X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=30f8cf4bd5a8cc09f1e99143a861f424cda52afc;hb=64ef25e1cadb4b840a4cedfe0adaddecb2d7ca42;hp=cd5785b1985683f6f2ba118bca6ccb133f12c9ba;hpb=51b61705e90b352de08519835fa1c63b81bca616;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index cd5785b1..30f8cf4b 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -1,633 +1,1377 @@ -#include "gdcm.h" -extern "C" { -#include "glib.h" -} -#include -// For nthos: -#ifdef _MSC_VER -#include -#else -#include -#endif -#include -#include +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmHeader.cxx,v $ + Language: C++ + Date: $Date: 2004/09/20 18:14:23 $ + Version: $Revision: 1.187 $ + + Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de + l'Image). All rights reserved. See Doc/License.txt or + http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details. + + This software is distributed WITHOUT ANY WARRANTY; without even + the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR + PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ + +#include "gdcmHeader.h" +#include "gdcmGlobal.h" #include "gdcmUtil.h" +#include "gdcmDebug.h" +#include "gdcmTS.h" +#include "gdcmValEntry.h" + +#include -#define HEADER_LENGHT_TO_READ 256 // on ne lit plus que le debut - -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)) - -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; -} - -gdcmHeader::gdcmHeader (const char* InFilename) { - filename = InFilename; - Initialise(); - fp=fopen(InFilename,"rw"); - dbg.Error(!fp, "gdcmHeader::gdcmHeader cannot open file", InFilename); - ParseHeader(); -} - -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"; // 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; +//----------------------------------------------------------------------------- +// Constructor / Destructor +/** + * \brief Constructor + * @param filename name of the file whose header we want to analyze + */ +gdcmHeader::gdcmHeader( std::string const & filename ): + gdcmDocument( filename ) +{ + // 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. + // Note: this IS the right place for the code + + // Image Location + std::string imgLocation = GetEntryByNumber(0x0028, 0x0200); + if ( imgLocation == GDCM_UNFOUND ) + { + // default value + GrPixel = 0x7fe0; + } + else + { + GrPixel = (uint16_t) atoi( imgLocation.c_str() ); + } + + // sometimes Image Location value doesn't follow + // the supposed processor endianity. + // see gdcmData/cr172241.dcm + if ( GrPixel == 0xe07f ) + { + GrPixel = 0x7fe0; + } + + if ( GrPixel != 0x7fe0 ) + { + // This is a kludge for old dirty Philips imager. + NumPixel = 0x1010; + } + else + { + NumPixel = 0x0010; + } +} + +/** + * \brief Constructor + */ +gdcmHeader::gdcmHeader() + :gdcmDocument() +{ } /** * \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. - * - * (il faudrait avoir des fonctions auxquelles - * on passe le code Swap en parametre, pour faire des essais 'manuels') + * \brief Canonical destructor. + */ +gdcmHeader::~gdcmHeader () +{ +} + + +/** + * \brief Performs some consistency checking on various 'File related' + * (as opposed to 'DicomDir related') entries + * then writes in a file all the (Dicom Elements) included the Pixels + * @param fp file pointer on an already open file + * @param filetype Type of the File to be written + * (ACR-NEMA, ExplicitVR, ImplicitVR) */ -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; -} - -/** - * \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. - * - * 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) - * - * DICOM en explicit Value Representation : - * GroupNumber (2 Octets) - * ElementNumber (2 Octets) - * ValueRepresentation (2 Octets) - * ElementSize (2 Octets) - * - * 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) - * - * @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 +void gdcmHeader::Write(FILE* fp,FileType filetype) +{ + // Bits Allocated + if ( GetEntryByNumber(0x0028,0x0100) == "12") + { + SetEntryByNumber("16", 0x0028,0x0100); + } + + // TODO : correct 'Pixel group' Length if necessary + + int i_lgPix = GetEntryLengthByNumber(GrPixel, NumPixel); + if (i_lgPix != -2) + { + // no (GrPixel, NumPixel) element + char* dumm = new char[20]; + sprintf(dumm ,"%d", i_lgPix+12); + std::string s_lgPix = dumm; + delete[] dumm; + ReplaceOrCreateByNumber(s_lgPix,GrPixel, 0x0000); + } + + // FIXME : should be nice if we could move it to gdcmFile + // (or in future gdcmPixelData class) + + // Drop Palette Color, if necessary + + if ( GetEntryByNumber(0x0028,0x0002).c_str()[0] == '3' ) + { + // if SamplesPerPixel = 3, sure we don't need any LUT ! + // Drop 0028|1101, 0028|1102, 0028|1103 + // Drop 0028|1201, 0028|1202, 0028|1203 + + gdcmDocEntry* e = GetDocEntryByNumber(0x0028,0x01101); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntryByNumber(0x0028,0x1102); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntryByNumber(0x0028,0x1103); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntryByNumber(0x0028,0x01201); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntryByNumber(0x0028,0x1202); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntryByNumber(0x0028,0x1203); + if (e) + { + RemoveEntryNoDestroy(e); + } + } + gdcmDocument::Write(fp,filetype); +} + +//----------------------------------------------------------------------------- +// Print + + +//----------------------------------------------------------------------------- +// Public + +/** + * \brief This predicate, based on hopefully reasonable heuristics, + * decides whether or not the current gdcmHeader was properly parsed + * and contains the mandatory information for being considered as + * a well formed and usable Dicom/Acr File. + * @return true when gdcmHeader is the one of a reasonable Dicom/Acr file, + * false otherwise. */ +bool gdcmHeader::IsReadable() +{ + if( !gdcmDocument::IsReadable() ) + { + return false; + } -void gdcmHeader::FindVR( ElValue *ElVal) { - 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()) { - ElVal->SetVR(FoundVR); - return; - } - - // We thought this was explicit VR, but we end up with an - // implicit VR tag. Let's backtrack. - ElVal->SetVR("Implicit"); - fseek(fp, PositionOnEntry, SEEK_SET); -} - -void gdcmHeader::FindLength( ElValue * ElVal) { - guint32 length32; - guint16 length16; - - string vr = ElVal->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); - length32 = ReadInt32(); - - } else { - // Length is encoded on 2 bytes. - length16 = ReadInt16(); - - if ( length16 == 0xffff) { - length32 = 0; - } else { - length32 = length16; - } - } - } else { - // Either implicit VR or an explicit VR that (at least for this - // element) lied a little bit. Length is on 4 bytes. - length32 = ReadInt32(); - } - - // Traitement des curiosites sur la longueur - if ( length32 == 0xffffffff) - length32=0; - - ElVal->SetLength(length32); + std::string res = GetEntryByNumber(0x0028, 0x0005); + if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) + { + return false; // Image Dimensions + } + if ( !GetDocEntryByNumber(0x0028, 0x0100) ) + { + return false; // "Bits Allocated" + } + if ( !GetDocEntryByNumber(0x0028, 0x0101) ) + { + return false; // "Bits Stored" + } + if ( !GetDocEntryByNumber(0x0028, 0x0102) ) + { + return false; // "High Bit" + } + if ( !GetDocEntryByNumber(0x0028, 0x0103) ) + { + return false; // "Pixel Representation" i.e. 'Sign' + } + + return true; } +/** + * \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 + */ +int gdcmHeader::GetXSize() +{ + 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 ACR-NEMA file contains a Signal, not an Image). + */ +int gdcmHeader::GetYSize() +{ + std::string strSize = GetEntryByNumber(0x0028,0x0010); + if ( strSize != GDCM_UNFOUND ) + { + return atoi( strSize.c_str() ); + } + if ( IsDicomV3() ) + { + return 0; + } + + // 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 ACR-NEMA "Planes" tag content. + * @return The encountered size when found, 1 by default (single image). */ -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::GetZSize() +{ + // 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 + strSize = GetEntryByNumber(0x0028,0x0012); + if ( strSize != GDCM_UNFOUND ) + { + return atoi( strSize.c_str() ); + } + + return 1; +} + +/** + * \ingroup gdcmHeader + * \brief gets the info from 0028,0030 : Pixel Spacing + * else 1.0 + * @return X dimension of a pixel + */ +float gdcmHeader::GetXSpacing() +{ + float xspacing, yspacing; + std::string strSpacing = GetEntryByNumber(0x0028,0x0030); + + if ( strSpacing == GDCM_UNFOUND ) + { + dbg.Verbose(0, "gdcmHeader::GetXSpacing: unfound Pixel Spacing (0028,0030)"); + return 1.; + } + + int nbValues; + if( ( nbValues = sscanf( strSpacing.c_str(), + "%f\\%f", &yspacing, &xspacing)) != 2 ) + { + // if single value is found, xspacing is defaulted to yspacing + if ( nbValues == 1 ) + { + return yspacing; + } + } + if ( xspacing == 0.) + { + dbg.Verbose(0, "gdcmHeader::GetYSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem"); + // seems to be a bug in the header ... + sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing); + } + + return xspacing; +} + +/** + * \ingroup gdcmHeader + * \brief gets the info from 0028,0030 : Pixel Spacing + * else 1.0 + * @return Y dimension of a pixel + */ +float gdcmHeader::GetYSpacing() +{ + float yspacing = 0; + std::string strSpacing = GetEntryByNumber(0x0028,0x0030); + + if ( strSpacing == GDCM_UNFOUND ) + { + dbg.Verbose(0, "gdcmHeader::GetYSpacing: unfound Pixel Spacing (0028,0030)"); + return 1.; + } + + // if sscanf cannot read any float value, it won't affect yspacing + sscanf( strSpacing.c_str(), "%f", &yspacing); + + return yspacing; +} + +/** + *\ingroup gdcmHeader + *\brief gets the info from 0018,0088 : Space Between Slices + * else from 0018,0050 : Slice Thickness + * else 1.0 + * @return Z dimension of a voxel-to be + */ +float gdcmHeader::GetZSpacing() +{ + // Spacing Between Slices : distance entre le milieu de chaque coupe + // Les coupes peuvent etre : + // jointives (Spacing between Slices = Slice Thickness) + // chevauchantes (Spacing between Slices < Slice Thickness) + // disjointes (Spacing between Slices > Slice Thickness) + // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal + // ca interesse le physicien de l'IRM, pas le visualisateur de volumes ... + // Si le Spacing Between Slices est absent, + // on suppose que les coupes sont jointives + + std::string strSpacingBSlices = GetEntryByNumber(0x0018,0x0088); + + if ( strSpacingBSlices == GDCM_UNFOUND ) + { + dbg.Verbose(0, "gdcmHeader::GetZSpacing: unfound StrSpacingBSlices"); + std::string strSliceThickness = GetEntryByNumber(0x0018,0x0050); + if ( strSliceThickness == GDCM_UNFOUND ) + { + return 1.; + } + else + { + // if no 'Spacing Between Slices' is found, + // we assume slices join together + // (no overlapping, no interslice gap) + // if they don't, we're fucked up + return atof( strSliceThickness.c_str() ); + } + } + else + { + return atof( strSpacingBSlices.c_str() ); + } +} + +/** + *\ingroup gdcmHeader + *\brief gets the info from 0028,1052 : Rescale Intercept + * @return Rescale Intercept + */ +float gdcmHeader::GetRescaleIntercept() +{ + float resInter = 0.; + std::string strRescInter = GetEntryByNumber(0x0028,0x1052); //0028 1052 DS IMG Rescale Intercept + if ( strRescInter != GDCM_UNFOUND ) + { + if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 ) + { + // bug in the element 0x0028,0x1052 + dbg.Verbose(0, "gdcmHeader::GetRescaleIntercept: Rescale Slope is empty"); + } + } + + return resInter; +} + +/** + *\ingroup gdcmHeader + *\brief gets the info from 0028,1053 : Rescale Slope + * @return Rescale Slope + */ +float gdcmHeader::GetRescaleSlope() +{ + float resSlope = 1.; + std::string strRescSlope = GetEntryByNumber(0x0028,0x1053); //0028 1053 DS IMG Rescale Slope + if ( strRescSlope != GDCM_UNFOUND ) + { + if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1) + { + // bug in the element 0x0028,0x1053 + dbg.Verbose(0, "gdcmHeader::GetRescaleSlope: Rescale Slope is empty"); + } + } + + return resSlope; +} + +/** + * \ingroup gdcmHeader + * \brief This function is intended to user who doesn't want + * to have to manage a LUT and expects to get an RBG Pixel image + * (or a monochrome one ...) + * \warning to be used with GetImagePixels() + * @return 1 if Gray level, 3 if Color (RGB, YBR or PALETTE COLOR) + */ +int gdcmHeader::GetNumberOfScalarComponents() +{ + if ( GetSamplesPerPixel() == 3 ) + { + return 3; + } + + // 0028 0100 US IMG Bits Allocated + // (in order no to be messed up by old RGB images) + if ( GetEntryByNumber(0x0028,0x0100) == "24" ) + { + return 3; + } + + std::string strPhotometricInterpretation = GetEntryByNumber(0x0028,0x0004); + + if ( ( strPhotometricInterpretation == "PALETTE COLOR ") ) + { + if ( HasLUT() )// PALETTE COLOR is NOT enough + { + return 3; + } + else + { + return 1; + } + } + + // beware of trailing space at end of string + // DICOM tags are never of odd length + if ( strPhotometricInterpretation == GDCM_UNFOUND || + strPhotometricInterpretation == "MONOCHROME1 " || + strPhotometricInterpretation == "MONOCHROME2 " ) + { + return 1; + } + else + { + // we assume that *all* kinds of YBR are dealt with + return 3; + } +} + +/** + * \ingroup gdcmHeader + * \brief This function is intended to user that DOESN'T want + * to get RGB pixels image when it's stored as a PALETTE COLOR image + * - the (vtk) user is supposed to know how deal with LUTs - + * \warning to be used with GetImagePixelsRaw() + * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -) + */ +int gdcmHeader::GetNumberOfScalarComponentsRaw() +{ + // 0028 0100 US IMG Bits Allocated + // (in order no to be messed up by old RGB images) + if ( gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24" ) + { + return 3; + } + + // we assume that *all* kinds of YBR are dealt with + return GetSamplesPerPixel(); +} + +// +// -------------- Remember ! ---------------------------------- +// +// Image Position Patient (0020,0032): +// If not found (ACR_NEMA) we try Image Position (0020,0030) +// If not found (ACR-NEMA), we consider Slice Location (0020,1041) +// or Location (0020,0050) +// as the Z coordinate, +// 0. for all the coordinates if nothing is found + +// \todo find a way to inform the caller nothing was found +// \todo How to tell the caller a wrong number of values was found? +// +// --------------------------------------------------------------- +// + +/** + * \brief gets the info from 0020,0032 : Image Position Patient + * else from 0020,0030 : Image Position (RET) + * else 0. + * @return up-left image corner X position + */ + +float gdcmHeader::GetXOrigin() +{ + float xImPos, yImPos, zImPos; + std::string strImPos = GetEntryByNumber(0x0020,0x0032); + + if ( strImPos == GDCM_UNFOUND ) + { + dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position Patient (0020,0032)"); + strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images + if ( strImPos == GDCM_UNFOUND ) + { + dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position (RET) (0020,0030)"); + /// \todo How to tell the caller nothing was found ? + return 0.; + } + } + + if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 ) + { + return 0.; + } + + return xImPos; +} + +/** + * \brief gets the info from 0020,0032 : Image Position Patient + * else from 0020,0030 : Image Position (RET) + * else 0. + * @return up-left image corner Y position + */ +float gdcmHeader::GetYOrigin() +{ + float xImPos, yImPos, zImPos; + std::string strImPos = GetEntryByNumber(0x0020,0x0032); + + if ( strImPos == GDCM_UNFOUND) + { + dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position Patient (0020,0032)"); + strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images + if ( strImPos == GDCM_UNFOUND ) + { + dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position (RET) (0020,0030)"); + /// \todo How to tell the caller nothing was found ? + return 0.; + } + } + + if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 ) + { + return 0.; + } + + return yImPos; +} + +/** + * \brief gets the info from 0020,0032 : Image Position Patient + * \ else from 0020,0030 : Image Position (RET) + * \ else from 0020,1041 : Slice Location + * \ else from 0020,0050 : Location + * \ else 0. + * @return up-left image corner Z position + */ +float gdcmHeader::GetZOrigin() +{ + float xImPos, yImPos, zImPos; + std::string strImPos = GetEntryByNumber(0x0020,0x0032); + + if ( strImPos != GDCM_UNFOUND ) + { + if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) + { + dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position Patient (0020,0032)"); + return 0.; // bug in the element 0x0020,0x0032 + } + else + { + return zImPos; + } + } + + strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images + if ( strImPos != GDCM_UNFOUND ) + { + if( sscanf( strImPos.c_str(), + "%f\\%f\\%f", &xImPos, &yImPos, &zImPos ) != 3 ) + { + dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position (RET) (0020,0030)"); + return 0.; // bug in the element 0x0020,0x0032 + } + else + { + return zImPos; + } + } + + std::string strSliceLocation = GetEntryByNumber(0x0020,0x1041); // for *very* old ACR-NEMA images + if ( strSliceLocation != GDCM_UNFOUND ) + { + if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1) + { + dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Slice Location (0020,1041)"); + return 0.; // bug in the element 0x0020,0x1041 + } + else + { + return zImPos; + } + } + dbg.Verbose(0, "gdcmHeader::GetZImagePosition: unfound Slice Location (0020,1041)"); + + std::string strLocation = GetEntryByNumber(0x0020,0x0050); + if ( strLocation != GDCM_UNFOUND ) + { + if( sscanf( strLocation.c_str(), "%f", &zImPos) != 1) + { + dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Location (0020,0050)"); + return 0.; // bug in the element 0x0020,0x0050 + } + else + { + return zImPos; + } + } + dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Location (0020,0050)"); + + return 0.; // Hopeless +} + +/** + * \brief gets the info from 0020,0013 : Image Number + * \ else 0. + * @return image number + */ +int gdcmHeader::GetImageNumber() +{ + // The function i atoi() takes the address of an area of memory as + // parameter and converts the string stored at that location to an integer + // using the external decimal to internal binary conversion rules. This may + // be preferable to sscanf() since atoi() is a much smaller, simpler and + // faster function. sscanf() can do all possible conversions whereas + // atoi() can only do single decimal integer conversions. + std::string strImNumber = GetEntryByNumber(0x0020,0x0013); //0020 0013 IS REL Image Number + if ( strImNumber != GDCM_UNFOUND ) + { + return atoi( strImNumber.c_str() ); + } + return 0; //Hopeless +} + +/** + * \brief gets the info from 0008,0060 : Modality + * @return Modality Type + */ +ModalityType gdcmHeader::GetModality() +{ + // 0008 0060 CS ID Modality + std::string strModality = GetEntryByNumber(0x0008,0x0060); + if ( strModality != GDCM_UNFOUND ) + { + if ( strModality.find("AU") < strModality.length()) return AU; + else if ( strModality.find("AS") < strModality.length()) return AS; + else if ( strModality.find("BI") < strModality.length()) return BI; + else if ( strModality.find("CF") < strModality.length()) return CF; + else if ( strModality.find("CP") < strModality.length()) return CP; + else if ( strModality.find("CR") < strModality.length()) return CR; + else if ( strModality.find("CT") < strModality.length()) return CT; + else if ( strModality.find("CS") < strModality.length()) return CS; + else if ( strModality.find("DD") < strModality.length()) return DD; + else if ( strModality.find("DF") < strModality.length()) return DF; + else if ( strModality.find("DG") < strModality.length()) return DG; + else if ( strModality.find("DM") < strModality.length()) return DM; + else if ( strModality.find("DS") < strModality.length()) return DS; + else if ( strModality.find("DX") < strModality.length()) return DX; + else if ( strModality.find("ECG") < strModality.length()) return ECG; + else if ( strModality.find("EPS") < strModality.length()) return EPS; + else if ( strModality.find("FA") < strModality.length()) return FA; + else if ( strModality.find("FS") < strModality.length()) return FS; + else if ( strModality.find("HC") < strModality.length()) return HC; + else if ( strModality.find("HD") < strModality.length()) return HD; + else if ( strModality.find("LP") < strModality.length()) return LP; + else if ( strModality.find("LS") < strModality.length()) return LS; + else if ( strModality.find("MA") < strModality.length()) return MA; + else if ( strModality.find("MR") < strModality.length()) return MR; + else if ( strModality.find("NM") < strModality.length()) return NM; + else if ( strModality.find("OT") < strModality.length()) return OT; + else if ( strModality.find("PT") < strModality.length()) return PT; + else if ( strModality.find("RF") < strModality.length()) return RF; + else if ( strModality.find("RG") < strModality.length()) return RG; + else if ( strModality.find("RTDOSE") < strModality.length()) return RTDOSE; + else if ( strModality.find("RTIMAGE") < strModality.length()) return RTIMAGE; + else if ( strModality.find("RTPLAN") < strModality.length()) return RTPLAN; + else if ( strModality.find("RTSTRUCT") < strModality.length()) return RTSTRUCT; + else if ( strModality.find("SM") < strModality.length()) return SM; + else if ( strModality.find("ST") < strModality.length()) return ST; + else if ( strModality.find("TG") < strModality.length()) return TG; + else if ( strModality.find("US") < strModality.length()) return US; + else if ( strModality.find("VF") < strModality.length()) return VF; + else if ( strModality.find("XA") < strModality.length()) return XA; + else if ( strModality.find("XC") < strModality.length()) return XC; + + else + { + /// \todo throw error return value ??? + /// specified <> unknow in our database + return Unknow; + } + } + + return Unknow; } /** * \ingroup gdcmHeader - * \brief remet les octets dans un ordre compatible avec celui du processeur + * \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() +{ + std::string strSize = GetEntryByNumber(0x0028,0x0101); + if ( strSize == GDCM_UNFOUND ) + { + dbg.Verbose(0, "gdcmHeader::GetBitsStored: this is supposed to be mandatory"); + return 0; // It's supposed to be mandatory + // the caller will have to check + } + return atoi( strSize.c_str() ); +} - * @return longueur retenue pour le champ +/** + * \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 ! */ -guint16 gdcmHeader::SwapShort(guint16 a) { - if ( (sw==4321) || (sw==2143) ) - a =(((a<<8) & 0x0ff00) | ((a>>8)&0x00ff)); - return (a); -} - -void gdcmHeader::SkipElementValue(ElValue * ElVal) { - //FIXME don't dump the returned value - (void)fseek(fp, (long)ElVal->GetLength(), SEEK_CUR); -} - -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(); - fseek(fp, (long)ElVal->GetOffset(), SEEK_SET); - - // Sequences not treated yet ! - if( vr == "SQ" ) { - SkipElementValue(ElVal); - ElVal->SetLength(0); - return; - } - // 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) { - SkipElementValue(ElVal); - ElVal->SetLength(0); - return; - } - - if ( IsAnInteger(group, elem, vr, length) ) { - 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 - char* NewValue = (char*)g_malloc(length+1); - if( !NewValue) { - dbg.Verbose(1, "LoadElementValue: Failed to allocate NewValue"); - return; - } - NewValue[length]= 0; - - // FIXME les elements trop long (seuil a fixer a la main) ne devraient - // pas etre charge's !!!! Voir TODO. - item_read = fread(NewValue, (size_t)length, (size_t)1, fp); - if ( item_read != 1 ) { - g_free(NewValue); - Error::FileReadError(fp, "gdcmHeader::LoadElementValue"); - ElVal->SetValue("gdcm::UnRead"); - return; - } - ElVal->SetValue(NewValue); -} - - -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; +int gdcmHeader::GetBitsAllocated() +{ + std::string strSize = GetEntryByNumber(0x0028,0x0100); + if ( strSize == GDCM_UNFOUND ) + { + dbg.Verbose(0, "gdcmHeader::GetBitsStored: this is supposed to be mandatory"); + return 0; // It's supposed to be mandatory + // the caller will have to check + } + return atoi( strSize.c_str() ); } /** * \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 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() +{ + std::string strSize = GetEntryByNumber(0x0028,0x0002); + if ( strSize == GDCM_UNFOUND ) + { + dbg.Verbose(0, "gdcmHeader::GetBitsStored: this is supposed to be mandatory"); + return 1; // Well, it's supposed to be mandatory ... + // but sometimes it's missing : *we* assume Gray pixels + } + return atoi( strSize.c_str() ); +} -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, "Unknown", "Unknown", "Unkown"); - - NewElVal = new ElValue(NewTag); - if (!NewElVal) { - dbg.Verbose(1, "ReadNextElement: failed to allocate ElValue"); - return (ElValue*)0; - } - - FindVR(NewElVal); - FindLength(NewElVal); - NewElVal->SetOffset(ftell(fp)); - return NewElVal; -} - -bool gdcmHeader::IsAnInteger(guint16 group, guint16 element, - string vr, guint32 length ) { - // When we have some semantics on the element we just read, and we - // a priori now we are dealing with an integer, then we can swap it's - // element value properly. - if ( element == 0 ) { // This is the group length of the group - if (length != 4) - dbg.Error("gdcmHeader::ShouldBeSwaped", "should be four"); - return true; - } - - 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 ? - return true; - - if ( (group == 0x0028) && (element == 0x0200) ) - // This tag is retained from ACR/NEMA - return true; - - return false; +/** + * \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() +{ + std::string strSize = GetEntryByNumber(0x0028,0x0006); + 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 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 */ -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 == "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.GetElement(grPixel, numPixel); - if (PixelElement) - return PixelElement->GetOffset(); - else - return 0; -} - -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; -} - -string gdcmHeader::GetPubElValByNumber(guint16 group, guint16 element) { - return PubElVals.GetElValue(group, element); -} - -string gdcmHeader::GetPubElValByName(string TagName) { - return PubElVals.GetElValue(TagName); +int gdcmHeader::GetPixelSize() +{ + // 0028 0100 US IMG Bits Allocated + // (in order no to be messed up by old RGB images) + // if (gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24") + // return 3; + + 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; + } + if ( pixelType == "FD" ) + { + return 8; + } + dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type"); + return 0; } /** * \ingroup gdcmHeader - * \brief Parses the header of the file but does NOT load element values. + * \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, + * - FD floating double 64 bits (Not kosher DICOM, but so usefull!) + * \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 */ -void gdcmHeader::ParseHeader(void) { - ElValue * newElValue = (ElValue *)0; - - rewind(fp); - CheckSwap(); - while ( (newElValue = ReadNextElement()) ) { - SkipElementValue(newElValue); - PubElVals.Add(newElValue); - } +std::string gdcmHeader::GetPixelType() +{ + std::string bitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated + if ( bitsAlloc == GDCM_UNFOUND ) + { + dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated"); + bitsAlloc = "16"; + } + + if ( bitsAlloc == "64" ) + { + return "FD"; + } + if ( bitsAlloc == "12" ) + { + // It will be unpacked + bitsAlloc = "16"; + } + else if ( bitsAlloc == "24" ) + { + // (in order no to be messed up + bitsAlloc = "8"; // by old RGB images) + } + + std::string sign = GetEntryByNumber(0x0028, 0x0103); // "Pixel Representation" + + if (sign == GDCM_UNFOUND ) + { + dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation"); + bitsAlloc = "0"; + } + if ( sign == "0" ) + { + sign = "U"; + } + else + { + sign = "S"; + } + return bitsAlloc + sign; } + /** * \ingroup gdcmHeader - * \brief Loads the element values of all the elements present in the - * public tag based hash table. + * \brief Recover the offset (from the beginning of the file) + * of *image* pixels (not *icone image* pixels, if any !) + * @return Pixel Offset + */ +size_t gdcmHeader::GetPixelOffset() +{ + gdcmDocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel); + if ( pxlElement ) + { + return pxlElement->GetOffset(); + } + else + { +#ifdef GDCM_DEBUG + std::cout << "Big trouble : Pixel Element (" + << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" + << std::endl; +#endif //GDCM_DEBUG + return 0; + } +} + +// TODO : unify those two (previous one and next one) +/** + * \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() +{ + gdcmDocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel); + if ( pxlElement ) + { + return pxlElement->GetLength(); + } + else + { +#ifdef GDCM_DEBUG + std::cout << "Big trouble : Pixel Element (" + << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" + << std::endl; +#endif //GDCM_DEBUG + 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 + * Please warn me if you know sbdy that *does* know ... jprx + * @return true if LUT Descriptors and LUT Tables were found + */ +bool gdcmHeader::HasLUT() +{ + // Check the presence of the LUT Descriptors, and LUT Tables + // LutDescriptorRed + if ( !GetDocEntryByNumber(0x0028,0x1101) ) + { + return false; + } + // LutDescriptorGreen + if ( !GetDocEntryByNumber(0x0028,0x1102) ) + { + return false; + } + // LutDescriptorBlue + if ( !GetDocEntryByNumber(0x0028,0x1103) ) + { + return false; + } + // Red Palette Color Lookup Table Data + if ( !GetDocEntryByNumber(0x0028,0x1201) ) + { + return false; + } + // Green Palette Color Lookup Table Data + if ( !GetDocEntryByNumber(0x0028,0x1202) ) + { + return false; + } + // Blue Palette Color Lookup Table Data + if ( !GetDocEntryByNumber(0x0028,0x1203) ) + { + return false; + } + + // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent) + // NOT taken into account, but we don't know how to use it ... + 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 ] + * @ return bit number of each LUT item + */ +int gdcmHeader::GetLUTNbits() +{ + std::vector tokens; + 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.clear(); // 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 + */ +uint8_t* gdcmHeader::GetLUTRGBA() +{ + // 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; + } + + // lengthR: Red LUT length in Bytes + // debR: subscript of the first Lut Value + // nbitsR: Lut item size (in Bits) + int nbRead = sscanf( lutDescriptionR.c_str(), "%d\\%d\\%d", + &lengthR, &debR, &nbitsR ); + if( nbRead != 3 ) + { + dbg.Verbose(0, "gdcmHeader::GetLUTRGBA: trouble reading red LUT"); + } + + // lengthG: Green LUT length in Bytes + // debG: subscript of the first Lut Value + // nbitsG: Lut item size (in Bits) + nbRead = sscanf( lutDescriptionG.c_str(), "%d\\%d\\%d", + &lengthG, &debG, &nbitsG ); + if( nbRead != 3 ) + { + dbg.Verbose(0, "gdcmHeader::GetLUTRGBA: trouble reading green LUT"); + } + + // lengthB: Blue LUT length in Bytes + // debB: subscript of the first Lut Value + // nbitsB: Lut item size (in Bits) + nbRead = sscanf( lutDescriptionB.c_str(), "%d\\%d\\%d", + &lengthB, &debB, &nbitsB ); + if( nbRead != 3 ) + { + dbg.Verbose(0, "gdcmHeader::GetLUTRGBA: trouble reading blue LUT"); + } + + // Load LUTs into memory, (as they were stored on disk) + uint8_t* lutR = (uint8_t*) GetEntryVoidAreaByNumber(0x0028,0x1201); + uint8_t* lutG = (uint8_t*) GetEntryVoidAreaByNumber(0x0028,0x1202); + uint8_t* lutB = (uint8_t*) GetEntryVoidAreaByNumber(0x0028,0x1203); + + if ( !lutR || !lutG || !lutB ) + { + dbg.Verbose(0, "gdcmHeader::GetLUTRGBA: trouble with one of the LUT"); + return NULL; + } + // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT + + uint8_t* LUTRGBA = new uint8_t[1024]; // 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) + uint8_t* a; + int i; + + a = LUTRGBA + 0; + for( i=0; i < lengthR; ++i) + { + *a = lutR[i*mult+1]; + a += 4; + } + + a = LUTRGBA + 1; + for( i=0; i < lengthG; ++i) + { + *a = lutG[i*mult+1]; + a += 4; + } + + a = LUTRGBA + 2; + for(i=0; i < lengthB; ++i) + { + *a = lutB[i*mult+1]; + a += 4; + } + + a = LUTRGBA + 3; + for(i=0; i < 256; ++i) + { + *a = 1; // Alpha component + a += 4; + } + return LUTRGBA; +} + +/** + * \brief Accesses the info from 0002,0010 : Transfert Syntax and gdcmTS + * else 1. + * @return The full Transfert Syntax Name (as opposed to Transfert Syntax UID) */ -void gdcmHeader::LoadElements(void) { - rewind(fp); - TagElValueHT ht = PubElVals.GetTagHt(); - for (TagElValueHT::iterator tag = ht.begin(); tag != ht.end(); ++tag) - LoadElementValue(tag->second); +std::string gdcmHeader::GetTransfertSyntaxName() +{ + // use the gdcmTS (TS : Transfert Syntax) + std::string transfertSyntax = GetEntryByNumber(0x0002,0x0010); + + if ( transfertSyntax == GDCM_NOTLOADED ) { // fusible + std::cout << "Transfert Syntax not loaded. " << std::endl + << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE" + << std::endl; + return "Uncompressed ACR-NEMA"; + } + if ( transfertSyntax == GDCM_UNFOUND ) + { + dbg.Verbose(0, "gdcmHeader::GetTransfertSyntaxName:" + " unfound Transfert Syntax (0002,0010)"); + return "Uncompressed ACR-NEMA"; + } + + while ( ! isdigit(transfertSyntax[transfertSyntax.length()-1]) ) + { + transfertSyntax.erase(transfertSyntax.length()-1, 1); + } + // we do it only when we need it + gdcmTS* ts = gdcmGlobal::GetTS(); + std::string tsName = ts->GetValue( transfertSyntax ); + + //delete ts; /// \todo Seg Fault when deleted ?! + return tsName; } -void gdcmHeader::PrintPubElVal(ostream & os) { - PubElVals.Print(os); +/** + * \brief Sets the Pixel Area size in the Header + * --> not-for-rats function + * @param ImageDataSize new Pixel Area Size + * warning : nothing else is checked + */ +void gdcmHeader::SetImageDataSize(size_t ImageDataSize) +{ + char car[20]; + sprintf(car,"%d",ImageDataSize); + + gdcmDocEntry *a = GetDocEntryByNumber(GrPixel, NumPixel); + a->SetLength(ImageDataSize); + + ImageDataSize += 8; + sprintf(car,"%d",ImageDataSize); + + const std::string content1 = car; + SetEntryByNumber(content1, GrPixel, NumPixel); } -void gdcmHeader::PrintPubDict(ostream & os) { - RefPubDict->Print(os); +//----------------------------------------------------------------------------- +// Protected + +/** + * \brief anonymize a Header (removes Patient's personal info) + * (read the code to see which ones ...) + */ +bool gdcmHeader::AnonymizeHeader() +{ + // If exist, replace by spaces + SetEntryByNumber (" ",0x0010, 0x2154); // Telephone + SetEntryByNumber (" ",0x0010, 0x1040); // Adress + SetEntryByNumber (" ",0x0010, 0x0020); // Patient ID + + gdcmDocEntry* patientNameHE = GetDocEntryByNumber (0x0010, 0x0010); + + if ( patientNameHE ) // we replace it by Study Instance UID (why not) + { + std::string studyInstanceUID = GetEntryByNumber (0x0020, 0x000d); + if ( studyInstanceUID != GDCM_UNFOUND ) + { + ReplaceOrCreateByNumber(studyInstanceUID, 0x0010, 0x0010); + } + else + { + ReplaceOrCreateByNumber(std::string("anonymised"), 0x0010, 0x0010); + } + } + + // Just for fun :-( + // (if any) remove or replace all the stuff that contains a Date + +//0008 0012 DA ID Instance Creation Date +//0008 0020 DA ID Study Date +//0008 0021 DA ID Series Date +//0008 0022 DA ID Acquisition Date +//0008 0023 DA ID Content Date +//0008 0024 DA ID Overlay Date +//0008 0025 DA ID Curve Date +//0008 002a DT ID Acquisition Datetime +//0018 9074 DT ACQ Frame Acquisition Datetime +//0018 9151 DT ACQ Frame Reference Datetime +//0018 a002 DT ACQ Contribution Date Time +//0020 3403 SH REL Modified Image Date (RET) +//0032 0032 DA SDY Study Verified Date +//0032 0034 DA SDY Study Read Date +//0032 1000 DA SDY Scheduled Study Start Date +//0032 1010 DA SDY Scheduled Study Stop Date +//0032 1040 DA SDY Study Arrival Date +//0032 1050 DA SDY Study Completion Date +//0038 001a DA VIS Scheduled Admission Date +//0038 001c DA VIS Scheduled Discharge Date +//0038 0020 DA VIS Admitting Date +//0038 0030 DA VIS Discharge Date +//0040 0002 DA PRC Scheduled Procedure Step Start Date +//0040 0004 DA PRC Scheduled Procedure Step End Date +//0040 0244 DA PRC Performed Procedure Step Start Date +//0040 0250 DA PRC Performed Procedure Step End Date +//0040 2004 DA PRC Issue Date of Imaging Service Request +//0040 4005 DT PRC Scheduled Procedure Step Start Date and Time +//0040 4011 DT PRC Expected Completion Date and Time +//0040 a030 DT PRC Verification Date Time +//0040 a032 DT PRC Observation Date Time +//0040 a120 DT PRC DateTime +//0040 a121 DA PRC Date +//0040 a13a DT PRC Referenced Datetime +//0070 0082 DA ??? Presentation Creation Date +//0100 0420 DT ??? SOP Autorization Date and Time +//0400 0105 DT ??? Digital Signature DateTime +//2100 0040 DA PJ Creation Date +//3006 0008 DA SSET Structure Set Date +//3008 0024 DA ??? Treatment Control Point Date +//3008 0054 DA ??? First Treatment Date +//3008 0056 DA ??? Most Recent Treatment Date +//3008 0162 DA ??? Safe Position Exit Date +//3008 0166 DA ??? Safe Position Return Date +//3008 0250 DA ??? Treatment Date +//300a 0006 DA RT RT Plan Date +//300a 022c DA RT Air Kerma Rate Reference Date +//300e 0004 DA RT Review Date + + return true; +} + +/** + * \brief gets the info from 0020,0037 : Image Orientation Patient + * @param iop adress of the (6)float aray to receive values + * @return cosines of image orientation patient + */ +void gdcmHeader::GetImageOrientationPatient( float iop[6] ) +{ + std::string strImOriPat; + //iop is supposed to be float[6] + iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.; + + // 0020 0037 DS REL Image Orientation (Patient) + if ( (strImOriPat = GetEntryByNumber(0x0020,0x0037)) != GDCM_UNFOUND ) + { + if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f", + &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) + { + dbg.Verbose(0, "gdcmHeader::GetImageOrientationPatient: wrong Image Orientation Patient (0020,0037)"); + // bug in the element 0x0020,0x0037 + } + } + //For ACR-NEMA + // 0020 0035 DS REL Image Orientation (RET) + else if ( (strImOriPat = GetEntryByNumber(0x0020,0x0035)) != GDCM_UNFOUND ) + { + if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f", + &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) + { + dbg.Verbose(0, "gdcmHeader::GetImageOrientationPatient: wrong Image Orientation Patient (0020,0035)"); + // bug in the element 0x0020,0x0035 + } + } } + +//----------------------------------------------------------------------------- +// Private + +//-----------------------------------------------------------------------------