X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmParser.cxx;h=7f6384f85edb59a4aa795a984ceface39f445775;hb=8402492c91eb411888fb7e220e0f02b3d94c59db;hp=93f2f56f0767306992aa7bc80d43d65d98048278;hpb=45bf98d79625d7efdb227b07c8746a918b49568b;p=gdcm.git diff --git a/src/gdcmParser.cxx b/src/gdcmParser.cxx index 93f2f56f..7f6384f8 100644 --- a/src/gdcmParser.cxx +++ b/src/gdcmParser.cxx @@ -104,8 +104,9 @@ 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 @@ -223,12 +224,12 @@ bool gdcmParser::SetShaDict(DictKey dictName){ * false otherwise. */ bool gdcmParser::IsReadable(void) { -cout << "filetype [" << filetype <<"]" << endl; - if(filetype==Unknown) + if(filetype==Unknown) { return(false); -cout << "trouv filetype" << endl; - if(listEntries.size()<=0) + } + if(listEntries.size()<=0) { return(false); + } return(true); } @@ -352,10 +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); } @@ -383,7 +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 @@ -433,7 +434,7 @@ bool gdcmParser::Write(FILE *fp, FileType type) { UpdateGroupLength(true,ACR); */ - WriteEntries(type, fp); + WriteEntries(fp,type); return(true); } @@ -754,6 +755,7 @@ void *gdcmParser::LoadEntryVoidArea(guint16 Group, guint16 Elem) free(a); return NULL; } + return a; } @@ -996,11 +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; @@ -1008,28 +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(); -//cout << hex << gr << " " << el << " "<< vr << " " << val << endl; // JPR + voidArea = (*tag2)->GetVoidArea(); if ( type == ACR ) { @@ -1052,21 +1060,30 @@ void gdcmParser::WriteEntries(FileType type, FILE * _fp) { // EXPLICIT VR guint16 z=0, shortLgr; - if (gr != 0xfffe) // JPR - fwrite (vr.c_str(),(size_t)2 ,(size_t)1 ,_fp); - - if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") || gr == 0xfffe) // JPR - { - if (gr != 0xfffe) - 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 { @@ -1078,6 +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 @@ -1103,11 +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 } } @@ -1176,18 +1204,22 @@ guint16 gdcmParser::UnswapShort(guint16 a) { /** * \ingroup gdcmParser * \brief Parses the header of the file but WITHOUT loading element values. + * @return false if file is not ACR-NEMA / DICOM */ -void gdcmParser::Parse(bool exception_on_error) throw(gdcmFormatError) { - gdcmHeaderEntry *newHeaderEntry = (gdcmHeaderEntry *)0; +bool gdcmParser::ParseHeader(bool exception_on_error) throw(gdcmFormatError) { rewind(fp); - CheckSwap(); + if (!CheckSwap()) + return false; + + gdcmHeaderEntry *newHeaderEntry = (gdcmHeaderEntry *)0; while ( (newHeaderEntry = ReadNextHeaderEntry()) ) { SkipHeaderEntry(newHeaderEntry); - if ( (ignoreShadow==0) || (newHeaderEntry->GetGroup()%2) == 0) { //JPR + if ( (ignoreShadow==0) || (newHeaderEntry->GetGroup()%2) == 0) { AddHeaderEntry(newHeaderEntry); } } + return true; } /** @@ -1217,8 +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 // @@ -1241,9 +1275,8 @@ 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() + * \brief Loads the element content if its length doesn't exceed + * the value specified with gdcmParser::SetMaxSizeLoadEntry() * @param Entry Header Entry (Dicom Element) to be dealt with */ void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry *Entry) { @@ -1295,7 +1328,7 @@ void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry *Entry) { // 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) @@ -1346,7 +1379,7 @@ void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry *Entry) { } if( (vr == "UI") ) // Because of correspondance with the VR dic - Entry->SetValue(NewValue.c_str()); + Entry->SetValue(NewValue.c_str()); // ??? JPR ??? else Entry->SetValue(NewValue); } @@ -1356,7 +1389,7 @@ void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry *Entry) { * \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 */ @@ -1378,11 +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()) ) @@ -1497,7 +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 @@ -1508,7 +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)) { @@ -1563,14 +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 ) { @@ -1635,7 +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 @@ -1720,19 +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::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 @@ -1742,8 +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 } @@ -1810,7 +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()); } @@ -1941,19 +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() { +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]; @@ -1989,12 +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 - // 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:", @@ -2006,6 +2066,7 @@ void gdcmParser::CheckSwap() { dbg.Verbose(1, "gdcmParser::CheckSwap:", "not an explicit Value Representation"); } + if (net2host) { sw = 4321; @@ -2023,7 +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 @@ -2041,40 +2102,70 @@ 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)); + s32 = *((guint32 *)(entCur)); - switch (s) { + 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 : - dbg.Verbose(0, "gdcmParser::CheckSwap:", - "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. + // 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; - // Then the only info we have is the net2host one. - if (! net2host ) - sw = 0; - else + return true; + case 0x0200 : + case 0x0400 : + case 0x0800 : sw = 4321; - return; + filetype = ACR; + return true; + default : + dbg.Verbose(0, "gdcmParser::CheckSwap:", + "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; } } @@ -2243,7 +2334,6 @@ gdcmHeaderEntry *gdcmParser::ReadNextHeaderEntry(void) { return NULL; } NewEntry->SetOffset(ftell(fp)); - //if ( (g==0x7fe0) && (n==0x0010) ) return NewEntry; } @@ -2258,7 +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) @@ -2312,6 +2402,7 @@ gdcmHeaderEntry *gdcmParser::NewHeaderEntryByNumber(guint16 Group, guint16 Elem) return NewEntry; } +// Never used; commented out, waiting for removal. /** * \ingroup gdcmParser * \brief Small utility function that creates a new manually crafted @@ -2322,28 +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 *NewEntry = NULL; - guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info - guint32 FreeElem = 0; - gdcmDictEntry *DictEntry = NULL; - - FreeElem = GenerateFreeTagKeyInGroup(StuffGroup); - if (FreeElem == UINT32_MAX) - { - dbg.Verbose(1, "gdcmHeader::NewManualHeaderEntryToPubDict", - "Group 0xffff in Public Dict is full"); - return NULL; - } - - DictEntry = NewVirtualDictEntry(StuffGroup, FreeElem, - VR, "GDCM", NewTagName); - NewEntry = new gdcmHeaderEntry(DictEntry); - AddHeaderEntry(NewEntry); - return NewEntry; -} +//gdcmHeaderEntry *gdcmParser::NewManualHeaderEntryToPubDict(std::string NewTagName, +// std::string VR) +//{ +// gdcmHeaderEntry *NewEntry = NULL; +// guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info +// guint32 FreeElem = 0; +// gdcmDictEntry *DictEntry = NULL; +// +// FreeElem = GenerateFreeTagKeyInGroup(StuffGroup); +// if (FreeElem == UINT32_MAX) +// { +// dbg.Verbose(1, "gdcmHeader::NewManualHeaderEntryToPubDict", +// "Group 0xffff in Public Dict is full"); +// return NULL; +// } +// +// DictEntry = NewVirtualDictEntry(StuffGroup, FreeElem, +// VR, "GDCM", NewTagName); +// NewEntry = new gdcmHeaderEntry(DictEntry); +// AddHeaderEntry(NewEntry); +// return NewEntry; +//} /** * \ingroup gdcmParser