X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDicomDir.cxx;h=60d533666df3716d0c55b59c9040a40afeed9da1;hb=a770affb0ae95b1a1c0647ce7ee84f179e6714da;hp=f25fefd786f195de9111b89d1e89b500ff3f659b;hpb=6003c9cbddd74caa0f6a7de58d5f1e3f8a4c38c4;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index f25fefd7..60d53366 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDicomDir.cxx,v $ Language: C++ - Date: $Date: 2005/02/06 14:31:09 $ - Version: $Revision: 1.129 $ + Date: $Date: 2005/07/08 10:13:38 $ + Version: $Revision: 1.145 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -55,21 +55,23 @@ // ---------------------------------------------------------------------------- // // 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-èlevel directory Entity +// in the next lower-level directory Entity // -// (Root directory Entity) PATIENT +// (Root directory Entity) PATIENT, TOPIC, PRIVATE // -// PATIENT STUDY +// PATIENT STUDY, PRIVATE // -// STUDY SERIES, VISIT, RESULTS, STUDY COMPONENT +// STUDY SERIES, VISIT, RESULTS, STUDY COMPONENT, PRIVATE // // 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 +// RAW DATA, REGISTRATION, FIDUCIAL, PRIVATE, +// ENCAP DOC // IMAGE // OVERLAY // MODALITY LUT @@ -88,6 +90,8 @@ // RAW DATA // REGISTRATION // FIDUCIAL +// PRIVATE +// ENCAP DOC // // ---------------------- // The current gdcm version only deals with : @@ -96,7 +100,7 @@ // PATIENT STUDY // STUDY SERIES // SERIES IMAGE -// IMAGE +// IMAGE / // // DicomDir::CreateDicomDir will have to be completed // Treelike structure management will have to be upgraded @@ -113,6 +117,7 @@ DicomDir::DicomDir() :Document( ) { Initialize(); // sets all private fields to NULL + ParseDir = false; NewMeta(); } @@ -129,82 +134,135 @@ DicomDir::DicomDir() * and wants to use it */ DicomDir::DicomDir(std::string const &fileName, bool parseDir ): - Document( fileName ) + Document( ) { // At this step, Document constructor is already executed, - // whatever user passed (a root directory or a DICOMDIR) + // 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); + + ClearPatient(); + if ( MetaElems ) + { + delete MetaElems; + } +} + +//----------------------------------------------------------------------------- +// Public + +/** + * \brief Loader. use SetLoadMode(), SetFileName() before ! + * @return false if file cannot be open or no swap info was found, + * or no tag was found. + */ +bool DicomDir::Load( ) +{ + // We should clean out anything that already exists. Initialize(); // sets all private fields to NULL - // if user passed a root directory, sure we didn't get anything + if (!ParseDir) + { + if ( ! this->Document::Load( ) ) + return false; + } + return DoTheLoadingJob( ); +} + +/** + * \brief Loader. (DEPRECATED : 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. + */ +bool DicomDir::Load(std::string const &fileName ) +{ + // We should clean out anything that already exists. + Initialize(); // sets all private fields to NULL - if ( GetFirstEntry() == 0 ) // when user passed a Directory to parse + SetFileName( fileName ); + if (!ParseDir) { - if (!parseDir) - gdcmWarningMacro( "Entry HT empty for file: "<Document::Load( ) ) + return false; + } + return DoTheLoadingJob( ); +} - // Only if user passed a root directory - // ------------------------------------ - if ( fileName == "." ) +/** + * \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( ) +{ + // We should clean out anything that already exists. + Initialize(); // sets all private fields to NULL + + if (!ParseDir) + { + // Only if user passed a DICOMDIR + // ------------------------------ + Fp = 0; + if ( !OpenFile() ) { - // 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 + return false; } - - if ( parseDir ) // user asked for a recursive parsing of a root directory + if (!Document::Load() ) { - NewMeta(); - - gdcmWarningMacro( "Parse directory and create the DicomDir"); - ParseDirectory(); + return false; } - else + + if ( GetFirstEntry() == 0 ) // when user passed a Directory to parse { - /// \todo if parseDir == false, it should be tagged as an error - // NO ! user may just call ParseDirectory() *after* constructor + gdcmWarningMacro( "Entry HT empty for file: "<< GetFileName()); + return false; } - } - // Only if user passed a DICOMDIR - // ------------------------------ - else - { // Directory record sequence DocEntry *e = GetDocEntry(0x0004, 0x1220); if ( !e ) { gdcmWarningMacro( "NO 'Directory record sequence' (0x0004,0x1220)" - << " in file " << fileName); - /// \todo FIXME : what do we do when the parsed file IS NOT a - /// DICOMDIR file ? + << " in file " << GetFileName()); + return false; } else CreateDicomDir(); } -} - -/** - * \brief Canonical destructor - */ -DicomDir::~DicomDir() -{ - SetStartMethod(NULL); - SetProgressMethod(NULL); - SetEndMethod(NULL); - - ClearPatient(); - if ( MetaElems ) + else { - delete MetaElems; + // Only if user passed a root directory + // ------------------------------------ + 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 + } + NewMeta(); + gdcmWarningMacro( "Parse directory and create the DicomDir : " + << GetFileName() ); + ParseDirectory(); } + return true; } -//----------------------------------------------------------------------------- -// Public /** * \brief This predicate, based on hopefully reasonable heuristics, * decides whether or not the current document was properly parsed @@ -215,17 +273,17 @@ DicomDir::~DicomDir() */ bool DicomDir::IsReadable() { - if( Filetype == Unknown) + if ( Filetype == Unknown ) { gdcmWarningMacro( "Wrong filetype"); return false; } - if( !MetaElems ) + if ( !MetaElems ) { gdcmWarningMacro( "Meta Elements missing in DicomDir"); return false; } - if( Patients.size() <= 0 ) + if ( Patients.size() <= 0 ) { gdcmWarningMacro( "NO Patient in DicomDir"); return false; @@ -239,18 +297,18 @@ bool DicomDir::IsReadable() */ DicomDirMeta *DicomDir::NewMeta() { - if( MetaElems ) + if ( MetaElems ) delete MetaElems; DocEntry *entry = GetFirstEntry(); - if( entry ) + if ( entry ) { - MetaElems = new DicomDirMeta(true); + MetaElems = new DicomDirMeta(true); // true = empty entry = GetFirstEntry(); while( entry ) { - if( dynamic_cast(entry) ) + if ( dynamic_cast(entry) ) break; RemoveEntryNoDestroy(entry); @@ -261,7 +319,7 @@ DicomDirMeta *DicomDir::NewMeta() } else // after root directory parsing { - MetaElems = new DicomDirMeta(false); + MetaElems = new DicomDirMeta(false); // false = not empty } MetaElems->SetSQItemNumber(0); // To avoid further missprinting return MetaElems; @@ -339,7 +397,7 @@ void DicomDir::ParseDirectory() void DicomDir::SetStartMethod( DicomDir::Method *method, void *arg, DicomDir::Method *argDelete ) { - if( StartArg && StartMethodArgDelete ) + if ( StartArg && StartMethodArgDelete ) { StartMethodArgDelete( StartArg ); } @@ -349,6 +407,7 @@ void DicomDir::SetStartMethod( DicomDir::Method *method, void *arg, StartMethodArgDelete = argDelete; } + /** * \brief Set the progress method to call when the parsing of the * directory progress @@ -360,7 +419,7 @@ void DicomDir::SetStartMethod( DicomDir::Method *method, void *arg, void DicomDir::SetProgressMethod( DicomDir::Method *method, void *arg, DicomDir::Method *argDelete ) { - if( ProgressArg && ProgressMethodArgDelete ) + if ( ProgressArg && ProgressMethodArgDelete ) { ProgressMethodArgDelete( ProgressArg ); } @@ -380,7 +439,7 @@ void DicomDir::SetProgressMethod( DicomDir::Method *method, void *arg, void DicomDir::SetEndMethod( DicomDir::Method *method, void *arg, DicomDir::Method *argDelete ) { - if( EndArg && EndMethodArgDelete ) + if ( EndArg && EndMethodArgDelete ) { EndMethodArgDelete( EndArg ); } @@ -427,9 +486,6 @@ void DicomDir::SetEndMethodArgDelete( DicomDir::Method *method ) * \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 */ @@ -442,7 +498,7 @@ bool DicomDir::WriteDicomDir(std::string const &fileName) std::ofstream *fp = new std::ofstream(fileName.c_str(), std::ios::out | std::ios::binary); - if( !fp ) + if ( !fp ) { gdcmWarningMacro("Failed to open(write) File: " << fileName.c_str()); return false; @@ -450,7 +506,7 @@ bool DicomDir::WriteDicomDir(std::string const &fileName) char filePreamble[128]; memset(filePreamble, 0, 128); - fp->write(filePreamble, 128); //FIXME + fp->write(filePreamble, 128); binary_write( *fp, "DICM"); DicomDirMeta *ptrMeta = GetMeta(); @@ -481,6 +537,45 @@ 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 /** @@ -493,7 +588,7 @@ void DicomDir::CreateDicomDirChainedList(std::string const &path) DirList dirList(path,1); // gets recursively the file list unsigned int count = 0; VectDocument list; - File *header; + File *f; DirListType fileList = dirList.GetFilenames(); @@ -503,27 +598,30 @@ void DicomDir::CreateDicomDirChainedList(std::string const &path) { Progress = (float)(count+1)/(float)fileList.size(); CallProgressMethod(); - if( Abort ) + if ( Abort ) { break; } - header = new File( it->c_str() ); - if( !header ) - { - gdcmWarningMacro( "Failure in new gdcm::File " << it->c_str() ); - continue; - } + f = new File( ); + f->SetLoadMode(LoadMode); // we allow user not to load Sequences... + f->Load( it->c_str() ); + +// if ( !f ) +// { +// gdcmWarningMacro( "Failure in new gdcm::File " << it->c_str() ); +// continue; +// } - if( header->IsReadable() ) + if ( f->IsReadable() ) { // Add the file to the chained list: - list.push_back(header); + list.push_back(f); gdcmWarningMacro( "Readable " << it->c_str() ); } else { - delete header; + delete f; } count++; } @@ -550,7 +648,7 @@ void DicomDir::CallStartMethod() { Progress = 0.0f; Abort = false; - if( StartMethod ) + if ( StartMethod ) { StartMethod( StartArg ); } @@ -561,7 +659,7 @@ void DicomDir::CallStartMethod() */ void DicomDir::CallProgressMethod() { - if( ProgressMethod ) + if ( ProgressMethod ) { ProgressMethod( ProgressArg ); } @@ -573,7 +671,7 @@ void DicomDir::CallProgressMethod() void DicomDir::CallEndMethod() { Progress = 1.0f; - if( EndMethod ) + if ( EndMethod ) { EndMethod( EndArg ); } @@ -603,7 +701,7 @@ void DicomDir::Initialize() } /** - * \brief create a 'DicomDir' from a DICOMDIR Header + * \brief create a 'gdcm::DicomDir' from a DICOMDIR Header */ void DicomDir::CreateDicomDir() { @@ -620,7 +718,6 @@ void DicomDir::CreateDicomDir() if ( !e ) { gdcmWarningMacro( "No Directory Record Sequence (0004,1220) found"); - /// \todo FIXME: what to do when the parsed file IS NOT a DICOMDIR file ? return; } @@ -647,57 +744,67 @@ void DicomDir::CreateDicomDir() } else { - gdcmWarningMacro( "Not a ValEntry."); + gdcmWarningMacro( "(0004,1430) not a ValEntry ?!?"); continue; } - if( v == "PATIENT " ) + // A decent DICOMDIR has much more images than series, + // more series than studies, and so on. + // This is the right order to preform the tests + + if ( v == "IMAGE " ) { - si = new DicomDirPatient(true); - if( !AddPatientToEnd( static_cast(si)) ) + si = new DicomDirImage(true); + if ( !AddImageToEnd( static_cast(si)) ) { delete si; si = NULL; - gdcmErrorMacro( "Add PatientToEnd failed"); + gdcmErrorMacro( "Add AddImageToEnd failed"); } } - else if( v == "STUDY " ) + else if ( v == "SERIES" ) { - si = new DicomDirStudy(true); - if( !AddStudyToEnd( static_cast(si)) ) + si = new DicomDirSerie(true); + if ( !AddSerieToEnd( static_cast(si)) ) { delete si; si = NULL; - gdcmErrorMacro( "Add AddStudyToEnd failed"); + gdcmErrorMacro( "Add AddSerieToEnd failed"); } } - else if( v == "SERIES" ) + else if ( v == "STUDY " ) { - si = new DicomDirSerie(true); - if( !AddSerieToEnd( static_cast(si)) ) + si = new DicomDirStudy(true); + if ( !AddStudyToEnd( static_cast(si)) ) { delete si; si = NULL; - gdcmErrorMacro( "Add AddSerieToEnd failed"); + gdcmErrorMacro( "Add AddStudyToEnd failed"); } } - else if( v == "IMAGE " ) + else if ( v == "PATIENT " ) { - si = new DicomDirImage(true); - if( !AddImageToEnd( static_cast(si)) ) + si = new DicomDirPatient(true); + if ( !AddPatientToEnd( static_cast(si)) ) { delete si; si = NULL; - gdcmErrorMacro( "Add AddImageToEnd failed"); + gdcmErrorMacro( "Add PatientToEnd failed"); } } else { - // It was not a 'PATIENT', nor a 'STUDY', nor a 'SERIE', - // neither an 'IMAGE' SQItem. Skip to next item. - continue; + // It was neither a 'PATIENT', nor a 'STUDY', nor a 'SERIE', + // nor an 'IMAGE' SQItem. Skip to next item. + gdcmWarningMacro( " -------------------------------------------" + << "a non PATIENT/STUDY/SERIE/IMAGE SQItem was found : " + << v); + + // FIXME : deal with other item types ! + tmpSI=s->GetNextSQItem(); // To avoid infinite loop + continue; } - if( si ) + if ( si ) MoveSQItem(si,tmpSI); tmpSI=s->GetNextSQItem(); @@ -721,7 +828,7 @@ bool DicomDir::AddPatientToEnd(DicomDirPatient *dd) */ bool DicomDir::AddStudyToEnd(DicomDirStudy *dd) { - if( Patients.size() > 0 ) + if ( Patients.size() > 0 ) { ListDicomDirPatient::iterator itp = Patients.end(); itp--; @@ -737,13 +844,13 @@ bool DicomDir::AddStudyToEnd(DicomDirStudy *dd) */ bool DicomDir::AddSerieToEnd(DicomDirSerie *dd) { - if( Patients.size() > 0 ) + if ( Patients.size() > 0 ) { ListDicomDirPatient::iterator itp = Patients.end(); itp--; DicomDirStudy *study = (*itp)->GetLastStudy(); - if( study ) + if ( study ) { study->AddSerie(dd); return true; @@ -758,16 +865,16 @@ bool DicomDir::AddSerieToEnd(DicomDirSerie *dd) */ bool DicomDir::AddImageToEnd(DicomDirImage *dd) { - if( Patients.size() > 0 ) + if ( Patients.size() > 0 ) { ListDicomDirPatient::iterator itp = Patients.end(); itp--; DicomDirStudy *study = (*itp)->GetLastStudy(); - if( study ) + if ( study ) { DicomDirSerie *serie = study->GetLastSerie(); - if( serie ) + if ( serie ) { serie->AddImage(dd); return true; @@ -809,26 +916,25 @@ void DicomDir::SetElements(std::string const &path, VectDocument const &list) serCurInstanceUID = (*it)->GetEntryValue(0x0020,0x000e); serCurID = (*it)->GetEntryValue(0x0020,0x0011); - if( patCurName != patPrevName || patCurID != patPrevID || first ) + 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 + // 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 + // 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 @@ -855,7 +961,7 @@ void DicomDir::SetElements(std::string const &path, VectDocument const &list) 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; @@ -868,7 +974,7 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, case GDCM_DICOMDIR_IMAGE: elemList = Global::GetDicomDirElements()->GetDicomDirImageElements(); si = new DicomDirImage(true); - if( !AddImageToEnd(static_cast(si)) ) + if ( !AddImageToEnd(static_cast(si)) ) { delete si; gdcmErrorMacro( "Add ImageToEnd failed"); @@ -877,7 +983,7 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, case GDCM_DICOMDIR_SERIE: elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements(); si = new DicomDirSerie(true); - if( !AddSerieToEnd(static_cast(si)) ) + if ( !AddSerieToEnd(static_cast(si)) ) { delete si; gdcmErrorMacro( "Add SerieToEnd failed"); @@ -886,7 +992,7 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, case GDCM_DICOMDIR_STUDY: elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements(); si = new DicomDirStudy(true); - if( !AddStudyToEnd(static_cast(si)) ) + if ( !AddStudyToEnd(static_cast(si)) ) { delete si; gdcmErrorMacro( "Add StudyToEnd failed"); @@ -895,7 +1001,7 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, case GDCM_DICOMDIR_PATIENT: elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements(); si = new DicomDirPatient(true); - if( !AddPatientToEnd(static_cast(si)) ) + if ( !AddPatientToEnd(static_cast(si)) ) { delete si; gdcmErrorMacro( "Add PatientToEnd failed"); @@ -904,7 +1010,7 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, case GDCM_DICOMDIR_META: elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements(); si = new DicomDirMeta(true); - if( MetaElems ) + if ( MetaElems ) { delete MetaElems; gdcmErrorMacro( "MetaElements already exist, they will be destroyed"); @@ -935,7 +1041,7 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, entry->SetOffset(0); // just to avoid further missprinting - if( header ) + if ( header ) { // NULL when we Build Up (ex nihilo) a DICOMDIR // or when we add the META elems @@ -946,16 +1052,16 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, val = GDCM_UNFOUND; } - if( val == GDCM_UNFOUND) + if ( val == GDCM_UNFOUND) { - if( tmpGr == 0x0004 && tmpEl == 0x1130 ) // File-set ID + if ( tmpGr == 0x0004 && tmpEl == 0x1130 ) // File-set ID { // force to the *end* File Name val = Util::GetName( path ); } - else if( tmpGr == 0x0004 && tmpEl == 0x1500 ) // Only used for image + else if ( tmpGr == 0x0004 && tmpEl == 0x1500 ) // Only used for image { - if( header->GetFileName().substr(0, path.length()) != path ) + if ( header->GetFileName().substr(0, path.length()) != path ) { gdcmWarningMacro( "The base path of file name is incorrect"); val = header->GetFileName(); @@ -1023,7 +1129,7 @@ bool DicomDir::HeaderLessThan(Document *header1, Document *header2) */ void DicomDir::Print(std::ostream &os, std::string const & ) { - if( MetaElems ) + if ( MetaElems ) { MetaElems->SetPrintLevel(PrintLevel); MetaElems->Print(os);