X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDicomDir.cxx;h=f1fd2561784fa24e016817f60594168d37a82ffc;hb=35ee8ee8af32946514713d271177df8bb2298eb2;hp=1a47080925328ad312a6fd473843c6a7315c4d0f;hpb=5ac625c72835828d687ebdef878691d0913ae41b;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index 1a470809..f1fd2561 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDicomDir.cxx,v $ Language: C++ - Date: $Date: 2005/11/29 12:48:45 $ - Version: $Revision: 1.176 $ + Date: $Date: 2010/04/09 15:23:40 $ + Version: $Revision: 1.198 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -26,6 +26,7 @@ #include "gdcmDicomDirSerie.h" #include "gdcmDicomDirVisit.h" #include "gdcmDicomDirImage.h" +#include "gdcmDicomDirPrivate.h" #include "gdcmDicomDirPatient.h" #include "gdcmDicomDirMeta.h" #include "gdcmDicomDirElement.h" @@ -53,6 +54,11 @@ #else # include #endif + +#if defined(__BORLANDC__) + #include // for memset +#endif + // ---------------------------------------------------------------------------- // Note for future developpers // ---------------------------------------------------------------------------- @@ -96,6 +102,64 @@ // 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 : // @@ -110,7 +174,7 @@ // Treelike structure management will have to be upgraded // ---------------------------------------------------------------------------- -namespace gdcm +namespace GDCM_NAME_SPACE { //----------------------------------------------------------------------------- // Constructor / Destructor @@ -124,6 +188,38 @@ DicomDir::DicomDir() 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 + * - of the root directory (parseDir = true) + * - of the DICOMDIR (parseDir = false) + * @param parseDir boolean + * - true if user passed an entry point + * and wants to explore recursively the directories + * - false if user passed an already built DICOMDIR file + * and wants to use it + * @deprecated use : new DicomDir() + [ SetLoadMode(lm) + ] SetDirectoryName(name) + * or : new DicomDir() + SetFileName(name) + */ + /* +DicomDir::DicomDir(std::string const &fileName, bool parseDir ): + Document( ) +{ + // At this step, Document constructor is already executed, + // whatever user passed (either a root directory or a DICOMDIR) + // and whatever the value of parseDir was. + // (nothing is checked in Document constructor, to avoid overhead) + + ParseDir = parseDir; + SetLoadMode (LD_ALL); // concerns only dicom files + SetFileName( fileName ); + Load( ); +} +*/ +//#endif + /** * \brief Canonical destructor */ @@ -154,6 +250,30 @@ bool DicomDir::Load( ) } 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 + + SetFileName( fileName ); + if (!ParseDir) + { + if ( ! this->Document::Load( ) ) + return false; + } + return DoTheLoadingJob( ); +} +*/ +//#endif /** * \brief Does the Loading Job (internal use only) @@ -189,7 +309,9 @@ bool DicomDir::DoTheLoadingJob( ) return false; } else + { CreateDicomDir(); + } } else { @@ -202,13 +324,13 @@ bool DicomDir::DoTheLoadingJob( ) char buf[2048]; const char *cwd = getcwd(buf, 2048); if( cwd ) - { - SetFileName( buf ); // will be converted into a string - } + { + SetFileName( buf ); // will be converted into a string + } else - { - gdcmErrorMacro( "Path was too long to fit on 2048 bytes" ); - } + { + gdcmErrorMacro( "Path was too long to fit on 2048 bytes" ); + } } NewMeta(); gdcmDebugMacro( "Parse directory and create the DicomDir : " @@ -253,8 +375,9 @@ bool DicomDir::IsReadable() DicomDirMeta *DicomDir::NewMeta() { if ( MetaElems ) + { MetaElems->Delete(); - + } DocEntry *entry = GetFirstEntry(); if ( entry ) { @@ -353,11 +476,11 @@ bool DicomDir::Write(std::string const &fileName) { int i; uint16_t sq[6] = { 0x0004, 0x1220, 0x5153, 0x0000, 0xffff, 0xffff }; - uint16_t sqt[4]= { 0xfffe, 0xe0dd, 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 ) { gdcmWarningMacro("Failed to open(write) File: " << fileName.c_str()); return false; @@ -369,7 +492,7 @@ bool DicomDir::Write(std::string const &fileName) 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<6;++i) @@ -381,13 +504,13 @@ bool DicomDir::Write(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(); @@ -438,7 +561,7 @@ bool DicomDir::Anonymize() /** * \brief Copies all the attributes from an other DocEntrySet * @param set entry to copy from - * @remarks The contained DocEntries a not copied, only referenced + * @remarks The contained DocEntries are not copied, only referenced */ void DicomDir::Copy(DocEntrySet *set) { @@ -477,12 +600,12 @@ void DicomDir::CreateDicomDirChainedList(std::string const &path) 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 ) { @@ -523,32 +646,6 @@ void DicomDir::CreateDicomDirChainedList(std::string const &path) } } -/** - * \brief CallStartMethod - */ -void DicomDir::CallStartMethod() -{ - Progress = 0.0f; - Abort = false; - CommandManager::ExecuteCommand(this,CMD_STARTPROGRESS); -} - -/** - * \brief CallProgressMethod - */ -void DicomDir::CallProgressMethod() -{ - CommandManager::ExecuteCommand(this,CMD_PROGRESS); -} - -/** - * \brief CallEndMethod - */ -void DicomDir::CallEndMethod() -{ - Progress = 1.0f; - CommandManager::ExecuteCommand(this,CMD_ENDPROGRESS); -} //----------------------------------------------------------------------------- // Private @@ -570,6 +667,7 @@ 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 @@ -614,11 +712,11 @@ void DicomDir::CreateDicomDir() // 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 + // This is the right order to perform the tests if ( v == "IMAGE " ) { - si = DicomDirImage::New(true); + si = DicomDirImage::New(true); // true = empty if ( !AddImageToEnd( static_cast(si)) ) { si->Delete(); @@ -628,7 +726,7 @@ void DicomDir::CreateDicomDir() } else if ( v == "SERIES" ) { - si = DicomDirSerie::New(true); + si = DicomDirSerie::New(true); // true = empty if ( !AddSerieToEnd( static_cast(si)) ) { si->Delete(); @@ -638,7 +736,7 @@ void DicomDir::CreateDicomDir() } else if ( v == "VISIT " ) { - si = DicomDirVisit::New(true); + si = DicomDirVisit::New(true); // true = empty if ( !AddVisitToEnd( static_cast(si)) ) { si->Delete(); @@ -648,7 +746,7 @@ void DicomDir::CreateDicomDir() } else if ( v == "STUDY " ) { - si = DicomDirStudy::New(true); + si = DicomDirStudy::New(true); // true = empty if ( !AddStudyToEnd( static_cast(si)) ) { si->Delete(); @@ -658,7 +756,7 @@ void DicomDir::CreateDicomDir() } else if ( v == "PATIENT " ) { - si = DicomDirPatient::New(true); + si = DicomDirPatient::New(true); // true = empty if ( !AddPatientToEnd( static_cast(si)) ) { si->Delete(); @@ -666,12 +764,28 @@ void DicomDir::CreateDicomDir() 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 neither a 'PATIENT', nor a 'STUDY', nor a 'SERIE', // nor an 'IMAGE' SQItem. Skip to next item. - gdcmDebugMacro( " -------------------------------------------" - << "a non PATIENT/STUDY/SERIE/IMAGE SQItem was found : " + gdcmWarningMacro( " -------------------------------------------" + << "a non PATIENT/STUDY/SERIE/IMAGE /VISIT/PRIVATE SQItem was found : " << v); // FIXME : deal with other item types ! @@ -778,6 +892,32 @@ bool DicomDir::AddImageToEnd(DicomDirImage *dd) return false; } +/** + * \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 @@ -804,6 +944,8 @@ void DicomDir::SetElements(std::string const &path, VectDocument const &list) { // get the current file characteristics patCurName = (*it)->GetEntryString(0x0010,0x0010); + if (patCurName == "") // to prevent further troubles when wild anonymization was performed + patCurName = "gdcm^Patient"; patCurID = (*it)->GetEntryString(0x0010,0x0011); studCurInstanceUID = (*it)->GetEntryString(0x0020,0x000d); studCurID = (*it)->GetEntryString(0x0020,0x0010); @@ -858,11 +1000,10 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, ListDicomDirElem elemList; ListDicomDirElem::const_iterator it; uint16_t tmpGr, tmpEl; - DictEntry *dictEntry; + //DictEntry *dictEntry; DataEntry *entry; std::string val; SQItem *si; - switch( type ) { case GDCM_DICOMDIR_IMAGE: @@ -901,7 +1042,7 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, gdcmErrorMacro( "Add PatientToEnd failed"); } break; - case GDCM_DICOMDIR_META: + case GDCM_DICOMDIR_META: // never used ?!? --> Done within DoTheLoadingJob if ( MetaElems ) { MetaElems->Delete(); @@ -914,9 +1055,9 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, 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 @@ -931,17 +1072,15 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, { tmpGr = it->Group; tmpEl = it->Elem; - dictEntry = GetPubDict()->GetEntry(tmpGr, tmpEl); - - entry = DataEntry::New( dictEntry ); + + 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); + val = header->GetEntryString(tmpGr, tmpEl); } else { @@ -949,55 +1088,74 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, } 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 0x1130: // File-set ID + // force to the *end* File Name + val = Util::GetName( path ); + break; - case 0x1500: // Only used for image + 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(); + { + gdcmWarningMacro( "The base path of file name is incorrect"); + val = header->GetFileName(); } else - { - val = &(header->GetFileName().c_str()[path.length()+1]); + { + // 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; + break; - case 0x1510: // Referenced SOP Class UID in File - referencedVal = header->GetEntryString(0x0008, 0x0016); - // FIXME : probabely something to check - val = referencedVal; - 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 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; + 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; - } + 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'! @@ -1012,12 +1170,14 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, 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(); } @@ -1029,15 +1189,16 @@ void DicomDir::SetElement(std::string const &path, DicomDirType type, * @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) { + dst->AddEntry(entry); // use it, *before* removing it! src->RemoveEntry(entry); - dst->AddEntry(entry); // we destroyed -> the current iterator is not longer valid entry = src->GetFirstEntry(); }