X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=9cdc5beb8606f7a56c9e7a1e413d26064378a8ca;hb=f04b9ef9bad66e1847e8139db9cd4126e4340301;hp=13da756dc1bde8eecaabd7bc93872e5051b7e24e;hpb=35d42d4166f9dae6312ec59765e08b48f9ef946f;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index 13da756d..9cdc5beb 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -1,4 +1,4 @@ -// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.101 2003/10/15 15:01:16 jpr Exp $ +// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.112 2003/11/10 09:21:40 jpr Exp $ #include "gdcmHeader.h" @@ -122,7 +122,7 @@ gdcmHeader::~gdcmHeader (void) { // Fourth semantics: // -// ---> Warning : This fourth fiels is NOT part +// ---> Warning : This fourth field is NOT part // of the 'official' Dicom Dictionnary // and should NOT be used. // (Not defined for all the groups @@ -394,7 +394,7 @@ void gdcmHeader::FindVR( gdcmElValue *ElVal) { 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 . @@ -508,7 +508,7 @@ 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; + if (Element->GetValue() == "1.2.840.10008.1.2.4.57") return true; return false; } @@ -629,15 +629,38 @@ 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 ... - if (FoundLength == 13) + else if (FoundLength == 13) { // The following 'if' will be removed when there is no more - // images on Creatis HD with a 13 length for Manufacturer... - if ( (ElVal->GetGroup() != 0x0008) || (ElVal->GetElement() ) ) + // 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; + } + // end of fix + + // to try to 'go inside' SeQuences (with length), and not to ship them + else if ( ElVal->GetVR() == "SQ") { + 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->SetLength(FoundLength); } @@ -658,23 +681,19 @@ 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 @@ -686,8 +705,7 @@ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { } 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); @@ -725,7 +743,8 @@ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { ElVal->SetLength(FindLengthOB()); return; } - FixFoundLength(ElVal, length32); + FixFoundLength(ElVal, length32); + return; } @@ -808,8 +827,7 @@ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { * \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) { @@ -863,7 +881,7 @@ guint16 gdcmHeader::SwapShort(guint16 a) { * @return */ void gdcmHeader::SkipElementValue(gdcmElValue * ElVal) { - SkipBytes(ElVal->GetLength()); + SkipBytes(ElVal->GetLength()); } /** @@ -904,17 +922,17 @@ 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; @@ -939,6 +957,7 @@ 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; } @@ -946,9 +965,9 @@ 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; @@ -1115,7 +1134,6 @@ gdcmElValue* gdcmHeader::NewElValueByNumber(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 @@ -1155,6 +1173,7 @@ 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 @@ -1162,7 +1181,7 @@ 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; @@ -1242,9 +1261,8 @@ 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 @@ -1298,6 +1316,40 @@ 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 @@ -1393,7 +1445,7 @@ 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. */ @@ -1410,7 +1462,7 @@ 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. */ @@ -1425,8 +1477,8 @@ 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. */ @@ -1443,8 +1495,8 @@ 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. */ @@ -1459,7 +1511,7 @@ 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. */ @@ -1476,7 +1528,7 @@ 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. */ @@ -1492,8 +1544,8 @@ 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. */ @@ -1514,8 +1566,8 @@ 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. */ @@ -1531,7 +1583,7 @@ 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. */ @@ -1552,7 +1604,7 @@ 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. */ @@ -1646,7 +1698,7 @@ void gdcmHeader::ParseHeader(bool exception_on_error) throw(gdcmFormatError) { rewind(fp); CheckSwap(); - while ( (newElValue = ReadNextElement()) ) { + while ( (newElValue = ReadNextElement()) ) { SkipElementValue(newElValue); PubElValSet.Add(newElValue); } @@ -1654,7 +1706,7 @@ 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. @@ -1713,11 +1765,22 @@ gdcmElValue* gdcmHeader::NewManualElValToPubDict(std::string NewTagName, * 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 + // we 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 @@ -1763,7 +1826,7 @@ void gdcmHeader::PrintPubElVal(std::ostream & os) { /** * \ingroup gdcmHeader - * \brief + * \brief * @return */ void gdcmHeader::PrintPubDict(std::ostream & os) { @@ -1773,12 +1836,11 @@ 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) + // TODO : move the following lines (and a lot of others, to be written) // to a future function CheckAndCorrectHeader if (type == ImplicitVR) { @@ -1828,7 +1890,7 @@ void * gdcmHeader::LoadElementVoidArea(guint16 Group, guint16 Elem) { << 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) { @@ -1836,7 +1898,8 @@ void * gdcmHeader::LoadElementVoidArea(guint16 Group, guint16 Elem) { << std::hex << Group << " " << Elem << std::endl; free(a); return NULL; - } + } + return a; } /** @@ -1959,11 +2022,24 @@ 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. */ @@ -2017,6 +2093,7 @@ 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) { @@ -2026,9 +2103,11 @@ 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) { @@ -2038,6 +2117,8 @@ 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); @@ -2066,39 +2147,33 @@ 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; - if( (LutDescriptionR != LutDescriptionG) || (LutDescriptionR != LutDescriptionB) ) { - dbg.Verbose(0, "gdcmHeader::GetLUTLength: The CLUT R,G,B are not equal"); + // It is not enough + // we check also + if (GetPubElValByNumber(0x0028,0x1201) == GDCM_UNFOUND) + return 0; + if (GetPubElValByNumber(0x0028,0x1202) == GDCM_UNFOUND) + return 0; + 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(); - // Warning : Any value for nBits as to be considered as 8 - // Any value for Length as to be considered as 256 - // That's DICOM ... + tokens.erase(tokens.begin(),tokens.end()); // clean any previous value + Tokenize (LutDescriptionG, tokens, "\\"); + lengthG=atoi(tokens[0].c_str()); // Green LUT length in Bytes + debG =atoi(tokens[1].c_str()); + nbitsG =atoi(tokens[2].c_str()); + 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 tokens; - tokens.erase(tokens.begin(),tokens.end()); // clean any previous value - Tokenize ((const std::string)x, tokens, "\\"); - for (unsigned int i=0; i