the DicomDir.dic + // FIXME : troubles found when it's a SeqEntry for( it = elemList.begin(); it != elemList.end(); ++it) { - tmpGr = it->group; - tmpEl = it->elem; - dictEntry = GetPubDict()->GetDictEntryByNumber(tmpGr, tmpEl); - entry = new gdcmValEntry( dictEntry ); // Be sure it's never a BinEntry ! + tmpGr = it->Group; + tmpEl = it->Elem; + dictEntry = GetPubDict()->GetDictEntry(tmpGr, tmpEl); + + entry = new ValEntry( dictEntry ); // Be sure it's never a BinEntry ! entry->SetOffset(0); // just to avoid further missprinting if( header ) { - val = header->GetEntryByNumber(tmpGr, tmpEl); + // NULL when we Build Up (ex nihilo) a DICOMDIR + // or when we add the META elems + val = header->GetEntry(tmpGr, tmpEl); } else { @@ -612,109 +622,87 @@ void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type, if( tmpGr == 0x0004 && tmpEl == 0x1130 ) // File-set ID { // force to the *end* File Name - val = GetName( path ); + val = Util::GetName( path ); } else if( tmpGr == 0x0004 && tmpEl == 0x1500 ) // Only used for image { if( header->GetFileName().substr(0, path.length()) != path ) { - dbg.Verbose(0, "gdcmDicomDir::SetElement : the base path" - " of file name is incorrect"); + gdcmVerboseMacro( "The base path of file name is incorrect"); val = header->GetFileName(); } else { val = &(header->GetFileName().c_str()[path.length()]); - } + } } else { - val = it->value; + val = it->Value; } } else { - if ( header->GetEntryLengthByNumber(tmpGr,tmpEl) == 0 ) - { - val = it->value; - } + if ( header->GetEntryLength(tmpGr,tmpEl) == 0 ) + val = it->Value; } - entry->SetValue( val ); + entry->SetValue( val ); // troubles expected when vr=SQ ... - if( dictEntry ) + if ( type == GDCM_DICOMDIR_META ) // fusible : should never print ! { - 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() ); - } + std::cout << "GDCM_DICOMDIR_META ?!? should never print that" + << std::endl; } - //AddDocEntry(entry); // both in H Table and in chained list - tagHT[entry->GetKey()] = entry; // FIXME : use a SEQUENCE ! + si->AddEntry(entry); } } +//----------------------------------------------------------------------------- /** * \brief CallStartMethod */ -void gdcmDicomDir::CallStartMethod() +void DicomDir::CallStartMethod() { - progress = 0.0f; - abort = false; - if( startMethod ) + Progress = 0.0f; + Abort = false; + if( StartMethod ) { - startMethod( startArg ); + StartMethod( StartArg ); } } +//----------------------------------------------------------------------------- /** - * \ingroup gdcmDicomDir * \brief CallProgressMethod */ -void gdcmDicomDir::CallProgressMethod() +void DicomDir::CallProgressMethod() { - if( progressMethod ) + if( ProgressMethod ) { - progressMethod( progressArg ); + ProgressMethod( ProgressArg ); } } +//----------------------------------------------------------------------------- /** - * \ingroup gdcmDicomDir * \brief CallEndMethod */ -void gdcmDicomDir::CallEndMethod() +void DicomDir::CallEndMethod() { - progress = 1.0f; - if( endMethod ) + Progress = 1.0f; + if( EndMethod ) { - endMethod( endArg ); + EndMethod( EndArg ); } } //----------------------------------------------------------------------------- // Private /** - * \ingroup gdcmDicomDir - * \brief create a 'gdcmDicomDir' from a DICOMDIR gdcmHeader + * \brief create a 'DicomDir' from a DICOMDIR Header */ -void gdcmDicomDir::CreateDicomDir() +void DicomDir::CreateDicomDir() { // The list is parsed. // When a DicomDir tag ("PATIENT", "STUDY", "SERIE", "IMAGE") is found : @@ -724,68 +712,63 @@ void gdcmDicomDir::CreateDicomDir() // + we create the object for the precedent tag // + loop to 1 - - gdcmDicomDirType type = gdcmDicomDir::GDCM_DICOMDIR_META; - // Directory record sequence - gdcmDocEntry *e = GetDocEntryByNumber(0x0004, 0x1220); + DocEntry *e = GetDocEntry(0x0004, 0x1220); if ( !e ) { - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : NO Directory record" - " sequence (0x0004,0x1220)"); + gdcmVerboseMacro( "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); + SeqEntry *s = dynamic_cast(e); if ( !s ) { - dbg.Verbose(0, "gdcmDicomDir::CreateDicomDir: no SeqEntry present"); + gdcmVerboseMacro( "No SeqEntry present"); + // useless : (0x0004,0x1220) IS a Sequence ! return; } + MetaElems = NewMeta(); + ListSQItem listItems = s->GetSQItems(); - gdcmDicomDirMeta *m = new gdcmDicomDirMeta(&tagHT); - (void)m; //?? - gdcmDocEntry * d; + DocEntry *d; std::string v; + SQItem *si; for( ListSQItem::iterator i = listItems.begin(); i !=listItems.end(); ++i ) { - d = (*i)->GetDocEntryByNumber(0x0004, 0x1430); // Directory Record Type - if ( gdcmValEntry* ValEntry = dynamic_cast< gdcmValEntry* >(d) ) + d = (*i)->GetDocEntry(0x0004, 0x1430); // Directory Record Type + if ( ValEntry* valEntry = dynamic_cast(d) ) { - v = ValEntry->GetValue(); + v = valEntry->GetValue(); } else { - dbg.Verbose(0, "gdcmDicomDir::CreateDicomDir: not a ValEntry."); + gdcmVerboseMacro( "Not a ValEntry."); continue; } if( v == "PATIENT " ) { - AddDicomDirPatientToEnd( *i ); - //AddObjectToEnd(type,*i); - type = gdcmDicomDir::GDCM_DICOMDIR_PATIENT; + si = new DicomDirPatient(); + AddDicomDirPatientToEnd( static_cast(si) ); } else if( v == "STUDY " ) { - AddDicomDirStudyToEnd( *i ); - // AddObjectToEnd(type,*i); - type = gdcmDicomDir::GDCM_DICOMDIR_STUDY; + si = new DicomDirStudy(); + AddDicomDirStudyToEnd( static_cast(si) ); } else if( v == "SERIES" ) { - AddDicomDirSerieToEnd( *i ); - // AddObjectToEnd(type,*i); - type = gdcmDicomDir::GDCM_DICOMDIR_SERIE; + si = new DicomDirSerie(); + AddDicomDirSerieToEnd( static_cast(si) ); } else if( v == "IMAGE " ) { - AddDicomDirImageToEnd( *i ); - // AddObjectToEnd(type,*i); - type = gdcmDicomDir::GDCM_DICOMDIR_IMAGE; + si = new DicomDirImage(); + AddDicomDirImageToEnd( static_cast(si) ); } else { @@ -793,143 +776,112 @@ void gdcmDicomDir::CreateDicomDir() // neither an 'IMAGE' SQItem. Skip to next item. continue; } + MoveSQItem(si,*i); } + TagHT.clear(); } /** - * \ingroup gdcmDicomDir - * \brief AddObjectToEnd - * @param type - * @param begin iterator on the first DocEntry within the chained List - * @param end iterator on the last DocEntry within the chained List - */ - -// now useless ? - -/*void gdcmDicomDir::AddObjectToEnd(gdcmDicomDirType type,gdcmSQItem *s) -{ - if(s==NULL) // ?? - return; - - switch(type) - { - case gdcmDicomDir::GDCM_DICOMDIR_META: - AddDicomDirMeta(); - break; - case gdcmDicomDir::GDCM_DICOMDIR_PATIENT: - AddDicomDirPatientToEnd(s); - break; - case gdcmDicomDir::GDCM_DICOMDIR_STUDY: - AddDicomDirStudyToEnd(s); - break; - case gdcmDicomDir::GDCM_DICOMDIR_SERIE: - AddDicomDirSerieToEnd(s); - break; - case gdcmDicomDir::GDCM_DICOMDIR_IMAGE: - AddDicomDirImageToEnd(s); - break; - case gdcmDicomDir::GDCM_DICOMDIR_NONE: - AddDicomDirImageToEnd(s); //FIXME - break; - } -} - -*/ - -/** - * \ingroup gdcmDicomDir * \brief Well ... there is only one occurence */ -void gdcmDicomDir::AddDicomDirMeta() +bool DicomDir::AddDicomDirMeta() { - if( metaElems ) + if( MetaElems ) { - delete metaElems; + delete MetaElems; } - metaElems = new gdcmDicomDirMeta( &tagHT ); + MetaElems = new DicomDirMeta(); + return true; } /** - * \ingroup gdcmDicomDir * \brief AddDicomDirPatientToEnd - * @param s SQ Item to enqueue to the DicomPatient chained List + * @param dd SQ Item to enqueue to the DicomPatient chained List */ -void gdcmDicomDir::AddDicomDirPatientToEnd(gdcmSQItem *s) +bool DicomDir::AddDicomDirPatientToEnd(DicomDirPatient *dd) { - patients.push_back(new gdcmDicomDirPatient(s, &tagHT)); + Patients.push_back(dd); + return true; } /** - * \ingroup gdcmDicomDir * \brief AddDicomDirStudyToEnd - * @param s SQ Item to enqueue to the DicomDirStudy chained List + * @param dd SQ Item to enqueue to the DicomDirStudy chained List */ - void gdcmDicomDir::AddDicomDirStudyToEnd(gdcmSQItem *s) +bool DicomDir::AddDicomDirStudyToEnd(DicomDirStudy *dd) { - if( patients.size() > 0 ) + if( Patients.size() > 0 ) { - ListDicomDirPatient::iterator itp = patients.end(); + ListDicomDirPatient::iterator itp = Patients.end(); itp--; - (*itp)->AddDicomDirStudy(new gdcmDicomDirStudy(s, &tagHT)); + (*itp)->AddDicomDirStudy(dd); + return true; } + return false; } /** - * \ingroup gdcmDicomDir * \brief AddDicomDirSerieToEnd - * @param s SQ Item to enqueue to the DicomDirSerie chained List + * @param dd SQ Item to enqueue to the DicomDirSerie chained List */ -void gdcmDicomDir::AddDicomDirSerieToEnd(gdcmSQItem *s) +bool DicomDir::AddDicomDirSerieToEnd(DicomDirSerie *dd) { - if( patients.size() > 0 ) + if( Patients.size() > 0 ) { - ListDicomDirPatient::iterator itp = patients.end(); + ListDicomDirPatient::iterator itp = Patients.end(); itp--; if( (*itp)->GetDicomDirStudies().size() > 0 ) { - ListDicomDirStudy::iterator itst=(*itp)->GetDicomDirStudies().end(); + ListDicomDirStudy::const_iterator itst = + (*itp)->GetDicomDirStudies().end(); itst--; - (*itst)->AddDicomDirSerie(new gdcmDicomDirSerie(s, &tagHT)); + (*itst)->AddDicomDirSerie(dd); + return true; } } + return false; } /** - * \ingroup gdcmDicomDir * \brief AddDicomDirImageToEnd - * @param s SQ Item to enqueue to the DicomDirImage chained List + * @param dd SQ Item to enqueue to the DicomDirImage chained List */ - void gdcmDicomDir::AddDicomDirImageToEnd(gdcmSQItem *s) +bool DicomDir::AddDicomDirImageToEnd(DicomDirImage *dd) { - if( patients.size() > 0 ) + if( Patients.size() > 0 ) { - ListDicomDirPatient::iterator itp = patients.end(); + ListDicomDirPatient::iterator itp = Patients.end(); itp--; if( (*itp)->GetDicomDirStudies().size() > 0 ) { - ListDicomDirStudy::iterator itst = (*itp)->GetDicomDirStudies().end(); + ListDicomDirStudy::const_iterator itst = + (*itp)->GetDicomDirStudies().end(); itst--; if( (*itst)->GetDicomDirSeries().size() > 0 ) { - ListDicomDirSerie::iterator its = (*itst)->GetDicomDirSeries().end(); + ListDicomDirSerie::const_iterator its = (*itst)->GetDicomDirSeries().end(); its--; - (*its)->AddDicomDirImage(new gdcmDicomDirImage(s, &tagHT)); + (*its)->AddDicomDirImage(dd); + return true; } } } + return false; } /** - * \ingroup gdcmDicomDir * \brief for each Header of the chained list, add/update the Patient/Study/Serie/Image info * @param path path of the root directory * @param list chained list of Headers */ -void gdcmDicomDir::SetElements(std::string &path, VectDocument &list) +void DicomDir::SetElements(std::string const & path, VectDocument const &list) { + TagHT.clear(); + Patients.clear(); + std::string patPrevName = "", patPrevID = ""; std::string studPrevInstanceUID = "", studPrevID = ""; std::string serPrevInstanceUID = "", serPrevID = ""; @@ -938,34 +890,38 @@ void gdcmDicomDir::SetElements(std::string &path, VectDocument &list) std::string studCurInstanceUID, studCurID; std::string serCurInstanceUID, serCurID; - SetElement( path, GDCM_DICOMDIR_META,NULL); - - for( VectDocument::iterator it = list.begin(); - it != list.end(); ++it ) + bool first = true; + for( VectDocument::const_iterator it = list.begin(); + it != list.end(); ++it ) { // get the current file characteristics - patCurName = (*it)->GetEntryByNumber(0x0010,0x0010); - patCurID = (*it)->GetEntryByNumber(0x0010,0x0011); - studCurInstanceUID = (*it)->GetEntryByNumber(0x0020,0x000d); - studCurID = (*it)->GetEntryByNumber(0x0020,0x0010); - serCurInstanceUID = (*it)->GetEntryByNumber(0x0020,0x000e); - serCurID = (*it)->GetEntryByNumber(0x0020,0x0011); - - if( patCurName != patPrevName || patCurID != patPrevID) + patCurName = (*it)->GetEntry(0x0010,0x0010); + patCurID = (*it)->GetEntry(0x0010,0x0011); + studCurInstanceUID = (*it)->GetEntry(0x0020,0x000d); + studCurID = (*it)->GetEntry(0x0020,0x0010); + serCurInstanceUID = (*it)->GetEntry(0x0020,0x000e); + serCurID = (*it)->GetEntry(0x0020,0x0011); + + if( patCurName != patPrevName || patCurID != patPrevID || first ) { SetElement(path, GDCM_DICOMDIR_PATIENT, *it); + first = true; } // if new Study Deal with 'STUDY' Elements - if( studCurInstanceUID != studPrevInstanceUID || studCurID != studPrevID ) + if( studCurInstanceUID != studPrevInstanceUID || studCurID != studPrevID + || first ) { SetElement(path, GDCM_DICOMDIR_STUDY, *it); + first = true; } // if new Serie Deal with 'SERIE' Elements - if( serCurInstanceUID != serPrevInstanceUID || serCurID != serPrevID ) + if( serCurInstanceUID != serPrevInstanceUID || serCurID != serPrevID + || first ) { SetElement(path, GDCM_DICOMDIR_SERIE, *it); + first = true; } // Always Deal with 'IMAGE' Elements @@ -977,48 +933,67 @@ void gdcmDicomDir::SetElements(std::string &path, VectDocument &list) studPrevID = studCurID; serPrevInstanceUID = serCurInstanceUID; serPrevID = serCurID; + first = false; + } +} + +/** + * \brief Move the content of the source SQItem to the destination SQItem + * Only DocEntry's are moved + * @param dst destination SQItem + * @param src source SQItem + */ +void DicomDir::MoveSQItem(SQItem *dst,SQItem *src) +{ + DocEntry *entry; + + entry = src->GetFirstEntry(); + while(entry) + { + src->RemoveEntryNoDestroy(entry); + dst->AddEntry(entry); + entry = src->GetNextEntry(); } } /** - * \ingroup gdcmDicomDir * \brief compares two dgcmHeaders */ -bool gdcmDicomDir::HeaderLessThan(gdcmDocument *header1, gdcmDocument *header2) +bool DicomDir::HeaderLessThan(Document *header1, Document *header2) { return *header1 < *header2; } + /** - * \brief Sets the accurate value for the (0x0004,0x1220) element of a DICOMDIR - */ -void gdcmDicomDir::UpdateDirectoryRecordSequenceLength() + * \brief Get the first entry while visiting the DicomDirPatients + * \return The first DicomDirPatient if found, otherwhise NULL + */ +DicomDirPatient *DicomDir::GetFirstEntry() { + ItDicomDirPatient = Patients.begin(); + if ( ItDicomDirPatient != Patients.end() ) + return *ItDicomDirPatient; + return NULL; +} -/// \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; -/// +/** + * \brief Get the next entry while visiting the DicomDirPatients + * \note : meaningfull only if GetFirstEntry already called + * \return The next DicomDirPatient if found, otherwhise NULL + */ +DicomDirPatient *DicomDir::GetNextEntry() +{ + gdcmAssertMacro (ItDicomDirPatient != Patients.end()); + { + ++ItDicomDirPatient; + if ( ItDicomDirPatient != Patients.end() ) + return *ItDicomDirPatient; + } + return NULL; } + +} // end namespace gdcm + //-----------------------------------------------------------------------------