X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=a16d0693841a40f35696f18e52fc917dd1c5aebd;hb=f41fb331c46df02fd4e284960f0473d7155573a2;hp=38763a3af7dac7d28fc142e18dc93dc45f674a74;hpb=21dc537d0c6c274bf1bc49084813a9f4e4cf29eb;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index 38763a3a..a16d0693 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -13,6 +13,8 @@ #include "gdcmUtil.h" #include "gdcmHeader.h" +#include + // Refer to gdcmHeader::CheckSwap() #define HEADER_LENGTH_TO_READ 256 // Refer to gdcmHeader::SetMaxSizeLoadElementValue() @@ -41,6 +43,7 @@ gdcmHeader::gdcmHeader(const char *InFilename, bool exception_on_error) else dbg.Error(!fp, "gdcmHeader::gdcmHeader cannot open file", InFilename); ParseHeader(); + LoadElements(); AddAndDefaultElements(); } @@ -128,8 +131,9 @@ void gdcmHeader::CheckSwap() 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 +143,12 @@ 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) { + if( (memcmp(entCur, "UL", (size_t)2) == 0) || + (memcmp(entCur, "OB", (size_t)2) == 0) ) + { filetype = ExplicitVR; dbg.Verbose(1, "gdcmHeader::CheckSwap:", "explicit Value Representation"); @@ -241,7 +247,11 @@ 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 +260,7 @@ 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 +296,7 @@ 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 +344,7 @@ 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 = PubElVals.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -352,7 +362,7 @@ 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 = PubElVals.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -370,7 +380,7 @@ 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 = PubElVals.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -388,12 +398,12 @@ 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 = PubElVals.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 +416,7 @@ 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 = PubElVals.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -416,6 +426,20 @@ bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) { return false; } +// faire qq chose d'intelligent a la place de ça + +bool gdcmHeader::IsJPEGLossless(void) { + gdcmElValue* Element = PubElVals.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 +448,7 @@ 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 = PubElVals.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -442,7 +466,7 @@ 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 = PubElVals.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -461,7 +485,7 @@ bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) { * other cases. */ bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) { - ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -477,7 +501,7 @@ 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 +545,7 @@ 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; @@ -660,7 +684,7 @@ 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 +704,7 @@ 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(); @@ -706,16 +730,7 @@ 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; @@ -741,21 +756,44 @@ void gdcmHeader::LoadElementValue(ElValue * 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. - 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; - } + + // pour les elements de Value Multiplicity > 1 + // on aura en fait une serie d'entiers + + // on devrait pouvoir faire + compact (?) + + if ( IsAnInteger(ElVal) ) { + guint32 NewInt; + ostringstream s; + int nbInt; + if (vr == "US" || vr == "SS") { + nbInt = length / 2; + NewInt = ReadInt16(); + s << NewInt; + if (nbInt > 1) { + for (int i=1; i < nbInt; i++) { + s << '\\'; + NewInt = ReadInt16(); + s << NewInt; + //printf("%s\n", s.str().c_str()); + } + } + + } else if (vr == "UL" || vr == "SL") { + nbInt = length / 4; + NewInt = ReadInt32(); + s << NewInt; + if (nbInt > 1) { + for (int i=1; i < nbInt; i++) { + s << '\\'; + NewInt = ReadInt32(); + s << NewInt; + } + } + } + ElVal->SetValue(s.str()); + return; + } // FIXME The exact size should be length if we move to strings or whatever char* NewValue = (char*)malloc(length+1); @@ -783,7 +821,7 @@ 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); @@ -826,17 +864,17 @@ 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; } @@ -848,17 +886,17 @@ 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; } @@ -868,24 +906,24 @@ 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) { +gdcmElValue * gdcmHeader::ReadNextElement(void) { guint16 g; guint16 n; - ElValue * NewElVal; + 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; } @@ -897,7 +935,7 @@ 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(); @@ -980,7 +1018,7 @@ size_t gdcmHeader::GetPixelOffset(void) { numPixel = 0x1010; else numPixel = 0x0010; - ElValue* PixelElement = PubElVals.GetElementByNumber(grPixel, numPixel); + gdcmElValue* PixelElement = PubElVals.GetElementByNumber(grPixel, numPixel); if (PixelElement) return PixelElement->GetOffset(); else @@ -1071,7 +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 = PubElVals.GetElementByNumber(group, element); if ( !elem ) return "gdcm::Unfound"; return elem->GetVR(); @@ -1103,7 +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 = PubElVals.GetElementByName(TagName); if ( !elem ) return "gdcm::Unfound"; return elem->GetVR(); @@ -1137,7 +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 = ShaElVals.GetElementByNumber(group, element); if ( !elem ) return "gdcm::Unfound"; return elem->GetVR(); @@ -1169,7 +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 = ShaElVals.GetElementByName(TagName); if ( !elem ) return "gdcm::Unfound"; return elem->GetVR(); @@ -1253,7 +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 PubElVals of this instance * through it's (group, element) and modifies it's content with * the given value. * @param content new value to substitute with @@ -1268,7 +1306,7 @@ int gdcmHeader::SetPubElValByNumber(string content, guint16 group, /** * \ingroup gdcmHeader - * \brief Accesses an existing ElValue in the PubElVals of this instance + * \brief Accesses an existing gdcmElValue in the PubElVals 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 @@ -1279,7 +1317,7 @@ int gdcmHeader::SetPubElValByName(string content, string TagName) { /** * \ingroup gdcmHeader - * \brief Accesses an existing ElValue in the PubElVals of this instance + * \brief Accesses an existing gdcmElValue in the PubElVals of this instance * through it's (group, element) and modifies it's length with * the given value. * NOT FOR BOZOs ! @@ -1295,7 +1333,7 @@ int gdcmHeader::SetPubElValLengthByNumber(guint32 lgr, guint16 group, /** * \ingroup gdcmHeader - * \brief Accesses an existing ElValue in the ShaElVals of this instance + * \brief Accesses an existing gdcmElValue in the ShaElVals of this instance * through it's (group, element) and modifies it's content with * the given value. * @param content new value to substitute with @@ -1308,12 +1346,9 @@ int gdcmHeader::SetShaElValByNumber(string content, return ( ShaElVals.SetElValueByNumber (content, group, element) ); } - - - /** * \ingroup gdcmHeader - * \brief Accesses an existing ElValue in the ShaElVals of this instance + * \brief Accesses an existing gdcmElValue in the ShaElVals 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 @@ -1327,7 +1362,7 @@ 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(); @@ -1340,7 +1375,7 @@ void gdcmHeader::ParseHeader(bool exception_on_error) throw(gdcmFormatError) { /** * \ingroup gdcmHeader * \brief Once the header is parsed add some gdcm convenience/helper elements - * in the ElValSet. For example add: + * in the gdcmElValSet. 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) @@ -1350,19 +1385,64 @@ void gdcmHeader::ParseHeader(bool exception_on_error) throw(gdcmFormatError) { * the ones of the official DICOM fields Rows, Columns and Planes. */ void gdcmHeader::AddAndDefaultElements(void) { - ElValue* NewEntry = (ElValue*)0; + gdcmElValue* NewElVal = (gdcmElValue*)0; + string NewVal; + + NewElVal = NewManualElValToPubDict("gdcmXSize", "US"); + if (!NewElVal) return; + NewVal = GetElValByName("Rows"); + if (NewVal != "gdcm::Unfound") + NewElVal->SetValue(NewVal); + else + NewElVal->SetValue("0"); + + + NewElVal = NewManualElValToPubDict("gdcmYSize", "US"); + if (!NewElVal) return; + NewVal = GetElValByName("Columns"); + if (NewVal != "gdcm::Unfound") + NewElVal->SetValue(NewVal); + else + NewElVal->SetValue("0"); - NewEntry = NewElValueByName("gdcmXSize"); - NewEntry->SetValue(GetElValByName("Rows")); - PubElVals.Add(NewEntry); - NewEntry = NewElValueByName("gdcmYSize"); - NewEntry->SetValue(GetElValByName("Columns")); - PubElVals.Add(NewEntry); + NewElVal = NewManualElValToPubDict("gdcmZSize", "US"); + if (!NewElVal) return; + NewVal = GetElValByName("Planes"); + if (NewVal != "gdcm::Unfound") + NewElVal->SetValue(NewVal); + else + NewElVal->SetValue("0"); +} - NewEntry = NewElValueByName("gdcmZSize"); - NewEntry->SetValue(GetElValByName("Planes")); - PubElVals.Add(NewEntry); +/** + * \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. + * Refer to gdcmHeader::AddAndDefaultElements for a typical usage. + * \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 = PubElVals.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); + PubElVals.Add(NewElVal); + return NewElVal; } /**