X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=4f2d2affb872a154c12ec4bd148249eb939ec6dd;hb=a1f0a28f71d3813042483bfa4cf07b00f3462d7c;hp=231b5bc4196a4af75b51695e5de8329c3c56a965;hpb=d5e17ffd70201ed72ebb59a2d0c09c8eac177c52;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index 231b5bc4..4f2d2aff 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -13,6 +13,8 @@ #include "gdcmUtil.h" #include "gdcmHeader.h" +#include "iddcmjpeg.h" + // Refer to gdcmHeader::CheckSwap() #define HEADER_LENGTH_TO_READ 256 // Refer to gdcmHeader::SetMaxSizeLoadElementValue() @@ -41,7 +43,7 @@ gdcmHeader::gdcmHeader(const char *InFilename, bool exception_on_error) else dbg.Error(!fp, "gdcmHeader::gdcmHeader cannot open file", InFilename); ParseHeader(); - AddAndDefaultElements(); + LoadElements(); } @@ -119,17 +121,11 @@ void gdcmHeader::CheckSwap() entCur = deb + 128; if(memcmp(entCur, "DICM", (size_t)4) == 0) { - filetype = TrueDicom; dbg.Verbose(1, "gdcmHeader::CheckSwap:", "looks like DICOM Version3"); - } else { - filetype = Unknown; - dbg.Verbose(1, "gdcmHeader::CheckSwap:", "not a DICOM Version3 file"); - } - - if(filetype == TrueDicom) { // Next, determine the value representation (VR). Let's skip to the - // first element (0002, 0000) and check there if we find "UL", in - // which case we (almost) know it is explicit VR. + // first element (0002, 0000) and check there if we find "UL" + // - or "OB" if the 1st one is (0002,0001) -, + // in which case we (almost) know it is explicit VR. // WARNING: if it happens to be implicit VR then what we will read // is the length of the group. If this ascii representation of this // length happens to be "UL" then we shall believe it is explicit VR. @@ -139,10 +135,16 @@ void gdcmHeader::CheckSwap() // We need to skip : // * the 128 bytes of File Preamble (often padded with zeroes), // * the 4 bytes of "DICM" string, - // * the 4 bytes of the first tag (0002, 0000), + // * the 4 bytes of the first tag (0002, 0000),or (0002, 0001) // i.e. a total of 136 bytes. entCur = deb + 136; - if(memcmp(entCur, "UL", (size_t)2) == 0) { + // FIXME + // Use gdcmHeader::dicom_vr to test all the possibilities + // instead of just checking for UL, OB and UI !? + if( (memcmp(entCur, "UL", (size_t)2) == 0) || + (memcmp(entCur, "OB", (size_t)2) == 0) || + (memcmp(entCur, "UI", (size_t)2) == 0) ) + { filetype = ExplicitVR; dbg.Verbose(1, "gdcmHeader::CheckSwap:", "explicit Value Representation"); @@ -167,11 +169,12 @@ void gdcmHeader::CheckSwap() rewind(fp); fseek (fp, 132L, SEEK_SET); return; - } // End of TrueDicom + } // End of DicomV3 // Alas, this is not a DicomV3 file and whatever happens there is no file // preamble. We can reset the file position indicator to where the data // is (i.e. the beginning of the file). + dbg.Verbose(1, "gdcmHeader::CheckSwap:", "not a DICOM Version3 file"); rewind(fp); // Our next best chance would be to be considering a 'clean' ACR/NEMA file. @@ -211,6 +214,7 @@ void gdcmHeader::CheckSwap() // 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. Then the only info we have is the net2host one. + filetype = Unknown; if (! net2host ) sw = 0; else @@ -241,7 +245,11 @@ void gdcmHeader::GetPixels(size_t lgrTotale, void* _Pixels) { size_t pixelsOffset; pixelsOffset = GetPixelOffset(); fseek(fp, pixelsOffset, SEEK_SET); - fread(_Pixels, 1, lgrTotale, fp); + if (IsJPEGLossless()) { + _Pixels=_IdDcmJpegRead(fp); + } else { + fread(_Pixels, 1, lgrTotale, fp); + } } @@ -250,7 +258,7 @@ void gdcmHeader::GetPixels(size_t lgrTotale, void* _Pixels) { * \ingroup gdcmHeader * \brief Find the value representation of the current tag. */ -void gdcmHeader::FindVR( ElValue *ElVal) { +void gdcmHeader::FindVR( gdcmElValue *ElVal) { if (filetype != ExplicitVR) return; @@ -286,7 +294,7 @@ void gdcmHeader::FindVR( ElValue *ElVal) { // PostPone this test in an optional integrity check at the end // of parsing or only in debug mode. if ( RealExplicit && !dicom_vr->count(vr) ) - RealExplicit = false; + RealExplicit= false; if ( RealExplicit ) { if ( ElVal->IsVrUnknown() ) { @@ -334,7 +342,7 @@ void gdcmHeader::FindVR( ElValue *ElVal) { * @return True when ImplicitVRLittleEndian found. False in all other cases. */ bool gdcmHeader::IsImplicitVRLittleEndianTransferSyntax(void) { - ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -352,7 +360,7 @@ bool gdcmHeader::IsImplicitVRLittleEndianTransferSyntax(void) { * @return True when ExplicitVRLittleEndian found. False in all other cases. */ bool gdcmHeader::IsExplicitVRLittleEndianTransferSyntax(void) { - ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -370,7 +378,7 @@ bool gdcmHeader::IsExplicitVRLittleEndianTransferSyntax(void) { * @return True when DeflatedExplicitVRLittleEndian found. False in all other cases. */ bool gdcmHeader::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) { - ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -388,12 +396,12 @@ bool gdcmHeader::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) { * @return True when big endian found. False in all other cases. */ bool gdcmHeader::IsExplicitVRBigEndianTransferSyntax(void) { - ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.2" ) + if ( Transfer == "1.2.840.10008.1.2.2" ) //1.2.2 ??? A verifier ! return true; return false; } @@ -406,7 +414,7 @@ bool gdcmHeader::IsExplicitVRBigEndianTransferSyntax(void) { * @return True when JPEGBaseLineProcess1found. False in all other cases. */ bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) { - ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -416,6 +424,20 @@ bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) { return false; } +// faire qq chose d'intelligent a la place de ça + +bool gdcmHeader::IsJPEGLossless(void) { + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); + if ( !Element ) + return false; + LoadElementValueSafe(Element); + 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; + return false; +} + + /** * \ingroup gdcmHeader * \brief Determines if the Transfer Syntax was allready encountered @@ -424,7 +446,7 @@ bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) { * @return True when JPEGExtendedProcess2-4 found. False in all other cases. */ bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) { - ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -442,7 +464,7 @@ bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) { * @return True when JPEGExtendedProcess3-5 found. False in all other cases. */ bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) { - ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -461,7 +483,7 @@ bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) { * other cases. */ bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) { - ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -470,6 +492,17 @@ bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) { return true; return false; } +/** + * \ingroup gdcmHeader + * \brief Predicate for dicom version 3 file. + * @return True when the file is a dicom version 3. + */ +bool gdcmHeader::IsDicomV3(void) { + if ( (filetype == ExplicitVR) + || (filetype == ImplicitVR) ) + return true; + return false; +} /** * \ingroup gdcmHeader @@ -477,7 +510,7 @@ bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) { * the parser went Jabberwocky) one can hope improving things by * applying this heuristic. */ -void gdcmHeader::FixFoundLength(ElValue * ElVal, guint32 FoundLength) { +void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { if ( FoundLength == 0xffffffff) FoundLength = 0; ElVal->SetLength(FoundLength); @@ -521,7 +554,7 @@ guint32 gdcmHeader::FindLengthOB(void) { return TotalLength; } -void gdcmHeader::FindLength(ElValue * ElVal) { +void gdcmHeader::FindLength(gdcmElValue * ElVal) { guint16 element = ElVal->GetElement(); string vr = ElVal->GetVR(); guint16 length16; @@ -621,7 +654,6 @@ void gdcmHeader::FindLength(ElValue * ElVal) { * @return The suggested integer. */ guint32 gdcmHeader::SwapLong(guint32 a) { - // FIXME: il pourrait y avoir un pb pour les entiers negatifs ... switch (sw) { case 0 : break; @@ -660,7 +692,7 @@ void gdcmHeader::SkipBytes(guint32 NBytes) { (void)fseek(fp, (long)NBytes, SEEK_CUR); } -void gdcmHeader::SkipElementValue(ElValue * ElVal) { +void gdcmHeader::SkipElementValue(gdcmElValue * ElVal) { SkipBytes(ElVal->GetLength()); } @@ -680,7 +712,7 @@ void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) { * than the value specified with * gdcmHeader::SetMaxSizeLoadElementValue() */ -void gdcmHeader::LoadElementValue(ElValue * ElVal) { +void gdcmHeader::LoadElementValue(gdcmElValue * ElVal) { size_t item_read; guint16 group = ElVal->GetGroup(); guint16 elem = ElVal->GetElement(); @@ -690,13 +722,14 @@ void gdcmHeader::LoadElementValue(ElValue * ElVal) { fseek(fp, (long)ElVal->GetOffset(), SEEK_SET); - // Sequences not treated yet ! + // FIXME Sequences not treated yet ! // // Ne faudrait-il pas au contraire trouver immediatement // une maniere 'propre' de traiter les sequences (vr = SQ) // car commencer par les ignorer risque de conduire a qq chose // qui pourrait ne pas etre generalisable - // + // Well, I'm expecting your code !!! + if( vr == "SQ" ) SkipLoad = true; @@ -706,16 +739,7 @@ void gdcmHeader::LoadElementValue(ElValue * ElVal) { if( group == 0xfffe ) SkipLoad = true; - // The group length doesn't represent data to be loaded in memory, since - // each element of the group shall be loaded individualy. - if( elem == 0 ) - //SkipLoad = true; // modif sauvage JPR - // On charge la longueur du groupe - // quand l'element 0x0000 est présent ! - if ( SkipLoad ) { - // FIXME the following skip is not necessary - SkipElementValue(ElVal); ElVal->SetLength(0); ElVal->SetValue("gdcm::Skipped"); return; @@ -745,26 +769,6 @@ void gdcmHeader::LoadElementValue(ElValue * ElVal) { // pour les elements de Value Multiplicity > 1 // on aura en fait une serie d'entiers - // code original - - //if ( IsAnInteger(ElVal) ) { - // guint32 NewInt; - // if( length == 2 ) { - // NewInt = ReadInt16(); - // } else if( length == 4 ) { - // - // NewInt = ReadInt32(); - // } else - // dbg.Error(true, "LoadElementValue: Inconsistency when reading Int."); - // - // //FIXME: make the following an util fonction - // ostringstream s; - // s << NewInt; - // ElVal->SetValue(s.str()); - // return; - //} - - // modif proposee. JPR // on devrait pouvoir faire + compact (?) if ( IsAnInteger(ElVal) ) { @@ -780,7 +784,6 @@ void gdcmHeader::LoadElementValue(ElValue * ElVal) { s << '\\'; NewInt = ReadInt16(); s << NewInt; - //printf("%s\n", s.str().c_str()); } } @@ -800,8 +803,6 @@ void gdcmHeader::LoadElementValue(ElValue * ElVal) { return; } - - // FIXME The exact size should be length if we move to strings or whatever char* NewValue = (char*)malloc(length+1); if( !NewValue) { @@ -828,7 +829,7 @@ void gdcmHeader::LoadElementValue(ElValue * ElVal) { * @param ElVal Element whose value shall be loaded. * @return */ -void gdcmHeader::LoadElementValueSafe(ElValue * ElVal) { +void gdcmHeader::LoadElementValueSafe(gdcmElValue * ElVal) { long PositionOnEntry = ftell(fp); LoadElementValue(ElVal); fseek(fp, PositionOnEntry, SEEK_SET); @@ -863,6 +864,16 @@ guint32 gdcmHeader::ReadInt32(void) { return g; } + + + +// +// TODO : JPR Pour des raisons d'homogeneité de noms, +// remplacer les quelques GetxxxByKey +// par des GetxxxByNumber, lorsqu'on passe gr, el en param. +// il peut etre interessant de rajouter des GetxxxByKey, auxquels on passe *vraiment* une TagKey +// + /** * \ingroup gdcmHeader * \brief Build a new Element Value from all the low level arguments. @@ -871,21 +882,35 @@ guint32 gdcmHeader::ReadInt32(void) { * @param Group group of the underlying DictEntry * @param Elem element of the underlying DictEntry */ -ElValue* gdcmHeader::NewElValueByKey(guint16 Group, guint16 Elem) { +gdcmElValue* gdcmHeader::NewElValueByKey(guint16 Group, guint16 Elem) { // Find out if the tag we encountered is in the dictionaries: gdcmDictEntry * NewTag = GetDictEntryByKey(Group, Elem); if (!NewTag) NewTag = new gdcmDictEntry(Group, Elem); - ElValue* NewElVal = new ElValue(NewTag); + gdcmElValue* NewElVal = new gdcmElValue(NewTag); if (!NewElVal) { dbg.Verbose(1, "gdcmHeader::NewElValueByKey", - "failed to allocate ElValue"); - return (ElValue*)0; + "failed to allocate gdcmElValue"); + return (gdcmElValue*)0; } return NewElVal; } +/** + * \ingroup gdcmHeader + * \brief TODO + * @param + */ +int gdcmHeader::ReplaceOrCreateByNumber(string Value, guint16 Group, guint16 Elem ) { + + gdcmElValue* nvElValue=NewElValueByKey(Group, Elem); + PubElValSet.Add(nvElValue); + PubElValSet.SetElValueByNumber(Value, Group, Elem); + return(1); +} + + /** * \ingroup gdcmHeader * \brief Build a new Element Value from all the low level arguments. @@ -893,17 +918,17 @@ ElValue* gdcmHeader::NewElValueByKey(guint16 Group, guint16 Elem) { * a default one when absent. * @param Name Name of the underlying DictEntry */ -ElValue* gdcmHeader::NewElValueByName(string Name) { +gdcmElValue* gdcmHeader::NewElValueByName(string Name) { gdcmDictEntry * NewTag = GetDictEntryByName(Name); if (!NewTag) NewTag = new gdcmDictEntry(0xffff, 0xffff, "LO", "Unknown", Name); - ElValue* NewElVal = new ElValue(NewTag); + gdcmElValue* NewElVal = new gdcmElValue(NewTag); if (!NewElVal) { dbg.Verbose(1, "gdcmHeader::ObtainElValueByName", - "failed to allocate ElValue"); - return (ElValue*)0; + "failed to allocate gdcmElValue"); + return (gdcmElValue*)0; } return NewElVal; } @@ -913,24 +938,24 @@ ElValue* gdcmHeader::NewElValueByName(string Name) { * \brief Read the next tag but WITHOUT loading it's value * @return On succes the newly created ElValue, NULL on failure. */ -ElValue * gdcmHeader::ReadNextElement(void) { - guint16 g; - guint16 n; - ElValue * NewElVal; +gdcmElValue * gdcmHeader::ReadNextElement(void) { + + guint16 g,n; + gdcmElValue * NewElVal; g = ReadInt16(); n = ReadInt16(); if (errno == 1) // We reached the EOF (or an error occured) and header parsing // has to be considered as finished. - return (ElValue *)0; + return (gdcmElValue *)0; NewElVal = NewElValueByKey(g, n); FindVR(NewElVal); FindLength(NewElVal); if (errno == 1) // Call it quits - return (ElValue *)0; + return (gdcmElValue *)0; NewElVal->SetOffset(ftell(fp)); return NewElVal; } @@ -942,7 +967,7 @@ ElValue * gdcmHeader::ReadNextElement(void) { * @param ElVal The element value on which to apply the predicate. * @return The result of the heuristical predicate. */ -bool gdcmHeader::IsAnInteger(ElValue * ElVal) { +bool gdcmHeader::IsAnInteger(gdcmElValue * ElVal) { guint16 group = ElVal->GetGroup(); guint16 element = ElVal->GetElement(); string vr = ElVal->GetVR(); @@ -954,48 +979,17 @@ bool gdcmHeader::IsAnInteger(ElValue * ElVal) { if ( element == 0 ) { // This is the group length of the group if (length == 4) return true; - else + else { + printf("Erroneous Group Length element length %d\n",length); + dbg.Error("gdcmHeader::IsAnInteger", - "Erroneous Group Length element length."); + "Erroneous Group Length element length."); + } } - /* - // on le traite tt de même (VR peut donner l'info) - // faire qq chose + ruse (pas de test si pas de VR) - if ( group % 2 != 0 ) - // We only have some semantics on documented elements, which are - // the even ones. - return false; - */ - - /* - if ( (length != 4) && ( length != 2) ) - // Swapping only make sense on integers which are 2 or 4 bytes long. - - // En fait, pour les entiers de 'Value Multiplicity' supérieur a 1 - // la longueur n'est pas forcement 2 ou 4 - // ET il faudra swapper. - return false; - */ - if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") ) return true; - - // est-ce encore utile? - // mieux vaut modifier le source du Dicom Dictionnaty - // et remplacer pour ces 2 cas RET par US - - if ( (group == 0x0028) && (element == 0x0005) ) - // The "Image Dimensions" tag is retained from ACR/NEMA and contains - // the number of dimensions of the contained object (1 for Signal, - // 2 for Image, 3 for Volume, 4 for Sequence). - return true; - - if ( (group == 0x0028) && (element == 0x0200) ) - // This tag is retained from ACR/NEMA - return true; - return false; } @@ -1010,7 +1004,7 @@ size_t gdcmHeader::GetPixelOffset(void) { // 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. + // When the "Image Location" is absent we default to group 0x7fe0. guint16 grPixel; guint16 numPixel; string ImageLocation = GetPubElValByName("Image Location"); @@ -1020,12 +1014,11 @@ size_t gdcmHeader::GetPixelOffset(void) { grPixel = (guint16) atoi( ImageLocation.c_str() ); } if (grPixel != 0x7fe0) - // FIXME is this still necessary ? - // Now, this looks like an old dirty fix for Philips imager + // This is a kludge for old dirty Philips imager. numPixel = 0x1010; else numPixel = 0x0010; - ElValue* PixelElement = PubElVals.GetElementByNumber(grPixel, numPixel); + gdcmElValue* PixelElement = PubElValSet.GetElementByNumber(grPixel, numPixel); if (PixelElement) return PixelElement->GetOffset(); else @@ -1045,7 +1038,7 @@ size_t gdcmHeader::GetPixelOffset(void) { gdcmDictEntry * gdcmHeader::GetDictEntryByKey(guint16 group, guint16 element) { gdcmDictEntry * found = (gdcmDictEntry*)0; if (!RefPubDict && !RefShaDict) { - dbg.Verbose(0, "FIXME in gdcmHeader::GetDictEntry", + dbg.Verbose(0, "gdcmHeader::GetDictEntry", "we SHOULD have a default dictionary"); } if (RefPubDict) { @@ -1072,7 +1065,7 @@ gdcmDictEntry * gdcmHeader::GetDictEntryByKey(guint16 group, guint16 element) { gdcmDictEntry * gdcmHeader::GetDictEntryByName(string Name) { gdcmDictEntry * found = (gdcmDictEntry*)0; if (!RefPubDict && !RefShaDict) { - dbg.Verbose(0, "FIXME in gdcmHeader::GetDictEntry", + dbg.Verbose(0, "gdcmHeader::GetDictEntry", "we SHOULD have a default dictionary"); } if (RefPubDict) { @@ -1098,7 +1091,7 @@ gdcmDictEntry * gdcmHeader::GetDictEntryByName(string Name) { * "gdcm::Unfound" otherwise. */ string gdcmHeader::GetPubElValByNumber(guint16 group, guint16 element) { - return PubElVals.GetElValueByNumber(group, element); + return PubElValSet.GetElValueByNumber(group, element); } /** @@ -1116,7 +1109,7 @@ string gdcmHeader::GetPubElValByNumber(guint16 group, guint16 element) { * and the string "gdcm::Unfound" otherwise. */ string gdcmHeader::GetPubElValRepByNumber(guint16 group, guint16 element) { - ElValue* elem = PubElVals.GetElementByNumber(group, element); + gdcmElValue* elem = PubElValSet.GetElementByNumber(group, element); if ( !elem ) return "gdcm::Unfound"; return elem->GetVR(); @@ -1131,7 +1124,7 @@ string gdcmHeader::GetPubElValRepByNumber(guint16 group, guint16 element) { * "gdcm::Unfound" otherwise. */ string gdcmHeader::GetPubElValByName(string TagName) { - return PubElVals.GetElValueByName(TagName); + return PubElValSet.GetElValueByName(TagName); } /** @@ -1148,7 +1141,7 @@ string gdcmHeader::GetPubElValByName(string TagName) { * and the string "gdcm::Unfound" otherwise. */ string gdcmHeader::GetPubElValRepByName(string TagName) { - ElValue* elem = PubElVals.GetElementByName(TagName); + gdcmElValue* elem = PubElValSet.GetElementByName(TagName); if ( !elem ) return "gdcm::Unfound"; return elem->GetVR(); @@ -1164,7 +1157,7 @@ string gdcmHeader::GetPubElValRepByName(string TagName) { * and the string "gdcm::Unfound" otherwise. */ string gdcmHeader::GetShaElValByNumber(guint16 group, guint16 element) { - return ShaElVals.GetElValueByNumber(group, element); + return ShaElValSet.GetElValueByNumber(group, element); } /** @@ -1182,7 +1175,7 @@ string gdcmHeader::GetShaElValByNumber(guint16 group, guint16 element) { * and the string "gdcm::Unfound" otherwise. */ string gdcmHeader::GetShaElValRepByNumber(guint16 group, guint16 element) { - ElValue* elem = ShaElVals.GetElementByNumber(group, element); + gdcmElValue* elem = ShaElValSet.GetElementByNumber(group, element); if ( !elem ) return "gdcm::Unfound"; return elem->GetVR(); @@ -1197,7 +1190,7 @@ string gdcmHeader::GetShaElValRepByNumber(guint16 group, guint16 element) { * "gdcm::Unfound" otherwise. */ string gdcmHeader::GetShaElValByName(string TagName) { - return ShaElVals.GetElValueByName(TagName); + return ShaElValSet.GetElValueByName(TagName); } /** @@ -1214,7 +1207,7 @@ string gdcmHeader::GetShaElValByName(string TagName) { * and the string "gdcm::Unfound" otherwise. */ string gdcmHeader::GetShaElValRepByName(string TagName) { - ElValue* elem = ShaElVals.GetElementByName(TagName); + gdcmElValue* elem = ShaElValSet.GetElementByName(TagName); if ( !elem ) return "gdcm::Unfound"; return elem->GetVR(); @@ -1298,7 +1291,7 @@ string gdcmHeader::GetElValRepByName(string TagName) { /** * \ingroup gdcmHeader - * \brief Accesses an existing ElValue in the PubElVals of this instance + * \brief Accesses an existing gdcmElValue in the PubElValSet of this instance * through it's (group, element) and modifies it's content with * the given value. * @param content new value to substitute with @@ -1308,63 +1301,61 @@ string gdcmHeader::GetElValRepByName(string TagName) { int gdcmHeader::SetPubElValByNumber(string content, guint16 group, guint16 element) { - return ( PubElVals.SetElValueByNumber (content, group, element) ); + return ( PubElValSet.SetElValueByNumber (content, group, element) ); } /** * \ingroup gdcmHeader - * \brief Accesses an existing ElValue in the PubElVals of this instance + * \brief Accesses an existing gdcmElValue in the PubElValSet of this instance * through tag name and modifies it's content with the given value. * @param content new value to substitute with * @param TagName name of the tag to be modified */ int gdcmHeader::SetPubElValByName(string content, string TagName) { - return ( PubElVals.SetElValueByName (content, TagName) ); + return ( PubElValSet.SetElValueByName (content, TagName) ); } /** * \ingroup gdcmHeader - * \brief Accesses an existing ElValue in the PubElVals of this instance + * \brief Accesses an existing gdcmElValue in the PubElValSet of this instance * through it's (group, element) and modifies it's length with * the given value. - * NOT FOR BOZOs ! - * @param contents new length to substitute with + * \warning Use with extreme caution. + * @param length new length to substitute with * @param group group of the ElVal to modify * @param element element of the ElVal to modify + * @return 1 on success, 0 otherwise. */ -int gdcmHeader::SetPubElValLengthByNumber(guint32 lgr, guint16 group, - guint16 element) -{ - return ( PubElVals.SetElValueLengthByNumber (lgr, group, element) ); + +int gdcmHeader::SetPubElValLengthByNumber(guint32 length, guint16 group, + guint16 element) { + return ( PubElValSet.SetElValueLengthByNumber (length, group, element) ); } /** * \ingroup gdcmHeader - * \brief Accesses an existing ElValue in the ShaElVals of this instance + * \brief Accesses an existing gdcmElValue in the ShaElValSet of this instance * through it's (group, element) and modifies it's content with * the given value. * @param content new value to substitute with * @param group group of the ElVal to modify * @param element element of the ElVal to modify + * @return 1 on success, 0 otherwise. */ int gdcmHeader::SetShaElValByNumber(string content, - guint16 group, guint16 element) -{ - return ( ShaElVals.SetElValueByNumber (content, group, element) ); + guint16 group, guint16 element) { + return ( ShaElValSet.SetElValueByNumber (content, group, element) ); } - - - /** * \ingroup gdcmHeader - * \brief Accesses an existing ElValue in the ShaElVals of this instance + * \brief Accesses an existing gdcmElValue in the ShaElValSet of this instance * through tag name and modifies it's content with the given value. * @param content new value to substitute with * @param TagName name of the tag to be modified */ int gdcmHeader::SetShaElValByName(string content, string TagName) { - return ( ShaElVals.SetElValueByName (content, TagName) ); + return ( ShaElValSet.SetElValueByName (content, TagName) ); } /** @@ -1372,42 +1363,165 @@ int gdcmHeader::SetShaElValByName(string content, string TagName) { * \brief Parses the header of the file but WITHOUT loading element values. */ void gdcmHeader::ParseHeader(bool exception_on_error) throw(gdcmFormatError) { - ElValue * newElValue = (ElValue *)0; + gdcmElValue * newElValue = (gdcmElValue *)0; rewind(fp); CheckSwap(); while ( (newElValue = ReadNextElement()) ) { SkipElementValue(newElValue); - PubElVals.Add(newElValue); + PubElValSet.Add(newElValue); } } /** * \ingroup gdcmHeader - * \brief Once the header is parsed add some gdcm convenience/helper elements - * in the ElValSet. For example add: - * - gdcmImageType which is an entry containing a short for the - * type of image and whose value ranges in - * I8 (unsigned 8 bit image) - * I16 (unsigned 8 bit image) - * IS16 (signed 8 bit image) - * - gdcmXsize, gdcmYsize, gdcmZsize whose values are respectively - * the ones of the official DICOM fields Rows, Columns and Planes. + * \brief Retrieve the number of columns of image. + * @return The encountered size when found, 0 by default. */ -void gdcmHeader::AddAndDefaultElements(void) { - ElValue* NewEntry = (ElValue*)0; +int gdcmHeader::GetXSize(void) { + // We cannot check for "Columns" because the "Columns" tag is present + // both in IMG (0028,0011) and OLY (6000,0011) sections of the dictionary. + string StrSize = GetPubElValByNumber(0x0028,0x0011); + if (StrSize == "gdcm::Unfound") + return 0; + return atoi(StrSize.c_str()); +} - NewEntry = NewElValueByName("gdcmXSize"); - NewEntry->SetValue(GetElValByName("Rows")); - PubElVals.Add(NewEntry); +/** + * \ingroup gdcmHeader + * \brief Retrieve the number of lines of image. + * \warning The defaulted value is 1 as opposed to gdcmHeader::GetXSize() + * @return The encountered size when found, 1 by default. + */ +int gdcmHeader::GetYSize(void) { + // We cannot check for "Rows" because the "Rows" tag is present + // both in IMG (0028,0010) and OLY (6000,0010) sections of the dictionary. + string StrSize = GetPubElValByNumber(0x0028,0x0010); + if (StrSize != "gdcm::Unfound") + return atoi(StrSize.c_str()); + if ( IsDicomV3() ) + return 0; + else + // The Rows (0028,0010) entry is optional for ACR/NEMA. It might + // hence be a signal (1d image). So we default to 1: + return 1; +} - NewEntry = NewElValueByName("gdcmYSize"); - NewEntry->SetValue(GetElValByName("Columns")); - PubElVals.Add(NewEntry); +/** + * \ingroup gdcmHeader + * \brief Retrieve the number of planes of volume or the number + * of frames of a multiframe. + * \warning When present we consider the "Number of Frames" as the third + * dimension. When absent we consider the third dimension as + * being the "Planes" tag content. + * @return The encountered size when found, 1 by default. + */ +int gdcmHeader::GetZSize(void) { + // Both in DicomV3 and ACR/Nema the consider the "Number of Frames" + // as the third dimension. + string StrSize = GetPubElValByNumber(0x0028,0x0008); + if (StrSize != "gdcm::Unfound") + return atoi(StrSize.c_str()); + + // We then consider the "Planes" entry as the third dimension [we + // cannot retrieve by name since "Planes tag is present both in + // IMG (0028,0012) and OLY (6000,0012) sections of the dictionary]. + StrSize = GetPubElValByNumber(0x0028,0x0012); + if (StrSize != "gdcm::Unfound") + return atoi(StrSize.c_str()); + return 1; +} + +/** + * \ingroup gdcmHeader + * \brief Build the Pixel Type of the image. + * Possible values are: + * - U8 unsigned 8 bit, + * - S8 signed 8 bit, + * - U16 unsigned 16 bit, + * - S16 signed 16 bit, + * - U32 unsigned 32 bit, + * - S32 signed 32 bit, + * \warning 12 bit images appear as 16 bit. + * @return + */ +string gdcmHeader::GetPixelType(void) { + string BitsAlloc; + BitsAlloc = GetElValByName("Bits Allocated"); + if (BitsAlloc == "gdcm::Unfound") { + dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated"); + BitsAlloc = string("16"); + } + if (BitsAlloc == "12") + BitsAlloc = string("16"); + + string Signed; + Signed = GetElValByName("Pixel Representation"); + if (Signed == "gdcm::Unfound") { + dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation"); + BitsAlloc = string("0"); + } + if (Signed == "0") + Signed = string("U"); + else + Signed = string("S"); + + return( BitsAlloc + Signed); +} + +/** + * \ingroup gdcmHeader + * \brief This predicate, based on hopefully reasonnable 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. + * @return true when gdcmHeader is the one of a reasonable Dicom file, + * false otherwise. + */ +bool gdcmHeader::IsReadable(void) { + if ( GetElValByName("Image Dimensions") != "gdcm::Unfound" + && atoi(GetElValByName("Image Dimensions").c_str()) > 4 ) { + return false; + } + if ( GetElValByName("Bits Allocated") == "gdcm::Unfound" ) + return false; + if ( GetElValByName("Bits Stored") == "gdcm::Unfound" ) + return false; + if ( GetElValByName("High Bit") == "gdcm::Unfound" ) + return false; + if ( GetElValByName("Pixel Representation") == "gdcm::Unfound" ) + return false; + return true; +} + +/** + * \ingroup gdcmHeader + * \brief Small utility function that creates a new manually crafted + * (as opposed as read from the file) gdcmElValue with user + * specified name and adds it to the public tag hash table. + * \note A fake TagKey is generated so the PubDict can keep it's coherence. + * @param NewTagName The name to be given to this new tag. + * @param VR The Value Representation to be given to this new tag. + * @ return The newly hand crafted Element Value. + */ +gdcmElValue* gdcmHeader::NewManualElValToPubDict(string NewTagName, string VR) { + gdcmElValue* NewElVal = (gdcmElValue*)0; + guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info + guint32 FreeElem = 0; + gdcmDictEntry* NewEntry = (gdcmDictEntry*)0; + + FreeElem = PubElValSet.GenerateFreeTagKeyInGroup(StuffGroup); + if (FreeElem == UINT32_MAX) { + dbg.Verbose(1, "gdcmHeader::NewManualElValToPubDict", + "Group 0xffff in Public Dict is full"); + return (gdcmElValue*)0; + } + NewEntry = new gdcmDictEntry(StuffGroup, FreeElem, + VR, "GDCM", NewTagName); + NewElVal = new gdcmElValue(NewEntry); + PubElValSet.Add(NewElVal); + return NewElVal; - NewEntry = NewElValueByName("gdcmZSize"); - NewEntry->SetValue(GetElValByName("Planes")); - PubElVals.Add(NewEntry); } /** @@ -1417,16 +1531,20 @@ void gdcmHeader::AddAndDefaultElements(void) { */ void gdcmHeader::LoadElements(void) { rewind(fp); - TagElValueHT ht = PubElVals.GetTagHt(); + TagElValueHT ht = PubElValSet.GetTagHt(); for (TagElValueHT::iterator tag = ht.begin(); tag != ht.end(); ++tag) { LoadElementValue(tag->second); } } void gdcmHeader::PrintPubElVal(ostream & os) { - PubElVals.Print(os); + PubElValSet.Print(os); } void gdcmHeader::PrintPubDict(ostream & os) { RefPubDict->Print(os); } + +int gdcmHeader::Write(FILE * fp, FileType type) { + return PubElValSet.Write(fp, type); +}