X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=30806b6775ec81a831f470558abf8151a2470fc3;hb=f58ef7f4b7e1e6c25c4fb7b78cd658e1b6efc639;hp=b280fd62ca0cbcd718182c7551bb43de47429793;hpb=cbdf7d814e2c43c37dff624581dd77ac178e9ce7;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index b280fd62..30806b67 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -1,5 +1,16 @@ +// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.83 2003/09/11 11:12:59 jpr Exp $ -// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.74 2003/07/01 15:48:27 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 @@ -14,6 +25,7 @@ #include "gdcmUtil.h" #include "gdcmHeader.h" using namespace std; +#include "gdcmTS.h" // TODO : remove DEBUG @@ -22,8 +34,8 @@ using namespace std; // 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 @@ -42,15 +54,15 @@ void gdcmHeader::Initialise(void) { * @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(); +gdcmHeader::gdcmHeader(const char *InFilename, bool exception_on_error) { + SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_); + filename = InFilename; + Initialise(); + if ( !OpenFile(exception_on_error)) + return; + ParseHeader(); + LoadElements(); + CloseFile(); } /** @@ -85,7 +97,7 @@ gdcmHeader::gdcmHeader(bool exception_on_error) { /** * \ingroup gdcmHeader * \brief - * @return + * @return TRUE if the close was successfull */ bool gdcmHeader::CloseFile(void) { int closed = fclose(fp); @@ -137,6 +149,7 @@ gdcmHeader::~gdcmHeader (void) { // CRV Curve // OLY Overlays // PXL Pixels +// DL Delimiters // /** @@ -152,7 +165,7 @@ 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; @@ -193,9 +206,9 @@ 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"); @@ -204,7 +217,6 @@ void gdcmHeader::CheckSwap() dbg.Verbose(1, "gdcmHeader::CheckSwap:", "not an explicit Value Representation"); } - if (net2host) { sw = 4321; dbg.Verbose(1, "gdcmHeader::CheckSwap:", @@ -299,6 +311,7 @@ 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) @@ -383,7 +396,7 @@ 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. @@ -401,7 +414,7 @@ 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. @@ -419,7 +432,7 @@ 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. @@ -437,7 +450,7 @@ 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. @@ -455,7 +468,7 @@ 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. @@ -492,7 +505,7 @@ 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. @@ -510,7 +523,7 @@ 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. @@ -528,7 +541,7 @@ 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 @@ -545,6 +558,45 @@ bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) { 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); + 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); + 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. @@ -588,31 +640,26 @@ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { g = ReadInt16(); n = ReadInt16(); - if (DEBUG) printf ("dans FindLengthOB (%04x,%04x)\n",g,n); - long l = ftell(fp); - if (DEBUG) printf("en %d o(%o) x(%x)\n",l,l,l); + long l = ftell(fp); if (errno == 1) return 0; TotalLength += 4; // We even have to decount the group and element - if ( g != 0xfffe && g!=0xb00c ) /*for bogus headerJPR */ { + 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); - if (DEBUG) printf("en %d o(%o) x(%x)\n",l,l,l); errno = 1; return 0; } - - if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) /* for bogus header JPR */ + if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) /* for bogus header */ FoundSequenceDelimiter = true; 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); - if (DEBUG) printf("wrong element (%04x) for an item sequence (%04x,%04x)\n",n, g,n); errno = 1; return 0; } @@ -620,7 +667,6 @@ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { TotalLength += ItemLength + 4; // We add 4 bytes since we just read // the ItemLength with ReadInt32 - if (DEBUG) printf("TotalLength %d\n",TotalLength); SkipBytes(ItemLength); } fseek(fp, PositionOnEntry, SEEK_SET); @@ -635,13 +681,12 @@ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { */ void gdcmHeader::FindLength (gdcmElValue * ElVal) { guint16 element = ElVal->GetElement(); - guint16 group = ElVal->GetGroup(); // JPR a virer + guint16 group = ElVal->GetGroup(); string vr = ElVal->GetVR(); guint16 length16; - if( (element == 0x0010) && (group == 0x7fe0) ) {// JPR - - dbg.SetDebug(10); - dbg.Verbose(2, "gdcmHeader::FindLength: ", // JPR + if( (element == 0x0010) && (group == 0x7fe0) ) { + dbg.SetDebug(0); + dbg.Verbose(2, "gdcmHeader::FindLength: ", "on est sur 7fe0 0010"); } @@ -687,7 +732,7 @@ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { // 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 @@ -789,7 +834,7 @@ guint16 gdcmHeader::SwapShort(guint16 a) { /** * \ingroup gdcmHeader * \brief - * + * @param ElVal * @return */ void gdcmHeader::SkipElementValue(gdcmElValue * ElVal) { @@ -799,7 +844,7 @@ guint16 gdcmHeader::SwapShort(guint16 a) { /** * \ingroup gdcmHeader * \brief - * + * @param NewSize * @return */ void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) { @@ -841,6 +886,11 @@ 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; @@ -872,8 +922,7 @@ 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) ) { @@ -943,20 +992,21 @@ void gdcmHeader::LoadElementValueSafe(gdcmElValue * ElVal) { /** * \ingroup gdcmHeader - * \brief + * \brief Reads a supposed to be 16 Bits integer + * \ (swaps it depending on processor endianity) * - * @return + * @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); if ( item_read != 1 ) { - dbg.Verbose(1, "gdcmHeader::ReadInt16", " Failed to read :"); - if(feof(fp)) - dbg.Verbose(1, "gdcmHeader::ReadInt16", " End of File encountered"); - if(ferror(fp)) - dbg.Verbose(1, "gdcmHeader::ReadInt16", " File 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; } @@ -967,7 +1017,8 @@ guint16 gdcmHeader::ReadInt16(void) { /** * \ingroup gdcmHeader - * \brief + * \brief Reads a supposed to be 32 Bits integer + * \ (swaps it depending on processor endianity) * * @return */ @@ -975,13 +1026,12 @@ guint32 gdcmHeader::ReadInt32(void) { guint32 g; size_t item_read; item_read = fread (&g, (size_t)4,(size_t)1, fp); - if ( item_read != 1 ) { - - dbg.Verbose(1, "gdcmHeader::ReadInt32", " Failed to read :"); - if(feof(fp)) - dbg.Verbose(1, "gdcmHeader::ReadInt32", " End of File encountered"); + 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(1, "gdcmHeader::ReadInt32", " File Error"); + dbg.Verbose(0, "gdcmHeader::ReadInt32", " File Error"); errno = 1; return 0; } @@ -1033,7 +1083,10 @@ 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 ) { @@ -1053,8 +1106,12 @@ int gdcmHeader::ReplaceOrCreateByNumber(string Value, guint16 Group, guint16 Ele /** * \ingroup gdcmHeader - * \brief TODO - * @param + * \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 ) { @@ -1065,17 +1122,37 @@ int gdcmHeader::ReplaceOrCreateByNumber(char* Value, guint16 Group, guint16 Elem return(1); } + /** * \ingroup gdcmHeader - * \brief TODO - * @param + * \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); + 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. @@ -1555,19 +1632,211 @@ 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); + } + rewind(fp); + + // Load 'non string' values + 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 + // + 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) { + cout << "Big Broblem (LoadElementVoidArea, malloc) " + << hex << Group << " " << Elem << "\n"; + return NULL; + } + int res = PubElValSet.SetVoidAreaByNumber(a, Group, Elem); + // TODO check the result + size_t l2 = fread(a, 1, l ,fp); + if(l != l2) { + cout << "Big Broblem (LoadElementVoidArea, fread) " + << hex << Group << " " << Elem << "\n"; + 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(); +} + // -// TODO : JPR -// des que les element values sont chargees, stocker, -// en une seule fois, dans des entiers -// NX, NY, NZ, Bits allocated, Bits Stored, High Bit, Samples Per Pixel -// (TODO : preciser les autres) -// et refaire ceux des accesseurs qui renvoient les entiers correspondants +// ============================================================================= +// Heuristics based accessors +//============================================================================== // -// --> peut etre dangereux ? -// si l'utilisateur modifie 'manuellement' l'un des paramètres -// l'entier de sera pas modifié ... -// (pb de la mise à jour en cas de redondance :-( + +// TODO : move to an other file. + /** * \ingroup gdcmHeader @@ -1642,6 +1911,7 @@ int gdcmHeader::GetBitsStored(void) { return atoi(StrSize.c_str()); } + /** * \ingroup gdcmHeader * \brief Retrieve the number of Samples Per Pixel @@ -1656,6 +1926,20 @@ int gdcmHeader::GetSamplesPerPixel(void) { 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) { + 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. @@ -1711,314 +1995,199 @@ string gdcmHeader::GetPixelType(void) { return( BitsAlloc + Signed); } - -/** - * \ingroup gdcmHeader - * \brief This predicate, based on hopefully reasonnable heuristics, - * decides whether or not the current gdcmHeader was properly parsed - * and contains the mandatory information for being considered as - * a well formed and usable image. - * @return true when gdcmHeader is the one of a reasonable Dicom file, - * false otherwise. - */ -bool gdcmHeader::IsReadable(void) { - if ( GetElValByName("Image Dimensions") != "gdcm::Unfound" - && atoi(GetElValByName("Image Dimensions").c_str()) > 4 ) { - return false; - } - if ( GetElValByName("Bits Allocated") == "gdcm::Unfound" ) - return false; - if ( GetElValByName("Bits Stored") == "gdcm::Unfound" ) - return false; - if ( GetElValByName("High Bit") == "gdcm::Unfound" ) - return false; - if ( GetElValByName("Pixel Representation") == "gdcm::Unfound" ) - return false; - return true; -} - /** - * \ingroup gdcmHeader - * \brief Small utility function that creates a new manually crafted - * (as opposed as read from the file) gdcmElValue with user - * specified name and adds it to the public tag hash table. - * \note A fake TagKey is generated so the PubDict can keep it's coherence. - * @param NewTagName The name to be given to this new tag. - * @param VR The Value Representation to be given to this new tag. - * @ return The newly hand crafted Element Value. - */ -gdcmElValue* gdcmHeader::NewManualElValToPubDict(string NewTagName, string VR) { - gdcmElValue* NewElVal = (gdcmElValue*)0; - guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info - guint32 FreeElem = 0; - gdcmDictEntry* NewEntry = (gdcmDictEntry*)0; - - FreeElem = PubElValSet.GenerateFreeTagKeyInGroup(StuffGroup); - if (FreeElem == UINT32_MAX) { - dbg.Verbose(1, "gdcmHeader::NewManualElValToPubDict", - "Group 0xffff in Public Dict is full"); - return (gdcmElValue*)0; - } - NewEntry = new gdcmDictEntry(StuffGroup, FreeElem, - VR, "GDCM", NewTagName); - NewElVal = new gdcmElValue(NewEntry); - PubElValSet.Add(NewElVal); - return NewElVal; -} - -/** - * \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 0002,0010 : Transfert Syntax + * \ else 1. + * @return Transfert Syntax Name (as oposite to Transfert Syntax UID) + */ +string gdcmHeader::GetTransferSyntaxName(void) { + string TransfertSyntax = GetPubElValByNumber(0x0002,0x0010); + if (TransfertSyntax == "gdcm::Unfound") { + dbg.Verbose(0, "gdcmHeader::GetTransferSyntaxName: unfound Transfert Syntax (0002,0010)"); + return "Uncompressed ACR-NEMA"; } + // we do it only when we need it + gdcmTS * ts = gdcmGlobal::GetTS(); + string tsName=ts->GetValue(TransfertSyntax); + //delete ts; // Seg Fault when deleted ?! + return tsName; } -/** - * \ingroup gdcmHeader - * \brief - * @return - */ -void gdcmHeader::PrintPubElVal(std::ostream & os) { - PubElValSet.Print(os); -} +// -------------------------------- Lookup Table related functions ------------ /** * \ingroup gdcmHeader - * \brief - * @return - */ -void gdcmHeader::PrintPubDict(std::ostream & os) { - RefPubDict->Print(os); -} - -/** - * \ingroup gdcmHeader - * \brief - * @return + * \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::Write(FILE * fp, FileType type) { - return PubElValSet.Write(fp, type); +int gdcmHeader::GetLUTLength(void) { + vector tokens; + int LutLength; + //int LutDepth; + //int LutNbits; + // Just hope Lookup Table Desc-Red = Lookup Table Desc-Red = Lookup Table Desc-Blue + string LutDescriptionR = GetPubElValByNumber(0x0028,0x1101); + if (LutDescriptionR == "gdcm::Unfound") + return 0; + string LutDescriptionG = GetPubElValByNumber(0x0028,0x1102); + if (LutDescriptionG == "gdcm::Unfound") + return 0; + 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; + } + cout << "Lut Description " << LutDescriptionR <<"\n"; + tokens.erase(tokens.begin(),tokens.end()); // clean any previous value + Tokenize (LutDescriptionR, tokens, "\\"); + LutLength=atoi(tokens[0].c_str()); + //LutDepth=atoi(tokens[1].c_str()); + //LutNbits=atoi(tokens[2].c_str()); + tokens.clear(); + return LutLength; } /** * \ingroup gdcmHeader - * \brief - * @return + * \brief gets the info from 0028,1101 : Lookup Table Desc-Red + * \ else 0 + * @return Lookup Table nBit + * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] */ -float gdcmHeader::GetXSpacing(void) { - float xspacing, yspacing; - string StrSpacing = GetPubElValByNumber(0x0028,0x0030); - - if (StrSpacing == "gdcm::Unfound") { - dbg.Verbose(0, "gdcmHeader::GetXSpacing: unfound Pixel Spacing"); - return 1.; - } - if( sscanf( StrSpacing.c_str(), "%f\\%f", &xspacing, &yspacing) != 2) - return 0.; - //else - return xspacing; + +int gdcmHeader::GetLUTNbits(void) { + vector 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 + 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 - * @return - */ -float gdcmHeader::GetYSpacing(void) { - float xspacing, yspacing; - string StrSpacing = GetPubElValByNumber(0x0028,0x0030); - if (StrSpacing == "gdcm::Unfound") { - dbg.Verbose(0, "gdcmHeader::GetYSpacing: unfound Pixel Spacing"); - 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; -} - /** * \ingroup gdcmHeader - * \brief - * @return - */ -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()); - } + * \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); } -// -// 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 (20,1041) -// 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 - * @return - */ -float gdcmHeader::GetXImagePosition(void) { - float xImPos, yImPos, zImPos; - // 0020,0032 : Image Position Patient - // 0020,0030 : Image Position (RET) - // 0020,1041 : Slice Location - - 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)"); - string StrSliceLoc = GetPubElValByNumber(0x0020,0x1041); // for *very* old ACR-NEMA images - if (StrSliceLoc == "gdcm::Unfound") { - dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Slice Location (0020,1041)"); - // How to tell the caller nothing was found? - } - } - return 0.; - } - if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) - // How to tell the caller a wrong number of values was found? - return 0.; - //else - return xImPos; + * \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); } /** * \ingroup gdcmHeader - * \brief - * @return - */ -float gdcmHeader::GetYImagePosition(void) { - float xImPos, yImPos, zImPos; - // 0020,0032 : Image Position Patient - // 0020,1041 : Slice Location - // 0020,0050 : Location - 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)"); - string StrSliceLoc = GetPubElValByNumber(0x0020,0x1041); // for *very* old ACR-NEMA images - if (StrSliceLoc == "gdcm::Unfound") { - dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Slice Location (0020,1041)"); - // How to tell the caller nothing was found? - } - } - return 0.; - } - if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) - // How to tell the caller a wrong number of values was found? - return 0.; - return yImPos; + * \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); } /** * \ingroup gdcmHeader - * \brief - * @return - */ -float gdcmHeader::GetZImagePosition(void) { - float xImPos, yImPos, zImPos; - // 0020,0032 : Image Position Patient - // 0020,1041 : Slice Location - // 0020,0050 : Location - - // TODO : How to tell the caller nothing was found? - // TODO : How to tell the caller a wrong number of values was found? + * \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. - 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; - } - } + l= GetLUTLength(); + if(l==0) + return (NULL); + int nBits=GetLUTNbits(); + // a virer quand on aura trouve UNE image + // qui correspond VRAIMENT à la definition ! + cout << "l " << l << " nBits " << nBits; - 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; + 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