X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=79ad3c0bd87135df6d27bb7385ecc8feb02059d2;hb=ea14e11cdd726f9c7e6d6384c7e9e508bc6efc2d;hp=a398ad35926dfdb3d1d2a461c8b36a2394ae0bbc;hpb=191decf8eab0497d96e871b0a49bf1d12d7b4529;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index a398ad35..79ad3c0b 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -1,4 +1,4 @@ -// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.106 2003/10/31 11:29:59 malaterre Exp $ +// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.113 2003/11/10 14:17:12 jpr Exp $ #include "gdcmHeader.h" @@ -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; } @@ -627,6 +627,9 @@ bool gdcmHeader::IsDicomV3(void) { * applying this heuristic. */ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { + + ElVal->SetReadLength(FoundLength); // will be updated only if a bug is found + if ( FoundLength == 0xffffffff) FoundLength = 0; @@ -635,19 +638,36 @@ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { 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)) { + 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->SetLength(FoundLength); + ( (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 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->SetUsableLength(FoundLength); } /** @@ -729,7 +749,7 @@ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { ElVal->SetLength(FindLengthOB()); return; } - FixFoundLength(ElVal, length32); + FixFoundLength(ElVal, length32); return; } @@ -753,7 +773,7 @@ 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 @@ -806,6 +826,7 @@ 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; } /** @@ -866,7 +887,7 @@ guint16 gdcmHeader::SwapShort(guint16 a) { * @return */ void gdcmHeader::SkipElementValue(gdcmElValue * ElVal) { - SkipBytes(ElVal->GetLength()); + SkipBytes(ElVal->GetLength()); } /** @@ -907,14 +928,17 @@ 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; - // A sequence "contains" a set of Elements. + // 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 SQuence just ended + // (fffe e0dd) tells us the current SeQuence just ended if( group == 0xfffe ) SkipLoad = true; @@ -939,6 +963,7 @@ 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 +971,9 @@ 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 +1140,6 @@ 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 @@ -1226,6 +1250,7 @@ gdcmElValue * gdcmHeader::ReadNextElement(void) { NewElVal = NewElValueByNumber(g, n); FindVR(NewElVal); FindLength(NewElVal); + if (errno == 1) { // Call it quits return (gdcmElValue *)0; @@ -1427,7 +1452,7 @@ 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. */ @@ -1444,7 +1469,7 @@ 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. */ @@ -1459,8 +1484,8 @@ 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. */ @@ -1477,8 +1502,8 @@ 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. */ @@ -1493,7 +1518,7 @@ 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. */ @@ -1510,7 +1535,7 @@ 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. */ @@ -1526,8 +1551,8 @@ 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. */ @@ -1548,8 +1573,8 @@ 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. */ @@ -1565,7 +1590,7 @@ 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. */ @@ -1586,7 +1611,7 @@ 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. */ @@ -1680,7 +1705,7 @@ void gdcmHeader::ParseHeader(bool exception_on_error) throw(gdcmFormatError) { rewind(fp); CheckSwap(); - while ( (newElValue = ReadNextElement()) ) { + while ( (newElValue = ReadNextElement()) ) { SkipElementValue(newElValue); PubElValSet.Add(newElValue); } @@ -1688,7 +1713,7 @@ 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. @@ -1747,11 +1772,22 @@ 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 + // 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 @@ -1811,8 +1847,7 @@ void gdcmHeader::PrintPubDict(std::ostream & os) { */ 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) { @@ -2011,7 +2046,7 @@ int gdcmHeader::GetBitsAllocated(void) { /** * \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. */ @@ -2065,6 +2100,7 @@ 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) { @@ -2074,9 +2110,11 @@ 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) { @@ -2086,6 +2124,8 @@ 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); @@ -2115,12 +2155,15 @@ std::string gdcmHeader::GetTransferSyntaxName(void) { /** * \ingroup gdcmHeader * \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::HasLUT(void) { - // Just hope checking the presence of the LUT Descriptors is enough + // Check the presence of the LUT Descriptors if (GetPubElValByNumber(0x0028,0x1101) == GDCM_UNFOUND) return 0; // LutDescriptorGreen @@ -2128,7 +2171,15 @@ int gdcmHeader::HasLUT(void) { return 0; // 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 (GetPubElValByNumber(0x0028,0x1203) == GDCM_UNFOUND) + return 0; return 1; } @@ -2243,7 +2294,7 @@ void * gdcmHeader::GetLUTRGBA(void) { } // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT - char *LUTRGBA = (char *)calloc(1024,1); // 256 * 4 (R, G, B, Alpha) + unsigned char *LUTRGBA = (unsigned char *)calloc(1024,1); // 256 * 4 (R, G, B, Alpha) if (!LUTRGBA) { return NULL; } @@ -2269,8 +2320,9 @@ void * gdcmHeader::GetLUTRGBA(void) { // if it works, we shall have to check the 3 Palettes // to see which byte is ==0 (first one, or second one) // and fix the code - // We give up the checking to avoid some overhead - char *a; + // We give up the checking to avoid some overhead + + unsigned char *a; int i; a= LUTRGBA+0; for(i=0;i