X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=002aed724d6b6b5b27e84427cb6fc68248b9dc44;hb=00bc08e9b8fd5aadac41221a071783ef3d485f94;hp=6a6a277ae681c7250ebbbfbed2da5cdff66be044;hpb=dcbbe0ecd3fe72f4b97aee8ee6145d06063400cb;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index 6a6a277a..002aed72 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -1,4 +1,4 @@ -// gdcmHeader.cxx +// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.65 2003/05/12 14:32:43 frog Exp $ #include #include @@ -13,81 +13,89 @@ #include "gdcmUtil.h" #include "gdcmHeader.h" -#include - // Refer to gdcmHeader::CheckSwap() #define HEADER_LENGTH_TO_READ 256 // Refer to gdcmHeader::SetMaxSizeLoadElementValue() #define _MaxSizeLoadElementValue_ 1024 -VRHT * gdcmHeader::dicom_vr = (VRHT*)0; - void gdcmHeader::Initialise(void) { - if (!gdcmHeader::dicom_vr) - InitVRDict(); - Dicts = new gdcmDictSet(); + dicom_vr = gdcmGlobal::GetVR(); + Dicts = gdcmGlobal::GetDicts(); RefPubDict = Dicts->GetDefaultPubDict(); RefShaDict = (gdcmDict*)0; } -gdcmHeader::gdcmHeader(const char *InFilename, bool exception_on_error) - throw(gdcmFileError) { +gdcmHeader::gdcmHeader(const char *InFilename, bool exception_on_error) { SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_); filename = InFilename; Initialise(); - fp=fopen(InFilename,"rb"); + if ( !OpenFile(exception_on_error)) + return; + ParseHeader(); + LoadElements(); + CloseFile(); +} + +bool gdcmHeader::OpenFile(bool exception_on_error) + throw(gdcmFileError) { + fp=fopen(filename.c_str(),"rb"); if(exception_on_error) { if(!fp) throw gdcmFileError("gdcmHeader::gdcmHeader(const char *, bool)"); } - else - dbg.Error(!fp, "gdcmHeader::gdcmHeader cannot open file", InFilename); - ParseHeader(); - LoadElements(); - AddAndDefaultElements(); + if ( fp ) + return true; + dbg.Verbose(0, "gdcmHeader::gdcmHeader cannot open file", filename.c_str()); + return false; } +bool gdcmHeader::CloseFile(void) { + int closed = fclose(fp); + fp = (FILE *)0; + if (! closed) + return false; + return true; +} gdcmHeader::~gdcmHeader (void) { - //FIXME obviously there is much to be done here ! - fclose(fp); + dicom_vr = (gdcmVR*)0; + Dicts = (gdcmDictSet*)0; + RefPubDict = (gdcmDict*)0; + RefShaDict = (gdcmDict*)0; return; } -void gdcmHeader::InitVRDict (void) { - if (dicom_vr) { - dbg.Verbose(0, "gdcmHeader::InitVRDict:", "VR dictionary allready set"); - return; - } - VRHT *vr = new VRHT; - (*vr)["AE"] = "Application Entity"; // At most 16 bytes - (*vr)["AS"] = "Age String"; // Exactly 4 bytes - (*vr)["AT"] = "Attribute Tag"; // 2 16-bit unsigned short integers - (*vr)["CS"] = "Code String"; // At most 16 bytes - (*vr)["DA"] = "Date"; // Exactly 8 bytes - (*vr)["DS"] = "Decimal String"; // At most 16 bytes - (*vr)["DT"] = "Date Time"; // At most 26 bytes - (*vr)["FL"] = "Floating Point Single"; // 32-bit IEEE 754:1985 float - (*vr)["FD"] = "Floating Point Double"; // 64-bit IEEE 754:1985 double - (*vr)["IS"] = "Integer String"; // At most 12 bytes - (*vr)["LO"] = "Long String"; // At most 64 chars - (*vr)["LT"] = "Long Text"; // At most 10240 chars - (*vr)["OB"] = "Other Byte String"; // String of bytes (vr independant) - (*vr)["OW"] = "Other Word String"; // String of 16-bit words (vr dep) - (*vr)["PN"] = "Person Name"; // At most 64 chars - (*vr)["SH"] = "Short String"; // At most 16 chars - (*vr)["SL"] = "Signed Long"; // Exactly 4 bytes - (*vr)["SQ"] = "Sequence of Items"; // Not Applicable - (*vr)["SS"] = "Signed Short"; // Exactly 2 bytes - (*vr)["ST"] = "Short Text"; // At most 1024 chars - (*vr)["TM"] = "Time"; // At most 16 bytes - (*vr)["UI"] = "Unique Identifier"; // At most 64 bytes - (*vr)["UL"] = "Unsigned Long "; // Exactly 4 bytes - (*vr)["UN"] = "Unknown"; // Any length of bytes - (*vr)["US"] = "Unsigned Short "; // Exactly 2 bytes - (*vr)["UT"] = "Unlimited Text"; // At most 2^32 -1 chars - dicom_vr = vr; -} +// Fourth semantics: +// CMD Command +// META Meta Information +// DIR Directory +// ID +// PAT Patient +// ACQ Acquisition +// REL Related +// IMG Image +// SDY Study +// VIS Visit +// WAV Waveform +// PRC +// DEV Device +// NMI Nuclear Medicine +// MED +// BFS Basic Film Session +// BFB Basic Film Box +// BIB Basic Image Box +// BAB +// IOB +// PJ +// PRINTER +// RT Radio Therapy +// DVH +// SSET +// RES Results +// CRV Curve +// OLY Overlays +// PXL Pixels +// /** * \ingroup gdcmHeader @@ -122,14 +130,7 @@ 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" // - or "OB" if the 1st one is (0002,0001) -, @@ -146,8 +147,12 @@ void gdcmHeader::CheckSwap() // * the 4 bytes of the first tag (0002, 0000),or (0002, 0001) // i.e. a total of 136 bytes. entCur = deb + 136; + // 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, "OB", (size_t)2) == 0) || + (memcmp(entCur, "UI", (size_t)2) == 0) ) { filetype = ExplicitVR; dbg.Verbose(1, "gdcmHeader::CheckSwap:", @@ -173,11 +178,12 @@ 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. @@ -217,6 +223,7 @@ 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 @@ -243,19 +250,6 @@ void gdcmHeader::SwitchSwapToBigEndian(void) { sw = 3412; } -void gdcmHeader::GetPixels(size_t lgrTotale, void* _Pixels) { - size_t pixelsOffset; - pixelsOffset = GetPixelOffset(); - fseek(fp, pixelsOffset, SEEK_SET); - if (IsJPEGLossless()) { - _Pixels=_IdDcmJpegRead(fp); - } else { - fread(_Pixels, 1, lgrTotale, fp); - } -} - - - /** * \ingroup gdcmHeader * \brief Find the value representation of the current tag. @@ -295,7 +289,7 @@ void gdcmHeader::FindVR( gdcmElValue *ElVal) { // CLEANME searching the dicom_vr at each occurence is expensive. // PostPone this test in an optional integrity check at the end // of parsing or only in debug mode. - if ( RealExplicit && !dicom_vr->count(vr) ) + if ( RealExplicit && !dicom_vr->Count(vr) ) RealExplicit= false; if ( RealExplicit ) { @@ -344,7 +338,7 @@ void gdcmHeader::FindVR( gdcmElValue *ElVal) { * @return True when ImplicitVRLittleEndian found. False in all other cases. */ bool gdcmHeader::IsImplicitVRLittleEndianTransferSyntax(void) { - gdcmElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -362,7 +356,7 @@ bool gdcmHeader::IsImplicitVRLittleEndianTransferSyntax(void) { * @return True when ExplicitVRLittleEndian found. False in all other cases. */ bool gdcmHeader::IsExplicitVRLittleEndianTransferSyntax(void) { - gdcmElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -380,7 +374,7 @@ bool gdcmHeader::IsExplicitVRLittleEndianTransferSyntax(void) { * @return True when DeflatedExplicitVRLittleEndian found. False in all other cases. */ bool gdcmHeader::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) { - gdcmElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -398,7 +392,7 @@ bool gdcmHeader::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) { * @return True when big endian found. False in all other cases. */ bool gdcmHeader::IsExplicitVRBigEndianTransferSyntax(void) { - gdcmElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -416,7 +410,7 @@ bool gdcmHeader::IsExplicitVRBigEndianTransferSyntax(void) { * @return True when JPEGBaseLineProcess1found. False in all other cases. */ bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) { - gdcmElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -429,11 +423,12 @@ bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) { // faire qq chose d'intelligent a la place de ça bool gdcmHeader::IsJPEGLossless(void) { - gdcmElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); const char * Transfert = Element->GetValue().c_str(); + printf("TransfertSyntx %s\n",Transfert); if ( memcmp(Transfert+strlen(Transfert)-2 ,"70",2)==0) return true; if ( memcmp(Transfert+strlen(Transfert)-2 ,"55",2)==0) return true; return false; @@ -448,7 +443,7 @@ bool gdcmHeader::IsJPEGLossless(void) { * @return True when JPEGExtendedProcess2-4 found. False in all other cases. */ bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) { - gdcmElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -466,7 +461,7 @@ bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) { * @return True when JPEGExtendedProcess3-5 found. False in all other cases. */ bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) { - gdcmElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -485,7 +480,7 @@ bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) { * other cases. */ bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) { - gdcmElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -494,6 +489,17 @@ 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 @@ -608,7 +614,8 @@ void gdcmHeader::FindLength(gdcmElValue * ElVal) { // and the dictionary entry depending on them. guint16 CorrectGroup = SwapShort(ElVal->GetGroup()); guint16 CorrectElem = SwapShort(ElVal->GetElement()); - gdcmDictEntry * NewTag = GetDictEntryByKey(CorrectGroup, CorrectElem); + gdcmDictEntry * NewTag = GetDictEntryByNumber(CorrectGroup, + CorrectElem); if (!NewTag) { // This correct tag is not in the dictionary. Create a new one. NewTag = new gdcmDictEntry(CorrectGroup, CorrectElem); @@ -645,7 +652,6 @@ void gdcmHeader::FindLength(gdcmElValue * 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; @@ -776,7 +782,6 @@ void gdcmHeader::LoadElementValue(gdcmElValue * ElVal) { s << '\\'; NewInt = ReadInt16(); s << NewInt; - //printf("%s\n", s.str().c_str()); } } @@ -796,7 +801,7 @@ void gdcmHeader::LoadElementValue(gdcmElValue * ElVal) { return; } - // FIXME The exact size should be length if we move to strings or whatever + // We need an additional byte for storing \0 that is not on disk char* NewValue = (char*)malloc(length+1); if( !NewValue) { dbg.Verbose(1, "LoadElementValue: Failed to allocate NewValue"); @@ -812,6 +817,7 @@ void gdcmHeader::LoadElementValue(gdcmElValue * ElVal) { return; } ElVal->SetValue(NewValue); + free(NewValue); } /** @@ -857,6 +863,18 @@ guint32 gdcmHeader::ReadInt32(void) { return g; } + +gdcmElValue* gdcmHeader::GetElValueByNumber(guint16 Group, guint16 Elem) { + + gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem); + if (!elValue) { + dbg.Verbose(1, "gdcmHeader::GetElValueByNumber", + "failed to Locate gdcmElValue"); + return (gdcmElValue*)0; + } + return elValue; +} + /** * \ingroup gdcmHeader * \brief Build a new Element Value from all the low level arguments. @@ -865,21 +883,35 @@ guint32 gdcmHeader::ReadInt32(void) { * @param Group group of the underlying DictEntry * @param Elem element of the underlying DictEntry */ -gdcmElValue* gdcmHeader::NewElValueByKey(guint16 Group, guint16 Elem) { +gdcmElValue* gdcmHeader::NewElValueByNumber(guint16 Group, guint16 Elem) { // Find out if the tag we encountered is in the dictionaries: - gdcmDictEntry * NewTag = GetDictEntryByKey(Group, Elem); + gdcmDictEntry * NewTag = GetDictEntryByNumber(Group, Elem); if (!NewTag) NewTag = new gdcmDictEntry(Group, Elem); gdcmElValue* NewElVal = new gdcmElValue(NewTag); if (!NewElVal) { - dbg.Verbose(1, "gdcmHeader::NewElValueByKey", + dbg.Verbose(1, "gdcmHeader::NewElValueByNumber", "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=NewElValueByNumber(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. @@ -908,8 +940,8 @@ gdcmElValue* gdcmHeader::NewElValueByName(string Name) { * @return On succes the newly created ElValue, NULL on failure. */ gdcmElValue * gdcmHeader::ReadNextElement(void) { - guint16 g; - guint16 n; + + guint16 g,n; gdcmElValue * NewElVal; g = ReadInt16(); @@ -919,7 +951,7 @@ gdcmElValue * gdcmHeader::ReadNextElement(void) { // has to be considered as finished. return (gdcmElValue *)0; - NewElVal = NewElValueByKey(g, n); + NewElVal = NewElValueByNumber(g, n); FindVR(NewElVal); FindLength(NewElVal); if (errno == 1) @@ -948,48 +980,18 @@ bool gdcmHeader::IsAnInteger(gdcmElValue * 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 (%04x , %04x) : %d\n", + group, element,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; } @@ -1004,7 +1006,7 @@ 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"); @@ -1014,12 +1016,12 @@ 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; - gdcmElValue* PixelElement = PubElVals.GetElementByNumber(grPixel, numPixel); + gdcmElValue* PixelElement = PubElValSet.GetElementByNumber(grPixel, + numPixel); if (PixelElement) return PixelElement->GetOffset(); else @@ -1036,19 +1038,20 @@ size_t gdcmHeader::GetPixelOffset(void) { * @param element element of the searched DictEntry * @return Corresponding DictEntry when it exists, NULL otherwise. */ -gdcmDictEntry * gdcmHeader::GetDictEntryByKey(guint16 group, guint16 element) { +gdcmDictEntry * gdcmHeader::GetDictEntryByNumber(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) { - found = RefPubDict->GetTagByKey(group, element); + found = RefPubDict->GetTagByNumber(group, element); if (found) return found; } if (RefShaDict) { - found = RefShaDict->GetTagByKey(group, element); + found = RefShaDict->GetTagByNumber(group, element); if (found) return found; } @@ -1066,7 +1069,7 @@ 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) { @@ -1092,7 +1095,7 @@ 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); } /** @@ -1110,7 +1113,7 @@ string gdcmHeader::GetPubElValByNumber(guint16 group, guint16 element) { * and the string "gdcm::Unfound" otherwise. */ string gdcmHeader::GetPubElValRepByNumber(guint16 group, guint16 element) { - gdcmElValue* elem = PubElVals.GetElementByNumber(group, element); + gdcmElValue* elem = PubElValSet.GetElementByNumber(group, element); if ( !elem ) return "gdcm::Unfound"; return elem->GetVR(); @@ -1125,7 +1128,7 @@ string gdcmHeader::GetPubElValRepByNumber(guint16 group, guint16 element) { * "gdcm::Unfound" otherwise. */ string gdcmHeader::GetPubElValByName(string TagName) { - return PubElVals.GetElValueByName(TagName); + return PubElValSet.GetElValueByName(TagName); } /** @@ -1142,7 +1145,7 @@ string gdcmHeader::GetPubElValByName(string TagName) { * and the string "gdcm::Unfound" otherwise. */ string gdcmHeader::GetPubElValRepByName(string TagName) { - gdcmElValue* elem = PubElVals.GetElementByName(TagName); + gdcmElValue* elem = PubElValSet.GetElementByName(TagName); if ( !elem ) return "gdcm::Unfound"; return elem->GetVR(); @@ -1158,7 +1161,7 @@ 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); } /** @@ -1176,7 +1179,7 @@ string gdcmHeader::GetShaElValByNumber(guint16 group, guint16 element) { * and the string "gdcm::Unfound" otherwise. */ string gdcmHeader::GetShaElValRepByNumber(guint16 group, guint16 element) { - gdcmElValue* elem = ShaElVals.GetElementByNumber(group, element); + gdcmElValue* elem = ShaElValSet.GetElementByNumber(group, element); if ( !elem ) return "gdcm::Unfound"; return elem->GetVR(); @@ -1191,7 +1194,7 @@ string gdcmHeader::GetShaElValRepByNumber(guint16 group, guint16 element) { * "gdcm::Unfound" otherwise. */ string gdcmHeader::GetShaElValByName(string TagName) { - return ShaElVals.GetElValueByName(TagName); + return ShaElValSet.GetElValueByName(TagName); } /** @@ -1208,7 +1211,7 @@ string gdcmHeader::GetShaElValByName(string TagName) { * and the string "gdcm::Unfound" otherwise. */ string gdcmHeader::GetShaElValRepByName(string TagName) { - gdcmElValue* elem = ShaElVals.GetElementByName(TagName); + gdcmElValue* elem = ShaElValSet.GetElementByName(TagName); if ( !elem ) return "gdcm::Unfound"; return elem->GetVR(); @@ -1292,7 +1295,7 @@ string gdcmHeader::GetElValRepByName(string TagName) { /** * \ingroup gdcmHeader - * \brief Accesses an existing gdcmElValue 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 @@ -1301,61 +1304,66 @@ string gdcmHeader::GetElValRepByName(string TagName) { */ int gdcmHeader::SetPubElValByNumber(string content, guint16 group, guint16 element) + +//TODO : homogeneiser les noms : SetPubElValByNumber qui appelle PubElValSet.SetElValueByNumber +// pourquoi pas SetPubElValueByNumber ?? { - return ( PubElVals.SetElValueByNumber (content, group, element) ); + + return ( PubElValSet.SetElValueByNumber (content, group, element) ); } /** * \ingroup gdcmHeader - * \brief Accesses an existing gdcmElValue 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 gdcmElValue 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 gdcmElValue 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 gdcmElValue 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) ); } /** @@ -1369,51 +1377,122 @@ void gdcmHeader::ParseHeader(bool exception_on_error) throw(gdcmFormatError) { 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 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) - * 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) { - 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); +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()); +} + +/** + * \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 - NewElVal->SetValue("0"); + // 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; +} + +/** + * \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 Return the size (in bytes) of a single pixel of data. + * @return The size in bytes of a single pixel of data. + * + */ +int gdcmHeader::GetPixelSize(void) { + string PixelType = GetPixelType(); + if (PixelType == "8U" || PixelType == "8S") + return 1; + if (PixelType == "16U" || PixelType == "16S") + return 2; + if (PixelType == "32U" || PixelType == "32S") + return 4; + dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type"); + return 0; +} - NewElVal = NewManualElValToPubDict("gdcmZSize", "US"); - if (!NewElVal) return; - NewVal = GetElValByName("Planes"); - if (NewVal != "gdcm::Unfound") - NewElVal->SetValue(NewVal); +/** + * \ingroup gdcmHeader + * \brief Build the Pixel Type of the image. + * Possible values are: + * - 8U unsigned 8 bit, + * - 8S signed 8 bit, + * - 16U unsigned 16 bit, + * - 16S signed 16 bit, + * - 32U unsigned 32 bit, + * - 32S 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 - NewElVal->SetValue("0"); + Signed = string("S"); + + return( BitsAlloc + Signed); } /** @@ -1441,13 +1520,11 @@ bool gdcmHeader::IsReadable(void) { 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. - * 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. @@ -1459,7 +1536,7 @@ gdcmElValue* gdcmHeader::NewManualElValToPubDict(string NewTagName, string VR) { guint32 FreeElem = 0; gdcmDictEntry* NewEntry = (gdcmDictEntry*)0; - FreeElem = PubElVals.GenerateFreeTagKeyInGroup(StuffGroup); + FreeElem = PubElValSet.GenerateFreeTagKeyInGroup(StuffGroup); if (FreeElem == UINT32_MAX) { dbg.Verbose(1, "gdcmHeader::NewManualElValToPubDict", "Group 0xffff in Public Dict is full"); @@ -1468,8 +1545,9 @@ gdcmElValue* gdcmHeader::NewManualElValToPubDict(string NewTagName, string VR) { NewEntry = new gdcmDictEntry(StuffGroup, FreeElem, VR, "GDCM", NewTagName); NewElVal = new gdcmElValue(NewEntry); - PubElVals.Add(NewElVal); + PubElValSet.Add(NewElVal); return NewElVal; + } /** @@ -1479,16 +1557,20 @@ gdcmElValue* gdcmHeader::NewManualElValToPubDict(string NewTagName, string VR) { */ 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); +}