X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=a8b156974a0786e52f97150d9a9203145f60102b;hb=5bf7c51796867388334836847a6874640bc83f89;hp=37966499bb038759d5d188a47fce182a6a0f29ab;hpb=3fd520b58c8d1939994de2c63cc038c3e7ac9522;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 37966499..a8b15697 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,12 +3,12 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2004/08/26 15:29:53 $ - Version: $Revision: 1.68 $ + Date: $Date: 2004/10/20 14:30:40 $ + Version: $Revision: 1.106 $ 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 @@ -20,7 +20,6 @@ #include "gdcmValEntry.h" #include "gdcmBinEntry.h" #include "gdcmSeqEntry.h" - #include "gdcmGlobal.h" #include "gdcmUtil.h" #include "gdcmDebug.h" @@ -34,7 +33,10 @@ #include #endif -# include +#include + +namespace gdcm +{ // Implicit VR Little Endian #define UI1_2_840_10008_1_2 "1.2.840.10008.1.2" @@ -69,22 +71,22 @@ #define str2num(str, typeNum) *((typeNum *)(str)) //----------------------------------------------------------------------------- -// Refer to gdcmDocument::CheckSwap() -const unsigned int gdcmDocument::HEADER_LENGTH_TO_READ = 256; +// Refer to Document::CheckSwap() +const unsigned int Document::HEADER_LENGTH_TO_READ = 256; -// Refer to gdcmDocument::SetMaxSizeLoadEntry() -const unsigned int gdcmDocument::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096 -const unsigned int gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff; +// Refer to Document::SetMaxSizeLoadEntry() +const unsigned int Document::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096 +const unsigned int Document::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff; //----------------------------------------------------------------------------- // Constructor / Destructor /** * \brief constructor - * @param inFilename file to be opened for parsing + * @param filename file to be opened for parsing */ -gdcmDocument::gdcmDocument( std::string const & filename ) - : gdcmElementSet(-1) +Document::Document( std::string const & filename ) + : ElementSet(-1) { SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Filename = filename; @@ -95,7 +97,7 @@ gdcmDocument::gdcmDocument( std::string const & filename ) return; } - dbg.Verbose(0, "gdcmDocument::gdcmDocument: starting parsing of file: ", + dbg.Verbose(0, "Document::Document: starting parsing of file: ", Filename.c_str()); rewind(Fp); @@ -107,10 +109,7 @@ gdcmDocument::gdcmDocument( std::string const & filename ) long beg = ftell(Fp); lgt -= beg; - SQDepthLevel = 0; - - long l = ParseDES( this, beg, lgt, false); // le Load sera fait a la volee - (void)l; //is l used anywhere ? + ParseDES( this, beg, lgt, false); // le Load sera fait a la volee rewind(Fp); @@ -119,17 +118,35 @@ gdcmDocument::gdcmDocument( std::string const & filename ) std::string PhotometricInterpretation = GetEntryByNumber(0x0028,0x0004); if( PhotometricInterpretation == "PALETTE COLOR " ) { - LoadEntryVoidArea(0x0028,0x1200); // gray LUT - LoadEntryVoidArea(0x0028,0x1201); // R LUT - LoadEntryVoidArea(0x0028,0x1202); // G LUT - LoadEntryVoidArea(0x0028,0x1203); // B LUT + LoadEntryBinArea(0x0028,0x1200); // gray LUT + /// FIXME FIXME FIXME + /// The tags refered by the three following lines used to be CORRECTLY + /// defined as having an US Value Representation in the public + /// dictionnary. BUT the semantics implied by the three following + /// lines state that the corresponding tag contents are in fact + /// the ones of a BinEntry. + /// In order to fix things "Quick and Dirty" the dictionnary was + /// altered on PURPOUS but now contains a WRONG value. + /// In order to fix things and restore the dictionary to its + /// correct value, one needs to decided of the semantics by deciding + /// wether the following tags are either: + /// - multivaluated US, and hence loaded as ValEntry, but afterwards + /// also used as BinEntry, which requires the proper conversion, + /// - OW, and hence loaded as BinEntry, but afterwards also used + /// as ValEntry, which requires the proper conversion. + LoadEntryBinArea(0x0028,0x1201); // R LUT + LoadEntryBinArea(0x0028,0x1202); // G LUT + LoadEntryBinArea(0x0028,0x1203); // B LUT - LoadEntryVoidArea(0x0028,0x1221); // Segmented Red Palette Color LUT Data - LoadEntryVoidArea(0x0028,0x1222); // Segmented Green Palette Color LUT Data - LoadEntryVoidArea(0x0028,0x1223); // Segmented Blue Palette Color LUT Data + // Segmented Red Palette Color LUT Data + LoadEntryBinArea(0x0028,0x1221); + // Segmented Green Palette Color LUT Data + LoadEntryBinArea(0x0028,0x1222); + // Segmented Blue Palette Color LUT Data + LoadEntryBinArea(0x0028,0x1223); } //FIXME later : how to use it? - LoadEntryVoidArea(0x0028,0x3006); //LUT Data (CTX dependent) + LoadEntryBinArea(0x0028,0x3006); //LUT Data (CTX dependent) CloseFile(); @@ -149,7 +166,7 @@ gdcmDocument::gdcmDocument( std::string const & filename ) RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares // with "little-endian strings" { - Filetype = gdcmACR_LIBIDO; + Filetype = ACR_LIBIDO; std::string rows = GetEntryByNumber(0x0028, 0x0010); std::string columns = GetEntryByNumber(0x0028, 0x0011); SetEntryByNumber(columns, 0x0028, 0x0010); @@ -162,10 +179,10 @@ gdcmDocument::gdcmDocument( std::string const & filename ) /** * \brief This default constructor doesn't parse the file. You should - * then invoke \ref gdcmDocument::SetFileName and then the parsing. + * then invoke \ref Document::SetFileName and then the parsing. */ -gdcmDocument::gdcmDocument() - :gdcmElementSet(-1) +Document::Document() + :ElementSet(-1) { SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Initialise(); @@ -175,7 +192,7 @@ gdcmDocument::gdcmDocument() /** * \brief Canonical destructor. */ -gdcmDocument::~gdcmDocument () +Document::~Document () { RefPubDict = NULL; RefShaDict = NULL; @@ -184,7 +201,7 @@ gdcmDocument::~gdcmDocument () for (TagDocEntryHT::const_iterator it = TagHT.begin(); it != TagHT.end(); ++it ) { - delete it->second; + //delete it->second; //temp remove } TagHT.clear(); } @@ -196,7 +213,7 @@ gdcmDocument::~gdcmDocument () * \brief Prints The Dict Entries of THE public Dicom Dictionary * @return */ -void gdcmDocument::PrintPubDict(std::ostream & os) +void Document::PrintPubDict(std::ostream & os) { RefPubDict->Print(os); } @@ -205,7 +222,7 @@ void gdcmDocument::PrintPubDict(std::ostream & os) * \brief Prints The Dict Entries of THE shadow Dicom Dictionary * @return */ -void gdcmDocument::PrintShaDict(std::ostream & os) +void Document::PrintShaDict(std::ostream & os) { RefShaDict->Print(os); } @@ -215,7 +232,7 @@ void gdcmDocument::PrintShaDict(std::ostream & os) /** * \brief Get the public dictionary used */ -gdcmDict *gdcmDocument::GetPubDict() +Dict* Document::GetPubDict() { return RefPubDict; } @@ -223,7 +240,7 @@ gdcmDict *gdcmDocument::GetPubDict() /** * \brief Get the shadow dictionary used */ -gdcmDict *gdcmDocument::GetShaDict() +Dict* Document::GetShaDict() { return RefShaDict; } @@ -232,7 +249,7 @@ gdcmDict *gdcmDocument::GetShaDict() * \brief Set the shadow dictionary used * \param dict dictionary to use in shadow */ -bool gdcmDocument::SetShaDict(gdcmDict *dict) +bool Document::SetShaDict(Dict *dict) { RefShaDict = dict; return !RefShaDict; @@ -242,31 +259,31 @@ bool gdcmDocument::SetShaDict(gdcmDict *dict) * \brief Set the shadow dictionary used * \param dictName name of the dictionary to use in shadow */ -bool gdcmDocument::SetShaDict(DictKey const & dictName) +bool Document::SetShaDict(DictKey const & dictName) { - RefShaDict = gdcmGlobal::GetDicts()->GetDict(dictName); + RefShaDict = Global::GetDicts()->GetDict(dictName); return !RefShaDict; } /** * \brief This predicate, based on hopefully reasonable heuristics, - * decides whether or not the current gdcmDocument 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 Dicom/Acr File. - * @return true when gdcmDocument is the one of a reasonable Dicom/Acr file, + * @return true when Document is the one of a reasonable Dicom/Acr file, * false otherwise. */ -bool gdcmDocument::IsReadable() +bool Document::IsReadable() { - if( Filetype == gdcmUnknown) + if( Filetype == Unknown) { - dbg.Verbose(0, "gdcmDocument::IsReadable: wrong filetype"); + dbg.Verbose(0, "Document::IsReadable: wrong filetype"); return false; } if( TagHT.empty() ) { - dbg.Verbose(0, "gdcmDocument::IsReadable: no tags in internal" + dbg.Verbose(0, "Document::IsReadable: no tags in internal" " hash table."); return false; } @@ -278,14 +295,14 @@ bool gdcmDocument::IsReadable() /** * \brief Internal function that checks whether the Transfer Syntax given * as argument is the one present in the current document. - * @param SyntaxToCheck The transfert syntax we need to check against. + * @param syntaxToCheck The transfert syntax we need to check against. * @return True when SyntaxToCheck corresponds to the Transfer Syntax of * the current document. False either when the document contains * no Transfer Syntax, or when the Tranfer Syntaxes doesn't match. */ -bool gdcmDocument::IsGivenTransferSyntax(std::string const & syntaxToCheck) +bool Document::IsGivenTransferSyntax(std::string const & syntaxToCheck) { - gdcmDocEntry *entry = GetDocEntryByNumber(0x0002, 0x0010); + DocEntry *entry = GetDocEntryByNumber(0x0002, 0x0010); if ( !entry ) { return false; @@ -294,7 +311,7 @@ bool gdcmDocument::IsGivenTransferSyntax(std::string const & syntaxToCheck) // The entry might be present but not loaded (parsing and loading // happen at different stages): try loading and proceed with check... LoadDocEntrySafe(entry); - if (gdcmValEntry* valEntry = dynamic_cast< gdcmValEntry* >(entry) ) + if (ValEntry* valEntry = dynamic_cast< ValEntry* >(entry) ) { std::string transfer = valEntry->GetValue(); // The actual transfer (as read from disk) might be padded. We @@ -319,10 +336,10 @@ bool gdcmDocument::IsGivenTransferSyntax(std::string const & syntaxToCheck) * \brief Determines if the Transfer Syntax of the present document * corresponds to a Implicit Value Representation of * Little Endian. - * \sa \ref gdcmDocument::IsGivenTransferSyntax. + * \sa \ref Document::IsGivenTransferSyntax. * @return True when ImplicitVRLittleEndian found. False in all other cases. */ -bool gdcmDocument::IsImplicitVRLittleEndianTransferSyntax() +bool Document::IsImplicitVRLittleEndianTransferSyntax() { return IsGivenTransferSyntax(UI1_2_840_10008_1_2); } @@ -332,7 +349,7 @@ bool gdcmDocument::IsImplicitVRLittleEndianTransferSyntax() * and if it corresponds to a ExplicitVRLittleEndian one. * @return True when ExplicitVRLittleEndian found. False in all other cases. */ -bool gdcmDocument::IsExplicitVRLittleEndianTransferSyntax() +bool Document::IsExplicitVRLittleEndianTransferSyntax() { return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1); } @@ -342,7 +359,7 @@ bool gdcmDocument::IsExplicitVRLittleEndianTransferSyntax() * and if it corresponds to a DeflatedExplicitVRLittleEndian one. * @return True when DeflatedExplicitVRLittleEndian found. False in all other cases. */ -bool gdcmDocument::IsDeflatedExplicitVRLittleEndianTransferSyntax() +bool Document::IsDeflatedExplicitVRLittleEndianTransferSyntax() { return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1_99); } @@ -352,7 +369,7 @@ bool gdcmDocument::IsDeflatedExplicitVRLittleEndianTransferSyntax() * and if it corresponds to a Explicit VR Big Endian one. * @return True when big endian found. False in all other cases. */ -bool gdcmDocument::IsExplicitVRBigEndianTransferSyntax() +bool Document::IsExplicitVRBigEndianTransferSyntax() { return IsGivenTransferSyntax(UI1_2_840_10008_1_2_2); } @@ -362,7 +379,7 @@ bool gdcmDocument::IsExplicitVRBigEndianTransferSyntax() * and if it corresponds to a JPEGBaseLineProcess1 one. * @return True when JPEGBaseLineProcess1found. False in all other cases. */ -bool gdcmDocument::IsJPEGBaseLineProcess1TransferSyntax() +bool Document::IsJPEGBaseLineProcess1TransferSyntax() { return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_50); } @@ -372,7 +389,7 @@ bool gdcmDocument::IsJPEGBaseLineProcess1TransferSyntax() * and if it corresponds to a JPEGExtendedProcess2-4 one. * @return True when JPEGExtendedProcess2-4 found. False in all other cases. */ -bool gdcmDocument::IsJPEGExtendedProcess2_4TransferSyntax() +bool Document::IsJPEGExtendedProcess2_4TransferSyntax() { return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_51); } @@ -382,7 +399,7 @@ bool gdcmDocument::IsJPEGExtendedProcess2_4TransferSyntax() * and if it corresponds to a JPEGExtendeProcess3-5 one. * @return True when JPEGExtendedProcess3-5 found. False in all other cases. */ -bool gdcmDocument::IsJPEGExtendedProcess3_5TransferSyntax() +bool Document::IsJPEGExtendedProcess3_5TransferSyntax() { return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_52); } @@ -393,7 +410,7 @@ bool gdcmDocument::IsJPEGExtendedProcess3_5TransferSyntax() * @return True when JPEGSpectralSelectionProcess6-8 found. False in all * other cases. */ -bool gdcmDocument::IsJPEGSpectralSelectionProcess6_8TransferSyntax() +bool Document::IsJPEGSpectralSelectionProcess6_8TransferSyntax() { return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_53); } @@ -404,7 +421,7 @@ bool gdcmDocument::IsJPEGSpectralSelectionProcess6_8TransferSyntax() * @return True when RLE Lossless found. False in all * other cases. */ -bool gdcmDocument::IsRLELossLessTransferSyntax() +bool Document::IsRLELossLessTransferSyntax() { return IsGivenTransferSyntax(UI1_2_840_10008_1_2_5); } @@ -416,7 +433,7 @@ bool gdcmDocument::IsRLELossLessTransferSyntax() * other cases. */ -bool gdcmDocument::IsJPEGLossless() +bool Document::IsJPEGLossless() { return ( IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_55) || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_57) @@ -429,17 +446,44 @@ bool gdcmDocument::IsJPEGLossless() * @return True when JPEG2000 (Lossly or LossLess) found. False in all * other cases. */ -bool gdcmDocument::IsJPEG2000() +bool Document::IsJPEG2000() { return ( IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_90) || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_91) ); } +/** + * \brief Determines if the Transfer Syntax corresponds to any form + * of Jpeg encoded Pixel data. + * @return True when any form of JPEG found. False otherwise. + */ +bool Document::IsJPEGTransferSyntax() +{ + return ( IsJPEGBaseLineProcess1TransferSyntax() + || IsJPEGExtendedProcess2_4TransferSyntax() + || IsJPEGExtendedProcess3_5TransferSyntax() + || IsJPEGSpectralSelectionProcess6_8TransferSyntax() + || IsJPEGLossless() + || IsJPEG2000() ); +} + + +/** + * \brief Determines if the Transfer Syntax corresponds to encapsulated + * of encoded Pixel Data (as opposed to native). + * @return True when encapsulated. False when native. + */ +bool Document::IsEncapsulateTransferSyntax() +{ + return ( IsJPEGTransferSyntax() + || IsRLELossLessTransferSyntax() ); +} + /** * \brief Predicate for dicom version 3 file. * @return True when the file is a dicom version 3. */ -bool gdcmDocument::IsDicomV3() +bool Document::IsDicomV3() { // Checking if Transfert Syntax exists is enough // Anyway, it's to late check if the 'Preamble' was found ... @@ -453,24 +497,24 @@ bool gdcmDocument::IsDicomV3() * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown) * @return the FileType code */ -FileType gdcmDocument::GetFileType() +FileType Document::GetFileType() { return Filetype; } /** - * \brief Tries to open the file \ref gdcmDocument::Filename and + * \brief Tries to open the file \ref Document::Filename and * checks the preamble when existing. * @return The FILE pointer on success. */ -FILE* gdcmDocument::OpenFile() +FILE* Document::OpenFile() { Fp = fopen(Filename.c_str(),"rb"); if(!Fp) { dbg.Verbose( 0, - "gdcmDocument::OpenFile cannot open file: ", + "Document::OpenFile cannot open file: ", Filename.c_str()); return 0; } @@ -495,7 +539,7 @@ FILE* gdcmDocument::OpenFile() fclose(Fp); dbg.Verbose( 0, - "gdcmDocument::OpenFile not DICOM/ACR (missing preamble)", + "Document::OpenFile not DICOM/ACR (missing preamble)", Filename.c_str()); return 0; @@ -505,7 +549,7 @@ FILE* gdcmDocument::OpenFile() * \brief closes the file * @return TRUE if the close was successfull */ -bool gdcmDocument::CloseFile() +bool Document::CloseFile() { int closed = fclose(Fp); Fp = 0; @@ -520,17 +564,14 @@ bool gdcmDocument::CloseFile() * (ACR-NEMA, ExplicitVR, ImplicitVR) * \return Always true. */ -void gdcmDocument::Write(FILE* fp,FileType filetype) +void Document::Write(FILE* fp,FileType filetype) { /// \todo move the following lines (and a lot of others, to be written) - /// to a future function CheckAndCorrectHeader - - /// WARNING : Si on veut ecrire du DICOM V3 a partir d'un DcmHeader ACR-NEMA - /// no way (check : FileType est un champ de gdcmDocument ...) - /// a moins de se livrer a un tres complique ajout des champs manquants. - /// faire un CheckAndCorrectHeader (?) - - if (filetype == gdcmImplicitVR) + /// to a future function CheckAndCorrectHeader + /// (necessary if user wants to write a DICOM V3 file + /// starting from an ACR-NEMA (V2) Header + + if (filetype == ImplicitVR) { std::string implicitVRTransfertSyntax = UI1_2_840_10008_1_2; ReplaceOrCreateByNumber(implicitVRTransfertSyntax,0x0002, 0x0010); @@ -543,7 +584,7 @@ void gdcmDocument::Write(FILE* fp,FileType filetype) SetEntryLengthByNumber(18, 0x0002, 0x0010); } - if (filetype == gdcmExplicitVR) + if (filetype == ExplicitVR) { std::string explicitVRTransfertSyntax = UI1_2_840_10008_1_2_1; ReplaceOrCreateByNumber(explicitVRTransfertSyntax,0x0002, 0x0010); @@ -568,61 +609,78 @@ void gdcmDocument::Write(FILE* fp,FileType filetype) * UpdateGroupLength(true,ACR); */ - gdcmElementSet::Write(fp, filetype); // This one is recursive + ElementSet::Write(fp, filetype); // This one is recursive } /** * \brief Modifies the value of a given Header Entry (Dicom Element) * when it exists. Create it with the given value when unexistant. - * @param Value (string) Value to be set - * @param Group Group number of the Entry - * @param Elem Element number of the Entry + * @param value (string) Value to be set + * @param group Group number of the Entry + * @param elem Element number of the Entry + * @param VR V(alue) R(epresentation) of the Entry -if private Entry- * \return pointer to the modified/created Header Entry (NULL when creation * failed). - */ - -gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber( + */ +ValEntry* Document::ReplaceOrCreateByNumber( std::string const & value, uint16_t group, - uint16_t elem ) + uint16_t elem, + std::string const & VR ) { - gdcmValEntry* valEntry = 0; - - gdcmDocEntry* currentEntry = GetDocEntryByNumber( group, elem); + ValEntry* valEntry = 0; + DocEntry* currentEntry = GetDocEntryByNumber( group, elem); + if (!currentEntry) { - // The entry wasn't present and we simply create the required ValEntry: - currentEntry = NewDocEntryByNumber(group, elem); + // check if (group,element) DictEntry exists + // if it doesn't, create an entry in DictSet::VirtualEntry + // and use it + + // Find out if the tag we received is in the dictionaries: + Dict *pubDict = Global::GetDicts()->GetDefaultPubDict(); + DictEntry* dictEntry = pubDict->GetDictEntryByNumber(group, elem); + if (!dictEntry) + { + currentEntry = NewDocEntryByNumber(group, elem,VR); + } + else + { + currentEntry = NewDocEntryByNumber(group, elem); + } + if (!currentEntry) { - dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: call to" + dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: call to" " NewDocEntryByNumber failed."); return NULL; } - valEntry = new gdcmValEntry(currentEntry); + valEntry = new ValEntry(currentEntry); if ( !AddEntry(valEntry)) { - dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: AddEntry" + dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry" " failed allthough this is a creation."); } } else { - valEntry = dynamic_cast< gdcmValEntry* >(currentEntry); - if ( !valEntry ) + valEntry = dynamic_cast< ValEntry* >(currentEntry); + if ( !valEntry ) // Euuuuh? It wasn't a ValEntry + // then we change it to a ValEntry ? + // Shouldn't it be considered as an error ? { - // We need to promote the gdcmDocEntry to a gdcmValEntry: - valEntry = new gdcmValEntry(currentEntry); + // We need to promote the DocEntry to a ValEntry: + valEntry = new ValEntry(currentEntry); if (!RemoveEntry(currentEntry)) { - dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: removal" + dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: removal" " of previous DocEntry failed."); return NULL; } if ( !AddEntry(valEntry)) { - dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: adding" + dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: adding" " promoted ValEntry failed."); return NULL; } @@ -637,36 +695,80 @@ gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber( /* * \brief Modifies the value of a given Header Entry (Dicom Element) * when it exists. Create it with the given value when unexistant. - * @param voidArea (binary) value to be set + * @param binArea (binary) value to be set * @param Group Group number of the Entry * @param Elem Element number of the Entry * \return pointer to the modified/created Header Entry (NULL when creation * failed). */ -gdcmBinEntry * gdcmDocument::ReplaceOrCreateByNumber( - void *voidArea, +BinEntry* Document::ReplaceOrCreateByNumber( + uint8_t* binArea, int lgth, uint16_t group, - uint16_t elem) + uint16_t elem, + std::string const& VR ) { - gdcmBinEntry* b = 0; - gdcmDocEntry* a = GetDocEntryByNumber( group, elem); - if (!a) + BinEntry* binEntry = 0; + DocEntry* currentEntry = GetDocEntryByNumber( group, elem); + if (!currentEntry) { - a = NewBinEntryByNumber(group, elem); - if (!a) + + // check if (group,element) DictEntry exists + // if it doesn't, create an entry in DictSet::VirtualEntry + // and use it + + // Find out if the tag we received is in the dictionaries: + Dict *pubDict = Global::GetDicts()->GetDefaultPubDict(); + DictEntry *dictEntry = pubDict->GetDictEntryByNumber(group, elem); + + if (!dictEntry) { - return 0; + currentEntry = NewDocEntryByNumber(group, elem, VR); + } + else + { + currentEntry = NewDocEntryByNumber(group, elem); + } + if (!currentEntry) + { + dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: call to" + " NewDocEntryByNumber failed."); + return NULL; + } + binEntry = new BinEntry(currentEntry); + if ( !AddEntry(binEntry)) + { + dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry" + " failed allthough this is a creation."); } + } + else + { + binEntry = dynamic_cast< BinEntry* >(currentEntry); + if ( !binEntry ) // Euuuuh? It wasn't a BinEntry + // then we change it to a BinEntry ? + // Shouldn't it be considered as an error ? + { + // We need to promote the DocEntry to a BinEntry: + binEntry = new BinEntry(currentEntry); + if (!RemoveEntry(currentEntry)) + { + dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: removal" + " of previous DocEntry failed."); + return NULL; + } + if ( !AddEntry(binEntry)) + { + dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: adding" + " promoted BinEntry failed."); + return NULL; + } + } + } - b = new gdcmBinEntry(a); - AddEntry(b); - b->SetVoidArea(voidArea); - } - SetEntryByNumber(voidArea, lgth, group, elem); - //b->SetVoidArea(voidArea); //what if b == 0 !! + SetEntryByNumber(binArea, lgth, group, elem); - return b; + return binEntry; } @@ -678,12 +780,12 @@ gdcmBinEntry * gdcmDocument::ReplaceOrCreateByNumber( * \return pointer to the modified/created SeqEntry (NULL when creation * failed). */ -gdcmSeqEntry * gdcmDocument::ReplaceOrCreateByNumber( +SeqEntry* Document::ReplaceOrCreateByNumber( uint16_t group, uint16_t elem) { - gdcmSeqEntry* b = 0; - gdcmDocEntry* a = GetDocEntryByNumber( group, elem); + SeqEntry* b = 0; + DocEntry* a = GetDocEntryByNumber( group, elem); if (!a) { a = NewSeqEntryByNumber(group, elem); @@ -692,7 +794,7 @@ gdcmSeqEntry * gdcmDocument::ReplaceOrCreateByNumber( return 0; } - b = new gdcmSeqEntry(a, 1); // FIXME : 1 (Depth) + b = new SeqEntry(a, 1); // FIXME : 1 (Depth) AddEntry(b); } return b; @@ -701,12 +803,12 @@ gdcmSeqEntry * gdcmDocument::ReplaceOrCreateByNumber( /** * \brief Set a new value if the invoked element exists * Seems to be useless !!! - * @param Value new element value - * @param Group group number of the Entry - * @param Elem element number of the Entry + * @param value new element value + * @param group group number of the Entry + * @param elem element number of the Entry * \return boolean */ -bool gdcmDocument::ReplaceIfExistByNumber(std::string const & value, +bool Document::ReplaceIfExistByNumber(std::string const & value, uint16_t group, uint16_t elem ) { SetEntryByNumber(value, group, elem); @@ -721,11 +823,11 @@ bool gdcmDocument::ReplaceIfExistByNumber(std::string const & value, * \brief Checks if a given Dicom Element exists within the H table * @param group Group number of the searched Dicom Element * @param element Element number of the searched Dicom Element - * @return number of occurences + * @return true is found */ -int gdcmDocument::CheckIfEntryExistByNumber(uint16_t group, uint16_t element ) +bool Document::CheckIfEntryExistByNumber(uint16_t group, uint16_t element ) { - const std::string &key = gdcmDictEntry::TranslateToKey(group, element ); + const std::string &key = DictEntry::TranslateToKey(group, element ); return TagHT.count(key); } @@ -738,9 +840,9 @@ int gdcmDocument::CheckIfEntryExistByNumber(uint16_t group, uint16_t element ) * @return Corresponding element value when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string gdcmDocument::GetEntryByName(TagName const & tagName) +std::string Document::GetEntryByName(TagName const& tagName) { - gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); + DictEntry* dictEntry = RefPubDict->GetDictEntryByName(tagName); if( !dictEntry ) { return GDCM_UNFOUND; @@ -762,20 +864,19 @@ std::string gdcmDocument::GetEntryByName(TagName const & tagName) * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string gdcmDocument::GetEntryVRByName(TagName const & tagName) +std::string Document::GetEntryVRByName(TagName const& tagName) { - gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); + DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( dictEntry == NULL) { return GDCM_UNFOUND; } - gdcmDocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(), + DocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(), dictEntry->GetElement()); return elem->GetVR(); } - /** * \brief Searches within Header Entries (Dicom Elements) parsed with * the public and private dictionaries @@ -785,16 +886,16 @@ std::string gdcmDocument::GetEntryVRByName(TagName const & tagName) * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string gdcmDocument::GetEntryByNumber(uint16_t group, uint16_t element) +std::string Document::GetEntryByNumber(uint16_t group, uint16_t element) { - gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element); + TagKey key = DictEntry::TranslateToKey(group, element); /// \todo use map methods, instead of multimap JPR if ( !TagHT.count(key)) { return GDCM_UNFOUND; } - return ((gdcmValEntry *)TagHT.find(key)->second)->GetValue(); + return ((ValEntry *)TagHT.find(key)->second)->GetValue(); } /** @@ -811,9 +912,9 @@ std::string gdcmDocument::GetEntryByNumber(uint16_t group, uint16_t element) * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string gdcmDocument::GetEntryVRByNumber(uint16_t group, uint16_t element) +std::string Document::GetEntryVRByNumber(uint16_t group, uint16_t element) { - gdcmDocEntry* elem = GetDocEntryByNumber(group, element); + DocEntry* elem = GetDocEntryByNumber(group, element); if ( !elem ) { return GDCM_UNFOUND; @@ -829,9 +930,9 @@ std::string gdcmDocument::GetEntryVRByNumber(uint16_t group, uint16_t element) * @param element Element number of the searched tag. * @return Corresponding element length; -2 if not found */ -int gdcmDocument::GetEntryLengthByNumber(uint16_t group, uint16_t element) +int Document::GetEntryLengthByNumber(uint16_t group, uint16_t element) { - gdcmDocEntry* elem = GetDocEntryByNumber(group, element); + DocEntry* elem = GetDocEntryByNumber(group, element); if ( !elem ) { return -2; //magic number @@ -844,9 +945,9 @@ int gdcmDocument::GetEntryLengthByNumber(uint16_t group, uint16_t element) * @param tagName name of the searched Dicom Element. * @return true when found */ -bool gdcmDocument::SetEntryByName(std::string const & content,std::string const & tagName) +bool Document::SetEntryByName(std::string const & content,std::string const & tagName) { - gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); + DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( !dictEntry ) { return false; @@ -857,66 +958,74 @@ bool gdcmDocument::SetEntryByName(std::string const & content,std::string const } /** - * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element) + * \brief Accesses an existing DocEntry (i.e. a Dicom Element) * through it's (group, element) and modifies it's content with * the given value. * @param content new value (string) to substitute with * @param group group number of the Dicom Element to modify * @param element element number of the Dicom Element to modify */ -bool gdcmDocument::SetEntryByNumber(std::string const & content, +bool Document::SetEntryByNumber(std::string const& content, uint16_t group, uint16_t element) { - gdcmValEntry* valEntry = GetValEntryByNumber(group, element); + int c; + int l; + + ValEntry* valEntry = GetValEntryByNumber(group, element); if (!valEntry ) { - dbg.Verbose(0, "gdcmDocument::SetEntryByNumber: no corresponding", + dbg.Verbose(0, "Document::SetEntryByNumber: no corresponding", " ValEntry (try promotion first)."); return false; } // Non even content must be padded with a space (020H)... - std::string evenContent = content; - if( evenContent.length() % 2 ) + std::string finalContent = content; + if( finalContent.length() % 2 ) { - evenContent += '\0'; // ... therefore we padd with (000H) .!?! + finalContent += '\0'; // ... therefore we padd with (000H) .!?! } - valEntry->SetValue(evenContent); + valEntry->SetValue(finalContent); // Integers have a special treatement for their length: - gdcmVRKey vr = valEntry->GetVR(); - if( vr == "US" || vr == "SS" ) - { - valEntry->SetLength(2); - } - else if( vr == "UL" || vr == "SL" ) - { - valEntry->SetLength(4); - } - else - { - valEntry->SetLength(evenContent.length()); - } + l = finalContent.length(); + if ( l != 0) // To avoid to be cheated by 'zero length' integers + { + VRKey vr = valEntry->GetVR(); + if( vr == "US" || vr == "SS" ) + { + // for multivaluated items + c = Util::CountSubstring(content, "\\") + 1; + l = c*2; + } + else if( vr == "UL" || vr == "SL" ) + { + // for multivaluated items + c = Util::CountSubstring(content, "\\") + 1; + l = c*4;; + } + } + valEntry->SetLength(l); return true; } /** - * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element) + * \brief Accesses an existing DocEntry (i.e. a Dicom Element) * through it's (group, element) and modifies it's content with * the given value. - * @param content new value (void *) to substitute with + * @param content new value (void* -> uint8_t*) to substitute with * @param lgth new value length * @param group group number of the Dicom Element to modify * @param element element number of the Dicom Element to modify */ -bool gdcmDocument::SetEntryByNumber(void *content, +bool Document::SetEntryByNumber(uint8_t*content, int lgth, uint16_t group, uint16_t element) { (void)lgth; //not used - gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element); + TagKey key = DictEntry::TranslateToKey(group, element); if ( !TagHT.count(key)) { return false; @@ -929,15 +1038,16 @@ bool gdcmDocument::SetEntryByNumber(void *content, //content = content + '\0'; // fing a trick to enlarge a binary field? } */ - gdcmBinEntry* a = (gdcmBinEntry *)TagHT[key]; - a->SetVoidArea(content); - //a->SetLength(lgth); // ??? + BinEntry* a = (BinEntry *)TagHT[key]; + a->SetBinArea(content); + a->SetLength(lgth); + a->SetValue(GDCM_BINLOADED); return true; } /** - * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element) + * \brief Accesses an existing DocEntry (i.e. a Dicom Element) * in the PubDocEntrySet of this instance * through it's (group, element) and modifies it's length with * the given value. @@ -947,12 +1057,12 @@ bool gdcmDocument::SetEntryByNumber(void *content, * @param element element number of the Entry to modify * @return true on success, false otherwise. */ -bool gdcmDocument::SetEntryLengthByNumber(uint32_t l, +bool Document::SetEntryLengthByNumber(uint32_t l, uint16_t group, uint16_t element) { /// \todo use map methods, instead of multimap JPR - gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element); + TagKey key = DictEntry::TranslateToKey(group, element); if ( !TagHT.count(key) ) { return false; @@ -969,16 +1079,16 @@ bool gdcmDocument::SetEntryLengthByNumber(uint32_t l, /** * \brief Gets (from Header) the offset of a 'non string' element value * (LoadElementValues has already be executed) - * @param Group group number of the Entry - * @param Elem element number of the Entry + * @param group group number of the Entry + * @param elem element number of the Entry * @return File Offset of the Element Value */ -size_t gdcmDocument::GetEntryOffsetByNumber(uint16_t group, uint16_t elem) +size_t Document::GetEntryOffsetByNumber(uint16_t group, uint16_t elem) { - gdcmDocEntry* entry = GetDocEntryByNumber(group, elem); + DocEntry* entry = GetDocEntryByNumber(group, elem); if (!entry) { - dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber: no entry present."); + dbg.Verbose(1, "Document::GetDocEntryByNumber: no entry present."); return 0; } return entry->GetOffset(); @@ -987,30 +1097,35 @@ size_t gdcmDocument::GetEntryOffsetByNumber(uint16_t group, uint16_t elem) /** * \brief Gets (from Header) a 'non string' element value * (LoadElementValues has already be executed) - * @param Group group number of the Entry - * @param Elem element number of the Entry + * @param group group number of the Entry + * @param elem element number of the Entry * @return Pointer to the 'non string' area */ -void * gdcmDocument::GetEntryVoidAreaByNumber(uint16_t group, uint16_t elem) +void* Document::GetEntryBinAreaByNumber(uint16_t group, uint16_t elem) { - gdcmDocEntry* entry = GetDocEntryByNumber(group, elem); + DocEntry* entry = GetDocEntryByNumber(group, elem); if (!entry) { - dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber: no entry"); + dbg.Verbose(1, "Document::GetDocEntryByNumber: no entry"); return 0; } - return ((gdcmBinEntry *)entry)->GetVoidArea(); + if ( BinEntry* binEntry = dynamic_cast(entry) ) + { + return binEntry->GetBinArea(); + } + + return 0; } /** * \brief Loads (from disk) the element content * when a string is not suitable - * @param Group group number of the Entry - * @param Elem element number of the Entry + * @param group group number of the Entry + * @param elem element number of the Entry */ -void *gdcmDocument::LoadEntryVoidArea(uint16_t group, uint16_t elem) +void* Document::LoadEntryBinArea(uint16_t group, uint16_t elem) { - gdcmDocEntry *docElement = GetDocEntryByNumber(group, elem); + DocEntry *docElement = GetDocEntryByNumber(group, elem); if ( !docElement ) { return NULL; @@ -1018,10 +1133,10 @@ void *gdcmDocument::LoadEntryVoidArea(uint16_t group, uint16_t elem) size_t o =(size_t)docElement->GetOffset(); fseek(Fp, o, SEEK_SET); size_t l = docElement->GetLength(); - char* a = new char[l]; + uint8_t* a = new uint8_t[l]; if(!a) { - dbg.Verbose(0, "gdcmDocument::LoadEntryVoidArea cannot allocate a"); + dbg.Verbose(0, "Document::LoadEntryBinArea cannot allocate a"); return NULL; } size_t l2 = fread(a, 1, l , Fp); @@ -1031,27 +1146,29 @@ void *gdcmDocument::LoadEntryVoidArea(uint16_t group, uint16_t elem) return NULL; } /// \todo Drop any already existing void area! JPR - SetEntryVoidAreaByNumber(a, group, elem); - + if( !SetEntryBinAreaByNumber( a, group, elem ) ) + { + dbg.Verbose(0, "Document::LoadEntryBinArea setting failed."); + } return a; } /** * \brief Loads (from disk) the element content * when a string is not suitable - * @param Element Entry whose voidArea is going to be loaded + * @param element Entry whose binArea is going to be loaded */ -void *gdcmDocument::LoadEntryVoidArea(gdcmBinEntry *element) +void* Document::LoadEntryBinArea(BinEntry* element) { size_t o =(size_t)element->GetOffset(); fseek(Fp, o, SEEK_SET); size_t l = element->GetLength(); - char* a = new char[l]; + uint8_t* a = new uint8_t[l]; if( !a ) { - dbg.Verbose(0, "gdcmDocument::LoadEntryVoidArea cannot allocate a"); + dbg.Verbose(0, "Document::LoadEntryBinArea cannot allocate a"); return NULL; } - element->SetVoidArea((void *)a); + element->SetBinArea((uint8_t*)a); /// \todo check the result size_t l2 = fread(a, 1, l , Fp); if( l != l2 ) @@ -1070,19 +1187,20 @@ void *gdcmDocument::LoadEntryVoidArea(gdcmBinEntry *element) * @param element Element number of the searched Dicom Element * @return */ -bool gdcmDocument::SetEntryVoidAreaByNumber(void * area, +bool Document::SetEntryBinAreaByNumber(uint8_t* area, uint16_t group, uint16_t element) { - gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element); - if ( !TagHT.count(key)) + DocEntry* currentEntry = GetDocEntryByNumber(group, element); + if ( !currentEntry ) { return false; } - - // This was for multimap ? - (( gdcmBinEntry *)( ((TagHT.equal_range(key)).first)->second ))->SetVoidArea(area); - + if ( BinEntry* binEntry = dynamic_cast(currentEntry) ) + { + binEntry->SetBinArea( area ); + return true; + } return true; } @@ -1090,9 +1208,9 @@ bool gdcmDocument::SetEntryVoidAreaByNumber(void * area, * \brief Update the entries with the shadow dictionary. * Only non even entries are analyzed */ -void gdcmDocument::UpdateShaEntries() +void Document::UpdateShaEntries() { - //gdcmDictEntry *entry; + //DictEntry *entry; std::string vr; /// \todo TODO : still any use to explore recursively the whole structure? @@ -1141,9 +1259,9 @@ void gdcmDocument::UpdateShaEntries() * @return Corresponding Dicom Element when it exists, and NULL * otherwise. */ -gdcmDocEntry* gdcmDocument::GetDocEntryByName(std::string const & tagName) +DocEntry* Document::GetDocEntryByName(std::string const & tagName) { - gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); + DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( !dictEntry ) { return NULL; @@ -1162,10 +1280,10 @@ gdcmDocEntry* gdcmDocument::GetDocEntryByName(std::string const & tagName) * @param element Element number of the searched Dicom Element * @return */ -gdcmDocEntry* gdcmDocument::GetDocEntryByNumber(uint16_t group, +DocEntry* Document::GetDocEntryByNumber(uint16_t group, uint16_t element) { - gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element); + TagKey key = DictEntry::TranslateToKey(group, element); if ( !TagHT.count(key)) { return NULL; @@ -1174,24 +1292,24 @@ gdcmDocEntry* gdcmDocument::GetDocEntryByNumber(uint16_t group, } /** - * \brief Same as \ref gdcmDocument::GetDocEntryByNumber except it only + * \brief Same as \ref Document::GetDocEntryByNumber except it only * returns a result when the corresponding entry is of type * ValEntry. * @return When present, the corresponding ValEntry. */ -gdcmValEntry* gdcmDocument::GetValEntryByNumber(uint16_t group, +ValEntry* Document::GetValEntryByNumber(uint16_t group, uint16_t element) { - gdcmDocEntry* currentEntry = GetDocEntryByNumber(group, element); + DocEntry* currentEntry = GetDocEntryByNumber(group, element); if ( !currentEntry ) { return 0; } - if ( gdcmValEntry* valEntry = dynamic_cast(currentEntry) ) + if ( ValEntry* valEntry = dynamic_cast(currentEntry) ) { return valEntry; } - dbg.Verbose(0, "gdcmDocument::GetValEntryByNumber: unfound ValEntry."); + dbg.Verbose(0, "Document::GetValEntryByNumber: unfound ValEntry."); return 0; } @@ -1203,7 +1321,7 @@ gdcmValEntry* gdcmDocument::GetValEntryByNumber(uint16_t group, * @param entry Header Entry whose value shall be loaded. * @return */ -void gdcmDocument::LoadDocEntrySafe(gdcmDocEntry * entry) +void Document::LoadDocEntrySafe(DocEntry * entry) { long PositionOnEntry = ftell(Fp); LoadDocEntry(entry); @@ -1215,7 +1333,7 @@ void gdcmDocument::LoadDocEntrySafe(gdcmDocEntry * entry) * processor order. * @return The properly swaped 32 bits integer. */ -uint32_t gdcmDocument::SwapLong(uint32_t a) +uint32_t Document::SwapLong(uint32_t a) { switch (SwapCode) { @@ -1235,7 +1353,7 @@ uint32_t gdcmDocument::SwapLong(uint32_t a) break; default : //std::cout << "swapCode= " << SwapCode << std::endl; - dbg.Error(" gdcmDocument::SwapLong : unset swap code"); + dbg.Error(" Document::SwapLong : unset swap code"); a = 0; } return a; @@ -1246,7 +1364,7 @@ uint32_t gdcmDocument::SwapLong(uint32_t a) * processor order. * @return The properly unswaped 32 bits integer. */ -uint32_t gdcmDocument::UnswapLong(uint32_t a) +uint32_t Document::UnswapLong(uint32_t a) { return SwapLong(a); } @@ -1255,7 +1373,7 @@ uint32_t gdcmDocument::UnswapLong(uint32_t a) * \brief Swaps the bytes so they agree with the processor order * @return The properly swaped 16 bits integer. */ -uint16_t gdcmDocument::SwapShort(uint16_t a) +uint16_t Document::SwapShort(uint16_t a) { if ( SwapCode == 4321 || SwapCode == 2143 ) { @@ -1268,7 +1386,7 @@ uint16_t gdcmDocument::SwapShort(uint16_t a) * \brief Unswaps the bytes so they agree with the processor order * @return The properly unswaped 16 bits integer. */ -uint16_t gdcmDocument::UnswapShort(uint16_t a) +uint16_t Document::UnswapShort(uint16_t a) { return SwapShort(a); } @@ -1280,17 +1398,13 @@ uint16_t gdcmDocument::UnswapShort(uint16_t a) * \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries) * @return length of the parsed set. */ - -long gdcmDocument::ParseDES(gdcmDocEntrySet *set, +void Document::ParseDES(DocEntrySet *set, long offset, long l_max, bool delim_mode) { - gdcmDocEntry *newDocEntry = 0; - gdcmValEntry *newValEntry = 0; - unsigned long l = 0; + DocEntry *newDocEntry = 0; - int depth = set->GetDepthLevel(); while (true) { if ( !delim_mode && (ftell(Fp)-offset) >= l_max) @@ -1303,18 +1417,35 @@ long gdcmDocument::ParseDES(gdcmDocEntrySet *set, break; } - gdcmVRKey vr = newDocEntry->GetVR(); + VRKey vr = newDocEntry->GetVR(); if ( vr != "SQ" ) { - if ( gdcmGlobal::GetVR()->IsVROfGdcmStringRepresentable(vr) ) + if ( Global::GetVR()->IsVROfGdcmStringRepresentable(vr) ) { - /////// ValEntry - newValEntry = new gdcmValEntry(newDocEntry->GetDictEntry()); - newValEntry->Copy(newDocEntry); - newValEntry->SetDepthLevel(depth); - set->AddEntry(newValEntry); - LoadDocEntry(newValEntry); + /////////////////////// ValEntry + ValEntry* newValEntry = + new ValEntry( newDocEntry->GetDictEntry() ); + newValEntry->Copy( newDocEntry ); + + // When "set" is a Document, then we are at the top of the + // hierarchy and the Key is simply of the form ( group, elem )... + if (Document* dummy = dynamic_cast< Document* > ( set ) ) + { + (void)dummy; + newValEntry->SetKey( newValEntry->GetKey() ); + } + // ...but when "set" is a SQItem, we are inserting this new + // valEntry in a sequence item. Hence the key has the + // generalized form (refer to \ref BaseTagKey): + if (SQItem* parentSQItem = dynamic_cast< SQItem* > ( set ) ) + { + newValEntry->SetKey( parentSQItem->GetBaseTagKey() + + newValEntry->GetKey() ); + } + + set->AddEntry( newValEntry ); + LoadDocEntry( newValEntry ); if (newValEntry->IsItemDelimitor()) { break; @@ -1326,46 +1457,65 @@ long gdcmDocument::ParseDES(gdcmDocEntrySet *set, } else { - if ( ! gdcmGlobal::GetVR()->IsVROfGdcmBinaryRepresentable(vr) ) + if ( ! Global::GetVR()->IsVROfGdcmBinaryRepresentable(vr) ) { ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR - dbg.Verbose(0, "gdcmDocument::ParseDES: neither Valentry, " + dbg.Verbose(0, "Document::ParseDES: neither Valentry, " "nor BinEntry. Probably unknown VR."); } - ////// BinEntry or UNKOWN VR: - gdcmBinEntry *bn = new gdcmBinEntry(newDocEntry->GetDictEntry()); - bn->Copy(newDocEntry); - set->AddEntry(bn); - LoadDocEntry(bn); + //////////////////// BinEntry or UNKOWN VR: + BinEntry* newBinEntry = + new BinEntry( newDocEntry->GetDictEntry() ); + newBinEntry->Copy( newDocEntry ); + + // When "this" is a Document the Key is simply of the + // form ( group, elem )... + if (Document* dummy = dynamic_cast< Document* > ( set ) ) + { + (void)dummy; + newBinEntry->SetKey( newBinEntry->GetKey() ); + } + // but when "this" is a SQItem, we are inserting this new + // valEntry in a sequence item, and the kay has the + // generalized form (refer to \ref BaseTagKey): + if (SQItem* parentSQItem = dynamic_cast< SQItem* > ( set ) ) + { + newBinEntry->SetKey( parentSQItem->GetBaseTagKey() + + newBinEntry->GetKey() ); + } + + set->AddEntry( newBinEntry ); + LoadDocEntry( newBinEntry ); } - if (newDocEntry->GetGroup() == 0x7fe0 && - newDocEntry->GetElement() == 0x0010 ) + if ( ( newDocEntry->GetGroup() == 0x7fe0 ) + && ( newDocEntry->GetElement() == 0x0010 ) ) { - if (newDocEntry->GetReadLength()==0xffffffff) + if ( IsRLELossLessTransferSyntax() ) { - // Broken US.3405.1.dcm - Parse7FE0(); // to skip the pixels - // (multipart JPEG/RLE are trouble makers) + long PositionOnEntry = ftell(Fp); + fseek( Fp, newDocEntry->GetOffset(), SEEK_SET ); + ComputeRLEInfo(); + fseek( Fp, PositionOnEntry, SEEK_SET ); } - else + else + if ( IsJPEGTransferSyntax() ) { - SkipToNextDocEntry(newDocEntry); - l = newDocEntry->GetFullLength(); + long PositionOnEntry = ftell(Fp); + fseek( Fp, newDocEntry->GetOffset(), SEEK_SET ); + ComputeJPEGFragmentInfo(); + fseek( Fp, PositionOnEntry, SEEK_SET ); } } - else - { - // to be sure we are at the beginning - SkipToNextDocEntry(newDocEntry); - l = newDocEntry->GetFullLength(); - } + + // Just to make sure we are at the beginning of next entry. + SkipToNextDocEntry(newDocEntry); } else { // VR = "SQ" - l = newDocEntry->GetReadLength(); + unsigned long l = newDocEntry->GetReadLength(); if ( l != 0 ) // don't mess the delim_mode for zero-length sequence { if ( l == 0xffffffff ) @@ -1378,20 +1528,38 @@ long gdcmDocument::ParseDES(gdcmDocEntrySet *set, } } // no other way to create it ... - gdcmSeqEntry *sq = new gdcmSeqEntry(newDocEntry->GetDictEntry(), - set->GetDepthLevel()); - sq->Copy(newDocEntry); - sq->SetDelimitorMode(delim_mode); - sq->SetDepthLevel(depth); + SeqEntry* newSeqEntry = + new SeqEntry( newDocEntry->GetDictEntry() ); + newSeqEntry->Copy( newDocEntry ); + newSeqEntry->SetDelimitorMode( delim_mode ); + + // At the top of the hierarchy, stands a Document. When "set" + // is a Document, then we are building the first depth level. + // Hence the SeqEntry we are building simply has a depth + // level of one: + if (Document* dummy = dynamic_cast< Document* > ( set ) ) + { + (void)dummy; + newSeqEntry->SetDepthLevel( 1 ); + newSeqEntry->SetKey( newSeqEntry->GetKey() ); + } + // But when "set" is allready a SQItem, we are building a nested + // sequence, and hence the depth level of the new SeqEntry + // we are building, is one level deeper: + if (SQItem* parentSQItem = dynamic_cast< SQItem* > ( set ) ) + { + newSeqEntry->SetDepthLevel( parentSQItem->GetDepthLevel() + 1 ); + newSeqEntry->SetKey( parentSQItem->GetBaseTagKey() + + newSeqEntry->GetKey() ); + } if ( l != 0 ) { // Don't try to parse zero-length sequences - long lgt = ParseSQ( sq, - newDocEntry->GetOffset(), - l, delim_mode); - (void)lgt; //not used... + ParseSQ( newSeqEntry, + newDocEntry->GetOffset(), + l, delim_mode); } - set->AddEntry(sq); + set->AddEntry( newSeqEntry ); if ( !delim_mode && (ftell(Fp)-offset) >= l_max) { break; @@ -1399,24 +1567,21 @@ long gdcmDocument::ParseDES(gdcmDocEntrySet *set, } delete newDocEntry; } - return l; // Probably useless } /** * \brief Parses a Sequence ( SeqEntry after SeqEntry) * @return parsed length for this level */ -long gdcmDocument::ParseSQ(gdcmSeqEntry *set, - long offset, long l_max, bool delim_mode) +void Document::ParseSQ( SeqEntry* seqEntry, + long offset, long l_max, bool delim_mode) { int SQItemNumber = 0; bool dlm_mod; - //int depth = set->GetDepthLevel(); - //(void)depth; //not used while (true) { - gdcmDocEntry *newDocEntry = ReadNextDocEntry(); + DocEntry* newDocEntry = ReadNextDocEntry(); if ( !newDocEntry ) { // FIXME Should warn user @@ -1426,7 +1591,7 @@ long gdcmDocument::ParseSQ(gdcmSeqEntry *set, { if ( newDocEntry->IsSequenceDelimitor() ) { - set->SetSequenceDelimitationItem( newDocEntry ); + seqEntry->SetSequenceDelimitationItem( newDocEntry ); break; } } @@ -1435,8 +1600,13 @@ long gdcmDocument::ParseSQ(gdcmSeqEntry *set, break; } - gdcmSQItem *itemSQ = new gdcmSQItem(set->GetDepthLevel()); - itemSQ->AddEntry(newDocEntry); + SQItem *itemSQ = new SQItem( seqEntry->GetDepthLevel() ); + std::ostringstream newBase; + newBase << seqEntry->GetKey() + << "/" + << SQItemNumber + << "#"; + itemSQ->SetBaseTagKey( newBase.str() ); unsigned int l = newDocEntry->GetReadLength(); if ( l == 0xffffffff ) @@ -1448,27 +1618,23 @@ long gdcmDocument::ParseSQ(gdcmSeqEntry *set, dlm_mod = false; } - int lgr = ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod); - (void)lgr; //FIXME not used + ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod); - set->AddEntry(itemSQ, SQItemNumber); + seqEntry->AddEntry( itemSQ, SQItemNumber ); SQItemNumber++; - if ( !delim_mode && (ftell(Fp)-offset) >= l_max) + if ( !delim_mode && ( ftell(Fp) - offset ) >= l_max ) { break; } } - - int lgth = ftell(Fp) - offset; - return lgth; } /** * \brief Loads the element content if its length doesn't exceed - * the value specified with gdcmDocument::SetMaxSizeLoadEntry() - * @param Entry Header Entry (Dicom Element) to be dealt with + * the value specified with Document::SetMaxSizeLoadEntry() + * @param entry Header Entry (Dicom Element) to be dealt with */ -void gdcmDocument::LoadDocEntry(gdcmDocEntry* entry) +void Document::LoadDocEntry(DocEntry* entry) { size_t item_read; uint16_t group = entry->GetGroup(); @@ -1490,7 +1656,7 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry* entry) // When the length is zero things are easy: if ( length == 0 ) { - ((gdcmValEntry *)entry)->SetValue(""); + ((ValEntry *)entry)->SetValue(""); return; } @@ -1501,45 +1667,43 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry* entry) std::ostringstream s; if (length > MaxSizeLoadEntry) { - if (gdcmBinEntry* binEntryPtr = dynamic_cast< gdcmBinEntry* >(entry) ) - { - s << "gdcm::NotLoaded (BinEntry)"; + if (BinEntry* binEntryPtr = dynamic_cast< BinEntry* >(entry) ) + { + //s << "gdcm::NotLoaded (BinEntry)"; + s << GDCM_NOTLOADED; s << " Address:" << (long)entry->GetOffset(); s << " Length:" << entry->GetLength(); s << " x(" << std::hex << entry->GetLength() << ")"; binEntryPtr->SetValue(s.str()); } - // to be sure we are at the end of the value ... - fseek(Fp, (long)entry->GetOffset()+(long)entry->GetLength(), SEEK_SET); - // Following return introduced by JPR on version 1.25. Since the - // treatement of a ValEntry is never executed (doh!) this means - // we were lucky up to now because we NEVER encountered a ValEntry - // whose length was bigger thant MaxSizeLoadEntry !? I can't believe - // this could ever work... - return; //FIXME FIXME FIXME FIXME JPR ???? - // Be carefull : a BinEntry IS_A ValEntry ... - if (gdcmValEntry* valEntryPtr = dynamic_cast< gdcmValEntry* >(entry) ) + else if (ValEntry* valEntryPtr = dynamic_cast< ValEntry* >(entry) ) { - s << "gdcm::NotLoaded. (ValEntry)"; + // s << "gdcm::NotLoaded. (ValEntry)"; + s << GDCM_NOTLOADED; s << " Address:" << (long)entry->GetOffset(); s << " Length:" << entry->GetLength(); s << " x(" << std::hex << entry->GetLength() << ")"; valEntryPtr->SetValue(s.str()); } + else + { + // fusible + std::cout<< "MaxSizeLoadEntry exceeded, neither a BinEntry " + << "nor a ValEntry ?! Should never print that !" << std::endl; + } + // to be sure we are at the end of the value ... fseek(Fp,(long)entry->GetOffset()+(long)entry->GetLength(),SEEK_SET); - return; } // When we find a BinEntry not very much can be done : - if (gdcmBinEntry* binEntryPtr = dynamic_cast< gdcmBinEntry* >(entry) ) + if (BinEntry* binEntryPtr = dynamic_cast< BinEntry* >(entry) ) { - - LoadEntryVoidArea(binEntryPtr); - s << "gdcm::Loaded (BinEntry)"; + s << GDCM_BINLOADED; binEntryPtr->SetValue(s.str()); + LoadEntryBinArea(binEntryPtr); // last one, not to erase length ! return; } @@ -1547,7 +1711,6 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry* entry) if ( IsDocEntryAnInteger(entry) ) { uint32_t NewInt; - //std::ostringstream s; //shadow previous declaration int nbInt; // When short integer(s) are expected, read and convert the following // n *two characters properly i.e. consider them as short integers as @@ -1589,7 +1752,7 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry* entry) s << std::ends; // to avoid oddities on Solaris #endif //GDCM_NO_ANSI_STRING_STREAM - ((gdcmValEntry *)entry)->SetValue(s.str()); + ((ValEntry *)entry)->SetValue(s.str()); return; } @@ -1602,13 +1765,13 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry* entry) str[length] = '\0'; std::string newValue = str; delete[] str; - if ( gdcmValEntry* valEntry = dynamic_cast(entry) ) + if ( ValEntry* valEntry = dynamic_cast(entry) ) { if ( item_read != 1 ) { - dbg.Verbose(1, "gdcmDocument::LoadDocEntry", + dbg.Verbose(1, "Document::LoadDocEntry", "unread element value"); - valEntry->SetValue("gdcm::UnRead"); + valEntry->SetValue(GDCM_UNREAD); return; } @@ -1624,7 +1787,7 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry* entry) } else { - dbg.Error(true, "gdcmDocument::LoadDocEntry" + dbg.Error(true, "Document::LoadDocEntry" "Should have a ValEntry, here !"); } } @@ -1632,33 +1795,35 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry* entry) /** * \brief Find the value Length of the passed Header Entry - * @param Entry Header Entry whose length of the value shall be loaded. + * @param entry Header Entry whose length of the value shall be loaded. */ -void gdcmDocument::FindDocEntryLength( gdcmDocEntry *entry ) - throw ( gdcmFormatError ) +void Document::FindDocEntryLength( DocEntry *entry ) + throw ( FormatError ) { uint16_t element = entry->GetElement(); std::string vr = entry->GetVR(); uint16_t length16; - if ( Filetype == gdcmExplicitVR && !entry->IsImplicitVR() ) + if ( Filetype == ExplicitVR && !entry->IsImplicitVR() ) { if ( vr == "OB" || vr == "OW" || vr == "SQ" || vr == "UN" ) { - // The following reserved two bytes (see PS 3.5-2001, section - // 7.1.2 Data element structure with explicit vr p27) must be + // The following reserved two bytes (see PS 3.5-2003, section + // "7.1.2 Data element structure with explicit vr", p 27) must be // skipped before proceeding on reading the length on 4 bytes. fseek(Fp, 2L, SEEK_CUR); uint32_t length32 = ReadInt32(); - if ( vr == "OB" && length32 == 0xffffffff ) + if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff ) { uint32_t lengthOB; try { + /// \todo rename that to FindDocEntryLengthOBOrOW since + /// the above test is on both OB and OW... lengthOB = FindDocEntryLengthOB(); } - catch ( gdcmFormatUnexpected ) + catch ( FormatUnexpected ) { // Computing the length failed (this happens with broken // files like gdcm-JPEG-LossLess3a.dcm). We still have a @@ -1713,8 +1878,8 @@ void gdcmDocument::FindDocEntryLength( gdcmDocEntry *entry ) { if ( !IsExplicitVRBigEndianTransferSyntax() ) { - throw gdcmFormatError( "gdcmDocument::FindDocEntryLength()", - " not explicit VR." ); + throw FormatError( "Document::FindDocEntryLength()", + " not explicit VR." ); return; } length16 = 4; @@ -1723,7 +1888,7 @@ void gdcmDocument::FindDocEntryLength( gdcmDocEntry *entry ) // and the dictionary entry depending on them. uint16_t correctGroup = SwapShort( entry->GetGroup() ); uint16_t correctElem = SwapShort( entry->GetElement() ); - gdcmDictEntry* newTag = GetDictEntryByNumber( correctGroup, + DictEntry* newTag = GetDictEntryByNumber( correctGroup, correctElem ); if ( !newTag ) { @@ -1760,11 +1925,11 @@ void gdcmDocument::FindDocEntryLength( gdcmDocEntry *entry ) /** * \brief Find the Value Representation of the current Dicom Element. - * @param Entry + * @param entry */ -void gdcmDocument::FindDocEntryVR( gdcmDocEntry *entry ) +void Document::FindDocEntryVR( DocEntry *entry ) { - if ( Filetype != gdcmExplicitVR ) + if ( Filetype != ExplicitVR ) { return; } @@ -1803,14 +1968,14 @@ void gdcmDocument::FindDocEntryVR( gdcmDocEntry *entry ) * \brief Check the correspondance between the VR of the header entry * and the taken VR. If they are different, the header entry is * updated with the new VR. - * @param Entry Header Entry to check + * @param entry Header Entry to check * @param vr Dicom Value Representation * @return false if the VR is incorrect of if the VR isn't referenced * otherwise, it returns true */ -bool gdcmDocument::CheckDocEntryVR(gdcmDocEntry *entry, gdcmVRKey vr) +bool Document::CheckDocEntryVR(DocEntry *entry, VRKey vr) { - char msg[100]; // for sprintf + std::string msg; bool realExplicit = true; // Assume we are reading a falsely explicit VR file i.e. we reached @@ -1829,7 +1994,7 @@ bool gdcmDocument::CheckDocEntryVR(gdcmDocEntry *entry, gdcmVRKey vr) // CLEANME searching the dicom_vr at each occurence is expensive. // PostPone this test in an optional integrity check at the end // of parsing or only in debug mode. - if ( realExplicit && !gdcmGlobal::GetVR()->Count(vr) ) + if ( realExplicit && !Global::GetVR()->Count(vr) ) { realExplicit = false; } @@ -1838,14 +2003,14 @@ bool gdcmDocument::CheckDocEntryVR(gdcmDocEntry *entry, gdcmVRKey vr) { // We thought this was explicit VR, but we end up with an // implicit VR tag. Let's backtrack. - sprintf(msg,"Falsely explicit vr file (%04x,%04x)\n", - entry->GetGroup(), entry->GetElement()); - dbg.Verbose(1, "gdcmDocument::FindVR: ",msg); + msg = Util::Format("Falsely explicit vr file (%04x,%04x)\n", + entry->GetGroup(), entry->GetElement()); + dbg.Verbose(1, "Document::FindVR: ", msg.c_str()); if( entry->GetGroup() % 2 && entry->GetElement() == 0x0000) { // Group length is UL ! - gdcmDictEntry* newEntry = NewVirtualDictEntry( + DictEntry* newEntry = NewVirtualDictEntry( entry->GetGroup(), entry->GetElement(), "UL", "FIXME", "Group Length"); entry->SetDictEntry( newEntry ); @@ -1873,7 +2038,7 @@ bool gdcmDocument::CheckDocEntryVR(gdcmDocEntry *entry, gdcmVRKey vr) // be unwise to overwrite the VR of a dictionary (since it would // compromise it's next user), we need to clone the actual DictEntry // and change the VR for the read one. - gdcmDictEntry* newEntry = NewVirtualDictEntry( + DictEntry* newEntry = NewVirtualDictEntry( entry->GetGroup(), entry->GetElement(), vr, "FIXME", entry->GetName()); entry->SetDictEntry(newEntry); @@ -1886,14 +2051,14 @@ bool gdcmDocument::CheckDocEntryVR(gdcmDocEntry *entry, gdcmVRKey vr) * \brief Get the transformed value of the header entry. The VR value * is used to define the transformation to operate on the value * \warning NOT end user intended method ! - * @param Entry + * @param entry entry to tranform * @return Transformed entry value */ -std::string gdcmDocument::GetDocEntryValue(gdcmDocEntry *entry) +std::string Document::GetDocEntryValue(DocEntry *entry) { if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() ) { - std::string val = ((gdcmValEntry *)entry)->GetValue(); + std::string val = ((ValEntry *)entry)->GetValue(); std::string vr = entry->GetVR(); uint32_t length = entry->GetLength(); std::ostringstream s; @@ -1954,7 +2119,7 @@ std::string gdcmDocument::GetDocEntryValue(gdcmDocEntry *entry) return s.str(); } - return ((gdcmValEntry *)entry)->GetValue(); + return ((ValEntry *)entry)->GetValue(); } /** @@ -1962,10 +2127,10 @@ std::string gdcmDocument::GetDocEntryValue(gdcmDocEntry *entry) * value is used to define the reverse transformation to operate on * the value * \warning NOT end user intended method ! - * @param Entry + * @param entry Entry to reverse transform * @return Reverse transformed entry value */ -std::string gdcmDocument::GetDocEntryUnvalue(gdcmDocEntry* entry) +std::string Document::GetDocEntryUnvalue(DocEntry* entry) { if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() ) { @@ -1978,7 +2143,7 @@ std::string gdcmDocument::GetDocEntryUnvalue(gdcmDocEntry* entry) uint16_t newInt16; tokens.erase( tokens.begin(), tokens.end()); // clean any previous value - Tokenize (((gdcmValEntry *)entry)->GetValue(), tokens, "\\"); + Util::Tokenize (((ValEntry *)entry)->GetValue(), tokens, "\\"); for (unsigned int i=0; iGetValue(), tokens, "\\"); + Util::Tokenize (((ValEntry *)entry)->GetValue(), tokens, "\\"); for (unsigned int i=0; iGetValue(); + return ((ValEntry *)entry)->GetValue(); } /** * \brief Skip a given Header Entry * \warning NOT end user intended method ! - * @param entry + * @param entry entry to skip */ -void gdcmDocument::SkipDocEntry(gdcmDocEntry *entry) +void Document::SkipDocEntry(DocEntry *entry) { SkipBytes(entry->GetLength()); } @@ -2026,9 +2191,9 @@ void gdcmDocument::SkipDocEntry(gdcmDocEntry *entry) /** * \brief Skips to the begining of the next Header Entry * \warning NOT end user intended method ! - * @param entry + * @param entry entry to skip */ -void gdcmDocument::SkipToNextDocEntry(gdcmDocEntry *entry) +void Document::SkipToNextDocEntry(DocEntry *entry) { fseek(Fp, (long)(entry->GetOffset()), SEEK_SET); fseek(Fp, (long)(entry->GetReadLength()), SEEK_CUR); @@ -2038,8 +2203,10 @@ void gdcmDocument::SkipToNextDocEntry(gdcmDocEntry *entry) * \brief When the length of an element value is obviously wrong (because * the parser went Jabberwocky) one can hope improving things by * applying some heuristics. + * @param entry entry to check + * @param foundLength fist assumption about length */ -void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *entry, +void Document::FixDocEntryFoundLength(DocEntry *entry, uint32_t foundLength) { entry->SetReadLength( foundLength ); // will be updated only if a bug is found @@ -2115,10 +2282,10 @@ void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *entry, /** * \brief Apply some heuristics to predict whether the considered * element value contains/represents an integer or not. - * @param Entry The element value on which to apply the predicate. + * @param entry The element value on which to apply the predicate. * @return The result of the heuristical predicate. */ -bool gdcmDocument::IsDocEntryAnInteger(gdcmDocEntry *entry) +bool Document::IsDocEntryAnInteger(DocEntry *entry) { uint16_t element = entry->GetElement(); uint16_t group = entry->GetGroup(); @@ -2144,12 +2311,12 @@ bool gdcmDocument::IsDocEntryAnInteger(gdcmDocEntry *entry) // encounter such an ill-formed image, we simply display a warning // message and proceed on parsing (while crossing fingers). std::ostringstream s; - int filePosition = ftell(Fp); + long filePosition = ftell(Fp); s << "Erroneous Group Length element length on : (" \ << std::hex << group << " , " << element << ") -before- position x(" << filePosition << ")" << "lgt : " << length; - dbg.Verbose(0, "gdcmDocument::IsDocEntryAnInteger", s.str().c_str() ); + dbg.Verbose(0, "Document::IsDocEntryAnInteger", s.str().c_str() ); } } @@ -2167,8 +2334,8 @@ bool gdcmDocument::IsDocEntryAnInteger(gdcmDocEntry *entry) * @return */ -uint32_t gdcmDocument::FindDocEntryLengthOB() - throw( gdcmFormatUnexpected ) +uint32_t Document::FindDocEntryLengthOB() + throw( FormatUnexpected ) { // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data. long positionOnEntry = ftell(Fp); @@ -2184,10 +2351,10 @@ uint32_t gdcmDocument::FindDocEntryLengthOB() group = ReadInt16(); elem = ReadInt16(); } - catch ( gdcmFormatError ) + catch ( FormatError ) { - throw gdcmFormatError("gdcmDocument::FindDocEntryLengthOB()", - " group or element not present."); + throw FormatError("Document::FindDocEntryLengthOB()", + " group or element not present."); } // We have to decount the group and element we just read @@ -2195,12 +2362,12 @@ uint32_t gdcmDocument::FindDocEntryLengthOB() if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) ) { - dbg.Verbose(1, "gdcmDocument::FindDocEntryLengthOB: neither an Item " + dbg.Verbose(1, "Document::FindDocEntryLengthOB: neither an Item " "tag nor a Sequence delimiter tag."); fseek(Fp, positionOnEntry, SEEK_SET); - throw gdcmFormatUnexpected("gdcmDocument::FindDocEntryLengthOB()", - "Neither an Item tag nor a Sequence " - "delimiter tag."); + throw FormatUnexpected("Document::FindDocEntryLengthOB()", + "Neither an Item tag nor a Sequence " + "delimiter tag."); } if ( elem == 0xe0dd ) @@ -2227,8 +2394,8 @@ uint32_t gdcmDocument::FindDocEntryLengthOB() * (swaps it depending on processor endianity) * @return read value */ -uint16_t gdcmDocument::ReadInt16() - throw( gdcmFormatError ) +uint16_t Document::ReadInt16() + throw( FormatError ) { uint16_t g; size_t item_read = fread (&g, (size_t)2,(size_t)1, Fp); @@ -2236,9 +2403,9 @@ uint16_t gdcmDocument::ReadInt16() { if( ferror(Fp) ) { - throw gdcmFormatError( "gdcmDocument::ReadInt16()", " file error." ); + throw FormatError( "Document::ReadInt16()", " file error." ); } - throw gdcmFormatError( "gdcmDocument::ReadInt16()", "EOF." ); + throw FormatError( "Document::ReadInt16()", "EOF." ); } g = SwapShort(g); return g; @@ -2249,8 +2416,8 @@ uint16_t gdcmDocument::ReadInt16() * (swaps it depending on processor endianity) * @return read value */ -uint32_t gdcmDocument::ReadInt32() - throw( gdcmFormatError ) +uint32_t Document::ReadInt32() + throw( FormatError ) { uint32_t g; size_t item_read = fread (&g, (size_t)4,(size_t)1, Fp); @@ -2258,9 +2425,9 @@ uint32_t gdcmDocument::ReadInt32() { if( ferror(Fp) ) { - throw gdcmFormatError( "gdcmDocument::ReadInt16()", " file error." ); + throw FormatError( "Document::ReadInt16()", " file error." ); } - throw gdcmFormatError( "gdcmDocument::ReadInt32()", "EOF." ); + throw FormatError( "Document::ReadInt32()", "EOF." ); } g = SwapLong(g); return g; @@ -2271,7 +2438,7 @@ uint32_t gdcmDocument::ReadInt32() * \warning NOT end user intended method ! * @return */ -void gdcmDocument::SkipBytes(uint32_t nBytes) +void Document::SkipBytes(uint32_t nBytes) { //FIXME don't dump the returned value (void)fseek(Fp, (long)nBytes, SEEK_CUR); @@ -2281,10 +2448,12 @@ void gdcmDocument::SkipBytes(uint32_t nBytes) * \brief Loads all the needed Dictionaries * \warning NOT end user intended method ! */ -void gdcmDocument::Initialise() +void Document::Initialise() { - RefPubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict(); + RefPubDict = Global::GetDicts()->GetDefaultPubDict(); RefShaDict = NULL; + RLEInfo = new RLEFramesInfo; + JPEGInfo = new JPEGFragmentsInfo; } /** @@ -2295,7 +2464,7 @@ void gdcmDocument::Initialise() * it's neither ACR-NEMA nor DICOM * true when we hope ours assuptions are OK */ -bool gdcmDocument::CheckSwap() +bool Document::CheckSwap() { // The only guaranted way of finding the swap code is to find a // group tag since we know it's length has to be of four bytes i.e. @@ -2328,7 +2497,7 @@ bool gdcmDocument::CheckSwap() char *entCur = deb + 128; if( memcmp(entCur, "DICM", (size_t)4) == 0 ) { - dbg.Verbose(1, "gdcmDocument::CheckSwap:", "looks like DICOM Version3"); + dbg.Verbose(1, "Document::CheckSwap:", "looks like DICOM Version3"); // Next, determine the value representation (VR). Let's skip to the // first element (0002, 0000) and check there if we find "UL" @@ -2358,30 +2527,30 @@ bool gdcmDocument::CheckSwap() memcmp(entCur, "CS", (size_t)2) == 0 ) // CS, to remove later // when Write DCM *adds* // FIXME - // Use gdcmDocument::dicom_vr to test all the possibilities + // Use Document::dicom_vr to test all the possibilities // instead of just checking for UL, OB and UI !? group 0000 { - Filetype = gdcmExplicitVR; - dbg.Verbose(1, "gdcmDocument::CheckSwap:", + Filetype = ExplicitVR; + dbg.Verbose(1, "Document::CheckSwap:", "explicit Value Representation"); } else { - Filetype = gdcmImplicitVR; - dbg.Verbose(1, "gdcmDocument::CheckSwap:", + Filetype = ImplicitVR; + dbg.Verbose(1, "Document::CheckSwap:", "not an explicit Value Representation"); } if ( net2host ) { SwapCode = 4321; - dbg.Verbose(1, "gdcmDocument::CheckSwap:", + dbg.Verbose(1, "Document::CheckSwap:", "HostByteOrder != NetworkByteOrder"); } else { SwapCode = 0; - dbg.Verbose(1, "gdcmDocument::CheckSwap:", + dbg.Verbose(1, "Document::CheckSwap:", "HostByteOrder = NetworkByteOrder"); } @@ -2395,7 +2564,7 @@ bool gdcmDocument::CheckSwap() // Alas, this is not a DicomV3 file and whatever happens there is no file // preamble. We can reset the file position indicator to where the data // is (i.e. the beginning of the file). - dbg.Verbose(1, "gdcmDocument::CheckSwap:", "not a DICOM Version3 file"); + dbg.Verbose(1, "Document::CheckSwap:", "not a DICOM Version3 file"); rewind(Fp); // Our next best chance would be to be considering a 'clean' ACR/NEMA file. @@ -2413,19 +2582,19 @@ bool gdcmDocument::CheckSwap() { case 0x00040000 : SwapCode = 3412; - Filetype = gdcmACR; + Filetype = ACR; return true; case 0x04000000 : SwapCode = 4321; - Filetype = gdcmACR; + Filetype = ACR; return true; case 0x00000400 : SwapCode = 2143; - Filetype = gdcmACR; + Filetype = ACR; return true; case 0x00000004 : SwapCode = 0; - Filetype = gdcmACR; + Filetype = ACR; return true; default : // We are out of luck. It is not a DicomV3 nor a 'clean' ACR/NEMA file. @@ -2451,18 +2620,18 @@ bool gdcmDocument::CheckSwap() case 0x0004 : case 0x0008 : SwapCode = 0; - Filetype = gdcmACR; + Filetype = ACR; return true; case 0x0200 : case 0x0400 : case 0x0800 : SwapCode = 4321; - Filetype = gdcmACR; + Filetype = ACR; return true; default : - dbg.Verbose(0, "gdcmDocument::CheckSwap:", + dbg.Verbose(0, "Document::CheckSwap:", "ACR/NEMA unfound swap info (Really hopeless !)"); - Filetype = gdcmUnknown; + Filetype = Unknown; return false; } // Then the only info we have is the net2host one. @@ -2478,9 +2647,9 @@ bool gdcmDocument::CheckSwap() * \brief Restore the unproperly loaded values i.e. the group, the element * and the dictionary entry depending on them. */ -void gdcmDocument::SwitchSwapToBigEndian() +void Document::SwitchSwapToBigEndian() { - dbg.Verbose(1, "gdcmDocument::SwitchSwapToBigEndian", + dbg.Verbose(1, "Document::SwitchSwapToBigEndian", "Switching to BigEndian mode."); if ( SwapCode == 0 ) { @@ -2502,9 +2671,9 @@ void gdcmDocument::SwitchSwapToBigEndian() /** * \brief during parsing, Header Elements too long are not loaded in memory - * @param NewSize + * @param newSize */ -void gdcmDocument::SetMaxSizeLoadEntry(long newSize) +void Document::SetMaxSizeLoadEntry(long newSize) { if ( newSize < 0 ) { @@ -2521,10 +2690,10 @@ void gdcmDocument::SetMaxSizeLoadEntry(long newSize) /** * \brief Header Elements too long will not be printed - * \todo See comments of \ref gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE - * @param NewSize + * \todo See comments of \ref Document::MAX_SIZE_PRINT_ELEMENT_VALUE + * @param newSize */ -void gdcmDocument::SetMaxSizePrintEntry(long newSize) +void Document::SetMaxSizePrintEntry(long newSize) { //DOH !! This is exactly SetMaxSizeLoadEntry FIXME FIXME if ( newSize < 0 ) @@ -2548,7 +2717,7 @@ void gdcmDocument::SetMaxSizePrintEntry(long newSize) * gets the VR, gets the length, gets the offset value) * @return On succes the newly created DocEntry, NULL on failure. */ -gdcmDocEntry* gdcmDocument::ReadNextDocEntry() +DocEntry* Document::ReadNextDocEntry() { uint16_t group; uint16_t elem; @@ -2558,7 +2727,7 @@ gdcmDocEntry* gdcmDocument::ReadNextDocEntry() group = ReadInt16(); elem = ReadInt16(); } - catch ( gdcmFormatError e ) + catch ( FormatError e ) { // We reached the EOF (or an error occured) therefore // header parsing has to be considered as finished. @@ -2566,14 +2735,14 @@ gdcmDocEntry* gdcmDocument::ReadNextDocEntry() return 0; } - gdcmDocEntry *newEntry = NewDocEntryByNumber(group, elem); + DocEntry *newEntry = NewDocEntryByNumber(group, elem); FindDocEntryVR(newEntry); try { FindDocEntryLength(newEntry); } - catch ( gdcmFormatError e ) + catch ( FormatError e ) { // Call it quits //std::cout << e; @@ -2588,16 +2757,16 @@ gdcmDocEntry* gdcmDocument::ReadNextDocEntry() /** - * \brief Generate a free gdcmTagKey i.e. a gdcmTagKey that is not present + * \brief Generate a free TagKey i.e. a TagKey that is not present * in the TagHt dictionary. * @param group The generated tag must belong to this group. * @return The element of tag with given group which is fee. */ -uint32_t gdcmDocument::GenerateFreeTagKeyInGroup(uint16_t group) +uint32_t Document::GenerateFreeTagKeyInGroup(uint16_t group) { for (uint32_t elem = 0; elem < UINT32_MAX; elem++) { - gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, elem); + TagKey key = DictEntry::TranslateToKey(group, elem); if (TagHT.count(key) == 0) { return elem; @@ -2607,19 +2776,19 @@ uint32_t gdcmDocument::GenerateFreeTagKeyInGroup(uint16_t group) } /** - * \brief Assuming the internal file pointer \ref gdcmDocument::fp + * \brief Assuming the internal file pointer \ref Document::Fp * is placed at the beginning of a tag check whether this * tag is (TestGroup, TestElement). - * \warning On success the internal file pointer \ref gdcmDocument::fp + * \warning On success the internal file pointer \ref Document::Fp * is modified to point after the tag. * On failure (i.e. when the tag wasn't the expected tag * (TestGroup, TestElement) the internal file pointer - * \ref gdcmDocument::fp is restored to it's original position. - * @param TestGroup The expected group of the tag. - * @param TestElement The expected Element of the tag. + * \ref Document::Fp is restored to it's original position. + * @param testGroup The expected group of the tag. + * @param testElement The expected Element of the tag. * @return True on success, false otherwise. */ -bool gdcmDocument::ReadTag(uint16_t testGroup, uint16_t testElement) +bool Document::ReadTag(uint16_t testGroup, uint16_t testElement) { long positionOnEntry = ftell(Fp); long currentPosition = ftell(Fp); // On debugging purposes @@ -2637,7 +2806,7 @@ bool gdcmDocument::ReadTag(uint16_t testGroup, uint16_t testElement) s << std::hex << itemTagGroup << "," << itemTagElement << ")" << std::endl; s << " at address: " << (unsigned)currentPosition << std::endl; - dbg.Verbose(0, "gdcmDocument::ReadItemTagLength: wrong Item Tag found:"); + dbg.Verbose(0, "Document::ReadItemTagLength: wrong Item Tag found:"); dbg.Verbose(0, s.str().c_str()); fseek(Fp, positionOnEntry, SEEK_SET); @@ -2647,20 +2816,20 @@ bool gdcmDocument::ReadTag(uint16_t testGroup, uint16_t testElement) } /** - * \brief Assuming the internal file pointer \ref gdcmDocument::fp + * \brief Assuming the internal file pointer \ref Document::Fp * is placed at the beginning of a tag (TestGroup, TestElement), * read the length associated to the Tag. - * \warning On success the internal file pointer \ref gdcmDocument::fp + * \warning On success the internal file pointer \ref Document::Fp * is modified to point after the tag and it's length. * On failure (i.e. when the tag wasn't the expected tag * (TestGroup, TestElement) the internal file pointer - * \ref gdcmDocument::fp is restored to it's original position. - * @param TestGroup The expected group of the tag. - * @param TestElement The expected Element of the tag. + * \ref Document::Fp is restored to it's original position. + * @param testGroup The expected group of the tag. + * @param testElement The expected Element of the tag. * @return On success returns the length associated to the tag. On failure * returns 0. */ -uint32_t gdcmDocument::ReadTagLength(uint16_t testGroup, uint16_t testElement) +uint32_t Document::ReadTagLength(uint16_t testGroup, uint16_t testElement) { long positionOnEntry = ftell(Fp); (void)positionOnEntry; @@ -2678,126 +2847,282 @@ uint32_t gdcmDocument::ReadTagLength(uint16_t testGroup, uint16_t testElement) s << "Basic Item Length is: " << itemLength << std::endl; s << " at address: " << (unsigned)currentPosition << std::endl; - dbg.Verbose(0, "gdcmDocument::ReadItemTagLength: ", s.str().c_str()); + dbg.Verbose(0, "Document::ReadItemTagLength: ", s.str().c_str()); } return itemLength; } /** - * \brief Parse pixel data from disk for multi-fragment Jpeg/Rle files - * No other way so 'skip' the Data - * + * \brief When parsing the Pixel Data of an encapsulated file, read + * the basic offset table (when present, and BTW dump it). */ -void gdcmDocument::Parse7FE0 () +void Document::ReadAndSkipEncapsulatedBasicOffsetTable() { - gdcmDocEntry* element = GetDocEntryByNumber(0x0002, 0x0010); - if ( !element ) - { - // Should warn user FIXME - return; - } - - if ( IsImplicitVRLittleEndianTransferSyntax() - || IsExplicitVRLittleEndianTransferSyntax() - || IsExplicitVRBigEndianTransferSyntax() /// \todo 1.2.2 ??? A verifier ! - || IsDeflatedExplicitVRLittleEndianTransferSyntax() ) - { - return; - } - - // ---------------- for Parsing : Position on begining of Jpeg/RLE Pixels - //// Read the Basic Offset Table Item Tag length... uint32_t itemLength = ReadTagLength(0xfffe, 0xe000); - //// ... and then read length[s] itself[themselves]. We don't use - // the values read (BTW what is the purpous of those lengths ?) + // When present, read the basic offset table itself. + // Notes: - since the presence of this basic offset table is optional + // we can't rely on it for the implementation, and we will simply + // trash it's content (when present). + // - still, when present, we could add some further checks on the + // lengths, but we won't bother with such fuses for the time being. if ( itemLength != 0 ) { - // BTW, what is the purpous of those length anyhow !? char* basicOffsetTableItemValue = new char[itemLength + 1]; fread(basicOffsetTableItemValue, itemLength, 1, Fp); +#ifdef GDCM_DEBUG for (unsigned int i=0; i < itemLength; i += 4 ) { - uint32_t individualLength = str2num(&basicOffsetTableItemValue[i],uint32_t); + uint32_t individualLength = str2num( &basicOffsetTableItemValue[i], + uint32_t); std::ostringstream s; s << " Read one length: "; s << std::hex << individualLength << std::endl; - dbg.Verbose(0, "gdcmDocument::Parse7FE0: ", s.str().c_str()); + dbg.Verbose(0, + "Document::ReadAndSkipEncapsulatedBasicOffsetTable: ", + s.str().c_str()); } +#endif //GDCM_DEBUG + delete[] basicOffsetTableItemValue; } +} +/** + * \brief Parse pixel data from disk of [multi-]fragment RLE encoding. + * Compute the RLE extra information and store it in \ref RLEInfo + * for later pixel retrieval usage. + */ +void Document::ComputeRLEInfo() +{ if ( ! IsRLELossLessTransferSyntax() ) { - // JPEG Image - - //// We then skip (not reading them) all the fragments of images: - while ( (itemLength = ReadTagLength(0xfffe, 0xe000)) ) + return; + } + + // Encoded pixel data: for the time being we are only concerned with + // Jpeg or RLE Pixel data encodings. + // As stated in PS 3.5-2003, section 8.2 p44: + // "If sent in Encapsulated Format (i.e. other than the Native Format) the + // value representation OB is used". + // Hence we expect an OB value representation. Concerning OB VR, + // the section PS 3.5-2003, section A.4.c p 58-59, states: + // "For the Value Representations OB and OW, the encoding shall meet the + // following specifications depending on the Data element tag:" + // [...snip...] + // - the first item in the sequence of items before the encoded pixel + // data stream shall be basic offset table item. The basic offset table + // item value, however, is not required to be present" + + ReadAndSkipEncapsulatedBasicOffsetTable(); + + // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G) + // Loop on the individual frame[s] and store the information + // on the RLE fragments in a RLEFramesInfo. + // Note: - when only a single frame is present, this is a + // classical image. + // - when more than one frame are present, then we are in + // the case of a multi-frame image. + long frameLength; + while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) ) + { + // Parse the RLE Header and store the corresponding RLE Segment + // Offset Table information on fragments of this current Frame. + // Note that the fragment pixels themselves are not loaded + // (but just skipped). + long frameOffset = ftell(Fp); + + uint32_t nbRleSegments = ReadInt32(); + + uint32_t rleSegmentOffsetTable[15]; + for( int k = 1; k <= 15; k++ ) { - SkipBytes(itemLength); + rleSegmentOffsetTable[k] = ReadInt32(); } + + // Deduce from both the RLE Header and the frameLength the + // fragment length, and again store this info in a + // RLEFramesInfo. + long rleSegmentLength[15]; + // skipping (not reading) RLE Segments + if ( nbRleSegments > 1) + { + for(unsigned int k = 1; k <= nbRleSegments-1; k++) + { + rleSegmentLength[k] = rleSegmentOffsetTable[k+1] + - rleSegmentOffsetTable[k]; + SkipBytes(rleSegmentLength[k]); + } + } + + rleSegmentLength[nbRleSegments] = frameLength + - rleSegmentOffsetTable[nbRleSegments]; + SkipBytes(rleSegmentLength[nbRleSegments]); + + // Store the collected info + RLEFrame* newFrameInfo = new RLEFrame; + newFrameInfo->NumberFragments = nbRleSegments; + for( unsigned int uk = 1; uk <= nbRleSegments; uk++ ) + { + newFrameInfo->Offset[uk] = frameOffset + rleSegmentOffsetTable[uk]; + newFrameInfo->Length[uk] = rleSegmentLength[uk]; + } + RLEInfo->Frames.push_back( newFrameInfo ); } - else + + // Make sure that at the end of the item we encounter a 'Sequence + // Delimiter Item': + if ( !ReadTag(0xfffe, 0xe0dd) ) { - // RLE Image - long ftellRes; - long rleSegmentLength[15], fragmentLength; + dbg.Verbose(0, "Document::ComputeRLEInfo: no sequence delimiter "); + dbg.Verbose(0, " item at end of RLE item sequence"); + } +} - // While we find some items: - while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) ) - { - // Parse fragments of the current Fragment (Frame) - //------------------ scanning (not reading) fragment pixels - uint32_t nbRleSegments = ReadInt32(); - - //// Reading RLE Segments Offset Table - uint32_t rleSegmentOffsetTable[15]; - for(int k=1; k<=15; k++) - { - ftellRes = ftell(Fp); - rleSegmentOffsetTable[k] = ReadInt32(); - } +/** + * \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding. + * Compute the jpeg extra information (fragment[s] offset[s] and + * length) and store it[them] in \ref JPEGInfo for later pixel + * retrieval usage. + */ +void Document::ComputeJPEGFragmentInfo() +{ + // If you need to, look for comments of ComputeRLEInfo(). + if ( ! IsJPEGTransferSyntax() ) + { + return; + } + + ReadAndSkipEncapsulatedBasicOffsetTable(); + + // Loop on the fragments[s] and store the parsed information in a + // JPEGInfo. + long fragmentLength; + while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) ) + { + long fragmentOffset = ftell(Fp); + + // Store the collected info + JPEGFragment* newFragment = new JPEGFragment; + newFragment->Offset = fragmentOffset; + newFragment->Length = fragmentLength; + JPEGInfo->Fragments.push_back( newFragment ); + + SkipBytes( fragmentLength ); + } + + // Make sure that at the end of the item we encounter a 'Sequence + // Delimiter Item': + if ( !ReadTag(0xfffe, 0xe0dd) ) + { + dbg.Verbose(0, "Document::ComputeRLEInfo: no sequence delimiter "); + dbg.Verbose(0, " item at end of JPEG item sequence"); + } +} - // skipping (not reading) RLE Segments - if ( nbRleSegments > 1) +/** + * \brief Walk recursively the given \ref DocEntrySet, and feed + * the given hash table (\ref TagDocEntryHT) with all the + * \ref DocEntry (Dicom entries) encountered. + * This method does the job for \ref BuildFlatHashTable. + * @param builtHT Where to collect all the \ref DocEntry encountered + * when recursively walking the given set. + * @param set The structure to be traversed (recursively). + */ +void Document::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT, + DocEntrySet* set ) +{ + if (ElementSet* elementSet = dynamic_cast< ElementSet* > ( set ) ) + { + TagDocEntryHT* currentHT = elementSet->GetTagHT(); + for( TagDocEntryHT::const_iterator i = currentHT->begin(); + i != currentHT->end(); + ++i) + { + DocEntry* entry = i->second; + if ( SeqEntry* seqEntry = dynamic_cast(entry) ) { - for(unsigned int k = 1; k <= nbRleSegments-1; k++) + ListSQItem& items = seqEntry->GetSQItems(); + for( ListSQItem::const_iterator item = items.begin(); + item != items.end(); + ++item) { - rleSegmentLength[k] = rleSegmentOffsetTable[k+1] - - rleSegmentOffsetTable[k]; - ftellRes = ftell(Fp); - SkipBytes(rleSegmentLength[k]); - } - } - - rleSegmentLength[nbRleSegments] = fragmentLength - - rleSegmentOffsetTable[nbRleSegments]; - ftellRes = ftell(Fp); - SkipBytes(rleSegmentLength[nbRleSegments]); + BuildFlatHashTableRecurse( builtHT, *item ); + } + continue; + } + builtHT[entry->GetKey()] = entry; } + return; + } - // Make sure that at the end of the item we encounter a 'Sequence - // Delimiter Item': - if ( !ReadTag(0xfffe, 0xe0dd) ) + if (SQItem* SQItemSet = dynamic_cast< SQItem* > ( set ) ) + { + ListDocEntry& currentList = SQItemSet->GetDocEntries(); + for (ListDocEntry::iterator i = currentList.begin(); + i != currentList.end(); + ++i) { - dbg.Verbose(0, "gdcmDocument::Parse7FE0: no sequence delimiter item"); - dbg.Verbose(0, " at end of RLE item sequence"); + DocEntry* entry = *i; + if ( SeqEntry* seqEntry = dynamic_cast(entry) ) + { + ListSQItem& items = seqEntry->GetSQItems(); + for( ListSQItem::const_iterator item = items.begin(); + item != items.end(); + ++item) + { + BuildFlatHashTableRecurse( builtHT, *item ); + } + continue; + } + builtHT[entry->GetKey()] = entry; } + } } +/** + * \brief Build a \ref TagDocEntryHT (i.e. a std::map<>) from the current + * Document. + * + * The structure used by a Document (through \ref ElementSet), + * in order to old the parsed entries of a Dicom header, is a recursive + * one. This is due to the fact that the sequences (when present) + * can be nested. Additionaly, the sequence items (represented in + * gdcm as \ref SQItem) add an extra complexity to the data + * structure. Hence, a gdcm user whishing to visit all the entries of + * a Dicom header will need to dig in the gdcm internals (which + * implies exposing all the internal data structures to the API). + * In order to avoid this burden to the user, \ref BuildFlatHashTable + * recursively builds a temporary hash table, which holds all the + * Dicom entries in a flat structure (a \ref TagDocEntryHT i.e. a + * std::map<>). + * \warning Of course there is NO integrity constrain between the + * returned \ref TagDocEntryHT and the \ref ElementSet used + * to build it. Hence if the underlying \ref ElementSet is + * altered, then it is the caller responsability to invoke + * \ref BuildFlatHashTable again... + * @return The flat std::map<> we juste build. + */ +TagDocEntryHT* Document::BuildFlatHashTable() +{ + TagDocEntryHT* FlatHT = new TagDocEntryHT; + BuildFlatHashTableRecurse( *FlatHT, this ); + return FlatHT; +} + /** - * \brief Compares two documents, according to \ref gdcmDicomDir rules + * \brief Compares two documents, according to \ref DicomDir rules * \warning Does NOT work with ACR-NEMA files * \todo Find a trick to solve the pb (use RET fields ?) * @param document * @return true if 'smaller' */ -bool gdcmDocument::operator<(gdcmDocument &document) +bool Document::operator<(Document &document) { // Patient Name std::string s1 = GetEntryByNumber(0x0010,0x0010); @@ -2806,7 +3131,7 @@ bool gdcmDocument::operator<(gdcmDocument &document) { return true; } - else if(s1 > s2) + else if( s1 > s2 ) { return false; } @@ -2821,7 +3146,7 @@ bool gdcmDocument::operator<(gdcmDocument &document) } else if ( s1 > s2 ) { - return true; + return false; } else { @@ -2840,7 +3165,7 @@ bool gdcmDocument::operator<(gdcmDocument &document) { // Serie Instance UID s1 = GetEntryByNumber(0x0020,0x000e); - s2 = document.GetEntryByNumber(0x0020,0x000e); + s2 = document.GetEntryByNumber(0x0020,0x000e); if ( s1 < s2 ) { return true; @@ -2855,5 +3180,6 @@ bool gdcmDocument::operator<(gdcmDocument &document) return false; } +} // end namespace gdcm //-----------------------------------------------------------------------------