X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=7cb2cad0fad356999bfcf623eec6399ea0256169;hb=efc4d18faced64c24c75448b61685f92f2d799ce;hp=1c65feb5d2bf9c0f2058eed2babb374313a14282;hpb=9d7bc1062abc4ca53c072f752c8938b08748fff8;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index 1c65feb5..7cb2cad0 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -1,16 +1,6 @@ -// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.88 2003/09/24 13:45:11 jpr Exp $ +// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.103 2003/10/23 12:08:32 jpr Exp $ -//This is needed when compiling in debug mode -#ifdef _MSC_VER -//'identifier' : not all control paths return a value -//#pragma warning ( disable : 4715 ) -// 'identifier' : class 'type' needs to have dll-interface to be used by -// clients of class 'type2' -#pragma warning ( disable : 4251 ) -// 'identifier' : identifier was truncated to 'number' characters in the -// debug information -#pragma warning ( disable : 4786 ) -#endif //_MSC_VER +#include "gdcmHeader.h" #include #include @@ -23,7 +13,6 @@ #include // for isalpha #include #include "gdcmUtil.h" -#include "gdcmHeader.h" #include "gdcmTS.h" // Refer to gdcmHeader::CheckSwap() @@ -38,7 +27,7 @@ void gdcmHeader::Initialise(void) { dicom_vr = gdcmGlobal::GetVR(); dicom_ts = gdcmGlobal::GetTS(); - Dicts = gdcmGlobal::GetDicts(); + Dicts = gdcmGlobal::GetDicts(); RefPubDict = Dicts->GetDefaultPubDict(); RefShaDict = (gdcmDict*)0; } @@ -83,9 +72,26 @@ gdcmHeader::gdcmHeader(bool exception_on_error) { if(!fp) throw gdcmFileError("gdcmHeader::gdcmHeader(const char *, bool)"); } - if ( fp ) - return true; - dbg.Verbose(0, "gdcmHeader::gdcmHeader cannot open file", filename.c_str()); + + if ( fp ) { + guint16 zero; + fread(&zero, (size_t)2, (size_t)1, fp); + + //ACR -- or DICOM with no Preamble + if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200) + return true; + //DICOM + fseek(fp, 126L, SEEK_CUR); + char dicm[4]; + fread(dicm, (size_t)4, (size_t)1, fp); + if( memcmp(dicm, "DICM", 4) == 0 ) + return true; + fclose(fp); + dbg.Verbose(0, "gdcmHeader::gdcmHeader not DICOM/ACR", filename.c_str()); + } + else { + dbg.Verbose(0, "gdcmHeader::gdcmHeader cannot open file", filename.c_str()); + } return false; } @@ -115,6 +121,13 @@ gdcmHeader::~gdcmHeader (void) { } // 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 @@ -375,7 +388,8 @@ void gdcmHeader::FindVR( gdcmElValue *ElVal) { // 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()); + sprintf(msg,"Falsely explicit vr file (%04x,%04x)\n", + ElVal->GetGroup(),ElVal->GetElement()); dbg.Verbose(1, "gdcmHeader::FindVR: ",msg); fseek(fp, PositionOnEntry, SEEK_SET); @@ -494,6 +508,8 @@ bool gdcmHeader::IsJPEGLossless(void) { const char * Transfert = Element->GetValue().c_str(); if ( memcmp(Transfert+strlen(Transfert)-2 ,"70",2)==0) return true; if ( memcmp(Transfert+strlen(Transfert)-2 ,"55",2)==0) return true; + if (Element->GetValue() == "1.2.840.10008.1.2.4.57") return true; + return false; } @@ -613,6 +629,24 @@ bool gdcmHeader::IsDicomV3(void) { void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { if ( FoundLength == 0xffffffff) FoundLength = 0; + + // Sorry for the patch! + // XMedCom did the trick to read some nasty GE images ... + else 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)) { + // end of remove area + FoundLength =10; + } + } + // 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) ) ) + FoundLength =4; + ElVal->SetLength(FoundLength); } @@ -633,35 +667,31 @@ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { while ( ! FoundSequenceDelimiter) { g = ReadInt16(); - n = ReadInt16(); - - long l = ftell(fp); - + n = ReadInt16(); if (errno == 1) return 0; TotalLength += 4; // We even have to decount the group and element - if ( g != 0xfffe && g!=0xb00c ) /*for bogus header */ { + if ( g != 0xfffe && g!=0xb00c ) /*for bogus header */ { char msg[100]; // for sprintf. Sorry sprintf(msg,"wrong group (%04x) for an item sequence (%04x,%04x)\n",g, g,n); dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",msg); - long l = ftell(fp); errno = 1; return 0; } - if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) /* for bogus header */ + if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) /* for bogus header */ FoundSequenceDelimiter = true; else if ( n != 0xe000 ){ char msg[100]; // for sprintf. Sorry - sprintf(msg,"wrong element (%04x) for an item sequence (%04x,%04x)\n",n, g,n); + sprintf(msg,"wrong element (%04x) for an item sequence (%04x,%04x)\n", + n, g,n); dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",msg); errno = 1; return 0; } ItemLength = ReadInt32(); TotalLength += ItemLength + 4; // We add 4 bytes since we just read - // the ItemLength with ReadInt32 - + // the ItemLength with ReadInt32 SkipBytes(ItemLength); } fseek(fp, PositionOnEntry, SEEK_SET); @@ -677,12 +707,12 @@ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { void gdcmHeader::FindLength (gdcmElValue * ElVal) { guint16 element = ElVal->GetElement(); guint16 group = ElVal->GetGroup(); - std::string vr = ElVal->GetVR(); + std::string vr = ElVal->GetVR(); guint16 length16; if( (element == 0x0010) && (group == 0x7fe0) ) { dbg.SetDebug(0); dbg.Verbose(2, "gdcmHeader::FindLength: ", - "on est sur 7fe0 0010"); + "we reached 7fe0 0010"); } if ( (filetype == ExplicitVR) && ! ElVal->IsImplicitVr() ) { @@ -694,6 +724,7 @@ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { fseek(fp, 2L, SEEK_CUR); guint32 length32 = ReadInt32(); + if ( (vr == "OB") && (length32 == 0xffffffff) ) { ElVal->SetLength(FindLengthOB()); return; @@ -758,9 +789,12 @@ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { // Heuristic: well some files are really ill-formed. if ( length16 == 0xffff) { length16 = 0; - dbg.Verbose(0, "gdcmHeader::FindLength", - "Erroneous element length fixed."); + //dbg.Verbose(0, "gdcmHeader::FindLength", + // "Erroneous element length fixed."); + // Actually, length= 0xffff means that we deal with + // Unknown Sequence Length } + FixFoundLength(ElVal, (guint32)length16); return; } @@ -861,7 +895,7 @@ guint16 gdcmHeader::SwapShort(guint16 a) { void gdcmHeader::LoadElementValue(gdcmElValue * ElVal) { size_t item_read; guint16 group = ElVal->GetGroup(); - std::string vr = ElVal->GetVR(); + std::string vr= ElVal->GetVR(); guint32 length = ElVal->GetLength(); bool SkipLoad = false; @@ -1083,7 +1117,8 @@ gdcmElValue* gdcmHeader::NewElValueByNumber(guint16 Group, guint16 Elem) { * @param Elem * \return integer acts as a boolean */ -int gdcmHeader::ReplaceOrCreateByNumber(std::string Value, guint16 Group, guint16 Elem ) { +int gdcmHeader::ReplaceOrCreateByNumber(std::string Value, + guint16 Group, guint16 Elem ) { // TODO : FIXME JPRx // curieux, non ? @@ -1091,9 +1126,12 @@ int gdcmHeader::ReplaceOrCreateByNumber(std::string Value, guint16 Group, guint1 // on l'ajoute au ElValSet // on affecte une valeur a cette ElValue a l'interieur du ElValSet // --> devrait pouvoir etre fait + simplement ??? - - gdcmElValue* nvElValue=NewElValueByNumber(Group, Elem); - PubElValSet.Add(nvElValue); + if (CheckIfExistByNumber(Group, Elem) == 0) { + gdcmElValue* a =NewElValueByNumber(Group, Elem); + if (a == NULL) + return 0; + PubElValSet.Add(a); + } PubElValSet.SetElValueByNumber(Value, Group, Elem); return(1); } @@ -1101,7 +1139,7 @@ int gdcmHeader::ReplaceOrCreateByNumber(std::string Value, guint16 Group, guint1 /** * \ingroup gdcmHeader - * \brief Modify or (Creates if not found) an element + * \brief Modify (or Creates if not found) an element * @param Value new value * @param Group * @param Elem @@ -1121,6 +1159,7 @@ int gdcmHeader::ReplaceOrCreateByNumber(char* Value, guint16 Group, guint16 Elem /** * \ingroup gdcmHeader * \brief Set a new value if the invoked element exists + * Seems to be useless !!! * @param Value * @param Group * @param Elem @@ -1128,7 +1167,7 @@ int gdcmHeader::ReplaceOrCreateByNumber(char* Value, guint16 Group, guint16 Elem */ int gdcmHeader::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 Elem ) { - gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem); + //gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem); std::string v = Value; PubElValSet.SetElValueByNumber(v, Group, Elem); return 1; @@ -1182,9 +1221,7 @@ gdcmElValue * gdcmHeader::ReadNextElement(void) { g = ReadInt16(); n = ReadInt16(); - - if ( (g==0x7fe0) && (n==0x0010) ) - + if (errno == 1) // We reached the EOF (or an error occured) and header parsing // has to be considered as finished. @@ -1198,7 +1235,7 @@ gdcmElValue * gdcmHeader::ReadNextElement(void) { return (gdcmElValue *)0; } NewElVal->SetOffset(ftell(fp)); - if ( (g==0x7fe0) && (n==0x0010) ) + //if ( (g==0x7fe0) && (n==0x0010) ) return NewElVal; } @@ -1210,9 +1247,8 @@ gdcmElValue * gdcmHeader::ReadNextElement(void) { * @return The result of the heuristical predicate. */ bool gdcmHeader::IsAnInteger(gdcmElValue * ElVal) { - guint16 group = ElVal->GetGroup(); guint16 element = ElVal->GetElement(); - std::string vr = ElVal->GetVR(); + std::string vr = ElVal->GetVR(); guint32 length = ElVal->GetLength(); // When we have some semantics on the element we just read, and if we @@ -1543,7 +1579,8 @@ std::string gdcmHeader::GetElValRepByName(std::string TagName) { int gdcmHeader::SetPubElValByNumber(std::string content, guint16 group, guint16 element) -//TODO : homogeneiser les noms : SetPubElValByNumber qui appelle PubElValSet.SetElValueByNumber +//TODO : homogeneiser les noms : SetPubElValByNumber +// qui appelle PubElValSet.SetElValueByNumber // pourquoi pas SetPubElValueByNumber ?? { @@ -1654,7 +1691,8 @@ bool gdcmHeader::IsReadable(void) { * @param VR The Value Representation to be given to this new tag. * @ return The newly hand crafted Element Value. */ -gdcmElValue* gdcmHeader::NewManualElValToPubDict(std::string NewTagName, std::string VR) { +gdcmElValue* gdcmHeader::NewManualElValToPubDict(std::string NewTagName, + std::string VR) { gdcmElValue* NewElVal = (gdcmElValue*)0; guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info guint32 FreeElem = 0; @@ -1729,7 +1767,7 @@ void gdcmHeader::PrintPubElVal(std::ostream & os) { /** * \ingroup gdcmHeader - * \brief + * \brief * @return */ void gdcmHeader::PrintPubDict(std::ostream & os) { @@ -1739,9 +1777,36 @@ void gdcmHeader::PrintPubDict(std::ostream & os) { /** * \ingroup gdcmHeader * \brief - * @return + * @return integer, acts as a Boolean */ int gdcmHeader::Write(FILE * fp, FileType type) { + + + // TODO : move the following lines (and a lot of others) + // to a future function CheckAndCorrectHeader + + if (type == ImplicitVR) { + std::string implicitVRTransfertSyntax = "1.2.840.10008.1.2"; + ReplaceOrCreateByNumber(implicitVRTransfertSyntax,0x0002, 0x0010); + + //FIXME Refer to standards on page 21, chapter 6.2 "Value representation": + // values with a VR of UI shall be padded with a single trailing null + // Dans le cas suivant on doit pader manuellement avec un 0 + + PubElValSet.SetElValueLengthByNumber(18, 0x0002, 0x0010); + } + + if (type == ExplicitVR) { + std::string explicitVRTransfertSyntax = "1.2.840.10008.1.2.1"; + ReplaceOrCreateByNumber(explicitVRTransfertSyntax,0x0002, 0x0010); + + //FIXME Refer to standards on page 21, chapter 6.2 "Value representation": + // values with a VR of UI shall be padded with a single trailing null + // Dans le cas suivant on doit pader manuellement avec un 0 + + PubElValSet.SetElValueLengthByNumber(20, 0x0002, 0x0010); + } + return PubElValSet.Write(fp, type); } @@ -1763,19 +1828,20 @@ void * gdcmHeader::LoadElementVoidArea(guint16 Group, guint16 Elem) { int l=Element->GetLength(); void * a = malloc(l); if(!a) { - cout << "Big Broblem (LoadElementVoidArea, malloc) " - << std::hex << Group << " " << Elem << std::endl; + std::cout << "Big Broblem (LoadElementVoidArea, malloc) " + << std::hex << Group << " " << Elem << std::endl; return NULL; } - int res = PubElValSet.SetVoidAreaByNumber(a, Group, Elem); + /* int res = */ PubElValSet.SetVoidAreaByNumber(a, Group, Elem); // TODO check the result size_t l2 = fread(a, 1, l ,fp); if(l != l2) { - cout << "Big Broblem (LoadElementVoidArea, fread) " - << std::hex << Group << " " << Elem << std::endl; + std::cout << "Big Broblem (LoadElementVoidArea, fread) " + << std::hex << Group << " " << Elem << std::endl; free(a); return NULL; - } + } + return a; } /** @@ -1790,7 +1856,7 @@ void * gdcmHeader::LoadElementVoidArea(guint16 Group, guint16 Elem) { gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem); if (!elValue) { dbg.Verbose(1, "gdcmHeader::GetElValueByNumber", - "failed to Locate gdcmElValue"); + "failed to Locate gdcmElValue"); return (size_t)0; } return elValue->GetOffset(); @@ -1898,6 +1964,19 @@ int gdcmHeader::GetBitsStored(void) { return atoi(StrSize.c_str()); } +/** + * \ingroup gdcmHeader + * \brief Retrieve the number of Bits Allocated + * (8, 12 -compacted ACR-NEMA files, 16, ...) + * + * @return The encountered number of Bits Allocated, 0 by default. + */ +int gdcmHeader::GetBitsAllocated(void) { + std::string StrSize = GetPubElValByNumber(0x0028,0x0100); + if (StrSize == GDCM_UNFOUND) + return 1; + return atoi(StrSize.c_str()); +} /** * \ingroup gdcmHeader @@ -2030,7 +2109,7 @@ int gdcmHeader::GetLUTLength(void) { dbg.Verbose(0, "gdcmHeader::GetLUTLength: The CLUT R,G,B are not equal"); return 0; } - cout << "Lut Description " << LutDescriptionR < tokens; + tokens.erase(tokens.begin(),tokens.end()); // clean any previous value + Tokenize ((const std::string)x, tokens, "\\"); + for (unsigned int i=0; i