X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDicomDir.cxx;h=1226e49598d9b3ca02ef9a6a7d47d7f3d0d8f9ff;hb=fbd2698cb0545343abc2d8aefe92bab1f5b3eaa3;hp=35726eac96b77eb1e632e162b00347daed4cb68d;hpb=1d69b92978803204089d270599133917d944c651;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index 35726eac..1226e495 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDicomDir.cxx,v $ Language: C++ - Date: $Date: 2004/10/12 04:35:44 $ - Version: $Revision: 1.73 $ + Date: $Date: 2005/07/07 16:37:40 $ + Version: $Revision: 1.144 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -16,53 +16,114 @@ =========================================================================*/ +//----------------------------------------------------------------------------- +// For full DICOMDIR description, see: +// PS 3.3-2003, pages 731-750 +//----------------------------------------------------------------------------- #include "gdcmDicomDir.h" #include "gdcmDicomDirStudy.h" #include "gdcmDicomDirSerie.h" #include "gdcmDicomDirImage.h" +#include "gdcmDicomDirPatient.h" +#include "gdcmDicomDirMeta.h" +#include "gdcmDicomDirElement.h" #include "gdcmDirList.h" #include "gdcmUtil.h" #include "gdcmDebug.h" #include "gdcmGlobal.h" -#include "gdcmHeader.h" +#include "gdcmFile.h" #include "gdcmSeqEntry.h" #include "gdcmSQItem.h" #include "gdcmValEntry.h" +#include #include #include #include -#ifdef _MSC_VER - #include +#ifdef _MSC_VER +# define getcwd _getcwd +#endif + +#if defined(_MSC_VER) || defined(__BORLANDC__) +# include #else - #include +# include #endif +// ---------------------------------------------------------------------------- +// Note for future developpers +// ---------------------------------------------------------------------------- +// +// Dicom PS 3.3 describes the relationship between Directory Records, as follow +// (see also PS 4.3, 2004, page 50 for Entity-Relationship model) +// +// Directory Record Type Directory Record Types which may be included +// in the next lower-level directory Entity +// +// (Root directory Entity) PATIENT, TOPIC, PRIVATE +// +// PATIENT STUDY, PRIVATE +// +// STUDY SERIES, VISIT, RESULTS, STUDY COMPONENT, PRIVATE +// +// SERIES IMAGE, OVERLAYS, MODALITY LUT, VOI LUT, +// CURVE, STORED PRINT, RT DOSE, RT STRUCTURE SET +// RT PLAN, RT TREAT RECORD, PRESENTATION, WAVEFORM, +// SR DOCUMENT, KEY OBJECT DOC, SPECTROSCOPY, +// RAW DATA, REGISTRATION, FIDUCIAL, PRIVATE, +// ENCAP DOC +// IMAGE +// OVERLAY +// MODALITY LUT +// VOI LUT +// CURVE +// STORED PRINT +// RT DOSE +// RT STRUCTURE SET +// RT PLAN +// RT TREAT RECORD +// PRESENTATION +// WAVEFORM +// SR DOCUMENT +// KEY OBJECT DOC +// SPECTROSCOPY +// RAW DATA +// REGISTRATION +// FIDUCIAL +// PRIVATE +// ENCAP DOC +// +// ---------------------- +// The current gdcm version only deals with : +// +// (Root directory Entity) PATIENT +// PATIENT STUDY +// STUDY SERIES +// SERIES IMAGE +// IMAGE / +// +// DicomDir::CreateDicomDir will have to be completed +// Treelike structure management will have to be upgraded +// ---------------------------------------------------------------------------- + namespace gdcm { - -//----------------------------------------------------------------------------- -// For full DICOMDIR description, see: -// PS 3.3-2003, pages 731-750 //----------------------------------------------------------------------------- // Constructor / Destructor - /** - * \ingroup DicomDir * \brief Constructor : creates an empty DicomDir */ DicomDir::DicomDir() - :Document( ) -{ + :Document( ) +{ Initialize(); // sets all private fields to NULL - std::string pathBidon = "Bidon"; // Sorry, NULL not allowed ... - MetaElems = NewMeta(); + NewMeta(); } /** * \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 @@ -71,57 +132,17 @@ DicomDir::DicomDir() * - false if user passed an already built DICOMDIR file * and wants to use it */ -DicomDir::DicomDir(std::string const & fileName, bool parseDir ): - Document( fileName ) +DicomDir::DicomDir(std::string const &fileName, bool parseDir ): + Document( ) { - // Whatever user passed (a root directory or a DICOMDIR) - // and whatever the value of parseDir was, - // Document is already executed - Initialize(); // sets all private fields to NULL - - // if user passed a root directory, sure we didn't get anything - - if ( TagHT.begin() == TagHT.end() ) // when user passed a Directory to parse - { - dbg.Verbose(0, "DicomDir::DicomDir : entry HT empty"); - - if ( fileName.size() == 1 && fileName[0] == '.' ) - { - // 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 - } - - if ( parseDir ) // user asked for a recursive parsing of a root directory - { - MetaElems = NewMeta(); - - dbg.Verbose(0, "DicomDir::DicomDir : Parse directory" - " and create the DicomDir"); - ParseDirectory(); - } - else - { - /// \todo if parseDir == false, it should be tagged as an error - // NON ! il suffit d'appeler ParseDirectory() - // apres le constructeur - } - } - else // Only if user passed a DICOMDIR - { - // Directory record sequence - DocEntry *e = GetDocEntryByNumber(0x0004, 0x1220); - if ( !e ) - { - dbg.Verbose(0, "DicomDir::DicomDir : NO Directory record" - " sequence (0x0004,0x1220)"); - /// \todo FIXME : what do we do when the parsed file IS NOT a - /// DICOMDIR file ? - } - CreateDicomDir(); - } + // 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 cheked in Document constructor, to avoid overhead) + + ParseDir = parseDir; + SetLoadMode (0x00000000); // concerns only dicom files + Load( fileName ); } /** @@ -132,12 +153,8 @@ DicomDir::~DicomDir() SetStartMethod(NULL); SetProgressMethod(NULL); SetEndMethod(NULL); - for(ListDicomDirPatient::iterator cc = Patients.begin(); - cc!= Patients.end(); - ++cc) - { - delete *cc; - } + + ClearPatient(); if ( MetaElems ) { delete MetaElems; @@ -145,31 +162,109 @@ DicomDir::~DicomDir() } //----------------------------------------------------------------------------- -// Print +// Public + /** - * \brief Canonical Printer + * \brief Loader. use SetLoadMode(), SetFileName() before ! + * @return false if file cannot be open or no swap info was found, + * or no tag was found. */ -void DicomDir::Print(std::ostream &os) +bool DicomDir::Load( ) { - if( MetaElems ) + // We should clean out anything that already exists. + Initialize(); // sets all private fields to NULL + + if (!ParseDir) { - MetaElems->SetPrintLevel(PrintLevel); - MetaElems->Print(os); - } - for(ListDicomDirPatient::iterator cc = Patients.begin(); - cc != Patients.end(); - ++cc) + if ( ! this->Document::Load( ) ) + return false; + } + return DoTheLoadingJob( ); +} + +/** + * \brief Loader. (DEPRECATED : not to break the API) + * @param fileName file to be open for parsing + * @return false if file cannot be open or no swap info was found, + * or no tag was found. + */ +bool DicomDir::Load(std::string const &fileName ) +{ + // We should clean out anything that already exists. + Initialize(); // sets all private fields to NULL + + SetFileName( fileName ); + if (!ParseDir) { - (*cc)->SetPrintLevel( PrintLevel ); - (*cc)->Print( os ); + if ( ! this->Document::Load( ) ) + return false; } + return DoTheLoadingJob( ); +} + +/** + * \brief Does the Loading Job (internal use only) + * @return false if file cannot be open or no swap info was found, + * or no tag was found. + */ +bool DicomDir::DoTheLoadingJob( ) +{ + // We should clean out anything that already exists. + Initialize(); // sets all private fields to NULL + + if (!ParseDir) + { + // Only if user passed a DICOMDIR + // ------------------------------ + Fp = 0; + if ( !OpenFile() ) + { + return false; + } + if (!Document::Load() ) + { + return false; + } + + if ( GetFirstEntry() == 0 ) // when user passed a Directory to parse + { + gdcmWarningMacro( "Entry HT empty for file: "<< GetFileName()); + return false; + } + // Directory record sequence + DocEntry *e = GetDocEntry(0x0004, 0x1220); + if ( !e ) + { + gdcmWarningMacro( "NO 'Directory record sequence' (0x0004,0x1220)" + << " in file " << GetFileName()); + return false; + } + else + CreateDicomDir(); + } + else + { + // Only if user passed a root directory + // ------------------------------------ + if ( GetFileName() == "." ) + { + // user passed '.' as Name + // we get current directory name + char dummy[1000]; + getcwd(dummy, (size_t)1000); + SetFileName( dummy ); // will be converted into a string + } + NewMeta(); + gdcmWarningMacro( "Parse directory and create the DicomDir : " + << GetFileName() ); + ParseDirectory(); + } + return true; } -//----------------------------------------------------------------------------- -// Public /** * \brief This predicate, based on hopefully reasonable heuristics, - * decides whether or not the current header was properly parsed + * 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, @@ -177,16 +272,19 @@ void DicomDir::Print(std::ostream &os) */ bool DicomDir::IsReadable() { - if( !Document::IsReadable() ) + if ( Filetype == Unknown ) { + gdcmWarningMacro( "Wrong filetype"); return false; } - if( !MetaElems ) + if ( !MetaElems ) { + gdcmWarningMacro( "Meta Elements missing in DicomDir"); return false; } - if( Patients.size() <= 0 ) + if ( Patients.size() <= 0 ) { + gdcmWarningMacro( "NO Patient in DicomDir"); return false; } @@ -194,30 +292,91 @@ bool DicomDir::IsReadable() } /** - * \brief Sets all fields to NULL - */ + * \brief adds *the* Meta to a partially created DICOMDIR + */ +DicomDirMeta *DicomDir::NewMeta() +{ + if ( MetaElems ) + delete MetaElems; -void DicomDir::Initialize() + DocEntry *entry = GetFirstEntry(); + if ( entry ) + { + MetaElems = new DicomDirMeta(true); // true = empty + + entry = GetFirstEntry(); + while( entry ) + { + if ( dynamic_cast(entry) ) + break; + + RemoveEntryNoDestroy(entry); + MetaElems->AddEntry(entry); + + entry = GetFirstEntry(); + } + } + else // after root directory parsing + { + MetaElems = new DicomDirMeta(false); // false = not empty + } + MetaElems->SetSQItemNumber(0); // To avoid further missprinting + return MetaElems; +} + +/** + * \brief adds a new Patient (with the basic elements) to a partially created + * DICOMDIR + */ +DicomDirPatient *DicomDir::NewPatient() { - StartMethod = NULL; - ProgressMethod = NULL; - EndMethod = NULL; - StartMethodArgDelete = NULL; - ProgressMethodArgDelete = NULL; - EndMethodArgDelete = NULL; - StartArg = NULL; - ProgressArg = NULL; - EndArg = NULL; + DicomDirPatient *p = new DicomDirPatient(); + AddPatientToEnd( p ); + return p; +} - Progress = 0.0; - Abort = false; +/** + * \brief Remove all Patients + */ +void DicomDir::ClearPatient() +{ + for(ListDicomDirPatient::iterator cc = Patients.begin(); + cc!= Patients.end(); + ++cc) + { + delete *cc; + } + Patients.clear(); +} - MetaElems = 0; +/** + * \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; +} /** - * \ingroup DicomDir * \brief fills the whole structure, starting from a root Directory */ void DicomDir::ParseDirectory() @@ -227,17 +386,17 @@ void DicomDir::ParseDirectory() } /** - * \ingroup DicomDir - * \brief Set the start method to call when the parsing of the directory starts + * \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(Method* method, void* arg, - Method* argDelete ) +void DicomDir::SetStartMethod( DicomDir::Method *method, void *arg, + DicomDir::Method *argDelete ) { - if( StartArg && StartMethodArgDelete ) + if ( StartArg && StartMethodArgDelete ) { StartMethodArgDelete( StartArg ); } @@ -247,30 +406,19 @@ void DicomDir::SetStartMethod(Method* method, void* arg, StartMethodArgDelete = argDelete; } -/** - * \ingroup DicomDir - * \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(Method* method) -{ - StartMethodArgDelete = method; -} /** - * \ingroup DicomDir - * \brief Set the progress method to call when the parsing of the directory progress + * \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(Method* method, void* arg, - Method* argDelete ) +void DicomDir::SetProgressMethod( DicomDir::Method *method, void *arg, + DicomDir::Method *argDelete ) { - if( ProgressArg && ProgressMethodArgDelete ) + if ( ProgressArg && ProgressMethodArgDelete ) { ProgressMethodArgDelete( ProgressArg ); } @@ -281,29 +429,16 @@ void DicomDir::SetProgressMethod(Method* method, void* arg, } /** - * \ingroup DicomDir - * \brief Set the method to delete the argument - * The argument is destroyed when the method is changed or when the - * class is destroyed - * @param method Method to call to delete the argument - */ -void DicomDir::SetProgressMethodArgDelete(Method* method) -{ - ProgressMethodArgDelete = method; -} - -/** - * \ingroup DicomDir * \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 */ -void DicomDir::SetEndMethod(Method* method, void* arg, - Method* argDelete ) +void DicomDir::SetEndMethod( DicomDir::Method *method, void *arg, + DicomDir::Method *argDelete ) { - if( EndArg && EndMethodArgDelete ) + if ( EndArg && EndMethodArgDelete ) { EndMethodArgDelete( EndArg ); } @@ -314,430 +449,262 @@ void DicomDir::SetEndMethod(Method* method, void* arg, } /** - * \ingroup DicomDir * \brief Set the method to delete the argument - * The argument is destroyed when the method is changed or when the class - * is destroyed + * The argument is destroyed when the method is changed or when the + * class is destroyed + * @param method Method to call to delete the argument + */ +void DicomDir::SetStartMethodArgDelete( DicomDir::Method *method ) +{ + StartMethodArgDelete = method; +} + +/** + * \brief Set the method to delete the argument + * The argument is destroyed when the method is changed or when the + * class is destroyed + * @param method Method to call to delete the argument + */ +void DicomDir::SetProgressMethodArgDelete( DicomDir::Method *method ) +{ + ProgressMethodArgDelete = method; +} + +/** + * \brief Set the 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(Method* method) +void DicomDir::SetEndMethodArgDelete( DicomDir::Method *method ) { EndMethodArgDelete = method; } /** - * \ingroup DicomDir - * \brief writes on disc a DICOMDIR + * \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::WriteDicomDir(std::string const &fileName) { + int i; uint16_t sq[4] = { 0x0004, 0x1220, 0xffff, 0xffff }; uint16_t sqt[4]= { 0xfffe, 0xe0dd, 0xffff, 0xffff }; - FILE* fp = fopen(fileName.c_str(), "wb"); - if( !fp ) + 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()); + gdcmWarningMacro("Failed to open(write) File: " << fileName.c_str()); return false; } - uint8_t filePreamble[128]; + char filePreamble[128]; memset(filePreamble, 0, 128); - fwrite(filePreamble,128,1,fp); - fwrite("DICM",4,1,fp); + fp->write(filePreamble, 128); + binary_write( *fp, "DICM"); - DicomDirMeta *ptrMeta = GetDicomDirMeta(); - ptrMeta->Write(fp, ExplicitVR); + DicomDirMeta *ptrMeta = GetMeta(); + ptrMeta->WriteContent(fp, ExplicitVR); // force writing 0004|1220 [SQ ], that CANNOT exist within DicomDirMeta - fwrite(&sq[0],8,1,fp); // 0004 1220 ffff ffff + for(i=0;i<4;++i) + { + binary_write(*fp, sq[i]); + } for(ListDicomDirPatient::iterator cc = Patients.begin(); cc != Patients.end(); ++cc ) { - (*cc)->Write( fp, ExplicitVR ); + (*cc)->WriteContent( fp, ExplicitVR ); } // force writing Sequence Delimitation Item - fwrite(&sqt[0],8,1,fp); // fffe e0dd ffff ffff + for(i=0;i<4;++i) + { + binary_write(*fp, sqt[i]); // fffe e0dd ffff ffff + } - fclose( fp ); + fp->close(); + delete fp; + + return true; +} + +/** + * \brief Anonymize a DICOMDIR + * @return true + */ + +bool DicomDir::AnonymizeDicomDir() +{ + ValEntry *v; + // Something clever to be found to forge the Patient names + std::ostringstream s; + int i = 1; + for(ListDicomDirPatient::iterator cc = Patients.begin(); + cc!= Patients.end(); + ++cc) + { + s << i; + v = (*cc)->GetValEntry(0x0010, 0x0010) ; // Patient's Name + if (v) + { + v->SetValue(s.str()); + } + + v = (*cc)->GetValEntry(0x0010, 0x0020) ; // Patient ID + if (v) + { + v->SetValue(" "); + } + + v = (*cc)->GetValEntry(0x0010, 0x0030) ; // Patient's BirthDate + if (v) + { + v->SetValue(" "); + } + s << ""; + i++; + } return true; } //----------------------------------------------------------------------------- // Protected - /** - * \ingroup DicomDir * \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 fileList(path,1); // gets recursively the file list + DirList dirList(path,1); // gets recursively the file list unsigned int count = 0; VectDocument list; - Header *header; + File *f; - TagHT.clear(); - Patients.clear(); + DirListType fileList = dirList.GetFilenames(); - for( DirList::iterator it = fileList.begin(); + for( DirListType::iterator it = fileList.begin(); it != fileList.end(); ++it ) { Progress = (float)(count+1)/(float)fileList.size(); CallProgressMethod(); - if( Abort ) + if ( Abort ) { break; } - header = new Header( it->c_str() ); - if( !header ) - { - dbg.Verbose( 1, - "DicomDir::CreateDicomDirChainedList: " - "failure in new Header ", - it->c_str() ); - } + f = new File( ); + f->SetLoadMode(LoadMode); // we allow user not to load Sequences... + f->Load( it->c_str() ); + +// if ( !f ) +// { +// gdcmWarningMacro( "Failure in new gdcm::File " << it->c_str() ); +// continue; +// } - if( header->IsReadable() ) + if ( f->IsReadable() ) { - // Add the file header to the chained list: - list.push_back(header); - dbg.Verbose( 1, - "DicomDir::CreateDicomDirChainedList: readable ", - it->c_str() ); - + // Add the file to the chained list: + list.push_back(f); + gdcmWarningMacro( "Readable " << it->c_str() ); } else { - delete header; + delete f; } count++; } // sorts Patient/Study/Serie/ std::sort(list.begin(), list.end(), DicomDir::HeaderLessThan ); - std::string tmp = fileList.GetDirName(); - //for each Header of the chained list, add/update the Patient/Study/Serie/Image info + std::string tmp = dirList.GetDirName(); + //for each File of the chained list, add/update the Patient/Study/Serie/Image info SetElements(tmp, list); CallEndMethod(); + + for(VectDocument::iterator itDoc=list.begin(); + itDoc!=list.end(); + ++itDoc) + { + delete dynamic_cast(*itDoc); + } } /** - * \ingroup DicomDir - * \brief adds *the* Meta to a partially created DICOMDIR + * \brief CallStartMethod */ - -DicomDirMeta * DicomDir::NewMeta() +void DicomDir::CallStartMethod() { - DicomDirMeta *m = new DicomDirMeta( &TagHT ); - - if ( TagHT.begin() != TagHT.end() ) // after Document Parsing - { - TagDocEntryHT::iterator lastOneButSequence = TagHT.end(); - lastOneButSequence --; - // ALL the 'out of Sequence' Tags belong to Meta Elems - // (we skip 0004|1220 [Directory record sequence] ) - for ( TagDocEntryHT::iterator cc = TagHT.begin(); - cc != lastOneButSequence; - ++cc) - { - m->AddDocEntry( cc->second ); - } - } - else // after root directory parsing + Progress = 0.0f; + Abort = false; + if ( StartMethod ) { - std::list elemList; - elemList=Global::GetDicomDirElements()->GetDicomDirMetaElements(); - m->FillObject(elemList); - } - m->SetSQItemNumber(0); // To avoid further missprinting - return m; + StartMethod( StartArg ); + } } /** - * \brief adds a new Patient (with the basic elements) to a partially created DICOMDIR + * \brief CallProgressMethod */ -DicomDirPatient * DicomDir::NewPatient() +void DicomDir::CallProgressMethod() { - std::list::iterator it; - uint16_t tmpGr,tmpEl; - DictEntry *dictEntry; - ValEntry *entry; - - std::list elemList; - elemList=Global::GetDicomDirElements()->GetDicomDirPatientElements(); - SQItem *s = new SQItem(0); - - // for all the DicomDirPatient Elements - for( it = elemList.begin(); it != elemList.end(); ++it ) + if ( ProgressMethod ) { - tmpGr = it->Group; - tmpEl = it->Elem; - dictEntry = GetPubDict()->GetDictEntryByNumber(tmpGr, tmpEl); - entry = new ValEntry( dictEntry ); - entry->SetOffset(0); // just to avoid further missprinting - entry->SetValue( it->Value ); - - // dealing with value length ... - - if( dictEntry->GetGroup() == 0xfffe) - { - entry->SetLength(entry->GetValue().length()); - } - else if( dictEntry->GetVR() == "UL" || dictEntry->GetVR() == "SL" ) - { - 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() ); - } - s->AddDocEntry( entry ); - } - - DicomDirPatient *p = new DicomDirPatient(s, &TagHT); - Patients.push_front( p ); - - return p; -} + ProgressMethod( ProgressArg ); + } +} /** - * \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 + * \brief CallEndMethod */ -void DicomDir::SetElement(std::string &path,DicomDirType type, - Document *header) +void DicomDir::CallEndMethod() { - std::list elemList; - std::list::iterator it; - uint16_t tmpGr, tmpEl; - DictEntry *dictEntry; - ValEntry *entry; - std::string val; - SQItem *si = new SQItem(0); // all the items will be at level 1 - switch( type ) - { - case GDCM_DICOMDIR_IMAGE: - elemList = Global::GetDicomDirElements()->GetDicomDirImageElements(); - break; - - case GDCM_DICOMDIR_SERIE: - elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements(); - break; - - case GDCM_DICOMDIR_STUDY: - elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements(); - break; - - case GDCM_DICOMDIR_PATIENT: - elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements(); - break; - - case GDCM_DICOMDIR_META: - elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements(); - 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()->GetDictEntryByNumber(tmpGr, tmpEl); - - entry = new ValEntry( dictEntry ); // Be sure it's never a BinEntry ! - - entry->SetOffset(0); // just to avoid further missprinting - entry->SetLength(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->GetEntryByNumber(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 ) - { - dbg.Verbose(0, "DicomDir::SetElement : 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->GetEntryLengthByNumber(tmpGr,tmpEl) == 0 ) - val = it->Value; - } - - // GDCM_UNFOUND or not ! - - entry->SetValue( val ); // troubles expected when vr=SQ ... - - if( dictEntry ) - { - if( dictEntry->GetGroup() == 0xfffe ) - { - entry->SetLength( entry->GetValue().length() ); // FIXME - } - else if( dictEntry->GetVR() == "UL" || dictEntry->GetVR() == "SL" ) - { - 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() ); - } - } - - if ( type == GDCM_DICOMDIR_META ) // fusible : should never print ! - { - std::cout << "GDCM_DICOMDIR_META ?!? should never print that" - << std::endl; - } - si->AddEntry(entry); - } - switch( type ) + Progress = 1.0f; + if ( EndMethod ) { - case GDCM_DICOMDIR_IMAGE: - AddDicomDirImageToEnd(si); - break; - - case GDCM_DICOMDIR_SERIE: - AddDicomDirSerieToEnd(si); - break; - - case GDCM_DICOMDIR_STUDY: - AddDicomDirStudyToEnd(si); - break; - - case GDCM_DICOMDIR_PATIENT: - AddDicomDirPatientToEnd(si); - break; - - default: - return; + EndMethod( EndArg ); } - //int count=1; // find a trick to increment - //s->AddEntry(si, count); // Seg Faults - } +//----------------------------------------------------------------------------- +// Private /** - * \brief CallStartMethod + * \brief Sets all fields to NULL */ -void DicomDir::CallStartMethod() +void DicomDir::Initialize() { - Progress = 0.0f; - Abort = false; - if( StartMethod ) - { - StartMethod( StartArg ); - } -} + StartMethod = NULL; + ProgressMethod = NULL; + EndMethod = NULL; + StartMethodArgDelete = NULL; + ProgressMethodArgDelete = NULL; + EndMethodArgDelete = NULL; + StartArg = NULL; + ProgressArg = NULL; + EndArg = NULL; -/** - * \ingroup DicomDir - * \brief CallProgressMethod - */ -void DicomDir::CallProgressMethod() -{ - if( ProgressMethod ) - { - ProgressMethod( ProgressArg ); - } -} + Progress = 0.0; + Abort = false; -/** - * \ingroup DicomDir - * \brief CallEndMethod - */ -void DicomDir::CallEndMethod() -{ - Progress = 1.0f; - if( EndMethod ) - { - EndMethod( EndArg ); - } + MetaElems = NULL; } -//----------------------------------------------------------------------------- -// Private /** - * \ingroup DicomDir - * \brief create a 'DicomDir' from a DICOMDIR Header + * \brief create a 'gdcm::DicomDir' from a DICOMDIR Header */ void DicomDir::CreateDicomDir() { - // The list is parsed. + // The SeqEntries of "Directory Record Sequence" are parsed. // When a DicomDir tag ("PATIENT", "STUDY", "SERIE", "IMAGE") is found : // 1 - we save the beginning iterator // 2 - we continue to parse @@ -746,167 +713,187 @@ void DicomDir::CreateDicomDir() // + loop to 1 - // Directory record sequence - DocEntry *e = GetDocEntryByNumber(0x0004, 0x1220); + DocEntry *e = GetDocEntry(0x0004, 0x1220); if ( !e ) { - dbg.Verbose(0, "DicomDir::DicomDir : NO Directory record" - " sequence (0x0004,0x1220)"); - /// \todo FIXME: what to do when the parsed file IS NOT a DICOMDIR file ? + gdcmWarningMacro( "No Directory Record Sequence (0004,1220) found"); return; } - SeqEntry* s = dynamic_cast(e); + SeqEntry *s = dynamic_cast(e); if ( !s ) { - dbg.Verbose(0, "DicomDir::CreateDicomDir: no SeqEntry present"); - // useless : (0x0004,0x1220) IS a Sequence ! + gdcmWarningMacro( "Element (0004,1220) is not a Sequence ?!?"); return; } - DicomDirType type = DicomDir::GDCM_DICOMDIR_META; - MetaElems = NewMeta(); - - ListSQItem listItems = s->GetSQItems(); + NewMeta(); - DocEntry * d; + DocEntry *d; std::string v; - for( ListSQItem::iterator i = listItems.begin(); - i !=listItems.end(); ++i ) + SQItem *si; + + SQItem *tmpSI=s->GetFirstSQItem(); + while(tmpSI) { - d = (*i)->GetDocEntryByNumber(0x0004, 0x1430); // Directory Record Type - if ( ValEntry* valEntry = dynamic_cast< ValEntry* >(d) ) + d = tmpSI->GetDocEntry(0x0004, 0x1430); // Directory Record Type + if ( ValEntry* valEntry = dynamic_cast(d) ) { v = valEntry->GetValue(); } else { - dbg.Verbose(0, "DicomDir::CreateDicomDir: not a ValEntry."); + gdcmWarningMacro( "(0004,1430) not a ValEntry ?!?"); continue; } - if( v == "PATIENT " ) + // A decent DICOMDIR has much more images than series, + // more series than studies, and so on. + // This is the right order to preform the tests + + if ( v == "IMAGE " ) { - AddDicomDirPatientToEnd( *i ); - type = DicomDir::GDCM_DICOMDIR_PATIENT; + si = new DicomDirImage(true); + if ( !AddImageToEnd( static_cast(si)) ) + { + delete si; + si = NULL; + gdcmErrorMacro( "Add AddImageToEnd failed"); + } } - else if( v == "STUDY " ) + else if ( v == "SERIES" ) { - AddDicomDirStudyToEnd( *i ); - type = DicomDir::GDCM_DICOMDIR_STUDY; + si = new DicomDirSerie(true); + if ( !AddSerieToEnd( static_cast(si)) ) + { + delete si; + si = NULL; + gdcmErrorMacro( "Add AddSerieToEnd failed"); + } } - else if( v == "SERIES" ) + else if ( v == "STUDY " ) { - AddDicomDirSerieToEnd( *i ); - type = DicomDir::GDCM_DICOMDIR_SERIE; + si = new DicomDirStudy(true); + if ( !AddStudyToEnd( static_cast(si)) ) + { + delete si; + si = NULL; + gdcmErrorMacro( "Add AddStudyToEnd failed"); + } } - else if( v == "IMAGE " ) + else if ( v == "PATIENT " ) { - AddDicomDirImageToEnd( *i ); - type = DicomDir::GDCM_DICOMDIR_IMAGE; + si = new DicomDirPatient(true); + if ( !AddPatientToEnd( static_cast(si)) ) + { + delete si; + si = NULL; + gdcmErrorMacro( "Add PatientToEnd failed"); + } } else { - // It was not a 'PATIENT', nor a 'STUDY', nor a 'SERIE', - // neither an 'IMAGE' SQItem. Skip to next item. - continue; + // It was neither a 'PATIENT', nor a 'STUDY', nor a 'SERIE', + // nor an 'IMAGE' SQItem. Skip to next item. + gdcmWarningMacro( " -------------------------------------------" + << "a non PATIENT/STUDY/SERIE/IMAGE SQItem was found : " + << v); + + // FIXME : deal with other item types ! + tmpSI=s->GetNextSQItem(); // To avoid infinite loop + continue; } - } -} + if ( si ) + MoveSQItem(si,tmpSI); -/** - * \ingroup DicomDir - * \brief Well ... there is only one occurence - */ -void DicomDir::AddDicomDirMeta() -{ - if( MetaElems ) - { - delete MetaElems; + tmpSI=s->GetNextSQItem(); } - MetaElems = new DicomDirMeta( &TagHT ); + ClearEntry(); } /** - * \ingroup DicomDir - * \brief AddDicomDirPatientToEnd - * @param s SQ Item to enqueue to the DicomPatient chained List + * \brief AddPatientToEnd + * @param dd SQ Item to enqueue to the DicomPatient chained List */ -void DicomDir::AddDicomDirPatientToEnd(SQItem *s) +bool DicomDir::AddPatientToEnd(DicomDirPatient *dd) { - Patients.push_back(new DicomDirPatient(s, &TagHT)); + Patients.push_back(dd); + return true; } /** - * \ingroup DicomDir - * \brief AddDicomDirStudyToEnd - * @param s SQ Item to enqueue to the DicomDirStudy chained List + * \brief AddStudyToEnd + * @param dd SQ Item to enqueue to the DicomDirStudy chained List */ - void DicomDir::AddDicomDirStudyToEnd(SQItem *s) +bool DicomDir::AddStudyToEnd(DicomDirStudy *dd) { - if( Patients.size() > 0 ) + if ( Patients.size() > 0 ) { ListDicomDirPatient::iterator itp = Patients.end(); itp--; - (*itp)->AddDicomDirStudy(new DicomDirStudy(s, &TagHT)); + (*itp)->AddStudy(dd); + return true; } + return false; } /** - * \ingroup DicomDir - * \brief AddDicomDirSerieToEnd - * @param s SQ Item to enqueue to the DicomDirSerie chained List + * \brief AddSerieToEnd + * @param dd SQ Item to enqueue to the DicomDirSerie chained List */ -void DicomDir::AddDicomDirSerieToEnd(SQItem *s) +bool DicomDir::AddSerieToEnd(DicomDirSerie *dd) { - if( Patients.size() > 0 ) + if ( Patients.size() > 0 ) { ListDicomDirPatient::iterator itp = Patients.end(); itp--; - if( (*itp)->GetDicomDirStudies().size() > 0 ) + DicomDirStudy *study = (*itp)->GetLastStudy(); + if ( study ) { - ListDicomDirStudy::iterator itst=(*itp)->GetDicomDirStudies().end(); - itst--; - (*itst)->AddDicomDirSerie(new DicomDirSerie(s, &TagHT)); + study->AddSerie(dd); + return true; } } + return false; } /** - * \ingroup DicomDir - * \brief AddDicomDirImageToEnd - * @param s SQ Item to enqueue to the DicomDirImage chained List + * \brief AddImageToEnd + * @param dd SQ Item to enqueue to the DicomDirImage chained List */ - void DicomDir::AddDicomDirImageToEnd(SQItem *s) +bool DicomDir::AddImageToEnd(DicomDirImage *dd) { - if( Patients.size() > 0 ) + if ( Patients.size() > 0 ) { ListDicomDirPatient::iterator itp = Patients.end(); itp--; - if( (*itp)->GetDicomDirStudies().size() > 0 ) + DicomDirStudy *study = (*itp)->GetLastStudy(); + if ( study ) { - ListDicomDirStudy::iterator itst = (*itp)->GetDicomDirStudies().end(); - itst--; - - if( (*itst)->GetDicomDirSeries().size() > 0 ) + DicomDirSerie *serie = study->GetLastSerie(); + if ( serie ) { - ListDicomDirSerie::iterator its = (*itst)->GetDicomDirSeries().end(); - its--; - (*its)->AddDicomDirImage(new DicomDirImage(s, &TagHT)); + serie->AddImage(dd); + return true; } } } + return false; } /** - * \ingroup DicomDir - * \brief for each Header of the chained list, add/update the Patient/Study/Serie/Image info + * \brief for each Header of the chained list, + * add/update the Patient/Study/Serie/Image info * @param path path of the root directory * @param list chained list of Headers */ -void DicomDir::SetElements(std::string &path, VectDocument &list) +void DicomDir::SetElements(std::string const &path, VectDocument const &list) { + ClearEntry(); + ClearPatient(); + std::string patPrevName = "", patPrevID = ""; std::string studPrevInstanceUID = "", studPrevID = ""; std::string serPrevInstanceUID = "", serPrevID = ""; @@ -915,30 +902,36 @@ void DicomDir::SetElements(std::string &path, VectDocument &list) std::string studCurInstanceUID, studCurID; std::string serCurInstanceUID, serCurID; - for( VectDocument::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); - - if( patCurName != patPrevName || patCurID != patPrevID) + patCurName = (*it)->GetEntryValue(0x0010,0x0010); + patCurID = (*it)->GetEntryValue(0x0010,0x0011); + studCurInstanceUID = (*it)->GetEntryValue(0x0020,0x000d); + studCurID = (*it)->GetEntryValue(0x0020,0x0010); + serCurInstanceUID = (*it)->GetEntryValue(0x0020,0x000e); + serCurID = (*it)->GetEntryValue(0x0020,0x0011); + + if ( patCurName != patPrevName || patCurID != patPrevID || first ) { SetElement(path, GDCM_DICOMDIR_PATIENT, *it); + first = true; } - // if new Study Deal with 'STUDY' Elements - if( studCurInstanceUID != studPrevInstanceUID || studCurID != studPrevID ) + // if new Study, deal with 'STUDY' Elements + if ( studCurInstanceUID != studPrevInstanceUID || studCurID != studPrevID + || first ) { SetElement(path, GDCM_DICOMDIR_STUDY, *it); + first = true; } - // if new Serie Deal with 'SERIE' Elements - if( serCurInstanceUID != serPrevInstanceUID || serCurID != serPrevID ) + // if new Serie, deal with 'SERIE' Elements + if ( serCurInstanceUID != serPrevInstanceUID || serCurID != serPrevID + || first ) { SetElement(path, GDCM_DICOMDIR_SERIE, *it); } @@ -952,17 +945,202 @@ void DicomDir::SetElements(std::string &path, VectDocument &list) studPrevID = studCurID; serPrevInstanceUID = serCurInstanceUID; serPrevID = serCurID; + first = false; + } +} + +/** + * \brief adds to the HTable + * the Entries (Dicom Elements) corresponding to the given type + * @param path full path file name (only used when type = GDCM_DICOMDIR_IMAGE + * @param type DicomDirObject type to create (GDCM_DICOMDIR_PATIENT, + * GDCM_DICOMDIR_STUDY, GDCM_DICOMDIR_SERIE ...) + * @param header Header of the current file + */ +void DicomDir::SetElement(std::string const &path, DicomDirType type, + Document *header) +{ + ListDicomDirElem elemList; + ListDicomDirElem::const_iterator it; + uint16_t tmpGr, tmpEl; + DictEntry *dictEntry; + ValEntry *entry; + std::string val; + SQItem *si; + + switch( type ) + { + case GDCM_DICOMDIR_IMAGE: + elemList = Global::GetDicomDirElements()->GetDicomDirImageElements(); + si = new DicomDirImage(true); + if ( !AddImageToEnd(static_cast(si)) ) + { + delete si; + gdcmErrorMacro( "Add ImageToEnd failed"); + } + break; + case GDCM_DICOMDIR_SERIE: + elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements(); + si = new DicomDirSerie(true); + if ( !AddSerieToEnd(static_cast(si)) ) + { + delete si; + gdcmErrorMacro( "Add SerieToEnd failed"); + } + break; + case GDCM_DICOMDIR_STUDY: + elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements(); + si = new DicomDirStudy(true); + if ( !AddStudyToEnd(static_cast(si)) ) + { + delete si; + gdcmErrorMacro( "Add StudyToEnd failed"); + } + break; + case GDCM_DICOMDIR_PATIENT: + elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements(); + si = new DicomDirPatient(true); + if ( !AddPatientToEnd(static_cast(si)) ) + { + delete si; + gdcmErrorMacro( "Add PatientToEnd failed"); + } + break; + case GDCM_DICOMDIR_META: + elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements(); + si = new DicomDirMeta(true); + if ( MetaElems ) + { + delete MetaElems; + gdcmErrorMacro( "MetaElements already exist, they will be destroyed"); + } + MetaElems = static_cast(si); + break; + default: + return; + } + // removed all the seems-to-be-useless stuff about Referenced Image Sequence + // to avoid further troubles + // imageElem 0008 1140 "" // Referenced Image Sequence + // imageElem fffe e000 "" // 'no length' item : length to be set to 0xffffffff later + // imageElem 0008 1150 "" // Referenced SOP Class UID : to be set/forged later + // imageElem 0008 1155 "" // Referenced SOP Instance UID : to be set/forged later + // imageElem fffe e00d "" // Item delimitation : length to be set to ZERO later + + // FIXME : troubles found when it's a SeqEntry + + // for all the relevant elements found in their own spot of the DicomDir.dic + for( it = elemList.begin(); it != elemList.end(); ++it) + { + tmpGr = it->Group; + tmpEl = it->Elem; + dictEntry = GetPubDict()->GetEntry(tmpGr, tmpEl); + + entry = new ValEntry( dictEntry ); // Be sure it's never a BinEntry ! + + entry->SetOffset(0); // just to avoid further missprinting + + if ( header ) + { + // NULL when we Build Up (ex nihilo) a DICOMDIR + // or when we add the META elems + val = header->GetEntryValue(tmpGr, tmpEl); + } + else + { + val = GDCM_UNFOUND; + } + + if ( val == GDCM_UNFOUND) + { + if ( tmpGr == 0x0004 && tmpEl == 0x1130 ) // File-set ID + { + // force to the *end* File Name + val = Util::GetName( path ); + } + else if ( tmpGr == 0x0004 && tmpEl == 0x1500 ) // Only used for image + { + if ( header->GetFileName().substr(0, path.length()) != path ) + { + gdcmWarningMacro( "The base path of file name is incorrect"); + val = header->GetFileName(); + } + else + { + val = &(header->GetFileName().c_str()[path.length()]); + } + } + else + { + val = it->Value; + } + } + else + { + if ( header->GetEntryLength(tmpGr,tmpEl) == 0 ) + val = it->Value; + } + + entry->SetValue( val ); // troubles expected when vr=SQ ... + + if ( type == GDCM_DICOMDIR_META ) // fusible : should never print ! + { + gdcmWarningMacro("GDCM_DICOMDIR_META ?!? should never print that"); + } + si->AddEntry(entry); + } +} + +/** + * \brief Move the content of the source SQItem to the destination SQItem + * Only DocEntry's are moved + * @param dst destination SQItem + * @param src source SQItem + */ +void DicomDir::MoveSQItem(DocEntrySet *dst,DocEntrySet *src) +{ + DocEntry *entry; + + entry = src->GetFirstEntry(); + while(entry) + { + src->RemoveEntryNoDestroy(entry); + dst->AddEntry(entry); + // we destroyed -> the current iterator is not longer valid + entry = src->GetFirstEntry(); } } /** - * \ingroup DicomDir - * \brief compares two dgcmHeaders + * \brief compares two files */ bool DicomDir::HeaderLessThan(Document *header1, Document *header2) { return *header1 < *header2; } -} // end namespace gdcm //----------------------------------------------------------------------------- +// Print +/** + * \brief Canonical Printer + * @param os ostream we want to print in + * @param indent Indentation string to be prepended during printing + */ +void DicomDir::Print(std::ostream &os, std::string const & ) +{ + if ( MetaElems ) + { + MetaElems->SetPrintLevel(PrintLevel); + MetaElems->Print(os); + } + for(ListDicomDirPatient::iterator cc = Patients.begin(); + cc != Patients.end(); + ++cc) + { + (*cc)->SetPrintLevel(PrintLevel); + (*cc)->Print(os); + } +} + +//----------------------------------------------------------------------------- +} // end namespace gdcm