X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=10fd52f39b03b6b8e7301947ab205a10aa755220;hb=ab62b1a706df8e2ab1fbf26fa5037d6c22293655;hp=7f87beacd41a43e9ed9bc2425fd49c6fcf86a883;hpb=e49dda75179644e228e33af72931535878799dff;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 7f87beac..10fd52f3 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -1,12 +1,30 @@ -// gdcmDocument.cxx -//----------------------------------------------------------------------------- +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmDocument.cxx,v $ + Language: C++ + Date: $Date: 2004/08/02 16:42:14 $ + Version: $Revision: 1.65 $ + + Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de + l'Image). All rights reserved. See Doc/License.txt or + http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details. + + 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: @@ -18,24 +36,45 @@ # include +// Implicit VR Little Endian #define UI1_2_840_10008_1_2 "1.2.840.10008.1.2" +// Explicit VR Little Endian #define UI1_2_840_10008_1_2_1 "1.2.840.10008.1.2.1" -#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" - -typedef struct { - guint32 totalSQlength; - guint32 alreadyParsedlength; -} pileElem; +// 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 gdcmDocument::SetMaxSizeLoadEntry() -const unsigned int gdcmDocument::MAX_SIZE_LOAD_ELEMENT_VALUE = 4096; - -const unsigned int gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE = 64; +const unsigned int gdcmDocument::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096 +const unsigned int gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff; //----------------------------------------------------------------------------- // Constructor / Destructor @@ -43,88 +82,122 @@ const unsigned int gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE = 64; /** * \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) { - enableSequences=enable_sequences; - ignoreShadow =ignore_shadow; - + */ +gdcmDocument::gdcmDocument( std::string const & filename ) + : gdcmElementSet(-1) +{ SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); - filename = inFilename; + Filename = filename; Initialise(); - if ( !OpenFile(exception_on_error)) + if ( !OpenFile() ) + { return; + } + + dbg.Verbose(0, "gdcmDocument::gdcmDocument: starting parsing of file: ", + Filename.c_str()); + rewind(Fp); + + fseek(Fp,0L,SEEK_END); + long lgt = ftell(Fp); + + rewind(Fp); + CheckSwap(); + long beg = ftell(Fp); + lgt -= beg; + + SQDepthLevel = 0; + + long l = ParseDES( this, beg, lgt, false); // le Load sera fait a la volee + (void)l; //is l used anywhere ? - rewind(fp); - if (!CheckSwap()) - return NULL; // Du menage à faire avant de sortir ? - LoadDocEntries(); - CloseFile(); + rewind(Fp); + + // Load 'non string' values + + std::string PhotometricInterpretation = GetEntryByNumber(0x0028,0x0004); + if( PhotometricInterpretation == "PALETTE COLOR " ) + { + LoadEntryVoidArea(0x0028,0x1200); // gray LUT + LoadEntryVoidArea(0x0028,0x1201); // R LUT + LoadEntryVoidArea(0x0028,0x1202); // G LUT + LoadEntryVoidArea(0x0028,0x1203); // B LUT + + LoadEntryVoidArea(0x0028,0x1221); // Segmented Red Palette Color LUT Data + LoadEntryVoidArea(0x0028,0x1222); // Segmented Green Palette Color LUT Data + LoadEntryVoidArea(0x0028,0x1223); // Segmented Blue Palette Color LUT Data + } + //FIXME later : how to use it? + LoadEntryVoidArea(0x0028,0x3006); //LUT Data (CTX dependent) + + CloseFile(); + + // -------------------------------------------------------------- + // 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 + // + std::string RecCode; + RecCode = GetEntryByNumber(0x0008, 0x0010); // recognition code + if (RecCode == "ACRNEMA_LIBIDO_1.1" || + RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares + // with "little-endian strings" + { + Filetype = gdcmACR_LIBIDO; + std::string rows = GetEntryByNumber(0x0028, 0x0010); + std::string columns = GetEntryByNumber(0x0028, 0x0011); + SetEntryByNumber(columns, 0x0028, 0x0010); + SetEntryByNumber(rows , 0x0028, 0x0011); + } + // ----------------- End of ACR-LibIDO kludge ------------------ - wasUpdated = 0; // will be set to 1 if user adds an entry - 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 gdcmDocument::SetFileName and then the parsing. */ -gdcmDocument::gdcmDocument(bool exception_on_error) { - (void)exception_on_error; - enableSequences=0; - +gdcmDocument::gdcmDocument() + :gdcmElementSet(-1) +{ SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Initialise(); - - wasUpdated = 0; // will be set to 1 if user adds an entry - printLevel = 1; // 'Medium' print level by default + PrintLevel = 1; // 'Medium' print level by default } /** * \brief Canonical destructor. */ -gdcmDocument::~gdcmDocument (void) { +gdcmDocument::~gdcmDocument () +{ RefPubDict = NULL; RefShaDict = NULL; + + // Recursive clean up of sequences + for (TagDocEntryHT::const_iterator it = TagHT.begin(); + it != TagHT.end(); ++it ) + { + delete it->second; + } + TagHT.clear(); } //----------------------------------------------------------------------------- // Print -/** - * \brief Prints the Doc Entries (Dicom Elements) - * from the chained list - * @return - */ -void gdcmDocument::PrintEntry(std::ostream & os) { - - for (ListTag::iterator i = listEntries.begin(); - i != listEntries.end(); - ++i) - { - (*i)->SetPrintLevel(printLevel); - (*i)->Print(os); - } -} - /** * \brief Prints The Dict Entries of THE public Dicom Dictionary * @return */ -void gdcmDocument::PrintPubDict(std::ostream & os) { +void gdcmDocument::PrintPubDict(std::ostream & os) +{ RefPubDict->Print(os); } @@ -132,7 +205,8 @@ void gdcmDocument::PrintPubDict(std::ostream & os) { * \brief Prints The Dict Entries of THE shadow Dicom Dictionary * @return */ -void gdcmDocument::PrintShaDict(std::ostream & os) { +void gdcmDocument::PrintShaDict(std::ostream & os) +{ RefShaDict->Print(os); } @@ -141,33 +215,37 @@ void gdcmDocument::PrintShaDict(std::ostream & os) { /** * \brief Get the public dictionary used */ -gdcmDict *gdcmDocument::GetPubDict(void) { - return(RefPubDict); +gdcmDict *gdcmDocument::GetPubDict() +{ + return RefPubDict; } /** * \brief Get the shadow dictionary used */ -gdcmDict *gdcmDocument::GetShaDict(void) { - return(RefShaDict); +gdcmDict *gdcmDocument::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 gdcmDocument::SetShaDict(gdcmDict *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 gdcmDocument::SetShaDict(DictKey const & dictName) +{ + RefShaDict = gdcmGlobal::GetDicts()->GetDict(dictName); + return !RefShaDict; } /** @@ -178,49 +256,87 @@ bool gdcmDocument::SetShaDict(DictKey dictName){ * @return true when gdcmDocument is the one of a reasonable Dicom/Acr file, * false otherwise. */ -bool gdcmDocument::IsReadable(void) { - if(filetype==Unknown) { - return(false); +bool gdcmDocument::IsReadable() +{ + if( Filetype == gdcmUnknown) + { + std::cout << " gdcmDocument::IsReadable: Filetype " << Filetype + << " " << "gdcmUnknown " << gdcmUnknown << std::endl; //JPR + dbg.Verbose(0, "gdcmDocument::IsReadable: wrong filetype"); + return false; } - if(listEntries.size()<=0) { - return(false); + + if( TagHT.empty() ) + { + dbg.Verbose(0, "gdcmDocument::IsReadable: no tags in internal" + " hash table."); + return false; } - return(true); + return true; } + /** - * \brief Determines if the Transfer Syntax was already encountered - * and if it corresponds to a ImplicitVRLittleEndian one. - * @return True when ImplicitVRLittleEndian found. False in all other cases. + * \brief Internal function that checks whether the Transfer Syntax given + * as argument is the one present in the current document. + * @param SyntaxToCheck The transfert syntax we need to check against. + * @return True when SyntaxToCheck corresponds to the Transfer Syntax of + * the current document. False either when the document contains + * no Transfer Syntax, or when the Tranfer Syntaxes doesn't match. */ -bool gdcmDocument::IsImplicitVRLittleEndianTransferSyntax(void) { - gdcmHeaderEntry *Element = GetHeaderEntryByNumber(0x0002, 0x0010); - if ( !Element ) +bool gdcmDocument::IsGivenTransferSyntax(std::string const & syntaxToCheck) +{ + gdcmDocEntry *entry = GetDocEntryByNumber(0x0002, 0x0010); + if ( !entry ) + { return false; - LoadHeaderEntrySafe(Element); + } - std::string Transfer = Element->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 (gdcmValEntry* valEntry = dynamic_cast< gdcmValEntry* >(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 gdcmDocument::IsGivenTransferSyntax. + * @return True when ImplicitVRLittleEndian found. False in all other cases. + */ +bool gdcmDocument::IsImplicitVRLittleEndianTransferSyntax() +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2); +} + /** * \brief Determines if the Transfer Syntax was already encountered * and if it corresponds to a ExplicitVRLittleEndian one. * @return True when ExplicitVRLittleEndian found. False in all other cases. */ -bool gdcmDocument::IsExplicitVRLittleEndianTransferSyntax(void) { - gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadHeaderEntrySafe(Element); - - std::string Transfer = Element->GetValue(); - if ( Transfer == UI1_2_840_10008_1_2_1 ) - return true; - return false; +bool gdcmDocument::IsExplicitVRLittleEndianTransferSyntax() +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1); } /** @@ -228,16 +344,9 @@ 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) { - gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadHeaderEntrySafe(Element); - - std::string Transfer = Element->GetValue(); - if ( Transfer == UI1_2_840_10008_1_2_1_99 ) - return true; - return false; +bool gdcmDocument::IsDeflatedExplicitVRLittleEndianTransferSyntax() +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1_99); } /** @@ -245,109 +354,185 @@ 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) { - gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadHeaderEntrySafe(Element); +bool gdcmDocument::IsExplicitVRBigEndianTransferSyntax() +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_2); +} - std::string Transfer = Element->GetValue(); - if ( Transfer == UI1_2_840_10008_1_2_2 ) //1.2.2 ??? A verifier ! - return true; - return false; +/** + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEGBaseLineProcess1 one. + * @return True when JPEGBaseLineProcess1found. False in all other cases. + */ +bool gdcmDocument::IsJPEGBaseLineProcess1TransferSyntax() +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_50); +} + +/** + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEGExtendedProcess2-4 one. + * @return True when JPEGExtendedProcess2-4 found. False in all other cases. + */ +bool gdcmDocument::IsJPEGExtendedProcess2_4TransferSyntax() +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_51); +} + +/** + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEGExtendeProcess3-5 one. + * @return True when JPEGExtendedProcess3-5 found. False in all other cases. + */ +bool gdcmDocument::IsJPEGExtendedProcess3_5TransferSyntax() +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_52); } /** - * \brief returns the File Type - * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown) - * @return the FileType code + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEGSpectralSelectionProcess6-8 one. + * @return True when JPEGSpectralSelectionProcess6-8 found. False in all + * other cases. */ -FileType gdcmDocument::GetFileType(void) { - return(filetype); +bool gdcmDocument::IsJPEGSpectralSelectionProcess6_8TransferSyntax() +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_53); } /** - * \brief opens the file - * @param exception_on_error - * @return + * \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. */ -FILE *gdcmDocument::OpenFile(bool exception_on_error) - throw(gdcmFileError) +bool gdcmDocument::IsRLELossLessTransferSyntax() { - fp=fopen(filename.c_str(),"rb"); - if(exception_on_error) - { - if(!fp) - throw gdcmFileError("gdcmDocument::gdcmDocument(const char *, bool)"); - } + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_5); +} - if ( fp ) - { - guint16 zero; - fread(&zero, (size_t)2, (size_t)1, fp); +/** + * \brief Determines if Transfer Syntax was already encountered + * and if it corresponds to a JPEG Lossless one. + * @return True when RLE Lossless found. False in all + * other cases. + */ + +bool gdcmDocument::IsJPEGLossless() +{ + return ( IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_55) + || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_57) + || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_70) ); +} + +/** + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEG2000 one + * @return True when JPEG2000 (Lossly or LossLess) found. False in all + * other cases. + */ +bool gdcmDocument::IsJPEG2000() +{ + return ( IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_90) + || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_91) ); +} + +/** + * \brief Predicate for dicom version 3 file. + * @return True when the file is a dicom version 3. + */ +bool gdcmDocument::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; +} - //ACR -- or DICOM with no Preamble -- - if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200) - return(fp); +/** + * \brief returns the File Type + * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown) + * @return the FileType code + */ +FileType gdcmDocument::GetFileType() +{ + return Filetype; +} - //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); +/** + * \brief Tries to open the file \ref gdcmDocument::Filename and + * checks the preamble when existing. + * @return The FILE pointer on success. + */ +FILE* gdcmDocument::OpenFile() +{ + Fp = fopen(Filename.c_str(),"rb"); - 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, + "gdcmDocument::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, + "gdcmDocument::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 gdcmDocument::CloseFile() +{ + int closed = fclose(Fp); + Fp = 0; + + return closed; } /** - * \brief Writes in a file all the Doc Entries (Dicom Elements) - * of the Chained List + * \brief Writes in a file all the Header Entries (Dicom Elements) * @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 GroupHT from the gdcmDocument) -/// To be checked -/// ============= - +void gdcmDocument::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 + /// no way (check : FileType est un champ de gdcmDocument ...) /// a moins de se livrer a un tres complique ajout des champs manquants. - /// faire un CheckAndCorrectHeader (?) - - if (type == ImplicitVR) + /// faire un CheckAndCorrectHeader (?) + + if (filetype == gdcmImplicitVR) { std::string implicitVRTransfertSyntax = UI1_2_840_10008_1_2; ReplaceOrCreateByNumber(implicitVRTransfertSyntax,0x0002, 0x0010); @@ -355,12 +540,12 @@ 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 == ExplicitVR) + if (filetype == gdcmExplicitVR) { std::string explicitVRTransfertSyntax = UI1_2_840_10008_1_2_1; ReplaceOrCreateByNumber(explicitVRTransfertSyntax,0x0002, 0x0010); @@ -372,63 +557,133 @@ 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); */ + + gdcmElementSet::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. - * \warning Adds the Header Entry to the HTable, NOT to the chained List - * @param Value Value to be set - * @param Group Group of the Entry - * @param Elem Element of the Entry + * @param Value (string) 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). */ -gdcmHeaderEntry * gdcmDocument::ReplaceOrCreateByNumber( - std::string Value, - guint16 Group, - guint16 Elem ){ - gdcmHeaderEntry* a; - a = GetHeaderEntryByNumber( Group, Elem); - if (a == NULL) { - a =NewHeaderEntryByNumber(Group, Elem); - if (a == NULL) + +gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber( + std::string const & value, + uint16_t group, + uint16_t elem ) +{ + gdcmValEntry* valEntry = 0; + + gdcmDocEntry* currentEntry = GetDocEntryByNumber( group, elem); + if (!currentEntry) + { + // The entry wasn't present and we simply create the required ValEntry: + currentEntry = NewDocEntryByNumber(group, elem); + if (!currentEntry) + { + dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: call to" + " NewDocEntryByNumber failed."); return NULL; - AddHeaderEntry(a); - } - //CLEANME SetEntryByNumber(Value, Group, Elem); - a->SetValue(Value); - return(a); + } + valEntry = new gdcmValEntry(currentEntry); + if ( !AddEntry(valEntry)) + { + dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: AddEntry" + " failed allthough this is a creation."); + } + } + else + { + valEntry = dynamic_cast< gdcmValEntry* >(currentEntry); + if ( !valEntry ) + { + // We need to promote the gdcmDocEntry to a gdcmValEntry: + valEntry = new gdcmValEntry(currentEntry); + if (!RemoveEntry(currentEntry)) + { + dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: removal" + " of previous DocEntry failed."); + return NULL; + } + if ( !AddEntry(valEntry)) + { + dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: adding" + " promoted ValEntry failed."); + 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 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, + int lgth, + uint16_t group, + uint16_t elem) +{ + gdcmBinEntry* b = 0; + gdcmDocEntry* a = GetDocEntryByNumber( group, elem); + if (!a) + { + a = NewBinEntryByNumber(group, elem); + if (!a) + { + return 0; + } + + b = new gdcmBinEntry(a); + AddEntry(b); + b->SetVoidArea(voidArea); + } + SetEntryByNumber(voidArea, lgth, group, elem); + //b->SetVoidArea(voidArea); //what if b == 0 !! + + return b; +} + /** * \brief Set a new value if the invoked element exists * Seems to be useless !!! * @param Value new element value - * @param Group group of the Entry - * @param Elem element of the Entry + * @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 gdcmDocument::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; } @@ -436,19 +691,19 @@ bool gdcmDocument::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 El // Protected /** - * \brief Checks if a given Dicom Element exists - * within the H table - * @param group Group number of the searched Dicom Element + * \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 */ -int gdcmDocument::CheckIfEntryExistByNumber(guint16 group, guint16 element ) { - std::string key = gdcmDictEntry::TranslateToKey(group, element ); - return (tagHT.count(key)); +int gdcmDocument::CheckIfEntryExistByNumber(uint16_t group, uint16_t element ) +{ + const std::string &key = gdcmDictEntry::TranslateToKey(group, element ); + return TagHT.count(key); } /** - * \brief Searches within Doc Entries (Dicom Elements) parsed with + * \brief Searches within Header Entries (Dicom Elements) parsed with * the public and private dictionaries * for the element value of a given tag. * \warning Don't use any longer : use GetPubEntryByName @@ -456,16 +711,19 @@ 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) { +std::string gdcmDocument::GetEntryByName(TagName const & tagName) +{ gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); - if( dictEntry == NULL) + if( !dictEntry ) + { return GDCM_UNFOUND; + } - return(GetEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement())); + return GetEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()); } /** - * \brief Searches within Doc Entries (Dicom Elements) parsed with + * \brief Searches within Header Entries (Dicom Elements) parsed with * the public and private dictionaries * for the element value representation of a given tag. * @@ -477,35 +735,43 @@ 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) { +std::string gdcmDocument::GetEntryVRByName(TagName const & tagName) +{ gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( dictEntry == NULL) + { return GDCM_UNFOUND; + } - gdcmHeaderEntry* elem = GetHeaderEntryByNumber(dictEntry->GetGroup(), - dictEntry->GetElement()); + gdcmDocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(), + dictEntry->GetElement()); return elem->GetVR(); } /** - * \brief Searches within Doc Entries (Dicom Elements) parsed with + * \brief Searches within Header Entries (Dicom Elements) parsed with * the public and private dictionaries * for the element value representation of a given tag. - * @param group Group of the searched tag. - * @param element Element of the searched tag. + * @param group Group number of the searched tag. + * @param element Element number of the searched tag. * @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 gdcmDocument::GetEntryByNumber(uint16_t group, uint16_t element) +{ + gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element); + /// \todo use map methods, instead of multimap JPR + if ( !TagHT.count(key)) + { return GDCM_UNFOUND; - return tagHT.find(key)->second->GetValue(); + } + + return ((gdcmValEntry *)TagHT.find(key)->second)->GetValue(); } /** - * \brief Searches within Doc Entries (Dicom Elements) parsed with + * \brief Searches within Header Entries (Dicom Elements) parsed with * the public and private dictionaries * for the element value representation of a given tag.. * @@ -513,30 +779,36 @@ std::string gdcmDocument::GetEntryByNumber(guint16 group, guint16 element){ * to convert the string typed content to caller's native type * (think of C++ vs Python). The VR is actually of a higher level * of semantics than just the native C++ type. - * @param group Group of the searched tag. - * @param element Element of the searched tag. + * @param group Group number of the searched tag. + * @param element Element number of the searched tag. * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string gdcmDocument::GetEntryVRByNumber(guint16 group, guint16 element) { - gdcmHeaderEntry* elem = GetHeaderEntryByNumber(group, element); +std::string gdcmDocument::GetEntryVRByNumber(uint16_t group, uint16_t element) +{ + gdcmDocEntry* elem = GetDocEntryByNumber(group, element); if ( !elem ) + { return GDCM_UNFOUND; + } return elem->GetVR(); } /** - * \brief Searches within Doc Entries (Dicom Elements) parsed with + * \brief Searches within Header Entries (Dicom Elements) parsed with * the public and private dictionaries * for the value length of a given tag.. - * @param group Group of the searched tag. - * @param element Element of the searched tag. + * @param group Group number of the searched tag. + * @param element Element number of the searched tag. * @return Corresponding element length; -2 if not found */ -int gdcmDocument::GetEntryLengthByNumber(guint16 group, guint16 element) { - gdcmHeaderEntry* elem = GetHeaderEntryByNumber(group, element); +int gdcmDocument::GetEntryLengthByNumber(uint16_t group, uint16_t element) +{ + gdcmDocEntry* elem = GetDocEntryByNumber(group, element); if ( !elem ) - return -2; + { + return -2; //magic number + } return elem->GetLength(); } /** @@ -545,85 +817,124 @@ 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) { +bool gdcmDocument::SetEntryByName(std::string const & content,std::string const & tagName) +{ gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); - if( dictEntry == NULL) - return false; + if( !dictEntry ) + { + return false; + } - return(SetEntryByNumber(content,dictEntry->GetGroup(), - dictEntry->GetElement())); + return SetEntryByNumber(content,dictEntry->GetGroup(), + dictEntry->GetElement()); } /** - * \brief Accesses an existing gdcmHeaderEntry (i.e. a Dicom Element) + * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element) * through it's (group, element) and modifies it's content with * the given value. - * \warning Don't use any longer : use SetPubEntryByNumber - * @param content new value to substitute with - * @param group group of the Dicom Element to modify - * @param element element of the Dicom Element to modify + * @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 gdcmDocument::SetEntryByNumber(std::string const & content, + uint16_t group, + uint16_t element) { - TagKey key = gdcmDictEntry::TranslateToKey(group, element); - if ( ! tagHT.count(key)) + gdcmValEntry* valEntry = GetValEntryByNumber(group, element); + if (!valEntry ) + { + dbg.Verbose(0, "gdcmDocument::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'; } - - gdcmHeaderEntry * a; - IterHT p; - TagHeaderEntryHT::iterator p2; - // DO NOT remove the following lines : they explain the stuff - //p= tagHT.equal_range(key); // get a pair of iterators first-last synonym - //p2=p.first; // iterator on the first synonym - //a=p2->second; // H Table target column (2-nd col) - - // or, easier : - a = ((tagHT.equal_range(key)).first)->second; - - a-> SetValue(content); - - std::string vr = a->GetVR(); + // Non even content must be padded with a space (020H)... + std::string evenContent = content; + if( evenContent.length() % 2 ) + { + evenContent += '\0'; // ... therefore we padd with (000H) .!?! + } + valEntry->SetValue(evenContent); - guint32 lgr; - if( (vr == "US") || (vr == "SS") ) - lgr = 2; - else if( (vr == "UL") || (vr == "SL") ) - lgr = 4; + // Integers have a special treatement for their length: + gdcmVRKey vr = valEntry->GetVR(); + if( vr == "US" || vr == "SS" ) + { + valEntry->SetLength(2); + } + else if( vr == "UL" || vr == "SL" ) + { + valEntry->SetLength(4); + } else - lgr = l; + { + valEntry->SetLength(evenContent.length()); + } - a->SetLength(lgr); return true; -} +} /** - * \brief Accesses an existing gdcmHeaderEntry (i.e. a Dicom Element) - * in the PubHeaderEntrySet of this instance + * \brief Accesses an existing gdcmDocEntry (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 lgth new value length + * @param group group number of the Dicom Element to modify + * @param element element number of the Dicom Element to modify + */ +bool gdcmDocument::SetEntryByNumber(void *content, + int lgth, + uint16_t group, + uint16_t element) +{ + (void)lgth; //not used + gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element); + if ( !TagHT.count(key)) + { + return false; + } + +/* Hope Binary field length is *never* wrong + if(lgth%2) // Non even length are padded with a space (020H). + { + lgth++; + //content = content + '\0'; // fing a trick to enlarge a binary field? + } +*/ + gdcmBinEntry* a = (gdcmBinEntry *)TagHT[key]; + a->SetVoidArea(content); + //a->SetLength(lgth); // ??? + + return true; +} + +/** + * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element) + * in the PubDocEntrySet of this instance * through it's (group, element) and modifies it's length with * the given value. * \warning Use with extreme caution. * @param l new length to substitute with - * @param group group of the Entry to modify - * @param element element of the Entry to modify + * @param group group number of the Entry to modify + * @param element element number of the Entry to modify * @return true on success, false otherwise. */ -bool gdcmDocument::SetEntryLengthByNumber(guint32 l, - guint16 group, - guint16 element) +bool gdcmDocument::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 + gdcmTagKey key = gdcmDictEntry::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 ; } @@ -631,86 +942,120 @@ 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 of the Entry - * @param Elem element 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 gdcmDocument::GetEntryOffsetByNumber(uint16_t group, uint16_t elem) { - gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem); - if (!Entry) + gdcmDocEntry* entry = GetDocEntryByNumber(group, elem); + if (!entry) { - dbg.Verbose(1, "gdcmDocument::GetHeaderEntryByNumber", - "failed to Locate gdcmHeaderEntry"); - return (size_t)0; + dbg.Verbose(1, "gdcmDocument::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 of the Entry - * @param Elem element 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 * gdcmDocument::GetEntryVoidAreaByNumber(uint16_t group, uint16_t elem) { - gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem); - if (!Entry) + gdcmDocEntry* entry = GetDocEntryByNumber(group, elem); + if (!entry) { - dbg.Verbose(1, "gdcmDocument::GetHeaderEntryByNumber", - "failed to Locate gdcmHeaderEntry"); - return (NULL); + dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber: no entry"); + return 0; } - return Entry->GetVoidArea(); + return ((gdcmBinEntry *)entry)->GetVoidArea(); } /** * \brief Loads (from disk) the element content * when a string is not suitable - * @param Group group of the Entry - * @param Elem element 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 *gdcmDocument::LoadEntryVoidArea(uint16_t group, uint16_t elem) { - gdcmHeaderEntry * Element= GetHeaderEntryByNumber(Group, Elem); - if ( !Element ) + gdcmDocEntry *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(); + } + size_t o =(size_t)docElement->GetOffset(); + fseek(Fp, o, SEEK_SET); + size_t l = docElement->GetLength(); char* a = new char[l]; - if(!a) + if(!a) + { + dbg.Verbose(0, "gdcmDocument::LoadEntryVoidArea cannot allocate a"); + return NULL; + } + size_t l2 = fread(a, 1, l , Fp); + if( l != l2 ) + { + delete[] a; return NULL; + } + /// \todo Drop any already existing void area! JPR + SetEntryVoidAreaByNumber(a, group, elem); - SetEntryVoidAreaByNumber(a, Group, Elem); + return a; +} +/** + * \brief Loads (from disk) the element content + * when a string is not suitable + * @param Element Entry whose voidArea is going to be loaded + */ +void *gdcmDocument::LoadEntryVoidArea(gdcmBinEntry *element) +{ + size_t o =(size_t)element->GetOffset(); + fseek(Fp, o, SEEK_SET); + size_t l = element->GetLength(); + char* a = new char[l]; + if( !a ) + { + dbg.Verbose(0, "gdcmDocument::LoadEntryVoidArea cannot allocate a"); + return NULL; + } + element->SetVoidArea((void *)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 group Group number of the searched Dicom Element + * @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) + uint16_t group, + uint16_t element) { - TagKey key = gdcmDictEntry::TranslateToKey(group, element); - if ( ! tagHT.count(key)) + gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element); + if ( !TagHT.count(key)) + { return false; - ( ((tagHT.equal_range(key)).first)->second )->SetVoidArea(area); + } + + // This was for multimap ? + (( gdcmBinEntry *)( ((TagHT.equal_range(key)).first)->second ))->SetVoidArea(area); + return true; } @@ -718,10 +1063,13 @@ 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 gdcmDocument::UpdateShaEntries() +{ + //gdcmDictEntry *entry; std::string vr; - + + /// \todo TODO : still any use to explore recursively the whole structure? +/* for(ListTag::iterator it=listEntries.begin(); it!=listEntries.end(); ++it) @@ -741,13 +1089,14 @@ void gdcmDocument::UpdateShaEntries(void) { else vr=(*it)->GetVR(); - (*it)->SetValue(GetHeaderEntryUnvalue(*it)); + (*it)->SetValue(GetDocEntryUnvalue(*it)); // to go on compiling if(entry){ // Set the new entry and the new value (*it)->SetDictEntry(entry); - CheckHeaderEntryVR(*it,vr); + CheckDocEntryVR(*it,vr); - (*it)->SetValue(GetHeaderEntryValue(*it)); + (*it)->SetValue(GetDocEntryValue(*it)); // to go on compiling + } else { @@ -755,21 +1104,25 @@ void gdcmDocument::UpdateShaEntries(void) { (*it)->SetDictEntry(NewVirtualDictEntry((*it)->GetGroup(),(*it)->GetElement(),vr)); } } +*/ } /** - * \brief Searches within the Doc Entries for a Dicom Element of + * \brief Searches within the Header Entries for a Dicom Element of * a given tag. * @param tagName name of the searched Dicom Element. * @return Corresponding Dicom Element when it exists, and NULL * otherwise. */ - gdcmHeaderEntry *gdcmDocument::GetHeaderEntryByName(std::string tagName) { +gdcmDocEntry* gdcmDocument::GetDocEntryByName(std::string const & tagName) +{ gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); - if( dictEntry == NULL) + if( !dictEntry ) + { return NULL; + } - return(GetHeaderEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement())); + return GetDocEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()); } /** @@ -782,372 +1135,52 @@ void gdcmDocument::UpdateShaEntries(void) { * @param element Element number of the searched Dicom Element * @return */ -gdcmHeaderEntry* gdcmDocument::GetHeaderEntryByNumber(guint16 group, guint16 element) +gdcmDocEntry* gdcmDocument::GetDocEntryByNumber(uint16_t group, + uint16_t element) { - TagKey key = gdcmDictEntry::TranslateToKey(group, element); - if ( ! tagHT.count(key)) + gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element); + if ( !TagHT.count(key)) + { return NULL; - return tagHT.find(key)->second; -} - -/** - * \brief retrieves the Dicom Elements (all of them) using (group, element) - * @param group Group number of the searched Dicom Element. - * @param element Element number of the searched Dicom Element. - * @return a range (i.e.pair<,>) containing all elements whose key is group|element) - */ - -IterHT gdcmDocument::GetHeaderEntrySameNumber(guint16 group, guint16 element){ - TagKey key = gdcmDictEntry::TranslateToKey(group, element); - return (tagHT.equal_range(key)); -} - -/** - * \brief Loads the element while preserving the current - * underlying file position indicator as opposed to - * to LoadHeaderEntry that modifies it. - * @param entry Header Entry whose value shall be loaded. - * @return - */ -void gdcmDocument::LoadHeaderEntrySafe(gdcmHeaderEntry * entry) { - long PositionOnEntry = ftell(fp); - LoadHeaderEntry(entry); - fseek(fp, PositionOnEntry, SEEK_SET); -} - -/** - * \brief Re-computes the length of a ACR-NEMA/Dicom group from a DcmHeader - * \warning : to be re-written using the chained list instead of the H table. - * \warning : DO NOT use (doesn't work any longer because of the multimap) - * \todo : to be re-written using the chained list instead of the H table - * @param SkipSequence TRUE if we don't want to write Sequences (ACR-NEMA Files) - * @param type Type of the File (ExplicitVR,ImplicitVR, ACR, ...) - */ -void gdcmDocument::UpdateGroupLength(bool SkipSequence, FileType type) { - guint16 gr, el; - std::string vr; - - gdcmHeaderEntry *elem; - char trash[10]; - std::string str_trash; - - GroupKey key; - GroupHT groupHt; // to hold the length of each group - TagKey tk; - // remember : - // typedef std::map GroupHT; - - gdcmHeaderEntry *elemZ; - - // for each Tag in the DCM Header - - for (TagHeaderEntryHT::iterator tag2 = tagHT.begin(); - tag2 != tagHT.end(); - ++tag2) - { - elem = tag2->second; - gr = elem->GetGroup(); - el = elem->GetElement(); - vr = elem->GetVR(); - - sprintf(trash, "%04x", gr); - key = trash; // generate 'group tag' - - // if the caller decided not to take SEQUENCEs into account - // e.g : he wants to write an ACR-NEMA File - - if (SkipSequence && vr == "SQ") - continue; - - // Still unsolved problem : - // we cannot find the 'Sequence Delimitation Item' - // since it's at the end of the Hash Table - // (fffe,e0dd) - - // there is SEQUENCE in ACR-NEMA - // WARNING : - // --> la descente a l'interieur' des SQ - // devrait etre faite avec une liste chainee, pas avec une HTable... - - if ( groupHt.count(key) == 0) // we just read the first elem of a given group - { - if (el == 0x0000) // the first elem is 0x0000 - { - groupHt[key] = 0; // initialize group length - } - else - { - groupHt[key] = 2 + 2 + 4 + elem->GetLength(); // non 0x0000 first group elem - } - } - else // any elem but the first - { - if (type == ExplicitVR) - { - if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") ) - { - groupHt[key] += 4; // explicit VR AND OB, OW, SQ : 4 more bytes - } - } - groupHt[key] += 2 + 2 + 4 + elem->GetLength(); - } } - - unsigned short int gr_bid; - - for (GroupHT::iterator g = groupHt.begin(); // for each group we found - g != groupHt.end(); - ++g) - { - // FIXME: g++ -Wall -Wstrict-prototypes reports on following line: - // warning: unsigned int format, different type arg - sscanf(g->first.c_str(),"%x",&gr_bid); //FIXME - tk = g->first + "|0000"; // generate the element full tag - - if ( tagHT.count(tk) == 0) // if element 0x0000 not found - { - gdcmDictEntry * tagZ = new gdcmDictEntry(gr_bid, 0x0000, "UL"); - elemZ = new gdcmHeaderEntry(tagZ); - elemZ->SetLength(4); - AddHeaderEntry(elemZ); // create it - } - else - { - elemZ=GetHeaderEntryByNumber(gr_bid, 0x0000); - } - sprintf(trash ,"%d",g->second); - str_trash=trash; - elemZ->SetValue(str_trash); - } + return TagHT.find(key)->second; } /** - * \brief Writes in a file (according to the requested format) - * the group, the element, the value representation and the length - * of a single gdcmHeaderEntry passed as argument. - * @param tag pointer on the gdcmHeaderEntry to be written - * @param _fp already open file pointer - * @param type type of the File to be written - */ -void gdcmDocument::WriteEntryTagVRLength(gdcmHeaderEntry *tag, - FILE *_fp, - FileType type) -{ - guint16 group = tag->GetGroup(); - std::string 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 == ExplicitVR ) { - - // 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); - } -} - -/** - * \brief Writes in a file (according to the requested format) - * the value of a single gdcmHeaderEntry passed as argument. - * @param tag Pointer on the gdcmHeaderEntry to be written - * @param _fp Already open file pointer - * @param type type of the File to be written + * \brief Same as \ref gdcmDocument::GetDocEntryByNumber except it only + * returns a result when the corresponding entry is of type + * ValEntry. + * @return When present, the corresponding ValEntry. */ -void gdcmDocument::WriteEntryValue(gdcmHeaderEntry *tag, FILE *_fp,FileType type) +gdcmValEntry* gdcmDocument::GetValEntryByNumber(uint16_t group, + uint16_t element) { - (void)type; - guint16 group = tag->GetGroup(); - std::string vr = tag->GetVR(); - guint32 lgr = tag->GetReadLength(); - - if (vr == "SQ") - // SeQuences have no value: - return; - if (group == 0xfffe) - // Delimiters have no associated value: - return; - - void *voidArea; - voidArea = tag->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") + gdcmDocEntry* currentEntry = GetDocEntryByNumber(group, element); + if ( !currentEntry ) { - // 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 (tag->GetValue(), tokens, "\\"); - for (unsigned int i=0; i(currentEntry) ) { - std::vector tokens; - tokens.erase(tokens.begin(),tokens.end()); // clean any previous value - Tokenize (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 gdcmHeaderEntry passed as argument. - * \sa WriteEntryValue, WriteEntryTagVRLength. - * @param tag Pointer on the gdcmHeaderEntry to be written - * @param _fp Already open file pointer - * @param type type of the File to be written - */ - -bool gdcmDocument::WriteEntry(gdcmHeaderEntry *tag, FILE *_fp,FileType type) -{ - guint32 length = tag->GetLength(); - - // 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); + return valEntry; } + dbg.Verbose(0, "gdcmDocument::GetValEntryByNumber: unfound ValEntry."); - WriteEntryTagVRLength(tag, _fp, type); - WriteEntryValue(tag, _fp, type); - return true; + return 0; } /** - * \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!) - * \sa WriteEntriesDeprecated (Special temporary method for Theralys) - * @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) -{ - /// \todo (?) check write failures (after *each* fwrite) - - for (ListTag::iterator tag2=listEntries.begin(); - tag2 != listEntries.end(); - ++tag2) - { - if ( type == ACR ){ - if ((*tag2)->GetGroup() < 0x0008) - // Ignore pure DICOM V3 groups - continue; - if ((*tag2)->GetElement() %2) - // Ignore the "shadow" groups - continue; - if ((*tag2)->GetVR() == "SQ" ) // ignore Sequences - continue; - if ((*tag2)->GetSQDepthLevel() != 0) // Not only ignore the SQ element - continue; - } - if (! WriteEntry(*tag2,_fp,type) ) - return false; - } - return true; -} - -/** - * \brief writes on disc according to the requested format - * (ACR-NEMA, ExplicitVR, ImplicitVR) the image, - * using only the last synonym of each mutimap H Table post. - * \warning Uses the H Table, instead of the Chained List - * in order to be compliant with the old way to proceed - * (added elements taken in to account) - * Only THERALYS, during a transitory phase is supposed - * to use this method !!! - * \warning DON'T try, right now, to write a DICOM image - * from an ACR Header (meta elements will be missing!) - * \sa WriteEntries - * @param _fp already open file pointer - * @param type type of the File to be written - * (ACR-NEMA, ExplicitVR, ImplicitVR) + * \brief Loads the element while preserving the current + * underlying file position indicator as opposed to + * to LoadDocEntry that modifies it. + * @param entry Header Entry whose value shall be loaded. + * @return */ -void gdcmDocument::WriteEntriesDeprecated(FILE *_fp,FileType type) { - - // restent a tester les echecs en ecriture (apres chaque fwrite) - - for (TagHeaderEntryHT::iterator tag2=tagHT.begin(); - tag2 != tagHT.end(); - ++tag2){ - if ( type == ACR ){ - if ((*tag2->second).GetGroup() < 0x0008) continue; // ignore pure DICOM V3 groups - if ((*tag2->second).GetElement() %2) continue; // ignore shadow groups - if ((*tag2->second).GetVR() == "SQ" ) continue; // ignore Sequences - if ((*tag2->second).GetSQDepthLevel() != 0) continue; // Not only ignore the SQ element - } - if ( ! WriteEntry(tag2->second,_fp,type)) - break; - } +void gdcmDocument::LoadDocEntrySafe(gdcmDocEntry * entry) +{ + long PositionOnEntry = ftell(Fp); + LoadDocEntry(entry); + fseek(Fp, PositionOnEntry, SEEK_SET); } /** @@ -1155,8 +1188,10 @@ void gdcmDocument::WriteEntriesDeprecated(FILE *_fp,FileType type) { * processor order. * @return The properly swaped 32 bits integer. */ -guint32 gdcmDocument::SwapLong(guint32 a) { - switch (sw) { +uint32_t gdcmDocument::SwapLong(uint32_t a) +{ + switch (SwapCode) + { case 0 : break; case 4321 : @@ -1169,117 +1204,355 @@ 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= " << SwapCode << std::endl; dbg.Error(" gdcmDocument::SwapLong : unset swap code"); - a=0; + 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 gdcmDocument::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 gdcmDocument::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 gdcmDocument::UnswapShort(uint16_t a) +{ + return SwapShort(a); } //----------------------------------------------------------------------------- // Private +/** + * \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries) + * @return length of the parsed set. + */ + +long gdcmDocument::ParseDES(gdcmDocEntrySet *set, + long offset, + long l_max, + bool delim_mode) +{ + gdcmDocEntry *newDocEntry = 0; + gdcmValEntry *newValEntry = 0; + unsigned long l = 0; + + int depth = set->GetDepthLevel(); + while (true) + { + if ( !delim_mode && (ftell(Fp)-offset) >= l_max) + { + break; + } + newDocEntry = ReadNextDocEntry( ); + if ( !newDocEntry ) + { + break; + } + + gdcmVRKey vr = newDocEntry->GetVR(); + if ( vr != "SQ" ) + { + + if ( gdcmGlobal::GetVR()->IsVROfGdcmStringRepresentable(vr) ) + { + /////// ValEntry + newValEntry = new gdcmValEntry(newDocEntry->GetDictEntry()); + newValEntry->Copy(newDocEntry); + newValEntry->SetDepthLevel(depth); + set->AddEntry(newValEntry); + LoadDocEntry(newValEntry); + if (newValEntry->IsItemDelimitor()) + { + break; + } + if ( !delim_mode && (ftell(Fp)-offset) >= l_max) + { + break; + } + } + else + { + if ( ! gdcmGlobal::GetVR()->IsVROfGdcmBinaryRepresentable(vr) ) + { + ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR + dbg.Verbose(0, "gdcmDocument::ParseDES: neither Valentry, " + "nor BinEntry. Probably unknown VR."); + } + + ////// BinEntry or UNKOWN VR: + gdcmBinEntry *bn = new gdcmBinEntry(newDocEntry->GetDictEntry()); + bn->Copy(newDocEntry); + set->AddEntry(bn); + LoadDocEntry(bn); + } + + if (newDocEntry->GetGroup() == 0x7fe0 && + newDocEntry->GetElement() == 0x0010 ) + { + if (newDocEntry->GetReadLength()==0xffffffff) + { + // Broken US.3405.1.dcm + Parse7FE0(); // to skip the pixels + // (multipart JPEG/RLE are trouble makers) + } + else + { + SkipToNextDocEntry(newDocEntry); + l = newDocEntry->GetFullLength(); + } + } + else + { + // 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 ) + { + delim_mode = true; + } + else + { + delim_mode = false; + } + } + // no other way to create it ... + gdcmSeqEntry *sq = new gdcmSeqEntry(newDocEntry->GetDictEntry(), + set->GetDepthLevel()); + sq->Copy(newDocEntry); + sq->SetDelimitorMode(delim_mode); + sq->SetDepthLevel(depth); + + if ( l != 0 ) + { // Don't try to parse zero-length sequences + long lgt = ParseSQ( sq, + newDocEntry->GetOffset(), + l, delim_mode); + (void)lgt; //not used... + } + set->AddEntry(sq); + if ( !delim_mode && (ftell(Fp)-offset) >= l_max) + { + break; + } + } + delete newDocEntry; + } + + return l; // Probably useless +} + +/** + * \brief Parses a Sequence ( SeqEntry after SeqEntry) + * @return parsed length for this level + */ +long gdcmDocument::ParseSQ(gdcmSeqEntry *set, + long offset, long l_max, bool delim_mode) +{ + int SQItemNumber = 0; + bool dlm_mod; + //int depth = set->GetDepthLevel(); + //(void)depth; //not used + + while (true) + { + gdcmDocEntry *newDocEntry = ReadNextDocEntry(); + if ( !newDocEntry ) + { + // FIXME Should warn user + break; + } + if( delim_mode ) + { + if ( newDocEntry->IsSequenceDelimitor() ) + { + set->SetSequenceDelimitationItem( newDocEntry ); + break; + } + } + if ( !delim_mode && (ftell(Fp)-offset) >= l_max) + { + break; + } + + gdcmSQItem *itemSQ = new gdcmSQItem(set->GetDepthLevel()); + itemSQ->AddEntry(newDocEntry); + unsigned int l = newDocEntry->GetReadLength(); + + if ( l == 0xffffffff ) + { + dlm_mod = true; + } + else + { + dlm_mod = false; + } + + int lgr = ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod); + (void)lgr; //FIXME not used + + set->AddEntry(itemSQ, SQItemNumber); + SQItemNumber++; + if ( !delim_mode && (ftell(Fp)-offset) >= l_max) + { + break; + } + } + + int lgth = ftell(Fp) - offset; + return lgth; +} + /** * \brief Loads the element content if its length doesn't exceed * the value specified with gdcmDocument::SetMaxSizeLoadEntry() * @param Entry Header Entry (Dicom Element) to be dealt with */ -void gdcmDocument::LoadHeaderEntry(gdcmHeaderEntry *Entry) { +void gdcmDocument::LoadDocEntry(gdcmDocEntry* 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 ) { - Entry->SetValue("gdcm::Skipped"); + if( group == 0xfffe ) + { + // NO more value field for SQ ! return; } // When the length is zero things are easy: - if ( length == 0 ) { - Entry->SetValue(""); + if ( length == 0 ) + { + ((gdcmValEntry *)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) { - std::ostringstream s; - s << "gdcm::NotLoaded."; - s << " Address:" << (long)Entry->GetOffset(); - s << " Length:" << Entry->GetLength(); - s << " x(" << std::hex << Entry->GetLength() << ")"; - Entry->SetValue(s.str()); + + std::ostringstream s; + if (length > MaxSizeLoadEntry) + { + if (gdcmBinEntry* binEntryPtr = dynamic_cast< gdcmBinEntry* >(entry) ) + { + s << "gdcm::NotLoaded (BinEntry)"; + s << " Address:" << (long)entry->GetOffset(); + s << " Length:" << entry->GetLength(); + s << " x(" << std::hex << entry->GetLength() << ")"; + binEntryPtr->SetValue(s.str()); + } + // to be sure we are at the end of the value ... + fseek(Fp, (long)entry->GetOffset()+(long)entry->GetLength(), SEEK_SET); + // Following return introduced by JPR on version 1.25. Since the + // treatement of a ValEntry is never executed (doh!) this means + // we were lucky up to now because we NEVER encountered a ValEntry + // whose length was bigger thant MaxSizeLoadEntry !? I can't believe + // this could ever work... + return; //FIXME FIXME FIXME FIXME JPR ???? + + // Be carefull : a BinEntry IS_A ValEntry ... + if (gdcmValEntry* valEntryPtr = dynamic_cast< gdcmValEntry* >(entry) ) + { + s << "gdcm::NotLoaded. (ValEntry)"; + s << " Address:" << (long)entry->GetOffset(); + s << " Length:" << entry->GetLength(); + s << " x(" << std::hex << entry->GetLength() << ")"; + valEntryPtr->SetValue(s.str()); + } + // to be sure we are at the end of the value ... + fseek(Fp,(long)entry->GetOffset()+(long)entry->GetLength(),SEEK_SET); + + return; + } + + // When we find a BinEntry not very much can be done : + if (gdcmBinEntry* binEntryPtr = dynamic_cast< gdcmBinEntry* >(entry) ) + { + + LoadEntryVoidArea(binEntryPtr); + s << "gdcm::Loaded (BinEntry)"; + binEntryPtr->SetValue(s.str()); return; } - // Any compacter code suggested (?) - if ( IsHeaderEntryAnInteger(Entry) ) { - guint32 NewInt; + /// \todo Any compacter code suggested (?) + if ( IsDocEntryAnInteger(entry) ) + { + uint32_t NewInt; std::ostringstream s; 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; @@ -1290,67 +1563,94 @@ void gdcmDocument::LoadHeaderEntry(gdcmHeaderEntry *Entry) { s << std::ends; // to avoid oddities on Solaris #endif //GDCM_NO_ANSI_STRING_STREAM - Entry->SetValue(s.str()); + ((gdcmValEntry *)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"); - 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 ( gdcmValEntry* valEntry = dynamic_cast(entry) ) + { + if ( item_read != 1 ) + { + dbg.Verbose(1, "gdcmDocument::LoadDocEntry", + "unread element value"); + valEntry->SetValue("gdcm::UnRead"); + return; + } - if( (vr == "UI") ) // Because of correspondance with the VR dic - Entry->SetValue(NewValue.c_str()); + if( vr == "UI" ) + { + // Because of correspondance with the VR dic + valEntry->SetValue(newValue); + } + else + { + valEntry->SetValue(newValue); + } + } else - Entry->SetValue(NewValue); + { + dbg.Error(true, "gdcmDocument::LoadDocEntry" + "Should have a ValEntry, here !"); + } } -/** - * \brief add a new Dicom Element pointer to - * the H Table and at the end of the chained List - * \warning push_bash in listEntries ONLY during ParseHeader - * \todo something to allow further Elements addition, - * (at their right place in the chained list) - * when position to be taken care of - * @param newHeaderEntry - */ -void gdcmDocument::AddHeaderEntry(gdcmHeaderEntry *newHeaderEntry) { - tagHT.insert( PairHT( newHeaderEntry->GetKey(),newHeaderEntry) ); - listEntries.push_back(newHeaderEntry); - wasUpdated = 1; -} /** * \brief Find the value Length of the passed Header Entry * @param Entry Header Entry whose length of the value shall be loaded. */ - void gdcmDocument::FindHeaderEntryLength (gdcmHeaderEntry *Entry) { - guint16 element = Entry->GetElement(); - //guint16 group = Entry->GetGroup(); //FIXME - std::string vr = Entry->GetVR(); - guint16 length16; +void gdcmDocument::FindDocEntryLength( gdcmDocEntry *entry ) + throw ( gdcmFormatError ) +{ + uint16_t element = entry->GetElement(); + std::string vr = entry->GetVR(); + uint16_t length16; - if ( (filetype == ExplicitVR) && (! Entry->IsImplicitVR()) ) + if ( Filetype == gdcmExplicitVR && !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 // 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" && length32 == 0xffffffff ) { - Entry->SetLength(FindHeaderEntryLengthOB()); + uint32_t lengthOB; + try + { + lengthOB = FindDocEntryLengthOB(); + } + catch ( gdcmFormatUnexpected ) + { + // 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; } - FixHeaderEntryFoundLength(Entry, length32); + FixDocEntryFoundLength(entry, length32); return; } @@ -1384,42 +1684,39 @@ void gdcmDocument::AddHeaderEntry(gdcmHeaderEntry *newHeaderEntry) { // 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 gdcmFormatError( "gdcmDocument::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() ); + gdcmDictEntry* 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 } - FixHeaderEntryFoundLength(Entry, (guint32)length16); + FixDocEntryFoundLength( entry, (uint32_t)length16 ); return; } else @@ -1431,7 +1728,7 @@ void gdcmDocument::AddHeaderEntry(gdcmHeaderEntry *newHeaderEntry) { // not coexist in a Data Set and Data Sets nested within it".] // Length is on 4 bytes. - FixHeaderEntryFoundLength(Entry, ReadInt32()); + FixDocEntryFoundLength( entry, ReadInt32() ); return; } } @@ -1440,14 +1737,16 @@ void gdcmDocument::AddHeaderEntry(gdcmHeaderEntry *newHeaderEntry) { * \brief Find the Value Representation of the current Dicom Element. * @param Entry */ -void gdcmDocument::FindHeaderEntryVR( gdcmHeaderEntry *Entry) +void gdcmDocument::FindDocEntryVR( gdcmDocEntry *entry ) { - if (filetype != ExplicitVR) + if ( Filetype != gdcmExplicitVR ) + { 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 @@ -1456,19 +1755,22 @@ void gdcmDocument::FindHeaderEntryVR( gdcmHeaderEntry *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(!CheckHeaderEntryVR(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(); } } @@ -1481,10 +1783,10 @@ void gdcmDocument::FindHeaderEntryVR( gdcmHeaderEntry *Entry) * @return false if the VR is incorrect of if the VR isn't referenced * otherwise, it returns true */ -bool gdcmDocument::CheckHeaderEntryVR(gdcmHeaderEntry *Entry, VRKey vr) +bool gdcmDocument::CheckDocEntryVR(gdcmDocEntry *entry, gdcmVRKey vr) { char msg[100]; // for sprintf - bool RealExplicit = true; + 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 @@ -1494,53 +1796,65 @@ bool gdcmDocument::CheckHeaderEntryVR(gdcmHeaderEntry *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 && !gdcmGlobal::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()); + entry->GetGroup(), entry->GetElement()); dbg.Verbose(1, "gdcmDocument::FindVR: ",msg); - if (Entry->GetGroup()%2 && Entry->GetElement() == 0x0000) { // Group length is UL ! - gdcmDictEntry* NewEntry = NewVirtualDictEntry( - Entry->GetGroup(),Entry->GetElement(), - "UL","FIXME","Group Length"); - Entry->SetDictEntry(NewEntry); + + if( entry->GetGroup() % 2 && entry->GetElement() == 0x0000) + { + // Group length is UL ! + gdcmDictEntry* 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); + gdcmDictEntry* newEntry = NewVirtualDictEntry( + entry->GetGroup(), entry->GetElement(), + vr, "FIXME", entry->GetName()); + entry->SetDictEntry(newEntry); } - return(true); + + return true; } /** @@ -1550,66 +1864,72 @@ bool gdcmDocument::CheckHeaderEntryVR(gdcmHeaderEntry *Entry, VRKey vr) * @param Entry * @return Transformed entry value */ -std::string gdcmDocument::GetHeaderEntryValue(gdcmHeaderEntry *Entry) +std::string gdcmDocument::GetDocEntryValue(gdcmDocEntry *entry) { - if ( (IsHeaderEntryAnInteger(Entry)) && (Entry->IsImplicitVR()) ) + if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() ) { - std::string val=Entry->GetValue(); - std::string vr=Entry->GetVR(); - guint32 length = Entry->GetLength(); + std::string val = ((gdcmValEntry *)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(Entry->GetValue()); + return ((gdcmValEntry *)entry)->GetValue(); } /** @@ -1620,38 +1940,41 @@ std::string gdcmDocument::GetHeaderEntryValue(gdcmHeaderEntry *Entry) * @param Entry * @return Reverse transformed entry value */ -std::string gdcmDocument::GetHeaderEntryUnvalue(gdcmHeaderEntry *Entry) +std::string gdcmDocument::GetDocEntryUnvalue(gdcmDocEntry* entry) { - if ( (IsHeaderEntryAnInteger(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 (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 (Entry->GetValue(), tokens, "\\"); + Tokenize (((gdcmValEntry *)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(); } @@ -1659,10 +1982,10 @@ std::string gdcmDocument::GetHeaderEntryUnvalue(gdcmHeaderEntry *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(Entry->GetValue()); + return ((gdcmValEntry *)entry)->GetValue(); } /** @@ -1670,73 +1993,98 @@ std::string gdcmDocument::GetHeaderEntryUnvalue(gdcmHeaderEntry *Entry) * \warning NOT end user intended method ! * @param entry */ -void gdcmDocument::SkipHeaderEntry(gdcmHeaderEntry *entry) +void gdcmDocument::SkipDocEntry(gdcmDocEntry *entry) +{ + SkipBytes(entry->GetLength()); +} + +/** + * \brief Skips to the begining of the next Header Entry + * \warning NOT end user intended method ! + * @param entry + */ +void gdcmDocument::SkipToNextDocEntry(gdcmDocEntry *entry) { - SkipBytes(entry->GetLength()); + fseek(Fp, (long)(entry->GetOffset()), SEEK_SET); + fseek(Fp, (long)(entry->GetReadLength()), SEEK_CUR); } /** * \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. */ -void gdcmDocument::FixHeaderEntryFoundLength(gdcmHeaderEntry *Entry, guint32 FoundLength) +void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *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 + //////// 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 !? } } - // 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 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); } /** @@ -1745,92 +2093,108 @@ void gdcmDocument::FixHeaderEntryFoundLength(gdcmHeaderEntry *Entry, guint32 Fou * @param Entry The element value on which to apply the predicate. * @return The result of the heuristical predicate. */ -bool gdcmDocument::IsHeaderEntryAnInteger(gdcmHeaderEntry *Entry) { - guint16 element = Entry->GetElement(); - guint16 group = Entry->GetGroup(); - std::string vr = Entry->GetVR(); - guint32 length = Entry->GetLength(); +bool gdcmDocument::IsDocEntryAnInteger(gdcmDocEntry *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); + int 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::IsHeaderEntryAnInteger", - // s.str().c_str()); + dbg.Verbose(0, "gdcmDocument::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::FindHeaderEntryLengthOB(void) { +uint32_t gdcmDocument::FindDocEntryLengthOB() + throw( gdcmFormatUnexpected ) +{ // 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 ( gdcmFormatError ) + { + throw gdcmFormatError("gdcmDocument::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, "gdcmDocument::FindDocEntryLengthOB: neither an Item " + "tag nor a Sequence delimiter tag."); + fseek(Fp, positionOnEntry, SEEK_SET); + throw gdcmFormatUnexpected("gdcmDocument::FindDocEntryLengthOB()", + "Neither an Item tag nor a Sequence " + "delimiter tag."); } - 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; } /** @@ -1838,18 +2202,20 @@ bool gdcmDocument::IsHeaderEntryAnInteger(gdcmHeaderEntry *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 gdcmDocument::ReadInt16() + throw( gdcmFormatError ) +{ + uint16_t g; + size_t item_read = fread (&g, (size_t)2,(size_t)1, Fp); + if ( item_read != 1 ) + { + if( ferror(Fp) ) + { + throw gdcmFormatError( "gdcmDocument::ReadInt16()", " file error." ); + } + throw gdcmFormatError( "gdcmDocument::ReadInt16()", "EOF." ); } - errno = 0; - g = SwapShort(g); + g = SwapShort(g); return g; } @@ -1858,17 +2224,19 @@ 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 gdcmDocument::ReadInt32() + throw( gdcmFormatError ) +{ + uint32_t g; + size_t item_read = fread (&g, (size_t)4,(size_t)1, Fp); + if ( item_read != 1 ) + { + if( ferror(Fp) ) + { + throw gdcmFormatError( "gdcmDocument::ReadInt16()", " file error." ); + } + throw gdcmFormatError( "gdcmDocument::ReadInt32()", "EOF." ); } - errno = 0; g = SwapLong(g); return g; } @@ -1878,19 +2246,20 @@ guint32 gdcmDocument::ReadInt32(void) { * \warning NOT end user intended method ! * @return */ -void gdcmDocument::SkipBytes(guint32 NBytes) { +void gdcmDocument::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 gdcmDocument::Initialise() { RefPubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict(); - RefShaDict = (gdcmDict*)0; + RefShaDict = NULL; } /** @@ -1901,35 +2270,39 @@ void gdcmDocument::Initialise(void) * it's neither ACR-NEMA nor DICOM * true when we hope ours assuptions are OK */ -bool gdcmDocument::CheckSwap() { - +bool gdcmDocument::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) { + char *entCur = deb + 128; + if( memcmp(entCur, "DICM", (size_t)4) == 0 ) + { dbg.Verbose(1, "gdcmDocument::CheckSwap:", "looks like DICOM Version3"); // Next, determine the value representation (VR). Let's skip to the @@ -1954,43 +2327,43 @@ 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 // instead of just checking for UL, OB and UI !? group 0000 { - filetype = ExplicitVR; + Filetype = gdcmExplicitVR; dbg.Verbose(1, "gdcmDocument::CheckSwap:", "explicit Value Representation"); } else { - filetype = ImplicitVR; + Filetype = gdcmImplicitVR; dbg.Verbose(1, "gdcmDocument::CheckSwap:", "not an explicit Value Representation"); } - if (net2host) + if ( net2host ) { - sw = 4321; + SwapCode = 4321; dbg.Verbose(1, "gdcmDocument::CheckSwap:", "HostByteOrder != NetworkByteOrder"); - } + } else { - sw = 0; + SwapCode = 0; dbg.Verbose(1, "gdcmDocument::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 @@ -1998,7 +2371,7 @@ bool gdcmDocument::CheckSwap() { // 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); + 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. @@ -2009,69 +2382,69 @@ 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 = ACR; + SwapCode = 3412; + Filetype = gdcmACR; return true; case 0x04000000 : - sw = 4321; - filetype = ACR; + SwapCode = 4321; + Filetype = gdcmACR; return true; case 0x00000400 : - sw = 2143; - filetype = ACR; + SwapCode = 2143; + Filetype = gdcmACR; return true; case 0x00000004 : - sw = 0; - filetype = ACR; + SwapCode = 0; + Filetype = gdcmACR; 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 = ACR; - return true; - case 0x0200 : - case 0x0400 : - case 0x0800 : - sw = 4321; - filetype = ACR; - return true; - default : - dbg.Verbose(0, "gdcmDocument::CheckSwap:", + switch ( s16 ) + { + case 0x0002 : + case 0x0004 : + case 0x0008 : + SwapCode = 0; + Filetype = gdcmACR; + return true; + case 0x0200 : + case 0x0400 : + case 0x0800 : + SwapCode = 4321; + Filetype = gdcmACR; + return true; + default : + dbg.Verbose(0, "gdcmDocument::CheckSwap:", "ACR/NEMA unfound swap info (Really hopeless !)"); - filetype = Unknown; - return false; - } - - // Then the only info we have is the net2host one. - //if (! net2host ) - // sw = 0; + Filetype = gdcmUnknown; + return false; + } + // Then the only info we have is the net2host one. + //if (! net2host ) + // SwapCode = 0; //else - // sw = 4321; + // SwapCode = 4321; //return; } } @@ -2080,43 +2453,44 @@ 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 gdcmDocument::SwitchSwapToBigEndian() { dbg.Verbose(1, "gdcmDocument::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 */ -void gdcmDocument::SetMaxSizeLoadEntry(long NewSize) +void gdcmDocument::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; } @@ -2125,226 +2499,336 @@ void gdcmDocument::SetMaxSizeLoadEntry(long NewSize) * \todo See comments of \ref gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE * @param NewSize */ -void gdcmDocument::SetMaxSizePrintEntry(long NewSize) +void gdcmDocument::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; } + + /** - * \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 Read the next tag but WITHOUT loading it's value + * (read the 'Group Number', the 'Element Number', + * gets the Dict Entry + * gets the VR, gets the length, gets the offset value) + * @return On succes the newly created DocEntry, NULL on failure. */ -gdcmDictEntry *gdcmDocument::GetDictEntryByName(std::string Name) +gdcmDocEntry* gdcmDocument::ReadNextDocEntry() { - gdcmDictEntry *found = (gdcmDictEntry *)0; - if (!RefPubDict && !RefShaDict) + uint16_t group; + uint16_t elem; + + try + { + group = ReadInt16(); + elem = ReadInt16(); + } + catch ( gdcmFormatError e ) { - dbg.Verbose(0, "gdcmDocument::GetDictEntry", - "we SHOULD have a default dictionary"); + // We reached the EOF (or an error occured) therefore + // header parsing has to be considered as finished. + std::cout << e; + return 0; } - if (RefPubDict) + + gdcmDocEntry *newEntry = NewDocEntryByNumber(group, elem); + FindDocEntryVR(newEntry); + + try { - found = RefPubDict->GetDictEntryByName(Name); - if (found) - return found; + FindDocEntryLength(newEntry); } - if (RefShaDict) + catch ( gdcmFormatError e ) { - found = RefShaDict->GetDictEntryByName(Name); - if (found) - return found; + // Call it quits + std::cout << e; + delete newEntry; + return 0; } - return found; + + newEntry->SetOffset(ftell(Fp)); + + return newEntry; } + /** - * \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 of the searched DictEntry - * @param element element of the searched DictEntry - * @return Corresponding DictEntry when it exists, NULL otherwise. + * \brief Generate a free gdcmTagKey i.e. a gdcmTagKey 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. */ -gdcmDictEntry *gdcmDocument::GetDictEntryByNumber(guint16 group,guint16 element) +uint32_t gdcmDocument::GenerateFreeTagKeyInGroup(uint16_t group) { - gdcmDictEntry *found = (gdcmDictEntry *)0; - if (!RefPubDict && !RefShaDict) - { - dbg.Verbose(0, "gdcmDocument::GetDictEntry", - "we SHOULD have a default dictionary"); - } - if (RefPubDict) - { - found = RefPubDict->GetDictEntryByNumber(group, element); - if (found) - return found; - } - if (RefShaDict) + for (uint32_t elem = 0; elem < UINT32_MAX; elem++) { - found = RefShaDict->GetDictEntryByNumber(group, element); - if (found) - return found; + gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, elem); + if (TagHT.count(key) == 0) + { + return elem; + } } - return found; + return UINT32_MAX; } /** - * \brief Read the next tag but WITHOUT loading it's value - * @return On succes the newly created HeaderEntry, NULL on failure. + * \brief Assuming the internal file pointer \ref gdcmDocument::fp + * is placed at the beginning of a tag check whether this + * tag is (TestGroup, TestElement). + * \warning On success the internal file pointer \ref gdcmDocument::fp + * is modified to point after the tag. + * On failure (i.e. when the tag wasn't the expected tag + * (TestGroup, TestElement) the internal file pointer + * \ref gdcmDocument::fp is restored to it's original position. + * @param TestGroup The expected group of the tag. + * @param TestElement The expected Element of the tag. + * @return True on success, false otherwise. */ -gdcmHeaderEntry *gdcmDocument::ReadNextHeaderEntry(void) { - guint16 g,n; - gdcmHeaderEntry *NewEntry; - g = ReadInt16(); - n = ReadInt16(); - - if (errno == 1) - // We reached the EOF (or an error occured) therefore - // header parsing has to be considered as finished. - return (gdcmHeaderEntry *)0; - -// Pb : how to propagate the element length (used in SkipHeaderEntry) -// 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 (gdcmHeaderEntry *)1; // to tell caller it's NOT finished - - NewEntry = NewHeaderEntryByNumber(g, n); - FindHeaderEntryVR(NewEntry); - FindHeaderEntryLength(NewEntry); +bool gdcmDocument::ReadTag(uint16_t testGroup, uint16_t testElement) +{ + 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 ) + { + std::ostringstream s; + s << " We should have found tag ("; + s << std::hex << testGroup << "," << testElement << ")" << std::endl; + s << " but instead we encountered tag ("; + s << std::hex << itemTagGroup << "," << itemTagElement << ")" + << std::endl; + s << " at address: " << (unsigned)currentPosition << std::endl; + dbg.Verbose(0, "gdcmDocument::ReadItemTagLength: wrong Item Tag found:"); + dbg.Verbose(0, s.str().c_str()); + fseek(Fp, positionOnEntry, SEEK_SET); - if (errno == 1) { - // Call it quits - return NULL; + return false; } - NewEntry->SetOffset(ftell(fp)); - 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 Name Name of the underlying DictEntry + * \brief Assuming the internal file pointer \ref gdcmDocument::fp + * is placed at the beginning of a tag (TestGroup, TestElement), + * read the length associated to the Tag. + * \warning On success the internal file pointer \ref gdcmDocument::fp + * is modified to point after the tag and it's length. + * On failure (i.e. when the tag wasn't the expected tag + * (TestGroup, TestElement) the internal file pointer + * \ref gdcmDocument::fp is restored to it's original position. + * @param TestGroup The expected group of the tag. + * @param TestElement The expected Element of the tag. + * @return On success returns the length associated to the tag. On failure + * returns 0. */ -gdcmHeaderEntry *gdcmDocument::NewHeaderEntryByName(std::string Name) +uint32_t gdcmDocument::ReadTagLength(uint16_t testGroup, uint16_t testElement) { - gdcmDictEntry *NewTag = GetDictEntryByName(Name); - if (!NewTag) - NewTag = NewVirtualDictEntry(0xffff, 0xffff, "LO", "unkn", Name); + long positionOnEntry = ftell(Fp); + (void)positionOnEntry; - gdcmHeaderEntry* NewEntry = new gdcmHeaderEntry(NewTag); - if (!NewEntry) + if ( !ReadTag(testGroup, testElement) ) + { + return 0; + } + + //// Then read the associated Item Length + long currentPosition = ftell(Fp); + uint32_t itemLength = ReadInt32(); { - dbg.Verbose(1, "gdcmDocument::ObtainHeaderEntryByName", - "failed to allocate gdcmHeaderEntry"); - return (gdcmHeaderEntry *)0; + std::ostringstream s; + s << "Basic Item Length is: " + << itemLength << std::endl; + s << " at address: " << (unsigned)currentPosition << std::endl; + dbg.Verbose(0, "gdcmDocument::ReadItemTagLength: ", s.str().c_str()); } - return NewEntry; -} + return itemLength; +} /** - * \brief Request a new virtual dict entry to the dict set - * @param group group of the underlying DictEntry - * @param element element of the underlying DictEntry - * @param vr VR of the underlying DictEntry - * @param fourth owner group - * @param name english name + * \brief Parse pixel data from disk for multi-fragment Jpeg/Rle files + * No other way so 'skip' the Data + * */ -gdcmDictEntry *gdcmDocument::NewVirtualDictEntry(guint16 group, guint16 element, - std::string vr, - std::string fourth, - std::string name) +void gdcmDocument::Parse7FE0 () { - return gdcmGlobal::GetDicts()->NewVirtualDictEntry(group,element,vr,fourth,name); + gdcmDocEntry* element = GetDocEntryByNumber(0x0002, 0x0010); + if ( !element ) + { + // Should warn user FIXME + return; + } + + if ( IsImplicitVRLittleEndianTransferSyntax() + || IsExplicitVRLittleEndianTransferSyntax() + || IsExplicitVRBigEndianTransferSyntax() /// \todo 1.2.2 ??? A verifier ! + || IsDeflatedExplicitVRLittleEndianTransferSyntax() ) + { + return; + } + + // ---------------- for Parsing : Position on begining of Jpeg/RLE Pixels + + //// Read the Basic Offset Table Item Tag length... + uint32_t itemLength = ReadTagLength(0xfffe, 0xe000); + + //// ... and then read length[s] itself[themselves]. We don't use + // the values read (BTW what is the purpous of those lengths ?) + if ( itemLength != 0 ) + { + // BTW, what is the purpous of those length anyhow !? + char* basicOffsetTableItemValue = new char[itemLength + 1]; + fread(basicOffsetTableItemValue, itemLength, 1, Fp); + + for (unsigned int i=0; i < itemLength; i += 4 ) + { + uint32_t individualLength = str2num(&basicOffsetTableItemValue[i],uint32_t); + std::ostringstream s; + s << " Read one length: "; + s << std::hex << individualLength << std::endl; + dbg.Verbose(0, "gdcmDocument::Parse7FE0: ", s.str().c_str()); + } + delete[] basicOffsetTableItemValue; + } + + if ( ! IsRLELossLessTransferSyntax() ) + { + // JPEG Image + + //// We then skip (not reading them) all the fragments of images: + while ( (itemLength = ReadTagLength(0xfffe, 0xe000)) ) + { + SkipBytes(itemLength); + } + } + else + { + // RLE Image + long ftellRes; + long rleSegmentLength[15], fragmentLength; + + // While we find some items: + while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) ) + { + // Parse fragments of the current Fragment (Frame) + //------------------ scanning (not reading) fragment pixels + uint32_t nbRleSegments = ReadInt32(); + + //// Reading RLE Segments Offset Table + uint32_t rleSegmentOffsetTable[15]; + for(int k=1; k<=15; k++) + { + ftellRes = ftell(Fp); + rleSegmentOffsetTable[k] = ReadInt32(); + } + + // skipping (not reading) RLE Segments + if ( nbRleSegments > 1) + { + for(unsigned int k = 1; k <= nbRleSegments-1; k++) + { + rleSegmentLength[k] = rleSegmentOffsetTable[k+1] + - rleSegmentOffsetTable[k]; + ftellRes = ftell(Fp); + SkipBytes(rleSegmentLength[k]); + } + } + + rleSegmentLength[nbRleSegments] = fragmentLength + - rleSegmentOffsetTable[nbRleSegments]; + ftellRes = ftell(Fp); + SkipBytes(rleSegmentLength[nbRleSegments]); + } + + // Make sure that at the end of the item we encounter a 'Sequence + // Delimiter Item': + if ( !ReadTag(0xfffe, 0xe0dd) ) + { + dbg.Verbose(0, "gdcmDocument::Parse7FE0: no sequence delimiter item"); + dbg.Verbose(0, " at end of RLE item sequence"); + } + } } + + /** - * \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 of the underlying DictEntry - * @param Elem element of the underlying DictEntry + * \brief Compares two documents, according to \ref gdcmDicomDir 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' */ -gdcmHeaderEntry *gdcmDocument::NewHeaderEntryByNumber(guint16 Group, guint16 Elem) +bool gdcmDocument::operator<(gdcmDocument &document) { - // Find out if the tag we encountered is in the dictionaries: - gdcmDictEntry *DictEntry = GetDictEntryByNumber(Group, Elem); - if (!DictEntry) - DictEntry = NewVirtualDictEntry(Group, Elem); - - gdcmHeaderEntry *NewEntry = new gdcmHeaderEntry(DictEntry); - if (!NewEntry) + // Patient Name + std::string s1 = GetEntryByNumber(0x0010,0x0010); + std::string s2 = document.GetEntryByNumber(0x0010,0x0010); + if(s1 < s2) { - dbg.Verbose(1, "gdcmDocument::NewHeaderEntryByNumber", - "failed to allocate gdcmHeaderEntry"); - return NULL; + return true; } - return NewEntry; -} - -/// \todo Never used; commented out, waiting for removal. -/** - * \brief Small utility function that creates a new manually crafted - * (as opposed as read from the file) gdcmHeaderEntry with user - * specified name and adds it to the public tag hash table. - * \note A fake TagKey is generated so the PubDict can keep it's coherence. - * @param NewTagName The name to be given to this new tag. - * @param VR The Value Representation to be given to this new tag. - * @return The newly hand crafted Element Value. - */ -//gdcmHeaderEntry *gdcmDocument::NewManualHeaderEntryToPubDict(std::string NewTagName, -// std::string VR) -//{ -// gdcmHeaderEntry *NewEntry = NULL; -// guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info -// guint32 FreeElem = 0; -// gdcmDictEntry *DictEntry = NULL; -// -// FreeElem = GenerateFreeTagKeyInGroup(StuffGroup); -// if (FreeElem == UINT32_MAX) -// { -// dbg.Verbose(1, "gdcmHeader::NewManualHeaderEntryToPubDict", -// "Group 0xffff in Public Dict is full"); -// return NULL; -// } -// -// DictEntry = NewVirtualDictEntry(StuffGroup, FreeElem, -// VR, "GDCM", NewTagName); -// NewEntry = new gdcmHeaderEntry(DictEntry); -// AddHeaderEntry(NewEntry); -// return NewEntry; -//} - -/** - * \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. - */ -guint32 gdcmDocument::GenerateFreeTagKeyInGroup(guint16 group) -{ - for (guint32 elem = 0; elem < UINT32_MAX; elem++) + else if(s1 > s2) { - TagKey key = gdcmDictEntry::TranslateToKey(group, elem); - if (tagHT.count(key) == 0) - return elem; + return false; } - return UINT32_MAX; + else + { + // Patient ID + s1 = GetEntryByNumber(0x0010,0x0020); + s2 = document.GetEntryByNumber(0x0010,0x0020); + if ( s1 < s2 ) + { + return true; + } + else if ( s1 > s2 ) + { + return true; + } + else + { + // Study Instance UID + 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 = GetEntryByNumber(0x0020,0x000e); + s2 = document.GetEntryByNumber(0x0020,0x000e); + if ( s1 < s2 ) + { + return true; + } + else if( s1 > s2 ) + { + return false; + } + } + } + } + return false; } + //-----------------------------------------------------------------------------