X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=c5d391396cc11c60b7b040b24e07c9d19869ce90;hb=0b01703cc07d46a6ae718e01c6beee14599a9da1;hp=9b5b2ac4e7f03d731f94e20a56c93b2a3b378f87;hpb=f4618aed21f60eeca799cf5807b3dca987831591;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 9b5b2ac4..c5d39139 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,12 +3,12 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2004/09/10 18:54:38 $ - Version: $Revision: 1.74 $ + Date: $Date: 2004/11/24 11:17:47 $ + Version: $Revision: 1.136 $ 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 @@ -20,61 +20,64 @@ #include "gdcmValEntry.h" #include "gdcmBinEntry.h" #include "gdcmSeqEntry.h" - #include "gdcmGlobal.h" #include "gdcmUtil.h" #include "gdcmDebug.h" #include +#include // For nthos: -#ifdef _MSC_VER +#if defined(_MSC_VER) || defined(__BORLANDC__) #include #else #include #endif -# include - -// Implicit VR Little Endian -#define UI1_2_840_10008_1_2 "1.2.840.10008.1.2" -// Explicit VR Little Endian -#define UI1_2_840_10008_1_2_1 "1.2.840.10008.1.2.1" -// Deflated Explicit VR Little Endian -#define UI1_2_840_10008_1_2_1_99 "1.2.840.10008.1.2.1.99" -// Explicit VR Big Endian -#define UI1_2_840_10008_1_2_2 "1.2.840.10008.1.2.2" -// JPEG Baseline (Process 1) -#define UI1_2_840_10008_1_2_4_50 "1.2.840.10008.1.2.4.50" -// JPEG Extended (Process 2 & 4) -#define UI1_2_840_10008_1_2_4_51 "1.2.840.10008.1.2.4.51" -// JPEG Extended (Process 3 & 5) -#define UI1_2_840_10008_1_2_4_52 "1.2.840.10008.1.2.4.52" -// JPEG Spectral Selection, Non-Hierarchical (Process 6 & 8) -#define UI1_2_840_10008_1_2_4_53 "1.2.840.10008.1.2.4.53" -// JPEG Full Progression, Non-Hierarchical (Process 10 & 12) -#define UI1_2_840_10008_1_2_4_55 "1.2.840.10008.1.2.4.55" -// JPEG Lossless, Non-Hierarchical (Process 14) -#define UI1_2_840_10008_1_2_4_57 "1.2.840.10008.1.2.4.57" -// JPEG Lossless, Hierarchical, First-Order Prediction (Process 14, -// [Selection Value 1]) -#define UI1_2_840_10008_1_2_4_70 "1.2.840.10008.1.2.4.70" -// JPEG 2000 Lossless -#define UI1_2_840_10008_1_2_4_90 "1.2.840.10008.1.2.4.90" -// JPEG 2000 -#define UI1_2_840_10008_1_2_4_91 "1.2.840.10008.1.2.4.91" -// RLE Lossless -#define UI1_2_840_10008_1_2_5 "1.2.840.10008.1.2.5" -// UI1_1_2_840_10008_1_2_5 -#define str2num(str, typeNum) *((typeNum *)(str)) +namespace gdcm +{ +static const char *TransferSyntaxStrings[] = { + // Implicit VR Little Endian + "1.2.840.10008.1.2", + // Implicit VR Little Endian DLX G.E? + "1.2.840.113619.5.2", + // Explicit VR Little Endian + "1.2.840.10008.1.2.1", + // Deflated Explicit VR Little Endian + "1.2.840.10008.1.2.1.99", + // Explicit VR Big Endian + "1.2.840.10008.1.2.2", + // JPEG Baseline (Process 1) + "1.2.840.10008.1.2.4.50", + // JPEG Extended (Process 2 & 4) + "1.2.840.10008.1.2.4.51", + // JPEG Extended (Process 3 & 5) + "1.2.840.10008.1.2.4.52", + // JPEG Spectral Selection, Non-Hierarchical (Process 6 & 8) + "1.2.840.10008.1.2.4.53", + // JPEG Full Progression, Non-Hierarchical (Process 10 & 12) + "1.2.840.10008.1.2.4.55", + // JPEG Lossless, Non-Hierarchical (Process 14) + "1.2.840.10008.1.2.4.57", + // JPEG Lossless, Hierarchical, First-Order Prediction (Process 14, [Selection Value 1]) + "1.2.840.10008.1.2.4.70", + // JPEG 2000 Lossless + "1.2.840.10008.1.2.4.90", + // JPEG 2000 + "1.2.840.10008.1.2.4.91", + // RLE Lossless + "1.2.840.10008.1.2.5", + // Unknown + "Unknown Transfer Syntax" +}; //----------------------------------------------------------------------------- -// 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 @@ -83,53 +86,68 @@ const unsigned int gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff; * \brief constructor * @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; Initialise(); + Fp = 0; if ( !OpenFile() ) { return; } - dbg.Verbose(0, "gdcmDocument::gdcmDocument: starting parsing of file: ", + dbg.Verbose(0, "Document::Document: starting parsing of file: ", Filename.c_str()); - rewind(Fp); + Fp->seekg( 0, std::ios_base::beg); - fseek(Fp,0L,SEEK_END); - long lgt = ftell(Fp); + Fp->seekg(0, std::ios_base::end); + long lgt = Fp->tellg(); - rewind(Fp); + Fp->seekg( 0, std::ios_base::beg); CheckSwap(); - long beg = ftell(Fp); + long beg = Fp->tellg(); 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); + Fp->seekg( 0, std::ios_base::beg); // Load 'non string' values 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 +167,7 @@ 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); @@ -162,31 +180,29 @@ 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) { + Fp = 0; + SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Initialise(); + SwapCode = 0; + Filetype = ExplicitVR; PrintLevel = 1; // 'Medium' print level by default } /** * \brief Canonical destructor. */ -gdcmDocument::~gdcmDocument () +Document::~Document () { RefPubDict = NULL; RefShaDict = NULL; - // Recursive clean up of sequences - for (TagDocEntryHT::const_iterator it = TagHT.begin(); - it != TagHT.end(); ++it ) - { - delete it->second; - } - TagHT.clear(); + delete RLEInfo; + delete JPEGInfo; } //----------------------------------------------------------------------------- @@ -196,7 +212,7 @@ 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 +221,7 @@ 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 +231,7 @@ void gdcmDocument::PrintShaDict(std::ostream & os) /** * \brief Get the public dictionary used */ -gdcmDict *gdcmDocument::GetPubDict() +Dict* Document::GetPubDict() { return RefPubDict; } @@ -223,7 +239,7 @@ gdcmDict *gdcmDocument::GetPubDict() /** * \brief Get the shadow dictionary used */ -gdcmDict *gdcmDocument::GetShaDict() +Dict* Document::GetShaDict() { return RefShaDict; } @@ -232,7 +248,7 @@ 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 +258,31 @@ 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; } @@ -274,172 +290,101 @@ bool gdcmDocument::IsReadable() return true; } - /** - * \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. - * @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. + * \brief Accessor to the Transfer Syntax (when present) of the + * current document (it internally handles reading the + * value from disk when only parsing occured). + * @return The encountered Transfer Syntax of the current document. */ -bool gdcmDocument::IsGivenTransferSyntax(std::string const & syntaxToCheck) +TransferSyntaxType Document::GetTransferSyntax() { - gdcmDocEntry *entry = GetDocEntryByNumber(0x0002, 0x0010); + DocEntry *entry = GetDocEntryByNumber(0x0002, 0x0010); if ( !entry ) { - return false; + return UnknownTS; } // 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 // first need to remove the potential padding. We can make the // weak assumption that padding was not executed with digits... - if ( transfer.length() == 0 ) { // for brain damaged headers - return false; + if ( transfer.length() == 0 ) + { + // for brain damaged headers + return UnknownTS; } - while ( ! isdigit(transfer[transfer.length()-1]) ) + while ( !isdigit((unsigned char)transfer[transfer.length()-1]) ) { transfer.erase(transfer.length()-1, 1); } - if ( transfer == syntaxToCheck ) + for (int i = 0; TransferSyntaxStrings[i] != NULL; i++) { - return true; + if ( TransferSyntaxStrings[i] == transfer ) + { + return TransferSyntaxType(i); + } } } - return false; -} - -/** - * \brief Determines if the Transfer Syntax of the present document - * corresponds to a Implicit Value Representation of - * Little Endian. - * \sa \ref gdcmDocument::IsGivenTransferSyntax. - * @return True when ImplicitVRLittleEndian found. False in all other cases. - */ -bool gdcmDocument::IsImplicitVRLittleEndianTransferSyntax() -{ - return IsGivenTransferSyntax(UI1_2_840_10008_1_2); -} - -/** - * \brief Determines if the Transfer Syntax was already encountered - * and if it corresponds to a ExplicitVRLittleEndian one. - * @return True when ExplicitVRLittleEndian found. False in all other cases. - */ -bool gdcmDocument::IsExplicitVRLittleEndianTransferSyntax() -{ - return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1); + return UnknownTS; } -/** - * \brief Determines if the Transfer Syntax was already encountered - * and if it corresponds to a DeflatedExplicitVRLittleEndian one. - * @return True when DeflatedExplicitVRLittleEndian found. False in all other cases. - */ -bool gdcmDocument::IsDeflatedExplicitVRLittleEndianTransferSyntax() +bool Document::IsJPEGLossless() { - return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1_99); -} - -/** - * \brief Determines if the Transfer Syntax was already encountered - * 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() -{ - return IsGivenTransferSyntax(UI1_2_840_10008_1_2_2); -} - -/** - * \brief Determines if the Transfer Syntax was already encountered - * and if it corresponds to a JPEGBaseLineProcess1 one. - * @return True when JPEGBaseLineProcess1found. False in all other cases. - */ -bool gdcmDocument::IsJPEGBaseLineProcess1TransferSyntax() -{ - return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_50); + TransferSyntaxType r = GetTransferSyntax(); + return r == JPEGFullProgressionProcess10_12 + || r == JPEGLosslessProcess14 + || r == JPEGLosslessProcess14_1; } /** * \brief Determines if the Transfer Syntax was already encountered - * and if it corresponds to a JPEGExtendedProcess2-4 one. - * @return True when JPEGExtendedProcess2-4 found. False in all other cases. - */ -bool gdcmDocument::IsJPEGExtendedProcess2_4TransferSyntax() -{ - return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_51); -} - -/** - * \brief Determines if the Transfer Syntax was already encountered - * and if it corresponds to a JPEGExtendeProcess3-5 one. - * @return True when JPEGExtendedProcess3-5 found. False in all other cases. - */ -bool gdcmDocument::IsJPEGExtendedProcess3_5TransferSyntax() -{ - return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_52); -} - -/** - * \brief Determines if the Transfer Syntax was already encountered - * and if it corresponds to a JPEGSpectralSelectionProcess6-8 one. - * @return True when JPEGSpectralSelectionProcess6-8 found. False in all + * and if it corresponds to a JPEG2000 one + * @return True when JPEG2000 (Lossly or LossLess) found. False in all * other cases. */ -bool gdcmDocument::IsJPEGSpectralSelectionProcess6_8TransferSyntax() +bool Document::IsJPEG2000() { - return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_53); + TransferSyntaxType r = GetTransferSyntax(); + return r == JPEG2000Lossless || r == JPEG2000; } /** - * \brief Determines if the Transfer Syntax was already encountered - * and if it corresponds to a RLE Lossless one. - * @return True when RLE Lossless found. False in all - * other cases. + * \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 gdcmDocument::IsRLELossLessTransferSyntax() +bool Document::IsJPEG() { - return IsGivenTransferSyntax(UI1_2_840_10008_1_2_5); + TransferSyntaxType r = GetTransferSyntax(); + return r == JPEGBaselineProcess1 + || r == JPEGExtendedProcess2_4 + || r == JPEGExtendedProcess3_5 + || r == JPEGSpectralSelectionProcess6_8 + || IsJPEGLossless() + || IsJPEG2000(); } /** - * \brief Determines if Transfer Syntax was already encountered - * and if it corresponds to a JPEG Lossless one. - * @return True when RLE Lossless found. False in all - * other cases. + * \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 gdcmDocument::IsJPEGLossless() +bool Document::IsEncapsulate() { - return ( IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_55) - || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_57) - || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_70) ); -} - -/** - * \brief Determines if the Transfer Syntax was already encountered - * and if it corresponds to a JPEG2000 one - * @return True when JPEG2000 (Lossly or LossLess) found. False in all - * other cases. - */ -bool gdcmDocument::IsJPEG2000() -{ - return ( IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_90) - || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_91) ); + TransferSyntaxType r = GetTransferSyntax(); + return IsJPEG() || r == RLELossless; } /** * \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 ... @@ -453,49 +398,61 @@ 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() +std::ifstream* Document::OpenFile() { - Fp = fopen(Filename.c_str(),"rb"); + if (Filename.length() == 0) return 0; + if(Fp) + { + dbg.Verbose( 0, + "Document::OpenFile is already opened when opening: ", + Filename.c_str()); + } + + Fp = new std::ifstream(Filename.c_str(), std::ios::in | std::ios::binary); if(!Fp) { dbg.Verbose( 0, - "gdcmDocument::OpenFile cannot open file: ", + "Document::OpenFile cannot open file: ", Filename.c_str()); return 0; } uint16_t zero; - fread(&zero, (size_t)2, (size_t)1, Fp); + Fp->read((char*)&zero, (size_t)2 ); - //ACR -- or DICOM with no Preamble -- - if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200 ) + //ACR -- or DICOM with no Preamble; may start with a Shadow Group -- + if( + zero == 0x0001 || zero == 0x0100 || zero == 0x0002 || zero == 0x0200 || + zero == 0x0003 || zero == 0x0300 || zero == 0x0004 || zero == 0x0400 || + zero == 0x0005 || zero == 0x0500 || zero == 0x0006 || zero == 0x0600 || + zero == 0x0007 || zero == 0x0700 || zero == 0x0008 || zero == 0x0800 ) { return Fp; } //DICOM - fseek(Fp, 126L, SEEK_CUR); + Fp->seekg(126L, std::ios_base::cur); char dicm[4]; - fread(dicm, (size_t)4, (size_t)1, Fp); + Fp->read(dicm, (size_t)4); if( memcmp(dicm, "DICM", 4) == 0 ) { return Fp; } - fclose(Fp); + CloseFile(); dbg.Verbose( 0, - "gdcmDocument::OpenFile not DICOM/ACR (missing preamble)", + "Document::OpenFile not DICOM/ACR (missing preamble)", Filename.c_str()); return 0; @@ -505,12 +462,16 @@ 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; + if( Fp ) + { + Fp->close(); + delete Fp; + Fp = 0; + } - return closed; + return true; //FIXME how do we detect a non-close ifstream ? } /** @@ -520,20 +481,18 @@ bool gdcmDocument::CloseFile() * (ACR-NEMA, ExplicitVR, ImplicitVR) * \return Always true. */ -void gdcmDocument::Write(FILE* fp,FileType filetype) +void Document::Write(std::ofstream* 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); + std::string ts = + Util::DicomString( TransferSyntaxStrings[ImplicitVRLittleEndian] ); + ReplaceOrCreateByNumber(ts, 0x0002, 0x0010); /// \todo Refer to standards on page 21, chapter 6.2 /// "Value representation": values with a VR of UI shall be @@ -543,10 +502,11 @@ 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); + std::string ts = + Util::DicomString( TransferSyntaxStrings[ExplicitVRLittleEndian] ); + ReplaceOrCreateByNumber(ts, 0x0002, 0x0010); //LEAK /// \todo Refer to standards on page 21, chapter 6.2 /// "Value representation": values with a VR of UI shall be @@ -568,7 +528,7 @@ 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 } @@ -578,53 +538,75 @@ void gdcmDocument::Write(FILE* fp,FileType filetype) * @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, + TagName 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); + delete currentEntry; + if ( !AddEntry(valEntry)) { - dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: AddEntry" + delete valEntry; + dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry" " failed allthough this is a creation."); + return NULL; } } else { - valEntry = dynamic_cast< gdcmValEntry* >(currentEntry); + 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" + delete valEntry; + dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: removal" " of previous DocEntry failed."); return NULL; } if ( !AddEntry(valEntry)) { - dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: adding" + delete valEntry; + dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: adding" " promoted ValEntry failed."); return NULL; } @@ -639,36 +621,97 @@ 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 + * A copy of the binArea is made to be kept in the Document. + * @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, + TagName 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 !! + uint8_t *tmpArea; + if (lgth>0 && binArea) + { + tmpArea = new uint8_t[lgth]; + memcpy(tmpArea,binArea,lgth); + } + else + { + tmpArea = 0; + } + if (!SetEntryByNumber(tmpArea, lgth, group, elem)) + { + if (tmpArea) + { + delete[] tmpArea; + } + } - return b; + return binEntry; } @@ -680,12 +723,10 @@ gdcmBinEntry * gdcmDocument::ReplaceOrCreateByNumber( * \return pointer to the modified/created SeqEntry (NULL when creation * failed). */ -gdcmSeqEntry * gdcmDocument::ReplaceOrCreateByNumber( - uint16_t group, - uint16_t elem) +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); @@ -694,7 +735,7 @@ 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; @@ -708,8 +749,8 @@ gdcmSeqEntry * gdcmDocument::ReplaceOrCreateByNumber( * @param elem element number of the Entry * \return boolean */ -bool gdcmDocument::ReplaceIfExistByNumber(std::string const & value, - uint16_t group, uint16_t elem ) +bool Document::ReplaceIfExistByNumber(std::string const & value, + uint16_t group, uint16_t elem ) { SetEntryByNumber(value, group, elem); @@ -725,10 +766,10 @@ bool gdcmDocument::ReplaceIfExistByNumber(std::string const & value, * @param element Element number of the searched Dicom Element * @return true is found */ -bool 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 ); - return TagHT.count(key); + const std::string &key = DictEntry::TranslateToKey(group, element ); + return TagHT.count(key) != 0; } /** @@ -740,9 +781,9 @@ bool 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; @@ -764,20 +805,19 @@ 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(), - dictEntry->GetElement()); + DocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(), + dictEntry->GetElement()); return elem->GetVR(); } - /** * \brief Searches within Header Entries (Dicom Elements) parsed with * the public and private dictionaries @@ -787,16 +827,16 @@ 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(); } /** @@ -813,9 +853,9 @@ 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; @@ -831,9 +871,9 @@ 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 @@ -846,9 +886,10 @@ 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, + TagName const & tagName) { - gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); + DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( !dictEntry ) { return false; @@ -859,68 +900,68 @@ 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, - uint16_t group, - uint16_t element) +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 ) - { - evenContent += '\0'; // ... therefore we padd with (000H) .!?! - } - valEntry->SetValue(evenContent); - + std::string finalContent = Util::DicomString( content.c_str() ); + assert( !(finalContent.size() % 2) ); + valEntry->SetValue(finalContent); + // Integers have a special treatement for their length: - gdcmVRKey vr = valEntry->GetVR(); - if( vr == "US" || vr == "SS" ) - { - int c = CountSubstring(content, "\\"); // for multivaluated items - valEntry->SetLength((c+1)*2); - } - else if( vr == "UL" || vr == "SL" ) - { - int c = CountSubstring(content, "\\"); // for multivaluated items - valEntry->SetLength((c+1)*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, - int lgth, - uint16_t group, - uint16_t element) +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; @@ -933,15 +974,16 @@ 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* entry = (BinEntry *)TagHT[key]; + entry->SetBinArea(content); + entry->SetLength(lgth); + entry->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. @@ -951,12 +993,11 @@ 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, - uint16_t group, - uint16_t element) +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; @@ -977,12 +1018,12 @@ bool gdcmDocument::SetEntryLengthByNumber(uint32_t l, * @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(); @@ -995,15 +1036,20 @@ size_t gdcmDocument::GetEntryOffsetByNumber(uint16_t group, uint16_t elem) * @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; } /** @@ -1012,59 +1058,78 @@ void * gdcmDocument::GetEntryVoidAreaByNumber(uint16_t group, uint16_t elem) * @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); + // Search the corresponding DocEntry + DocEntry *docElement = GetDocEntryByNumber(group, elem); if ( !docElement ) - { - return NULL; - } - size_t o =(size_t)docElement->GetOffset(); - fseek(Fp, o, SEEK_SET); + return; + + BinEntry *binElement = dynamic_cast(docElement); + if( !binElement ) + return; + + LoadEntryBinArea(binElement); +/* size_t o =(size_t)docElement->GetOffset(); + Fp->seekg( o, std::ios_base::beg); 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"); - return NULL; + dbg.Verbose(0, "Document::LoadEntryBinArea cannot allocate a"); + return; } - size_t l2 = fread(a, 1, l , Fp); - if( l != l2 ) + + // Read the value + Fp->read((char*)a, l); + if( Fp->fail() || Fp->eof() )//Fp->gcount() == 1 { delete[] a; - return NULL; + return; } - /// \TODO Drop any already existing void area! JPR - SetEntryVoidAreaByNumber(a, group, elem); - return a; + // Set the value to the DocEntry + if( !SetEntryBinAreaByNumber( a, group, elem ) ) + { + delete[] a; + dbg.Verbose(0, "Document::LoadEntryBinArea setting failed."); + }*/ } + /** * \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) { + bool openFile = !Fp; + if(openFile) + OpenFile(); + size_t o =(size_t)element->GetOffset(); - fseek(Fp, o, SEEK_SET); + Fp->seekg(o, std::ios_base::beg); + 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"); - return NULL; + dbg.Verbose(0, "Document::LoadEntryBinArea cannot allocate a"); + return; } - element->SetVoidArea((void *)a); + /// \todo check the result - size_t l2 = fread(a, 1, l , Fp); - if( l != l2 ) + Fp->read((char*)a, l); + if( Fp->fail() || Fp->eof()) //Fp->gcount() == 1 { delete[] a; - return NULL; + return; } - return a; + element->SetBinArea(a); + + if(openFile) + CloseFile(); } /** @@ -1074,29 +1139,31 @@ void *gdcmDocument::LoadEntryVoidArea(gdcmBinEntry *element) * @param element Element number of the searched Dicom Element * @return */ -bool gdcmDocument::SetEntryVoidAreaByNumber(void * area, - uint16_t group, - uint16_t element) +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); - - return true; + if ( BinEntry* binEntry = dynamic_cast(currentEntry) ) + { + binEntry->SetBinArea( area ); + return true; + } + + return false; } /** * \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? @@ -1145,9 +1212,9 @@ void gdcmDocument::UpdateShaEntries() * @return Corresponding Dicom Element when it exists, and NULL * otherwise. */ -gdcmDocEntry* gdcmDocument::GetDocEntryByName(std::string const & tagName) +DocEntry* Document::GetDocEntryByName(TagName const & tagName) { - gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); + DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( !dictEntry ) { return NULL; @@ -1166,10 +1233,9 @@ gdcmDocEntry* gdcmDocument::GetDocEntryByName(std::string const & tagName) * @param element Element number of the searched Dicom Element * @return */ -gdcmDocEntry* gdcmDocument::GetDocEntryByNumber(uint16_t group, - uint16_t element) +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; @@ -1178,24 +1244,23 @@ 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, - uint16_t element) +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; } @@ -1207,11 +1272,11 @@ 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); + long PositionOnEntry = Fp->tellg(); LoadDocEntry(entry); - fseek(Fp, PositionOnEntry, SEEK_SET); + Fp->seekg(PositionOnEntry, std::ios_base::beg); } /** @@ -1219,7 +1284,7 @@ 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) { @@ -1239,7 +1304,7 @@ 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; @@ -1250,7 +1315,7 @@ 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); } @@ -1259,7 +1324,7 @@ 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 ) { @@ -1272,7 +1337,7 @@ 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); } @@ -1284,20 +1349,14 @@ 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, - long offset, - long l_max, - bool delim_mode) +void Document::ParseDES(DocEntrySet *set, long offset, + long l_max, bool delim_mode) { - gdcmDocEntry *newDocEntry = 0; - gdcmValEntry *newValEntry = 0; - unsigned long l = 0; - - int depth = set->GetDepthLevel(); + DocEntry *newDocEntry = 0; + while (true) - { - if ( !delim_mode && (ftell(Fp)-offset) >= l_max) + { + if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { break; } @@ -1307,69 +1366,119 @@ 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); - if (newValEntry->IsItemDelimitor()) + /////////////////////// ValEntry + ValEntry* newValEntry = + new ValEntry( newDocEntry->GetDictEntry() ); //LEAK + 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() ); + } + + LoadDocEntry( newValEntry ); + bool delimitor=newValEntry->IsItemDelimitor(); + if( !set->AddEntry( newValEntry ) ) + { + // If here expect big troubles + delete newValEntry; //otherwise mem leak + } + + if (delimitor) + { + delete newDocEntry; break; } - if ( !delim_mode && (ftell(Fp)-offset) >= l_max) + if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { + delete newDocEntry; break; } } 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() ); //LEAK + newBinEntry->Copy( newDocEntry );*/ + BinEntry* newBinEntry = new BinEntry( newDocEntry ); //LEAK + + // 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() ); + } + + LoadDocEntry( newBinEntry ); + if( !set->AddEntry( newBinEntry ) ) + { + //Expect big troubles if here + delete newBinEntry; + } } - if (newDocEntry->GetGroup() == 0x7fe0 && - newDocEntry->GetElement() == 0x0010 ) + if ( ( newDocEntry->GetGroup() == 0x7fe0 ) + && ( newDocEntry->GetElement() == 0x0010 ) ) { - if (newDocEntry->GetReadLength()==0xffffffff) + TransferSyntaxType ts = GetTransferSyntax(); + if ( ts == RLELossless ) { - // Broken US.3405.1.dcm - Parse7FE0(); // to skip the pixels - // (multipart JPEG/RLE are trouble makers) + long PositionOnEntry = Fp->tellg(); + Fp->seekg( newDocEntry->GetOffset(), std::ios_base::beg ); + ComputeRLEInfo(); + Fp->seekg( PositionOnEntry, std::ios_base::beg ); } - else + else if ( IsJPEG() ) { - SkipToNextDocEntry(newDocEntry); - l = newDocEntry->GetFullLength(); + long PositionOnEntry = Fp->tellg(); + Fp->seekg( newDocEntry->GetOffset(), std::ios_base::beg ); + ComputeJPEGFragmentInfo(); + Fp->seekg( PositionOnEntry, std::ios_base::beg ); } } - 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); + //delete 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 ) @@ -1382,45 +1491,61 @@ 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); - if ( !delim_mode && (ftell(Fp)-offset) >= l_max) + set->AddEntry( newSeqEntry ); + if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { + delete newDocEntry; break; } } 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 @@ -1430,17 +1555,23 @@ long gdcmDocument::ParseSQ(gdcmSeqEntry *set, { if ( newDocEntry->IsSequenceDelimitor() ) { - set->SetSequenceDelimitationItem( newDocEntry ); + seqEntry->SetSequenceDelimitationItem( newDocEntry ); break; } } - if ( !delim_mode && (ftell(Fp)-offset) >= l_max) + if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { - break; + delete newDocEntry; + 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 ) @@ -1452,34 +1583,30 @@ 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); + delete newDocEntry; - set->AddEntry(itemSQ, SQItemNumber); + seqEntry->AddEntry( itemSQ, SQItemNumber ); SQItemNumber++; - if ( !delim_mode && (ftell(Fp)-offset) >= l_max) + if ( !delim_mode && ((long)(Fp->tellg())-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() + * 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(); std::string vr = entry->GetVR(); uint32_t length = entry->GetLength(); - fseek(Fp, (long)entry->GetOffset(), SEEK_SET); + Fp->seekg((long)entry->GetOffset(), std::ios_base::beg); // A SeQuence "contains" a set of Elements. // (fffe e000) tells us an Element is beginning @@ -1494,7 +1621,7 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry* entry) // When the length is zero things are easy: if ( length == 0 ) { - ((gdcmValEntry *)entry)->SetValue(""); + ((ValEntry *)entry)->SetValue(""); return; } @@ -1505,7 +1632,7 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry* entry) std::ostringstream s; if (length > MaxSizeLoadEntry) { - if (gdcmBinEntry* binEntryPtr = dynamic_cast< gdcmBinEntry* >(entry) ) + if (BinEntry* binEntryPtr = dynamic_cast< BinEntry* >(entry) ) { //s << "gdcm::NotLoaded (BinEntry)"; s << GDCM_NOTLOADED; @@ -1514,8 +1641,8 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry* entry) s << " x(" << std::hex << entry->GetLength() << ")"; binEntryPtr->SetValue(s.str()); } - // Be carefull : a BinEntry IS_A ValEntry ... - else if (gdcmValEntry* valEntryPtr = dynamic_cast< gdcmValEntry* >(entry) ) + // Be carefull : a BinEntry IS_A ValEntry ... + else if (ValEntry* valEntryPtr = dynamic_cast< ValEntry* >(entry) ) { // s << "gdcm::NotLoaded. (ValEntry)"; s << GDCM_NOTLOADED; @@ -1532,16 +1659,17 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry* entry) } // to be sure we are at the end of the value ... - fseek(Fp,(long)entry->GetOffset()+(long)entry->GetLength(),SEEK_SET); + Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(), + std::ios_base::beg); 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) ) { - s << "gdcm::Loaded (BinEntry)"; + s << GDCM_BINLOADED; binEntryPtr->SetValue(s.str()); - LoadEntryVoidArea(binEntryPtr); // last one, not to erase length ! + LoadEntryBinArea(binEntryPtr); // last one, not to erase length ! return; } @@ -1549,7 +1677,6 @@ 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 @@ -1591,24 +1718,35 @@ 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; } - // We need an additional byte for storing \0 that is not on disk - //std::string newValue(length,0); - //item_read = fread(&(newValue[0]), (size_t)length, (size_t)1, Fp); - //rah !! I can't believe it could work, normally this is a const char* !!! + // FIXME: We need an additional byte for storing \0 that is not on disk char *str = new char[length+1]; - item_read = fread(str, (size_t)length, (size_t)1, Fp); - str[length] = '\0'; - std::string newValue = str; + Fp->read(str, (size_t)length); + str[length] = '\0'; //this is only useful when length is odd + // Special DicomString call to properly handle \0 and even length + std::string newValue; + if( length % 2 ) + { + newValue = Util::DicomString(str, length+1); + //dbg.Verbose(0, "Warning: bad length: ", length ); + dbg.Verbose(0, "For string :", newValue.c_str()); + // Since we change the length of string update it length + entry->SetReadLength(length+1); + } + else + { + newValue = Util::DicomString(str, length); + } delete[] str; - if ( gdcmValEntry* valEntry = dynamic_cast(entry) ) - { - if ( item_read != 1 ) + + if ( ValEntry* valEntry = dynamic_cast(entry) ) + { + if ( Fp->fail() || Fp->eof())//Fp->gcount() == 1 { - dbg.Verbose(1, "gdcmDocument::LoadDocEntry", + dbg.Verbose(1, "Document::LoadDocEntry", "unread element value"); valEntry->SetValue(GDCM_UNREAD); return; @@ -1626,7 +1764,7 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry* entry) } else { - dbg.Error(true, "gdcmDocument::LoadDocEntry" + dbg.Error(true, "Document::LoadDocEntry" "Should have a ValEntry, here !"); } } @@ -1636,41 +1774,43 @@ 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. */ -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); + Fp->seekg( 2L, std::ios_base::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 // chance to get the pixels by deciding the element goes // until the end of the file. Hence we artificially fix the // the length and proceed. - long currentPosition = ftell(Fp); - fseek(Fp,0L,SEEK_END); - long lengthUntilEOF = ftell(Fp) - currentPosition; - fseek(Fp, currentPosition, SEEK_SET); + long currentPosition = Fp->tellg(); + Fp->seekg(0L,std::ios_base::end); + long lengthUntilEOF = (long)(Fp->tellg())-currentPosition; + Fp->seekg(currentPosition, std::ios_base::beg); entry->SetLength(lengthUntilEOF); return; } @@ -1713,10 +1853,11 @@ void gdcmDocument::FindDocEntryLength( gdcmDocEntry *entry ) // big endian and proceed... if ( element == 0x0000 && length16 == 0x0400 ) { - if ( !IsExplicitVRBigEndianTransferSyntax() ) + TransferSyntaxType ts = GetTransferSyntax(); + if ( ts != ExplicitVRBigEndian ) { - throw gdcmFormatError( "gdcmDocument::FindDocEntryLength()", - " not explicit VR." ); + throw FormatError( "Document::FindDocEntryLength()", + " not explicit VR." ); return; } length16 = 4; @@ -1725,7 +1866,7 @@ 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 ) { @@ -1764,16 +1905,16 @@ void gdcmDocument::FindDocEntryLength( gdcmDocEntry *entry ) * \brief Find the Value Representation of the current Dicom Element. * @param entry */ -void gdcmDocument::FindDocEntryVR( gdcmDocEntry *entry ) +void Document::FindDocEntryVR( DocEntry *entry ) { - if ( Filetype != gdcmExplicitVR ) + if ( Filetype != ExplicitVR ) { return; } char vr[3]; - long positionOnEntry = ftell(Fp); + long positionOnEntry = Fp->tellg(); // Warning: we believe this is explicit VR (Value Representation) because // we used a heuristic that found "UL" in the first tag. Alas this // doesn't guarantee that all the tags will be in explicit VR. In some @@ -1782,12 +1923,12 @@ void gdcmDocument::FindDocEntryVR( gdcmDocEntry *entry ) // is in explicit VR and try to fix things if it happens not to be // the case. - fread (vr, (size_t)2,(size_t)1, Fp); + Fp->read (vr, (size_t)2); vr[2] = 0; if( !CheckDocEntryVR(entry, vr) ) { - fseek(Fp, positionOnEntry, SEEK_SET); + Fp->seekg(positionOnEntry, std::ios_base::beg); // When this element is known in the dictionary we shall use, e.g. for // the semantics (see the usage of IsAnInteger), the VR proposed by the // dictionary entry. Still we have to flag the element as implicit since @@ -1810,9 +1951,9 @@ void gdcmDocument::FindDocEntryVR( gdcmDocEntry *entry ) * @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 @@ -1823,7 +1964,7 @@ bool gdcmDocument::CheckDocEntryVR(gdcmDocEntry *entry, gdcmVRKey vr) // expected VR read happens to be non-ascii characters we consider // we hit falsely explicit VR tag. - if ( !isalpha(vr[0]) && !isalpha(vr[1]) ) + if ( !isalpha((unsigned char)vr[0]) && !isalpha((unsigned char)vr[1]) ) { realExplicit = false; } @@ -1831,7 +1972,7 @@ 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; } @@ -1840,14 +1981,14 @@ 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 ); @@ -1875,7 +2016,7 @@ 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); @@ -1891,11 +2032,11 @@ bool gdcmDocument::CheckDocEntryVR(gdcmDocEntry *entry, gdcmVRKey vr) * @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; @@ -1956,7 +2097,7 @@ std::string gdcmDocument::GetDocEntryValue(gdcmDocEntry *entry) return s.str(); } - return ((gdcmValEntry *)entry)->GetValue(); + return ((ValEntry *)entry)->GetValue(); } /** @@ -1967,7 +2108,7 @@ std::string gdcmDocument::GetDocEntryValue(gdcmDocEntry *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() ) { @@ -1980,7 +2121,7 @@ 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(); } /** @@ -2020,7 +2161,7 @@ std::string gdcmDocument::GetDocEntryUnvalue(gdcmDocEntry* entry) * \warning NOT end user intended method ! * @param entry entry to skip */ -void gdcmDocument::SkipDocEntry(gdcmDocEntry *entry) +void Document::SkipDocEntry(DocEntry *entry) { SkipBytes(entry->GetLength()); } @@ -2030,10 +2171,10 @@ void gdcmDocument::SkipDocEntry(gdcmDocEntry *entry) * \warning NOT end user intended method ! * @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); + Fp->seekg((long)(entry->GetOffset()), std::ios_base::beg); + Fp->seekg( (long)(entry->GetReadLength()), std::ios_base::cur); } /** @@ -2043,8 +2184,8 @@ void gdcmDocument::SkipToNextDocEntry(gdcmDocEntry *entry) * @param entry entry to check * @param foundLength fist assumption about length */ -void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *entry, - uint32_t foundLength) +void Document::FixDocEntryFoundLength(DocEntry *entry, + uint32_t foundLength) { entry->SetReadLength( foundLength ); // will be updated only if a bug is found if ( foundLength == 0xffffffff) @@ -2122,11 +2263,11 @@ void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *entry, * @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(); - std::string vr = entry->GetVR(); + const std::string & vr = entry->GetVR(); uint32_t length = entry->GetLength(); // When we have some semantics on the element we just read, and if we @@ -2148,12 +2289,12 @@ 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 = Fp->tellg(); 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() ); } } @@ -2171,11 +2312,11 @@ 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); + long positionOnEntry = Fp->tellg(); bool foundSequenceDelimiter = false; uint32_t totalLength = 0; @@ -2188,10 +2329,10 @@ 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 @@ -2199,12 +2340,12 @@ 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."); + Fp->seekg(positionOnEntry, std::ios_base::beg); + throw FormatUnexpected("Document::FindDocEntryLengthOB()", + "Neither an Item tag nor a Sequence " + "delimiter tag."); } if ( elem == 0xe0dd ) @@ -2222,7 +2363,7 @@ uint32_t gdcmDocument::FindDocEntryLengthOB() break; } } - fseek(Fp, positionOnEntry, SEEK_SET); + Fp->seekg( positionOnEntry, std::ios_base::beg); return totalLength; } @@ -2231,18 +2372,18 @@ 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); - if ( item_read != 1 ) + Fp->read ((char*)&g, (size_t)2); + if ( Fp->fail() ) { - if( ferror(Fp) ) - { - throw gdcmFormatError( "gdcmDocument::ReadInt16()", " file error." ); - } - throw gdcmFormatError( "gdcmDocument::ReadInt16()", "EOF." ); + throw FormatError( "Document::ReadInt16()", " file error." ); + } + if( Fp->eof() ) + { + throw FormatError( "Document::ReadInt16()", "EOF." ); } g = SwapShort(g); return g; @@ -2253,18 +2394,18 @@ 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); - if ( item_read != 1 ) + Fp->read ((char*)&g, (size_t)4); + if ( Fp->fail() ) { - if( ferror(Fp) ) - { - throw gdcmFormatError( "gdcmDocument::ReadInt16()", " file error." ); - } - throw gdcmFormatError( "gdcmDocument::ReadInt32()", "EOF." ); + throw FormatError( "Document::ReadInt32()", " file error." ); + } + if( Fp->eof() ) + { + throw FormatError( "Document::ReadInt32()", "EOF." ); } g = SwapLong(g); return g; @@ -2275,20 +2416,22 @@ 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); + Fp->seekg((long)nBytes, std::ios_base::cur); } /** * \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; } /** @@ -2299,7 +2442,7 @@ 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. @@ -2311,7 +2454,7 @@ bool gdcmDocument::CheckSwap() uint32_t s32; uint16_t s16; - char deb[HEADER_LENGTH_TO_READ]; + char deb[256]; //HEADER_LENGTH_TO_READ]; // First, compare HostByteOrder and NetworkByteOrder in order to // determine if we shall need to swap bytes (i.e. the Endian type). @@ -2326,13 +2469,12 @@ bool gdcmDocument::CheckSwap() // The easiest case is the one of a DICOM header, since it possesses a // file preamble where it suffice to look for the string "DICM". - int lgrLue = fread(deb, 1, HEADER_LENGTH_TO_READ, Fp); - (void)lgrLue; //FIXME not used + Fp->read(deb, HEADER_LENGTH_TO_READ); 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" @@ -2362,45 +2504,45 @@ 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"); } // Position the file position indicator at first tag (i.e. // after the file preamble and the "DICM" string). - rewind(Fp); - fseek (Fp, 132L, SEEK_SET); + Fp->seekg(0, std::ios_base::beg); + Fp->seekg ( 132L, std::ios_base::beg); return true; } // End of DicomV3 // 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"); - rewind(Fp); + dbg.Verbose(1, "Document::CheckSwap:", "not a DICOM Version3 file"); + Fp->seekg(0, std::ios_base::beg); // Our next best chance would be to be considering a 'clean' ACR/NEMA file. // By clean we mean that the length of the first tag is written down. @@ -2417,19 +2559,19 @@ 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. @@ -2437,13 +2579,13 @@ bool gdcmDocument::CheckSwap() // So, let's check if this file wouldn't happen to be 'dirty' ACR/NEMA, // i.e. the 'group length' element is not present : - // check the supposed to be 'group number' - // 0x0002 or 0x0004 or 0x0008 + // check the supposed-to-be 'group number' + // in ( 0x0001 .. 0x0008 ) // to determine ' SwapCode' value . // Only 0 or 4321 will be possible // (no oportunity to check for the formerly well known // ACR-NEMA 'Bad Big Endian' or 'Bad Little Endian' - // if unsuccessfull (i.e. neither 0x0002 nor 0x0200 etc -4, 8-) + // if unsuccessfull (i.e. neither 0x0002 nor 0x0200 etc -3, 4, ..., 8-) // the file IS NOT ACR-NEMA nor DICOM V3 // Find a trick to tell it the caller... @@ -2451,22 +2593,32 @@ bool gdcmDocument::CheckSwap() switch ( s16 ) { + case 0x0001 : case 0x0002 : + case 0x0003 : case 0x0004 : - case 0x0008 : + case 0x0005 : + case 0x0006 : + case 0x0007 : + case 0x0008 : SwapCode = 0; - Filetype = gdcmACR; + Filetype = ACR; return true; + case 0x0100 : case 0x0200 : + case 0x0300 : case 0x0400 : - case 0x0800 : + case 0x0500 : + case 0x0600 : + case 0x0700 : + case 0x0800 : SwapCode = 4321; - Filetype = gdcmACR; + Filetype = ACR; return true; default : - dbg.Verbose(0, "gdcmDocument::CheckSwap:", - "ACR/NEMA unfound swap info (Really hopeless !)"); - Filetype = gdcmUnknown; + dbg.Verbose(0, "Document::CheckSwap:", + "ACR/NEMA unfound swap info (Really hopeless !)"); + Filetype = Unknown; return false; } // Then the only info we have is the net2host one. @@ -2478,13 +2630,15 @@ 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 ) { @@ -2508,7 +2662,7 @@ void gdcmDocument::SwitchSwapToBigEndian() * \brief during parsing, Header Elements too long are not loaded in memory * @param newSize */ -void gdcmDocument::SetMaxSizeLoadEntry(long newSize) +void Document::SetMaxSizeLoadEntry(long newSize) { if ( newSize < 0 ) { @@ -2525,10 +2679,10 @@ 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 + * \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 ) @@ -2545,6 +2699,35 @@ void gdcmDocument::SetMaxSizePrintEntry(long newSize) +/** + * \brief Handle broken private tag from Philips NTSCAN + * where the endianess is being switch to BigEndian for no + * apparent reason + * @return no return + */ +void Document::HandleBrokenEndian(uint16_t group, uint16_t elem) +{ + // Endian reversion. Some files contain groups of tags with reversed endianess. + static int reversedEndian = 0; + // try to fix endian switching in the middle of headers + if ((group == 0xfeff) && (elem == 0x00e0)) + { + // start endian swap mark for group found + reversedEndian++; + SwitchSwapToBigEndian(); + // fix the tag + group = 0xfffe; + elem = 0xe000; + } + else if ((group == 0xfffe) && (elem == 0xe00d) && reversedEndian) + { + // end of reversed endian group + reversedEndian--; + SwitchSwapToBigEndian(); + } + +} + /** * \brief Read the next tag but WITHOUT loading it's value * (read the 'Group Number', the 'Element Number', @@ -2552,7 +2735,7 @@ 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; @@ -2562,7 +2745,7 @@ 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. @@ -2570,14 +2753,15 @@ gdcmDocEntry* gdcmDocument::ReadNextDocEntry() return 0; } - gdcmDocEntry *newEntry = NewDocEntryByNumber(group, elem); + HandleBrokenEndian(group, elem); + DocEntry *newEntry = NewDocEntryByNumber(group, elem); FindDocEntryVR(newEntry); try { FindDocEntryLength(newEntry); } - catch ( gdcmFormatError e ) + catch ( FormatError e ) { // Call it quits //std::cout << e; @@ -2585,23 +2769,23 @@ gdcmDocEntry* gdcmDocument::ReadNextDocEntry() return 0; } - newEntry->SetOffset(ftell(Fp)); + newEntry->SetOffset(Fp->tellg()); return newEntry; } /** - * \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; @@ -2611,27 +2795,37 @@ 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. + * \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 + long positionOnEntry = Fp->tellg(); + long currentPosition = Fp->tellg(); // On debugging purposes //// Read the Item Tag group and element, and make // sure they are what we expected: - uint16_t itemTagGroup = ReadInt16(); - uint16_t itemTagElement = ReadInt16(); + uint16_t itemTagGroup; + uint16_t itemTagElement; + try + { + itemTagGroup = ReadInt16(); + itemTagElement = ReadInt16(); + } + catch ( FormatError e ) + { + //std::cerr << e << std::endl; + return false; + } if ( itemTagGroup != testGroup || itemTagElement != testElement ) { std::ostringstream s; @@ -2641,9 +2835,9 @@ 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); + Fp->seekg(positionOnEntry, std::ios_base::beg); return false; } @@ -2651,22 +2845,22 @@ 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. + * \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); + long positionOnEntry = Fp->tellg(); (void)positionOnEntry; if ( !ReadTag(testGroup, testElement) ) @@ -2675,133 +2869,295 @@ uint32_t gdcmDocument::ReadTagLength(uint16_t testGroup, uint16_t testElement) } //// Then read the associated Item Length - long currentPosition = ftell(Fp); + long currentPosition = Fp->tellg(); uint32_t itemLength = ReadInt32(); { std::ostringstream s; 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); + Fp->read(basicOffsetTableItemValue, itemLength); +#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; } +} - if ( ! IsRLELossLessTransferSyntax() ) +/** + * \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() +{ + TransferSyntaxType ts = GetTransferSyntax(); + if ( ts != RLELossless ) { - // 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 = Fp->tellg(); + + uint32_t nbRleSegments = ReadInt32(); + if ( nbRleSegments > 16 ) + { + // There should be at most 15 segments (refer to RLEFrame class) + dbg.Verbose(0, "Document::ComputeRLEInfo: too many segments."); + } + + uint32_t rleSegmentOffsetTable[16]; + 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 ( ! IsJPEG() ) + { + return; + } - // skipping (not reading) RLE Segments - if ( nbRleSegments > 1) + ReadAndSkipEncapsulatedBasicOffsetTable(); + + // Loop on the fragments[s] and store the parsed information in a + // JPEGInfo. + long fragmentLength; + while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) ) + { + long fragmentOffset = Fp->tellg(); + + // 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"); + } +} + +/** + * \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 const & 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++) + const 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 ) ) + { + const ListDocEntry& currentList = SQItemSet->GetDocEntries(); + for (ListDocEntry::const_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) ) + { + const 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 hold 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); @@ -2859,5 +3215,6 @@ bool gdcmDocument::operator<(gdcmDocument &document) return false; } +} // end namespace gdcm //-----------------------------------------------------------------------------