X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDicomDir.cxx;h=0a9a714244c26bdef80e039535f130fe13ab57c6;hb=3f8964856e65c2447beab900b04a63d003192bf9;hp=05981583d5024377644d51c73a35125e6bc54fe2;hpb=6383e4f567672c46fefb1c67c0bb821dee5b8bff;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index 05981583..0a9a7142 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDicomDir.cxx,v $ Language: C++ - Date: $Date: 2005/07/03 12:45:53 $ - Version: $Revision: 1.143 $ + Date: $Date: 2005/11/07 10:14:44 $ + Version: $Revision: 1.172 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -21,8 +21,10 @@ // PS 3.3-2003, pages 731-750 //----------------------------------------------------------------------------- #include "gdcmDicomDir.h" +#include "gdcmDicomDirObject.h" #include "gdcmDicomDirStudy.h" #include "gdcmDicomDirSerie.h" +#include "gdcmDicomDirVisit.h" #include "gdcmDicomDirImage.h" #include "gdcmDicomDirPatient.h" #include "gdcmDicomDirMeta.h" @@ -34,7 +36,7 @@ #include "gdcmFile.h" #include "gdcmSeqEntry.h" #include "gdcmSQItem.h" -#include "gdcmValEntry.h" +#include "gdcmDataEntry.h" #include #include @@ -98,7 +100,8 @@ // // (Root directory Entity) PATIENT // PATIENT STUDY -// STUDY SERIES +// STUDY SERIES +// STUDY VISIT // SERIES IMAGE // IMAGE / // @@ -117,73 +120,94 @@ DicomDir::DicomDir() :Document( ) { Initialize(); // sets all private fields to NULL + ParseDir = false; 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 - */ -DicomDir::DicomDir(std::string const &fileName, bool parseDir ): - Document( ) -{ - // At this step, Document constructor is already executed, - // whatever user passed (either a root directory or a DICOMDIR) - // and whatever the value of parseDir was. - // (nothing is cheked in Document constructor, to avoid overhead) - - ParseDir = parseDir; - SetLoadMode (0x00000000); // concerns only dicom files - Load( fileName ); -} - /** * \brief Canonical destructor */ DicomDir::~DicomDir() { - SetStartMethod(NULL); - SetProgressMethod(NULL); - SetEndMethod(NULL); + SetStartMethod(NULL,NULL,NULL); + SetProgressMethod(NULL,NULL,NULL); + SetEndMethod(NULL,NULL,NULL); ClearPatient(); if ( MetaElems ) { - delete MetaElems; + MetaElems->Delete(); } } //----------------------------------------------------------------------------- // Public +/** + * \brief Loader. use SetFileName(fn) + * or SetLoadMode(lm) + SetDirectoryName(dn) before ! + * @return false if file cannot be open or no swap info was found, + * or no tag was found. + */ +bool DicomDir::Load( ) +{ + if (!ParseDir) + { + if ( ! this->Document::Load( ) ) + return false; + } + return DoTheLoadingJob( ); +} + +#ifndef GDCM_LEGACY_REMOVE +/* * + * \ brief Loader. (DEPRECATED : kept not to break the API) + * @ param fileName file to be open for parsing + * @ return false if file cannot be open or no swap info was found, + * or no tag was found. + * @ deprecated use SetFileName(n) + Load() instead + */ bool DicomDir::Load(std::string const &fileName ) { - Filename = fileName; - // We should clean out anything that already exists. + SetFileName(fileName); + return Load(); +} - Initialize(); // sets all private fields to NULL +/// DEPRECATED : use SetDirectoryName(dname) instead +/* * + * \brief Loader. (DEPRECATED : kept not to break the API) + * @param paseDir Parse Dir + * @deprecated use SetDirectoryName(dname) instead + */ +void DicomDir::SetParseDir(bool parseDir) +{ + ParseDir = parseDir; +} +#endif + +/** + * \brief Does the Loading Job (internal use only) + * @return false if file cannot be open or no swap info was found, + * or no tag was found. + */ +bool DicomDir::DoTheLoadingJob( ) +{ + Progress = 0.0f; + Abort = false; if (!ParseDir) { // Only if user passed a DICOMDIR // ------------------------------ Fp = 0; - if ( !OpenFile() ) + if (!Document::Load() ) { return false; } - Document::Load(fileName); + if ( GetFirstEntry() == 0 ) // when user passed a Directory to parse { - gdcmWarningMacro( "Entry HT empty for file: "<< fileName); + gdcmWarningMacro( "Entry HT empty for file: "<< GetFileName()); return false; } // Directory record sequence @@ -191,7 +215,7 @@ bool DicomDir::Load(std::string const &fileName ) if ( !e ) { gdcmWarningMacro( "NO 'Directory record sequence' (0x0004,0x1220)" - << " in file " << fileName); + << " in file " << GetFileName()); return false; } else @@ -201,17 +225,24 @@ bool DicomDir::Load(std::string const &fileName ) { // Only if user passed a root directory // ------------------------------------ - if ( fileName == "." ) + if ( GetFileName() == "." ) { // 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 + char buf[2048]; + const char *cwd = getcwd(buf, 2048); + if( cwd ) + { + SetFileName( buf ); // will be converted into a string + } + else + { + gdcmErrorMacro( "Path was too long to fit on 2048 bytes" ); + } } NewMeta(); - gdcmWarningMacro( "Parse directory and create the DicomDir : " << Filename ); - + gdcmDebugMacro( "Parse directory and create the DicomDir : " + << GetFileName() ); ParseDirectory(); } return true; @@ -229,7 +260,7 @@ bool DicomDir::IsReadable() { if ( Filetype == Unknown ) { - gdcmWarningMacro( "Wrong filetype"); + gdcmErrorMacro( "Wrong filetype for " << GetFileName()); return false; } if ( !MetaElems ) @@ -252,12 +283,12 @@ bool DicomDir::IsReadable() DicomDirMeta *DicomDir::NewMeta() { if ( MetaElems ) - delete MetaElems; + MetaElems->Delete(); DocEntry *entry = GetFirstEntry(); if ( entry ) { - MetaElems = new DicomDirMeta(true); // true = empty + MetaElems = DicomDirMeta::New(true); // true = empty entry = GetFirstEntry(); while( entry ) @@ -265,15 +296,15 @@ DicomDirMeta *DicomDir::NewMeta() if ( dynamic_cast(entry) ) break; - RemoveEntryNoDestroy(entry); MetaElems->AddEntry(entry); + RemoveEntry(entry); entry = GetFirstEntry(); } } else // after root directory parsing { - MetaElems = new DicomDirMeta(false); // false = not empty + MetaElems = DicomDirMeta::New(false); // false = not empty } MetaElems->SetSQItemNumber(0); // To avoid further missprinting return MetaElems; @@ -285,9 +316,9 @@ DicomDirMeta *DicomDir::NewMeta() */ DicomDirPatient *DicomDir::NewPatient() { - DicomDirPatient *p = new DicomDirPatient(); - AddPatientToEnd( p ); - return p; + DicomDirPatient *dd = DicomDirPatient::New(); + AddPatientToEnd( dd ); + return dd; } /** @@ -299,7 +330,7 @@ void DicomDir::ClearPatient() cc!= Patients.end(); ++cc) { - delete *cc; + (*cc)->Unregister(); } Patients.clear(); } @@ -340,6 +371,21 @@ void DicomDir::ParseDirectory() CreateDicomDir(); } +void DicomDir::SetStartMethod( DicomDir::Method *method, void *arg ) +{ + SetStartMethod(method,arg,NULL); +} + +void DicomDir::SetProgressMethod( DicomDir::Method *method, void *arg ) +{ + SetProgressMethod(method,arg,NULL); +} + +void DicomDir::SetEndMethod( DicomDir::Method *method, void *arg ) +{ + SetEndMethod(method,arg,NULL); +} + /** * \brief Set the start method to call when the parsing of the * directory starts. @@ -444,10 +490,10 @@ void DicomDir::SetEndMethodArgDelete( DicomDir::Method *method ) * @return false only when fail to open */ -bool DicomDir::WriteDicomDir(std::string const &fileName) +bool DicomDir::Write(std::string const &fileName) { int i; - uint16_t sq[4] = { 0x0004, 0x1220, 0xffff, 0xffff }; + uint16_t sq[6] = { 0x0004, 0x1220, 0x5153, 0x0000, 0xffff, 0xffff }; uint16_t sqt[4]= { 0xfffe, 0xe0dd, 0xffff, 0xffff }; std::ofstream *fp = new std::ofstream(fileName.c_str(), @@ -467,7 +513,7 @@ bool DicomDir::WriteDicomDir(std::string const &fileName) ptrMeta->WriteContent(fp, ExplicitVR); // force writing 0004|1220 [SQ ], that CANNOT exist within DicomDirMeta - for(i=0;i<4;++i) + for(i=0;i<6;++i) { binary_write(*fp, sq[i]); } @@ -496,9 +542,9 @@ bool DicomDir::WriteDicomDir(std::string const &fileName) * @return true */ -bool DicomDir::AnonymizeDicomDir() +bool DicomDir::Anonymize() { - ValEntry *v; + DataEntry *v; // Something clever to be found to forge the Patient names std::ostringstream s; int i = 1; @@ -507,22 +553,22 @@ bool DicomDir::AnonymizeDicomDir() ++cc) { s << i; - v = (*cc)->GetValEntry(0x0010, 0x0010) ; // Patient's Name + v = (*cc)->GetDataEntry(0x0010, 0x0010) ; // Patient's Name if (v) { - v->SetValue(s.str()); + v->SetString(s.str()); } - v = (*cc)->GetValEntry(0x0010, 0x0020) ; // Patient ID + v = (*cc)->GetDataEntry(0x0010, 0x0020) ; // Patient ID if (v) { - v->SetValue(" "); + v->SetString(" "); } - v = (*cc)->GetValEntry(0x0010, 0x0030) ; // Patient's BirthDate + v = (*cc)->GetDataEntry(0x0010, 0x0030) ; // Patient's BirthDate if (v) { - v->SetValue(" "); + v->SetString(" "); } s << ""; i++; @@ -557,25 +603,21 @@ void DicomDir::CreateDicomDirChainedList(std::string const &path) break; } - f = new File( ); - f->SetLoadMode(LoadMode); // we allow user not to load Sequences... - f->Load( it->c_str() ); + f = File::New( ); + f->SetLoadMode(LoadMode); // we allow user not to load Sequences, + // or Shadow groups, or ...... + f->SetFileName( it->c_str() ); + f->Load( ); -// if ( !f ) -// { -// gdcmWarningMacro( "Failure in new gdcm::File " << it->c_str() ); -// continue; -// } - if ( f->IsReadable() ) { // Add the file to the chained list: list.push_back(f); - gdcmWarningMacro( "Readable " << it->c_str() ); + gdcmDebugMacro( "Readable " << it->c_str() ); } else { - delete f; + f->Delete(); } count++; } @@ -591,7 +633,7 @@ void DicomDir::CreateDicomDirChainedList(std::string const &path) itDoc!=list.end(); ++itDoc) { - delete dynamic_cast(*itDoc); + dynamic_cast(*itDoc)->Delete(); } } @@ -666,6 +708,7 @@ void DicomDir::CreateDicomDir() // 3 - we find an other tag // + we create the object for the precedent tag // + loop to 1 - + gdcmDebugMacro("Create DicomDir"); // Directory record sequence DocEntry *e = GetDocEntry(0x0004, 0x1220); @@ -692,13 +735,13 @@ void DicomDir::CreateDicomDir() while(tmpSI) { d = tmpSI->GetDocEntry(0x0004, 0x1430); // Directory Record Type - if ( ValEntry* valEntry = dynamic_cast(d) ) + if ( DataEntry *dataEntry = dynamic_cast(d) ) { - v = valEntry->GetValue(); + v = dataEntry->GetString(); } else { - gdcmWarningMacro( "(0004,1430) not a ValEntry ?!?"); + gdcmWarningMacro( "(0004,1430) not a DataEntry ?!?"); continue; } @@ -708,40 +751,50 @@ void DicomDir::CreateDicomDir() if ( v == "IMAGE " ) { - si = new DicomDirImage(true); + si = DicomDirImage::New(true); if ( !AddImageToEnd( static_cast(si)) ) { - delete si; + si->Delete(); si = NULL; gdcmErrorMacro( "Add AddImageToEnd failed"); } } else if ( v == "SERIES" ) { - si = new DicomDirSerie(true); + si = DicomDirSerie::New(true); if ( !AddSerieToEnd( static_cast(si)) ) { - delete si; + si->Delete(); si = NULL; gdcmErrorMacro( "Add AddSerieToEnd failed"); } } + else if ( v == "VISIT " ) + { + si = DicomDirVisit::New(true); + if ( !AddVisitToEnd( static_cast(si)) ) + { + si->Delete(); + si = NULL; + gdcmErrorMacro( "Add AddVisitToEnd failed"); + } + } else if ( v == "STUDY " ) { - si = new DicomDirStudy(true); + si = DicomDirStudy::New(true); if ( !AddStudyToEnd( static_cast(si)) ) { - delete si; + si->Delete(); si = NULL; gdcmErrorMacro( "Add AddStudyToEnd failed"); } } else if ( v == "PATIENT " ) { - si = new DicomDirPatient(true); + si = DicomDirPatient::New(true); if ( !AddPatientToEnd( static_cast(si)) ) { - delete si; + si->Delete(); si = NULL; gdcmErrorMacro( "Add PatientToEnd failed"); } @@ -750,7 +803,7 @@ void DicomDir::CreateDicomDir() { // It was neither a 'PATIENT', nor a 'STUDY', nor a 'SERIE', // nor an 'IMAGE' SQItem. Skip to next item. - gdcmWarningMacro( " -------------------------------------------" + gdcmDebugMacro( " -------------------------------------------" << "a non PATIENT/STUDY/SERIE/IMAGE SQItem was found : " << v); @@ -759,7 +812,7 @@ void DicomDir::CreateDicomDir() continue; } if ( si ) - MoveSQItem(si,tmpSI); + si->MoveObject(tmpSI); // New code : Copies the List tmpSI=s->GetNextSQItem(); } @@ -813,6 +866,26 @@ bool DicomDir::AddSerieToEnd(DicomDirSerie *dd) return false; } +/** + * \brief AddVisitToEnd + * @param dd SQ Item to enqueue to the DicomDirVisit chained List + */ +bool DicomDir::AddVisitToEnd(DicomDirVisit *dd) +{ + if ( Patients.size() > 0 ) + { + ListDicomDirPatient::iterator itp = Patients.end(); + itp--; + + DicomDirStudy *study = (*itp)->GetLastStudy(); + if ( study ) + { + study->AddVisit(dd); + return true; + } + } + return false; +} /** * \brief AddImageToEnd * @param dd SQ Item to enqueue to the DicomDirImage chained List @@ -863,12 +936,12 @@ void DicomDir::SetElements(std::string const &path, VectDocument const &list) ++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); + patCurName = (*it)->GetEntryString(0x0010,0x0010); + patCurID = (*it)->GetEntryString(0x0010,0x0011); + studCurInstanceUID = (*it)->GetEntryString(0x0020,0x000d); + studCurID = (*it)->GetEntryString(0x0020,0x0010); + serCurInstanceUID = (*it)->GetEntryString(0x0020,0x000e); + serCurID = (*it)->GetEntryString(0x0020,0x0011); if ( patCurName != patPrevName || patCurID != patPrevID || first ) { @@ -919,7 +992,7 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, ListDicomDirElem::const_iterator it; uint16_t tmpGr, tmpEl; DictEntry *dictEntry; - ValEntry *entry; + DataEntry *entry; std::string val; SQItem *si; @@ -927,53 +1000,56 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, { case GDCM_DICOMDIR_IMAGE: elemList = Global::GetDicomDirElements()->GetDicomDirImageElements(); - si = new DicomDirImage(true); + si = DicomDirImage::New(true); if ( !AddImageToEnd(static_cast(si)) ) { - delete si; + si->Delete(); gdcmErrorMacro( "Add ImageToEnd failed"); } break; case GDCM_DICOMDIR_SERIE: elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements(); - si = new DicomDirSerie(true); + si = DicomDirSerie::New(true); if ( !AddSerieToEnd(static_cast(si)) ) { - delete si; + si->Delete(); gdcmErrorMacro( "Add SerieToEnd failed"); } break; case GDCM_DICOMDIR_STUDY: elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements(); - si = new DicomDirStudy(true); + si = DicomDirStudy::New(true); if ( !AddStudyToEnd(static_cast(si)) ) { - delete si; + si->Delete(); gdcmErrorMacro( "Add StudyToEnd failed"); } break; case GDCM_DICOMDIR_PATIENT: elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements(); - si = new DicomDirPatient(true); + si = DicomDirPatient::New(true); if ( !AddPatientToEnd(static_cast(si)) ) { - delete si; + si->Delete(); gdcmErrorMacro( "Add PatientToEnd failed"); } break; case GDCM_DICOMDIR_META: - elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements(); - si = new DicomDirMeta(true); if ( MetaElems ) { - delete MetaElems; + MetaElems->Delete(); gdcmErrorMacro( "MetaElements already exist, they will be destroyed"); } - MetaElems = static_cast(si); + elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements(); + MetaElems = DicomDirMeta::New(true); + si = MetaElems; break; default: return; } + + // FIXME : troubles found when it's a SeqEntry + // removed all the seems-to-be-useless stuff about Referenced Image Sequence // to avoid further troubles // imageElem 0008 1140 "" // Referenced Image Sequence @@ -982,8 +1058,7 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, // imageElem 0008 1155 "" // Referenced SOP Instance UID : to be set/forged later // imageElem fffe e00d "" // Item delimitation : length to be set to ZERO later - // FIXME : troubles found when it's a SeqEntry - + std::string referencedVal; // for all the relevant elements found in their own spot of the DicomDir.dic for( it = elemList.begin(); it != elemList.end(); ++it) { @@ -991,15 +1066,15 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, tmpEl = it->Elem; dictEntry = GetPubDict()->GetEntry(tmpGr, tmpEl); - entry = new ValEntry( dictEntry ); // Be sure it's never a BinEntry ! - + entry = DataEntry::New( dictEntry ); 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->GetEntryValue(tmpGr, tmpEl); + + val = header->GetEntryString(tmpGr, tmpEl); } else { @@ -1007,27 +1082,49 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, } 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 ) - { - gdcmWarningMacro( "The base path of file name is incorrect"); - val = header->GetFileName(); - } - else - { - val = &(header->GetFileName().c_str()[path.length()]); - } - } - else + { + if ( tmpGr == 0x0004 ) // never present in File ! { - val = it->Value; + switch (tmpEl) + { + case 0x1130: // File-set ID + // force to the *end* File Name + val = Util::GetName( path ); + break; + + case 0x1500: // Only used for image + if ( header->GetFileName().substr(0, path.length()) != path ) + { + gdcmWarningMacro( "The base path of file name is incorrect"); + val = header->GetFileName(); + } + else + { + val = &(header->GetFileName().c_str()[path.length()+1]); + } + break; + + case 0x1510: // Referenced SOP Class UID in File + referencedVal = header->GetEntryString(0x0008, 0x0016); + // FIXME : probabely something to check + val = referencedVal; + break; + + case 0x1511: // Referenced SOP Instance UID in File + referencedVal = header->GetEntryString(0x0008, 0x0018); + // FIXME : probabely something to check + val = referencedVal; + break; + + case 0x1512: // Referenced Transfer Syntax UID in File + referencedVal = header->GetEntryString(0x0002, 0x0010); + // FIXME : probabely something to check + val = referencedVal; + break; + + default : + val = it->Value; + } } } else @@ -1036,13 +1133,26 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, val = it->Value; } - entry->SetValue( val ); // troubles expected when vr=SQ ... +/* FIX later the pb of creating the 'Implementation Version Name'! + + if (val == GDCM_UNFOUND) + val = ""; + + if ( tmpGr == 0x0002 && tmpEl == 0x0013) + { + // 'Implementation Version Name' + std::string val = "GDCM "; + val += Util::GetVersion(); + } +*/ + entry->SetString( val ); // troubles expected when vr=SQ ... if ( type == GDCM_DICOMDIR_META ) // fusible : should never print ! { - gdcmWarningMacro("GDCM_DICOMDIR_META ?!? should never print that"); + gdcmDebugMacro("GDCM_DICOMDIR_META ?!? should never print that"); } si->AddEntry(entry); + entry->Delete(); } } @@ -1053,13 +1163,13 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, * @param src source SQItem */ void DicomDir::MoveSQItem(DocEntrySet *dst,DocEntrySet *src) -{ +{ DocEntry *entry; entry = src->GetFirstEntry(); while(entry) { - src->RemoveEntryNoDestroy(entry); + src->RemoveEntry(entry); dst->AddEntry(entry); // we destroyed -> the current iterator is not longer valid entry = src->GetFirstEntry();