X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=b6801f8b88955802c6ee3ac9e19aa0aee749e7ef;hb=1d69b92978803204089d270599133917d944c651;hp=eb927e3c314dd8d3cb1d526bbd91a6d265c02c1a;hpb=aba8714645174c0c7d3c7aadf6af1832743e2971;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index eb927e3c..b6801f8b 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -1,495 +1,948 @@ -// gdcmHeader.cxx -//----------------------------------------------------------------------------- -#include "gdcmHeader.h" - -#include -#include -// For nthos: -#ifdef _MSC_VER -#include -#else -#include -#endif -#include // for isalpha - -#ifdef GDCM_NO_ANSI_STRING_STREAM -# include -# define ostringstream ostrstream -# else -# include -#endif +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmHeader.cxx,v $ + Language: C++ + Date: $Date: 2004/10/12 04:35:46 $ + Version: $Revision: 1.193 $ + + 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.html 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" -//----------------------------------------------------------------------------- -// Refer to gdcmHeader::CheckSwap() -const unsigned int gdcmHeader::HEADER_LENGTH_TO_READ = 256; +#include -// Refer to gdcmHeader::SetMaxSizeLoadElementValue() -const unsigned int gdcmHeader::MAX_SIZE_LOAD_ELEMENT_VALUE = 4096; +namespace gdcm +{ //----------------------------------------------------------------------------- // 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 + * \brief Constructor + * @param filename name of the file whose header we want to analyze */ -gdcmHeader::gdcmHeader(const char *InFilename, - bool exception_on_error, - bool enable_sequences ) { - if (enable_sequences) - enableSequences = 1; +Header::Header( std::string const & filename ): + Document( 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 - enableSequences = 0; - - SetMaxSizeLoadElementValue(MAX_SIZE_LOAD_ELEMENT_VALUE); - filename = InFilename; - Initialise(); - if ( !OpenFile(exception_on_error)) - return; - ParseHeader(); - LoadElements(); - CloseFile(); + { + 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; + } } /** - * \ingroup gdcmHeader - * \brief - * @param exception_on_error + * \brief Constructor */ -gdcmHeader::gdcmHeader(bool exception_on_error) { - SetMaxSizeLoadElementValue(MAX_SIZE_LOAD_ELEMENT_VALUE); - Initialise(); +Header::Header() + :Document() +{ } /** - * \ingroup gdcmHeader * \brief Canonical destructor. */ -gdcmHeader::~gdcmHeader (void) { - dicom_vr = (gdcmVR*)0; - Dicts = (gdcmDictSet*)0; - RefPubDict = (gdcmDict*)0; - RefShaDict = (gdcmDict*)0; - return; +Header::~Header () +{ } -//----------------------------------------------------------------------------- -// Print /** - * \ingroup gdcmHeader - * \brief - * @return - */ -void gdcmHeader::PrintPubElVal(std::ostream & os) { - PubElValSet.Print(os); -} + * \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 Header::Write(FILE* fp,FileType filetype) +{ + // Bits Allocated + if ( GetEntryByNumber(0x0028,0x0100) == "12") + { + SetEntryByNumber("16", 0x0028,0x0100); + } -/** - * \ingroup gdcmHeader - * \brief - * @return - */ -void gdcmHeader::PrintPubDict(std::ostream & os) { - RefPubDict->Print(os); + /// \todo correct 'Pixel group' Length if necessary + + int i_lgPix = GetEntryLengthByNumber(GrPixel, NumPixel); + if (i_lgPix != -2) + { + // no (GrPixel, NumPixel) element + std::string s_lgPix; + s_lgPix = Util::Format("%d", i_lgPix+12); + ReplaceOrCreateByNumber(s_lgPix,GrPixel, 0x0000); + } + + // FIXME : should be nice if we could move it to File + // (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 + + DocEntry* 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); + } + } + Document::Write(fp,filetype); } +//----------------------------------------------------------------------------- +// Print + + //----------------------------------------------------------------------------- // Public + /** - * \ingroup gdcmHeader * \brief This predicate, based on hopefully reasonable heuristics, - * decides whether or not the current gdcmHeader was properly parsed + * decides whether or not the current Header was properly parsed * and contains the mandatory information for being considered as - * a well formed and usable image. - * @return true when gdcmHeader is the one of a reasonable Dicom file, + * a well formed and usable Dicom/Acr File. + * @return true when Header is the one of a reasonable Dicom/Acr file, * false otherwise. */ -bool gdcmHeader::IsReadable(void) { - std::string res = GetPubElValByNumber(0x0028, 0x0005); - if ( res != GDCM_UNFOUND - && atoi(res.c_str()) > 4 ) { +bool Header::IsReadable() +{ + if( !Document::IsReadable() ) + { + return false; + } + + std::string res = GetEntryByNumber(0x0028, 0x0005); + if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) + { return false; // Image Dimensions } - if ( GetPubElValByNumber(0x0028, 0x0100) == GDCM_UNFOUND ) + if ( !GetDocEntryByNumber(0x0028, 0x0100) ) + { return false; // "Bits Allocated" - if ( GetPubElValByNumber(0x0028, 0x0101) == GDCM_UNFOUND ) + } + if ( !GetDocEntryByNumber(0x0028, 0x0101) ) + { return false; // "Bits Stored" - if ( GetPubElValByNumber(0x0028, 0x0102) == GDCM_UNFOUND ) + } + if ( !GetDocEntryByNumber(0x0028, 0x0102) ) + { return false; // "High Bit" - if ( GetPubElValByNumber(0x0028, 0x0103) == GDCM_UNFOUND ) - return false; // "Pixel Representation" + } + if ( !GetDocEntryByNumber(0x0028, 0x0103) ) + { + return false; // "Pixel Representation" i.e. 'Sign' + } + return true; } /** - * \ingroup gdcmHeader - * \brief Determines if the Transfer Syntax was already encountered - * and if it corresponds to a ImplicitVRLittleEndian one. - * - * @return True when ImplicitVRLittleEndian found. False in all other cases. + * \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 */ -bool gdcmHeader::IsImplicitVRLittleEndianTransferSyntax(void) { - gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadElementValueSafe(Element); - std::string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2" ) - return true; - return false; -} +int Header::GetXSize() +{ + std::string strSize; + strSize = GetEntryByNumber(0x0028,0x0011); + if ( strSize == GDCM_UNFOUND ) + { + return 0; + } -/** - * \ingroup gdcmHeader - * \brief Determines if the Transfer Syntax was already encountered - * and if it corresponds to a ExplicitVRLittleEndian one. - * - * @return True when ExplicitVRLittleEndian found. False in all other cases. - */ -bool gdcmHeader::IsExplicitVRLittleEndianTransferSyntax(void) { - gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadElementValueSafe(Element); - std::string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.1" ) - return true; - return false; + return atoi( strSize.c_str() ); } /** - * \ingroup gdcmHeader - * \brief Determines if the Transfer Syntax was already encountered - * and if it corresponds to a DeflatedExplicitVRLittleEndian one. - * - * @return True when DeflatedExplicitVRLittleEndian found. False in all other cases. + * \brief Retrieve the number of lines of image. + * \warning The defaulted value is 1 as opposed to Header::GetXSize() + * @return The encountered size when found, 1 by default + * (The ACR-NEMA file contains a Signal, not an Image). */ -bool gdcmHeader::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) { - gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadElementValueSafe(Element); - std::string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.1.99" ) - return true; - return false; +int Header::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; } /** - * \ingroup gdcmHeader - * \brief Determines if the Transfer Syntax was already encountered - * and if it corresponds to a Explicit VR Big Endian one. - * - * @return True when big endian found. False in all other cases. + * \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). */ -bool gdcmHeader::IsExplicitVRBigEndianTransferSyntax(void) { - gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadElementValueSafe(Element); - std::string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.2" ) //1.2.2 ??? A verifier ! - return true; - return false; +int Header::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 Determines if the Transfer Syntax was already encountered - * and if it corresponds to a JPEGBaseLineProcess1 one. - * - * @return True when JPEGBaseLineProcess1found. False in all other cases. - */ -bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) { - gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadElementValueSafe(Element); - std::string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.4.50" ) - return true; - return false; + * \brief gets the info from 0028,0030 : Pixel Spacing + * else 1.0 + * @return X dimension of a pixel + */ +float Header::GetXSpacing() +{ + float xspacing, yspacing; + std::string strSpacing = GetEntryByNumber(0x0028,0x0030); + + if ( strSpacing == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::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, "Header::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 Determines if the Transfer Syntax was already encountered - * and if it corresponds to a JPEGExtendedProcess2-4 one. - * - * @return True when JPEGExtendedProcess2-4 found. False in all other cases. - */ -bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) { - gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadElementValueSafe(Element); - std::string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.4.51" ) - return true; - return false; -} + * \brief gets the info from 0028,0030 : Pixel Spacing + * else 1.0 + * @return Y dimension of a pixel + */ +float Header::GetYSpacing() +{ + float yspacing = 0; + std::string strSpacing = GetEntryByNumber(0x0028,0x0030); + + if ( strSpacing == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::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 Determines if the Transfer Syntax was already encountered - * and if it corresponds to a JPEGExtendeProcess3-5 one. - * - * @return True when JPEGExtendedProcess3-5 found. False in all other cases. + * \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 */ -bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) { - gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadElementValueSafe(Element); - std::string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.4.52" ) - return true; - return false; +float Header::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, "Header::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 Determines if the Transfer Syntax was already encountered - * and if it corresponds to a JPEGSpectralSelectionProcess6-8 one. - * - * @return True when JPEGSpectralSelectionProcess6-8 found. False in all - * other cases. + *\brief gets the info from 0028,1052 : Rescale Intercept + * @return Rescale Intercept */ -bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) { - gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadElementValueSafe(Element); - std::string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.4.53" ) - return true; - return false; +float Header::GetRescaleIntercept() +{ + float resInter = 0.; + /// 0028 1052 DS IMG Rescale Intercept + std::string strRescInter = GetEntryByNumber(0x0028,0x1052); + if ( strRescInter != GDCM_UNFOUND ) + { + if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 ) + { + // bug in the element 0x0028,0x1052 + dbg.Verbose(0, "Header::GetRescaleIntercept: Rescale Slope " + "is empty"); + } + } + + return resInter; } /** - * \ingroup gdcmHeader - * \brief Determines if the Transfer Syntax was already encountered - * and if it corresponds to a RLE Lossless one. - * - * @return True when RLE Lossless found. False in all - * other cases. + *\brief gets the info from 0028,1053 : Rescale Slope + * @return Rescale Slope */ -bool gdcmHeader::IsRLELossLessTransferSyntax(void) { - gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadElementValueSafe(Element); - std::string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.5" ) - return true; - return false; +float Header::GetRescaleSlope() +{ + float resSlope = 1.; + //0028 1053 DS IMG Rescale Slope + std::string strRescSlope = GetEntryByNumber(0x0028,0x1053); + if ( strRescSlope != GDCM_UNFOUND ) + { + if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1) + { + // bug in the element 0x0028,0x1053 + dbg.Verbose(0, "Header::GetRescaleSlope: Rescale Slope is empty"); + } + } + + return resSlope; } /** - * \ingroup gdcmHeader - * \brief - * - * @return + * \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) */ -bool gdcmHeader::IsJPEGLossless(void) { - gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); - // faire qq chose d'intelligent a la place de ça - if ( !Element ) - return false; - LoadElementValueSafe(Element); - const char * Transfert = Element->GetValue().c_str(); - if ( memcmp(Transfert+strlen(Transfert)-2 ,"70",2)==0) return true; - if ( memcmp(Transfert+strlen(Transfert)-2 ,"55",2)==0) return true; - if (Element->GetValue() == "1.2.840.10008.1.2.4.57") return true; +int Header::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); - return false; + 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 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. + * \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' -) */ -bool gdcmHeader::IsJPEG2000(void) { - gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadElementValueSafe(Element); - std::string Transfer = Element->GetValue(); - if ( (Transfer == "1.2.840.10008.1.2.4.90") - || (Transfer == "1.2.840.10008.1.2.4.91") ) - return true; - return false; +int Header::GetNumberOfScalarComponentsRaw() +{ + // 0028 0100 US IMG Bits Allocated + // (in order no to be messed up by old RGB images) + if ( Header::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? +// +// --------------------------------------------------------------- +// + /** - * \ingroup gdcmHeader - * \brief Predicate for dicom version 3 file. - * @return True when the file is a dicom version 3. + * \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 */ -bool gdcmHeader::IsDicomV3(void) { - if ( (filetype == ExplicitVR) - || (filetype == ImplicitVR) ) - return true; - return false; +float Header::GetXOrigin() +{ + float xImPos, yImPos, zImPos; + std::string strImPos = GetEntryByNumber(0x0020,0x0032); + + if ( strImPos == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::GetXImagePosition: unfound Image " + "Position Patient (0020,0032)"); + strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images + if ( strImPos == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::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; } /** - * \ingroup gdcmHeader - * \brief - * @return + * \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 */ -FileType gdcmHeader::GetFileType(void) +float Header::GetYOrigin() { - return(filetype); + float xImPos, yImPos, zImPos; + std::string strImPos = GetEntryByNumber(0x0020,0x0032); + + if ( strImPos == GDCM_UNFOUND) + { + dbg.Verbose(0, "Header::GetYImagePosition: unfound Image " + "Position Patient (0020,0032)"); + strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images + if ( strImPos == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::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; } /** - * \ingroup gdcmHeader - * \brief Retrieve the number of columns of image. - * @return The encountered size when found, 0 by default. + * \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 */ -int gdcmHeader::GetXSize(void) { - // We cannot check for "Columns" because the "Columns" tag is present - // both in IMG (0028,0011) and OLY (6000,0011) sections of the dictionary. - std::string StrSize = GetPubElValByNumber(0x0028,0x0011); - if (StrSize == GDCM_UNFOUND) - return 0; - return atoi(StrSize.c_str()); +float Header::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, "Header::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, "Header::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, "Header::GetZImagePosition: wrong Slice Location (0020,1041)"); + return 0.; // bug in the element 0x0020,0x1041 + } + else + { + return zImPos; + } + } + dbg.Verbose(0, "Header::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, "Header::GetZImagePosition: wrong Location (0020,0050)"); + return 0.; // bug in the element 0x0020,0x0050 + } + else + { + return zImPos; + } + } + dbg.Verbose(0, "Header::GetYImagePosition: unfound Location (0020,0050)"); + + return 0.; // Hopeless } /** - * \ingroup gdcmHeader - * \brief Retrieve the number of lines of image. - * \warning The defaulted value is 1 as opposed to gdcmHeader::GetXSize() - * @return The encountered size when found, 1 by default. + * \brief gets the info from 0020,0013 : Image Number else 0. + * @return image number */ -int gdcmHeader::GetYSize(void) { - // We cannot check for "Rows" because the "Rows" tag is present - // both in IMG (0028,0010) and OLY (6000,0010) sections of the dictionary. - std::string StrSize = GetPubElValByNumber(0x0028,0x0010); - if (StrSize != GDCM_UNFOUND) - return atoi(StrSize.c_str()); - if ( IsDicomV3() ) - return 0; - else - // The Rows (0028,0010) entry is optional for ACR/NEMA. It might - // hence be a signal (1d image). So we default to 1: - return 1; +int Header::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. + //0020 0013 IS REL Image Number + std::string strImNumber = GetEntryByNumber(0x0020,0x0013); + if ( strImNumber != GDCM_UNFOUND ) + { + return atoi( strImNumber.c_str() ); + } + return 0; //Hopeless } /** - * \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. + * \brief gets the info from 0008,0060 : Modality + * @return Modality Type */ -int gdcmHeader::GetZSize(void) { - // Both DicomV3 and ACR/Nema consider the "Number of Frames" - // as the third dimension. - std::string StrSize = GetPubElValByNumber(0x0028,0x0008); - if (StrSize != GDCM_UNFOUND) - return atoi(StrSize.c_str()); - - // We then consider the "Planes" entry as the third dimension [we - // cannot retrieve by name since "Planes tag is present both in - // IMG (0028,0012) and OLY (6000,0012) sections of the dictionary]. - StrSize = GetPubElValByNumber(0x0028,0x0012); - if (StrSize != GDCM_UNFOUND) - return atoi(StrSize.c_str()); - return 1; +ModalityType Header::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 Retrieve the number of Bits Stored + * \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 = GetPubElValByNumber(0x0028,0x0101); - if (StrSize == GDCM_UNFOUND) - return 1; - return atoi(StrSize.c_str()); +int Header::GetBitsStored() +{ + std::string strSize = GetEntryByNumber( 0x0028, 0x0101 ); + if ( strSize == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::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 Retrieve the number of Bits Allocated - * (8, 12 -compacted ACR-NEMA files, 16, ...) - * - * @return The encountered number of Bits Allocated, 0 by default. + * \brief Retrieve the high bit position. + * \warning The method defaults to 0 when information is absent. + * The responsability of checking this value is left to the caller. + * @return The high bit positin when present. 0 when absent. */ -int gdcmHeader::GetBitsAllocated(void) { - std::string StrSize = GetPubElValByNumber(0x0028,0x0100); - if (StrSize == GDCM_UNFOUND) - return 1; - return atoi(StrSize.c_str()); +int Header::GetHighBitPosition() +{ + std::string strSize = GetEntryByNumber( 0x0028, 0x0102 ); + if ( strSize == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::GetHighBitPosition: this is supposed " + "to be mandatory"); + return 0; + } + return atoi( strSize.c_str() ); } /** - * \ingroup gdcmHeader - * \brief Retrieve the number of Samples Per Pixel + * \brief Check wether the pixels are signed or UNsigned data. + * \warning The method defaults to false (UNsigned) when information is absent. + * The responsability of checking this value is left to the caller. + * @return True when signed, false when UNsigned + */ +bool Header::IsSignedPixelData() +{ + std::string strSize = GetEntryByNumber( 0x0028, 0x0103 ); + if ( strSize == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::IsSignedPixelData: this is supposed " + "to be mandatory"); + return false; + } + int sign = atoi( strSize.c_str() ); + if ( sign == 0 ) + { + return false; + } + return true; +} + +/** + * \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 Header::GetBitsAllocated() +{ + std::string strSize = GetEntryByNumber(0x0028,0x0100); + if ( strSize == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::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() ); +} + +/** + * \brief Retrieve the number of Samples Per Pixel * (1 : gray level, 3 : RGB -1 or 3 Planes-) - * * @return The encountered number of Samples Per Pixel, 1 by default. + * (Gray level Pixels) */ -int gdcmHeader::GetSamplesPerPixel(void) { - std::string StrSize = GetPubElValByNumber(0x0028,0x0002); - if (StrSize == GDCM_UNFOUND) +int Header::GetSamplesPerPixel() +{ + std::string strSize = GetEntryByNumber(0x0028,0x0002); + if ( strSize == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::GetBitsStored: this is supposed to " + "be mandatory"); return 1; // Well, it's supposed to be mandatory ... - return atoi(StrSize.c_str()); + // but sometimes it's missing : *we* assume Gray pixels + } + return atoi( strSize.c_str() ); +} + +/** + * \brief Check wether this a monochrome picture or not by accessing + * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). + * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise. + */ +bool Header::IsMonochrome() +{ + std::string PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 ); + if ( PhotometricInterp == "MONOCHROME1 " + || PhotometricInterp == "MONOCHROME2 " ) + { + return true; + } + if ( PhotometricInterp == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::IsMonochrome: absent Photometric " + "Interpretation"); + } + return false; +} + +/** + * \brief Check wether this a "PALETTE COLOR" picture or not by accessing + * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). + * @return true when "PALETTE COLOR". False otherwise. + */ +bool Header::IsPaletteColor() +{ + std::string PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 ); + if ( PhotometricInterp == "PALETTE COLOR " ) + { + return true; + } + if ( PhotometricInterp == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::IsPaletteColor: absent Photometric " + "Interpretation"); + } + return false; +} + +/** + * \brief Check wether this a "YBR_FULL" color picture or not by accessing + * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). + * @return true when "YBR_FULL". False otherwise. + */ +bool Header::IsYBRFull() +{ + std::string PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 ); + if ( PhotometricInterp == "YBR_FULL" ) + { + return true; + } + if ( PhotometricInterp == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::IsYBRFull: absent Photometric " + "Interpretation"); + } + 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(void) { - std::string StrSize = GetPubElValByNumber(0x0028,0x0006); - if (StrSize == GDCM_UNFOUND) +int Header::GetPlanarConfiguration() +{ + std::string strSize = GetEntryByNumber(0x0028,0x0006); + if ( strSize == GDCM_UNFOUND ) + { return 0; - return atoi(StrSize.c_str()); + } + 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. - * + * @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") +int Header::GetPixelSize() +{ + // 0028 0100 US IMG Bits Allocated + // (in order no to be messed up by old RGB images) + // if (Header::GetEntryByNumber(0x0028,0x0100) == "24") + // return 3; + + std::string pixelType = GetPixelType(); + if ( pixelType == "8U" || pixelType == "8S" ) + { return 1; - if (PixelType == "16U" || PixelType == "16S") + } + if ( pixelType == "16U" || pixelType == "16S") + { return 2; - if (PixelType == "32U" || PixelType == "32S") + } + if ( pixelType == "32U" || pixelType == "32S") + { return 4; - dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type"); + } + if ( pixelType == "FD" ) + { + return 8; + } + dbg.Verbose(0, "Header::GetPixelSize: Unknown pixel type"); return 0; } /** - * \ingroup gdcmHeader * \brief Build the Pixel Type of the image. * Possible values are: * - 8U unsigned 8 bit, @@ -498,1867 +951,522 @@ int gdcmHeader::GetPixelSize(void) { * - 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 + * 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; - BitsAlloc = GetPubElValByNumber(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; - Signed = GetPubElValByNumber(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"); +std::string Header::GetPixelType() +{ + std::string bitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated + if ( bitsAlloc == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::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) + } - return( BitsAlloc + Signed); + std::string sign = GetEntryByNumber(0x0028, 0x0103);//"Pixel Representation" + + if (sign == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::GetPixelType: unfound Pixel Representation"); + bitsAlloc = "0"; + } + if ( sign == "0" ) + { + sign = "U"; + } + else + { + sign = "S"; + } + return bitsAlloc + sign; } + /** - * \ingroup gdcmHeader - * \brief Recover the offset (from the beginning of the file) of the pixels. + * \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(void) { - // If this file complies with the norm we should encounter the - // "Image Location" tag (0x0028, 0x0200). This tag contains the - // the group that contains the pixel data (hence the "Pixel Data" - // is found by indirection through the "Image Location"). - // Inside the group pointed by "Image Location" the searched element - // is conventionally the element 0x0010 (when the norm is respected). - // When the "Image Location" is absent we default to group 0x7fe0. - guint16 grPixel; - guint16 numPixel; - std::string ImageLocation = GetPubElValByNumber(0x0028, 0x0200); - if ( ImageLocation == GDCM_UNFOUND ) { // Image Location - grPixel = 0x7fe0; - } else { - grPixel = (guint16) atoi( ImageLocation.c_str() ); - } - if (grPixel != 0x7fe0) - // This is a kludge for old dirty Philips imager. - numPixel = 0x1010; - else - numPixel = 0x0010; - - gdcmElValue* PixelElement = PubElValSet.GetElementByNumber(grPixel, - numPixel); - if (PixelElement) - return PixelElement->GetOffset(); +size_t Header::GetPixelOffset() +{ + DocEntry* 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 TODO : unify those two (previous one and next one) /** - * \ingroup gdcmHeader - * \brief Recover the pixel area length (in Bytes) . + * \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) { - // If this file complies with the norm we should encounter the - // "Image Location" tag (0x0028, 0x0200). This tag contains the - // the group that contains the pixel data (hence the "Pixel Data" - // is found by indirection through the "Image Location"). - // Inside the group pointed by "Image Location" the searched element - // is conventionally the element 0x0010 (when the norm is respected). - // When the "Image Location" is absent we default to group 0x7fe0. - guint16 grPixel; - guint16 numPixel; - std::string ImageLocation = GetPubElValByNumber(0x0028, 0x0200); - if ( ImageLocation == GDCM_UNFOUND ) { - grPixel = 0x7fe0; - } else { - grPixel = (guint16) atoi( ImageLocation.c_str() ); - } - if (grPixel != 0x7fe0) - // This is a kludge for old dirty Philips imager. - numPixel = 0x1010; - else - numPixel = 0x0010; - - gdcmElValue* PixelElement = PubElValSet.GetElementByNumber(grPixel, - numPixel); - if (PixelElement) - return PixelElement->GetLength(); +size_t Header::GetPixelAreaLength() +{ + DocEntry* 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 - * @return int acts as a Boolean + * \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(void) { - - // Check the presence of the LUT Descriptors - if (GetPubElValByNumber(0x0028,0x1101) == GDCM_UNFOUND) +bool Header::HasLUT() +{ + // Check the presence of the LUT Descriptors, and LUT Tables + // LutDescriptorRed + if ( !GetDocEntryByNumber(0x0028,0x1101) ) + { return false; + } // LutDescriptorGreen - if (GetPubElValByNumber(0x0028,0x1102) == GDCM_UNFOUND) + if ( !GetDocEntryByNumber(0x0028,0x1102) ) + { return false; + } // LutDescriptorBlue - if (GetPubElValByNumber(0x0028,0x1103) == GDCM_UNFOUND) + if ( !GetDocEntryByNumber(0x0028,0x1103) ) + { return false; - // It is not enough - // we check also - if (GetPubElValByNumber(0x0028,0x1201) == GDCM_UNFOUND) - return false; - if (GetPubElValByNumber(0x0028,0x1202) == GDCM_UNFOUND) + } + // Red Palette Color Lookup Table Data + if ( !GetDocEntryByNumber(0x0028,0x1201) ) + { return false; - if (GetPubElValByNumber(0x0028,0x1203) == GDCM_UNFOUND) - 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 nBit - * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] + * 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(void) { +int Header::GetLUTNbits() +{ std::vector tokens; - //int LutLength; - //int LutDepth; - int LutNbits; - //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red = Lookup Table Desc-Blue + int lutNbits; + + //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red + // = Lookup Table Desc-Blue // Consistency already checked in GetLUTLength - std::string LutDescription = GetPubElValByNumber(0x0028,0x1101); - if (LutDescription == GDCM_UNFOUND) + 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, "\\"); + } + + tokens.clear(); // clean any previous value + Util::Tokenize ( lutDescription, tokens, "\\" ); //LutLength=atoi(tokens[0].c_str()); //LutDepth=atoi(tokens[1].c_str()); - LutNbits=atoi(tokens[2].c_str()); + + lutNbits = atoi( tokens[2].c_str() ); tokens.clear(); - return LutNbits; + + 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 + * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] + * and (0028,1101),(0028,1102),(0028,1102) + * - xxx Palette Color Lookup Table Descriptor - are found + * and (0028,1201),(0028,1202),(0028,1202) + * - xxx Palette Color Lookup Table Data - are found * \warning does NOT deal with : - * \ 0028 1100 Gray Lookup Table Descriptor (Retired) - * \ 0028 1221 Segmented Red Palette Color Lookup Table Data - * \ 0028 1222 Segmented Green Palette Color Lookup Table Data - * \ 0028 1223 Segmented Blue Palette Color Lookup Table Data - * \ no known Dicom reader deails with them :-( - * @return Lookup Table RGBA + * 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 -// and OT-PAL-8-face.dcm +uint8_t* Header::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 (gdcmHeader::GetPubElValByNumber(0x0028,0x0004) != "PALETTE COLOR ") { - return NULL; - } + 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 = GetPubElValByNumber(0x0028,0x1101); - if (LutDescriptionR == GDCM_UNFOUND) + // 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 = GetPubElValByNumber(0x0028,0x1102); - if (LutDescriptionG == GDCM_UNFOUND) - return NULL; - std::string LutDescriptionB = GetPubElValByNumber(0x0028,0x1103); - if (LutDescriptionB == GDCM_UNFOUND) + } + + std::string lutDescriptionG = GetEntryByNumber(0x0028,0x1102); + if ( lutDescriptionG == GDCM_UNFOUND ) + { return NULL; - - std::vector tokens; - - tokens.erase(tokens.begin(),tokens.end()); // clean any previous value - Tokenize (LutDescriptionR, tokens, "\\"); - lengthR=atoi(tokens[0].c_str()); // Red LUT length in Bytes - debR =atoi(tokens[1].c_str()); // subscript of the first Lut Value - nbitsR =atoi(tokens[2].c_str()); // Lut item size (in Bits) - tokens.clear(); - - tokens.erase(tokens.begin(),tokens.end()); // clean any previous value - Tokenize (LutDescriptionG, tokens, "\\"); - lengthG=atoi(tokens[0].c_str()); // Green LUT length in Bytes - debG =atoi(tokens[1].c_str()); - nbitsG =atoi(tokens[2].c_str()); - tokens.clear(); + } + + 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, "Header::GetLUTRGBA: trouble reading red LUT"); + } - tokens.erase(tokens.begin(),tokens.end()); // clean any previous value - Tokenize (LutDescriptionB, tokens, "\\"); - lengthB=atoi(tokens[0].c_str()); // Blue LUT length in Bytes - debB =atoi(tokens[1].c_str()); - nbitsB =atoi(tokens[2].c_str()); - tokens.clear(); + // 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, "Header::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, "Header::GetLUTRGBA: trouble reading blue LUT"); + } -// Load LUTs into memory, (as they were stored on disk) - unsigned char *lutR = (unsigned char *) - GetPubElValVoidAreaByNumber(0x0028,0x1201); - unsigned char *lutG = (unsigned char *) - GetPubElValVoidAreaByNumber(0x0028,0x1202); - unsigned char *lutB = (unsigned char *) - GetPubElValVoidAreaByNumber(0x0028,0x1203); - - if (!lutR || !lutG || !lutB ) { - return NULL; + // Load LUTs into memory, (as they were stored on disk) + uint8_t* lutR = (uint8_t*) GetEntryBinAreaByNumber(0x0028,0x1201); + uint8_t* lutG = (uint8_t*) GetEntryBinAreaByNumber(0x0028,0x1202); + uint8_t* lutB = (uint8_t*) GetEntryBinAreaByNumber(0x0028,0x1203); + + if ( !lutR || !lutG || !lutB ) + { + dbg.Verbose(0, "Header::GetLUTRGBA: trouble with one of the LUT"); + 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 + // 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 = GetPubElValByNumber(0x0028,0x0100); - if (str_nb == GDCM_UNFOUND ) { + 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; - + } + else + { + nb = atoi( str_nb.c_str() ); + } + int mult; + + if ( nbitsR == 16 && nb == 8) + { + // when LUT item size is different than pixel size + mult = 2; // high byte must be = low byte + } + else + { + // See PS 3.3-2003 C.11.1.1.2 p 619 + mult = 1; + } + // if we get a black image, let's just remove the '+1' // from 'i*mult+1' and check again // if it works, we shall have to check the 3 Palettes // to see which byte is ==0 (first one, or second one) // and fix the code - // We give up the checking to avoid some overhead - unsigned char *a; - int i; - - a = LUTRGBA+0; - for(i=0;iGetValue(TransfertSyntax); - //delete ts; // Seg Fault when deleted ?! - return tsName; -} -/** - * \ingroup gdcmHeader - * \brief Searches within the public dictionary for element value of - * a given tag. - * @param tagName name of the searched element. - * @return Corresponding element value when it exists, and the string - * GDCM_UNFOUND ("gdcm::Unfound") otherwise. - */ -std::string gdcmHeader::GetPubElValByName(std::string tagName) { - gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName); - if( dictEntry == NULL) - return GDCM_UNFOUND; - return(PubElValSet.GetElValueByNumber(dictEntry->GetGroup(), - dictEntry->GetElement())); -} - -/** - * \ingroup gdcmHeader - * \brief Searches within the elements parsed with the public dictionary for - * the element value representation of a given tag. - * - * Obtaining the VR (Value Representation) might be needed by caller - * to convert the string typed content to caller's native type - * (think of C++ vs Python). The VR is actually of a higher level - * of semantics than just the native C++ type. - * @param tagName name of the searched element. - * @return Corresponding element value representation when it exists, - * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. - */ -std::string gdcmHeader::GetPubElValRepByName(std::string tagName) { - gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName); - if( dictEntry == NULL) - return GDCM_UNFOUND; - gdcmElValue* elem = PubElValSet.GetElementByNumber( - dictEntry->GetGroup(), - dictEntry->GetElement()); - return elem->GetVR(); -} - -/** - * \ingroup gdcmHeader - * \brief Searches within the public dictionary for element value of - * a given tag. - * @param group Group of the researched tag. - * @param element Element of the researched tag. - * @return Corresponding element value when it exists, and the string - * GDCM_UNFOUND ("gdcm::Unfound") otherwise. - */ -std::string gdcmHeader::GetPubElValByNumber(guint16 group, guint16 element) { - return PubElValSet.GetElValueByNumber(group, element); -} - -/** - * \ingroup gdcmHeader - * \brief Searches within the public dictionary for element value - * representation of a given tag. - * - * Obtaining the VR (Value Representation) might be needed by caller - * to convert the string typed content to caller's native type - * (think of C++ vs Python). The VR is actually of a higher level - * of semantics than just the native C++ type. - * @param group Group of the researched tag. - * @param element Element of the researched tag. - * @return Corresponding element value representation when it exists, - * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. - */ -std::string gdcmHeader::GetPubElValRepByNumber(guint16 group, guint16 element) { - gdcmElValue* elem = PubElValSet.GetElementByNumber(group, element); - if ( !elem ) - return GDCM_UNFOUND; - return elem->GetVR(); -} - -/** - * \ingroup gdcmHeader - * \brief Accesses an existing gdcmElValue in the PubElValSet of this instance - * through tag name and modifies it's content with the given value. - * @param content new value to substitute with - * @param tagName name of the tag to be modified - */ -bool gdcmHeader::SetPubElValByName(std::string content, std::string tagName) { - //return ( PubElValSet.SetElValueByName (content, tagName) ); - gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName); - if( dictEntry == NULL) - return false; - return(PubElValSet.SetElValueByNumber(content, - dictEntry->GetGroup(), - dictEntry->GetElement())); -} + a = LUTRGBA + 3; + for(i=0; i < 256; ++i) + { + *a = 1; // Alpha component + a += 4; + } + return LUTRGBA; +} /** - * \ingroup gdcmHeader - * \brief Accesses an existing gdcmElValue (i.e. a Dicom Element) - * in the PubElValSet of this instance - * through it's (group, element) and modifies it's content with - * the given value. - * @param content new value to substitute with - * @param group group of the Dicom Element to modify - * @param element element of the Dicom Element to modify + * \brief Accesses the info from 0002,0010 : Transfert Syntax and TS + * else 1. + * @return The full Transfert Syntax Name (as opposed to Transfert Syntax UID) */ -bool gdcmHeader::SetPubElValByNumber(std::string content, guint16 group, - guint16 element) - -//TODO : homogeneiser les noms : SetPubElValByNumber -// qui appelle PubElValSet.SetElValueByNumber -// pourquoi pas SetPubElValueByNumber ?? +std::string Header::GetTransfertSyntaxName() { - return ( PubElValSet.SetElValueByNumber (content, group, element) ); -} - -/** - * \ingroup gdcmHeader - * \brief Accesses an existing gdcmElValue in the PubElValSet of this instance - * through it's (group, element) and modifies it's length with - * the given value. - * \warning Use with extreme caution. - * @param length new length to substitute with - * @param group group of the ElVal to modify - * @param element element of the ElVal to modify - * @return 1 on success, 0 otherwise. - */ - -bool gdcmHeader::SetPubElValLengthByNumber(guint32 length, guint16 group, - guint16 element) { - return ( PubElValSet.SetElValueLengthByNumber (length, group, element) ); -} - -/** - * \ingroup gdcmHeader - * \brief Searches within elements parsed with the public dictionary - * and then within the elements parsed with the shadow dictionary - * for the element value of a given tag. - * @param tagName name of the searched element. - * @return Corresponding element value when it exists, - * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. - */ -std::string gdcmHeader::GetElValByName(std::string tagName) { - std::string pub = GetPubElValByName(tagName); - return pub; -} - -/** - * \ingroup gdcmHeader - * \brief Searches within elements parsed with the public dictionary - * and then within the elements parsed with the shadow dictionary - * for the element value representation of a given tag. - * - * Obtaining the VR (Value Representation) might be needed by caller - * to convert the string typed content to caller's native type - * (think of C++ vs Python). The VR is actually of a higher level - * of semantics than just the native C++ type. - * @param tagName name of the searched element. - * @return Corresponding element value representation when it exists, - * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. - */ -std::string gdcmHeader::GetElValRepByName(std::string tagName) { - std::string pub = GetPubElValRepByName(tagName); - return pub; -} - -/** - * \ingroup gdcmHeader - * \brief Searches within elements parsed with the public dictionary - * and then within the elements parsed with the shadow dictionary - * for the element value of a given tag. - * @param group Group of the searched tag. - * @param element Element of the searched tag. - * @return Corresponding element value representation when it exists, - * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. - */ -std::string gdcmHeader::GetElValByNumber(guint16 group, guint16 element) { - std::string pub = GetPubElValByNumber(group, element); - return pub; -} - -/** - * \ingroup gdcmHeader - * \brief Searches within elements parsed with the public dictionary - * and then within the elements parsed with the shadow dictionary - * for the element value representation of a given tag. - * - * Obtaining the VR (Value Representation) might be needed by caller - * to convert the string typed content to caller's native type - * (think of C++ vs Python). The VR is actually of a higher level - * of semantics than just the native C++ type. - * @param group Group of the searched tag. - * @param element Element of the searched tag. - * @return Corresponding element value representation when it exists, - * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. - */ -std::string gdcmHeader::GetElValRepByNumber(guint16 group, guint16 element) { - std::string pub = GetPubElValRepByNumber(group, element); - return pub; -} - -/** - * \ingroup gdcmElValSet - * \brief Sets the value (string) of the target Dicom Element - * @param content string value of the Dicom Element - * @param tagName name of the searched Dicom Element. - * @return true when found - */ -bool gdcmHeader::SetElValueByName(std::string content, - std::string tagName) { - - gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName); - if( dictEntry == NULL) - return false; - - - TagKey key = gdcmDictEntry::TranslateToKey(dictEntry->GetGroup(), - dictEntry->GetElement()); - if ( ! PubElValSet.GetTagHt().count(key)) - return false; - int l = content.length(); - if(l%2) { // Odd length are padded with a space (020H). - l++; - content = content + '\0'; + // use the TS (TS : Transfert Syntax) + std::string transfertSyntax = GetEntryByNumber(0x0002,0x0010); + + if ( transfertSyntax == GDCM_NOTLOADED ) + { + std::cout << "Transfert Syntax not loaded. " << std::endl + << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE" + << std::endl; + return "Uncompressed ACR-NEMA"; } - - //tagHt[key]->SetValue(content); - gdcmElValue * a; - IterHT p; - TagElValueHT::iterator p2; - // DO NOT remove the following lines : they explain the stuff - //p= tagHt.equal_range(key); // get a pair of iterators first-last synonym - //p2=p.first; // iterator on the first synonym - //a=p2->second; // H Table target column (2-nd col) - - // or, easier : - a = ((PubElValSet.GetTagHt().equal_range(key)).first)->second; - - a-> SetValue(content); - - //std::string vr = tagHt[key]->GetVR(); - std::string vr = a->GetVR(); - - guint32 lgr; - if( (vr == "US") || (vr == "SS") ) - lgr = 2; - else if( (vr == "UL") || (vr == "SL") ) - lgr = 4; - else - lgr = l; - //tagHt[key]->SetLength(lgr); - a->SetLength(lgr); - return true; -} - -/** - * \ingroup gdcmHeader - * \brief - * @param exception_on_error - * @return - */ -FILE *gdcmHeader::OpenFile(bool exception_on_error) - throw(gdcmFileError) { - fp=fopen(filename.c_str(),"rb"); - if(exception_on_error) { - if(!fp) - throw gdcmFileError("gdcmHeader::gdcmHeader(const char *, bool)"); - } - - if ( fp ) { - guint16 zero; - fread(&zero, (size_t)2, (size_t)1, fp); - - //ACR -- or DICOM with no Preamble - if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200) - return(fp); - - //DICOM - fseek(fp, 126L, SEEK_CUR); - char dicm[4]; - fread(dicm, (size_t)4, (size_t)1, fp); - if( memcmp(dicm, "DICM", 4) == 0 ) - return(fp); - - fclose(fp); - dbg.Verbose(0, "gdcmHeader::gdcmHeader not DICOM/ACR", filename.c_str()); - } - else { - dbg.Verbose(0, "gdcmHeader::gdcmHeader cannot open file", filename.c_str()); - } - return(NULL); -} - -/** - * \ingroup gdcmHeader - * \brief - * @return TRUE if the close was successfull - */ -bool gdcmHeader::CloseFile(void) { - int closed = fclose(fp); - fp = (FILE *)0; - if (! closed) - return false; - return true; -} - -/** - * \ingroup gdcmHeader - * \brief Parses the header of the file but WITHOUT loading element values. - */ -void gdcmHeader::ParseHeader(bool exception_on_error) throw(gdcmFormatError) { - gdcmElValue * newElValue = (gdcmElValue *)0; - - rewind(fp); - CheckSwap(); - while ( (newElValue = ReadNextElement()) ) { - SkipElementValue(newElValue); - PubElValSet.Add(newElValue); + if ( transfertSyntax == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::GetTransfertSyntaxName:" + " unfound Transfert Syntax (0002,0010)"); + return "Uncompressed ACR-NEMA"; } -} - -/** - * \ingroup gdcmHeader - * \brief - * @return integer, acts as a Boolean - */ -bool gdcmHeader::Write(FILE * fp, FileType type) { - - // TODO : move the following lines (and a lot of others, to be written) - // to a future function CheckAndCorrectHeader - - if (type == ImplicitVR) { - std::string implicitVRTransfertSyntax = "1.2.840.10008.1.2"; - ReplaceOrCreateByNumber(implicitVRTransfertSyntax,0x0002, 0x0010); - - //FIXME Refer to standards on page 21, chapter 6.2 "Value representation": - // values with a VR of UI shall be padded with a single trailing null - // Dans le cas suivant on doit pader manuellement avec un 0 - - PubElValSet.SetElValueLengthByNumber(18, 0x0002, 0x0010); - } - if (type == ExplicitVR) { - std::string explicitVRTransfertSyntax = "1.2.840.10008.1.2.1"; - ReplaceOrCreateByNumber(explicitVRTransfertSyntax,0x0002, 0x0010); - - //FIXME Refer to standards on page 21, chapter 6.2 "Value representation": - // values with a VR of UI shall be padded with a single trailing null - // Dans le cas suivant on doit pader manuellement avec un 0 - - PubElValSet.SetElValueLengthByNumber(20, 0x0002, 0x0010); + while ( ! isdigit(transfertSyntax[transfertSyntax.length()-1]) ) + { + transfertSyntax.erase(transfertSyntax.length()-1, 1); } + // we do it only when we need it + TS* ts = Global::GetTS(); + std::string tsName = ts->GetValue( transfertSyntax ); - return PubElValSet.Write(fp, type); + //delete ts; /// \todo Seg Fault when deleted ?! + return tsName; } /** - * \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 ElValue (0x7fe0, 0x0010) exists ... - sprintf(car,"%d",ImageDataSize); +void Header::SetImageDataSize(size_t ImageDataSize) +{ + ///FIXME I don't understand this code wh ydo we set two times 'car' ? + std::string car = Util::Format("%d", ImageDataSize); - gdcmElValue *a = GetElValueByNumber(0x7fe0, 0x0010); + DocEntry *a = GetDocEntryByNumber(GrPixel, NumPixel); a->SetLength(ImageDataSize); - - ImageDataSize+=8; - sprintf(car,"%d",ImageDataSize); - content1=car; - SetPubElValByNumber(content1, 0x7fe0, 0x0000); -} -/** - * \ingroup gdcmHeader - * \brief Swaps back the bytes of 4-byte long integer accordingly to - * processor order. - * @return The properly swaped 32 bits integer. - */ -guint32 gdcmHeader::SwapLong(guint32 a) { - 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); -} + ImageDataSize += 8; + car = Util::Format("%d", ImageDataSize); -/** - * \ingroup gdcmHeader - * \brief Swaps the bytes so they agree with the processor order - * @return The properly swaped 16 bits integer. - */ -guint16 gdcmHeader::SwapShort(guint16 a) { - if ( (sw==4321) || (sw==2143) ) - a =(((a<<8) & 0x0ff00) | ((a>>8)&0x00ff)); - return (a); + SetEntryByNumber(car, GrPixel, NumPixel); } //----------------------------------------------------------------------------- // Protected -/** - * \ingroup gdcmHeader - * \brief - * - * @return - */ -gdcmElValue* gdcmHeader::GetElValueByNumber(guint16 Group, guint16 Elem) { - - gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem); - if (!elValue) { - dbg.Verbose(1, "gdcmHeader::GetElValueByNumber", - "failed to Locate gdcmElValue"); - return (gdcmElValue*)0; - } - return elValue; -} - -/** - * \ingroup gdcmHeader - * \brief Checks if a given ElValue (group,number) - * \ exists in the Public ElValSet - * @param Group - * @param Elem - * @return integer acts as a boolean - */ -bool gdcmHeader::CheckIfExistByNumber(guint16 Group, guint16 Elem ) { - return (PubElValSet.CheckIfExistByNumber(Group, Elem)>0); -} - -/** - * \ingroup gdcmHeader - * \brief Gets (from Header) the offset of a 'non string' element value - * \ (LoadElementValue has already be executed) - * @param Group - * @param Elem - * @return File Offset of the Element Value - */ -size_t gdcmHeader::GetPubElValOffsetByNumber(guint16 Group, guint16 Elem) { - gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem); - if (!elValue) { - dbg.Verbose(1, "gdcmHeader::GetElValueByNumber", - "failed to Locate gdcmElValue"); - return (size_t)0; - } - return elValue->GetOffset(); -} - -/** - * \ingroup gdcmHeader - * \brief Gets (from Header) a 'non string' element value - * \ (LoadElementValue has already be executed) - * @param Group - * @param Elem - * @return Pointer to the 'non string' area - */ -void * gdcmHeader::GetPubElValVoidAreaByNumber(guint16 Group, guint16 Elem) { - gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem); - if (!elValue) { - dbg.Verbose(1, "gdcmHeader::GetElValueByNumber", - "failed to Locate gdcmElValue"); - return (NULL); - } - return elValue->GetVoidArea(); -} - -/** - * \ingroup gdcmHeader - * \brief Loads (from disk) the element content - * when a string is not suitable - */ -void * gdcmHeader::LoadElementVoidArea(guint16 Group, guint16 Elem) { - gdcmElValue * Element= PubElValSet.GetElementByNumber(Group, Elem); - if ( !Element ) - return NULL; - size_t o =(size_t)Element->GetOffset(); - fseek(fp, o, SEEK_SET); - int l=Element->GetLength(); - void * a = malloc(l); - if(!a) { - return NULL; - } - /* int res = */ PubElValSet.SetVoidAreaByNumber(a, Group, Elem); - // TODO check the result - size_t l2 = fread(a, 1, l ,fp); - if(l != l2) { - free(a); - return NULL; - } - return a; -} - -/** - * \ingroup gdcmHeader - * \brief TODO - * @param Value - * @param Group - * @param Elem - * \return integer acts as a boolean - */ -bool gdcmHeader::ReplaceOrCreateByNumber(std::string Value, - guint16 Group, guint16 Elem ) { - // TODO : FIXME JPRx - // curieux, non ? - // on (je) cree une Elvalue ne contenant pas de valeur - // on l'ajoute au ElValSet - // on affecte une valeur a cette ElValue a l'interieur du ElValSet - // --> devrait pouvoir etre fait + simplement ??? - if (CheckIfExistByNumber(Group, Elem) == 0) { - gdcmElValue* a =NewElValueByNumber(Group, Elem); - if (a == NULL) - return false; - PubElValSet.Add(a); - } - PubElValSet.SetElValueByNumber(Value, Group, Elem); - return(true); -} - -/** - * \ingroup gdcmHeader - * \brief Modify (or Creates if not found) an element - * @param Value new value - * @param Group - * @param Elem - * \return integer acts as a boolean - * - */ -bool gdcmHeader::ReplaceOrCreateByNumber(char* Value, guint16 Group, guint16 Elem ) { - - gdcmElValue* nvElValue=NewElValueByNumber(Group, Elem); - // TODO : check if fails - PubElValSet.Add(nvElValue); - std::string v = Value; - PubElValSet.SetElValueByNumber(v, Group, Elem); - return(true); -} - -/** - * \ingroup gdcmHeader - * \brief Set a new value if the invoked element exists - * Seems to be useless !!! - * @param Value - * @param Group - * @param Elem - * \return integer acts as a boolean - */ -bool gdcmHeader::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 Elem ) { - - //gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem); - std::string v = Value; - PubElValSet.SetElValueByNumber(v, Group, Elem); - return true; -} - -//----------------------------------------------------------------------------- -// Private -/** - * \ingroup gdcmHeader - * \brief Loads the element values of all the elements present in the - * public tag based hash table. - */ -void gdcmHeader::LoadElements(void) { - rewind(fp); - - // We don't use any longer the HashTable, since a lot a stuff is missing - // when SeQuences were encountered - // - //TagElValueHT ht = PubElValSet.GetTagHt(); - //for (TagElValueHT::iterator tag = ht.begin(); tag != ht.end(); ++tag) { - // LoadElementValue(tag->second); - //} - - for (ListTag::iterator i = GetPubListElem().begin(); - i != GetPubListElem().end(); - ++i){ - LoadElementValue(*i); - } - - rewind(fp); - - // Load 'non string' values - std::string PhotometricInterpretation = GetPubElValByNumber(0x0028,0x0004); - if( PhotometricInterpretation == "PALETTE COLOR " ){ - LoadElementVoidArea(0x0028,0x1200); // gray LUT - LoadElementVoidArea(0x0028,0x1201); // R LUT - LoadElementVoidArea(0x0028,0x1202); // G LUT - LoadElementVoidArea(0x0028,0x1203); // B LUT - - LoadElementVoidArea(0x0028,0x1221); // Segmented Red Palette Color LUT Data - LoadElementVoidArea(0x0028,0x1222); // Segmented Green Palette Color LUT Data - LoadElementVoidArea(0x0028,0x1223); // Segmented Blue Palette Color LUT Data - } - - // -------------------------------------------------------------- - // Special Patch to allow gdcm to read ACR-LibIDO formated images - // - // if recognition code tells us we deal with a LibIDO image - // we switch lineNumber and columnNumber - // - std::string RecCode; - RecCode = GetPubElValByNumber(0x0008, 0x0010); - if (RecCode == "ACRNEMA_LIBIDO_1.1" || - RecCode == "CANRME_AILIBOD1_1." ) { - filetype = ACR_LIBIDO; - std::string rows = GetPubElValByNumber(0x0028, 0x0010); - std::string columns = GetPubElValByNumber(0x0028, 0x0011); - SetPubElValByNumber(columns, 0x0028, 0x0010); - SetPubElValByNumber(rows , 0x0028, 0x0011); - } - // ----------------- End of Special Patch ---------------- -} - -/** - * \ingroup gdcmHeader - * \brief Loads the element content if it's length is not bigger - * than the value specified with - * gdcmHeader::SetMaxSizeLoadElementValue() - * @param ElVal string value of the Dicom Element - */ -void gdcmHeader::LoadElementValue(gdcmElValue * ElVal) { - size_t item_read; - guint16 group = ElVal->GetGroup(); - std::string vr= ElVal->GetVR(); - guint32 length = ElVal->GetLength(); - bool SkipLoad = false; - - fseek(fp, (long)ElVal->GetOffset(), SEEK_SET); - - // the test was commented out to 'go inside' the SeQuences - // we don't any longer skip them ! - - // if( vr == "SQ" ) - // SkipLoad = true; - - // A SeQuence "contains" a set of Elements. - // (fffe e000) tells us an Element is beginning - // (fffe e00d) tells us an Element just ended - // (fffe e0dd) tells us the current SeQuence just ended - if( group == 0xfffe ) - SkipLoad = true; - - if ( SkipLoad ) { - ElVal->SetLength(0); - ElVal->SetValue("gdcm::Skipped"); - return; - } - - // When the length is zero things are easy: - if ( length == 0 ) { - ElVal->SetValue(""); - return; - } - - // The elements whose length is bigger than the specified upper bound - // are not loaded. Instead we leave a short notice of the offset of - // the element content and it's length. - if (length > MaxSizeLoadElementValue) { - std::ostringstream s; - s << "gdcm::NotLoaded."; - s << " Address:" << (long)ElVal->GetOffset(); - s << " Length:" << ElVal->GetLength(); - s << " x(" << std::hex << ElVal->GetLength() << ")"; - ElVal->SetValue(s.str()); - return; - } - - // When an integer is expected, read and convert the following two or - // four bytes properly i.e. as an integer as opposed to a string. - - // Actually, elements with Value Multiplicity > 1 - // contain a set of integers (not a single one) - // Any compacter code suggested (?) - if ( IsAnInteger(ElVal) ) { - guint32 NewInt; - std::ostringstream s; - int nbInt; - if (vr == "US" || vr == "SS") { - nbInt = length / 2; - NewInt = ReadInt16(); - s << NewInt; - if (nbInt > 1) { - for (int i=1; i < nbInt; i++) { - s << '\\'; - NewInt = ReadInt16(); - s << NewInt; - } - } - - } else if (vr == "UL" || vr == "SL") { - nbInt = length / 4; - NewInt = ReadInt32(); - s << NewInt; - if (nbInt > 1) { - for (int i=1; i < nbInt; i++) { - s << '\\'; - NewInt = ReadInt32(); - s << NewInt; - } - } - } -#ifdef GDCM_NO_ANSI_STRING_STREAM - s << std::ends; // to avoid oddities on Solaris -#endif //GDCM_NO_ANSI_STRING_STREAM - ElVal->SetValue(s.str()); - return; - } - - // We need an additional byte for storing \0 that is not on disk - char* NewValue = (char*)malloc(length+1); - if( !NewValue) { - dbg.Verbose(1, "LoadElementValue: Failed to allocate NewValue"); - return; - } - NewValue[length]= 0; - - item_read = fread(NewValue, (size_t)length, (size_t)1, fp); - if ( item_read != 1 ) { - free(NewValue); - dbg.Verbose(1, "gdcmHeader::LoadElementValue","unread element value"); - ElVal->SetValue("gdcm::UnRead"); - return; - } - ElVal->SetValue(NewValue); - free(NewValue); -} - -/** - * \ingroup gdcmHeader - * \brief Loads the element while preserving the current - * underlying file position indicator as opposed to - * to LoadElementValue that modifies it. - * @param ElVal Element whose value shall be loaded. - * @return - */ -void gdcmHeader::LoadElementValueSafe(gdcmElValue * ElVal) { - long PositionOnEntry = ftell(fp); - LoadElementValue(ElVal); - fseek(fp, PositionOnEntry, SEEK_SET); -} - -/** - * \ingroup gdcmHeader - * \brief - * - * @return - */ - void gdcmHeader::FindLength (gdcmElValue * ElVal) { - guint16 element = ElVal->GetElement(); - guint16 group = ElVal->GetGroup(); - std::string vr = ElVal->GetVR(); - guint16 length16; - if( (element == 0x0010) && (group == 0x7fe0) ) { - dbg.SetDebug(-1); - dbg.Verbose(2, "gdcmHeader::FindLength: ", - "we reached 7fe0 0010"); - } - - if ( (filetype == ExplicitVR) && ! ElVal->IsImplicitVr() ) { - if ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") ) { - - // The following reserved two bytes (see PS 3.5-2001, section - // 7.1.2 Data element structure with explicit vr p27) must be - // skipped before proceeding on reading the length on 4 bytes. - fseek(fp, 2L, SEEK_CUR); - - guint32 length32 = ReadInt32(); - - if ( (vr == "OB") && (length32 == 0xffffffff) ) { - ElVal->SetLength(FindLengthOB()); - return; - } - FixFoundLength(ElVal, length32); - return; - } - - // Length is encoded on 2 bytes. - length16 = ReadInt16(); - - // We can tell the current file is encoded in big endian (like - // Data/US-RGB-8-epicard) when we find the "Transfer Syntax" tag - // and it's value is the one of the encoding of a big endian file. - // In order to deal with such big endian encoded files, we have - // (at least) two strategies: - // * when we load the "Transfer Syntax" tag with value of big endian - // encoding, we raise the proper flags. Then we wait for the end - // of the META group (0x0002) among which is "Transfer Syntax", - // before switching the swap code to big endian. We have to postpone - // the switching of the swap code since the META group is fully encoded - // in little endian, and big endian coding only starts at the next - // group. The corresponding code can be hard to analyse and adds - // many additional unnecessary tests for regular tags. - // * the second strategy consists in waiting for trouble, that shall - // appear when we find the first group with big endian encoding. This - // is easy to detect since the length of a "Group Length" tag (the - // ones with zero as element number) has to be of 4 (0x0004). When we - // encounter 1024 (0x0400) chances are the encoding changed and we - // found a group with big endian encoding. - // We shall use this second strategy. In order to make sure that we - // can interpret the presence of an apparently big endian encoded - // length of a "Group Length" without committing a big mistake, we - // add an additional check: we look in the already parsed elements - // for the presence of a "Transfer Syntax" whose value has to be "big - // endian encoding". When this is the case, chances are we have got our - // hands on a big endian encoded file: we switch the swap code to - // big endian and proceed... - if ( (element == 0x0000) && (length16 == 0x0400) ) { - if ( ! IsExplicitVRBigEndianTransferSyntax() ) { - dbg.Verbose(0, "gdcmHeader::FindLength", "not explicit VR"); - errno = 1; - return; - } - length16 = 4; - SwitchSwapToBigEndian(); - // Restore the unproperly loaded values i.e. the group, the element - // and the dictionary entry depending on them. - guint16 CorrectGroup = SwapShort(ElVal->GetGroup()); - guint16 CorrectElem = SwapShort(ElVal->GetElement()); - gdcmDictEntry * NewTag = GetDictEntryByNumber(CorrectGroup, - CorrectElem); - if (!NewTag) { - // This correct tag is not in the dictionary. Create a new one. - NewTag = new gdcmDictEntry(CorrectGroup, CorrectElem); - } - // FIXME this can create a memory leaks on the old entry that be - // left unreferenced. - ElVal->SetDictEntry(NewTag); - } - - // Heuristic: well some files are really ill-formed. - if ( length16 == 0xffff) { - length16 = 0; - //dbg.Verbose(0, "gdcmHeader::FindLength", - // "Erroneous element length fixed."); - // Actually, length= 0xffff means that we deal with - // Unknown Sequence Length - } - - FixFoundLength(ElVal, (guint32)length16); - return; - } - - // Either implicit VR or a non DICOM conformal (see not below) explicit - // VR that ommited the VR of (at least) this element. Farts happen. - // [Note: according to the part 5, PS 3.5-2001, section 7.1 p25 - // on Data elements "Implicit and Explicit VR Data Elements shall - // not coexist in a Data Set and Data Sets nested within it".] - // Length is on 4 bytes. - FixFoundLength(ElVal, ReadInt32()); - return; -} - -/** - * \ingroup gdcmHeader - * \brief Find the value representation of the current tag. - * @param ElVal - */ -void gdcmHeader::FindVR( gdcmElValue *ElVal) { - if (filetype != ExplicitVR) - return; - - char VR[3]; - std::string vr; - int lgrLue; - char msg[100]; // for sprintf. Sorry - - long PositionOnEntry = ftell(fp); - // Warning: we believe this is explicit VR (Value Representation) because - // we used a heuristic that found "UL" in the first tag. Alas this - // doesn't guarantee that all the tags will be in explicit VR. In some - // cases (see e-film filtered files) one finds implicit VR tags mixed - // within an explicit VR file. Hence we make sure the present tag - // is in explicit VR and try to fix things if it happens not to be - // the case. - bool RealExplicit = true; - - lgrLue=fread (&VR, (size_t)2,(size_t)1, fp); - VR[2]=0; - vr = std::string(VR); - - // Assume we are reading a falsely explicit VR file i.e. we reached - // a tag where we expect reading a VR but are in fact we read the - // first to bytes of the length. Then we will interogate (through find) - // the dicom_vr dictionary with oddities like "\004\0" which crashes - // both GCC and VC++ implementations of the STL map. Hence when the - // expected VR read happens to be non-ascii characters we consider - // we hit falsely explicit VR tag. - - if ( (!isalpha(VR[0])) && (!isalpha(VR[1])) ) - RealExplicit = false; - - // CLEANME searching the dicom_vr at each occurence is expensive. - // PostPone this test in an optional integrity check at the end - // of parsing or only in debug mode. - if ( RealExplicit && !dicom_vr->Count(vr) ) - RealExplicit= false; - - if ( RealExplicit ) { - if ( ElVal->IsVRUnknown() ) { - // When not a dictionary entry, we can safely overwrite the vr. - ElVal->SetVR(vr); - return; - } - if ( ElVal->GetVR() == vr ) { - // The vr we just read and the dictionary agree. Nothing to do. - return; - } - // The vr present in the file and the dictionary disagree. We assume - // the file writer knew best and use the vr of the file. Since it would - // be unwise to overwrite the vr of a dictionary (since it would - // compromise it's next user), we need to clone the actual DictEntry - // and change the vr for the read one. - gdcmDictEntry* NewTag = new gdcmDictEntry(ElVal->GetGroup(), - ElVal->GetElement(), - vr, - "FIXME", - ElVal->GetName()); - ElVal->SetDictEntry(NewTag); - return; - } - - // We thought this was explicit VR, but we end up with an - // implicit VR tag. Let's backtrack. - - sprintf(msg,"Falsely explicit vr file (%04x,%04x)\n", - ElVal->GetGroup(),ElVal->GetElement()); - dbg.Verbose(1, "gdcmHeader::FindVR: ",msg); - - fseek(fp, PositionOnEntry, SEEK_SET); - // When this element is known in the dictionary we shall use, e.g. for - // the semantics (see the usage of IsAnInteger), the vr proposed by the - // dictionary entry. Still we have to flag the element as implicit since - // we know now our assumption on expliciteness is not furfilled. - // avoid . - if ( ElVal->IsVRUnknown() ) - ElVal->SetVR("Implicit"); - ElVal->SetImplicitVr(); -} /** - * \ingroup gdcmHeader - * \brief - * - * @return + * \brief anonymize a Header (removes Patient's personal info) + * (read the code to see which ones ...) */ - guint32 gdcmHeader::FindLengthOB(void) { - // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data. - guint16 g; - guint16 n; - long PositionOnEntry = ftell(fp); - bool FoundSequenceDelimiter = false; - guint32 TotalLength = 0; - guint32 ItemLength; - - while ( ! FoundSequenceDelimiter) { - g = ReadInt16(); - n = ReadInt16(); - if (errno == 1) - return 0; - TotalLength += 4; // We even have to decount the group and element - - if ( g != 0xfffe && g!=0xb00c ) /*for bogus header */ { - char msg[100]; // for sprintf. Sorry - sprintf(msg,"wrong group (%04x) for an item sequence (%04x,%04x)\n",g, g,n); - dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",msg); - errno = 1; - return 0; - } - if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) /* for bogus header */ - FoundSequenceDelimiter = true; - else if ( n != 0xe000 ){ - char msg[100]; // for sprintf. Sorry - sprintf(msg,"wrong element (%04x) for an item sequence (%04x,%04x)\n", - n, g,n); - dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",msg); - errno = 1; - return 0; - } - ItemLength = ReadInt32(); - TotalLength += ItemLength + 4; // We add 4 bytes since we just read - // the ItemLength with ReadInt32 - SkipBytes(ItemLength); - } - fseek(fp, PositionOnEntry, SEEK_SET); - return TotalLength; -} - -/** - * \ingroup gdcmHeader - * \brief - * @param ElVal - * @return - */ -void gdcmHeader::SkipElementValue(gdcmElValue * ElVal) { - SkipBytes(ElVal->GetLength()); -} - -/** - * \ingroup gdcmHeader - * \brief When the length of an element value is obviously wrong (because - * the parser went Jabberwocky) one can hope improving things by - * applying this heuristic. - */ -void gdcmHeader::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { +bool Header::AnonymizeHeader() +{ + // If exist, replace by spaces + SetEntryByNumber (" ",0x0010, 0x2154); // Telephone + SetEntryByNumber (" ",0x0010, 0x1040); // Adress + SetEntryByNumber (" ",0x0010, 0x0020); // Patient ID - ElVal->SetReadLength(FoundLength); // will be updated only if a bug is found - - if ( FoundLength == 0xffffffff) { - FoundLength = 0; - } - - // Sorry for the patch! - // XMedCom did the trick to read some nasty GE images ... - else if (FoundLength == 13) { - // The following 'if' will be removed when there is no more - // images on Creatis HDs with a 13 length for Manufacturer... - if ( (ElVal->GetGroup() != 0x0008) || - ( (ElVal->GetElement() != 0x0070) && (ElVal->GetElement() != 0x0080) ) ) { - // end of remove area - FoundLength =10; - ElVal->SetReadLength(10); // a bug is to be fixed + DocEntry* 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); } - } - // to fix some garbage 'Leonardo' Siemens images - // May be commented out to avoid overhead - else if ( (ElVal->GetGroup() == 0x0009) && - ( (ElVal->GetElement() == 0x1113) || (ElVal->GetElement() == 0x1114) ) ){ - FoundLength =4; - ElVal->SetReadLength(4); // a bug is to be fixed - } - // end of fix - - // to try to 'go inside' SeQuences (with length), and not to skip them - else if ( ElVal->GetVR() == "SQ") { - if (enableSequences) // only if the user does want to ! - FoundLength =0; - } - - ElVal->SetUsableLength(FoundLength); -} - -/** - * \ingroup gdcmHeader - * \brief Apply some heuristics to predict wether the considered - * element value contains/represents an integer or not. - * @param ElVal The element value on which to apply the predicate. - * @return The result of the heuristical predicate. - */ -bool gdcmHeader::IsAnInteger(gdcmElValue * ElVal) { - guint16 element = ElVal->GetElement(); - guint16 group = ElVal->GetGroup(); - std::string vr = ElVal->GetVR(); - guint32 length = ElVal->GetLength(); - - // When we have some semantics on the element we just read, and if we - // a priori know we are dealing with an integer, then we shall be - // able to swap it's element value properly. - if ( element == 0 ) { // This is the group length of the group - if (length == 4) - return true; - else { - std::ostringstream s; - s << "Erroneous Group Length element length on :" \ - << std::hex << group << " , " << element; - dbg.Error("gdcmHeader::IsAnInteger", - s.str().c_str()); + else + { + ReplaceOrCreateByNumber(std::string("anonymised"), 0x0010, 0x0010); } } - if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") ) - return true; - - return false; -} -/** - * \ingroup gdcmHeader - * \brief Reads a supposed to be 16 Bits integer - * \ (swaps it depending on processor endianity) - * - * @return integer acts as a boolean - */ -guint16 gdcmHeader::ReadInt16(void) { - guint16 g; - size_t item_read; - item_read = fread (&g, (size_t)2,(size_t)1, fp); - if ( item_read != 1 ) { - // dbg.Verbose(0, "gdcmHeader::ReadInt16", " Failed to read :"); - // if(feof(fp)) - // dbg.Verbose(0, "gdcmHeader::ReadInt16", " End of File encountered"); - if(ferror(fp)) - dbg.Verbose(0, "gdcmHeader::ReadInt16", " File Error"); - errno = 1; - return 0; - } - errno = 0; - g = SwapShort(g); - return g; -} - -/** - * \ingroup gdcmHeader - * \brief Reads a supposed to be 32 Bits integer - * \ (swaps it depending on processor endianity) - * - * @return - */ -guint32 gdcmHeader::ReadInt32(void) { - guint32 g; - size_t item_read; - item_read = fread (&g, (size_t)4,(size_t)1, fp); - if ( item_read != 1 ) { - //dbg.Verbose(0, "gdcmHeader::ReadInt32", " Failed to read :"); - //if(feof(fp)) - // dbg.Verbose(0, "gdcmHeader::ReadInt32", " End of File encountered"); - if(ferror(fp)) - dbg.Verbose(0, "gdcmHeader::ReadInt32", " File Error"); - errno = 1; - return 0; - } - errno = 0; - g = SwapLong(g); - return g; -} + // 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 -/** - * \ingroup gdcmHeader - * \brief - * - * @return - */ -void gdcmHeader::SkipBytes(guint32 NBytes) { - //FIXME don't dump the returned value - (void)fseek(fp, (long)NBytes, SEEK_CUR); -} - -/** - * \ingroup gdcmHeader - * \brief - */ -void gdcmHeader::Initialise(void) { - dicom_vr = gdcmGlobal::GetVR(); - dicom_ts = gdcmGlobal::GetTS(); - Dicts = gdcmGlobal::GetDicts(); - RefPubDict = Dicts->GetDefaultPubDict(); - RefShaDict = (gdcmDict*)0; + return true; } /** - * \ingroup gdcmHeader - * \brief Discover what the swap code is (among little endian, big endian, - * bad little endian, bad big endian). - * - */ -void gdcmHeader::CheckSwap() + * \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 Header::GetImageOrientationPatient( float iop[6] ) { - // Fourth semantics: - // - // ---> Warning : This fourth field is NOT part - // of the 'official' Dicom Dictionnary - // and should NOT be used. - // (Not defined for all the groups - // may be removed in a future release) - // - // CMD Command - // META Meta Information - // DIR Directory - // ID - // PAT Patient - // ACQ Acquisition - // REL Related - // IMG Image - // SDY Study - // VIS Visit - // WAV Waveform - // PRC - // DEV Device - // NMI Nuclear Medicine - // MED - // BFS Basic Film Session - // BFB Basic Film Box - // BIB Basic Image Box - // BAB - // IOB - // PJ - // PRINTER - // RT Radio Therapy - // DVH - // SSET - // RES Results - // CRV Curve - // OLY Overlays - // PXL Pixels - // DL Delimiters - // - - // The only guaranted way of finding the swap code is to find a - // group tag since we know it's length has to be of four bytes i.e. - // 0x00000004. Finding the swap code in then straigthforward. Trouble - // occurs when we can't find such group... - guint32 s; - guint32 x=4; // x : for ntohs - bool net2host; // true when HostByteOrder is the same as NetworkByteOrder - - int lgrLue; - char * entCur; - char deb[HEADER_LENGTH_TO_READ]; - - // First, compare HostByteOrder and NetworkByteOrder in order to - // determine if we shall need to swap bytes (i.e. the Endian type). - if (x==ntohs(x)) - net2host = true; - else - net2host = false; - //cout << net2host << endl; - - // The easiest case is the one of a DICOM header, since it possesses a - // file preamble where it suffice to look for the string "DICM". - lgrLue = fread(deb, 1, HEADER_LENGTH_TO_READ, fp); - - entCur = deb + 128; - if(memcmp(entCur, "DICM", (size_t)4) == 0) { - dbg.Verbose(1, "gdcmHeader::CheckSwap:", "looks like DICOM Version3"); - // Next, determine the value representation (VR). Let's skip to the - // first element (0002, 0000) and check there if we find "UL" - // - or "OB" if the 1st one is (0002,0001) -, - // 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),or (0002, 0001) - // i.e. a total of 136 bytes. - entCur = deb + 136; - // FIXME - // Use gdcmHeader::dicom_vr to test all the possibilities - // instead of just checking for UL, OB and UI !? - if( (memcmp(entCur, "UL", (size_t)2) == 0) || - (memcmp(entCur, "OB", (size_t)2) == 0) || - (memcmp(entCur, "UI", (size_t)2) == 0) ) + 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 ) { - filetype = ExplicitVR; - dbg.Verbose(1, "gdcmHeader::CheckSwap:", - "explicit Value Representation"); - } else { - filetype = ImplicitVR; - dbg.Verbose(1, "gdcmHeader::CheckSwap:", - "not an explicit Value Representation"); + dbg.Verbose(0, "Header::GetImageOrientationPatient: " + "wrong Image Orientation Patient (0020,0037)"); } - if (net2host) { - sw = 4321; - dbg.Verbose(1, "gdcmHeader::CheckSwap:", - "HostByteOrder != NetworkByteOrder"); - } else { - sw = 0; - dbg.Verbose(1, "gdcmHeader::CheckSwap:", - "HostByteOrder = NetworkByteOrder"); + } + //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, "Header::GetImageOrientationPatient: " + "wrong Image Orientation Patient (0020,0035)"); } - - // 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 DicomV3 - - // Alas, this is not a DicomV3 file and whatever happens there is no file - // preamble. We can reset the file position indicator to where the data - // is (i.e. the beginning of the file). - dbg.Verbose(1, "gdcmHeader::CheckSwap:", "not a DICOM Version3 file"); - rewind(fp); - - // Our next best chance would be to be considering a 'clean' ACR/NEMA file. - // 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; - // We assume the array of char we are considering contains the binary - // representation of a 32 bits integer. Hence the following dirty - // trick : - s = *((guint32 *)(entCur)); - - switch (s) { - case 0x00040000 : - sw = 3412; - filetype = ACR; - return; - case 0x04000000 : - sw = 4321; - filetype = ACR; - return; - case 0x00000400 : - sw = 2143; - filetype = ACR; - return; - case 0x00000004 : - sw = 0; - filetype = ACR; - return; - default : - dbg.Verbose(0, "gdcmHeader::CheckSwap:", - "ACR/NEMA unfound swap info (time to raise bets)"); - } - - // We are out of luck. It is not a DicomV3 nor a 'clean' ACR/NEMA file. - // It is time for despaired wild guesses. So, let's assume this file - // happens to be 'dirty' ACR/NEMA, i.e. the length of the group is - // not present. Then the only info we have is the net2host one. - filetype = Unknown; - if (! net2host ) - sw = 0; - else - sw = 4321; - return; -} - -/** - * \ingroup gdcmHeader - * \brief - */ -void gdcmHeader::SwitchSwapToBigEndian(void) { - dbg.Verbose(1, "gdcmHeader::SwitchSwapToBigEndian", - "Switching to BigEndian mode."); - if ( sw == 0 ) { - sw = 4321; - return; - } - if ( sw == 4321 ) { - sw = 0; - return; - } - if ( sw == 3412 ) { - sw = 2143; - return; - } - if ( sw == 2143 ) - sw = 3412; -} - -/** - * \ingroup gdcmHeader - * \brief - * @param NewSize - * @return - */ -void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) { - if (NewSize < 0) - return; - if ((guint32)NewSize >= (guint32)0xffffffff) { - MaxSizeLoadElementValue = 0xffffffff; - return; - } - MaxSizeLoadElementValue = NewSize; -} - -/** - * \ingroup gdcmHeader - * \brief Searches both the public and the shadow dictionary (when they - * exist) for the presence of the DictEntry with given - * group and element. The public dictionary has precedence on the - * shadow one. - * @param group group of the searched DictEntry - * @param element element of the searched DictEntry - * @return Corresponding DictEntry when it exists, NULL otherwise. - */ -gdcmDictEntry * gdcmHeader::GetDictEntryByNumber(guint16 group, - guint16 element) { - gdcmDictEntry * found = (gdcmDictEntry*)0; - if (!RefPubDict && !RefShaDict) { - dbg.Verbose(0, "gdcmHeader::GetDictEntry", - "we SHOULD have a default dictionary"); - } - if (RefPubDict) { - found = RefPubDict->GetTagByNumber(group, element); - if (found) - return found; - } - if (RefShaDict) { - found = RefShaDict->GetTagByNumber(group, element); - if (found) - return found; - } - return found; -} - -/** - * \ingroup gdcmHeader - * \brief Searches both the public and the shadow dictionary (when they - * exist) for the presence of the DictEntry with given name. - * The public dictionary has precedence on the shadow one. - * @param Name name of the searched DictEntry - * @return Corresponding DictEntry when it exists, NULL otherwise. - */ -gdcmDictEntry * gdcmHeader::GetDictEntryByName(std::string Name) { - gdcmDictEntry * found = (gdcmDictEntry*)0; - if (!RefPubDict && !RefShaDict) { - dbg.Verbose(0, "gdcmHeader::GetDictEntry", - "we SHOULD have a default dictionary"); - } - if (RefPubDict) { - found = RefPubDict->GetTagByName(Name); - if (found) - return found; - } - if (RefShaDict) { - found = RefShaDict->GetTagByName(Name); - if (found) - return found; - } - return found; -} - -/** - * \ingroup gdcmHeader - * \brief Read the next tag but WITHOUT loading it's value - * @return On succes the newly created ElValue, NULL on failure. - */ -gdcmElValue * gdcmHeader::ReadNextElement(void) { - - guint16 g,n; - gdcmElValue * NewElVal; - - g = ReadInt16(); - n = ReadInt16(); - - if (errno == 1) - // We reached the EOF (or an error occured) and header parsing - // has to be considered as finished. - return (gdcmElValue *)0; - - NewElVal = NewElValueByNumber(g, n); - FindVR(NewElVal); - FindLength(NewElVal); - - if (errno == 1) { - // Call it quits - return (gdcmElValue *)0; - } - NewElVal->SetOffset(ftell(fp)); - //if ( (g==0x7fe0) && (n==0x0010) ) - return NewElVal; -} - -/** - * \ingroup gdcmHeader - * \brief Build a new Element Value from all the low level arguments. - * Check for existence of dictionary entry, and build - * a default one when absent. - * @param Name Name of the underlying DictEntry - */ -gdcmElValue* gdcmHeader::NewElValueByName(std::string Name) { - - gdcmDictEntry * NewTag = GetDictEntryByName(Name); - if (!NewTag) - NewTag = new gdcmDictEntry(0xffff, 0xffff, "LO", "Unknown", Name); - - gdcmElValue* NewElVal = new gdcmElValue(NewTag); - if (!NewElVal) { - dbg.Verbose(1, "gdcmHeader::ObtainElValueByName", - "failed to allocate gdcmElValue"); - return (gdcmElValue*)0; } - return NewElVal; -} - -/** - * \ingroup gdcmHeader - * \brief Build a new Element Value from all the low level arguments. - * Check for existence of dictionary entry, and build - * a default one when absent. - * @param Group group of the underlying DictEntry - * @param Elem element of the underlying DictEntry - */ -gdcmElValue* gdcmHeader::NewElValueByNumber(guint16 Group, guint16 Elem) { - // Find out if the tag we encountered is in the dictionaries: - gdcmDictEntry * NewTag = GetDictEntryByNumber(Group, Elem); - if (!NewTag) - NewTag = new gdcmDictEntry(Group, Elem); - - gdcmElValue* NewElVal = new gdcmElValue(NewTag); - if (!NewElVal) { - dbg.Verbose(1, "gdcmHeader::NewElValueByNumber", - "failed to allocate gdcmElValue"); - return (gdcmElValue*)0; - } - return NewElVal; -} - -/** - * \ingroup gdcmHeader - * \brief Searches within the public dictionary for a Dicom Element of - * a given tag. - * @param tagName name of the searched Dicom Element. - * @return Corresponding Dicom Element when it exists, and NULL - * otherwise. - */ - gdcmElValue* gdcmHeader::GetElementByName(std::string tagName) { - gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName); - if( dictEntry == NULL) - return (gdcmElValue*)NULL; - return(PubElValSet.GetElementByNumber(dictEntry->GetGroup(), - dictEntry->GetElement())); } -/** - * \ingroup gdcmHeader - * \brief Small utility function that creates a new manually crafted - * (as opposed as read from the file) gdcmElValue with user - * specified name and adds it to the public tag hash table. - * \note A fake TagKey is generated so the PubDict can keep it's coherence. - * @param NewTagName The name to be given to this new tag. - * @param VR The Value Representation to be given to this new tag. - * @ return The newly hand crafted Element Value. - */ -gdcmElValue* gdcmHeader::NewManualElValToPubDict(std::string NewTagName, - std::string VR) { - gdcmElValue* NewElVal = (gdcmElValue*)0; - guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info - guint32 FreeElem = 0; - gdcmDictEntry* NewEntry = (gdcmDictEntry*)0; - - FreeElem = PubElValSet.GenerateFreeTagKeyInGroup(StuffGroup); - if (FreeElem == UINT32_MAX) { - dbg.Verbose(1, "gdcmHeader::NewManualElValToPubDict", - "Group 0xffff in Public Dict is full"); - return (gdcmElValue*)0; - } - NewEntry = new gdcmDictEntry(StuffGroup, FreeElem, - VR, "GDCM", NewTagName); - NewElVal = new gdcmElValue(NewEntry); - PubElValSet.Add(NewElVal); - return NewElVal; -} +//----------------------------------------------------------------------------- +// Private //----------------------------------------------------------------------------- + +} // end namespace gdcm