X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=ae50bc8a2cbd31b55893e6e57c672bb5f84939d0;hb=d72e3cb0326093093f99863964f8f4df382c83e1;hp=9d3d59ea0717c461339377ef9e3acd388e8d540d;hpb=175fcae3621cded83810f560ae3e440e532bce68;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 9d3d59ea..ae50bc8a 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2004/10/08 08:38:54 $ - Version: $Revision: 1.98 $ + Date: $Date: 2005/01/11 23:06:35 $ + Version: $Revision: 1.180 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -23,57 +23,34 @@ #include "gdcmGlobal.h" #include "gdcmUtil.h" #include "gdcmDebug.h" +#include "gdcmTS.h" +#include "gdcmException.h" +#include "gdcmDictSet.h" +#include "gdcmRLEFramesInfo.h" +#include "gdcmJPEGFragmentsInfo.h" +#include "gdcmDocEntrySet.h" +#include "gdcmSQItem.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 +{ //----------------------------------------------------------------------------- -// 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 @@ -82,37 +59,38 @@ 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: ", - Filename.c_str()); - rewind(Fp); + Group0002Parsed = false; + + gdcmVerboseMacro( "Starting parsing of file: " << Filename.c_str()); + // Fp->seekg( 0, std::ios::beg); - fseek(Fp,0L,SEEK_END); - long lgt = ftell(Fp); + Fp->seekg(0, std::ios::end); + long lgt = Fp->tellg(); - rewind(Fp); + Fp->seekg( 0, std::ios::beg); CheckSwap(); - long beg = ftell(Fp); + long beg = Fp->tellg(); lgt -= beg; ParseDES( this, beg, lgt, false); // le Load sera fait a la volee - rewind(Fp); + Fp->seekg( 0, std::ios::beg); // Load 'non string' values - std::string PhotometricInterpretation = GetEntryByNumber(0x0028,0x0004); + std::string PhotometricInterpretation = GetEntry(0x0028,0x0004); if( PhotometricInterpretation == "PALETTE COLOR " ) { LoadEntryBinArea(0x0028,0x1200); // gray LUT @@ -121,16 +99,16 @@ gdcmDocument::gdcmDocument( std::string const & filename ) /// 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 gdcmBinEntry. + /// 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 gdcmValEntry, but afterwards - /// also used as gdcmBinEntry, which requires the proper conversion, - /// - OW, and hence loaded as gdcmBinEntry, but afterwards also used - /// as gdcmValEntry, which requires the proper conversion. + /// - 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 @@ -158,49 +136,45 @@ gdcmDocument::gdcmDocument( std::string const & filename ) // we switch lineNumber and columnNumber // std::string RecCode; - RecCode = GetEntryByNumber(0x0008, 0x0010); // recognition code + RecCode = GetEntry(0x0008, 0x0010); // recognition code if (RecCode == "ACRNEMA_LIBIDO_1.1" || RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares // with "little-endian strings" { - Filetype = gdcmACR_LIBIDO; - std::string rows = GetEntryByNumber(0x0028, 0x0010); - std::string columns = GetEntryByNumber(0x0028, 0x0011); - SetEntryByNumber(columns, 0x0028, 0x0010); - SetEntryByNumber(rows , 0x0028, 0x0011); + Filetype = ACR_LIBIDO; + std::string rows = GetEntry(0x0028, 0x0010); + std::string columns = GetEntry(0x0028, 0x0011); + SetEntry(columns, 0x0028, 0x0010); + SetEntry(rows , 0x0028, 0x0011); } // ----------------- End of ACR-LibIDO kludge ------------------ - - PrintLevel = 1; // 'Medium' print level by default } /** * \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(); - PrintLevel = 1; // 'Medium' print level by default + SwapCode = 1234; + Filetype = ExplicitVR; + Group0002Parsed = false; } /** * \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; //temp remove - } - TagHT.clear(); + delete RLEInfo; + delete JPEGInfo; } //----------------------------------------------------------------------------- @@ -210,8 +184,9 @@ 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->SetPrintLevel(PrintLevel); RefPubDict->Print(os); } @@ -219,8 +194,9 @@ 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->SetPrintLevel(PrintLevel); RefShaDict->Print(os); } @@ -229,7 +205,7 @@ void gdcmDocument::PrintShaDict(std::ostream & os) /** * \brief Get the public dictionary used */ -gdcmDict* gdcmDocument::GetPubDict() +Dict *Document::GetPubDict() { return RefPubDict; } @@ -237,16 +213,16 @@ gdcmDict* gdcmDocument::GetPubDict() /** * \brief Get the shadow dictionary used */ -gdcmDict* gdcmDocument::GetShaDict() +Dict *Document::GetShaDict() { return RefShaDict; } /** * \brief Set the shadow dictionary used - * \param dict dictionary to use in shadow + * @param dict dictionary to use in shadow */ -bool gdcmDocument::SetShaDict(gdcmDict *dict) +bool Document::SetShaDict(Dict *dict) { RefShaDict = dict; return !RefShaDict; @@ -254,228 +230,87 @@ bool gdcmDocument::SetShaDict(gdcmDict *dict) /** * \brief Set the shadow dictionary used - * \param dictName name of the dictionary to use in shadow + * @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"); + gdcmVerboseMacro( "Wrong filetype"); return false; } if( TagHT.empty() ) { - dbg.Verbose(0, "gdcmDocument::IsReadable: no tags in internal" - " hash table."); + gdcmVerboseMacro( "No tags in internal hash table."); return false; } 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) +std::string Document::GetTransferSyntax() { - gdcmDocEntry *entry = GetDocEntryByNumber(0x0002, 0x0010); + DocEntry *entry = GetDocEntry(0x0002, 0x0010); if ( !entry ) { - return false; + return GDCM_UNKNOWN; } // 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; - } - while ( ! isdigit(transfer[transfer.length()-1]) ) + if ( transfer.length() == 0 ) { - transfer.erase(transfer.length()-1, 1); + // for brain damaged headers + return GDCM_UNKNOWN; } - if ( transfer == syntaxToCheck ) + while ( !isdigit((unsigned char)transfer[transfer.length()-1]) ) { - return true; + transfer.erase(transfer.length()-1, 1); } + return transfer; } - 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); -} - -/** - * \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() -{ - 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); -} - -/** - * \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 - * other cases. - */ -bool gdcmDocument::IsJPEGSpectralSelectionProcess6_8TransferSyntax() -{ - return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_53); -} - -/** - * \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. - */ -bool gdcmDocument::IsRLELossLessTransferSyntax() -{ - return IsGivenTransferSyntax(UI1_2_840_10008_1_2_5); -} - -/** - * \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. - */ - -bool gdcmDocument::IsJPEGLossless() -{ - 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) ); -} - -/** - * \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::IsEncapsulateTransferSyntax() -{ - return ( IsJPEGBaseLineProcess1TransferSyntax() - || IsJPEGExtendedProcess2_4TransferSyntax() - || IsJPEGExtendedProcess3_5TransferSyntax() - || IsJPEGSpectralSelectionProcess6_8TransferSyntax() - || IsRLELossLessTransferSyntax() - || IsJPEGLossless() - || IsJPEG2000() ); + return GDCM_UNKNOWN; } /** * \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 + // Checking if Transfer Syntax exists is enough // Anyway, it's to late check if the 'Preamble' was found ... // And ... would it be a rich idea to check ? // (some 'no Preamble' DICOM images exist !) - return GetDocEntryByNumber(0x0002, 0x0010) != NULL; + return GetDocEntry(0x0002, 0x0010) != NULL; } /** @@ -483,50 +318,77 @@ 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(!Fp) + HasDCMPreamble = false; + if (Filename.length() == 0) + { + return 0; + } + + if(Fp) + { + gdcmVerboseMacro( "File already open: " << 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: ", - Filename.c_str()); + gdcmVerboseMacro( "Cannot open file: " << Filename.c_str()); + delete Fp; + Fp = 0; return 0; } uint16_t zero; - fread(&zero, (size_t)2, (size_t)1, Fp); - - //ACR -- or DICOM with no Preamble -- - if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200 ) + Fp->read((char*)&zero, (size_t)2); + if( Fp->eof() ) { + CloseFile(); + return 0; + } + + //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 ) + { + std::string msg + = Util::Format("ACR/DICOM with no preamble: (%04x)\n", zero); + gdcmVerboseMacro( msg.c_str() ); return Fp; } //DICOM - fseek(Fp, 126L, SEEK_CUR); + Fp->seekg(126L, std::ios::cur); char dicm[4]; - fread(dicm, (size_t)4, (size_t)1, Fp); + Fp->read(dicm, (size_t)4); + if( Fp->eof() ) + { + CloseFile(); + return 0; + } if( memcmp(dicm, "DICM", 4) == 0 ) { + HasDCMPreamble = true; return Fp; } - fclose(Fp); - dbg.Verbose( 0, - "gdcmDocument::OpenFile not DICOM/ACR (missing preamble)", - Filename.c_str()); + CloseFile(); + gdcmVerboseMacro( "Not DICOM/ACR (missing preamble)" << Filename.c_str()); return 0; } @@ -535,12 +397,16 @@ 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 ? } /** @@ -550,39 +416,22 @@ bool gdcmDocument::CloseFile() * (ACR-NEMA, ExplicitVR, ImplicitVR) * \return Always true. */ -void gdcmDocument::Write(FILE* fp,FileType filetype) +void Document::WriteContent(std::ofstream *fp, FileType filetype) { /// \todo move the following lines (and a lot of others, to be written) /// to a future function CheckAndCorrectHeader /// (necessary if user wants to write a DICOM V3 file - /// starting from an ACR-NEMA (V2) gdcmHeader + /// starting from an ACR-NEMA (V2) Header - if (filetype == gdcmImplicitVR) + if ( filetype == ImplicitVR || filetype == ExplicitVR ) { - std::string implicitVRTransfertSyntax = UI1_2_840_10008_1_2; - ReplaceOrCreateByNumber(implicitVRTransfertSyntax,0x0002, 0x0010); - - /// \todo Refer to standards on page 21, chapter 6.2 - /// "Value representation": values with a VR of UI shall be - /// padded with a single trailing null - /// in the following case we have to padd manually with a 0 - - SetEntryLengthByNumber(18, 0x0002, 0x0010); - } - - if (filetype == gdcmExplicitVR) - { - std::string explicitVRTransfertSyntax = UI1_2_840_10008_1_2_1; - ReplaceOrCreateByNumber(explicitVRTransfertSyntax,0x0002, 0x0010); - - /// \todo Refer to standards on page 21, chapter 6.2 - /// "Value representation": values with a VR of UI shall be - /// padded with a single trailing null - /// Dans le cas suivant on doit pader manuellement avec un 0 - - SetEntryLengthByNumber(20, 0x0002, 0x0010); + // writing Dicom File Preamble + char filePreamble[128]; + memset(filePreamble, 0, 128); + fp->write(filePreamble, 128); + fp->write("DICM", 4); } - + /** * \todo rewrite later, if really usefull * - 'Group Length' element is optional in DICOM @@ -595,169 +444,145 @@ void gdcmDocument::Write(FILE* fp,FileType filetype) * UpdateGroupLength(true,ACR); */ - gdcmElementSet::Write(fp, filetype); // This one is recursive - + ElementSet::WriteContent(fp, filetype); // This one is recursive } /** - * \brief Modifies the value of a given Header Entry (Dicom Element) + * \brief Modifies the value of a given Doc Entry (Dicom Element) * when it exists. Create it with the given value when unexistant. * @param value (string) Value to be set * @param group Group number of the Entry * @param elem Element number of the Entry - * @param VR V(alue) R(epresentation) of the Entry -if private 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( - std::string const & value, - uint16_t group, - uint16_t elem, - std::string const & VR ) -{ - gdcmValEntry* valEntry = 0; - gdcmDocEntry* currentEntry = GetDocEntryByNumber( group, elem); +ValEntry *Document::ReplaceOrCreate(std::string const &value, + uint16_t group, + uint16_t elem, + TagName const &vr ) +{ + ValEntry *valEntry = 0; + DocEntry *currentEntry = GetDocEntry( group, elem); - if (!currentEntry) + if (currentEntry) { - // check if (group,element) DictEntry exists - // if it doesn't, create an entry in gdcmDictSet::VirtualEntry - // and use it + valEntry = dynamic_cast< ValEntry* >(currentEntry); - // Find out if the tag we received is in the dictionaries: - gdcmDict *pubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict(); - gdcmDictEntry* dictEntry = pubDict->GetDictEntryByNumber(group, elem); - if (!dictEntry) - { - currentEntry = NewDocEntryByNumber(group, elem,VR); - } - else - { - currentEntry = NewDocEntryByNumber(group, elem); - } + // Verify the VR + if( valEntry ) + if( valEntry->GetVR()!=vr ) + valEntry=NULL; - if (!currentEntry) + // if currentEntry doesn't correspond to the requested valEntry + if( !valEntry) { - dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: call to" - " NewDocEntryByNumber failed."); - return NULL; - } - valEntry = new gdcmValEntry(currentEntry); - if ( !AddEntry(valEntry)) - { - dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: AddEntry" - " failed allthough this is a creation."); - } - } - else - { - valEntry = dynamic_cast< gdcmValEntry* >(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); if (!RemoveEntry(currentEntry)) { - dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: removal" - " of previous DocEntry failed."); - return NULL; - } - if ( !AddEntry(valEntry)) - { - dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: adding" - " promoted ValEntry failed."); + gdcmVerboseMacro( "Removal of previous DocEntry failed."); + return NULL; } } } - SetEntryByNumber(value, group, elem); + // Create a new valEntry if necessary + if (!valEntry) + { + valEntry = NewValEntry(group, elem, vr); + + if ( !AddEntry(valEntry)) + { + gdcmVerboseMacro("AddEntry failed although this is a creation."); + + delete valEntry; + return NULL; + } + } + // Set the binEntry value + SetEntry(value, valEntry); return valEntry; } /* * \brief Modifies the value of a given Header Entry (Dicom Element) * when it exists. Create it with the given value when unexistant. + * 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 + * @param vr V(alue) R(epresentation) of the Entry -if private Entry- * \return pointer to the modified/created Header Entry (NULL when creation * failed). */ -gdcmBinEntry* gdcmDocument::ReplaceOrCreateByNumber( - uint8_t* binArea, - int lgth, - uint16_t group, - uint16_t elem, - std::string const& VR ) +BinEntry *Document::ReplaceOrCreate(uint8_t *binArea, + int lgth, + uint16_t group, + uint16_t elem, + TagName const &vr ) { - gdcmBinEntry* binEntry = 0; - gdcmDocEntry* currentEntry = GetDocEntryByNumber( group, elem); - if (!currentEntry) - { + BinEntry *binEntry = 0; + DocEntry *currentEntry = GetDocEntry( group, elem); - // check if (group,element) DictEntry exists - // if it doesn't, create an entry in gdcmDictSet::VirtualEntry - // and use it + // Verify the currentEntry + if (currentEntry) + { + binEntry = dynamic_cast< BinEntry* >(currentEntry); - // Find out if the tag we received is in the dictionaries: - gdcmDict *pubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict(); - gdcmDictEntry *dictEntry = pubDict->GetDictEntryByNumber(group, elem); + // Verify the VR + if( binEntry ) + if( binEntry->GetVR()!=vr ) + binEntry=NULL; - if (!dictEntry) - { - currentEntry = NewDocEntryByNumber(group, elem, VR); - } - else - { - currentEntry = NewDocEntryByNumber(group, elem); - } - if (!currentEntry) + // if currentEntry doesn't correspond to the requested valEntry + if( !binEntry) { - dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: call to" - " NewDocEntryByNumber failed."); - return NULL; + if (!RemoveEntry(currentEntry)) + { + gdcmVerboseMacro( "Removal of previous DocEntry failed."); + + return NULL; + } } - binEntry = new gdcmBinEntry(currentEntry); + } + + // Create a new binEntry if necessary + if (!binEntry) + { + binEntry = NewBinEntry(group, elem, vr); + if ( !AddEntry(binEntry)) { - dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: AddEntry" - " failed allthough this is a creation."); + gdcmVerboseMacro( "AddEntry failed allthough this is a creation."); + + delete binEntry; + return NULL; } } + + // Set the binEntry value + uint8_t *tmpArea; + if (lgth>0 && binArea) + { + tmpArea = new uint8_t[lgth]; + memcpy(tmpArea,binArea,lgth); + } else { - binEntry = dynamic_cast< gdcmBinEntry* >(currentEntry); - if ( !binEntry ) // Euuuuh? It wasn't a BinEntry - // then we change it to a BinEntry ? - // Shouldn't it be considered as an error ? + tmpArea = 0; + } + if (!SetEntry(tmpArea,lgth,binEntry)) + { + if (tmpArea) { - // We need to promote the gdcmDocEntry to a gdcmBinEntry: - binEntry = new gdcmBinEntry(currentEntry); - if (!RemoveEntry(currentEntry)) - { - dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: removal" - " of previous DocEntry failed."); - return NULL; - } - if ( !AddEntry(binEntry)) - { - dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: adding" - " promoted BinEntry failed."); - return NULL; - } + delete[] tmpArea; } } - SetEntryByNumber(binArea, lgth, group, elem); - return binEntry; } - /* * \brief Modifies the value of a given Header Entry (Dicom Element) * when it exists. Create it when unexistant. @@ -766,24 +591,48 @@ 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::ReplaceOrCreate( uint16_t group, uint16_t elem) { - gdcmSeqEntry* b = 0; - gdcmDocEntry* a = GetDocEntryByNumber( group, elem); - if (!a) + SeqEntry *seqEntry = 0; + DocEntry *currentEntry = GetDocEntry( group, elem); + + // Verify the currentEntry + if (currentEntry) + { + seqEntry = dynamic_cast< SeqEntry* >(currentEntry); + + // Verify the VR + if( seqEntry ) + if( seqEntry->GetVR()!="SQ" ) + seqEntry=NULL; + + // if currentEntry doesn't correspond to the requested valEntry + if( !seqEntry) + { + if (!RemoveEntry(currentEntry)) + { + gdcmVerboseMacro( "Removal of previous DocEntry failed."); + + return NULL; + } + } + } + + // Create a new seqEntry if necessary + if (!seqEntry) { - a = NewSeqEntryByNumber(group, elem); - if (!a) + seqEntry = NewSeqEntry(group, elem); + + if ( !AddEntry(seqEntry)) { - return 0; + gdcmVerboseMacro( "AddEntry failed allthough this is a creation."); + + delete seqEntry; + return NULL; } + } - b = new gdcmSeqEntry(a, 1); // FIXME : 1 (Depth) - AddEntry(b); - } - return b; + return seqEntry; } /** @@ -794,10 +643,10 @@ 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::ReplaceIfExist(std::string const &value, + uint16_t group, uint16_t elem ) { - SetEntryByNumber(value, group, elem); + SetEntry(value, group, elem); return true; } @@ -811,57 +660,12 @@ 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::CheckIfEntryExist(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; } -/** - * \brief Searches within Header Entries (Dicom Elements) parsed with - * the public and private dictionaries - * for the element value of a given tag. - * \warning Don't use any longer : use GetPubEntryByName - * @param tagName name of the searched element. - * @return Corresponding element value when it exists, - * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. - */ -std::string gdcmDocument::GetEntryByName(TagName const& tagName) -{ - gdcmDictEntry* dictEntry = RefPubDict->GetDictEntryByName(tagName); - if( !dictEntry ) - { - return GDCM_UNFOUND; - } - - return GetEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()); -} - -/** - * \brief Searches within Header Entries (Dicom Elements) parsed with - * the public and private dictionaries - * for the element value representation of a given tag. - * - * Obtaining the VR (Value Representation) might be needed by caller - * to convert the string typed content to caller's native type - * (think of C++ vs Python). The VR is actually of a higher level - * of semantics than just the native C++ type. - * @param tagName name of the searched element. - * @return Corresponding element value representation when it exists, - * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. - */ -std::string gdcmDocument::GetEntryVRByName(TagName const& tagName) -{ - gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); - if( dictEntry == NULL) - { - return GDCM_UNFOUND; - } - - gdcmDocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(), - dictEntry->GetElement()); - return elem->GetVR(); -} /** * \brief Searches within Header Entries (Dicom Elements) parsed with @@ -872,16 +676,15 @@ 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::GetEntry(uint16_t group, uint16_t element) { - gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element); - /// \todo use map methods, instead of multimap JPR + TagKey key = DictEntry::TranslateToKey(group, element); if ( !TagHT.count(key)) { return GDCM_UNFOUND; } - return ((gdcmValEntry *)TagHT.find(key)->second)->GetValue(); + return ((ValEntry *)TagHT.find(key)->second)->GetValue(); } /** @@ -898,9 +701,9 @@ 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::GetEntryVR(uint16_t group, uint16_t element) { - gdcmDocEntry* elem = GetDocEntryByNumber(group, element); + DocEntry *elem = GetDocEntry(group, element); if ( !elem ) { return GDCM_UNFOUND; @@ -916,86 +719,38 @@ 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::GetEntryLength(uint16_t group, uint16_t element) { - gdcmDocEntry* elem = GetDocEntryByNumber(group, element); + DocEntry *elem = GetDocEntry(group, element); if ( !elem ) { return -2; //magic number } return elem->GetLength(); } -/** - * \brief Sets the value (string) of the Header Entry (Dicom Element) - * @param content string value of the Dicom Element - * @param tagName name of the searched Dicom Element. - * @return true when found - */ -bool gdcmDocument::SetEntryByName(std::string const & content,std::string const & tagName) -{ - gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); - if( !dictEntry ) - { - return false; - } - - return SetEntryByNumber(content,dictEntry->GetGroup(), - dictEntry->GetElement()); -} /** - * \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::SetEntry(std::string const& content, + uint16_t group, uint16_t element) { - int c; - int l; - - gdcmValEntry* valEntry = GetValEntryByNumber(group, element); - if (!valEntry ) + ValEntry *entry = GetValEntry(group, element); + if (!entry ) { - dbg.Verbose(0, "gdcmDocument::SetEntryByNumber: no corresponding", - " ValEntry (try promotion first)."); + gdcmVerboseMacro( "No corresponding ValEntry (try promotion first)."); return false; } - // Non even content must be padded with a space (020H)... - std::string finalContent = content; - if( finalContent.length() % 2 ) - { - finalContent += '\0'; // ... therefore we padd with (000H) .!?! - } - valEntry->SetValue(finalContent); - - // Integers have a special treatement for their length: - - l = finalContent.length(); - if ( l != 0) // To avoid to be cheated by 'zero length' integers - { - gdcmVRKey vr = valEntry->GetVR(); - if( vr == "US" || vr == "SS" ) - { - c = CountSubstring(content, "\\") + 1; // for multivaluated items - l = c*2; - } - else if( vr == "UL" || vr == "SL" ) - { - c = CountSubstring(content, "\\") + 1; // for multivaluated items - l = c*4;; - } - } - valEntry->SetLength(l); - return true; + return SetEntry(content,entry); } /** - * \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* -> uint8_t*) to substitute with @@ -1003,79 +758,59 @@ bool gdcmDocument::SetEntryByNumber(std::string const& content, * @param group group number of the Dicom Element to modify * @param element element number of the Dicom Element to modify */ -bool gdcmDocument::SetEntryByNumber(uint8_t*content, - int lgth, - uint16_t group, - uint16_t element) +bool Document::SetEntry(uint8_t*content, int lgth, + uint16_t group, uint16_t element) { - (void)lgth; //not used - gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element); - if ( !TagHT.count(key)) + BinEntry *entry = GetBinEntry(group, element); + if (!entry ) { + gdcmVerboseMacro( "No corresponding ValEntry (try promotion first)."); return false; } -/* Hope Binary field length is *never* wrong - if(lgth%2) // Non even length are padded with a space (020H). - { - lgth++; - //content = content + '\0'; // fing a trick to enlarge a binary field? - } -*/ - gdcmBinEntry* a = (gdcmBinEntry *)TagHT[key]; - a->SetBinArea(content); - a->SetLength(lgth); - a->SetValue(GDCM_BINLOADED); - - return true; + return SetEntry(content,lgth,entry); } /** - * \brief Accesses an existing gdcmDocEntry (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. - * \warning Use with extreme caution. - * @param l new length to substitute with - * @param group group number of the Entry to modify - * @param element element number of the Entry to modify - * @return true on success, false otherwise. + * \brief Accesses an existing DocEntry (i.e. a Dicom Element) + * and modifies it's content with the given value. + * @param content new value (string) to substitute with + * @param entry Entry to be modified */ -bool gdcmDocument::SetEntryLengthByNumber(uint32_t l, - uint16_t group, - uint16_t element) +bool Document::SetEntry(std::string const &content,ValEntry *entry) { - /// \todo use map methods, instead of multimap JPR - gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element); - if ( !TagHT.count(key) ) - { - return false; - } - if ( l % 2 ) + if(entry) { - l++; // length must be even + entry->SetValue(content); + return true; } - ( ((TagHT.equal_range(key)).first)->second )->SetLength(l); - - return true ; + return false; } /** - * \brief Gets (from Header) the offset of a 'non string' element value - * (LoadElementValues has already be executed) - * @param group group number of the Entry - * @param elem element number of the Entry - * @return File Offset of the Element Value + * \brief Accesses an existing BinEntry (i.e. a Dicom Element) + * and modifies it's content with the given value. + * @param content new value (void* -> uint8_t*) to substitute with + * @param entry Entry to be modified + * @param lgth new value length */ -size_t gdcmDocument::GetEntryOffsetByNumber(uint16_t group, uint16_t elem) +bool Document::SetEntry(uint8_t *content, int lgth, BinEntry *entry) { - gdcmDocEntry* entry = GetDocEntryByNumber(group, elem); - if (!entry) + if(entry) { - dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber: no entry present."); - return 0; + // Hope Binary field length is *never* wrong + /*if(lgth%2) // Non even length are padded with a space (020H). + { + lgth++; + //content = content + '\0'; // fing a trick to enlarge a binary field? + }*/ + + entry->SetBinArea(content); + entry->SetLength(lgth); + entry->SetValue(GDCM_BINLOADED); + return true; } - return entry->GetOffset(); + return false; } /** @@ -1085,15 +820,20 @@ 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::GetEntryBinAreaByNumber(uint16_t group, uint16_t elem) +void *Document::GetEntryBinArea(uint16_t group, uint16_t elem) { - gdcmDocEntry* entry = GetDocEntryByNumber(group, elem); + DocEntry *entry = GetDocEntry(group, elem); if (!entry) { - dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber: no entry"); + gdcmVerboseMacro( "No entry"); return 0; } - return ((gdcmBinEntry *)entry)->GetBinArea(); + if ( BinEntry *binEntry = dynamic_cast(entry) ) + { + return binEntry->GetBinArea(); + } + + return 0; } /** @@ -1102,61 +842,57 @@ void* gdcmDocument::GetEntryBinAreaByNumber(uint16_t group, uint16_t elem) * @param group group number of the Entry * @param elem element number of the Entry */ -void* gdcmDocument::LoadEntryBinArea(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 = GetDocEntry(group, elem); if ( !docElement ) - { - return NULL; - } - size_t o =(size_t)docElement->GetOffset(); - fseek(Fp, o, SEEK_SET); - size_t l = docElement->GetLength(); - uint8_t* a = new uint8_t[l]; - if(!a) - { - dbg.Verbose(0, "gdcmDocument::LoadEntryBinArea cannot allocate a"); - return NULL; - } - size_t l2 = fread(a, 1, l , Fp); - if( l != l2 ) - { - delete[] a; - return NULL; - } - /// \todo Drop any already existing void area! JPR - if( !SetEntryBinAreaByNumber( a, group, elem ) ); - { - dbg.Verbose(0, "gdcmDocument::LoadEntryBinArea setting failed."); - } - return a; + return; + + BinEntry *binElement = dynamic_cast(docElement); + if( !binElement ) + return; + + LoadEntryBinArea(binElement); } + /** * \brief Loads (from disk) the element content * when a string is not suitable * @param element Entry whose binArea is going to be loaded */ -void* gdcmDocument::LoadEntryBinArea(gdcmBinEntry* element) +void Document::LoadEntryBinArea(BinEntry *element) { + if(element->GetBinArea()) + return; + + bool openFile = !Fp; + if(openFile) + OpenFile(); + size_t o =(size_t)element->GetOffset(); - fseek(Fp, o, SEEK_SET); + Fp->seekg(o, std::ios::beg); + size_t l = element->GetLength(); - uint8_t* a = new uint8_t[l]; + uint8_t *a = new uint8_t[l]; if( !a ) { - dbg.Verbose(0, "gdcmDocument::LoadEntryBinArea cannot allocate a"); - return NULL; + gdcmVerboseMacro( "Cannot allocate a"); + return; } - element->SetBinArea((uint8_t*)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()) { delete[] a; - return NULL; + return; } - return a; + element->SetBinArea(a); + + if(openFile) + CloseFile(); } /** @@ -1166,88 +902,23 @@ void* gdcmDocument::LoadEntryBinArea(gdcmBinEntry* element) * @param element Element number of the searched Dicom Element * @return */ -bool gdcmDocument::SetEntryBinAreaByNumber(uint8_t* area, - uint16_t group, - uint16_t element) +/*bool Document::SetEntryBinArea(uint8_t *area, + uint16_t group, uint16_t element) { - gdcmDocEntry* currentEntry = GetDocEntryByNumber(group, element); + DocEntry *currentEntry = GetDocEntry(group, element); if ( !currentEntry ) { return false; } - if ( gdcmBinEntry* binEntry = dynamic_cast(currentEntry) ) + + if ( BinEntry *binEntry = dynamic_cast(currentEntry) ) { binEntry->SetBinArea( area ); return true; } - return true; -} - -/** - * \brief Update the entries with the shadow dictionary. - * Only non even entries are analyzed - */ -void gdcmDocument::UpdateShaEntries() -{ - //gdcmDictEntry *entry; - std::string vr; - - /// \todo TODO : still any use to explore recursively the whole structure? -/* - for(ListTag::iterator it=listEntries.begin(); - it!=listEntries.end(); - ++it) - { - // Odd group => from public dictionary - if((*it)->GetGroup()%2==0) - continue; - - // Peer group => search the corresponding dict entry - if(RefShaDict) - entry=RefShaDict->GetDictEntryByNumber((*it)->GetGroup(),(*it)->GetElement()); - else - entry=NULL; - - if((*it)->IsImplicitVR()) - vr="Implicit"; - else - vr=(*it)->GetVR(); - - (*it)->SetValue(GetDocEntryUnvalue(*it)); // to go on compiling - if(entry){ - // Set the new entry and the new value - (*it)->SetDictEntry(entry); - CheckDocEntryVR(*it,vr); - - (*it)->SetValue(GetDocEntryValue(*it)); // to go on compiling - - } - else - { - // Remove precedent value transformation - (*it)->SetDictEntry(NewVirtualDictEntry((*it)->GetGroup(),(*it)->GetElement(),vr)); - } - } -*/ -} - -/** - * \brief Searches within the Header Entries for a Dicom Element of - * a given tag. - * @param tagName name of the searched Dicom Element. - * @return Corresponding Dicom Element when it exists, and NULL - * otherwise. - */ -gdcmDocEntry* gdcmDocument::GetDocEntryByName(std::string const & tagName) -{ - gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); - if( !dictEntry ) - { - return NULL; - } - return GetDocEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()); -} + return false; +}*/ /** * \brief retrieves a Dicom Element (the first one) using (group, element) @@ -1259,10 +930,9 @@ 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::GetDocEntry(uint16_t group, uint16_t element) { - gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element); + TagKey key = DictEntry::TranslateToKey(group, element); if ( !TagHT.count(key)) { return NULL; @@ -1271,40 +941,64 @@ gdcmDocEntry* gdcmDocument::GetDocEntryByNumber(uint16_t group, } /** - * \brief Same as \ref gdcmDocument::GetDocEntryByNumber except it only + * \brief Same as \ref Document::GetDocEntry 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::GetValEntry(uint16_t group, uint16_t element) { - gdcmDocEntry* currentEntry = GetDocEntryByNumber(group, element); + DocEntry *currentEntry = GetDocEntry(group, element); if ( !currentEntry ) { return 0; } - if ( gdcmValEntry* valEntry = dynamic_cast(currentEntry) ) + if ( ValEntry *entry = dynamic_cast(currentEntry) ) { - return valEntry; + return entry; } - dbg.Verbose(0, "gdcmDocument::GetValEntryByNumber: unfound ValEntry."); + gdcmVerboseMacro( "Unfound ValEntry."); + + return 0; +} + +/** + * \brief Same as \ref Document::GetDocEntry except it only + * returns a result when the corresponding entry is of type + * BinEntry. + * @return When present, the corresponding BinEntry. + */ +BinEntry *Document::GetBinEntry(uint16_t group, uint16_t element) +{ + DocEntry *currentEntry = GetDocEntry(group, element); + if ( !currentEntry ) + { + return 0; + } + if ( BinEntry *entry = dynamic_cast(currentEntry) ) + { + return entry; + } + gdcmVerboseMacro( "Unfound BinEntry."); return 0; } /** * \brief Loads the element while preserving the current - * underlying file position indicator as opposed to + * underlying file position indicator as opposed to * to LoadDocEntry that modifies it. * @param entry Header Entry whose value shall be loaded. * @return */ -void gdcmDocument::LoadDocEntrySafe(gdcmDocEntry * entry) +void Document::LoadDocEntrySafe(DocEntry *entry) { - long PositionOnEntry = ftell(Fp); - LoadDocEntry(entry); - fseek(Fp, PositionOnEntry, SEEK_SET); + if(Fp) + { + long PositionOnEntry = Fp->tellg(); + LoadDocEntry(entry); + Fp->seekg(PositionOnEntry, std::ios::beg); + } } /** @@ -1312,11 +1006,11 @@ 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) { - case 0 : + case 1234 : break; case 4321 : a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) | @@ -1331,8 +1025,7 @@ uint32_t gdcmDocument::SwapLong(uint32_t a) a=( ((a<< 8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) ); break; default : - //std::cout << "swapCode= " << SwapCode << std::endl; - dbg.Error(" gdcmDocument::SwapLong : unset swap code"); + gdcmErrorMacro( "Unset swap code:" << SwapCode ); a = 0; } return a; @@ -1343,7 +1036,7 @@ 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); } @@ -1352,7 +1045,7 @@ 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 ) { @@ -1365,7 +1058,7 @@ 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); } @@ -1377,116 +1070,135 @@ uint16_t gdcmDocument::UnswapShort(uint16_t a) * \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries) * @return length of the parsed set. */ -void 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; - + DocEntry *newDocEntry = 0; + ValEntry *newValEntry; + BinEntry *newBinEntry; + SeqEntry *newSeqEntry; + VRKey vr; + bool used=false; + while (true) - { - if ( !delim_mode && (ftell(Fp)-offset) >= l_max) + { + if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { break; } + + used=true; newDocEntry = ReadNextDocEntry( ); if ( !newDocEntry ) { break; } - gdcmVRKey vr = newDocEntry->GetVR(); - if ( vr != "SQ" ) - { - - if ( gdcmGlobal::GetVR()->IsVROfGdcmStringRepresentable(vr) ) + vr = newDocEntry->GetVR(); + newValEntry = dynamic_cast(newDocEntry); + newBinEntry = dynamic_cast(newDocEntry); + newSeqEntry = dynamic_cast(newDocEntry); + + if ( newValEntry || newBinEntry ) + { + if ( newBinEntry ) + { + if ( ! Global::GetVR()->IsVROfBinaryRepresentable(vr) ) + { + ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR + gdcmVerboseMacro( "Neither Valentry, nor BinEntry." + "Probably unknown VR."); + } + + //////////////////// BinEntry or UNKOWN VR: + // 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; + used=false; + } + } + else { /////////////////////// ValEntry - gdcmValEntry* newValEntry = - new gdcmValEntry( newDocEntry->GetDictEntry() ); - newValEntry->Copy( newDocEntry ); - - // When "set" is a gdcmDocument, then we are at the top of the + // 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 (gdcmDocument* dummy = dynamic_cast< gdcmDocument* > ( set ) ) + if (Document *dummy = dynamic_cast< Document* > ( set ) ) { (void)dummy; newValEntry->SetKey( newValEntry->GetKey() ); } - // ...but when "set" is a gdcmSQItem, we are inserting this new + // ...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 gdcmBaseTagKey): - if (gdcmSQItem* parentSQItem = dynamic_cast< gdcmSQItem* > ( set ) ) + // generalized form (refer to \ref BaseTagKey): + if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) ) { newValEntry->SetKey( parentSQItem->GetBaseTagKey() + newValEntry->GetKey() ); } - set->AddEntry( newValEntry ); LoadDocEntry( newValEntry ); - if (newValEntry->IsItemDelimitor()) - { - break; - } - if ( !delim_mode && (ftell(Fp)-offset) >= l_max) + bool delimitor=newValEntry->IsItemDelimitor(); + if( !set->AddEntry( newValEntry ) ) { - break; - } - } - else - { - if ( ! gdcmGlobal::GetVR()->IsVROfGdcmBinaryRepresentable(vr) ) - { - ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR - dbg.Verbose(0, "gdcmDocument::ParseDES: neither Valentry, " - "nor BinEntry. Probably unknown VR."); + // If here expect big troubles + //delete newValEntry; //otherwise mem leak + used=false; } - //////////////////// BinEntry or UNKOWN VR: - gdcmBinEntry* newBinEntry = - new gdcmBinEntry( newDocEntry->GetDictEntry() ); - newBinEntry->Copy( newDocEntry ); - - // When "this" is a gdcmDocument the Key is simply of the - // form ( group, elem )... - if (gdcmDocument* dummy = dynamic_cast< gdcmDocument* > ( set ) ) + if (delimitor) { - newBinEntry->SetKey( newBinEntry->GetKey() ); + if(!used) + delete newDocEntry; + break; } - // 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 gdcmBaseTagKey): - if (gdcmSQItem* parentSQItem = dynamic_cast< gdcmSQItem* > ( set ) ) + if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { - newBinEntry->SetKey( parentSQItem->GetBaseTagKey() - + newBinEntry->GetKey() ); + if(!used) + delete newDocEntry; + break; } - - set->AddEntry( newBinEntry ); - LoadDocEntry( newBinEntry ); } - if (newDocEntry->GetGroup() == 0x7fe0 && - newDocEntry->GetElement() == 0x0010 ) + if ( ( newDocEntry->GetGroup() == 0x7fe0 ) + && ( newDocEntry->GetElement() == 0x0010 ) ) { - if ( IsRLELossLessTransferSyntax() ) + std::string ts = GetTransferSyntax(); + if ( Global::GetTS()->IsRLELossless(ts) ) { - long PositionOnEntry = ftell(Fp); - fseek(Fp, newDocEntry->GetOffset(), SEEK_SET); + long positionOnEntry = Fp->tellg(); + Fp->seekg( newDocEntry->GetOffset(), std::ios::beg ); ComputeRLEInfo(); - fseek(Fp, PositionOnEntry, SEEK_SET); + Fp->seekg( positionOnEntry, std::ios::beg ); } - else + else if ( Global::GetTS()->IsJPEG(ts) ) { - SkipToNextDocEntry(newDocEntry); + long positionOnEntry = Fp->tellg(); + Fp->seekg( newDocEntry->GetOffset(), std::ios::beg ); + ComputeJPEGFragmentInfo(); + Fp->seekg( positionOnEntry, std::ios::beg ); } } - else - { - // to be sure we are at the beginning - SkipToNextDocEntry(newDocEntry); - } + + // Just to make sure we are at the beginning of next entry. + SkipToNextDocEntry(newDocEntry); } else { @@ -1504,25 +1216,22 @@ void gdcmDocument::ParseDES(gdcmDocEntrySet *set, } } // no other way to create it ... - gdcmSeqEntry* newSeqEntry = - new gdcmSeqEntry( newDocEntry->GetDictEntry() ); - newSeqEntry->Copy( newDocEntry ); newSeqEntry->SetDelimitorMode( delim_mode ); - // At the top of the hierarchy, stands a gdcmDocument. When "set" - // is a gdcmDocument, then we are building the first depth level. - // Hence the gdcmSeqEntry we are building simply has a depth + // 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 (gdcmDocument* dummy = dynamic_cast< gdcmDocument* > ( set ) ) + 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 gdcmSeqEntry + // sequence, and hence the depth level of the new SeqEntry // we are building, is one level deeper: - if (gdcmSQItem* parentSQItem = dynamic_cast< gdcmSQItem* > ( set ) ) + if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) ) { newSeqEntry->SetDepthLevel( parentSQItem->GetDepthLevel() + 1 ); newSeqEntry->SetKey( parentSQItem->GetBaseTagKey() @@ -1536,12 +1245,14 @@ void gdcmDocument::ParseDES(gdcmDocEntrySet *set, l, delim_mode); } set->AddEntry( newSeqEntry ); - if ( !delim_mode && (ftell(Fp)-offset) >= l_max) + if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { break; } } - delete newDocEntry; + + if(!used) + delete newDocEntry; } } @@ -1549,15 +1260,15 @@ void gdcmDocument::ParseDES(gdcmDocEntrySet *set, * \brief Parses a Sequence ( SeqEntry after SeqEntry) * @return parsed length for this level */ -void gdcmDocument::ParseSQ( gdcmSeqEntry* seqEntry, - 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; while (true) { - gdcmDocEntry* newDocEntry = ReadNextDocEntry(); + DocEntry *newDocEntry = ReadNextDocEntry(); if ( !newDocEntry ) { // FIXME Should warn user @@ -1567,16 +1278,17 @@ void gdcmDocument::ParseSQ( gdcmSeqEntry* seqEntry, { if ( newDocEntry->IsSequenceDelimitor() ) { - seqEntry->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( seqEntry->GetDepthLevel() ); + SQItem *itemSQ = new SQItem( seqEntry->GetDepthLevel() ); std::ostringstream newBase; newBase << seqEntry->GetKey() << "/" @@ -1595,10 +1307,11 @@ void gdcmDocument::ParseSQ( gdcmSeqEntry* seqEntry, } ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod); + delete newDocEntry; seqEntry->AddEntry( itemSQ, SQItemNumber ); SQItemNumber++; - if ( !delim_mode && ( ftell(Fp) - offset ) >= l_max ) + if ( !delim_mode && ((long)(Fp->tellg())-offset ) >= l_max ) { break; } @@ -1607,17 +1320,16 @@ void gdcmDocument::ParseSQ( gdcmSeqEntry* seqEntry, /** * \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::beg); // A SeQuence "contains" a set of Elements. // (fffe e000) tells us an Element is beginning @@ -1632,7 +1344,7 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry* entry) // When the length is zero things are easy: if ( length == 0 ) { - ((gdcmValEntry *)entry)->SetValue(""); + ((ValEntry *)entry)->SetValue(""); return; } @@ -1643,7 +1355,7 @@ 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; @@ -1652,8 +1364,8 @@ 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; @@ -1665,24 +1377,25 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry* entry) else { // fusible - std::cout<< "MaxSizeLoadEntry exceeded, neither a BinEntry " - << "nor a ValEntry ?! Should never print that !" << std::endl; + gdcmErrorMacro( "MaxSizeLoadEntry exceeded, neither a BinEntry " + << "nor a ValEntry ?! Should never print that !" ); } // 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::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_BINLOADED; binEntryPtr->SetValue(s.str()); LoadEntryBinArea(binEntryPtr); // last one, not to erase length ! return; } - + /// \todo Any compacter code suggested (?) if ( IsDocEntryAnInteger(entry) ) { @@ -1728,25 +1441,35 @@ 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); + gdcmVerboseMacro("Warning: bad length: " << length << + ",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()) { - dbg.Verbose(1, "gdcmDocument::LoadDocEntry", - "unread element value"); + gdcmVerboseMacro("Unread element value"); valEntry->SetValue(GDCM_UNREAD); return; } @@ -1763,8 +1486,7 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry* entry) } else { - dbg.Error(true, "gdcmDocument::LoadDocEntry" - "Should have a ValEntry, here !"); + gdcmErrorMacro( "Should have a ValEntry, here !"); } } @@ -1773,21 +1495,21 @@ 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 3.5-2003, 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::cur); uint32_t length32 = ReadInt32(); if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff ) @@ -1795,24 +1517,26 @@ void gdcmDocument::FindDocEntryLength( gdcmDocEntry *entry ) uint32_t lengthOB; try { - /// \todo rename that to FindDocEntryLengthOBOrOW since - /// the above test is on both OB and OW... - lengthOB = FindDocEntryLengthOB(); + lengthOB = FindDocEntryLengthOBOrOW(); } - 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::end); + + long lengthUntilEOF = (long)(Fp->tellg())-currentPosition; + Fp->seekg(currentPosition, std::ios::beg); + + entry->SetReadLength(lengthUntilEOF); entry->SetLength(lengthUntilEOF); return; } + entry->SetReadLength(lengthOB); entry->SetLength(lengthOB); return; } @@ -1852,20 +1576,22 @@ void gdcmDocument::FindDocEntryLength( gdcmDocEntry *entry ) // big endian and proceed... if ( element == 0x0000 && length16 == 0x0400 ) { - if ( !IsExplicitVRBigEndianTransferSyntax() ) + std::string ts = GetTransferSyntax(); + if ( Global::GetTS()->GetSpecialTransferSyntax(ts) + != TS::ExplicitVRBigEndian ) { - throw gdcmFormatError( "gdcmDocument::FindDocEntryLength()", - " not explicit VR." ); + throw FormatError( "Document::FindDocEntryLength()", + " not explicit VR." ); return; } length16 = 4; - SwitchSwapToBigEndian(); + SwitchByteSwapCode(); + // Restore the unproperly loaded values i.e. the group, the element // and the dictionary entry depending on them. uint16_t correctGroup = SwapShort( entry->GetGroup() ); uint16_t correctElem = SwapShort( entry->GetElement() ); - gdcmDictEntry* newTag = GetDictEntryByNumber( correctGroup, - correctElem ); + DictEntry *newTag = GetDictEntry( correctGroup, correctElem ); if ( !newTag ) { // This correct tag is not in the dictionary. Create a new one. @@ -1901,18 +1627,14 @@ void gdcmDocument::FindDocEntryLength( gdcmDocEntry *entry ) /** * \brief Find the Value Representation of the current Dicom Element. - * @param entry + * @return Value Representation of the current Entry */ -void gdcmDocument::FindDocEntryVR( gdcmDocEntry *entry ) +std::string Document::FindDocEntryVR() { - if ( Filetype != gdcmExplicitVR ) - { - return; - } - - char vr[3]; + if ( Filetype != ExplicitVR ) + return GDCM_UNKNOWN; - 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 @@ -1920,105 +1642,34 @@ void gdcmDocument::FindDocEntryVR( gdcmDocEntry *entry ) // within an explicit VR file. Hence we make sure the present tag // 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); + + char vr[3]; + Fp->read (vr, (size_t)2); vr[2] = 0; - if( !CheckDocEntryVR(entry, vr) ) + if( !CheckDocEntryVR(vr) ) { - fseek(Fp, positionOnEntry, SEEK_SET); - // 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 - // we know now our assumption on expliciteness is not furfilled. - // avoid . - if ( entry->IsVRUnknown() ) - { - entry->SetVR("Implicit"); - } - entry->SetImplicitVR(); + Fp->seekg(positionOnEntry, std::ios::beg); + return GDCM_UNKNOWN; } + return vr; } /** * \brief Check the correspondance between the VR of the header entry * and the taken VR. If they are different, the header entry is * updated with the new VR. - * @param entry Header Entry to check * @param vr Dicom Value Representation * @return false if the VR is incorrect of if the VR isn't referenced * otherwise, it returns true */ -bool gdcmDocument::CheckDocEntryVR(gdcmDocEntry *entry, gdcmVRKey vr) +bool Document::CheckDocEntryVR(VRKey vr) { - char msg[100]; // for sprintf - bool realExplicit = true; - - // Assume we are reading a falsely explicit VR file i.e. we reached - // a tag where we expect reading a VR but are in fact we read the - // first to bytes of the length. Then we will interogate (through find) - // the dicom_vr dictionary with oddities like "\004\0" which crashes - // both GCC and VC++ implementations of the STL map. Hence when the - // expected VR read happens to be non-ascii characters we consider - // we hit falsely explicit VR tag. - - if ( !isalpha(vr[0]) && !isalpha(vr[1]) ) - { - realExplicit = false; - } - // 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) ) - { - realExplicit = false; - } - - if ( !realExplicit ) - { - // 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); - - if( entry->GetGroup() % 2 && entry->GetElement() == 0x0000) - { - // Group length is UL ! - gdcmDictEntry* newEntry = NewVirtualDictEntry( - entry->GetGroup(), entry->GetElement(), - "UL", "FIXME", "Group Length"); - entry->SetDictEntry( newEntry ); - } + if ( !Global::GetVR()->IsValidVR(vr) ) return false; - } - - if ( entry->IsVRUnknown() ) - { - // When not a dictionary entry, we can safely overwrite the VR. - if( entry->GetElement() == 0x0000 ) - { - // Group length is UL ! - entry->SetVR("UL"); - } - else - { - entry->SetVR(vr); - } - } - else if ( entry->GetVR() != vr ) - { - // The VR present in the file and the dictionary disagree. We assume - // the file writer knew best and use the VR of the file. Since it would - // 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( - entry->GetGroup(), entry->GetElement(), - vr, "FIXME", entry->GetName()); - entry->SetDictEntry(newEntry); - } return true; } @@ -2030,11 +1681,11 @@ 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; @@ -2095,7 +1746,7 @@ std::string gdcmDocument::GetDocEntryValue(gdcmDocEntry *entry) return s.str(); } - return ((gdcmValEntry *)entry)->GetValue(); + return ((ValEntry *)entry)->GetValue(); } /** @@ -2106,7 +1757,7 @@ 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() ) { @@ -2119,7 +1770,7 @@ 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(); } /** @@ -2159,7 +1810,7 @@ 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()); } @@ -2167,12 +1818,12 @@ void gdcmDocument::SkipDocEntry(gdcmDocEntry *entry) /** * \brief Skips to the begining of the next Header Entry * \warning NOT end user intended method ! - * @param entry entry to skip + * @param currentDocEntry entry to skip */ -void gdcmDocument::SkipToNextDocEntry(gdcmDocEntry *entry) +void Document::SkipToNextDocEntry(DocEntry *currentDocEntry) { - fseek(Fp, (long)(entry->GetOffset()), SEEK_SET); - fseek(Fp, (long)(entry->GetReadLength()), SEEK_CUR); + Fp->seekg((long)(currentDocEntry->GetOffset()), std::ios::beg); + Fp->seekg( (long)(currentDocEntry->GetReadLength()),std::ios::cur); } /** @@ -2180,10 +1831,10 @@ void gdcmDocument::SkipToNextDocEntry(gdcmDocEntry *entry) * the parser went Jabberwocky) one can hope improving things by * applying some heuristics. * @param entry entry to check - * @param foundLength fist assumption about length + * @param foundLength first 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) @@ -2191,30 +1842,25 @@ void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *entry, foundLength = 0; } - uint16_t gr = entry->GetGroup(); - uint16_t el = entry->GetElement(); + uint16_t gr = entry->GetGroup(); + uint16_t elem = entry->GetElement(); if ( foundLength % 2) { - std::ostringstream s; - s << "Warning : Tag with uneven length " - << foundLength - << " in x(" << std::hex << gr << "," << el <<")" << std::dec; - dbg.Verbose(0, s.str().c_str()); + gdcmVerboseMacro( "Warning : Tag with uneven length " << foundLength + << " in x(" << std::hex << gr << "," << elem <<")"); } //////// Fix for some naughty General Electric images. // Allthough not recent many such GE corrupted images are still present // on Creatis hard disks. Hence this fix shall remain when such images - // are no longer in user (we are talking a few years, here)... + // are no longer in use (we are talking a few years, here)... // Note: XMedCom probably uses such a trick since it is able to read // those pesky GE images ... if ( foundLength == 13) { // Only happens for this length ! - if ( entry->GetGroup() != 0x0008 - || ( entry->GetElement() != 0x0070 - && entry->GetElement() != 0x0080 ) ) + if ( gr != 0x0008 || ( elem != 0x0070 && elem != 0x0080 ) ) { foundLength = 10; entry->SetReadLength(10); /// \todo a bug is to be fixed !? @@ -2225,9 +1871,7 @@ void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *entry, // Occurence of such images is quite low (unless one leaves close to a // 'Leonardo' source. Hence, one might consider commenting out the // following fix on efficiency reasons. - else if ( entry->GetGroup() == 0x0009 - && ( entry->GetElement() == 0x1113 - || entry->GetElement() == 0x1114 ) ) + else if ( gr == 0x0009 && ( elem == 0x1113 || elem == 0x1114 ) ) { foundLength = 4; entry->SetReadLength(4); /// \todo a bug is to be fixed !? @@ -2241,7 +1885,7 @@ void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *entry, //////// We encountered a 'delimiter' element i.e. a tag of the form // "fffe|xxxx" which is just a marker. Delimiters length should not be // taken into account. - else if( entry->GetGroup() == 0xfffe ) + else if( gr == 0xfffe ) { // According to the norm, fffe|0000 shouldn't exist. BUT the Philips // image gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm happens to @@ -2252,7 +1896,7 @@ void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *entry, } } - entry->SetUsableLength(foundLength); + entry->SetLength(foundLength); } /** @@ -2261,17 +1905,17 @@ 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 elem = 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 // a priori know we are dealing with an integer, then we shall be // able to swap it's element value properly. - if ( element == 0 ) // This is the group length of the group + if ( elem == 0 ) // This is the group length of the group { if ( length == 4 ) { @@ -2286,21 +1930,18 @@ bool gdcmDocument::IsDocEntryAnInteger(gdcmDocEntry *entry) // test is useless (and might even look a bit paranoid), when we // 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); - s << "Erroneous Group Length element length on : (" \ - << std::hex << group << " , " << element + long filePosition = Fp->tellg(); + gdcmVerboseMacro( "Erroneous Group Length element length on : (" + << std::hex << group << " , " << elem << ") -before- position x(" << filePosition << ")" - << "lgt : " << length; - dbg.Verbose(0, "gdcmDocument::IsDocEntryAnInteger", s.str().c_str() ); + << "lgt : " << length ); } } if ( vr == "UL" || vr == "US" || vr == "SL" || vr == "SS" ) { return true; - } - + } return false; } @@ -2310,11 +1951,11 @@ bool gdcmDocument::IsDocEntryAnInteger(gdcmDocEntry *entry) * @return */ -uint32_t gdcmDocument::FindDocEntryLengthOB() - throw( gdcmFormatUnexpected ) +uint32_t Document::FindDocEntryLengthOBOrOW() + 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; @@ -2327,10 +1968,10 @@ uint32_t gdcmDocument::FindDocEntryLengthOB() group = ReadInt16(); elem = ReadInt16(); } - catch ( gdcmFormatError ) + catch ( FormatError ) { - throw gdcmFormatError("gdcmDocument::FindDocEntryLengthOB()", - " group or element not present."); + throw FormatError("Unexpected end of file encountered during ", + "Document::FindDocEntryLengthOBOrOW()"); } // We have to decount the group and element we just read @@ -2338,12 +1979,13 @@ uint32_t gdcmDocument::FindDocEntryLengthOB() if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) ) { - dbg.Verbose(1, "gdcmDocument::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."); + long filePosition = Fp->tellg(); + gdcmVerboseMacro( "Neither an Item tag nor a Sequence delimiter tag on :" + << std::hex << group << " , " << elem + << ") -before- position x(" << filePosition << ")" ); + + Fp->seekg(positionOnEntry, std::ios::beg); + throw FormatUnexpected( "Neither an Item tag nor a Sequence delimiter tag."); } if ( elem == 0xe0dd ) @@ -2361,7 +2003,7 @@ uint32_t gdcmDocument::FindDocEntryLengthOB() break; } } - fseek(Fp, positionOnEntry, SEEK_SET); + Fp->seekg( positionOnEntry, std::ios::beg); return totalLength; } @@ -2370,18 +2012,18 @@ 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; @@ -2392,18 +2034,18 @@ 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; @@ -2414,20 +2056,23 @@ 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::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; + Filetype = Unknown; } /** @@ -2438,7 +2083,7 @@ 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. @@ -2450,7 +2095,7 @@ bool gdcmDocument::CheckSwap() uint32_t s32; uint16_t s16; - char deb[HEADER_LENGTH_TO_READ]; + char deb[256]; // First, compare HostByteOrder and NetworkByteOrder in order to // determine if we shall need to swap bytes (i.e. the Endian type). @@ -2465,13 +2110,12 @@ 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, 256); char *entCur = deb + 128; if( memcmp(entCur, "DICM", (size_t)4) == 0 ) { - dbg.Verbose(1, "gdcmDocument::CheckSwap:", "looks like DICOM Version3"); + gdcmVerboseMacro( "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" @@ -2492,7 +2136,7 @@ bool gdcmDocument::CheckSwap() // FIXME : FIXME: // Sometimes (see : gdcmData/icone.dcm) group 0x0002 *is* Explicit VR, - // but elem 0002,0010 (Transfert Syntax) tells us the file is + // but elem 0002,0010 (Transfer Syntax) tells us the file is // *Implicit* VR. -and it is !- if( memcmp(entCur, "UL", (size_t)2) == 0 || @@ -2501,45 +2145,41 @@ 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:", - "explicit Value Representation"); + Filetype = ExplicitVR; + gdcmVerboseMacro( "Explicit Value Representation"); } else { - Filetype = gdcmImplicitVR; - dbg.Verbose(1, "gdcmDocument::CheckSwap:", - "not an explicit Value Representation"); + Filetype = ImplicitVR; + gdcmVerboseMacro( "Not an explicit Value Representation"); } if ( net2host ) { SwapCode = 4321; - dbg.Verbose(1, "gdcmDocument::CheckSwap:", - "HostByteOrder != NetworkByteOrder"); + gdcmVerboseMacro( "HostByteOrder != NetworkByteOrder"); } else { - SwapCode = 0; - dbg.Verbose(1, "gdcmDocument::CheckSwap:", - "HostByteOrder = NetworkByteOrder"); + SwapCode = 1234; + gdcmVerboseMacro( "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::beg); + Fp->seekg ( 132L, std::ios::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); + gdcmVerboseMacro( "Not a DICOM Version3 file"); + Fp->seekg(0, std::ios::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. @@ -2551,24 +2191,24 @@ bool gdcmDocument::CheckSwap() // representation of a 32 bits integer. Hence the following dirty // trick : s32 = *((uint32_t *)(entCur)); - + switch( s32 ) { 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; + SwapCode = 1234; + Filetype = ACR; return true; default : // We are out of luck. It is not a DicomV3 nor a 'clean' ACR/NEMA file. @@ -2576,13 +2216,13 @@ 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... @@ -2590,48 +2230,57 @@ bool gdcmDocument::CheckSwap() switch ( s16 ) { + case 0x0001 : case 0x0002 : + case 0x0003 : case 0x0004 : - case 0x0008 : - SwapCode = 0; - Filetype = gdcmACR; + case 0x0005 : + case 0x0006 : + case 0x0007 : + case 0x0008 : + SwapCode = 1234; + 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; + gdcmVerboseMacro( "ACR/NEMA unfound swap info (Really hopeless !)"); + Filetype = Unknown; return false; } // Then the only info we have is the net2host one. //if (! net2host ) - // SwapCode = 0; + // SwapCode = 1234; //else // SwapCode = 4321; //return; } } + + /** - * \brief Restore the unproperly loaded values i.e. the group, the element - * and the dictionary entry depending on them. + * \brief Change the Byte Swap code. */ -void gdcmDocument::SwitchSwapToBigEndian() +void Document::SwitchByteSwapCode() { - dbg.Verbose(1, "gdcmDocument::SwitchSwapToBigEndian", - "Switching to BigEndian mode."); - if ( SwapCode == 0 ) + gdcmVerboseMacro( "Switching Byte Swap code."); + if ( SwapCode == 1234 ) { SwapCode = 4321; } else if ( SwapCode == 4321 ) { - SwapCode = 0; + SwapCode = 1234; } else if ( SwapCode == 3412 ) { @@ -2647,7 +2296,7 @@ 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 ) { @@ -2664,10 +2313,10 @@ 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 ) @@ -2684,14 +2333,107 @@ 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++; + SwitchByteSwapCode(); + // fix the tag + group = 0xfffe; + elem = 0xe000; + } + else if (group == 0xfffe && elem == 0xe00d && reversedEndian) + { + // end of reversed endian group + reversedEndian--; + SwitchByteSwapCode(); + } +} + +/** + * \brief Accesses the info from 0002,0010 : Transfer Syntax and TS + * else 1. + * @return The full Transfer Syntax Name (as opposed to Transfer Syntax UID) + */ +std::string Document::GetTransferSyntaxName() +{ + // use the TS (TS : Transfer Syntax) + std::string transferSyntax = GetEntry(0x0002,0x0010); + + if ( transferSyntax == GDCM_NOTLOADED ) + { + gdcmVerboseMacro( "Transfer Syntax not loaded. " << std::endl + << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE" ); + return "Uncompressed ACR-NEMA"; + } + if ( transferSyntax == GDCM_UNFOUND ) + { + gdcmVerboseMacro( "Unfound Transfer Syntax (0002,0010)"); + return "Uncompressed ACR-NEMA"; + } + + while ( ! isdigit((unsigned char)transferSyntax[transferSyntax.length()-1]) ) + { + transferSyntax.erase(transferSyntax.length()-1, 1); + } + // we do it only when we need it + TS* ts = Global::GetTS(); + std::string tsName = ts->GetValue( transferSyntax ); + + // Global::GetTS() is a global static you shall never try to delete it! + return tsName; +} + +/** + * \brief Group 0002 is always coded Little Endian + * whatever Transfer Syntax is + * @return no return + */ +void Document::HandleOutOfGroup0002(uint16_t group) +{ + // Endian reversion. Some files contain groups of tags with reversed endianess. + if ( !Group0002Parsed && group != 0x0002) + { + Group0002Parsed = true; + // we just came out of group 0002 + // if Transfer syntax is Big Endian we have to change CheckSwap + + std::string ts = GetTransferSyntaxName(); + if ( !Global::GetTS()->IsTransferSyntax(ts) ) + { + gdcmVerboseMacro("True DICOM File, with NO Tansfer Syntax: " << ts ); + return; + } + + // FIXME Strangely, this works with + //'Implicit VR Transfer Syntax (GE Private) + if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian ) + { + gdcmVerboseMacro("Tansfer Syntax = Explicit VR - Big Endian"); + SwitchByteSwapCode(); + } + } +} + /** * \brief Read the next tag but WITHOUT loading it's value * (read the 'Group Number', the 'Element Number', - * gets the Dict Entry + * gets the Dict Entry * 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; @@ -2701,7 +2443,7 @@ 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. @@ -2709,14 +2451,50 @@ gdcmDocEntry* gdcmDocument::ReadNextDocEntry() return 0; } - gdcmDocEntry *newEntry = NewDocEntryByNumber(group, elem); - FindDocEntryVR(newEntry); + // Sometimes file contains groups of tags with reversed endianess. + HandleBrokenEndian(group, elem); + +// In 'true DICOM' files Group 0002 is allways little endian + if ( HasDCMPreamble ) + HandleOutOfGroup0002(group); + + std::string vr = FindDocEntryVR(); + std::string realVR = vr; + + if( vr == GDCM_UNKNOWN) + { + DictEntry *dictEntry = GetDictEntry(group,elem); + if( dictEntry ) + realVR = dictEntry->GetVR(); + } + + DocEntry *newEntry; + if( Global::GetVR()->IsVROfSequence(realVR) ) + newEntry = NewSeqEntry(group, elem); + else if( Global::GetVR()->IsVROfStringRepresentable(realVR) ) + newEntry = NewValEntry(group, elem,vr); + else + newEntry = NewBinEntry(group, elem,vr); + + if( vr == GDCM_UNKNOWN ) + { + if( Filetype == ExplicitVR ) + { + // We thought this was explicit VR, but we end up with an + // implicit VR tag. Let's backtrack. + std::string msg; + msg = Util::Format("Falsely explicit vr file (%04x,%04x)\n", + newEntry->GetGroup(), newEntry->GetElement()); + gdcmVerboseMacro( msg.c_str() ); + } + newEntry->SetImplicitVR(); + } try { FindDocEntryLength(newEntry); } - catch ( gdcmFormatError e ) + catch ( FormatError e ) { // Call it quits //std::cout << e; @@ -2724,23 +2502,23 @@ 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; @@ -2750,39 +2528,47 @@ 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; - s << " We should have found tag ("; - s << std::hex << testGroup << "," << testElement << ")" << std::endl; - s << " but instead we encountered tag ("; - 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, s.str().c_str()); - fseek(Fp, positionOnEntry, SEEK_SET); + gdcmVerboseMacro( "Wrong Item Tag found:" + << " We should have found tag (" + << std::hex << testGroup << "," << testElement << ")" << std::endl + << " but instead we encountered tag (" + << std::hex << itemTagGroup << "," << itemTagElement << ")" + << " at address: " << " 0x(" << (unsigned int)currentPosition << ")" + ) ; + Fp->seekg(positionOnEntry, std::ios::beg); return false; } @@ -2790,22 +2576,22 @@ 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) ) @@ -2814,29 +2600,63 @@ 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()); + gdcmVerboseMacro( "Basic Item Length is: " + << itemLength << std::endl + << " at address: " << std::hex << (unsigned int)currentPosition); } return itemLength; } +/** + * \brief When parsing the Pixel Data of an encapsulated file, read + * the basic offset table (when present, and BTW dump it). + */ +void Document::ReadAndSkipEncapsulatedBasicOffsetTable() +{ + //// Read the Basic Offset Table Item Tag length... + uint32_t itemLength = ReadTagLength(0xfffe, 0xe000); + + // 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 ) + { + char *basicOffsetTableItemValue = new char[itemLength + 1]; + Fp->read(basicOffsetTableItemValue, itemLength); + +#ifdef GDCM_DEBUG + for (unsigned int i=0; i < itemLength; i += 4 ) + { + uint32_t individualLength = str2num( &basicOffsetTableItemValue[i], + uint32_t); + gdcmVerboseMacro( "Read one length: " << + std::hex << individualLength ); + } +#endif //GDCM_DEBUG + + delete[] basicOffsetTableItemValue; + } +} + /** * \brief Parse pixel data from disk of [multi-]fragment RLE encoding. * Compute the RLE extra information and store it in \ref RLEInfo * for later pixel retrieval usage. */ -void gdcmDocument::ComputeRLEInfo() +void Document::ComputeRLEInfo() { - if ( ! IsRLELossLessTransferSyntax() ) + std::string ts = GetTransferSyntax(); + if ( !Global::GetTS()->IsRLELossless(ts) ) { 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: @@ -2851,54 +2671,32 @@ void gdcmDocument::ComputeRLEInfo() // data stream shall be basic offset table item. The basic offset table // item value, however, is not required to be present" - //// Read the Basic Offset Table Item Tag length... - uint32_t itemLength = ReadTagLength(0xfffe, 0xe000); - - // 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 ) - { - char* basicOffsetTableItemValue = new char[itemLength + 1]; - fread(basicOffsetTableItemValue, itemLength, 1, Fp); - - for (unsigned int i=0; i < itemLength; i += 4 ) - { - 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::ComputeRLEInfo: ", s.str().c_str()); - } - delete[] basicOffsetTableItemValue; - } + ReadAndSkipEncapsulatedBasicOffsetTable(); // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G) - // Loop on the frame[s] and store the parsed information in a - // gdcmRLEFramesInfo. - long frameLength; - // Loop on the individual frame[s] and store the information - // on the RLE fragments in a gdcmRLEFramesInfo. + // on the RLE fragments in a RLEFramesInfo. // Note: - when only a single frame is present, this is a // classical image. // - when more than one frame are present, then we are in // the case of a multi-frame image. + long frameLength; while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) ) { // Parse the RLE Header and store the corresponding RLE Segment // Offset Table information on fragments of this current Frame. // Note that the fragment pixels themselves are not loaded // (but just skipped). - long frameOffset = ftell(Fp); + long frameOffset = Fp->tellg(); uint32_t nbRleSegments = ReadInt32(); + if ( nbRleSegments > 16 ) + { + // There should be at most 15 segments (refer to RLEFrame class) + gdcmVerboseMacro( "Too many segments."); + } - uint32_t rleSegmentOffsetTable[15]; + uint32_t rleSegmentOffsetTable[16]; for( int k = 1; k <= 15; k++ ) { rleSegmentOffsetTable[k] = ReadInt32(); @@ -2906,7 +2704,7 @@ void gdcmDocument::ComputeRLEInfo() // Deduce from both the RLE Header and the frameLength the // fragment length, and again store this info in a - // gdcmRLEFramesInfo. + // RLEFramesInfo. long rleSegmentLength[15]; // skipping (not reading) RLE Segments if ( nbRleSegments > 1) @@ -2924,48 +2722,88 @@ void gdcmDocument::ComputeRLEInfo() SkipBytes(rleSegmentLength[nbRleSegments]); // Store the collected info - gdcmRLEFrame* newFrameInfo = new gdcmRLEFrame; + 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 ); + RLEInfo->Frames.push_back( newFrameInfo ); + } + + // Make sure that at the end of the item we encounter a 'Sequence + // Delimiter Item': + if ( !ReadTag(0xfffe, 0xe0dd) ) + { + gdcmVerboseMacro( "No sequence delimiter item at end of RLE item sequence"); + } +} + +/** + * \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(). + std::string ts = GetTransferSyntax(); + if ( ! Global::GetTS()->IsJPEG(ts) ) + { + return; + } + + 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, "gdcmDocument::ComputeRLEInfo: no sequence delimiter "); - dbg.Verbose(0, " item at end of RLE item sequence"); + gdcmVerboseMacro( "No sequence delimiter item at end of JPEG item sequence"); } } /** - * \brief Walk recursively the given \ref gdcmDocEntrySet, and feed + * \brief Walk recursively the given \ref DocEntrySet, and feed * the given hash table (\ref TagDocEntryHT) with all the - * \ref gdcmDocEntry (Dicom entries) encountered. + * \ref DocEntry (Dicom entries) encountered. * This method does the job for \ref BuildFlatHashTable. - * @param builtHT Where to collect all the \ref gdcmDocEntry encountered + * @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 gdcmDocument::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT, - gdcmDocEntrySet* set ) +void Document::BuildFlatHashTableRecurse( TagDocEntryHT &builtHT, + DocEntrySet *set ) { - if (gdcmElementSet* elementSet = dynamic_cast< gdcmElementSet* > ( set ) ) + if (ElementSet *elementSet = dynamic_cast< ElementSet* > ( set ) ) { - TagDocEntryHT* currentHT = elementSet->GetTagHT(); - for( TagDocEntryHT::const_iterator i = currentHT->begin(); - i != currentHT->end(); + TagDocEntryHT const ¤tHT = elementSet->GetTagHT(); + for( TagDocEntryHT::const_iterator i = currentHT.begin(); + i != currentHT.end(); ++i) { - gdcmDocEntry* entry = i->second; - if ( gdcmSeqEntry* seqEntry = dynamic_cast(entry) ) + DocEntry *entry = i->second; + if ( SeqEntry *seqEntry = dynamic_cast(entry) ) { - ListSQItem& items = seqEntry->GetSQItems(); + const ListSQItem& items = seqEntry->GetSQItems(); for( ListSQItem::const_iterator item = items.begin(); item != items.end(); ++item) @@ -2979,17 +2817,17 @@ void gdcmDocument::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT, return; } - if (gdcmSQItem* SQItemSet = dynamic_cast< gdcmSQItem* > ( set ) ) + if (SQItem *SQItemSet = dynamic_cast< SQItem* > ( set ) ) { - ListDocEntry& currentList = SQItemSet->GetDocEntries(); - for (ListDocEntry::iterator i = currentList.begin(); - i != currentList.end(); - ++i) + const ListDocEntry& currentList = SQItemSet->GetDocEntries(); + for (ListDocEntry::const_iterator i = currentList.begin(); + i != currentList.end(); + ++i) { - gdcmDocEntry* entry = *i; - if ( gdcmSeqEntry* seqEntry = dynamic_cast(entry) ) + DocEntry *entry = *i; + if ( SeqEntry *seqEntry = dynamic_cast(entry) ) { - ListSQItem& items = seqEntry->GetSQItems(); + const ListSQItem& items = seqEntry->GetSQItems(); for( ListSQItem::const_iterator item = items.begin(); item != items.end(); ++item) @@ -3006,13 +2844,13 @@ void gdcmDocument::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT, /** * \brief Build a \ref TagDocEntryHT (i.e. a std::map<>) from the current - * gdcmDocument. + * Document. * - * The structure used by a gdcmDocument (through \ref gdcmElementSet), - * in order to old the parsed entries of a Dicom header, is a recursive + * 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 gdcmSQItem) add an extra complexity to the data + * 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). @@ -3021,15 +2859,15 @@ void gdcmDocument::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT, * 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 gdcmElementSet used - * to build it. Hence if the underlying \ref gdcmElementSet is + * 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* gdcmDocument::BuildFlatHashTable() +TagDocEntryHT *Document::BuildFlatHashTable() { - TagDocEntryHT* FlatHT = new TagDocEntryHT; + TagDocEntryHT *FlatHT = new TagDocEntryHT; BuildFlatHashTableRecurse( *FlatHT, this ); return FlatHT; } @@ -3037,17 +2875,17 @@ TagDocEntryHT* gdcmDocument::BuildFlatHashTable() /** - * \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); - std::string s2 = document.GetEntryByNumber(0x0010,0x0010); + std::string s1 = GetEntry(0x0010,0x0010); + std::string s2 = document.GetEntry(0x0010,0x0010); if(s1 < s2) { return true; @@ -3059,8 +2897,8 @@ bool gdcmDocument::operator<(gdcmDocument &document) else { // Patient ID - s1 = GetEntryByNumber(0x0010,0x0020); - s2 = document.GetEntryByNumber(0x0010,0x0020); + s1 = GetEntry(0x0010,0x0020); + s2 = document.GetEntry(0x0010,0x0020); if ( s1 < s2 ) { return true; @@ -3072,8 +2910,8 @@ bool gdcmDocument::operator<(gdcmDocument &document) else { // Study Instance UID - s1 = GetEntryByNumber(0x0020,0x000d); - s2 = document.GetEntryByNumber(0x0020,0x000d); + s1 = GetEntry(0x0020,0x000d); + s2 = document.GetEntry(0x0020,0x000d); if ( s1 < s2 ) { return true; @@ -3085,8 +2923,8 @@ bool gdcmDocument::operator<(gdcmDocument &document) else { // Serie Instance UID - s1 = GetEntryByNumber(0x0020,0x000e); - s2 = document.GetEntryByNumber(0x0020,0x000e); + s1 = GetEntry(0x0020,0x000e); + s2 = document.GetEntry(0x0020,0x000e); if ( s1 < s2 ) { return true; @@ -3102,4 +2940,51 @@ bool gdcmDocument::operator<(gdcmDocument &document) } +/** + * \brief Re-computes the length of a ACR-NEMA/Dicom group from a DcmHeader + * @param filetype Type of the File to be written + */ +int Document::ComputeGroup0002Length( FileType filetype ) +{ + uint16_t gr, el; + std::string vr; + + int groupLength = 0; + bool found0002 = false; + + // for each zero-level Tag in the DCM Header + DocEntry *entry; + + Initialize(); + entry = GetNextEntry(); + while(entry) + { + gr = entry->GetGroup(); + + if (gr == 0x0002) + { + found0002 = true; + + el = entry->GetElement(); + vr = entry->GetVR(); + + if (filetype == ExplicitVR) + { + if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") ) + { + groupLength += 4; // explicit VR AND OB, OW, SQ : 4 more bytes + } + } + groupLength += 2 + 2 + 4 + entry->GetLength(); + } + else if (found0002 ) + break; + + entry = GetNextEntry(); + } + return groupLength; +} + +} // end namespace gdcm + //-----------------------------------------------------------------------------