X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=e9ae38fc4c71c315e2f68879429bb3a6fc330da7;hb=5d5448482dc2b56be816c48df294af6884746547;hp=f94d9dc1b625eca7dfe56321d1cd04ef018e42c0;hpb=47438101c70c750ccdcb19df4816169a87fc6c1d;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index f94d9dc1..e9ae38fc 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -1,4 +1,6 @@ -// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.72 2003/07/01 09:29:56 jpr Exp $ +// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.117 2003/11/13 18:08:34 jpr Exp $ + +#include "gdcmHeader.h" #include #include @@ -11,28 +13,21 @@ #include // for isalpha #include #include "gdcmUtil.h" -#include "gdcmHeader.h" -using namespace std; - - -// TODO : remove DEBUG -#define DEBUG 0 +#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 - * @param none - * @return */ - void gdcmHeader::Initialise(void) { +void gdcmHeader::Initialise(void) { dicom_vr = gdcmGlobal::GetVR(); dicom_ts = gdcmGlobal::GetTS(); - Dicts = gdcmGlobal::GetDicts(); + Dicts = gdcmGlobal::GetDicts(); RefPubDict = Dicts->GetDefaultPubDict(); RefShaDict = (gdcmDict*)0; } @@ -40,27 +35,33 @@ using namespace std; /** * \ingroup gdcmHeader * \brief - * @param - * @return - */ - gdcmHeader::gdcmHeader(const char *InFilename, bool exception_on_error) { - SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_); - filename = InFilename; - Initialise(); - if ( !OpenFile(exception_on_error)) - return; - ParseHeader(); - LoadElements(); - CloseFile(); + * @param InFilename + * @param exception_on_error + */ +gdcmHeader::gdcmHeader(const char *InFilename, + bool exception_on_error, + bool enable_sequences ) { + if (enable_sequences) + enableSequences = 1; + else + enableSequences = 0; + + SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_); + filename = InFilename; + Initialise(); + if ( !OpenFile(exception_on_error)) + return; + ParseHeader(); + LoadElements(); + CloseFile(); } /** * \ingroup gdcmHeader * \brief - * @param - * @return + * @param exception_on_error */ - gdcmHeader::gdcmHeader(bool exception_on_error) { +gdcmHeader::gdcmHeader(bool exception_on_error) { SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_); Initialise(); } @@ -68,7 +69,7 @@ using namespace std; /** * \ingroup gdcmHeader * \brief - * @param + * @param exception_on_error * @return */ bool gdcmHeader::OpenFile(bool exception_on_error) @@ -78,19 +79,35 @@ using namespace std; if(!fp) throw gdcmFileError("gdcmHeader::gdcmHeader(const char *, bool)"); } - if ( fp ) - return true; - dbg.Verbose(0, "gdcmHeader::gdcmHeader cannot open file", filename.c_str()); + + if ( fp ) { + guint16 zero; + fread(&zero, (size_t)2, (size_t)1, fp); + + //ACR -- or DICOM with no Preamble + if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200) + return true; + //DICOM + fseek(fp, 126L, SEEK_CUR); + char dicm[4]; + fread(dicm, (size_t)4, (size_t)1, fp); + if( memcmp(dicm, "DICM", 4) == 0 ) + return true; + fclose(fp); + dbg.Verbose(0, "gdcmHeader::gdcmHeader not DICOM/ACR", filename.c_str()); + } + else { + dbg.Verbose(0, "gdcmHeader::gdcmHeader cannot open file", filename.c_str()); + } return false; } /** * \ingroup gdcmHeader * \brief - * @param - * @return + * @return TRUE if the close was successfull */ - bool gdcmHeader::CloseFile(void) { +bool gdcmHeader::CloseFile(void) { int closed = fclose(fp); fp = (FILE *)0; if (! closed) @@ -100,19 +117,24 @@ using namespace std; /** * \ingroup gdcmHeader - * \brief - * @param - * @return + * \brief Canonical destructor. */ - gdcmHeader::~gdcmHeader (void) { - dicom_vr = (gdcmVR*)0; - Dicts = (gdcmDictSet*)0; - RefPubDict = (gdcmDict*)0; - RefShaDict = (gdcmDict*)0; - return; +gdcmHeader::~gdcmHeader (void) { + dicom_vr = (gdcmVR*)0; + Dicts = (gdcmDictSet*)0; + RefPubDict = (gdcmDict*)0; + RefShaDict = (gdcmDict*)0; + return; } // Fourth semantics: +// +// ---> Warning : This fourth field is NOT part +// of the 'official' Dicom Dictionnary +// and should NOT be used. +// (Not defined for all the groups +// may be removed in a future release) +// // CMD Command // META Meta Information // DIR Directory @@ -142,6 +164,7 @@ using namespace std; // CRV Curve // OLY Overlays // PXL Pixels +// DL Delimiters // /** @@ -157,7 +180,7 @@ 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; @@ -198,9 +221,9 @@ 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"); @@ -209,7 +232,6 @@ void gdcmHeader::CheckSwap() dbg.Verbose(1, "gdcmHeader::CheckSwap:", "not an explicit Value Representation"); } - if (net2host) { sw = 4321; dbg.Verbose(1, "gdcmHeader::CheckSwap:", @@ -281,10 +303,8 @@ void gdcmHeader::CheckSwap() /** * \ingroup gdcmHeader * \brief - * @param - * @return */ - void gdcmHeader::SwitchSwapToBigEndian(void) { +void gdcmHeader::SwitchSwapToBigEndian(void) { dbg.Verbose(1, "gdcmHeader::SwitchSwapToBigEndian", "Switching to BigEndian mode."); if ( sw == 0 ) { @@ -306,13 +326,14 @@ void gdcmHeader::CheckSwap() /** * \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 @@ -328,7 +349,7 @@ 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 @@ -374,12 +395,13 @@ void gdcmHeader::FindVR( gdcmElValue *ElVal) { // We thought this was explicit VR, but we end up with an // implicit VR tag. Let's backtrack. - sprintf(msg,"Falsely explicit vr file (%04x,%04x)\n", ElVal->GetGroup(),ElVal->GetElement()); + 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 + // the semantics (see the usage of IsAnInteger), the vr proposed by the // dictionary entry. Still we have to flag the element as implicit since // we know now our assumption on expliciteness is not furfilled. // avoid . @@ -390,7 +412,7 @@ 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. @@ -400,7 +422,7 @@ 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; @@ -408,7 +430,7 @@ 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. @@ -418,7 +440,7 @@ 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; @@ -426,7 +448,7 @@ 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. @@ -436,7 +458,7 @@ 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; @@ -444,7 +466,7 @@ 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. @@ -454,7 +476,7 @@ 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; @@ -462,7 +484,7 @@ 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. @@ -472,7 +494,7 @@ 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; @@ -493,13 +515,15 @@ bool gdcmHeader::IsJPEGLossless(void) { const char * Transfert = Element->GetValue().c_str(); if ( memcmp(Transfert+strlen(Transfert)-2 ,"70",2)==0) return true; if ( memcmp(Transfert+strlen(Transfert)-2 ,"55",2)==0) return true; + if (Element->GetValue() == "1.2.840.10008.1.2.4.57") return true; + return false; } /** * \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. @@ -509,7 +533,7 @@ 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; @@ -517,7 +541,7 @@ 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. @@ -527,7 +551,7 @@ 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; @@ -535,7 +559,7 @@ 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 @@ -546,12 +570,51 @@ 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. @@ -571,9 +634,49 @@ bool gdcmHeader::IsDicomV3(void) { * applying this heuristic. */ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { - if ( FoundLength == 0xffffffff) + + ElVal->SetReadLength(FoundLength); // will be updated only if a bug is found + + if ( FoundLength == 0xffffffff) { FoundLength = 0; - ElVal->SetLength(FoundLength); + } + + // Sorry for the patch! + // XMedCom did the trick to read some nasty GE images ... + else if (FoundLength == 13) { + // The following 'if' will be removed when there is no more + // images on Creatis HDs with a 13 length for Manufacturer... + if ( (ElVal->GetGroup() != 0x0008) && + ( (ElVal->GetElement() != 0x0070) || (ElVal->GetElement() != 0x0080) ) ) { + // end of remove area + FoundLength =10; + ElVal->SetReadLength(10); // a bug is to be fixed + } + } + // to fix some garbage 'Leonardo' Siemens images + // May be commented out to avoid overhead + else if ( (ElVal->GetGroup() == 0x0009) + && + ( (ElVal->GetElement() == 0x1113) || (ElVal->GetElement() == 0x1114) ) ){ + FoundLength =4; + ElVal->SetReadLength(4); // a bug is to be fixed + } + // end of fix + + // to try to 'go inside' SeQuences (with length), and not to skip them + else if ( ElVal->GetVR() == "SQ") { + if (enableSequences) // only if the user does want to ! + FoundLength =0; + } + + // a SeQuence Element is beginning + // Let's forget it's length + // (we want to 'go inside') + else if(ElVal->GetGroup() == 0xfffe){ + FoundLength =0; + } + + ElVal->SetUsableLength(FoundLength); } /** @@ -593,41 +696,31 @@ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { while ( ! FoundSequenceDelimiter) { 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); - + n = ReadInt16(); 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); + 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; } ItemLength = ReadInt32(); TotalLength += ItemLength + 4; // We add 4 bytes since we just read - // the ItemLength with ReadInt32 - - if (DEBUG) printf("TotalLength %d\n",TotalLength); + // the ItemLength with ReadInt32 SkipBytes(ItemLength); } fseek(fp, PositionOnEntry, SEEK_SET); @@ -642,14 +735,13 @@ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { */ void gdcmHeader::FindLength (gdcmElValue * ElVal) { guint16 element = ElVal->GetElement(); - guint16 group = ElVal->GetGroup(); // JPR a virer - string vr = ElVal->GetVR(); + guint16 group = ElVal->GetGroup(); + std::string vr = ElVal->GetVR(); guint16 length16; - if( (element == 0x0010) && (group == 0x7fe0) ) {// JPR - - dbg.SetDebug(10); - dbg.Verbose(2, "gdcmHeader::FindLength: ", // JPR - "on est sur 7fe0 0010"); + if( (element == 0x0010) && (group == 0x7fe0) ) { + dbg.SetDebug(0); + dbg.Verbose(2, "gdcmHeader::FindLength: ", + "we reached 7fe0 0010"); } if ( (filetype == ExplicitVR) && ! ElVal->IsImplicitVr() ) { @@ -661,11 +753,12 @@ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { fseek(fp, 2L, SEEK_CUR); guint32 length32 = ReadInt32(); + if ( (vr == "OB") && (length32 == 0xffffffff) ) { ElVal->SetLength(FindLengthOB()); return; } - FixFoundLength(ElVal, length32); + FixFoundLength(ElVal, length32); return; } @@ -689,12 +782,12 @@ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { // appear when we find the first group with big endian encoding. This // is easy to detect since the length of a "Group Length" tag (the // ones with zero as element number) has to be of 4 (0x0004). When we - // encouter 1024 (0x0400) chances are the encoding changed and we + // encounter 1024 (0x0400) chances are the encoding changed and we // found a group with big endian encoding. // 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 @@ -725,9 +818,12 @@ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { // Heuristic: well some files are really ill-formed. if ( length16 == 0xffff) { length16 = 0; - dbg.Verbose(0, "gdcmHeader::FindLength", - "Erroneous element length fixed."); + //dbg.Verbose(0, "gdcmHeader::FindLength", + // "Erroneous element length fixed."); + // Actually, length= 0xffff means that we deal with + // Unknown Sequence Length } + FixFoundLength(ElVal, (guint32)length16); return; } @@ -739,14 +835,14 @@ void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { // not coexist in a Data Set and Data Sets nested within it".] // Length is on 4 bytes. FixFoundLength(ElVal, ReadInt32()); + return; } /** * \ingroup gdcmHeader * \brief Swaps back the bytes of 4-byte long integer accordingly to * processor order. - * - * @return The suggested integer. + * @return The properly swaped 32 bits integer. */ guint32 gdcmHeader::SwapLong(guint32 a) { switch (sw) { @@ -796,17 +892,17 @@ guint16 gdcmHeader::SwapShort(guint16 a) { /** * \ingroup gdcmHeader * \brief - * + * @param ElVal * @return */ void gdcmHeader::SkipElementValue(gdcmElValue * ElVal) { - SkipBytes(ElVal->GetLength()); + SkipBytes(ElVal->GetLength()); } /** * \ingroup gdcmHeader * \brief - * + * @param NewSize * @return */ void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) { @@ -828,7 +924,7 @@ guint16 gdcmHeader::SwapShort(guint16 a) { void gdcmHeader::LoadElementValue(gdcmElValue * ElVal) { size_t item_read; guint16 group = ElVal->GetGroup(); - string vr = ElVal->GetVR(); + std::string vr= ElVal->GetVR(); guint32 length = ElVal->GetLength(); bool SkipLoad = false; @@ -841,13 +937,18 @@ void gdcmHeader::LoadElementValue(gdcmElValue * ElVal) { // car commencer par les ignorer risque de conduire a qq chose // qui pourrait ne pas etre generalisable // Well, I'm expecting your code !!! + + // the test was commented out to 'go inside' the SeQuences + // we don't any longer skip them ! - if( vr == "SQ" ) - SkipLoad = true; + // if( vr == "SQ" ) + // SkipLoad = true; - // 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). + // A SeQuence "contains" a set of Elements. + // (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; @@ -867,10 +968,11 @@ 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(); + s << " x(" << std::hex << ElVal->GetLength() << ")"; ElVal->SetValue(s.str()); return; } @@ -878,14 +980,13 @@ void gdcmHeader::LoadElementValue(gdcmElValue * ElVal) { // When an integer is expected, read and convert the following two or // four bytes properly i.e. as an integer as opposed to a string. - // pour les elements de Value Multiplicity > 1 - // on aura en fait une serie d'entiers - - // on devrait pouvoir faire + compact (?) + // Actually, elements with Value Multiplicity > 1 + // contain a set of integers (not a single one) + // Any compacter code suggested (?) if ( IsAnInteger(ElVal) ) { guint32 NewInt; - ostringstream s; + std::ostringstream s; int nbInt; if (vr == "US" || vr == "SS") { nbInt = length / 2; @@ -910,7 +1011,8 @@ void gdcmHeader::LoadElementValue(gdcmElValue * ElVal) { s << NewInt; } } - } + } + s << '\0'; // to avoid oddities on Solaris ElVal->SetValue(s.str()); return; } @@ -950,20 +1052,21 @@ 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; } @@ -974,7 +1077,8 @@ guint16 gdcmHeader::ReadInt16(void) { /** * \ingroup gdcmHeader - * \brief + * \brief Reads a supposed to be 32 Bits integer + * \ (swaps it depending on processor endianity) * * @return */ @@ -982,13 +1086,12 @@ 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; } @@ -1040,49 +1143,80 @@ 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 ) { - +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); + if (CheckIfExistByNumber(Group, Elem) == 0) { + gdcmElValue* a =NewElValueByNumber(Group, Elem); + if (a == NULL) + return 0; + PubElValSet.Add(a); + } + PubElValSet.SetElValueByNumber(Value, Group, Elem); + return(1); } /** * \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 ) { - gdcmElValue* nvElValue=NewElValueByNumber(Group, Elem); - PubElValSet.Add(nvElValue); - string v = Value; - PubElValSet.SetElValueByNumber(v, Group, Elem); - return(1); + gdcmElValue* nvElValue=NewElValueByNumber(Group, Elem); + PubElValSet.Add(nvElValue); + std::string v = Value; + PubElValSet.SetElValueByNumber(v, Group, Elem); + return(1); } + /** * \ingroup gdcmHeader - * \brief TODO - * @param + * \brief Set a new value if the invoked element exists + * Seems to be useless !!! + * @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)); +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. @@ -1090,7 +1224,7 @@ int gdcmHeader::ReplaceOrCreateByNumber(char* Value, guint16 Group, guint16 Elem * 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) @@ -1117,11 +1251,7 @@ gdcmElValue * gdcmHeader::ReadNextElement(void) { g = ReadInt16(); n = ReadInt16(); - - if ( (g==0x7fe0) && (n==0x0010) ) - if (DEBUG) - printf("in gdcmHeader::ReadNextElement try to read 7fe0 0010 \n"); - + if (errno == 1) // We reached the EOF (or an error occured) and header parsing // has to be considered as finished. @@ -1130,15 +1260,13 @@ gdcmElValue * gdcmHeader::ReadNextElement(void) { NewElVal = NewElValueByNumber(g, n); FindVR(NewElVal); FindLength(NewElVal); + if (errno == 1) { // Call it quits - if (DEBUG) printf("in gdcmHeader::ReadNextElement : g %04x n %04x errno %d\n",g, n, errno); return (gdcmElValue *)0; } NewElVal->SetOffset(ftell(fp)); - if ( (g==0x7fe0) && (n==0x0010) ) - if (DEBUG) - printf("sortie de gdcmHeader::ReadNextElement 7fe0 0010 \n"); + //if ( (g==0x7fe0) && (n==0x0010) ) return NewElVal; } @@ -1150,9 +1278,8 @@ gdcmElValue * gdcmHeader::ReadNextElement(void) { * @return The result of the heuristical predicate. */ 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 @@ -1162,9 +1289,6 @@ bool gdcmHeader::IsAnInteger(gdcmElValue * ElVal) { if (length == 4) return true; else { - if (DEBUG) printf("Erroneous Group Length element length (%04x , %04x) : %d\n", - group, element,length); - dbg.Error("gdcmHeader::IsAnInteger", "Erroneous Group Length element length."); } @@ -1189,8 +1313,8 @@ 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() ); @@ -1209,6 +1333,40 @@ size_t gdcmHeader::GetPixelOffset(void) { return 0; } +/** + * \ingroup gdcmHeader + * \brief Recover the pixel area length (in Bytes) . + */ +size_t gdcmHeader::GetPixelAreaLength(void) { + // If this file complies with the norm we should encounter the + // "Image Location" tag (0x0028, 0x0200). This tag contains the + // the group that contains the pixel data (hence the "Pixel Data" + // is found by indirection through the "Image Location"). + // Inside the group pointed by "Image Location" the searched element + // is conventionally the element 0x0010 (when the norm is respected). + // When the "Image Location" is absent we default to group 0x7fe0. + guint16 grPixel; + guint16 numPixel; + std::string ImageLocation = GetPubElValByName("Image Location"); + if ( ImageLocation == GDCM_UNFOUND ) { + grPixel = 0x7fe0; + } else { + grPixel = (guint16) atoi( ImageLocation.c_str() ); + } + if (grPixel != 0x7fe0) + // This is a kludge for old dirty Philips imager. + numPixel = 0x1010; + else + numPixel = 0x0010; + + gdcmElValue* PixelElement = PubElValSet.GetElementByNumber(grPixel, + numPixel); + if (PixelElement) + return PixelElement->GetLength(); + else + return 0; +} + /** * \ingroup gdcmHeader * \brief Searches both the public and the shadow dictionary (when they @@ -1247,7 +1405,7 @@ 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", @@ -1273,9 +1431,9 @@ 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); } @@ -1291,12 +1449,12 @@ 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(); } @@ -1304,11 +1462,11 @@ string gdcmHeader::GetPubElValRepByNumber(guint16 group, guint16 element) { * \ingroup gdcmHeader * \brief Searches within the public dictionary for element value of * a given tag. - * @param TagName name of the researched element. + * @param TagName name of the searched 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); } @@ -1321,14 +1479,14 @@ string gdcmHeader::GetPubElValByName(string TagName) { * to convert the string typed content to caller's native type * (think of C++ vs Python). The VR is actually of a higher level * of semantics than just the native C++ type. - * @param TagName name of the researched element. + * @param TagName name of the searched 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(); } @@ -1336,12 +1494,12 @@ string gdcmHeader::GetPubElValRepByName(string TagName) { * \ingroup gdcmHeader * \brief Searches within elements parsed with the SHADOW dictionary * for the element value of a given tag. - * @param group Group of the researched tag. - * @param element Element of the researched tag. + * @param group Group of the searched tag. + * @param element Element of the searched 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); } @@ -1354,15 +1512,15 @@ string gdcmHeader::GetShaElValByNumber(guint16 group, guint16 element) { * to convert the string typed content to caller's native type * (think of C++ vs Python). The VR is actually of a higher level * of semantics than just the native C++ type. - * @param group Group of the researched tag. - * @param element Element of the researched tag. + * @param group Group of the searched tag. + * @param element Element of the searched 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(); } @@ -1370,11 +1528,11 @@ string gdcmHeader::GetShaElValRepByNumber(guint16 group, guint16 element) { * \ingroup gdcmHeader * \brief Searches within the elements parsed with the shadow dictionary * for an element value of given tag. - * @param TagName name of the researched element. + * @param TagName name of the searched 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); } @@ -1387,14 +1545,14 @@ string gdcmHeader::GetShaElValByName(string TagName) { * to convert the string typed content to caller's native type * (think of C++ vs Python). The VR is actually of a higher level * of semantics than just the native C++ type. - * @param TagName name of the researched element. + * @param TagName name of the searched 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(); } @@ -1403,13 +1561,13 @@ string gdcmHeader::GetShaElValRepByName(string TagName) { * \brief Searches within elements parsed with the public dictionary * and then within the elements parsed with the shadow dictionary * for the element value of a given tag. - * @param group Group of the researched tag. - * @param element Element of the researched tag. + * @param group Group of the searched tag. + * @param element Element of the searched 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); @@ -1425,13 +1583,13 @@ string gdcmHeader::GetElValByNumber(guint16 group, guint16 element) { * to convert the string typed content to caller's native type * (think of C++ vs Python). The VR is actually of a higher level * of semantics than just the native C++ type. - * @param group Group of the researched tag. - * @param element Element of the researched tag. + * @param group Group of the searched tag. + * @param element Element of the searched 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); @@ -1442,12 +1600,12 @@ string gdcmHeader::GetElValRepByNumber(guint16 group, guint16 element) { * \brief Searches within elements parsed with the public dictionary * and then within the elements parsed with the shadow dictionary * for the element value of a given tag. - * @param TagName name of the researched element. + * @param TagName name of the searched 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); @@ -1463,12 +1621,12 @@ string gdcmHeader::GetElValByName(string TagName) { * to convert the string typed content to caller's native type * (think of C++ vs Python). The VR is actually of a higher level * of semantics than just the native C++ type. - * @param TagName name of the researched element. + * @param TagName name of the searched 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); @@ -1483,10 +1641,11 @@ 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 +//TODO : homogeneiser les noms : SetPubElValByNumber +// qui appelle PubElValSet.SetElValueByNumber // pourquoi pas SetPubElValueByNumber ?? { @@ -1500,7 +1659,7 @@ 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) ); } @@ -1531,7 +1690,7 @@ 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) ); } @@ -1541,10 +1700,10 @@ 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) ); } /** @@ -1556,25 +1715,256 @@ void gdcmHeader::ParseHeader(bool exception_on_error) throw(gdcmFormatError) { rewind(fp); CheckSwap(); - while ( (newElValue = ReadNextElement()) ) { + while ( (newElValue = ReadNextElement()) ) { SkipElementValue(newElValue); PubElValSet.Add(newElValue); } } +/** + * \ingroup gdcmHeader + * \brief This predicate, based on hopefully reasonable 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); + + // We don't use any longer the HashTable, since a lot a stuff is missing + // when SeQuences were encountered + // + //TagElValueHT ht = PubElValSet.GetTagHt(); + //for (TagElValueHT::iterator tag = ht.begin(); tag != ht.end(); ++tag) { + // LoadElementValue(tag->second); + //} + + for (ListTag::iterator i = GetListElem().begin(); + i != GetListElem().end(); + ++i){ + LoadElementValue(*i); + } + + 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 integer, acts as a Boolean + */ +int gdcmHeader::Write(FILE * fp, FileType type) { + + // TODO : move the following lines (and a lot of others, to be written) + // to a future function CheckAndCorrectHeader + + if (type == ImplicitVR) { + std::string implicitVRTransfertSyntax = "1.2.840.10008.1.2"; + ReplaceOrCreateByNumber(implicitVRTransfertSyntax,0x0002, 0x0010); + + //FIXME Refer to standards on page 21, chapter 6.2 "Value representation": + // values with a VR of UI shall be padded with a single trailing null + // Dans le cas suivant on doit pader manuellement avec un 0 + + PubElValSet.SetElValueLengthByNumber(18, 0x0002, 0x0010); + } + + if (type == ExplicitVR) { + std::string explicitVRTransfertSyntax = "1.2.840.10008.1.2.1"; + ReplaceOrCreateByNumber(explicitVRTransfertSyntax,0x0002, 0x0010); + + //FIXME Refer to standards on page 21, chapter 6.2 "Value representation": + // values with a VR of UI shall be padded with a single trailing null + // Dans le cas suivant on doit pader manuellement avec un 0 + + PubElValSet.SetElValueLengthByNumber(20, 0x0002, 0x0010); + } + + return PubElValSet.Write(fp, type); +} // -// 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 +// ------------------------ 'non string' elements related functions // -// --> 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 :-( + +/** + * \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; + } + return a; +} + +/** + * \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 @@ -1584,8 +1974,8 @@ 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()); } @@ -1599,8 +1989,8 @@ 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; @@ -1622,20 +2012,19 @@ 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 @@ -1644,26 +2033,54 @@ int gdcmHeader::GetZSize(void) { * @return The encountered number of Bits Stored, 0 by default. */ int gdcmHeader::GetBitsStored(void) { - string StrSize = GetPubElValByNumber(0x0028,0x0101); - if (StrSize == "gdcm::Unfound") + std::string StrSize = GetPubElValByNumber(0x0028,0x0101); + if (StrSize == GDCM_UNFOUND) return 1; return atoi(StrSize.c_str()); } +/** + * \ingroup gdcmHeader + * \brief Retrieve the number of Bits Allocated + * (8, 12 -compacted ACR-NEMA files, 16, ...) + * + * @return The encountered number of Bits Allocated, 0 by default. + */ +int gdcmHeader::GetBitsAllocated(void) { + std::string StrSize = GetPubElValByNumber(0x0028,0x0100); + 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) + * (1 : gray level, 3 : RGB -1 or 3 Planes-) * * @return The encountered number of Samples Per Pixel, 1 by default. */ int gdcmHeader::GetSamplesPerPixel(void) { - string StrSize = GetPubElValByNumber(0x0028,0x0002); - if (StrSize == "gdcm::Unfound") + 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. @@ -1671,7 +2088,7 @@ int gdcmHeader::GetSamplesPerPixel(void) { * */ int gdcmHeader::GetPixelSize(void) { - string PixelType = GetPixelType(); + std::string PixelType = GetPixelType(); if (PixelType == "8U" || PixelType == "8S") return 1; if (PixelType == "16U" || PixelType == "16S") @@ -1693,333 +2110,253 @@ int gdcmHeader::GetPixelSize(void) { * - 32U unsigned 32 bit, * - 32S signed 32 bit, * \warning 12 bit images appear as 16 bit. + * \ 24 bit images appear as 8 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"); - - string Signed; + if (BitsAlloc == "12") // It will be unpacked + BitsAlloc = std::string("16"); + else if (BitsAlloc == "24") // (in order no to be messed up + BitsAlloc = std::string("8"); // by old RGB images) + + 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"); - - 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); - } -} +std::cout << "GetPixelType : " << BitsAlloc + Signed << std::endl; + Signed = std::string("S"); -/** - * \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); + return( BitsAlloc + Signed); } /** * \ingroup gdcmHeader - * \brief - * @return + * \brief gets the info from 0002,0010 : Transfert Syntax + * \ else 1. + * @return Transfert Syntax Name (as oposite to Transfert Syntax UID) */ - -int gdcmHeader::Write(FILE * fp, FileType type) { - return PubElValSet.Write(fp, type); +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"; + } + // 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 - * @return - */ -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; -} +// -------------------------------- Lookup Table related functions ------------ /** * \ingroup gdcmHeader - * \brief - * @return + * \brief tells us if LUT are used + * \warning Right now, Segmented xxx Palette Color Lookup Table Data + * \ are NOT considered as LUT, since nobody knows + *\ how to deal with them + * @return int acts as a Boolean */ -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; -} - +int gdcmHeader::HasLUT(void) { -/** - * \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 - return atof(StrSliceThickness.c_str()); - } else { - return atof(StrSpacingBSlices.c_str()); - } -} - -// -// Image Position Patient : -// If not found (AVR-NEMA), we consider Slice Location (20,1041) -// or Location (20,50) as the Z coordinate, -// 0. for all the coordinates if Slice Location not 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 - // 0020,1041 : 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; + // Check the presence of the LUT Descriptors + if (GetPubElValByNumber(0x0028,0x1101) == GDCM_UNFOUND) + return 0; + // LutDescriptorGreen + if (GetPubElValByNumber(0x0028,0x1102) == GDCM_UNFOUND) + return 0; + // LutDescriptorBlue + if (GetPubElValByNumber(0x0028,0x1103) == GDCM_UNFOUND) + return 0; + // It is not enough + // we check also + if (GetPubElValByNumber(0x0028,0x1201) == GDCM_UNFOUND) + return 0; + if (GetPubElValByNumber(0x0028,0x1202) == GDCM_UNFOUND) + return 0; + if (GetPubElValByNumber(0x0028,0x1203) == GDCM_UNFOUND) + return 0; + return 1; } /** * \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::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.; - //else - return yImPos; + +int gdcmHeader::GetLUTNbits(void) { + std::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 + 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 - * @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 builts Red/Green/Blue/Alpha LUT from Header + * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] + * \ and (0028,1101),(0028,1102),(0028,1102) + * \ - xxx Palette Color Lookup Table Descriptor - are found + * \ and (0028,1201),(0028,1202),(0028,1202) + * \ - xxx Palette Color Lookup Table Data - are found + * \warning does NOT deal with : + * \ 0028 1100 Gray Lookup Table Descriptor (Retired) + * \ 0028 1221 Segmented Red Palette Color Lookup Table Data + * \ 0028 1222 Segmented Green Palette Color Lookup Table Data + * \ 0028 1223 Segmented Blue Palette Color Lookup Table Data + * \ no known Dicom reader deails with them :-( + * @return Lookup Table RGBA + */ - 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; - } - } +unsigned char * gdcmHeader::GetLUTRGBA(void) { +// Not so easy : see +// http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables +// and OT-PAL-8-face.dcm + +// if Photometric Interpretation # PALETTE COLOR, no LUT to be done + + if (gdcmHeader::GetPubElValByNumber(0x0028,0x0004) != "PALETTE COLOR ") { + return NULL; + } + + int lengthR, debR, nbitsR; + int lengthG, debG, nbitsG; + int lengthB, debB, nbitsB; - StrImPos = GetPubElValByNumber(0x0020,0x0030); // For ACR-NEMA images - if (StrImPos != "gdcm::Unfound") { - if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) { - dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position (RET) (0020,0030)"); - return 0.; // bug in the element 0x0020,0x0032 - } else { - return zImPos; - } - } - - string StrSliceLocation = GetPubElValByNumber(0x0020,0x1041);// for *very* old ACR-NEMA images - if (StrSliceLocation != "gdcm::Unfound") { - if( sscanf( StrSliceLocation.c_str(), "%f", &zImPos) !=1) { - dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Slice Location (0020,1041)"); - return 0.; // bug in the element 0x0020,0x1041 - } else { - return zImPos; - } - } - dbg.Verbose(0, "gdcmHeader::GetZImagePosition: unfound Slice Location (0020,1041)"); - - string StrLocation = GetPubElValByNumber(0x0020,0x0050); - if (StrLocation != "gdcm::Unfound") { - if( sscanf( StrLocation.c_str(), "%f", &zImPos) !=1) { - dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Location (0020,0050)"); - return 0.; // bug in the element 0x0020,0x0050 - } else { - return zImPos; - } - } - dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Slice Location"); +// Get info from Lut Descriptors +// (the 3 LUT descriptors may be different) - return 0.; // Hopeless -} - - + std::string LutDescriptionR = GetPubElValByNumber(0x0028,0x1101); + if (LutDescriptionR == GDCM_UNFOUND) + return NULL; + std::string LutDescriptionG = GetPubElValByNumber(0x0028,0x1102); + if (LutDescriptionG == GDCM_UNFOUND) + return NULL; + std::string LutDescriptionB = GetPubElValByNumber(0x0028,0x1103); + if (LutDescriptionB == GDCM_UNFOUND) + return NULL; + + std::vector tokens; + + tokens.erase(tokens.begin(),tokens.end()); // clean any previous value + Tokenize (LutDescriptionR, tokens, "\\"); + lengthR=atoi(tokens[0].c_str()); // Red LUT length in Bytes + debR =atoi(tokens[1].c_str()); // subscript of the first Lut Value + nbitsR =atoi(tokens[2].c_str()); // Lut item size (in Bits) + tokens.clear(); + + tokens.erase(tokens.begin(),tokens.end()); // clean any previous value + Tokenize (LutDescriptionG, tokens, "\\"); + lengthG=atoi(tokens[0].c_str()); // Green LUT length in Bytes + debG =atoi(tokens[1].c_str()); + nbitsG =atoi(tokens[2].c_str()); + tokens.clear(); + + tokens.erase(tokens.begin(),tokens.end()); // clean any previous value + Tokenize (LutDescriptionB, tokens, "\\"); + lengthB=atoi(tokens[0].c_str()); // Blue LUT length in Bytes + debB =atoi(tokens[1].c_str()); + nbitsB =atoi(tokens[2].c_str()); + tokens.clear(); + +// Load LUTs into memory, (as they were stored on disk) + + unsigned char *lutR =(unsigned char *) + GetPubElValVoidAreaByNumber(0x0028,0x1201); + unsigned char *lutG =(unsigned char *) + GetPubElValVoidAreaByNumber(0x0028,0x1202); + unsigned char *lutB =(unsigned char *) + GetPubElValVoidAreaByNumber(0x0028,0x1203); + + if (!lutR || !lutG || !lutB ) { + return NULL; + } + // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT + + unsigned char *LUTRGBA = (unsigned char *)calloc(1024,1); // 256 * 4 (R, G, B, Alpha) + if (!LUTRGBA) { + return NULL; + } + memset(LUTRGBA, 0, 1024); + // Bits Allocated + int nb; + std::string str_nb = GetPubElValByNumber(0x0028,0x0100); + if (str_nb == GDCM_UNFOUND ) { + nb = 16; + } else { + nb = atoi(str_nb.c_str() ); + } + int mult; + + if (nbitsR==16 && nb==8) // when LUT item size is different than pixel size + mult=2; // high byte must be = low byte + else // See PS 3.3-2003 C.11.1.1.2 p 619 + mult=1; + + + // if we get a black image, let's just remove the '+1' + // from 'i*mult+1' and check again + // if it works, we shall have to check the 3 Palettes + // to see which byte is ==0 (first one, or second one) + // and fix the code + // We give up the checking to avoid some overhead + + unsigned char *a; + int i; + a= LUTRGBA+0; + for(i=0;i