X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;ds=sidebyside;f=src%2FgdcmDicomDir.cxx;h=6ad223049f8f724052dc0e40e82d92ce34367fec;hb=6efceb0f2d025e536c69ea4345a83555a059cfa6;hp=f3dc73156f2f5185462ac7620ea50508debabf0c;hpb=c437a99c0660bfd7712b98b4d60d37fac051d658;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index f3dc7315..6ad22304 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDicomDir.cxx,v $ Language: C++ - Date: $Date: 2004/07/27 15:04:10 $ - Version: $Revision: 1.59 $ + Date: $Date: 2004/08/27 15:48:44 $ + Version: $Revision: 1.65 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -19,7 +19,6 @@ #include #include #include -#include #ifdef _MSC_VER #include @@ -49,12 +48,11 @@ /** * \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): - gdcmDocument( exception_on_error ) +gdcmDicomDir::gdcmDicomDir() + :gdcmDocument( ) { - Initialize(); + Initialize(); // sets all private fields to NULL std::string pathBidon = "Bidon"; // Sorry, NULL not allowed ... SetElement(pathBidon, GDCM_DICOMDIR_META, NULL); // Set the META elements @@ -72,21 +70,19 @@ gdcmDicomDir::gdcmDicomDir(bool exception_on_error): * 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 +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 deja lance gdcmDocument - Initialize(); + Initialize(); // sets all private fields to NULL // gdcmDocument already executed // if user passed a root directory, sure we didn't get anything - if ( TagHT.begin() == TagHT.end() ) + if ( TagHT.begin() == TagHT.end() ) // when user passed a Directory to parse { dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : entry HT empty"); @@ -96,13 +92,14 @@ gdcmDicomDir::gdcmDicomDir(std::string const & fileName, bool parseDir, // 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 ) // user asked for a recursive parsing of a root directory { + metaElems = NewMeta(); + dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : Parse directory" " and create the DicomDir"); ParseDirectory(); @@ -114,7 +111,7 @@ gdcmDicomDir::gdcmDicomDir(std::string const & fileName, bool parseDir, // apres le constructeur } } - else + else // Only if user passed a DICOMDIR { // Directory record sequence gdcmDocEntry *e = GetDocEntryByNumber(0x0004, 0x1220); @@ -137,18 +134,16 @@ gdcmDicomDir::~gdcmDicomDir() SetStartMethod(NULL); SetProgressMethod(NULL); SetEndMethod(NULL); - - if ( metaElems ) - { - delete metaElems; - } - for(ListDicomDirPatient::iterator cc = patients.begin(); cc!= patients.end(); ++cc) { delete *cc; } + if ( metaElems ) + { + delete metaElems; + } } //----------------------------------------------------------------------------- @@ -219,7 +214,7 @@ void gdcmDicomDir::Initialize() progress = 0.0; abort = false; - metaElems = (gdcmDicomDirMeta *)0; + metaElems = 0; } @@ -345,83 +340,46 @@ void gdcmDicomDir::SetEndMethodArgDelete(gdcmMethod *method) */ bool gdcmDicomDir::Write(std::string const & fileName) -{ - FILE * fp1; +{ + uint16_t sq[5] = { 0x0004, 0x1220, 0x0000, 0xffff, 0xffff }; + uint16_t sqt[4]= { 0xfffe, 0xe0dd, 0xffff, 0xffff }; - fp1 = fopen(fileName.c_str(), "wb"); - if( !fp1 ) + FILE * fp = fopen(fileName.c_str(), "wb"); + if( !fp ) { printf("Failed to open(write) File [%s] \n", fileName.c_str()); return false; } - char * filePreamble = new char[128]; - fwrite(filePreamble,128,1,fp1); - fwrite("DICM",4,1,fp1); + uint8_t* filePreamble = new uint8_t[128]; + memset(filePreamble, 0, 128); + fwrite(filePreamble,128,1,fp); + fwrite("DICM",4,1,fp); delete[] filePreamble; - UpdateDirectoryRecordSequenceLength(); - WriteEntries(fp1); + + // UpdateDirectoryRecordSequenceLength(); // TODO (if *really* usefull) + + gdcmDicomDirMeta *ptrMeta = GetDicomDirMeta(); + ptrMeta->Write(fp, gdcmExplicitVR); + + // force writing 0004|1220 [SQ ], that CANNOT exist within gdcmDicomDirMeta + fwrite(&sq[0],4,1,fp); // 0004 1220 + //fwrite("SQ" ,2,1,fp); // SQ // VR no written for 'No length' Sequences ! + //fwrite(&sq[2],6,1,fp); // 00 ffffffff + fwrite(&sq[3],4,1,fp); // ffffffff + + 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( fp1 ); + fclose( fp ); 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 @@ -452,29 +410,36 @@ void gdcmDicomDir::CreateDicomDirChainedList(std::string const & path) break; } - header = new gdcmHeader(it->c_str(),false,true); - if(!header) { - std::cout << "failure in 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 gdcmHeader( it->c_str() ); + if( !header ) { - delete header; + dbg.Verbose( 1, + "gdcmDicomDir::CreateDicomDirChainedList: " + "failure in new Header ", + it->c_str() ); } - count++; - + 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(); //for each Header of the chained list, add/update the Patient/Study/Serie/Image info - SetElements(tmp, list); - + SetElements(tmp, list); CallEndMethod(); } @@ -482,18 +447,35 @@ void gdcmDicomDir::CreateDicomDirChainedList(std::string const & path) * \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() { gdcmDicomDirMeta *m = new gdcmDicomDirMeta( &TagHT ); - for ( TagDocEntryHT::iterator cc = TagHT.begin(); - cc != TagHT.end(); ++cc) - { - m->AddDocEntry( cc->second ); + + if ( TagHT.begin() != TagHT.end() ) // after Document Parsing + { + TagDocEntryHT::iterator lastOneButSequence = TagHT.end(); + lastOneButSequence --; + // This works because 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 + { + //cout << "gdcmDicomDir::NewMeta avec FillObject" << endl; + std::list elemList; + elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirMetaElements(); + m->FillObject(elemList); + // we create the Sequence manually + //gdcmSeqEntry *se =NewSeqEntryByNumber(0x0004, 0x1220); // NOT YET! + //m->AddEntry(se); + } + m->SetSQItemNumber(0); // To avoid further missprinting return m; } @@ -577,7 +559,7 @@ void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type, gdcmDictEntry *dictEntry; gdcmValEntry *entry; std::string val; - //gdcmObject *o; + gdcmSQItem *si = new gdcmSQItem(0); // all the items will be at level 1 switch( type ) { case GDCM_DICOMDIR_IMAGE: @@ -598,30 +580,38 @@ void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type, case GDCM_DICOMDIR_META: elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirMetaElements(); + // add already done ? 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 ! 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) { @@ -639,24 +629,20 @@ void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type, 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 ); + // GDCM_UNFOUND or not ! + + entry->SetValue( val ); // troubles expected when vr=SQ ... if( dictEntry ) { @@ -681,13 +667,38 @@ void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type, entry->SetLength( entry->GetValue().length() ); } } - std::cout << " was TagHT[entry->GetKey()] = entry " << std::endl; - if ( type == GDCM_DICOMDIR_META ) { + + if ( type == GDCM_DICOMDIR_META ) // fusible : should never print ! + { std::cout << " special Treatment for GDCM_DICOMDIR_META" << std::endl; - + entry->Print(); // just to see } - //TagHT[entry->GetKey()] = entry; // FIXME : use a SEQUENCE ! + si->AddEntry(entry); } + switch( type ) + { + case GDCM_DICOMDIR_IMAGE: + AddDicomDirImageToEnd(si); + break; + + case GDCM_DICOMDIR_SERIE: + AddDicomDirSerieToEnd(si); + break; + + case GDCM_DICOMDIR_STUDY: + AddDicomDirStudyToEnd(si); + break; + + case GDCM_DICOMDIR_PATIENT: + AddDicomDirPatientToEnd(si); + break; + + default: + return; + } + //int count=1; // find a trick to increment + //s->AddEntry(si, count); // Seg Faults + } /** @@ -786,25 +797,21 @@ void gdcmDicomDir::CreateDicomDir() if( v == "PATIENT " ) { AddDicomDirPatientToEnd( *i ); - //AddObjectToEnd(type,*i); type = gdcmDicomDir::GDCM_DICOMDIR_PATIENT; } else if( v == "STUDY " ) { 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 @@ -816,46 +823,6 @@ void gdcmDicomDir::CreateDicomDir() } } -/** - * \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 @@ -958,7 +925,7 @@ void gdcmDicomDir::SetElements(std::string &path, VectDocument &list) std::string studCurInstanceUID, studCurID; std::string serCurInstanceUID, serCurID; - SetElement( path, GDCM_DICOMDIR_META,NULL); + //SetElement( path, GDCM_DICOMDIR_META,NULL); // already done (NewMeta) for( VectDocument::iterator it = list.begin(); it != list.end(); ++it )