X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=e9ae38fc4c71c315e2f68879429bb3a6fc330da7;hb=5d5448482dc2b56be816c48df294af6884746547;hp=5e6c2c876cd2c1c4b6146b12c9b6b5215243ff57;hpb=bb2cb788a245b6377a70de3e8a502dab036165ab;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index 5e6c2c87..e9ae38fc 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -1,4 +1,6 @@ -// gdcmHeader.cxx +// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.117 2003/11/13 18:08:34 jpr Exp $ + +#include "gdcmHeader.h" #include #include @@ -11,83 +13,159 @@ #include // for isalpha #include #include "gdcmUtil.h" -#include "gdcmHeader.h" - -#include "iddcmjpeg.h" +#include "gdcmTS.h" // Refer to gdcmHeader::CheckSwap() #define HEADER_LENGTH_TO_READ 256 // Refer to gdcmHeader::SetMaxSizeLoadElementValue() -#define _MaxSizeLoadElementValue_ 1024 - -VRHT * gdcmHeader::dicom_vr = (VRHT*)0; - +//#define _MaxSizeLoadElementValue_ 1024 +#define _MaxSizeLoadElementValue_ 4096 +/** + * \ingroup gdcmHeader + * \brief + */ 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) { +/** + * \ingroup gdcmHeader + * \brief + * @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 exception_on_error + */ +gdcmHeader::gdcmHeader(bool exception_on_error) { SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_); - filename = InFilename; Initialise(); - fp=fopen(InFilename,"rb"); +} + +/** + * \ingroup gdcmHeader + * \brief + * @param exception_on_error + * @return + */ + bool gdcmHeader::OpenFile(bool exception_on_error) + throw(gdcmFileError) { + fp=fopen(filename.c_str(),"rb"); if(exception_on_error) { if(!fp) throw gdcmFileError("gdcmHeader::gdcmHeader(const char *, bool)"); } - else - dbg.Error(!fp, "gdcmHeader::gdcmHeader cannot open file", InFilename); - ParseHeader(); - LoadElements(); - AddAndDefaultElements(); + + 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 + * @return TRUE if the close was successfull + */ +bool gdcmHeader::CloseFile(void) { + int closed = fclose(fp); + fp = (FILE *)0; + if (! closed) + return false; + return true; +} +/** + * \ingroup gdcmHeader + * \brief Canonical destructor. + */ gdcmHeader::~gdcmHeader (void) { - //FIXME obviously there is much to be done here ! - fclose(fp); - return; + 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: +// +// ---> 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 +// 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 +// DL Delimiters +// /** * \ingroup gdcmHeader @@ -102,7 +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; @@ -122,14 +200,7 @@ 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" // - or "OB" if the 1st one is (0002,0001) -, @@ -146,9 +217,13 @@ void gdcmHeader::CheckSwap() // * the 4 bytes of the first tag (0002, 0000),or (0002, 0001) // i.e. a total of 136 bytes. entCur = deb + 136; + // 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, "OB", (size_t)2) == 0) || + (memcmp(entCur, "UI", (size_t)2) == 0) ) + { filetype = ExplicitVR; dbg.Verbose(1, "gdcmHeader::CheckSwap:", "explicit Value Representation"); @@ -157,7 +232,6 @@ void gdcmHeader::CheckSwap() dbg.Verbose(1, "gdcmHeader::CheckSwap:", "not an explicit Value Representation"); } - if (net2host) { sw = 4321; dbg.Verbose(1, "gdcmHeader::CheckSwap:", @@ -173,11 +247,12 @@ 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. @@ -217,6 +292,7 @@ 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 @@ -224,6 +300,10 @@ void gdcmHeader::CheckSwap() return; } +/** + * \ingroup gdcmHeader + * \brief + */ void gdcmHeader::SwitchSwapToBigEndian(void) { dbg.Verbose(1, "gdcmHeader::SwitchSwapToBigEndian", "Switching to BigEndian mode."); @@ -243,30 +323,20 @@ void gdcmHeader::SwitchSwapToBigEndian(void) { sw = 3412; } -void gdcmHeader::GetPixels(size_t lgrTotale, void* _Pixels) { - size_t pixelsOffset; - pixelsOffset = GetPixelOffset(); - fseek(fp, pixelsOffset, SEEK_SET); - if (IsJPEGLossless()) { - _Pixels=_IdDcmJpegRead(fp); - } else { - fread(_Pixels, 1, lgrTotale, fp); - } -} - - - /** * \ingroup gdcmHeader * \brief Find the value representation of the current tag. + * @param ElVal */ void gdcmHeader::FindVR( gdcmElValue *ElVal) { if (filetype != ExplicitVR) return; char VR[3]; - string vr; + std::string vr; int lgrLue; + char msg[100]; // for sprintf. Sorry + long PositionOnEntry = ftell(fp); // Warning: we believe this is explicit VR (Value Representation) because // we used a heuristic that found "UL" in the first tag. Alas this @@ -279,7 +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 @@ -295,7 +365,7 @@ void gdcmHeader::FindVR( gdcmElValue *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) ) + if ( RealExplicit && !dicom_vr->Count(vr) ) RealExplicit= false; if ( RealExplicit ) { @@ -323,11 +393,15 @@ void gdcmHeader::FindVR( gdcmElValue *ElVal) { } // We thought this was explicit VR, but we end up with an - // implicit VR tag. Let's backtrack. - dbg.Verbose(1, "gdcmHeader::FindVR:", "Falsely explicit vr file"); + // implicit VR tag. Let's backtrack. + + sprintf(msg,"Falsely explicit vr file (%04x,%04x)\n", + ElVal->GetGroup(),ElVal->GetElement()); + dbg.Verbose(1, "gdcmHeader::FindVR: ",msg); + fseek(fp, PositionOnEntry, SEEK_SET); // When this element is known in the dictionary we shall use, e.g. for - // the semantics (see the usage of IsAnInteger), the vr proposed by the + // 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 . @@ -338,7 +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. @@ -348,7 +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; @@ -356,7 +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. @@ -366,7 +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; @@ -374,7 +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. @@ -384,7 +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; @@ -392,7 +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. @@ -402,7 +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; @@ -410,7 +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. @@ -420,29 +494,36 @@ bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) { if ( !Element ) return false; LoadElementValueSafe(Element); - string Transfer = Element->GetValue(); + std::string Transfer = Element->GetValue(); if ( Transfer == "1.2.840.10008.1.2.4.50" ) return true; return false; } -// faire qq chose d'intelligent a la place de ça - +/** + * \ingroup gdcmHeader + * \brief + * + * @return + */ bool gdcmHeader::IsJPEGLossless(void) { gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); + // faire qq chose d'intelligent a la place de ça if ( !Element ) return false; LoadElementValueSafe(Element); const char * Transfert = Element->GetValue().c_str(); 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. @@ -452,7 +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; @@ -460,7 +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. @@ -470,7 +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; @@ -478,7 +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 @@ -489,12 +570,63 @@ 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. + * @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 @@ -502,12 +634,58 @@ bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(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); } -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; @@ -518,51 +696,69 @@ guint32 gdcmHeader::FindLengthOB(void) { while ( ! FoundSequenceDelimiter) { g = ReadInt16(); - n = ReadInt16(); + n = ReadInt16(); if (errno == 1) return 0; TotalLength += 4; // We even have to decount the group and element - if ( g != 0xfffe ) { - dbg.Verbose(1, "gdcmHeader::FindLengthOB: ", - "wrong group for an item sequence."); + + if ( g != 0xfffe && g!=0xb00c ) /*for bogus header */ { + char msg[100]; // for sprintf. Sorry + sprintf(msg,"wrong group (%04x) for an item sequence (%04x,%04x)\n",g, g,n); + dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",msg); errno = 1; return 0; } - if ( n == 0xe0dd ) + if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) /* for bogus header */ FoundSequenceDelimiter = true; - else if ( n != 0xe000) { - dbg.Verbose(1, "gdcmHeader::FindLengthOB: ", - "wrong element for an item sequence."); + else if ( n != 0xe000 ){ + char msg[100]; // for sprintf. Sorry + sprintf(msg,"wrong element (%04x) for an item sequence (%04x,%04x)\n", + n, g,n); + dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",msg); errno = 1; return 0; } ItemLength = ReadInt32(); TotalLength += ItemLength + 4; // We add 4 bytes since we just read - // the ItemLength with ReadInt32 + // the ItemLength with ReadInt32 SkipBytes(ItemLength); } fseek(fp, PositionOnEntry, SEEK_SET); return TotalLength; } -void gdcmHeader::FindLength(gdcmElValue * ElVal) { +/** + * \ingroup gdcmHeader + * \brief + * + * @return + */ + void gdcmHeader::FindLength (gdcmElValue * ElVal) { guint16 element = ElVal->GetElement(); - string vr = ElVal->GetVR(); + guint16 group = ElVal->GetGroup(); + std::string vr = ElVal->GetVR(); guint16 length16; + if( (element == 0x0010) && (group == 0x7fe0) ) { + dbg.SetDebug(0); + dbg.Verbose(2, "gdcmHeader::FindLength: ", + "we reached 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; } @@ -586,17 +782,17 @@ void gdcmHeader::FindLength(gdcmElValue * ElVal) { // 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 // 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; @@ -608,7 +804,8 @@ void gdcmHeader::FindLength(gdcmElValue * 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); @@ -621,9 +818,12 @@ void gdcmHeader::FindLength(gdcmElValue * ElVal) { // 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; } @@ -635,17 +835,16 @@ void gdcmHeader::FindLength(gdcmElValue * ElVal) { // 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) { - // FIXME: il pourrait y avoir un pb pour les entiers negatifs ... switch (sw) { case 0 : break; @@ -679,16 +878,34 @@ guint16 gdcmHeader::SwapShort(guint16 a) { return (a); } -void gdcmHeader::SkipBytes(guint32 NBytes) { +/** + * \ingroup gdcmHeader + * \brief + * + * @return + */ + void gdcmHeader::SkipBytes(guint32 NBytes) { //FIXME don't dump the returned value (void)fseek(fp, (long)NBytes, SEEK_CUR); } -void gdcmHeader::SkipElementValue(gdcmElValue * ElVal) { - SkipBytes(ElVal->GetLength()); +/** + * \ingroup gdcmHeader + * \brief + * @param ElVal + * @return + */ + void gdcmHeader::SkipElementValue(gdcmElValue * ElVal) { + SkipBytes(ElVal->GetLength()); } -void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) { +/** + * \ingroup gdcmHeader + * \brief + * @param NewSize + * @return + */ + void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) { if (NewSize < 0) return; if ((guint32)NewSize >= (guint32)0xffffffff) { @@ -707,8 +924,7 @@ void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) { void gdcmHeader::LoadElementValue(gdcmElValue * ElVal) { size_t item_read; guint16 group = ElVal->GetGroup(); - guint16 elem = ElVal->GetElement(); - string vr = ElVal->GetVR(); + std::string vr= ElVal->GetVR(); guint32 length = ElVal->GetLength(); bool SkipLoad = false; @@ -721,13 +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; @@ -747,10 +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; } @@ -758,45 +980,44 @@ 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; - int nbInt; - if (vr == "US" || vr == "SS") { - nbInt = length / 2; - NewInt = ReadInt16(); - s << NewInt; - if (nbInt > 1) { - for (int i=1; i < nbInt; i++) { - s << '\\'; - NewInt = ReadInt16(); - s << NewInt; - //printf("%s\n", s.str().c_str()); - } - } + if ( IsAnInteger(ElVal) ) { + guint32 NewInt; + std::ostringstream s; + int nbInt; + if (vr == "US" || vr == "SS") { + nbInt = length / 2; + NewInt = ReadInt16(); + s << NewInt; + if (nbInt > 1) { + for (int i=1; i < nbInt; i++) { + s << '\\'; + NewInt = ReadInt16(); + s << NewInt; + } + } - } else if (vr == "UL" || vr == "SL") { - nbInt = length / 4; - NewInt = ReadInt32(); - s << NewInt; - if (nbInt > 1) { - for (int i=1; i < nbInt; i++) { - s << '\\'; - NewInt = ReadInt32(); - s << NewInt; - } - } - } - ElVal->SetValue(s.str()); - return; - } + } else if (vr == "UL" || vr == "SL") { + nbInt = length / 4; + NewInt = ReadInt32(); + s << NewInt; + if (nbInt > 1) { + for (int i=1; i < nbInt; i++) { + s << '\\'; + NewInt = ReadInt32(); + s << NewInt; + } + } + } + s << '\0'; // to avoid oddities on Solaris + ElVal->SetValue(s.str()); + 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"); @@ -812,6 +1033,7 @@ void gdcmHeader::LoadElementValue(gdcmElValue * ElVal) { return; } ElVal->SetValue(NewValue); + free(NewValue); } /** @@ -828,35 +1050,73 @@ void gdcmHeader::LoadElementValueSafe(gdcmElValue * ElVal) { fseek(fp, PositionOnEntry, SEEK_SET); } - +/** + * \ingroup gdcmHeader + * \brief Reads a supposed to be 16 Bits integer + * \ (swaps it depending on processor endianity) + * + * @return integer acts as a boolean + */ guint16 gdcmHeader::ReadInt16(void) { guint16 g; size_t item_read; item_read = fread (&g, (size_t)2,(size_t)1, fp); - errno = 0; if ( item_read != 1 ) { - dbg.Verbose(1, "gdcmHeader::ReadInt16", " File read error"); + // dbg.Verbose(0, "gdcmHeader::ReadInt16", " Failed to read :"); + // if(feof(fp)) + // dbg.Verbose(0, "gdcmHeader::ReadInt16", " End of File encountered"); + if(ferror(fp)) + dbg.Verbose(0, "gdcmHeader::ReadInt16", " File Error"); errno = 1; return 0; } + errno = 0; g = SwapShort(g); return g; } +/** + * \ingroup gdcmHeader + * \brief Reads a supposed to be 32 Bits integer + * \ (swaps it depending on processor endianity) + * + * @return + */ guint32 gdcmHeader::ReadInt32(void) { guint32 g; size_t item_read; item_read = fread (&g, (size_t)4,(size_t)1, fp); - errno = 0; - if ( item_read != 1 ) { - dbg.Verbose(1, "gdcmHeader::ReadInt32", " File read error"); + if ( item_read != 1 ) { + //dbg.Verbose(0, "gdcmHeader::ReadInt32", " Failed to read :"); + //if(feof(fp)) + // dbg.Verbose(0, "gdcmHeader::ReadInt32", " End of File encountered"); + if(ferror(fp)) + dbg.Verbose(0, "gdcmHeader::ReadInt32", " File Error"); errno = 1; return 0; } + errno = 0; g = SwapLong(g); return g; } +/** + * \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. @@ -865,15 +1125,15 @@ guint32 gdcmHeader::ReadInt32(void) { * @param Group group of the underlying DictEntry * @param Elem element of the underlying DictEntry */ -gdcmElValue* 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); gdcmElValue* NewElVal = new gdcmElValue(NewTag); if (!NewElVal) { - dbg.Verbose(1, "gdcmHeader::NewElValueByKey", + dbg.Verbose(1, "gdcmHeader::NewElValueByNumber", "failed to allocate gdcmElValue"); return (gdcmElValue*)0; } @@ -883,17 +1143,80 @@ gdcmElValue* gdcmHeader::NewElValueByKey(guint16 Group, guint16 Elem) { /** * \ingroup gdcmHeader * \brief TODO - * @param + * @param Value + * @param Group + * @param Elem + * \return integer acts as a boolean */ -int gdcmHeader::ReplaceOrCreateByNumber(guint16 Group, guint16 Elem, string Value) { - - gdcmElValue* nvElValue=NewElValueByKey(Group, Elem); - PubElValSet.Add(nvElValue); - PubElValSet.SetElValueByNumber(Value, Group, Elem); - return(1); +int gdcmHeader::ReplaceOrCreateByNumber(std::string Value, + guint16 Group, guint16 Elem ) { + // TODO : FIXME JPRx + // curieux, non ? + // on (je) cree une Elvalue ne contenant pas de valeur + // on l'ajoute au ElValSet + // on affecte une valeur a cette ElValue a l'interieur du ElValSet + // --> devrait pouvoir etre fait + simplement ??? + 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 Modify (or Creates if not found) an element + * @param Value new value + * @param Group + * @param Elem + * \return integer acts as a boolean + * + */ +int gdcmHeader::ReplaceOrCreateByNumber(char* Value, guint16 Group, guint16 Elem ) { + + gdcmElValue* nvElValue=NewElValueByNumber(Group, Elem); + PubElValSet.Add(nvElValue); + std::string v = Value; + PubElValSet.SetElValueByNumber(v, Group, Elem); + return(1); +} + + +/** + * \ingroup gdcmHeader + * \brief Set a new value if the invoked element exists + * 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)); + } + /** * \ingroup gdcmHeader * \brief Build a new Element Value from all the low level arguments. @@ -901,7 +1224,7 @@ int gdcmHeader::ReplaceOrCreateByNumber(guint16 Group, guint16 Elem, string Valu * 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) @@ -928,18 +1251,22 @@ gdcmElValue * gdcmHeader::ReadNextElement(void) { g = ReadInt16(); n = ReadInt16(); + if (errno == 1) // We reached the EOF (or an error occured) and header parsing // has to be considered as finished. 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 (gdcmElValue *)0; - NewElVal->SetOffset(ftell(fp)); + } + NewElVal->SetOffset(ftell(fp)); + //if ( (g==0x7fe0) && (n==0x0010) ) return NewElVal; } @@ -951,9 +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 @@ -962,48 +1288,14 @@ bool gdcmHeader::IsAnInteger(gdcmElValue * ElVal) { if ( element == 0 ) { // This is the group length of the group if (length == 4) return true; - else + else { 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; } @@ -1018,28 +1310,63 @@ 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"); - if ( ImageLocation == "gdcm::Unfound" ) { + std::string ImageLocation = GetPubElValByName("Image Location"); + if ( ImageLocation == GDCM_UNFOUND ) { grPixel = 0x7fe0; } else { 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; - gdcmElValue* PixelElement = PubElValSet.GetElementByNumber(grPixel, numPixel); + + gdcmElValue* PixelElement = PubElValSet.GetElementByNumber(grPixel, + numPixel); if (PixelElement) return PixelElement->GetOffset(); else 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 @@ -1050,19 +1377,20 @@ 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; } @@ -1077,10 +1405,10 @@ gdcmDictEntry * gdcmHeader::GetDictEntryByKey(guint16 group, guint16 element) { * @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, "FIXME in gdcmHeader::GetDictEntry", + dbg.Verbose(0, "gdcmHeader::GetDictEntry", "we SHOULD have a default dictionary"); } if (RefPubDict) { @@ -1103,9 +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); } @@ -1121,12 +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(); } @@ -1134,11 +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); } @@ -1151,14 +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(); } @@ -1166,12 +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); } @@ -1184,15 +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(); } @@ -1200,11 +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); } @@ -1217,14 +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(); } @@ -1233,13 +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); @@ -1255,13 +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); @@ -1272,12 +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); @@ -1293,12 +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); @@ -1313,9 +1641,14 @@ 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 +// pourquoi pas SetPubElValueByNumber ?? { + return ( PubElValSet.SetElValueByNumber (content, group, element) ); } @@ -1326,7 +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) ); } @@ -1357,7 +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) ); } @@ -1367,10 +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) ); } /** @@ -1382,7 +1715,7 @@ void gdcmHeader::ParseHeader(bool exception_on_error) throw(gdcmFormatError) { rewind(fp); CheckSwap(); - while ( (newElValue = ReadNextElement()) ) { + while ( (newElValue = ReadNextElement()) ) { SkipElementValue(newElValue); PubElValSet.Add(newElValue); } @@ -1390,56 +1723,7 @@ void gdcmHeader::ParseHeader(bool exception_on_error) throw(gdcmFormatError) { /** * \ingroup gdcmHeader - * \brief Once the header is parsed add some gdcm convenience/helper elements - * in the gdcmElValSet. 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. - */ -void gdcmHeader::AddAndDefaultElements(void) { - gdcmElValue* NewElVal = (gdcmElValue*)0; - string NewVal; - - NewElVal = NewManualElValToPubDict("gdcmXSize", "US"); - if (!NewElVal) return; - NewVal = GetElValByName("Rows"); - if (NewVal != "gdcm::Unfound") - NewElVal->SetValue(NewVal); - else - NewElVal->SetValue("0"); - - NewElVal = NewManualElValToPubDict("gdcmYSize", "US"); - if (!NewElVal) return; - NewVal = GetElValByName("Columns"); - if (NewVal != "gdcm::Unfound") - NewElVal->SetValue(NewVal); - else - NewElVal->SetValue("0"); - - - NewElVal = NewManualElValToPubDict("gdcmZSize", "US"); - if (!NewElVal) return; - NewVal = GetElValByNumber(0x0028,0x0008); // 0028 0008 IS IMG Number of Frames (DICOM) - if (NewVal == "gdcm::Unfound") { - NewVal = GetElValByNumber(0x0028,0x0012); // 028 0012 US IMG Planes (ACR-NEMA) - if (NewVal == "gdcm::Unfound") { // Warning !!! : 6000 0012 US OLY Planes - NewElVal->SetValue("0"); - } else { - NewElVal->SetValue(NewVal); - } - } else { - NewElVal->SetValue(NewVal); - } // length is still wrong -} // do we care about it? - - -/** - * \ingroup gdcmHeader - * \brief This predicate, based on hopefully reasonnable heuristics, + * \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. @@ -1447,34 +1731,33 @@ void gdcmHeader::AddAndDefaultElements(void) { * false otherwise. */ bool gdcmHeader::IsReadable(void) { - if ( GetElValByName("Image Dimensions") != "gdcm::Unfound" + if ( GetElValByName("Image Dimensions") != GDCM_UNFOUND && atoi(GetElValByName("Image Dimensions").c_str()) > 4 ) { return false; } - if ( GetElValByName("Bits Allocated") == "gdcm::Unfound" ) + if ( GetElValByName("Bits Allocated") == GDCM_UNFOUND ) return false; - if ( GetElValByName("Bits Stored") == "gdcm::Unfound" ) + if ( GetElValByName("Bits Stored") == GDCM_UNFOUND ) return false; - if ( GetElValByName("High Bit") == "gdcm::Unfound" ) + if ( GetElValByName("High Bit") == GDCM_UNFOUND ) return false; - if ( GetElValByName("Pixel Representation") == "gdcm::Unfound" ) + 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. - * Refer to gdcmHeader::AddAndDefaultElements for a typical usage. * \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* 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; @@ -1491,7 +1774,6 @@ gdcmElValue* gdcmHeader::NewManualElValToPubDict(string NewTagName, string VR) { NewElVal = new gdcmElValue(NewEntry); PubElValSet.Add(NewElVal); return NewElVal; - } /** @@ -1500,17 +1782,581 @@ gdcmElValue* gdcmHeader::NewManualElValToPubDict(string NewTagName, string VR) { * public tag based hash table. */ void gdcmHeader::LoadElements(void) { - rewind(fp); - TagElValueHT ht = PubElValSet.GetTagHt(); - for (TagElValueHT::iterator tag = ht.begin(); tag != ht.end(); ++tag) { - LoadElementValue(tag->second); - } + rewind(fp); + + // 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 ---------------- } -void gdcmHeader::PrintPubElVal(ostream & 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 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); +} + +// +// ------------------------ 'non string' elements related functions +// + +/** + * \ingroup gdcmHeader + * \brief Loads (from disk) the element content + * when a string is not suitable + */ +void * gdcmHeader::LoadElementVoidArea(guint16 Group, guint16 Elem) { + gdcmElValue * Element= PubElValSet.GetElementByNumber(Group, Elem); + if ( !Element ) + return NULL; + size_t o =(size_t)Element->GetOffset(); + fseek(fp, o, SEEK_SET); + int l=Element->GetLength(); + void * a = malloc(l); + if(!a) { + std::cout << "Big Broblem (LoadElementVoidArea, malloc) " + << std::hex << Group << " " << Elem << std::endl; + return NULL; + } + /* int res = */ PubElValSet.SetVoidAreaByNumber(a, Group, Elem); + // TODO check the result + size_t l2 = fread(a, 1, l ,fp); + if(l != l2) { + std::cout << "Big Broblem (LoadElementVoidArea, fread) " + << std::hex << Group << " " << Elem << std::endl; + free(a); + return NULL; + } + 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 + * \brief Retrieve the number of columns of image. + * @return The encountered size when found, 0 by default. + */ +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. + std::string StrSize = GetPubElValByNumber(0x0028,0x0011); + if (StrSize == GDCM_UNFOUND) + return 0; + return atoi(StrSize.c_str()); +} + +/** + * \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. + std::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; +} + +/** + * \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. + 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) + return atoi(StrSize.c_str()); + return 1; +} + +/** + * \ingroup gdcmHeader + * \brief Retrieve the number of Bits Stored + * (as opposite to number of Bits Allocated) + * + * @return The encountered number of Bits Stored, 0 by default. + */ +int gdcmHeader::GetBitsStored(void) { + std::string StrSize = GetPubElValByNumber(0x0028,0x0101); + if (StrSize == GDCM_UNFOUND) + return 1; + return atoi(StrSize.c_str()); +} + +/** + * \ingroup gdcmHeader + * \brief Retrieve the number of 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 or 3 Planes-) + * + * @return The encountered number of Samples Per Pixel, 1 by default. + */ +int gdcmHeader::GetSamplesPerPixel(void) { + std::string StrSize = GetPubElValByNumber(0x0028,0x0002); + if (StrSize == GDCM_UNFOUND) + return 1; // Well, it's supposed to be mandatory ... + return atoi(StrSize.c_str()); +} + +/** + * \ingroup gdcmHeader + * \brief Retrieve the Planar Configuration for RGB images + * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane) + * + * @return The encountered Planar Configuration, 0 by default. + */ +int gdcmHeader::GetPlanarConfiguration(void) { + std::string StrSize = GetPubElValByNumber(0x0028,0x0006); + if (StrSize == GDCM_UNFOUND) + return 0; + return atoi(StrSize.c_str()); +} + +/** + * \ingroup gdcmHeader + * \brief Return the size (in bytes) of a single pixel of data. + * @return The size in bytes of a single pixel of data. + * + */ +int gdcmHeader::GetPixelSize(void) { + std::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. + * \ 24 bit images appear as 8 bit + * @return + */ +std::string gdcmHeader::GetPixelType(void) { + std::string BitsAlloc; + BitsAlloc = GetElValByName("Bits Allocated"); + if (BitsAlloc == GDCM_UNFOUND) { + dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated"); + BitsAlloc = std::string("16"); + } + 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) { + dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation"); + BitsAlloc = std::string("0"); + } + if (Signed == "0") + Signed = std::string("U"); + else + +std::cout << "GetPixelType : " << BitsAlloc + Signed << std::endl; + Signed = std::string("S"); + + return( BitsAlloc + Signed); +} + +/** + * \ingroup gdcmHeader + * \brief gets the info from 0002,0010 : Transfert Syntax + * \ else 1. + * @return Transfert Syntax Name (as oposite to Transfert Syntax UID) + */ +std::string gdcmHeader::GetTransferSyntaxName(void) { + std::string TransfertSyntax = GetPubElValByNumber(0x0002,0x0010); + if (TransfertSyntax == GDCM_UNFOUND) { + dbg.Verbose(0, "gdcmHeader::GetTransferSyntaxName: unfound Transfert Syntax (0002,0010)"); + return "Uncompressed ACR-NEMA"; + } + // 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; +} + +// -------------------------------- Lookup Table related functions ------------ + +/** + * \ingroup gdcmHeader + * \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 + */ + +int gdcmHeader::HasLUT(void) { + + // 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 gets the info from 0028,1101 : Lookup Table Desc-Red + * \ else 0 + * @return Lookup Table nBit + * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] + */ + +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 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 + */ + +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; + +// Get info from Lut Descriptors +// (the 3 LUT descriptors may be different) + + 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