X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=837db41455e4d60857fcedf3052525291b264979;hb=10aa56aa534bae643e3833474a49309330235196;hp=38763a3af7dac7d28fc142e18dc93dc45f674a74;hpb=21dc537d0c6c274bf1bc49084813a9f4e4cf29eb;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index 38763a3a..837db414 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -1,4 +1,4 @@ -// gdcmHeader.cxx +// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.69 2003/06/17 17:44:48 jpr Exp $ #include #include @@ -12,79 +12,101 @@ #include #include "gdcmUtil.h" #include "gdcmHeader.h" +using namespace std; + + +// TODO : remove DEBUG +#define DEBUG 0 // Refer to gdcmHeader::CheckSwap() #define HEADER_LENGTH_TO_READ 256 // Refer to gdcmHeader::SetMaxSizeLoadElementValue() #define _MaxSizeLoadElementValue_ 1024 -VRHT * gdcmHeader::dicom_vr = (VRHT*)0; - void gdcmHeader::Initialise(void) { - if (!gdcmHeader::dicom_vr) - InitVRDict(); - Dicts = new gdcmDictSet(); + dicom_vr = gdcmGlobal::GetVR(); + dicom_ts = gdcmGlobal::GetTS(); + Dicts = gdcmGlobal::GetDicts(); RefPubDict = Dicts->GetDefaultPubDict(); RefShaDict = (gdcmDict*)0; } -gdcmHeader::gdcmHeader(const char *InFilename, bool exception_on_error) - throw(gdcmFileError) { +gdcmHeader::gdcmHeader(const char *InFilename, bool exception_on_error) { SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_); filename = InFilename; Initialise(); - fp=fopen(InFilename,"rb"); + if ( !OpenFile(exception_on_error)) + return; + ParseHeader(); + LoadElements(); + CloseFile(); +} + +gdcmHeader::gdcmHeader(bool exception_on_error) { + SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_); + Initialise(); +} + +bool gdcmHeader::OpenFile(bool exception_on_error) + throw(gdcmFileError) { + fp=fopen(filename.c_str(),"rb"); if(exception_on_error) { if(!fp) throw gdcmFileError("gdcmHeader::gdcmHeader(const char *, bool)"); } - else - dbg.Error(!fp, "gdcmHeader::gdcmHeader cannot open file", InFilename); - ParseHeader(); - AddAndDefaultElements(); + if ( fp ) + return true; + dbg.Verbose(0, "gdcmHeader::gdcmHeader cannot open file", filename.c_str()); + return false; } +bool gdcmHeader::CloseFile(void) { + int closed = fclose(fp); + fp = (FILE *)0; + if (! closed) + return false; + return true; +} gdcmHeader::~gdcmHeader (void) { - //FIXME obviously there is much to be done here ! - fclose(fp); + dicom_vr = (gdcmVR*)0; + Dicts = (gdcmDictSet*)0; + RefPubDict = (gdcmDict*)0; + RefShaDict = (gdcmDict*)0; return; } -void gdcmHeader::InitVRDict (void) { - if (dicom_vr) { - dbg.Verbose(0, "gdcmHeader::InitVRDict:", "VR dictionary allready set"); - return; - } - VRHT *vr = new VRHT; - (*vr)["AE"] = "Application Entity"; // At most 16 bytes - (*vr)["AS"] = "Age String"; // Exactly 4 bytes - (*vr)["AT"] = "Attribute Tag"; // 2 16-bit unsigned short integers - (*vr)["CS"] = "Code String"; // At most 16 bytes - (*vr)["DA"] = "Date"; // Exactly 8 bytes - (*vr)["DS"] = "Decimal String"; // At most 16 bytes - (*vr)["DT"] = "Date Time"; // At most 26 bytes - (*vr)["FL"] = "Floating Point Single"; // 32-bit IEEE 754:1985 float - (*vr)["FD"] = "Floating Point Double"; // 64-bit IEEE 754:1985 double - (*vr)["IS"] = "Integer String"; // At most 12 bytes - (*vr)["LO"] = "Long String"; // At most 64 chars - (*vr)["LT"] = "Long Text"; // At most 10240 chars - (*vr)["OB"] = "Other Byte String"; // String of bytes (vr independant) - (*vr)["OW"] = "Other Word String"; // String of 16-bit words (vr dep) - (*vr)["PN"] = "Person Name"; // At most 64 chars - (*vr)["SH"] = "Short String"; // At most 16 chars - (*vr)["SL"] = "Signed Long"; // Exactly 4 bytes - (*vr)["SQ"] = "Sequence of Items"; // Not Applicable - (*vr)["SS"] = "Signed Short"; // Exactly 2 bytes - (*vr)["ST"] = "Short Text"; // At most 1024 chars - (*vr)["TM"] = "Time"; // At most 16 bytes - (*vr)["UI"] = "Unique Identifier"; // At most 64 bytes - (*vr)["UL"] = "Unsigned Long "; // Exactly 4 bytes - (*vr)["UN"] = "Unknown"; // Any length of bytes - (*vr)["US"] = "Unsigned Short "; // Exactly 2 bytes - (*vr)["UT"] = "Unlimited Text"; // At most 2^32 -1 chars - dicom_vr = vr; -} +// Fourth semantics: +// CMD Command +// META Meta Information +// DIR Directory +// ID +// PAT Patient +// ACQ Acquisition +// REL Related +// IMG Image +// SDY Study +// VIS Visit +// WAV Waveform +// PRC +// DEV Device +// NMI Nuclear Medicine +// MED +// BFS Basic Film Session +// BFB Basic Film Box +// BIB Basic Image Box +// BAB +// IOB +// PJ +// PRINTER +// RT Radio Therapy +// DVH +// SSET +// RES Results +// CRV Curve +// OLY Overlays +// PXL Pixels +// /** * \ingroup gdcmHeader @@ -119,17 +141,11 @@ void gdcmHeader::CheckSwap() entCur = deb + 128; if(memcmp(entCur, "DICM", (size_t)4) == 0) { - filetype = TrueDicom; dbg.Verbose(1, "gdcmHeader::CheckSwap:", "looks like DICOM Version3"); - } else { - filetype = Unknown; - dbg.Verbose(1, "gdcmHeader::CheckSwap:", "not a DICOM Version3 file"); - } - - if(filetype == TrueDicom) { // Next, determine the value representation (VR). Let's skip to the - // first element (0002, 0000) and check there if we find "UL", in - // which case we (almost) know it is explicit VR. + // first element (0002, 0000) and check there if we find "UL" + // - or "OB" if the 1st one is (0002,0001) -, + // in which case we (almost) know it is explicit VR. // WARNING: if it happens to be implicit VR then what we will read // is the length of the group. If this ascii representation of this // length happens to be "UL" then we shall believe it is explicit VR. @@ -139,10 +155,16 @@ void gdcmHeader::CheckSwap() // We need to skip : // * the 128 bytes of File Preamble (often padded with zeroes), // * the 4 bytes of "DICM" string, - // * the 4 bytes of the first tag (0002, 0000), + // * the 4 bytes of the first tag (0002, 0000),or (0002, 0001) // i.e. a total of 136 bytes. entCur = deb + 136; - if(memcmp(entCur, "UL", (size_t)2) == 0) { + // FIXME + // Use gdcmHeader::dicom_vr to test all the possibilities + // instead of just checking for UL, OB and UI !? + if( (memcmp(entCur, "UL", (size_t)2) == 0) || + (memcmp(entCur, "OB", (size_t)2) == 0) || + (memcmp(entCur, "UI", (size_t)2) == 0) ) + { filetype = ExplicitVR; dbg.Verbose(1, "gdcmHeader::CheckSwap:", "explicit Value Representation"); @@ -167,11 +189,12 @@ void gdcmHeader::CheckSwap() rewind(fp); fseek (fp, 132L, SEEK_SET); return; - } // End of TrueDicom + } // End of DicomV3 // Alas, this is not a DicomV3 file and whatever happens there is no file // preamble. We can reset the file position indicator to where the data // is (i.e. the beginning of the file). + dbg.Verbose(1, "gdcmHeader::CheckSwap:", "not a DICOM Version3 file"); rewind(fp); // Our next best chance would be to be considering a 'clean' ACR/NEMA file. @@ -211,6 +234,7 @@ void gdcmHeader::CheckSwap() // It is time for despaired wild guesses. So, let's assume this file // happens to be 'dirty' ACR/NEMA, i.e. the length of the group is // not present. Then the only info we have is the net2host one. + filetype = Unknown; if (! net2host ) sw = 0; else @@ -237,26 +261,19 @@ void gdcmHeader::SwitchSwapToBigEndian(void) { sw = 3412; } -void gdcmHeader::GetPixels(size_t lgrTotale, void* _Pixels) { - size_t pixelsOffset; - pixelsOffset = GetPixelOffset(); - fseek(fp, pixelsOffset, SEEK_SET); - fread(_Pixels, 1, lgrTotale, fp); -} - - - /** * \ingroup gdcmHeader * \brief Find the value representation of the current tag. */ -void gdcmHeader::FindVR( ElValue *ElVal) { +void gdcmHeader::FindVR( gdcmElValue *ElVal) { if (filetype != ExplicitVR) return; char VR[3]; string vr; int lgrLue; + char msg[100]; // for sprintf. Sorry + long PositionOnEntry = ftell(fp); // Warning: we believe this is explicit VR (Value Representation) because // we used a heuristic that found "UL" in the first tag. Alas this @@ -285,8 +302,8 @@ void gdcmHeader::FindVR( ElValue *ElVal) { // CLEANME searching the dicom_vr at each occurence is expensive. // PostPone this test in an optional integrity check at the end // of parsing or only in debug mode. - if ( RealExplicit && !dicom_vr->count(vr) ) - RealExplicit = false; + if ( RealExplicit && !dicom_vr->Count(vr) ) + RealExplicit= false; if ( RealExplicit ) { if ( ElVal->IsVrUnknown() ) { @@ -313,8 +330,11 @@ void gdcmHeader::FindVR( ElValue *ElVal) { } // We thought this was explicit VR, but we end up with an - // implicit VR tag. Let's backtrack. - dbg.Verbose(1, "gdcmHeader::FindVR:", "Falsely explicit vr file"); + // implicit VR tag. Let's backtrack. + + sprintf(msg,"Falsely explicit vr file (%04x,%04x)\n", ElVal->GetGroup(),ElVal->GetElement()); + dbg.Verbose(1, "gdcmHeader::FindVR: ",msg); + fseek(fp, PositionOnEntry, SEEK_SET); // When this element is known in the dictionary we shall use, e.g. for // the semantics (see the usage of IsAnInteger), the vr proposed by the @@ -334,7 +354,7 @@ void gdcmHeader::FindVR( ElValue *ElVal) { * @return True when ImplicitVRLittleEndian found. False in all other cases. */ bool gdcmHeader::IsImplicitVRLittleEndianTransferSyntax(void) { - ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -352,7 +372,7 @@ bool gdcmHeader::IsImplicitVRLittleEndianTransferSyntax(void) { * @return True when ExplicitVRLittleEndian found. False in all other cases. */ bool gdcmHeader::IsExplicitVRLittleEndianTransferSyntax(void) { - ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -370,7 +390,7 @@ bool gdcmHeader::IsExplicitVRLittleEndianTransferSyntax(void) { * @return True when DeflatedExplicitVRLittleEndian found. False in all other cases. */ bool gdcmHeader::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) { - ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -388,12 +408,12 @@ bool gdcmHeader::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) { * @return True when big endian found. False in all other cases. */ bool gdcmHeader::IsExplicitVRBigEndianTransferSyntax(void) { - ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.2" ) + if ( Transfer == "1.2.840.10008.1.2.2" ) //1.2.2 ??? A verifier ! return true; return false; } @@ -406,7 +426,7 @@ bool gdcmHeader::IsExplicitVRBigEndianTransferSyntax(void) { * @return True when JPEGBaseLineProcess1found. False in all other cases. */ bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) { - ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -416,6 +436,25 @@ bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) { return false; } +/** + * \ingroup gdcmHeader + * \brief + * + * @return + */ +bool gdcmHeader::IsJPEGLossless(void) { + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); + // faire qq chose d'intelligent a la place de ça + if ( !Element ) + return false; + LoadElementValueSafe(Element); + const char * Transfert = Element->GetValue().c_str(); + if ( memcmp(Transfert+strlen(Transfert)-2 ,"70",2)==0) return true; + if ( memcmp(Transfert+strlen(Transfert)-2 ,"55",2)==0) return true; + return false; +} + + /** * \ingroup gdcmHeader * \brief Determines if the Transfer Syntax was allready encountered @@ -424,7 +463,7 @@ bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) { * @return True when JPEGExtendedProcess2-4 found. False in all other cases. */ bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) { - ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -442,7 +481,7 @@ bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) { * @return True when JPEGExtendedProcess3-5 found. False in all other cases. */ bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) { - ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -461,7 +500,7 @@ bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) { * other cases. */ bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) { - ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); + gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); @@ -471,19 +510,37 @@ bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) { return false; } +/** + * \ingroup gdcmHeader + * \brief Predicate for dicom version 3 file. + * @return True when the file is a dicom version 3. + */ +bool gdcmHeader::IsDicomV3(void) { + if ( (filetype == ExplicitVR) + || (filetype == ImplicitVR) ) + return true; + return false; +} + /** * \ingroup gdcmHeader * \brief When the length of an element value is obviously wrong (because * the parser went Jabberwocky) one can hope improving things by * applying this heuristic. */ -void gdcmHeader::FixFoundLength(ElValue * ElVal, guint32 FoundLength) { +void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { if ( FoundLength == 0xffffffff) FoundLength = 0; ElVal->SetLength(FoundLength); } -guint32 gdcmHeader::FindLengthOB(void) { +/** + * \ingroup gdcmHeader + * \brief + * + * @return + */ + guint32 gdcmHeader::FindLengthOB(void) { // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data. guint16 g; guint16 n; @@ -495,50 +552,78 @@ guint32 gdcmHeader::FindLengthOB(void) { 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); + if (errno == 1) return 0; TotalLength += 4; // We even have to decount the group and element - if ( g != 0xfffe ) { - dbg.Verbose(1, "gdcmHeader::FindLengthOB: ", - "wrong group for an item sequence."); + + if ( g != 0xfffe && g!=0xb00c ) /*for bogus headerJPR */ { + 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 ) + + if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) /* for bogus header JPR */ FoundSequenceDelimiter = true; - else if ( n != 0xe000) { - dbg.Verbose(1, "gdcmHeader::FindLengthOB: ", - "wrong element for an item sequence."); + else if ( n != 0xe000 ){ + char msg[100]; // for sprintf. Sorry + sprintf(msg,"wrong element (%04x) for an item sequence (%04x,%04x)\n",n, g,n); + dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",msg); + 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); SkipBytes(ItemLength); } fseek(fp, PositionOnEntry, SEEK_SET); return TotalLength; } -void gdcmHeader::FindLength(ElValue * ElVal) { +/** + * \ingroup gdcmHeader + * \brief + * + * @return + */ + void gdcmHeader::FindLength (gdcmElValue * ElVal) { guint16 element = ElVal->GetElement(); + guint16 group = ElVal->GetGroup(); // JPR a virer string vr = ElVal->GetVR(); guint16 length16; + if( (element == 0x0010) && (group == 0x7fe0) ) {// JPR + + dbg.SetDebug(1); + dbg.Verbose(2, "gdcmHeader::FindLength: ", // JPR + "on est sur 7fe0 0010"); + } if ( (filetype == ExplicitVR) && ! ElVal->IsImplicitVr() ) { - if ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") ) { + // The following reserved two bytes (see PS 3.5-2001, section // 7.1.2 Data element structure with explicit vr p27) must be // skipped before proceeding on reading the length on 4 bytes. fseek(fp, 2L, SEEK_CUR); + guint32 length32 = ReadInt32(); if ( (vr == "OB") && (length32 == 0xffffffff) ) { ElVal->SetLength(FindLengthOB()); return; } - FixFoundLength(ElVal, length32); + FixFoundLength(ElVal, length32); return; } @@ -572,7 +657,7 @@ void gdcmHeader::FindLength(ElValue * ElVal) { // endian encoding". When this is the case, chances are we have got our // hands on a big endian encoded file: we switch the swap code to // big endian and proceed... - if ( (element == 0x000) && (length16 == 0x0400) ) { + if ( (element == 0x0000) && (length16 == 0x0400) ) { if ( ! IsExplicitVRBigEndianTransferSyntax() ) { dbg.Verbose(0, "gdcmHeader::FindLength", "not explicit VR"); errno = 1; @@ -584,7 +669,8 @@ void gdcmHeader::FindLength(ElValue * ElVal) { // and the dictionary entry depending on them. guint16 CorrectGroup = SwapShort(ElVal->GetGroup()); guint16 CorrectElem = SwapShort(ElVal->GetElement()); - gdcmDictEntry * NewTag = GetDictEntryByKey(CorrectGroup, CorrectElem); + gdcmDictEntry * NewTag = GetDictEntryByNumber(CorrectGroup, + CorrectElem); if (!NewTag) { // This correct tag is not in the dictionary. Create a new one. NewTag = new gdcmDictEntry(CorrectGroup, CorrectElem); @@ -621,7 +707,6 @@ void gdcmHeader::FindLength(ElValue * ElVal) { * @return The suggested integer. */ guint32 gdcmHeader::SwapLong(guint32 a) { - // FIXME: il pourrait y avoir un pb pour les entiers negatifs ... switch (sw) { case 0 : break; @@ -655,16 +740,34 @@ guint16 gdcmHeader::SwapShort(guint16 a) { return (a); } -void gdcmHeader::SkipBytes(guint32 NBytes) { +/** + * \ingroup gdcmHeader + * \brief + * + * @return + */ + void gdcmHeader::SkipBytes(guint32 NBytes) { //FIXME don't dump the returned value (void)fseek(fp, (long)NBytes, SEEK_CUR); } -void gdcmHeader::SkipElementValue(ElValue * ElVal) { +/** + * \ingroup gdcmHeader + * \brief + * + * @return + */ + void gdcmHeader::SkipElementValue(gdcmElValue * ElVal) { SkipBytes(ElVal->GetLength()); } -void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) { +/** + * \ingroup gdcmHeader + * \brief + * + * @return + */ + void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) { if (NewSize < 0) return; if ((guint32)NewSize >= (guint32)0xffffffff) { @@ -680,23 +783,23 @@ void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) { * than the value specified with * gdcmHeader::SetMaxSizeLoadElementValue() */ -void gdcmHeader::LoadElementValue(ElValue * ElVal) { +void gdcmHeader::LoadElementValue(gdcmElValue * ElVal) { size_t item_read; guint16 group = ElVal->GetGroup(); - guint16 elem = ElVal->GetElement(); string vr = ElVal->GetVR(); guint32 length = ElVal->GetLength(); bool SkipLoad = false; fseek(fp, (long)ElVal->GetOffset(), SEEK_SET); - // Sequences not treated yet ! + // FIXME Sequences not treated yet ! // // Ne faudrait-il pas au contraire trouver immediatement // une maniere 'propre' de traiter les sequences (vr = SQ) // car commencer par les ignorer risque de conduire a qq chose // qui pourrait ne pas etre generalisable - // + // Well, I'm expecting your code !!! + if( vr == "SQ" ) SkipLoad = true; @@ -706,16 +809,7 @@ void gdcmHeader::LoadElementValue(ElValue * ElVal) { if( group == 0xfffe ) SkipLoad = true; - // The group length doesn't represent data to be loaded in memory, since - // each element of the group shall be loaded individualy. - if( elem == 0 ) - //SkipLoad = true; // modif sauvage JPR - // On charge la longueur du groupe - // quand l'element 0x0000 est présent ! - if ( SkipLoad ) { - // FIXME the following skip is not necessary - SkipElementValue(ElVal); ElVal->SetLength(0); ElVal->SetValue("gdcm::Skipped"); return; @@ -741,23 +835,45 @@ void gdcmHeader::LoadElementValue(ElValue * 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 (?) + if ( IsAnInteger(ElVal) ) { guint32 NewInt; - if( length == 2 ) { + ostringstream s; + int nbInt; + if (vr == "US" || vr == "SS") { + nbInt = length / 2; NewInt = ReadInt16(); - } else if( length == 4 ) { + s << NewInt; + if (nbInt > 1) { + for (int i=1; i < nbInt; i++) { + s << '\\'; + NewInt = ReadInt16(); + s << NewInt; + } + } + + } else if (vr == "UL" || vr == "SL") { + nbInt = length / 4; NewInt = ReadInt32(); - } else - dbg.Error(true, "LoadElementValue: Inconsistency when reading Int."); - - //FIXME: make the following an util fonction - ostringstream s; - s << NewInt; + s << NewInt; + if (nbInt > 1) { + for (int i=1; i < nbInt; i++) { + s << '\\'; + NewInt = ReadInt32(); + s << NewInt; + } + } + } ElVal->SetValue(s.str()); - return; + return; } - // FIXME The exact size should be length if we move to strings or whatever + // We need an additional byte for storing \0 that is not on disk char* NewValue = (char*)malloc(length+1); if( !NewValue) { dbg.Verbose(1, "LoadElementValue: Failed to allocate NewValue"); @@ -773,6 +889,7 @@ void gdcmHeader::LoadElementValue(ElValue * ElVal) { return; } ElVal->SetValue(NewValue); + free(NewValue); } /** @@ -783,41 +900,78 @@ void gdcmHeader::LoadElementValue(ElValue * ElVal) { * @param ElVal Element whose value shall be loaded. * @return */ -void gdcmHeader::LoadElementValueSafe(ElValue * ElVal) { +void gdcmHeader::LoadElementValueSafe(gdcmElValue * ElVal) { long PositionOnEntry = ftell(fp); LoadElementValue(ElVal); fseek(fp, PositionOnEntry, SEEK_SET); } - +/** + * \ingroup gdcmHeader + * \brief + * + * @return + */ guint16 gdcmHeader::ReadInt16(void) { guint16 g; size_t item_read; item_read = fread (&g, (size_t)2,(size_t)1, fp); - errno = 0; if ( item_read != 1 ) { - dbg.Verbose(1, "gdcmHeader::ReadInt16", " File read error"); + dbg.Verbose(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"); errno = 1; return 0; } + errno = 0; g = SwapShort(g); return g; } +/** + * \ingroup gdcmHeader + * \brief + * + * @return + */ guint32 gdcmHeader::ReadInt32(void) { guint32 g; size_t item_read; item_read = fread (&g, (size_t)4,(size_t)1, fp); - errno = 0; if ( item_read != 1 ) { - dbg.Verbose(1, "gdcmHeader::ReadInt32", " File read error"); + + dbg.Verbose(1, "gdcmHeader::ReadInt32", " Failed to read :"); + if(feof(fp)) + dbg.Verbose(1, "gdcmHeader::ReadInt32", " End of File encountered"); + if(ferror(fp)) + dbg.Verbose(1, "gdcmHeader::ReadInt32", " File Error"); errno = 1; return 0; } + errno = 0; g = SwapLong(g); return g; } +/** + * \ingroup gdcmHeader + * \brief + * + * @return + */ + gdcmElValue* gdcmHeader::GetElValueByNumber(guint16 Group, guint16 Elem) { + + gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem); + if (!elValue) { + dbg.Verbose(1, "gdcmHeader::GetElValueByNumber", + "failed to Locate gdcmElValue"); + return (gdcmElValue*)0; + } + return elValue; +} + /** * \ingroup gdcmHeader * \brief Build a new Element Value from all the low level arguments. @@ -826,21 +980,34 @@ guint32 gdcmHeader::ReadInt32(void) { * @param Group group of the underlying DictEntry * @param Elem element of the underlying DictEntry */ -ElValue* gdcmHeader::NewElValueByKey(guint16 Group, guint16 Elem) { +gdcmElValue* gdcmHeader::NewElValueByNumber(guint16 Group, guint16 Elem) { // Find out if the tag we encountered is in the dictionaries: - gdcmDictEntry * NewTag = GetDictEntryByKey(Group, Elem); + gdcmDictEntry * NewTag = GetDictEntryByNumber(Group, Elem); if (!NewTag) NewTag = new gdcmDictEntry(Group, Elem); - ElValue* NewElVal = new ElValue(NewTag); + gdcmElValue* NewElVal = new gdcmElValue(NewTag); if (!NewElVal) { - dbg.Verbose(1, "gdcmHeader::NewElValueByKey", - "failed to allocate ElValue"); - return (ElValue*)0; + dbg.Verbose(1, "gdcmHeader::NewElValueByNumber", + "failed to allocate gdcmElValue"); + return (gdcmElValue*)0; } return NewElVal; } +/** + * \ingroup gdcmHeader + * \brief TODO + * @param + */ +int gdcmHeader::ReplaceOrCreateByNumber(string Value, guint16 Group, guint16 Elem ) { + + gdcmElValue* nvElValue=NewElValueByNumber(Group, Elem); + PubElValSet.Add(nvElValue); + PubElValSet.SetElValueByNumber(Value, Group, Elem); + return(1); +} + /** * \ingroup gdcmHeader * \brief Build a new Element Value from all the low level arguments. @@ -848,17 +1015,17 @@ ElValue* gdcmHeader::NewElValueByKey(guint16 Group, guint16 Elem) { * a default one when absent. * @param Name Name of the underlying DictEntry */ -ElValue* gdcmHeader::NewElValueByName(string Name) { +gdcmElValue* gdcmHeader::NewElValueByName(string Name) { gdcmDictEntry * NewTag = GetDictEntryByName(Name); if (!NewTag) NewTag = new gdcmDictEntry(0xffff, 0xffff, "LO", "Unknown", Name); - ElValue* NewElVal = new ElValue(NewTag); + gdcmElValue* NewElVal = new gdcmElValue(NewTag); if (!NewElVal) { dbg.Verbose(1, "gdcmHeader::ObtainElValueByName", - "failed to allocate ElValue"); - return (ElValue*)0; + "failed to allocate gdcmElValue"); + return (gdcmElValue*)0; } return NewElVal; } @@ -868,25 +1035,35 @@ ElValue* gdcmHeader::NewElValueByName(string Name) { * \brief Read the next tag but WITHOUT loading it's value * @return On succes the newly created ElValue, NULL on failure. */ -ElValue * gdcmHeader::ReadNextElement(void) { - guint16 g; - guint16 n; - ElValue * NewElVal; +gdcmElValue * gdcmHeader::ReadNextElement(void) { + + guint16 g,n; + gdcmElValue * NewElVal; 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. - return (ElValue *)0; + return (gdcmElValue *)0; - NewElVal = NewElValueByKey(g, n); + NewElVal = NewElValueByNumber(g, n); FindVR(NewElVal); FindLength(NewElVal); - if (errno == 1) + if (errno == 1) { // Call it quits - return (ElValue *)0; - NewElVal->SetOffset(ftell(fp)); + 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"); return NewElVal; } @@ -897,7 +1074,7 @@ ElValue * gdcmHeader::ReadNextElement(void) { * @param ElVal The element value on which to apply the predicate. * @return The result of the heuristical predicate. */ -bool gdcmHeader::IsAnInteger(ElValue * ElVal) { +bool gdcmHeader::IsAnInteger(gdcmElValue * ElVal) { guint16 group = ElVal->GetGroup(); guint16 element = ElVal->GetElement(); string vr = ElVal->GetVR(); @@ -909,48 +1086,17 @@ bool gdcmHeader::IsAnInteger(ElValue * ElVal) { if ( element == 0 ) { // This is the group length of the group if (length == 4) return true; - else + 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."); + "Erroneous Group Length element length."); + } } - - /* - // on le traite tt de même (VR peut donner l'info) - // faire qq chose + ruse (pas de test si pas de VR) - if ( group % 2 != 0 ) - // We only have some semantics on documented elements, which are - // the even ones. - return false; - */ - - /* - if ( (length != 4) && ( length != 2) ) - // Swapping only make sense on integers which are 2 or 4 bytes long. - - // En fait, pour les entiers de 'Value Multiplicity' supérieur a 1 - // la longueur n'est pas forcement 2 ou 4 - // ET il faudra swapper. - return false; - */ - if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") ) return true; - - // est-ce encore utile? - // mieux vaut modifier le source du Dicom Dictionnaty - // et remplacer pour ces 2 cas RET par US - - if ( (group == 0x0028) && (element == 0x0005) ) - // The "Image Dimensions" tag is retained from ACR/NEMA and contains - // the number of dimensions of the contained object (1 for Signal, - // 2 for Image, 3 for Volume, 4 for Sequence). - return true; - - if ( (group == 0x0028) && (element == 0x0200) ) - // This tag is retained from ACR/NEMA - return true; - return false; } @@ -965,7 +1111,7 @@ size_t gdcmHeader::GetPixelOffset(void) { // is found by indirection through the "Image Location"). // Inside the group pointed by "Image Location" the searched element // is conventionally the element 0x0010 (when the norm is respected). - // When the "Image Location" is absent we default to group 0x7fe0. + // When the "Image Location" is absent we default to group 0x7fe0. guint16 grPixel; guint16 numPixel; string ImageLocation = GetPubElValByName("Image Location"); @@ -975,12 +1121,13 @@ size_t gdcmHeader::GetPixelOffset(void) { grPixel = (guint16) atoi( ImageLocation.c_str() ); } if (grPixel != 0x7fe0) - // FIXME is this still necessary ? - // Now, this looks like an old dirty fix for Philips imager + // This is a kludge for old dirty Philips imager. numPixel = 0x1010; else numPixel = 0x0010; - ElValue* PixelElement = PubElVals.GetElementByNumber(grPixel, numPixel); + + gdcmElValue* PixelElement = PubElValSet.GetElementByNumber(grPixel, + numPixel); if (PixelElement) return PixelElement->GetOffset(); else @@ -997,19 +1144,20 @@ size_t gdcmHeader::GetPixelOffset(void) { * @param element element of the searched DictEntry * @return Corresponding DictEntry when it exists, NULL otherwise. */ -gdcmDictEntry * gdcmHeader::GetDictEntryByKey(guint16 group, guint16 element) { +gdcmDictEntry * gdcmHeader::GetDictEntryByNumber(guint16 group, + guint16 element) { gdcmDictEntry * found = (gdcmDictEntry*)0; if (!RefPubDict && !RefShaDict) { - dbg.Verbose(0, "FIXME in gdcmHeader::GetDictEntry", + dbg.Verbose(0, "gdcmHeader::GetDictEntry", "we SHOULD have a default dictionary"); } if (RefPubDict) { - found = RefPubDict->GetTagByKey(group, element); + found = RefPubDict->GetTagByNumber(group, element); if (found) return found; } if (RefShaDict) { - found = RefShaDict->GetTagByKey(group, element); + found = RefShaDict->GetTagByNumber(group, element); if (found) return found; } @@ -1027,7 +1175,7 @@ gdcmDictEntry * gdcmHeader::GetDictEntryByKey(guint16 group, guint16 element) { gdcmDictEntry * gdcmHeader::GetDictEntryByName(string Name) { gdcmDictEntry * found = (gdcmDictEntry*)0; if (!RefPubDict && !RefShaDict) { - dbg.Verbose(0, "FIXME in gdcmHeader::GetDictEntry", + dbg.Verbose(0, "gdcmHeader::GetDictEntry", "we SHOULD have a default dictionary"); } if (RefPubDict) { @@ -1053,7 +1201,7 @@ gdcmDictEntry * gdcmHeader::GetDictEntryByName(string Name) { * "gdcm::Unfound" otherwise. */ string gdcmHeader::GetPubElValByNumber(guint16 group, guint16 element) { - return PubElVals.GetElValueByNumber(group, element); + return PubElValSet.GetElValueByNumber(group, element); } /** @@ -1071,7 +1219,7 @@ string gdcmHeader::GetPubElValByNumber(guint16 group, guint16 element) { * and the string "gdcm::Unfound" otherwise. */ string gdcmHeader::GetPubElValRepByNumber(guint16 group, guint16 element) { - ElValue* elem = PubElVals.GetElementByNumber(group, element); + gdcmElValue* elem = PubElValSet.GetElementByNumber(group, element); if ( !elem ) return "gdcm::Unfound"; return elem->GetVR(); @@ -1086,7 +1234,7 @@ string gdcmHeader::GetPubElValRepByNumber(guint16 group, guint16 element) { * "gdcm::Unfound" otherwise. */ string gdcmHeader::GetPubElValByName(string TagName) { - return PubElVals.GetElValueByName(TagName); + return PubElValSet.GetElValueByName(TagName); } /** @@ -1103,7 +1251,7 @@ string gdcmHeader::GetPubElValByName(string TagName) { * and the string "gdcm::Unfound" otherwise. */ string gdcmHeader::GetPubElValRepByName(string TagName) { - ElValue* elem = PubElVals.GetElementByName(TagName); + gdcmElValue* elem = PubElValSet.GetElementByName(TagName); if ( !elem ) return "gdcm::Unfound"; return elem->GetVR(); @@ -1119,7 +1267,7 @@ string gdcmHeader::GetPubElValRepByName(string TagName) { * and the string "gdcm::Unfound" otherwise. */ string gdcmHeader::GetShaElValByNumber(guint16 group, guint16 element) { - return ShaElVals.GetElValueByNumber(group, element); + return ShaElValSet.GetElValueByNumber(group, element); } /** @@ -1137,7 +1285,7 @@ string gdcmHeader::GetShaElValByNumber(guint16 group, guint16 element) { * and the string "gdcm::Unfound" otherwise. */ string gdcmHeader::GetShaElValRepByNumber(guint16 group, guint16 element) { - ElValue* elem = ShaElVals.GetElementByNumber(group, element); + gdcmElValue* elem = ShaElValSet.GetElementByNumber(group, element); if ( !elem ) return "gdcm::Unfound"; return elem->GetVR(); @@ -1152,7 +1300,7 @@ string gdcmHeader::GetShaElValRepByNumber(guint16 group, guint16 element) { * "gdcm::Unfound" otherwise. */ string gdcmHeader::GetShaElValByName(string TagName) { - return ShaElVals.GetElValueByName(TagName); + return ShaElValSet.GetElValueByName(TagName); } /** @@ -1169,7 +1317,7 @@ string gdcmHeader::GetShaElValByName(string TagName) { * and the string "gdcm::Unfound" otherwise. */ string gdcmHeader::GetShaElValRepByName(string TagName) { - ElValue* elem = ShaElVals.GetElementByName(TagName); + gdcmElValue* elem = ShaElValSet.GetElementByName(TagName); if ( !elem ) return "gdcm::Unfound"; return elem->GetVR(); @@ -1253,7 +1401,7 @@ string gdcmHeader::GetElValRepByName(string TagName) { /** * \ingroup gdcmHeader - * \brief Accesses an existing ElValue in the PubElVals of this instance + * \brief Accesses an existing gdcmElValue in the PubElValSet of this instance * through it's (group, element) and modifies it's content with * the given value. * @param content new value to substitute with @@ -1262,64 +1410,66 @@ string gdcmHeader::GetElValRepByName(string TagName) { */ int gdcmHeader::SetPubElValByNumber(string content, guint16 group, guint16 element) + +//TODO : homogeneiser les noms : SetPubElValByNumber qui appelle PubElValSet.SetElValueByNumber +// pourquoi pas SetPubElValueByNumber ?? { - return ( PubElVals.SetElValueByNumber (content, group, element) ); + + return ( PubElValSet.SetElValueByNumber (content, group, element) ); } /** * \ingroup gdcmHeader - * \brief Accesses an existing ElValue in the PubElVals of this instance + * \brief Accesses an existing gdcmElValue in the PubElValSet of this instance * through tag name and modifies it's content with the given value. * @param content new value to substitute with * @param TagName name of the tag to be modified */ int gdcmHeader::SetPubElValByName(string content, string TagName) { - return ( PubElVals.SetElValueByName (content, TagName) ); + return ( PubElValSet.SetElValueByName (content, TagName) ); } /** * \ingroup gdcmHeader - * \brief Accesses an existing ElValue in the PubElVals of this instance + * \brief Accesses an existing gdcmElValue in the PubElValSet of this instance * through it's (group, element) and modifies it's length with * the given value. - * NOT FOR BOZOs ! - * @param contents new length to substitute with + * \warning Use with extreme caution. + * @param length new length to substitute with * @param group group of the ElVal to modify * @param element element of the ElVal to modify + * @return 1 on success, 0 otherwise. */ -int gdcmHeader::SetPubElValLengthByNumber(guint32 lgr, guint16 group, - guint16 element) -{ - return ( PubElVals.SetElValueLengthByNumber (lgr, group, element) ); + +int gdcmHeader::SetPubElValLengthByNumber(guint32 length, guint16 group, + guint16 element) { + return ( PubElValSet.SetElValueLengthByNumber (length, group, element) ); } /** * \ingroup gdcmHeader - * \brief Accesses an existing ElValue in the ShaElVals of this instance + * \brief Accesses an existing gdcmElValue in the ShaElValSet of this instance * through it's (group, element) and modifies it's content with * the given value. * @param content new value to substitute with * @param group group of the ElVal to modify * @param element element of the ElVal to modify + * @return 1 on success, 0 otherwise. */ int gdcmHeader::SetShaElValByNumber(string content, - guint16 group, guint16 element) -{ - return ( ShaElVals.SetElValueByNumber (content, group, element) ); + guint16 group, guint16 element) { + return ( ShaElValSet.SetElValueByNumber (content, group, element) ); } - - - /** * \ingroup gdcmHeader - * \brief Accesses an existing ElValue in the ShaElVals of this instance + * \brief Accesses an existing gdcmElValue in the ShaElValSet of this instance * through tag name and modifies it's content with the given value. * @param content new value to substitute with * @param TagName name of the tag to be modified */ int gdcmHeader::SetShaElValByName(string content, string TagName) { - return ( ShaElVals.SetElValueByName (content, TagName) ); + return ( ShaElValSet.SetElValueByName (content, TagName) ); } /** @@ -1327,42 +1477,226 @@ int gdcmHeader::SetShaElValByName(string content, string TagName) { * \brief Parses the header of the file but WITHOUT loading element values. */ void gdcmHeader::ParseHeader(bool exception_on_error) throw(gdcmFormatError) { - ElValue * newElValue = (ElValue *)0; + gdcmElValue * newElValue = (gdcmElValue *)0; rewind(fp); CheckSwap(); while ( (newElValue = ReadNextElement()) ) { SkipElementValue(newElValue); - PubElVals.Add(newElValue); + PubElValSet.Add(newElValue); } } + +// +// 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 +// +// --> 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 Once the header is parsed add some gdcm convenience/helper elements - * in the ElValSet. For example add: - * - gdcmImageType which is an entry containing a short for the - * type of image and whose value ranges in - * I8 (unsigned 8 bit image) - * I16 (unsigned 8 bit image) - * IS16 (signed 8 bit image) - * - gdcmXsize, gdcmYsize, gdcmZsize whose values are respectively - * the ones of the official DICOM fields Rows, Columns and Planes. + * \brief Retrieve the number of columns of image. + * @return The encountered size when found, 0 by default. */ -void gdcmHeader::AddAndDefaultElements(void) { - ElValue* NewEntry = (ElValue*)0; +int gdcmHeader::GetXSize(void) { + // We cannot check for "Columns" because the "Columns" tag is present + // both in IMG (0028,0011) and OLY (6000,0011) sections of the dictionary. + string StrSize = GetPubElValByNumber(0x0028,0x0011); + if (StrSize == "gdcm::Unfound") + return 0; + return atoi(StrSize.c_str()); +} - NewEntry = NewElValueByName("gdcmXSize"); - NewEntry->SetValue(GetElValByName("Rows")); - PubElVals.Add(NewEntry); +/** + * \ingroup gdcmHeader + * \brief Retrieve the number of lines of image. + * \warning The defaulted value is 1 as opposed to gdcmHeader::GetXSize() + * @return The encountered size when found, 1 by default. + */ +int gdcmHeader::GetYSize(void) { + // We cannot check for "Rows" because the "Rows" tag is present + // both in IMG (0028,0010) and OLY (6000,0010) sections of the dictionary. + string StrSize = GetPubElValByNumber(0x0028,0x0010); + if (StrSize != "gdcm::Unfound") + return atoi(StrSize.c_str()); + if ( IsDicomV3() ) + return 0; + else + // The Rows (0028,0010) entry is optional for ACR/NEMA. It might + // hence be a signal (1d image). So we default to 1: + return 1; +} - NewEntry = NewElValueByName("gdcmYSize"); - NewEntry->SetValue(GetElValByName("Columns")); - PubElVals.Add(NewEntry); +/** + * \ingroup gdcmHeader + * \brief Retrieve the number of planes of volume or the number + * of frames of a multiframe. + * \warning When present we consider the "Number of Frames" as the third + * dimension. When absent we consider the third dimension as + * being the "Planes" tag content. + * @return The encountered size when found, 1 by default. + */ +int gdcmHeader::GetZSize(void) { + // Both in DicomV3 and ACR/Nema the consider the "Number of Frames" + // as the third dimension. + string StrSize = GetPubElValByNumber(0x0028,0x0008); + if (StrSize != "gdcm::Unfound") + return atoi(StrSize.c_str()); + + // We then consider the "Planes" entry as the third dimension [we + // cannot retrieve by name since "Planes tag is present both in + // IMG (0028,0012) and OLY (6000,0012) sections of the dictionary]. + StrSize = GetPubElValByNumber(0x0028,0x0012); + if (StrSize != "gdcm::Unfound") + return atoi(StrSize.c_str()); + return 1; +} - NewEntry = NewElValueByName("gdcmZSize"); - NewEntry->SetValue(GetElValByName("Planes")); - PubElVals.Add(NewEntry); + +/** + * \ingroup gdcmHeader + * \brief Retrieve the number of Bits Stored + * (as opposite to number of Bits Allocated) + * + * @return The encountered number of Bits Stored, 0 by default. + */ +int gdcmHeader::GetBitsStored(void) { + string StrSize = GetPubElValByNumber(0x0028,0x0101); + if (StrSize == "gdcm::Unfound") + return 1; + return atoi(StrSize.c_str()); +} + + +/** + * \ingroup gdcmHeader + * \brief Retrieve the number of Samples Per Pixel + * (1 : gray level, 3 : RGB) + * + * @return The encountered number of Samples Per Pixel, 1 by default. + */ +int gdcmHeader::GetSamplesPerPixel(void) { + string StrSize = GetPubElValByNumber(0x0028,0x0002); + if (StrSize == "gdcm::Unfound") + return 1; // Well, it's supposed to be mandatory ... + return atoi(StrSize.c_str()); +} +/** + * \ingroup gdcmHeader + * \brief Return the size (in bytes) of a single pixel of data. + * @return The size in bytes of a single pixel of data. + * + */ +int gdcmHeader::GetPixelSize(void) { + string PixelType = GetPixelType(); + if (PixelType == "8U" || PixelType == "8S") + return 1; + if (PixelType == "16U" || PixelType == "16S") + return 2; + if (PixelType == "32U" || PixelType == "32S") + return 4; + dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type"); + return 0; +} + +/** + * \ingroup gdcmHeader + * \brief Build the Pixel Type of the image. + * Possible values are: + * - 8U unsigned 8 bit, + * - 8S signed 8 bit, + * - 16U unsigned 16 bit, + * - 16S signed 16 bit, + * - 32U unsigned 32 bit, + * - 32S signed 32 bit, + * \warning 12 bit images appear as 16 bit. + * @return + */ +string gdcmHeader::GetPixelType(void) { + string BitsAlloc; + BitsAlloc = GetElValByName("Bits Allocated"); + if (BitsAlloc == "gdcm::Unfound") { + dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated"); + BitsAlloc = string("16"); + } + if (BitsAlloc == "12") + BitsAlloc = string("16"); + + string Signed; + Signed = GetElValByName("Pixel Representation"); + if (Signed == "gdcm::Unfound") { + dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation"); + BitsAlloc = string("0"); + } + if (Signed == "0") + Signed = string("U"); + else + 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; } /** @@ -1372,16 +1706,232 @@ void gdcmHeader::AddAndDefaultElements(void) { */ void gdcmHeader::LoadElements(void) { rewind(fp); - TagElValueHT ht = PubElVals.GetTagHt(); + TagElValueHT ht = PubElValSet.GetTagHt(); for (TagElValueHT::iterator tag = ht.begin(); tag != ht.end(); ++tag) { LoadElementValue(tag->second); - } + } } -void gdcmHeader::PrintPubElVal(ostream & os) { - PubElVals.Print(os); +/** + * \ingroup gdcmHeader + * \brief + * @return + */ +void gdcmHeader::PrintPubElVal(std::ostream & os) { + PubElValSet.Print(os); } -void gdcmHeader::PrintPubDict(ostream & 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); +} + +/** + * \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; +} + +/** + * \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 + 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"); + string StrSliceLoc = GetPubElValByNumber(0x0020,0x1041); + if (StrSliceLoc == "gdcm::Unfound") { + dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Slice Location"); + // 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; +} + +/** + * \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"); + string StrSliceLoc = GetPubElValByNumber(0x0020,0x1041); + if (StrSliceLoc == "gdcm::Unfound") { + dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Slice Location"); + // How to tell the caller nothing was found? + string StrLocation = GetPubElValByNumber(0x0020,0x0050); + if (StrSliceLoc == "gdcm::Unfound") { + dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Slice Location"); + } + } + 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; +} + +/** + * \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? + + 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"); + return 0.; // bug in the element 0x0020,0x0032 + } else { + return zImPos; + } + } + dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position Patient"); + + string StrSliceLocation = GetPubElValByNumber(0x0020,0x1041); + if (StrSliceLocation != "gdcm::Unfound") { + if( sscanf( StrSliceLocation.c_str(), "%f", &zImPos) !=1) { + dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Slice Location"); + return 0.; // bug in the element 0x0020,0x1041 + } else { + return zImPos; + } + } + dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Slice Location"); + + string StrLocation = GetPubElValByNumber(0x0020,0x0050); + if (StrLocation != "gdcm::Unfound") { + if( sscanf( StrLocation.c_str(), "%f", &zImPos) !=1) { + dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Location"); + return 0.; // bug in the element 0x0020,0x0050 + } else { + return zImPos; + } + } + dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Slice Location"); + + return 0.; // Hopeless +} + + +