X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmParser.cxx;h=7f6384f85edb59a4aa795a984ceface39f445775;hb=8402492c91eb411888fb7e220e0f02b3d94c59db;hp=797d50c8c7227cec8a124730e060e6279c977f17;hpb=e8235a5f13987040aac69069bf6e1667cfe36507;p=gdcm.git diff --git a/src/gdcmParser.cxx b/src/gdcmParser.cxx index 797d50c8..7f6384f8 100644 --- a/src/gdcmParser.cxx +++ b/src/gdcmParser.cxx @@ -17,14 +17,64 @@ # 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() 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 /** @@ -35,15 +85,18 @@ 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; @@ -51,12 +104,13 @@ gdcmParser::gdcmParser(const char *InFilename, if ( !OpenFile(exception_on_error)) return; - Parse(); - LoadHeaderEntries(); + if (ParseHeader()) { + 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 } /** @@ -64,27 +118,23 @@ 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) -{ - dicom_vr = (gdcmVR*)0; - Dicts = (gdcmDictSet*)0; - RefPubDict = (gdcmDict*)0; - RefShaDict = (gdcmDict*)0; +gdcmParser::~gdcmParser (void) { + RefPubDict = NULL; + RefShaDict = NULL; } //----------------------------------------------------------------------------- @@ -95,16 +145,9 @@ 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; -// guint32 lgth; -// char greltag[10]; //group element tag - - s << "------------ using listEntries ----------------" << std::endl; - -// char st[20]; for (ListTag::iterator i = listEntries.begin(); i != listEntries.end(); ++i) @@ -120,8 +163,7 @@ 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); } @@ -130,13 +172,48 @@ 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); } //----------------------------------------------------------------------------- // Public +/** + * \ingroup gdcmParser + * \brief Get the public dictionary used + */ +gdcmDict *gdcmParser::GetPubDict(void) { + return(RefPubDict); +} + +/** + * \ingroup gdcmParser + * \brief Get the shadow dictionary used + */ +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){ + 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){ + RefShaDict=gdcmGlobal::GetDicts()->GetDict(dictName); + return(!RefShaDict); +} + /** * \ingroup gdcmParser * \brief This predicate, based on hopefully reasonable heuristics, @@ -146,23 +223,15 @@ void gdcmParser::PrintShaDict(std::ostream & os) * @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) { + if(filetype==Unknown) { + return(false); + } + 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); } /** @@ -172,15 +241,14 @@ 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; } @@ -192,15 +260,14 @@ 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; } @@ -212,15 +279,14 @@ 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; } @@ -232,15 +298,14 @@ 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; } @@ -288,11 +353,10 @@ 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 { - std::cerr<GetTagByName(tagName); +std::string gdcmParser::GetEntryByName(std::string tagName) { + gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( dictEntry == NULL) return GDCM_UNFOUND; @@ -502,9 +546,8 @@ 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) -{ - gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName); +std::string gdcmParser::GetEntryVRByName(std::string tagName) { + gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( dictEntry == NULL) return GDCM_UNFOUND; @@ -523,8 +566,7 @@ 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; @@ -546,8 +588,7 @@ 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; @@ -561,48 +602,13 @@ 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) -{ - gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName); +bool gdcmParser::SetEntryByName(std::string content,std::string tagName) { + gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( dictEntry == NULL) return false; return(SetEntryByNumber(content,dictEntry->GetGroup(), dictEntry->GetElement())); -/* TagKey key = gdcmDictEntry::TranslateToKey(dictEntry->GetGroup(), - dictEntry->GetElement()); - if ( GetPubEntry().count(key) == 0 ) - return false; - - int l = content.length(); - if(l%2) // Odd length are padded with a space (020H). - { - l++; - content = content + '\0'; - } - - //tagHt[key]->SetValue(content); - gdcmHeaderEntry * a; - IterHT p; - TagHeaderEntryHT::iterator p2; - // DO NOT remove the following lines : they explain how the stuff works - //p= tagHt.equal_range(key); // get a pair of iterators first-last synonym - //p2=p.first; // iterator on the first synonym - //a=p2->second; // H Table target column (2-nd col) - // or, easier : - a = ((GetPubEntry().equal_range(key)).first)->second; - a-> SetValue(content); - std::string vr = a->GetVR(); - - guint32 lgr; - if( (vr == "US") || (vr == "SS") ) - lgr = 2; - else if( (vr == "UL") || (vr == "SL") ) - lgr = 4; - else - lgr = l; - a->SetLength(lgr); - return true;*/ } /** @@ -629,7 +635,6 @@ bool gdcmParser::SetEntryByNumber(std::string content, content = content + '\0'; } - //tagHT[key]->SetValue(content); gdcmHeaderEntry * a; IterHT p; TagHeaderEntryHT::iterator p2; @@ -643,7 +648,6 @@ bool gdcmParser::SetEntryByNumber(std::string content, a-> SetValue(content); - //std::string vr = tagHT[key]->GetVR(); std::string vr = a->GetVR(); guint32 lgr; @@ -654,7 +658,6 @@ bool gdcmParser::SetEntryByNumber(std::string content, else lgr = l; - //tagHT[key]->SetLength(lgr); a->SetLength(lgr); return true; } @@ -667,19 +670,19 @@ bool gdcmParser::SetEntryByNumber(std::string content, * the given value. * \warning Use with extreme caution. * @param length new length to substitute with - * @param group group of the ElVal to modify - * @param element element of the ElVal to modify + * @param group group of the entry to modify + * @param element element of the Entry to modify * @return 1 on success, 0 otherwise. */ 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 ; @@ -729,6 +732,8 @@ 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) { @@ -750,6 +755,7 @@ void *gdcmParser::LoadEntryVoidArea(guint16 Group, guint16 Elem) free(a); return NULL; } + return a; } @@ -761,16 +767,61 @@ 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; } +/** + * \ingroup gdcmParser + * \brief Update the entries with the shadow dictionary. Only odd entries are + * analized + */ +void gdcmParser::UpdateShaEntries(void) { + gdcmDictEntry *entry; + std::string vr; + + for(ListTag::iterator it=listEntries.begin(); + it!=listEntries.end(); + ++it) + { + // Odd group => from public dictionary + if((*it)->GetGroup()%2==0) + continue; + + // Peer group => search the corresponding dict 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)); + } + } +} + /** * \ingroup gdcmParser * \brief Searches within the Header Entries for a Dicom Element of @@ -779,9 +830,8 @@ bool gdcmParser::SetEntryVoidAreaByNumber(void * area,guint16 group, guint16 ele * @return Corresponding Dicom Element when it exists, and NULL * otherwise. */ - gdcmHeaderEntry *gdcmParser::GetHeaderEntryByName(std::string tagName) - { - gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName); + gdcmHeaderEntry *gdcmParser::GetHeaderEntryByName(std::string tagName) { + gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( dictEntry == NULL) return NULL; @@ -807,6 +857,19 @@ 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 @@ -815,8 +878,7 @@ 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); @@ -831,8 +893,7 @@ 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; @@ -937,11 +998,13 @@ void gdcmParser::UpdateGroupLength(bool SkipSequence, FileType type) * \ warning does NOT add the missing elements in the header : * \ it's up to the user doing it ! * \ (function CheckHeaderCoherence to be written) + * \ warning DON'T try, right now, to write a DICOM image + * \ from an ACR Header (meta elements will be missing!) * @param type type of the File to be written * (ACR-NEMA, ExplicitVR, ImplicitVR) * @param _fp already open file pointer */ -void gdcmParser::WriteEntries(FileType type, FILE * _fp) +void gdcmParser::WriteEntries(FILE *_fp,FileType type) { guint16 gr, el; guint32 lgr; @@ -949,27 +1012,32 @@ void gdcmParser::WriteEntries(FileType type, FILE * _fp) std::string vr; guint32 val_uint32; guint16 val_uint16; - + guint16 valZero =0; + void *voidArea; std::vector tokens; + // TODO : function CheckHeaderCoherence to be written + // 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; - + // TODO (?) tester les echecs en ecriture (apres chaque fwrite) - + int compte =0; + for (ListTag::iterator tag2=listEntries.begin(); tag2 != listEntries.end(); ++tag2) { gr = (*tag2)->GetGroup(); el = (*tag2)->GetElement(); - lgr = (*tag2)->GetLength(); + lgr = (*tag2)->GetReadLength(); val = (*tag2)->GetValue().c_str(); vr = (*tag2)->GetVR(); + voidArea = (*tag2)->GetVoidArea(); if ( type == ACR ) { @@ -983,30 +1051,55 @@ 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 ( (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 - { + if (vr == "unkn") { // Unknown was 'written' shortLgr=lgr; fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp); - } + fwrite ( &z, (size_t)2 ,(size_t)1 ,_fp); + } else { + if (gr != 0xfffe) { // NO value for 'delimiters' + if (vr == "unkn") // Unknown was 'written' + 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") || gr == 0xfffe) + { + if (gr != 0xfffe) + fwrite ( &z, (size_t)2 ,(size_t)1 ,_fp); + fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp); + } + else + { + shortLgr=lgr; + 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; // no "value" to write for the SEQuences + if (gr == 0xfffe)continue; + + if (voidArea != NULL) { // there is a 'non string' LUT, overlay, etc + fwrite ( voidArea,(size_t)lgr ,(size_t)1 ,_fp); // Elem value + continue; + } + if (vr == "US" || vr == "SS") { tokens.erase(tokens.begin(),tokens.end()); // clean any previous value @@ -1032,11 +1125,17 @@ void gdcmParser::WriteEntries(FileType type, FILE * _fp) } tokens.clear(); continue; - } + } + // Pixels are never loaded in the element ! - if ((gr == 0x7fe0) && (el == 0x0010) ) - break; - + // we stop writting when Pixel are processed + // FIX : we loose trailing elements (RAB, right now) + + if ((gr == GrPixel) && (el == NumPixel) ) { + compte++; + if (compte == countGrPixel) // we passed *all* the GrPixel,NumPixel + break; + } fwrite ( val,(size_t)lgr ,(size_t)1 ,_fp); // Elem value } } @@ -1047,10 +1146,8 @@ 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 : @@ -1072,41 +1169,78 @@ 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. + * @return false if file is not ACR-NEMA / DICOM + */ +bool gdcmParser::ParseHeader(bool exception_on_error) throw(gdcmFormatError) { + + rewind(fp); + if (!CheckSwap()) + return false; + + gdcmHeaderEntry *newHeaderEntry = (gdcmHeaderEntry *)0; + while ( (newHeaderEntry = ReadNextHeaderEntry()) ) { + SkipHeaderEntry(newHeaderEntry); + if ( (ignoreShadow==0) || (newHeaderEntry->GetGroup()%2) == 0) { + AddHeaderEntry(newHeaderEntry); + } + } + return true; +} + /** * \ingroup gdcmParser * \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 = GetPubListEntry().begin(); - i != GetPubListEntry().end(); + 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 @@ -1115,8 +1249,10 @@ 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 : how to use it? + LoadEntryVoidArea(0x0028,0x3006); //LUT Data (CTX dependent) + // -------------------------------------------------------------- // Special Patch to allow gdcm to read ACR-LibIDO formated images // @@ -1139,20 +1275,18 @@ void gdcmParser::LoadHeaderEntries(void) /** * \ingroup gdcmParser - * \brief Loads the element content if it's length is not bigger - * than the value specified with - * gdcmParser::SetMaxSizeLoadEntry() - * @param ElVal Header Entry (Dicom Element) to be dealt with + * \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 * ElVal) -{ +void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry *Entry) { size_t item_read; - guint16 group = ElVal->GetGroup(); - std::string vr= ElVal->GetVR(); - guint32 length = ElVal->GetLength(); + guint16 group = Entry->GetGroup(); + std::string vr= Entry->GetVR(); + guint32 length = Entry->GetLength(); bool SkipLoad = false; - fseek(fp, (long)ElVal->GetOffset(), SEEK_SET); + fseek(fp, (long)Entry->GetOffset(), SEEK_SET); // the test was commented out to 'go inside' the SeQuences // we don't any longer skip them ! @@ -1167,103 +1301,87 @@ void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry * ElVal) if( group == 0xfffe ) SkipLoad = true; - if ( SkipLoad ) - { - ElVal->SetLength(0); - ElVal->SetValue("gdcm::Skipped"); + if ( SkipLoad ) { + Entry->SetLength(0); + Entry->SetValue("gdcm::Skipped"); return; } // When the length is zero things are easy: - if ( length == 0 ) - { - ElVal->SetValue(""); + if ( length == 0 ) { + Entry->SetValue(""); return; } // The elements whose length is bigger than the specified upper bound // are not loaded. Instead we leave a short notice of the offset of // the element content and it's length. - if (length > MaxSizeLoadEntry) - { + if (length > MaxSizeLoadEntry) { std::ostringstream s; s << "gdcm::NotLoaded."; - s << " Address:" << (long)ElVal->GetOffset(); - s << " Length:" << ElVal->GetLength(); - s << " x(" << std::hex << ElVal->GetLength() << ")"; - ElVal->SetValue(s.str()); + s << " Address:" << (long)Entry->GetOffset(); + s << " Length:" << Entry->GetLength(); + s << " x(" << std::hex << Entry->GetLength() << ")"; + 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. + // properly i.e. as integers as opposed to strings. // Elements with Value Multiplicity > 1 // contain a set of integers (not a single one) // Any compacter code suggested (?) - if ( IsHeaderEntryAnInteger(ElVal) ) - { + 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 - ElVal->SetValue(s.str()); + + 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"); - ElVal->SetValue("gdcm::UnRead"); + Entry->SetValue("gdcm::UnRead"); return; } - ElVal->SetValue(NewValue); - free(NewValue); + + if( (vr == "UI") ) // Because of correspondance with the VR dic + Entry->SetValue(NewValue.c_str()); // ??? JPR ??? + else + Entry->SetValue(NewValue); } /** @@ -1271,12 +1389,11 @@ void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry * ElVal) * \brief add a new Dicom Element pointer to * the H Table and to the chained List * \warning push_bash in listEntries ONLY during ParseHeader - * \todo something to allow further Elements addition, + * \TODO something to allow further Elements addition, * \ 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; @@ -1285,24 +1402,23 @@ void gdcmParser::AddHeaderEntry(gdcmHeaderEntry * newHeaderEntry) /** * \ingroup gdcmParser * \brief - * @param ElVal : Header Entry whose length of the value shall be loaded. + * @param Entry Header Entry whose length of the value shall be loaded. * @return */ - void gdcmParser::FindHeaderEntryLength (gdcmHeaderEntry * ElVal) - { - guint16 element = ElVal->GetElement(); - guint16 group = ElVal->GetGroup(); - std::string vr = ElVal->GetVR(); + void gdcmParser::FindHeaderEntryLength (gdcmHeaderEntry *Entry) { + guint16 element = Entry->GetElement(); + guint16 group = Entry->GetGroup(); + std::string vr = Entry->GetVR(); guint16 length16; - if( (element == 0x0010) && (group == 0x7fe0) ) + if( (element == NumPixel) && (group == GrPixel) ) { dbg.SetDebug(-1); dbg.Verbose(2, "gdcmParser::FindLength: ", - "we reached 7fe0 0010"); + "we reached (GrPixel,NumPixel)"); } - if ( (filetype == ExplicitVR) && ! ElVal->IsImplicitVr() ) + if ( (filetype == ExplicitVR) && (! Entry->IsImplicitVR()) ) { if ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") ) { @@ -1314,10 +1430,10 @@ void gdcmParser::AddHeaderEntry(gdcmHeaderEntry * newHeaderEntry) if ( (vr == "OB") && (length32 == 0xffffffff) ) { - ElVal->SetLength(FindHeaderEntryLengthOB()); + Entry->SetLength(FindHeaderEntryLengthOB()); return; } - FixHeaderEntryFoundLength(ElVal, length32); + FixHeaderEntryFoundLength(Entry, length32); return; } @@ -1363,18 +1479,18 @@ void gdcmParser::AddHeaderEntry(gdcmHeaderEntry * newHeaderEntry) SwitchSwapToBigEndian(); // Restore the unproperly loaded values i.e. the group, the element // and the dictionary entry depending on them. - guint16 CorrectGroup = SwapShort(ElVal->GetGroup()); - guint16 CorrectElem = SwapShort(ElVal->GetElement()); + guint16 CorrectGroup = SwapShort(Entry->GetGroup()); + guint16 CorrectElem = SwapShort(Entry->GetElement()); gdcmDictEntry * NewTag = GetDictEntryByNumber(CorrectGroup, CorrectElem); if (!NewTag) { // This correct tag is not in the dictionary. Create a new one. - NewTag = Dicts->NewVirtualDictEntry(CorrectGroup, CorrectElem); + NewTag = NewVirtualDictEntry(CorrectGroup, CorrectElem); } // FIXME this can create a memory leaks on the old entry that be // left unreferenced. - ElVal->SetDictEntry(NewTag); + Entry->SetDictEntry(NewTag); } // Heuristic: well some files are really ill-formed. @@ -1387,34 +1503,33 @@ void gdcmParser::AddHeaderEntry(gdcmHeaderEntry * newHeaderEntry) // Unknown Sequence Length } - FixHeaderEntryFoundLength(ElVal, (guint32)length16); + FixHeaderEntryFoundLength(Entry, (guint32)length16); + 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; } - - // 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(ElVal, ReadInt32()); - return; } /** * \ingroup gdcmParser * \brief Find the Value Representation of the current Dicom Element. - * @param ElVal + * @param Entry */ -void gdcmParser::FindHeaderEntryVR( gdcmHeaderEntry *ElVal) +void gdcmParser::FindHeaderEntryVR( gdcmHeaderEntry *Entry) { if (filetype != ExplicitVR) return; char VR[3]; - std::string vr; - int lgrLue; - char msg[100]; // for sprintf. Sorry long PositionOnEntry = ftell(fp); // Warning: we believe this is explicit VR (Value Representation) because @@ -1424,12 +1539,38 @@ void gdcmParser::FindHeaderEntryVR( gdcmHeaderEntry *ElVal) // within an explicit VR file. Hence we make sure the present tag // is in explicit VR and try to fix things if it happens not to be // the case. - bool RealExplicit = true; - lgrLue=fread (&VR, (size_t)2,(size_t)1, fp); + int lgrLue=fread (&VR, (size_t)2,(size_t)1, fp); // lgrLue not used VR[2]=0; - vr = std::string(VR); - + if(!CheckHeaderEntryVR(Entry,VR)) + { + fseek(fp, PositionOnEntry, SEEK_SET); + // When this element is known in the dictionary we shall use, e.g. for + // the semantics (see the usage of IsAnInteger), the VR proposed by the + // dictionary entry. Still we have to flag the element as implicit since + // we know now our assumption on expliciteness is not furfilled. + // avoid . + if ( Entry->IsVRUnknown() ) + Entry->SetVR("Implicit"); + Entry->SetImplicitVR(); + } +} + +/** + * \ingroup gdcmParser + * \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 + * @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) +{ + char msg[100]; // for sprintf + bool RealExplicit = true; + // Assume we are reading a falsely explicit VR file i.e. we reached // a tag where we expect reading a VR but are in fact we read the // first to bytes of the length. Then we will interogate (through find) @@ -1438,68 +1579,173 @@ void gdcmParser::FindHeaderEntryVR( gdcmHeaderEntry *ElVal) // expected VR read happens to be non-ascii characters we consider // we hit falsely explicit VR tag. - if ( (!isalpha(VR[0])) && (!isalpha(VR[1])) ) + if ( (!isalpha(vr[0])) && (!isalpha(vr[1])) ) RealExplicit = false; // CLEANME searching the dicom_vr at each occurence is expensive. // PostPone this test in an optional integrity check at the end // of parsing or only in debug mode. - if ( RealExplicit && !dicom_vr->Count(vr) ) + if ( RealExplicit && !gdcmGlobal::GetVR()->Count(vr) ) RealExplicit= false; - if ( RealExplicit ) + if ( !RealExplicit ) { - if ( ElVal->IsVRUnknown() ) - { - // When not a dictionary entry, we can safely overwrite the VR. - ElVal->SetVR(vr); - return; + // We thought this was explicit VR, but we end up with an + // implicit VR tag. Let's backtrack. + sprintf(msg,"Falsely explicit vr file (%04x,%04x)\n", + Entry->GetGroup(),Entry->GetElement()); + dbg.Verbose(1, "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); } - if ( ElVal->GetVR() == vr ) - { - // The VR we just read and the dictionary agree. Nothing to do. - return; + return(false); + } + + if ( Entry->IsVRUnknown() ) + { + // When not a dictionary entry, we can safely overwrite the VR. + if (Entry->GetElement() == 0x0000) { // Group length is UL ! + Entry->SetVR("UL"); + } else { + Entry->SetVR(vr); } + } + else if ( Entry->GetVR() != vr ) + { // The VR present in the file and the dictionary disagree. We assume // the file writer knew best and use the VR of the file. Since it would // be unwise to overwrite the VR of a dictionary (since it would // compromise it's next user), we need to clone the actual DictEntry // and change the VR for the read one. - gdcmDictEntry* NewTag = Dicts->NewVirtualDictEntry(ElVal->GetGroup(), - ElVal->GetElement(), - vr, - "FIXME", - ElVal->GetName()); - ElVal->SetDictEntry(NewTag); - return; + gdcmDictEntry* NewEntry = NewVirtualDictEntry( + Entry->GetGroup(),Entry->GetElement(), + vr,"FIXME",Entry->GetName()); + Entry->SetDictEntry(NewEntry); } - - // We thought this was explicit VR, but we end up with an - // implicit VR tag. Let's backtrack. - - sprintf(msg,"Falsely explicit vr file (%04x,%04x)\n", - ElVal->GetGroup(),ElVal->GetElement()); - dbg.Verbose(1, "gdcmParser::FindVR: ",msg); - - fseek(fp, PositionOnEntry, SEEK_SET); - // When this element is known in the dictionary we shall use, e.g. for - // the semantics (see the usage of IsAnInteger), the VR proposed by the - // dictionary entry. Still we have to flag the element as implicit since - // we know now our assumption on expliciteness is not furfilled. - // avoid . - if ( ElVal->IsVRUnknown() ) - ElVal->SetVR("Implicit"); - ElVal->SetImplicitVr(); + 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) +void gdcmParser::SkipHeaderEntry(gdcmHeaderEntry *entry) { SkipBytes(entry->GetLength()); } @@ -1510,44 +1756,49 @@ void gdcmParser::SkipHeaderEntry(gdcmHeaderEntry * entry) * the parser went Jabberwocky) one can hope improving things by * applying this heuristic. */ -void gdcmParser::FixHeaderEntryFoundLength(gdcmHeaderEntry * ElVal, guint32 FoundLength) +void gdcmParser::FixHeaderEntryFoundLength(gdcmHeaderEntry *Entry, guint32 FoundLength) { - ElVal->SetReadLength(FoundLength); // will be updated only if a bug is found + Entry->SetReadLength(FoundLength); // will be updated only if a bug is found - if ( FoundLength == 0xffffffff) - { + if ( FoundLength == 0xffffffff) { FoundLength = 0; } + + guint16 gr =Entry->GetGroup(); + guint16 el =Entry->GetElement(); + + if (FoundLength%2) { + std::cout << "Warning : Tag with uneven length " << FoundLength + << " in x(" << std::hex << gr << "," << el <<")" << std::endl; + } // Sorry for the patch! // XMedCom did the trick to read some nasty GE images ... - else if (FoundLength == 13) - { + 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 ( (ElVal->GetGroup() != 0x0008) || - ( (ElVal->GetElement() != 0x0070) && (ElVal->GetElement() != 0x0080) ) ) { + if ( (Entry->GetGroup() != 0x0008) || + ( (Entry->GetElement() != 0x0070) && (Entry->GetElement() != 0x0080) ) ){ // end of remove area FoundLength =10; - ElVal->SetReadLength(10); // a bug is to be fixed + Entry->SetReadLength(10); // a bug is to be fixed } } // to fix some garbage 'Leonardo' Siemens images // May be commented out to avoid overhead - else if ( (ElVal->GetGroup() == 0x0009) && - ( (ElVal->GetElement() == 0x1113) || (ElVal->GetElement() == 0x1114) ) ) - { + else if ( (Entry->GetGroup() == 0x0009) && + ( (Entry->GetElement() == 0x1113) || (Entry->GetElement() == 0x1114) ) ){ FoundLength =4; - ElVal->SetReadLength(4); // a bug is to be fixed + 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 ( ElVal->GetVR() == "SQ") + 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 @@ -1559,7 +1810,7 @@ void gdcmParser::FixHeaderEntryFoundLength(gdcmHeaderEntry * ElVal, guint32 Foun // if we set the length to zero IsHeaderEntryAnInteger() breaks... // if we don't, we lost 28800 characters from the Header :-( - else if(ElVal->GetGroup() == 0xfffe) + else if(Entry->GetGroup() == 0xfffe) { // sometimes, length seems to be wrong FoundLength =0; // some more clever checking to be done ! @@ -1568,23 +1819,21 @@ void gdcmParser::FixHeaderEntryFoundLength(gdcmHeaderEntry * ElVal, guint32 Foun // causes troubles :-( } - ElVal->SetUsableLength(FoundLength); + Entry->SetUsableLength(FoundLength); } /** * \ingroup gdcmParser * \brief Apply some heuristics to predict wether the considered * element value contains/represents an integer or not. - * @param ElVal The element value on which to apply the predicate. + * @param Entry The element value on which to apply the predicate. * @return The result of the heuristical predicate. */ -bool gdcmParser::IsHeaderEntryAnInteger(gdcmHeaderEntry * ElVal) -{ - guint16 element = ElVal->GetElement(); - guint16 group = ElVal->GetGroup(); - std::string vr = ElVal->GetVR(); - guint32 length = ElVal->GetLength(); - +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. @@ -1595,10 +1844,22 @@ bool gdcmParser::IsHeaderEntryAnInteger(gdcmHeaderEntry * ElVal) 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") ) @@ -1613,8 +1874,7 @@ bool gdcmParser::IsHeaderEntryAnInteger(gdcmHeaderEntry * ElVal) * * @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; @@ -1664,22 +1924,20 @@ bool gdcmParser::IsHeaderEntryAnInteger(gdcmHeaderEntry * ElVal) * \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; } @@ -1688,15 +1946,13 @@ 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; @@ -1713,8 +1969,7 @@ 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); } @@ -1725,10 +1980,7 @@ void gdcmParser::SkipBytes(guint32 NBytes) */ void gdcmParser::Initialise(void) { - dicom_vr = gdcmGlobal::GetVR(); - dicom_ts = gdcmGlobal::GetTS(); - Dicts = gdcmGlobal::GetDicts(); - RefPubDict = Dicts->GetDefaultPubDict(); + RefPubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict(); RefShaDict = (gdcmDict*)0; } @@ -1736,58 +1988,23 @@ 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]; @@ -1798,16 +2015,15 @@ 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) -, @@ -1824,12 +2040,21 @@ 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:", @@ -1841,6 +2066,7 @@ void gdcmParser::CheckSwap() dbg.Verbose(1, "gdcmParser::CheckSwap:", "not an explicit Value Representation"); } + if (net2host) { sw = 4321; @@ -1858,7 +2084,7 @@ 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 @@ -1876,41 +2102,71 @@ 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; } /** @@ -1944,7 +2200,6 @@ void gdcmParser::SwitchSwapToBigEndian(void) * \ingroup gdcmParser * \brief * @param NewSize - * @return */ void gdcmParser::SetMaxSizeLoadEntry(long NewSize) { @@ -1958,6 +2213,28 @@ void gdcmParser::SetMaxSizeLoadEntry(long NewSize) MaxSizeLoadEntry = NewSize; } + +/** + * \ingroup gdcmParser + * \brief + * \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 @@ -1976,13 +2253,13 @@ gdcmDictEntry *gdcmParser::GetDictEntryByName(std::string Name) } if (RefPubDict) { - found = RefPubDict->GetTagByName(Name); + found = RefPubDict->GetDictEntryByName(Name); if (found) return found; } if (RefShaDict) { - found = RefShaDict->GetTagByName(Name); + found = RefShaDict->GetDictEntryByName(Name); if (found) return found; } @@ -2009,13 +2286,13 @@ gdcmDictEntry *gdcmParser::GetDictEntryByNumber(guint16 group,guint16 element) } if (RefPubDict) { - found = RefPubDict->GetTagByNumber(group, element); + found = RefPubDict->GetDictEntryByNumber(group, element); if (found) return found; } if (RefShaDict) { - found = RefShaDict->GetTagByNumber(group, element); + found = RefShaDict->GetDictEntryByNumber(group, element); if (found) return found; } @@ -2027,31 +2304,37 @@ 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 *NewElVal; + 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 ? - NewElVal = NewHeaderEntryByNumber(g, n); - FindHeaderEntryVR(NewElVal); - FindHeaderEntryLength(NewElVal); + 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; } - NewElVal->SetOffset(ftell(fp)); - //if ( (g==0x7fe0) && (n==0x0010) ) - return NewElVal; + NewEntry->SetOffset(ftell(fp)); + return NewEntry; } /** @@ -2065,18 +2348,35 @@ gdcmHeaderEntry *gdcmParser::NewHeaderEntryByName(std::string Name) { gdcmDictEntry *NewTag = GetDictEntryByName(Name); if (!NewTag) - NewTag = Dicts->NewVirtualDictEntry(0xffff, 0xffff, "LO", "Unknown", Name); + NewTag = NewVirtualDictEntry(0xffff, 0xffff, "LO", "unkn", Name); - gdcmHeaderEntry* NewElVal = new gdcmHeaderEntry(NewTag); - if (!NewElVal) + gdcmHeaderEntry* NewEntry = new gdcmHeaderEntry(NewTag); + if (!NewEntry) { dbg.Verbose(1, "gdcmParser::ObtainHeaderEntryByName", "failed to allocate gdcmHeaderEntry"); return (gdcmHeaderEntry *)0; } - return NewElVal; + return NewEntry; } +/** + * \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 vr VR of the underlying DictEntry + * @param fourth owner group + * @param name english name + */ +gdcmDictEntry *gdcmParser::NewVirtualDictEntry(guint16 group, guint16 element, + std::string vr, + std::string fourth, + std::string name) +{ + return gdcmGlobal::GetDicts()->NewVirtualDictEntry(group,element,vr,fourth,name); +} + /** * \ingroup gdcmParser * \brief Build a new Element Value from all the low level arguments. @@ -2088,20 +2388,21 @@ gdcmHeaderEntry *gdcmParser::NewHeaderEntryByName(std::string Name) 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 = Dicts->NewVirtualDictEntry(Group, Elem); + gdcmDictEntry *DictEntry = GetDictEntryByNumber(Group, Elem); + if (!DictEntry) + DictEntry = NewVirtualDictEntry(Group, Elem); - gdcmHeaderEntry* NewElVal = new gdcmHeaderEntry(NewTag); - if (!NewElVal) + gdcmHeaderEntry *NewEntry = new gdcmHeaderEntry(DictEntry); + if (!NewEntry) { dbg.Verbose(1, "gdcmParser::NewHeaderEntryByNumber", "failed to allocate gdcmHeaderEntry"); return NULL; } - return NewElVal; + return NewEntry; } +// Never used; commented out, waiting for removal. /** * \ingroup gdcmParser * \brief Small utility function that creates a new manually crafted @@ -2112,28 +2413,28 @@ 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 *NewElVal = (gdcmHeaderEntry *)0; - guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info - guint32 FreeElem = 0; - gdcmDictEntry *NewEntry = (gdcmDictEntry *)0; - - FreeElem = GenerateFreeTagKeyInGroup(StuffGroup); - if (FreeElem == UINT32_MAX) - { - dbg.Verbose(1, "gdcmHeader::NewManualElValToPubDict", - "Group 0xffff in Public Dict is full"); - return NULL; - } - - NewEntry = Dicts->NewVirtualDictEntry(StuffGroup, FreeElem, - VR, "GDCM", NewTagName); - NewElVal = new gdcmHeaderEntry(NewEntry); - AddHeaderEntry(NewElVal); - return NewElVal; -} +//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