X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDicomDir.cxx;h=9145817176fed5f65f028c9f21af06b5c0dd2ffc;hb=42b5b1fda1b91860c4708a5706600a913da219f3;hp=58e58b631a8692475feabaffbb23a362f5059a6d;hpb=ba78e6c6d47d6db1528e8e88e5ebde7296a26692;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index 58e58b63..91458171 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDicomDir.cxx,v $ Language: C++ - Date: $Date: 2004/12/03 20:16:57 $ - Version: $Revision: 1.85 $ + Date: $Date: 2005/03/09 19:29:38 $ + Version: $Revision: 1.136 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -16,6 +16,10 @@ =========================================================================*/ +//----------------------------------------------------------------------------- +// For full DICOMDIR description, see: +// PS 3.3-2003, pages 731-750 +//----------------------------------------------------------------------------- #include "gdcmDicomDir.h" #include "gdcmDicomDirStudy.h" #include "gdcmDicomDirSerie.h" @@ -27,7 +31,7 @@ #include "gdcmUtil.h" #include "gdcmDebug.h" #include "gdcmGlobal.h" -#include "gdcmHeader.h" +#include "gdcmFile.h" #include "gdcmSeqEntry.h" #include "gdcmSQItem.h" #include "gdcmValEntry.h" @@ -38,39 +42,85 @@ #include #ifdef _MSC_VER -#define getcwd _getcwd +# define getcwd _getcwd #endif -#if defined( _MSC_VER) || defined(__BORLANDC__) - #include +#if defined(_MSC_VER) || defined(__BORLANDC__) +# include #else - #include +# include #endif - +// ---------------------------------------------------------------------------- +// Note for future developpers +// ---------------------------------------------------------------------------- +// +// Dicom PS 3.3 describes the relationship between Directory Records, as follow +// (see also PS 4.3, 2004, page 50 for Entity-Relationship model) +// +// Directory Record Type Directory Record Types which may be included +// in the next lower-level directory Entity +// +// (Root directory Entity) PATIENT +// +// PATIENT STUDY +// +// STUDY SERIES, VISIT, RESULTS, STUDY COMPONENT +// +// SERIES IMAGE, OVERLAYS, MODALITY LUT, VOI LUT, +// CURVE, STORED PRINT, RT DOSE, RT STRUCTURE SET +// RT PLAN, RT TREAT RECORD, PRESENTATION, WAVEFORM, +// SR DOCUMENT, KEY OBJECT DOC, SPECTROSCOPY, +// RAW DATA, REGISTRATION, FIDUCIAL +// IMAGE +// OVERLAY +// MODALITY LUT +// VOI LUT +// CURVE +// STORED PRINT +// RT DOSE +// RT STRUCTURE SET +// RT PLAN +// RT TREAT RECORD +// PRESENTATION +// WAVEFORM +// SR DOCUMENT +// KEY OBJECT DOC +// SPECTROSCOPY +// RAW DATA +// REGISTRATION +// FIDUCIAL +// +// ---------------------- +// The current gdcm version only deals with : +// +// (Root directory Entity) PATIENT +// PATIENT STUDY +// STUDY SERIES +// SERIES IMAGE +// IMAGE / +// +// DicomDir::CreateDicomDir will have to be completed +// Treelike structure management will have to be upgraded +// ---------------------------------------------------------------------------- + namespace gdcm { - -//----------------------------------------------------------------------------- -// For full DICOMDIR description, see: -// PS 3.3-2003, pages 731-750 //----------------------------------------------------------------------------- // Constructor / Destructor - /** - * \ingroup DicomDir * \brief Constructor : creates an empty DicomDir */ DicomDir::DicomDir() - :Document( ) -{ + :Document( ) +{ Initialize(); // sets all private fields to NULL - MetaElems = NewMeta(); + 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 @@ -79,20 +129,26 @@ DicomDir::DicomDir() * - false if user passed an already built DICOMDIR file * and wants to use it */ -DicomDir::DicomDir(std::string const & fileName, bool parseDir ): +DicomDir::DicomDir(std::string const &fileName, bool parseDir ): Document( fileName ) { - // Whatever user passed (a root directory or a DICOMDIR) - // and whatever the value of parseDir was, - // Document is already executed + // At this step, Document constructor is already executed, + // whatever user passed (a root directory or a DICOMDIR) + // and whatever the value of parseDir was. + // (nothing is cheked in Document constructor, to avoid overhead) + Initialize(); // sets all private fields to NULL // if user passed a root directory, sure we didn't get anything - if ( TagHT.begin() == TagHT.end() ) // when user passed a Directory to parse + + if ( GetFirstEntry() == 0 ) // when user passed a Directory to parse { - dbg.Verbose(0, "DicomDir::DicomDir : entry HT empty"); + if (!parseDir) + gdcmWarningMacro( "Entry HT empty for file: "<SetPrintLevel(PrintLevel); - MetaElems->Print(os); - } - for(ListDicomDirPatient::iterator cc = Patients.begin(); - cc != Patients.end(); - ++cc) - { - (*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 + * decides whether or not the current document 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, @@ -186,16 +215,19 @@ void DicomDir::Print(std::ostream &os) */ bool DicomDir::IsReadable() { - if( !Document::IsReadable() ) + if( Filetype == Unknown) { + gdcmWarningMacro( "Wrong filetype"); return false; } if( !MetaElems ) { + gdcmWarningMacro( "Meta Elements missing in DicomDir"); return false; } if( Patients.size() <= 0 ) { + gdcmWarningMacro( "NO Patient in DicomDir"); return false; } @@ -203,30 +235,91 @@ bool DicomDir::IsReadable() } /** - * \brief Sets all fields to NULL - */ + * \brief adds *the* Meta to a partially created DICOMDIR + */ +DicomDirMeta *DicomDir::NewMeta() +{ + if( MetaElems ) + delete MetaElems; -void DicomDir::Initialize() + DocEntry *entry = GetFirstEntry(); + if( entry ) + { + MetaElems = new DicomDirMeta(true); + + entry = GetFirstEntry(); + while( entry ) + { + if( dynamic_cast(entry) ) + break; + + RemoveEntryNoDestroy(entry); + MetaElems->AddEntry(entry); + + entry = GetFirstEntry(); + } + } + else // after root directory parsing + { + MetaElems = new DicomDirMeta(false); + } + MetaElems->SetSQItemNumber(0); // To avoid further missprinting + return MetaElems; +} + +/** + * \brief adds a new Patient (with the basic elements) to a partially created + * DICOMDIR + */ +DicomDirPatient *DicomDir::NewPatient() { - StartMethod = NULL; - ProgressMethod = NULL; - EndMethod = NULL; - StartMethodArgDelete = NULL; - ProgressMethodArgDelete = NULL; - EndMethodArgDelete = NULL; - StartArg = NULL; - ProgressArg = NULL; - EndArg = NULL; + DicomDirPatient *p = new DicomDirPatient(); + AddPatientToEnd( p ); + return p; +} - Progress = 0.0; - Abort = false; +/** + * \brief Remove all Patients + */ +void DicomDir::ClearPatient() +{ + for(ListDicomDirPatient::iterator cc = Patients.begin(); + cc!= Patients.end(); + ++cc) + { + delete *cc; + } + Patients.clear(); +} - MetaElems = NULL; +/** + * \brief Get the first entry while visiting the DicomDirPatients + * \return The first DicomDirPatient if found, otherwhise NULL + */ +DicomDirPatient *DicomDir::GetFirstPatient() +{ + ItPatient = Patients.begin(); + if ( ItPatient != Patients.end() ) + return *ItPatient; + return NULL; } +/** + * \brief Get the next entry while visiting the DicomDirPatients + * \note : meaningfull only if GetFirstEntry already called + * \return The next DicomDirPatient if found, otherwhise NULL + */ +DicomDirPatient *DicomDir::GetNextPatient() +{ + gdcmAssertMacro (ItPatient != Patients.end()); + + ++ItPatient; + if ( ItPatient != Patients.end() ) + return *ItPatient; + return NULL; +} /** - * \ingroup DicomDir * \brief fills the whole structure, starting from a root Directory */ void DicomDir::ParseDirectory() @@ -236,7 +329,6 @@ void DicomDir::ParseDirectory() } /** - * \ingroup DicomDir * \brief Set the start method to call when the parsing of the * directory starts. * @param method Method to call @@ -244,8 +336,8 @@ void DicomDir::ParseDirectory() * @param argDelete Argument * \warning In python : the arg parameter isn't considered */ -void DicomDir::SetStartMethod( DicomDir::Method* method, void* arg, - DicomDir::Method* argDelete ) +void DicomDir::SetStartMethod( DicomDir::Method *method, void *arg, + DicomDir::Method *argDelete ) { if( StartArg && StartMethodArgDelete ) { @@ -258,19 +350,6 @@ void DicomDir::SetStartMethod( DicomDir::Method* method, void* arg, } /** - * \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 @@ -278,8 +357,8 @@ void DicomDir::SetStartMethodArgDelete( DicomDir::Method* method ) * @param argDelete Argument * \warning In python : the arg parameter isn't considered */ -void DicomDir::SetProgressMethod( DicomDir::Method* method, void* arg, - DicomDir::Method* argDelete ) +void DicomDir::SetProgressMethod( DicomDir::Method *method, void *arg, + DicomDir::Method *argDelete ) { if( ProgressArg && ProgressMethodArgDelete ) { @@ -292,27 +371,14 @@ void DicomDir::SetProgressMethod( DicomDir::Method* method, void* arg, } /** - * \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::SetProgressMethodArgDelete( DicomDir::Method* method ) -{ - ProgressMethodArgDelete = method; -} - -/** - * \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 ) +void DicomDir::SetEndMethod( DicomDir::Method *method, void *arg, + DicomDir::Method *argDelete ) { if( EndArg && EndMethodArgDelete ) { @@ -325,49 +391,66 @@ void DicomDir::SetEndMethod( DicomDir::Method* method, void* arg, } /** - * \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; +} + +/** + * \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::SetProgressMethodArgDelete( DicomDir::Method *method ) +{ + ProgressMethodArgDelete = method; +} + +/** * \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::SetEndMethodArgDelete( DicomDir::Method* method ) +void DicomDir::SetEndMethodArgDelete( DicomDir::Method *method ) { EndMethodArgDelete = method; } /** - * \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) +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::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()); + gdcmWarningMacro("Failed to open(write) File: " << fileName.c_str()); return false; } char filePreamble[128]; memset(filePreamble, 0, 128); - fp->write(filePreamble, 128); //FIXME + fp->write(filePreamble, 128); binary_write( *fp, "DICM"); - DicomDirMeta *ptrMeta = GetDicomDirMeta(); + DicomDirMeta *ptrMeta = GetMeta(); ptrMeta->WriteContent(fp, ExplicitVR); // force writing 0004|1220 [SQ ], that CANNOT exist within DicomDirMeta @@ -395,23 +478,61 @@ bool DicomDir::WriteDicomDir(std::string const& fileName) return true; } +/** + * \brief Anonymize a DICOMDIR + * @return true + */ + +bool DicomDir::AnonymizeDicomDir() +{ + ValEntry *v; + // Something clever to be found to forge the Patient names + std::ostringstream s; + int i = 1; + for(ListDicomDirPatient::iterator cc = Patients.begin(); + cc!= Patients.end(); + ++cc) + { + s << i; + v = (*cc)->GetValEntry(0x0010, 0x0010) ; // Patient's Name + if (v) + { + v->SetValue(s.str()); + } + + v = (*cc)->GetValEntry(0x0010, 0x0020) ; // Patient ID + if (v) + { + v->SetValue(" "); + } + + v = (*cc)->GetValEntry(0x0010, 0x0030) ; // Patient's BirthDate + if (v) + { + v->SetValue(" "); + } + s << ""; + i++; + } + return true; +} //----------------------------------------------------------------------------- // Protected - /** - * \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) +void DicomDir::CreateDicomDirChainedList(std::string const &path) { CallStartMethod(); - DirList fileList(path,1); // gets recursively the file list + DirList dirList(path,1); // gets recursively the file list unsigned int count = 0; VectDocument list; - Header *header; + File *header; + + DirListType fileList = dirList.GetFilenames(); - for( DirList::iterator it = fileList.begin(); + for( DirListType::iterator it = fileList.begin(); it != fileList.end(); ++it ) { @@ -422,24 +543,18 @@ void DicomDir::CreateDicomDirChainedList(std::string const & path) break; } -std::cerr<<"File : "<c_str()<c_str() ); + header = new File( it->c_str() ); if( !header ) { - dbg.Verbose( 1, - "DicomDir::CreateDicomDirChainedList: " - "failure in new Header ", - it->c_str() ); + gdcmWarningMacro( "Failure in new gdcm::File " << it->c_str() ); continue; } if( header->IsReadable() ) { - // Add the file header to the chained list: + // Add the file to the chained list: list.push_back(header); - dbg.Verbose( 1, - "DicomDir::CreateDicomDirChainedList: readable ", - it->c_str() ); + gdcmWarningMacro( "Readable " << it->c_str() ); } else { @@ -450,103 +565,316 @@ std::cerr<<"File : "<c_str()<(*it); + delete dynamic_cast(*itDoc); } } /** - * \ingroup DicomDir - * \brief adds *the* Meta to a partially created DICOMDIR + * \brief CallStartMethod */ - -DicomDirMeta * DicomDir::NewMeta() +void DicomDir::CallStartMethod() { - 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->AddDocEntry( cc->second ); - } + Progress = 0.0f; + Abort = false; + if( StartMethod ) + { + StartMethod( StartArg ); } - else // after root directory parsing +} + +/** + * \brief CallProgressMethod + */ +void DicomDir::CallProgressMethod() +{ + if( ProgressMethod ) { - ListDicomDirMetaElem const & elemList = - Global::GetDicomDirElements()->GetDicomDirMetaElements(); - m->FillObject(elemList); + ProgressMethod( ProgressArg ); } - m->SetSQItemNumber(0); // To avoid further missprinting - return m; } /** - * \brief adds a new Patient (with the basic elements) to a partially created DICOMDIR + * \brief CallEndMethod */ -DicomDirPatient * DicomDir::NewPatient() +void DicomDir::CallEndMethod() { - ListDicomDirPatientElem::const_iterator it; - uint16_t tmpGr,tmpEl; - DictEntry *dictEntry; - ValEntry *entry; + Progress = 1.0f; + if( EndMethod ) + { + EndMethod( EndArg ); + } +} - ListDicomDirPatientElem const & elemList = - Global::GetDicomDirElements()->GetDicomDirPatientElements(); - DicomDirPatient *p = new DicomDirPatient(); +//----------------------------------------------------------------------------- +// Private +/** + * \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 = NULL; +} + +/** + * \brief create a 'DicomDir' from a DICOMDIR Header + */ +void DicomDir::CreateDicomDir() +{ + // The SeqEntries of "Directory Record Sequence" are 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 - - // for all the DicomDirPatient Elements - for( it = elemList.begin(); it != elemList.end(); ++it ) + // Directory record sequence + DocEntry *e = GetDocEntry(0x0004, 0x1220); + if ( !e ) { - 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 ); + gdcmWarningMacro( "No Directory Record Sequence (0004,1220) found"); + return; + } + + SeqEntry *s = dynamic_cast(e); + if ( !s ) + { + gdcmWarningMacro( "Element (0004,1220) is not a Sequence ?!?"); + return; + } - // dealing with value length ... - - if( dictEntry->GetGroup() == 0xfffe) + NewMeta(); + + DocEntry *d; + std::string v; + SQItem *si; + + SQItem *tmpSI=s->GetFirstSQItem(); + while(tmpSI) + { + d = tmpSI->GetDocEntry(0x0004, 0x1430); // Directory Record Type + if ( ValEntry* valEntry = dynamic_cast(d) ) { - entry->SetLength(entry->GetValue().length()); + v = valEntry->GetValue(); } - else if( dictEntry->GetVR() == "UL" || dictEntry->GetVR() == "SL" ) + else { - entry->SetLength( 4 ); - } - else if( dictEntry->GetVR() == "US" || dictEntry->GetVR() == "SS" ) + gdcmWarningMacro( "(0004,1430) not a ValEntry ?!?"); + continue; + } + + if( v == "PATIENT " ) { - entry->SetLength(2); - } - else if( dictEntry->GetVR() == "SQ" ) + si = new DicomDirPatient(true); + if( !AddPatientToEnd( static_cast(si)) ) + { + delete si; + si = NULL; + gdcmErrorMacro( "Add PatientToEnd failed"); + } + } + else if( v == "STUDY " ) { - entry->SetLength( 0xffffffff ); + si = new DicomDirStudy(true); + if( !AddStudyToEnd( static_cast(si)) ) + { + delete si; + si = NULL; + gdcmErrorMacro( "Add AddStudyToEnd failed"); + } } - else + else if( v == "SERIES" ) { - entry->SetLength( entry->GetValue().length() ); + si = new DicomDirSerie(true); + if( !AddSerieToEnd( static_cast(si)) ) + { + delete si; + si = NULL; + gdcmErrorMacro( "Add AddSerieToEnd failed"); + } } - p->AddDocEntry( entry ); - } + else if( v == "IMAGE " ) + { + si = new DicomDirImage(true); + if( !AddImageToEnd( static_cast(si)) ) + { + delete si; + si = NULL; + gdcmErrorMacro( "Add AddImageToEnd failed"); + } + } + else + { + // It was not a 'PATIENT', nor a 'STUDY', nor a 'SERIE', + // neither an 'IMAGE' SQItem. Skip to next item. + continue; + } + if( si ) + MoveSQItem(si,tmpSI); - Patients.push_front( p ); + tmpSI=s->GetNextSQItem(); + } + ClearEntry(); +} - return p; +/** + * \brief AddPatientToEnd + * @param dd SQ Item to enqueue to the DicomPatient chained List + */ +bool DicomDir::AddPatientToEnd(DicomDirPatient *dd) +{ + Patients.push_back(dd); + return true; +} + +/** + * \brief AddStudyToEnd + * @param dd SQ Item to enqueue to the DicomDirStudy chained List + */ +bool DicomDir::AddStudyToEnd(DicomDirStudy *dd) +{ + if( Patients.size() > 0 ) + { + ListDicomDirPatient::iterator itp = Patients.end(); + itp--; + (*itp)->AddStudy(dd); + return true; + } + return false; +} + +/** + * \brief AddSerieToEnd + * @param dd SQ Item to enqueue to the DicomDirSerie chained List + */ +bool DicomDir::AddSerieToEnd(DicomDirSerie *dd) +{ + if( Patients.size() > 0 ) + { + ListDicomDirPatient::iterator itp = Patients.end(); + itp--; + + DicomDirStudy *study = (*itp)->GetLastStudy(); + if( study ) + { + study->AddSerie(dd); + return true; + } + } + return false; +} + +/** + * \brief AddImageToEnd + * @param dd SQ Item to enqueue to the DicomDirImage chained List + */ +bool DicomDir::AddImageToEnd(DicomDirImage *dd) +{ + if( Patients.size() > 0 ) + { + ListDicomDirPatient::iterator itp = Patients.end(); + itp--; + + DicomDirStudy *study = (*itp)->GetLastStudy(); + if( study ) + { + DicomDirSerie *serie = study->GetLastSerie(); + if( serie ) + { + serie->AddImage(dd); + return true; + } + } + } + return false; +} + +/** + * \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 DicomDir::SetElements(std::string const &path, VectDocument const &list) +{ + ClearEntry(); + ClearPatient(); + + std::string patPrevName = "", patPrevID = ""; + std::string studPrevInstanceUID = "", studPrevID = ""; + std::string serPrevInstanceUID = "", serPrevID = ""; + + std::string patCurName, patCurID; + std::string studCurInstanceUID, studCurID; + std::string serCurInstanceUID, serCurID; + + bool first = true; + for( VectDocument::const_iterator it = list.begin(); + it != list.end(); + ++it ) + { + // get the current file characteristics + patCurName = (*it)->GetEntryValue(0x0010,0x0010); + patCurID = (*it)->GetEntryValue(0x0010,0x0011); + studCurInstanceUID = (*it)->GetEntryValue(0x0020,0x000d); + studCurID = (*it)->GetEntryValue(0x0020,0x0010); + serCurInstanceUID = (*it)->GetEntryValue(0x0020,0x000e); + serCurID = (*it)->GetEntryValue(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 + || first ) + { + SetElement(path, GDCM_DICOMDIR_STUDY, *it); + first = true; + } + + // if new Serie Deal with 'SERIE' Elements + if( serCurInstanceUID != serPrevInstanceUID || serCurID != serPrevID + || first ) + { + 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; + first = false; + } } /** @@ -557,10 +885,10 @@ DicomDirPatient * DicomDir::NewPatient() * GDCM_DICOMDIR_STUDY, GDCM_DICOMDIR_SERIE ...) * @param header Header of the current file */ -void DicomDir::SetElement(std::string const & path, DicomDirType type, +void DicomDir::SetElement(std::string const &path, DicomDirType type, Document *header) { - ListDicomDirElem elemList; //FIXME this is going to be a by copy operation + ListDicomDirElem elemList; ListDicomDirElem::const_iterator it; uint16_t tmpGr, tmpEl; DictEntry *dictEntry; @@ -572,48 +900,47 @@ void DicomDir::SetElement(std::string const & path, DicomDirType type, { case GDCM_DICOMDIR_IMAGE: elemList = Global::GetDicomDirElements()->GetDicomDirImageElements(); - si = new DicomDirImage(); - if( !AddDicomDirImageToEnd(static_cast(si)) ) + si = new DicomDirImage(true); + if( !AddImageToEnd(static_cast(si)) ) { - dbg.Verbose(0,"DicomDir::SetElement:", - "Add DicomDirImageToEnd failed"); + delete si; + gdcmErrorMacro( "Add ImageToEnd failed"); } break; case GDCM_DICOMDIR_SERIE: elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements(); - si = new DicomDirSerie(); - if( !AddDicomDirSerieToEnd(static_cast(si)) ) + si = new DicomDirSerie(true); + if( !AddSerieToEnd(static_cast(si)) ) { - dbg.Verbose(0,"DicomDir::SetElement:", - "Add DicomDirSerieToEnd failed"); + delete si; + gdcmErrorMacro( "Add SerieToEnd failed"); } break; case GDCM_DICOMDIR_STUDY: elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements(); - si = new DicomDirStudy(); - if( !AddDicomDirStudyToEnd(static_cast(si)) ) + si = new DicomDirStudy(true); + if( !AddStudyToEnd(static_cast(si)) ) { - dbg.Verbose(0,"DicomDir::SetElement:", - "Add DicomDirStudyToEnd failed"); + delete si; + gdcmErrorMacro( "Add StudyToEnd failed"); } break; case GDCM_DICOMDIR_PATIENT: elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements(); - si = new DicomDirPatient(); - if( !AddDicomDirPatientToEnd(static_cast(si)) ) + si = new DicomDirPatient(true); + if( !AddPatientToEnd(static_cast(si)) ) { - dbg.Verbose(0,"DicomDir::SetElement:", - "Add DicomDirPatientToEnd failed"); + delete si; + gdcmErrorMacro( "Add PatientToEnd failed"); } break; case GDCM_DICOMDIR_META: elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements(); - si = new DicomDirMeta(); + si = new DicomDirMeta(true); if( MetaElems ) { - dbg.Verbose(0,"DicomDir::SetElement:", - "MetaElements already exist, they will be destroyed"); delete MetaElems; + gdcmErrorMacro( "MetaElements already exist, they will be destroyed"); } MetaElems = static_cast(si); break; @@ -627,25 +954,25 @@ void DicomDir::SetElement(std::string const & path, DicomDirType type, // 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 all the relevant elements found in their own spot of the DicomDir.dic for( it = elemList.begin(); it != elemList.end(); ++it) { tmpGr = it->Group; tmpEl = it->Elem; - dictEntry = GetPubDict()->GetDictEntryByNumber(tmpGr, tmpEl); + dictEntry = GetPubDict()->GetEntry(tmpGr, tmpEl); 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 ) { // NULL when we Build Up (ex nihilo) a DICOMDIR // or when we add the META elems - val = header->GetEntryByNumber(tmpGr, tmpEl); + val = header->GetEntryValue(tmpGr, tmpEl); } else { @@ -663,8 +990,7 @@ void DicomDir::SetElement(std::string const & path, DicomDirType type, { if( header->GetFileName().substr(0, path.length()) != path ) { - dbg.Verbose(0, "DicomDir::SetElement : the base path" - " of file name is incorrect"); + gdcmWarningMacro( "The base path of file name is incorrect"); val = header->GetFileName(); } else @@ -679,371 +1005,70 @@ void DicomDir::SetElement(std::string const & path, DicomDirType type, } else { - if ( header->GetEntryLengthByNumber(tmpGr,tmpEl) == 0 ) + if ( header->GetEntryLength(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 << "GDCM_DICOMDIR_META ?!? should never print that" - << std::endl; + gdcmWarningMacro("GDCM_DICOMDIR_META ?!? should never print that"); } si->AddEntry(entry); } } -//----------------------------------------------------------------------------- /** - * \brief CallStartMethod + * \brief Move the content of the source SQItem to the destination SQItem + * Only DocEntry's are moved + * @param dst destination SQItem + * @param src source SQItem */ -void DicomDir::CallStartMethod() +void DicomDir::MoveSQItem(DocEntrySet *dst,DocEntrySet *src) { - Progress = 0.0f; - Abort = false; - if( StartMethod ) - { - StartMethod( StartArg ); - } -} + DocEntry *entry; -//----------------------------------------------------------------------------- -/** - * \ingroup DicomDir - * \brief CallProgressMethod - */ -void DicomDir::CallProgressMethod() -{ - if( ProgressMethod ) + entry = src->GetFirstEntry(); + while(entry) { - ProgressMethod( ProgressArg ); + src->RemoveEntryNoDestroy(entry); + dst->AddEntry(entry); + // we destroyed -> the current iterator is not longer valid + entry = src->GetFirstEntry(); } } -//----------------------------------------------------------------------------- /** - * \ingroup DicomDir - * \brief CallEndMethod + * \brief compares two files */ -void DicomDir::CallEndMethod() +bool DicomDir::HeaderLessThan(Document *header1, Document *header2) { - Progress = 1.0f; - if( EndMethod ) - { - EndMethod( EndArg ); - } + return *header1 < *header2; } //----------------------------------------------------------------------------- -// 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(); -} - +// Print /** - * \ingroup DicomDir - * \brief Well ... there is only one occurence + * \brief Canonical Printer + * @param os ostream we want to print in + * @param indent Indentation string to be prepended during printing */ -bool DicomDir::AddDicomDirMeta() +void DicomDir::Print(std::ostream &os, std::string const & ) { 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)->AddDicomDirStudy(dd); - return true; - } - return false; -} - -/** - * \ingroup DicomDir - * \brief AddDicomDirSerieToEnd - * @param s SQ Item to enqueue to the DicomDirSerie chained List - */ -bool DicomDir::AddDicomDirSerieToEnd(DicomDirSerie *dd) -{ - if( Patients.size() > 0 ) - { - ListDicomDirPatient::iterator itp = Patients.end(); - itp--; - - if( (*itp)->GetDicomDirStudies().size() > 0 ) - { - ListDicomDirStudy::const_iterator itst = - (*itp)->GetDicomDirStudies().end(); - itst--; - (*itst)->AddDicomDirSerie(dd); - return true; - } - } - return false; -} - -/** - * \ingroup DicomDir - * \brief AddDicomDirImageToEnd - * @param s SQ Item to enqueue to the DicomDirImage chained List - */ -bool DicomDir::AddDicomDirImageToEnd(DicomDirImage *dd) -{ - if( Patients.size() > 0 ) - { - ListDicomDirPatient::iterator itp = Patients.end(); - itp--; - - if( (*itp)->GetDicomDirStudies().size() > 0 ) - { - ListDicomDirStudy::const_iterator itst = - (*itp)->GetDicomDirStudies().end(); - itst--; - - if( (*itst)->GetDicomDirSeries().size() > 0 ) - { - ListDicomDirSerie::const_iterator its = (*itst)->GetDicomDirSeries().end(); - its--; - (*its)->AddDicomDirImage(dd); - return true; - } - } - } - return false; -} - -/** - * \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 DicomDir::SetElements(std::string const & path, VectDocument const &list) -{ - TagHT.clear(); - Patients.clear(); - - std::string patPrevName = "", patPrevID = ""; - std::string studPrevInstanceUID = "", studPrevID = ""; - std::string serPrevInstanceUID = "", serPrevID = ""; - - std::string patCurName, patCurID; - std::string studCurInstanceUID, studCurID; - std::string serCurInstanceUID, serCurID; - - 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 || first ) - { - SetElement(path, GDCM_DICOMDIR_PATIENT, *it); - first = true; - } - - // if new Study Deal with 'STUDY' Elements - 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 - || first ) - { - SetElement(path, GDCM_DICOMDIR_SERIE, *it); - first = true; - } - - // Always Deal with 'IMAGE' Elements - SetElement(path, GDCM_DICOMDIR_IMAGE, *it); - - patPrevName = patCurName; - patPrevID = patCurID; - studPrevInstanceUID = studCurInstanceUID; - studPrevID = studCurID; - serPrevInstanceUID = serCurInstanceUID; - serPrevID = serCurID; - first = false; - } -} - -/** - * \ingroup DicomDir - * \brief Move the content of the src SQItem to the dst SQItem - * Only DocEntry's are moved - * - */ -void DicomDir::MoveSQItem(SQItem* dst,SQItem *src) -{ - DocEntry *entry; - - src->Initialize(); - entry = src->GetNextEntry(); - while(entry) + MetaElems->SetPrintLevel(PrintLevel); + MetaElems->Print(os); + } + for(ListDicomDirPatient::iterator cc = Patients.begin(); + cc != Patients.end(); + ++cc) { - src->RemoveEntryNoDestroy(entry); - dst->AddEntry(entry); - - src->Initialize(); - entry = src->GetNextEntry(); + (*cc)->SetPrintLevel(PrintLevel); + (*cc)->Print(os); } } -/** - * \ingroup DicomDir - * \brief compares two dgcmHeaders - */ -bool DicomDir::HeaderLessThan(Document *header1, Document *header2) -{ - return *header1 < *header2; -} -} // end namespace gdcm - //----------------------------------------------------------------------------- +} // end namespace gdcm