X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDicomDir.cxx;h=b7f4cb00d04bfa18f3376856c1c2f893daaad918;hb=559c3639fc5b255b36a951f352db1addead9f78f;hp=7a18df16f7d28230eda48d4c2e06238e89678b5a;hpb=746c9ec7ec0fbe389b0894c80a8393ecd5472479;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index 7a18df16..b7f4cb00 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -3,12 +3,12 @@ Program: gdcm Module: $RCSfile: gdcmDicomDir.cxx,v $ Language: C++ - Date: $Date: 2004/06/28 09:30:58 $ - Version: $Revision: 1.53 $ + Date: $Date: 2004/11/03 20:52:13 $ + Version: $Revision: 1.77 $ 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 @@ -16,17 +16,6 @@ =========================================================================*/ -#include -#include -#include -#include - -#ifdef _MSC_VER - #include -#else - #include -#endif - #include "gdcmDicomDir.h" #include "gdcmDicomDirStudy.h" #include "gdcmDicomDirSerie.h" @@ -40,35 +29,41 @@ #include "gdcmSQItem.h" #include "gdcmValEntry.h" +#include +#include +#include +#include + +#ifdef _MSC_VER + #include +#else + #include +#endif +namespace gdcm +{ + //----------------------------------------------------------------------------- // For full DICOMDIR description, see: // PS 3.3-2003, pages 731-750 //----------------------------------------------------------------------------- // Constructor / Destructor -void gdcmDicomDir::Initialize(void) -{ - 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; +/** + * \ingroup DicomDir + * \brief Constructor : creates an empty DicomDir + */ +DicomDir::DicomDir() + :Document( ) +{ + 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 @@ -76,89 +71,78 @@ void gdcmDicomDir::Initialize(void) * 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(const char *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 lance gdcmDocument - Initialize(); + // Whatever user passed (a root directory or a DICOMDIR) + // and whatever the value of parseDir was, + // Document 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( GetEntry().begin() == GetEntry().end() ) + if ( TagHT.begin() == TagHT.end() ) // when user passed a Directory to parse { - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : entry HT empty"); + dbg.Verbose(0, "DicomDir::DicomDir : entry HT empty"); - if(strlen(FileName)==1 && FileName[0]=='.') { // user passed '.' as Name - // we get current directory name - char* dummy= new char[1000]; + if ( fileName.size() == 1 && fileName[0] == '.' ) + { + // user passed '.' as Name + // we get current directory name + char dummy[1000]; getcwd(dummy, (size_t)1000); - SetFileName(dummy); // will be converted into a string - delete[] dummy; // no longer needed + SetFileName( dummy ); // will be converted into a string } - if(parseDir) + if ( parseDir ) // user asked for a recursive parsing of a root directory { - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : Parse directory" + MetaElems = NewMeta(); + + dbg.Verbose(0, "DicomDir::DicomDir : Parse directory" " and create the DicomDir"); ParseDirectory(); - } else { + } + else + { /// \todo if parseDir == false, it should be tagged as an error + // NON ! il suffit d'appeler ParseDirectory() + // apres le constructeur } } - else + else // Only if user passed a DICOMDIR { // Directory record sequence - gdcmDocEntry *e = GetDocEntryByNumber(0x0004, 0x1220); - if (e==NULL) { - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : NO Directory record" + DocEntry *e = GetDocEntryByNumber(0x0004, 0x1220); + if ( !e ) + { + dbg.Verbose(0, "DicomDir::DicomDir : NO Directory record" " sequence (0x0004,0x1220)"); - /// \todo FIXME : what to do when the parsed file IS NOT a + /// \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): - gdcmDocument(exception_on_error) -{ - - Initialize(); - - std::string pathBidon = "Bidon"; // Sorry, NULL not allowed ... - SetElement(pathBidon, GDCM_DICOMDIR_META, NULL); // Set the META elements - AddDicomDirMeta(); + } } /** * \brief Canonical destructor */ -gdcmDicomDir::~gdcmDicomDir() +DicomDir::~DicomDir() { SetStartMethod(NULL); SetProgressMethod(NULL); SetEndMethod(NULL); - - if(metaElems) - delete metaElems; - - for(ListDicomDirPatient::iterator cc = patients.begin(); - cc!= patients.end(); + for(ListDicomDirPatient::iterator cc = Patients.begin(); + cc!= Patients.end(); ++cc) { delete *cc; } + if ( MetaElems ) + { + delete MetaElems; + } } //----------------------------------------------------------------------------- @@ -166,19 +150,19 @@ gdcmDicomDir::~gdcmDicomDir() /** * \brief Canonical Printer */ -void gdcmDicomDir::Print(std::ostream &os) +void DicomDir::Print(std::ostream &os) { - if(metaElems) + if( MetaElems ) { - metaElems->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 ); } } @@ -189,123 +173,161 @@ 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(void) +bool DicomDir::IsReadable() { - if(!gdcmDocument::IsReadable()) - return(false); - if(!metaElems) - return(false); - if(patients.size()<=0) - return(false); - - return(true); + if( !Document::IsReadable() ) + { + return false; + } + if( !MetaElems ) + { + return false; + } + if( Patients.size() <= 0 ) + { + return false; + } + + return true; } /** - * \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 = 0; +} + + +/** + * \ingroup DicomDir * \brief fills the whole structure, starting from a root Directory */ -void gdcmDicomDir::ParseDirectory(void) +void DicomDir::ParseDirectory() { - CreateDicomDirChainedList(GetFileName()); + CreateDicomDirChainedList( GetFileName() ); CreateDicomDir(); } /** - * \ingroup gdcmDicomDir + * \ingroup DicomDir * \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(Method* method, void* arg, + Method* 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 + * \ingroup DicomDir * \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(Method* method) { - startMethodArgDelete=method; + StartMethodArgDelete = method; } /** - * \ingroup gdcmDicomDir + * \ingroup DicomDir * \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(Method* method, void* arg, + Method* 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 + * \ingroup DicomDir * \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(Method* method) { - progressMethodArgDelete=method; + ProgressMethodArgDelete = method; } /** - * \ingroup gdcmDicomDir + * \ingroup DicomDir * \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(Method* method, void* arg, + Method* 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 + * \ingroup DicomDir * \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::SetEndMethodArgDelete(gdcmMethod *method) +void DicomDir::SetEndMethodArgDelete(Method* method) { - endMethodArgDelete=method; + EndMethodArgDelete = method; } /** - * \ingroup gdcmDicomDir + * \ingroup 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 ! @@ -316,362 +338,416 @@ void gdcmDicomDir::SetEndMethodArgDelete(gdcmMethod *method) * @return false only when fail to open */ -bool gdcmDicomDir::Write(std::string fileName) -{ - FILE * fp1; - - fp1=fopen(fileName.c_str(),"wb"); - if(fp1==NULL) +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()); - return(false); + dbg.Verbose(2, "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->Write(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)->Write( fp, ExplicitVR ); + } + + // force writing Sequence Delimitation Item + for(i=0;i<4;++i) + { + binary_write(*fp, sqt[i]); // fffe e0dd ffff ffff + } - fclose(fp1); + fp->close(); 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 + * \ingroup DicomDir + * \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 path) +void DicomDir::CreateDicomDirChainedList(std::string const & path) { CallStartMethod(); - gdcmDirList fileList(path,1); // gets recursively the file list - unsigned int count=0; + DirList fileList(path,1); // gets recursively the file list + unsigned int count = 0; VectDocument list; - gdcmHeader *header; + Header *header; - tagHT.clear(); - patients.clear(); + TagHT.clear(); + Patients.clear(); - for(gdcmDirList::iterator it=fileList.begin(); - it!=fileList.end(); - ++it) + for( DirList::iterator it = fileList.begin(); + it != fileList.end(); + ++it ) { - std::cout << "nom fichier " << it->c_str() << std::endl; //JPR - - progress=(float)(count+1)/(float)fileList.size(); + Progress = (float)(count+1)/(float)fileList.size(); CallProgressMethod(); - if(abort) - break; - - header=new gdcmHeader(it->c_str()); - if(!header) { - std::cout << "echec new Header " << it->c_str() << std::endl; // JPR + if( Abort ) + { + break; } - if(header->IsReadable()) { - list.push_back(header); // adds the file header to the chained list - std::cout << "readable : " <c_str() << std::endl; - } - else - delete header; - count++; + header = new Header( it->c_str() ); + if( !header ) + { + dbg.Verbose( 1, + "DicomDir::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, + "DicomDir::CreateDicomDirChainedList: readable ", + it->c_str() ); + } + else + { + delete header; + } + count++; } // sorts Patient/Study/Serie/ - std::sort(list.begin(),list.end(),gdcmDicomDir::HeaderLessThan); - - std::string tmp=fileList.GetDirName(); - + std::sort(list.begin(), list.end(), DicomDir::HeaderLessThan ); + + std::string tmp = fileList.GetDirName(); //for each Header of the chained list, add/update the Patient/Study/Serie/Image info - SetElements(tmp,list); - + SetElements(tmp, list); CallEndMethod(); } /** - * \ingroup gdcmDicomDir + * \ingroup DicomDir * \brief adds *the* Meta to a partially created DICOMDIR */ - - // FIXME : Heuuuuu ! Il prend les Entries du Document deja parse, - // il ne fabrique rien ! -gdcmDicomDirMeta * gdcmDicomDir::NewMeta(void) { - gdcmDicomDirMeta *m = new gdcmDicomDirMeta(&tagHT); - for (TagDocEntryHT::iterator cc = tagHT.begin();cc != tagHT.end();++cc) { - m->AddDocEntry(cc->second); +DicomDirMeta * DicomDir::NewMeta() +{ + DicomDirMeta *m = new DicomDirMeta( &TagHT ); + + if ( TagHT.begin() != TagHT.end() ) // after Document Parsing + { + TagDocEntryHT::iterator lastOneButSequence = TagHT.end(); + lastOneButSequence --; + // ALL the 'out of Sequence' Tags belong to Meta Elems + // (we skip 0004|1220 [Directory record sequence] ) + for ( TagDocEntryHT::iterator cc = TagHT.begin(); + cc != lastOneButSequence; + ++cc) + { + m->AddDocEntry( cc->second ); + } } + else // after root directory parsing + { + ListDicomDirMetaElem const & elemList = + Global::GetDicomDirElements()->GetDicomDirMetaElements(); + m->FillObject(elemList); + } + m->SetSQItemNumber(0); // To avoid further missprinting return m; } - /** - * \ingroup gdcmDicomDir * \brief adds a new Patient (with the basic elements) to a partially created DICOMDIR */ -gdcmDicomDirPatient * gdcmDicomDir::NewPatient(void) { - std::list elemList; - std::list::iterator it; - guint16 tmpGr,tmpEl; - gdcmDictEntry *dictEntry; - gdcmValEntry *entry; - - gdcmSQItem *s = new gdcmSQItem(0); - - elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirPatientElements(); - - // TODO : use FillObject !!! +DicomDirPatient * DicomDir::NewPatient() +{ + ListDicomDirPatientElem::const_iterator it; + uint16_t tmpGr,tmpEl; + DictEntry *dictEntry; + ValEntry *entry; + + ListDicomDirPatientElem const & elemList = + Global::GetDicomDirElements()->GetDicomDirPatientElements(); + SQItem *s = new SQItem(0); - // for all the DicomDirPatient Elements - - for(it=elemList.begin();it!=elemList.end();++it) + // 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()->GetDictEntryByNumber(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); - } + 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); + { + entry->SetLength( entry->GetValue().length() ); + } + s->AddDocEntry( entry ); } - gdcmDicomDirPatient *p = new gdcmDicomDirPatient(s, &tagHT); - patients.push_front(p); + DicomDirPatient *p = new DicomDirPatient(s, &TagHT); + Patients.push_front( 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; - guint16 tmpGr, tmpEl; - gdcmDictEntry *dictEntry; - gdcmValEntry *entry; + ListDicomDirElem elemList; //FIXME this is going to be a by copy operation + ListDicomDirElem::const_iterator it; + uint16_t tmpGr, tmpEl; + DictEntry *dictEntry; + ValEntry *entry; std::string val; + SQItem *si = new SQItem(0); // all the items will be at level 1 + switch( type ) + { + case GDCM_DICOMDIR_IMAGE: + elemList = Global::GetDicomDirElements()->GetDicomDirImageElements(); + break; - switch(type){ - case GDCM_DICOMDIR_PATIENT: - elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirPatientElements(); + case GDCM_DICOMDIR_SERIE: + elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements(); break; + case GDCM_DICOMDIR_STUDY: - elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirStudyElements(); - break; - case GDCM_DICOMDIR_SERIE: - elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirSerieElements(); + elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements(); break; - case GDCM_DICOMDIR_IMAGE: - elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirImageElements(); + + case GDCM_DICOMDIR_PATIENT: + elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements(); break; + case GDCM_DICOMDIR_META: - elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirMetaElements(); + elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements(); break; + default: return; } + // removed all the seems-to-be-useless stuff about Referenced Image Sequence + // to avoid further troubles + // imageElem 0008 1140 "" // Referenced Image Sequence + // imageElem fffe e000 "" // 'no length' item : length to be set to 0xffffffff later + // imageElem 0008 1150 "" // Referenced SOP Class UID : to be set/forged later + // imageElem 0008 1155 "" // Referenced SOP Instance UID : to be set/forged later + // imageElem fffe e00d "" // Item delimitation : length to be set to ZERO later + // for all the relevant elements found in their own spot of the DicomDir.dic + // FIXME : troubles found when it's a SeqEntry + + for( it = elemList.begin(); it != elemList.end(); ++it) + { + tmpGr = it->Group; + tmpEl = it->Elem; + dictEntry = GetPubDict()->GetDictEntryByNumber(tmpGr, tmpEl); - 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 = new ValEntry( 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) - val=header->GetEntryByNumber(tmpGr,tmpEl); + 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; + { + val = GDCM_UNFOUND; + } - if(val==GDCM_UNFOUND) + if( val == GDCM_UNFOUND) { - if((tmpGr==0x0004) &&(tmpEl==0x1130) ) // File-set ID + 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 + else if( tmpGr == 0x0004 && tmpEl == 0x1500 ) // Only used for image { - if(header->GetFileName().substr(0,path.length())!=path) + if( header->GetFileName().substr(0, path.length()) != path ) { - dbg.Verbose(0, "gdcmDicomDir::SetElement : the base path" + dbg.Verbose(0, "DicomDir::SetElement : the base path" " of file name is incorrect"); - val=header->GetFileName(); + val = header->GetFileName(); } else { - val=&(header->GetFileName().c_str()[path.length()]); - } + 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->GetEntryLengthByNumber(tmpGr,tmpEl) == 0 ) + val = it->Value; } - - entry->SetValue(val); - if(dictEntry) + // GDCM_UNFOUND or not ! + + entry->SetValue( val ); // troubles expected when vr=SQ ... + + if( dictEntry ) { - if(dictEntry->GetGroup()==0xfffe) { - entry->SetLength(entry->GetValue().length()); - } - else if( (dictEntry->GetVR()=="UL") || (dictEntry->GetVR()=="SL") ) + if( dictEntry->GetGroup() == 0xfffe ) + { + entry->SetLength( entry->GetValue().length() ); // FIXME + } + else if( dictEntry->GetVR() == "UL" || dictEntry->GetVR() == "SL" ) { entry->SetLength(4); - } - else if( (dictEntry->GetVR()=="US") || (dictEntry->GetVR()=="SS") ) + } + else if( dictEntry->GetVR() == "US" || dictEntry->GetVR() == "SS" ) { entry->SetLength(2); - } - else if(dictEntry->GetVR()=="SQ") + } + else if( dictEntry->GetVR() == "SQ" ) { - entry->SetLength(0xffffffff); + entry->SetLength( 0xffffffff ); } - else + else { - entry->SetLength(entry->GetValue().length()); + entry->SetLength( entry->GetValue().length() ); } } - //AddDocEntry(entry); // both in H Table and in chained list - tagHT[entry->GetKey()] = entry; // FIXME : use a SEQUENCE ! - } + + if ( type == GDCM_DICOMDIR_META ) // fusible : should never print ! + { + std::cout << "GDCM_DICOMDIR_META ?!? should never print that" + << std::endl; + } + si->AddEntry(entry); + } + switch( type ) + { + case GDCM_DICOMDIR_IMAGE: + AddDicomDirImageToEnd(si); + break; + + 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 + } +//----------------------------------------------------------------------------- /** * \brief CallStartMethod */ -void gdcmDicomDir::CallStartMethod(void) +void DicomDir::CallStartMethod() { - progress=0.0f; - abort=false; - if(startMethod) - startMethod(startArg); + Progress = 0.0f; + Abort = false; + if( StartMethod ) + { + StartMethod( StartArg ); + } } + +//----------------------------------------------------------------------------- /** - * \ingroup gdcmDicomDir + * \ingroup DicomDir * \brief CallProgressMethod */ -void gdcmDicomDir::CallProgressMethod(void) +void DicomDir::CallProgressMethod() { - if(progressMethod) - progressMethod(progressArg); + if( ProgressMethod ) + { + ProgressMethod( ProgressArg ); + } } + +//----------------------------------------------------------------------------- /** - * \ingroup gdcmDicomDir + * \ingroup DicomDir * \brief CallEndMethod */ -void gdcmDicomDir::CallEndMethod(void) +void DicomDir::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 + * \ingroup DicomDir + * \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 : @@ -681,293 +757,226 @@ 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); - if (e==NULL) + DocEntry *e = GetDocEntryByNumber(0x0004, 0x1220); + if ( !e ) { - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : NO Directory record" + dbg.Verbose(0, "DicomDir::DicomDir : 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) + SeqEntry* s = dynamic_cast(e); + if ( !s ) { - dbg.Verbose(0, "gdcmDicomDir::CreateDicomDir: no SeqEntry present"); + dbg.Verbose(0, "DicomDir::CreateDicomDir: no SeqEntry present"); + // useless : (0x0004,0x1220) IS a Sequence ! return; } + DicomDirType type = DicomDir::GDCM_DICOMDIR_META; + MetaElems = NewMeta(); + ListSQItem listItems = s->GetSQItems(); - gdcmDicomDirMeta *m = new gdcmDicomDirMeta(&tagHT); - (void)m; //?? - gdcmDocEntry * d; + DocEntry * d; std::string v; - 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) ) + for( ListSQItem::iterator i = listItems.begin(); + i !=listItems.end(); ++i ) + { + d = (*i)->GetDocEntryByNumber(0x0004, 0x1430); // Directory Record Type + if ( ValEntry* valEntry = dynamic_cast< ValEntry* >(d) ) { - v = ValEntry->GetValue(); + v = valEntry->GetValue(); } - else + else { - dbg.Verbose(0, "gdcmDicomDir::CreateDicomDir: not a ValEntry."); + dbg.Verbose(0, "DicomDir::CreateDicomDir: not a ValEntry."); continue; - } - - if(v=="PATIENT ") - { - AddDicomDirPatientToEnd(*i); - //AddObjectToEnd(type,*i); - type=gdcmDicomDir::GDCM_DICOMDIR_PATIENT; } - else if(v=="STUDY ") + if( v == "PATIENT " ) { - AddDicomDirStudyToEnd(*i); - // AddObjectToEnd(type,*i); - type=gdcmDicomDir::GDCM_DICOMDIR_STUDY; + AddDicomDirPatientToEnd( *i ); + type = DicomDir::GDCM_DICOMDIR_PATIENT; } - - else if(v=="SERIES") + else if( v == "STUDY " ) { - AddDicomDirSerieToEnd(*i); - // AddObjectToEnd(type,*i); - type=gdcmDicomDir::GDCM_DICOMDIR_SERIE; + AddDicomDirStudyToEnd( *i ); + type = DicomDir::GDCM_DICOMDIR_STUDY; } - - else if(v=="IMAGE ") + else if( v == "SERIES" ) { - AddDicomDirImageToEnd(*i); - // AddObjectToEnd(type,*i); - type=gdcmDicomDir::GDCM_DICOMDIR_IMAGE; + AddDicomDirSerieToEnd( *i ); + type = DicomDir::GDCM_DICOMDIR_SERIE; + } + else if( v == "IMAGE " ) + { + AddDicomDirImageToEnd( *i ); + type = DicomDir::GDCM_DICOMDIR_IMAGE; } - else + { // It was not a 'PATIENT', nor a 'STUDY', nor a 'SERIE', // neither an 'IMAGE' SQItem. Skip to next item. continue; + } } } + /** - * \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 + * \ingroup DicomDir + * \brief Well ... there is only one occurence */ - -// now useless ? - -/*void gdcmDicomDir::AddObjectToEnd(gdcmDicomDirType type,gdcmSQItem *s) +void DicomDir::AddDicomDirMeta() { - if(s==NULL) // ?? - return; - - switch(type) + if( MetaElems ) { - 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; + delete MetaElems; } -} - -*/ - -/** - * \ingroup gdcmDicomDir - * \brief Well ... there is only one occurence -*/ -void gdcmDicomDir::AddDicomDirMeta() -{ - if(metaElems) - delete metaElems; - metaElems = new gdcmDicomDirMeta(&tagHT); + MetaElems = new DicomDirMeta( &TagHT ); } /** - * \ingroup gdcmDicomDir + * \ingroup DicomDir * \brief AddDicomDirPatientToEnd * @param s SQ Item to enqueue to the DicomPatient chained List -*/ -void gdcmDicomDir::AddDicomDirPatientToEnd(gdcmSQItem *s) + */ +void DicomDir::AddDicomDirPatientToEnd(SQItem *s) { - patients.push_back(new gdcmDicomDirPatient(s, &tagHT)); + Patients.push_back(new DicomDirPatient(s, &TagHT)); } /** - * \ingroup gdcmDicomDir + * \ingroup DicomDir * \brief AddDicomDirStudyToEnd * @param s SQ Item to enqueue to the DicomDirStudy chained List */ - void gdcmDicomDir::AddDicomDirStudyToEnd(gdcmSQItem *s) + void DicomDir::AddDicomDirStudyToEnd(SQItem *s) { - 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(new DicomDirStudy(s, &TagHT)); } } + /** - * \ingroup gdcmDicomDir + * \ingroup DicomDir * \brief AddDicomDirSerieToEnd * @param s SQ Item to enqueue to the DicomDirSerie chained List */ -void gdcmDicomDir::AddDicomDirSerieToEnd(gdcmSQItem *s) +void DicomDir::AddDicomDirSerieToEnd(SQItem *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::const_iterator itst = + (*itp)->GetDicomDirStudies().end(); itst--; - (*itst)->AddDicomDirSerie(new gdcmDicomDirSerie(s, &tagHT)); + (*itst)->AddDicomDirSerie(new DicomDirSerie(s, &TagHT)); } } } /** - * \ingroup gdcmDicomDir + * \ingroup DicomDir * \brief AddDicomDirImageToEnd * @param s SQ Item to enqueue to the DicomDirImage chained List */ - void gdcmDicomDir::AddDicomDirImageToEnd(gdcmSQItem *s) + void DicomDir::AddDicomDirImageToEnd(SQItem *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::const_iterator itst = + (*itp)->GetDicomDirStudies().end(); itst--; - if((*itst)->GetDicomDirSeries().size()>0) + 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(new DicomDirImage(s, &TagHT)); } } } } /** - * \ingroup gdcmDicomDir + * \ingroup DicomDir * \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) { - 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); - - for(VectDocument::iterator it=list.begin();it!=list.end();++it) + 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) - 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 + * \ingroup DicomDir * \brief compares two dgcmHeaders */ -bool gdcmDicomDir::HeaderLessThan(gdcmDocument *header1,gdcmDocument *header2) +bool DicomDir::HeaderLessThan(Document *header1, Document *header2) { - return(*header1<*header2); -} - -/** - * \ingroup gdcmDicomDir - * \brief Sets the accurate value for the (0x0004,0x1220) element of a DICOMDIR - */ - -void gdcmDicomDir::UpdateDirectoryRecordSequenceLength() { - -// FIXME : to go on compiling - -// to be re written ! -/* - int offset = 0; - ListTag::iterator it; - guint16 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; - */ + return *header1 < *header2; } +} // end namespace gdcm //-----------------------------------------------------------------------------