X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDicomDir.cxx;h=6ad223049f8f724052dc0e40e82d92ce34367fec;hb=6efceb0f2d025e536c69ea4345a83555a059cfa6;hp=edd6e84e527588956432f60843097609f78e89b5;hpb=bfbd90327a5e45d972546843b0d9e4185e16cb24;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index edd6e84e..6ad22304 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -1,194 +1,1011 @@ -// gdcmDicomDir.cxx -//----------------------------------------------------------------------------- -#include "gdcmDicomDir.h" -#include "gdcmStudy.h" -#include "gdcmSerie.h" -#include "gdcmImage.h" -#include "gdcmUtil.h" +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmDicomDir.cxx,v $ + Language: C++ + 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 + http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details. + + This software is distributed WITHOUT ANY WARRANTY; without even + the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR + PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ #include +#include +#include + +#ifdef _MSC_VER + #include +#else + #include +#endif +#include "gdcmDicomDir.h" +#include "gdcmDicomDirStudy.h" +#include "gdcmDicomDirSerie.h" +#include "gdcmDicomDirImage.h" +#include "gdcmDirList.h" +#include "gdcmUtil.h" +#include "gdcmDebug.h" +#include "gdcmGlobal.h" +#include "gdcmHeader.h" +#include "gdcmSeqEntry.h" +#include "gdcmSQItem.h" +#include "gdcmValEntry.h" + +//----------------------------------------------------------------------------- +// For full DICOMDIR description, see: +// PS 3.3-2003, pages 731-750 //----------------------------------------------------------------------------- // Constructor / Destructor -gdcmDicomDir::gdcmDicomDir(std::string & FileName, - bool exception_on_error): - gdcmParser(FileName.c_str(),exception_on_error, true ) + +/** + * \ingroup gdcmDicomDir + * \brief Constructor : creates an empty gdcmDicomDir + */ +gdcmDicomDir::gdcmDicomDir() + :gdcmDocument( ) +{ + 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 + AddDicomDirMeta(); +} + +/** + * \brief Constructor Parses recursively the directory and creates the DicomDir + * or uses an already built DICOMDIR, depending on 'parseDir' value. + * @param FileName name + * - of the root directory (parseDir = true) + * - of the DICOMDIR (parseDir = false) + * @param parseDir boolean + * - true if user passed an entry point + * and wants to explore recursively the directories + * - false if user passed an already built DICOMDIR file + * and wants to use it + */ +gdcmDicomDir::gdcmDicomDir(std::string const & fileName, bool parseDir ): + gdcmDocument( fileName ) { - if ( GetListEntry().begin() == GetListEntry().end() ) + // 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(); // 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() ) // when user passed a Directory to parse { - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir entry list empty"); - } + dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : entry HT empty"); - CreateDicomDir(); -} + if ( fileName.size() == 1 && fileName[0] == '.' ) + { + // user passed '.' as Name + // we get current directory name + char* dummy = new char[1000]; + getcwd(dummy, (size_t)1000); + SetFileName( dummy ); // will be converted into a string + delete[] dummy; // no longer needed + } + + 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(); + } + else + { + /// \todo if parseDir == false, it should be tagged as an error + // NON ! il suffit d'appeler ParseDirectory() + // apres le constructeur + } + } + else // Only if user passed a DICOMDIR + { + // Directory record sequence + gdcmDocEntry *e = GetDocEntryByNumber(0x0004, 0x1220); + if ( !e ) + { + dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : NO Directory record" + " sequence (0x0004,0x1220)"); + /// \todo FIXME : what do we do when the parsed file IS NOT a + /// DICOMDIR file ? + } + CreateDicomDir(); + } +} +/** + * \brief Canonical destructor + */ gdcmDicomDir::~gdcmDicomDir() { - for(ListPatient::iterator cc = patients.begin();cc!=patients.end();++cc) + SetStartMethod(NULL); + SetProgressMethod(NULL); + SetEndMethod(NULL); + for(ListDicomDirPatient::iterator cc = patients.begin(); + cc!= patients.end(); + ++cc) { delete *cc; } + if ( metaElems ) + { + delete metaElems; + } } //----------------------------------------------------------------------------- // Print +/** + * \brief Canonical Printer + */ void gdcmDicomDir::Print(std::ostream &os) { - for(ListPatient::iterator cc = patients.begin();cc!=patients.end();++cc) + if(metaElems) + { + metaElems->SetPrintLevel(PrintLevel); + metaElems->Print(os); + } + for(ListDicomDirPatient::iterator cc = patients.begin(); + cc != patients.end(); + ++cc) { - (*cc)->SetPrintLevel(printLevel); - (*cc)->Print(os); + (*cc)->SetPrintLevel( PrintLevel ); + (*cc)->Print( os ); } } //----------------------------------------------------------------------------- // Public +/** + * \brief This predicate, based on hopefully reasonable heuristics, + * 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, + * false otherwise. + */ +bool gdcmDicomDir::IsReadable() +{ + if( !gdcmDocument::IsReadable() ) + { + return false; + } + if( !metaElems ) + { + return false; + } + if( patients.size() <= 0 ) + { + return false; + } + + return true; +} + +/** + * \brief Sets all fields to NULL + */ + +void gdcmDicomDir::Initialize() +{ + startMethod = NULL; + progressMethod = NULL; + endMethod = NULL; + startMethodArgDelete = NULL; + progressMethodArgDelete = NULL; + endMethodArgDelete = NULL; + startArg = NULL; + progressArg = NULL; + endArg = NULL; + + progress = 0.0; + abort = false; + + metaElems = 0; +} + + +/** + * \ingroup gdcmDicomDir + * \brief fills the whole structure, starting from a root Directory + */ +void gdcmDicomDir::ParseDirectory() +{ + CreateDicomDirChainedList( GetFileName() ); + CreateDicomDir(); +} + +/** + * \ingroup gdcmDicomDir + * \brief Set the start method to call when the parsing of the directory starts + * @param method Method to call + * @param arg Argument to pass to the method + * @param argDelete Argument + * \warning In python : the arg parameter isn't considered + */ +void gdcmDicomDir::SetStartMethod(gdcmMethod *method, void *arg, + gdcmMethod *argDelete ) +{ + if( startArg && startMethodArgDelete ) + { + startMethodArgDelete( startArg ); + } + + 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) +{ + startMethodArgDelete = method; +} + +/** + * \ingroup gdcmDicomDir + * \brief Set the progress method to call when the parsing of the directory progress + * @param method Method to call + * @param arg Argument to pass to the method + * @param argDelete Argument + * \warning In python : the arg parameter isn't considered + */ +void gdcmDicomDir::SetProgressMethod(gdcmMethod *method, void *arg, + gdcmMethod *argDelete ) +{ + if( progressArg && progressMethodArgDelete ) + { + progressMethodArgDelete( progressArg ); + } + + 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) +{ + 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 ) +{ + if( endArg && endMethodArgDelete ) + { + endMethodArgDelete( endArg ); + } + + 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 + * @param method Method to call to delete the argument + */ +void gdcmDicomDir::SetEndMethodArgDelete(gdcmMethod *method) +{ + endMethodArgDelete = method; +} + +/** + * \ingroup gdcmDicomDir + * \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 + * *not* the chained list + * (does NOT exist if the DICOMDIR is user-forged !) + * @param fileName file to be written to + * @return false only when fail to open + */ + +bool gdcmDicomDir::Write(std::string const & fileName) +{ + uint16_t sq[5] = { 0x0004, 0x1220, 0x0000, 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; + } + + uint8_t* filePreamble = new uint8_t[128]; + memset(filePreamble, 0, 128); + fwrite(filePreamble,128,1,fp); + fwrite("DICM",4,1,fp); + delete[] filePreamble; + + // 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( fp ); + return true; +} //----------------------------------------------------------------------------- // Protected -//----------------------------------------------------------------------------- -// Private -void gdcmDicomDir::CreateDicomDir(void) +/** + * \ingroup gdcmDicomDir + * \brief create a gdcmDocument-like chained list from a root Directory + * @param path entry point of the tree-like structure + */ +void gdcmDicomDir::CreateDicomDirChainedList(std::string const & path) { - // The list is parsed. When a tag is found : - // 1 - we save the beginning iterator - // 2 - we continue to parse - // 3 - we find an other tag - // + we create the object for the precedent tag - // + loop to 1 - + CallStartMethod(); + gdcmDirList fileList(path,1); // gets recursively the file list + unsigned int count = 0; + VectDocument list; + gdcmHeader *header; - gdcmDicomDirType type=gdcmDicomDir::GDCM_NONE; - ListTag::iterator begin; - ListTag::iterator end; + TagHT.clear(); + patients.clear(); - begin=GetListEntry().begin(); - end=begin; - for(ListTag::iterator i=GetListEntry().begin();i != GetListEntry().end();++i) + for( gdcmDirList::iterator it = fileList.begin(); + it != fileList.end(); + ++it ) { - // std::cout << std::hex << (*i)->GetGroup() << - // " " << (*i)->GetElement() << endl; + progress = (float)(count+1)/(float)fileList.size(); + CallProgressMethod(); + if( abort ) + { + break; + } - std::string v = (*i)->GetValue(); - if (v == "PATIENT ") + header = new gdcmHeader( it->c_str() ); + if( !header ) + { + dbg.Verbose( 1, + "gdcmDicomDir::CreateDicomDirChainedList: " + "failure in new Header ", + it->c_str() ); + } + if( header->IsReadable() ) { -// std::cout<<"PATIENT"<c_str() ); + } + else + { + delete header; + } + count++; + } - type=gdcmDicomDir::GDCM_PATIENT; - begin=end; - } + // sorts Patient/Study/Serie/ + std::sort(list.begin(), list.end(), gdcmDicomDir::HeaderLessThan ); - if (v == "STUDY ") - { -// std::cout<<"STUDY"<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; +} - if (v == "SERIES") - { -// std::cout<<"SERIES"<::iterator it; + uint16_t tmpGr,tmpEl; + gdcmDictEntry *dictEntry; + gdcmValEntry *entry; - if (v == "IMAGE ") - { -// std::cout<<"IMAGE"< elemList; + elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirPatientElements(); +// Looks nice, but gdcmDicomDir IS NOT a gdcmObject ... +// gdcmDicomDirPatient *p = new gdcmDicomDirPatient(ptagHT); +// FillObject(elemList); +// patients.push_front( p ); +// return p; +/// \todo TODO : find a trick to use FillObject !!! + + gdcmSQItem *s = new gdcmSQItem(0); + + // for all the DicomDirPatient Elements + for( it = elemList.begin(); it != elemList.end(); ++it ) + { + tmpGr = it->group; + tmpEl = it->elem; + dictEntry = GetPubDict()->GetDictEntryByNumber(tmpGr, tmpEl); + entry = new gdcmValEntry( dictEntry ); + entry->SetOffset(0); // just to avoid further missprinting + entry->SetValue( it->value ); - type=gdcmDicomDir::GDCM_IMAGE; - begin=end; + // 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 ); } - end=i; - AddObjectToEnd(type,begin,end); + gdcmDicomDirPatient *p = new gdcmDicomDirPatient(s, &TagHT); + patients.push_front( p ); + + return p; } -void gdcmDicomDir::AddObjectToEnd(gdcmDicomDirType type,ListTag::iterator begin,ListTag::iterator end) +/** + * \brief adds to the HTable + * the gdcmEntries (Dicom Elements) corresponding to the given type + * @param path full path file name (only used when type = GDCM_DICOMDIR_IMAGE + * @param type gdcmObject type to create (GDCM_DICOMDIR_PATIENT, + * GDCM_DICOMDIR_STUDY, GDCM_DICOMDIR_SERIE ...) + * @param header gdcmHeader of the current file + */ +void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type, + gdcmDocument *header) { - if(begin==end) - return; + std::list elemList; + std::list::iterator it; + uint16_t tmpGr, tmpEl; + gdcmDictEntry *dictEntry; + gdcmValEntry *entry; + std::string val; + gdcmSQItem *si = new gdcmSQItem(0); // all the items will be at level 1 + switch( type ) + { + case GDCM_DICOMDIR_IMAGE: + elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirImageElements(); + break; - switch(type) + case GDCM_DICOMDIR_SERIE: + elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirSerieElements(); + break; + + case GDCM_DICOMDIR_STUDY: + elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirStudyElements(); + break; + + case GDCM_DICOMDIR_PATIENT: + elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirPatientElements(); + break; + + case GDCM_DICOMDIR_META: + elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirMetaElements(); + // 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) { - case gdcmDicomDir::GDCM_PATIENT: - AddPatientToEnd(begin,end); + 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) + { + if( tmpGr == 0x0004 && tmpEl == 0x1130 ) // File-set ID + { + // force to the *end* File Name + val = GetName( path ); + } + else if( tmpGr == 0x0004 && tmpEl == 0x1500 ) // Only used for image + { + if( header->GetFileName().substr(0, path.length()) != path ) + { + dbg.Verbose(0, "gdcmDicomDir::SetElement : the base path" + " of file name is incorrect"); + val = header->GetFileName(); + } + else + val = &(header->GetFileName().c_str()[path.length()]); + } + else + val = it->value; + } + else + { + if ( header->GetEntryLengthByNumber(tmpGr,tmpEl) == 0 ) + val = it->value; + } + + // GDCM_UNFOUND or not ! + + entry->SetValue( val ); // troubles expected when vr=SQ ... + + if( dictEntry ) + { + if( dictEntry->GetGroup() == 0xfffe ) + { + entry->SetLength( entry->GetValue().length() ); // FIXME + } + else if( dictEntry->GetVR() == "UL" || dictEntry->GetVR() == "SL" ) + { + entry->SetLength(4); + } + else if( dictEntry->GetVR() == "US" || dictEntry->GetVR() == "SS" ) + { + entry->SetLength(2); + } + else if( dictEntry->GetVR() == "SQ" ) + { + entry->SetLength( 0xffffffff ); + } + else + { + entry->SetLength( entry->GetValue().length() ); + } + } + + if ( type == GDCM_DICOMDIR_META ) // fusible : should never print ! + { + std::cout << " special Treatment for GDCM_DICOMDIR_META" << std::endl; + entry->Print(); // just to see + } + si->AddEntry(entry); + } + switch( type ) + { + case GDCM_DICOMDIR_IMAGE: + AddDicomDirImageToEnd(si); break; - case gdcmDicomDir::GDCM_STUDY: - AddStudyToEnd(begin,end); + + case GDCM_DICOMDIR_SERIE: + AddDicomDirSerieToEnd(si); break; - case gdcmDicomDir::GDCM_SERIE: - AddSerieToEnd(begin,end); + + case GDCM_DICOMDIR_STUDY: + AddDicomDirStudyToEnd(si); break; - case gdcmDicomDir::GDCM_IMAGE: - AddImageToEnd(begin,end); + + 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() +{ + progress = 0.0f; + abort = false; + if( startMethod ) + { + startMethod( startArg ); + } +} + +/** + * \ingroup gdcmDicomDir + * \brief CallProgressMethod + */ +void gdcmDicomDir::CallProgressMethod() +{ + if( progressMethod ) + { + progressMethod( progressArg ); + } +} + +/** + * \ingroup gdcmDicomDir + * \brief CallEndMethod + */ +void gdcmDicomDir::CallEndMethod() +{ + progress = 1.0f; + if( endMethod ) + { + endMethod( endArg ); + } +} + +//----------------------------------------------------------------------------- +// Private +/** + * \ingroup gdcmDicomDir + * \brief create a 'gdcmDicomDir' from a DICOMDIR gdcmHeader + */ +void gdcmDicomDir::CreateDicomDir() +{ + // The list is parsed. + // When a DicomDir tag ("PATIENT", "STUDY", "SERIE", "IMAGE") is found : + // 1 - we save the beginning iterator + // 2 - we continue to parse + // 3 - we find an other tag + // + we create the object for the precedent tag + // + loop to 1 - + + // Directory record sequence + gdcmDocEntry *e = GetDocEntryByNumber(0x0004, 0x1220); + if ( !e ) + { + dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : NO Directory record" + " sequence (0x0004,0x1220)"); + /// \todo FIXME: what to do when the parsed file IS NOT a DICOMDIR file ? + return; + } + + gdcmSeqEntry* s = dynamic_cast(e); + if ( !s ) + { + dbg.Verbose(0, "gdcmDicomDir::CreateDicomDir: no SeqEntry present"); + // useless : (0x0004,0x1220) IS a Sequence ! + return; } + + gdcmDicomDirType type = gdcmDicomDir::GDCM_DICOMDIR_META; + metaElems = NewMeta(); + + ListSQItem listItems = s->GetSQItems(); + + gdcmDocEntry * 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) ) + { + v = ValEntry->GetValue(); + } + else + { + dbg.Verbose(0, "gdcmDicomDir::CreateDicomDir: not a ValEntry."); + continue; + } + + if( v == "PATIENT " ) + { + AddDicomDirPatientToEnd( *i ); + type = gdcmDicomDir::GDCM_DICOMDIR_PATIENT; + } + else if( v == "STUDY " ) + { + AddDicomDirStudyToEnd( *i ); + type = gdcmDicomDir::GDCM_DICOMDIR_STUDY; + } + else if( v == "SERIES" ) + { + AddDicomDirSerieToEnd( *i ); + type = gdcmDicomDir::GDCM_DICOMDIR_SERIE; + } + else if( v == "IMAGE " ) + { + AddDicomDirImageToEnd( *i ); + type = gdcmDicomDir::GDCM_DICOMDIR_IMAGE; + } + else + { + // It was not a 'PATIENT', nor a 'STUDY', nor a 'SERIE', + // neither an 'IMAGE' SQItem. Skip to next item. + continue; + } + } +} + +/** + * \ingroup gdcmDicomDir + * \brief Well ... there is only one occurence + */ +void gdcmDicomDir::AddDicomDirMeta() +{ + if( metaElems ) + { + delete metaElems; + } + metaElems = new gdcmDicomDirMeta( &TagHT ); } -void gdcmDicomDir::AddPatientToEnd(ListTag::iterator begin,ListTag::iterator end) +/** + * \ingroup gdcmDicomDir + * \brief AddDicomDirPatientToEnd + * @param s SQ Item to enqueue to the DicomPatient chained List + */ +void gdcmDicomDir::AddDicomDirPatientToEnd(gdcmSQItem *s) { - patients.push_back(new gdcmPatient(begin,end)); + patients.push_back(new gdcmDicomDirPatient(s, &TagHT)); } -void gdcmDicomDir::AddStudyToEnd(ListTag::iterator begin,ListTag::iterator end) +/** + * \ingroup gdcmDicomDir + * \brief AddDicomDirStudyToEnd + * @param s SQ Item to enqueue to the DicomDirStudy chained List + */ + void gdcmDicomDir::AddDicomDirStudyToEnd(gdcmSQItem *s) { - if(patients.size()>0) + if( patients.size() > 0 ) { - ListPatient::iterator itp=patients.end(); + ListDicomDirPatient::iterator itp = patients.end(); itp--; - (*itp)->AddStudy(new gdcmStudy(begin,end)); + (*itp)->AddDicomDirStudy(new gdcmDicomDirStudy(s, &TagHT)); } } -void gdcmDicomDir::AddSerieToEnd(ListTag::iterator begin,ListTag::iterator end) +/** + * \ingroup gdcmDicomDir + * \brief AddDicomDirSerieToEnd + * @param s SQ Item to enqueue to the DicomDirSerie chained List + */ +void gdcmDicomDir::AddDicomDirSerieToEnd(gdcmSQItem *s) { - if(patients.size()>0) + if( patients.size() > 0 ) { - ListPatient::iterator itp=patients.end(); + ListDicomDirPatient::iterator itp = patients.end(); itp--; - if((*itp)->GetStudies().size()>0) + if( (*itp)->GetDicomDirStudies().size() > 0 ) { - ListStudy::iterator itst=(*itp)->GetStudies().end(); + ListDicomDirStudy::iterator itst=(*itp)->GetDicomDirStudies().end(); itst--; - (*itst)->AddSerie(new gdcmSerie(begin,end)); + (*itst)->AddDicomDirSerie(new gdcmDicomDirSerie(s, &TagHT)); } } } -void gdcmDicomDir::AddImageToEnd(ListTag::iterator begin,ListTag::iterator end) +/** + * \ingroup gdcmDicomDir + * \brief AddDicomDirImageToEnd + * @param s SQ Item to enqueue to the DicomDirImage chained List + */ + void gdcmDicomDir::AddDicomDirImageToEnd(gdcmSQItem *s) { - if(patients.size()>0) + if( patients.size() > 0 ) { - ListPatient::iterator itp=patients.end(); + ListDicomDirPatient::iterator itp = patients.end(); itp--; - if((*itp)->GetStudies().size()>0) + if( (*itp)->GetDicomDirStudies().size() > 0 ) { - ListStudy::iterator itst=(*itp)->GetStudies().end(); + ListDicomDirStudy::iterator itst = (*itp)->GetDicomDirStudies().end(); itst--; - if((*itst)->GetSeries().size()>0) + if( (*itst)->GetDicomDirSeries().size() > 0 ) { - ListSerie::iterator its=(*itst)->GetSeries().end(); + ListDicomDirSerie::iterator its = (*itst)->GetDicomDirSeries().end(); its--; - (*its)->AddImage(new gdcmImage(begin,end)); + (*its)->AddDicomDirImage(new gdcmDicomDirImage(s, &TagHT)); } } } } +/** + * \ingroup gdcmDicomDir + * \brief for each Header of the chained list, add/update the Patient/Study/Serie/Image info + * @param path path of the root directory + * @param list chained list of Headers + */ +void gdcmDicomDir::SetElements(std::string &path, VectDocument &list) +{ + 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); // already done (NewMeta) + + for( VectDocument::iterator it = list.begin(); + it != list.end(); ++it ) + { + // get the current file characteristics + patCurName = (*it)->GetEntryByNumber(0x0010,0x0010); + patCurID = (*it)->GetEntryByNumber(0x0010,0x0011); + studCurInstanceUID = (*it)->GetEntryByNumber(0x0020,0x000d); + studCurID = (*it)->GetEntryByNumber(0x0020,0x0010); + serCurInstanceUID = (*it)->GetEntryByNumber(0x0020,0x000e); + serCurID = (*it)->GetEntryByNumber(0x0020,0x0011); + + if( patCurName != patPrevName || patCurID != patPrevID) + { + SetElement(path, GDCM_DICOMDIR_PATIENT, *it); + } + + // if new Study Deal with 'STUDY' Elements + 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); + } + + // Always Deal with 'IMAGE' Elements + SetElement(path, GDCM_DICOMDIR_IMAGE, *it); + + patPrevName = patCurName; + patPrevID = patCurID; + studPrevInstanceUID = studCurInstanceUID; + studPrevID = studCurID; + serPrevInstanceUID = serCurInstanceUID; + serPrevID = serCurID; + } +} + +/** + * \ingroup gdcmDicomDir + * \brief compares two dgcmHeaders + */ +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; +/// +} + //-----------------------------------------------------------------------------