X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDicomDir.cxx;h=7ab7f7d6d3c3b7c0f6add43c6d8de4c5044b6f46;hb=d31dacbd4792e49cccecc51ffd9d93fd71541561;hp=23f33438381c7bcaba3c3defa3d39e2095ff7e62;hpb=e785350bf905bcac85e241f9cf9f07d03eae345d;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index 23f33438..7ab7f7d6 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -1,522 +1,1000 @@ -// gdcmDicomDir.cxx -//----------------------------------------------------------------------------- +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmDicomDir.cxx,v $ + Language: C++ + Date: $Date: 2004/12/07 13:39:33 $ + Version: $Revision: 1.88 $ + + 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.html 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 "gdcmDicomDir.h" -#include "gdcmStudy.h" -#include "gdcmSerie.h" -#include "gdcmImage.h" +#include "gdcmDicomDirStudy.h" +#include "gdcmDicomDirSerie.h" +#include "gdcmDicomDirImage.h" +#include "gdcmDicomDirPatient.h" +#include "gdcmDicomDirMeta.h" +#include "gdcmDicomDirElement.h" #include "gdcmDirList.h" #include "gdcmUtil.h" - +#include "gdcmDebug.h" +#include "gdcmGlobal.h" +#include "gdcmHeader.h" +#include "gdcmSeqEntry.h" +#include "gdcmSQItem.h" +#include "gdcmValEntry.h" + +#include #include #include - #include -#include + +#ifdef _MSC_VER +#define getcwd _getcwd +#endif + +#if defined( _MSC_VER) || defined(__BORLANDC__) + #include +#else + #include +#endif + +namespace gdcm +{ + //----------------------------------------------------------------------------- // For full DICOMDIR description, see: // PS 3.3-2003, pages 731-750 //----------------------------------------------------------------------------- // Constructor / Destructor -/* - * \ingroup gdcmDicomDir - * \brief Constructor - * @param Filename - * @param exception_on_error + +/** + * \ingroup DicomDir + * \brief Constructor : creates an empty DicomDir + */ +DicomDir::DicomDir() + :Document( ) +{ + Initialize(); // sets all private fields to NULL + MetaElems = NewMeta(); +} + +/** + * \brief Constructor Parses recursively the directory and creates the DicomDir + * or uses an already built DICOMDIR, depending on 'parseDir' value. + * @param fileName name + * - 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(const char *FileName, bool parseDir, - bool exception_on_error): - gdcmParser(FileName,exception_on_error,true) +DicomDir::DicomDir(std::string const & fileName, bool parseDir ): + Document( fileName ) { - metaElems=NULL; + // 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 - if( GetListEntry().begin()==GetListEntry().end() ) + // if user passed a root directory, sure we didn't get anything + if ( TagHT.begin() == TagHT.end() ) // when user passed a Directory to parse { - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : entry list empty"); + dbg.Verbose(0, "DicomDir::DicomDir : entry HT empty"); - if(parseDir) + if ( fileName.size() == 1 && fileName[0] == '.' ) { - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : Parse directory and create the DicomDir"); + // 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 + } + + if ( parseDir ) // user asked for a recursive parsing of a root directory + { + MetaElems = NewMeta(); + + dbg.Verbose(0, "DicomDir::DicomDir : 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 + DocEntry *e = GetDocEntryByNumber(0x0004, 0x1220); + if ( !e ) + { + dbg.Verbose(0, "DicomDir::DicomDir : NO Directory record" + " sequence (0x0004,0x1220)"); + /// \todo FIXME : what do we do when the parsed file IS NOT a + /// DICOMDIR file ? + } + else + CreateDicomDir(); } - else - CreateDicomDir(); } -/* - * \ingroup gdcmDicomDir +/** * \brief Canonical destructor */ -gdcmDicomDir::~gdcmDicomDir() +DicomDir::~DicomDir() { - if(metaElems) - delete metaElems; - - 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 -/* - * \ingroup 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); - } - - for(ListPatient::iterator cc=patients.begin();cc!=patients.end();++cc) + 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 /** - * \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 ! - * @param fileName file to be written to - * @return false only when fail to open + * \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 Document is the one of a reasonable DicomDir, + * false otherwise. */ -bool gdcmDicomDir::Write(std::string fileName) +bool DicomDir::IsReadable() { - FILE * fp1; - - fp1=fopen(fileName.c_str(),"wb"); - if(fp1==NULL) + if( !Document::IsReadable() ) { - printf("Failed to open(write) File [%s] \n",fileName.c_str()); - return(false); + return false; + } + if( !MetaElems ) + { + return false; + } + if( Patients.size() <= 0 ) + { + return false; } - char * filePreamble; - filePreamble=(char*)calloc(128,1); - fwrite(filePreamble,128,1,fp1); - fwrite("DICM",4,1,fp1); - free(filePreamble); - - WriteEntries(fp1,DICOMDIR); + return true; +} - fclose(fp1); +/** + * \brief Sets all fields to NULL + */ - return true; +void DicomDir::Initialize() +{ + StartMethod = NULL; + ProgressMethod = NULL; + EndMethod = NULL; + StartMethodArgDelete = NULL; + ProgressMethodArgDelete = NULL; + EndMethodArgDelete = NULL; + StartArg = NULL; + ProgressArg = NULL; + EndArg = NULL; + + Progress = 0.0; + Abort = false; + + MetaElems = NULL; } -/* - * \ingroup gdcmDicomDir - * \brief fills whole the structure + +/** + * \ingroup DicomDir + * \brief fills the whole structure, starting from a root Directory */ -void gdcmDicomDir::ParseDirectory(void) +void DicomDir::ParseDirectory() { - NewDicomDir(GetPath()); + CreateDicomDirChainedList( GetFileName() ); CreateDicomDir(); } -//----------------------------------------------------------------------------- -// Protected -/* - * \ingroup gdcmDicomDir - * \brief create a gdcmDicomDir from a root Directory - * @param path entry point of the stree-like structure +/** + * \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::NewDicomDir(std::string path) +void DicomDir::SetStartMethod( DicomDir::Method* method, void* arg, + DicomDir::Method* argDelete ) { - gdcmDirList fileList(path,1); - ListHeader list; - gdcmHeader *header; + if( StartArg && StartMethodArgDelete ) + { + StartMethodArgDelete( StartArg ); + } - listEntries.clear(); - patients.clear(); + StartMethod = method; + StartArg = arg; + StartMethodArgDelete = argDelete; +} - for(gdcmDirList::iterator it=fileList.begin(); - it!=fileList.end(); ++it) +/** + * \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 DicomDir::SetStartMethodArgDelete( DicomDir::Method* method ) +{ + StartMethodArgDelete = method; +} + +/** + * \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 DicomDir::SetProgressMethod( DicomDir::Method* method, void* arg, + DicomDir::Method* argDelete ) +{ + if( ProgressArg && ProgressMethodArgDelete ) { - std::cout<<*it<c_str()); - if(header->IsReadable()) - list.push_back(header); - else - delete header; + ProgressMethodArgDelete( ProgressArg ); } - std::sort(list.begin(),list.end(),gdcmDicomDir::HeaderLessThan); - - std::string tmp=fileList.GetDirName(); - SetElements(tmp,list); + ProgressMethod = method; + ProgressArg = arg; + ProgressMethodArgDelete = argDelete; } -/* - * \ingroup gdcmDicomDir - * \brief Get the DicomDir path - * @param +/** + * \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 */ -std::string gdcmDicomDir::GetPath(void) +void DicomDir::SetProgressMethodArgDelete( DicomDir::Method* method ) { - std::string path=GetFileName(); + ProgressMethodArgDelete = method; +} - int pos1=path.rfind("/"); - int pos2=path.rfind("\\"); - if(pos1>pos2) - path.resize(pos1); - else - path.resize(pos2); +/** + * \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 DicomDir::SetEndMethod( DicomDir::Method* method, void* arg, + DicomDir::Method* argDelete ) +{ + if( EndArg && EndMethodArgDelete ) + { + EndMethodArgDelete( EndArg ); + } - return(path); + EndMethod = method; + EndArg = arg; + EndMethodArgDelete = argDelete; } -//----------------------------------------------------------------------------- -// Private -/* - * \ingroup gdcmDicomDir - * \brief create a 'gdcmDicomDir' from a DICOMDIR gdcmHeader +/** + * \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::CreateDicomDir() +void DicomDir::SetEndMethodArgDelete( DicomDir::Method* method ) { - // 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 - + EndMethodArgDelete = method; +} - gdcmDicomDirType type=gdcmDicomDir::GDCM_META; - ListTag::iterator begin; - ListTag::iterator end; +/** + * \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 ! + * \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 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 ) + { + dbg.Verbose(2, "Failed to open(write) File: ", fileName.c_str()); + return false; + } - begin=listEntries.begin(); - end=begin; - for(ListTag::iterator i=end;i !=listEntries.end();++i) + char filePreamble[128]; + memset(filePreamble, 0, 128); + fp->write(filePreamble, 128); //FIXME + binary_write( *fp, "DICM"); + + DicomDirMeta *ptrMeta = GetDicomDirMeta(); + ptrMeta->WriteContent(fp, ExplicitVR); + + // force writing 0004|1220 [SQ ], that CANNOT exist within DicomDirMeta + for(i=0;i<4;++i) { - std::string v=(*i)->GetValue(); - if(v=="PATIENT ") - { - end=i; - AddObjectToEnd(type,begin,end); + binary_write(*fp, sq[i]); + } + + for(ListDicomDirPatient::iterator cc = Patients.begin(); + cc != Patients.end(); + ++cc ) + { + (*cc)->WriteContent( fp, ExplicitVR ); + } + + // force writing Sequence Delimitation Item + for(i=0;i<4;++i) + { + binary_write(*fp, sqt[i]); // fffe e0dd ffff ffff + } - type=gdcmDicomDir::GDCM_PATIENT; - begin=end; - } + fp->close(); + delete fp; - if(v=="STUDY ") - { - end=i; - AddObjectToEnd(type,begin,end); + return true; +} - type=gdcmDicomDir::GDCM_STUDY; - begin=end; - } +//----------------------------------------------------------------------------- +// Protected - if(v=="SERIES") +/** + * \ingroup DicomDir + * \brief create a Document-like chained list from a root Directory + * @param path entry point of the tree-like structure + */ +void DicomDir::CreateDicomDirChainedList(std::string const & path) +{ + CallStartMethod(); + DirList fileList(path,1); // gets recursively the file list + unsigned int count = 0; + VectDocument list; + Header *header; + + for( DirList::iterator it = fileList.begin(); + it != fileList.end(); + ++it ) + { + Progress = (float)(count+1)/(float)fileList.size(); + CallProgressMethod(); + if( Abort ) { - end=i; - AddObjectToEnd(type,begin,end); - - type=gdcmDicomDir::GDCM_SERIE; - begin=end; + break; } - if(v=="IMAGE ") +std::cerr<<"File : "<c_str()<c_str() ); + if( !header ) { - end=i; - AddObjectToEnd(type,begin,end); + dbg.Verbose( 1, + "DicomDir::CreateDicomDirChainedList: " + "failure in new Header ", + it->c_str() ); + continue; + } + + 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(), 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); + CallEndMethod(); + + for(VectDocument::iterator itDoc=list.begin(); + itDoc!=list.end(); + ++itDoc) + { + delete dynamic_cast
(*itDoc); + } +} - type=gdcmDicomDir::GDCM_IMAGE; - begin=end; +/** + * \ingroup DicomDir + * \brief adds *the* Meta to a partially created DICOMDIR + */ + +DicomDirMeta * DicomDir::NewMeta() +{ + DicomDirMeta *m = new DicomDirMeta(); + + if ( TagHT.begin() != TagHT.end() ) // after Document Parsing + { + TagDocEntryHT::iterator lastOneButSequence = TagHT.end(); + lastOneButSequence --; + // ALL the 'out of Sequence' Tags belong to Meta Elems + // (we skip 0004|1220 [Directory record sequence] ) + for ( TagDocEntryHT::iterator cc = TagHT.begin(); + cc != lastOneButSequence; + ++cc) + { + m->AddEntry( cc->second ); } } + else // after root directory parsing + { + ListDicomDirMetaElem const & elemList = + Global::GetDicomDirElements()->GetDicomDirMetaElements(); + m->FillObject(elemList); + } + m->SetSQItemNumber(0); // To avoid further missprinting + return m; +} + +/** + * \brief adds a new Patient (with the basic elements) to a partially created DICOMDIR + */ +DicomDirPatient * DicomDir::NewPatient() +{ + ListDicomDirPatientElem::const_iterator it; + uint16_t tmpGr,tmpEl; + DictEntry *dictEntry; + ValEntry *entry; - if(begin!=end) + ListDicomDirPatientElem const & elemList = + Global::GetDicomDirElements()->GetDicomDirPatientElements(); + DicomDirPatient *p = new DicomDirPatient(); + + // for all the DicomDirPatient Elements + for( it = elemList.begin(); it != elemList.end(); ++it ) { - end=GetListEntry().end(); - AddObjectToEnd(type,begin,end); + 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 ); + + p->AddEntry( entry ); } + + Patients.push_front( p ); + + return p; } -/* - * \ingroup gdcmDicomDir - * \brief - * @param type - * @param begin - * @param end + +/** + * \brief adds to the HTable + * the Entries (Dicom Elements) corresponding to the given type + * @param path full path file name (only used when type = GDCM_DICOMDIR_IMAGE + * @param type DicomDirObject type to create (GDCM_DICOMDIR_PATIENT, + * GDCM_DICOMDIR_STUDY, GDCM_DICOMDIR_SERIE ...) + * @param header Header of the current file */ -void gdcmDicomDir::AddObjectToEnd(gdcmDicomDirType type,ListTag::iterator begin,ListTag::iterator end) +void DicomDir::SetElement(std::string const & path, DicomDirType type, + Document *header) { - if(begin==end) - return; + 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; - switch(type) + switch( type ) { - case gdcmDicomDir::GDCM_META: - AddMetaToEnd(begin,end); - break; - case gdcmDicomDir::GDCM_PATIENT: - AddPatientToEnd(begin,end); + case GDCM_DICOMDIR_IMAGE: + elemList = Global::GetDicomDirElements()->GetDicomDirImageElements(); + si = new DicomDirImage(); + if( !AddDicomDirImageToEnd(static_cast(si)) ) + { + dbg.Verbose(0,"DicomDir::SetElement:", + "Add DicomDirImageToEnd failed"); + } break; - case gdcmDicomDir::GDCM_STUDY: - AddStudyToEnd(begin,end); + case GDCM_DICOMDIR_SERIE: + elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements(); + si = new DicomDirSerie(); + if( !AddDicomDirSerieToEnd(static_cast(si)) ) + { + dbg.Verbose(0,"DicomDir::SetElement:", + "Add DicomDirSerieToEnd failed"); + } break; - case gdcmDicomDir::GDCM_SERIE: - AddSerieToEnd(begin,end); + case GDCM_DICOMDIR_STUDY: + elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements(); + si = new DicomDirStudy(); + if( !AddDicomDirStudyToEnd(static_cast(si)) ) + { + dbg.Verbose(0,"DicomDir::SetElement:", + "Add DicomDirStudyToEnd failed"); + } break; - case gdcmDicomDir::GDCM_IMAGE: - AddImageToEnd(begin,end); + case GDCM_DICOMDIR_PATIENT: + elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements(); + si = new DicomDirPatient(); + if( !AddDicomDirPatientToEnd(static_cast(si)) ) + { + dbg.Verbose(0,"DicomDir::SetElement:", + "Add DicomDirPatientToEnd failed"); + } break; + case GDCM_DICOMDIR_META: + elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements(); + si = new DicomDirMeta(); + if( MetaElems ) + { + dbg.Verbose(0,"DicomDir::SetElement:", + "MetaElements already exist, they will be destroyed"); + delete MetaElems; + } + MetaElems = static_cast(si); + break; + default: + return; + } + // removed all the seems-to-be-useless stuff about Referenced Image Sequence + // to avoid further troubles + // imageElem 0008 1140 "" // Referenced Image Sequence + // imageElem fffe e000 "" // 'no length' item : length to be set to 0xffffffff later + // imageElem 0008 1150 "" // Referenced SOP Class UID : to be set/forged later + // imageElem 0008 1155 "" // Referenced SOP Instance UID : to be set/forged later + // imageElem fffe e00d "" // Item delimitation : length to be set to ZERO later + // for all the relevant elements found in their own spot of the DicomDir.dic + // FIXME : troubles found when it's a SeqEntry + + for( it = elemList.begin(); it != elemList.end(); ++it) + { + tmpGr = it->Group; + tmpEl = it->Elem; + dictEntry = GetPubDict()->GetDictEntryByNumber(tmpGr, tmpEl); + + entry = new ValEntry( dictEntry ); // Be sure it's never a BinEntry ! + + entry->SetOffset(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 = Util::GetName( path ); + } + else if( tmpGr == 0x0004 && tmpEl == 0x1500 ) // Only used for image + { + if( header->GetFileName().substr(0, path.length()) != path ) + { + dbg.Verbose(0, "DicomDir::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; + } + + entry->SetValue( val ); // troubles expected when vr=SQ ... + + if ( type == GDCM_DICOMDIR_META ) // fusible : should never print ! + { + std::cout << "GDCM_DICOMDIR_META ?!? should never print that" + << std::endl; + } + si->AddEntry(entry); } } -/* - * \ingroup gdcmDicomDir - * \brief Well ... Not realy to end, there is only one occurence - * @param begin - * @param end -*/ -void gdcmDicomDir::AddMetaToEnd(ListTag::iterator begin,ListTag::iterator end) +//----------------------------------------------------------------------------- +/** + * \brief CallStartMethod + */ +void DicomDir::CallStartMethod() { - if(metaElems) - delete metaElems; - metaElems = new gdcmMeta(begin,end); + Progress = 0.0f; + Abort = false; + if( StartMethod ) + { + StartMethod( StartArg ); + } } -/* - * \ingroup gdcmDicomDir - * \brief - * @param begin - * @param end -*/ -void gdcmDicomDir::AddPatientToEnd(ListTag::iterator begin,ListTag::iterator end) +//----------------------------------------------------------------------------- +/** + * \ingroup DicomDir + * \brief CallProgressMethod + */ +void DicomDir::CallProgressMethod() { - patients.push_back(new gdcmPatient(begin,end)); + if( ProgressMethod ) + { + ProgressMethod( ProgressArg ); + } } -/* - * \ingroup gdcmDicomDir - * \brief - * @param begin - * @param end +//----------------------------------------------------------------------------- +/** + * \ingroup DicomDir + * \brief CallEndMethod */ - void gdcmDicomDir::AddStudyToEnd(ListTag::iterator begin,ListTag::iterator end) +void DicomDir::CallEndMethod() { - if(patients.size()>0) + Progress = 1.0f; + if( EndMethod ) { - ListPatient::iterator itp=patients.end(); + EndMethod( EndArg ); + } +} + +//----------------------------------------------------------------------------- +// Private +/** + * \ingroup DicomDir + * \brief create a 'DicomDir' from a DICOMDIR Header + */ +void DicomDir::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 + 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 DICOMDIR file ? + return; + } + + SeqEntry* s = dynamic_cast(e); + if ( !s ) + { + 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(); + + DocEntry * d; + std::string v; + SQItem * si; + for( ListSQItem::iterator i = listItems.begin(); + i !=listItems.end(); ++i ) + { + d = (*i)->GetDocEntryByNumber(0x0004, 0x1430); // Directory Record Type + if ( ValEntry* valEntry = dynamic_cast< ValEntry* >(d) ) + { + v = valEntry->GetValue(); + } + else + { + dbg.Verbose(0, "DicomDir::CreateDicomDir: not a ValEntry."); + continue; + } + + if( v == "PATIENT " ) + { + si = new DicomDirPatient(); + AddDicomDirPatientToEnd( static_cast(si) ); + type = DicomDir::GDCM_DICOMDIR_PATIENT; + } + else if( v == "STUDY " ) + { + si = new DicomDirStudy(); + AddDicomDirStudyToEnd( static_cast(si) ); + type = DicomDir::GDCM_DICOMDIR_STUDY; + } + else if( v == "SERIES" ) + { + si = new DicomDirSerie(); + AddDicomDirSerieToEnd( static_cast(si) ); + type = DicomDir::GDCM_DICOMDIR_SERIE; + } + else if( v == "IMAGE " ) + { + si = new DicomDirImage(); + AddDicomDirImageToEnd( static_cast(si) ); + 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; + } + MoveSQItem(si,*i); + } + TagHT.clear(); +} + +/** + * \ingroup DicomDir + * \brief Well ... there is only one occurence + */ +bool DicomDir::AddDicomDirMeta() +{ + if( MetaElems ) + { + delete MetaElems; + } + MetaElems = new DicomDirMeta(); + return true; +} + +/** + * \ingroup DicomDir + * \brief AddDicomDirPatientToEnd + * @param s SQ Item to enqueue to the DicomPatient chained List + */ +bool DicomDir::AddDicomDirPatientToEnd(DicomDirPatient *dd) +{ + Patients.push_back(dd); + return true; +} + +/** + * \ingroup DicomDir + * \brief AddDicomDirStudyToEnd + * @param s SQ Item to enqueue to the DicomDirStudy chained List + */ +bool DicomDir::AddDicomDirStudyToEnd(DicomDirStudy *dd) +{ + if( Patients.size() > 0 ) + { + ListDicomDirPatient::iterator itp = Patients.end(); itp--; - (*itp)->AddStudy(new gdcmStudy(begin,end)); + (*itp)->AddDicomDirStudy(dd); + return true; } + return false; } -/* - * \ingroup gdcmDicomDir - * \brief - * @param begin - * @param end + +/** + * \ingroup DicomDir + * \brief AddDicomDirSerieToEnd + * @param s SQ Item to enqueue to the DicomDirSerie chained List */ -void gdcmDicomDir::AddSerieToEnd(ListTag::iterator begin,ListTag::iterator end) +bool DicomDir::AddDicomDirSerieToEnd(DicomDirSerie *dd) { - 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::const_iterator itst = + (*itp)->GetDicomDirStudies().end(); itst--; - (*itst)->AddSerie(new gdcmSerie(begin,end)); + (*itst)->AddDicomDirSerie(dd); + return true; } } + return false; } -/* - * \ingroup gdcmDicomDir - * @param begin - * @param end - * @param +/** + * \ingroup DicomDir + * \brief AddDicomDirImageToEnd + * @param s SQ Item to enqueue to the DicomDirImage chained List */ - void gdcmDicomDir::AddImageToEnd(ListTag::iterator begin,ListTag::iterator end) +bool DicomDir::AddDicomDirImageToEnd(DicomDirImage *dd) { - 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::const_iterator itst = + (*itp)->GetDicomDirStudies().end(); itst--; - if((*itst)->GetSeries().size()>0) + if( (*itst)->GetDicomDirSeries().size() > 0 ) { - ListSerie::iterator its=(*itst)->GetSeries().end(); + ListDicomDirSerie::const_iterator its = (*itst)->GetDicomDirSeries().end(); its--; - (*its)->AddImage(new gdcmImage(begin,end)); + (*its)->AddDicomDirImage(dd); + return true; } } } + return false; } -/* - * \ingroup gdcmDicomDir - * \brief - * @param path - * @param list +/** + * \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,ListHeader &list) +void DicomDir::SetElements(std::string const & path, VectDocument const &list) { - std::string patPrevName="", patPrevID=""; - std::string studPrevInstanceUID="", studPrevID=""; - std::string serPrevInstanceUID="", serPrevID=""; + TagHT.clear(); + Patients.clear(); - std::string patCurName, patCurID; - std::string studCurInstanceUID, studCurID; - std::string serCurInstanceUID, serCurID; + std::string patPrevName = "", patPrevID = ""; + std::string studPrevInstanceUID = "", studPrevID = ""; + std::string serPrevInstanceUID = "", serPrevID = ""; - SetElement(path,GDCM_NONE,NULL); + std::string patCurName, patCurID; + std::string studCurInstanceUID, studCurID; + std::string serCurInstanceUID, serCurID; - ListTag::iterator debPat=listEntries.begin(); - for(ListHeader::iterator it=list.begin();it!=list.end();++it) + bool first = true; + for( VectDocument::const_iterator it = list.begin(); + it != list.end(); ++it ) { // get the current file characteristics - patCurName=(*it)->GetEntryByNumber(0x0010,0x0010); - patCurID=(*it)->GetEntryByNumber(0x0010,0x0011); - studCurInstanceUID=(*it)->GetEntryByNumber(0x0020,0x000d); - studCurID=(*it)->GetEntryByNumber(0x0020,0x0010); - serCurInstanceUID=(*it)->GetEntryByNumber(0x0020,0x000e); - serCurID=(*it)->GetEntryByNumber(0x0020,0x0011); - - if(patCurName!=patPrevName || patCurID!=patPrevID) - SetElement(path,GDCM_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 || first ) + { + SetElement(path, GDCM_DICOMDIR_PATIENT, *it); + first = true; + } // if new Study Deal with 'STUDY' Elements - if(studCurInstanceUID!=studPrevInstanceUID || studCurID!=studPrevID) - SetElement(path,GDCM_STUDY,*it); + if( studCurInstanceUID != studPrevInstanceUID || studCurID != studPrevID + || first ) + { + SetElement(path, GDCM_DICOMDIR_STUDY, *it); + first = true; + } // if new Serie Deal with 'SERIE' Elements - if(serCurInstanceUID!=serPrevInstanceUID || serCurID!=serPrevID) - SetElement(path,GDCM_SERIE,*it); + if( serCurInstanceUID != serPrevInstanceUID || serCurID != serPrevID + || first ) + { + SetElement(path, GDCM_DICOMDIR_SERIE, *it); + first = true; + } // Always Deal with 'IMAGE' Elements - SetElement(path,GDCM_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; + first = false; } } -/* - * \ingroup gdcmDicomDir - * \brief - * @param path - * @param type - * @param header +/** + * \ingroup DicomDir + * \brief Move the content of the src SQItem to the dst SQItem + * Only DocEntry's are moved + * */ -void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type,gdcmHeader *header) +void DicomDir::MoveSQItem(SQItem* dst,SQItem *src) { - std::list elemList; - std::list::iterator it; - guint16 tmpGr, tmpEl; - gdcmDictEntry *dictEntry; - gdcmHeaderEntry *entry; - std::string val; + DocEntry *entry; - switch(type) + src->Initialize(); + entry = src->GetNextEntry(); + while(entry) { - case GDCM_PATIENT: - elemList=gdcmGlobal::GetDicomDirElements()->GetPatientElements(); - break; - case GDCM_STUDY: - elemList=gdcmGlobal::GetDicomDirElements()->GetStudyElements(); - break; - case GDCM_SERIE: - elemList=gdcmGlobal::GetDicomDirElements()->GetSerieElements(); - break; - case GDCM_IMAGE: - elemList=gdcmGlobal::GetDicomDirElements()->GetImageElements(); - break; - case GDCM_NONE: - elemList=gdcmGlobal::GetDicomDirElements()->GetMetaElements(); - break; - default: - return; - } - - for(it=elemList.begin();it!=elemList.end();++it) - { - tmpGr=it->group; - tmpEl=it->elem; + src->RemoveEntryNoDestroy(entry); + dst->AddEntry(entry); - dictEntry=GetPubDict()->GetDictEntryByNumber(tmpGr,tmpEl); - entry=new gdcmHeaderEntry(dictEntry); - entry->SetOffset(0); // just to avoid missprinting - - if(header) - val=header->GetEntryByNumber(tmpGr,tmpEl); - else - val=GDCM_UNFOUND; - - if(val==GDCM_UNFOUND) - { - if((tmpGr==0x0004) &&(tmpEl==0x1130) ) - { - // TODO force the *end* File Name(remove path) - val=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()[path.length()]); - } - else - { - val=it->value; - } - } - entry->SetValue(val); - - if(dictEntry) - { - 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()); - } - } - - listEntries.push_back(entry); - } + src->Initialize(); + entry = src->GetNextEntry(); + } } -bool gdcmDicomDir::HeaderLessThan(gdcmHeader *header1,gdcmHeader *header2) +/** + * \ingroup DicomDir + * \brief compares two dgcmHeaders + */ +bool DicomDir::HeaderLessThan(Document *header1, Document *header2) { - return(*header1<*header2); + return *header1 < *header2; } +} // end namespace gdcm //-----------------------------------------------------------------------------