X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmParser.cxx;h=fc523630d76271f9ffb1b76d19583710f4f88328;hb=d4faf2fa2fcd6beba4ba8da5557b3841adfe36dd;hp=ec1dcb9f06b7d4dcc2085e97aa9fdc7a2689f7e8;hpb=65467b71ee500909b0ef7c31d442ca0c160d6a15;p=gdcm.git diff --git a/src/gdcmParser.cxx b/src/gdcmParser.cxx index ec1dcb9f..fc523630 100644 --- a/src/gdcmParser.cxx +++ b/src/gdcmParser.cxx @@ -17,6 +17,52 @@ # else # include #endif +# include + +#define UI1_2_840_10008_1_2 "1.2.840.10008.1.2" +#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" +#define UI1_2_840_10008_1_2_1_99 "1.2.840.10008.1.2.1.99" + + // 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 + // //----------------------------------------------------------------------------- // Refer to gdcmParser::CheckSwap() @@ -35,15 +81,18 @@ const unsigned int gdcmParser::MAX_SIZE_LOAD_ELEMENT_VALUE = 4096; * @param enable_sequences = true to allow the header * 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 + * @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; @@ -56,7 +105,7 @@ gdcmParser::gdcmParser(const char *InFilename, 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 } /** @@ -64,23 +113,21 @@ gdcmParser::gdcmParser(const char *InFilename, * \brief * @param exception_on_error */ -gdcmParser::gdcmParser(bool exception_on_error) -{ +gdcmParser::gdcmParser(bool 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; } @@ -93,11 +140,9 @@ gdcmParser::~gdcmParser (void) * both from the H Table and the chained list * @return */ -void gdcmParser::PrintPubEntry(std::ostream & os) -{ +void gdcmParser::PrintEntry(std::ostream & os) { std::ostringstream s; - s << "------------ using listEntries ----------------" << std::endl; for (ListTag::iterator i = listEntries.begin(); i != listEntries.end(); ++i) @@ -113,8 +158,7 @@ void gdcmParser::PrintPubEntry(std::ostream & os) * \brief Prints The Dict Entries of THE public Dicom Dictionnry * @return */ -void gdcmParser::PrintPubDict(std::ostream & os) -{ +void gdcmParser::PrintPubDict(std::ostream & os) { RefPubDict->Print(os); } @@ -123,8 +167,7 @@ void gdcmParser::PrintPubDict(std::ostream & os) * \brief Prints The Dict Entries of THE shadow Dicom Dictionnry * @return */ -void gdcmParser::PrintShaDict(std::ostream & os) -{ +void gdcmParser::PrintShaDict(std::ostream & os) { RefShaDict->Print(os); } @@ -134,8 +177,7 @@ void gdcmParser::PrintShaDict(std::ostream & os) * \ingroup gdcmParser * \brief Get the public dictionary used */ -gdcmDict *gdcmParser::GetPubDict(void) -{ +gdcmDict *gdcmParser::GetPubDict(void) { return(RefPubDict); } @@ -143,8 +185,7 @@ gdcmDict *gdcmParser::GetPubDict(void) * \ingroup gdcmParser * \brief Get the shadow dictionary used */ -gdcmDict *gdcmParser::GetShaDict(void) -{ +gdcmDict *gdcmParser::GetShaDict(void) { return(RefShaDict); } @@ -153,8 +194,7 @@ gdcmDict *gdcmParser::GetShaDict(void) * \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); } @@ -164,8 +204,7 @@ bool gdcmParser::SetShaDict(gdcmDict *dict) * \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); } @@ -179,23 +218,15 @@ 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 - } +bool gdcmParser::IsReadable(void) { +cout << "filetype [" << filetype <<"]" << endl; + if(filetype==Unknown) + return(false); +cout << "trouv filetype" << endl; + if(listEntries.size()<=0) + return(false); - 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; + return(true); } /** @@ -205,15 +236,14 @@ bool gdcmParser::IsReadable(void) * * @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; LoadHeaderEntrySafe(Element); std::string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2" ) + if ( Transfer == UI1_2_840_10008_1_2 ) return true; return false; } @@ -225,15 +255,14 @@ bool gdcmParser::IsImplicitVRLittleEndianTransferSyntax(void) * * @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; LoadHeaderEntrySafe(Element); std::string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.1" ) + if ( Transfer == UI1_2_840_10008_1_2_1 ) return true; return false; } @@ -245,15 +274,14 @@ bool gdcmParser::IsExplicitVRLittleEndianTransferSyntax(void) * * @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; LoadHeaderEntrySafe(Element); std::string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.1.99" ) + if ( Transfer == UI1_2_840_10008_1_2_1_99 ) return true; return false; } @@ -265,15 +293,14 @@ bool gdcmParser::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) * * @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; LoadHeaderEntrySafe(Element); std::string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.2" ) //1.2.2 ??? A verifier ! + if ( Transfer == UI1_2_840_10008_1_2_2 ) //1.2.2 ??? A verifier ! return true; return false; } @@ -324,7 +351,6 @@ FILE *gdcmParser::OpenFile(bool exception_on_error) dbg.Verbose(0, "gdcmParser::gdcmParser not DICOM/ACR", filename.c_str()); } else { - std::cerr<GetDictEntryByName(tagName); if( dictEntry == NULL) return GDCM_UNFOUND; @@ -518,8 +541,7 @@ 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; @@ -539,8 +561,7 @@ 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; @@ -562,8 +583,7 @@ 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; @@ -577,8 +597,7 @@ 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; @@ -611,7 +630,6 @@ bool gdcmParser::SetEntryByNumber(std::string content, content = content + '\0'; } - //tagHT[key]->SetValue(content); gdcmHeaderEntry * a; IterHT p; TagHeaderEntryHT::iterator p2; @@ -625,7 +643,6 @@ bool gdcmParser::SetEntryByNumber(std::string content, a-> SetValue(content); - //std::string vr = tagHT[key]->GetVR(); std::string vr = a->GetVR(); guint32 lgr; @@ -636,7 +653,6 @@ bool gdcmParser::SetEntryByNumber(std::string content, else lgr = l; - //tagHT[key]->SetLength(lgr); a->SetLength(lgr); return true; } @@ -655,13 +671,13 @@ bool gdcmParser::SetEntryByNumber(std::string content, */ bool gdcmParser::SetEntryLengthByNumber(guint32 length, - guint16 group, guint16 element) + 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 ; @@ -711,6 +727,8 @@ void * gdcmParser::GetEntryVoidAreaByNumber(guint16 Group, guint16 Elem) * \ingroup gdcmParser * \brief Loads (from disk) the element content * when a string is not suitable + * @param Group + * @param Elem */ void *gdcmParser::LoadEntryVoidArea(guint16 Group, guint16 Elem) { @@ -743,12 +761,13 @@ 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); return true; } @@ -758,11 +777,7 @@ bool gdcmParser::SetEntryVoidAreaByNumber(void * area,guint16 group, guint16 ele * \brief Update the entries with the shadow dictionary. Only odd entries are * analized */ -void gdcmParser::UpdateShaEntries(void) -{ - if(!RefShaDict) - return; - +void gdcmParser::UpdateShaEntries(void) { gdcmDictEntry *entry; std::string vr; @@ -771,16 +786,32 @@ void gdcmParser::UpdateShaEntries(void) ++it) { // Odd group => from public dictionary - if((*it)->GetGroup()%1==0) + if((*it)->GetGroup()%2==0) continue; // Peer group => search the corresponding dict entry - entry=RefShaDict->GetDictEntryByNumber((*it)->GetGroup(),(*it)->GetElement()); - if(entry) - { - (*it)->SetDictEntry(entry); + if(RefShaDict) + entry=RefShaDict->GetDictEntryByNumber((*it)->GetGroup(),(*it)->GetElement()); + else + entry=NULL; + + if((*it)->IsImplicitVR()) + vr="Implicit"; + else vr=(*it)->GetVR(); + + (*it)->SetValue(GetHeaderEntryUnvalue(*it)); + if(entry){ + // Set the new entry and the new value + (*it)->SetDictEntry(entry); CheckHeaderEntryVR(*it,vr); + + (*it)->SetValue(GetHeaderEntryValue(*it)); + } + else + { + // Remove precedent value transformation + (*it)->SetDictEntry(NewVirtualDictEntry((*it)->GetGroup(),(*it)->GetElement(),vr)); } } } @@ -793,8 +824,7 @@ 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; @@ -821,6 +851,19 @@ gdcmHeaderEntry* gdcmParser::GetHeaderEntryByNumber(guint16 group, guint16 eleme 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 @@ -829,8 +872,7 @@ 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); @@ -845,8 +887,7 @@ 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; @@ -984,6 +1025,7 @@ void gdcmParser::WriteEntries(FileType type, FILE * _fp) lgr = (*tag2)->GetLength(); val = (*tag2)->GetValue().c_str(); vr = (*tag2)->GetVR(); +//cout << hex << gr << " " << el << " "<< vr << " " << val << endl; // JPR if ( type == ACR ) { @@ -997,16 +1039,22 @@ void gdcmParser::WriteEntries(FileType type, FILE * _fp) fwrite ( &gr,(size_t)2 ,(size_t)1 ,_fp); //group fwrite ( &el,(size_t)2 ,(size_t)1 ,_fp); //element - - if ( (type == ExplicitVR) && (gr <= 0x0002) ) + + // === Deal with the length + // -------------------- + + // if ( (type == ExplicitVR) && (gr <= 0x0002) ) // ?!? < 2 + if ( (type == ExplicitVR) || (type == DICOMDIR) ) { // EXPLICIT VR guint16 z=0, shortLgr; - fwrite (vr.c_str(),(size_t)2 ,(size_t)1 ,_fp); + if (gr != 0xfffe) // JPR + fwrite (vr.c_str(),(size_t)2 ,(size_t)1 ,_fp); - if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") ) + if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") || gr == 0xfffe) // JPR { - fwrite ( &z, (size_t)2 ,(size_t)1 ,_fp); + if (gr != 0xfffe) + fwrite ( &z, (size_t)2 ,(size_t)1 ,_fp); fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp); } @@ -1016,11 +1064,16 @@ void gdcmParser::WriteEntries(FileType type, FILE * _fp) fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp); } } - else // IMPLICIT VR + else // IMPLICIT VR { fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp); } - + + // === Deal with the value + // ------------------- + if (vr == "SQ") continue; // vo "value" to write for the SEQuences + if (gr == 0xfffe)continue; + if (vr == "US" || vr == "SS") { tokens.erase(tokens.begin(),tokens.end()); // clean any previous value @@ -1061,10 +1114,8 @@ 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 : @@ -1086,34 +1137,52 @@ guint32 gdcmParser::SwapLong(guint32 a) return(a); } +/** + * \ingroup gdcmParser + * \brief Unswaps back the bytes of 4-byte long integer accordingly to + * processor order. + * @return The properly unswaped 32 bits integer. + */ +guint32 gdcmParser::UnswapLong(guint32 a) { + return (SwapLong(a)); +} + /** * \ingroup gdcmParser * \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); } +/** + * \ingroup gdcmParser + * \brief Unswaps the bytes so they agree with the processor order + * @return The properly unswaped 16 bits integer. + */ +guint16 gdcmParser::UnswapShort(guint16 a) { + return (SwapShort(a)); +} + //----------------------------------------------------------------------------- // Private /** * \ingroup gdcmParser * \brief Parses the header of the file but WITHOUT loading element values. */ -void gdcmParser::Parse(bool exception_on_error) throw(gdcmFormatError) -{ +void gdcmParser::Parse(bool exception_on_error) throw(gdcmFormatError) { gdcmHeaderEntry *newHeaderEntry = (gdcmHeaderEntry *)0; rewind(fp); CheckSwap(); - while ( (newHeaderEntry = ReadNextHeaderEntry()) ) - { - SkipHeaderEntry(newHeaderEntry); - AddHeaderEntry(newHeaderEntry); + while ( (newHeaderEntry = ReadNextHeaderEntry()) ) { + SkipHeaderEntry(newHeaderEntry); + if ( (ignoreShadow==0) || (newHeaderEntry->GetGroup()%2) == 0) { //JPR + AddHeaderEntry(newHeaderEntry); + } } } @@ -1122,22 +1191,20 @@ void gdcmParser::Parse(bool exception_on_error) throw(gdcmFormatError) * \brief Loads the element values of all the Header Entries pointed in the * public Chained List. */ -void gdcmParser::LoadHeaderEntries(void) -{ +void gdcmParser::LoadHeaderEntries(void) { rewind(fp); for (ListTag::iterator i = GetListEntry().begin(); i != GetListEntry().end(); ++i) { - LoadHeaderEntry(*i); - } + LoadHeaderEntry(*i); + } rewind(fp); // 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 @@ -1175,8 +1242,7 @@ void gdcmParser::LoadHeaderEntries(void) * 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(); @@ -1198,16 +1264,14 @@ void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry *Entry) if( group == 0xfffe ) SkipLoad = true; - if ( SkipLoad ) - { + if ( SkipLoad ) { Entry->SetLength(0); Entry->SetValue("gdcm::Skipped"); return; } // When the length is zero things are easy: - if ( length == 0 ) - { + if ( length == 0 ) { Entry->SetValue(""); return; } @@ -1215,8 +1279,7 @@ 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(); @@ -1233,68 +1296,55 @@ void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry *Entry) // 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") - { + 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") - { + } + } + 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; } } - } + } #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; } // We need an additional byte for storing \0 that is not on disk - char* NewValue = (char*)malloc(length+1); - if( !NewValue) - { - dbg.Verbose(1, "LoadElementValue: Failed to allocate NewValue"); - return; - } - NewValue[length]= 0; - - item_read = fread(NewValue, (size_t)length, (size_t)1, fp); - if ( item_read != 1 ) - { - free(NewValue); + std::string NewValue(length,0); + item_read = fread(&(NewValue[0]), (size_t)length, (size_t)1, fp); + if ( item_read != 1 ) { dbg.Verbose(1, "gdcmParser::LoadElementValue","unread element value"); Entry->SetValue("gdcm::UnRead"); return; } - Entry->SetValue(NewValue); - free(NewValue); + + if( (vr == "UI") ) // Because of correspondance with the VR dic + Entry->SetValue(NewValue.c_str()); + else + Entry->SetValue(NewValue); } /** @@ -1306,8 +1356,7 @@ void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry *Entry) * \ 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; @@ -1320,8 +1369,7 @@ void gdcmParser::AddHeaderEntry(gdcmHeaderEntry * newHeaderEntry) * @return */ - void gdcmParser::FindHeaderEntryLength (gdcmHeaderEntry * Entry) - { + void gdcmParser::FindHeaderEntryLength (gdcmHeaderEntry *Entry) { guint16 element = Entry->GetElement(); guint16 group = Entry->GetGroup(); std::string vr = Entry->GetVR(); @@ -1333,7 +1381,7 @@ void gdcmParser::AddHeaderEntry(gdcmHeaderEntry * newHeaderEntry) "we reached 7fe0 0010"); } - if ( (filetype == ExplicitVR) && ! Entry->IsImplicitVr() ) + if ( (filetype == ExplicitVR) && (! Entry->IsImplicitVR()) ) { if ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") ) { @@ -1421,15 +1469,17 @@ void gdcmParser::AddHeaderEntry(gdcmHeaderEntry * newHeaderEntry) FixHeaderEntryFoundLength(Entry, (guint32)length16); return; } - - // Either implicit VR or a non DICOM conformal (see not 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; + else + { + // Either implicit VR or a non DICOM conformal (see not 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; + } } /** @@ -1466,7 +1516,7 @@ void gdcmParser::FindHeaderEntryVR( gdcmHeaderEntry *Entry) // avoid . if ( Entry->IsVRUnknown() ) Entry->SetVR("Implicit"); - Entry->SetImplicitVr(); + Entry->SetImplicitVR(); } } @@ -1480,7 +1530,7 @@ void gdcmParser::FindHeaderEntryVR( gdcmHeaderEntry *Entry) * @return false if the VR is incorrect of if the VR isn't referenced * otherwise, it returns true */ -bool gdcmParser::CheckHeaderEntryVR (gdcmHeaderEntry *Entry, VRKey vr) +bool gdcmParser::CheckHeaderEntryVR(gdcmHeaderEntry *Entry, VRKey vr) { char msg[100]; // for sprintf bool RealExplicit = true; @@ -1525,22 +1575,131 @@ bool gdcmParser::CheckHeaderEntryVR (gdcmHeaderEntry *Entry, VRKey vr) // 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* NewTag = NewVirtualDictEntry(Entry->GetGroup(), - Entry->GetElement(), - vr, - "FIXME", - Entry->GetName()); - Entry->SetDictEntry(NewTag); + gdcmDictEntry* NewEntry = NewVirtualDictEntry( + Entry->GetGroup(),Entry->GetElement(), + vr,"FIXME",Entry->GetName()); + Entry->SetDictEntry(NewEntry); } return(true); } /** * \ingroup gdcmParser - * \brief Skip a given Header Entry + * \brief Get the transformed value of the header entry. The VR value + * is used to define the transformation to operate on the value * \warning NOT end user intended method ! - * @param entry - * @return + * @param Entry + * @return Transformed entry value + */ +std::string gdcmParser::GetHeaderEntryValue(gdcmHeaderEntry *Entry) +{ + if ( (IsHeaderEntryAnInteger(Entry)) && (Entry->IsImplicitVR()) ) + { + std::string val=Entry->GetValue(); + std::string vr=Entry->GetVR(); + guint32 length = Entry->GetLength(); + std::ostringstream s; + int nbInt; + + if (vr == "US" || vr == "SS") + { + guint16 NewInt16; + + nbInt = length / 2; + for (int i=0; i < nbInt; i++) + { + if(i!=0) + s << '\\'; + NewInt16 = (val[2*i+0]&0xFF)+((val[2*i+1]&0xFF)<<8); + NewInt16 = SwapShort(NewInt16); + s << NewInt16; + } + } + + else if (vr == "UL" || vr == "SL") + { + guint32 NewInt32; + + nbInt = length / 4; + for (int i=0; i < nbInt; i++) + { + 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; + } + } + +#ifdef GDCM_NO_ANSI_STRING_STREAM + s << std::ends; // to avoid oddities on Solaris +#endif //GDCM_NO_ANSI_STRING_STREAM + return(s.str()); + } + + return(Entry->GetValue()); +} + +/** + * \ingroup gdcmParser + * \brief Get the reverse transformed value of the header entry. The VR + * value is used to define the reverse transformation to operate on + * the value + * \warning NOT end user intended method ! + * @param Entry + * @return Reverse transformed entry value + */ +std::string gdcmParser::GetHeaderEntryUnvalue(gdcmHeaderEntry *Entry) +{ + if ( (IsHeaderEntryAnInteger(Entry)) && (Entry->IsImplicitVR()) ) + { + std::string vr=Entry->GetVR(); + std::ostringstream s; + std::vector tokens; + + if (vr == "US" || vr == "SS") + { + guint16 NewInt16; + + tokens.erase(tokens.begin(),tokens.end()); // clean any previous value + Tokenize (Entry->GetValue(), tokens, "\\"); + for (unsigned int i=0; i>8)&0xFF); + } + tokens.clear(); + } + if (vr == "UL" || vr == "SL") + { + guint32 NewInt32; + + tokens.erase(tokens.begin(),tokens.end()); // clean any previous value + Tokenize (Entry->GetValue(), tokens, "\\"); + for (unsigned int i=0; i>8)&0xFF) + <<(char)((NewInt32>>16)&0xFF)<<(char)((NewInt32>>24)&0xFF); + } + tokens.clear(); + } + +#ifdef GDCM_NO_ANSI_STRING_STREAM + s << std::ends; // to avoid oddities on Solaris +#endif //GDCM_NO_ANSI_STRING_STREAM + return(s.str()); + } + + return(Entry->GetValue()); +} + +/** + * \ingroup gdcmParser + * \brief Skip a given Header Entry + * \warning NOT end user intended method ! + * @param entry */ void gdcmParser::SkipHeaderEntry(gdcmHeaderEntry *entry) { @@ -1590,7 +1749,7 @@ void gdcmParser::FixHeaderEntryFoundLength(gdcmHeaderEntry *Entry, guint32 Found 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 @@ -1621,13 +1780,11 @@ void gdcmParser::FixHeaderEntryFoundLength(gdcmHeaderEntry *Entry, guint32 Found * @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. @@ -1638,10 +1795,20 @@ 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") ) @@ -1656,8 +1823,7 @@ bool gdcmParser::IsHeaderEntryAnInteger(gdcmHeaderEntry *Entry) * * @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; @@ -1707,22 +1873,20 @@ bool gdcmParser::IsHeaderEntryAnInteger(gdcmHeaderEntry *Entry) * \brief Reads a supposed to be 16 Bits integer * \ (swaps it depending on processor endianity) * - * @return integer acts as a boolean + * @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; } @@ -1731,15 +1895,13 @@ guint16 gdcmParser::ReadInt16(void) * \brief Reads a supposed to be 32 Bits integer * \ (swaps it depending on processor endianity) * - * @return + * @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; @@ -1756,8 +1918,7 @@ guint32 gdcmParser::ReadInt32(void) * * @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); } @@ -1778,52 +1939,13 @@ void gdcmParser::Initialise(void) * bad little endian, bad big endian). * */ -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 - // +void 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 @@ -1838,16 +1960,15 @@ 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) -, @@ -1867,7 +1988,7 @@ void gdcmParser::CheckSwap() // 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) || + if( (memcmp(entCur, "UL", (size_t)2) == 0) || (memcmp(entCur, "OB", (size_t)2) == 0) || (memcmp(entCur, "UI", (size_t)2) == 0) ) { @@ -1917,9 +2038,8 @@ void gdcmParser::CheckSwap() // representation of a 32 bits integer. Hence the following dirty // trick : s = *((guint32 *)(entCur)); - - switch (s) - { + + switch (s) { case 0x00040000 : sw = 3412; filetype = ACR; @@ -1938,19 +2058,20 @@ void gdcmParser::CheckSwap() return; default : dbg.Verbose(0, "gdcmParser::CheckSwap:", - "ACR/NEMA unfound swap info (time to raise bets)"); + "ACR/NEMA unfound swap info (time to raise bets)"); + + // 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. + filetype = ACR; + // 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; } /** @@ -2067,8 +2188,7 @@ 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; @@ -2076,16 +2196,24 @@ gdcmHeaderEntry *gdcmParser::ReadNextHeaderEntry(void) 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) //JPR + // 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; } @@ -2145,11 +2273,11 @@ gdcmDictEntry *gdcmParser::NewVirtualDictEntry(guint16 group, guint16 element, gdcmHeaderEntry *gdcmParser::NewHeaderEntryByNumber(guint16 Group, guint16 Elem) { // Find out if the tag we encountered is in the dictionaries: - gdcmDictEntry *NewTag = GetDictEntryByNumber(Group, Elem); - if (!NewTag) - NewTag = NewVirtualDictEntry(Group, Elem); + gdcmDictEntry *DictEntry = GetDictEntryByNumber(Group, Elem); + if (!DictEntry) + DictEntry = NewVirtualDictEntry(Group, Elem); - gdcmHeaderEntry* NewEntry = new gdcmHeaderEntry(NewTag); + gdcmHeaderEntry *NewEntry = new gdcmHeaderEntry(DictEntry); if (!NewEntry) { dbg.Verbose(1, "gdcmParser::NewHeaderEntryByNumber",