X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmParser.cxx;h=acd248eb3f5230b4cc34ae0c9db1d227d19d87d3;hb=ccc795ae220f0d14496d0ef2473f66d8eae48c7a;hp=384aa6e045beb73fd36eafe99c6ad616f2a64896;hpb=41cc62fb86c116bd195581980c27480c213c958b;p=gdcm.git diff --git a/src/gdcmParser.cxx b/src/gdcmParser.cxx index 384aa6e0..acd248eb 100644 --- a/src/gdcmParser.cxx +++ b/src/gdcmParser.cxx @@ -1,8 +1,15 @@ -// gdcmHeader.cxx +// gdcmParser.cxx //----------------------------------------------------------------------------- +//#define UINT32_MAX (4294967295U) + + #include "gdcmParser.h" +#include "gdcmGlobal.h" #include "gdcmUtil.h" +#include "gdcmDebug.h" + #include +#include // For nthos: #ifdef _MSC_VER @@ -11,12 +18,6 @@ #include #endif -#ifdef GDCM_NO_ANSI_STRING_STREAM -# include -# define ostringstream ostrstream -# else -# include -#endif # include #define UI1_2_840_10008_1_2 "1.2.840.10008.1.2" @@ -24,69 +25,81 @@ #define UI1_2_840_10008_1_2_2 "1.2.840.10008.1.2.2" #define UI1_2_840_10008_1_2_1_99 "1.2.840.10008.1.2.1.99" +typedef struct { + guint32 totalSQlength; + guint32 alreadyParsedlength; +} pileElem; + //----------------------------------------------------------------------------- // Refer to gdcmParser::CheckSwap() const unsigned int gdcmParser::HEADER_LENGTH_TO_READ = 256; -// Refer to gdcmParser::SetMaxSizeLoadElementValue() +// Refer to gdcmParser::SetMaxSizeLoadEntry() const unsigned int gdcmParser::MAX_SIZE_LOAD_ELEMENT_VALUE = 4096; +// Refer to gdcmParser::SetMaxSizePrintEntry() +// TODO : Right now, better see "define, in gdcmHederEntry.cxx +const unsigned int gdcmParser::MAX_SIZE_PRINT_ELEMENT_VALUE = 64; + //----------------------------------------------------------------------------- // Constructor / Destructor + /** - * \ingroup gdcmParser - * \brief - * @param InFilename - * @param exception_on_error + * \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, + * to be parsed *inside* the SeQuences, * when they have an actual length - *\TODO may be we need one more bool, - * to allow skipping the private elements while parsing the header - * in order to save space - */ -gdcmParser::gdcmParser(const char *InFilename, + * \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') + */ +gdcmParser::gdcmParser(const char *inFilename, bool exception_on_error, - bool enable_sequences ) -{ + bool enable_sequences, + bool ignore_shadow) { enableSequences=enable_sequences; + ignoreShadow =ignore_shadow; - SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); - filename = InFilename; + SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); + filename = inFilename; Initialise(); if ( !OpenFile(exception_on_error)) return; - Parse(); - LoadHeaderEntries(); + + LoadHeaderEntries(); CloseFile(); wasUpdated = 0; // will be set to 1 if user adds an entry - printLevel = 1; // 'Heavy' header print by default + printLevel = 1; // 'Medium' print level by default } /** * \ingroup gdcmParser - * \brief + * \brief constructor * @param exception_on_error */ -gdcmParser::gdcmParser(bool exception_on_error) -{ +gdcmParser::gdcmParser(bool exception_on_error) { + (void)exception_on_error; enableSequences=0; SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Initialise(); wasUpdated = 0; // will be set to 1 if user adds an entry - printLevel = 1; // 'Heavy' header print by default + printLevel = 1; // 'Medium' print level by default } /** * \ingroup gdcmParser * \brief Canonical destructor. */ -gdcmParser::~gdcmParser (void) -{ +gdcmParser::~gdcmParser (void) { RefPubDict = NULL; RefShaDict = NULL; } @@ -96,88 +109,72 @@ gdcmParser::~gdcmParser (void) /** * \ingroup gdcmParser * \brief Prints the Header Entries (Dicom Elements) - * both from the H Table and the chained list + * from the chained list * @return */ -void gdcmParser::PrintEntry(std::ostream & os) -{ - std::ostringstream s; - - s << "------------ using listEntries ----------------" << std::endl; +void gdcmParser::PrintEntry(std::ostream & os) { + for (ListTag::iterator i = listEntries.begin(); - i != listEntries.end(); - ++i) + i != listEntries.end(); + ++i) { - (*i)->SetPrintLevel(printLevel); - (*i)->Print(os); + (*i)->SetPrintLevel(printLevel); + (*i)->Print(os); } - os<Print(os); } /** - * \ingroup gdcmParser - * \brief Prints The Dict Entries of THE shadow Dicom Dictionnry + * \brief Prints The Dict Entries of THE shadow Dicom Dictionary * @return */ -void gdcmParser::PrintShaDict(std::ostream & os) -{ +void gdcmParser::PrintShaDict(std::ostream & os) { RefShaDict->Print(os); } //----------------------------------------------------------------------------- // Public /** - * \ingroup gdcmParser * \brief Get the public dictionary used */ -gdcmDict *gdcmParser::GetPubDict(void) -{ +gdcmDict *gdcmParser::GetPubDict(void) { return(RefPubDict); } /** - * \ingroup gdcmParser * \brief Get the shadow dictionary used */ -gdcmDict *gdcmParser::GetShaDict(void) -{ +gdcmDict *gdcmParser::GetShaDict(void) { return(RefShaDict); } /** - * \ingroup gdcmParser * \brief Set the shadow dictionary used * \param dict dictionary to use in shadow */ -bool gdcmParser::SetShaDict(gdcmDict *dict) -{ +bool gdcmParser::SetShaDict(gdcmDict *dict){ RefShaDict=dict; return(!RefShaDict); } /** - * \ingroup gdcmParser * \brief Set the shadow dictionary used * \param dictName name of the dictionary to use in shadow */ -bool gdcmParser::SetShaDict(DictKey dictName) -{ +bool gdcmParser::SetShaDict(DictKey dictName){ RefShaDict=gdcmGlobal::GetDicts()->GetDict(dictName); return(!RefShaDict); } /** - * \ingroup gdcmParser * \brief This predicate, based on hopefully reasonable heuristics, * decides whether or not the current gdcmParser was properly parsed * and contains the mandatory information for being considered as @@ -185,32 +182,23 @@ bool gdcmParser::SetShaDict(DictKey dictName) * @return true when gdcmParser is the one of a reasonable Dicom/Acr file, * false otherwise. */ -bool gdcmParser::IsReadable(void) -{ - std::string res = GetEntryByNumber(0x0028, 0x0005); - if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) - return false; // Image Dimensions - - if ( !GetHeaderEntryByNumber(0x0028, 0x0100) ) - return false; // "Bits Allocated" - if ( !GetHeaderEntryByNumber(0x0028, 0x0101) ) - return false; // "Bits Stored" - if ( !GetHeaderEntryByNumber(0x0028, 0x0102) ) - return false; // "High Bit" - if ( !GetHeaderEntryByNumber(0x0028, 0x0103) ) - return false; // "Pixel Representation" - return true; +bool gdcmParser::IsReadable(void) { + if(filetype==Unknown) { + return(false); + } + if(listEntries.size()<=0) { + return(false); + } + + return(true); } /** - * \ingroup gdcmParser * \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. */ -bool gdcmParser::IsImplicitVRLittleEndianTransferSyntax(void) -{ +bool gdcmParser::IsImplicitVRLittleEndianTransferSyntax(void) { gdcmHeaderEntry *Element = GetHeaderEntryByNumber(0x0002, 0x0010); if ( !Element ) return false; @@ -226,11 +214,9 @@ bool gdcmParser::IsImplicitVRLittleEndianTransferSyntax(void) * \ingroup gdcmParser * \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 gdcmParser::IsExplicitVRLittleEndianTransferSyntax(void) -{ +bool gdcmParser::IsExplicitVRLittleEndianTransferSyntax(void) { gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); if ( !Element ) return false; @@ -243,14 +229,11 @@ bool gdcmParser::IsExplicitVRLittleEndianTransferSyntax(void) } /** - * \ingroup gdcmParser * \brief Determines if the Transfer Syntax was already encountered * and if it corresponds to a DeflatedExplicitVRLittleEndian one. - * * @return True when DeflatedExplicitVRLittleEndian found. False in all other cases. */ -bool gdcmParser::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) -{ +bool gdcmParser::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) { gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); if ( !Element ) return false; @@ -263,14 +246,11 @@ bool gdcmParser::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) } /** - * \ingroup gdcmParser * \brief Determines if the Transfer Syntax was already encountered * and if it corresponds to a Explicit VR Big Endian one. - * * @return True when big endian found. False in all other cases. */ -bool gdcmParser::IsExplicitVRBigEndianTransferSyntax(void) -{ +bool gdcmParser::IsExplicitVRBigEndianTransferSyntax(void) { gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); if ( !Element ) return false; @@ -283,17 +263,15 @@ bool gdcmParser::IsExplicitVRBigEndianTransferSyntax(void) } /** - * \ingroup gdcmParser * \brief returns the File Type * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown) - * @return + * @return the FileType code */ FileType gdcmParser::GetFileType(void) { return(filetype); } /** - * \ingroup gdcmParser * \brief opens the file * @param exception_on_error * @return @@ -325,21 +303,19 @@ FILE *gdcmParser::OpenFile(bool exception_on_error) return(fp); fclose(fp); - dbg.Verbose(0, "gdcmParser::gdcmParser not DICOM/ACR", filename.c_str()); + dbg.Verbose(0, "gdcmParser::OpenFile not DICOM/ACR", filename.c_str()); } else { - dbg.Verbose(0, "gdcmParser::gdcmParser cannot open file", filename.c_str()); + dbg.Verbose(0, "gdcmParser::OpenFile cannot open file", filename.c_str()); } return(NULL); } /** - * \ingroup gdcmParser * \brief closes the file * @return TRUE if the close was successfull */ -bool gdcmParser::CloseFile(void) -{ +bool gdcmParser::CloseFile(void) { int closed = fclose(fp); fp = (FILE *)0; if (! closed) @@ -348,17 +324,16 @@ bool gdcmParser::CloseFile(void) } /** - * \ingroup gdcmParser - * \brief + * \brief Writes in a file all the Header Entries (Dicom Elements) + * of the Chained List * @param fp file pointer on an already open file - * @param type type of the File to be written + * @param type Type of the File to be written * (ACR-NEMA, ExplicitVR, ImplicitVR) - * @return always "True" ?! + * \return Always true. */ -bool gdcmParser::Write(FILE *fp, FileType type) -{ +bool gdcmParser::Write(FILE *fp, FileType type) { // ============== -// TODO The stuff has been rewritten using the chained list instead +// TODO The stuff was rewritten using the chained list instead // of the H table // so we could remove the GroupHT from the gdcmParser // To be checked @@ -367,14 +342,13 @@ bool gdcmParser::Write(FILE *fp, FileType type) // TODO : move the following lines (and a lot of others, to be written) // to a future function CheckAndCorrectHeader - // Question : - // Comment pourrait-on savoir si le DcmHeader vient d'un fichier DicomV3 ou non - // (FileType est un champ de gdcmParser ...) - // WARNING : Si on veut ecrire du DICOM V3 a partir d'un DcmHeader ACR-NEMA - // no way - // a moins de se livrer a un tres complique ajout des champs manquants. - // faire un CheckAndCorrectHeader (?) - + // Question : + // Comment pourrait-on savoir si le DcmHeader vient d'un fichier + // DicomV3 ou non (FileType est un champ de gdcmParser ...) + // WARNING : Si on veut ecrire du DICOM V3 a partir d'un DcmHeader ACR-NEMA + // no way + // a moins de se livrer a un tres complique ajout des champs manquants. + // faire un CheckAndCorrectHeader (?) if (type == ImplicitVR) { @@ -400,92 +374,77 @@ bool gdcmParser::Write(FILE *fp, FileType type) SetEntryLengthByNumber(20, 0x0002, 0x0010); } +/* TODO : rewrite later, if really usefull + +--> 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) UpdateGroupLength(true,ACR); +*/ - WriteEntries(type, fp); + WriteEntries(fp,type); return(true); - } +} /** - * \ingroup gdcmParser * \brief Modifies the value of a given Header Entry (Dicom Element) - * if it exists; Creates it with the given value if it doesn't - * @param Value passed as a std::string - * @param Group - * @param Elem - * \return boolean - */ -bool gdcmParser::ReplaceOrCreateByNumber(std::string Value, - guint16 Group, guint16 Elem ) -{ - if (CheckIfEntryExistByNumber(Group, Elem) == 0) { - gdcmHeaderEntry *a =NewHeaderEntryByNumber(Group, Elem); + * 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 + * \return pointer to the modified/created Header Entry (NULL when creation + * failed). + */ +gdcmHeaderEntry * gdcmParser::ReplaceOrCreateByNumber( + std::string Value, + guint16 Group, + guint16 Elem ){ + gdcmHeaderEntry* a; + a = GetHeaderEntryByNumber( Group, Elem); + if (a == NULL) { + a =NewHeaderEntryByNumber(Group, Elem); if (a == NULL) - return false; + return NULL; AddHeaderEntry(a); } - SetEntryByNumber(Value, Group, Elem); - return(true); + //CLEANME SetEntryByNumber(Value, Group, Elem); + a->SetValue(Value); + return(a); } /** - * \ingroup gdcmParser - * \brief Modifies the value of a given Header Entry (Dicom Element) - * if it exists; Creates it with the given value if it doesn't - * @param Value passed as a char* - * @param Group - * @param Elem - * \return boolean - * - */ -bool gdcmParser::ReplaceOrCreateByNumber(char* Value, guint16 Group, guint16 Elem ) -{ - gdcmHeaderEntry* nvHeaderEntry=NewHeaderEntryByNumber(Group, Elem); - - if(!nvHeaderEntry) - return(false); - - AddHeaderEntry(nvHeaderEntry); - - std::string v = Value; - SetEntryByNumber(v, Group, Elem); - return(true); -} - -/** - * \ingroup gdcmParser - * \brief Set a new value if the invoked element exists - * Seems to be useless !!! - * @param Value - * @param Group - * @param Elem + * \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 * \return boolean */ bool gdcmParser::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 Elem ) { - std::string v = Value; + std::string v = Value; SetEntryByNumber(v, Group, Elem); return true; } //----------------------------------------------------------------------------- // Protected + /** - * \ingroup gdcmParser * \brief Checks if a given Dicom Element exists - * \ within the H table + * 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 gdcmParser::CheckIfEntryExistByNumber(guint16 group, guint16 element ) -{ - std::string key = gdcmDictEntry::TranslateToKey(group, element ); - return (tagHT.count(key)); +int gdcmParser::CheckIfEntryExistByNumber(guint16 group, guint16 element ) { + std::string key = gdcmDictEntry::TranslateToKey(group, element ); + return (tagHT.count(key)); } /** @@ -498,8 +457,7 @@ int gdcmParser::CheckIfEntryExistByNumber(guint16 group, guint16 element ) * @return Corresponding element value when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string gdcmParser::GetEntryByName(std::string tagName) -{ +std::string gdcmParser::GetEntryByName(std::string tagName) { gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( dictEntry == NULL) return GDCM_UNFOUND; @@ -521,17 +479,17 @@ std::string gdcmParser::GetEntryByName(std::string tagName) * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string gdcmParser::GetEntryVRByName(std::string tagName) -{ +std::string gdcmParser::GetEntryVRByName(std::string tagName) { gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( dictEntry == NULL) return GDCM_UNFOUND; gdcmHeaderEntry* elem = GetHeaderEntryByNumber(dictEntry->GetGroup(), - dictEntry->GetElement()); + dictEntry->GetElement()); return elem->GetVR(); } + /** * \ingroup gdcmParser * \brief Searches within Header Entries (Dicom Elements) parsed with @@ -542,8 +500,7 @@ std::string gdcmParser::GetEntryVRByName(std::string tagName) * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string gdcmParser::GetEntryByNumber(guint16 group, guint16 element) -{ +std::string gdcmParser::GetEntryByNumber(guint16 group, guint16 element){ TagKey key = gdcmDictEntry::TranslateToKey(group, element); if ( ! tagHT.count(key)) return GDCM_UNFOUND; @@ -565,14 +522,28 @@ std::string gdcmParser::GetEntryByNumber(guint16 group, guint16 element) * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string gdcmParser::GetEntryVRByNumber(guint16 group, guint16 element) -{ +std::string gdcmParser::GetEntryVRByNumber(guint16 group, guint16 element) { gdcmHeaderEntry* elem = GetHeaderEntryByNumber(group, element); if ( !elem ) return GDCM_UNFOUND; return elem->GetVR(); } +/** + * \ingroup gdcmParser + * \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. + * @return Corresponding element length; -2 if not found + */ +int gdcmParser::GetEntryLengthByNumber(guint16 group, guint16 element) { + gdcmHeaderEntry* elem = GetHeaderEntryByNumber(group, element); + if ( !elem ) + return -2; + return elem->GetLength(); +} /** * \ingroup gdcmParser * \brief Sets the value (string) of the Header Entry (Dicom Element) @@ -580,11 +551,10 @@ std::string gdcmParser::GetEntryVRByNumber(guint16 group, guint16 element) * @param tagName name of the searched Dicom Element. * @return true when found */ -bool gdcmParser::SetEntryByName(std::string content,std::string tagName) -{ +bool gdcmParser::SetEntryByName(std::string content,std::string tagName) { gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( dictEntry == NULL) - return false; + return false; return(SetEntryByNumber(content,dictEntry->GetGroup(), dictEntry->GetElement())); @@ -608,13 +578,12 @@ bool gdcmParser::SetEntryByNumber(std::string content, if ( ! tagHT.count(key)) return false; int l = content.length(); - if(l%2) // Odd length are padded with a space (020H). + if(l%2) // Non even length are padded with a space (020H). { l++; content = content + '\0'; } - //tagHT[key]->SetValue(content); gdcmHeaderEntry * a; IterHT p; TagHeaderEntryHT::iterator p2; @@ -628,7 +597,6 @@ bool gdcmParser::SetEntryByNumber(std::string content, a-> SetValue(content); - //std::string vr = tagHT[key]->GetVR(); std::string vr = a->GetVR(); guint32 lgr; @@ -637,12 +605,11 @@ bool gdcmParser::SetEntryByNumber(std::string content, else if( (vr == "UL") || (vr == "SL") ) lgr = 4; else - lgr = l; + lgr = l; - //tagHT[key]->SetLength(lgr); a->SetLength(lgr); return true; -} +} /** * \ingroup gdcmParser @@ -651,36 +618,35 @@ bool gdcmParser::SetEntryByNumber(std::string content, * through it's (group, element) and modifies it's length with * the given value. * \warning Use with extreme caution. - * @param length new length to substitute with - * @param group group of the entry to modify - * @param element element of the Entry to modify - * @return 1 on success, 0 otherwise. + * @param l new length to substitute with + * @param group group of the Entry to modify + * @param element element of the Entry to modify + * @return true on success, false otherwise. */ - -bool gdcmParser::SetEntryLengthByNumber(guint32 length, - guint16 group, guint16 element) +bool gdcmParser::SetEntryLengthByNumber(guint32 l, + guint16 group, + guint16 element) { TagKey key = gdcmDictEntry::TranslateToKey(group, element); if ( ! tagHT.count(key)) return false; - if (length%2) length++; // length must be even - //tagHT[key]->SetLength(length); - ( ((tagHT.equal_range(key)).first)->second )->SetLength(length); - - return true ; + if (l%2) l++; // length must be even + ( ((tagHT.equal_range(key)).first)->second )->SetLength(l); + + return true ; } /** * \ingroup gdcmParser * \brief Gets (from Header) the offset of a 'non string' element value - * \ (LoadElementValues has already be executed) - * @param Group - * @param Elem + * (LoadElementValues has already be executed) + * @param Group group of the Entry + * @param Elem element of the Entry * @return File Offset of the Element Value */ size_t gdcmParser::GetEntryOffsetByNumber(guint16 Group, guint16 Elem) { - gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem); + gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem); if (!Entry) { dbg.Verbose(1, "gdcmParser::GetHeaderEntryByNumber", @@ -693,14 +659,14 @@ size_t gdcmParser::GetEntryOffsetByNumber(guint16 Group, guint16 Elem) /** * \ingroup gdcmParser * \brief Gets (from Header) a 'non string' element value - * \ (LoadElementValues has already be executed) - * @param Group - * @param Elem + * (LoadElementValues has already be executed) + * @param Group group of the Entry + * @param Elem element of the Entry * @return Pointer to the 'non string' area */ void * gdcmParser::GetEntryVoidAreaByNumber(guint16 Group, guint16 Elem) { - gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem); + gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem); if (!Entry) { dbg.Verbose(1, "gdcmParser::GetHeaderEntryByNumber", @@ -711,9 +677,10 @@ void * gdcmParser::GetEntryVoidAreaByNumber(guint16 Group, guint16 Elem) } /** - * \ingroup gdcmParser * \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 */ void *gdcmParser::LoadEntryVoidArea(guint16 Group, guint16 Elem) { @@ -722,19 +689,20 @@ void *gdcmParser::LoadEntryVoidArea(guint16 Group, guint16 Elem) return NULL; size_t o =(size_t)Element->GetOffset(); fseek(fp, o, SEEK_SET); - int l=Element->GetLength(); - void * a = malloc(l); + size_t l=Element->GetLength(); + char* a = new char[l]; if(!a) - return NULL; + return NULL; SetEntryVoidAreaByNumber(a, Group, Elem); // TODO check the result size_t l2 = fread(a, 1, l ,fp); if(l != l2) { - free(a); - return NULL; + delete[] a; + return NULL; } + return a; } @@ -746,23 +714,23 @@ void *gdcmParser::LoadEntryVoidArea(guint16 Group, guint16 Elem) * @param element Element number of the searched Dicom Element * @return */ -bool gdcmParser::SetEntryVoidAreaByNumber(void * area,guint16 group, guint16 element) +bool gdcmParser::SetEntryVoidAreaByNumber(void * area, + guint16 group, + guint16 element) { TagKey key = gdcmDictEntry::TranslateToKey(group, element); if ( ! tagHT.count(key)) return false; - //tagHT[key]->SetVoidArea(area); - ( ((tagHT.equal_range(key)).first)->second )->SetVoidArea(area); + ( ((tagHT.equal_range(key)).first)->second )->SetVoidArea(area); return true; } /** * \ingroup gdcmParser - * \brief Update the entries with the shadow dictionary. Only odd entries are - * analized + * \brief Update the entries with the shadow dictionary. + * Only non even entries are analyzed */ -void gdcmParser::UpdateShaEntries(void) -{ +void gdcmParser::UpdateShaEntries(void) { gdcmDictEntry *entry; std::string vr; @@ -786,8 +754,7 @@ void gdcmParser::UpdateShaEntries(void) vr=(*it)->GetVR(); (*it)->SetValue(GetHeaderEntryUnvalue(*it)); - if(entry) - { + if(entry){ // Set the new entry and the new value (*it)->SetDictEntry(entry); CheckHeaderEntryVR(*it,vr); @@ -810,8 +777,7 @@ void gdcmParser::UpdateShaEntries(void) * @return Corresponding Dicom Element when it exists, and NULL * otherwise. */ - gdcmHeaderEntry *gdcmParser::GetHeaderEntryByName(std::string tagName) - { + gdcmHeaderEntry *gdcmParser::GetHeaderEntryByName(std::string tagName) { gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( dictEntry == NULL) return NULL; @@ -822,7 +788,7 @@ void gdcmParser::UpdateShaEntries(void) /** * \ingroup gdcmParser * \brief retrieves a Dicom Element (the first one) using (group, element) - * \ warning (group, element) IS NOT an identifier inside the Dicom Header + * \warning (group, element) IS NOT an identifier inside the Dicom Header * if you think it's NOT UNIQUE, check the count number * and use iterators to retrieve ALL the Dicoms Elements within * a given couple (group, element) @@ -832,12 +798,25 @@ void gdcmParser::UpdateShaEntries(void) */ gdcmHeaderEntry* gdcmParser::GetHeaderEntryByNumber(guint16 group, guint16 element) { - TagKey key = gdcmDictEntry::TranslateToKey(group, element); + TagKey key = gdcmDictEntry::TranslateToKey(group, element); if ( ! tagHT.count(key)) return NULL; return tagHT.find(key)->second; } +/** + * \ingroup gdcmParser + * \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 gdcmParser::GetHeaderEntrySameNumber(guint16 group, guint16 element){ + TagKey key = gdcmDictEntry::TranslateToKey(group, element); + return (tagHT.equal_range(key)); +} + /** * \ingroup gdcmParser * \brief Loads the element while preserving the current @@ -846,15 +825,13 @@ gdcmHeaderEntry* gdcmParser::GetHeaderEntryByNumber(guint16 group, guint16 eleme * @param entry Header Entry whose value shall be loaded. * @return */ -void gdcmParser::LoadHeaderEntrySafe(gdcmHeaderEntry * entry) -{ +void gdcmParser::LoadHeaderEntrySafe(gdcmHeaderEntry * entry) { long PositionOnEntry = ftell(fp); LoadHeaderEntry(entry); fseek(fp, PositionOnEntry, SEEK_SET); } /** - * \ingroup gdcmParser * \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) @@ -862,8 +839,7 @@ void gdcmParser::LoadHeaderEntrySafe(gdcmHeaderEntry * entry) * @param SkipSequence TRUE if we don't want to write Sequences (ACR-NEMA Files) * @param type Type of the File (ExplicitVR,ImplicitVR, ACR, ...) */ -void gdcmParser::UpdateGroupLength(bool SkipSequence, FileType type) -{ +void gdcmParser::UpdateGroupLength(bool SkipSequence, FileType type) { guint16 gr, el; std::string vr; @@ -891,7 +867,7 @@ void gdcmParser::UpdateGroupLength(bool SkipSequence, FileType type) vr = elem->GetVR(); sprintf(trash, "%04x", gr); - key = trash; // generate 'group tag' + 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 @@ -904,7 +880,7 @@ void gdcmParser::UpdateGroupLength(bool SkipSequence, FileType type) // since it's at the end of the Hash Table // (fffe,e0dd) - // pas SEQUENCE en ACR-NEMA + // 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... @@ -912,8 +888,8 @@ void gdcmParser::UpdateGroupLength(bool SkipSequence, FileType type) 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 + { + groupHt[key] = 0; // initialize group length } else { @@ -941,15 +917,15 @@ void gdcmParser::UpdateGroupLength(bool SkipSequence, FileType type) { // FIXME: g++ -Wall -Wstrict-prototypes reports on following line: // warning: unsigned int format, different type arg - sscanf(g->first.c_str(),"%x",&gr_bid); - tk = g->first + "|0000"; // generate the element full tag + 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 + AddHeaderEntry(elemZ); // create it } else { @@ -962,113 +938,232 @@ void gdcmParser::UpdateGroupLength(bool SkipSequence, FileType type) } /** - * \ingroup gdcmParser - * \brief writes on disc according to the requested format - * \ (ACR-NEMA, ExplicitVR, ImplicitVR) the image - * \ warning does NOT add the missing elements in the header : - * \ it's up to the user doing it ! - * \ (function CheckHeaderCoherence to be written) - * @param type type of the File to be written - * (ACR-NEMA, ExplicitVR, ImplicitVR) - * @param _fp already open file pointer + * \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 gdcmParser::WriteEntries(FileType type, FILE * _fp) +void gdcmParser::WriteEntryTagVRLength(gdcmHeaderEntry *tag, + FILE *_fp, + FileType type) { - guint16 gr, el; - guint32 lgr; - const char * val; - std::string vr; - guint32 val_uint32; - guint16 val_uint16; - - std::vector tokens; - - // uses now listEntries to iterate, not TagHt! - // - // pb : gdcmParser.Add does NOT update listEntries - // TODO : find a trick (in STL?) to do it, at low cost ! - - void *ptr; + guint16 group = tag->GetGroup(); + std::string vr = tag->GetVR(); + guint16 el = tag->GetElement(); + guint32 lgr = tag->GetReadLength(); - // TODO (?) tester les echecs en ecriture (apres chaque fwrite) + 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; - for (ListTag::iterator tag2=listEntries.begin(); - tag2 != listEntries.end(); - ++tag2) - { - gr = (*tag2)->GetGroup(); - el = (*tag2)->GetElement(); - lgr = (*tag2)->GetLength(); - val = (*tag2)->GetValue().c_str(); - vr = (*tag2)->GetVR(); + fwrite ( &group,(size_t)2 ,(size_t)1 ,_fp); //group + fwrite ( &el,(size_t)2 ,(size_t)1 ,_fp); //element - if ( type == ACR ) - { - if (gr < 0x0008) continue; // ignore pure DICOM V3 groups - if (gr %2) continue; // ignore shadow groups - if (vr == "SQ" ) continue; // ignore Sequences - // TODO : find a trick to *skip* the SeQuences ! - // Not only ignore the SQ element - if (gr == 0xfffe ) continue; // ignore delimiters - } + if ( type == ExplicitVR ) { - fwrite ( &gr,(size_t)2 ,(size_t)1 ,_fp); //group - fwrite ( &el,(size_t)2 ,(size_t)1 ,_fp); //element + // 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 - if ( (type == ExplicitVR) && (gr <= 0x0002) ) - { - // EXPLICIT VR - guint16 z=0, shortLgr; - fwrite (vr.c_str(),(size_t)2 ,(size_t)1 ,_fp); + int ff=0xffffffff; + fwrite (&ff,(size_t)4 ,(size_t)1 ,_fp); + return; + } - if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") ) + 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 - { - shortLgr=lgr; + } else { fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp); } - } - else // IMPLICIT VR - { - fwrite ( &lgr,(size_t)4 ,(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 + */ +void gdcmParser::WriteEntryValue(gdcmHeaderEntry *tag, FILE *_fp,FileType type) +{ + (void)type; + guint16 group = tag->GetGroup(); + std::string vr = tag->GetVR(); + guint32 lgr = tag->GetReadLength(); - if (vr == "US" || vr == "SS") + 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") + { + // 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; iGetValue(), tokens, "\\"); - for (unsigned int i=0; i tokens; + tokens.erase(tokens.begin(),tokens.end()); // clean any previous value + Tokenize (tag->GetValue(), tokens, "\\"); + for (unsigned int i=0; iGetValue(), 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 gdcmParser::WriteEntry(gdcmHeaderEntry *tag, FILE *_fp,FileType type) +{ + guint32 length = tag->GetLength(); - fwrite ( val,(size_t)lgr ,(size_t)1 ,_fp); // Elem value + // The value of a tag MUST (see the DICOM norm) be an odd number of + // bytes. When this is not the case, pad with an additional byte: + if(length%2==1) + { + tag->SetValue(tag->GetValue()+"\0"); + tag->SetLength(tag->GetReadLength()+1); + } + + WriteEntryTagVRLength(tag, _fp, type); + WriteEntryValue(tag, _fp, type); + return true; +} + +/** + * \brief writes on disc according to the requested format + * (ACR-NEMA, ExplicitVR, ImplicitVR) the image + * using the Chained List + * \warning does NOT add the missing elements in the header : + * it's up to the user doing it ! + * (function CheckHeaderCoherence to be written) + * \warning DON'T try, right now, to write a DICOM image + * from an ACR Header (meta elements will be missing!) + * \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 gdcmParser::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; +} + +/** + * \ingroup gdcmParser + * \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) + */ +void gdcmParser::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; } } @@ -1078,10 +1173,8 @@ void gdcmParser::WriteEntries(FileType type, FILE * _fp) * processor order. * @return The properly swaped 32 bits integer. */ -guint32 gdcmParser::SwapLong(guint32 a) -{ - switch (sw) - { +guint32 gdcmParser::SwapLong(guint32 a) { + switch (sw) { case 0 : break; case 4321 : @@ -1109,8 +1202,7 @@ guint32 gdcmParser::SwapLong(guint32 a) * processor order. * @return The properly unswaped 32 bits integer. */ -guint32 gdcmParser::UnswapLong(guint32 a) -{ +guint32 gdcmParser::UnswapLong(guint32 a) { return (SwapLong(a)); } @@ -1119,8 +1211,7 @@ guint32 gdcmParser::UnswapLong(guint32 a) * \brief Swaps the bytes so they agree with the processor order * @return The properly swaped 16 bits integer. */ -guint16 gdcmParser::SwapShort(guint16 a) -{ +guint16 gdcmParser::SwapShort(guint16 a) { if ( (sw==4321) || (sw==2143) ) a =(((a<<8) & 0x0ff00) | ((a>>8)&0x00ff)); return (a); @@ -1131,8 +1222,7 @@ guint16 gdcmParser::SwapShort(guint16 a) * \brief Unswaps the bytes so they agree with the processor order * @return The properly unswaped 16 bits integer. */ -guint16 gdcmParser::UnswapShort(guint16 a) -{ +guint16 gdcmParser::UnswapShort(guint16 a) { return (SwapShort(a)); } @@ -1140,42 +1230,29 @@ guint16 gdcmParser::UnswapShort(guint16 a) // Private /** * \ingroup gdcmParser - * \brief Parses the header of the file but WITHOUT loading element values. + * \brief Parses the header of the file and load element values. + * @return false if file is not ACR-NEMA / DICOM */ -void gdcmParser::Parse(bool exception_on_error) throw(gdcmFormatError) -{ - gdcmHeaderEntry *newHeaderEntry = (gdcmHeaderEntry *)0; - +bool gdcmParser::LoadHeaderEntries(bool exception_on_error) throw(gdcmFormatError) { + (void)exception_on_error; rewind(fp); - CheckSwap(); - while ( (newHeaderEntry = ReadNextHeaderEntry()) ) - { - SkipHeaderEntry(newHeaderEntry); - AddHeaderEntry(newHeaderEntry); - } -} - -/** - * \ingroup gdcmParser - * \brief Loads the element values of all the Header Entries pointed in the - * public Chained List. - */ -void gdcmParser::LoadHeaderEntries(void) -{ - rewind(fp); - for (ListTag::iterator i = GetListEntry().begin(); - i != GetListEntry().end(); - ++i) - { - LoadHeaderEntry(*i); + if (!CheckSwap()) + return false; + + gdcmHeaderEntry *newHeaderEntry = (gdcmHeaderEntry *)0; + while ( (newHeaderEntry = ReadNextHeaderEntry()) ) { + SkipHeaderEntry(newHeaderEntry); + if ( (ignoreShadow==0) || (newHeaderEntry->GetGroup()%2) == 0) { + AddHeaderEntry(newHeaderEntry); + LoadHeaderEntry(newHeaderEntry); + } } - rewind(fp); - // Load 'non string' values + // Load 'non string' values + std::string PhotometricInterpretation = GetEntryByNumber(0x0028,0x0004); - if( PhotometricInterpretation == "PALETTE COLOR " ) - { + if( PhotometricInterpretation == "PALETTE COLOR " ) { LoadEntryVoidArea(0x0028,0x1200); // gray LUT LoadEntryVoidArea(0x0028,0x1201); // R LUT LoadEntryVoidArea(0x0028,0x1202); // G LUT @@ -1184,15 +1261,17 @@ void gdcmParser::LoadHeaderEntries(void) 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) + // -------------------------------------------------------------- // Special Patch to allow gdcm to read ACR-LibIDO formated images // // if recognition code tells us we deal with a LibIDO image // we switch lineNumber and columnNumber // - std::string RecCode; + std::string RecCode; RecCode = GetEntryByNumber(0x0008, 0x0010); // recognition code if (RecCode == "ACRNEMA_LIBIDO_1.1" || RecCode == "CANRME_AILIBOD1_1." ) @@ -1203,49 +1282,35 @@ void gdcmParser::LoadHeaderEntries(void) SetEntryByNumber(columns, 0x0028, 0x0010); SetEntryByNumber(rows , 0x0028, 0x0011); } - // ----------------- End of Special Patch ---------------- + // ----------------- End of Special Patch ---------------- + return true; } /** * \ingroup gdcmParser - * \brief Loads the element content if it's length is not bigger - * than the value specified with - * gdcmParser::SetMaxSizeLoadEntry() + * \brief Loads the element content if its length doesn't exceed + * the value specified with gdcmParser::SetMaxSizeLoadEntry() * @param Entry Header Entry (Dicom Element) to be dealt with */ -void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry *Entry) -{ +void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry *Entry) { size_t item_read; guint16 group = Entry->GetGroup(); std::string vr= Entry->GetVR(); guint32 length = Entry->GetLength(); - bool SkipLoad = false; fseek(fp, (long)Entry->GetOffset(), SEEK_SET); - - // the test was commented out to 'go inside' the SeQuences - // we don't any longer skip them ! - - // if( vr == "SQ" ) // (DO NOT remove this comment) - // SkipLoad = true; // 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 ) - SkipLoad = true; - - if ( SkipLoad ) - { - Entry->SetLength(0); + if( group == 0xfffe ) { Entry->SetValue("gdcm::Skipped"); return; } // When the length is zero things are easy: - if ( length == 0 ) - { + if ( length == 0 ) { Entry->SetValue(""); return; } @@ -1253,8 +1318,7 @@ void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry *Entry) // The elements whose length is bigger than the specified upper bound // are not loaded. Instead we leave a short notice of the offset of // the element content and it's length. - if (length > MaxSizeLoadEntry) - { + if (length > MaxSizeLoadEntry) { std::ostringstream s; s << "gdcm::NotLoaded."; s << " Address:" << (long)Entry->GetOffset(); @@ -1263,44 +1327,38 @@ void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry *Entry) Entry->SetValue(s.str()); return; } - - // When integer(s) are expected, read and convert the following - // n *(two or four bytes) - // properly i.e. as integers as opposed to a strings. - // Elements with Value Multiplicity > 1 - // contain a set of integers (not a single one) - + // Any compacter code suggested (?) - if ( IsHeaderEntryAnInteger(Entry) ) - { + if ( IsHeaderEntryAnInteger(Entry) ) { guint32 NewInt; std::ostringstream s; int nbInt; - if (vr == "US" || vr == "SS") - { + // 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") { 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; } } - } - else if (vr == "UL" || vr == "SL") - { + // 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") { 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; @@ -1310,15 +1368,15 @@ void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry *Entry) #ifdef GDCM_NO_ANSI_STRING_STREAM s << std::ends; // to avoid oddities on Solaris #endif //GDCM_NO_ANSI_STRING_STREAM + Entry->SetValue(s.str()); - return; + 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 ) - { + if ( item_read != 1 ) { dbg.Verbose(1, "gdcmParser::LoadElementValue","unread element value"); Entry->SetValue("gdcm::UnRead"); return; @@ -1333,14 +1391,14 @@ void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry *Entry) /** * \ingroup gdcmParser * \brief add a new Dicom Element pointer to - * the H Table and to the chained List + * 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, - * \ when position to be taken care of + * (at their right place in the chained list) + * when position to be taken care of * @param newHeaderEntry */ -void gdcmParser::AddHeaderEntry(gdcmHeaderEntry *newHeaderEntry) -{ +void gdcmParser::AddHeaderEntry(gdcmHeaderEntry *newHeaderEntry) { tagHT.insert( PairHT( newHeaderEntry->GetKey(),newHeaderEntry) ); listEntries.push_back(newHeaderEntry); wasUpdated = 1; @@ -1348,23 +1406,15 @@ void gdcmParser::AddHeaderEntry(gdcmHeaderEntry *newHeaderEntry) /** * \ingroup gdcmParser - * \brief - * @param Entry Header Entry whose length of the value shall be loaded. - - * @return + * \brief Find the value Length of the passed Header Entry + * @param Entry Header Entry whose length of the value shall be loaded. */ - void gdcmParser::FindHeaderEntryLength (gdcmHeaderEntry *Entry) - { + void gdcmParser::FindHeaderEntryLength (gdcmHeaderEntry *Entry) { guint16 element = Entry->GetElement(); - guint16 group = Entry->GetGroup(); + //guint16 group = Entry->GetGroup(); //FIXME std::string vr = Entry->GetVR(); guint16 length16; - if( (element == 0x0010) && (group == 0x7fe0) ) - { - dbg.SetDebug(-1); - dbg.Verbose(2, "gdcmParser::FindLength: ", - "we reached 7fe0 0010"); - } + if ( (filetype == ExplicitVR) && (! Entry->IsImplicitVR()) ) { @@ -1450,18 +1500,18 @@ void gdcmParser::AddHeaderEntry(gdcmHeaderEntry *newHeaderEntry) // Actually, length= 0xffff means that we deal with // Unknown Sequence Length } - FixHeaderEntryFoundLength(Entry, (guint32)length16); return; } else { - // Either implicit VR or a non DICOM conformal (see not below) explicit + // Either implicit VR or a non DICOM conformal (see note below) explicit // VR that ommited the VR of (at least) this element. Farts happen. // [Note: according to the part 5, PS 3.5-2001, section 7.1 p25 // on Data elements "Implicit and Explicit VR Data Elements shall // not coexist in a Data Set and Data Sets nested within it".] // Length is on 4 bytes. + FixHeaderEntryFoundLength(Entry, ReadInt32()); return; } @@ -1478,7 +1528,6 @@ void gdcmParser::FindHeaderEntryVR( gdcmHeaderEntry *Entry) return; char VR[3]; - int lgrLue; long PositionOnEntry = ftell(fp); // Warning: we believe this is explicit VR (Value Representation) because @@ -1489,7 +1538,7 @@ void gdcmParser::FindHeaderEntryVR( gdcmHeaderEntry *Entry) // is in explicit VR and try to fix things if it happens not to be // the case. - lgrLue=fread (&VR, (size_t)2,(size_t)1, fp); + (void)fread (&VR, (size_t)2,(size_t)1, fp); VR[2]=0; if(!CheckHeaderEntryVR(Entry,VR)) { @@ -1510,8 +1559,8 @@ void gdcmParser::FindHeaderEntryVR( gdcmHeaderEntry *Entry) * \brief Check the correspondance between the VR of the header entry * and the taken VR. If they are different, the header entry is * updated with the new VR. - * @param Entry - * @param VR + * @param Entry Header Entry to check + * @param vr Dicom Value Representation * @return false if the VR is incorrect of if the VR isn't referenced * otherwise, it returns true */ @@ -1544,14 +1593,23 @@ bool gdcmParser::CheckHeaderEntryVR(gdcmHeaderEntry *Entry, VRKey vr) sprintf(msg,"Falsely explicit vr file (%04x,%04x)\n", Entry->GetGroup(),Entry->GetElement()); dbg.Verbose(1, "gdcmParser::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); + } return(false); } if ( Entry->IsVRUnknown() ) { // When not a dictionary entry, we can safely overwrite the VR. - Entry->SetVR(vr); + if (Entry->GetElement() == 0x0000) { // Group length is UL ! + Entry->SetVR("UL"); + } else { + Entry->SetVR(vr); + } } else if ( Entry->GetVR() != vr ) { @@ -1586,6 +1644,13 @@ std::string gdcmParser::GetHeaderEntryValue(gdcmHeaderEntry *Entry) 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) + if (vr == "US" || vr == "SS") { guint16 NewInt16; @@ -1601,6 +1666,12 @@ std::string gdcmParser::GetHeaderEntryValue(gdcmHeaderEntry *Entry) } } + // 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; @@ -1616,7 +1687,6 @@ std::string gdcmParser::GetHeaderEntryValue(gdcmHeaderEntry *Entry) s << NewInt32; } } - #ifdef GDCM_NO_ANSI_STRING_STREAM s << std::ends; // to avoid oddities on Solaris #endif //GDCM_NO_ANSI_STRING_STREAM @@ -1699,21 +1769,28 @@ void gdcmParser::SkipHeaderEntry(gdcmHeaderEntry *entry) */ void gdcmParser::FixHeaderEntryFoundLength(gdcmHeaderEntry *Entry, guint32 FoundLength) { - Entry->SetReadLength(FoundLength); // will be updated only if a bug is found - - if ( FoundLength == 0xffffffff) - { + 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(); + + 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()); + } // Sorry for the patch! - // XMedCom did the trick to read some nasty GE images ... - else if (FoundLength == 13) - { + // 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) ) ) { + ( (Entry->GetElement() != 0x0070) && (Entry->GetElement() != 0x0080) ) ){ // end of remove area FoundLength =10; Entry->SetReadLength(10); // a bug is to be fixed @@ -1723,55 +1800,44 @@ void gdcmParser::FixHeaderEntryFoundLength(gdcmHeaderEntry *Entry, guint32 Found // 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) ) ) - { + ( (Entry->GetElement() == 0x1113) || (Entry->GetElement() == 0x1114) ) ){ FoundLength =4; Entry->SetReadLength(4); // 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; + FoundLength =0; // ReadLength is unchanged } - // a SeQuence Element is beginning - // Let's forget it's length - // (we want to 'go inside') - - // Pb : *normaly* fffe|e000 is just a marker, its length *should be* zero - // in gdcm-MR-PHILIPS-16-Multi-Seq.dcm we find lengthes as big as 28800 - // if we set the length to zero IsHeaderEntryAnInteger() breaks... - // if we don't, we lost 28800 characters from the Header :-( - + // we found a 'delimiter' element + // fffe|xxxx is just a marker, we don't take its length into account else if(Entry->GetGroup() == 0xfffe) - { - // sometimes, length seems to be wrong - FoundLength =0; // some more clever checking to be done ! - // I give up! - // only gdcm-MR-PHILIPS-16-Multi-Seq.dcm - // causes troubles :-( - } - + { + // *normally, fffe|0000 doesn't exist ! + if( Entry->GetElement() != 0x0000 ) // gdcm-MR-PHILIPS-16-Multi-Seq.dcm + // causes extra troubles :-( + FoundLength =0; + } + Entry->SetUsableLength(FoundLength); } /** * \ingroup gdcmParser - * \brief Apply some heuristics to predict wether the considered + * \brief Apply some heuristics to predict whether the considered * element value contains/represents an integer or not. * @param Entry The element value on which to apply the predicate. * @return The result of the heuristical predicate. */ -bool gdcmParser::IsHeaderEntryAnInteger(gdcmHeaderEntry *Entry) -{ +bool gdcmParser::IsHeaderEntryAnInteger(gdcmHeaderEntry *Entry) { guint16 element = Entry->GetElement(); guint16 group = Entry->GetGroup(); std::string vr = Entry->GetVR(); guint32 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. @@ -1782,10 +1848,21 @@ bool gdcmParser::IsHeaderEntryAnInteger(gdcmHeaderEntry *Entry) else { std::ostringstream s; - s << "Erroneous Group Length element length on :" \ - << std::hex << group << " , " << element; - dbg.Error("gdcmParser::IsAnInteger", - s.str().c_str()); + 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("gdcmParser::IsHeaderEntryAnInteger", + // s.str().c_str()); } } if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") ) @@ -1793,15 +1870,14 @@ bool gdcmParser::IsHeaderEntryAnInteger(gdcmHeaderEntry *Entry) return false; } - /** * \ingroup gdcmParser - * \brief - * + * \brief Find the Length till the next sequence delimiter + * \warning NOT end user intended method ! * @return */ - guint32 gdcmParser::FindHeaderEntryLengthOB(void) - { + + guint32 gdcmParser::FindHeaderEntryLengthOB(void) { // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data. guint16 g; guint16 n; @@ -1818,7 +1894,7 @@ bool gdcmParser::IsHeaderEntryAnInteger(gdcmHeaderEntry *Entry) return 0; TotalLength += 4; // We even have to decount the group and element - if ( g != 0xfffe && g!=0xb00c ) /*for bogus header */ + if ( g != 0xfffe && g!=0xb00c ) //for bogus header { char msg[100]; // for sprintf. Sorry sprintf(msg,"wrong group (%04x) for an item sequence (%04x,%04x)\n",g, g,n); @@ -1826,7 +1902,7 @@ bool gdcmParser::IsHeaderEntryAnInteger(gdcmHeaderEntry *Entry) errno = 1; return 0; } - if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) /* for bogus header */ + if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) // for bogus header FoundSequenceDelimiter = true; else if ( n != 0xe000 ) { @@ -1849,41 +1925,35 @@ bool gdcmParser::IsHeaderEntryAnInteger(gdcmHeaderEntry *Entry) /** * \ingroup gdcmParser * \brief Reads a supposed to be 16 Bits integer - * \ (swaps it depending on processor endianity) - * - * @return integer acts as a boolean + * (swaps it depending on processor endianity) + * @return read value */ -guint16 gdcmParser::ReadInt16(void) -{ +guint16 gdcmParser::ReadInt16(void) { guint16 g; size_t item_read; item_read = fread (&g, (size_t)2,(size_t)1, fp); - if ( item_read != 1 ) - { + if ( item_read != 1 ) { if(ferror(fp)) dbg.Verbose(0, "gdcmParser::ReadInt16", " File Error"); errno = 1; return 0; } errno = 0; - g = SwapShort(g); + g = SwapShort(g); return g; } /** * \ingroup gdcmParser * \brief Reads a supposed to be 32 Bits integer - * \ (swaps it depending on processor endianity) - * - * @return + * (swaps it depending on processor endianity) + * @return read value */ -guint32 gdcmParser::ReadInt32(void) -{ +guint32 gdcmParser::ReadInt32(void) { guint32 g; size_t item_read; item_read = fread (&g, (size_t)4,(size_t)1, fp); - if ( item_read != 1 ) - { + if ( item_read != 1 ) { if(ferror(fp)) dbg.Verbose(0, "gdcmParser::ReadInt32", " File Error"); errno = 1; @@ -1896,19 +1966,19 @@ guint32 gdcmParser::ReadInt32(void) /** * \ingroup gdcmParser - * \brief - * + * \brief skips bytes inside the source file + * \warning NOT end user intended method ! * @return */ -void gdcmParser::SkipBytes(guint32 NBytes) -{ +void gdcmParser::SkipBytes(guint32 NBytes) { //FIXME don't dump the returned value (void)fseek(fp, (long)NBytes, SEEK_CUR); } /** * \ingroup gdcmParser - * \brief + * \brief Loads all the needed Dictionaries + * \warning NOT end user intended method ! */ void gdcmParser::Initialise(void) { @@ -1920,58 +1990,23 @@ void gdcmParser::Initialise(void) * \ingroup gdcmParser * \brief Discover what the swap code is (among little endian, big endian, * bad little endian, bad big endian). - * + * sw is set + * @return false when we are absolutely sure + * it's neither ACR-NEMA nor DICOM + * true when we hope ours assuptions are OK */ -void gdcmParser::CheckSwap() -{ - // Fourth semantics: - // - // ---> Warning : This fourth field is NOT part - // of the 'official' Dicom Dictionnary - // and should NOT be used. - // (Not defined for all the groups - // may be removed in a future release) - // - // CMD Command - // META Meta Information - // DIR Directory - // ID - // PAT Patient - // ACQ Acquisition - // REL Related - // IMG Image - // SDY Study - // VIS Visit - // WAV Waveform - // PRC - // DEV Device - // NMI Nuclear Medicine - // MED - // BFS Basic Film Session - // BFB Basic Film Box - // BIB Basic Image Box - // BAB - // IOB - // PJ - // PRINTER - // RT Radio Therapy - // DVH - // SSET - // RES Results - // CRV Curve - // OLY Overlays - // PXL Pixels - // DL Delimiters - // +bool gdcmParser::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 s; + guint32 x=4; // x : for ntohs bool net2host; // true when HostByteOrder is the same as NetworkByteOrder - + guint32 s32; + guint16 s16; + int lgrLue; char *entCur; char deb[HEADER_LENGTH_TO_READ]; @@ -1982,16 +2017,15 @@ void gdcmParser::CheckSwap() net2host = true; else net2host = false; - //cout << net2host << endl; // 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); entCur = deb + 128; - if(memcmp(entCur, "DICM", (size_t)4) == 0) - { + if(memcmp(entCur, "DICM", (size_t)4) == 0) { dbg.Verbose(1, "gdcmParser::CheckSwap:", "looks like DICOM Version3"); + // Next, determine the value representation (VR). Let's skip to the // first element (0002, 0000) and check there if we find "UL" // - or "OB" if the 1st one is (0002,0001) -, @@ -2008,12 +2042,20 @@ void gdcmParser::CheckSwap() // * the 4 bytes of the first tag (0002, 0000),or (0002, 0001) // i.e. a total of 136 bytes. entCur = deb + 136; + + // FIXME : FIXME: + // Sometimes (see : gdcmData/icone.dcm) group 0x0002 *is* Explicit VR, + // 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 + // when Write DCM *adds* // FIXME // Use gdcmParser::dicom_vr to test all the possibilities - // instead of just checking for UL, OB and UI !? - if( (memcmp(entCur, "UL", (size_t)2) == 0) || - (memcmp(entCur, "OB", (size_t)2) == 0) || - (memcmp(entCur, "UI", (size_t)2) == 0) ) + // instead of just checking for UL, OB and UI !? group 0000 { filetype = ExplicitVR; dbg.Verbose(1, "gdcmParser::CheckSwap:", @@ -2025,6 +2067,7 @@ void gdcmParser::CheckSwap() dbg.Verbose(1, "gdcmParser::CheckSwap:", "not an explicit Value Representation"); } + if (net2host) { sw = 4321; @@ -2042,7 +2085,7 @@ void gdcmParser::CheckSwap() // after the file preamble and the "DICM" string). rewind(fp); fseek (fp, 132L, SEEK_SET); - return; + return true; } // End of DicomV3 // Alas, this is not a DicomV3 file and whatever happens there is no file @@ -2060,46 +2103,77 @@ void gdcmParser::CheckSwap() // We assume the array of char we are considering contains the binary // representation of a 32 bits integer. Hence the following dirty // trick : - s = *((guint32 *)(entCur)); - - switch (s) - { + s32 = *((guint32 *)(entCur)); + + switch (s32) { case 0x00040000 : sw = 3412; filetype = ACR; - return; + return true; case 0x04000000 : sw = 4321; filetype = ACR; - return; + return true; case 0x00000400 : sw = 2143; filetype = ACR; - return; + return true; case 0x00000004 : sw = 0; filetype = ACR; - return; + 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... + + s16 = *((guint16 *)(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, "gdcmParser::CheckSwap:", - "ACR/NEMA unfound swap info (time to raise bets)"); + "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; + //else + // sw = 4321; + //return; } - - // 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 assume this file - // happens to be 'dirty' ACR/NEMA, i.e. the length of the group is - // not present. Then the only info we have is the net2host one. - filetype = Unknown; - if (! net2host ) - sw = 0; - else - sw = 4321; - return; } /** * \ingroup gdcmParser - * \brief + * \brief Restore the unproperly loaded values i.e. the group, the element + * and the dictionary entry depending on them. */ void gdcmParser::SwitchSwapToBigEndian(void) { @@ -2126,9 +2200,8 @@ void gdcmParser::SwitchSwapToBigEndian(void) /** * \ingroup gdcmParser - * \brief + * \brief during parsing, Header Elements too long are not loaded in memory * @param NewSize - * @return */ void gdcmParser::SetMaxSizeLoadEntry(long NewSize) { @@ -2142,6 +2215,29 @@ void gdcmParser::SetMaxSizeLoadEntry(long NewSize) MaxSizeLoadEntry = NewSize; } + +/** + * \ingroup gdcmParser + * \brief Header Elements too long will not be printed + * \warning + * \todo : not yet usable + * (see MAX_SIZE_PRINT_ELEMENT_VALUE + * in gdcmHeaderEntry gdcmLoadEntry) + * + * @param NewSize + */ +void gdcmParser::SetMaxSizePrintEntry(long NewSize) +{ + if (NewSize < 0) + return; + if ((guint32)NewSize >= (guint32)0xffffffff) + { + MaxSizePrintEntry = 0xffffffff; + return; + } + MaxSizePrintEntry = NewSize; +} + /** * \ingroup gdcmParser * \brief Searches both the public and the shadow dictionary (when they @@ -2211,30 +2307,35 @@ gdcmDictEntry *gdcmParser::GetDictEntryByNumber(guint16 group,guint16 element) * \brief Read the next tag but WITHOUT loading it's value * @return On succes the newly created HeaderEntry, NULL on failure. */ -gdcmHeaderEntry *gdcmParser::ReadNextHeaderEntry(void) -{ +gdcmHeaderEntry *gdcmParser::ReadNextHeaderEntry(void) { guint16 g,n; gdcmHeaderEntry *NewEntry; - g = ReadInt16(); n = ReadInt16(); if (errno == 1) - // We reached the EOF (or an error occured) and header parsing - // has to be considered as finished. + // 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); - - if (errno == 1) - { + + if (errno == 1) { // Call it quits return NULL; } NewEntry->SetOffset(ftell(fp)); - //if ( (g==0x7fe0) && (n==0x0010) ) return NewEntry; } @@ -2249,7 +2350,7 @@ gdcmHeaderEntry *gdcmParser::NewHeaderEntryByName(std::string Name) { gdcmDictEntry *NewTag = GetDictEntryByName(Name); if (!NewTag) - NewTag = NewVirtualDictEntry(0xffff, 0xffff, "LO", "Unknown", Name); + NewTag = NewVirtualDictEntry(0xffff, 0xffff, "LO", "unkn", Name); gdcmHeaderEntry* NewEntry = new gdcmHeaderEntry(NewTag); if (!NewEntry) @@ -2265,7 +2366,7 @@ gdcmHeaderEntry *gdcmParser::NewHeaderEntryByName(std::string Name) * \ingroup gdcmParser * \brief Request a new virtual dict entry to the dict set * @param group group of the underlying DictEntry - * @param elem element 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 @@ -2303,6 +2404,7 @@ gdcmHeaderEntry *gdcmParser::NewHeaderEntryByNumber(guint16 Group, guint16 Elem) return NewEntry; } +// Never used; commented out, waiting for removal. /** * \ingroup gdcmParser * \brief Small utility function that creates a new manually crafted @@ -2313,28 +2415,28 @@ gdcmHeaderEntry *gdcmParser::NewHeaderEntryByNumber(guint16 Group, guint16 Elem) * @param VR The Value Representation to be given to this new tag. * @return The newly hand crafted Element Value. */ -gdcmHeaderEntry *gdcmParser::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; -} +//gdcmHeaderEntry *gdcmParser::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; +//} /** * \ingroup gdcmParser