X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;ds=sidebyside;f=src%2FgdcmParser.cxx;h=9a2f98143eb823756b79099c77cbb143cb05cb82;hb=0574f31372f78bf8399e42ee04bd0010e684c440;hp=ffbe647e827bcf3770a5b38cd492f42847ce4cfb;hpb=76a33f0c9aee18505341e737d0c37ff7d7e1f9b4;p=gdcm.git diff --git a/src/gdcmParser.cxx b/src/gdcmParser.cxx index ffbe647e..9a2f9814 100644 --- a/src/gdcmParser.cxx +++ b/src/gdcmParser.cxx @@ -224,10 +224,12 @@ bool gdcmParser::SetShaDict(DictKey dictName){ * false otherwise. */ bool gdcmParser::IsReadable(void) { - if(filetype==Unknown) + if(filetype==Unknown) { return(false); - if(listEntries.size()<=0) + } + if(listEntries.size()<=0) { return(false); + } return(true); } @@ -351,10 +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 { - dbg.Verbose(0, "gdcmParser::gdcmParser cannot open file", filename.c_str()); + dbg.Verbose(0, "gdcmParser::OpenFile cannot open file", filename.c_str()); } return(NULL); } @@ -432,7 +434,7 @@ bool gdcmParser::Write(FILE *fp, FileType type) { UpdateGroupLength(true,ACR); */ - WriteEntries(type, fp); + WriteEntries(fp,type); return(true); } @@ -672,7 +674,6 @@ bool gdcmParser::SetEntryByNumber(std::string content, * @param element element of the Entry to modify * @return 1 on success, 0 otherwise. */ - bool gdcmParser::SetEntryLengthByNumber(guint32 length, guint16 group, guint16 element) @@ -753,6 +754,7 @@ void *gdcmParser::LoadEntryVoidArea(guint16 Group, guint16 Elem) free(a); return NULL; } + return a; } @@ -1001,15 +1003,17 @@ void gdcmParser::UpdateGroupLength(bool SkipSequence, FileType type) { * (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; + std::string value; const char * val; std::string vr; guint32 val_uint32; guint16 val_uint16; guint16 valZero =0; + void *voidArea; std::vector tokens; // TODO : function CheckHeaderCoherence to be written @@ -1020,7 +1024,7 @@ void gdcmParser::WriteEntries(FileType type, FILE * _fp) // 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; @@ -1028,11 +1032,21 @@ void gdcmParser::WriteEntries(FileType type, FILE * _fp) tag2 != listEntries.end(); ++tag2) { - gr = (*tag2)->GetGroup(); - el = (*tag2)->GetElement(); - lgr = (*tag2)->GetReadLength(); - val = (*tag2)->GetValue().c_str(); - vr = (*tag2)->GetVR(); + // === Deal with the length + // -------------------- + if(((*tag2)->GetLength())%2==1) + { + (*tag2)->SetValue((*tag2)->GetValue()+"\0"); + (*tag2)->SetLength((*tag2)->GetLength()+1); + } + + gr = (*tag2)->GetGroup(); + el = (*tag2)->GetElement(); + lgr = (*tag2)->GetReadLength(); + val = (*tag2)->GetValue().c_str(); + vr = (*tag2)->GetVR(); + voidArea = (*tag2)->GetVoidArea(); + if ( type == ACR ) { if (gr < 0x0008) continue; // ignore pure DICOM V3 groups @@ -1046,38 +1060,39 @@ 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 - // === Deal with the length - // -------------------- - // if ( (type == ExplicitVR) && (gr <= 0x0002) ) // ?!? < 2 if ( (type == ExplicitVR) || (type == DICOMDIR) ) { // EXPLICIT VR guint16 z=0, shortLgr; - if (vr == "Unknown") { // Unknown was 'written' + 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 == "Unknown") // Unknown was 'written' - fwrite(&z,(size_t)2 ,(size_t)1 ,_fp); - else - fwrite (vr.c_str(),(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) // JPR + + 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); + 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 { @@ -1089,6 +1104,12 @@ void gdcmParser::WriteEntries(FileType type, FILE * _fp) 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 @@ -1122,7 +1143,7 @@ void gdcmParser::WriteEntries(FileType type, FILE * _fp) if ((gr == GrPixel) && (el == NumPixel) ) { compte++; - if (compte == countGrPixel) // we passed *all* the GrPixel,NumPixel + if (compte == countGrPixel) // we passed *all* the GrPixel,NumPixel break; } fwrite ( val,(size_t)lgr ,(size_t)1 ,_fp); // Elem value @@ -1238,7 +1259,9 @@ 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 @@ -1517,7 +1540,6 @@ void gdcmParser::FindHeaderEntryVR( gdcmHeaderEntry *Entry) return; char VR[3]; - int lgrLue; long PositionOnEntry = ftell(fp); // Warning: we believe this is explicit VR (Value Representation) because @@ -1528,7 +1550,7 @@ void gdcmParser::FindHeaderEntryVR( gdcmHeaderEntry *Entry) // is in explicit VR and try to fix things if it happens not to be // the case. - lgrLue=fread (&VR, (size_t)2,(size_t)1, fp); + int lgrLue=fread (&VR, (size_t)2,(size_t)1, fp); // lgrLue not used VR[2]=0; if(!CheckHeaderEntryVR(Entry,VR)) { @@ -1550,7 +1572,7 @@ void gdcmParser::FindHeaderEntryVR( gdcmHeaderEntry *Entry) * and the taken VR. If they are different, the header entry is * updated with the new VR. * @param Entry - * @param VR + * @param vr * @return false if the VR is incorrect of if the VR isn't referenced * otherwise, it returns true */ @@ -1583,14 +1605,23 @@ bool gdcmParser::CheckHeaderEntryVR(gdcmHeaderEntry *Entry, VRKey vr) sprintf(msg,"Falsely explicit vr file (%04x,%04x)\n", Entry->GetGroup(),Entry->GetElement()); dbg.Verbose(1, "gdcmParser::FindVR: ",msg); - + if (Entry->GetGroup()%2 && Entry->GetElement() == 0x0000) { // Group length is UL ! + gdcmDictEntry* NewEntry = NewVirtualDictEntry( + Entry->GetGroup(),Entry->GetElement(), + "UL","FIXME","Group Length"); + Entry->SetDictEntry(NewEntry); + } return(false); } if ( Entry->IsVRUnknown() ) { // When not a dictionary entry, we can safely overwrite the VR. - Entry->SetVR(vr); + if (Entry->GetElement() == 0x0000) { // Group length is UL ! + Entry->SetVR("UL"); + } else { + Entry->SetVR(vr); + } } else if ( Entry->GetVR() != vr ) { @@ -1655,7 +1686,6 @@ std::string gdcmParser::GetHeaderEntryValue(gdcmHeaderEntry *Entry) s << NewInt32; } } - #ifdef GDCM_NO_ANSI_STRING_STREAM s << std::ends; // to avoid oddities on Solaris #endif //GDCM_NO_ANSI_STRING_STREAM @@ -1749,7 +1779,7 @@ void gdcmParser::FixHeaderEntryFoundLength(gdcmHeaderEntry *Entry, guint32 Found if (FoundLength%2) { std::cout << "Warning : Tag with uneven length " << FoundLength - << "in x(" << std::hex << gr << "," << el <<")" << std::endl; + << " in x(" << std::hex << gr << "," << el <<")" << std::dec << std::endl; } // Sorry for the patch! @@ -1835,7 +1865,9 @@ bool gdcmParser::IsHeaderEntryAnInteger(gdcmHeaderEntry *Entry) { // 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; + + //std::cout << s.str().c_str() << std::endl; + // dbg.Error("gdcmParser::IsHeaderEntryAnInteger", // s.str().c_str()); } @@ -2018,21 +2050,21 @@ bool 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 - // Use gdcmParser::dicom_vr to test all the possibilities - // instead of just checking for UL, OB and UI !? - + // 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 !- - // The following test is *absolutely useless*, since everything *goes right* - // with a *100 % wrong* assumption !!! - if( (memcmp(entCur, "UL", (size_t)2) == 0) || (memcmp(entCur, "OB", (size_t)2) == 0) || - (memcmp(entCur, "UI", (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 !? // group 0000 + { filetype = ExplicitVR; dbg.Verbose(1, "gdcmParser::CheckSwap:", @@ -2044,6 +2076,7 @@ bool gdcmParser::CheckSwap() { dbg.Verbose(1, "gdcmParser::CheckSwap:", "not an explicit Value Representation"); } + if (net2host) { sw = 4321; @@ -2284,7 +2317,6 @@ gdcmDictEntry *gdcmParser::GetDictEntryByNumber(guint16 group,guint16 element) gdcmHeaderEntry *gdcmParser::ReadNextHeaderEntry(void) { guint16 g,n; gdcmHeaderEntry *NewEntry; - g = ReadInt16(); n = ReadInt16(); @@ -2325,7 +2357,7 @@ gdcmHeaderEntry *gdcmParser::NewHeaderEntryByName(std::string Name) { gdcmDictEntry *NewTag = GetDictEntryByName(Name); if (!NewTag) - NewTag = NewVirtualDictEntry(0xffff, 0xffff, "LO", "Unknown", Name); + NewTag = NewVirtualDictEntry(0xffff, 0xffff, "LO", "unkn", Name); gdcmHeaderEntry* NewEntry = new gdcmHeaderEntry(NewTag); if (!NewEntry)