X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDicomDir.cxx;h=22720bd8c572cac2c5f505df20ec02a473861de6;hb=0bcc188c6d5185375f809253e8b9b97c856d2eac;hp=196156a7d7c8010705cd44eb6d631f88a1dc9509;hpb=e62d57cbd05c8e864fd2ba197a271cdcac9a2128;p=gdcm.git diff --git a/src/gdcmDicomDir.cxx b/src/gdcmDicomDir.cxx index 196156a7..22720bd8 100644 --- a/src/gdcmDicomDir.cxx +++ b/src/gdcmDicomDir.cxx @@ -3,12 +3,12 @@ Program: gdcm Module: $RCSfile: gdcmDicomDir.cxx,v $ Language: C++ - Date: $Date: 2004/09/24 11:39:21 $ - Version: $Revision: 1.69 $ + 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.htm for details. + 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 @@ -16,51 +16,183 @@ =========================================================================*/ -#include -#include -#include - -#ifdef _MSC_VER - #include -#else - #include -#endif - +//----------------------------------------------------------------------------- +// For full DICOMDIR description, see: +// PS 3.3-2003, pages 731-750 +//----------------------------------------------------------------------------- #include "gdcmDicomDir.h" +#include "gdcmDicomDirObject.h" #include "gdcmDicomDirStudy.h" #include "gdcmDicomDirSerie.h" +#include "gdcmDicomDirVisit.h" #include "gdcmDicomDirImage.h" +#include "gdcmDicomDirPrivate.h" +#include "gdcmDicomDirPatient.h" +#include "gdcmDicomDirMeta.h" +#include "gdcmDicomDirElement.h" #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 "gdcmDataEntry.h" +#include "gdcmCommandManager.h" -//----------------------------------------------------------------------------- -// For full DICOMDIR description, see: -// PS 3.3-2003, pages 731-750 +#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 Constructor : creates an empty gdcmDicomDir + * \brief Constructor : creates an empty DicomDir */ -gdcmDicomDir::gdcmDicomDir() - :gdcmDocument( ) -{ +DicomDir::DicomDir() +{ Initialize(); // sets all private fields to NULL - std::string pathBidon = "Bidon"; // Sorry, NULL not allowed ... - metaElems = NewMeta(); + ParseDir = false; + NewMeta(); } +//#ifndef GDCM_LEGACY_REMOVE /** * \brief Constructor Parses recursively the directory and creates the DicomDir * or uses an already built DICOMDIR, depending on 'parseDir' value. - * @param fileName name + * @param fileName name * - of the root directory (parseDir = true) * - of the DICOMDIR (parseDir = false) * @param parseDir boolean @@ -68,124 +200,169 @@ gdcmDicomDir::gdcmDicomDir() * 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) */ -gdcmDicomDir::gdcmDicomDir(std::string const & fileName, bool parseDir ): - gdcmDocument( 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, - // gdcmDocument 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, "gdcmDicomDir::gdcmDicomDir : entry HT empty"); - - if ( fileName.size() == 1 && fileName[0] == '.' ) - { - // user passed '.' as Name - // we get current directory name - char* dummy = new char[1000]; - getcwd(dummy, (size_t)1000); - SetFileName( dummy ); // will be converted into a string - delete[] dummy; // no longer needed - } - - if ( parseDir ) // user asked for a recursive parsing of a root directory - { - metaElems = NewMeta(); + // 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 - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : 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 +/** + * \brief Canonical destructor + */ +DicomDir::~DicomDir() +{ + ClearPatient(); + if ( MetaElems ) { - // Directory record sequence - gdcmDocEntry *e = GetDocEntryByNumber(0x0004, 0x1220); - if ( !e ) - { - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : NO Directory record" - " sequence (0x0004,0x1220)"); - /// \todo FIXME : what do we do when the parsed file IS NOT a - /// DICOMDIR file ? - } - CreateDicomDir(); + MetaElems->Delete(); } } +//----------------------------------------------------------------------------- +// Public + /** - * \brief Canonical destructor + * \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. */ -gdcmDicomDir::~gdcmDicomDir() +bool DicomDir::Load( ) { - SetStartMethod(NULL); - SetProgressMethod(NULL); - SetEndMethod(NULL); - for(ListDicomDirPatient::iterator cc = patients.begin(); - cc!= patients.end(); - ++cc) + if (!ParseDir) { - delete *cc; + if ( ! this->Document::Load( ) ) + return false; } - if ( metaElems ) + 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) { - delete metaElems; + if ( ! this->Document::Load( ) ) + return false; } + return DoTheLoadingJob( ); } +*/ +//#endif -//----------------------------------------------------------------------------- -// Print /** - * \brief Canonical Printer + * \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. */ -void gdcmDicomDir::Print(std::ostream &os) +bool DicomDir::DoTheLoadingJob( ) { - if(metaElems) + Progress = 0.0f; + Abort = false; + + if (!ParseDir) { - metaElems->SetPrintLevel(PrintLevel); - metaElems->Print(os); - } - for(ListDicomDirPatient::iterator cc = patients.begin(); - cc != patients.end(); - ++cc) + // Only if user passed a DICOMDIR + // ------------------------------ + Fp = 0; + 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 { - (*cc)->SetPrintLevel( PrintLevel ); - (*cc)->Print( os ); + // Only if user passed a root directory + // ------------------------------------ + if ( GetFileName() == "." ) + { + // user passed '.' as Name + // we get current directory name + char buf[2048]; + const char *cwd = getcwd(buf, 2048); + if( cwd ) + { + SetFileName( buf ); // will be converted into a string + } + else + { + gdcmErrorMacro( "Path was too long to fit on 2048 bytes" ); + } + } + NewMeta(); + gdcmDebugMacro( "Parse directory and create the DicomDir : " + << GetFileName() ); + ParseDirectory(); } + return true; } -//----------------------------------------------------------------------------- -// Public /** * \brief This predicate, based on hopefully reasonable heuristics, - * decides whether or not the current 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 gdcmDocument is the one of a reasonable DicomDir, + * @return true when Document is the one of a reasonable DicomDir, * false otherwise. */ -bool gdcmDicomDir::IsReadable() +bool DicomDir::IsReadable() { - if( !gdcmDocument::IsReadable() ) + if ( Filetype == Unknown ) { + gdcmErrorMacro( "Wrong filetype for " << GetFileName()); 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; } @@ -193,709 +370,565 @@ bool gdcmDicomDir::IsReadable() } /** - * \brief Sets all fields to NULL - */ - -void gdcmDicomDir::Initialize() + * \brief adds *the* Meta to a partially created DICOMDIR + */ +DicomDirMeta *DicomDir::NewMeta() { - startMethod = NULL; - progressMethod = NULL; - endMethod = NULL; - startMethodArgDelete = NULL; - progressMethodArgDelete = NULL; - endMethodArgDelete = NULL; - startArg = NULL; - progressArg = NULL; - endArg = NULL; - - progress = 0.0; - abort = false; - - metaElems = 0; -} + if ( MetaElems ) + { + MetaElems->Delete(); + } + DocEntry *entry = GetFirstEntry(); + if ( entry ) + { + MetaElems = DicomDirMeta::New(true); // true = empty + entry = GetFirstEntry(); + while( entry ) + { + if ( dynamic_cast(entry) ) + break; -/** - * \ingroup gdcmDicomDir - * \brief fills the whole structure, starting from a root Directory - */ -void gdcmDicomDir::ParseDirectory() -{ - CreateDicomDirChainedList( GetFileName() ); - CreateDicomDir(); -} + MetaElems->AddEntry(entry); + RemoveEntry(entry); -/** - * \ingroup gdcmDicomDir - * \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 gdcmDicomDir::SetStartMethod(gdcmMethod* method, void* arg, - gdcmMethod* argDelete ) -{ - if( startArg && startMethodArgDelete ) + entry = GetFirstEntry(); + } + } + else // after root directory parsing { - startMethodArgDelete( startArg ); + MetaElems = DicomDirMeta::New(false); // false = not empty } - - startMethod = method; - startArg = arg; - startMethodArgDelete = argDelete; + MetaElems->SetSQItemNumber(0); // To avoid further missprinting + return MetaElems; } /** - * \ingroup gdcmDicomDir - * \brief Set the method to delete the argument - * The argument is destroyed when the method is changed or when the - * class is destroyed - * @param method Method to call to delete the argument + * \brief adds a new Patient (with the basic elements) to a partially created + * DICOMDIR */ -void gdcmDicomDir::SetStartMethodArgDelete(gdcmMethod* method) +DicomDirPatient *DicomDir::NewPatient() { - startMethodArgDelete = method; + DicomDirPatient *dd = DicomDirPatient::New(); + AddPatientToEnd( dd ); + return dd; } /** - * \ingroup gdcmDicomDir - * \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 + * \brief Remove all Patients */ -void gdcmDicomDir::SetProgressMethod(gdcmMethod* method, void* arg, - gdcmMethod* argDelete ) +void DicomDir::ClearPatient() { - if( progressArg && progressMethodArgDelete ) + for(ListDicomDirPatient::iterator cc = Patients.begin(); + cc!= Patients.end(); + ++cc) { - progressMethodArgDelete( progressArg ); + (*cc)->Unregister(); } - - progressMethod = method; - progressArg = arg; - progressMethodArgDelete = argDelete; + Patients.clear(); } /** - * \ingroup gdcmDicomDir - * \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 gdcmDicomDir::SetProgressMethodArgDelete(gdcmMethod* method) + * \brief Get the first entry while visiting the DicomDirPatients + * \return The first DicomDirPatient if found, otherwhise NULL + */ +DicomDirPatient *DicomDir::GetFirstPatient() { - progressMethodArgDelete = method; + ItPatient = Patients.begin(); + if ( ItPatient != Patients.end() ) + return *ItPatient; + return NULL; } /** - * \ingroup gdcmDicomDir - * \brief Set the end method to call when the parsing of the directory ends - * @param method Method to call - * @param arg Argument to pass to the method - * @param argDelete Argument - * \warning In python : the arg parameter isn't considered + * \brief Get the next entry while visiting the DicomDirPatients + * \note : meaningfull only if GetFirstEntry already called + * \return The next DicomDirPatient if found, otherwhise NULL */ -void gdcmDicomDir::SetEndMethod(gdcmMethod* method, void* arg, - gdcmMethod* argDelete ) +DicomDirPatient *DicomDir::GetNextPatient() { - if( endArg && endMethodArgDelete ) - { - endMethodArgDelete( endArg ); - } + gdcmAssertMacro (ItPatient != Patients.end()); - endMethod = method; - endArg = arg; - endMethodArgDelete = argDelete; + ++ItPatient; + if ( ItPatient != Patients.end() ) + return *ItPatient; + return NULL; } /** - * \ingroup gdcmDicomDir - * \brief Set the method to delete the argument - * The argument is destroyed when the method is changed or when the class - * is destroyed - * @param method Method to call to delete the argument + * \brief fills the whole structure, starting from a root Directory */ -void gdcmDicomDir::SetEndMethodArgDelete(gdcmMethod* method) +void DicomDir::ParseDirectory() { - endMethodArgDelete = method; + CreateDicomDirChainedList( GetFileName() ); + CreateDicomDir(); } /** - * \ingroup gdcmDicomDir - * \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 gdcmDicomDir::WriteDicomDir(std::string const& fileName) +bool DicomDir::Write(std::string const &fileName) { - uint16_t sq[4] = { 0x0004, 0x1220, 0xffff, 0xffff }; - uint16_t sqt[4]= { 0xfffe, 0xe0dd, 0xffff, 0xffff }; + int i; + uint16_t sq[6] = { 0x0004, 0x1220, 0x5153, 0x0000, 0xffff, 0xffff }; + uint16_t sqt[4]= { 0xfffe, 0xe0dd, 0x0000, 0x0000 }; - 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 = new uint8_t[128]; + char filePreamble[128]; memset(filePreamble, 0, 128); - fwrite(filePreamble,128,1,fp); - fwrite("DICM",4,1,fp); - delete[] filePreamble; + fp->write(filePreamble, 128); + binary_write( *fp, "DICM"); - gdcmDicomDirMeta *ptrMeta = GetDicomDirMeta(); - ptrMeta->Write(fp, gdcmExplicitVR); + DicomDirMeta *ptrMeta = GetMeta(); + ptrMeta->WriteContent(fp, ExplicitVR, true, false); - // force writing 0004|1220 [SQ ], that CANNOT exist within gdcmDicomDirMeta - fwrite(&sq[0],8,1,fp); // 0004 1220 ffff ffff + // 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) + for(ListDicomDirPatient::iterator cc = Patients.begin(); + cc != Patients.end(); + ++cc ) { - (*cc)->Write( fp, gdcmExplicitVR ); + (*cc)->WriteContent( fp, ExplicitVR, false, true ); } // 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 0000 0000 + } + + fp->close(); + delete fp; - fclose( fp ); return true; } -//----------------------------------------------------------------------------- -// Protected - /** - * \ingroup gdcmDicomDir - * \brief create a gdcmDocument-like chained list from a root Directory - * @param path entry point of the tree-like structure + * \brief Anonymize a DICOMDIR + * @return true */ -void gdcmDicomDir::CreateDicomDirChainedList(std::string const & path) + +bool DicomDir::Anonymize() { - CallStartMethod(); - gdcmDirList fileList(path,1); // gets recursively the file list - unsigned int count = 0; - VectDocument list; - gdcmHeader *header; - - TagHT.clear(); - patients.clear(); - - for( gdcmDirList::iterator it = fileList.begin(); - it != fileList.end(); - ++it ) + 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) { - progress = (float)(count+1)/(float)fileList.size(); - CallProgressMethod(); - if( abort ) + s << i; + v = (*cc)->GetDataEntry(0x0010, 0x0010) ; // Patient's Name + if (v) { - break; + v->SetString(s.str()); } - header = new gdcmHeader( it->c_str() ); - if( !header ) + v = (*cc)->GetDataEntry(0x0010, 0x0020) ; // Patient ID + if (v) { - dbg.Verbose( 1, - "gdcmDicomDir::CreateDicomDirChainedList: " - "failure in new Header ", - it->c_str() ); + v->SetString(" "); } - - if( header->IsReadable() ) - { - // Add the file header to the chained list: - list.push_back(header); - dbg.Verbose( 1, - "gdcmDicomDir::CreateDicomDirChainedList: readable ", - it->c_str() ); - - } - else - { - delete header; - } - count++; - } - // sorts Patient/Study/Serie/ - std::sort(list.begin(), list.end(), gdcmDicomDir::HeaderLessThan ); - - std::string tmp = fileList.GetDirName(); - //for each Header of the chained list, add/update the Patient/Study/Serie/Image info - SetElements(tmp, list); - CallEndMethod(); -} -/** - * \ingroup gdcmDicomDir - * \brief adds *the* Meta to a partially created DICOMDIR - */ - -gdcmDicomDirMeta * gdcmDicomDir::NewMeta() -{ - gdcmDicomDirMeta *m = new gdcmDicomDirMeta( &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) + v = (*cc)->GetDataEntry(0x0010, 0x0030) ; // Patient's BirthDate + if (v) { - m->AddDocEntry( cc->second ); + v->SetString(" "); } + s << ""; + i++; } - else // after root directory parsing - { - std::list elemList; - elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirMetaElements(); - m->FillObject(elemList); - } - m->SetSQItemNumber(0); // To avoid further missprinting - return m; + return true; } /** - * \brief adds a new Patient (with the basic elements) to a partially created DICOMDIR + * \brief Copies all the attributes from an other DocEntrySet + * @param set entry to copy from + * @remarks The contained DocEntries are not copied, only referenced */ -gdcmDicomDirPatient * gdcmDicomDir::NewPatient() +void DicomDir::Copy(DocEntrySet *set) { - std::list::iterator it; - uint16_t tmpGr,tmpEl; - gdcmDictEntry *dictEntry; - gdcmValEntry *entry; - - std::list elemList; - elemList=gdcmGlobal::GetDicomDirElements()->GetDicomDirPatientElements(); - gdcmSQItem *s = new gdcmSQItem(0); - - // for all the DicomDirPatient Elements - for( it = elemList.begin(); it != elemList.end(); ++it ) - { - tmpGr = it->group; - tmpEl = it->elem; - dictEntry = GetPubDict()->GetDictEntryByNumber(tmpGr, tmpEl); - entry = new gdcmValEntry( dictEntry ); - entry->SetOffset(0); // just to avoid further missprinting - entry->SetValue( it->value ); + // Remove all previous childs + ClearPatient(); - // 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 ); - } - - gdcmDicomDirPatient *p = new gdcmDicomDirPatient(s, &TagHT); - patients.push_front( p ); + Document::Copy(set); - return p; + DicomDir *dd = dynamic_cast(set); + if( dd ) + { + if(MetaElems) + MetaElems->Unregister(); + MetaElems = dd->MetaElems; + if(MetaElems) + MetaElems->Register(); + + Patients = dd->Patients; + for(ItPatient = Patients.begin();ItPatient != Patients.end();++ItPatient) + (*ItPatient)->Register(); + } } +//----------------------------------------------------------------------------- +// Protected /** - * \brief adds to the HTable - * the gdcmEntries (Dicom Elements) corresponding to the given type - * @param path full path file name (only used when type = GDCM_DICOMDIR_IMAGE - * @param type gdcmDicomDirObject type to create (GDCM_DICOMDIR_PATIENT, - * GDCM_DICOMDIR_STUDY, GDCM_DICOMDIR_SERIE ...) - * @param header gdcmHeader of the current file + * \brief create a Document-like chained list from a root Directory + * @param path entry point of the tree-like structure */ -void gdcmDicomDir::SetElement(std::string &path,gdcmDicomDirType type, - gdcmDocument *header) +void DicomDir::CreateDicomDirChainedList(std::string const &path) { - std::list elemList; - std::list::iterator it; - uint16_t tmpGr, tmpEl; - gdcmDictEntry *dictEntry; - gdcmValEntry *entry; - std::string val; - gdcmSQItem *si = new gdcmSQItem(0); // all the items will be at level 1 - switch( type ) - { - case GDCM_DICOMDIR_IMAGE: - elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirImageElements(); - break; - - case GDCM_DICOMDIR_SERIE: - elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirSerieElements(); - break; - - case GDCM_DICOMDIR_STUDY: - elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirStudyElements(); - break; - - case GDCM_DICOMDIR_PATIENT: - elemList = gdcmGlobal::GetDicomDirElements()->GetDicomDirPatientElements(); - break; - - case GDCM_DICOMDIR_META: - elemList = gdcmGlobal::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 + CallStartMethod(); + DirList dirList(path,1); // gets recursively the file list + unsigned int count = 0; + VectDocument list; + File *f; - for( it = elemList.begin(); it != elemList.end(); ++it) + DirListType fileList = dirList.GetFilenames(); + unsigned int nbFile = fileList.size(); + for( DirListType::iterator it = fileList.begin(); + it != fileList.end(); + ++it ) { - tmpGr = it->group; - tmpEl = it->elem; - dictEntry = GetPubDict()->GetDictEntryByNumber(tmpGr, tmpEl); - - entry = new gdcmValEntry( 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 = GetName( path ); - } - else if( tmpGr == 0x0004 && tmpEl == 0x1500 ) // Only used for image - { - if( header->GetFileName().substr(0, path.length()) != path ) - { - dbg.Verbose(0, "gdcmDicomDir::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 + Progress = (float)(count+1)/(float)nbFile; + CallProgressMethod(); + if ( Abort ) { - if ( header->GetEntryLengthByNumber(tmpGr,tmpEl) == 0 ) - val = it->value; + break; } - // GDCM_UNFOUND or not ! + f = File::New( ); + f->SetLoadMode(LoadMode); // we allow user not to load Sequences, + // or Shadow groups, or ...... + f->SetFileName( it->c_str() ); + f->Load( ); - entry->SetValue( val ); // troubles expected when vr=SQ ... - - if( dictEntry ) + if ( f->IsReadable() ) { - 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 ) - { - 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; + // Add the file to the chained list: + list.push_back(f); + gdcmDebugMacro( "Readable " << it->c_str() ); + } + else + { + f->Delete(); + } + count++; } - //int count=1; // find a trick to increment - //s->AddEntry(si, count); // Seg Faults - -} + // 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(); -/** - * \brief CallStartMethod - */ -void gdcmDicomDir::CallStartMethod() -{ - progress = 0.0f; - abort = false; - if( startMethod ) + for(VectDocument::iterator itDoc=list.begin(); + itDoc!=list.end(); + ++itDoc) { - startMethod( startArg ); + dynamic_cast(*itDoc)->Delete(); } } -/** - * \ingroup gdcmDicomDir - * \brief CallProgressMethod - */ -void gdcmDicomDir::CallProgressMethod() -{ - if( progressMethod ) - { - progressMethod( progressArg ); - } -} +//----------------------------------------------------------------------------- +// Private /** - * \ingroup gdcmDicomDir - * \brief CallEndMethod + * \brief Sets all fields to NULL */ -void gdcmDicomDir::CallEndMethod() +void DicomDir::Initialize() { - progress = 1.0f; - if( endMethod ) - { - endMethod( endArg ); - } + Progress = 0.0; + Abort = false; + + MetaElems = NULL; } -//----------------------------------------------------------------------------- -// Private /** - * \ingroup gdcmDicomDir - * \brief create a 'gdcmDicomDir' from a DICOMDIR gdcmHeader + * \brief create a 'gdcm::DicomDir' from a DICOMDIR Header */ -void gdcmDicomDir::CreateDicomDir() +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 : + // N.B. : VISIT, PRIVATE not fully dealt with // 1 - we save the beginning iterator // 2 - we continue to parse // 3 - we find an other tag // + we create the object for the precedent tag // + loop to 1 - + gdcmDebugMacro("Create DicomDir"); // Directory record sequence - gdcmDocEntry *e = GetDocEntryByNumber(0x0004, 0x1220); + DocEntry *e = GetDocEntry(0x0004, 0x1220); if ( !e ) { - dbg.Verbose(0, "gdcmDicomDir::gdcmDicomDir : 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; } - gdcmSeqEntry* s = dynamic_cast(e); + SeqEntry *s = dynamic_cast(e); if ( !s ) { - dbg.Verbose(0, "gdcmDicomDir::CreateDicomDir: no SeqEntry present"); - // useless : (0x0004,0x1220) IS a Sequence ! + gdcmWarningMacro( "Element (0004,1220) is not a Sequence ?!?"); return; } - gdcmDicomDirType type = gdcmDicomDir::GDCM_DICOMDIR_META; - metaElems = NewMeta(); - - ListSQItem listItems = s->GetSQItems(); + NewMeta(); - gdcmDocEntry * 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 ( gdcmValEntry* ValEntry = dynamic_cast< gdcmValEntry* >(d) ) + d = tmpSI->GetDocEntry(0x0004, 0x1430); // Directory Record Type + if ( DataEntry *dataEntry = dynamic_cast(d) ) { - v = ValEntry->GetValue(); + v = dataEntry->GetString(); } else { - dbg.Verbose(0, "gdcmDicomDir::CreateDicomDir: not a ValEntry."); + gdcmWarningMacro( "(0004,1430) not a DataEntry ?!?"); continue; } - if( v == "PATIENT " ) + // A decent DICOMDIR has much more images than series, + // more series than studies, and so on. + // This is the right order to perform the tests + + if ( v == "IMAGE " ) { - AddDicomDirPatientToEnd( *i ); - type = gdcmDicomDir::GDCM_DICOMDIR_PATIENT; + si = DicomDirImage::New(true); // true = empty + if ( !AddImageToEnd( static_cast(si)) ) + { + si->Delete(); + si = NULL; + gdcmErrorMacro( "Add AddImageToEnd failed"); + } } - else if( v == "STUDY " ) + else if ( v == "SERIES" ) { - AddDicomDirStudyToEnd( *i ); - type = gdcmDicomDir::GDCM_DICOMDIR_STUDY; + si = DicomDirSerie::New(true); // true = empty + if ( !AddSerieToEnd( static_cast(si)) ) + { + si->Delete(); + si = NULL; + gdcmErrorMacro( "Add AddSerieToEnd failed"); + } + } + else if ( v == "VISIT " ) + { + si = DicomDirVisit::New(true); // true = empty + if ( !AddVisitToEnd( static_cast(si)) ) + { + si->Delete(); + si = NULL; + gdcmErrorMacro( "Add AddVisitToEnd failed"); + } } - else if( v == "SERIES" ) + else if ( v == "STUDY " ) { - AddDicomDirSerieToEnd( *i ); - type = gdcmDicomDir::GDCM_DICOMDIR_SERIE; + si = DicomDirStudy::New(true); // true = empty + if ( !AddStudyToEnd( static_cast(si)) ) + { + si->Delete(); + si = NULL; + gdcmErrorMacro( "Add AddStudyToEnd failed"); + } } - else if( v == "IMAGE " ) + else if ( v == "PATIENT " ) { - AddDicomDirImageToEnd( *i ); - type = gdcmDicomDir::GDCM_DICOMDIR_IMAGE; + si = DicomDirPatient::New(true); // true = empty + if ( !AddPatientToEnd( static_cast(si)) ) + { + si->Delete(); + si = NULL; + gdcmErrorMacro( "Add PatientToEnd failed"); + } } + /// \todo : deal with PRIVATE (not so easy, since PRIVATE appears + /// at different levels ?!? ) + + else if ( v == "PRIVATE " ) // for SIEMENS 'CSA Non Image' + { + + gdcmWarningMacro( " -------------------------------------------" + << "a PRIVATE SQItem was found : " << v); + si = DicomDirPrivate::New(true); // true = empty + if ( !AddPrivateToEnd( static_cast(si)) ) + { + si->Delete(); + si = NULL; + gdcmErrorMacro( "Add PrivateToEnd failed"); + } + } else { - // It was not a 'PATIENT', nor a 'STUDY', nor a 'SERIE', - // neither an 'IMAGE' SQItem. Skip to next item. - continue; + // It was neither a 'PATIENT', nor a 'STUDY', nor a 'SERIE', + // nor an 'IMAGE' SQItem. Skip to next item. + gdcmWarningMacro( " -------------------------------------------" + << "a non PATIENT/STUDY/SERIE/IMAGE /VISIT/PRIVATE SQItem was found : " + << v); + + // FIXME : deal with other item types ! + tmpSI=s->GetNextSQItem(); // To avoid infinite loop + continue; } + if ( si ) + si->Copy(tmpSI); + + tmpSI=s->GetNextSQItem(); } + ClearEntry(); +} + +/** + * \brief AddPatientToEnd + * @param dd SQ Item to enqueue to the DicomPatient chained List + */ +bool DicomDir::AddPatientToEnd(DicomDirPatient *dd) +{ + Patients.push_back(dd); + return true; } /** - * \ingroup gdcmDicomDir - * \brief Well ... there is only one occurence + * \brief AddStudyToEnd + * @param dd SQ Item to enqueue to the DicomDirStudy chained List */ -void gdcmDicomDir::AddDicomDirMeta() +bool DicomDir::AddStudyToEnd(DicomDirStudy *dd) { - if( metaElems ) + if ( Patients.size() > 0 ) { - delete metaElems; + ListDicomDirPatient::iterator itp = Patients.end(); + itp--; + (*itp)->AddStudy(dd); + return true; } - metaElems = new gdcmDicomDirMeta( &TagHT ); + return false; } /** - * \ingroup gdcmDicomDir - * \brief AddDicomDirPatientToEnd - * @param s SQ Item to enqueue to the DicomPatient chained List + * \brief AddSerieToEnd + * @param dd SQ Item to enqueue to the DicomDirSerie chained List */ -void gdcmDicomDir::AddDicomDirPatientToEnd(gdcmSQItem *s) +bool DicomDir::AddSerieToEnd(DicomDirSerie *dd) { - patients.push_back(new gdcmDicomDirPatient(s, &TagHT)); + 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 AddDicomDirStudyToEnd - * @param s SQ Item to enqueue to the DicomDirStudy chained List + * \brief AddVisitToEnd + * @param dd SQ Item to enqueue to the DicomDirVisit chained List */ - void gdcmDicomDir::AddDicomDirStudyToEnd(gdcmSQItem *s) +bool DicomDir::AddVisitToEnd(DicomDirVisit *dd) { - if( patients.size() > 0 ) + if ( Patients.size() > 0 ) { - ListDicomDirPatient::iterator itp = patients.end(); + ListDicomDirPatient::iterator itp = Patients.end(); itp--; - (*itp)->AddDicomDirStudy(new gdcmDicomDirStudy(s, &TagHT)); + + DicomDirStudy *study = (*itp)->GetLastStudy(); + if ( study ) + { + study->AddVisit(dd); + return true; + } } + return false; } - /** - * \ingroup gdcmDicomDir - * \brief AddDicomDirSerieToEnd - * @param s SQ Item to enqueue to the DicomDirSerie chained List + * \brief AddImageToEnd + * @param dd SQ Item to enqueue to the DicomDirImage chained List */ -void gdcmDicomDir::AddDicomDirSerieToEnd(gdcmSQItem *s) +bool DicomDir::AddImageToEnd(DicomDirImage *dd) { - if( patients.size() > 0 ) + if ( Patients.size() > 0 ) { - ListDicomDirPatient::iterator itp = patients.end(); + 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 gdcmDicomDirSerie(s, &TagHT)); + DicomDirSerie *serie = study->GetLastSerie(); + if ( serie ) + { + serie->AddImage(dd); + return true; + } } } + return false; } /** - * \ingroup gdcmDicomDir - * \brief AddDicomDirImageToEnd - * @param s SQ Item to enqueue to the DicomDirImage chained List + * \brief AddPrivateToEnd + * @param dd SQ Item to enqueue to the DicomDirPrivate chained List + * (checked for SIEMENS 'CSA non image') */ - void gdcmDicomDir::AddDicomDirImageToEnd(gdcmSQItem *s) +bool DicomDir::AddPrivateToEnd(DicomDirPrivate *dd) { - if( patients.size() > 0 ) + if ( Patients.size() > 0 ) { - ListDicomDirPatient::iterator itp = patients.end(); + 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 gdcmDicomDirImage(s, &TagHT)); + serie->AddPrivate(dd); + return true; } } } + return false; } /** - * \ingroup gdcmDicomDir - * \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 gdcmDicomDir::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 = ""; @@ -904,30 +937,36 @@ void gdcmDicomDir::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)->GetEntryString(0x0010,0x0010); + patCurID = (*it)->GetEntryString(0x0010,0x0011); + studCurInstanceUID = (*it)->GetEntryString(0x0020,0x000d); + studCurID = (*it)->GetEntryString(0x0020,0x0010); + serCurInstanceUID = (*it)->GetEntryString(0x0020,0x000e); + serCurID = (*it)->GetEntryString(0x0020,0x0011); + + if ( patCurName != patPrevName || patCurID != patPrevID || first ) { SetElement(path, GDCM_DICOMDIR_PATIENT, *it); + first = true; } - // if new Study Deal with 'STUDY' Elements - if( studCurInstanceUID != studPrevInstanceUID || studCurID != studPrevID ) + // if new Study, deal with 'STUDY' Elements + if ( studCurInstanceUID != studPrevInstanceUID || studCurID != studPrevID + || first ) { SetElement(path, GDCM_DICOMDIR_STUDY, *it); + first = true; } - // if new Serie Deal with 'SERIE' Elements - if( serCurInstanceUID != serPrevInstanceUID || serCurID != serPrevID ) + // if new Serie, deal with 'SERIE' Elements + if ( serCurInstanceUID != serPrevInstanceUID || serCurID != serPrevID + || first ) { SetElement(path, GDCM_DICOMDIR_SERIE, *it); } @@ -941,16 +980,258 @@ void gdcmDicomDir::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; + DataEntry *entry; + std::string val; + SQItem *si; + switch( type ) + { + case GDCM_DICOMDIR_IMAGE: + elemList = Global::GetDicomDirElements()->GetDicomDirImageElements(); + si = DicomDirImage::New(true); + if ( !AddImageToEnd(static_cast(si)) ) + { + si->Delete(); + gdcmErrorMacro( "Add ImageToEnd failed"); + } + break; + case GDCM_DICOMDIR_SERIE: + elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements(); + si = DicomDirSerie::New(true); + if ( !AddSerieToEnd(static_cast(si)) ) + { + si->Delete(); + gdcmErrorMacro( "Add SerieToEnd failed"); + } + break; + case GDCM_DICOMDIR_STUDY: + elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements(); + si = DicomDirStudy::New(true); + if ( !AddStudyToEnd(static_cast(si)) ) + { + si->Delete(); + gdcmErrorMacro( "Add StudyToEnd failed"); + } + break; + case GDCM_DICOMDIR_PATIENT: + elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements(); + si = DicomDirPatient::New(true); + if ( !AddPatientToEnd(static_cast(si)) ) + { + si->Delete(); + gdcmErrorMacro( "Add PatientToEnd failed"); + } + break; + case GDCM_DICOMDIR_META: // never used ?!? --> Done within DoTheLoadingJob + if ( MetaElems ) + { + MetaElems->Delete(); + gdcmErrorMacro( "MetaElements already exist, they will be destroyed"); + } + elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements(); + MetaElems = DicomDirMeta::New(true); + si = MetaElems; + break; + default: + return; + } + + // FIXME : troubles found when it's a SeqEntry + + // removed all the seems-to-be-useless stuff about Referenced Image Sequence + // to avoid further troubles + // imageElem 0008 1140 "" // Referenced Image Sequence + // imageElem fffe e000 "" // 'no length' item : length to be set to 0xffffffff later + // imageElem 0008 1150 "" // Referenced SOP Class UID : to be set/forged later + // imageElem 0008 1155 "" // Referenced SOP Instance UID : to be set/forged later + // imageElem fffe e00d "" // Item delimitation : length to be set to ZERO later + + std::string referencedVal; + // for all the relevant elements found in their own spot of the DicomDir.dic + for( it = elemList.begin(); it != elemList.end(); ++it) + { + tmpGr = it->Group; + tmpEl = it->Elem; + + entry = DataEntry::New(tmpGr, tmpEl, it->VR); // dicomelements file was modified, to store VR + entry->SetOffset(0); // just to avoid further missprinting + + if ( header ) + { + // NULL when we Build Up (ex nihilo) a DICOMDIR + // or when we add the META elems + val = header->GetEntryString(tmpGr, tmpEl); + } + else + { + val = GDCM_UNFOUND; + } + + if ( val == GDCM_UNFOUND) + { + if ( tmpGr == 0x0004 ) // never present in File ! + { + switch (tmpEl) + { + case 0x1130: // File-set ID + // force to the *end* File Name + val = Util::GetName( path ); + break; + + case 0x1500: // Only used for image + if ( header->GetFileName().substr(0, path.length()) != path ) + { + gdcmWarningMacro( "The base path of file name is incorrect"); + val = header->GetFileName(); + } + else + { + // avoid the first '/' in File name ! + if ( header->GetFileName().c_str()[path.length()] + == GDCM_FILESEPARATOR ) + val = &(header->GetFileName().c_str()[path.length()+1]); + else + val = &(header->GetFileName().c_str()[path.length()]); + } + break; + + case 0x1510: // Referenced SOP Class UID in File + referencedVal = header->GetEntryString(0x0008, 0x0016); + // FIXME : probabely something to check + val = referencedVal; + break; + + case 0x1511: // Referenced SOP Instance UID in File + referencedVal = header->GetEntryString(0x0008, 0x0018); + // FIXME : probabely something to check + val = referencedVal; + break; + + case 0x1512: // Referenced Transfer Syntax UID in File + referencedVal = header->GetEntryString(0x0002, 0x0010); + // FIXME : probabely something to check + val = referencedVal; + break; + + default : + val = it->Value; + } + } + else + { + // If the entry is not found in the Header, don't write its 'value' in the DICOMDIR ! + entry->Delete(); + continue; + } + } + else + { + if ( header->GetEntryLength(tmpGr,tmpEl) == 0 ) + { + val = it->Value; + // Don't polute the DICOMDIR with empty fields + if (val == "") + { + entry->Delete(); + continue; + } + } + } + +/* FIX later the pb of creating the 'Implementation Version Name'! + + if (val == GDCM_UNFOUND) + val = ""; + + if ( tmpGr == 0x0002 && tmpEl == 0x0013) + { + // 'Implementation Version Name' + std::string val = "GDCM "; + val += Util::GetVersion(); + } +*/ + + entry->SetString( val ); // troubles expected when vr=SQ ... + + if ( type == GDCM_DICOMDIR_META ) // fusible : should never print ! + { + gdcmDebugMacro("GDCM_DICOMDIR_META ?!? should never print that"); + } + + si->AddEntry(entry); + entry->Delete(); + } +} + +/** + * \brief Move the content of the source SQItem to the destination SQItem + * Only DocEntry's are moved + * @param dst destination SQItem + * @param src source SQItem + */ +void DicomDir::MoveSQItem(DocEntrySet *dst, DocEntrySet *src) +{ + 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(); } } /** - * \ingroup gdcmDicomDir - * \brief compares two dgcmHeaders + * \brief compares two files */ -bool gdcmDicomDir::HeaderLessThan(gdcmDocument *header1, gdcmDocument *header2) +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