X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDicomDir.cxx;h=05981583d5024377644d51c73a35125e6bc54fe2;hb=0a63df7d5417e936948123cb00a80d58addcae66;hp=769ce05901da1ceb26b72674f8383b3a45a78d18;hpb=cc8f86d8d77d1e831a04d5c80ec95f2f125c5313;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index 769ce059..05981583 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDicomDir.cxx,v $ Language: C++ - Date: $Date: 2005/02/02 14:52:24 $ - Version: $Revision: 1.127 $ + Date: $Date: 2005/07/03 12:45:53 $ + Version: $Revision: 1.143 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -50,7 +50,62 @@ #else # 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, TOPIC, PRIVATE +// +// PATIENT STUDY, PRIVATE +// +// 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, PRIVATE, +// ENCAP DOC +// 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 +// PRIVATE +// ENCAP DOC +// +// ---------------------- +// 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 { //----------------------------------------------------------------------------- @@ -78,82 +133,90 @@ 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) - Initialize(); // sets all private fields to NULL + ParseDir = parseDir; + SetLoadMode (0x00000000); // concerns only dicom files + Load( fileName ); +} - // if user passed a root directory, sure we didn't get anything +/** + * \brief Canonical destructor + */ +DicomDir::~DicomDir() +{ + SetStartMethod(NULL); + SetProgressMethod(NULL); + SetEndMethod(NULL); - if ( GetFirstEntry() == 0 ) // when user passed a Directory to parse + ClearPatient(); + if ( MetaElems ) { - if (!parseDir) - gdcmVerboseMacro( "Entry HT empty for file: "<(entry) ) + if ( dynamic_cast(entry) ) break; RemoveEntryNoDestroy(entry); @@ -210,7 +273,7 @@ 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; @@ -288,7 +351,7 @@ void DicomDir::ParseDirectory() void DicomDir::SetStartMethod( DicomDir::Method *method, void *arg, DicomDir::Method *argDelete ) { - if( StartArg && StartMethodArgDelete ) + if ( StartArg && StartMethodArgDelete ) { StartMethodArgDelete( StartArg ); } @@ -298,6 +361,7 @@ void DicomDir::SetStartMethod( DicomDir::Method *method, void *arg, StartMethodArgDelete = argDelete; } + /** * \brief Set the progress method to call when the parsing of the * directory progress @@ -309,7 +373,7 @@ 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 ); } @@ -329,7 +393,7 @@ 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 ); } @@ -376,9 +440,6 @@ 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 */ @@ -391,15 +452,15 @@ 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 ) { - gdcmVerboseMacro("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 = GetMeta(); @@ -430,6 +491,45 @@ 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 /** @@ -442,7 +542,7 @@ 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(); @@ -452,27 +552,30 @@ 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 ) - { - gdcmVerboseMacro( "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); - gdcmVerboseMacro( "Readable " << it->c_str() ); + list.push_back(f); + gdcmWarningMacro( "Readable " << it->c_str() ); } else { - delete header; + delete f; } count++; } @@ -499,7 +602,7 @@ void DicomDir::CallStartMethod() { Progress = 0.0f; Abort = false; - if( StartMethod ) + if ( StartMethod ) { StartMethod( StartArg ); } @@ -510,7 +613,7 @@ void DicomDir::CallStartMethod() */ void DicomDir::CallProgressMethod() { - if( ProgressMethod ) + if ( ProgressMethod ) { ProgressMethod( ProgressArg ); } @@ -522,7 +625,7 @@ void DicomDir::CallProgressMethod() void DicomDir::CallEndMethod() { Progress = 1.0f; - if( EndMethod ) + if ( EndMethod ) { EndMethod( EndArg ); } @@ -552,7 +655,7 @@ void DicomDir::Initialize() } /** - * \brief create a 'DicomDir' from a DICOMDIR Header + * \brief create a 'gdcm::DicomDir' from a DICOMDIR Header */ void DicomDir::CreateDicomDir() { @@ -568,15 +671,14 @@ void DicomDir::CreateDicomDir() DocEntry *e = GetDocEntry(0x0004, 0x1220); if ( !e ) { - gdcmVerboseMacro( "No Directory Record Sequence (0004,1220) found"); - /// \todo FIXME: what to do when the parsed file IS NOT a DICOMDIR file ? + gdcmWarningMacro( "No Directory Record Sequence (0004,1220) found"); return; } SeqEntry *s = dynamic_cast(e); if ( !s ) { - gdcmVerboseMacro( "Element (0004,1220) is not a Sequence ?!?"); + gdcmWarningMacro( "Element (0004,1220) is not a Sequence ?!?"); return; } @@ -596,57 +698,67 @@ void DicomDir::CreateDicomDir() } else { - gdcmVerboseMacro( "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(); @@ -670,7 +782,7 @@ bool DicomDir::AddPatientToEnd(DicomDirPatient *dd) */ bool DicomDir::AddStudyToEnd(DicomDirStudy *dd) { - if( Patients.size() > 0 ) + if ( Patients.size() > 0 ) { ListDicomDirPatient::iterator itp = Patients.end(); itp--; @@ -686,13 +798,13 @@ 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; @@ -707,16 +819,16 @@ 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; @@ -732,7 +844,7 @@ bool DicomDir::AddImageToEnd(DicomDirImage *dd) * @param path path of the root directory * @param list chained list of Headers */ -void DicomDir::SetElements(std::string const & path, VectDocument const &list) +void DicomDir::SetElements(std::string const &path, VectDocument const &list) { ClearEntry(); ClearPatient(); @@ -747,7 +859,8 @@ void DicomDir::SetElements(std::string const & path, VectDocument const &list) bool first = true; for( VectDocument::const_iterator it = list.begin(); - it != list.end(); ++it ) + it != list.end(); + ++it ) { // get the current file characteristics patCurName = (*it)->GetEntryValue(0x0010,0x0010); @@ -757,26 +870,25 @@ 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 @@ -803,7 +915,7 @@ 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; @@ -816,7 +928,7 @@ 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"); @@ -825,7 +937,7 @@ 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"); @@ -834,7 +946,7 @@ 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"); @@ -843,7 +955,7 @@ 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"); @@ -852,7 +964,7 @@ 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"); @@ -869,10 +981,10 @@ 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; @@ -883,7 +995,7 @@ 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 @@ -894,18 +1006,18 @@ 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 ) { - gdcmVerboseMacro( "The base path of file name is incorrect"); + gdcmWarningMacro( "The base path of file name is incorrect"); val = header->GetFileName(); } else @@ -928,7 +1040,7 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, if ( type == GDCM_DICOMDIR_META ) // fusible : should never print ! { - gdcmVerboseMacro("GDCM_DICOMDIR_META ?!? should never print that"); + gdcmWarningMacro("GDCM_DICOMDIR_META ?!? should never print that"); } si->AddEntry(entry); } @@ -971,7 +1083,7 @@ 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);