X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=51f36d756b53809fbbbea55fe2822499a8c884df;hb=412e45113080662e115ad6a5771ae607fab2e7ea;hp=eeba821686d59ccbcdd8b577f12ddb916e940e6b;hpb=3e78befc911eac2ecc70747854911d1f803797b5;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index eeba8216..51f36d75 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -1,4 +1,16 @@ -// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.67 2003/05/21 16:26:28 regrain Exp $ +// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.89 2003/09/24 13:52:46 jpr Exp $ + +//This is needed when compiling in debug mode +#ifdef _MSC_VER +//'identifier' : not all control paths return a value +//#pragma warning ( disable : 4715 ) +// 'identifier' : class 'type' needs to have dll-interface to be used by +// clients of class 'type2' +#pragma warning ( disable : 4251 ) +// 'identifier' : identifier was truncated to 'number' characters in the +// debug information +#pragma warning ( disable : 4786 ) +#endif //_MSC_VER #include #include @@ -12,32 +24,59 @@ #include #include "gdcmUtil.h" #include "gdcmHeader.h" -using namespace std; +#include "gdcmTS.h" // Refer to gdcmHeader::CheckSwap() #define HEADER_LENGTH_TO_READ 256 // Refer to gdcmHeader::SetMaxSizeLoadElementValue() -#define _MaxSizeLoadElementValue_ 1024 - +//#define _MaxSizeLoadElementValue_ 1024 +#define _MaxSizeLoadElementValue_ 4096 +/** + * \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(); - if ( !OpenFile(exception_on_error)) - return; - 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) { @@ -50,6 +89,11 @@ bool gdcmHeader::OpenFile(bool exception_on_error) return false; } +/** + * \ingroup gdcmHeader + * \brief + * @return TRUE if the close was successfull + */ bool gdcmHeader::CloseFile(void) { int closed = fclose(fp); fp = (FILE *)0; @@ -58,12 +102,16 @@ bool gdcmHeader::CloseFile(void) { return true; } +/** + * \ingroup gdcmHeader + * \brief Canonical destructor. + */ gdcmHeader::~gdcmHeader (void) { - dicom_vr = (gdcmVR*)0; - Dicts = (gdcmDictSet*)0; - RefPubDict = (gdcmDict*)0; - RefShaDict = (gdcmDict*)0; - return; + dicom_vr = (gdcmVR*)0; + Dicts = (gdcmDictSet*)0; + RefPubDict = (gdcmDict*)0; + RefShaDict = (gdcmDict*)0; + return; } // Fourth semantics: @@ -96,6 +144,7 @@ gdcmHeader::~gdcmHeader (void) { // CRV Curve // OLY Overlays // PXL Pixels +// DL Delimiters // /** @@ -111,7 +160,7 @@ void gdcmHeader::CheckSwap() // 0x00000004. Finding the swap code in then straigthforward. Trouble // occurs when we can't find such group... guint32 s; - guint32 x=4; // x : pour ntohs + guint32 x=4; // x : for ntohs bool net2host; // true when HostByteOrder is the same as NetworkByteOrder int lgrLue; @@ -152,9 +201,9 @@ 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"); @@ -163,7 +212,6 @@ void gdcmHeader::CheckSwap() dbg.Verbose(1, "gdcmHeader::CheckSwap:", "not an explicit Value Representation"); } - if (net2host) { sw = 4321; dbg.Verbose(1, "gdcmHeader::CheckSwap:", @@ -232,6 +280,10 @@ void gdcmHeader::CheckSwap() return; } +/** + * \ingroup gdcmHeader + * \brief + */ void gdcmHeader::SwitchSwapToBigEndian(void) { dbg.Verbose(1, "gdcmHeader::SwitchSwapToBigEndian", "Switching to BigEndian mode."); @@ -254,14 +306,17 @@ 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) return; char VR[3]; - string vr; + std::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 @@ -274,7 +329,7 @@ void gdcmHeader::FindVR( gdcmElValue *ElVal) { lgrLue=fread (&VR, (size_t)2,(size_t)1, fp); VR[2]=0; - vr = string(VR); + vr = std::string(VR); // Assume we are reading a falsely explicit VR file i.e. we reached // a tag where we expect reading a VR but are in fact we read the @@ -318,8 +373,11 @@ 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 @@ -333,7 +391,7 @@ 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. @@ -343,7 +401,7 @@ bool gdcmHeader::IsImplicitVRLittleEndianTransferSyntax(void) { if ( !Element ) return false; LoadElementValueSafe(Element); - string Transfer = Element->GetValue(); + std::string Transfer = Element->GetValue(); if ( Transfer == "1.2.840.10008.1.2" ) return true; return false; @@ -351,7 +409,7 @@ 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. @@ -361,7 +419,7 @@ bool gdcmHeader::IsExplicitVRLittleEndianTransferSyntax(void) { if ( !Element ) return false; LoadElementValueSafe(Element); - string Transfer = Element->GetValue(); + std::string Transfer = Element->GetValue(); if ( Transfer == "1.2.840.10008.1.2.1" ) return true; return false; @@ -369,7 +427,7 @@ 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. @@ -379,7 +437,7 @@ bool gdcmHeader::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) { if ( !Element ) return false; LoadElementValueSafe(Element); - string Transfer = Element->GetValue(); + std::string Transfer = Element->GetValue(); if ( Transfer == "1.2.840.10008.1.2.1.99" ) return true; return false; @@ -387,7 +445,7 @@ 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. @@ -397,7 +455,7 @@ bool gdcmHeader::IsExplicitVRBigEndianTransferSyntax(void) { if ( !Element ) return false; LoadElementValueSafe(Element); - string Transfer = Element->GetValue(); + std::string Transfer = Element->GetValue(); if ( Transfer == "1.2.840.10008.1.2.2" ) //1.2.2 ??? A verifier ! return true; return false; @@ -405,7 +463,7 @@ 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. @@ -415,21 +473,25 @@ bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) { if ( !Element ) return false; LoadElementValueSafe(Element); - string Transfer = Element->GetValue(); + std::string Transfer = Element->GetValue(); if ( Transfer == "1.2.840.10008.1.2.4.50" ) return true; 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; @@ -438,7 +500,7 @@ 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. @@ -448,7 +510,7 @@ bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) { if ( !Element ) return false; LoadElementValueSafe(Element); - string Transfer = Element->GetValue(); + std::string Transfer = Element->GetValue(); if ( Transfer == "1.2.840.10008.1.2.4.51" ) return true; return false; @@ -456,7 +518,7 @@ 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. @@ -466,7 +528,7 @@ bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) { if ( !Element ) return false; LoadElementValueSafe(Element); - string Transfer = Element->GetValue(); + std::string Transfer = Element->GetValue(); if ( Transfer == "1.2.840.10008.1.2.4.52" ) return true; return false; @@ -474,7 +536,7 @@ 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 @@ -485,11 +547,51 @@ bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) { if ( !Element ) return false; LoadElementValueSafe(Element); - string Transfer = Element->GetValue(); + std::string Transfer = Element->GetValue(); if ( Transfer == "1.2.840.10008.1.2.4.53" ) return true; return false; } + +/** + * \ingroup gdcmHeader + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a RLE Lossless one. + * + * @return True when RLE Lossless found. False in all + * other cases. + */ +bool gdcmHeader::IsRLELossLessTransferSyntax(void) { + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); + if ( !Element ) + return false; + LoadElementValueSafe(Element); + std::string Transfer = Element->GetValue(); + if ( Transfer == "1.2.840.10008.1.2.5" ) + return true; + return false; +} + +/** + * \ingroup gdcmHeader + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEG200 one.0 + * + * @return True when JPEG2000 (Lossly or LossLess) found. False in all + * other cases. + */ +bool gdcmHeader::IsJPEG2000(void) { + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); + if ( !Element ) + return false; + LoadElementValueSafe(Element); + std::string Transfer = Element->GetValue(); + if ( (Transfer == "1.2.840.10008.1.2.4.90") + || (Transfer == "1.2.840.10008.1.2.4.91") ) + return true; + return false; +} + /** * \ingroup gdcmHeader * \brief Predicate for dicom version 3 file. @@ -514,7 +616,13 @@ 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; @@ -526,50 +634,71 @@ 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(); - string vr = ElVal->GetVR(); + guint16 group = ElVal->GetGroup(); + std::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; } @@ -598,12 +727,12 @@ 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; @@ -686,16 +815,34 @@ 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 + * @param ElVal + * @return + */ + void gdcmHeader::SkipElementValue(gdcmElValue * ElVal) { SkipBytes(ElVal->GetLength()); } -void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) { +/** + * \ingroup gdcmHeader + * \brief + * @param NewSize + * @return + */ + void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) { if (NewSize < 0) return; if ((guint32)NewSize >= (guint32)0xffffffff) { @@ -714,8 +861,7 @@ 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(); + std::string vr = ElVal->GetVR(); guint32 length = ElVal->GetLength(); bool SkipLoad = false; @@ -735,6 +881,11 @@ void gdcmHeader::LoadElementValue(gdcmElValue * ElVal) { // Heuristic : a sequence "contains" a set of tags (called items). It looks // like the last tag of a sequence (the one that terminates the sequence) // has a group of 0xfffe (with a dummy length). + // Well ... + // Actually (fffe e000) tells us an Element is beginning + // (fffe e00d) tells us an Element just ended + // (fffe e0dd) tells us the current SEQuence just ended + if( group == 0xfffe ) SkipLoad = true; @@ -754,7 +905,7 @@ void gdcmHeader::LoadElementValue(gdcmElValue * ElVal) { // are not loaded. Instead we leave a short notice of the offset of // the element content and it's length. if (length > MaxSizeLoadElementValue) { - ostringstream s; + std::ostringstream s; s << "gdcm::NotLoaded."; s << " Address:" << (long)ElVal->GetOffset(); s << " Length:" << ElVal->GetLength(); @@ -766,41 +917,40 @@ 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; + std::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); @@ -835,37 +985,63 @@ void gdcmHeader::LoadElementValueSafe(gdcmElValue * ElVal) { fseek(fp, PositionOnEntry, SEEK_SET); } - +/** + * \ingroup gdcmHeader + * \brief Reads a supposed to be 16 Bits integer + * \ (swaps it depending on processor endianity) + * + * @return integer acts as a boolean + */ 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 Reads a supposed to be 32 Bits integer + * \ (swaps it depending on processor endianity) + * + * @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) { @@ -902,17 +1078,76 @@ gdcmElValue* gdcmHeader::NewElValueByNumber(guint16 Group, guint16 Elem) { /** * \ingroup gdcmHeader * \brief TODO - * @param + * @param Value + * @param Group + * @param Elem + * \return integer acts as a boolean */ -int gdcmHeader::ReplaceOrCreateByNumber(string Value, guint16 Group, guint16 Elem ) { - - gdcmElValue* nvElValue=NewElValueByNumber(Group, Elem); - PubElValSet.Add(nvElValue); - PubElValSet.SetElValueByNumber(Value, Group, Elem); - return(1); +int gdcmHeader::ReplaceOrCreateByNumber(std::string Value, guint16 Group, guint16 Elem ) { + + // TODO : FIXME JPRx + // curieux, non ? + // on (je) cree une Elvalue ne contenant pas de valeur + // 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 Modify or (Creates if not found) an element + * @param Value new value + * @param Group + * @param Elem + * \return integer acts as a boolean + * + */ +int gdcmHeader::ReplaceOrCreateByNumber(char* Value, guint16 Group, guint16 Elem ) { + + gdcmElValue* nvElValue=NewElValueByNumber(Group, Elem); + PubElValSet.Add(nvElValue); + std::string v = Value; + PubElValSet.SetElValueByNumber(v, Group, Elem); + return(1); +} + + +/** + * \ingroup gdcmHeader + * \brief Set a new value if the invoked element exists + * @param Value + * @param Group + * @param Elem + * \return integer acts as a boolean + */ +int gdcmHeader::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 Elem ) { + + gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem); + std::string v = Value; + PubElValSet.SetElValueByNumber(v, Group, Elem); + return 1; +} + + +/** + * \ingroup gdcmHeader + * \brief Checks if a given ElValue (group,number) + * \ exists in the Public ElValSet + * @param Group + * @param Elem + * @return integer acts as a boolean + */ + +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. @@ -920,7 +1155,7 @@ int gdcmHeader::ReplaceOrCreateByNumber(string Value, guint16 Group, guint16 Ele * a default one when absent. * @param Name Name of the underlying DictEntry */ -gdcmElValue* gdcmHeader::NewElValueByName(string Name) { +gdcmElValue* gdcmHeader::NewElValueByName(std::string Name) { gdcmDictEntry * NewTag = GetDictEntryByName(Name); if (!NewTag) @@ -947,6 +1182,9 @@ gdcmElValue * gdcmHeader::ReadNextElement(void) { g = ReadInt16(); n = ReadInt16(); + + if ( (g==0x7fe0) && (n==0x0010) ) + if (errno == 1) // We reached the EOF (or an error occured) and header parsing // has to be considered as finished. @@ -955,10 +1193,12 @@ gdcmElValue * gdcmHeader::ReadNextElement(void) { NewElVal = NewElValueByNumber(g, n); FindVR(NewElVal); FindLength(NewElVal); - if (errno == 1) + if (errno == 1) { // Call it quits return (gdcmElValue *)0; - NewElVal->SetOffset(ftell(fp)); + } + NewElVal->SetOffset(ftell(fp)); + if ( (g==0x7fe0) && (n==0x0010) ) return NewElVal; } @@ -972,7 +1212,7 @@ gdcmElValue * gdcmHeader::ReadNextElement(void) { bool gdcmHeader::IsAnInteger(gdcmElValue * ElVal) { guint16 group = ElVal->GetGroup(); guint16 element = ElVal->GetElement(); - string vr = ElVal->GetVR(); + std::string vr = ElVal->GetVR(); guint32 length = ElVal->GetLength(); // When we have some semantics on the element we just read, and if we @@ -982,14 +1222,10 @@ bool gdcmHeader::IsAnInteger(gdcmElValue * ElVal) { if (length == 4) return true; else { - 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; @@ -1010,8 +1246,8 @@ size_t gdcmHeader::GetPixelOffset(void) { // When the "Image Location" is absent we default to group 0x7fe0. guint16 grPixel; guint16 numPixel; - string ImageLocation = GetPubElValByName("Image Location"); - if ( ImageLocation == "gdcm::Unfound" ) { + std::string ImageLocation = GetPubElValByName("Image Location"); + if ( ImageLocation == GDCM_UNFOUND ) { grPixel = 0x7fe0; } else { grPixel = (guint16) atoi( ImageLocation.c_str() ); @@ -1021,6 +1257,7 @@ size_t gdcmHeader::GetPixelOffset(void) { numPixel = 0x1010; else numPixel = 0x0010; + gdcmElValue* PixelElement = PubElValSet.GetElementByNumber(grPixel, numPixel); if (PixelElement) @@ -1067,7 +1304,7 @@ gdcmDictEntry * gdcmHeader::GetDictEntryByNumber(guint16 group, * @param Name name of the searched DictEntry * @return Corresponding DictEntry when it exists, NULL otherwise. */ -gdcmDictEntry * gdcmHeader::GetDictEntryByName(string Name) { +gdcmDictEntry * gdcmHeader::GetDictEntryByName(std::string Name) { gdcmDictEntry * found = (gdcmDictEntry*)0; if (!RefPubDict && !RefShaDict) { dbg.Verbose(0, "gdcmHeader::GetDictEntry", @@ -1093,9 +1330,9 @@ gdcmDictEntry * gdcmHeader::GetDictEntryByName(string Name) { * @param group Group of the researched tag. * @param element Element of the researched tag. * @return Corresponding element value when it exists, and the string - * "gdcm::Unfound" otherwise. + * GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -string gdcmHeader::GetPubElValByNumber(guint16 group, guint16 element) { +std::string gdcmHeader::GetPubElValByNumber(guint16 group, guint16 element) { return PubElValSet.GetElValueByNumber(group, element); } @@ -1111,12 +1348,12 @@ string gdcmHeader::GetPubElValByNumber(guint16 group, guint16 element) { * @param group Group of the researched tag. * @param element Element of the researched tag. * @return Corresponding element value representation when it exists, - * and the string "gdcm::Unfound" otherwise. + * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -string gdcmHeader::GetPubElValRepByNumber(guint16 group, guint16 element) { +std::string gdcmHeader::GetPubElValRepByNumber(guint16 group, guint16 element) { gdcmElValue* elem = PubElValSet.GetElementByNumber(group, element); if ( !elem ) - return "gdcm::Unfound"; + return GDCM_UNFOUND; return elem->GetVR(); } @@ -1126,9 +1363,9 @@ string gdcmHeader::GetPubElValRepByNumber(guint16 group, guint16 element) { * a given tag. * @param TagName name of the researched element. * @return Corresponding element value when it exists, and the string - * "gdcm::Unfound" otherwise. + * GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -string gdcmHeader::GetPubElValByName(string TagName) { +std::string gdcmHeader::GetPubElValByName(std::string TagName) { return PubElValSet.GetElValueByName(TagName); } @@ -1143,12 +1380,12 @@ string gdcmHeader::GetPubElValByName(string TagName) { * of semantics than just the native C++ type. * @param TagName name of the researched element. * @return Corresponding element value representation when it exists, - * and the string "gdcm::Unfound" otherwise. + * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -string gdcmHeader::GetPubElValRepByName(string TagName) { +std::string gdcmHeader::GetPubElValRepByName(std::string TagName) { gdcmElValue* elem = PubElValSet.GetElementByName(TagName); if ( !elem ) - return "gdcm::Unfound"; + return GDCM_UNFOUND; return elem->GetVR(); } @@ -1159,9 +1396,9 @@ string gdcmHeader::GetPubElValRepByName(string TagName) { * @param group Group of the researched tag. * @param element Element of the researched tag. * @return Corresponding element value representation when it exists, - * and the string "gdcm::Unfound" otherwise. + * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -string gdcmHeader::GetShaElValByNumber(guint16 group, guint16 element) { +std::string gdcmHeader::GetShaElValByNumber(guint16 group, guint16 element) { return ShaElValSet.GetElValueByNumber(group, element); } @@ -1177,12 +1414,12 @@ string gdcmHeader::GetShaElValByNumber(guint16 group, guint16 element) { * @param group Group of the researched tag. * @param element Element of the researched tag. * @return Corresponding element value representation when it exists, - * and the string "gdcm::Unfound" otherwise. + * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -string gdcmHeader::GetShaElValRepByNumber(guint16 group, guint16 element) { +std::string gdcmHeader::GetShaElValRepByNumber(guint16 group, guint16 element) { gdcmElValue* elem = ShaElValSet.GetElementByNumber(group, element); if ( !elem ) - return "gdcm::Unfound"; + return GDCM_UNFOUND; return elem->GetVR(); } @@ -1192,9 +1429,9 @@ string gdcmHeader::GetShaElValRepByNumber(guint16 group, guint16 element) { * for an element value of given tag. * @param TagName name of the researched element. * @return Corresponding element value when it exists, and the string - * "gdcm::Unfound" otherwise. + * GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -string gdcmHeader::GetShaElValByName(string TagName) { +std::string gdcmHeader::GetShaElValByName(std::string TagName) { return ShaElValSet.GetElValueByName(TagName); } @@ -1209,12 +1446,12 @@ string gdcmHeader::GetShaElValByName(string TagName) { * of semantics than just the native C++ type. * @param TagName name of the researched element. * @return Corresponding element value representation when it exists, - * and the string "gdcm::Unfound" otherwise. + * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -string gdcmHeader::GetShaElValRepByName(string TagName) { +std::string gdcmHeader::GetShaElValRepByName(std::string TagName) { gdcmElValue* elem = ShaElValSet.GetElementByName(TagName); if ( !elem ) - return "gdcm::Unfound"; + return GDCM_UNFOUND; return elem->GetVR(); } @@ -1226,10 +1463,10 @@ string gdcmHeader::GetShaElValRepByName(string TagName) { * @param group Group of the researched tag. * @param element Element of the researched tag. * @return Corresponding element value representation when it exists, - * and the string "gdcm::Unfound" otherwise. + * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -string gdcmHeader::GetElValByNumber(guint16 group, guint16 element) { - string pub = GetPubElValByNumber(group, element); +std::string gdcmHeader::GetElValByNumber(guint16 group, guint16 element) { + std::string pub = GetPubElValByNumber(group, element); if (pub.length()) return pub; return GetShaElValByNumber(group, element); @@ -1248,10 +1485,10 @@ string gdcmHeader::GetElValByNumber(guint16 group, guint16 element) { * @param group Group of the researched tag. * @param element Element of the researched tag. * @return Corresponding element value representation when it exists, - * and the string "gdcm::Unfound" otherwise. + * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -string gdcmHeader::GetElValRepByNumber(guint16 group, guint16 element) { - string pub = GetPubElValRepByNumber(group, element); +std::string gdcmHeader::GetElValRepByNumber(guint16 group, guint16 element) { + std::string pub = GetPubElValRepByNumber(group, element); if (pub.length()) return pub; return GetShaElValRepByNumber(group, element); @@ -1264,10 +1501,10 @@ string gdcmHeader::GetElValRepByNumber(guint16 group, guint16 element) { * for the element value of a given tag. * @param TagName name of the researched element. * @return Corresponding element value when it exists, - * and the string "gdcm::Unfound" otherwise. + * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -string gdcmHeader::GetElValByName(string TagName) { - string pub = GetPubElValByName(TagName); +std::string gdcmHeader::GetElValByName(std::string TagName) { + std::string pub = GetPubElValByName(TagName); if (pub.length()) return pub; return GetShaElValByName(TagName); @@ -1285,10 +1522,10 @@ string gdcmHeader::GetElValByName(string TagName) { * of semantics than just the native C++ type. * @param TagName name of the researched element. * @return Corresponding element value representation when it exists, - * and the string "gdcm::Unfound" otherwise. + * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -string gdcmHeader::GetElValRepByName(string TagName) { - string pub = GetPubElValRepByName(TagName); +std::string gdcmHeader::GetElValRepByName(std::string TagName) { + std::string pub = GetPubElValRepByName(TagName); if (pub.length()) return pub; return GetShaElValRepByName(TagName); @@ -1303,7 +1540,7 @@ string gdcmHeader::GetElValRepByName(string TagName) { * @param group group of the ElVal to modify * @param element element of the ElVal to modify */ -int gdcmHeader::SetPubElValByNumber(string content, guint16 group, +int gdcmHeader::SetPubElValByNumber(std::string content, guint16 group, guint16 element) //TODO : homogeneiser les noms : SetPubElValByNumber qui appelle PubElValSet.SetElValueByNumber @@ -1320,7 +1557,7 @@ int gdcmHeader::SetPubElValByNumber(string content, guint16 group, * @param content new value to substitute with * @param TagName name of the tag to be modified */ -int gdcmHeader::SetPubElValByName(string content, string TagName) { +int gdcmHeader::SetPubElValByName(std::string content, std::string TagName) { return ( PubElValSet.SetElValueByName (content, TagName) ); } @@ -1351,7 +1588,7 @@ int gdcmHeader::SetPubElValLengthByNumber(guint32 length, guint16 group, * @param element element of the ElVal to modify * @return 1 on success, 0 otherwise. */ -int gdcmHeader::SetShaElValByNumber(string content, +int gdcmHeader::SetShaElValByNumber(std::string content, guint16 group, guint16 element) { return ( ShaElValSet.SetElValueByNumber (content, group, element) ); } @@ -1361,10 +1598,10 @@ 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(std::string content, std::string ShadowTagName) { + return ( ShaElValSet.SetElValueByName (content, ShadowTagName) ); } /** @@ -1382,6 +1619,212 @@ 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(std::string NewTagName, std::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); + } + rewind(fp); + + // Load 'non string' values + std::string PhotometricInterpretation = GetPubElValByNumber(0x0028,0x0004); + if( PhotometricInterpretation == "PALETTE COLOR " ){ + LoadElementVoidArea(0x0028,0x1200); // gray LUT + LoadElementVoidArea(0x0028,0x1201); // R LUT + LoadElementVoidArea(0x0028,0x1202); // G LUT + LoadElementVoidArea(0x0028,0x1203); // B LUT + + LoadElementVoidArea(0x0028,0x1221); // Segmented Red Palette Color LUT Data + LoadElementVoidArea(0x0028,0x1222); // Segmented Green Palette Color LUT Data + LoadElementVoidArea(0x0028,0x1223); // Segmented Blue Palette Color LUT Data + } + + // -------------------------------------------------------------- + // Special Patch to allow gdcm to read ACR-LibIDO formated images + // + // if recognition code tells us we deal with a LibIDO image + // we switch lineNumber and columnNumber + // + std::string RecCode; + RecCode = GetPubElValByNumber(0x0008, 0x0010); + if (RecCode == "ACRNEMA_LIBIDO_1.1" || + RecCode == "CANRME_AILIBOD1_1." ) { + filetype = ACR_LIBIDO; + std::string rows = GetPubElValByNumber(0x0028, 0x0010); + std::string columns = GetPubElValByNumber(0x0028, 0x0011); + SetPubElValByNumber(columns, 0x0028, 0x0010); + SetPubElValByNumber(rows , 0x0028, 0x0011); + } + // ----------------- End of Special Patch ---------------- +} + +/** + * \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); +} + +// +// ------------------------ 'non string' elements related functions +// + +/** + * \ingroup gdcmHeader + * \brief Loads (from disk) the element content + * when a string is not suitable + */ +void * gdcmHeader::LoadElementVoidArea(guint16 Group, guint16 Elem) { + gdcmElValue * Element= PubElValSet.GetElementByNumber(Group, Elem); + if ( !Element ) + return NULL; + size_t o =(size_t)Element->GetOffset(); + fseek(fp, o, SEEK_SET); + int l=Element->GetLength(); + void * a = malloc(l); + if(!a) { + std::cout << "Big Broblem (LoadElementVoidArea, malloc) " + << std::hex << Group << " " << Elem << std::endl; + return NULL; + } + int res = PubElValSet.SetVoidAreaByNumber(a, Group, Elem); + // TODO check the result + size_t l2 = fread(a, 1, l ,fp); + if(l != l2) { + std::cout << "Big Broblem (LoadElementVoidArea, fread) " + << std::hex << Group << " " << Elem << std::endl; + free(a); + return NULL; + } +} + +/** + * \ingroup gdcmHeader + * \brief Gets (from Header) the offset of a 'non string' element value + * \ (LoadElementValue has already be executed) + * @param Group + * @param Elem + * @return File Offset of the Element Value + */ + size_t gdcmHeader::GetPubElValOffsetByNumber(guint16 Group, guint16 Elem) { + gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem); + if (!elValue) { + dbg.Verbose(1, "gdcmHeader::GetElValueByNumber", + "failed to Locate gdcmElValue"); + return (size_t)0; + } + return elValue->GetOffset(); +} + +/** + * \ingroup gdcmHeader +* \brief Gets (from Header) a 'non string' element value + * \ (LoadElementValue has already be executed) + * @param Group + * @param Elem + * @return Pointer to the 'non string' area + + */ + void * gdcmHeader::GetPubElValVoidAreaByNumber(guint16 Group, guint16 Elem) { + gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem); + if (!elValue) { + dbg.Verbose(1, "gdcmHeader::GetElValueByNumber", + "failed to Locate gdcmElValue"); + return (NULL); + } + return elValue->GetVoidArea(); +} + + +// +// ============================================================================= +// Heuristics based accessors +//============================================================================== +// + +// TODO : move to an other file. + + /** * \ingroup gdcmHeader * \brief Retrieve the number of columns of image. @@ -1390,8 +1833,8 @@ void gdcmHeader::ParseHeader(bool exception_on_error) throw(gdcmFormatError) { 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") + std::string StrSize = GetPubElValByNumber(0x0028,0x0011); + if (StrSize == GDCM_UNFOUND) return 0; return atoi(StrSize.c_str()); } @@ -1405,8 +1848,8 @@ int gdcmHeader::GetXSize(void) { 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") + std::string StrSize = GetPubElValByNumber(0x0028,0x0010); + if (StrSize != GDCM_UNFOUND) return atoi(StrSize.c_str()); if ( IsDicomV3() ) return 0; @@ -1428,19 +1871,62 @@ int gdcmHeader::GetYSize(void) { 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") + std::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") + if (StrSize != GDCM_UNFOUND) return atoi(StrSize.c_str()); 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) { + std::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) { + std::string StrSize = GetPubElValByNumber(0x0028,0x0002); + if (StrSize == GDCM_UNFOUND) + return 1; // Well, it's supposed to be mandatory ... + return atoi(StrSize.c_str()); +} + +/** + * \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) { + std::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. @@ -1448,8 +1934,8 @@ int gdcmHeader::GetZSize(void) { * */ int gdcmHeader::GetPixelSize(void) { - string PixelType = GetPixelType(); - if (PixelType == "8U" || PixelType == "8S") + std::string PixelType = GetPixelType(); + if (PixelType == "8U" || PixelType == "8S") return 1; if (PixelType == "16U" || PixelType == "16S") return 2; @@ -1472,106 +1958,223 @@ int gdcmHeader::GetPixelSize(void) { * \warning 12 bit images appear as 16 bit. * @return */ -string gdcmHeader::GetPixelType(void) { - string BitsAlloc; +std::string gdcmHeader::GetPixelType(void) { + std::string BitsAlloc; BitsAlloc = GetElValByName("Bits Allocated"); - if (BitsAlloc == "gdcm::Unfound") { + if (BitsAlloc == GDCM_UNFOUND) { dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated"); - BitsAlloc = string("16"); + BitsAlloc = std::string("16"); } if (BitsAlloc == "12") - BitsAlloc = string("16"); + BitsAlloc = std::string("16"); - string Signed; + std::string Signed; Signed = GetElValByName("Pixel Representation"); - if (Signed == "gdcm::Unfound") { + if (Signed == GDCM_UNFOUND) { dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation"); - BitsAlloc = string("0"); + BitsAlloc = std::string("0"); } if (Signed == "0") - Signed = string("U"); + Signed = std::string("U"); else - Signed = string("S"); + Signed = std::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; + * \ingroup gdcmHeader + * \brief gets the info from 0002,0010 : Transfert Syntax + * \ else 1. + * @return Transfert Syntax Name (as oposite to Transfert Syntax UID) + */ +std::string gdcmHeader::GetTransferSyntaxName(void) { + std::string TransfertSyntax = GetPubElValByNumber(0x0002,0x0010); + if (TransfertSyntax == GDCM_UNFOUND) { + dbg.Verbose(0, "gdcmHeader::GetTransferSyntaxName: unfound Transfert Syntax (0002,0010)"); + return "Uncompressed ACR-NEMA"; } - 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; + // we do it only when we need it + gdcmTS * ts = gdcmGlobal::GetTS(); + std::string tsName=ts->GetValue(TransfertSyntax); + //delete ts; // Seg Fault when deleted ?! + return tsName; } -/** - * \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; +// -------------------------------- Lookup Table related functions ------------ - 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 0028,1101 : Lookup Table Desc-Red + * \ else 0 + * @return Lookup Table Length + * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] + */ + +int gdcmHeader::GetLUTLength(void) { + std::vector tokens; + int LutLength; + //int LutDepth; + //int LutNbits; + // Just hope Lookup Table Desc-Red = Lookup Table Desc-Red = Lookup Table Desc-Blue + std::string LutDescriptionR = GetPubElValByNumber(0x0028,0x1101); + if (LutDescriptionR == GDCM_UNFOUND) + return 0; + std::string LutDescriptionG = GetPubElValByNumber(0x0028,0x1102); + if (LutDescriptionG == GDCM_UNFOUND) + return 0; + std::string LutDescriptionB = GetPubElValByNumber(0x0028,0x1103); + if (LutDescriptionB == GDCM_UNFOUND) + return 0; + if( (LutDescriptionR != LutDescriptionG) || (LutDescriptionR != LutDescriptionB) ) { + dbg.Verbose(0, "gdcmHeader::GetLUTLength: The CLUT R,G,B are not equal"); + return 0; + } + std::cout << "Lut Description " << LutDescriptionR < tokens; + //int LutLength; + //int LutDepth; + int LutNbits; + // Just hope Lookup Table Desc-Red = Lookup Table Desc-Red = Lookup Table Desc-Blue + // Consistency already checked in GetLUTLength + std::string LutDescription = GetPubElValByNumber(0x0028,0x1101); + if (LutDescription == GDCM_UNFOUND) + return 0; + tokens.erase(tokens.begin(),tokens.end()); // clean any previous value + Tokenize (LutDescription, tokens, "\\"); + //LutLength=atoi(tokens[0].c_str()); + //LutDepth=atoi(tokens[1].c_str()); + LutNbits=atoi(tokens[2].c_str()); + tokens.clear(); + return LutNbits; } + /** - * \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 0028,1201 : Lookup Table Red + * \ else 0 + * @return Lookup Table Red + * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] + */ +void * gdcmHeader::GetLUTRed(void) { + return GetPubElValVoidAreaByNumber(0x0028,0x1201); } -void gdcmHeader::PrintPubElVal(std::ostream & os) { - PubElValSet.Print(os); +/** + * \ingroup gdcmHeader + * \brief gets the info from 0028,1202 : Lookup Table Green + * \ else 0 + * @return Lookup Table Red + * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] + */ + void * gdcmHeader::GetLUTGreen(void) { + return GetPubElValVoidAreaByNumber(0x0028,0x1202); } -void gdcmHeader::PrintPubDict(std::ostream & os) { - RefPubDict->Print(os); +/** + * \ingroup gdcmHeader + * \brief gets the info from 0028,1202 : Lookup Table Blue + * \ else 0 + * @return Lookup Table Blue + * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] + */ +void * gdcmHeader::GetLUTBlue(void) { + return GetPubElValVoidAreaByNumber(0x0028,0x1203); } -int gdcmHeader::Write(FILE * fp, FileType type) { - return PubElValSet.Write(fp, type); +/** + * \ingroup gdcmHeader + * \brief + * @return Lookup Table RGB + * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] + * \ and (0028,1201),(0028,1202),(0028,1202) are found + * \warning : hazardous ! Use better GetPubElValVoidAreaByNumber + */ +void * gdcmHeader::GetLUTRGB(void) { +// Not so easy : see +// http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables +// and OT-PAL-8-face.dcm + + if (GetPubElValByNumber(0x0028,0x0004) == GDCM_UNFOUND) { + dbg.Verbose(0, "gdcmHeader::GetLUTRGB: unfound Photometric Interpretation"); + return NULL; + } + void * LutR,*LutG,*LutB; + int l; + + // Maybe, some day we get an image + // that respects the definition ... + // Let's consider no ones does. + + l= GetLUTLength(); + if(l==0) + return (NULL); + int nBits=GetLUTNbits(); + // a virer quand on aura trouve UNE image + // qui correspond VRAIMENT à la definition ! + std::cout << "l " << l << " nBits " << nBits; + + l= l/(nBits/8); + + LutR =GetPubElValVoidAreaByNumber(0x0028,0x1201); + LutG =GetPubElValVoidAreaByNumber(0x0028,0x1202); + LutB =GetPubElValVoidAreaByNumber(0x0028,0x1203); + + // Warning : Any value for nBits as to be considered as 8 + // Any value for Length as to be considered as 256 + // That's DICOM ... + + // Just wait before removing the following code + /* + if (nBits == 16) { + guint16 * LUTRGB, *rgb; + LUTRGB = rgb = (guint16 *) malloc(3*l*sizeof( guint16)); + guint16 * r = (guint16 *)LutR; + guint16 * g = (guint16 *)LutG; + guint16 * b = (guint16 *)LutB; + for(int i=0;i