X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDicomDir.cxx;h=6b758ed193b858919c233c5d0c1cb7dc73f80c93;hb=f6dbab059809959b586408f89330264a03cfe656;hp=3959a469bd712cfb07f1f7faa73e5f814cd56ec3;hpb=ab62b1a706df8e2ab1fbf26fa5037d6c22293655;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index 3959a469..6b758ed1 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDicomDir.cxx,v $ Language: C++ - Date: $Date: 2004/08/02 16:42:14 $ - Version: $Revision: 1.63 $ + Date: $Date: 2004/08/31 14:24:47 $ + Version: $Revision: 1.67 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -52,17 +52,15 @@ gdcmDicomDir::gdcmDicomDir() :gdcmDocument( ) { - Initialize(); - - std::string pathBidon = "Bidon"; // Sorry, NULL not allowed ... - SetElement(pathBidon, GDCM_DICOMDIR_META, NULL); // Set the META elements - AddDicomDirMeta(); + Initialize(); // sets all private fields to NULL + std::string pathBidon = "Bidon"; // Sorry, NULL not allowed ... + metaElems = NewMeta(); } /** * \brief Constructor Parses recursively the directory and creates the DicomDir * or uses an already built DICOMDIR, depending on 'parseDir' value. - * @param FileName name + * @param fileName name * - of the root directory (parseDir = true) * - of the DICOMDIR (parseDir = false) * @param parseDir boolean @@ -74,15 +72,14 @@ gdcmDicomDir::gdcmDicomDir() 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(); + // Whatever user passed (a root directory or a DICOMDIR) + // and whatever the value of parseDir was, + // gdcmDocument is already executed + Initialize(); // sets all private fields to NULL - // 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"); @@ -92,13 +89,14 @@ 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(); @@ -110,7 +108,7 @@ 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); @@ -133,18 +131,16 @@ 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; + } } //----------------------------------------------------------------------------- @@ -340,82 +336,42 @@ void gdcmDicomDir::SetEndMethodArgDelete(gdcmMethod *method) * @return false only when fail to open */ -bool gdcmDicomDir::Write(std::string const & fileName) -{ - FILE * fp1 = fopen(fileName.c_str(), "wb"); - if( !fp1 ) +bool gdcmDicomDir::WriteDicomDir(std::string const & fileName) +{ + uint16_t sq[4] = { 0x0004, 0x1220, 0xffff, 0xffff }; + uint16_t sqt[4]= { 0xfffe, 0xe0dd, 0xffff, 0xffff }; + + 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); + + gdcmDicomDirMeta *ptrMeta = GetDicomDirMeta(); + ptrMeta->Write(fp, gdcmExplicitVR); + + // force writing 0004|1220 [SQ ], that CANNOT exist within gdcmDicomDirMeta + fwrite(&sq[0],8,1,fp); // 0004 1220 ffff ffff + + for(ListDicomDirPatient::iterator cc = patients.begin();cc!=patients.end();++cc) + { + (*cc)->Write( fp, gdcmExplicitVR ); + } + + // force writing Sequence Delimitation Item + fwrite(&sqt[0],8,1,fp); // fffe e0dd ffff ffff - fclose( 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 @@ -454,6 +410,7 @@ void gdcmDicomDir::CreateDicomDirChainedList(std::string const & path) "failure in new Header ", it->c_str() ); } + if( header->IsReadable() ) { // Add the file header to the chained list: @@ -461,6 +418,7 @@ void gdcmDicomDir::CreateDicomDirChainedList(std::string const & path) dbg.Verbose( 1, "gdcmDicomDir::CreateDicomDirChainedList: readable ", it->c_str() ); + } else { @@ -468,15 +426,12 @@ void gdcmDicomDir::CreateDicomDirChainedList(std::string const & path) } count++; } - // sorts Patient/Study/Serie/ 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); - CallEndMethod(); } @@ -484,22 +439,34 @@ 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 --; + // ALL the 'out of Sequence' Tags belong to Meta Elems + // (we skip 0004|1220 [Directory record sequence] ) + for ( TagDocEntryHT::iterator cc = TagHT.begin(); + cc != lastOneButSequence; + ++cc) + { + m->AddDocEntry( cc->second ); + } } + else // after root directory parsing + { + std::list elemList; + elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirMetaElements(); + m->FillObject(elemList); + } + m->SetSQItemNumber(0); // To avoid further missprinting return m; } - /** * \brief adds a new Patient (with the basic elements) to a partially created DICOMDIR */ @@ -512,13 +479,6 @@ gdcmDicomDirPatient * gdcmDicomDir::NewPatient() 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 @@ -579,7 +539,7 @@ 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: @@ -605,25 +565,32 @@ void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type, 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) { @@ -641,24 +608,20 @@ 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 ) { @@ -683,13 +646,38 @@ 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 ) { - std::cout << " special Treatment for GDCM_DICOMDIR_META" << std::endl; - + + if ( type == GDCM_DICOMDIR_META ) // fusible : should never print ! + { + std::cout << "GDCM_DICOMDIR_META ?!? should never print that" + << std::endl; } - //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 + } /** @@ -788,25 +776,21 @@ 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 @@ -818,46 +802,6 @@ 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 @@ -960,8 +904,6 @@ 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 ) { @@ -1011,36 +953,4 @@ bool gdcmDicomDir::HeaderLessThan(gdcmDocument *header1, gdcmDocument *header2) return *header1 < *header2; } -/** - * \brief Sets the accurate value for the (0x0004,0x1220) element of a DICOMDIR - */ -void gdcmDicomDir::UpdateDirectoryRecordSequenceLength() -{ - -/// \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; -/// -} - //-----------------------------------------------------------------------------