X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=b6801f8b88955802c6ee3ac9e19aa0aee749e7ef;hb=1d69b92978803204089d270599133917d944c651;hp=5e01a8f37ecdc30f4a940207709bfb3ac9fd108c;hpb=4c8c80589b3770976ea27fc03b290b97db5da3e6;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index 5e01a8f3..b6801f8b 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -3,12 +3,12 @@ Program: gdcm Module: $RCSfile: gdcmHeader.cxx,v $ Language: C++ - Date: $Date: 2004/07/30 11:40:13 $ - Version: $Revision: 1.179 $ + 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.htm for details. + 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 @@ -25,21 +25,17 @@ #include +namespace gdcm +{ + //----------------------------------------------------------------------------- // Constructor / Destructor /** * \brief Constructor * @param filename name of the file whose header we want to analyze - * @param exception_on_error whether we want to throw an exception or not - * @param ignore_shadow = true if user wants to skip shadow groups - * during parsing, to save memory space */ -gdcmHeader::gdcmHeader( std::string const & filename, - bool exception_on_error, - bool ignore_shadow ): - gdcmDocument( filename, - exception_on_error, - ignore_shadow ) +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 @@ -49,8 +45,7 @@ gdcmHeader::gdcmHeader( std::string const & filename, // Inside the group pointed by "Image Location" the searched element // is conventionally the element 0x0010 (when the norm is respected). // When the "Image Location" is absent we default to group 0x7fe0. - - // This IS the right place for the code + // Note: this IS the right place for the code // Image Location std::string imgLocation = GetEntryByNumber(0x0028, 0x0200); @@ -85,18 +80,16 @@ gdcmHeader::gdcmHeader( std::string const & filename, /** * \brief Constructor - * @param exception_on_error whether we want to throw an exception or not */ -gdcmHeader::gdcmHeader(bool exception_on_error) : - gdcmDocument( exception_on_error ) +Header::Header() + :Document() { } /** - * \ingroup gdcmHeader * \brief Canonical destructor. */ -gdcmHeader::~gdcmHeader () +Header::~Header () { } @@ -109,57 +102,68 @@ gdcmHeader::~gdcmHeader () * @param filetype Type of the File to be written * (ACR-NEMA, ExplicitVR, ImplicitVR) */ -void gdcmHeader::Write(FILE* fp,FileType filetype) { - +void Header::Write(FILE* fp,FileType filetype) +{ // Bits Allocated - if ( GetEntryByNumber(0x0028,0x0100) == "12") { + if ( GetEntryByNumber(0x0028,0x0100) == "12") + { SetEntryByNumber("16", 0x0028,0x0100); } - // correct Pixel group Length if necessary - - // TODO : create a gdcmHeader::Write method and move this part. - // (only gdcmHeader knows GrPixel, NumPixel) + /// \todo correct 'Pixel group' Length if necessary int i_lgPix = GetEntryLengthByNumber(GrPixel, NumPixel); - if (i_lgPix != -2) { // no (GrPixel, NumPixel) element - char * dumm = new char[20]; - sprintf(dumm ,"%d", i_lgPix+12); - std::string s_lgPix = dumm; - delete dumm; + 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 - - gdcmDocEntry *e; - e=GetDocEntryByNumber(0x0028,0x01101); - if (e) - RemoveEntry(e); - e=GetDocEntryByNumber(0x0028,0x1102); - if (e) - RemoveEntry(e); - e=GetDocEntryByNumber(0x0028,0x1103); - - if (e) - RemoveEntry(e); - e=GetDocEntryByNumber(0x0028,0x01201); - if (e) - RemoveEntry(e); - e=GetDocEntryByNumber(0x0028,0x1202); - if (e) - RemoveEntry(e); - e=GetDocEntryByNumber(0x0028,0x1203); - if (e) - RemoveEntry(e); - } - - gdcmDocument::Write(fp,filetype); + 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); } //----------------------------------------------------------------------------- @@ -171,15 +175,15 @@ void gdcmHeader::Write(FILE* fp,FileType filetype) { /** * \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 Dicom/Acr File. - * @return true when gdcmHeader is the one of a reasonable Dicom/Acr file, + * @return true when Header is the one of a reasonable Dicom/Acr file, * false otherwise. */ -bool gdcmHeader::IsReadable() +bool Header::IsReadable() { - if( !gdcmDocument::IsReadable() ) + if( !Document::IsReadable() ) { return false; } @@ -214,7 +218,7 @@ bool gdcmHeader::IsReadable() * @return The encountered size when found, 0 by default. * 0 means the file is NOT USABLE. The caller will have to check */ -int gdcmHeader::GetXSize() +int Header::GetXSize() { std::string strSize; strSize = GetEntryByNumber(0x0028,0x0011); @@ -227,13 +231,12 @@ int gdcmHeader::GetXSize() } /** - * \ingroup gdcmHeader * \brief Retrieve the number of lines of image. - * \warning The defaulted value is 1 as opposed to gdcmHeader::GetXSize() + * \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). */ -int gdcmHeader::GetYSize() +int Header::GetYSize() { std::string strSize = GetEntryByNumber(0x0028,0x0010); if ( strSize != GDCM_UNFOUND ) @@ -251,7 +254,6 @@ int gdcmHeader::GetYSize() } /** - * \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 @@ -259,7 +261,7 @@ int gdcmHeader::GetYSize() * being the ACR-NEMA "Planes" tag content. * @return The encountered size when found, 1 by default (single image). */ -int gdcmHeader::GetZSize() +int Header::GetZSize() { // Both DicomV3 and ACR/Nema consider the "Number of Frames" // as the third dimension. @@ -280,19 +282,18 @@ int gdcmHeader::GetZSize() } /** - * \ingroup gdcmHeader * \brief gets the info from 0028,0030 : Pixel Spacing * else 1.0 * @return X dimension of a pixel */ -float gdcmHeader::GetXSpacing() +float Header::GetXSpacing() { float xspacing, yspacing; std::string strSpacing = GetEntryByNumber(0x0028,0x0030); if ( strSpacing == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetXSpacing: unfound Pixel Spacing (0028,0030)"); + dbg.Verbose(0, "Header::GetXSpacing: unfound Pixel Spacing (0028,0030)"); return 1.; } @@ -308,7 +309,7 @@ float gdcmHeader::GetXSpacing() } if ( xspacing == 0.) { - dbg.Verbose(0, "gdcmHeader::GetYSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem"); + 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); } @@ -317,19 +318,18 @@ float gdcmHeader::GetXSpacing() } /** - * \ingroup gdcmHeader * \brief gets the info from 0028,0030 : Pixel Spacing * else 1.0 * @return Y dimension of a pixel */ -float gdcmHeader::GetYSpacing() +float Header::GetYSpacing() { float yspacing = 0; std::string strSpacing = GetEntryByNumber(0x0028,0x0030); if ( strSpacing == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetYSpacing: unfound Pixel Spacing (0028,0030)"); + dbg.Verbose(0, "Header::GetYSpacing: unfound Pixel Spacing (0028,0030)"); return 1.; } @@ -340,13 +340,12 @@ float gdcmHeader::GetYSpacing() } /** - *\ingroup gdcmHeader - *\brief gets the info from 0018,0088 : Space Between Slices - * else from 0018,0050 : Slice Thickness - * else 1.0 - * @return Z dimension of a voxel-to be - */ -float gdcmHeader::GetZSpacing() + * \brief gets the info from 0018,0088 : Space Between Slices + * else from 0018,0050 : Slice Thickness + * else 1.0 + * @return Z dimension of a voxel-to be + */ +float Header::GetZSpacing() { // Spacing Between Slices : distance entre le milieu de chaque coupe // Les coupes peuvent etre : @@ -362,7 +361,7 @@ float gdcmHeader::GetZSpacing() if ( strSpacingBSlices == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetZSpacing: unfound StrSpacingBSlices"); + dbg.Verbose(0, "Header::GetZSpacing: unfound StrSpacingBSlices"); std::string strSliceThickness = GetEntryByNumber(0x0018,0x0050); if ( strSliceThickness == GDCM_UNFOUND ) { @@ -384,41 +383,42 @@ float gdcmHeader::GetZSpacing() } /** - *\ingroup gdcmHeader - *\brief gets the info from 0028,1052 : Rescale Intercept - * @return Rescale Intercept + *\brief gets the info from 0028,1052 : Rescale Intercept + * @return Rescale Intercept */ -float gdcmHeader::GetRescaleIntercept() +float Header::GetRescaleIntercept() { float resInter = 0.; - std::string strRescInter = GetEntryByNumber(0x0028,0x1052); //0028 1052 DS IMG Rescale Intercept + /// 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, "gdcmHeader::GetRescaleIntercept: Rescale Slope is empty"); + dbg.Verbose(0, "Header::GetRescaleIntercept: Rescale Slope " + "is empty"); } } - return resInter; + return resInter; } /** - *\ingroup gdcmHeader - *\brief gets the info from 0028,1053 : Rescale Slope - * @return Rescale Slope + *\brief gets the info from 0028,1053 : Rescale Slope + * @return Rescale Slope */ -float gdcmHeader::GetRescaleSlope() +float Header::GetRescaleSlope() { float resSlope = 1.; - std::string strRescSlope = GetEntryByNumber(0x0028,0x1053); //0028 1053 DS IMG Rescale Slope + //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, "gdcmHeader::GetRescaleSlope: Rescale Slope is empty"); + dbg.Verbose(0, "Header::GetRescaleSlope: Rescale Slope is empty"); } } @@ -426,14 +426,13 @@ float gdcmHeader::GetRescaleSlope() } /** - * \ingroup gdcmHeader - * \brief This function is intended to user who doesn't want - * to have to manage a LUT and expects to get an RBG Pixel image - * (or a monochrome one ...) - * \warning to be used with GetImagePixels() - * @return 1 if Gray level, 3 if Color (RGB, YBR or PALETTE COLOR) - */ -int gdcmHeader::GetNumberOfScalarComponents() + * \brief This function is intended to user who doesn't want + * to have to manage a LUT and expects to get an RBG Pixel image + * (or a monochrome one ...) + * \warning to be used with GetImagePixels() + * @return 1 if Gray level, 3 if Color (RGB, YBR or PALETTE COLOR) + */ +int Header::GetNumberOfScalarComponents() { if ( GetSamplesPerPixel() == 3 ) { @@ -477,18 +476,17 @@ int gdcmHeader::GetNumberOfScalarComponents() } /** - * \ingroup gdcmHeader - * \brief This function is intended to user that DOESN'T want - * to get RGB pixels image when it's stored as a PALETTE COLOR image - * - the (vtk) user is supposed to know how deal with LUTs - - * \warning to be used with GetImagePixelsRaw() - * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -) - */ -int gdcmHeader::GetNumberOfScalarComponentsRaw() + * \brief This function is intended to user that DOESN'T want + * to get RGB pixels image when it's stored as a PALETTE COLOR image + * - the (vtk) user is supposed to know how deal with LUTs - + * \warning to be used with GetImagePixelsRaw() + * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -) + */ +int Header::GetNumberOfScalarComponentsRaw() { // 0028 0100 US IMG Bits Allocated // (in order no to be messed up by old RGB images) - if ( gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24" ) + if ( Header::GetEntryByNumber(0x0028,0x0100) == "24" ) { return 3; } @@ -514,24 +512,25 @@ int gdcmHeader::GetNumberOfScalarComponentsRaw() // /** - * \brief gets the info from 0020,0032 : Image Position Patient - * else from 0020,0030 : Image Position (RET) - * else 0. - * @return up-left image corner X position - */ - -float gdcmHeader::GetXOrigin() + * \brief gets the info from 0020,0032 : Image Position Patient + * else from 0020,0030 : Image Position (RET) + * else 0. + * @return up-left image corner X position + */ +float Header::GetXOrigin() { float xImPos, yImPos, zImPos; std::string strImPos = GetEntryByNumber(0x0020,0x0032); if ( strImPos == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position Patient (0020,0032)"); + 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, "gdcmHeader::GetXImagePosition: unfound Image Position (RET) (0020,0030)"); + dbg.Verbose(0, "Header::GetXImagePosition: unfound Image " + "Position (RET) (0020,0030)"); /// \todo How to tell the caller nothing was found ? return 0.; } @@ -539,30 +538,32 @@ float gdcmHeader::GetXOrigin() if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 ) { - return 0.; + return 0.; } return xImPos; } /** - * \brief gets the info from 0020,0032 : Image Position Patient - * else from 0020,0030 : Image Position (RET) - * else 0. - * @return up-left image corner Y position - */ -float gdcmHeader::GetYOrigin() + * \brief gets the info from 0020,0032 : Image Position Patient + * else from 0020,0030 : Image Position (RET) + * else 0. + * @return up-left image corner Y position + */ +float Header::GetYOrigin() { float xImPos, yImPos, zImPos; std::string strImPos = GetEntryByNumber(0x0020,0x0032); if ( strImPos == GDCM_UNFOUND) { - dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position Patient (0020,0032)"); + 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, "gdcmHeader::GetYImagePosition: unfound Image Position (RET) (0020,0030)"); + dbg.Verbose(0, "Header::GetYImagePosition: unfound Image " + "Position (RET) (0020,0030)"); /// \todo How to tell the caller nothing was found ? return 0.; } @@ -577,14 +578,14 @@ float gdcmHeader::GetYOrigin() } /** - * \brief gets the info from 0020,0032 : Image Position Patient - * \ else from 0020,0030 : Image Position (RET) - * \ else from 0020,1041 : Slice Location - * \ else from 0020,0050 : Location - * \ else 0. - * @return up-left image corner Z position - */ -float gdcmHeader::GetZOrigin() + * \brief gets the info from 0020,0032 : Image Position Patient + * else from 0020,0030 : Image Position (RET) + * else from 0020,1041 : Slice Location + * else from 0020,0050 : Location + * else 0. + * @return up-left image corner Z position + */ +float Header::GetZOrigin() { float xImPos, yImPos, zImPos; std::string strImPos = GetEntryByNumber(0x0020,0x0032); @@ -593,7 +594,8 @@ float gdcmHeader::GetZOrigin() { if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) { - dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position Patient (0020,0032)"); + dbg.Verbose(0, "Header::GetZImagePosition: wrong Image " + "Position Patient (0020,0032)"); return 0.; // bug in the element 0x0020,0x0032 } else @@ -608,7 +610,7 @@ float gdcmHeader::GetZOrigin() if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos ) != 3 ) { - dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position (RET) (0020,0030)"); + dbg.Verbose(0, "Header::GetZImagePosition: wrong Image Position (RET) (0020,0030)"); return 0.; // bug in the element 0x0020,0x0032 } else @@ -622,7 +624,7 @@ float gdcmHeader::GetZOrigin() { if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1) { - dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Slice Location (0020,1041)"); + dbg.Verbose(0, "Header::GetZImagePosition: wrong Slice Location (0020,1041)"); return 0.; // bug in the element 0x0020,0x1041 } else @@ -630,14 +632,14 @@ float gdcmHeader::GetZOrigin() return zImPos; } } - dbg.Verbose(0, "gdcmHeader::GetZImagePosition: unfound Slice Location (0020,1041)"); + 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, "gdcmHeader::GetZImagePosition: wrong Location (0020,0050)"); + dbg.Verbose(0, "Header::GetZImagePosition: wrong Location (0020,0050)"); return 0.; // bug in the element 0x0020,0x0050 } else @@ -645,17 +647,16 @@ float gdcmHeader::GetZOrigin() return zImPos; } } - dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Location (0020,0050)"); + dbg.Verbose(0, "Header::GetYImagePosition: unfound Location (0020,0050)"); return 0.; // Hopeless } /** - * \brief gets the info from 0020,0013 : Image Number - * \ else 0. - * @return image number - */ -int gdcmHeader::GetImageNumber() + * \brief gets the info from 0020,0013 : Image Number else 0. + * @return image number + */ +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 @@ -663,7 +664,8 @@ int gdcmHeader::GetImageNumber() // be preferable to sscanf() since atoi() is a much smaller, simpler and // faster function. sscanf() can do all possible conversions whereas // atoi() can only do single decimal integer conversions. - std::string strImNumber = GetEntryByNumber(0x0020,0x0013); //0020 0013 IS REL Image Number + //0020 0013 IS REL Image Number + std::string strImNumber = GetEntryByNumber(0x0020,0x0013); if ( strImNumber != GDCM_UNFOUND ) { return atoi( strImNumber.c_str() ); @@ -672,10 +674,10 @@ int gdcmHeader::GetImageNumber() } /** - * \brief gets the info from 0008,0060 : Modality - * @return Modality Type - */ -ModalityType gdcmHeader::GetModality() + * \brief gets the info from 0008,0060 : Modality + * @return Modality Type + */ +ModalityType Header::GetModality() { // 0008 0060 CS ID Modality std::string strModality = GetEntryByNumber(0x0008,0x0060); @@ -734,93 +736,189 @@ ModalityType gdcmHeader::GetModality() } /** - * \ingroup gdcmHeader * \brief Retrieve the number of Bits Stored (actually used) * (as opposite to number of Bits Allocated) * @return The encountered number of Bits Stored, 0 by default. * 0 means the file is NOT USABLE. The caller has to check it ! */ -int gdcmHeader::GetBitsStored() +int Header::GetBitsStored() { - std::string strSize = GetEntryByNumber(0x0028,0x0101); + std::string strSize = GetEntryByNumber( 0x0028, 0x0101 ); if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetBitsStored: this is supposed to be mandatory"); + 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 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 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 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 gdcmHeader::GetBitsAllocated() +int Header::GetBitsAllocated() { std::string strSize = GetEntryByNumber(0x0028,0x0100); if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetBitsStored: this is supposed to be mandatory"); + 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 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() +int Header::GetSamplesPerPixel() { std::string strSize = GetEntryByNumber(0x0028,0x0002); if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetBitsStored: this is supposed to be mandatory"); + dbg.Verbose(0, "Header::GetBitsStored: this is supposed to " + "be mandatory"); return 1; // Well, it's supposed to be mandatory ... // but sometimes it's missing : *we* assume Gray pixels } - return atoi( strSize.c_str() ); } /** - * \ingroup gdcmHeader + * \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; +} + +/** * \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() +int Header::GetPlanarConfiguration() { std::string strSize = GetEntryByNumber(0x0028,0x0006); if ( strSize == GDCM_UNFOUND ) { return 0; } - return atoi( strSize.c_str() ); } /** - * \ingroup gdcmHeader * \brief Return the size (in bytes) of a single pixel of data. * @return The size in bytes of a single pixel of data; 0 by default - * 0 means the file is NOT USABLE; the caller will have to check + * 0 means the file is NOT USABLE; the caller will have to check */ -int gdcmHeader::GetPixelSize() +int Header::GetPixelSize() { // 0028 0100 US IMG Bits Allocated // (in order no to be messed up by old RGB images) - // if (gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24") + // if (Header::GetEntryByNumber(0x0028,0x0100) == "24") // return 3; std::string pixelType = GetPixelType(); @@ -840,13 +938,11 @@ int gdcmHeader::GetPixelSize() { return 8; } - - dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type"); + 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, @@ -860,12 +956,12 @@ int gdcmHeader::GetPixelSize() * 24 bit images appear as 8 bit * @return 0S if nothing found. NOT USABLE file. The caller has to check */ -std::string gdcmHeader::GetPixelType() +std::string Header::GetPixelType() { std::string bitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated if ( bitsAlloc == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated"); + dbg.Verbose(0, "Header::GetPixelType: unfound Bits Allocated"); bitsAlloc = "16"; } @@ -884,11 +980,11 @@ std::string gdcmHeader::GetPixelType() bitsAlloc = "8"; // by old RGB images) } - std::string sign = GetEntryByNumber(0x0028, 0x0103); // "Pixel Representation" + std::string sign = GetEntryByNumber(0x0028, 0x0103);//"Pixel Representation" if (sign == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation"); + dbg.Verbose(0, "Header::GetPixelType: unfound Pixel Representation"); bitsAlloc = "0"; } if ( sign == "0" ) @@ -899,20 +995,18 @@ std::string gdcmHeader::GetPixelType() { sign = "S"; } - return bitsAlloc + sign; } /** - * \ingroup gdcmHeader * \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() +size_t Header::GetPixelOffset() { - gdcmDocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel); + DocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel); if ( pxlElement ) { return pxlElement->GetOffset(); @@ -928,18 +1022,17 @@ size_t gdcmHeader::GetPixelOffset() } } -// TODO : unify those two (previous one and next one) +/// \todo TODO : unify those two (previous one and next one) /** - * \ingroup gdcmHeader * \brief Recover the pixel area length (in Bytes) * @return Pixel Element Length, as stored in the header * (NOT the memory space necessary to hold the Pixels * -in case of embeded compressed image-) * 0 : NOT USABLE file. The caller has to check. */ -size_t gdcmHeader::GetPixelAreaLength() +size_t Header::GetPixelAreaLength() { - gdcmDocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel); + DocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel); if ( pxlElement ) { return pxlElement->GetLength(); @@ -956,7 +1049,6 @@ size_t gdcmHeader::GetPixelAreaLength() } /** - * \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 @@ -964,7 +1056,7 @@ size_t gdcmHeader::GetPixelAreaLength() * Please warn me if you know sbdy that *does* know ... jprx * @return true if LUT Descriptors and LUT Tables were found */ -bool gdcmHeader::HasLUT() +bool Header::HasLUT() { // Check the presence of the LUT Descriptors, and LUT Tables // LutDescriptorRed @@ -1004,19 +1096,19 @@ bool gdcmHeader::HasLUT() } /** - * \ingroup gdcmHeader * \brief gets the info from 0028,1101 : Lookup Table Desc-Red * else 0 * @return Lookup Table number of Bits , 0 by default * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] * @ return bit number of each LUT item */ -int gdcmHeader::GetLUTNbits() +int Header::GetLUTNbits() { std::vector tokens; int lutNbits; - //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red = Lookup Table Desc-Blue + //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red + // = Lookup Table Desc-Blue // Consistency already checked in GetLUTLength std::string lutDescription = GetEntryByNumber(0x0028,0x1101); if ( lutDescription == GDCM_UNFOUND ) @@ -1025,7 +1117,7 @@ int gdcmHeader::GetLUTNbits() } tokens.clear(); // clean any previous value - Tokenize ( lutDescription, tokens, "\\" ); + Util::Tokenize ( lutDescription, tokens, "\\" ); //LutLength=atoi(tokens[0].c_str()); //LutDepth=atoi(tokens[1].c_str()); @@ -1036,7 +1128,6 @@ int gdcmHeader::GetLUTNbits() } /** - * \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) @@ -1051,7 +1142,7 @@ int gdcmHeader::GetLUTNbits() * no known Dicom reader deals with them :-( * @return a RGBA Lookup Table */ -uint8_t* gdcmHeader::GetLUTRGBA() +uint8_t* Header::GetLUTRGBA() { // Not so easy : see // http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables @@ -1093,7 +1184,7 @@ uint8_t* gdcmHeader::GetLUTRGBA() &lengthR, &debR, &nbitsR ); if( nbRead != 3 ) { - dbg.Verbose(0, "gdcmHeader::GetLUTRGBA: trouble reading red LUT"); + dbg.Verbose(0, "Header::GetLUTRGBA: trouble reading red LUT"); } // lengthG: Green LUT length in Bytes @@ -1103,7 +1194,7 @@ uint8_t* gdcmHeader::GetLUTRGBA() &lengthG, &debG, &nbitsG ); if( nbRead != 3 ) { - dbg.Verbose(0, "gdcmHeader::GetLUTRGBA: trouble reading green LUT"); + dbg.Verbose(0, "Header::GetLUTRGBA: trouble reading green LUT"); } // lengthB: Blue LUT length in Bytes @@ -1113,17 +1204,17 @@ uint8_t* gdcmHeader::GetLUTRGBA() &lengthB, &debB, &nbitsB ); if( nbRead != 3 ) { - dbg.Verbose(0, "gdcmHeader::GetLUTRGBA: trouble reading blue LUT"); + dbg.Verbose(0, "Header::GetLUTRGBA: trouble reading blue LUT"); } // Load LUTs into memory, (as they were stored on disk) - uint8_t* lutR = (uint8_t*) GetEntryVoidAreaByNumber(0x0028,0x1201); - uint8_t* lutG = (uint8_t*) GetEntryVoidAreaByNumber(0x0028,0x1202); - uint8_t* lutB = (uint8_t*) GetEntryVoidAreaByNumber(0x0028,0x1203); + 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, "gdcmHeader::GetLUTRGBA: trouble with one of the LUT"); + dbg.Verbose(0, "Header::GetLUTRGBA: trouble with one of the LUT"); return NULL; } // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT @@ -1196,23 +1287,29 @@ uint8_t* gdcmHeader::GetLUTRGBA() *a = 1; // Alpha component a += 4; } - return LUTRGBA; } /** - * \brief Accesses the info from 0002,0010 : Transfert Syntax and gdcmTS + * \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) */ -std::string gdcmHeader::GetTransfertSyntaxName() +std::string Header::GetTransfertSyntaxName() { - // use the gdcmTS (TS : Transfert Syntax) + // 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"; + } if ( transfertSyntax == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetTransfertSyntaxName:" + dbg.Verbose(0, "Header::GetTransfertSyntaxName:" " unfound Transfert Syntax (0002,0010)"); return "Uncompressed ACR-NEMA"; } @@ -1222,7 +1319,7 @@ std::string gdcmHeader::GetTransfertSyntaxName() transfertSyntax.erase(transfertSyntax.length()-1, 1); } // we do it only when we need it - gdcmTS* ts = gdcmGlobal::GetTS(); + TS* ts = Global::GetTS(); std::string tsName = ts->GetValue( transfertSyntax ); //delete ts; /// \todo Seg Fault when deleted ?! @@ -1235,20 +1332,18 @@ std::string gdcmHeader::GetTransfertSyntaxName() * @param ImageDataSize new Pixel Area Size * warning : nothing else is checked */ -void gdcmHeader::SetImageDataSize(size_t ImageDataSize) +void Header::SetImageDataSize(size_t ImageDataSize) { - std::string content1; - char car[20]; - - sprintf(car,"%d",ImageDataSize); + ///FIXME I don't understand this code wh ydo we set two times 'car' ? + std::string car = Util::Format("%d", ImageDataSize); - gdcmDocEntry *a = GetDocEntryByNumber(GrPixel, NumPixel); + DocEntry *a = GetDocEntryByNumber(GrPixel, NumPixel); a->SetLength(ImageDataSize); - ImageDataSize+=8; - sprintf(car,"%d",ImageDataSize); - content1=car; - SetEntryByNumber(content1, GrPixel, NumPixel); + ImageDataSize += 8; + car = Util::Format("%d", ImageDataSize); + + SetEntryByNumber(car, GrPixel, NumPixel); } //----------------------------------------------------------------------------- @@ -1258,15 +1353,16 @@ void gdcmHeader::SetImageDataSize(size_t ImageDataSize) * \brief anonymize a Header (removes Patient's personal info) * (read the code to see which ones ...) */ -bool gdcmHeader::AnonymizeHeader() +bool Header::AnonymizeHeader() { - gdcmDocEntry* patientNameHE = GetDocEntryByNumber (0x0010, 0x0010); + // If exist, replace by spaces + SetEntryByNumber (" ",0x0010, 0x2154); // Telephone + SetEntryByNumber (" ",0x0010, 0x1040); // Adress + SetEntryByNumber (" ",0x0010, 0x0020); // Patient ID - ReplaceIfExistByNumber (" ",0x0010, 0x2154); // Telephone - ReplaceIfExistByNumber (" ",0x0010, 0x1040); // Adress - ReplaceIfExistByNumber (" ",0x0010, 0x0020); // Patient ID + DocEntry* patientNameHE = GetDocEntryByNumber (0x0010, 0x0010); - if ( patientNameHE ) + if ( patientNameHE ) // we replace it by Study Instance UID (why not) { std::string studyInstanceUID = GetEntryByNumber (0x0020, 0x000d); if ( studyInstanceUID != GDCM_UNFOUND ) @@ -1339,46 +1435,38 @@ bool gdcmHeader::AnonymizeHeader() * @param iop adress of the (6)float aray to receive values * @return cosines of image orientation patient */ -void gdcmHeader::GetImageOrientationPatient( float* iop ) +void Header::GetImageOrientationPatient( float iop[6] ) { + std::string strImOriPat; //iop is supposed to be float[6] - iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0; + iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.; // 0020 0037 DS REL Image Orientation (Patient) - std::string strImOriPat = GetEntryByNumber(0x0020,0x0037); - if ( strImOriPat != GDCM_UNFOUND ) + if ( (strImOriPat = GetEntryByNumber(0x0020,0x0037)) != GDCM_UNFOUND ) { if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f", &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) { - dbg.Verbose(0, "gdcmHeader::GetImageOrientationPatient: wrong Image Orientation Patient (0020,0037)"); - return ; // bug in the element 0x0020,0x0037 - } - else - { - return ; + dbg.Verbose(0, "Header::GetImageOrientationPatient: " + "wrong Image Orientation Patient (0020,0037)"); } } - //For ACR-NEMA // 0020 0035 DS REL Image Orientation (RET) - strImOriPat = GetEntryByNumber(0x0020,0x0035); - if ( strImOriPat != GDCM_UNFOUND ) + else if ( (strImOriPat = GetEntryByNumber(0x0020,0x0035)) != GDCM_UNFOUND ) { if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f", &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) { - dbg.Verbose(0, "gdcmHeader::GetImageOrientationPatient: wrong Image Orientation Patient (0020,0035)"); - return ; // bug in the element 0x0020,0x0035 + dbg.Verbose(0, "Header::GetImageOrientationPatient: " + "wrong Image Orientation Patient (0020,0035)"); } } - else - { - return; - } } //----------------------------------------------------------------------------- // Private //----------------------------------------------------------------------------- + +} // end namespace gdcm