X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDicomDir.cxx;h=9d44e72ffd059bf0158c9edb68b418f52b86796d;hb=80075429b6ab9db9e885b9bb9ae1427530c7bef8;hp=34f7025cf1dace136fe11e7a72a75abd66847923;hpb=8670efa6c3fc51c51fe71c2f62af2297a19b07e2;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index 34f7025c..9d44e72f 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDicomDir.cxx,v $ Language: C++ - Date: $Date: 2005/02/01 10:34:59 $ - Version: $Revision: 1.124 $ + Date: $Date: 2008/02/13 18:53:33 $ + Version: $Revision: 1.197 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -21,9 +21,12 @@ // 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 "gdcmDicomDirPrivate.h" #include "gdcmDicomDirPatient.h" #include "gdcmDicomDirMeta.h" #include "gdcmDicomDirElement.h" @@ -34,7 +37,8 @@ #include "gdcmFile.h" #include "gdcmSeqEntry.h" #include "gdcmSQItem.h" -#include "gdcmValEntry.h" +#include "gdcmDataEntry.h" +#include "gdcmCommandManager.h" #include #include @@ -51,7 +55,126 @@ # include #endif -namespace gdcm +#if defined(__BORLANDC__) + #include // for memset +#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 +// + +/* + +// see also : ftp://medical.nema.org/medical/dicom/final/cp343_ft.doc + +RELATIONSHIP BETWEEN DIRECTORY RECORDS + +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, 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, PRIVATE + +IMAGE PRIVATE +OVERLAY PRIVATE +MODALITY LUT PRIVATE +VOI LUT PRIVATE +CURVE PRIVATE +STORED PRINT PRIVATE +RT DOSE PRIVATE +RT STRUCTURE SET PRIVATE +RT PLAN PRIVATE +RT TREAT RECORD PRIVATE +PRESENTATION PRIVATE +WAVEFORM PRIVATE +SR DOCUMENT PRIVATE +KEY OBJECT DOC PRIVATE +SPECTROSCOPY PRIVATE +RAW DATA PRIVATE + +TOPIC STUDY, SERIES, 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, + PRIVATE + +VISIT PRIVATE + +RESULTS INTERPRETATION, PRIVATE + +INTERPRETATION PRIVATE +STUDY COMPONENT PRIVATE +PRIVATE PRIVATE, (any of the above as privately defined) +MRDR (Not applicable) + +Note : Directory Record Types PRINT QUEUE, FILM SESSION, FILM BOX, and + IMAGE BOX were previously defined in DICOM. They have been retired. + See PS 3.3-1998. +*/ + +// ---------------------- +// The current gdcm version only deals with : +// +// (Root directory Entity) PATIENT +// PATIENT STUDY +// STUDY SERIES +// STUDY VISIT +// SERIES IMAGE +// IMAGE / +// +// DicomDir::CreateDicomDir will have to be completed +// Treelike structure management will have to be upgraded +// ---------------------------------------------------------------------------- + +namespace GDCM_NAME_SPACE { //----------------------------------------------------------------------------- // Constructor / Destructor @@ -59,16 +182,17 @@ namespace gdcm * \brief Constructor : creates an empty DicomDir */ DicomDir::DicomDir() - :Document( ) { Initialize(); // sets all private fields to NULL + ParseDir = false; NewMeta(); } +//#ifndef GDCM_LEGACY_REMOVE /** * \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 @@ -76,84 +200,146 @@ DicomDir::DicomDir() * and wants to explore recursively the directories * - false if user passed an already built DICOMDIR file * and wants to use it + * @deprecated use : new DicomDir() + [ SetLoadMode(lm) + ] SetDirectoryName(name) + * or : new DicomDir() + SetFileName(name) */ + /* 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) + // (nothing is checked in Document constructor, to avoid overhead) - Initialize(); // sets all private fields to NULL + ParseDir = parseDir; + SetLoadMode (LD_ALL); // concerns only dicom files + SetFileName( fileName ); + Load( ); +} +*/ +//#endif + +/** + * \brief Canonical destructor + */ +DicomDir::~DicomDir() +{ + ClearPatient(); + if ( MetaElems ) + { + MetaElems->Delete(); + } +} - // if user passed a root directory, sure we didn't get anything +//----------------------------------------------------------------------------- +// Public - if ( GetFirstEntry() == 0 ) // when user passed a Directory to parse +/** + * \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 (!parseDir) - gdcmVerboseMacro( "Entry HT empty for file: "<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 ) +{ + // We should clean out anything that already exists. + Initialize(); // sets all private fields to NULL - // Only if user passed a root directory - // ------------------------------------ - if ( fileName == "." ) - { - // 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 - } + SetFileName( fileName ); + if (!ParseDir) + { + if ( ! this->Document::Load( ) ) + return false; + } + return DoTheLoadingJob( ); +} +*/ +//#endif - if ( parseDir ) // user asked for a recursive parsing of a root directory - { - NewMeta(); +/** + * \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; - gdcmVerboseMacro( "Parse directory and create the DicomDir"); - ParseDirectory(); + if (!ParseDir) + { + // Only if user passed a DICOMDIR + // ------------------------------ + Fp = 0; + if (!Document::Load() ) + { + 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 ) { - gdcmVerboseMacro( "NO 'Directory record sequence' (0x0004,0x1220)" - << " in file " << fileName); - /// \todo FIXME : what do we do when the parsed file IS NOT a - /// DICOMDIR file ? + gdcmWarningMacro( "NO 'Directory record sequence' (0x0004,0x1220)" + << " 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 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(); + gdcmDebugMacro( "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 @@ -164,19 +350,19 @@ DicomDir::~DicomDir() */ bool DicomDir::IsReadable() { - if( Filetype == Unknown) + if ( Filetype == Unknown ) { - gdcmVerboseMacro( "Wrong filetype"); + gdcmErrorMacro( "Wrong filetype for " << GetFileName()); 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; } @@ -184,107 +370,62 @@ bool DicomDir::IsReadable() } /** - * \brief fills the whole structure, starting from a root Directory - */ -void DicomDir::ParseDirectory() -{ - CreateDicomDirChainedList( GetFileName() ); - CreateDicomDir(); -} - -/** - * \brief Set the start method to call when the parsing of the - * directory starts. - * @param method Method to call - * @param arg Argument to pass to the method - * @param argDelete Argument - * \warning In python : the arg parameter isn't considered - */ -void DicomDir::SetStartMethod( DicomDir::Method *method, void *arg, - DicomDir::Method *argDelete ) + * \brief adds *the* Meta to a partially created DICOMDIR + */ +DicomDirMeta *DicomDir::NewMeta() { - if( StartArg && StartMethodArgDelete ) + if ( MetaElems ) { - StartMethodArgDelete( StartArg ); + MetaElems->Delete(); } + DocEntry *entry = GetFirstEntry(); + if ( entry ) + { + MetaElems = DicomDirMeta::New(true); // true = empty - StartMethod = method; - StartArg = arg; - StartMethodArgDelete = argDelete; -} + entry = GetFirstEntry(); + while( entry ) + { + if ( dynamic_cast(entry) ) + break; -/** - * \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; -} + MetaElems->AddEntry(entry); + RemoveEntry(entry); -/** - * \brief Set the progress method to call when the parsing of the - * directory progress - * @param method Method to call - * @param arg Argument to pass to the method - * @param argDelete Argument - * \warning In python : the arg parameter isn't considered - */ -void DicomDir::SetProgressMethod( DicomDir::Method *method, void *arg, - DicomDir::Method *argDelete ) -{ - if( ProgressArg && ProgressMethodArgDelete ) + entry = GetFirstEntry(); + } + } + else // after root directory parsing { - ProgressMethodArgDelete( ProgressArg ); + MetaElems = DicomDirMeta::New(false); // false = not empty } - - ProgressMethod = method; - ProgressArg = arg; - ProgressMethodArgDelete = argDelete; + MetaElems->SetSQItemNumber(0); // To avoid further missprinting + return MetaElems; } /** - * \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 + * \brief adds a new Patient (with the basic elements) to a partially created + * DICOMDIR */ -void DicomDir::SetProgressMethodArgDelete( DicomDir::Method *method ) +DicomDirPatient *DicomDir::NewPatient() { - ProgressMethodArgDelete = method; + DicomDirPatient *dd = DicomDirPatient::New(); + AddPatientToEnd( dd ); + return dd; } /** - * \brief Set the end method to call when the parsing of the directory ends - * @param method Method to call - * @param arg Argument to pass to the method - * @param argDelete Argument - * \warning In python : the arg parameter isn't considered + * \brief Remove all Patients */ -void DicomDir::SetEndMethod( DicomDir::Method *method, void *arg, - DicomDir::Method *argDelete ) +void DicomDir::ClearPatient() { - if( EndArg && EndMethodArgDelete ) + for(ListDicomDirPatient::iterator cc = Patients.begin(); + cc!= Patients.end(); + ++cc) { - EndMethodArgDelete( EndArg ); + (*cc)->Unregister(); } - - EndMethod = method; - EndArg = arg; - EndMethodArgDelete = 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::SetEndMethodArgDelete( DicomDir::Method *method ) -{ - EndMethodArgDelete = method; + Patients.clear(); } /** @@ -314,41 +455,47 @@ DicomDirPatient *DicomDir::GetNextPatient() return NULL; } +/** + * \brief fills the whole structure, starting from a root Directory + */ +void DicomDir::ParseDirectory() +{ + CreateDicomDirChainedList( GetFileName() ); + CreateDicomDir(); +} + /** * \brief writes on disc a DICOMDIR * \ warning does NOT add the missing elements in the header : * it's up to the user doing it ! - * \todo : to be re-written using the DICOMDIR tree-like structure - * *not* the chained list - * (does NOT exist if the DICOMDIR is user-forged !) * @param fileName file to be written to * @return false only when fail to open */ -bool DicomDir::WriteDicomDir(std::string const &fileName) +bool DicomDir::Write(std::string const &fileName) { int i; - uint16_t sq[4] = { 0x0004, 0x1220, 0xffff, 0xffff }; - uint16_t sqt[4]= { 0xfffe, 0xe0dd, 0xffff, 0xffff }; + uint16_t sq[6] = { 0x0004, 0x1220, 0x5153, 0x0000, 0xffff, 0xffff }; + uint16_t sqt[4]= { 0xfffe, 0xe0dd, 0x0000, 0x0000 }; 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(); - ptrMeta->WriteContent(fp, ExplicitVR); + ptrMeta->WriteContent(fp, ExplicitVR, true, false); // 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]); } @@ -357,13 +504,13 @@ bool DicomDir::WriteDicomDir(std::string const &fileName) cc != Patients.end(); ++cc ) { - (*cc)->WriteContent( fp, ExplicitVR ); + (*cc)->WriteContent( fp, ExplicitVR, false, true ); } // force writing Sequence Delimitation Item for(i=0;i<4;++i) { - binary_write(*fp, sqt[i]); // fffe e0dd ffff ffff + binary_write(*fp, sqt[i]); // fffe e0dd 0000 0000 } fp->close(); @@ -372,49 +519,114 @@ bool DicomDir::WriteDicomDir(std::string const &fileName) return true; } +/** + * \brief Anonymize a DICOMDIR + * @return true + */ + +bool DicomDir::Anonymize() +{ + DataEntry *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)->GetDataEntry(0x0010, 0x0010) ; // Patient's Name + if (v) + { + v->SetString(s.str()); + } + + v = (*cc)->GetDataEntry(0x0010, 0x0020) ; // Patient ID + if (v) + { + v->SetString(" "); + } + + v = (*cc)->GetDataEntry(0x0010, 0x0030) ; // Patient's BirthDate + if (v) + { + v->SetString(" "); + } + s << ""; + i++; + } + return true; +} + +/** + * \brief Copies all the attributes from an other DocEntrySet + * @param set entry to copy from + * @remarks The contained DocEntries are not copied, only referenced + */ +void DicomDir::Copy(DocEntrySet *set) +{ + // Remove all previous childs + ClearPatient(); + + Document::Copy(set); + + DicomDir *dd = dynamic_cast(set); + if( dd ) + { + if(MetaElems) + MetaElems->Unregister(); + MetaElems = dd->MetaElems; + if(MetaElems) + MetaElems->Register(); + + Patients = dd->Patients; + for(ItPatient = Patients.begin();ItPatient != Patients.end();++ItPatient) + (*ItPatient)->Register(); + } +} + //----------------------------------------------------------------------------- // 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) +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; + File *f; DirListType fileList = dirList.GetFilenames(); - + unsigned int nbFile = fileList.size(); for( DirListType::iterator it = fileList.begin(); it != fileList.end(); ++it ) { - Progress = (float)(count+1)/(float)fileList.size(); + Progress = (float)(count+1)/(float)nbFile; CallProgressMethod(); - if( Abort ) + if ( Abort ) { break; } - header = new File( it->c_str() ); - if( !header ) - { - gdcmVerboseMacro( "Failure in new gdcm::File " << it->c_str() ); - continue; - } - - if( header->IsReadable() ) + 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->IsReadable() ) { // Add the file to the chained list: - list.push_back(header); - gdcmVerboseMacro( "Readable " << it->c_str() ); + list.push_back(f); + gdcmDebugMacro( "Readable " << it->c_str() ); } else { - delete header; + f->Delete(); } count++; } @@ -430,244 +642,10 @@ void DicomDir::CreateDicomDirChainedList(std::string const & path) itDoc!=list.end(); ++itDoc) { - delete dynamic_cast(*itDoc); + dynamic_cast(*itDoc)->Delete(); } } -/** - * \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); - - entry = GetFirstEntry(); - while( entry ) - { - if( dynamic_cast(entry) ) - break; - - RemoveEntryNoDestroy(entry); - MetaElems->AddEntry(entry); - - entry = GetFirstEntry(); - } - } - else // after root directory parsing - { - MetaElems = new DicomDirMeta(false); - } - MetaElems->SetSQItemNumber(0); // To avoid further missprinting - return MetaElems; -} - -/** - * \brief adds a new Patient (with the basic elements) to a partially created - * DICOMDIR - */ -DicomDirPatient *DicomDir::NewPatient() -{ - 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 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()->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 ) - { - gdcmVerboseMacro( "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 ! - { - gdcmVerboseMacro("GDCM_DICOMDIR_META ?!? should never print that"); - } - si->AddEntry(entry); - } -} - -/** - * \brief CallStartMethod - */ -void DicomDir::CallStartMethod() -{ - Progress = 0.0f; - Abort = false; - if( StartMethod ) - { - StartMethod( StartArg ); - } -} - -/** - * \brief CallProgressMethod - */ -void DicomDir::CallProgressMethod() -{ - if( ProgressMethod ) - { - ProgressMethod( ProgressArg ); - } -} - -/** - * \brief CallEndMethod - */ -void DicomDir::CallEndMethod() -{ - Progress = 1.0f; - if( EndMethod ) - { - EndMethod( EndArg ); - } -} //----------------------------------------------------------------------------- // Private @@ -676,16 +654,6 @@ void DicomDir::CallEndMethod() */ void DicomDir::Initialize() { - StartMethod = NULL; - ProgressMethod = NULL; - EndMethod = NULL; - StartMethodArgDelete = NULL; - ProgressMethodArgDelete = NULL; - EndMethodArgDelete = NULL; - StartArg = NULL; - ProgressArg = NULL; - EndArg = NULL; - Progress = 0.0; Abort = false; @@ -693,31 +661,32 @@ void DicomDir::Initialize() } /** - * \brief create a 'DicomDir' from a DICOMDIR Header + * \brief create a 'gdcm::DicomDir' from a DICOMDIR Header */ void DicomDir::CreateDicomDir() { // The SeqEntries of "Directory Record Sequence" are parsed. // When a DicomDir tag ("PATIENT", "STUDY", "SERIE", "IMAGE") is found : + // N.B. : VISIT, PRIVATE not fully dealt with // 1 - we save the beginning iterator // 2 - we continue to parse // 3 - we find an other tag // + we create the object for the precedent tag // + loop to 1 - + gdcmDebugMacro("Create DicomDir"); // Directory record sequence 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; } @@ -731,64 +700,100 @@ 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 { - gdcmVerboseMacro( "Not a ValEntry."); + gdcmWarningMacro( "(0004,1430) not a DataEntry ?!?"); 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 perform the tests + + if ( v == "IMAGE " ) { - si = new DicomDirPatient(true); - if( !AddPatientToEnd( static_cast(si)) ) + si = DicomDirImage::New(true); // true = empty + if ( !AddImageToEnd( static_cast(si)) ) { - delete si; + si->Delete(); 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 = DicomDirSerie::New(true); // true = empty + if ( !AddSerieToEnd( static_cast(si)) ) { - delete si; + si->Delete(); si = NULL; - gdcmErrorMacro( "Add AddStudyToEnd failed"); + gdcmErrorMacro( "Add AddSerieToEnd failed"); } } - else if( v == "SERIES" ) + else if ( v == "VISIT " ) { - si = new DicomDirSerie(true); - if( !AddSerieToEnd( static_cast(si)) ) + si = DicomDirVisit::New(true); // true = empty + if ( !AddVisitToEnd( static_cast(si)) ) { - delete si; + si->Delete(); si = NULL; - gdcmErrorMacro( "Add AddSerieToEnd failed"); + gdcmErrorMacro( "Add AddVisitToEnd failed"); } } - else if( v == "IMAGE " ) + else if ( v == "STUDY " ) { - si = new DicomDirImage(true); - if( !AddImageToEnd( static_cast(si)) ) + si = DicomDirStudy::New(true); // true = empty + if ( !AddStudyToEnd( static_cast(si)) ) { - delete si; + si->Delete(); si = NULL; - gdcmErrorMacro( "Add AddImageToEnd failed"); + gdcmErrorMacro( "Add AddStudyToEnd failed"); + } + } + else if ( v == "PATIENT " ) + { + si = DicomDirPatient::New(true); // true = empty + if ( !AddPatientToEnd( static_cast(si)) ) + { + si->Delete(); + si = NULL; + gdcmErrorMacro( "Add PatientToEnd failed"); } } + /// \todo : deal with PRIVATE (not so easy, since PRIVATE appears + /// at different levels ?!? ) + + else if ( v == "PRIVATE " ) // for SIEMENS 'CSA Non Image' + { + + gdcmWarningMacro( " -------------------------------------------" + << "a PRIVATE SQItem was found : " << v); + si = DicomDirPrivate::New(true); // true = empty + if ( !AddPrivateToEnd( static_cast(si)) ) + { + si->Delete(); + si = NULL; + gdcmErrorMacro( "Add PrivateToEnd 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 /VISIT/PRIVATE SQItem was found : " + << v); + + // FIXME : deal with other item types ! + tmpSI=s->GetNextSQItem(); // To avoid infinite loop + continue; } - if( si ) - MoveSQItem(si,tmpSI); + if ( si ) + si->Copy(tmpSI); tmpSI=s->GetNextSQItem(); } @@ -811,7 +816,7 @@ bool DicomDir::AddPatientToEnd(DicomDirPatient *dd) */ bool DicomDir::AddStudyToEnd(DicomDirStudy *dd) { - if( Patients.size() > 0 ) + if ( Patients.size() > 0 ) { ListDicomDirPatient::iterator itp = Patients.end(); itp--; @@ -827,13 +832,13 @@ 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; @@ -842,22 +847,42 @@ 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 */ 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; @@ -868,11 +893,38 @@ bool DicomDir::AddImageToEnd(DicomDirImage *dd) } /** - * \brief for each Header of the chained list, add/update the Patient/Study/Serie/Image info + * \brief AddPrivateToEnd + * @param dd SQ Item to enqueue to the DicomDirPrivate chained List + * (checked for SIEMENS 'CSA non image') + */ +bool DicomDir::AddPrivateToEnd(DicomDirPrivate *dd) +{ + if ( Patients.size() > 0 ) + { + ListDicomDirPatient::iterator itp = Patients.end(); + itp--; + + DicomDirStudy *study = (*itp)->GetLastStudy(); + if ( study ) + { + DicomDirSerie *serie = study->GetLastSerie(); + if ( serie ) + { + serie->AddPrivate(dd); + return true; + } + } + } + return false; +} + +/** + * \brief for each Header of the chained list, + * add/update the Patient/Study/Serie/Image info * @param path path of the root directory * @param list chained list of Headers */ -void DicomDir::SetElements(std::string const & path, VectDocument const &list) +void DicomDir::SetElements(std::string const &path, VectDocument const &list) { ClearEntry(); ClearPatient(); @@ -887,36 +939,36 @@ 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)->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 ) + 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 ) { 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 @@ -932,21 +984,219 @@ 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; + DataEntry *entry; + std::string val; + SQItem *si; + switch( type ) + { + case GDCM_DICOMDIR_IMAGE: + elemList = Global::GetDicomDirElements()->GetDicomDirImageElements(); + si = DicomDirImage::New(true); + if ( !AddImageToEnd(static_cast(si)) ) + { + si->Delete(); + gdcmErrorMacro( "Add ImageToEnd failed"); + } + break; + case GDCM_DICOMDIR_SERIE: + elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements(); + si = DicomDirSerie::New(true); + if ( !AddSerieToEnd(static_cast(si)) ) + { + si->Delete(); + gdcmErrorMacro( "Add SerieToEnd failed"); + } + break; + case GDCM_DICOMDIR_STUDY: + elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements(); + si = DicomDirStudy::New(true); + if ( !AddStudyToEnd(static_cast(si)) ) + { + si->Delete(); + gdcmErrorMacro( "Add StudyToEnd failed"); + } + break; + case GDCM_DICOMDIR_PATIENT: + elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements(); + si = DicomDirPatient::New(true); + if ( !AddPatientToEnd(static_cast(si)) ) + { + si->Delete(); + gdcmErrorMacro( "Add PatientToEnd failed"); + } + break; + case GDCM_DICOMDIR_META: // never used ?!? --> Done within DoTheLoadingJob + if ( MetaElems ) + { + MetaElems->Delete(); + gdcmErrorMacro( "MetaElements already exist, they will be destroyed"); + } + 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 + // 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 + + 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) + { + tmpGr = it->Group; + tmpEl = it->Elem; + + entry = DataEntry::New(tmpGr, tmpEl, it->VR); // dicomelements file was modified, to store VR + 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->GetEntryString(tmpGr, tmpEl); + } + else + { + val = GDCM_UNFOUND; + } + + if ( val == GDCM_UNFOUND) + { + if ( tmpGr == 0x0004 ) // never present in File ! + { + 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 + { + // avoid the first '/' in File name ! + if ( header->GetFileName().c_str()[path.length()] + == GDCM_FILESEPARATOR ) + val = &(header->GetFileName().c_str()[path.length()+1]); + else + val = &(header->GetFileName().c_str()[path.length()]); + } + 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 + { + // If the entry is not found in the Header, don't write its 'value' in the DICOMDIR ! + entry->Delete(); + continue; + } + } + else + { + if ( header->GetEntryLength(tmpGr,tmpEl) == 0 ) + { + val = it->Value; + // Don't polute the DICOMDIR with empty fields + if (val == "") + { + entry->Delete(); + continue; + } + } + } + +/* 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 ! + { + gdcmDebugMacro("GDCM_DICOMDIR_META ?!? should never print that"); + } + + si->AddEntry(entry); + entry->Delete(); + } +} + /** * \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(DocEntrySet *dst,DocEntrySet *src) -{ +void DicomDir::MoveSQItem(DocEntrySet *dst, DocEntrySet *src) +{ DocEntry *entry; - +// todo : rewrite the whole stuff, without using RemoveEntry an AddEntry, +// to save time entry = src->GetFirstEntry(); while(entry) { - src->RemoveEntryNoDestroy(entry); - dst->AddEntry(entry); + dst->AddEntry(entry); // use it, *before* removing it! + src->RemoveEntry(entry); // we destroyed -> the current iterator is not longer valid entry = src->GetFirstEntry(); } @@ -969,7 +1219,7 @@ 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);