X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDicomDir.cxx;h=22720bd8c572cac2c5f505df20ec02a473861de6;hb=df832cf7f90b4ca5aca2f628c1756fb276779fac;hp=cc37127647324718cc4c51cb92a37ee15b989dcd;hpb=4a07b1470f68d316f570fef1f07b9f9c77e90ee1;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index cc371276..22720bd8 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -1,487 +1,1237 @@ -// gdcmDicomDir.cxx +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmDicomDir.cxx,v $ + Language: C++ + Date: $Date: 2007/09/17 12:21:56 $ + Version: $Revision: 1.196 $ + + Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de + l'Image). All rights reserved. See Doc/License.txt or + http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details. + + This software is distributed WITHOUT ANY WARRANTY; without even + the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR + PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ + +//----------------------------------------------------------------------------- +// For full DICOMDIR description, see: +// PS 3.3-2003, pages 731-750 //----------------------------------------------------------------------------- #include "gdcmDicomDir.h" -#include "gdcmStudy.h" -#include "gdcmSerie.h" -#include "gdcmImage.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" #include "gdcmDirList.h" #include "gdcmUtil.h" +#include "gdcmDebug.h" +#include "gdcmGlobal.h" +#include "gdcmFile.h" +#include "gdcmSeqEntry.h" +#include "gdcmSQItem.h" +#include "gdcmDataEntry.h" +#include "gdcmCommandManager.h" +#include #include - +#include #include -#include +#ifdef _MSC_VER +# define getcwd _getcwd +#endif + +#if defined(_MSC_VER) || defined(__BORLANDC__) +# include +#else +# include +#endif + +#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 -/* - * \ingroup gdcmDicomDir - * \brief - * @param Filename - * @param exception_on_error +/** + * \brief Constructor : creates an empty DicomDir */ -gdcmDicomDir::gdcmDicomDir(const char *FileName, bool parseDir, - bool exception_on_error): - gdcmParser(FileName,exception_on_error,true) +DicomDir::DicomDir() { - if( GetListEntry().begin()==GetListEntry().end() ) + 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 + * - 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 + */ +DicomDir::~DicomDir() +{ + ClearPatient(); + if ( MetaElems ) { - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : entry list empty"); + MetaElems->Delete(); + } +} + +//----------------------------------------------------------------------------- +// Public - if(parseDir) +/** + * \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 ( ! this->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 + + SetFileName( fileName ); + if (!ParseDir) + { + if ( ! this->Document::Load( ) ) + return false; + } + return DoTheLoadingJob( ); +} +*/ +//#endif + +/** + * \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; + + if (!ParseDir) + { + // Only if user passed a DICOMDIR + // ------------------------------ + Fp = 0; + if (!Document::Load() ) { - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : Parse directory and create the DicomDir"); - ParseDirectory(); + 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 - CreateDicomDir(); + { + // 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; } -/* - * \ingroup gdcmDicomDir - * \brief - * @param exception_on_error +/** + * \brief This predicate, based on hopefully reasonable heuristics, + * decides whether or not the current document was properly parsed + * and contains the mandatory information for being considered as + * a well formed and usable DicomDir. + * @return true when Document is the one of a reasonable DicomDir, + * false otherwise. */ -/*gdcmDicomDir::gdcmDicomDir(ListTag *l, - bool exception_on_error): - gdcmParser(exception_on_error ) -{ - listEntries=*l; - CreateDicomDir(); -}*/ +bool DicomDir::IsReadable() +{ + if ( Filetype == Unknown ) + { + gdcmErrorMacro( "Wrong filetype for " << GetFileName()); + return false; + } + if ( !MetaElems ) + { + gdcmWarningMacro( "Meta Elements missing in DicomDir"); + return false; + } + if ( Patients.size() <= 0 ) + { + gdcmWarningMacro( "NO Patient in DicomDir"); + return false; + } -/* - * \ingroup gdcmDicomDir - * \brief Canonical destructor - */ -gdcmDicomDir::~gdcmDicomDir() + return true; +} + +/** + * \brief adds *the* Meta to a partially created DICOMDIR + */ +DicomDirMeta *DicomDir::NewMeta() { - for(ListPatient::iterator cc=patients.begin();cc!=patients.end();++cc) + if ( MetaElems ) + { + MetaElems->Delete(); + } + DocEntry *entry = GetFirstEntry(); + if ( entry ) + { + MetaElems = DicomDirMeta::New(true); // true = empty + + entry = GetFirstEntry(); + while( entry ) + { + if ( dynamic_cast(entry) ) + break; + + MetaElems->AddEntry(entry); + RemoveEntry(entry); + + entry = GetFirstEntry(); + } + } + else // after root directory parsing { - delete *cc; + MetaElems = DicomDirMeta::New(false); // false = not empty } + MetaElems->SetSQItemNumber(0); // To avoid further missprinting + return MetaElems; } -//----------------------------------------------------------------------------- -// Print -void gdcmDicomDir::Print(std::ostream &os) +/** + * \brief adds a new Patient (with the basic elements) to a partially created + * DICOMDIR + */ +DicomDirPatient *DicomDir::NewPatient() +{ + DicomDirPatient *dd = DicomDirPatient::New(); + AddPatientToEnd( dd ); + return dd; +} + +/** + * \brief Remove all Patients + */ +void DicomDir::ClearPatient() { - for(ListPatient::iterator cc=patients.begin();cc!=patients.end();++cc) + for(ListDicomDirPatient::iterator cc = Patients.begin(); + cc!= Patients.end(); + ++cc) { - (*cc)->SetPrintLevel(printLevel); - (*cc)->Print(os); + (*cc)->Unregister(); } + 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; } -//----------------------------------------------------------------------------- -// Public /** - * \ingroup gdcmDicomDir - * \brief writes on disc a DICOMDIR + * \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 ! + * it's up to the user doing it ! * @param fileName file to be written to - * @return + * @return false only when fail to open */ -bool gdcmDicomDir::Write(std::string fileName) -{ - FILE * fp1; + +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, 0x0000, 0x0000 }; - fp1=fopen(fileName.c_str(),"wb"); - if(fp1==NULL) + std::ofstream *fp = new std::ofstream(fileName.c_str(), + std::ios::out | std::ios::binary); + if ( !fp ) { - printf("Failed to open(write) File [%s] \n",fileName.c_str()); - return(false); + gdcmWarningMacro("Failed to open(write) File: " << fileName.c_str()); + return false; } - char * filePreamble; - filePreamble=(char*)calloc(128,1); - fwrite(filePreamble,128,1,fp1); - fwrite("DICM",4,1,fp1); - free(filePreamble); - - WriteEntries(fp1,DICOMDIR); + char filePreamble[128]; + memset(filePreamble, 0, 128); + fp->write(filePreamble, 128); + binary_write( *fp, "DICM"); + + DicomDirMeta *ptrMeta = GetMeta(); + ptrMeta->WriteContent(fp, ExplicitVR, true, false); + + // force writing 0004|1220 [SQ ], that CANNOT exist within DicomDirMeta + for(i=0;i<6;++i) + { + binary_write(*fp, sq[i]); + } + + for(ListDicomDirPatient::iterator cc = Patients.begin(); + cc != Patients.end(); + ++cc ) + { + (*cc)->WriteContent( fp, ExplicitVR, false, true ); + } + + // force writing Sequence Delimitation Item + for(i=0;i<4;++i) + { + binary_write(*fp, sqt[i]); // fffe e0dd 0000 0000 + } - fclose(fp1); + fp->close(); + delete fp; return true; } -void gdcmDicomDir::ParseDirectory(void) +/** + * \brief Anonymize a DICOMDIR + * @return true + */ + +bool DicomDir::Anonymize() { - NewDicomDir(GetPath()); - CreateDicomDir(); + 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; } -//----------------------------------------------------------------------------- -// Protected -/* - * \ingroup gdcmDicomDir - * \brief - * @param +/** + * \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 gdcmDicomDir::NewDicomDir(std::string path) +void DicomDir::Copy(DocEntrySet *set) { - gdcmDirList fileList(path,1); - ListHeader list; - gdcmHeader *header; + // Remove all previous childs + ClearPatient(); - listEntries.clear(); - patients.clear(); + Document::Copy(set); - for(gdcmDirList::iterator it=fileList.begin(); - it!=fileList.end(); ++it) + DicomDir *dd = dynamic_cast(set); + if( dd ) { -// std::cout<<*it<c_str()); - if(header->IsReadable()) - list.push_back(header); - else - delete header; - } + if(MetaElems) + MetaElems->Unregister(); + MetaElems = dd->MetaElems; + if(MetaElems) + MetaElems->Register(); - SetElements(path,list); + Patients = dd->Patients; + for(ItPatient = Patients.begin();ItPatient != Patients.end();++ItPatient) + (*ItPatient)->Register(); + } } -/* - * \ingroup gdcmDicomDir - * \brief Get the dicom dir path - * @param +//----------------------------------------------------------------------------- +// Protected +/** + * \brief create a Document-like chained list from a root Directory + * @param path entry point of the tree-like structure */ -std::string gdcmDicomDir::GetPath(void) +void DicomDir::CreateDicomDirChainedList(std::string const &path) { - std::string path=GetFileName(); + CallStartMethod(); + DirList dirList(path,1); // gets recursively the file list + unsigned int count = 0; + VectDocument list; + File *f; - int pos1=path.rfind("/"); - int pos2=path.rfind("\\"); - if(pos1>pos2) - path.resize(pos1); - else - path.resize(pos2); + DirListType fileList = dirList.GetFilenames(); + unsigned int nbFile = fileList.size(); + for( DirListType::iterator it = fileList.begin(); + it != fileList.end(); + ++it ) + { + Progress = (float)(count+1)/(float)nbFile; + CallProgressMethod(); + if ( Abort ) + { + break; + } + + f = File::New( ); + f->SetLoadMode(LoadMode); // we allow user not to load Sequences, + // or Shadow groups, or ...... + f->SetFileName( it->c_str() ); + f->Load( ); - return(path); + if ( f->IsReadable() ) + { + // Add the file to the chained list: + list.push_back(f); + gdcmDebugMacro( "Readable " << it->c_str() ); + } + else + { + f->Delete(); + } + 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) + { + dynamic_cast(*itDoc)->Delete(); + } } + //----------------------------------------------------------------------------- // Private -/* - * \ingroup gdcmDicomDir - * \brief - * @param +/** + * \brief Sets all fields to NULL + */ +void DicomDir::Initialize() +{ + Progress = 0.0; + Abort = false; + + MetaElems = NULL; +} + +/** + * \brief create a 'gdcm::DicomDir' from a DICOMDIR Header */ -void gdcmDicomDir::CreateDicomDir() +void DicomDir::CreateDicomDir() { - // The list is parsed. When a tag is found : + // 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"); - gdcmDicomDirType type=gdcmDicomDir::GDCM_NONE; - ListTag::iterator begin; - ListTag::iterator end; - - begin=listEntries.begin(); - end=begin; - for(ListTag::iterator i=listEntries.begin();i !=listEntries.end();++i) + // Directory record sequence + DocEntry *e = GetDocEntry(0x0004, 0x1220); + if ( !e ) { - // std::cout << std::hex <<(*i)->GetGroup() << - // " " <<(*i)->GetElement() << endl; + gdcmWarningMacro( "No Directory Record Sequence (0004,1220) found"); + return; + } + + SeqEntry *s = dynamic_cast(e); + if ( !s ) + { + gdcmWarningMacro( "Element (0004,1220) is not a Sequence ?!?"); + return; + } + + NewMeta(); + + DocEntry *d; + std::string v; + SQItem *si; - std::string v=(*i)->GetValue(); - if(v=="PATIENT ") + SQItem *tmpSI=s->GetFirstSQItem(); + while(tmpSI) + { + d = tmpSI->GetDocEntry(0x0004, 0x1430); // Directory Record Type + if ( DataEntry *dataEntry = dynamic_cast(d) ) { - // std::cout<<"PATIENT"<GetString(); + } + else + { + gdcmWarningMacro( "(0004,1430) not a DataEntry ?!?"); + continue; + } - type=gdcmDicomDir::GDCM_PATIENT; - begin=end; - } + // 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=="STUDY ") + if ( v == "IMAGE " ) { - // std::cout<<"STUDY"<(si)) ) + { + si->Delete(); + si = NULL; + gdcmErrorMacro( "Add AddImageToEnd failed"); + } } - - if(v=="SERIES") + else if ( v == "SERIES" ) { - // std::cout<<"SERIES"<(si)) ) + { + si->Delete(); + si = NULL; + gdcmErrorMacro( "Add AddSerieToEnd failed"); + } } - - if(v=="IMAGE ") + else if ( v == "VISIT " ) { - // std::cout<<"IMAGE"<(si)) ) + { + si->Delete(); + si = NULL; + gdcmErrorMacro( "Add AddVisitToEnd failed"); + } + } + else if ( v == "STUDY " ) + { + si = DicomDirStudy::New(true); // true = empty + if ( !AddStudyToEnd( static_cast(si)) ) + { + si->Delete(); + si = NULL; + 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 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); - type=gdcmDicomDir::GDCM_IMAGE; - begin=end; + // FIXME : deal with other item types ! + tmpSI=s->GetNextSQItem(); // To avoid infinite loop + continue; } - } + if ( si ) + si->Copy(tmpSI); - end=GetListEntry().end(); - AddObjectToEnd(type,begin,end); + tmpSI=s->GetNextSQItem(); + } + ClearEntry(); } -/* - * \ingroup gdcmDicomDir - * \brief - * @param + +/** + * \brief AddPatientToEnd + * @param dd SQ Item to enqueue to the DicomPatient chained List */ -void gdcmDicomDir::AddObjectToEnd(gdcmDicomDirType type,ListTag::iterator begin,ListTag::iterator end) +bool DicomDir::AddPatientToEnd(DicomDirPatient *dd) { - if(begin==end) - return; + Patients.push_back(dd); + return true; +} - switch(type) +/** + * \brief AddStudyToEnd + * @param dd SQ Item to enqueue to the DicomDirStudy chained List + */ +bool DicomDir::AddStudyToEnd(DicomDirStudy *dd) +{ + if ( Patients.size() > 0 ) { - case gdcmDicomDir::GDCM_PATIENT: - AddPatientToEnd(begin,end); - break; - case gdcmDicomDir::GDCM_STUDY: - AddStudyToEnd(begin,end); - break; - case gdcmDicomDir::GDCM_SERIE: - AddSerieToEnd(begin,end); - break; - case gdcmDicomDir::GDCM_IMAGE: - AddImageToEnd(begin,end); - break; + ListDicomDirPatient::iterator itp = Patients.end(); + itp--; + (*itp)->AddStudy(dd); + return true; } + return false; } -/* - * \ingroup gdcmDicomDir - * \brief - * @param +/** + * \brief AddSerieToEnd + * @param dd SQ Item to enqueue to the DicomDirSerie chained List */ -void gdcmDicomDir::AddPatientToEnd(ListTag::iterator begin,ListTag::iterator end) +bool DicomDir::AddSerieToEnd(DicomDirSerie *dd) { - patients.push_back(new gdcmPatient(begin,end)); + if ( Patients.size() > 0 ) + { + ListDicomDirPatient::iterator itp = Patients.end(); + itp--; + + DicomDirStudy *study = (*itp)->GetLastStudy(); + if ( study ) + { + study->AddSerie(dd); + return true; + } + } + return false; } -/* - * \ingroup gdcmDicomDir - * \brief - * @param +/** + * \brief AddVisitToEnd + * @param dd SQ Item to enqueue to the DicomDirVisit chained List */ - void gdcmDicomDir::AddStudyToEnd(ListTag::iterator begin,ListTag::iterator end) +bool DicomDir::AddVisitToEnd(DicomDirVisit *dd) { - if(patients.size()>0) + if ( Patients.size() > 0 ) { - ListPatient::iterator itp=patients.end(); + ListDicomDirPatient::iterator itp = Patients.end(); itp--; - (*itp)->AddStudy(new gdcmStudy(begin,end)); + + DicomDirStudy *study = (*itp)->GetLastStudy(); + if ( study ) + { + study->AddVisit(dd); + return true; + } } + return false; } -/* - * \ingroup gdcmDicomDir - * \brief - * @param +/** + * \brief AddImageToEnd + * @param dd SQ Item to enqueue to the DicomDirImage chained List */ -void gdcmDicomDir::AddSerieToEnd(ListTag::iterator begin,ListTag::iterator end) +bool DicomDir::AddImageToEnd(DicomDirImage *dd) { - if(patients.size()>0) + if ( Patients.size() > 0 ) { - ListPatient::iterator itp=patients.end(); + ListDicomDirPatient::iterator itp = Patients.end(); itp--; - if((*itp)->GetStudies().size()>0) + DicomDirStudy *study = (*itp)->GetLastStudy(); + if ( study ) { - ListStudy::iterator itst=(*itp)->GetStudies().end(); - itst--; - (*itst)->AddSerie(new gdcmSerie(begin,end)); + DicomDirSerie *serie = study->GetLastSerie(); + if ( serie ) + { + serie->AddImage(dd); + return true; + } } } + return false; } -/* - * \ingroup gdcmDicomDir - * \brief - * @param +/** + * \brief AddPrivateToEnd + * @param dd SQ Item to enqueue to the DicomDirPrivate chained List + * (checked for SIEMENS 'CSA non image') */ - void gdcmDicomDir::AddImageToEnd(ListTag::iterator begin,ListTag::iterator end) +bool DicomDir::AddPrivateToEnd(DicomDirPrivate *dd) { - if(patients.size()>0) + if ( Patients.size() > 0 ) { - ListPatient::iterator itp=patients.end(); + ListDicomDirPatient::iterator itp = Patients.end(); itp--; - if((*itp)->GetStudies().size()>0) + DicomDirStudy *study = (*itp)->GetLastStudy(); + if ( study ) { - ListStudy::iterator itst=(*itp)->GetStudies().end(); - itst--; - - if((*itst)->GetSeries().size()>0) + DicomDirSerie *serie = study->GetLastSerie(); + if ( serie ) { - ListSerie::iterator its=(*itst)->GetSeries().end(); - its--; - (*its)->AddImage(new gdcmImage(begin,end)); + serie->AddPrivate(dd); + return true; } } } + return false; } -/* - * \ingroup gdcmDicomDir - * \brief - * @param +/** + * \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 gdcmDicomDir::SetElements(std::string &path,ListHeader &list) +void DicomDir::SetElements(std::string const &path, VectDocument const &list) { - std::string patPrevName="", patPrevID=""; - std::string studPrevInstanceUID="", studPrevID=""; - std::string serPrevInstanceUID="", serPrevID=""; + ClearEntry(); + ClearPatient(); - std::string patCurName, patCurID; - std::string studCurInstanceUID, studCurID; - std::string serCurInstanceUID, serCurID; + std::string patPrevName = "", patPrevID = ""; + std::string studPrevInstanceUID = "", studPrevID = ""; + std::string serPrevInstanceUID = "", serPrevID = ""; - SetElement(path,GDCM_NONE,NULL); + std::string patCurName, patCurID; + std::string studCurInstanceUID, studCurID; + std::string serCurInstanceUID, serCurID; - ListTag::iterator debPat=listEntries.begin(); - for(ListHeader::iterator it=list.begin();it!=list.end();++it) + bool first = true; + for( VectDocument::const_iterator it = list.begin(); + it != list.end(); + ++it ) { - // get the current file characteristics - patCurName=(*it)->GetEntryByNumber(0x0010,0x0010); - patCurID=(*it)->GetEntryByNumber(0x0010,0x0011); - studCurInstanceUID=(*it)->GetEntryByNumber(0x0020,0x000d); - studCurID=(*it)->GetEntryByNumber(0x0020,0x0010); - serCurInstanceUID=(*it)->GetEntryByNumber(0x0020,0x000e); - serCurID=(*it)->GetEntryByNumber(0x0020,0x0011); + // get the current file characteristics + 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) - SetElement(path,GDCM_PATIENT,*it); + 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) - SetElement(path,GDCM_STUDY,*it); + // 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_SERIE,*it); - } + SetElement(path, GDCM_DICOMDIR_SERIE, *it); + } // Always Deal with 'IMAGE' Elements - SetElement(path,GDCM_IMAGE,*it); + SetElement(path, GDCM_DICOMDIR_IMAGE, *it); - patPrevName=patCurName; - patPrevID=patCurID; - studPrevInstanceUID=studCurInstanceUID; - studPrevID=studCurID; - serPrevInstanceUID=serCurInstanceUID; - serPrevID=serCurID; + patPrevName = patCurName; + patPrevID = patCurID; + studPrevInstanceUID = studCurInstanceUID; + studPrevID = studCurID; + serPrevInstanceUID = serCurInstanceUID; + serPrevID = serCurID; + first = false; } } -/* - * \ingroup gdcmDicomDir - * \brief - * @param +/** + * \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 gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type,gdcmHeader *header) +void DicomDir::SetElement(std::string const &path, DicomDirType type, + Document *header) { - std::list elemList; - std::list::iterator it; - guint16 tmpGr, tmpEl; - gdcmDictEntry *dictEntry; - gdcmHeaderEntry *entry; + ListDicomDirElem elemList; + ListDicomDirElem::const_iterator it; + uint16_t tmpGr, tmpEl; + //DictEntry *dictEntry; + DataEntry *entry; std::string val; - - switch(type) + SQItem *si; + switch( type ) { - case GDCM_PATIENT: - elemList=gdcmGlobal::GetDicomDirElements()->GetPatientElements(); + 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_STUDY: - elemList=gdcmGlobal::GetDicomDirElements()->GetStudyElements(); + 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_SERIE: - elemList=gdcmGlobal::GetDicomDirElements()->GetSerieElements(); + 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_IMAGE: - elemList=gdcmGlobal::GetDicomDirElements()->GetImageElements(); + 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_NONE: - elemList=gdcmGlobal::GetDicomDirElements()->GetMetaElements(); + 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; } - for(it=elemList.begin();it!=elemList.end();++it) - { - tmpGr=it->group; - tmpEl=it->elem; + // FIXME : troubles found when it's a SeqEntry - dictEntry=GetPubDict()->GetDictEntryByNumber(tmpGr,tmpEl); - entry=new gdcmHeaderEntry(dictEntry); - entry->SetOffset(0); // just to avoid missprinting + // 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) - val=header->GetEntryByNumber(tmpGr,tmpEl); + 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; + { + val = GDCM_UNFOUND; + } - if(val==GDCM_UNFOUND) + if ( val == GDCM_UNFOUND) { - if((tmpGr==0x0004) &&(tmpEl==0x1130) ) + if ( tmpGr == 0x0004 ) // never present in File ! { - // TODO force the *end* File Name(remove path) - val=path; - } - else if( (tmpGr==0x0004) && (tmpEl==0x1500) ) // Only used for image - { - if(header->GetFileName().substr(0,path.length())!=path) + switch (tmpEl) { - dbg.Verbose(0, "gdcmDicomDir::SetElement : the base path of file name is incorrect"); - val=header->GetFileName(); - } - else - val=&(header->GetFileName()[path.length()]); + 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 { - val=it->value; - } + // If the entry is not found in the Header, don't write its 'value' in the DICOMDIR ! + entry->Delete(); + continue; + } } - entry->SetValue(val); - - if(dictEntry) + else { - if( (dictEntry->GetVR()=="UL") || (dictEntry->GetVR()=="SL") ) + if ( header->GetEntryLength(tmpGr,tmpEl) == 0 ) { - entry->SetLength(4); - } - else if( (dictEntry->GetVR()=="US") || (dictEntry->GetVR()=="SS") ) - { - entry->SetLength(2); - } - else if(dictEntry->GetVR()=="SQ") - { - entry->SetLength(0xffffffff); - } - else - { - entry->SetLength(entry->GetValue().length()); - } + val = it->Value; + // Don't polute the DICOMDIR with empty fields + if (val == "") + { + entry->Delete(); + continue; + } + } } - listEntries.push_back(entry); - } +/* 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) +{ + 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); + // we destroyed -> the current iterator is not longer valid + entry = src->GetFirstEntry(); + } +} + +/** + * \brief compares two files + */ +bool DicomDir::HeaderLessThan(Document *header1, Document *header2) +{ + return *header1 < *header2; +} + +//----------------------------------------------------------------------------- +// 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