X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=a8b156974a0786e52f97150d9a9203145f60102b;hb=5bf7c51796867388334836847a6874640bc83f89;hp=7476b4b0aeabbb27836db6a8a80650092f0c568c;hpb=75262e67ec39ad2f359c1efbf9ee805819a8e58a;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 7476b4b0..a8b15697 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -1,16 +1,29 @@ -// gdcmDocument.cxx -//----------------------------------------------------------------------------- +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmDocument.cxx,v $ + Language: C++ + Date: $Date: 2004/10/20 14:30:40 $ + Version: $Revision: 1.106 $ + + Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de + l'Image). All rights reserved. See Doc/License.txt or + http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details. + + This software is distributed WITHOUT ANY WARRANTY; without even + the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR + PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ #include "gdcmDocument.h" #include "gdcmValEntry.h" #include "gdcmBinEntry.h" #include "gdcmSeqEntry.h" - #include "gdcmGlobal.h" #include "gdcmUtil.h" #include "gdcmDebug.h" -#include #include // For nthos: @@ -20,76 +33,129 @@ #include #endif -# include +#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" -#define UI1_2_840_10008_1_2_2 "1.2.840.10008.1.2.2" +// Deflated Explicit VR Little Endian #define UI1_2_840_10008_1_2_1_99 "1.2.840.10008.1.2.1.99" -#define UI1_1_2_840_10008_1_2_5 "1.2.840.10008.1.2.5" - +// 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)) //----------------------------------------------------------------------------- -// 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 = 4096; - -const unsigned int gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE = 64; +// Refer to Document::SetMaxSizeLoadEntry() +const unsigned int Document::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096 +const unsigned int Document::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff; //----------------------------------------------------------------------------- // Constructor / Destructor /** * \brief constructor - * @param inFilename file to be opened for parsing - * @param exception_on_error whether we throw an exception or not - * @param enable_sequences = true to allow the header - * to be parsed *inside* the SeQuences, - * when they have an actual length - * \warning enable_sequences *has to be* true for reading PAPYRUS 3.0 files - * @param ignore_shadow to allow skipping the shadow elements, - * to save memory space. - * \warning The TRUE value for this param has to be used - * with a FALSE value for the 'enable_sequence' param. - * ('public elements' may be embedded in 'shadow Sequences') - */ -gdcmDocument::gdcmDocument(const char *inFilename, - bool exception_on_error, - bool enable_sequences, - bool ignore_shadow) - : gdcmElementSet(-1) { - enableSequences=enable_sequences; - ignoreShadow =ignore_shadow; - + * @param filename file to be opened for parsing + */ +Document::Document( std::string const & filename ) + : ElementSet(-1) +{ SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); - filename = inFilename; + Filename = filename; Initialise(); - if ( !OpenFile(exception_on_error)) + if ( !OpenFile() ) + { return; + } + + dbg.Verbose(0, "Document::Document: starting parsing of file: ", + Filename.c_str()); + rewind(Fp); - rewind(fp); - //if (!CheckSwap()) - // return false; // to go on compiling - - fseek(fp,0L,SEEK_END); - long lgt = ftell(fp); + fseek(Fp,0L,SEEK_END); + long lgt = ftell(Fp); - rewind(fp); + rewind(Fp); CheckSwap(); - long beg = ftell(fp); + long beg = ftell(Fp); lgt -= beg; - SQDepthLevel=0; + ParseDES( this, beg, lgt, false); // le Load sera fait a la volee + + rewind(Fp); - long l=ParseDES( this, beg, lgt, false); // le Load sera fait a la volee + // Load 'non string' values + + std::string PhotometricInterpretation = GetEntryByNumber(0x0028,0x0004); + if( PhotometricInterpretation == "PALETTE COLOR " ) + { + LoadEntryBinArea(0x0028,0x1200); // gray LUT + /// FIXME FIXME FIXME + /// The tags refered by the three following lines used to be CORRECTLY + /// defined as having an US Value Representation in the public + /// dictionnary. BUT the semantics implied by the three following + /// lines state that the corresponding tag contents are in fact + /// the ones of a BinEntry. + /// In order to fix things "Quick and Dirty" the dictionnary was + /// altered on PURPOUS but now contains a WRONG value. + /// In order to fix things and restore the dictionary to its + /// correct value, one needs to decided of the semantics by deciding + /// wether the following tags are either: + /// - multivaluated US, and hence loaded as ValEntry, but afterwards + /// also used as BinEntry, which requires the proper conversion, + /// - OW, and hence loaded as BinEntry, but afterwards also used + /// as ValEntry, which requires the proper conversion. + LoadEntryBinArea(0x0028,0x1201); // R LUT + LoadEntryBinArea(0x0028,0x1202); // G LUT + LoadEntryBinArea(0x0028,0x1203); // B LUT + + // Segmented Red Palette Color LUT Data + LoadEntryBinArea(0x0028,0x1221); + // Segmented Green Palette Color LUT Data + LoadEntryBinArea(0x0028,0x1222); + // Segmented Blue Palette Color LUT Data + LoadEntryBinArea(0x0028,0x1223); + } + //FIXME later : how to use it? + LoadEntryBinArea(0x0028,0x3006); //LUT Data (CTX dependent) + CloseFile(); // -------------------------------------------------------------- - // Special Patch to allow gdcm to read ACR-LibIDO formated images + // Specific code to allow gdcm to read ACR-LibIDO formated images + // Note: ACR-LibIDO is an extension of the ACR standard that was + // used at CREATIS. For the time being (say a couple years) + // we keep this kludge to allow a smooth move to gdcm for + // CREATIS developpers (sorry folks). // // if recognition code tells us we deal with a LibIDO image // we switch lineNumber and columnNumber @@ -100,50 +166,55 @@ gdcmDocument::gdcmDocument(const char *inFilename, RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares // with "little-endian strings" { - filetype = gdcmACR_LIBIDO; + Filetype = ACR_LIBIDO; std::string rows = GetEntryByNumber(0x0028, 0x0010); std::string columns = GetEntryByNumber(0x0028, 0x0011); SetEntryByNumber(columns, 0x0028, 0x0010); SetEntryByNumber(rows , 0x0028, 0x0011); } - // ----------------- End of Special Patch ---------------- + // ----------------- End of ACR-LibIDO kludge ------------------ - printLevel = 1; // 'Medium' print level by default + PrintLevel = 1; // 'Medium' print level by default } /** - * \brief constructor - * @param exception_on_error + * \brief This default constructor doesn't parse the file. You should + * then invoke \ref Document::SetFileName and then the parsing. */ -gdcmDocument::gdcmDocument(bool exception_on_error) - :gdcmElementSet(-1) { - (void)exception_on_error; - enableSequences=0; - +Document::Document() + :ElementSet(-1) +{ SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Initialise(); - - printLevel = 1; // 'Medium' print level by default + PrintLevel = 1; // 'Medium' print level by default } /** * \brief Canonical destructor. */ -gdcmDocument::~gdcmDocument (void) { +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(); } //----------------------------------------------------------------------------- // Print -/** - /** * \brief Prints The Dict Entries of THE public Dicom Dictionary * @return */ -void gdcmDocument::PrintPubDict(std::ostream & os) { +void Document::PrintPubDict(std::ostream & os) +{ RefPubDict->Print(os); } @@ -151,7 +222,8 @@ void gdcmDocument::PrintPubDict(std::ostream & os) { * \brief Prints The Dict Entries of THE shadow Dicom Dictionary * @return */ -void gdcmDocument::PrintShaDict(std::ostream & os) { +void Document::PrintShaDict(std::ostream & os) +{ RefShaDict->Print(os); } @@ -160,90 +232,126 @@ void gdcmDocument::PrintShaDict(std::ostream & os) { /** * \brief Get the public dictionary used */ -gdcmDict *gdcmDocument::GetPubDict(void) { - return(RefPubDict); +Dict* Document::GetPubDict() +{ + return RefPubDict; } /** * \brief Get the shadow dictionary used */ -gdcmDict *gdcmDocument::GetShaDict(void) { - return(RefShaDict); +Dict* Document::GetShaDict() +{ + return RefShaDict; } /** * \brief Set the shadow dictionary used * \param dict dictionary to use in shadow */ -bool gdcmDocument::SetShaDict(gdcmDict *dict){ - RefShaDict=dict; - return(!RefShaDict); +bool Document::SetShaDict(Dict *dict) +{ + RefShaDict = dict; + return !RefShaDict; } /** * \brief Set the shadow dictionary used * \param dictName name of the dictionary to use in shadow */ -bool gdcmDocument::SetShaDict(DictKey dictName){ - RefShaDict=gdcmGlobal::GetDicts()->GetDict(dictName); - return(!RefShaDict); +bool Document::SetShaDict(DictKey const & 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(void) { - if(filetype==gdcmUnknown) { - dbg.Verbose(0, "gdcmDocument::IsReadable: wrong filetype"); - return(false); +bool Document::IsReadable() +{ + if( Filetype == Unknown) + { + dbg.Verbose(0, "Document::IsReadable: wrong filetype"); + return false; } - if(!tagHT.empty()<=0) { - std::cout << "gdcmDocument::IsReadable: wrong tagHT size : " - << tagHT.size() - <GetValue(); - if ( Transfer == UI1_2_840_10008_1_2 ) - return true; + // The entry might be present but not loaded (parsing and loading + // happen at different stages): try loading and proceed with check... + LoadDocEntrySafe(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]) ) + { + transfer.erase(transfer.length()-1, 1); + } + if ( transfer == syntaxToCheck ) + { + return true; + } + } 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 gdcmDocument::IsExplicitVRLittleEndianTransferSyntax(void) { - gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadDocEntrySafe(Element); - - std::string Transfer = ((gdcmValEntry *)Element)->GetValue(); - if ( Transfer == UI1_2_840_10008_1_2_1 ) - return true; - return false; +bool Document::IsExplicitVRLittleEndianTransferSyntax() +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1); } /** @@ -251,16 +359,9 @@ bool gdcmDocument::IsExplicitVRLittleEndianTransferSyntax(void) { * and if it corresponds to a DeflatedExplicitVRLittleEndian one. * @return True when DeflatedExplicitVRLittleEndian found. False in all other cases. */ -bool gdcmDocument::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) { - gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadDocEntrySafe(Element); - - std::string Transfer = ((gdcmValEntry *)Element)->GetValue(); - if ( Transfer == UI1_2_840_10008_1_2_1_99 ) - return true; - return false; +bool Document::IsDeflatedExplicitVRLittleEndianTransferSyntax() +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1_99); } /** @@ -268,16 +369,9 @@ bool gdcmDocument::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) { * 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(void) { - gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadDocEntrySafe(Element); - - std::string Transfer = ((gdcmValEntry *)Element)->GetValue(); - if ( Transfer == UI1_2_840_10008_1_2_2 ) //1.2.2 ??? A verifier ! - return true; - return false; +bool Document::IsExplicitVRBigEndianTransferSyntax() +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_2); } /** @@ -285,16 +379,9 @@ bool gdcmDocument::IsExplicitVRBigEndianTransferSyntax(void) { * and if it corresponds to a JPEGBaseLineProcess1 one. * @return True when JPEGBaseLineProcess1found. False in all other cases. */ -bool gdcmDocument::IsJPEGBaseLineProcess1TransferSyntax(void) { - gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadDocEntrySafe(Element); - - std::string Transfer = ((gdcmValEntry *)Element)->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.4.50" ) - return true; - return false; +bool Document::IsJPEGBaseLineProcess1TransferSyntax() +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_50); } /** @@ -302,29 +389,19 @@ bool gdcmDocument::IsJPEGBaseLineProcess1TransferSyntax(void) { * and if it corresponds to a JPEGExtendedProcess2-4 one. * @return True when JPEGExtendedProcess2-4 found. False in all other cases. */ -bool gdcmDocument::IsJPEGExtendedProcess2_4TransferSyntax(void) { - gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadDocEntrySafe(Element); - return ( ((gdcmValEntry *)Element)->GetValue() == "1.2.840.10008.1.2.4.51" -);} +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 gdcmDocument::IsJPEGExtendedProcess3_5TransferSyntax(void) { - gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadDocEntrySafe(Element); - - std::string Transfer = ((gdcmValEntry *)Element)->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.4.52" ) - return true; - return false; +bool Document::IsJPEGExtendedProcess3_5TransferSyntax() +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_52); } /** @@ -333,35 +410,20 @@ bool gdcmDocument::IsJPEGExtendedProcess3_5TransferSyntax(void) { * @return True when JPEGSpectralSelectionProcess6-8 found. False in all * other cases. */ -bool gdcmDocument::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) { - gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadDocEntrySafe(Element); - - std::string Transfer = ((gdcmValEntry *)Element)->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.4.53" ) - return true; - return false; +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 gdcmDocument::IsRLELossLessTransferSyntax(void) { - gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadDocEntrySafe(Element); - - std::string Transfer = ((gdcmValEntry *)Element)->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.5" ) { - return true; - } - return false; +bool Document::IsRLELossLessTransferSyntax() +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_5); } /** @@ -370,22 +432,12 @@ bool gdcmDocument::IsRLELossLessTransferSyntax(void) { * @return True when RLE Lossless found. False in all * other cases. */ -bool gdcmDocument::IsJPEGLossless(void) { - gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); - // faire qq chose d'intelligent a la place de ça - if ( !Element ) - return false; - LoadDocEntrySafe(Element); - - const char * Transfert = ((gdcmValEntry *)Element)->GetValue().c_str(); - - if ( memcmp(Transfert+strlen(Transfert)-2 ,"70",2)==0) return true; - if ( memcmp(Transfert+strlen(Transfert)-2 ,"55",2)==0) return true; - - if (((gdcmValEntry *)Element)->GetValue() == "1.2.840.10008.1.2.4.57") -return true; - - return false; + +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) ); } /** @@ -394,29 +446,50 @@ return true; * @return True when JPEG2000 (Lossly or LossLess) found. False in all * other cases. */ -bool gdcmDocument::IsJPEG2000(void) { - gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadDocEntrySafe(Element); - - std::string Transfer = ((gdcmValEntry *)Element)->GetValue(); - if ( (Transfer == "1.2.840.10008.1.2.4.90") - || (Transfer == "1.2.840.10008.1.2.4.91") ) - return true; - return false; +bool Document::IsJPEG2000() +{ + return ( IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_90) + || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_91) ); +} + +/** + * \brief Determines if the Transfer Syntax corresponds to any form + * of Jpeg encoded Pixel data. + * @return True when any form of JPEG found. False otherwise. + */ +bool Document::IsJPEGTransferSyntax() +{ + return ( IsJPEGBaseLineProcess1TransferSyntax() + || IsJPEGExtendedProcess2_4TransferSyntax() + || IsJPEGExtendedProcess3_5TransferSyntax() + || IsJPEGSpectralSelectionProcess6_8TransferSyntax() + || IsJPEGLossless() + || IsJPEG2000() ); +} + + +/** + * \brief Determines if the Transfer Syntax corresponds to encapsulated + * of encoded Pixel Data (as opposed to native). + * @return True when encapsulated. False when native. + */ +bool Document::IsEncapsulateTransferSyntax() +{ + return ( IsJPEGTransferSyntax() + || IsRLELossLessTransferSyntax() ); } /** * \brief Predicate for dicom version 3 file. * @return True when the file is a dicom version 3. */ -bool gdcmDocument::IsDicomV3(void) { +bool Document::IsDicomV3() +{ // Checking if Transfert 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 GetDocEntryByNumber(0x0002, 0x0010) != NULL; } /** @@ -424,101 +497,81 @@ bool gdcmDocument::IsDicomV3(void) { * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown) * @return the FileType code */ -FileType gdcmDocument::GetFileType(void) { - return(filetype); +FileType Document::GetFileType() +{ + return Filetype; } /** - * \brief opens the file - * @param exception_on_error - * @return + * \brief Tries to open the file \ref Document::Filename and + * checks the preamble when existing. + * @return The FILE pointer on success. */ -FILE *gdcmDocument::OpenFile(bool exception_on_error) - throw(gdcmFileError) +FILE* Document::OpenFile() { - fp=fopen(filename.c_str(),"rb"); - - if(!fp) - { - if(exception_on_error) - throw gdcmFileError("gdcmDocument::gdcmDocument(const char *, bool)"); - else - { - std::cout <<"gdcmDocument::OpenFile cannot open file: " - << filename.c_str() << std::endl; - dbg.Verbose(0, "gdcmDocument::OpenFile cannot open file: ", - filename.c_str()); - return (NULL); - } - } + Fp = fopen(Filename.c_str(),"rb"); - if ( fp ) - { - guint16 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) - return(fp); - - //DICOM - fseek(fp, 126L, SEEK_CUR); - char dicm[4]; - fread(dicm, (size_t)4, (size_t)1, fp); - if( memcmp(dicm, "DICM", 4) == 0 ) - return(fp); - - fclose(fp); - dbg.Verbose(0, "gdcmDocument::OpenFile not DICOM/ACR", filename.c_str()); - } - else { - dbg.Verbose(0, "gdcmDocument::OpenFile cannot open file", filename.c_str()); - } - return(NULL); + if(!Fp) + { + dbg.Verbose( 0, + "Document::OpenFile cannot open file: ", + Filename.c_str()); + 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 ) + { + return Fp; + } + + //DICOM + fseek(Fp, 126L, SEEK_CUR); + char dicm[4]; + fread(dicm, (size_t)4, (size_t)1, Fp); + if( memcmp(dicm, "DICM", 4) == 0 ) + { + return Fp; + } + + fclose(Fp); + dbg.Verbose( 0, + "Document::OpenFile not DICOM/ACR (missing preamble)", + Filename.c_str()); + + return 0; } /** * \brief closes the file * @return TRUE if the close was successfull */ -bool gdcmDocument::CloseFile(void) { - int closed = fclose(fp); - fp = (FILE *)0; - if (! closed) - return false; - return true; +bool Document::CloseFile() +{ + int closed = fclose(Fp); + Fp = 0; + + return closed; } /** * \brief Writes in a file all the Header Entries (Dicom Elements) - * of the Chained List * @param fp file pointer on an already open file - * @param type Type of the File to be written + * @param filetype Type of the File to be written * (ACR-NEMA, ExplicitVR, ImplicitVR) * \return Always true. */ -bool gdcmDocument::Write(FILE *fp, FileType type) { -/// \todo -/// ============== -/// The stuff will have to be rewritten using the SeQuence based -/// tree-like stucture instead of the chained list . -/// (so we shall remove the Group*HT from the gdcmDocument) -/// To be checked -/// ============= - +void Document::Write(FILE* fp,FileType filetype) +{ /// \todo move the following lines (and a lot of others, to be written) - /// to a future function CheckAndCorrectHeader - - /// \todo - /// Question : - /// Comment pourrait-on savoir si le DcmHeader vient d'un fichier - /// DicomV3 ou non (FileType est un champ de gdcmDocument ...) - /// WARNING : Si on veut ecrire du DICOM V3 a partir d'un DcmHeader ACR-NEMA - /// no way - /// a moins de se livrer a un tres complique ajout des champs manquants. - /// faire un CheckAndCorrectHeader (?) + /// to a future function CheckAndCorrectHeader + /// (necessary if user wants to write a DICOM V3 file + /// starting from an ACR-NEMA (V2) Header - if (type == gdcmImplicitVR) + if (filetype == ImplicitVR) { std::string implicitVRTransfertSyntax = UI1_2_840_10008_1_2; ReplaceOrCreateByNumber(implicitVRTransfertSyntax,0x0002, 0x0010); @@ -526,12 +579,12 @@ bool gdcmDocument::Write(FILE *fp, FileType type) { /// \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 + /// in the following case we have to padd manually with a 0 SetEntryLengthByNumber(18, 0x0002, 0x0010); } - if (type == gdcmExplicitVR) + if (filetype == ExplicitVR) { std::string explicitVRTransfertSyntax = UI1_2_840_10008_1_2_1; ReplaceOrCreateByNumber(explicitVRTransfertSyntax,0x0002, 0x0010); @@ -543,99 +596,223 @@ bool gdcmDocument::Write(FILE *fp, FileType type) { SetEntryLengthByNumber(20, 0x0002, 0x0010); } - + /** * \todo rewrite later, if really usefull + * - 'Group Length' element is optional in DICOM + * - but un-updated odd groups lengthes can causes pb + * (xmedcon breaker) * - * --> Warning : un-updated odd groups lengths can causes pb - * --> (xmedcon breaks) - * --> to be re- written with future org. - * - * if ( (type == ImplicitVR) || (type == ExplicitVR) ) - * UpdateGroupLength(false,type); - * if ( type == ACR) + * if ( (filetype == ImplicitVR) || (filetype == ExplicitVR) ) + * UpdateGroupLength(false,filetype); + * if ( filetype == ACR) * UpdateGroupLength(true,ACR); */ + + ElementSet::Write(fp, filetype); // This one is recursive - WriteEntries(fp,type); - return(true); } /** * \brief Modifies the value of a given Header Entry (Dicom Element) * when it exists. Create it with the given value when unexistant. - * @param Value (string) Value to be set - * @param Group Group number of the Entry - * @param Elem Element number of the Entry + * @param value (string) Value to be set + * @param group Group number of the Entry + * @param elem Element number of the Entry + * @param VR V(alue) R(epresentation) of the Entry -if private Entry- * \return pointer to the modified/created Header Entry (NULL when creation * failed). - */ - -gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber( - std::string Value, - guint16 Group, - guint16 Elem ){ - gdcmDocEntry* a; - gdcmValEntry* b; - a = GetDocEntryByNumber( Group, Elem); - if (a == NULL) { - a =NewDocEntryByNumber(Group, Elem); - if (a == NULL) + */ +ValEntry* Document::ReplaceOrCreateByNumber( + std::string const & value, + uint16_t group, + uint16_t elem, + std::string const & VR ) +{ + ValEntry* valEntry = 0; + DocEntry* currentEntry = GetDocEntryByNumber( group, elem); + + if (!currentEntry) + { + // check if (group,element) DictEntry exists + // if it doesn't, create an entry in DictSet::VirtualEntry + // and use it + + // Find out if the tag we received is in the dictionaries: + Dict *pubDict = Global::GetDicts()->GetDefaultPubDict(); + DictEntry* dictEntry = pubDict->GetDictEntryByNumber(group, elem); + if (!dictEntry) + { + currentEntry = NewDocEntryByNumber(group, elem,VR); + } + else + { + currentEntry = NewDocEntryByNumber(group, elem); + } + + if (!currentEntry) + { + dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: call to" + " NewDocEntryByNumber failed."); return NULL; - b = new gdcmValEntry(a); - AddEntry(b); - } - SetEntryByNumber(Value, Group, Elem); - b->SetValue(Value); - return (gdcmValEntry*)b; -} + } + valEntry = new ValEntry(currentEntry); + if ( !AddEntry(valEntry)) + { + dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry" + " failed allthough this is a creation."); + } + } + else + { + valEntry = dynamic_cast< ValEntry* >(currentEntry); + if ( !valEntry ) // Euuuuh? It wasn't a ValEntry + // then we change it to a ValEntry ? + // Shouldn't it be considered as an error ? + { + // We need to promote the DocEntry to a ValEntry: + valEntry = new ValEntry(currentEntry); + if (!RemoveEntry(currentEntry)) + { + dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: removal" + " of previous DocEntry failed."); + return NULL; + } + if ( !AddEntry(valEntry)) + { + dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: adding" + " promoted ValEntry failed."); + return NULL; + } + } + } + SetEntryByNumber(value, group, elem); + + return valEntry; +} /* * \brief Modifies the value of a given Header Entry (Dicom Element) * when it exists. Create it with the given value when unexistant. - * @param voidArea (binary) value to be set + * @param binArea (binary) value to be set * @param Group Group number of the Entry * @param Elem Element number of the Entry * \return pointer to the modified/created Header Entry (NULL when creation * failed). */ - - -gdcmBinEntry * gdcmDocument::ReplaceOrCreateByNumber( - void *voidArea, +BinEntry* Document::ReplaceOrCreateByNumber( + uint8_t* binArea, int lgth, - guint16 Group, - guint16 Elem ){ - gdcmDocEntry* a; - gdcmBinEntry* b; - a = GetDocEntryByNumber( Group, Elem); - if (a == NULL) { - a =NewBinEntryByNumber(Group, Elem); - if (a == NULL) + uint16_t group, + uint16_t elem, + std::string const& VR ) +{ + BinEntry* binEntry = 0; + DocEntry* currentEntry = GetDocEntryByNumber( group, elem); + if (!currentEntry) + { + + // check if (group,element) DictEntry exists + // if it doesn't, create an entry in DictSet::VirtualEntry + // and use it + + // Find out if the tag we received is in the dictionaries: + Dict *pubDict = Global::GetDicts()->GetDefaultPubDict(); + DictEntry *dictEntry = pubDict->GetDictEntryByNumber(group, elem); + + if (!dictEntry) + { + currentEntry = NewDocEntryByNumber(group, elem, VR); + } + else + { + currentEntry = NewDocEntryByNumber(group, elem); + } + if (!currentEntry) + { + dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: call to" + " NewDocEntryByNumber failed."); return NULL; - b = new gdcmBinEntry(a); - AddEntry(b); - } - SetEntryByNumber(voidArea, lgth, Group, Elem); - b->SetVoidArea(voidArea); - return (gdcmBinEntry*)b; + } + binEntry = new BinEntry(currentEntry); + if ( !AddEntry(binEntry)) + { + dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry" + " failed allthough this is a creation."); + } + } + else + { + binEntry = dynamic_cast< BinEntry* >(currentEntry); + if ( !binEntry ) // Euuuuh? It wasn't a BinEntry + // then we change it to a BinEntry ? + // Shouldn't it be considered as an error ? + { + // We need to promote the DocEntry to a BinEntry: + binEntry = new BinEntry(currentEntry); + if (!RemoveEntry(currentEntry)) + { + dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: removal" + " of previous DocEntry failed."); + return NULL; + } + if ( !AddEntry(binEntry)) + { + dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: adding" + " promoted BinEntry failed."); + return NULL; + } + } + } + + 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. + * @param Group Group number of the Entry + * @param Elem Element number of the Entry + * \return pointer to the modified/created SeqEntry (NULL when creation + * failed). + */ +SeqEntry* Document::ReplaceOrCreateByNumber( + uint16_t group, + uint16_t elem) +{ + SeqEntry* b = 0; + DocEntry* a = GetDocEntryByNumber( group, elem); + if (!a) + { + a = NewSeqEntryByNumber(group, elem); + if (!a) + { + return 0; + } + b = new SeqEntry(a, 1); // FIXME : 1 (Depth) + AddEntry(b); + } + return b; +} + /** * \brief Set a new value if the invoked element exists * Seems to be useless !!! - * @param Value new element value - * @param Group group number of the Entry - * @param Elem element number of the Entry + * @param value new element value + * @param group group number of the Entry + * @param elem element number of the Entry * \return boolean */ -bool gdcmDocument::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 Elem ) +bool Document::ReplaceIfExistByNumber(std::string const & value, + uint16_t group, uint16_t elem ) { - std::string v = Value; - SetEntryByNumber(v, Group, Elem); + SetEntryByNumber(value, group, elem); + return true; } @@ -646,11 +823,12 @@ bool gdcmDocument::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 El * \brief Checks if a given Dicom Element exists within the H table * @param group Group number of the searched Dicom Element * @param element Element number of the searched Dicom Element - * @return number of occurences + * @return true is found */ -int gdcmDocument::CheckIfEntryExistByNumber(guint16 group, guint16 element ) { - std::string key = gdcmDictEntry::TranslateToKey(group, element ); - return (tagHT.count(key)); +bool Document::CheckIfEntryExistByNumber(uint16_t group, uint16_t element ) +{ + const std::string &key = DictEntry::TranslateToKey(group, element ); + return TagHT.count(key); } /** @@ -662,12 +840,15 @@ int gdcmDocument::CheckIfEntryExistByNumber(guint16 group, guint16 element ) { * @return Corresponding element value when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string gdcmDocument::GetEntryByName(std::string tagName) { - gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); - if( dictEntry == NULL) +std::string Document::GetEntryByName(TagName const& tagName) +{ + DictEntry* dictEntry = RefPubDict->GetDictEntryByName(tagName); + if( !dictEntry ) + { return GDCM_UNFOUND; + } - return(GetEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement())); + return GetEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()); } /** @@ -683,17 +864,19 @@ std::string gdcmDocument::GetEntryByName(std::string tagName) { * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string gdcmDocument::GetEntryVRByName(std::string tagName) { - gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); +std::string Document::GetEntryVRByName(TagName const& tagName) +{ + DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( dictEntry == NULL) + { return GDCM_UNFOUND; + } - gdcmDocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(), - dictEntry->GetElement()); + DocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(), + dictEntry->GetElement()); return elem->GetVR(); } - /** * \brief Searches within Header Entries (Dicom Elements) parsed with * the public and private dictionaries @@ -703,11 +886,16 @@ std::string gdcmDocument::GetEntryVRByName(std::string tagName) { * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string gdcmDocument::GetEntryByNumber(guint16 group, guint16 element){ - TagKey key = gdcmDictEntry::TranslateToKey(group, element); - if ( ! tagHT.count(key)) +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; - return ((gdcmValEntry *)tagHT.find(key)->second)->GetValue(); + } + + return ((ValEntry *)TagHT.find(key)->second)->GetValue(); } /** @@ -724,10 +912,13 @@ std::string gdcmDocument::GetEntryByNumber(guint16 group, guint16 element){ * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string gdcmDocument::GetEntryVRByNumber(guint16 group, guint16 element) { - gdcmDocEntry* elem = GetDocEntryByNumber(group, element); +std::string Document::GetEntryVRByNumber(uint16_t group, uint16_t element) +{ + DocEntry* elem = GetDocEntryByNumber(group, element); if ( !elem ) + { return GDCM_UNFOUND; + } return elem->GetVR(); } @@ -739,10 +930,13 @@ std::string gdcmDocument::GetEntryVRByNumber(guint16 group, guint16 element) { * @param element Element number of the searched tag. * @return Corresponding element length; -2 if not found */ -int gdcmDocument::GetEntryLengthByNumber(guint16 group, guint16 element) { - gdcmDocEntry* elem = GetDocEntryByNumber(group, element); +int Document::GetEntryLengthByNumber(uint16_t group, uint16_t element) +{ + DocEntry* elem = GetDocEntryByNumber(group, element); if ( !elem ) - return -2; + { + return -2; //magic number + } return elem->GetLength(); } /** @@ -751,89 +945,109 @@ int gdcmDocument::GetEntryLengthByNumber(guint16 group, guint16 element) { * @param tagName name of the searched Dicom Element. * @return true when found */ -bool gdcmDocument::SetEntryByName(std::string content,std::string tagName) { - gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); - if( dictEntry == NULL) - return false; +bool Document::SetEntryByName(std::string const & content,std::string const & tagName) +{ + DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); + if( !dictEntry ) + { + return false; + } - return(SetEntryByNumber(content,dictEntry->GetGroup(), - dictEntry->GetElement())); + 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 content, - guint16 group, - guint16 element) +bool Document::SetEntryByNumber(std::string const& content, + uint16_t group, + uint16_t element) { - TagKey key = gdcmDictEntry::TranslateToKey(group, element); - if ( ! tagHT.count(key)) + int c; + int l; + + ValEntry* valEntry = GetValEntryByNumber(group, element); + if (!valEntry ) + { + dbg.Verbose(0, "Document::SetEntryByNumber: no corresponding", + " ValEntry (try promotion first)."); return false; - int l = content.length(); - if(l%2) // Non even length are padded with a space (020H). - { - l++; - content = content + '\0'; } - - gdcmValEntry * a; - a = (gdcmValEntry *)tagHT[key]; - - a->SetValue(content); - - VRKey vr = a->GetVR(); + // 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); - guint32 lgr; - if( (vr == "US") || (vr == "SS") ) - lgr = 2; - else if( (vr == "UL") || (vr == "SL") ) - lgr = 4; - else - lgr = l; + // Integers have a special treatement for their length: - a->SetLength(lgr); + l = finalContent.length(); + if ( l != 0) // To avoid to be cheated by 'zero length' integers + { + VRKey vr = valEntry->GetVR(); + if( vr == "US" || vr == "SS" ) + { + // for multivaluated items + c = Util::CountSubstring(content, "\\") + 1; + l = c*2; + } + else if( vr == "UL" || vr == "SL" ) + { + // for multivaluated items + c = Util::CountSubstring(content, "\\") + 1; + l = c*4;; + } + } + valEntry->SetLength(l); return true; } /** - * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element) + * \brief Accesses an existing DocEntry (i.e. a Dicom Element) * through it's (group, element) and modifies it's content with * the given value. - * @param content new value (void *) to substitute with + * @param content new value (void* -> uint8_t*) to substitute with + * @param lgth new value length * @param group group number of the Dicom Element to modify * @param element element number of the Dicom Element to modify */ -bool gdcmDocument::SetEntryByNumber(void *content, - int lgth, - guint16 group, - guint16 element) +bool Document::SetEntryByNumber(uint8_t*content, + int lgth, + uint16_t group, + uint16_t element) { - TagKey key = gdcmDictEntry::TranslateToKey(group, element); - if ( ! tagHT.count(key)) + (void)lgth; //not used + TagKey key = DictEntry::TranslateToKey(group, element); + if ( !TagHT.count(key)) + { return false; - -/* Hope Binray field length is never wrong + } + +/* 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; - a = (gdcmBinEntry *)tagHT[key]; - a->SetVoidArea(content); - //a->SetLength(lgth); // ??? + BinEntry* a = (BinEntry *)TagHT[key]; + a->SetBinArea(content); + a->SetLength(lgth); + a->SetValue(GDCM_BINLOADED); + return true; } /** - * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element) + * \brief Accesses an existing DocEntry (i.e. a Dicom Element) * in the PubDocEntrySet of this instance * through it's (group, element) and modifies it's length with * the given value. @@ -843,15 +1057,21 @@ bool gdcmDocument::SetEntryByNumber(void *content, * @param element element number of the Entry to modify * @return true on success, false otherwise. */ -bool gdcmDocument::SetEntryLengthByNumber(guint32 l, - guint16 group, - guint16 element) +bool Document::SetEntryLengthByNumber(uint32_t l, + uint16_t group, + uint16_t element) { - TagKey key = gdcmDictEntry::TranslateToKey(group, element); - if ( ! tagHT.count(key)) + /// \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); + } + if ( l % 2 ) + { + l++; // length must be even + } + ( ((TagHT.equal_range(key)).first)->second )->SetLength(l); return true ; } @@ -859,88 +1079,128 @@ bool gdcmDocument::SetEntryLengthByNumber(guint32 l, /** * \brief Gets (from Header) the offset of a 'non string' element value * (LoadElementValues has already be executed) - * @param Group group number of the Entry - * @param Elem element number of the Entry + * @param group group number of the Entry + * @param elem element number of the Entry * @return File Offset of the Element Value */ -size_t gdcmDocument::GetEntryOffsetByNumber(guint16 Group, guint16 Elem) +size_t Document::GetEntryOffsetByNumber(uint16_t group, uint16_t elem) { - gdcmDocEntry* Entry = GetDocEntryByNumber(Group, Elem); - if (!Entry) + DocEntry* entry = GetDocEntryByNumber(group, elem); + if (!entry) { - dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber", - "failed to Locate gdcmDocEntry"); - return (size_t)0; + dbg.Verbose(1, "Document::GetDocEntryByNumber: no entry present."); + return 0; } - return Entry->GetOffset(); + return entry->GetOffset(); } /** * \brief Gets (from Header) a 'non string' element value * (LoadElementValues has already be executed) - * @param Group group number of the Entry - * @param Elem element number of the Entry + * @param group group number of the Entry + * @param elem element number of the Entry * @return Pointer to the 'non string' area */ -void * gdcmDocument::GetEntryVoidAreaByNumber(guint16 Group, guint16 Elem) +void* Document::GetEntryBinAreaByNumber(uint16_t group, uint16_t elem) { - gdcmDocEntry* Entry = GetDocEntryByNumber(Group, Elem); - if (!Entry) + DocEntry* entry = GetDocEntryByNumber(group, elem); + if (!entry) + { + dbg.Verbose(1, "Document::GetDocEntryByNumber: no entry"); + return 0; + } + if ( BinEntry* binEntry = dynamic_cast(entry) ) { - dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber", - "failed to Locate gdcmDocEntry"); - return (NULL); + return binEntry->GetBinArea(); } - return ((gdcmBinEntry *)Entry)->GetVoidArea(); + + return 0; } /** * \brief Loads (from disk) the element content * when a string is not suitable - * @param Group group number of the Entry - * @param Elem element number of the Entry + * @param group group number of the Entry + * @param elem element number of the Entry */ -void *gdcmDocument::LoadEntryVoidArea(guint16 Group, guint16 Elem) +void* Document::LoadEntryBinArea(uint16_t group, uint16_t elem) { - gdcmDocEntry * Element= GetDocEntryByNumber(Group, Elem); - if ( !Element ) + DocEntry *docElement = GetDocEntryByNumber(group, elem); + if ( !docElement ) + { return NULL; - size_t o =(size_t)Element->GetOffset(); - fseek(fp, o, SEEK_SET); - size_t l=Element->GetLength(); - char* a = new char[l]; - if(!a) + } + 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; - - SetEntryVoidAreaByNumber(a, Group, Elem); + } + 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; +} +/** + * \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) +{ + size_t o =(size_t)element->GetOffset(); + fseek(Fp, o, SEEK_SET); + size_t l = element->GetLength(); + uint8_t* a = new uint8_t[l]; + if( !a ) + { + dbg.Verbose(0, "Document::LoadEntryBinArea cannot allocate a"); + return NULL; + } + element->SetBinArea((uint8_t*)a); /// \todo check the result - size_t l2 = fread(a, 1, l ,fp); - if(l != l2) + size_t l2 = fread(a, 1, l , Fp); + if( l != l2 ) { delete[] a; return NULL; } - return a; + return a; } /** * \brief Sets a 'non string' value to a given Dicom Element - * @param area + * @param area area containing the 'non string' value * @param group Group number of the searched Dicom Element * @param element Element number of the searched Dicom Element * @return */ -bool gdcmDocument::SetEntryVoidAreaByNumber(void * area, - guint16 group, - guint16 element) +bool Document::SetEntryBinAreaByNumber(uint8_t* area, + uint16_t group, + uint16_t element) { - TagKey key = gdcmDictEntry::TranslateToKey(group, element); - if ( ! tagHT.count(key)) + DocEntry* currentEntry = GetDocEntryByNumber(group, element); + if ( !currentEntry ) + { return false; - // This was for multimap ? - (( gdcmBinEntry *)( ((tagHT.equal_range(key)).first)->second ))->SetVoidArea(area); - + } + if ( BinEntry* binEntry = dynamic_cast(currentEntry) ) + { + binEntry->SetBinArea( area ); + return true; + } return true; } @@ -948,11 +1208,12 @@ bool gdcmDocument::SetEntryVoidAreaByNumber(void * area, * \brief Update the entries with the shadow dictionary. * Only non even entries are analyzed */ -void gdcmDocument::UpdateShaEntries(void) { - gdcmDictEntry *entry; +void Document::UpdateShaEntries() +{ + //DictEntry *entry; std::string vr; - // TODO : if still any use (?) explore recursively the whole structure + /// \todo TODO : still any use to explore recursively the whole structure? /* for(ListTag::iterator it=listEntries.begin(); it!=listEntries.end(); @@ -980,7 +1241,7 @@ void gdcmDocument::UpdateShaEntries(void) { CheckDocEntryVR(*it,vr); (*it)->SetValue(GetDocEntryValue(*it)); // to go on compiling - + } else { @@ -998,12 +1259,15 @@ void gdcmDocument::UpdateShaEntries(void) { * @return Corresponding Dicom Element when it exists, and NULL * otherwise. */ - gdcmDocEntry *gdcmDocument::GetDocEntryByName(std::string tagName) { - gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); - if( dictEntry == NULL) +DocEntry* Document::GetDocEntryByName(std::string const & tagName) +{ + DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); + if( !dictEntry ) + { return NULL; + } - return(GetDocEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement())); + return GetDocEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()); } /** @@ -1016,12 +1280,38 @@ void gdcmDocument::UpdateShaEntries(void) { * @param element Element number of the searched Dicom Element * @return */ -gdcmDocEntry* gdcmDocument::GetDocEntryByNumber(guint16 group, guint16 element) +DocEntry* Document::GetDocEntryByNumber(uint16_t group, + uint16_t element) { - TagKey key = gdcmDictEntry::TranslateToKey(group, element); - if ( ! tagHT.count(key)) + TagKey key = DictEntry::TranslateToKey(group, element); + if ( !TagHT.count(key)) + { return NULL; - return tagHT.find(key)->second; + } + return TagHT.find(key)->second; +} + +/** + * \brief Same as \ref Document::GetDocEntryByNumber except it only + * returns a result when the corresponding entry is of type + * ValEntry. + * @return When present, the corresponding ValEntry. + */ +ValEntry* Document::GetValEntryByNumber(uint16_t group, + uint16_t element) +{ + DocEntry* currentEntry = GetDocEntryByNumber(group, element); + if ( !currentEntry ) + { + return 0; + } + if ( ValEntry* valEntry = dynamic_cast(currentEntry) ) + { + return valEntry; + } + dbg.Verbose(0, "Document::GetValEntryByNumber: unfound ValEntry."); + + return 0; } /** @@ -1031,253 +1321,22 @@ gdcmDocEntry* gdcmDocument::GetDocEntryByNumber(guint16 group, guint16 element) * @param entry Header Entry whose value shall be loaded. * @return */ -void gdcmDocument::LoadDocEntrySafe(gdcmDocEntry * entry) { - long PositionOnEntry = ftell(fp); - LoadDocEntry(entry); - fseek(fp, PositionOnEntry, SEEK_SET); -} - - -/** - * \brief Writes in a file (according to the requested format) - * the group, the element, the value representation and the length - * of a single gdcmDocEntry passed as argument. - * @param tag pointer on the gdcmDocEntry to be written - * @param _fp already open file pointer - * @param type type of the File to be written - */ -void gdcmDocument::WriteEntryTagVRLength(gdcmDocEntry *tag, - FILE *_fp, - FileType type) +void Document::LoadDocEntrySafe(DocEntry * entry) { - guint16 group = tag->GetGroup(); - VRKey vr = tag->GetVR(); - guint16 el = tag->GetElement(); - guint32 lgr = tag->GetReadLength(); - - if ( (group == 0xfffe) && (el == 0x0000) ) - // Fix in order to make some MR PHILIPS images e-film readable - // see gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm: - // we just *always* ignore spurious fffe|0000 tag ! - return; - - fwrite ( &group,(size_t)2 ,(size_t)1 ,_fp); //group - fwrite ( &el,(size_t)2 ,(size_t)1 ,_fp); //element - - if ( type == gdcmExplicitVR ) { - - // Special case of delimiters: - if (group == 0xfffe) { - // Delimiters have NO Value Representation and have NO length. - // Hence we skip writing the VR and length and we pad by writing - // 0xffffffff - - int ff=0xffffffff; - fwrite (&ff,(size_t)4 ,(size_t)1 ,_fp); - return; - } - - guint16 z=0; - guint16 shortLgr = lgr; - if (vr == "unkn") { // Unknown was 'written' - // deal with Little Endian - fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp); - fwrite ( &z, (size_t)2 ,(size_t)1 ,_fp); - } else { - fwrite (vr.c_str(),(size_t)2 ,(size_t)1 ,_fp); - if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") ) - { - fwrite ( &z, (size_t)2 ,(size_t)1 ,_fp); - fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp); - } else { - fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp); - } - } - } - else // IMPLICIT VR - { - fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp); - } + long PositionOnEntry = ftell(Fp); + LoadDocEntry(entry); + fseek(Fp, PositionOnEntry, SEEK_SET); } - -/** - * \brief Writes in a file (according to the requested format) - * the value of a single gdcmDocEntry passed as argument. - * @param tag Pointer on the gdcmDocEntry to be written - * @param _fp Already open file pointer - * @param type type of the File to be written - */ - - // TODO : to be re -written recursively ! - -void gdcmDocument::WriteEntryValue(gdcmDocEntry *tag, FILE *_fp,FileType type) -{ - (void)type; - guint16 group = tag->GetGroup(); - VRKey vr = tag->GetVR(); - guint32 lgr = tag->GetReadLength(); - - if (vr == "SQ") - // SeQuences have no value: - return; - if (group == 0xfffe) - // Delimiters have no associated value: - return; - - //-------------------------------- - // - // FIXME :right now, both value and voidArea belong to gdcmValue - // - // ------------------------------- - -// if (gdcmBinEntry* BinEntry = dynamic_cast< gdcmBinEntry* >(tag) ) { - void *voidArea; - gdcmBinEntry *BinEntry= (gdcmBinEntry *)tag;; - voidArea = BinEntry->GetVoidArea(); - if (voidArea != NULL) - { // there is a 'non string' LUT, overlay, etc - fwrite ( voidArea,(size_t)lgr ,(size_t)1 ,_fp); // Elem value - return; - } -// } - - if (vr == "US" || vr == "SS") - { - // some 'Short integer' fields may be mulivaluated - // each single value is separated from the next one by '\' - // we split the string and write each value as a short int - std::vector tokens; - tokens.erase(tokens.begin(),tokens.end()); // clean any previous value - Tokenize (((gdcmValEntry *)tag)->GetValue(), tokens, "\\"); - for (unsigned int i=0; i tokens; - tokens.erase(tokens.begin(),tokens.end()); // clean any previous value - Tokenize (((gdcmValEntry *)tag)->GetValue(), tokens, "\\"); - for (unsigned int i=0; iGetValue().c_str(), (size_t)lgr ,(size_t)1, _fp); // Elem value -} - -/** - * \brief Writes in a file (according to the requested format) - * a single gdcmDocEntry passed as argument. - * \sa WriteEntryValue, WriteEntryTagVRLength. - * @param tag Pointer on the gdcmDocEntry to be written - * @param _fp Already open file pointer - * @param type type of the File to be written - */ - -bool gdcmDocument::WriteEntry(gdcmDocEntry *tag, FILE *_fp,FileType type) -{ - guint32 length = tag->GetLength(); - - if (gdcmValEntry* ValEntry = dynamic_cast< gdcmValEntry* >(tag) ) { - // The value of a tag MUST (see the DICOM norm) be an odd number of - // bytes. When this is not the case, pad with an additional byte: - if(length%2==1) { - ValEntry->SetValue(ValEntry->GetValue()+"\0"); - ValEntry->SetLength(ValEntry->GetReadLength()+1); - } - WriteEntryTagVRLength(ValEntry, _fp, type); - WriteEntryValue(ValEntry, _fp, type); - return true; - } - - if (gdcmBinEntry* BinEntry = dynamic_cast< gdcmBinEntry* >(tag) ) { - // - // FIXME : when voidArea belong to gdcmBinEntry only, fix voidArea length - // - // The value of a tag MUST (see the DICOM norm) be an odd number of - // bytes. When this is not the case, pad with an additional byte: - /* - if(length%2==1) { - tag->SetValue(tag->GetValue()+"\0"); - tag->SetLength(tag->GetReadLength()+1); - } -*/ - WriteEntryTagVRLength(tag, _fp, type); - WriteEntryValue(tag, _fp, type); - return true; - } -} - -/** - * \brief writes on disc according to the requested format - * (ACR-NEMA, ExplicitVR, ImplicitVR) the image - * using the Chained List - * \warning does NOT add the missing elements in the header : - * it's up to the user doing it ! - * (function CheckHeaderCoherence to be written) - * \warning DON'T try, right now, to write a DICOM image - * from an ACR Header (meta elements will be missing!) - * @param type type of the File to be written - * (ACR-NEMA, ExplicitVR, ImplicitVR) - * @param _fp already open file pointer - */ - -bool gdcmDocument::WriteEntries(FILE *_fp,FileType type) -{ - -// FIXME : explore recursively the whole structure... - - /// \todo (?) check write failures (after *each* fwrite) - - std::cout << "--------------------- gdcmDocument::WriteEntries " << std::endl; - for (TagDocEntryHT::iterator tag2=tagHT.begin(); - tag2 != tagHT.end(); - ++tag2) - { - - (*tag2).second->Print(); - - if ( type == gdcmACR ){ - if ((*tag2).second->GetGroup() < 0x0008) - // Ignore pure DICOM V3 groups - continue; - if ((*tag2).second->GetGroup() %2) - // Ignore the "shadow" groups - continue; - if ((*tag2).second->GetVR() == "SQ" ) // ignore Sequences - continue; - } - if (! WriteEntry((*tag2).second,_fp,type) ) { - std::cout << "Write Failure " << std::endl; - return false; - } else { - - } - } - return true; -} - /** * \brief Swaps back the bytes of 4-byte long integer accordingly to * processor order. * @return The properly swaped 32 bits integer. */ -guint32 gdcmDocument::SwapLong(guint32 a) { - switch (sw) { +uint32_t Document::SwapLong(uint32_t a) +{ + switch (SwapCode) + { case 0 : break; case 4321 : @@ -1290,41 +1349,46 @@ guint32 gdcmDocument::SwapLong(guint32 a) { break; case 2143 : - a=( ((a<<8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) ); + a=( ((a<< 8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) ); break; default : - std::cout << "swapCode= " << sw << std::endl; - dbg.Error(" gdcmDocument::SwapLong : unset swap code"); - a=0; + //std::cout << "swapCode= " << SwapCode << std::endl; + dbg.Error(" Document::SwapLong : unset swap code"); + a = 0; } - return(a); -} + return a; +} /** * \brief Unswaps back the bytes of 4-byte long integer accordingly to * processor order. * @return The properly unswaped 32 bits integer. */ -guint32 gdcmDocument::UnswapLong(guint32 a) { - return (SwapLong(a)); +uint32_t Document::UnswapLong(uint32_t a) +{ + return SwapLong(a); } /** * \brief Swaps the bytes so they agree with the processor order * @return The properly swaped 16 bits integer. */ -guint16 gdcmDocument::SwapShort(guint16 a) { - if ( (sw==4321) || (sw==2143) ) - a =(((a<<8) & 0x0ff00) | ((a>>8)&0x00ff)); - return (a); +uint16_t Document::SwapShort(uint16_t a) +{ + if ( SwapCode == 4321 || SwapCode == 2143 ) + { + a = ((( a << 8 ) & 0x0ff00 ) | (( a >> 8 ) & 0x00ff ) ); + } + return a; } /** * \brief Unswaps the bytes so they agree with the processor order * @return The properly unswaped 16 bits integer. */ -guint16 gdcmDocument::UnswapShort(guint16 a) { - return (SwapShort(a)); +uint16_t Document::UnswapShort(uint16_t a) +{ + return SwapShort(a); } //----------------------------------------------------------------------------- @@ -1332,236 +1396,352 @@ guint16 gdcmDocument::UnswapShort(guint16 a) { /** * \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries) - * @return false if file is not ACR-NEMA / PAPYRUS / DICOM + * @return length of the parsed set. */ - -long gdcmDocument::ParseDES(gdcmDocEntrySet *set, long offset, long l_max, bool delim_mode) { - - gdcmDocEntry *NewDocEntry = (gdcmDocEntry *)0; - gdcmValEntry *vl; - gdcmBinEntry *bn; - gdcmSeqEntry *sq; - VRKey vr; - long l; - int depth; - - depth = set->GetDepthLevel(); - while (true) { +void Document::ParseDES(DocEntrySet *set, + long offset, + long l_max, + bool delim_mode) +{ + DocEntry *newDocEntry = 0; - if ( !delim_mode && ftell(fp)-offset >= l_max) { - break; + while (true) + { + if ( !delim_mode && (ftell(Fp)-offset) >= l_max) + { + break; } - NewDocEntry = ReadNextDocEntry( ); - if (!NewDocEntry) + newDocEntry = ReadNextDocEntry( ); + if ( !newDocEntry ) + { break; + } - vr = NewDocEntry->GetVR(); - if (vr!="SQ") { + VRKey vr = newDocEntry->GetVR(); + if ( vr != "SQ" ) + { - if ( gdcmGlobal::GetVR()->IsVROfGdcmStringRepresentable(vr) ) + if ( Global::GetVR()->IsVROfGdcmStringRepresentable(vr) ) { - /////// ValEntry - vl= new gdcmValEntry(NewDocEntry->GetDictEntry()); - vl->Copy(NewDocEntry); - vl->SetDepthLevel(depth); - set->AddEntry(vl); - LoadDocEntry(vl); - if (/*!delim_mode && */vl->isItemDelimitor()) + /////////////////////// ValEntry + ValEntry* newValEntry = + new ValEntry( newDocEntry->GetDictEntry() ); + newValEntry->Copy( newDocEntry ); + + // When "set" is a Document, then we are at the top of the + // hierarchy and the Key is simply of the form ( group, elem )... + if (Document* dummy = dynamic_cast< Document* > ( set ) ) + { + (void)dummy; + newValEntry->SetKey( newValEntry->GetKey() ); + } + // ...but when "set" is a SQItem, we are inserting this new + // valEntry in a sequence item. Hence the key has the + // generalized form (refer to \ref BaseTagKey): + if (SQItem* parentSQItem = dynamic_cast< SQItem* > ( set ) ) + { + newValEntry->SetKey( parentSQItem->GetBaseTagKey() + + newValEntry->GetKey() ); + } + + set->AddEntry( newValEntry ); + LoadDocEntry( newValEntry ); + if (newValEntry->IsItemDelimitor()) + { break; - if ( !delim_mode && ftell(fp)-offset >= l_max) + } + if ( !delim_mode && (ftell(Fp)-offset) >= l_max) { break; } } else { - if ( ! gdcmGlobal::GetVR()->IsVROfGdcmBinaryRepresentable(vr) ) + if ( ! Global::GetVR()->IsVROfGdcmBinaryRepresentable(vr) ) { ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR - dbg.Verbose(0, "gdcmDocument::ParseDES: neither Valentry, " + dbg.Verbose(0, "Document::ParseDES: neither Valentry, " "nor BinEntry. Probably unknown VR."); } - ////// BinEntry or UNKOWN VR: - bn = new gdcmBinEntry(NewDocEntry->GetDictEntry()); - bn->Copy(NewDocEntry); - set->AddEntry(bn); - LoadDocEntry(bn); + //////////////////// BinEntry or UNKOWN VR: + BinEntry* newBinEntry = + new BinEntry( newDocEntry->GetDictEntry() ); + newBinEntry->Copy( newDocEntry ); + + // When "this" is a Document the Key is simply of the + // form ( group, elem )... + if (Document* dummy = dynamic_cast< Document* > ( set ) ) + { + (void)dummy; + newBinEntry->SetKey( newBinEntry->GetKey() ); + } + // but when "this" is a SQItem, we are inserting this new + // valEntry in a sequence item, and the kay has the + // generalized form (refer to \ref BaseTagKey): + if (SQItem* parentSQItem = dynamic_cast< SQItem* > ( set ) ) + { + newBinEntry->SetKey( parentSQItem->GetBaseTagKey() + + newBinEntry->GetKey() ); + } + + set->AddEntry( newBinEntry ); + LoadDocEntry( newBinEntry ); } - if (NewDocEntry->GetGroup() == 0x7fe0 && - NewDocEntry->GetElement() == 0x0010 ) + if ( ( newDocEntry->GetGroup() == 0x7fe0 ) + && ( newDocEntry->GetElement() == 0x0010 ) ) { - if (NewDocEntry->GetLength()==0xffffffff) - // Broken US.3405.1.dcm - Parse7FE0(); // to skip the pixels - // (multipart JPEG/RLE are trouble makers) + if ( IsRLELossLessTransferSyntax() ) + { + long PositionOnEntry = ftell(Fp); + fseek( Fp, newDocEntry->GetOffset(), SEEK_SET ); + ComputeRLEInfo(); + fseek( Fp, PositionOnEntry, SEEK_SET ); + } + else + if ( IsJPEGTransferSyntax() ) + { + long PositionOnEntry = ftell(Fp); + fseek( Fp, newDocEntry->GetOffset(), SEEK_SET ); + ComputeJPEGFragmentInfo(); + fseek( Fp, PositionOnEntry, SEEK_SET ); + } } - else + + // Just to make sure we are at the beginning of next entry. + SkipToNextDocEntry(newDocEntry); + } + else + { + // VR = "SQ" + unsigned long l = newDocEntry->GetReadLength(); + if ( l != 0 ) // don't mess the delim_mode for zero-length sequence { - // to be sure we are at the beginning - SkipToNextDocEntry(NewDocEntry); - l = NewDocEntry->GetFullLength(); - } - } else { // VR = "SQ" - - l=NewDocEntry->GetReadLength(); - if (l != 0) // don't mess the delim_mode for zero-length sequence - if (l == 0xffffffff) + if ( l == 0xffffffff ) + { delim_mode = true; + } else + { delim_mode = false; + } + } // no other way to create it ... - sq = new gdcmSeqEntry(NewDocEntry->GetDictEntry(), - set->GetDepthLevel()); - sq->Copy(NewDocEntry); - sq->SetDelimitorMode(delim_mode); - sq->SetDepthLevel(depth); + SeqEntry* newSeqEntry = + new SeqEntry( newDocEntry->GetDictEntry() ); + newSeqEntry->Copy( newDocEntry ); + newSeqEntry->SetDelimitorMode( delim_mode ); + + // At the top of the hierarchy, stands a Document. When "set" + // is a Document, then we are building the first depth level. + // Hence the SeqEntry we are building simply has a depth + // level of one: + if (Document* dummy = dynamic_cast< Document* > ( set ) ) + { + (void)dummy; + newSeqEntry->SetDepthLevel( 1 ); + newSeqEntry->SetKey( newSeqEntry->GetKey() ); + } + // But when "set" is allready a SQItem, we are building a nested + // sequence, and hence the depth level of the new SeqEntry + // we are building, is one level deeper: + if (SQItem* parentSQItem = dynamic_cast< SQItem* > ( set ) ) + { + newSeqEntry->SetDepthLevel( parentSQItem->GetDepthLevel() + 1 ); + newSeqEntry->SetKey( parentSQItem->GetBaseTagKey() + + newSeqEntry->GetKey() ); + } - if (l != 0) + if ( l != 0 ) { // Don't try to parse zero-length sequences - long lgt = ParseSQ( sq, - NewDocEntry->GetOffset(), - l, delim_mode); + ParseSQ( newSeqEntry, + newDocEntry->GetOffset(), + l, delim_mode); } - // FIXME : on en fait quoi, de lgt ? - set->AddEntry(sq); - if ( !delim_mode && ftell(fp)-offset >= l_max) + set->AddEntry( newSeqEntry ); + if ( !delim_mode && (ftell(Fp)-offset) >= l_max) { break; } } + delete newDocEntry; } - delete NewDocEntry; - return l; // ?? } /** * \brief Parses a Sequence ( SeqEntry after SeqEntry) * @return parsed length for this level */ -long gdcmDocument::ParseSQ(gdcmSeqEntry *set, long offset, long l_max, bool delim_mode) { +void Document::ParseSQ( SeqEntry* seqEntry, + long offset, long l_max, bool delim_mode) +{ int SQItemNumber = 0; - gdcmDocEntry *NewDocEntry = (gdcmDocEntry *)0; - gdcmSQItem *itemSQ; bool dlm_mod; - int lgr, l, lgth; - int depth = set->GetDepthLevel(); - while (true) { - - NewDocEntry = ReadNextDocEntry(); - if(delim_mode) { - if (NewDocEntry->isSequenceDelimitor()) { - //add the Sequence Delimitor // TODO : find the trick to put it properly ! - set->SetSequenceDelimitationItem(NewDocEntry); - break; - } - } - if (!delim_mode && (ftell(fp)-offset) >= l_max) { - break; - } - itemSQ = new gdcmSQItem(set->GetDepthLevel()); - itemSQ->AddEntry(NewDocEntry); // no value, no voidArea. Think of it while printing ! - l= NewDocEntry->GetReadLength(); + + while (true) + { + DocEntry* newDocEntry = ReadNextDocEntry(); + if ( !newDocEntry ) + { + // FIXME Should warn user + break; + } + if( delim_mode ) + { + if ( newDocEntry->IsSequenceDelimitor() ) + { + seqEntry->SetSequenceDelimitationItem( newDocEntry ); + break; + } + } + if ( !delim_mode && (ftell(Fp)-offset) >= l_max) + { + break; + } + + SQItem *itemSQ = new SQItem( seqEntry->GetDepthLevel() ); + std::ostringstream newBase; + newBase << seqEntry->GetKey() + << "/" + << SQItemNumber + << "#"; + itemSQ->SetBaseTagKey( newBase.str() ); + unsigned int l = newDocEntry->GetReadLength(); - if (l ==0xffffffff) + if ( l == 0xffffffff ) + { dlm_mod = true; + } else - dlm_mod=false; - - lgr=ParseDES(itemSQ, NewDocEntry->GetOffset(), l, dlm_mod); + { + dlm_mod = false; + } + + ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod); - set->AddEntry(itemSQ,SQItemNumber); - SQItemNumber ++; - if (!delim_mode && (ftell(fp)-offset) >= l_max) { + seqEntry->AddEntry( itemSQ, SQItemNumber ); + SQItemNumber++; + if ( !delim_mode && ( ftell(Fp) - offset ) >= l_max ) + { break; - } + } } - lgth = ftell(fp) - offset; - return(lgth); } /** * \brief Loads the element content if its length doesn't exceed - * the value specified with gdcmDocument::SetMaxSizeLoadEntry() - * @param Entry Header Entry (Dicom Element) to be dealt with + * the value specified with Document::SetMaxSizeLoadEntry() + * @param entry Header Entry (Dicom Element) to be dealt with */ -void gdcmDocument::LoadDocEntry(gdcmDocEntry *Entry) { +void Document::LoadDocEntry(DocEntry* entry) +{ size_t item_read; - guint16 group = Entry->GetGroup(); - std::string vr= Entry->GetVR(); - guint32 length = Entry->GetLength(); + uint16_t group = entry->GetGroup(); + std::string vr = entry->GetVR(); + uint32_t length = entry->GetLength(); - fseek(fp, (long)Entry->GetOffset(), SEEK_SET); + fseek(Fp, (long)entry->GetOffset(), SEEK_SET); // A SeQuence "contains" a set of Elements. // (fffe e000) tells us an Element is beginning // (fffe e00d) tells us an Element just ended // (fffe e0dd) tells us the current SeQuence just ended - if( group == 0xfffe ) { + if( group == 0xfffe ) + { // NO more value field for SQ ! - //Entry->SetValue("gdcm::Skipped"); - // appel recursif de Load Value - // (meme pb que pour le parsing) return; } // When the length is zero things are easy: - if ( length == 0 ) { - ((gdcmValEntry *)Entry)->SetValue(""); + if ( length == 0 ) + { + ((ValEntry *)entry)->SetValue(""); return; } // The elements whose length is bigger than the specified upper bound // are not loaded. Instead we leave a short notice of the offset of // the element content and it's length. - if (length > MaxSizeLoadEntry) { - if (gdcmValEntry* ValEntryPtr = dynamic_cast< gdcmValEntry* >(Entry) ) + + std::ostringstream s; + if (length > MaxSizeLoadEntry) + { + if (BinEntry* binEntryPtr = dynamic_cast< BinEntry* >(entry) ) + { + //s << "gdcm::NotLoaded (BinEntry)"; + s << GDCM_NOTLOADED; + s << " Address:" << (long)entry->GetOffset(); + s << " Length:" << entry->GetLength(); + s << " x(" << std::hex << entry->GetLength() << ")"; + binEntryPtr->SetValue(s.str()); + } + // Be carefull : a BinEntry IS_A ValEntry ... + else if (ValEntry* valEntryPtr = dynamic_cast< ValEntry* >(entry) ) { - std::ostringstream s; - s << "gdcm::NotLoaded."; - s << " Address:" << (long)Entry->GetOffset(); - s << " Length:" << Entry->GetLength(); - s << " x(" << std::hex << Entry->GetLength() << ")"; - ValEntryPtr->SetValue(s.str()); + // s << "gdcm::NotLoaded. (ValEntry)"; + s << GDCM_NOTLOADED; + s << " Address:" << (long)entry->GetOffset(); + s << " Length:" << entry->GetLength(); + s << " x(" << std::hex << entry->GetLength() << ")"; + valEntryPtr->SetValue(s.str()); + } + else + { + // fusible + std::cout<< "MaxSizeLoadEntry exceeded, neither a BinEntry " + << "nor a ValEntry ?! Should never print that !" << std::endl; } + // to be sure we are at the end of the value ... - fseek(fp,(long)Entry->GetOffset()+(long)Entry->GetLength(),SEEK_SET); - + fseek(Fp,(long)entry->GetOffset()+(long)entry->GetLength(),SEEK_SET); + return; + } + + // When we find a BinEntry not very much can be done : + if (BinEntry* binEntryPtr = dynamic_cast< BinEntry* >(entry) ) + { + s << GDCM_BINLOADED; + binEntryPtr->SetValue(s.str()); + LoadEntryBinArea(binEntryPtr); // last one, not to erase length ! return; } - // Any compacter code suggested (?) - if ( IsDocEntryAnInteger(Entry) ) { - guint32 NewInt; - std::ostringstream s; + /// \todo Any compacter code suggested (?) + if ( IsDocEntryAnInteger(entry) ) + { + uint32_t NewInt; int nbInt; - // When short integer(s) are expected, read and convert the following - // n *two characters properly i.e. as short integers as opposed to strings. - // Elements with Value Multiplicity > 1 - // contain a set of integers (not a single one) - if (vr == "US" || vr == "SS") { + // When short integer(s) are expected, read and convert the following + // n *two characters properly i.e. consider them as short integers as + // opposed to strings. + // Elements with Value Multiplicity > 1 + // contain a set of integers (not a single one) + if (vr == "US" || vr == "SS") + { nbInt = length / 2; NewInt = ReadInt16(); s << NewInt; - if (nbInt > 1){ - for (int i=1; i < nbInt; i++) { + if (nbInt > 1) + { + for (int i=1; i < nbInt; i++) + { s << '\\'; NewInt = ReadInt16(); s << NewInt; } } } - // When integer(s) are expected, read and convert the following - // n * four characters properly i.e. as integers as opposed to strings. - // Elements with Value Multiplicity > 1 - // contain a set of integers (not a single one) - else if (vr == "UL" || vr == "SL") { + // See above comment on multiple integers (mutatis mutandis). + else if (vr == "UL" || vr == "SL") + { nbInt = length / 4; NewInt = ReadInt32(); s << NewInt; - if (nbInt > 1) { - for (int i=1; i < nbInt; i++) { + if (nbInt > 1) + { + for (int i=1; i < nbInt; i++) + { s << '\\'; NewInt = ReadInt32(); s << NewInt; @@ -1572,53 +1752,95 @@ 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); - if ( item_read != 1 ) { - dbg.Verbose(1, "gdcmDocument::LoadElementValue","unread element value"); - ((gdcmValEntry *)Entry)->SetValue("gdcm::UnRead"); - return; - } + //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* !!! + char *str = new char[length+1]; + item_read = fread(str, (size_t)length, (size_t)1, Fp); + str[length] = '\0'; + std::string newValue = str; + delete[] str; + if ( ValEntry* valEntry = dynamic_cast(entry) ) + { + if ( item_read != 1 ) + { + dbg.Verbose(1, "Document::LoadDocEntry", + "unread element value"); + valEntry->SetValue(GDCM_UNREAD); + return; + } - if( (vr == "UI") ) // Because of correspondance with the VR dic - ((gdcmValEntry *)Entry)->SetValue(NewValue.c_str()); + if( vr == "UI" ) + { + // Because of correspondance with the VR dic + valEntry->SetValue(newValue); + } + else + { + valEntry->SetValue(newValue); + } + } else - ((gdcmValEntry *)Entry)->SetValue(NewValue); + { + dbg.Error(true, "Document::LoadDocEntry" + "Should have a ValEntry, here !"); + } } /** * \brief Find the value Length of the passed Header Entry - * @param Entry Header Entry whose length of the value shall be loaded. + * @param entry Header Entry whose length of the value shall be loaded. */ - void gdcmDocument::FindDocEntryLength (gdcmDocEntry *Entry) { - guint16 element = Entry->GetElement(); - //guint16 group = Entry->GetGroup(); //FIXME - std::string vr = Entry->GetVR(); - guint16 length16; - +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") ) + if ( vr == "OB" || vr == "OW" || vr == "SQ" || vr == "UN" ) { - // The following reserved two bytes (see PS 3.5-2001, section - // 7.1.2 Data element structure with explicit vr p27) must be + // The following reserved two bytes (see PS 3.5-2003, section + // "7.1.2 Data element structure with explicit vr", p 27) must be // skipped before proceeding on reading the length on 4 bytes. - fseek(fp, 2L, SEEK_CUR); - guint32 length32 = ReadInt32(); + fseek(Fp, 2L, SEEK_CUR); + uint32_t length32 = ReadInt32(); - if ( (vr == "OB") && (length32 == 0xffffffff) ) + if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff ) { - Entry->SetLength(FindDocEntryLengthOB()); + uint32_t lengthOB; + try + { + /// \todo rename that to FindDocEntryLengthOBOrOW since + /// the above test is on both OB and OW... + lengthOB = FindDocEntryLengthOB(); + } + 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); + entry->SetLength(lengthUntilEOF); + return; + } + entry->SetLength(lengthOB); return; } - FixDocEntryFoundLength(Entry, length32); + FixDocEntryFoundLength(entry, length32); return; } @@ -1652,42 +1874,39 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry *Entry) { // endian encoding". When this is the case, chances are we have got our // hands on a big endian encoded file: we switch the swap code to // big endian and proceed... - if ( (element == 0x0000) && (length16 == 0x0400) ) + if ( element == 0x0000 && length16 == 0x0400 ) { - if ( ! IsExplicitVRBigEndianTransferSyntax() ) + if ( !IsExplicitVRBigEndianTransferSyntax() ) { - dbg.Verbose(0, "gdcmDocument::FindLength", "not explicit VR"); - errno = 1; + throw FormatError( "Document::FindDocEntryLength()", + " not explicit VR." ); return; } length16 = 4; SwitchSwapToBigEndian(); // Restore the unproperly loaded values i.e. the group, the element // and the dictionary entry depending on them. - guint16 CorrectGroup = SwapShort(Entry->GetGroup()); - guint16 CorrectElem = SwapShort(Entry->GetElement()); - gdcmDictEntry * NewTag = GetDictEntryByNumber(CorrectGroup, - CorrectElem); - if (!NewTag) + uint16_t correctGroup = SwapShort( entry->GetGroup() ); + uint16_t correctElem = SwapShort( entry->GetElement() ); + DictEntry* newTag = GetDictEntryByNumber( correctGroup, + correctElem ); + if ( !newTag ) { // This correct tag is not in the dictionary. Create a new one. - NewTag = NewVirtualDictEntry(CorrectGroup, CorrectElem); + newTag = NewVirtualDictEntry(correctGroup, correctElem); } // FIXME this can create a memory leaks on the old entry that be // left unreferenced. - Entry->SetDictEntry(NewTag); + entry->SetDictEntry( newTag ); } - // Heuristic: well some files are really ill-formed. + // Heuristic: well, some files are really ill-formed. if ( length16 == 0xffff) { + // 0xffff means that we deal with 'Unknown Length' Sequence length16 = 0; - //dbg.Verbose(0, "gdcmDocument::FindLength", - // "Erroneous element length fixed."); - // Actually, length= 0xffff means that we deal with - // Unknown Sequence Length } - FixDocEntryFoundLength(Entry, (guint32)length16); + FixDocEntryFoundLength( entry, (uint32_t)length16 ); return; } else @@ -1699,23 +1918,25 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry *Entry) { // not coexist in a Data Set and Data Sets nested within it".] // Length is on 4 bytes. - FixDocEntryFoundLength(Entry, ReadInt32()); + FixDocEntryFoundLength( entry, ReadInt32() ); return; } } /** * \brief Find the Value Representation of the current Dicom Element. - * @param Entry + * @param entry */ -void gdcmDocument::FindDocEntryVR( gdcmDocEntry *Entry) +void Document::FindDocEntryVR( DocEntry *entry ) { - if (filetype != gdcmExplicitVR) + if ( Filetype != ExplicitVR ) + { return; + } - char VR[3]; + char vr[3]; - long PositionOnEntry = ftell(fp); + long positionOnEntry = ftell(Fp); // 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 @@ -1724,19 +1945,22 @@ void gdcmDocument::FindDocEntryVR( gdcmDocEntry *Entry) // is in explicit VR and try to fix things if it happens not to be // the case. - (void)fread (&VR, (size_t)2,(size_t)1, fp); - VR[2]=0; - if(!CheckDocEntryVR(Entry,VR)) + fread (vr, (size_t)2,(size_t)1, Fp); + vr[2] = 0; + + if( !CheckDocEntryVR(entry, vr) ) { - fseek(fp, PositionOnEntry, SEEK_SET); + 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(); + if ( entry->IsVRUnknown() ) + { + entry->SetVR("Implicit"); + } + entry->SetImplicitVR(); } } @@ -1744,15 +1968,15 @@ void gdcmDocument::FindDocEntryVR( gdcmDocEntry *Entry) * \brief Check the correspondance between the VR of the header entry * and the taken VR. If they are different, the header entry is * updated with the new VR. - * @param Entry Header Entry to check + * @param entry Header Entry to check * @param vr Dicom Value Representation * @return false if the VR is incorrect of if the VR isn't referenced * otherwise, it returns true */ -bool gdcmDocument::CheckDocEntryVR(gdcmDocEntry *Entry, VRKey vr) +bool Document::CheckDocEntryVR(DocEntry *entry, VRKey vr) { - char msg[100]; // for sprintf - bool RealExplicit = true; + std::string msg; + 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 @@ -1762,122 +1986,140 @@ bool gdcmDocument::CheckDocEntryVR(gdcmDocEntry *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])) ) - RealExplicit = false; + 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 && !Global::GetVR()->Count(vr) ) + { + realExplicit = false; + } - if ( !RealExplicit ) + 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); + msg = Util::Format("Falsely explicit vr file (%04x,%04x)\n", + entry->GetGroup(), entry->GetElement()); + dbg.Verbose(1, "Document::FindVR: ", msg.c_str()); + + if( entry->GetGroup() % 2 && entry->GetElement() == 0x0000) + { + // Group length is UL ! + DictEntry* newEntry = NewVirtualDictEntry( + entry->GetGroup(), entry->GetElement(), + "UL", "FIXME", "Group Length"); + entry->SetDictEntry( newEntry ); } - return(false); + return false; } - if ( Entry->IsVRUnknown() ) + 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); + if( entry->GetElement() == 0x0000 ) + { + // Group length is UL ! + entry->SetVR("UL"); + } + else + { + entry->SetVR(vr); } } - else if ( Entry->GetVR() != 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); + DictEntry* newEntry = NewVirtualDictEntry( + entry->GetGroup(), entry->GetElement(), + vr, "FIXME", entry->GetName()); + entry->SetDictEntry(newEntry); } - return(true); + + return true; } /** * \brief Get the transformed value of the header entry. The VR value * is used to define the transformation to operate on the value * \warning NOT end user intended method ! - * @param Entry + * @param entry entry to tranform * @return Transformed entry value */ -std::string gdcmDocument::GetDocEntryValue(gdcmDocEntry *Entry) +std::string Document::GetDocEntryValue(DocEntry *entry) { - if ( (IsDocEntryAnInteger(Entry)) && (Entry->IsImplicitVR()) ) + if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() ) { - std::string val=((gdcmValEntry *)Entry)->GetValue(); - std::string vr=Entry->GetVR(); - guint32 length = Entry->GetLength(); + std::string val = ((ValEntry *)entry)->GetValue(); + std::string vr = entry->GetVR(); + uint32_t length = entry->GetLength(); std::ostringstream s; int nbInt; - // When short integer(s) are expected, read and convert the following - // n * 2 bytes properly i.e. as a multivaluated strings - // (each single value is separated fromthe next one by '\' - // as usual for standard multivaluated filels - // Elements with Value Multiplicity > 1 - // contain a set of short integers (not a single one) + // When short integer(s) are expected, read and convert the following + // n * 2 bytes properly i.e. as a multivaluated strings + // (each single value is separated fromthe next one by '\' + // as usual for standard multivaluated filels + // Elements with Value Multiplicity > 1 + // contain a set of short integers (not a single one) - if (vr == "US" || vr == "SS") + if( vr == "US" || vr == "SS" ) { - guint16 NewInt16; + uint16_t newInt16; nbInt = length / 2; for (int i=0; i < nbInt; i++) { - if(i!=0) + if( i != 0 ) + { s << '\\'; - NewInt16 = (val[2*i+0]&0xFF)+((val[2*i+1]&0xFF)<<8); - NewInt16 = SwapShort(NewInt16); - s << NewInt16; + } + newInt16 = ( val[2*i+0] & 0xFF ) + ( ( val[2*i+1] & 0xFF ) << 8); + newInt16 = SwapShort( newInt16 ); + s << newInt16; } } - // When integer(s) are expected, read and convert the following - // n * 4 bytes properly i.e. as a multivaluated strings - // (each single value is separated fromthe next one by '\' - // as usual for standard multivaluated filels - // Elements with Value Multiplicity > 1 - // contain a set of integers (not a single one) - else if (vr == "UL" || vr == "SL") + // When integer(s) are expected, read and convert the following + // n * 4 bytes properly i.e. as a multivaluated strings + // (each single value is separated fromthe next one by '\' + // as usual for standard multivaluated filels + // Elements with Value Multiplicity > 1 + // contain a set of integers (not a single one) + else if( vr == "UL" || vr == "SL" ) { - guint32 NewInt32; + uint32_t newInt32; nbInt = length / 4; for (int i=0; i < nbInt; i++) { - if(i!=0) + if( i != 0) + { s << '\\'; - NewInt32= (val[4*i+0]&0xFF)+((val[4*i+1]&0xFF)<<8)+ - ((val[4*i+2]&0xFF)<<16)+((val[4*i+3]&0xFF)<<24); - NewInt32=SwapLong(NewInt32); - s << NewInt32; + } + newInt32 = ( val[4*i+0] & 0xFF ) + + (( val[4*i+1] & 0xFF ) << 8 ) + + (( val[4*i+2] & 0xFF ) << 16 ) + + (( val[4*i+3] & 0xFF ) << 24 ); + newInt32 = SwapLong( newInt32 ); + s << newInt32; } } #ifdef GDCM_NO_ANSI_STRING_STREAM s << std::ends; // to avoid oddities on Solaris #endif //GDCM_NO_ANSI_STRING_STREAM - return(s.str()); + return s.str(); } - return(((gdcmValEntry *)Entry)->GetValue()); + return ((ValEntry *)entry)->GetValue(); } /** @@ -1885,41 +2127,44 @@ std::string gdcmDocument::GetDocEntryValue(gdcmDocEntry *Entry) * value is used to define the reverse transformation to operate on * the value * \warning NOT end user intended method ! - * @param Entry + * @param entry Entry to reverse transform * @return Reverse transformed entry value */ -std::string gdcmDocument::GetDocEntryUnvalue(gdcmDocEntry *Entry) +std::string Document::GetDocEntryUnvalue(DocEntry* entry) { - if ( (IsDocEntryAnInteger(Entry)) && (Entry->IsImplicitVR()) ) + if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() ) { - std::string vr=Entry->GetVR(); - std::ostringstream s; + std::string vr = entry->GetVR(); std::vector tokens; + std::ostringstream s; - if (vr == "US" || vr == "SS") + if ( vr == "US" || vr == "SS" ) { - guint16 NewInt16; + uint16_t newInt16; - tokens.erase(tokens.begin(),tokens.end()); // clean any previous value - Tokenize (((gdcmValEntry *)Entry)->GetValue(), tokens, "\\"); - for (unsigned int i=0; iGetValue(), tokens, "\\"); + for (unsigned int i=0; i>8)&0xFF); + newInt16 = atoi(tokens[i].c_str()); + s << ( newInt16 & 0xFF ) + << (( newInt16 >> 8 ) & 0xFF ); } tokens.clear(); } - if (vr == "UL" || vr == "SL") + if ( vr == "UL" || vr == "SL") { - guint32 NewInt32; + uint32_t newInt32; 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; i>8)&0xFF) - <<(char)((NewInt32>>16)&0xFF)<<(char)((NewInt32>>24)&0xFF); + newInt32 = atoi(tokens[i].c_str()); + s << (char)( newInt32 & 0xFF ) + << (char)(( newInt32 >> 8 ) & 0xFF ) + << (char)(( newInt32 >> 16 ) & 0xFF ) + << (char)(( newInt32 >> 24 ) & 0xFF ); } tokens.clear(); } @@ -1927,18 +2172,18 @@ std::string gdcmDocument::GetDocEntryUnvalue(gdcmDocEntry *Entry) #ifdef GDCM_NO_ANSI_STRING_STREAM s << std::ends; // to avoid oddities on Solaris #endif //GDCM_NO_ANSI_STRING_STREAM - return(s.str()); + return s.str(); } - return(((gdcmValEntry *)Entry)->GetValue()); + return ((ValEntry *)entry)->GetValue(); } /** * \brief Skip a given Header Entry * \warning NOT end user intended method ! - * @param entry + * @param entry entry to skip */ -void gdcmDocument::SkipDocEntry(gdcmDocEntry *entry) +void Document::SkipDocEntry(DocEntry *entry) { SkipBytes(entry->GetLength()); } @@ -1946,180 +2191,202 @@ void gdcmDocument::SkipDocEntry(gdcmDocEntry *entry) /** * \brief Skips to the begining of the next Header Entry * \warning NOT end user intended method ! - * @param entry + * @param entry entry to skip */ -void gdcmDocument::SkipToNextDocEntry(gdcmDocEntry *entry) +void Document::SkipToNextDocEntry(DocEntry *entry) { - (void)fseek(fp, (long)(entry->GetOffset()), SEEK_SET); - (void)fseek(fp, (long)(entry->GetReadLength()), SEEK_CUR); + fseek(Fp, (long)(entry->GetOffset()), SEEK_SET); + fseek(Fp, (long)(entry->GetReadLength()), SEEK_CUR); } -/** - * \brief Loads the value for a a given VLEntry - * \warning NOT end user intended method ! - * @param entry - */ -void gdcmDocument::LoadVLEntry(gdcmDocEntry *entry) -{ - //SkipBytes(entry->GetLength()); - LoadDocEntry(entry); -} /** * \brief When the length of an element value is obviously wrong (because * the parser went Jabberwocky) one can hope improving things by - * applying this heuristic. + * applying some heuristics. + * @param entry entry to check + * @param foundLength fist assumption about length */ -void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *Entry, guint32 FoundLength) +void Document::FixDocEntryFoundLength(DocEntry *entry, + uint32_t foundLength) { - Entry->SetReadLength(FoundLength); // will be updated only if a bug is found - if ( FoundLength == 0xffffffff) { - FoundLength = 0; + entry->SetReadLength( foundLength ); // will be updated only if a bug is found + if ( foundLength == 0xffffffff) + { + foundLength = 0; } - guint16 gr =Entry->GetGroup(); - guint16 el =Entry->GetElement(); + uint16_t gr = entry->GetGroup(); + uint16_t el = entry->GetElement(); - if (FoundLength%2) { + 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()); + s << "Warning : Tag with uneven length " + << foundLength + << " in x(" << std::hex << gr << "," << el <<")" << std::dec; + dbg.Verbose(0, s.str().c_str()); } - // Sorry for the patch! - // XMedCom did the trick to read some naughty GE images ... - if (FoundLength == 13) { - // The following 'if' will be removed when there is no more - // images on Creatis HDs with a 13 length for Manufacturer... - if ( (Entry->GetGroup() != 0x0008) || - ( (Entry->GetElement() != 0x0070) && (Entry->GetElement() != 0x0080) ) ){ - // end of remove area - FoundLength =10; - Entry->SetReadLength(10); // a bug is to be fixed - } - } - - // to fix some garbage 'Leonardo' Siemens images - // May be commented out to avoid overhead - else if ( (Entry->GetGroup() == 0x0009) && - ( (Entry->GetElement() == 0x1113) || (Entry->GetElement() == 0x1114) ) ){ - FoundLength =4; - Entry->SetReadLength(4); // a bug is to be fixed + //////// 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)... + // 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 ) ) + { + foundLength = 10; + entry->SetReadLength(10); /// \todo a bug is to be fixed !? + } + } + + //////// Fix for some brain-dead 'Leonardo' Siemens images. + // 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 ) ) + { + foundLength = 4; + entry->SetReadLength(4); /// \todo a bug is to be fixed !? } - // end of fix - // to try to 'go inside' SeQuences (with length), and not to skip them - else if ( Entry->GetVR() == "SQ") - { - if (enableSequences) // only if the user does want to ! - FoundLength =0; // ReadLength is unchanged + else if ( entry->GetVR() == "SQ" ) + { + foundLength = 0; // ReadLength is unchanged } - // we found a 'delimiter' element - // fffe|xxxx is just a marker, we don't take its length into account - else if(Entry->GetGroup() == 0xfffe) + //////// 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 ) { - // *normally, fffe|0000 doesn't exist ! - if( Entry->GetElement() != 0x0000 ) // gdcm-MR-PHILIPS-16-Multi-Seq.dcm - // causes extra troubles :-( - FoundLength =0; + // According to the norm, fffe|0000 shouldn't exist. BUT the Philips + // image gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm happens to + // causes extra troubles... + if( entry->GetElement() != 0x0000 ) + { + foundLength = 0; + } } - Entry->SetUsableLength(FoundLength); + entry->SetUsableLength(foundLength); } /** * \brief Apply some heuristics to predict whether the considered * element value contains/represents an integer or not. - * @param Entry The element value on which to apply the predicate. + * @param entry The element value on which to apply the predicate. * @return The result of the heuristical predicate. */ -bool gdcmDocument::IsDocEntryAnInteger(gdcmDocEntry *Entry) { - guint16 element = Entry->GetElement(); - guint16 group = Entry->GetGroup(); - std::string vr = Entry->GetVR(); - guint32 length = Entry->GetLength(); +bool Document::IsDocEntryAnInteger(DocEntry *entry) +{ + uint16_t element = entry->GetElement(); + uint16_t group = entry->GetGroup(); + 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 (length == 4) + if ( length == 4 ) + { return true; + } else { + // Allthough this should never happen, still some images have a + // corrupted group length [e.g. have a glance at offset x(8336) of + // gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm]. + // Since for dicom compliant and well behaved headers, the present + // 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); + long filePosition = ftell(Fp); s << "Erroneous Group Length element length on : (" \ << std::hex << group << " , " << element << ") -before- position x(" << filePosition << ")" << "lgt : " << length; - // These 2 lines commented out : a *very dirty* patch - // to go on PrintHeader'ing gdcm-MR-PHILIPS-16-Multi-Seq.dcm. - // have a glance at offset x(8336) ... - // For *regular* headers, the test is useless.. - // lets's print a warning message and go on, - // instead of giving up with an error message - - //std::cout << s.str().c_str() << std::endl; - // dbg.Error("gdcmDocument::IsDocEntryAnInteger", - // s.str().c_str()); + dbg.Verbose(0, "Document::IsDocEntryAnInteger", s.str().c_str() ); } } - if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") ) + + if ( vr == "UL" || vr == "US" || vr == "SL" || vr == "SS" ) + { return true; + } return false; } + /** * \brief Find the Length till the next sequence delimiter * \warning NOT end user intended method ! * @return */ - guint32 gdcmDocument::FindDocEntryLengthOB(void) { +uint32_t Document::FindDocEntryLengthOB() + throw( FormatUnexpected ) +{ // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data. - guint16 g; - guint16 n; - long PositionOnEntry = ftell(fp); - bool FoundSequenceDelimiter = false; - guint32 TotalLength = 0; - guint32 ItemLength; - - while ( ! FoundSequenceDelimiter) - { - g = ReadInt16(); - n = ReadInt16(); - if (errno == 1) - return 0; - TotalLength += 4; // We even have to decount the group and element + long positionOnEntry = ftell(Fp); + bool foundSequenceDelimiter = false; + uint32_t totalLength = 0; + + while ( !foundSequenceDelimiter ) + { + uint16_t group; + uint16_t elem; + try + { + group = ReadInt16(); + elem = ReadInt16(); + } + catch ( FormatError ) + { + throw FormatError("Document::FindDocEntryLengthOB()", + " group or element not present."); + } + + // We have to decount the group and element we just read + totalLength += 4; - if ( g != 0xfffe && g!=0xb00c ) //for bogus header + if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) ) { - char msg[100]; // for sprintf. Sorry - sprintf(msg,"wrong group (%04x) for an item sequence (%04x,%04x)\n",g, g,n); - dbg.Verbose(1, "gdcmDocument::FindLengthOB: ",msg); - errno = 1; - return 0; + dbg.Verbose(1, "Document::FindDocEntryLengthOB: neither an Item " + "tag nor a Sequence delimiter tag."); + fseek(Fp, positionOnEntry, SEEK_SET); + throw FormatUnexpected("Document::FindDocEntryLengthOB()", + "Neither an Item tag nor a Sequence " + "delimiter tag."); } - if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) // for bogus header - FoundSequenceDelimiter = true; - else if ( n != 0xe000 ) + + if ( elem == 0xe0dd ) { - char msg[100]; // for sprintf. Sorry - sprintf(msg,"wrong element (%04x) for an item sequence (%04x,%04x)\n", - n, g,n); - dbg.Verbose(1, "gdcmDocument::FindLengthOB: ",msg); - errno = 1; - return 0; + foundSequenceDelimiter = true; + } + + uint32_t itemLength = ReadInt32(); + // We add 4 bytes since we just read the ItemLength with ReadInt32 + totalLength += itemLength + 4; + SkipBytes(itemLength); + + if ( foundSequenceDelimiter ) + { + break; } - ItemLength = ReadInt32(); - TotalLength += ItemLength + 4; // We add 4 bytes since we just read - // the ItemLength with ReadInt32 - SkipBytes(ItemLength); } - fseek(fp, PositionOnEntry, SEEK_SET); - return TotalLength; + fseek(Fp, positionOnEntry, SEEK_SET); + return totalLength; } /** @@ -2127,18 +2394,20 @@ bool gdcmDocument::IsDocEntryAnInteger(gdcmDocEntry *Entry) { * (swaps it depending on processor endianity) * @return read value */ -guint16 gdcmDocument::ReadInt16(void) { - guint16 g; - size_t item_read; - item_read = fread (&g, (size_t)2,(size_t)1, fp); - if ( item_read != 1 ) { - if(ferror(fp)) - dbg.Verbose(0, "gdcmDocument::ReadInt16", " File Error"); - errno = 1; - return 0; +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 ) + { + if( ferror(Fp) ) + { + throw FormatError( "Document::ReadInt16()", " file error." ); + } + throw FormatError( "Document::ReadInt16()", "EOF." ); } - errno = 0; - g = SwapShort(g); + g = SwapShort(g); return g; } @@ -2147,17 +2416,19 @@ guint16 gdcmDocument::ReadInt16(void) { * (swaps it depending on processor endianity) * @return read value */ -guint32 gdcmDocument::ReadInt32(void) { - guint32 g; - size_t item_read; - item_read = fread (&g, (size_t)4,(size_t)1, fp); - if ( item_read != 1 ) { - if(ferror(fp)) - dbg.Verbose(0, "gdcmDocument::ReadInt32", " File Error"); - errno = 1; - return 0; +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 ) + { + if( ferror(Fp) ) + { + throw FormatError( "Document::ReadInt16()", " file error." ); + } + throw FormatError( "Document::ReadInt32()", "EOF." ); } - errno = 0; g = SwapLong(g); return g; } @@ -2167,19 +2438,22 @@ guint32 gdcmDocument::ReadInt32(void) { * \warning NOT end user intended method ! * @return */ -void gdcmDocument::SkipBytes(guint32 NBytes) { +void Document::SkipBytes(uint32_t nBytes) +{ //FIXME don't dump the returned value - (void)fseek(fp, (long)NBytes, SEEK_CUR); + (void)fseek(Fp, (long)nBytes, SEEK_CUR); } /** * \brief Loads all the needed Dictionaries * \warning NOT end user intended method ! */ -void gdcmDocument::Initialise(void) +void Document::Initialise() { - RefPubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict(); - RefShaDict = (gdcmDict*)0; + RefPubDict = Global::GetDicts()->GetDefaultPubDict(); + RefShaDict = NULL; + RLEInfo = new RLEFramesInfo; + JPEGInfo = new JPEGFragmentsInfo; } /** @@ -2190,36 +2464,40 @@ void gdcmDocument::Initialise(void) * 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. // 0x00000004. Finding the swap code in then straigthforward. Trouble // occurs when we can't find such group... - guint32 x=4; // x : for ntohs + uint32_t x = 4; // x : for ntohs bool net2host; // true when HostByteOrder is the same as NetworkByteOrder - guint32 s32; - guint16 s16; + uint32_t s32; + uint16_t s16; - int lgrLue; - char *entCur; char deb[HEADER_LENGTH_TO_READ]; // First, compare HostByteOrder and NetworkByteOrder in order to // determine if we shall need to swap bytes (i.e. the Endian type). - if (x==ntohs(x)) + if ( x == ntohs(x) ) + { net2host = true; + } else - net2host = false; + { + net2host = false; + } // 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". - lgrLue = fread(deb, 1, HEADER_LENGTH_TO_READ, fp); + int lgrLue = fread(deb, 1, HEADER_LENGTH_TO_READ, Fp); + (void)lgrLue; //FIXME not used - entCur = deb + 128; - if(memcmp(entCur, "DICM", (size_t)4) == 0) { - dbg.Verbose(1, "gdcmDocument::CheckSwap:", "looks like DICOM Version3"); + char *entCur = deb + 128; + if( memcmp(entCur, "DICM", (size_t)4) == 0 ) + { + dbg.Verbose(1, "Document::CheckSwap:", "looks like DICOM Version3"); // Next, determine the value representation (VR). Let's skip to the // first element (0002, 0000) and check there if we find "UL" @@ -2243,51 +2521,51 @@ bool gdcmDocument::CheckSwap() { // but elem 0002,0010 (Transfert Syntax) tells us the file is // *Implicit* VR. -and it is !- - if( (memcmp(entCur, "UL", (size_t)2) == 0) || - (memcmp(entCur, "OB", (size_t)2) == 0) || - (memcmp(entCur, "UI", (size_t)2) == 0) || - (memcmp(entCur, "CS", (size_t)2) == 0) ) // CS, to remove later + if( memcmp(entCur, "UL", (size_t)2) == 0 || + memcmp(entCur, "OB", (size_t)2) == 0 || + memcmp(entCur, "UI", (size_t)2) == 0 || + memcmp(entCur, "CS", (size_t)2) == 0 ) // CS, to remove later // when Write DCM *adds* // FIXME - // Use gdcmDocument::dicom_vr to test all the possibilities + // Use Document::dicom_vr to test all the possibilities // instead of just checking for UL, OB and UI !? group 0000 { - filetype = gdcmExplicitVR; - dbg.Verbose(1, "gdcmDocument::CheckSwap:", + Filetype = ExplicitVR; + dbg.Verbose(1, "Document::CheckSwap:", "explicit Value Representation"); } else { - filetype = gdcmImplicitVR; - dbg.Verbose(1, "gdcmDocument::CheckSwap:", + Filetype = ImplicitVR; + dbg.Verbose(1, "Document::CheckSwap:", "not an explicit Value Representation"); } - if (net2host) + if ( net2host ) { - sw = 4321; - dbg.Verbose(1, "gdcmDocument::CheckSwap:", + SwapCode = 4321; + dbg.Verbose(1, "Document::CheckSwap:", "HostByteOrder != NetworkByteOrder"); - } + } else { - sw = 0; - dbg.Verbose(1, "gdcmDocument::CheckSwap:", + SwapCode = 0; + dbg.Verbose(1, "Document::CheckSwap:", "HostByteOrder = NetworkByteOrder"); } // Position the file position indicator at first tag (i.e. // after the file preamble and the "DICM" string). - rewind(fp); - fseek (fp, 132L, SEEK_SET); + rewind(Fp); + fseek (Fp, 132L, SEEK_SET); return true; } // End of DicomV3 // Alas, this is not a DicomV3 file and whatever happens there is no file // preamble. We can reset the file position indicator to where the data // is (i.e. the beginning of the file). - dbg.Verbose(1, "gdcmDocument::CheckSwap:", "not a DICOM Version3 file"); - rewind(fp); + dbg.Verbose(1, "Document::CheckSwap:", "not a DICOM Version3 file"); + rewind(Fp); // 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. @@ -2298,69 +2576,69 @@ bool gdcmDocument::CheckSwap() { // We assume the array of char we are considering contains the binary // representation of a 32 bits integer. Hence the following dirty // trick : - s32 = *((guint32 *)(entCur)); + s32 = *((uint32_t *)(entCur)); - switch (s32) { + switch( s32 ) + { case 0x00040000 : - sw = 3412; - filetype = gdcmACR; + SwapCode = 3412; + Filetype = ACR; return true; case 0x04000000 : - sw = 4321; - filetype = gdcmACR; + SwapCode = 4321; + Filetype = ACR; return true; case 0x00000400 : - sw = 2143; - filetype = gdcmACR; + SwapCode = 2143; + Filetype = ACR; return true; case 0x00000004 : - sw = 0; - filetype = gdcmACR; + SwapCode = 0; + Filetype = ACR; return true; default : - - // We are out of luck. It is not a DicomV3 nor a 'clean' ACR/NEMA file. - // It is time for despaired wild guesses. - // 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 - // to determine ' sw' 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-) - // the file IS NOT ACR-NEMA nor DICOM V3 - // Find a trick to tell it the caller... + // We are out of luck. It is not a DicomV3 nor a 'clean' ACR/NEMA file. + // It is time for despaired wild guesses. + // 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 + // 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-) + // the file IS NOT ACR-NEMA nor DICOM V3 + // Find a trick to tell it the caller... - s16 = *((guint16 *)(deb)); + s16 = *((uint16_t *)(deb)); - switch (s16) { - case 0x0002 : - case 0x0004 : - case 0x0008 : - sw = 0; - filetype = gdcmACR; - return true; - case 0x0200 : - case 0x0400 : - case 0x0800 : - sw = 4321; - filetype = gdcmACR; - return true; - default : - dbg.Verbose(0, "gdcmDocument::CheckSwap:", + switch ( s16 ) + { + case 0x0002 : + case 0x0004 : + case 0x0008 : + SwapCode = 0; + Filetype = ACR; + return true; + case 0x0200 : + case 0x0400 : + case 0x0800 : + SwapCode = 4321; + Filetype = ACR; + return true; + default : + dbg.Verbose(0, "Document::CheckSwap:", "ACR/NEMA unfound swap info (Really hopeless !)"); - filetype = gdcmUnknown; - return false; - } - - // Then the only info we have is the net2host one. - //if (! net2host ) - // sw = 0; + Filetype = Unknown; + return false; + } + // Then the only info we have is the net2host one. + //if (! net2host ) + // SwapCode = 0; //else - // sw = 4321; + // SwapCode = 4321; //return; } } @@ -2369,61 +2647,65 @@ bool gdcmDocument::CheckSwap() { * \brief Restore the unproperly loaded values i.e. the group, the element * and the dictionary entry depending on them. */ -void gdcmDocument::SwitchSwapToBigEndian(void) +void Document::SwitchSwapToBigEndian() { - dbg.Verbose(1, "gdcmDocument::SwitchSwapToBigEndian", + dbg.Verbose(1, "Document::SwitchSwapToBigEndian", "Switching to BigEndian mode."); - if ( sw == 0 ) + if ( SwapCode == 0 ) { - sw = 4321; - return; + SwapCode = 4321; } - if ( sw == 4321 ) + else if ( SwapCode == 4321 ) { - sw = 0; - return; + SwapCode = 0; } - if ( sw == 3412 ) + else if ( SwapCode == 3412 ) { - sw = 2143; - return; + SwapCode = 2143; + } + else if ( SwapCode == 2143 ) + { + SwapCode = 3412; } - if ( sw == 2143 ) - sw = 3412; } /** * \brief during parsing, Header Elements too long are not loaded in memory - * @param NewSize + * @param newSize */ -void gdcmDocument::SetMaxSizeLoadEntry(long NewSize) +void Document::SetMaxSizeLoadEntry(long newSize) { - if (NewSize < 0) + if ( newSize < 0 ) + { return; - if ((guint32)NewSize >= (guint32)0xffffffff) + } + if ((uint32_t)newSize >= (uint32_t)0xffffffff ) { MaxSizeLoadEntry = 0xffffffff; return; } - MaxSizeLoadEntry = NewSize; + MaxSizeLoadEntry = newSize; } /** * \brief Header Elements too long will not be printed - * \todo See comments of \ref gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE - * @param NewSize + * \todo See comments of \ref Document::MAX_SIZE_PRINT_ELEMENT_VALUE + * @param newSize */ -void gdcmDocument::SetMaxSizePrintEntry(long NewSize) +void Document::SetMaxSizePrintEntry(long newSize) { - if (NewSize < 0) + //DOH !! This is exactly SetMaxSizeLoadEntry FIXME FIXME + if ( newSize < 0 ) + { return; - if ((guint32)NewSize >= (guint32)0xffffffff) + } + if ((uint32_t)newSize >= (uint32_t)0xffffffff ) { MaxSizePrintEntry = 0xffffffff; return; } - MaxSizePrintEntry = NewSize; + MaxSizePrintEntry = newSize; } @@ -2435,487 +2717,469 @@ void gdcmDocument::SetMaxSizePrintEntry(long NewSize) * gets the VR, gets the length, gets the offset value) * @return On succes the newly created DocEntry, NULL on failure. */ -gdcmDocEntry *gdcmDocument::ReadNextDocEntry(void) { - guint16 g,n; - gdcmDocEntry *NewEntry; - g = ReadInt16(); - n = ReadInt16(); - - if (errno == 1) +DocEntry* Document::ReadNextDocEntry() +{ + uint16_t group; + uint16_t elem; + + try + { + group = ReadInt16(); + elem = ReadInt16(); + } + catch ( FormatError e ) + { // We reached the EOF (or an error occured) therefore // header parsing has to be considered as finished. - return (gdcmDocEntry *)0; - -// Pb : how to propagate the element length (used in SkipDocEntry) -// direct call to SkipBytes ? - -// if (ignoreShadow == 1 && g%2 ==1) - // if user wants to skip shadow groups - // and current element *is* a shadow element - // we don't create anything -// return (gdcmDocEntry *)1; // to tell caller it's NOT finished - - NewEntry = NewDocEntryByNumber(g, n); - FindDocEntryVR(NewEntry); - FindDocEntryLength(NewEntry); - - if (errno == 1) { - // Call it quits - delete NewEntry; - return NULL; + //std::cout << e; + return 0; } - NewEntry->SetOffset(ftell(fp)); - return NewEntry; -} -/** - * \brief Build a new Element Value from all the low level arguments. - * Check for existence of dictionary entry, and build - * a default one when absent. - * @param Name Name of the underlying DictEntry - */ -gdcmDocEntry *gdcmDocument::NewDocEntryByName(std::string Name) -{ - gdcmDictEntry *NewTag = GetDictEntryByName(Name); - if (!NewTag) - NewTag = NewVirtualDictEntry(0xffff, 0xffff, "LO", "unkn", Name); + DocEntry *newEntry = NewDocEntryByNumber(group, elem); + FindDocEntryVR(newEntry); - gdcmDocEntry* NewEntry = new gdcmDocEntry(NewTag); - if (!NewEntry) + try { - dbg.Verbose(1, "gdcmDocument::ObtainDocEntryByName", - "failed to allocate gdcmDocEntry"); - return (gdcmDocEntry *)0; + FindDocEntryLength(newEntry); + } + catch ( FormatError e ) + { + // Call it quits + //std::cout << e; + delete newEntry; + return 0; } - return NewEntry; -} -/** - * \brief Request a new virtual dict entry to the dict set - * @param group group number of the underlying DictEntry - * @param element element number of the underlying DictEntry - * @param vr VR of the underlying DictEntry - * @param fourth owner group - * @param name english name - */ -gdcmDictEntry *gdcmDocument::NewVirtualDictEntry(guint16 group, guint16 element, - std::string vr, - std::string fourth, - std::string name) -{ - return gdcmGlobal::GetDicts()->NewVirtualDictEntry(group,element,vr,fourth,name); + newEntry->SetOffset(ftell(Fp)); + + return newEntry; } + /** - * \brief Build a new Element Value from all the low level arguments. - * Check for existence of dictionary entry, and build - * a default one when absent. - * @param Group group number of the underlying DictEntry - * @param Elem element number of the underlying DictEntry + * \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. */ -gdcmDocEntry *gdcmDocument::NewDocEntryByNumber(guint16 Group, guint16 Elem) +uint32_t Document::GenerateFreeTagKeyInGroup(uint16_t group) { - // Find out if the tag we encountered is in the dictionaries: - gdcmDictEntry *DictEntry = GetDictEntryByNumber(Group, Elem); - if (!DictEntry) - DictEntry = NewVirtualDictEntry(Group, Elem); - - gdcmDocEntry *NewEntry = new gdcmDocEntry(DictEntry); - if (!NewEntry) + for (uint32_t elem = 0; elem < UINT32_MAX; elem++) { - dbg.Verbose(1, "gdcmDocument::NewDocEntryByNumber", - "failed to allocate gdcmDocEntry"); - return NULL; + TagKey key = DictEntry::TranslateToKey(group, elem); + if (TagHT.count(key) == 0) + { + return elem; + } } - return NewEntry; + return UINT32_MAX; } - /** - * \brief Build a new Element Value from all the low level arguments. - * Check for existence of dictionary entry, and build - * a default one when absent. - * @param Group group number of the underlying DictEntry - * @param Elem element number of the underlying DictEntry + * \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 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 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. */ -gdcmValEntry *gdcmDocument::NewValEntryByNumber(guint16 Group, guint16 Elem) +bool Document::ReadTag(uint16_t testGroup, uint16_t testElement) { - // Find out if the tag we encountered is in the dictionaries: - gdcmDictEntry *DictEntry = GetDictEntryByNumber(Group, Elem); - if (!DictEntry) - DictEntry = NewVirtualDictEntry(Group, Elem); - - gdcmValEntry *NewEntry = new gdcmValEntry(DictEntry); - if (!NewEntry) + long positionOnEntry = ftell(Fp); + long currentPosition = ftell(Fp); // 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(); + if ( itemTagGroup != testGroup || itemTagElement != testElement ) { - dbg.Verbose(1, "gdcmDocument::NewValEntryByNumber", - "failed to allocate gdcmValEntry"); - return NULL; + 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, "Document::ReadItemTagLength: wrong Item Tag found:"); + dbg.Verbose(0, s.str().c_str()); + fseek(Fp, positionOnEntry, SEEK_SET); + + return false; } - return NewEntry; + return true; } - /** - * \brief Build a new Element Value from all the low level arguments. - * Check for existence of dictionary entry, and build - * a default one when absent. - * @param Group group number of the underlying DictEntry - * @param Elem element number of the underlying DictEntry + * \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 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 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. */ -gdcmBinEntry *gdcmDocument::NewBinEntryByNumber(guint16 Group, guint16 Elem) +uint32_t Document::ReadTagLength(uint16_t testGroup, uint16_t testElement) { - // Find out if the tag we encountered is in the dictionaries: - gdcmDictEntry *DictEntry = GetDictEntryByNumber(Group, Elem); - if (!DictEntry) - DictEntry = NewVirtualDictEntry(Group, Elem); + long positionOnEntry = ftell(Fp); + (void)positionOnEntry; - gdcmBinEntry *NewEntry = new gdcmBinEntry(DictEntry); - if (!NewEntry) + if ( !ReadTag(testGroup, testElement) ) { - dbg.Verbose(1, "gdcmDocument::NewBinEntryByNumber", - "failed to allocate gdcmBinEntry"); - return NULL; + return 0; + } + + //// Then read the associated Item Length + long currentPosition = ftell(Fp); + 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, "Document::ReadItemTagLength: ", s.str().c_str()); } - return NewEntry; + return itemLength; } /** - * \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. + * \brief When parsing the Pixel Data of an encapsulated file, read + * the basic offset table (when present, and BTW dump it). */ -guint32 gdcmDocument::GenerateFreeTagKeyInGroup(guint16 group) +void Document::ReadAndSkipEncapsulatedBasicOffsetTable() { - for (guint32 elem = 0; elem < UINT32_MAX; elem++) + //// 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 ) { - TagKey key = gdcmDictEntry::TranslateToKey(group, elem); - if (tagHT.count(key) == 0) - return elem; + char* basicOffsetTableItemValue = new char[itemLength + 1]; + fread(basicOffsetTableItemValue, itemLength, 1, Fp); + +#ifdef GDCM_DEBUG + for (unsigned int i=0; i < itemLength; i += 4 ) + { + uint32_t individualLength = str2num( &basicOffsetTableItemValue[i], + uint32_t); + std::ostringstream s; + s << " Read one length: "; + s << std::hex << individualLength << std::endl; + dbg.Verbose(0, + "Document::ReadAndSkipEncapsulatedBasicOffsetTable: ", + s.str().c_str()); + } +#endif //GDCM_DEBUG + + delete[] basicOffsetTableItemValue; } - return UINT32_MAX; } - /** - * \brief Searches both the public and the shadow dictionary (when they - * exist) for the presence of the DictEntry with given name. - * The public dictionary has precedence on the shadow one. - * @param Name name of the searched DictEntry - * @return Corresponding DictEntry when it exists, NULL otherwise. + * \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. */ -gdcmDictEntry *gdcmDocument::GetDictEntryByName(std::string Name) +void Document::ComputeRLEInfo() { - gdcmDictEntry *found = (gdcmDictEntry *)0; - if (!RefPubDict && !RefShaDict) + if ( ! IsRLELossLessTransferSyntax() ) { - dbg.Verbose(0, "gdcmDocument::GetDictEntry", - "we SHOULD have a default dictionary"); + return; } - if (RefPubDict) - { - found = RefPubDict->GetDictEntryByName(Name); - if (found) - return found; + + // Encoded pixel data: for the time being we are only concerned with + // Jpeg or RLE Pixel data encodings. + // As stated in PS 3.5-2003, section 8.2 p44: + // "If sent in Encapsulated Format (i.e. other than the Native Format) the + // value representation OB is used". + // Hence we expect an OB value representation. Concerning OB VR, + // the section PS 3.5-2003, section A.4.c p 58-59, states: + // "For the Value Representations OB and OW, the encoding shall meet the + // following specifications depending on the Data element tag:" + // [...snip...] + // - the first item in the sequence of items before the encoded pixel + // data stream shall be basic offset table item. The basic offset table + // item value, however, is not required to be present" + + ReadAndSkipEncapsulatedBasicOffsetTable(); + + // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G) + // Loop on the individual frame[s] and store the information + // on the RLE fragments in a RLEFramesInfo. + // Note: - when only a single frame is present, this is a + // classical image. + // - when more than one frame are present, then we are in + // the case of a multi-frame image. + long frameLength; + while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) ) + { + // Parse the RLE Header and store the corresponding RLE Segment + // Offset Table information on fragments of this current Frame. + // Note that the fragment pixels themselves are not loaded + // (but just skipped). + long frameOffset = ftell(Fp); + + uint32_t nbRleSegments = ReadInt32(); + + uint32_t rleSegmentOffsetTable[15]; + for( int k = 1; k <= 15; k++ ) + { + rleSegmentOffsetTable[k] = ReadInt32(); + } + + // Deduce from both the RLE Header and the frameLength the + // fragment length, and again store this info in a + // RLEFramesInfo. + long rleSegmentLength[15]; + // skipping (not reading) RLE Segments + if ( nbRleSegments > 1) + { + for(unsigned int k = 1; k <= nbRleSegments-1; k++) + { + rleSegmentLength[k] = rleSegmentOffsetTable[k+1] + - rleSegmentOffsetTable[k]; + SkipBytes(rleSegmentLength[k]); + } + } + + rleSegmentLength[nbRleSegments] = frameLength + - rleSegmentOffsetTable[nbRleSegments]; + SkipBytes(rleSegmentLength[nbRleSegments]); + + // Store the collected info + RLEFrame* newFrameInfo = new RLEFrame; + newFrameInfo->NumberFragments = nbRleSegments; + for( unsigned int uk = 1; uk <= nbRleSegments; uk++ ) + { + newFrameInfo->Offset[uk] = frameOffset + rleSegmentOffsetTable[uk]; + newFrameInfo->Length[uk] = rleSegmentLength[uk]; + } + RLEInfo->Frames.push_back( newFrameInfo ); } - if (RefShaDict) + + // Make sure that at the end of the item we encounter a 'Sequence + // Delimiter Item': + if ( !ReadTag(0xfffe, 0xe0dd) ) { - found = RefShaDict->GetDictEntryByName(Name); - if (found) - return found; + dbg.Verbose(0, "Document::ComputeRLEInfo: no sequence delimiter "); + dbg.Verbose(0, " item at end of RLE item sequence"); } - return found; } /** - * \brief Searches both the public and the shadow dictionary (when they - * exist) for the presence of the DictEntry with given - * group and element. The public dictionary has precedence on the - * shadow one. - * @param group group number of the searched DictEntry - * @param element element number of the searched DictEntry - * @return Corresponding DictEntry when it exists, NULL otherwise. + * \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. */ -gdcmDictEntry *gdcmDocument::GetDictEntryByNumber(guint16 group,guint16 element) +void Document::ComputeJPEGFragmentInfo() { - gdcmDictEntry *found = (gdcmDictEntry *)0; - if (!RefPubDict && !RefShaDict) + // If you need to, look for comments of ComputeRLEInfo(). + if ( ! IsJPEGTransferSyntax() ) { - dbg.Verbose(0, "gdcmDocument::GetDictEntry", - "we SHOULD have a default dictionary"); + return; } - if (RefPubDict) - { - found = RefPubDict->GetDictEntryByNumber(group, element); - if (found) - return found; + + ReadAndSkipEncapsulatedBasicOffsetTable(); + + // Loop on the fragments[s] and store the parsed information in a + // JPEGInfo. + long fragmentLength; + while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) ) + { + long fragmentOffset = ftell(Fp); + + // Store the collected info + JPEGFragment* newFragment = new JPEGFragment; + newFragment->Offset = fragmentOffset; + newFragment->Length = fragmentLength; + JPEGInfo->Fragments.push_back( newFragment ); + + SkipBytes( fragmentLength ); } - if (RefShaDict) + + // Make sure that at the end of the item we encounter a 'Sequence + // Delimiter Item': + if ( !ReadTag(0xfffe, 0xe0dd) ) { - found = RefShaDict->GetDictEntryByNumber(group, element); - if (found) - return found; + dbg.Verbose(0, "Document::ComputeRLEInfo: no sequence delimiter "); + dbg.Verbose(0, " item at end of JPEG item sequence"); } - return found; } - /** - * \ingroup gdcmDocument - * \brief Parse pixel data from disk for multi-fragment Jpeg/Rle files - * \ No other way so 'skip' the Data - * + * \brief Walk recursively the given \ref DocEntrySet, and feed + * the given hash table (\ref TagDocEntryHT) with all the + * \ref DocEntry (Dicom entries) encountered. + * This method does the job for \ref BuildFlatHashTable. + * @param builtHT Where to collect all the \ref DocEntry encountered + * when recursively walking the given set. + * @param set The structure to be traversed (recursively). */ -void gdcmDocument::Parse7FE0 (void) { - - gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return; - - std::string Transfer = ((gdcmValEntry *)Element)->GetValue(); - if (Transfer == UI1_2_840_10008_1_2 ) - return; - if ( Transfer == UI1_2_840_10008_1_2_1 ) - return; - if ( Transfer == UI1_2_840_10008_1_2_2 ) //1.2.2 ??? A verifier ! - return; - if ( Transfer == UI1_2_840_10008_1_2_1_99 ) - return; - - int nb; - std::string str_nb=GetEntryByNumber(0x0028,0x0100); - if (str_nb == GDCM_UNFOUND ) { - nb = 16; - } else { - nb = atoi(str_nb.c_str() ); - if (nb == 12) nb =16; - } - - guint16 ItemTagGr,ItemTagEl; - int ln; - long ftellRes; - - // -------------------- for Parsing : Position on begining of Jpeg/RLE Pixels - - if ( Transfer != UI1_1_2_840_10008_1_2_5 ) { // !RLELossLessTransferSyntax - // JPEG Image - ftellRes=ftell(fp); - fread(&ItemTagGr,2,1,fp); //Reading (fffe):Basic Offset Table Item Tag Gr - fread(&ItemTagEl,2,1,fp); //Reading (e000):Basic Offset Table Item Tag El - if(GetSwapCode()) { - ItemTagGr=SwapShort(ItemTagGr); - ItemTagEl=SwapShort(ItemTagEl); - } - printf ("at %x : ItemTag (should be fffe,e000): %04x,%04x\n", - (unsigned)ftellRes,ItemTagGr,ItemTagEl ); - ftellRes=ftell(fp); - fread(&ln,4,1,fp); - if(GetSwapCode()) - ln=SwapLong(ln); // Basic Offset Table Item Length - printf("at %x : Basic Offset Table Item Length (\?\?) %d x(%08x)\n", - (unsigned)ftellRes,ln,ln); - if (ln != 0) { - // What is it used for ?? - char * BasicOffsetTableItemValue= new char[ln+1]; - fread(BasicOffsetTableItemValue,ln,1,fp); - guint32 a; - for (int i=0;i ( set ) ) + { + TagDocEntryHT* currentHT = elementSet->GetTagHT(); + for( TagDocEntryHT::const_iterator i = currentHT->begin(); + i != currentHT->end(); + ++i) + { + DocEntry* entry = i->second; + if ( SeqEntry* seqEntry = dynamic_cast(entry) ) + { + ListSQItem& items = seqEntry->GetSQItems(); + for( ListSQItem::const_iterator item = items.begin(); + item != items.end(); + ++item) + { + BuildFlatHashTableRecurse( builtHT, *item ); + } + continue; } - printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n", - (unsigned)ftellRes,ItemTagGr,ItemTagEl ); - } + builtHT[entry->GetKey()] = entry; + } + return; + } - } else { - - // RLE Image - long RleSegmentLength[15],fragmentLength; - guint32 nbRleSegments; - guint32 RleSegmentOffsetTable[15]; - ftellRes=ftell(fp); - // Basic Offset Table with Item Value - // Item Tag - fread(&ItemTagGr,2,1,fp); //Reading (fffe):Basic Offset Table Item Tag Gr - fread(&ItemTagEl,2,1,fp); //Reading (e000):Basic Offset Table Item Tag El - if(GetSwapCode()) { - ItemTagGr=SwapShort(ItemTagGr); - ItemTagEl=SwapShort(ItemTagEl); - } - printf ("at %x : ItemTag (should be fffe,e000): %04x,%04x\n", - (unsigned)ftellRes,ItemTagGr,ItemTagEl ); - // Item Length - ftellRes=ftell(fp); - fread(&ln,4,1,fp); - if(GetSwapCode()) - ln=SwapLong(ln); // Basic Offset Table Item Length - printf("at %x : Basic Offset Table Item Length (\?\?) %d x(%08x)\n", - (unsigned)ftellRes,ln,ln); - if (ln != 0) { - // What is it used for ?? - char * BasicOffsetTableItemValue= new char[ln+1]; - fread(BasicOffsetTableItemValue,ln,1,fp); - guint32 a; - for (int i=0;i ( set ) ) + { + ListDocEntry& currentList = SQItemSet->GetDocEntries(); + for (ListDocEntry::iterator i = currentList.begin(); + i != currentList.end(); + ++i) + { + DocEntry* entry = *i; + if ( SeqEntry* seqEntry = dynamic_cast(entry) ) + { + ListSQItem& items = seqEntry->GetSQItems(); + for( ListSQItem::const_iterator item = items.begin(); + item != items.end(); + ++item) + { + BuildFlatHashTableRecurse( builtHT, *item ); + } + continue; } + builtHT[entry->GetKey()] = entry; + } - if (nbRleSegments>1) { // skipping (not reading) RLE Segments - for(unsigned int k=1; k<=nbRleSegments-1; k++) { - RleSegmentLength[k]= RleSegmentOffsetTable[k+1] - - RleSegmentOffsetTable[k]; - ftellRes=ftell(fp); - printf (" Segment %d : Length = %d x(%x) Start at %x\n", - k,(unsigned)RleSegmentLength[k],(unsigned)RleSegmentLength[k], (unsigned)ftellRes); - fseek(fp,RleSegmentLength[k],SEEK_CUR); - } - } - RleSegmentLength[nbRleSegments]= fragmentLength - - RleSegmentOffsetTable[nbRleSegments]; - ftellRes=ftell(fp); - printf (" Segment %d : Length = %d x(%x) Start at %x\n", - nbRleSegments,(unsigned)RleSegmentLength[nbRleSegments], - (unsigned)RleSegmentLength[nbRleSegments],(unsigned)ftellRes); - - fseek(fp,RleSegmentLength[nbRleSegments],SEEK_CUR); - - // ------------------ end of scanning fragment pixels - - ftellRes=ftell(fp); - fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr - fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El - if(GetSwapCode()) { - ItemTagGr=SwapShort(ItemTagGr); - ItemTagEl=SwapShort(ItemTagEl); - } - printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n", - (unsigned)ftellRes,ItemTagGr,ItemTagEl ); - } } - return; } /** - * \brief Compares two documents, according to \ref gdcmDicomDir rules + * \brief Build a \ref TagDocEntryHT (i.e. a std::map<>) from the current + * Document. + * + * The structure used by a Document (through \ref ElementSet), + * in order to old the parsed entries of a Dicom header, is a recursive + * one. This is due to the fact that the sequences (when present) + * can be nested. Additionaly, the sequence items (represented in + * gdcm as \ref SQItem) add an extra complexity to the data + * structure. Hence, a gdcm user whishing to visit all the entries of + * a Dicom header will need to dig in the gdcm internals (which + * implies exposing all the internal data structures to the API). + * In order to avoid this burden to the user, \ref BuildFlatHashTable + * recursively builds a temporary hash table, which holds all the + * Dicom entries in a flat structure (a \ref TagDocEntryHT i.e. a + * std::map<>). + * \warning Of course there is NO integrity constrain between the + * returned \ref TagDocEntryHT and the \ref ElementSet used + * to build it. Hence if the underlying \ref ElementSet is + * altered, then it is the caller responsability to invoke + * \ref BuildFlatHashTable again... + * @return The flat std::map<> we juste build. + */ +TagDocEntryHT* Document::BuildFlatHashTable() +{ + TagDocEntryHT* FlatHT = new TagDocEntryHT; + BuildFlatHashTableRecurse( *FlatHT, this ); + return FlatHT; +} + + + +/** + * \brief Compares two documents, according to \ref 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){ - std::string s1,s2; - +bool Document::operator<(Document &document) +{ // Patient Name - s1=this->GetEntryByNumber(0x0010,0x0010); - s2=document.GetEntryByNumber(0x0010,0x0010); + std::string s1 = GetEntryByNumber(0x0010,0x0010); + std::string s2 = document.GetEntryByNumber(0x0010,0x0010); if(s1 < s2) - return(true); - else if(s1 > s2) - return(false); + { + return true; + } + else if( s1 > s2 ) + { + return false; + } else { // Patient ID - s1=this->GetEntryByNumber(0x0010,0x0020); - s2=document.GetEntryByNumber(0x0010,0x0020); - if (s1 < s2) - return(true); - else if (s1 > s2) - return(1); + s1 = GetEntryByNumber(0x0010,0x0020); + s2 = document.GetEntryByNumber(0x0010,0x0020); + if ( s1 < s2 ) + { + return true; + } + else if ( s1 > s2 ) + { + return false; + } else { // Study Instance UID - s1=this->GetEntryByNumber(0x0020,0x000d); - s2=document.GetEntryByNumber(0x0020,0x000d); - if (s1 < s2) - return(true); - else if(s1 > s2) - return(false); + s1 = GetEntryByNumber(0x0020,0x000d); + s2 = document.GetEntryByNumber(0x0020,0x000d); + if ( s1 < s2 ) + { + return true; + } + else if( s1 > s2 ) + { + return false; + } else { // Serie Instance UID - s1=this->GetEntryByNumber(0x0020,0x000e); - s2=document.GetEntryByNumber(0x0020,0x000e); - if (s1 < s2) - return(true); - else if(s1 > s2) - return(false); + s1 = GetEntryByNumber(0x0020,0x000e); + s2 = document.GetEntryByNumber(0x0020,0x000e); + if ( s1 < s2 ) + { + return true; + } + else if( s1 > s2 ) + { + return false; + } } } } - return(false); + return false; } +} // end namespace gdcm //-----------------------------------------------------------------------------