X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=ddfe7557fa01dd342c22fe941493d55ca987845f;hb=822a234a022899ba97ad11831df13ff009eaacd0;hp=c1d8c0434d4fd539279691d6032a28627c2c0d74;hpb=af94ab6719e309d3dd9730d5656057c429106938;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index c1d8c043..ddfe7557 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -1,16 +1,6 @@ -// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.90 2003/09/24 16:18:32 jpr Exp $ +// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.115 2003/11/12 15:35:19 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; } @@ -49,16 +38,20 @@ void gdcmHeader::Initialise(void) { * @param InFilename * @param exception_on_error */ -gdcmHeader::gdcmHeader(const char *InFilename, bool exception_on_error) { +gdcmHeader::gdcmHeader(const char *InFilename, + bool exception_on_error, + bool enable_sequences ) { + if (enable_sequences) + enableSequences = 1; + else + enableSequences = 0; + SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_); filename = InFilename; Initialise(); if ( !OpenFile(exception_on_error)) return; -printf ("avant ParseHeader\n"); ParseHeader(); -printf ("avant LoadElements\n"); - LoadElements(); CloseFile(); } @@ -86,9 +79,26 @@ 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; } @@ -118,6 +128,13 @@ 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 @@ -378,12 +395,13 @@ 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); // 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 + // 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 . @@ -497,6 +515,8 @@ 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; } @@ -614,9 +634,49 @@ bool gdcmHeader::IsDicomV3(void) { * applying this heuristic. */ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { - if ( FoundLength == 0xffffffff) + + ElVal->SetReadLength(FoundLength); // will be updated only if a bug is found + + if ( FoundLength == 0xffffffff) { FoundLength = 0; - ElVal->SetLength(FoundLength); + } + + // 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) || (ElVal->GetElement() != 0x0080) ) ) { + // end of remove area + FoundLength =10; + ElVal->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) ) ){ + FoundLength =4; + ElVal->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") { + if (enableSequences) // only if the user does want to ! + FoundLength =0; + } + + // a SeQuence Element is beginning + // Let's forget it's length + // (we want to 'go inside') + else if(ElVal->GetGroup() == 0xfffe){ + FoundLength =0; + } + + ElVal->SetUsableLength(FoundLength); } /** @@ -636,35 +696,31 @@ 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); @@ -680,12 +736,12 @@ 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() ) { @@ -697,11 +753,12 @@ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { fseek(fp, 2L, SEEK_CUR); guint32 length32 = ReadInt32(); + if ( (vr == "OB") && (length32 == 0xffffffff) ) { ElVal->SetLength(FindLengthOB()); return; } - FixFoundLength(ElVal, length32); + FixFoundLength(ElVal, length32); return; } @@ -725,7 +782,7 @@ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { // appear when we find the first group with big endian encoding. This // is easy to detect since the length of a "Group Length" tag (the // ones with zero as element number) has to be of 4 (0x0004). When we - // encouter 1024 (0x0400) chances are the encoding changed and we + // encounter 1024 (0x0400) chances are the encoding changed and we // found a group with big endian encoding. // We shall use this second strategy. In order to make sure that we // can interpret the presence of an apparently big endian encoded @@ -761,9 +818,12 @@ 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; } @@ -775,14 +835,14 @@ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { // not coexist in a Data Set and Data Sets nested within it".] // Length is on 4 bytes. FixFoundLength(ElVal, ReadInt32()); + return; } /** * \ingroup gdcmHeader * \brief Swaps back the bytes of 4-byte long integer accordingly to * processor order. - * - * @return The suggested integer. + * @return The properly swaped 32 bits integer. */ guint32 gdcmHeader::SwapLong(guint32 a) { switch (sw) { @@ -836,7 +896,7 @@ guint16 gdcmHeader::SwapShort(guint16 a) { * @return */ void gdcmHeader::SkipElementValue(gdcmElValue * ElVal) { - SkipBytes(ElVal->GetLength()); + SkipBytes(ElVal->GetLength()); } /** @@ -864,7 +924,7 @@ 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; @@ -877,17 +937,17 @@ void gdcmHeader::LoadElementValue(gdcmElValue * ElVal) { // car commencer par les ignorer risque de conduire a qq chose // qui pourrait ne pas etre generalisable // Well, I'm expecting your code !!! + + // the test was commented out to 'go inside' the SeQuences + // we don't any longer skip them ! - if( vr == "SQ" ) - SkipLoad = true; + // if( vr == "SQ" ) + // SkipLoad = true; - // Heuristic : a sequence "contains" a set of tags (called items). It looks - // like the last tag of a sequence (the one that terminates the sequence) - // has a group of 0xfffe (with a dummy length). - // Well ... - // Actually (fffe e000) tells us an Element is beginning + // A SeQuence "contains" a set of Elements. + // (fffe e000) tells us an Element is beginning // (fffe e00d) tells us an Element just ended - // (fffe e0dd) tells us the current SEQuence just ended + // (fffe e0dd) tells us the current SeQuence just ended if( group == 0xfffe ) SkipLoad = true; @@ -912,6 +972,7 @@ void gdcmHeader::LoadElementValue(gdcmElValue * ElVal) { s << "gdcm::NotLoaded."; s << " Address:" << (long)ElVal->GetOffset(); s << " Length:" << ElVal->GetLength(); + s << " x(" << std::hex << ElVal->GetLength() << ")"; ElVal->SetValue(s.str()); return; } @@ -919,9 +980,9 @@ void gdcmHeader::LoadElementValue(gdcmElValue * ElVal) { // When an integer is expected, read and convert the following two or // four bytes properly i.e. as an integer as opposed to a string. - // pour les elements de Value Multiplicity > 1 - // on aura en fait une serie d'entiers - // on devrait pouvoir faire + compact (?) + // Actually, elements with Value Multiplicity > 1 + // contain a set of integers (not a single one) + // Any compacter code suggested (?) if ( IsAnInteger(ElVal) ) { guint32 NewInt; @@ -1086,17 +1147,20 @@ 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 ? // on (je) cree une Elvalue ne contenant pas de valeur // 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); } @@ -1104,7 +1168,7 @@ 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 @@ -1124,6 +1188,7 @@ 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 @@ -1131,7 +1196,7 @@ 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; @@ -1185,9 +1250,7 @@ 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. @@ -1196,6 +1259,7 @@ gdcmElValue * gdcmHeader::ReadNextElement(void) { NewElVal = NewElValueByNumber(g, n); FindVR(NewElVal); FindLength(NewElVal); + if (errno == 1) { // Call it quits return (gdcmElValue *)0; @@ -1213,9 +1277,8 @@ 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 @@ -1269,6 +1332,40 @@ size_t gdcmHeader::GetPixelOffset(void) { return 0; } +/** + * \ingroup gdcmHeader + * \brief Recover the pixel area length (in Bytes) . + */ +size_t gdcmHeader::GetPixelAreaLength(void) { + // If this file complies with the norm we should encounter the + // "Image Location" tag (0x0028, 0x0200). This tag contains the + // the group that contains the pixel data (hence the "Pixel Data" + // is found by indirection through the "Image Location"). + // Inside the group pointed by "Image Location" the searched element + // is conventionally the element 0x0010 (when the norm is respected). + // When the "Image Location" is absent we default to group 0x7fe0. + guint16 grPixel; + guint16 numPixel; + std::string ImageLocation = GetPubElValByName("Image Location"); + if ( ImageLocation == GDCM_UNFOUND ) { + grPixel = 0x7fe0; + } else { + grPixel = (guint16) atoi( ImageLocation.c_str() ); + } + if (grPixel != 0x7fe0) + // This is a kludge for old dirty Philips imager. + numPixel = 0x1010; + else + numPixel = 0x0010; + + gdcmElValue* PixelElement = PubElValSet.GetElementByNumber(grPixel, + numPixel); + if (PixelElement) + return PixelElement->GetLength(); + else + return 0; +} + /** * \ingroup gdcmHeader * \brief Searches both the public and the shadow dictionary (when they @@ -1364,7 +1461,7 @@ std::string gdcmHeader::GetPubElValRepByNumber(guint16 group, guint16 element) { * \ingroup gdcmHeader * \brief Searches within the public dictionary for element value of * a given tag. - * @param TagName name of the researched element. + * @param TagName name of the searched element. * @return Corresponding element value when it exists, and the string * GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ @@ -1381,7 +1478,7 @@ std::string gdcmHeader::GetPubElValByName(std::string TagName) { * to convert the string typed content to caller's native type * (think of C++ vs Python). The VR is actually of a higher level * of semantics than just the native C++ type. - * @param TagName name of the researched element. + * @param TagName name of the searched element. * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ @@ -1396,8 +1493,8 @@ std::string gdcmHeader::GetPubElValRepByName(std::string TagName) { * \ingroup gdcmHeader * \brief Searches within elements parsed with the SHADOW dictionary * for the element value of a given tag. - * @param group Group of the researched tag. - * @param element Element of the researched tag. + * @param group Group of the searched tag. + * @param element Element of the searched tag. * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ @@ -1414,8 +1511,8 @@ std::string gdcmHeader::GetShaElValByNumber(guint16 group, guint16 element) { * to convert the string typed content to caller's native type * (think of C++ vs Python). The VR is actually of a higher level * of semantics than just the native C++ type. - * @param group Group of the researched tag. - * @param element Element of the researched tag. + * @param group Group of the searched tag. + * @param element Element of the searched tag. * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ @@ -1430,7 +1527,7 @@ std::string gdcmHeader::GetShaElValRepByNumber(guint16 group, guint16 element) { * \ingroup gdcmHeader * \brief Searches within the elements parsed with the shadow dictionary * for an element value of given tag. - * @param TagName name of the researched element. + * @param TagName name of the searched element. * @return Corresponding element value when it exists, and the string * GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ @@ -1447,7 +1544,7 @@ std::string gdcmHeader::GetShaElValByName(std::string TagName) { * to convert the string typed content to caller's native type * (think of C++ vs Python). The VR is actually of a higher level * of semantics than just the native C++ type. - * @param TagName name of the researched element. + * @param TagName name of the searched element. * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ @@ -1463,8 +1560,8 @@ std::string gdcmHeader::GetShaElValRepByName(std::string TagName) { * \brief Searches within elements parsed with the public dictionary * and then within the elements parsed with the shadow dictionary * for the element value of a given tag. - * @param group Group of the researched tag. - * @param element Element of the researched tag. + * @param group Group of the searched tag. + * @param element Element of the searched tag. * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ @@ -1485,8 +1582,8 @@ std::string gdcmHeader::GetElValByNumber(guint16 group, guint16 element) { * to convert the string typed content to caller's native type * (think of C++ vs Python). The VR is actually of a higher level * of semantics than just the native C++ type. - * @param group Group of the researched tag. - * @param element Element of the researched tag. + * @param group Group of the searched tag. + * @param element Element of the searched tag. * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ @@ -1502,7 +1599,7 @@ std::string gdcmHeader::GetElValRepByNumber(guint16 group, guint16 element) { * \brief Searches within elements parsed with the public dictionary * and then within the elements parsed with the shadow dictionary * for the element value of a given tag. - * @param TagName name of the researched element. + * @param TagName name of the searched element. * @return Corresponding element value when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ @@ -1523,7 +1620,7 @@ std::string gdcmHeader::GetElValByName(std::string TagName) { * to convert the string typed content to caller's native type * (think of C++ vs Python). The VR is actually of a higher level * of semantics than just the native C++ type. - * @param TagName name of the researched element. + * @param TagName name of the searched element. * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ @@ -1546,7 +1643,8 @@ 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 ?? { @@ -1616,7 +1714,7 @@ void gdcmHeader::ParseHeader(bool exception_on_error) throw(gdcmFormatError) { rewind(fp); CheckSwap(); - while ( (newElValue = ReadNextElement()) ) { + while ( (newElValue = ReadNextElement()) ) { SkipElementValue(newElValue); PubElValSet.Add(newElValue); } @@ -1624,7 +1722,7 @@ void gdcmHeader::ParseHeader(bool exception_on_error) throw(gdcmFormatError) { /** * \ingroup gdcmHeader - * \brief This predicate, based on hopefully reasonnable heuristics, + * \brief This predicate, based on hopefully reasonable heuristics, * decides whether or not the current gdcmHeader was properly parsed * and contains the mandatory information for being considered as * a well formed and usable image. @@ -1657,7 +1755,8 @@ 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; @@ -1682,11 +1781,22 @@ gdcmElValue* gdcmHeader::NewManualElValToPubDict(std::string NewTagName, std::st * public tag based hash table. */ void gdcmHeader::LoadElements(void) { - rewind(fp); - TagElValueHT ht = PubElValSet.GetTagHt(); - for (TagElValueHT::iterator tag = ht.begin(); tag != ht.end(); ++tag) { - LoadElementValue(tag->second); - } + rewind(fp); + + // We don't use any longer the HashTable, since a lot a stuff is missing + // when SeQuences were encountered + // + //TagElValueHT ht = PubElValSet.GetTagHt(); + //for (TagElValueHT::iterator tag = ht.begin(); tag != ht.end(); ++tag) { + // LoadElementValue(tag->second); + //} + + for (std::list::iterator i = GetListElem().begin(); + i != GetListElem().end(); + ++i){ + LoadElementValue(*i); + } + rewind(fp); // Load 'non string' values @@ -1732,7 +1842,7 @@ void gdcmHeader::PrintPubElVal(std::ostream & os) { /** * \ingroup gdcmHeader - * \brief + * \brief * @return */ void gdcmHeader::PrintPubDict(std::ostream & os) { @@ -1742,9 +1852,35 @@ 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 be written) + // 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); } @@ -1767,18 +1903,19 @@ void * gdcmHeader::LoadElementVoidArea(guint16 Group, guint16 Elem) { void * a = malloc(l); if(!a) { std::cout << "Big Broblem (LoadElementVoidArea, malloc) " - << std::hex << Group << " " << Elem << std::endl; + << 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) { std::cout << "Big Broblem (LoadElementVoidArea, fread) " - << std::hex << Group << " " << Elem << std::endl; + << std::hex << Group << " " << Elem << std::endl; free(a); return NULL; - } + } + return a; } /** @@ -1793,7 +1930,7 @@ 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(); @@ -1901,11 +2038,24 @@ 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 * \brief Retrieve the number of Samples Per Pixel - * (1 : gray level, 3 : RGB) + * (1 : gray level, 3 : RGB -1 or 3 Planes-) * * @return The encountered number of Samples Per Pixel, 1 by default. */ @@ -1959,6 +2109,7 @@ int gdcmHeader::GetPixelSize(void) { * - 32U unsigned 32 bit, * - 32S signed 32 bit, * \warning 12 bit images appear as 16 bit. + * \ 24 bit images appear as 8 bit * @return */ std::string gdcmHeader::GetPixelType(void) { @@ -1968,9 +2119,11 @@ std::string gdcmHeader::GetPixelType(void) { dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated"); BitsAlloc = std::string("16"); } - if (BitsAlloc == "12") + if (BitsAlloc == "12") // It will be unpacked BitsAlloc = std::string("16"); - + else if (BitsAlloc == "24") // (in order no to be messed up + BitsAlloc = std::string("8"); // by old RGB images) + std::string Signed; Signed = GetElValByName("Pixel Representation"); if (Signed == GDCM_UNFOUND) { @@ -1980,6 +2133,8 @@ std::string gdcmHeader::GetPixelType(void) { if (Signed == "0") Signed = std::string("U"); else + +std::cout << "GetPixelType : " << BitsAlloc + Signed << std::endl; Signed = std::string("S"); return( BitsAlloc + Signed); @@ -2008,39 +2163,33 @@ std::string gdcmHeader::GetTransferSyntaxName(void) { /** * \ingroup gdcmHeader - * \brief gets the info from 0028,1101 : Lookup Table Desc-Red - * \ else 0 - * @return Lookup Table Length - * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] + * \brief tells us if LUT are used + * \warning Right now, Segmented xxx Palette Color Lookup Table Data + * \ are NOT considered as LUT, since nobody knows + *\ how to deal with them + * @return int acts as a Boolean */ -int gdcmHeader::GetLUTLength(void) { - std::vector tokens; - int LutLength; - //int LutDepth; - //int LutNbits; - // Just hope Lookup Table Desc-Red = Lookup Table Desc-Red = Lookup Table Desc-Blue - std::string LutDescriptionR = GetPubElValByNumber(0x0028,0x1101); - if (LutDescriptionR == GDCM_UNFOUND) +int gdcmHeader::HasLUT(void) { + + // Check the presence of the LUT Descriptors + if (GetPubElValByNumber(0x0028,0x1101) == GDCM_UNFOUND) return 0; - std::string LutDescriptionG = GetPubElValByNumber(0x0028,0x1102); - if (LutDescriptionG == GDCM_UNFOUND) + // LutDescriptorGreen + if (GetPubElValByNumber(0x0028,0x1102) == GDCM_UNFOUND) return 0; - std::string LutDescriptionB = GetPubElValByNumber(0x0028,0x1103); - if (LutDescriptionB == GDCM_UNFOUND) + // LutDescriptorBlue + if (GetPubElValByNumber(0x0028,0x1103) == GDCM_UNFOUND) + return 0; + // It is not enough + // we check also + if (GetPubElValByNumber(0x0028,0x1201) == GDCM_UNFOUND) + return 0; + if (GetPubElValByNumber(0x0028,0x1202) == GDCM_UNFOUND) return 0; - if( (LutDescriptionR != LutDescriptionG) || (LutDescriptionR != LutDescriptionB) ) { - dbg.Verbose(0, "gdcmHeader::GetLUTLength: The CLUT R,G,B are not equal"); + if (GetPubElValByNumber(0x0028,0x1203) == GDCM_UNFOUND) return 0; - } - std::cout << "Lut Description " << LutDescriptionR < tokens; + + tokens.erase(tokens.begin(),tokens.end()); // clean any previous value + Tokenize (LutDescriptionR, tokens, "\\"); + lengthR=atoi(tokens[0].c_str()); // Red LUT length in Bytes + debR =atoi(tokens[1].c_str()); // subscript of the first Lut Value + nbitsR =atoi(tokens[2].c_str()); // Lut item size (in Bits) + tokens.clear(); - // Just wait before removing the following code - /* - if (nBits == 16) { - guint16 * LUTRGB, *rgb; - LUTRGB = rgb = (guint16 *) malloc(3*l*sizeof( guint16)); - guint16 * r = (guint16 *)LutR; - guint16 * g = (guint16 *)LutG; - guint16 * b = (guint16 *)LutB; - for(int i=0;i