X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=0d21112109206bc53eaaf150f1639e067d87be2f;hb=8402492c91eb411888fb7e220e0f02b3d94c59db;hp=361aedd878f997036677fccddfeca4cf6d8dc870;hpb=81ed6935092ed908ca5c1af450f04c84baacf568;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index 361aedd8..6aa3cadb 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -1,1174 +1,796 @@ // gdcmHeader.cxx +//----------------------------------------------------------------------------- +#include "gdcmHeader.h" -#include "gdcm.h" #include -// For nthos: -#ifdef _MSC_VER -#include -#else -#include -#endif -#include // for isalpha -#include -#include -#include "gdcmUtil.h" - -#define HEADER_LENGTH_TO_READ 256 // on ne lit plus que le debut -#define _MaxSizeLoadElementValue_ 1024 // longueur au dela de laquelle on ne charge plus les valeurs - -namespace Error { - struct FileReadError { - FileReadError(FILE* fp, const char* Mesg) { - if (feof(fp)) - dbg.Verbose(1, "EOF encountered :", Mesg); - if (ferror(fp)) - dbg.Verbose(1, "Error on reading :", Mesg); - } - }; -} - -//FIXME: this looks dirty to me... - -#define str2num(str, typeNum) *((typeNum *)(str)) - -// str est un pointeur dans un tableau de caractères, qui doit contenir, -// à cet endroit la, la représentation binaire d'un entier (16 ou 32 bits) -// je veux récupérer ça ... dans un entier. -// s'il y a une autre solution, évitant des cast et les indirections, -// je suis preneur - -VRHT * gdcmHeader::dicom_vr = (VRHT*)0; -gdcmDictSet* gdcmHeader::Dicts = new gdcmDictSet(); - -void gdcmHeader::Initialise(void) { - if (!gdcmHeader::dicom_vr) - InitVRDict(); - RefPubDict = gdcmHeader::Dicts->GetDefaultPublicDict(); - RefShaDict = (gdcmDict*)0; -} +#include +#include // for isalpha -gdcmHeader::gdcmHeader (const char* InFilename) { - SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_); - filename = InFilename; - Initialise(); - fp=fopen(InFilename,"rw"); - dbg.Error(!fp, "gdcmHeader::gdcmHeader cannot open file", InFilename); - ParseHeader(); -} +#include "gdcmUtil.h" +#include "gdcmTS.h" -gdcmHeader::~gdcmHeader (void) { - fclose(fp); - 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; -} +//----------------------------------------------------------------------------- +// Constructor / Destructor /** * \ingroup gdcmHeader - * \brief Discover what the swap code is (among little endian, big endian, - * bad little endian, bad big endian). - * - */ -void gdcmHeader::CheckSwap() -{ - // The only guaranted way of finding the swap code is to find a - // group tag since we know it's length has to be of four bytes i.e. - // 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 - bool net2host; // true when HostByteOrder is the same as NetworkByteOrder - - int lgrLue; - char * entCur; - char deb[HEADER_LENGTH_TO_READ]; - - // First, compare HostByteOrder and NetworkByteOrder in order to - // determine if we shall need to swap bytes (i.e. the Endian type). - if (x==ntohs(x)) - net2host = true; - else - net2host = false; - - // The easiest case is the one of a DICOM header, since it possesses a - // file preamble where it suffice to look for the sting "DICM". - lgrLue = fread(deb, 1, HEADER_LENGTH_TO_READ, fp); - - 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. - // 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. - // FIXME: in order to fix the above warning, we could read the next - // element value (or a couple of elements values) in order to make - // sure we are not commiting a big mistake. - // 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), - // i.e. a total of 136 bytes. - entCur = deb + 136; - if(memcmp(entCur, "UL", (size_t)2) == 0) { - filetype = ExplicitVR; - dbg.Verbose(1, "gdcmHeader::CheckSwap:", - "explicit Value Representation"); - } else { - filetype = ImplicitVR; - dbg.Verbose(1, "gdcmHeader::CheckSwap:", - "not an explicit Value Representation"); - } - - if (net2host) { - sw = 4321; - dbg.Verbose(1, "gdcmHeader::CheckSwap:", - "HostByteOrder != NetworkByteOrder"); - } else { - sw = 0; - dbg.Verbose(1, "gdcmHeader::CheckSwap:", - "HostByteOrder = NetworkByteOrder"); - } - - // Position the file position indicator at first tag (i.e. - // after the file preamble and the "DICM" string). - rewind(fp); - fseek (fp, 132L, SEEK_SET); - return; - } // End of TrueDicom - - // 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). - rewind(fp); - - // Our next best chance would be to be considering a 'clean' ACR/NEMA file. - // By clean we mean that the length of the first tag is written down. - // If this is the case and since the length of the first group HAS to be - // four (bytes), then determining the proper swap code is straightforward. - - entCur = deb + 4; - s = str2num(entCur, guint32); - - switch (s) { - case 0x00040000 : - sw = 3412; - filetype = ACR; - return; - case 0x04000000 : - sw = 4321; - filetype = ACR; - return; - case 0x00000400 : - sw = 2143; - filetype = ACR; - return; - case 0x00000004 : - sw = 0; - filetype = ACR; - return; - default : - dbg.Verbose(0, "gdcmHeader::CheckSwap:", - "ACR/NEMA unfound swap info (time to raise bets)"); - } - - // We are out of luck. It is not a DicomV3 nor a 'clean' ACR/NEMA file. - // 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. - if (! net2host ) - sw = 0; - else - sw = 4321; - return; -} - -void gdcmHeader::SwitchSwapToBigEndian(void) { - dbg.Verbose(1, "gdcmHeader::SwitchSwapToBigEndian", - "Switching to BigEndian mode."); - if ( sw == 0 ) { - sw = 4321; - return; - } - if ( sw == 4321 ) { - sw = 0; - return; - } - if ( sw == 3412 ) { - sw = 2143; - return; - } - if ( sw == 2143 ) - 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. - * - * @param sw code swap - * @param skippedLength pointeur sur nombre d'octets que l'on a saute qd - * la lecture est finie - * @param longueurLue pointeur sur longueur (en nombre d'octets) - * effectivement lue - * @return longueur retenue pour le champ + * \brief + * @param InFilename + * @param exception_on_error + * @param enable_sequences = true to allow the header + * to be parsed *inside* the SeQuences, + * when they have an actual length + * @param ignore_shadow = true if user wants to skip shadow groups + during parsing, to save memory space + *\TODO : may be we need one more bool, + * to allow skipping the private elements while parsing the header + * in order to save space */ +gdcmHeader::gdcmHeader(const char *InFilename, + bool exception_on_error, + bool enable_sequences, + bool ignore_shadow): + gdcmParser(InFilename,exception_on_error,enable_sequences,ignore_shadow) +{ + + // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010 + // We may encounter the 'RETired' (0x0028, 0x0200) tag + // (Image Location") . This Element contains the number of + // 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. + + // This IS the right place for the code -// --> -// --> Oops -// --> C'etait la description de quoi, ca? -// --> - -void gdcmHeader::FindVR( ElValue *ElVal) { - if (filetype != ExplicitVR) - return; - - char VR[3]; - string vr; - int lgrLue; - 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 - // doesn't guarantee that all the tags will be in explicit VR. In some - // cases (see e-film filtered files) one finds implicit VR tags mixed - // within an explicit VR file. Hence we make sure the present tag - // is in explicit VR and try to fix things if it happens not to be - // the case. - bool RealExplicit = true; - - lgrLue=fread (&VR, (size_t)2,(size_t)1, fp); - VR[2]=0; - vr = 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 - // first to bytes of the length. Then we will interogate (through find) - // the dicom_vr dictionary with oddities like "\004\0" which crashes - // both GCC and VC++ implementations of the STL map. Hence when the - // expected VR read happens to be non-ascii characters we consider - // we hit falsely explicit VR tag. - - if ( (!isalpha(VR[0])) && (!isalpha(VR[1])) ) - RealExplicit = false; - - // 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 ) { - if ( ElVal->IsVrUnknown() ) { - // When not a dictionary entry, we can safely overwrite the vr. - ElVal->SetVR(vr); - return; - } - if ( ElVal->GetVR() == vr ) { - // The vr we just read and the dictionary agree. Nothing to do. - return; - } - // The vr present in the file and the dictionary disagree. We assume - // the file writer knew best and use the vr of the file. Since it would - // be unwise to overwrite the vr of a dictionary (since it would - // compromise it's next user), we need to clone the actual DictEntry - // and change the vr for the read one. - gdcmDictEntry* NewTag = new gdcmDictEntry(ElVal->GetGroup(), - ElVal->GetElement(), - vr, - "FIXME", - ElVal->GetName()); - ElVal->SetDictEntry(NewTag); - return; - } - - // 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"); - 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 - // dictionary entry. Still we have to flag the element as implicit since - // we know now our assumption on expliciteness is not furfilled. - // avoid . - if ( ElVal->IsVrUnknown() ) - ElVal->SetVR("Implicit"); - ElVal->SetImplicitVr(); -} - -/** - * \ingroup gdcmHeader - * \brief Determines if the Transfer Syntax was allready encountered - * and if it corresponds to a ImplicitVRLittleEndian one. - * - * @return True when ImplicitVRLittleEndian found. False in all other cases. - */ -bool gdcmHeader::IsImplicitVRLittleEndianTransferSyntax(void) { - ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadElementValueSafe(Element); - string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2" ) - return true; - return false; + std::string ImageLocation = GetEntryByNumber(0x0028, 0x0200); + if ( ImageLocation == GDCM_UNFOUND ) { // Image Location + GrPixel = 0x7fe0; // default value + } else { + GrPixel = (guint16) atoi( ImageLocation.c_str() ); + } + if (GrPixel == 0xe07f) // sometimes Image Location value doesn't follow + GrPixel = 0x7fe0; // the supposed processor endianity. + // see gdcmData/cr172241.dcm + if (GrPixel != 0x7fe0) + // This is a kludge for old dirty Philips imager. + NumPixel = 0x1010; + else + NumPixel = 0x0010; + + TagKey key = gdcmDictEntry::TranslateToKey(GrPixel, NumPixel); + countGrPixel = GetEntry().count(key); } /** * \ingroup gdcmHeader - * \brief Determines if the Transfer Syntax was allready encountered - * and if it corresponds to a ExplicitVRLittleEndian one. - * - * @return True when ExplicitVRLittleEndian found. False in all other cases. + * \brief + * @param exception_on_error */ -bool gdcmHeader::IsExplicitVRLittleEndianTransferSyntax(void) { - ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadElementValueSafe(Element); - string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.1" ) - return true; - return false; +gdcmHeader::gdcmHeader(bool exception_on_error) : + gdcmParser(exception_on_error) +{ } /** * \ingroup gdcmHeader - * \brief Determines if the Transfer Syntax was allready encountered - * and if it corresponds to a DeflatedExplicitVRLittleEndian one. - * - * @return True when DeflatedExplicitVRLittleEndian found. False in all other cases. + * \brief Canonical destructor. */ -bool gdcmHeader::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) { - ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadElementValueSafe(Element); - string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.1.99" ) - return true; - return false; +gdcmHeader::~gdcmHeader (void) { } +//----------------------------------------------------------------------------- +// Print +// see gdcmParser.cxx +//----------------------------------------------------------------------------- +// Public /** * \ingroup gdcmHeader - * \brief Determines if the Transfer Syntax was allready encountered - * and if it corresponds to a Explicit VR Big Endian one. - * - * @return True when big endian found. False in all other cases. + * \brief This predicate, based on hopefully reasonable heuristics, + * decides whether or not the current gdcmParser was properly parsed + * and contains the mandatory information for being considered as + * a well formed and usable Dicom/Acr File. + * @return true when gdcmParser is the one of a reasonable Dicom/Acr file, + * false otherwise. */ -bool gdcmHeader::IsExplicitVRBigEndianTransferSyntax(void) { - ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadElementValueSafe(Element); - string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.2" ) - return true; - return false; +bool gdcmHeader::IsReadable(void) { + if(!gdcmParser::IsReadable()) { + return(false); + } + std::string res = GetEntryByNumber(0x0028, 0x0005); + if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) + return false; // Image Dimensions + if ( !GetHeaderEntryByNumber(0x0028, 0x0100) ) + return false; // "Bits Allocated" + if ( !GetHeaderEntryByNumber(0x0028, 0x0101) ) + return false; // "Bits Stored" + if ( !GetHeaderEntryByNumber(0x0028, 0x0102) ) + return false; // "High Bit" + if ( !GetHeaderEntryByNumber(0x0028, 0x0103) ) + return false; // "Pixel Representation" + return true; } - /** * \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. */ bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) { - ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadElementValueSafe(Element); - string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.4.50" ) - return true; - return false; + gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + if ( !Element ) + return false; + LoadHeaderEntrySafe(Element); + + std::string Transfer = Element->GetValue(); + if ( Transfer == "1.2.840.10008.1.2.4.50" ) + 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. */ bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) { - ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadElementValueSafe(Element); - string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.4.51" ) - return true; - return false; + gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + if ( !Element ) + return false; + LoadHeaderEntrySafe(Element); + return ( Element->GetValue() == "1.2.840.10008.1.2.4.51" ); } - /** * \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. */ bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) { - ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadElementValueSafe(Element); - string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.4.52" ) - return true; - return false; + gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + if ( !Element ) + return false; + LoadHeaderEntrySafe(Element); + + std::string Transfer = Element->GetValue(); + if ( Transfer == "1.2.840.10008.1.2.4.52" ) + 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 JPEGSpectralSelectionProcess6-8 one. * - * @return True when JPEGSpectralSelectionProcess6-8 found. False in all other cases. + * @return True when JPEGSpectralSelectionProcess6-8 found. False in all + * other cases. */ bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) { - ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadElementValueSafe(Element); - string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.4.53" ) - return true; - return false; -} - -// -// Euhhhhhhh -// Il y en a encore DIX-SEPT, comme ça. -// Il faudrait trouver qq chose + rusé ... -// -// --> probablement TOUS les supprimer (Eric dixit) -// -void gdcmHeader::FixFoundLength(ElValue * ElVal, guint32 FoundLength) { - // Heuristic: a final fix. - if ( FoundLength == 0xffffffff) - FoundLength = 0; - ElVal->SetLength(FoundLength); -} - -guint32 gdcmHeader::FindLengthOB(void) { - // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data. - guint16 g; - guint16 n; - long PositionOnEntry = ftell(fp); - bool FoundSequenceDelimiter = false; - guint32 TotalLength = 0; - guint32 ItemLength; - - while ( ! FoundSequenceDelimiter) { - g = ReadInt16(); - n = ReadInt16(); - 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."); - throw Error::FileReadError(fp, "gdcmHeader::FindLengthOB"); - } - if ( n == 0xe0dd ) - FoundSequenceDelimiter = true; - else if ( n != 0xe000) { - dbg.Verbose(1, "gdcmHeader::FindLengthOB: ", - "wrong element for an item sequence."); - throw Error::FileReadError(fp, "gdcmHeader::FindLengthOB"); - } - ItemLength = ReadInt32(); - TotalLength += ItemLength + 4; // We add 4 bytes since we just read - // the ItemLength with ReadInt32 - SkipBytes(ItemLength); - } - fseek(fp, PositionOnEntry, SEEK_SET); - return TotalLength; -} - -void gdcmHeader::FindLength(ElValue * ElVal) { - guint16 element = ElVal->GetElement(); - string vr = ElVal->GetVR(); - guint16 length16; - - 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); - return; - } - - // Length is encoded on 2 bytes. - length16 = ReadInt16(); - - // We can tell the current file is encoded in big endian (like - // Data/US-RGB-8-epicard) when we find the "Transfer Syntax" tag - // and it's value is the one of the encoding of a big endian file. - // In order to deal with such big endian encoded files, we have - // (at least) two strategies: - // * when we load the "Transfer Syntax" tag with value of big endian - // encoding, we raise the proper flags. Then we wait for the end - // of the META group (0x0002) among which is "Transfer Syntax", - // before switching the swap code to big endian. We have to postpone - // the switching of the swap code since the META group is fully encoded - // in little endian, and big endian coding only starts at the next - // group. The corresponding code can be hard to analyse and adds - // many additional unnecessary tests for regular tags. - // * the second strategy consists in waiting for trouble, that shall 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 - // found a group with big endian encoding. - // We shall use this second strategy. In order 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 - // for the presence of a "Transfer Syntax" whose value has to be "big - // endian encoding". When this is the case, chances are we 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 ( ! IsExplicitVRBigEndianTransferSyntax() ) - throw Error::FileReadError(fp, "gdcmHeader::FindLength"); - length16 = 4; - SwitchSwapToBigEndian(); - // Restore the unproperly loaded values i.e. the group, the element - // and the dictionary entry depending on them. - guint16 CorrectGroup = SwapShort(ElVal->GetGroup()); - guint16 CorrectElem = SwapShort(ElVal->GetElement()); - gdcmDictEntry * NewTag = IsInDicts(CorrectGroup, CorrectElem); - if (!NewTag) { - // This correct tag is not in the dictionary. Create a new one. - NewTag = new gdcmDictEntry(CorrectGroup, CorrectElem); - } - // FIXME this can create a memory leaks on the old entry that be - // left unreferenced. - ElVal->SetDictEntry(NewTag); - } - - // Heuristic: well some files are really ill-formed. - if ( length16 == 0xffff) { - length16 = 0; - dbg.Verbose(0, "gdcmHeader::FindLength", - "Erroneous element length fixed."); - } - FixFoundLength(ElVal, (guint32)length16); - return; - } + gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + if ( !Element ) + return false; + LoadHeaderEntrySafe(Element); - // Either implicit VR or a non DICOM conformal (see not below) explicit - // VR that ommited the VR of (at least) this element. Farts happen. - // [Note: according to the part 5, PS 3.5-2001, section 7.1 p25 - // on Data elements "Implicit and Explicit VR Data Elements shall - // not coexist in a Data Set and Data Sets nested within it".] - // Length is on 4 bytes. - FixFoundLength(ElVal, ReadInt32()); + std::string Transfer = Element->GetValue(); + if ( Transfer == "1.2.840.10008.1.2.4.53" ) + return true; + return false; } /** * \ingroup gdcmHeader - * \brief Swaps back the bytes of 4-byte long integer accordingly to - * processor order. + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a RLE Lossless one. * - * @return The suggested integer. + * @return True when RLE Lossless found. False in all + * other cases. */ -guint32 gdcmHeader::SwapLong(guint32 a) { - // FIXME: il pourrait y avoir un pb pour les entiers negatifs ... - switch (sw) { - case 0 : - break; - case 4321 : - a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) | - ((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) ); - break; - - case 3412 : - a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) ); - break; - - case 2143 : - a=( ((a<<8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) ); - break; - default : - dbg.Error(" gdcmHeader::SwapLong : unset swap code"); - a=0; - } - return(a); +bool gdcmHeader::IsRLELossLessTransferSyntax(void) { + gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + if ( !Element ) + return false; + LoadHeaderEntrySafe(Element); + + std::string Transfer = Element->GetValue(); + if ( Transfer == "1.2.840.10008.1.2.5" ) { + return true; + } + return false; } /** * \ingroup gdcmHeader - * \brief Swaps the bytes so they agree with the processor order - * @return The properly swaped 16 bits integer. + * \brief Determines if Transfer Syntax was already encountered + * and if it corresponds to a JPEG Lossless one. + * + * @return True when RLE Lossless found. False in all + * other cases. */ -guint16 gdcmHeader::SwapShort(guint16 a) { - if ( (sw==4321) || (sw==2143) ) - a =(((a<<8) & 0x0ff00) | ((a>>8)&0x00ff)); - return (a); -} +bool gdcmHeader::IsJPEGLossless(void) { + gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + // faire qq chose d'intelligent a la place de ça + if ( !Element ) + return false; + LoadHeaderEntrySafe(Element); -void gdcmHeader::SkipBytes(guint32 NBytes) { - //FIXME don't dump the returned value - (void)fseek(fp, (long)NBytes, SEEK_CUR); -} + 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; -void gdcmHeader::SkipElementValue(ElValue * ElVal) { - SkipBytes(ElVal->GetLength()); -} - -void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) { - if (NewSize < 0) - return; - if ((guint32)NewSize >= (guint32)0xffffffff) { - MaxSizeLoadElementValue = 0xffffffff; - return; - } - MaxSizeLoadElementValue = NewSize; + return false; } /** - * \ingroup gdcmHeader - * \brief Loads the element if it's size is not to big. - * @param ElVal Element whose value shall be loaded. - * @param MaxSize Size treshold above which the element value is not - * loaded in memory. The element value is allways loaded - * when MaxSize is equal to UINT32_MAX. - * @return + * \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. */ -void gdcmHeader::LoadElementValue(ElValue * 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 ! - // - // 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 - // - if( vr == "SQ" ) - SkipLoad = true; +bool gdcmHeader::IsJPEG2000(void) { + gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + if ( !Element ) + return false; + LoadHeaderEntrySafe(Element); - // 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). - 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 - - if ( SkipLoad ) { - // FIXME the following skip is not necessary - SkipElementValue(ElVal); - ElVal->SetLength(0); - ElVal->SetValue("gdcm::Skipped"); - return; - } - - // When the length is zero things are easy: - if ( length == 0 ) { - ElVal->SetValue(""); - return; - } - - // Values bigger than specified are not loaded. - // - // En fait, c'est les elements dont la longueur est superieure - // a celle fixee qui ne sont pas charges - // - if (length > MaxSizeLoadElementValue) { - ostringstream s; - s << "gdcm::NotLoaded."; - s << " Address:" << (long)ElVal->GetOffset(); - s << " Length:" << ElVal->GetLength(); - //mesg += " Length:" + ElVal->GetLength(); - ElVal->SetValue(s.str()); - return; - } - - // 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. - if ( IsAnInteger(ElVal) ) { - guint32 NewInt; - if( length == 2 ) { - NewInt = ReadInt16(); - } else if( length == 4 ) { - NewInt = ReadInt32(); - } else - dbg.Error(true, "LoadElementValue: Inconsistency when reading Int."); - - //FIXME: make the following an util fonction - ostringstream s; - s << NewInt; - ElVal->SetValue(s.str()); - return; - } - - // FIXME The exact size should be length if we move to strings or whatever - - // - // QUESTION : y a-t-il une raison pour ne pas utiliser g_malloc ici ? - // - - char* NewValue = (char*)malloc(length+1); - if( !NewValue) { - dbg.Verbose(1, "LoadElementValue: Failed to allocate NewValue"); - return; - } - NewValue[length]= 0; - - item_read = fread(NewValue, (size_t)length, (size_t)1, fp); - if ( item_read != 1 ) { - free(NewValue); - Error::FileReadError(fp, "gdcmHeader::LoadElementValue"); - ElVal->SetValue("gdcm::UnRead"); - return; - } - ElVal->SetValue(NewValue); + 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 Loads the element while preserving the current - * underlying file position indicator as opposed to - * to LoadElementValue that modifies it. - * @param ElVal Element whose value shall be loaded. - * @return + * \ingroup gdcmHeader + * \brief Predicate for dicom version 3 file. + * @return True when the file is a dicom version 3. */ -void gdcmHeader::LoadElementValueSafe(ElValue * ElVal) { - long PositionOnEntry = ftell(fp); - LoadElementValue(ElVal); - fseek(fp, PositionOnEntry, SEEK_SET); -} - - -guint16 gdcmHeader::ReadInt16(void) { - guint16 g; - size_t item_read; - item_read = fread (&g, (size_t)2,(size_t)1, fp); - if ( item_read != 1 ) - throw Error::FileReadError(fp, "gdcmHeader::ReadInt16"); - g = SwapShort(g); - return g; -} - -guint32 gdcmHeader::ReadInt32(void) { - guint32 g; - size_t item_read; - item_read = fread (&g, (size_t)4,(size_t)1, fp); - if ( item_read != 1 ) - throw Error::FileReadError(fp, "gdcmHeader::ReadInt32"); - g = SwapLong(g); - return g; +bool gdcmHeader::IsDicomV3(void) { + // Checking if Transfert Syntax exists is enough + return (GetHeaderEntryByNumber(0x0002, 0x0010) != NULL); } /** * \ingroup gdcmHeader - * \brief Read the next tag without loading it's value - * @return On succes the newly created ElValue, NULL on failure. + * \brief Retrieve the number of columns of image. + * @return The encountered size when found, 0 by default. + * 0 means the file is NOT USABLE. The caller will have to check */ - -ElValue * gdcmHeader::ReadNextElement(void) { - guint16 g; - guint16 n; - ElValue * NewElVal; - - try { - g = ReadInt16(); - n = ReadInt16(); - } - catch ( Error::FileReadError ) { - // We reached the EOF (or an error occured) and header parsing - // has to be considered as finished. - return (ElValue *)0; - } - - // Find out if the tag we encountered is in the dictionaries: - gdcmDictEntry * NewTag = IsInDicts(g, n); - if (!NewTag) - NewTag = new gdcmDictEntry(g, n); - - NewElVal = new ElValue(NewTag); - if (!NewElVal) { - dbg.Verbose(1, "ReadNextElement: failed to allocate ElValue"); - return (ElValue*)0; - } - - FindVR(NewElVal); - try { FindLength(NewElVal); } - catch ( Error::FileReadError ) { // Call it quits - return (ElValue *)0; - } - NewElVal->SetOffset(ftell(fp)); - return NewElVal; -} - -bool gdcmHeader::IsAnInteger(ElValue * ElVal) { - guint16 group = ElVal->GetGroup(); - guint16 element = ElVal->GetElement(); - string vr = ElVal->GetVR(); - guint32 length = ElVal->GetLength(); - - // When we have some semantics on the element we just read, and if we - // a priori know we are dealing with an integer, then we shall be - // able to swap it's element value properly. - if ( element == 0 ) { // This is the group length of the group - if (length == 4) - return true; - else - dbg.Error("gdcmHeader::IsAnInteger", - "Erroneous Group Length element length."); - } - - 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. - return false; - - if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") ) - return true; - - if ( (group == 0x0028) && (element == 0x0005) ) - // This tag is retained from ACR/NEMA - // CHECKME Why should "Image Dimensions" be a single integer ? - // - // "Image Dimensions", c'est en fait le 'nombre de dimensions' - // de l'objet ACR-NEMA stocké - // 1 : Signal - // 2 : Image - // 3 : Volume - // 4 : Sequence - // - // DICOM V3 ne retient pas cette information - // Par defaut, tout est 'Image', - // C'est a l'utilisateur d'explorer l'ensemble des entetes - // pour savoir à quoi il a a faire - // - // Le Dicom Multiframe peut etre utilise pour stocker, - // dans un seul fichier, une serie temporelle (cardio vasculaire GE, p.ex) - // ou un volume (medecine Nucleaire, p.ex) - // - return true; - - if ( (group == 0x0028) && (element == 0x0200) ) - // This tag is retained from ACR/NEMA - return true; - - return false; +int gdcmHeader::GetXSize(void) { + std::string StrSize; + StrSize = GetEntryByNumber(0x0028,0x0011); + if (StrSize == GDCM_UNFOUND) + return 0; + return atoi(StrSize.c_str()); } /** * \ingroup gdcmHeader - * \brief Recover the offset (from the beginning of the file) of the pixels. + * \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 + * (The file contains a Signal, not an Image). */ -size_t gdcmHeader::GetPixelOffset(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; - 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 - numPixel = 0x1010; - else - numPixel = 0x0010; - ElValue* PixelElement = PubElVals.GetElementByNumber(grPixel, numPixel); - if (PixelElement) - return PixelElement->GetOffset(); - else - return 0; -} - -gdcmDictEntry * gdcmHeader::IsInDicts(guint32 group, guint32 element) { - // - // Y a-t-il une raison de lui passer des guint32 - // alors que group et element sont des guint16? - // - gdcmDictEntry * found = (gdcmDictEntry*)0; - if (!RefPubDict && !RefShaDict) { - //FIXME build a default dictionary ! - printf("FIXME in gdcmHeader::IsInDicts\n"); - } - if (RefPubDict) { - found = RefPubDict->GetTag(group, element); - if (found) - return found; - } - if (RefShaDict) { - found = RefShaDict->GetTag(group, element); - if (found) - return found; - } - return found; +int gdcmHeader::GetYSize(void) { + std::string StrSize = GetEntryByNumber(0x0028,0x0010); + if (StrSize != GDCM_UNFOUND) + return atoi(StrSize.c_str()); + if ( IsDicomV3() ) + return 0; + else + // The Rows (0028,0010) entry was optional for ACR/NEMA. It might + // hence be a signal (1d image). So we default to 1: + return 1; } -list * gdcmHeader::GetPubTagNames(void) { - list * Result = new list; - TagHT entries = RefPubDict->GetEntries(); - - for (TagHT::iterator tag = entries.begin(); tag != entries.end(); ++tag){ - Result->push_back( tag->second->GetName() ); - } - return Result; -} - -map > * gdcmHeader::GetPubTagNamesByCategory(void) { - map > * Result = new map >; - TagHT entries = RefPubDict->GetEntries(); - - for (TagHT::iterator tag = entries.begin(); tag != entries.end(); ++tag){ - (*Result)[tag->second->GetFourth()].push_back(tag->second->GetName()); - } - return Result; -} - -string gdcmHeader::GetPubElValByNumber(guint16 group, guint16 element) { - return PubElVals.GetElValueByNumber(group, element); -} - -string gdcmHeader::GetPubElValRepByNumber(guint16 group, guint16 element) { - ElValue* elem = PubElVals.GetElementByNumber(group, element); - if ( !elem ) - return "gdcm::Unfound"; - return elem->GetVR(); -} - -string gdcmHeader::GetPubElValByName(string TagName) { - return PubElVals.GetElValueByName(TagName); -} - -string gdcmHeader::GetPubElValRepByName(string TagName) { - ElValue* elem = PubElVals.GetElementByName(TagName); - if ( !elem ) - return "gdcm::Unfound"; - return elem->GetVR(); -} - -string gdcmHeader::GetShaElValByNumber(guint16 group, guint16 element) { - return ShaElVals.GetElValueByNumber(group, element); -} - -string gdcmHeader::GetShaElValRepByNumber(guint16 group, guint16 element) { - ElValue* elem = ShaElVals.GetElementByNumber(group, element); - if ( !elem ) - return "gdcm::Unfound"; - return elem->GetVR(); -} - -string gdcmHeader::GetShaElValByName(string TagName) { - return ShaElVals.GetElValueByName(TagName); -} - -string gdcmHeader::GetShaElValRepByName(string TagName) { - ElValue* elem = ShaElVals.GetElementByName(TagName); - if ( !elem ) - return "gdcm::Unfound"; - return elem->GetVR(); -} - - -string gdcmHeader::GetElValByNumber(guint16 group, guint16 element) { - string pub = GetPubElValByNumber(group, element); - if (pub.length()) - return pub; - return GetShaElValByNumber(group, element); +/** + * \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 (single image). + */ +int gdcmHeader::GetZSize(void) { + // Both DicomV3 and ACR/Nema consider the "Number of Frames" + // as the third dimension. + std::string StrSize = GetEntryByNumber(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 = GetEntryByNumber(0x0028,0x0012); + if (StrSize != GDCM_UNFOUND) + return atoi(StrSize.c_str()); + return 1; } -string gdcmHeader::GetElValRepByNumber(guint16 group, guint16 element) { - string pub = GetPubElValRepByNumber(group, element); - if (pub.length()) - return pub; - return GetShaElValRepByNumber(group, element); +/** + * \ingroup gdcmHeader + * \brief Retrieve the number of Bits Stored (actually used) + * (as opposite to number of Bits Allocated) + * + * @return The encountered number of Bits Stored, 0 by default. + * 0 means the file is NOT USABLE. The caller has to check it ! + */ +int gdcmHeader::GetBitsStored(void) { + std::string StrSize = GetEntryByNumber(0x0028,0x0101); + if (StrSize == GDCM_UNFOUND) + return 0; // It's supposed to be mandatory + // the caller will have to check + return atoi(StrSize.c_str()); } -string gdcmHeader::GetElValByName(string TagName) { - string pub = GetPubElValByName(TagName); - if (pub.length()) - return pub; - return GetShaElValByName(TagName); +/** + * \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. + * 0 means the file is NOT USABLE. The caller has to check it ! + */ +int gdcmHeader::GetBitsAllocated(void) { // TODO : move to gdcmFile + std::string StrSize = GetEntryByNumber(0x0028,0x0100); + if (StrSize == GDCM_UNFOUND) + return 0; // It's supposed to be mandatory + // the caller will have to check + return atoi(StrSize.c_str()); } -string gdcmHeader::GetElValRepByName(string TagName) { - string pub = GetPubElValRepByName(TagName); - if (pub.length()) - return pub; - return GetShaElValRepByName(TagName); +/** + * \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. + * (Gray level Pixels) + */ +int gdcmHeader::GetSamplesPerPixel(void) { // TODO : move to gdcmFile + std::string StrSize = GetEntryByNumber(0x0028,0x0002); + if (StrSize == GDCM_UNFOUND) + return 1; // Well, it's supposed to be mandatory ... + // but sometimes it's missing : we assume Gray pixels + return atoi(StrSize.c_str()); } /** * \ingroup gdcmHeader - * \brief Modifie la valeur d'un ElValue déja existant - * \ dans le PubElVals du gdcmHeader, - * \ accédé par ses numero de groupe et d'element. + * \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::SetPubElValByNumber(string content, guint16 group, guint16 element) { - //TagKey key = gdcmDictEntry::TranslateToKey(group, element); - //PubElVals.tagHt[key]->SetValue(content); - - return ( PubElVals.SetElValueByNumber (content, group, element) ); +int gdcmHeader::GetPlanarConfiguration(void) { + std::string StrSize = GetEntryByNumber(0x0028,0x0006); + if (StrSize == GDCM_UNFOUND) + return 0; + return atoi(StrSize.c_str()); } - /** * \ingroup gdcmHeader - * \brief Modifie la valeur d'un ElValue déja existant - * \ dans le PubElVals du gdcmHeader, - * \ accédé par son nom + * \brief Return the size (in bytes) of a single pixel of data. + * @return The size in bytes of a single pixel of data; 0 by default + * 0 means the file is NOT USABLE; the caller will have to check */ -int gdcmHeader::SetPubElValByName(string content, string TagName) { - //TagKey key = gdcmDictEntry::TranslateToKey(group, element); - //PubElVals.tagHt[key]->SetValue(content); - - return ( PubElVals.SetElValueByName (content, TagName) ); +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 Modifie la valeur d'un ElValue déja existant - * \ dans le ShaElVals du gdcmHeader, - * \ accédé par ses numero de groupe et d'element. + * \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 0S if nothing found. NOT USABLE file. The caller has to check */ -int gdcmHeader::SetShaElValByNumber(string content, guint16 group, guint16 element) { - - return ( ShaElVals.SetElValueByNumber (content, group, element) ); +std::string gdcmHeader::GetPixelType(void) { + std::string BitsAlloc = GetEntryByNumber(0x0028, 0x0100); // 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 = GetEntryByNumber(0x0028, 0x0103); // "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 + Signed = std::string("S"); + + return( BitsAlloc + Signed); } /** * \ingroup gdcmHeader - * \brief Modifie la valeur d'un ElValue déja existant - * \ dans le ShaElVals du gdcmHeader, - * \ accédé par son nom + * \brief Recover the offset (from the beginning of the file) + * \ of *image* pixels (not *icone image* pixels, if any !) */ -int gdcmHeader::SetShaElValByName(string content, string TagName) { - - return ( ShaElVals.SetElValueByName (content, TagName) ); -} +size_t gdcmHeader::GetPixelOffset(void) { + // + // If the element (0x0088,0x0200) 'icone image sequence' is found + // (grPixel,numPixel) is stored twice : the first one for the icon + // the second one for the image ... + // pb : sometimes , (0x0088,0x0200) exists, but doesn't contain *anything* + // see gdcmData/MxTwinLossLess.dcm ... + + //std::string icone = GetEntryByNumber(0x0088,0x0200); //icone image sequence + + IterHT it = GetHeaderEntrySameNumber(GrPixel,NumPixel); + TagKey key = gdcmDictEntry::TranslateToKey(GrPixel,NumPixel); + gdcmHeaderEntry* PixelElement; + if (countGrPixel == 1) + PixelElement = (it.first)->second; + else { + PixelElement = (++it.first)->second; // hope there are no more than 2 ! + } + if (PixelElement) { + return PixelElement->GetOffset(); + } else { + return 0; + std::cout << "Big trouble : Pixel Element (" + << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" + << std::endl; + } +} +// TODO : unify those two (previous one and next one) /** * \ingroup gdcmHeader - * \brief Parses the header of the file but does NOT load element values. + * \brief Recover the pixel area length (in Bytes) + * @return Pixel Element Length, as stored in the header + * (NOT the memory space necessary to hold the Pixels + * - in case of embeded compressed image-) + * 0 : NOT USABLE file. The caller has to check. */ -void gdcmHeader::ParseHeader(void) { - ElValue * newElValue = (ElValue *)0; - - rewind(fp); - CheckSwap(); - while ( (newElValue = ReadNextElement()) ) { - SkipElementValue(newElValue); - PubElVals.Add(newElValue); - } +size_t gdcmHeader::GetPixelAreaLength(void) { + + IterHT it = GetHeaderEntrySameNumber(GrPixel,NumPixel); + TagKey key = gdcmDictEntry::TranslateToKey(GrPixel,NumPixel); + gdcmHeaderEntry* PixelElement; + + if (countGrPixel==1) + PixelElement = (it.first)->second; + else + PixelElement = (++it.first)->second; + + if (PixelElement) { + return PixelElement->GetLength(); + } else { + std::cout << "Big trouble : Pixel Element (" + << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" + << std::endl; + return 0; + } } /** - * \ingroup gdcmHeader - * \brief Loads the element values of all the elements present in the - * public tag based hash table. - */ -void gdcmHeader::LoadElements(void) { - - rewind(fp); + * \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 a Boolean + */ +bool gdcmHeader::HasLUT(void) { + + // Check the presence of the LUT Descriptors + + // LutDescriptorRed + if ( !GetHeaderEntryByNumber(0x0028,0x1101) ) + return false; + // LutDescriptorGreen + if ( !GetHeaderEntryByNumber(0x0028,0x1102) ) + return false; + // LutDescriptorBlue + if ( !GetHeaderEntryByNumber(0x0028,0x1103) ) + return false; + + // It is not enough : + // we check also + + // Red Palette Color Lookup Table Data + if ( !GetHeaderEntryByNumber(0x0028,0x1201) ) + return false; + // Green Palette Color Lookup Table Data + if ( !GetHeaderEntryByNumber(0x0028,0x1202) ) + return false; + // Blue Palette Color Lookup Table Data + if ( !GetHeaderEntryByNumber(0x0028,0x1203) ) + return false; + return true; +} - TagElValueHT ht = PubElVals.GetTagHt(); - - for (TagElValueHT::iterator tag = ht.begin(); tag != ht.end(); ++tag) { - LoadElementValue(tag->second); - } +/** + * \ingroup gdcmHeader + * \brief gets the info from 0028,1101 : Lookup Table Desc-Red + * \ else 0 + * @return Lookup Table number of Bits , 0 by default + * \ 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 = GetEntryByNumber(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; } -void gdcmHeader::PrintPubElVal(ostream & os) { - PubElVals.Print(os); +/** + * \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 deals with them :-( + * @return a RGBA Lookup Table + */ +unsigned char * gdcmHeader::GetLUTRGBA(void) { +// Not so easy : see +// http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables + +// if Photometric Interpretation # PALETTE COLOR, no LUT to be done + if (GetEntryByNumber(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 = GetEntryByNumber(0x0028,0x1101); + if (LutDescriptionR == GDCM_UNFOUND) + return NULL; + std::string LutDescriptionG = GetEntryByNumber(0x0028,0x1102); + if (LutDescriptionG == GDCM_UNFOUND) + return NULL; + std::string LutDescriptionB = GetEntryByNumber(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()); // subscript of the first Lut Value + nbitsG =atoi(tokens[2].c_str()); // Lut item size (in Bits) + 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()); // subscript of the first Lut Value + nbitsB =atoi(tokens[2].c_str()); // Lut item size (in Bits) + tokens.clear(); + + // Load LUTs into memory, (as they were stored on disk) + unsigned char *lutR = (unsigned char *) + GetEntryVoidAreaByNumber(0x0028,0x1201); + unsigned char *lutG = (unsigned char *) + GetEntryVoidAreaByNumber(0x0028,0x1202); + unsigned char *lutB = (unsigned char *) + GetEntryVoidAreaByNumber(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 = GetEntryByNumber(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 (useless ?)overhead + // (optimistic asumption) + unsigned char *a; + int i; + + a = LUTRGBA+0; + for(i=0;iGetValue(TransfertSyntax); + //delete ts; // Seg Fault when deleted ?! + return tsName; } -void gdcmHeader::PrintPubDict(ostream & os) { - RefPubDict->Print(os); +/** + * \ingroup gdcmFile + * \brief Sets the Pixel Area size in the Header + * --> not-for-rats function + * + * \warning WARNING doit-etre etre publique ? + * TODO : y aurait il un inconvenient à fusionner ces 2 fonctions + * + * @param ImageDataSize new Pixel Area Size + * warning : nothing else is checked + */ +void gdcmHeader::SetImageDataSize(size_t ImageDataSize) { + std::string content1; + char car[20]; + + // Assumes HeaderEntry (GrPixel, NumPixel) is unique ... + // TODO deal with multiplicity (see gdcmData/icone.dcm) + sprintf(car,"%d",ImageDataSize); + + gdcmHeaderEntry *a = GetHeaderEntryByNumber(GrPixel, NumPixel); + a->SetLength(ImageDataSize); + + ImageDataSize+=8; + sprintf(car,"%d",ImageDataSize); + content1=car; + SetEntryByNumber(content1, GrPixel, NumPixel); } + +bool gdcmHeader::operator<(gdcmHeader &header) +{ + std::string s1,s2; + + // Patient Name + s1=this->GetEntryByNumber(0x0010,0x0010); + s2=header.GetEntryByNumber(0x0010,0x0010); + if(s1 < s2) + return(true); + else if(s1 > s2) + return(false); + else + { + // Patient ID + s1=this->GetEntryByNumber(0x0010,0x0020); + s2=header.GetEntryByNumber(0x0010,0x0020); + if (s1 < s2) + return(true); + else if (s1 > s2) + return(1); + else + { + // Study Instance UID + s1=this->GetEntryByNumber(0x0020,0x000d); + s2=header.GetEntryByNumber(0x0020,0x000d); + if (s1 < s2) + return(true); + else if(s1 > s2) + return(false); + else + { + // Serie Instance UID + s1=this->GetEntryByNumber(0x0020,0x000e); + s2=header.GetEntryByNumber(0x0020,0x000e); + if (s1 < s2) + return(true); + else if(s1 > s2) + return(false); + } + } + } + return(false); +} + +//----------------------------------------------------------------------------- +// Protected + +//----------------------------------------------------------------------------- +// Private + +//-----------------------------------------------------------------------------