X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDicomDir.cxx;h=1226e49598d9b3ca02ef9a6a7d47d7f3d0d8f9ff;hb=fbd2698cb0545343abc2d8aefe92bab1f5b3eaa3;hp=481ed229b2a7e0a38a6c9cd1075f8a6d2f6360e7;hpb=c094e185dd6404df031524ccae8e1b51e3b84871;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index 481ed229..1226e495 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDicomDir.cxx,v $ Language: C++ - Date: $Date: 2005/01/21 11:40:55 $ - Version: $Revision: 1.112 $ + Date: $Date: 2005/07/07 16:37:40 $ + Version: $Revision: 1.144 $ 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" @@ -46,21 +50,71 @@ #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 { - -//----------------------------------------------------------------------------- -// For full DICOMDIR description, see: -// PS 3.3-2003, pages 731-750 //----------------------------------------------------------------------------- // Constructor / Destructor - /** * \brief Constructor : creates an empty DicomDir */ DicomDir::DicomDir() - :Document( ) + :Document( ) { Initialize(); // sets all private fields to NULL NewMeta(); @@ -69,7 +123,7 @@ DicomDir::DicomDir() /** * \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 @@ -79,61 +133,16 @@ 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 - - // 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 (!parseDir) - gdcmVerboseMacro( "Entry HT empty for file: "<SetPrintLevel(PrintLevel); - MetaElems->Print(os); - } - for(ListDicomDirPatient::iterator cc = Patients.begin(); - cc != Patients.end(); - ++cc) + 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 + + SetFileName( fileName ); + if (!ParseDir) { - (*cc)->SetPrintLevel(PrintLevel); - (*cc)->Print(os); + if ( ! this->Document::Load( ) ) + return false; } + return DoTheLoadingJob( ); +} + +/** + * \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() ) + { + return false; + } + if (!Document::Load() ) + { + return false; + } + + if ( GetFirstEntry() == 0 ) // when user passed a Directory to parse + { + gdcmWarningMacro( "Entry HT empty for file: "<< GetFileName()); + return false; + } + // Directory record sequence + DocEntry *e = GetDocEntry(0x0004, 0x1220); + if ( !e ) + { + gdcmWarningMacro( "NO 'Directory record sequence' (0x0004,0x1220)" + << " in file " << GetFileName()); + return false; + } + else + CreateDicomDir(); + } + else + { + // 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 @@ -190,25 +272,110 @@ void DicomDir::Print(std::ostream &os, std::string const & ) */ bool DicomDir::IsReadable() { - if( Filetype == Unknown) + if ( Filetype == Unknown ) { - gdcmVerboseMacro( "Wrong filetype"); + gdcmWarningMacro( "Wrong filetype"); return false; } - if( !MetaElems ) + if ( !MetaElems ) { - gdcmVerboseMacro( "Meta Elements missing in DicomDir"); + gdcmWarningMacro( "Meta Elements missing in DicomDir"); return false; } - if( Patients.size() <= 0 ) + if ( Patients.size() <= 0 ) { - gdcmVerboseMacro( "NO Patient in DicomDir"); + gdcmWarningMacro( "NO Patient in DicomDir"); return false; } return true; } +/** + * \brief adds *the* Meta to a partially created DICOMDIR + */ +DicomDirMeta *DicomDir::NewMeta() +{ + if ( MetaElems ) + delete MetaElems; + + DocEntry *entry = GetFirstEntry(); + if ( entry ) + { + MetaElems = new DicomDirMeta(true); // true = empty + + 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); // false = not empty + } + 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() +{ + DicomDirPatient *p = new DicomDirPatient(); + AddPatientToEnd( p ); + return p; +} + +/** + * \brief Remove all Patients + */ +void DicomDir::ClearPatient() +{ + for(ListDicomDirPatient::iterator cc = Patients.begin(); + cc!= Patients.end(); + ++cc) + { + delete *cc; + } + Patients.clear(); +} + +/** + * \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; +} + /** * \brief fills the whole structure, starting from a root Directory */ @@ -229,7 +396,7 @@ void DicomDir::ParseDirectory() void DicomDir::SetStartMethod( DicomDir::Method *method, void *arg, DicomDir::Method *argDelete ) { - if( StartArg && StartMethodArgDelete ) + if ( StartArg && StartMethodArgDelete ) { StartMethodArgDelete( StartArg ); } @@ -239,16 +406,6 @@ void DicomDir::SetStartMethod( DicomDir::Method *method, void *arg, StartMethodArgDelete = argDelete; } -/** - * \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 progress method to call when the parsing of the @@ -261,7 +418,7 @@ void DicomDir::SetStartMethodArgDelete( DicomDir::Method *method ) void DicomDir::SetProgressMethod( DicomDir::Method *method, void *arg, DicomDir::Method *argDelete ) { - if( ProgressArg && ProgressMethodArgDelete ) + if ( ProgressArg && ProgressMethodArgDelete ) { ProgressMethodArgDelete( ProgressArg ); } @@ -271,17 +428,6 @@ void DicomDir::SetProgressMethod( DicomDir::Method *method, void *arg, ProgressMethodArgDelete = argDelete; } -/** - * \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 end method to call when the parsing of the directory ends * @param method Method to call @@ -292,7 +438,7 @@ void DicomDir::SetProgressMethodArgDelete( DicomDir::Method *method ) void DicomDir::SetEndMethod( DicomDir::Method *method, void *arg, DicomDir::Method *argDelete ) { - if( EndArg && EndMethodArgDelete ) + if ( EndArg && EndMethodArgDelete ) { EndMethodArgDelete( EndArg ); } @@ -304,50 +450,41 @@ void DicomDir::SetEndMethod( DicomDir::Method *method, void *arg, /** * \brief Set the method to delete the argument - * The argument is destroyed when the method is changed or when - * the class is destroyed + * 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::SetStartMethodArgDelete( DicomDir::Method *method ) { - EndMethodArgDelete = method; + StartMethodArgDelete = method; } /** - * \brief Get the first entry while visiting the DicomDirPatients - * \return The first DicomDirPatient if found, otherwhise NULL - */ -DicomDirPatient *DicomDir::GetFirstPatient() + * \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 ) { - ItPatient = Patients.begin(); - if ( ItPatient != Patients.end() ) - return *ItPatient; - return NULL; + ProgressMethodArgDelete = method; } /** - * \brief Get the next entry while visiting the DicomDirPatients - * \note : meaningfull only if GetFirstEntry already called - * \return The next DicomDirPatient if found, otherwhise NULL + * \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 */ -DicomDirPatient *DicomDir::GetNextPatient() +void DicomDir::SetEndMethodArgDelete( DicomDir::Method *method ) { - gdcmAssertMacro (ItPatient != Patients.end()); - { - ++ItPatient; - if ( ItPatient != Patients.end() ) - return *ItPatient; - } - return NULL; + EndMethodArgDelete = 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 */ @@ -360,15 +497,15 @@ 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(); @@ -399,254 +536,110 @@ bool DicomDir::WriteDicomDir(std::string const &fileName) return true; } -//----------------------------------------------------------------------------- -// Protected - -/** - * \brief create a Document-like chained list from a root Directory - * @param path entry point of the tree-like structure - */ -void DicomDir::CreateDicomDirChainedList(std::string const & path) -{ - CallStartMethod(); - DirList dirList(path,1); // gets recursively the file list - unsigned int count = 0; - VectDocument list; - File *header; - - DirListType fileList = dirList.GetFilenames(); - - for( DirListType::iterator it = fileList.begin(); - it != fileList.end(); - ++it ) - { - Progress = (float)(count+1)/(float)fileList.size(); - CallProgressMethod(); - if( Abort ) - { - break; - } - - header = new File( it->c_str() ); - if( !header ) - { - gdcmVerboseMacro( "Failure in new gdcm::File " << it->c_str() ); - continue; - } - - if( header->IsReadable() ) - { - // Add the file to the chained list: - list.push_back(header); - gdcmVerboseMacro( "Readable " << it->c_str() ); - } - else - { - delete header; - } - count++; - } - // sorts Patient/Study/Serie/ - std::sort(list.begin(), list.end(), DicomDir::HeaderLessThan ); - - std::string tmp = dirList.GetDirName(); - //for each File of the chained list, add/update the Patient/Study/Serie/Image info - SetElements(tmp, list); - CallEndMethod(); - - for(VectDocument::iterator itDoc=list.begin(); - itDoc!=list.end(); - ++itDoc) - { - delete dynamic_cast(*itDoc); - } -} - /** - * \brief adds *the* Meta to a partially created DICOMDIR + * \brief Anonymize a DICOMDIR + * @return true */ - -DicomDirMeta * DicomDir::NewMeta() + +bool DicomDir::AnonymizeDicomDir() { - if( MetaElems ) - delete MetaElems; - - - if ( TagHT.begin() != TagHT.end() ) // after Document Parsing - { - MetaElems = new DicomDirMeta(true); - - 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; + 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) - { - MetaElems->AddEntry( cc->second ); - } - } - 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() -{ - DicomDirPatient *p = new DicomDirPatient(); - AddPatientToEnd( p ); - return p; -} - -/** - * \brief adds to the HTable - * the Entries (Dicom Elements) corresponding to the given type - * @param path full path file name (only used when type = GDCM_DICOMDIR_IMAGE - * @param type DicomDirObject type to create (GDCM_DICOMDIR_PATIENT, - * GDCM_DICOMDIR_STUDY, GDCM_DICOMDIR_SERIE ...) - * @param header Header of the current file - */ -void DicomDir::SetElement(std::string const &path, DicomDirType type, - Document *header) -{ - ListDicomDirElem elemList; //FIXME this is going to be a by copy operation - ListDicomDirElem::const_iterator it; - uint16_t tmpGr, tmpEl; - DictEntry *dictEntry; - ValEntry *entry; - std::string val; - SQItem *si; - - switch( type ) { - case GDCM_DICOMDIR_IMAGE: - elemList = Global::GetDicomDirElements()->GetDicomDirImageElements(); - si = new DicomDirImage(true); - if( !AddImageToEnd(static_cast(si)) ) - { - delete si; - gdcmErrorMacro( "Add ImageToEnd failed"); - } - break; - case GDCM_DICOMDIR_SERIE: - elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements(); - si = new DicomDirSerie(true); - if( !AddSerieToEnd(static_cast(si)) ) - { - delete si; - gdcmErrorMacro( "Add SerieToEnd failed"); - } - break; - case GDCM_DICOMDIR_STUDY: - elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements(); - si = new DicomDirStudy(true); - if( !AddStudyToEnd(static_cast(si)) ) - { - delete si; - gdcmErrorMacro( "Add StudyToEnd failed"); - } - break; - case GDCM_DICOMDIR_PATIENT: - elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements(); - si = new DicomDirPatient(true); - if( !AddPatientToEnd(static_cast(si)) ) - { - delete si; - gdcmErrorMacro( "Add PatientToEnd failed"); - } - break; - case GDCM_DICOMDIR_META: - elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements(); - si = new DicomDirMeta(true); - if( MetaElems ) - { - delete MetaElems; - gdcmErrorMacro( "MetaElements already exist, they will be destroyed"); - } - MetaElems = static_cast(si); - break; - default: - return; - } - // removed all the seems-to-be-useless stuff about Referenced Image Sequence - // to avoid further troubles - // imageElem 0008 1140 "" // Referenced Image Sequence - // imageElem fffe e000 "" // 'no length' item : length to be set to 0xffffffff later - // imageElem 0008 1150 "" // Referenced SOP Class UID : to be set/forged later - // imageElem 0008 1155 "" // Referenced SOP Instance UID : to be set/forged later - // imageElem fffe e00d "" // Item delimitation : length to be set to ZERO later - // for all the relevant elements found in their own spot of the DicomDir.dic - // FIXME : troubles found when it's a SeqEntry - - for( it = elemList.begin(); it != elemList.end(); ++it) - { - tmpGr = it->Group; - tmpEl = it->Elem; - dictEntry = GetPubDict()->GetDictEntry(tmpGr, tmpEl); - - entry = new ValEntry( dictEntry ); // Be sure it's never a BinEntry ! - - entry->SetOffset(0); // just to avoid further missprinting - - if( header ) + s << i; + v = (*cc)->GetValEntry(0x0010, 0x0010) ; // Patient's Name + if (v) { - // NULL when we Build Up (ex nihilo) a DICOMDIR - // or when we add the META elems - val = header->GetEntry(tmpGr, tmpEl); + v->SetValue(s.str()); } - else + + v = (*cc)->GetValEntry(0x0010, 0x0020) ; // Patient ID + if (v) { - val = GDCM_UNFOUND; + v->SetValue(" "); } - if( val == GDCM_UNFOUND) + v = (*cc)->GetValEntry(0x0010, 0x0030) ; // Patient's BirthDate + if (v) { - 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 ) - { - gdcmVerboseMacro( "The base path of file name is incorrect"); - val = header->GetFileName(); - } - else - { - val = &(header->GetFileName().c_str()[path.length()]); - } - } - else - { - val = it->Value; - } + v->SetValue(" "); } - else + s << ""; + i++; + } + return true; +} + +//----------------------------------------------------------------------------- +// Protected +/** + * \brief create a Document-like chained list from a root Directory + * @param path entry point of the tree-like structure + */ +void DicomDir::CreateDicomDirChainedList(std::string const &path) +{ + CallStartMethod(); + DirList dirList(path,1); // gets recursively the file list + unsigned int count = 0; + VectDocument list; + File *f; + + DirListType fileList = dirList.GetFilenames(); + + for( DirListType::iterator it = fileList.begin(); + it != fileList.end(); + ++it ) + { + Progress = (float)(count+1)/(float)fileList.size(); + CallProgressMethod(); + if ( Abort ) { - if ( header->GetEntryLength(tmpGr,tmpEl) == 0 ) - val = it->Value; + break; } - entry->SetValue( val ); // troubles expected when vr=SQ ... + f = new File( ); + f->SetLoadMode(LoadMode); // we allow user not to load Sequences... + f->Load( it->c_str() ); - if ( type == GDCM_DICOMDIR_META ) // fusible : should never print ! +// if ( !f ) +// { +// gdcmWarningMacro( "Failure in new gdcm::File " << it->c_str() ); +// continue; +// } + + if ( f->IsReadable() ) { - gdcmVerboseMacro("GDCM_DICOMDIR_META ?!? should never print that"); - } - si->AddEntry(entry); + // Add the file to the chained list: + list.push_back(f); + gdcmWarningMacro( "Readable " << it->c_str() ); + } + else + { + delete f; + } + count++; + } + // sorts Patient/Study/Serie/ + std::sort(list.begin(), list.end(), DicomDir::HeaderLessThan ); + + std::string tmp = dirList.GetDirName(); + //for each File of the chained list, add/update the Patient/Study/Serie/Image info + SetElements(tmp, list); + CallEndMethod(); + + for(VectDocument::iterator itDoc=list.begin(); + itDoc!=list.end(); + ++itDoc) + { + delete dynamic_cast(*itDoc); } } -//----------------------------------------------------------------------------- /** * \brief CallStartMethod */ @@ -654,32 +647,30 @@ void DicomDir::CallStartMethod() { Progress = 0.0f; Abort = false; - if( StartMethod ) + if ( StartMethod ) { StartMethod( StartArg ); } } -//----------------------------------------------------------------------------- /** * \brief CallProgressMethod */ void DicomDir::CallProgressMethod() { - if( ProgressMethod ) + if ( ProgressMethod ) { ProgressMethod( ProgressArg ); } } -//----------------------------------------------------------------------------- /** * \brief CallEndMethod */ void DicomDir::CallEndMethod() { Progress = 1.0f; - if( EndMethod ) + if ( EndMethod ) { EndMethod( EndArg ); } @@ -709,11 +700,11 @@ void DicomDir::Initialize() } /** - * \brief create a 'DicomDir' from a DICOMDIR Header + * \brief create a 'gdcm::DicomDir' from a DICOMDIR Header */ void DicomDir::CreateDicomDir() { - // The list is parsed. + // 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 @@ -725,22 +716,18 @@ void DicomDir::CreateDicomDir() DocEntry *e = GetDocEntry(0x0004, 0x1220); if ( !e ) { - gdcmVerboseMacro( "NO Directory record sequence (0x0004,0x1220)"); - /// \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( "No SeqEntry present"); - // useless : (0x0004,0x1220) IS a Sequence ! + gdcmWarningMacro( "Element (0004,1220) is not a Sequence ?!?"); return; } NewMeta(); - - //ListSQItem listItems = s->GetSQItems(); DocEntry *d; std::string v; @@ -756,63 +743,72 @@ 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(); } - TagHT.clear(); + ClearEntry(); } /** @@ -831,7 +827,7 @@ bool DicomDir::AddPatientToEnd(DicomDirPatient *dd) */ bool DicomDir::AddStudyToEnd(DicomDirStudy *dd) { - if( Patients.size() > 0 ) + if ( Patients.size() > 0 ) { ListDicomDirPatient::iterator itp = Patients.end(); itp--; @@ -847,25 +843,17 @@ 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; } -/* if( (*itp)->GetDicomDirStudies().size() > 0 ) - { - ListDicomDirStudy::const_iterator itst = - (*itp)->GetDicomDirStudies().end(); - itst--; - (*itst)->AddSerie(dd); - return true; - }*/ } return false; } @@ -876,48 +864,35 @@ 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; } } -/* 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)->AddImage(dd); - return true; - } - }*/ } return false; } /** - * \brief for each Header of the chained list, add/update the Patient/Study/Serie/Image info + * \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) +void DicomDir::SetElements(std::string const &path, VectDocument const &list) { - TagHT.clear(); - Patients.clear(); + ClearEntry(); + ClearPatient(); std::string patPrevName = "", patPrevID = ""; std::string studPrevInstanceUID = "", studPrevID = ""; @@ -929,36 +904,36 @@ 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)->GetEntry(0x0010,0x0010); - patCurID = (*it)->GetEntry(0x0010,0x0011); - studCurInstanceUID = (*it)->GetEntry(0x0020,0x000d); - studCurID = (*it)->GetEntry(0x0020,0x0010); - serCurInstanceUID = (*it)->GetEntry(0x0020,0x000e); - serCurID = (*it)->GetEntry(0x0020,0x0011); - - if( patCurName != patPrevName || patCurID != patPrevID || first ) + 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 + // 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 @@ -974,13 +949,155 @@ void DicomDir::SetElements(std::string const & path, VectDocument const &list) } } +/** + * \brief adds to the HTable + * the Entries (Dicom Elements) corresponding to the given type + * @param path full path file name (only used when type = GDCM_DICOMDIR_IMAGE + * @param type DicomDirObject type to create (GDCM_DICOMDIR_PATIENT, + * GDCM_DICOMDIR_STUDY, GDCM_DICOMDIR_SERIE ...) + * @param header Header of the current file + */ +void DicomDir::SetElement(std::string const &path, DicomDirType type, + Document *header) +{ + ListDicomDirElem elemList; + ListDicomDirElem::const_iterator it; + uint16_t tmpGr, tmpEl; + DictEntry *dictEntry; + ValEntry *entry; + std::string val; + SQItem *si; + + switch( type ) + { + case GDCM_DICOMDIR_IMAGE: + elemList = Global::GetDicomDirElements()->GetDicomDirImageElements(); + si = new DicomDirImage(true); + if ( !AddImageToEnd(static_cast(si)) ) + { + delete si; + gdcmErrorMacro( "Add ImageToEnd failed"); + } + break; + case GDCM_DICOMDIR_SERIE: + elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements(); + si = new DicomDirSerie(true); + if ( !AddSerieToEnd(static_cast(si)) ) + { + delete si; + gdcmErrorMacro( "Add SerieToEnd failed"); + } + break; + case GDCM_DICOMDIR_STUDY: + elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements(); + si = new DicomDirStudy(true); + if ( !AddStudyToEnd(static_cast(si)) ) + { + delete si; + gdcmErrorMacro( "Add StudyToEnd failed"); + } + break; + case GDCM_DICOMDIR_PATIENT: + elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements(); + si = new DicomDirPatient(true); + if ( !AddPatientToEnd(static_cast(si)) ) + { + delete si; + gdcmErrorMacro( "Add PatientToEnd failed"); + } + break; + case GDCM_DICOMDIR_META: + elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements(); + si = new DicomDirMeta(true); + if ( MetaElems ) + { + delete MetaElems; + gdcmErrorMacro( "MetaElements already exist, they will be destroyed"); + } + MetaElems = static_cast(si); + break; + default: + return; + } + // removed all the seems-to-be-useless stuff about Referenced Image Sequence + // to avoid further troubles + // imageElem 0008 1140 "" // Referenced Image Sequence + // imageElem fffe e000 "" // 'no length' item : length to be set to 0xffffffff later + // imageElem 0008 1150 "" // Referenced SOP Class UID : to be set/forged later + // imageElem 0008 1155 "" // Referenced SOP Instance UID : to be set/forged later + // imageElem fffe e00d "" // Item delimitation : length to be set to ZERO later + + // 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()->GetEntry(tmpGr, tmpEl); + + entry = new ValEntry( dictEntry ); // Be sure it's never a BinEntry ! + + entry->SetOffset(0); // just to avoid further missprinting + + if ( header ) + { + // NULL when we Build Up (ex nihilo) a DICOMDIR + // or when we add the META elems + val = header->GetEntryValue(tmpGr, tmpEl); + } + else + { + val = GDCM_UNFOUND; + } + + if ( val == GDCM_UNFOUND) + { + if ( tmpGr == 0x0004 && tmpEl == 0x1130 ) // File-set ID + { + // force to the *end* File Name + val = Util::GetName( path ); + } + else if ( tmpGr == 0x0004 && tmpEl == 0x1500 ) // Only used for image + { + if ( header->GetFileName().substr(0, path.length()) != path ) + { + gdcmWarningMacro( "The base path of file name is incorrect"); + val = header->GetFileName(); + } + else + { + val = &(header->GetFileName().c_str()[path.length()]); + } + } + else + { + val = it->Value; + } + } + else + { + if ( header->GetEntryLength(tmpGr,tmpEl) == 0 ) + val = it->Value; + } + + entry->SetValue( val ); // troubles expected when vr=SQ ... + + if ( type == GDCM_DICOMDIR_META ) // fusible : should never print ! + { + gdcmWarningMacro("GDCM_DICOMDIR_META ?!? should never print that"); + } + si->AddEntry(entry); + } +} + /** * \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::MoveSQItem(SQItem *dst,SQItem *src) +void DicomDir::MoveSQItem(DocEntrySet *dst,DocEntrySet *src) { DocEntry *entry; @@ -995,13 +1112,35 @@ void DicomDir::MoveSQItem(SQItem *dst,SQItem *src) } /** - * \brief compares two dgcmHeaders + * \brief compares two files */ bool DicomDir::HeaderLessThan(Document *header1, Document *header2) { return *header1 < *header2; } -} // end namespace gdcm +//----------------------------------------------------------------------------- +// Print +/** + * \brief Canonical Printer + * @param os ostream we want to print in + * @param indent Indentation string to be prepended during printing + */ +void DicomDir::Print(std::ostream &os, std::string const & ) +{ + if ( MetaElems ) + { + MetaElems->SetPrintLevel(PrintLevel); + MetaElems->Print(os); + } + for(ListDicomDirPatient::iterator cc = Patients.begin(); + cc != Patients.end(); + ++cc) + { + (*cc)->SetPrintLevel(PrintLevel); + (*cc)->Print(os); + } +} //----------------------------------------------------------------------------- +} // end namespace gdcm