X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=62d542d2ecb414ab3b015dd0d410e91fe465d18a;hb=d31dacbd4792e49cccecc51ffd9d93fd71541561;hp=60ca2dff2fae566e9b8171cb07bef9e4b44839ae;hpb=bd1fa6ade44ea7dffa9d0fed99d5caa15cb7339a;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 60ca2dff..62d542d2 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2004/10/12 17:31:56 $ - Version: $Revision: 1.104 $ + Date: $Date: 2004/12/07 13:39:33 $ + Version: $Revision: 1.149 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -23,56 +23,65 @@ #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 - namespace gdcm { - -// 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)) - +//----------------------------------------------------------------------------- +static const char *TransferSyntaxStrings[] = { + // Implicit VR Little Endian + "1.2.840.10008.1.2", + // Implicit VR Little Endian DLX G.E? + "1.2.840.113619.5.2", + // Explicit VR Little Endian + "1.2.840.10008.1.2.1", + // Deflated Explicit VR Little Endian + "1.2.840.10008.1.2.1.99", + // Explicit VR Big Endian + "1.2.840.10008.1.2.2", + // JPEG Baseline (Process 1) + "1.2.840.10008.1.2.4.50", + // JPEG Extended (Process 2 & 4) + "1.2.840.10008.1.2.4.51", + // JPEG Extended (Process 3 & 5) + "1.2.840.10008.1.2.4.52", + // JPEG Spectral Selection, Non-Hierarchical (Process 6 & 8) + "1.2.840.10008.1.2.4.53", + // JPEG Full Progression, Non-Hierarchical (Process 10 & 12) + "1.2.840.10008.1.2.4.55", + // JPEG Lossless, Non-Hierarchical (Process 14) + "1.2.840.10008.1.2.4.57", + // JPEG Lossless, Hierarchical, First-Order Prediction (Process 14, [Selection Value 1]) + "1.2.840.10008.1.2.4.70", + // JPEG 2000 Lossless + "1.2.840.10008.1.2.4.90", + // JPEG 2000 + "1.2.840.10008.1.2.4.91", + // RLE Lossless + "1.2.840.10008.1.2.5", + // Unknown + "Unknown Transfer Syntax" +}; + //----------------------------------------------------------------------------- // Refer to Document::CheckSwap() -const unsigned int Document::HEADER_LENGTH_TO_READ = 256; +//const unsigned int Document::HEADER_LENGTH_TO_READ = 256; // Refer to Document::SetMaxSizeLoadEntry() const unsigned int Document::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096 @@ -85,13 +94,13 @@ const unsigned int Document::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff; * \brief constructor * @param filename file to be opened for parsing */ -Document::Document( std::string const & filename ) - : ElementSet(-1) +Document::Document( std::string const & filename ) : ElementSet(-1) { SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Filename = filename; Initialise(); + Fp = 0; if ( !OpenFile() ) { return; @@ -99,19 +108,19 @@ Document::Document( std::string const & filename ) dbg.Verbose(0, "Document::Document: starting parsing of file: ", Filename.c_str()); - rewind(Fp); + 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 @@ -181,11 +190,14 @@ Document::Document( std::string const & filename ) * \brief This default constructor doesn't parse the file. You should * then invoke \ref Document::SetFileName and then the parsing. */ -Document::Document() - :ElementSet(-1) +Document::Document() : ElementSet(-1) { + Fp = 0; + SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Initialise(); + SwapCode = 0; + Filetype = ExplicitVR; PrintLevel = 1; // 'Medium' print level by default } @@ -197,13 +209,8 @@ 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; } //----------------------------------------------------------------------------- @@ -291,21 +298,18 @@ bool Document::IsReadable() return true; } - /** - * \brief Internal function that checks whether the Transfer Syntax given - * as argument is the one present in the current document. - * @param syntaxToCheck The transfert syntax we need to check against. - * @return True when SyntaxToCheck corresponds to the Transfer Syntax of - * the current document. False either when the document contains - * no Transfer Syntax, or when the Tranfer Syntaxes doesn't match. + * \brief Accessor to the Transfer Syntax (when present) of the + * current document (it internally handles reading the + * value from disk when only parsing occured). + * @return The encountered Transfer Syntax of the current document. */ -bool Document::IsGivenTransferSyntax(std::string const & syntaxToCheck) +TransferSyntaxType Document::GetTransferSyntax() { DocEntry *entry = GetDocEntryByNumber(0x0002, 0x0010); if ( !entry ) { - return false; + return UnknownTS; } // The entry might be present but not loaded (parsing and loading @@ -317,127 +321,32 @@ bool Document::IsGivenTransferSyntax(std::string const & syntaxToCheck) // The actual transfer (as read from disk) might be padded. We // first need to remove the potential padding. We can make the // weak assumption that padding was not executed with digits... - if ( transfer.length() == 0 ) { // for brain damaged headers - return false; + if ( transfer.length() == 0 ) + { + // for brain damaged headers + return UnknownTS; } - while ( ! isdigit(transfer[transfer.length()-1]) ) + while ( !isdigit((unsigned char)transfer[transfer.length()-1]) ) { transfer.erase(transfer.length()-1, 1); } - if ( transfer == syntaxToCheck ) + for (int i = 0; TransferSyntaxStrings[i] != NULL; i++) { - return true; + if ( TransferSyntaxStrings[i] == transfer ) + { + return TransferSyntaxType(i); + } } } - return false; -} - -/** - * \brief Determines if the Transfer Syntax of the present document - * corresponds to a Implicit Value Representation of - * Little Endian. - * \sa \ref Document::IsGivenTransferSyntax. - * @return True when ImplicitVRLittleEndian found. False in all other cases. - */ -bool Document::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 Document::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 Document::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 Document::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 Document::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 Document::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 Document::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 Document::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 Document::IsRLELossLessTransferSyntax() -{ - return IsGivenTransferSyntax(UI1_2_840_10008_1_2_5); + return UnknownTS; } -/** - * \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 Document::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) ); + TransferSyntaxType r = GetTransferSyntax(); + return r == JPEGFullProgressionProcess10_12 + || r == JPEGLosslessProcess14 + || r == JPEGLosslessProcess14_1; } /** @@ -448,8 +357,8 @@ bool Document::IsJPEGLossless() */ bool Document::IsJPEG2000() { - return ( IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_90) - || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_91) ); + TransferSyntaxType r = GetTransferSyntax(); + return r == JPEG2000Lossless || r == JPEG2000; } /** @@ -457,26 +366,26 @@ bool Document::IsJPEG2000() * of Jpeg encoded Pixel data. * @return True when any form of JPEG found. False otherwise. */ -bool Document::IsJPEGTransferSyntax() +bool Document::IsJPEG() { - return ( IsJPEGBaseLineProcess1TransferSyntax() - || IsJPEGExtendedProcess2_4TransferSyntax() - || IsJPEGExtendedProcess3_5TransferSyntax() - || IsJPEGSpectralSelectionProcess6_8TransferSyntax() - || IsJPEGLossless() - || IsJPEG2000() ); + TransferSyntaxType r = GetTransferSyntax(); + return r == JPEGBaselineProcess1 + || r == JPEGExtendedProcess2_4 + || r == JPEGExtendedProcess3_5 + || r == JPEGSpectralSelectionProcess6_8 + || IsJPEGLossless() + || IsJPEG2000(); } - /** * \brief Determines if the Transfer Syntax corresponds to encapsulated * of encoded Pixel Data (as opposed to native). * @return True when encapsulated. False when native. */ -bool Document::IsEncapsulateTransferSyntax() +bool Document::IsEncapsulate() { - return ( IsJPEGTransferSyntax() - || IsRLELossLessTransferSyntax() ); + TransferSyntaxType r = GetTransferSyntax(); + return IsJPEG() || r == RLELossless; } /** @@ -507,37 +416,64 @@ FileType Document::GetFileType() * checks the preamble when existing. * @return The FILE pointer on success. */ -FILE* Document::OpenFile() +std::ifstream* Document::OpenFile() { - Fp = fopen(Filename.c_str(),"rb"); + if (Filename.length() == 0) + { + return 0; + } + + if(Fp) + { + dbg.Verbose( 0, + "Document::OpenFile is already opened when opening: ", + Filename.c_str()); + } - if(!Fp) + Fp = new std::ifstream(Filename.c_str(), std::ios::in | std::ios::binary); + if( ! *Fp ) { dbg.Verbose( 0, "Document::OpenFile cannot open file: ", Filename.c_str()); + delete Fp; + Fp = 0; return 0; } uint16_t zero; - fread(&zero, (size_t)2, (size_t)1, Fp); + Fp->read((char*)&zero, (size_t)2); + if( Fp->eof() ) + { + CloseFile(); + return 0; + } - //ACR -- or DICOM with no Preamble -- - if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200 ) + //ACR -- or DICOM with no Preamble; may start with a Shadow Group -- + if( + zero == 0x0001 || zero == 0x0100 || zero == 0x0002 || zero == 0x0200 || + zero == 0x0003 || zero == 0x0300 || zero == 0x0004 || zero == 0x0400 || + zero == 0x0005 || zero == 0x0500 || zero == 0x0006 || zero == 0x0600 || + zero == 0x0007 || zero == 0x0700 || zero == 0x0008 || zero == 0x0800 ) { return Fp; } //DICOM - fseek(Fp, 126L, SEEK_CUR); + Fp->seekg(126L, std::ios::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 ) { return Fp; } - fclose(Fp); + CloseFile(); dbg.Verbose( 0, "Document::OpenFile not DICOM/ACR (missing preamble)", Filename.c_str()); @@ -551,10 +487,14 @@ FILE* Document::OpenFile() */ 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 ? } /** @@ -564,39 +504,22 @@ bool Document::CloseFile() * (ACR-NEMA, ExplicitVR, ImplicitVR) * \return Always true. */ -void Document::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) Header - if (filetype == ImplicitVR) + 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 == ExplicitVR) - { - 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 @@ -609,8 +532,7 @@ void Document::Write(FILE* fp,FileType filetype) * UpdateGroupLength(true,ACR); */ - ElementSet::Write(fp, filetype); // This one is recursive - + ElementSet::WriteContent(fp, filetype); // This one is recursive } /** @@ -619,7 +541,7 @@ void Document::Write(FILE* fp,FileType filetype) * @param value (string) Value to be set * @param group Group number of the Entry * @param elem Element number of the Entry - * @param VR V(alue) R(epresentation) of the Entry -if private Entry- + * @param vr V(alue) R(epresentation) of the Entry -if private Entry- * \return pointer to the modified/created Header Entry (NULL when creation * failed). */ @@ -627,7 +549,7 @@ ValEntry* Document::ReplaceOrCreateByNumber( std::string const & value, uint16_t group, uint16_t elem, - std::string const & VR ) + TagName const & vr ) { ValEntry* valEntry = 0; DocEntry* currentEntry = GetDocEntryByNumber( group, elem); @@ -643,7 +565,7 @@ ValEntry* Document::ReplaceOrCreateByNumber( DictEntry* dictEntry = pubDict->GetDictEntryByNumber(group, elem); if (!dictEntry) { - currentEntry = NewDocEntryByNumber(group, elem,VR); + currentEntry = NewDocEntryByNumber(group, elem, vr); } else { @@ -656,11 +578,16 @@ ValEntry* Document::ReplaceOrCreateByNumber( " NewDocEntryByNumber failed."); return NULL; } + valEntry = new ValEntry(currentEntry); + delete currentEntry; + if ( !AddEntry(valEntry)) { + delete valEntry; dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry" " failed allthough this is a creation."); + return NULL; } } else @@ -674,12 +601,14 @@ ValEntry* Document::ReplaceOrCreateByNumber( valEntry = new ValEntry(currentEntry); if (!RemoveEntry(currentEntry)) { + delete valEntry; dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: removal" " of previous DocEntry failed."); return NULL; } if ( !AddEntry(valEntry)) { + delete valEntry; dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: adding" " promoted ValEntry failed."); return NULL; @@ -695,6 +624,7 @@ ValEntry* Document::ReplaceOrCreateByNumber( /* * \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 @@ -706,7 +636,7 @@ BinEntry* Document::ReplaceOrCreateByNumber( int lgth, uint16_t group, uint16_t elem, - std::string const& VR ) + TagName const & vr ) { BinEntry* binEntry = 0; DocEntry* currentEntry = GetDocEntryByNumber( group, elem); @@ -723,7 +653,7 @@ BinEntry* Document::ReplaceOrCreateByNumber( if (!dictEntry) { - currentEntry = NewDocEntryByNumber(group, elem, VR); + currentEntry = NewDocEntryByNumber(group, elem, vr); } else { @@ -741,6 +671,7 @@ BinEntry* Document::ReplaceOrCreateByNumber( dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry" " failed allthough this is a creation."); } + delete currentEntry; } else { @@ -766,7 +697,23 @@ BinEntry* Document::ReplaceOrCreateByNumber( } } - SetEntryByNumber(binArea, lgth, group, elem); + uint8_t *tmpArea; + if (lgth>0 && binArea) + { + tmpArea = new uint8_t[lgth]; + memcpy(tmpArea,binArea,lgth); + } + else + { + tmpArea = 0; + } + if (!SetEntryByNumber(tmpArea, lgth, group, elem)) + { + if (tmpArea) + { + delete[] tmpArea; + } + } return binEntry; } @@ -780,9 +727,7 @@ BinEntry* Document::ReplaceOrCreateByNumber( * \return pointer to the modified/created SeqEntry (NULL when creation * failed). */ -SeqEntry* Document::ReplaceOrCreateByNumber( - uint16_t group, - uint16_t elem) +SeqEntry* Document::ReplaceOrCreateByNumber( uint16_t group, uint16_t elem) { SeqEntry* b = 0; DocEntry* a = GetDocEntryByNumber( group, elem); @@ -809,13 +754,18 @@ SeqEntry* Document::ReplaceOrCreateByNumber( * \return boolean */ bool Document::ReplaceIfExistByNumber(std::string const & value, - uint16_t group, uint16_t elem ) + uint16_t group, uint16_t elem ) { SetEntryByNumber(value, group, elem); return true; } +std::string Document::GetTransferSyntaxValue(TransferSyntaxType type) +{ + return TransferSyntaxStrings[type]; +} + //----------------------------------------------------------------------------- // Protected @@ -828,7 +778,7 @@ bool Document::ReplaceIfExistByNumber(std::string const & value, bool Document::CheckIfEntryExistByNumber(uint16_t group, uint16_t element ) { const std::string &key = DictEntry::TranslateToKey(group, element ); - return TagHT.count(key); + return TagHT.count(key) != 0; } /** @@ -840,7 +790,7 @@ bool Document::CheckIfEntryExistByNumber(uint16_t group, uint16_t element ) * @return Corresponding element value when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string Document::GetEntryByName(TagName const& tagName) +std::string Document::GetEntryByName(TagName const & tagName) { DictEntry* dictEntry = RefPubDict->GetDictEntryByName(tagName); if( !dictEntry ) @@ -873,7 +823,7 @@ std::string Document::GetEntryVRByName(TagName const& tagName) } DocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(), - dictEntry->GetElement()); + dictEntry->GetElement()); return elem->GetVR(); } @@ -889,7 +839,6 @@ std::string Document::GetEntryVRByName(TagName const& tagName) std::string Document::GetEntryByNumber(uint16_t group, uint16_t element) { TagKey key = DictEntry::TranslateToKey(group, element); - /// \todo use map methods, instead of multimap JPR if ( !TagHT.count(key)) { return GDCM_UNFOUND; @@ -945,7 +894,8 @@ int Document::GetEntryLengthByNumber(uint16_t group, uint16_t element) * @param tagName name of the searched Dicom Element. * @return true when found */ -bool Document::SetEntryByName(std::string const & content,std::string const & tagName) +bool Document::SetEntryByName( std::string const & content, + TagName const & tagName) { DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( !dictEntry ) @@ -966,12 +916,8 @@ bool Document::SetEntryByName(std::string const & content,std::string const & ta * @param element element number of the Dicom Element to modify */ bool Document::SetEntryByNumber(std::string const& content, - uint16_t group, - uint16_t element) + uint16_t group, uint16_t element) { - int c; - int l; - ValEntry* valEntry = GetValEntryByNumber(group, element); if (!valEntry ) { @@ -980,33 +926,7 @@ bool Document::SetEntryByNumber(std::string const& content, 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 - { - VRKey vr = valEntry->GetVR(); - if( vr == "US" || vr == "SS" ) - { - // for multivaluated items - c = Util::CountSubstring(content, "\\") + 1; - l = c*2; - } - else if( vr == "UL" || vr == "SL" ) - { - // for multivaluated items - c = Util::CountSubstring(content, "\\") + 1; - l = c*4;; - } - } - valEntry->SetLength(l); + valEntry->SetValue(content); return true; } @@ -1019,10 +939,8 @@ bool Document::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 Document::SetEntryByNumber(uint8_t*content, - int lgth, - uint16_t group, - uint16_t element) +bool Document::SetEntryByNumber(uint8_t*content, int lgth, + uint16_t group, uint16_t element) { (void)lgth; //not used TagKey key = DictEntry::TranslateToKey(group, element); @@ -1038,62 +956,14 @@ bool Document::SetEntryByNumber(uint8_t*content, //content = content + '\0'; // fing a trick to enlarge a binary field? } */ - BinEntry* a = (BinEntry *)TagHT[key]; - a->SetBinArea(content); - a->SetLength(lgth); - a->SetValue(GDCM_BINLOADED); + BinEntry* entry = (BinEntry *)TagHT[key]; + entry->SetBinArea(content); + entry->SetLength(lgth); + entry->SetValue(GDCM_BINLOADED); return true; } -/** - * \brief Accesses an existing DocEntry (i.e. a Dicom Element) - * in the PubDocEntrySet of this instance - * through it's (group, element) and modifies it's length with - * the given value. - * \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. - */ -bool Document::SetEntryLengthByNumber(uint32_t l, - uint16_t group, - uint16_t element) -{ - /// \todo use map methods, instead of multimap JPR - TagKey key = DictEntry::TranslateToKey(group, element); - if ( !TagHT.count(key) ) - { - return false; - } - if ( l % 2 ) - { - l++; // length must be even - } - ( ((TagHT.equal_range(key)).first)->second )->SetLength(l); - - return true ; -} - -/** - * \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 - */ -size_t Document::GetEntryOffsetByNumber(uint16_t group, uint16_t elem) -{ - DocEntry* entry = GetDocEntryByNumber(group, elem); - if (!entry) - { - dbg.Verbose(1, "Document::GetDocEntryByNumber: no entry present."); - return 0; - } - return entry->GetOffset(); -} - /** * \brief Gets (from Header) a 'non string' element value * (LoadElementValues has already be executed) @@ -1109,7 +979,12 @@ void* Document::GetEntryBinAreaByNumber(uint16_t group, uint16_t elem) dbg.Verbose(1, "Document::GetDocEntryByNumber: no entry"); return 0; } - return ((BinEntry *)entry)->GetBinArea(); + if ( BinEntry* binEntry = dynamic_cast(entry) ) + { + return binEntry->GetBinArea(); + } + + return 0; } /** @@ -1118,61 +993,57 @@ void* Document::GetEntryBinAreaByNumber(uint16_t group, uint16_t elem) * @param group group number of the Entry * @param elem element number of the Entry */ -void* Document::LoadEntryBinArea(uint16_t group, uint16_t elem) +void Document::LoadEntryBinArea(uint16_t group, uint16_t elem) { + // Search the corresponding DocEntry DocEntry *docElement = GetDocEntryByNumber(group, elem); if ( !docElement ) - { - return NULL; - } - size_t o =(size_t)docElement->GetOffset(); - fseek(Fp, o, SEEK_SET); - size_t l = docElement->GetLength(); - uint8_t* a = new uint8_t[l]; - if(!a) - { - dbg.Verbose(0, "Document::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, "Document::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* Document::LoadEntryBinArea(BinEntry* 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]; if( !a ) { dbg.Verbose(0, "Document::LoadEntryBinArea cannot allocate a"); - return NULL; + 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()) //Fp->gcount() == 1 { delete[] a; - return NULL; + return; } - return a; + element->SetBinArea(a); + + if(openFile) + CloseFile(); } /** @@ -1182,22 +1053,23 @@ void* Document::LoadEntryBinArea(BinEntry* element) * @param element Element number of the searched Dicom Element * @return */ -bool Document::SetEntryBinAreaByNumber(uint8_t* area, - uint16_t group, - uint16_t element) +/*bool Document::SetEntryBinAreaByNumber(uint8_t* area, + uint16_t group, uint16_t element) { DocEntry* currentEntry = GetDocEntryByNumber(group, element); if ( !currentEntry ) { return false; } + if ( BinEntry* binEntry = dynamic_cast(currentEntry) ) { binEntry->SetBinArea( area ); return true; } - return true; -} + + return false; +}*/ /** * \brief Update the entries with the shadow dictionary. @@ -1254,7 +1126,7 @@ void Document::UpdateShaEntries() * @return Corresponding Dicom Element when it exists, and NULL * otherwise. */ -DocEntry* Document::GetDocEntryByName(std::string const & tagName) +DocEntry* Document::GetDocEntryByName(TagName const & tagName) { DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( !dictEntry ) @@ -1275,8 +1147,7 @@ DocEntry* Document::GetDocEntryByName(std::string const & tagName) * @param element Element number of the searched Dicom Element * @return */ -DocEntry* Document::GetDocEntryByNumber(uint16_t group, - uint16_t element) +DocEntry* Document::GetDocEntryByNumber(uint16_t group, uint16_t element) { TagKey key = DictEntry::TranslateToKey(group, element); if ( !TagHT.count(key)) @@ -1292,8 +1163,7 @@ DocEntry* Document::GetDocEntryByNumber(uint16_t group, * ValEntry. * @return When present, the corresponding ValEntry. */ -ValEntry* Document::GetValEntryByNumber(uint16_t group, - uint16_t element) +ValEntry* Document::GetValEntryByNumber(uint16_t group, uint16_t element) { DocEntry* currentEntry = GetDocEntryByNumber(group, element); if ( !currentEntry ) @@ -1318,9 +1188,12 @@ ValEntry* Document::GetValEntryByNumber(uint16_t group, */ 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); + } } /** @@ -1393,16 +1266,14 @@ uint16_t Document::UnswapShort(uint16_t a) * \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries) * @return length of the parsed set. */ -void Document::ParseDES(DocEntrySet *set, - long offset, - long l_max, - bool delim_mode) +void Document::ParseDES(DocEntrySet *set, long offset, + long l_max, bool delim_mode) { DocEntry *newDocEntry = 0; - + while (true) - { - if ( !delim_mode && (ftell(Fp)-offset) >= l_max) + { + if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { break; } @@ -1420,7 +1291,7 @@ void Document::ParseDES(DocEntrySet *set, { /////////////////////// ValEntry ValEntry* newValEntry = - new ValEntry( newDocEntry->GetDictEntry() ); + new ValEntry( newDocEntry->GetDictEntry() ); //LEAK newValEntry->Copy( newDocEntry ); // When "set" is a Document, then we are at the top of the @@ -1439,14 +1310,22 @@ void Document::ParseDES(DocEntrySet *set, + newValEntry->GetKey() ); } - set->AddEntry( newValEntry ); LoadDocEntry( newValEntry ); - if (newValEntry->IsItemDelimitor()) + bool delimitor=newValEntry->IsItemDelimitor(); + if( !set->AddEntry( newValEntry ) ) { + // If here expect big troubles + delete newValEntry; //otherwise mem leak + } + + if (delimitor) + { + delete newDocEntry; break; } - if ( !delim_mode && (ftell(Fp)-offset) >= l_max) + if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { + delete newDocEntry; break; } } @@ -1460,9 +1339,7 @@ void Document::ParseDES(DocEntrySet *set, } //////////////////// BinEntry or UNKOWN VR: - BinEntry* newBinEntry = - new BinEntry( newDocEntry->GetDictEntry() ); - newBinEntry->Copy( newDocEntry ); + BinEntry* newBinEntry = new BinEntry( newDocEntry ); //LEAK // When "this" is a Document the Key is simply of the // form ( group, elem )... @@ -1480,32 +1357,37 @@ void Document::ParseDES(DocEntrySet *set, + newBinEntry->GetKey() ); } - set->AddEntry( newBinEntry ); LoadDocEntry( newBinEntry ); + if( !set->AddEntry( newBinEntry ) ) + { + //Expect big troubles if here + delete newBinEntry; + } } if ( ( newDocEntry->GetGroup() == 0x7fe0 ) && ( newDocEntry->GetElement() == 0x0010 ) ) { - if ( IsRLELossLessTransferSyntax() ) + TransferSyntaxType ts = GetTransferSyntax(); + if ( ts == RLELossless ) { - 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 - if ( IsJPEGTransferSyntax() ) + else if ( IsJPEG() ) { - long PositionOnEntry = ftell(Fp); - fseek( Fp, newDocEntry->GetOffset(), SEEK_SET ); + long PositionOnEntry = Fp->tellg(); + Fp->seekg( newDocEntry->GetOffset(), std::ios::beg ); ComputeJPEGFragmentInfo(); - fseek( Fp, PositionOnEntry, SEEK_SET ); + Fp->seekg( PositionOnEntry, std::ios::beg ); } } // Just to make sure we are at the beginning of next entry. SkipToNextDocEntry(newDocEntry); + //delete newDocEntry; } else { @@ -1555,8 +1437,9 @@ void Document::ParseDES(DocEntrySet *set, l, delim_mode); } set->AddEntry( newSeqEntry ); - if ( !delim_mode && (ftell(Fp)-offset) >= l_max) + if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { + delete newDocEntry; break; } } @@ -1569,7 +1452,7 @@ void Document::ParseDES(DocEntrySet *set, * @return parsed length for this level */ void Document::ParseSQ( SeqEntry* seqEntry, - long offset, long l_max, bool delim_mode) + long offset, long l_max, bool delim_mode) { int SQItemNumber = 0; bool dlm_mod; @@ -1586,13 +1469,14 @@ void Document::ParseSQ( SeqEntry* 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; } SQItem *itemSQ = new SQItem( seqEntry->GetDepthLevel() ); @@ -1614,10 +1498,11 @@ void Document::ParseSQ( SeqEntry* 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; } @@ -1631,12 +1516,11 @@ void Document::ParseSQ( SeqEntry* seqEntry, */ 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 @@ -1671,7 +1555,7 @@ void Document::LoadDocEntry(DocEntry* entry) s << " x(" << std::hex << entry->GetLength() << ")"; binEntryPtr->SetValue(s.str()); } - // Be carefull : a BinEntry IS_A ValEntry ... + // Be carefull : a BinEntry IS_A ValEntry ... else if (ValEntry* valEntryPtr = dynamic_cast< ValEntry* >(entry) ) { // s << "gdcm::NotLoaded. (ValEntry)"; @@ -1689,7 +1573,8 @@ void Document::LoadDocEntry(DocEntry* entry) } // to be sure we are at the end of the value ... - fseek(Fp,(long)entry->GetOffset()+(long)entry->GetLength(),SEEK_SET); + Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(), + std::ios::beg); return; } @@ -1751,18 +1636,29 @@ void Document::LoadDocEntry(DocEntry* entry) return; } - // We need an additional byte for storing \0 that is not on disk - //std::string newValue(length,0); - //item_read = fread(&(newValue[0]), (size_t)length, (size_t)1, Fp); - //rah !! I can't believe it could work, normally this is a const char* !!! + // FIXME: We need an additional byte for storing \0 that is not on disk char *str = new char[length+1]; - item_read = fread(str, (size_t)length, (size_t)1, Fp); - str[length] = '\0'; - std::string newValue = str; + Fp->read(str, (size_t)length); + str[length] = '\0'; //this is only useful when length is odd + // Special DicomString call to properly handle \0 and even length + std::string newValue; + if( length % 2 ) + { + newValue = Util::DicomString(str, length+1); + //dbg.Verbose(0, "Warning: bad length: ", length ); + dbg.Verbose(0, "For string :", newValue.c_str()); + // Since we change the length of string update it length + entry->SetReadLength(length+1); + } + else + { + newValue = Util::DicomString(str, length); + } delete[] str; + if ( ValEntry* valEntry = dynamic_cast(entry) ) - { - if ( item_read != 1 ) + { + if ( Fp->fail() || Fp->eof())//Fp->gcount() == 1 { dbg.Verbose(1, "Document::LoadDocEntry", "unread element value"); @@ -1806,7 +1702,7 @@ void Document::FindDocEntryLength( DocEntry *entry ) // 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 ) @@ -1825,10 +1721,10 @@ void Document::FindDocEntryLength( DocEntry *entry ) // 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->SetLength(lengthUntilEOF); return; } @@ -1871,7 +1767,8 @@ void Document::FindDocEntryLength( DocEntry *entry ) // big endian and proceed... if ( element == 0x0000 && length16 == 0x0400 ) { - if ( !IsExplicitVRBigEndianTransferSyntax() ) + TransferSyntaxType ts = GetTransferSyntax(); + if ( ts != ExplicitVRBigEndian ) { throw FormatError( "Document::FindDocEntryLength()", " not explicit VR." ); @@ -1931,7 +1828,7 @@ void Document::FindDocEntryVR( DocEntry *entry ) char vr[3]; - long positionOnEntry = ftell(Fp); + long positionOnEntry = Fp->tellg(); // Warning: we believe this is explicit VR (Value Representation) because // we used a heuristic that found "UL" in the first tag. Alas this // doesn't guarantee that all the tags will be in explicit VR. In some @@ -1939,13 +1836,12 @@ void Document::FindDocEntryVR( DocEntry *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); + Fp->read (vr, (size_t)2); vr[2] = 0; if( !CheckDocEntryVR(entry, vr) ) { - fseek(Fp, positionOnEntry, SEEK_SET); + Fp->seekg(positionOnEntry, std::ios::beg); // When this element is known in the dictionary we shall use, e.g. for // the semantics (see the usage of IsAnInteger), the VR proposed by the // dictionary entry. Still we have to flag the element as implicit since @@ -1981,7 +1877,7 @@ bool Document::CheckDocEntryVR(DocEntry *entry, VRKey vr) // expected VR read happens to be non-ascii characters we consider // we hit falsely explicit VR tag. - if ( !isalpha(vr[0]) && !isalpha(vr[1]) ) + if ( !isalpha((unsigned char)vr[0]) && !isalpha((unsigned char)vr[1]) ) { realExplicit = false; } @@ -2190,8 +2086,8 @@ void Document::SkipDocEntry(DocEntry *entry) */ void Document::SkipToNextDocEntry(DocEntry *entry) { - fseek(Fp, (long)(entry->GetOffset()), SEEK_SET); - fseek(Fp, (long)(entry->GetReadLength()), SEEK_CUR); + Fp->seekg((long)(entry->GetOffset()), std::ios::beg); + Fp->seekg( (long)(entry->GetReadLength()), std::ios::cur); } /** @@ -2202,7 +2098,7 @@ void Document::SkipToNextDocEntry(DocEntry *entry) * @param foundLength fist assumption about length */ void Document::FixDocEntryFoundLength(DocEntry *entry, - uint32_t foundLength) + uint32_t foundLength) { entry->SetReadLength( foundLength ); // will be updated only if a bug is found if ( foundLength == 0xffffffff) @@ -2284,7 +2180,7 @@ bool Document::IsDocEntryAnInteger(DocEntry *entry) { uint16_t element = entry->GetElement(); uint16_t group = entry->GetGroup(); - std::string vr = entry->GetVR(); + const std::string & vr = entry->GetVR(); uint32_t length = entry->GetLength(); // When we have some semantics on the element we just read, and if we @@ -2306,7 +2202,7 @@ bool Document::IsDocEntryAnInteger(DocEntry *entry) // encounter such an ill-formed image, we simply display a warning // message and proceed on parsing (while crossing fingers). std::ostringstream s; - int filePosition = ftell(Fp); + long filePosition = Fp->tellg(); s << "Erroneous Group Length element length on : (" \ << std::hex << group << " , " << element << ") -before- position x(" << filePosition << ")" @@ -2333,7 +2229,7 @@ uint32_t Document::FindDocEntryLengthOB() throw( FormatUnexpected ) { // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data. - long positionOnEntry = ftell(Fp); + long positionOnEntry = Fp->tellg(); bool foundSequenceDelimiter = false; uint32_t totalLength = 0; @@ -2359,7 +2255,7 @@ uint32_t Document::FindDocEntryLengthOB() { dbg.Verbose(1, "Document::FindDocEntryLengthOB: neither an Item " "tag nor a Sequence delimiter tag."); - fseek(Fp, positionOnEntry, SEEK_SET); + Fp->seekg(positionOnEntry, std::ios::beg); throw FormatUnexpected("Document::FindDocEntryLengthOB()", "Neither an Item tag nor a Sequence " "delimiter tag."); @@ -2380,7 +2276,7 @@ uint32_t Document::FindDocEntryLengthOB() break; } } - fseek(Fp, positionOnEntry, SEEK_SET); + Fp->seekg( positionOnEntry, std::ios::beg); return totalLength; } @@ -2393,13 +2289,13 @@ 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() ) + { + throw FormatError( "Document::ReadInt16()", " file error." ); + } + if( Fp->eof() ) { - if( ferror(Fp) ) - { - throw FormatError( "Document::ReadInt16()", " file error." ); - } throw FormatError( "Document::ReadInt16()", "EOF." ); } g = SwapShort(g); @@ -2415,13 +2311,13 @@ 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() ) + { + throw FormatError( "Document::ReadInt32()", " file error." ); + } + if( Fp->eof() ) { - if( ferror(Fp) ) - { - throw FormatError( "Document::ReadInt16()", " file error." ); - } throw FormatError( "Document::ReadInt32()", "EOF." ); } g = SwapLong(g); @@ -2436,7 +2332,7 @@ uint32_t Document::ReadInt32() 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); } /** @@ -2447,6 +2343,9 @@ void Document::Initialise() { RefPubDict = Global::GetDicts()->GetDefaultPubDict(); RefShaDict = NULL; + RLEInfo = new RLEFramesInfo; + JPEGInfo = new JPEGFragmentsInfo; + Filetype = Unknown; } /** @@ -2469,7 +2368,7 @@ bool Document::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). @@ -2484,8 +2383,7 @@ bool Document::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 ) @@ -2549,8 +2447,8 @@ bool Document::CheckSwap() // 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 @@ -2558,7 +2456,7 @@ bool Document::CheckSwap() // preamble. We can reset the file position indicator to where the data // is (i.e. the beginning of the file). dbg.Verbose(1, "Document::CheckSwap:", "not a DICOM Version3 file"); - rewind(Fp); + 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. @@ -2570,7 +2468,7 @@ bool Document::CheckSwap() // representation of a 32 bits integer. Hence the following dirty // trick : s32 = *((uint32_t *)(entCur)); - + switch( s32 ) { case 0x00040000 : @@ -2595,13 +2493,13 @@ bool Document::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... @@ -2609,22 +2507,32 @@ bool Document::CheckSwap() switch ( s16 ) { + case 0x0001 : case 0x0002 : + case 0x0003 : case 0x0004 : - case 0x0008 : + case 0x0005 : + case 0x0006 : + case 0x0007 : + case 0x0008 : SwapCode = 0; 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 = ACR; return true; default : dbg.Verbose(0, "Document::CheckSwap:", - "ACR/NEMA unfound swap info (Really hopeless !)"); - Filetype = Unknown; + "ACR/NEMA unfound swap info (Really hopeless !)"); + Filetype = Unknown; return false; } // Then the only info we have is the net2host one. @@ -2636,6 +2544,8 @@ bool Document::CheckSwap() } } + + /** * \brief Restore the unproperly loaded values i.e. the group, the element * and the dictionary entry depending on them. @@ -2703,6 +2613,35 @@ void Document::SetMaxSizePrintEntry(long newSize) +/** + * \brief Handle broken private tag from Philips NTSCAN + * where the endianess is being switch to BigEndian for no + * apparent reason + * @return no return + */ +void Document::HandleBrokenEndian(uint16_t group, uint16_t elem) +{ + // Endian reversion. Some files contain groups of tags with reversed endianess. + static int reversedEndian = 0; + // try to fix endian switching in the middle of headers + if ((group == 0xfeff) && (elem == 0x00e0)) + { + // start endian swap mark for group found + reversedEndian++; + SwitchSwapToBigEndian(); + // fix the tag + group = 0xfffe; + elem = 0xe000; + } + else if ((group == 0xfffe) && (elem == 0xe00d) && reversedEndian) + { + // end of reversed endian group + reversedEndian--; + SwitchSwapToBigEndian(); + } + +} + /** * \brief Read the next tag but WITHOUT loading it's value * (read the 'Group Number', the 'Element Number', @@ -2728,6 +2667,7 @@ DocEntry* Document::ReadNextDocEntry() return 0; } + HandleBrokenEndian(group, elem); DocEntry *newEntry = NewDocEntryByNumber(group, elem); FindDocEntryVR(newEntry); @@ -2743,7 +2683,7 @@ DocEntry* Document::ReadNextDocEntry() return 0; } - newEntry->SetOffset(ftell(Fp)); + newEntry->SetOffset(Fp->tellg()); return newEntry; } @@ -2783,13 +2723,23 @@ uint32_t Document::GenerateFreeTagKeyInGroup(uint16_t group) */ 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; @@ -2801,7 +2751,7 @@ bool Document::ReadTag(uint16_t testGroup, uint16_t testElement) s << " at address: " << (unsigned)currentPosition << std::endl; dbg.Verbose(0, "Document::ReadItemTagLength: wrong Item Tag found:"); dbg.Verbose(0, s.str().c_str()); - fseek(Fp, positionOnEntry, SEEK_SET); + Fp->seekg(positionOnEntry, std::ios::beg); return false; } @@ -2824,7 +2774,7 @@ bool Document::ReadTag(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) ) @@ -2833,7 +2783,7 @@ uint32_t Document::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; @@ -2863,7 +2813,7 @@ void Document::ReadAndSkipEncapsulatedBasicOffsetTable() if ( itemLength != 0 ) { char* basicOffsetTableItemValue = new char[itemLength + 1]; - fread(basicOffsetTableItemValue, itemLength, 1, Fp); + Fp->read(basicOffsetTableItemValue, itemLength); #ifdef GDCM_DEBUG for (unsigned int i=0; i < itemLength; i += 4 ) @@ -2890,7 +2840,8 @@ void Document::ReadAndSkipEncapsulatedBasicOffsetTable() */ void Document::ComputeRLEInfo() { - if ( ! IsRLELossLessTransferSyntax() ) + TransferSyntaxType ts = GetTransferSyntax(); + if ( ts != RLELossless ) { return; } @@ -2925,11 +2876,16 @@ void Document::ComputeRLEInfo() // 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) + dbg.Verbose(0, "Document::ComputeRLEInfo: too many segments."); + } - uint32_t rleSegmentOffsetTable[15]; + uint32_t rleSegmentOffsetTable[16]; for( int k = 1; k <= 15; k++ ) { rleSegmentOffsetTable[k] = ReadInt32(); @@ -2962,7 +2918,7 @@ void Document::ComputeRLEInfo() 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 @@ -2983,7 +2939,7 @@ void Document::ComputeRLEInfo() void Document::ComputeJPEGFragmentInfo() { // If you need to, look for comments of ComputeRLEInfo(). - if ( ! IsJPEGTransferSyntax() ) + if ( ! IsJPEG() ) { return; } @@ -2995,13 +2951,13 @@ void Document::ComputeJPEGFragmentInfo() long fragmentLength; while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) ) { - long fragmentOffset = ftell(Fp); + long fragmentOffset = Fp->tellg(); // Store the collected info JPEGFragment* newFragment = new JPEGFragment; newFragment->Offset = fragmentOffset; newFragment->Length = fragmentLength; - JPEGInfo.Fragments.push_back( newFragment ); + JPEGInfo->Fragments.push_back( newFragment ); SkipBytes( fragmentLength ); } @@ -3025,19 +2981,19 @@ void Document::ComputeJPEGFragmentInfo() * @param set The structure to be traversed (recursively). */ void Document::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT, - DocEntrySet* set ) + DocEntrySet* set ) { if (ElementSet* elementSet = dynamic_cast< ElementSet* > ( set ) ) { - TagDocEntryHT* currentHT = elementSet->GetTagHT(); - for( TagDocEntryHT::const_iterator i = currentHT->begin(); - i != currentHT->end(); + TagDocEntryHT const & currentHT = elementSet->GetTagHT(); + for( TagDocEntryHT::const_iterator i = currentHT.begin(); + i != currentHT.end(); ++i) { DocEntry* entry = i->second; if ( SeqEntry* seqEntry = dynamic_cast(entry) ) { - ListSQItem& items = seqEntry->GetSQItems(); + const ListSQItem& items = seqEntry->GetSQItems(); for( ListSQItem::const_iterator item = items.begin(); item != items.end(); ++item) @@ -3053,15 +3009,15 @@ void Document::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT, 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) { 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) @@ -3081,7 +3037,7 @@ void Document::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT, * Document. * * The structure used by a Document (through \ref ElementSet), - * in order to old the parsed entries of a Dicom header, is a recursive + * in order to hold the parsed entries of a Dicom header, is a recursive * one. This is due to the fact that the sequences (when present) * can be nested. Additionaly, the sequence items (represented in * gdcm as \ref SQItem) add an extra complexity to the data