X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;ds=sidebyside;f=src%2FgdcmHeader.cxx;h=0d21112109206bc53eaaf150f1639e067d87be2f;hb=8402492c91eb411888fb7e220e0f02b3d94c59db;hp=955411202925e9d289de811cdd8ba5efe6f4fea8;hpb=baecaa4a3a8de7d236921b836a442ff7ac7e65ee;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index 95541120..6aa3cadb 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -1,616 +1,796 @@ -#include "gdcmlib.h" -extern "C" { -#include "glib.h" -} -#include -// For nthos: -#ifdef _MSC_VER -#include -#else -#include -#endif -#include -#include -#include "gdcmUtil.h" +// gdcmHeader.cxx +//----------------------------------------------------------------------------- +#include "gdcmHeader.h" -#define HEADER_LENGHT_TO_READ 256 // on ne lit plus que le debut +#include +#include +#include // for isalpha -//FIXME: this looks dirty to me... -#define str2num(str, typeNum) *((typeNum *)(str)) +#include "gdcmUtil.h" +#include "gdcmTS.h" -VRHT * gdcmHeader::dicom_vr = (VRHT*)0; -gdcmDictSet* gdcmHeader::Dicts = new gdcmDictSet(); -void gdcmHeader::Initialise(void) { - if (!gdcmHeader::dicom_vr) - InitVRDict(); - PixelPosition = (size_t)0; - PixelsTrouves = false; - RefPubDict = gdcmHeader::Dicts->GetDefaultPublicDict(); - RefShaDict = (gdcmDict*)0; +//----------------------------------------------------------------------------- +// Constructor / Destructor +/** + * \ingroup gdcmHeader + * \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 + + 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); } -gdcmHeader::gdcmHeader (char* InFilename) { - filename = InFilename; - Initialise(); - fp=fopen(InFilename,"rw"); - dbg.Error(!fp, "gdcmHeader::gdcmHeader cannot open file", InFilename); - BuildHeader(); - fclose(fp); +/** + * \ingroup gdcmHeader + * \brief + * @param exception_on_error + */ +gdcmHeader::gdcmHeader(bool exception_on_error) : + gdcmParser(exception_on_error) +{ } +/** + * \ingroup gdcmHeader + * \brief Canonical destructor. + */ gdcmHeader::~gdcmHeader (void) { - 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"; // 16 car max - (*vr)["AS"] = "Age String"; // 4 car fixe - (*vr)["AT"] = "Attribute Tag"; // 2 unsigned short int - (*vr)["CS"] = "Code String"; // 16 car max - (*vr)["DA"] = "Date"; // 8 car fixe - (*vr)["DS"] = "Decimal String"; // Decimal codé Binaire 16 max - (*vr)["DT"] = "Date Time"; // 26 car max - (*vr)["FL"] = "Floating Point Single"; // 4 octets IEEE 754:1985 - (*vr)["FD"] = "Floating Point Double"; // 8 octets IEEE 754:1985 - (*vr)["IS"] = "Integer String"; // en format externe 12 max - (*vr)["LO"] = "Long String"; // 64 octets max - (*vr)["LT"] = "Long Text"; // 10240 max - (*vr)["OB"] = "Other Byte String"; - (*vr)["OW"] = "Other Word String"; - (*vr)["PN"] = "Person Name"; - (*vr)["SH"] = "Short String"; // 16 car max - (*vr)["SL"] = "Signed Long"; - (*vr)["SQ"] = "Sequence of Items"; // Not Applicable - (*vr)["SS"] = "Signed Short"; // 2 octets - (*vr)["ST"] = "Short Text"; // 1024 car max - (*vr)["TM"] = "Time"; // 16 car max - (*vr)["UI"] = "Unique Identifier"; // 64 car max - (*vr)["UN"] = "Unknown"; - (*vr)["UT"] = "Unlimited Text"; // 2 puissance 32 -1 car max - (*vr)["UL"] = "Unsigned Long "; // 4 octets fixe - (*vr)["US"] = "Unsigned Short "; // 2 octets fixe - dicom_vr = vr; +//----------------------------------------------------------------------------- +// Print + +// see gdcmParser.cxx +//----------------------------------------------------------------------------- +// Public +/** + * \ingroup gdcmHeader + * \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::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 La seule maniere sure que l'on aie pour determiner - * si on est en LITTLE_ENDIAN, BIG-ENDIAN, - * BAD-LITTLE-ENDIAN, BAD-BIG-ENDIAN - * est de trouver l'element qui donne la longueur d'un 'GROUP' - * (on sait que la longueur de cet element vaut 0x00000004) - * et de regarder comment cette longueur est codee en memoire - * - * Le probleme vient de ce que parfois, il n'y en a pas ... - * - * On fait alors le pari qu'on a a faire a du LITTLE_ENDIAN propre. - * (Ce qui est la norme -pas respectee- depuis ACR-NEMA) - * Si ce n'est pas le cas, on ne peut rien faire. + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEGBaseLineProcess1 one. * - * (il faudrait avoir des fonctions auxquelles - * on passe le code Swap en parametre, pour faire des essais 'manuels') + * @return True when JPEGBaseLineProcess1found. False in all other cases. */ -void gdcmHeader::CheckSwap() -{ - 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_LENGHT_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_LENGHT_TO_READ, fp); - - entCur = deb + 128; - if(memcmp(entCur, "DICM", (size_t)4) == 0) { - filetype = TrueDicom; - dbg.Verbose(0, "gdcmHeader::CheckSwap:", "looks like DICOM Version3"); - } else { - filetype = Unknown; - dbg.Verbose(0, "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(0, "gdcmHeader::CheckSwap:", - "explicit Value Representation"); - } else { - filetype = ImplicitVR; - dbg.Verbose(0, "gdcmHeader::CheckSwap:", - "not an explicit Value Representation"); - } - - if (net2host) { - sw = 4321; - dbg.Verbose(0, "gdcmHeader::CheckSwap:", - "HostByteOrder != NetworkByteOrder"); - } else { - sw = 0; - dbg.Verbose(0, "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, int); - - 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:", - "ACE/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 it - // not present. Then the only info we have is the net2host one. - //FIXME Si c'est du RAW, ca degagera + tard - - if (! net2host ) - sw = 0; - else - sw = 4321; - return; +bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) { + gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + if ( !Element ) + return false; + LoadHeaderEntrySafe(Element); + + std::string Transfer = Element->GetValue(); + if ( Transfer == "1.2.840.10008.1.2.4.50" ) + return true; + return false; } /** - * \ingroup gdcmHeader - * \brief recupere la longueur d'un champ DICOM. - * Preconditions: - * 1/ le fichier doit deja avoir ete ouvert, - * 2/ CheckSwap() doit avoir ete appele - * 3/ la partie 'group' ainsi que la partie 'elem' - * de l'acr_element doivent avoir ete lues. + * \ingroup gdcmHeader + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEGExtendedProcess2-4 one. * - * ACR-NEMA : we allways get - * GroupNumber (2 Octets) - * ElementNumber (2 Octets) - * ElementSize (4 Octets) - * DICOM en implicit Value Representation : - * GroupNumber (2 Octets) - * ElementNumber (2 Octets) - * ElementSize (4 Octets) + * @return True when JPEGExtendedProcess2-4 found. False in all other cases. + */ +bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) { + 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 already encountered + * and if it corresponds to a JPEGExtendeProcess3-5 one. * - * DICOM en explicit Value Representation : - * GroupNumber (2 Octets) - * ElementNumber (2 Octets) - * ValueRepresentation (2 Octets) - * ElementSize (2 Octets) + * @return True when JPEGExtendedProcess3-5 found. False in all other cases. + */ +bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) { + gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + if ( !Element ) + return false; + LoadHeaderEntrySafe(Element); + + std::string Transfer = Element->GetValue(); + if ( Transfer == "1.2.840.10008.1.2.4.52" ) + return true; + return false; +} + +/** + * \ingroup gdcmHeader + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEGSpectralSelectionProcess6-8 one. * - * ATTENTION : dans le cas ou ValueRepresentation = OB, OW, SQ, UN - * GroupNumber (2 Octets) - * ElementNumber (2 Octets) - * ValueRepresentation (2 Octets) - * zone reservee (2 Octets) - * ElementSize (4 Octets) + * @return True when JPEGSpectralSelectionProcess6-8 found. False in all + * other cases. + */ +bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) { + gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + if ( !Element ) + return false; + LoadHeaderEntrySafe(Element); + + std::string Transfer = Element->GetValue(); + if ( Transfer == "1.2.840.10008.1.2.4.53" ) + return true; + return false; +} + +/** + * \ingroup gdcmHeader + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a RLE Lossless one. * - * @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 + * @return True when RLE Lossless found. False in all + * other cases. */ +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; +} -void gdcmHeader::FindVR( ElValue *pleCourant) { - char VR[3]; - int lgrLue; - long PositionOnEntry = ftell(fp); - - if (filetype != ExplicitVR) - return; - - lgrLue=fread (&VR, (size_t)2,(size_t)1, fp); - VR[2]=0; - - // 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. - - // FIXME There should be only one occurence returned. Avoid the - // first extraction by calling proper method. - VRAtr FoundVR = dicom_vr->find(string(VR))->first; - if ( ! FoundVR.empty()) { - pleCourant->SetVR(FoundVR); - return; - } - - // We thought this was explicit VR, but we end up with an - // implicit VR tag. Let's backtrack. - pleCourant->SetVR("Implicit"); - fseek(fp, PositionOnEntry, SEEK_SET); +/** + * \ingroup gdcmHeader + * \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. + */ +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); + + 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; } -void gdcmHeader::RecupLgr( ElValue *pleCourant) { - int lgrLue; - guint32 l_gr; - unsigned short int l_gr_2; - - string vr = pleCourant->GetVR(); - - if ( (filetype == ExplicitVR) && (vr != "Implicit") ) { - if ( ( vr == "OB" ) || ( vr == "OW" ) - || ( vr == "SQ" ) || ( vr == "UN" ) ) { - - // The following two bytes are reserved, so we skip them, - // and we proceed on reading the length on 4 bytes. - fseek(fp, 2L,SEEK_CUR); - lgrLue=fread (&l_gr, (size_t)4,(size_t)1, fp); - l_gr = SwapLong((guint32)l_gr); - - } else { - //on lit la lgr sur DEUX octets - lgrLue=fread (&l_gr_2, (size_t)2,(size_t)1, fp); - - l_gr_2 = SwapShort((unsigned short)l_gr_2); - - if ( l_gr_2 == 0xffff) { - l_gr = 0; - } else { - l_gr = l_gr_2; - } - } - } else { - // Explicit VR = 0 - //on lit la lgr sur QUATRE octets - lgrLue=fread (&l_gr, (size_t)4,(size_t)1, fp); - l_gr= SwapLong((long)l_gr); - } - - // Traitement des curiosites sur la longueur - if ( (int)l_gr == 0xffffffff) - l_gr=0; - - pleCourant->SetLgrElem(l_gr); +/** + * \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) { + gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + if ( !Element ) + return false; + LoadHeaderEntrySafe(Element); + + std::string Transfer = Element->GetValue(); + if ( (Transfer == "1.2.840.10008.1.2.4.90") + || (Transfer == "1.2.840.10008.1.2.4.91") ) + return true; + return false; } /** * \ingroup gdcmHeader - * \brief remet les octets dans un ordre compatible avec celui du processeur + * \brief Predicate for dicom version 3 file. + * @return True when the file is a dicom version 3. + */ +bool gdcmHeader::IsDicomV3(void) { + // Checking if Transfert Syntax exists is enough + return (GetHeaderEntryByNumber(0x0002, 0x0010) != NULL); +} - * @return longueur retenue pour le champ +/** + * \ingroup gdcmHeader + * \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 */ -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); +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 remet les octets dans un ordre compatible avec celui du processeur + * \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). + */ +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; +} - * @return longueur retenue pour le champ +/** + * \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). */ -short int gdcmHeader::SwapShort(short int a) { - if ( (sw==4321) || (sw==2143) ) - a =(((a<<8) & 0x0ff00) | ((a>>8)&0x00ff)); - return (a); +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; } /** - * \ingroup gdcmHeader - * \brief lit le dicom_element suivant. - * (le fichier doit deja avoir ete ouvert, - * _IdAcrCheckSwap(ID_DCM_HDR *e) avoir ete appele) - * @param e ID_DCM_HDR dans lequel effectuer la recherche. - * @param sw code swap. - * @return En cas de succes, 1 - * 0 en cas d'echec. + * \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()); +} -ElValue * gdcmHeader::ReadNextElement(void) { - unsigned short g; - unsigned short n; - guint32 l; - size_t lgrLue; - ElValue * nouvDcmElem; - - // ------------------------- Lecture Num group : g - lgrLue=fread (&g, (size_t)2,(size_t)1, fp); - - if (feof(fp)) { - dbg.Verbose(1, "ReadNextElement: EOF encountered"); - return (NULL); - } - if (ferror(fp)){ - dbg.Verbose(1, "ReadNextElement: failed to read NumGr"); - return (NULL); - } - - if (sw) g= SwapShort(((short)g)); - - // ------------------------- Lecture Num Elem : n - lgrLue=fread (&n, (size_t)2,(size_t)1, fp); - - if (feof(fp)) { - dbg.Verbose(1, "ReadNextElement: EOF encountered"); - return (NULL); - } - if (ferror(fp)){ - dbg.Verbose(1, "ReadNextElement: failed to read NumElem"); - return (NULL); - } - - if(sw) n= SwapShort(((short)n)); - - // Find out if the tag we encountered is in the dictionaries: - gdcmDictEntry * NewTag = IsInDicts(g, n); - if (!NewTag) - NewTag = new gdcmDictEntry(g, n, "Unknown", "Unknown", "Unkown"); - - nouvDcmElem = new ElValue(NewTag); - if (!nouvDcmElem) { - dbg.Verbose(1, "ReadNextElement: failed to allocate ElValue"); - return(NULL); - } - - // ------------------------- Lecture longueur element : l - - FindVR(nouvDcmElem); - RecupLgr(nouvDcmElem); - nouvDcmElem->SetOffset(ftell(fp)); - l = nouvDcmElem->GetLgrElem(); - - //FIXMEif(!memcmp( VR,"SQ",(size_t)2 )) { // ca annonce une SEQUENCE d'items ?! - //FIXME l_gr=0; // on lira donc les items de la sequence - //FIXME} - //FIXMEreturn(l_gr); - - - if(g==0xfffe) l=0; // pour sauter les indicateurs de 'SQ' - - - // ------------------------- Lecture Valeur element - - // FIXME The exact size should be l if we move to strings or whatever - // CLEAN ME NEWValue used to be nouvDcmElem->valeurElem - char* NewValue = (char*)g_malloc(l+1); - if(NewValue) { - NewValue[l]= 0; - } else { - return (NULL); - } - - // FIXME les elements trop long (seuil a fixer a la main) ne devraient - // pas etre charge's !!!! Voir TODO. - lgrLue=fread (NewValue, (size_t)l,(size_t)1, fp); - - - // ------------------------- Doit-on le Swapper ? - - if ((n==0) && sw) { // n=0 : lgr du groupe : guint32 - *(guint32 *) NewValue = SwapLong ((*(guint32 *) NewValue)); - } else { - if(sw) { - if ( (g/2)*2-g==0) { /* on ne teste pas les groupes impairs */ - - if ((l==4)||(l==2)) { // pour eviter de swapper les chaines - // de lgr 2 ou 4 - - // FIXME make reference to nouvDcmElem->GetTag - string VR = NewTag->GetVR(); - if ( (VR == "UL") || (VR == "US") - || (VR == "SL") || (VR == "SS") - || (g == 0x0028 && ( n == 0x0005 || n == 0x0200) )) { - // seuls (28,5) de vr RET et (28,200) sont des entiers - // ... jusqu'a preuve du contraire - - if(l==4) { - *(guint32 *) NewValue = - SwapLong ((*(guint32 *) NewValue)); - } else { - if(l==2) - *(unsigned short *) NewValue = - SwapShort ((*(unsigned short *)NewValue)); - } - } - } /* fin if l==2 ==4 */ - } /* fin if g pair */ - } /* fin sw */ - } - nouvDcmElem->value = NewValue; - return nouvDcmElem; +/** + * \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()); } /** * \ingroup gdcmHeader - * \brief If we encountered the offset of the pixels in the file - * (Pixel Data) then keep the info aside. + * \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) */ -void gdcmHeader::SetAsidePixelData(ElValue* elem) { - /// FIXME this wall process is bizarre: - // on peut pas lire pixel data et pixel location puis - // a la fin de la lecture aller interpreter ce qui existe ? - // penser a nettoyer les variables globales associes genre - // PixelsTrouve ou grPixelTrouve... - // - // They are two cases : - // * the pixel data (i.e. the image or the volume) is pointed by it's - // default official tag (0x7fe0,0x0010), - // * the writer of this file decided to put the image "address" (i.e the - // offset from the begining of the file) at a different tag. - // Then the "Pixel Data" offset might be found by indirection through - // the "Image Location" tag (0x0028, 0x0200). In other terms the Image - // Location tag contains the group where the "Pixel Data" offset is and - // inside this group the element is conventionally at element 0x0010 - // (when the norm is respected). - // - // Hence getting our hands on the Pixel Data is a two stage process: - // 1/ * find if the "Pixel Data" tag exists. - // * if it does not exist, look for the "Pixel Location" tag. - // 2/ look at the proper tag ("Pixel Data" or "Pixel Location" when - // it exists) what the offset is. - guint16 g; - guint16 n; - g = elem->GetGroup(); - n = elem->GetElement(); - if (!grPixelTrouve) { // on n a pas encore trouve les pixels - if (g > 0x0028) { - if (n > 0x0200 || g == 0x7FE0 ) { // on a depasse (28,200) - grPixel = 0x7FE0; - numPixel = 0x0010; - grPixelTrouve = true; - } - } else { // on est sur (28,200) - if (g == 0x0028) { - if (n == 0x0200) { - grPixelTrouve = 1; - char* NewValue = (char*)g_malloc(elem->GetLgrElem()+1); - // FIXME: not very elegant conversion - for(int i=0;i<4;i++) - *((char*)(&grPixel)+i) = *(NewValue+i); - elem->SetValue(NewValue); - - if (grPixel != 0x7FE0) // Vieux pb Philips - numPixel = 0x1010; // encore utile ?? - else - numPixel = 0x0010; - } - } - } - } else { // on vient de trouver les pixels - if (g == grPixel) { - if (n == numPixel) { - PixelPosition = elem->Offset; - PixelsTrouves = true; - dbg.Verbose(0, "gdcmHeader::SetAsidePixelData:", - "Pixel data found"); - } - } - } +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()); } -gdcmDictEntry * gdcmHeader::IsInDicts(guint32 group, guint32 element) { - 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; +/** + * \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 = GetEntryByNumber(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; 0 by default + * 0 means the file is NOT USABLE; the caller will have to check + */ +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; } -string gdcmHeader::GetPubElValByNumber(unsigned short, unsigned short) { +/** + * \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 0S if nothing found. NOT USABLE file. The caller has to check + */ +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 Recover the offset (from the beginning of the file) + * \ of *image* pixels (not *icone image* pixels, if any !) + */ +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 renvoie un pointeur sur le ID_DCM_HDR correspondant au fichier - * @param filename Nom du fichier ACR / LibIDO / DICOM - * @return le ID_DCM_HDR + * \ingroup gdcmHeader + * \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. */ +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 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; +} + +/** + * \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; +} + +/** + * \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; -void gdcmHeader::BuildHeader(void) { - ElValue * newElValue = (ElValue *)0; - - rewind(fp); - rewind(fp); - CheckSwap(); - while ( (newElValue = ReadNextElement()) ) { - PubElVals.Add(newElValue); - } + // 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; } -int gdcmHeader::PrintPubElVal(ostream & os) { - return PubElVals.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); } -void gdcmHeader::PrintPubDict(ostream & os) { - RefPubDict->Print(os); +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 + +//-----------------------------------------------------------------------------