X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=b92ba73707ebc92c146bf93a7cbd741433676721;hb=264e66944696bde25a73a246163731a820304ad9;hp=d98074f56aea75c3da92ba280bee6fb97edce8ef;hpb=ec7826d8a6e9f1bfb58ab5c6ec45702a5b3fa30d;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index d98074f5..b92ba737 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -1,4 +1,5 @@ -// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.62 2003/05/06 15:52:13 jpr Exp $ + +// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.78 2003/07/03 14:38:16 jpr Exp $ #include #include @@ -12,43 +13,80 @@ #include #include "gdcmUtil.h" #include "gdcmHeader.h" +using namespace std; + + +// TODO : remove DEBUG +#define DEBUG 0 // Refer to gdcmHeader::CheckSwap() #define HEADER_LENGTH_TO_READ 256 // Refer to gdcmHeader::SetMaxSizeLoadElementValue() #define _MaxSizeLoadElementValue_ 1024 +/** + * \ingroup gdcmHeader + * \brief + */ void gdcmHeader::Initialise(void) { dicom_vr = gdcmGlobal::GetVR(); - Dicts = gdcmGlobal::GetDicts(); + dicom_ts = gdcmGlobal::GetTS(); + Dicts = gdcmGlobal::GetDicts(); RefPubDict = Dicts->GetDefaultPubDict(); RefShaDict = (gdcmDict*)0; } +/** + * \ingroup gdcmHeader + * \brief + * @param InFilename + * @param exception_on_error + */ gdcmHeader::gdcmHeader(const char *InFilename, bool exception_on_error) { + SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_); + filename = InFilename; + Initialise(); + if ( !OpenFile(exception_on_error)) + return; + ParseHeader(); + LoadElements(); + CloseFile(); +} + +/** + * \ingroup gdcmHeader + * \brief + * @param exception_on_error + */ +gdcmHeader::gdcmHeader(bool exception_on_error) { SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_); - filename = InFilename; Initialise(); - OpenFile(exception_on_error); - ParseHeader(); - LoadElements(); - CloseFile(); } -bool gdcmHeader::OpenFile(bool exception_on_error) +/** + * \ingroup gdcmHeader + * \brief + * @param exception_on_error + * @return + */ + 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", filename.c_str()); if ( fp ) return true; + dbg.Verbose(0, "gdcmHeader::gdcmHeader cannot open file", filename.c_str()); return false; } +/** + * \ingroup gdcmHeader + * \brief + * @return + */ bool gdcmHeader::CloseFile(void) { int closed = fclose(fp); fp = (FILE *)0; @@ -57,9 +95,13 @@ bool gdcmHeader::CloseFile(void) { return true; } +/** + * \ingroup gdcmHeader + * \brief Canonical destructor. + */ gdcmHeader::~gdcmHeader (void) { - dicom_vr = (gdcmVR*)0; - Dicts = (gdcmDictSet*)0; + dicom_vr = (gdcmVR*)0; + Dicts = (gdcmDictSet*)0; RefPubDict = (gdcmDict*)0; RefShaDict = (gdcmDict*)0; return; @@ -151,9 +193,9 @@ void gdcmHeader::CheckSwap() // 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) ) - { + (memcmp(entCur, "OB", (size_t)2) == 0) || + (memcmp(entCur, "UI", (size_t)2) == 0) ) + { filetype = ExplicitVR; dbg.Verbose(1, "gdcmHeader::CheckSwap:", "explicit Value Representation"); @@ -162,7 +204,6 @@ void gdcmHeader::CheckSwap() dbg.Verbose(1, "gdcmHeader::CheckSwap:", "not an explicit Value Representation"); } - if (net2host) { sw = 4321; dbg.Verbose(1, "gdcmHeader::CheckSwap:", @@ -231,6 +272,10 @@ void gdcmHeader::CheckSwap() return; } +/** + * \ingroup gdcmHeader + * \brief + */ void gdcmHeader::SwitchSwapToBigEndian(void) { dbg.Verbose(1, "gdcmHeader::SwitchSwapToBigEndian", "Switching to BigEndian mode."); @@ -253,6 +298,7 @@ void gdcmHeader::SwitchSwapToBigEndian(void) { /** * \ingroup gdcmHeader * \brief Find the value representation of the current tag. + * @param ElVal */ void gdcmHeader::FindVR( gdcmElValue *ElVal) { if (filetype != ExplicitVR) @@ -261,6 +307,8 @@ void gdcmHeader::FindVR( gdcmElValue *ElVal) { char VR[3]; string vr; int lgrLue; + char msg[100]; // for sprintf. Sorry + long PositionOnEntry = ftell(fp); // Warning: we believe this is explicit VR (Value Representation) because // we used a heuristic that found "UL" in the first tag. Alas this @@ -317,8 +365,11 @@ void gdcmHeader::FindVR( gdcmElValue *ElVal) { } // We thought this was explicit VR, but we end up with an - // implicit VR tag. Let's backtrack. - dbg.Verbose(1, "gdcmHeader::FindVR:", "Falsely explicit vr file"); + // implicit VR tag. Let's backtrack. + + sprintf(msg,"Falsely explicit vr file (%04x,%04x)\n", ElVal->GetGroup(),ElVal->GetElement()); + dbg.Verbose(1, "gdcmHeader::FindVR: ",msg); + fseek(fp, PositionOnEntry, SEEK_SET); // When this element is known in the dictionary we shall use, e.g. for // the semantics (see the usage of IsAnInteger), the vr proposed by the @@ -332,7 +383,7 @@ void gdcmHeader::FindVR( gdcmElValue *ElVal) { /** * \ingroup gdcmHeader - * \brief Determines if the Transfer Syntax was allready encountered + * \brief Determines if the Transfer Syntax was already encountered * and if it corresponds to a ImplicitVRLittleEndian one. * * @return True when ImplicitVRLittleEndian found. False in all other cases. @@ -350,7 +401,7 @@ bool gdcmHeader::IsImplicitVRLittleEndianTransferSyntax(void) { /** * \ingroup gdcmHeader - * \brief Determines if the Transfer Syntax was allready encountered + * \brief Determines if the Transfer Syntax was already encountered * and if it corresponds to a ExplicitVRLittleEndian one. * * @return True when ExplicitVRLittleEndian found. False in all other cases. @@ -368,7 +419,7 @@ bool gdcmHeader::IsExplicitVRLittleEndianTransferSyntax(void) { /** * \ingroup gdcmHeader - * \brief Determines if the Transfer Syntax was allready encountered + * \brief Determines if the Transfer Syntax was already encountered * and if it corresponds to a DeflatedExplicitVRLittleEndian one. * * @return True when DeflatedExplicitVRLittleEndian found. False in all other cases. @@ -386,7 +437,7 @@ bool gdcmHeader::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) { /** * \ingroup gdcmHeader - * \brief Determines if the Transfer Syntax was allready encountered + * \brief Determines if the Transfer Syntax was already encountered * and if it corresponds to a Explicit VR Big Endian one. * * @return True when big endian found. False in all other cases. @@ -404,7 +455,7 @@ bool gdcmHeader::IsExplicitVRBigEndianTransferSyntax(void) { /** * \ingroup gdcmHeader - * \brief Determines if the Transfer Syntax was allready encountered + * \brief Determines if the Transfer Syntax was already encountered * and if it corresponds to a JPEGBaseLineProcess1 one. * * @return True when JPEGBaseLineProcess1found. False in all other cases. @@ -420,15 +471,19 @@ bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) { return false; } -// faire qq chose d'intelligent a la place de ça - +/** + * \ingroup gdcmHeader + * \brief + * + * @return + */ bool gdcmHeader::IsJPEGLossless(void) { gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); + // faire qq chose d'intelligent a la place de ça 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; @@ -437,7 +492,7 @@ bool gdcmHeader::IsJPEGLossless(void) { /** * \ingroup gdcmHeader - * \brief Determines if the Transfer Syntax was allready encountered + * \brief Determines if the Transfer Syntax was already encountered * and if it corresponds to a JPEGExtendedProcess2-4 one. * * @return True when JPEGExtendedProcess2-4 found. False in all other cases. @@ -455,7 +510,7 @@ bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) { /** * \ingroup gdcmHeader - * \brief Determines if the Transfer Syntax was allready encountered + * \brief Determines if the Transfer Syntax was already encountered * and if it corresponds to a JPEGExtendeProcess3-5 one. * * @return True when JPEGExtendedProcess3-5 found. False in all other cases. @@ -473,7 +528,7 @@ bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) { /** * \ingroup gdcmHeader - * \brief Determines if the Transfer Syntax was allready encountered + * \brief Determines if the Transfer Syntax was already encountered * and if it corresponds to a JPEGSpectralSelectionProcess6-8 one. * * @return True when JPEGSpectralSelectionProcess6-8 found. False in all @@ -489,6 +544,7 @@ bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) { return true; return false; } + /** * \ingroup gdcmHeader * \brief Predicate for dicom version 3 file. @@ -513,7 +569,13 @@ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { ElVal->SetLength(FoundLength); } -guint32 gdcmHeader::FindLengthOB(void) { +/** + * \ingroup gdcmHeader + * \brief + * + * @return + */ + guint32 gdcmHeader::FindLengthOB(void) { // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data. guint16 g; guint16 n; @@ -525,50 +587,71 @@ guint32 gdcmHeader::FindLengthOB(void) { while ( ! FoundSequenceDelimiter) { g = ReadInt16(); n = ReadInt16(); + + long l = ftell(fp); + if (errno == 1) return 0; TotalLength += 4; // We even have to decount the group and element - if ( g != 0xfffe ) { - dbg.Verbose(1, "gdcmHeader::FindLengthOB: ", - "wrong group for an item sequence."); + + if ( g != 0xfffe && g!=0xb00c ) /*for bogus header */ { + char msg[100]; // for sprintf. Sorry + sprintf(msg,"wrong group (%04x) for an item sequence (%04x,%04x)\n",g, g,n); + dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",msg); + long l = ftell(fp); errno = 1; return 0; } - if ( n == 0xe0dd ) + if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) /* for bogus header */ FoundSequenceDelimiter = true; - else if ( n != 0xe000) { - dbg.Verbose(1, "gdcmHeader::FindLengthOB: ", - "wrong element for an item sequence."); + else if ( n != 0xe000 ){ + char msg[100]; // for sprintf. Sorry + sprintf(msg,"wrong element (%04x) for an item sequence (%04x,%04x)\n",n, g,n); + dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",msg); errno = 1; return 0; } ItemLength = ReadInt32(); TotalLength += ItemLength + 4; // We add 4 bytes since we just read // the ItemLength with ReadInt32 + SkipBytes(ItemLength); } fseek(fp, PositionOnEntry, SEEK_SET); return TotalLength; } -void gdcmHeader::FindLength(gdcmElValue * ElVal) { +/** + * \ingroup gdcmHeader + * \brief + * + * @return + */ + void gdcmHeader::FindLength (gdcmElValue * ElVal) { guint16 element = ElVal->GetElement(); + guint16 group = ElVal->GetGroup(); string vr = ElVal->GetVR(); guint16 length16; + if( (element == 0x0010) && (group == 0x7fe0) ) { + dbg.SetDebug(0); + dbg.Verbose(2, "gdcmHeader::FindLength: ", + "on est sur 7fe0 0010"); + } if ( (filetype == ExplicitVR) && ! ElVal->IsImplicitVr() ) { - if ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") ) { + // The following reserved two bytes (see PS 3.5-2001, section // 7.1.2 Data element structure with explicit vr p27) must be // skipped before proceeding on reading the length on 4 bytes. fseek(fp, 2L, SEEK_CUR); + guint32 length32 = ReadInt32(); if ( (vr == "OB") && (length32 == 0xffffffff) ) { ElVal->SetLength(FindLengthOB()); return; } - FixFoundLength(ElVal, length32); + FixFoundLength(ElVal, length32); return; } @@ -597,12 +680,12 @@ void gdcmHeader::FindLength(gdcmElValue * ElVal) { // We shall use this second strategy. In order to make sure that we // can interpret the presence of an apparently big endian encoded // length of a "Group Length" without committing a big mistake, we - // add an additional check: we look in the allready parsed elements + // add an additional check: we look in the already parsed elements // for the presence of a "Transfer Syntax" whose value has to be "big // endian encoding". When this is the case, chances are we have got our // hands on a big endian encoded file: we switch the swap code to // big endian and proceed... - if ( (element == 0x000) && (length16 == 0x0400) ) { + if ( (element == 0x0000) && (length16 == 0x0400) ) { if ( ! IsExplicitVRBigEndianTransferSyntax() ) { dbg.Verbose(0, "gdcmHeader::FindLength", "not explicit VR"); errno = 1; @@ -685,16 +768,34 @@ guint16 gdcmHeader::SwapShort(guint16 a) { return (a); } -void gdcmHeader::SkipBytes(guint32 NBytes) { +/** + * \ingroup gdcmHeader + * \brief + * + * @return + */ + void gdcmHeader::SkipBytes(guint32 NBytes) { //FIXME don't dump the returned value (void)fseek(fp, (long)NBytes, SEEK_CUR); } -void gdcmHeader::SkipElementValue(gdcmElValue * ElVal) { +/** + * \ingroup gdcmHeader + * \brief + * + * @return + */ + void gdcmHeader::SkipElementValue(gdcmElValue * ElVal) { SkipBytes(ElVal->GetLength()); } -void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) { +/** + * \ingroup gdcmHeader + * \brief + * + * @return + */ + void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) { if (NewSize < 0) return; if ((guint32)NewSize >= (guint32)0xffffffff) { @@ -713,7 +814,6 @@ void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) { void gdcmHeader::LoadElementValue(gdcmElValue * ElVal) { size_t item_read; guint16 group = ElVal->GetGroup(); - guint16 elem = ElVal->GetElement(); string vr = ElVal->GetVR(); guint32 length = ElVal->GetLength(); bool SkipLoad = false; @@ -765,41 +865,40 @@ void gdcmHeader::LoadElementValue(gdcmElValue * ElVal) { // 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 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; - } - } + 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; + } + } - } 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; - } + } 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; + } // We need an additional byte for storing \0 that is not on disk char* NewValue = (char*)malloc(length+1); @@ -834,37 +933,61 @@ void gdcmHeader::LoadElementValueSafe(gdcmElValue * ElVal) { fseek(fp, PositionOnEntry, SEEK_SET); } - +/** + * \ingroup gdcmHeader + * \brief + * + * @return + */ guint16 gdcmHeader::ReadInt16(void) { guint16 g; size_t item_read; item_read = fread (&g, (size_t)2,(size_t)1, fp); - errno = 0; if ( item_read != 1 ) { - dbg.Verbose(1, "gdcmHeader::ReadInt16", " File read error"); + // dbg.Verbose(0, "gdcmHeader::ReadInt16", " Failed to read :"); + // if(feof(fp)) + // dbg.Verbose(0, "gdcmHeader::ReadInt16", " End of File encountered"); + if(ferror(fp)) + dbg.Verbose(0, "gdcmHeader::ReadInt16", " File Error"); errno = 1; return 0; } + errno = 0; g = SwapShort(g); return g; } +/** + * \ingroup gdcmHeader + * \brief + * + * @return + */ guint32 gdcmHeader::ReadInt32(void) { guint32 g; size_t item_read; item_read = fread (&g, (size_t)4,(size_t)1, fp); - errno = 0; - if ( item_read != 1 ) { - dbg.Verbose(1, "gdcmHeader::ReadInt32", " File read error"); + if ( item_read != 1 ) { + //dbg.Verbose(0, "gdcmHeader::ReadInt32", " Failed to read :"); + //if(feof(fp)) + // dbg.Verbose(0, "gdcmHeader::ReadInt32", " End of File encountered"); + if(ferror(fp)) + dbg.Verbose(0, "gdcmHeader::ReadInt32", " File Error"); errno = 1; return 0; } + errno = 0; g = SwapLong(g); return g; } - -gdcmElValue* gdcmHeader::GetElValueByNumber(guint16 Group, guint16 Elem) { +/** + * \ingroup gdcmHeader + * \brief + * + * @return + */ + gdcmElValue* gdcmHeader::GetElValueByNumber(guint16 Group, guint16 Elem) { gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem); if (!elValue) { @@ -901,17 +1024,54 @@ gdcmElValue* gdcmHeader::NewElValueByNumber(guint16 Group, guint16 Elem) { /** * \ingroup gdcmHeader * \brief TODO - * @param + * @param Value + * @param Group + * @param Elem */ int gdcmHeader::ReplaceOrCreateByNumber(string Value, guint16 Group, guint16 Elem ) { - gdcmElValue* nvElValue=NewElValueByNumber(Group, Elem); - PubElValSet.Add(nvElValue); - PubElValSet.SetElValueByNumber(Value, Group, Elem); - return(1); + // TODO : FIXME JPRx + // curieux, non ? + // on (je) cree une Elvalue ne contenant pas de valeur + // on l'ajoute au ElValSet + // on affecte une valeur a cette ElValue a l'interieur du ElValSet + // --> devrait pouvoir etre fait + simplement ??? + + gdcmElValue* nvElValue=NewElValueByNumber(Group, Elem); + PubElValSet.Add(nvElValue); + PubElValSet.SetElValueByNumber(Value, Group, Elem); + return(1); } +/** + * \ingroup gdcmHeader + * \brief TODO + * @param Value + * @param Group + * @param Elem + */ +int gdcmHeader::ReplaceOrCreateByNumber(char* Value, guint16 Group, guint16 Elem ) { + + gdcmElValue* nvElValue=NewElValueByNumber(Group, Elem); + PubElValSet.Add(nvElValue); + string v = Value; + PubElValSet.SetElValueByNumber(v, Group, Elem); + return(1); +} + +/** + * \ingroup gdcmHeader + * \brief TODO + * @param Group + * @param Elem + */ + +int gdcmHeader::CheckIfExistByNumber(guint16 Group, guint16 Elem ) { + return (PubElValSet.CheckIfExistByNumber(Group, Elem)); + } + + /** * \ingroup gdcmHeader * \brief Build a new Element Value from all the low level arguments. @@ -946,6 +1106,11 @@ gdcmElValue * gdcmHeader::ReadNextElement(void) { g = ReadInt16(); n = ReadInt16(); + + if ( (g==0x7fe0) && (n==0x0010) ) + if (DEBUG) + printf("in gdcmHeader::ReadNextElement try to read 7fe0 0010 \n"); + if (errno == 1) // We reached the EOF (or an error occured) and header parsing // has to be considered as finished. @@ -954,10 +1119,15 @@ gdcmElValue * gdcmHeader::ReadNextElement(void) { NewElVal = NewElValueByNumber(g, n); FindVR(NewElVal); FindLength(NewElVal); - if (errno == 1) + if (errno == 1) { // Call it quits + if (DEBUG) printf("in gdcmHeader::ReadNextElement : g %04x n %04x errno %d\n",g, n, errno); return (gdcmElValue *)0; - NewElVal->SetOffset(ftell(fp)); + } + NewElVal->SetOffset(ftell(fp)); + if ( (g==0x7fe0) && (n==0x0010) ) + if (DEBUG) + printf("sortie de gdcmHeader::ReadNextElement 7fe0 0010 \n"); return NewElVal; } @@ -981,14 +1151,13 @@ bool gdcmHeader::IsAnInteger(gdcmElValue * ElVal) { if (length == 4) return true; else { - printf("Erroneous Group Length element length (%04x , %04x) : %d\n", + if (DEBUG) printf("Erroneous Group Length element length (%04x , %04x) : %d\n", group, element,length); dbg.Error("gdcmHeader::IsAnInteger", "Erroneous Group Length element length."); } } - if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") ) return true; @@ -1020,6 +1189,7 @@ size_t gdcmHeader::GetPixelOffset(void) { numPixel = 0x1010; else numPixel = 0x0010; + gdcmElValue* PixelElement = PubElValSet.GetElementByNumber(grPixel, numPixel); if (PixelElement) @@ -1360,10 +1530,10 @@ int gdcmHeader::SetShaElValByNumber(string content, * \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 + * @param ShadowTagName name of the tag to be modified */ -int gdcmHeader::SetShaElValByName(string content, string TagName) { - return ( ShaElValSet.SetElValueByName (content, TagName) ); +int gdcmHeader::SetShaElValByName(string content, string ShadowTagName) { + return ( ShaElValSet.SetElValueByName (content, ShadowTagName) ); } /** @@ -1381,6 +1551,109 @@ void gdcmHeader::ParseHeader(bool exception_on_error) throw(gdcmFormatError) { } } +/** + * \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; +} + +/** + * \ingroup gdcmHeader + * \brief Loads the element values of all the elements present in the + * 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); + } +} + +/** + * \ingroup gdcmHeader + * \brief + * @return + */ +void gdcmHeader::PrintPubElVal(std::ostream & os) { + PubElValSet.Print(os); +} + +/** + * \ingroup gdcmHeader + * \brief + * @return + */ +void gdcmHeader::PrintPubDict(std::ostream & os) { + RefPubDict->Print(os); +} + +/** + * \ingroup gdcmHeader + * \brief + * @return + */ +int gdcmHeader::Write(FILE * fp, FileType type) { + return PubElValSet.Write(fp, type); +} + +// +// ============================================================================= +// Accesors with euristics +//============================================================================== +// + +// TODO : move to an other file. + + /** * \ingroup gdcmHeader * \brief Retrieve the number of columns of image. @@ -1440,18 +1713,83 @@ int gdcmHeader::GetZSize(void) { return 1; } +/** + * \ingroup gdcmHeader + * \brief Retrieve the number of Bits Stored + * (as opposite to number of Bits Allocated) + * + * @return The encountered number of Bits Stored, 0 by default. + */ +int gdcmHeader::GetBitsStored(void) { + string StrSize = GetPubElValByNumber(0x0028,0x0101); + if (StrSize == "gdcm::Unfound") + return 1; + return atoi(StrSize.c_str()); +} + + +/** + * \ingroup gdcmHeader + * \brief Retrieve the number of Samples Per Pixel + * (1 : gray level, 3 : RGB) + * + * @return The encountered number of Samples Per Pixel, 1 by default. + */ +int gdcmHeader::GetSamplesPerPixel(void) { + string StrSize = GetPubElValByNumber(0x0028,0x0002); + if (StrSize == "gdcm::Unfound") + return 1; // Well, it's supposed to be mandatory ... + return atoi(StrSize.c_str()); +} + + +/* ================ COMMENT OUT after unfreeze +** + * \ingroup gdcmHeader + * \brief Retrieve the Planar Configuration for RGB images + * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane) + * + * @return The encountered Planar Configuration, 0 by default. + * +int gdcmHeader::GetPlanarConfiguration(void) { + string StrSize = GetPubElValByNumber(0x0028,0x0006); + if (StrSize == "gdcm::Unfound") + return 0; + return atoi(StrSize.c_str()); +} + + ======================================= */ + +/** + * \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; +} + /** * \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, + * - 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 + * @return */ string gdcmHeader::GetPixelType(void) { string BitsAlloc; @@ -1478,81 +1816,198 @@ string gdcmHeader::GetPixelType(void) { } /** - * \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 gets the info from 0028,0030 : Pixel Spacing + * \ else 1. + * @return X dimension of a pixel + */ +float gdcmHeader::GetXSpacing(void) { + float xspacing, yspacing; + string StrSpacing = GetPubElValByNumber(0x0028,0x0030); + + if (StrSpacing == "gdcm::Unfound") { + dbg.Verbose(0, "gdcmHeader::GetXSpacing: unfound Pixel Spacing (0028,0030)"); + return 1.; + } + if( sscanf( StrSpacing.c_str(), "%f\\%f", &xspacing, &yspacing) != 2) + return 0.; + //else + return xspacing; } /** - * \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; + * \ingroup gdcmHeader + * \brief gets the info from 0028,0030 : Pixel Spacing + * \ else 1. + * @return Y dimension of a pixel + */ +float gdcmHeader::GetYSpacing(void) { + float xspacing, yspacing; + string StrSpacing = GetPubElValByNumber(0x0028,0x0030); + + if (StrSpacing == "gdcm::Unfound") { + dbg.Verbose(0, "gdcmHeader::GetYSpacing: unfound Pixel Spacing (0028,0030)"); + return 1.; + } + if( sscanf( StrSpacing.c_str(), "%f\\%f", &xspacing, &yspacing) != 2) + return 0.; + if (yspacing == 0.) { + dbg.Verbose(0, "gdcmHeader::GetYSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem"); + // seems to be a bug in the header ... + sscanf( StrSpacing.c_str(), "%f\\0\\%f", &xspacing, &yspacing); + } + return yspacing; +} - 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; +/** + *\ingroup gdcmHeader + *\brief gets the info from 0018,0088 : Space Between Slices + *\ else from 0018,0050 : Slice Thickness + *\ else 1. + * @return Z dimension of a voxel-to be + */ +float gdcmHeader::GetZSpacing(void) { + // TODO : translate into English + // Spacing Between Slices : distance entre le milieu de chaque coupe + // Les coupes peuvent etre : + // jointives (Spacing between Slices = Slice Thickness) + // chevauchantes (Spacing between Slices < Slice Thickness) + // disjointes (Spacing between Slices > Slice Thickness) + // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal + // ca interesse le physicien de l'IRM, pas le visualisateur de volumes ... + // Si le Spacing Between Slices est absent, + // on suppose que les coupes sont jointives + + string StrSpacingBSlices = GetPubElValByNumber(0x0018,0x0088); + + if (StrSpacingBSlices == "gdcm::Unfound") { + dbg.Verbose(0, "gdcmHeader::GetZSpacing: unfound StrSpacingBSlices"); + string StrSliceThickness = GetPubElValByNumber(0x0018,0x0050); + if (StrSliceThickness == "gdcm::Unfound") + return 1.; + else + // if no 'Spacing Between Slices' is found, + // we assume slices join together + // (no overlapping, no interslice gap) + // if they don't, we're fucked up + return atof(StrSliceThickness.c_str()); + } else { + return atof(StrSpacingBSlices.c_str()); + } } +// +// Image Position Patient (0020,0032): +// If not found (ACR_NEMA) we try Image Position (0020,0030) +// If not found (ACR-NEMA), we consider Slice Location (0020,1041) +// or Location (0020,0050) +// as the Z coordinate, +// 0. for all the coordinates if nothing is found + +// TODO : find a way to inform the caller nothing was found +// TODO : How to tell the caller a wrong number of values was found? + /** - * \ingroup gdcmHeader - * \brief Loads the element values of all the elements present in the - * 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); - } + * \ingroup gdcmHeader + * \brief gets the info from 0020,0032 : Image Position Patient + *\ else from 0020,0030 : Image Position (RET) + *\ else 0. + * @return up-left image corner position + */ +float gdcmHeader::GetXImagePosition(void) { + float xImPos, yImPos, zImPos; + string StrImPos = GetPubElValByNumber(0x0020,0x0032); + + if (StrImPos == "gdcm::Unfound") { + dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position Patient (0020,0032)"); + StrImPos = GetPubElValByNumber(0x0020,0x0030); // For ACR-NEMA images + if (StrImPos == "gdcm::Unfound") { + dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position (RET) (0020,0030)"); + // How to tell the caller nothing was found ? + } + return 0.; + } + if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) + return 0.; + return xImPos; } -void gdcmHeader::PrintPubElVal(ostream & os) { - PubElValSet.Print(os); +/** + * \ingroup gdcmHeader + * \brief gets the info from 0020,0032 : Image Position Patient + * \ else from 0020,0030 : Image Position (RET) + * \ else 0. + * @return up-left image corner position + */ +float gdcmHeader::GetYImagePosition(void) { + float xImPos, yImPos, zImPos; + string StrImPos = GetPubElValByNumber(0x0020,0x0032); + + if (StrImPos == "gdcm::Unfound") { + dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position Patient (0020,0032)"); + StrImPos = GetPubElValByNumber(0x0020,0x0030); // For ACR-NEMA images + if (StrImPos == "gdcm::Unfound") { + dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position (RET) (0020,0030)"); + } + return 0.; + } + if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) + return 0.; + return yImPos; } -void gdcmHeader::PrintPubDict(ostream & os) { - RefPubDict->Print(os); +/** + * \ingroup gdcmHeader + * \brief gets the info from 0020,0032 : Image Position Patient + * \ else from 0020,0030 : Image Position (RET) + * \ else from 0020,1041 : Slice Location + * \ else from 0020,0050 : Location + * \ else 0. + * @return up-left image corner position + */ +float gdcmHeader::GetZImagePosition(void) { + float xImPos, yImPos, zImPos; + string StrImPos = GetPubElValByNumber(0x0020,0x0032); + if (StrImPos != "gdcm::Unfound") { + if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) { + dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position Patient (0020,0032)"); + return 0.; // bug in the element 0x0020,0x0032 + } else { + return zImPos; + } + } + StrImPos = GetPubElValByNumber(0x0020,0x0030); // For ACR-NEMA images + if (StrImPos != "gdcm::Unfound") { + if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) { + dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position (RET) (0020,0030)"); + return 0.; // bug in the element 0x0020,0x0032 + } else { + return zImPos; + } + } + string StrSliceLocation = GetPubElValByNumber(0x0020,0x1041);// for *very* old ACR-NEMA images + if (StrSliceLocation != "gdcm::Unfound") { + if( sscanf( StrSliceLocation.c_str(), "%f", &zImPos) !=1) { + dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Slice Location (0020,1041)"); + return 0.; // bug in the element 0x0020,0x1041 + } else { + return zImPos; + } + } + dbg.Verbose(0, "gdcmHeader::GetZImagePosition: unfound Slice Location (0020,1041)"); + string StrLocation = GetPubElValByNumber(0x0020,0x0050); + if (StrLocation != "gdcm::Unfound") { + if( sscanf( StrLocation.c_str(), "%f", &zImPos) !=1) { + dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Location (0020,0050)"); + return 0.; // bug in the element 0x0020,0x0050 + } else { + return zImPos; + } + } + dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Location (0020,0050)"); + return 0.; // Hopeless } -int gdcmHeader::Write(FILE * fp, FileType type) { - return PubElValSet.Write(fp, type); -} + +