X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmParser.cxx;h=2bb771cbd2f1236d005d81e71ff6d28939d5eb71;hb=7b8dcad5fbb9b248952ad6819ef984e7880ef81e;hp=a155c2936265f7acd1cd7aaa1d2ff91f753e096d;hpb=a547ed6d41e444153f4bea38c47810fe7f50d88e;p=gdcm.git diff --git a/src/gdcmParser.cxx b/src/gdcmParser.cxx index a155c293..2bb771cb 100644 --- a/src/gdcmParser.cxx +++ b/src/gdcmParser.cxx @@ -104,8 +104,9 @@ gdcmParser::gdcmParser(const char *InFilename, if ( !OpenFile(exception_on_error)) return; - if (ParseHeader()) + if (ParseHeader()) { LoadHeaderEntries(); + } CloseFile(); wasUpdated = 0; // will be set to 1 if user adds an entry @@ -223,10 +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); } @@ -350,10 +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); } @@ -381,7 +384,7 @@ bool gdcmParser::CloseFile(void) { */ bool gdcmParser::Write(FILE *fp, FileType type) { // ============== -// TODO The stuff has been rewritten using the chained list instead +// TODO The stuff was rewritten using the chained list instead // of the H table // so we could remove the GroupHT from the gdcmParser // To be checked @@ -431,7 +434,7 @@ bool gdcmParser::Write(FILE *fp, FileType type) { UpdateGroupLength(true,ACR); */ - WriteEntries(type, fp); + WriteEntries(fp,type); return(true); } @@ -752,6 +755,7 @@ void *gdcmParser::LoadEntryVoidArea(guint16 Group, guint16 Elem) free(a); return NULL; } + return a; } @@ -1000,7 +1004,7 @@ 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; @@ -1009,6 +1013,7 @@ void gdcmParser::WriteEntries(FileType type, FILE * _fp) guint32 val_uint32; guint16 val_uint16; guint16 valZero =0; + void *voidArea; std::vector tokens; // TODO : function CheckHeaderCoherence to be written @@ -1019,15 +1024,10 @@ void gdcmParser::WriteEntries(FileType type, FILE * _fp) // TODO : find a trick (in STL?) to do it, at low cost ! void *ptr; - - // TODO : get grPixel and numPixel - guint16 grPixel =0x7fe0; - guint16 numPixel=0x0010; - //IterHT it = GetHeaderEntrySameNumber(grPixel,numPixel); - - + // TODO (?) tester les echecs en ecriture (apres chaque fwrite) - + int compte =0; + for (ListTag::iterator tag2=listEntries.begin(); tag2 != listEntries.end(); ++tag2) @@ -1037,7 +1037,8 @@ void gdcmParser::WriteEntries(FileType type, FILE * _fp) lgr = (*tag2)->GetReadLength(); val = (*tag2)->GetValue().c_str(); vr = (*tag2)->GetVR(); - cout << hex << gr << " " << el << " " << vr <<" lgr " << lgr << endl; + voidArea = (*tag2)->GetVoidArea(); + if ( type == ACR ) { if (gr < 0x0008) continue; // ignore pure DICOM V3 groups @@ -1059,19 +1060,19 @@ void gdcmParser::WriteEntries(FileType type, FILE * _fp) { // 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' + 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); @@ -1094,6 +1095,11 @@ 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 @@ -1119,14 +1125,17 @@ void gdcmParser::WriteEntries(FileType type, FILE * _fp) } tokens.clear(); continue; - } + } + // Pixels are never loaded in the element ! - - // TODO : FIX --> doesn't work when ICONE is found !!! - - if ((gr == grPixel) && (el == numPixel) ) - 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 } } @@ -1240,8 +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 // @@ -1400,11 +1411,11 @@ void gdcmParser::AddHeaderEntry(gdcmHeaderEntry *newHeaderEntry) { 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) && (! Entry->IsImplicitVR()) ) @@ -1519,7 +1530,6 @@ 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 @@ -1530,7 +1540,7 @@ 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)) { @@ -1585,14 +1595,23 @@ 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 ) { @@ -1657,7 +1676,6 @@ 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 @@ -1742,19 +1760,25 @@ void gdcmParser::FixHeaderEntryFoundLength(gdcmHeaderEntry *Entry, guint32 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::dec << 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 ( (Entry->GetGroup() != 0x0008) || - ( (Entry->GetElement() != 0x0070) && (Entry->GetElement() != 0x0080) ) ) { + ( (Entry->GetElement() != 0x0070) && (Entry->GetElement() != 0x0080) ) ){ // end of remove area FoundLength =10; Entry->SetReadLength(10); // a bug is to be fixed @@ -1764,8 +1788,7 @@ void gdcmParser::FixHeaderEntryFoundLength(gdcmHeaderEntry *Entry, guint32 Found // to fix some garbage 'Leonardo' Siemens images // May be commented out to avoid overhead else if ( (Entry->GetGroup() == 0x0009) && - ( (Entry->GetElement() == 0x1113) || (Entry->GetElement() == 0x1114) ) ) - { + ( (Entry->GetElement() == 0x1113) || (Entry->GetElement() == 0x1114) ) ){ FoundLength =4; Entry->SetReadLength(4); // a bug is to be fixed } @@ -1832,7 +1855,9 @@ 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()); } @@ -2015,12 +2040,21 @@ 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 !- + 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:", @@ -2032,6 +2066,7 @@ bool gdcmParser::CheckSwap() { dbg.Verbose(1, "gdcmParser::CheckSwap:", "not an explicit Value Representation"); } + if (net2host) { sw = 4321; @@ -2299,7 +2334,6 @@ gdcmHeaderEntry *gdcmParser::ReadNextHeaderEntry(void) { return NULL; } NewEntry->SetOffset(ftell(fp)); - //if ( (g==0x7fe0) && (n==0x0010) ) return NewEntry; } @@ -2314,7 +2348,7 @@ 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)