X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=90299a8a0ab45d4a08a4d685b8f7533b1390f508;hb=e6671b4378ba33a2cdf7c711e4e45250af74dbbc;hp=aa808aeb26e4d4e9bc5b78a7f3254e83cd23def5;hpb=19f72d139faa0f6a03f4e4a33be4c6b3e70b18b7;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index aa808aeb..90299a8a 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmHeader.cxx,v $ Language: C++ - Date: $Date: 2004/06/23 03:36:24 $ - Version: $Revision: 1.168 $ + Date: $Date: 2004/07/31 23:30:04 $ + Version: $Revision: 1.181 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -29,26 +29,14 @@ // Constructor / Destructor /** * \brief Constructor - * @param InFilename name of the file whose header we want to analyze + * @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 enable_sequences = true to allow the header - * to be parsed *inside* the SeQuences, when they have an actual length - * @param ignore_shadow = true if user wants to skip shadow groups - * during parsing, to save memory space */ -gdcmHeader::gdcmHeader(std::string const & filename, - bool exception_on_error, - bool enable_sequences, - bool ignore_shadow): - gdcmDocument(filename,exception_on_error,enable_sequences,ignore_shadow) -{ -/* - typedef struct { - guint32 totalSQlength; - guint32 alreadyParsedlength; - } pileElem; -*/ - +gdcmHeader::gdcmHeader( std::string const & filename, + bool exception_on_error ): + gdcmDocument( filename, + exception_on_error ) +{ // 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 @@ -57,22 +45,35 @@ 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 - std::string ImageLocation = GetEntryByNumber(0x0028, 0x0200); - if ( ImageLocation == GDCM_UNFOUND ) { // Image Location - GrPixel = 0x7fe0; // default value - } else { - GrPixel = (guint16) atoi( ImageLocation.c_str() ); + // Image Location + std::string imgLocation = GetEntryByNumber(0x0028, 0x0200); + if ( imgLocation == GDCM_UNFOUND ) + { + // default value + GrPixel = 0x7fe0; + } + else + { + GrPixel = (uint16_t) atoi( imgLocation.c_str() ); } - if (GrPixel == 0xe07f) // sometimes Image Location value doesn't follow - GrPixel = 0x7fe0; // the supposed processor endianity. - // see gdcmData/cr172241.dcm - if (GrPixel != 0x7fe0) { + + // 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 { + } + else + { NumPixel = 0x0010; } } @@ -82,7 +83,7 @@ gdcmHeader::gdcmHeader(std::string const & filename, * @param exception_on_error whether we want to throw an exception or not */ gdcmHeader::gdcmHeader(bool exception_on_error) : - gdcmDocument(exception_on_error) + gdcmDocument( exception_on_error ) { } @@ -90,7 +91,83 @@ gdcmHeader::gdcmHeader(bool exception_on_error) : * \ingroup gdcmHeader * \brief Canonical destructor. */ -gdcmHeader::~gdcmHeader () { +gdcmHeader::~gdcmHeader () +{ +} + + +/** + * \brief Performs some consistency checking on various 'File related' + * (as opposed to 'DicomDir related') entries + * then writes in a file all the (Dicom Elements) included the Pixels + * @param fp file pointer on an already open file + * @param filetype Type of the File to be written + * (ACR-NEMA, ExplicitVR, ImplicitVR) + */ +void gdcmHeader::Write(FILE* fp,FileType filetype) +{ + // Bits Allocated + 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) + + int i_lgPix = GetEntryLengthByNumber(GrPixel, NumPixel); + if (i_lgPix != -2) + { + // no (GrPixel, NumPixel) element + char* dumm = new char[20]; + sprintf(dumm ,"%d", i_lgPix+12); + std::string s_lgPix = dumm; + delete[] dumm; + ReplaceOrCreateByNumber(s_lgPix,GrPixel, 0x0000); + } + + // Drop Palette Color, if necessary + + if ( GetEntryByNumber(0x0028,0x0002).c_str()[0] == '3' ) + { + // if SamplesPerPixel = 3, sure we don't need any LUT ! + // Drop 0028|1101, 0028|1102, 0028|1103 + // Drop 0028|1201, 0028|1202, 0028|1203 + + gdcmDocEntry* e = GetDocEntryByNumber(0x0028,0x01101); + if (e) + { + 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); } //----------------------------------------------------------------------------- @@ -108,21 +185,35 @@ gdcmHeader::~gdcmHeader () { * @return true when gdcmHeader is the one of a reasonable Dicom/Acr file, * false otherwise. */ -bool gdcmHeader::IsReadable() { - if(!gdcmDocument::IsReadable()) { +bool gdcmHeader::IsReadable() +{ + if( !gdcmDocument::IsReadable() ) + { return false; } + std::string res = GetEntryByNumber(0x0028, 0x0005); - if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) + if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) + { return false; // Image Dimensions + } if ( !GetDocEntryByNumber(0x0028, 0x0100) ) + { return false; // "Bits Allocated" + } if ( !GetDocEntryByNumber(0x0028, 0x0101) ) + { return false; // "Bits Stored" + } if ( !GetDocEntryByNumber(0x0028, 0x0102) ) + { return false; // "High Bit" + } if ( !GetDocEntryByNumber(0x0028, 0x0103) ) + { return false; // "Pixel Representation" i.e. 'Sign' + } + return true; } @@ -131,12 +222,16 @@ 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() { - std::string StrSize; - StrSize = GetEntryByNumber(0x0028,0x0011); - if (StrSize == GDCM_UNFOUND) +int gdcmHeader::GetXSize() +{ + std::string strSize; + strSize = GetEntryByNumber(0x0028,0x0011); + if ( strSize == GDCM_UNFOUND ) + { return 0; - return atoi(StrSize.c_str()); + } + + return atoi( strSize.c_str() ); } /** @@ -144,18 +239,23 @@ int gdcmHeader::GetXSize() { * \brief Retrieve the number of lines of image. * \warning The defaulted value is 1 as opposed to gdcmHeader::GetXSize() * @return The encountered size when found, 1 by default - * (The ACR-MEMA file contains a Signal, not an Image). + * (The ACR-NEMA file contains a Signal, not an Image). */ -int gdcmHeader::GetYSize() { - std::string StrSize = GetEntryByNumber(0x0028,0x0010); - if (StrSize != GDCM_UNFOUND) - return atoi(StrSize.c_str()); +int gdcmHeader::GetYSize() +{ + std::string strSize = GetEntryByNumber(0x0028,0x0010); + if ( strSize != GDCM_UNFOUND ) + { + return atoi( strSize.c_str() ); + } if ( IsDicomV3() ) + { return 0; - else - // The Rows (0028,0010) entry was optional for ACR/NEMA. It might - // hence be a signal (1d image). So we default to 1: - return 1; + } + + // 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; } /** @@ -167,17 +267,23 @@ 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 gdcmHeader::GetZSize() +{ // Both DicomV3 and ACR/Nema consider the "Number of Frames" // as the third dimension. - std::string StrSize = GetEntryByNumber(0x0028,0x0008); - if (StrSize != GDCM_UNFOUND) - return atoi(StrSize.c_str()); + 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()); + strSize = GetEntryByNumber(0x0028,0x0012); + if ( strSize != GDCM_UNFOUND ) + { + return atoi( strSize.c_str() ); + } + return 1; } @@ -187,25 +293,35 @@ int gdcmHeader::GetZSize() { * else 1.0 * @return X dimension of a pixel */ -float gdcmHeader::GetXSpacing() { - float xspacing, yspacing; - std::string StrSpacing = GetEntryByNumber(0x0028,0x0030); - - if (StrSpacing == GDCM_UNFOUND) { +float gdcmHeader::GetXSpacing() +{ + float xspacing, yspacing; + std::string strSpacing = GetEntryByNumber(0x0028,0x0030); + + if ( strSpacing == GDCM_UNFOUND ) + { dbg.Verbose(0, "gdcmHeader::GetXSpacing: unfound Pixel Spacing (0028,0030)"); return 1.; - } - int nbValues; - if( (nbValues = sscanf( StrSpacing.c_str(), "%f\\%f", &yspacing, &xspacing)) != 2) { - if (nbValues==1) // if single value is found, xspacing is defaulted to yspacing - return yspacing; - } - if (xspacing == 0.) { - dbg.Verbose(0, "gdcmHeader::GetYSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem"); - // seems to be a bug in the header ... - sscanf( StrSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing); - } - return xspacing; + } + + int nbValues; + if( ( nbValues = sscanf( strSpacing.c_str(), + "%f\\%f", &yspacing, &xspacing)) != 2 ) + { + // if single value is found, xspacing is defaulted to yspacing + if ( nbValues == 1 ) + { + return yspacing; + } + } + if ( xspacing == 0.) + { + dbg.Verbose(0, "gdcmHeader::GetYSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem"); + // seems to be a bug in the header ... + sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing); + } + + return xspacing; } /** @@ -214,16 +330,21 @@ float gdcmHeader::GetXSpacing() { * else 1.0 * @return Y dimension of a pixel */ -float gdcmHeader::GetYSpacing() { - float yspacing; - std::string StrSpacing = GetEntryByNumber(0x0028,0x0030); +float gdcmHeader::GetYSpacing() +{ + float yspacing = 0; + std::string strSpacing = GetEntryByNumber(0x0028,0x0030); - if (StrSpacing == GDCM_UNFOUND) { + if ( strSpacing == GDCM_UNFOUND ) + { dbg.Verbose(0, "gdcmHeader::GetYSpacing: unfound Pixel Spacing (0028,0030)"); return 1.; } - sscanf( StrSpacing.c_str(), "%f", &yspacing); - return yspacing; + + // if sscanf cannot read any float value, it won't affect yspacing + sscanf( strSpacing.c_str(), "%f", &yspacing); + + return yspacing; } /** @@ -233,7 +354,8 @@ float gdcmHeader::GetYSpacing() { * else 1.0 * @return Z dimension of a voxel-to be */ -float gdcmHeader::GetZSpacing() { +float gdcmHeader::GetZSpacing() +{ // Spacing Between Slices : distance entre le milieu de chaque coupe // Les coupes peuvent etre : // jointives (Spacing between Slices = Slice Thickness) @@ -244,21 +366,28 @@ float gdcmHeader::GetZSpacing() { // Si le Spacing Between Slices est absent, // on suppose que les coupes sont jointives - std::string StrSpacingBSlices = GetEntryByNumber(0x0018,0x0088); + std::string strSpacingBSlices = GetEntryByNumber(0x0018,0x0088); - if (StrSpacingBSlices == GDCM_UNFOUND) { + if ( strSpacingBSlices == GDCM_UNFOUND ) + { dbg.Verbose(0, "gdcmHeader::GetZSpacing: unfound StrSpacingBSlices"); - std::string StrSliceThickness = GetEntryByNumber(0x0018,0x0050); - if (StrSliceThickness == GDCM_UNFOUND) + 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()); + return atof( strSliceThickness.c_str() ); + } + } + else + { + return atof( strSpacingBSlices.c_str() ); } } @@ -267,16 +396,20 @@ float gdcmHeader::GetZSpacing() { *\brief gets the info from 0028,1052 : Rescale Intercept * @return Rescale Intercept */ -float gdcmHeader::GetRescaleIntercept() { - float resInter = 0.; - std::string StrRescInter = GetEntryByNumber(0x0028,0x1052); //0028 1052 DS IMG Rescale Intercept - if (StrRescInter != GDCM_UNFOUND) { - if( sscanf( StrRescInter.c_str(), "%f", &resInter) != 1) { +float gdcmHeader::GetRescaleIntercept() +{ + float resInter = 0.; + std::string strRescInter = GetEntryByNumber(0x0028,0x1052); //0028 1052 DS IMG Rescale Intercept + if ( strRescInter != GDCM_UNFOUND ) + { + if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 ) + { + // bug in the element 0x0028,0x1052 dbg.Verbose(0, "gdcmHeader::GetRescaleIntercept: Rescale Slope is empty"); - // bug in the element 0x0028,0x1052 - } + } } - return resInter; + + return resInter; } /** @@ -284,15 +417,19 @@ float gdcmHeader::GetRescaleIntercept() { *\brief gets the info from 0028,1053 : Rescale Slope * @return Rescale Slope */ - float gdcmHeader::GetRescaleSlope() { - float resSlope = 1.; - std::string StrRescSlope = GetEntryByNumber(0x0028,0x1053); //0028 1053 DS IMG Rescale Slope - if (StrRescSlope != GDCM_UNFOUND) { - if( sscanf( StrRescSlope.c_str(), "%f", &resSlope) != 1) { +float gdcmHeader::GetRescaleSlope() +{ + float resSlope = 1.; + std::string strRescSlope = GetEntryByNumber(0x0028,0x1053); //0028 1053 DS IMG Rescale Slope + if ( strRescSlope != GDCM_UNFOUND ) + { + if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1) + { + // bug in the element 0x0028,0x1053 dbg.Verbose(0, "gdcmHeader::GetRescaleSlope: Rescale Slope is empty"); - // bug in the element 0x0028,0x1053 - } - } + } + } + return resSlope; } @@ -304,36 +441,47 @@ float gdcmHeader::GetRescaleIntercept() { * \warning to be used with GetImagePixels() * @return 1 if Gray level, 3 if Color (RGB, YBR or PALETTE COLOR) */ -int gdcmHeader::GetNumberOfScalarComponents() { - if (GetSamplesPerPixel() ==3) +int gdcmHeader::GetNumberOfScalarComponents() +{ + if ( GetSamplesPerPixel() == 3 ) + { return 3; + } - // 0028 0100 US IMG Bits Allocated - // (in order no to be messed up by old RGB images) - if (gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24") + // 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 PhotometricInterpretation = - gdcmHeader::GetEntryByNumber(0x0028,0x0004); + std::string strPhotometricInterpretation = GetEntryByNumber(0x0028,0x0004); - if ( ( PhotometricInterpretation == "PALETTE COLOR ") ) { - if (HasLUT()) // PALETTE COLOR is NOT enough + if ( ( strPhotometricInterpretation == "PALETTE COLOR ") ) + { + if ( HasLUT() )// PALETTE COLOR is NOT enough + { return 3; + } else - return 1; - } + { + return 1; + } + } - //beware of trailing space at end of string - if (PhotometricInterpretation.find(GDCM_UNFOUND) < - PhotometricInterpretation.length() || - PhotometricInterpretation.find("MONOCHROME1") < - PhotometricInterpretation.length() || - PhotometricInterpretation.find("MONOCHROME2") < - PhotometricInterpretation.length() ) - return 1; - else - // we assume that *all* kinds of YBR are dealt with + // 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; + } } /** @@ -344,55 +492,19 @@ int gdcmHeader::GetNumberOfScalarComponents() { * \warning to be used with GetImagePixelsRaw() * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -) */ -int gdcmHeader::GetNumberOfScalarComponentsRaw() { - - // 0028 0100 US IMG Bits Allocated - // (in order no to be messed up by old RGB images) - if (gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24") +int gdcmHeader::GetNumberOfScalarComponentsRaw() +{ + // 0028 0100 US IMG Bits Allocated + // (in order no to be messed up by old RGB images) + if ( gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24" ) + { return 3; + } - // we assume that *all* kinds of YBR are dealt with - return GetSamplesPerPixel(); + // we assume that *all* kinds of YBR are dealt with + return GetSamplesPerPixel(); } -/** - *\ingroup gdcmHeader - *\brief gets the info from 0020,000d : Study Instance UID - *\todo ? : return the ACR-NEMA element value if DICOM one is not found - * @return Study Instance UID - */ -//std::string gdcmHeader::GetStudyUID(){ -// return GetEntryByNumber(0x0020,0x000d); //0020 000d UI REL Study Instance UID -//} - -/** - *\ingroup gdcmHeader - *\brief gets the info from 0020,000e : Series Instance UID - *\todo ? : return the ACR-NEMA element value if DICOM one is not found - * @return Series Instance UID - */ -//std::string gdcmHeader::GetSeriesUID(){ -// return GetEntryByNumber(0x0020,0x000e); //0020 000e UI REL Series Instance UID -//} - -/** - *\ingroup gdcmHeader - *\brief gets the info from 0008,0016 : SOP Class UID - *\todo ? : return the ACR-NEMA element value if DICOM one is not found - * @return SOP Class UID - */ -//std::string gdcmHeader::GetClassUID(){ -// return GetEntryByNumber(0x0008,0x0016); //0008 0016 UI ID SOP Class UID -//} - -/** - *\brief gets the info from 0008,0018 : SOP Instance UID - *\todo ? : return the ACR-NEMA element value if DICOM one is not found - * @return SOP Instance UID - */ -//std::string gdcmHeader::GetInstanceUID(){ -// return GetEntryByNumber(0x0008,0x0018); //0008 0018 UI ID SOP Instance UID -//} // // -------------- Remember ! ---------------------------------- // @@ -416,21 +528,28 @@ int gdcmHeader::GetNumberOfScalarComponentsRaw() { * @return up-left image corner X position */ -float gdcmHeader::GetXOrigin() { - float xImPos, yImPos, zImPos; - std::string StrImPos = GetEntryByNumber(0x0020,0x0032); - - if (StrImPos == GDCM_UNFOUND) { - dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position Patient (0020,0032)"); - StrImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images - if (StrImPos == GDCM_UNFOUND) { - dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position (RET) (0020,0030)"); - /// \todo How to tell the caller nothing was found ? +float gdcmHeader::GetXOrigin() +{ + float xImPos, yImPos, zImPos; + std::string strImPos = GetEntryByNumber(0x0020,0x0032); + + if ( strImPos == GDCM_UNFOUND ) + { + dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position Patient (0020,0032)"); + strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images + if ( strImPos == GDCM_UNFOUND ) + { + dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position (RET) (0020,0030)"); + /// \todo How to tell the caller nothing was found ? return 0.; - } - } - if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) - return 0.; + } + } + + if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 ) + { + return 0.; + } + return xImPos; } @@ -440,21 +559,28 @@ float gdcmHeader::GetXOrigin() { * else 0. * @return up-left image corner Y position */ -float gdcmHeader::GetYOrigin() { - float xImPos, yImPos, zImPos; - std::string StrImPos = GetEntryByNumber(0x0020,0x0032); - - if (StrImPos == GDCM_UNFOUND) { - dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position Patient (0020,0032)"); - StrImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images - if (StrImPos == GDCM_UNFOUND) { - dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position (RET) (0020,0030)"); - /// \todo How to tell the caller nothing was found ? - return 0.; - } - } - if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) - return 0.; +float gdcmHeader::GetYOrigin() +{ + float xImPos, yImPos, zImPos; + std::string strImPos = GetEntryByNumber(0x0020,0x0032); + + if ( strImPos == GDCM_UNFOUND) + { + dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position Patient (0020,0032)"); + strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images + if ( strImPos == GDCM_UNFOUND ) + { + dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position (RET) (0020,0030)"); + /// \todo How to tell the caller nothing was found ? + return 0.; + } + } + + if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 ) + { + return 0.; + } + return yImPos; } @@ -466,46 +592,69 @@ float gdcmHeader::GetYOrigin() { * \ else 0. * @return up-left image corner Z position */ -float gdcmHeader::GetZOrigin() { +float gdcmHeader::GetZOrigin() +{ float xImPos, yImPos, zImPos; - std::string StrImPos = GetEntryByNumber(0x0020,0x0032); - if (StrImPos != GDCM_UNFOUND) { - if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) { + std::string strImPos = GetEntryByNumber(0x0020,0x0032); + + if ( strImPos != GDCM_UNFOUND ) + { + if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) + { dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position Patient (0020,0032)"); return 0.; // bug in the element 0x0020,0x0032 - } else { + } + 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) { + } + } + + strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images + if ( strImPos != GDCM_UNFOUND ) + { + if( sscanf( strImPos.c_str(), + "%f\\%f\\%f", &xImPos, &yImPos, &zImPos ) != 3 ) + { dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position (RET) (0020,0030)"); return 0.; // bug in the element 0x0020,0x0032 - } else { + } + 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) { + } + } + + std::string strSliceLocation = GetEntryByNumber(0x0020,0x1041); // for *very* old ACR-NEMA images + if ( strSliceLocation != GDCM_UNFOUND ) + { + if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1) + { dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Slice Location (0020,1041)"); return 0.; // bug in the element 0x0020,0x1041 - } else { + } + else + { return zImPos; } - } + } dbg.Verbose(0, "gdcmHeader::GetZImagePosition: unfound Slice Location (0020,1041)"); - std::string StrLocation = GetEntryByNumber(0x0020,0x0050); - if (StrLocation != GDCM_UNFOUND) { - if( sscanf( StrLocation.c_str(), "%f", &zImPos) !=1) { + + std::string strLocation = GetEntryByNumber(0x0020,0x0050); + if ( strLocation != GDCM_UNFOUND ) + { + if( sscanf( strLocation.c_str(), "%f", &zImPos) != 1) + { dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Location (0020,0050)"); return 0.; // bug in the element 0x0020,0x0050 - } else { + } + else + { return zImPos; } } dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Location (0020,0050)"); + return 0.; // Hopeless } @@ -514,77 +663,82 @@ float gdcmHeader::GetZOrigin() { * \ else 0. * @return image number */ -int gdcmHeader::GetImageNumber() { - // The function i atoi() takes the address of an area of memory as - // parameter and converts the string stored at that location to an integer - // using the external decimal to internal binary conversion rules. This may - // be preferable to sscanf() since atoi() is a much smaller, simpler and - // faster function. sscanf() can do all possible conversions whereas - // atoi() can only do single decimal integer conversions. - std::string StrImNumber = GetEntryByNumber(0x0020,0x0013); //0020 0013 IS REL Image Number - if (StrImNumber != GDCM_UNFOUND) { - return atoi( StrImNumber.c_str() ); - } - return 0; //Hopeless +int gdcmHeader::GetImageNumber() +{ + // The function i atoi() takes the address of an area of memory as + // parameter and converts the string stored at that location to an integer + // using the external decimal to internal binary conversion rules. This may + // be preferable to sscanf() since atoi() is a much smaller, simpler and + // faster function. sscanf() can do all possible conversions whereas + // atoi() can only do single decimal integer conversions. + std::string strImNumber = GetEntryByNumber(0x0020,0x0013); //0020 0013 IS REL Image Number + if ( strImNumber != GDCM_UNFOUND ) + { + return atoi( strImNumber.c_str() ); + } + return 0; //Hopeless } /** * \brief gets the info from 0008,0060 : Modality * @return Modality Type */ -ModalityType gdcmHeader::GetModality() { - // 0008 0060 CS ID Modality - std::string StrModality = GetEntryByNumber(0x0008,0x0060); - if (StrModality != GDCM_UNFOUND) { - if ( StrModality.find("AU") < StrModality.length()) return AU; - else if ( StrModality.find("AS") < StrModality.length()) return AS; - else if ( StrModality.find("BI") < StrModality.length()) return BI; - else if ( StrModality.find("CF") < StrModality.length()) return CF; - else if ( StrModality.find("CP") < StrModality.length()) return CP; - else if ( StrModality.find("CR") < StrModality.length()) return CR; - else if ( StrModality.find("CT") < StrModality.length()) return CT; - else if ( StrModality.find("CS") < StrModality.length()) return CS; - else if ( StrModality.find("DD") < StrModality.length()) return DD; - else if ( StrModality.find("DF") < StrModality.length()) return DF; - else if ( StrModality.find("DG") < StrModality.length()) return DG; - else if ( StrModality.find("DM") < StrModality.length()) return DM; - else if ( StrModality.find("DS") < StrModality.length()) return DS; - else if ( StrModality.find("DX") < StrModality.length()) return DX; - else if ( StrModality.find("ECG") < StrModality.length()) return ECG; - else if ( StrModality.find("EPS") < StrModality.length()) return EPS; - else if ( StrModality.find("FA") < StrModality.length()) return FA; - else if ( StrModality.find("FS") < StrModality.length()) return FS; - else if ( StrModality.find("HC") < StrModality.length()) return HC; - else if ( StrModality.find("HD") < StrModality.length()) return HD; - else if ( StrModality.find("LP") < StrModality.length()) return LP; - else if ( StrModality.find("LS") < StrModality.length()) return LS; - else if ( StrModality.find("MA") < StrModality.length()) return MA; - else if ( StrModality.find("MR") < StrModality.length()) return MR; - else if ( StrModality.find("NM") < StrModality.length()) return NM; - else if ( StrModality.find("OT") < StrModality.length()) return OT; - else if ( StrModality.find("PT") < StrModality.length()) return PT; - else if ( StrModality.find("RF") < StrModality.length()) return RF; - else if ( StrModality.find("RG") < StrModality.length()) return RG; - else if ( StrModality.find("RTDOSE") < StrModality.length()) return RTDOSE; - else if ( StrModality.find("RTIMAGE") < StrModality.length()) return RTIMAGE; - else if ( StrModality.find("RTPLAN") < StrModality.length()) return RTPLAN; - else if ( StrModality.find("RTSTRUCT")< StrModality.length()) return RTSTRUCT; - else if ( StrModality.find("SM") < StrModality.length()) return SM; - else if ( StrModality.find("ST") < StrModality.length()) return ST; - else if ( StrModality.find("TG") < StrModality.length()) return TG; - else if ( StrModality.find("US") < StrModality.length()) return US; - else if ( StrModality.find("VF") < StrModality.length()) return VF; - else if ( StrModality.find("XA") < StrModality.length()) return XA; - else if ( StrModality.find("XC") < StrModality.length()) return XC; - - else - { - /// \todo throw error return value ??? - /// specified <> unknow in our database - return Unknow; - } - } - return Unknow; +ModalityType gdcmHeader::GetModality() +{ + // 0008 0060 CS ID Modality + std::string strModality = GetEntryByNumber(0x0008,0x0060); + if ( strModality != GDCM_UNFOUND ) + { + if ( strModality.find("AU") < strModality.length()) return AU; + else if ( strModality.find("AS") < strModality.length()) return AS; + else if ( strModality.find("BI") < strModality.length()) return BI; + else if ( strModality.find("CF") < strModality.length()) return CF; + else if ( strModality.find("CP") < strModality.length()) return CP; + else if ( strModality.find("CR") < strModality.length()) return CR; + else if ( strModality.find("CT") < strModality.length()) return CT; + else if ( strModality.find("CS") < strModality.length()) return CS; + else if ( strModality.find("DD") < strModality.length()) return DD; + else if ( strModality.find("DF") < strModality.length()) return DF; + else if ( strModality.find("DG") < strModality.length()) return DG; + else if ( strModality.find("DM") < strModality.length()) return DM; + else if ( strModality.find("DS") < strModality.length()) return DS; + else if ( strModality.find("DX") < strModality.length()) return DX; + else if ( strModality.find("ECG") < strModality.length()) return ECG; + else if ( strModality.find("EPS") < strModality.length()) return EPS; + else if ( strModality.find("FA") < strModality.length()) return FA; + else if ( strModality.find("FS") < strModality.length()) return FS; + else if ( strModality.find("HC") < strModality.length()) return HC; + else if ( strModality.find("HD") < strModality.length()) return HD; + else if ( strModality.find("LP") < strModality.length()) return LP; + else if ( strModality.find("LS") < strModality.length()) return LS; + else if ( strModality.find("MA") < strModality.length()) return MA; + else if ( strModality.find("MR") < strModality.length()) return MR; + else if ( strModality.find("NM") < strModality.length()) return NM; + else if ( strModality.find("OT") < strModality.length()) return OT; + else if ( strModality.find("PT") < strModality.length()) return PT; + else if ( strModality.find("RF") < strModality.length()) return RF; + else if ( strModality.find("RG") < strModality.length()) return RG; + else if ( strModality.find("RTDOSE") < strModality.length()) return RTDOSE; + else if ( strModality.find("RTIMAGE") < strModality.length()) return RTIMAGE; + else if ( strModality.find("RTPLAN") < strModality.length()) return RTPLAN; + else if ( strModality.find("RTSTRUCT") < strModality.length()) return RTSTRUCT; + else if ( strModality.find("SM") < strModality.length()) return SM; + else if ( strModality.find("ST") < strModality.length()) return ST; + else if ( strModality.find("TG") < strModality.length()) return TG; + else if ( strModality.find("US") < strModality.length()) return US; + else if ( strModality.find("VF") < strModality.length()) return VF; + else if ( strModality.find("XA") < strModality.length()) return XA; + else if ( strModality.find("XC") < strModality.length()) return XC; + + else + { + /// \todo throw error return value ??? + /// specified <> unknow in our database + return Unknow; + } + } + + return Unknow; } /** @@ -594,12 +748,17 @@ ModalityType gdcmHeader::GetModality() { * @return The encountered number of Bits Stored, 0 by default. * 0 means the file is NOT USABLE. The caller has to check it ! */ -int gdcmHeader::GetBitsStored() { - std::string StrSize = GetEntryByNumber(0x0028,0x0101); - if (StrSize == GDCM_UNFOUND) +int gdcmHeader::GetBitsStored() +{ + std::string strSize = GetEntryByNumber(0x0028,0x0101); + if ( strSize == GDCM_UNFOUND ) + { + dbg.Verbose(0, "gdcmHeader::GetBitsStored: this is supposed to be mandatory"); return 0; // It's supposed to be mandatory // the caller will have to check - return atoi(StrSize.c_str()); + } + + return atoi( strSize.c_str() ); } /** @@ -609,12 +768,17 @@ int gdcmHeader::GetBitsStored() { * @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() { - std::string StrSize = GetEntryByNumber(0x0028,0x0100); - if (StrSize == GDCM_UNFOUND) +int gdcmHeader::GetBitsAllocated() +{ + std::string strSize = GetEntryByNumber(0x0028,0x0100); + if ( strSize == GDCM_UNFOUND ) + { + dbg.Verbose(0, "gdcmHeader::GetBitsStored: this is supposed to be mandatory"); return 0; // It's supposed to be mandatory // the caller will have to check - return atoi(StrSize.c_str()); + } + + return atoi( strSize.c_str() ); } /** @@ -624,12 +788,17 @@ int gdcmHeader::GetBitsAllocated() { * @return The encountered number of Samples Per Pixel, 1 by default. * (Gray level Pixels) */ -int gdcmHeader::GetSamplesPerPixel() { - std::string StrSize = GetEntryByNumber(0x0028,0x0002); - if (StrSize == GDCM_UNFOUND) +int gdcmHeader::GetSamplesPerPixel() +{ + std::string strSize = GetEntryByNumber(0x0028,0x0002); + if ( strSize == GDCM_UNFOUND ) + { + dbg.Verbose(0, "gdcmHeader::GetBitsStored: this is supposed to be mandatory"); return 1; // Well, it's supposed to be mandatory ... // but sometimes it's missing : *we* assume Gray pixels - return atoi(StrSize.c_str()); + } + + return atoi( strSize.c_str() ); } /** @@ -638,11 +807,15 @@ int gdcmHeader::GetSamplesPerPixel() { * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane) * @return The encountered Planar Configuration, 0 by default. */ -int gdcmHeader::GetPlanarConfiguration() { - std::string StrSize = GetEntryByNumber(0x0028,0x0006); - if (StrSize == GDCM_UNFOUND) +int gdcmHeader::GetPlanarConfiguration() +{ + std::string strSize = GetEntryByNumber(0x0028,0x0006); + if ( strSize == GDCM_UNFOUND ) + { return 0; - return atoi(StrSize.c_str()); + } + + return atoi( strSize.c_str() ); } /** @@ -651,21 +824,31 @@ int gdcmHeader::GetPlanarConfiguration() { * @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() { - // 0028 0100 US IMG Bits Allocated - // (in order no to be messed up by old RGB images) -// if (gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24") -// return 3; - - std::string PixelType = GetPixelType(); - if (PixelType == "8U" || PixelType == "8S") +int gdcmHeader::GetPixelSize() +{ + // 0028 0100 US IMG Bits Allocated + // (in order no to be messed up by old RGB images) + // if (gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24") + // return 3; + + std::string pixelType = GetPixelType(); + if ( pixelType == "8U" || pixelType == "8S" ) + { return 1; - if (PixelType == "16U" || PixelType == "16S") + } + if ( pixelType == "16U" || pixelType == "16S") + { return 2; - if (PixelType == "32U" || PixelType == "32S") + } + if ( pixelType == "32U" || pixelType == "32S") + { return 4; - if (PixelType == "FD") - return 8; + } + if ( pixelType == "FD" ) + { + return 8; + } + dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type"); return 0; } @@ -685,30 +868,47 @@ 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 BitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated - if (BitsAlloc == GDCM_UNFOUND) { +std::string gdcmHeader::GetPixelType() +{ + std::string bitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated + if ( bitsAlloc == GDCM_UNFOUND ) + { dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated"); - BitsAlloc = std::string("16"); - } - if (BitsAlloc == "64") // ) - return ("FD"); - if (BitsAlloc == "12") // It will be unpacked - BitsAlloc = std::string("16"); - else if (BitsAlloc == "24") // (in order no to be messed up - BitsAlloc = std::string("8"); // by old RGB images) - - std::string Signed = GetEntryByNumber(0x0028, 0x0103); // "Pixel Representation" - if (Signed == GDCM_UNFOUND) { + bitsAlloc = "16"; + } + + if ( bitsAlloc == "64" ) + { + return "FD"; + } + if ( bitsAlloc == "12" ) + { + // It will be unpacked + bitsAlloc = "16"; + } + else if ( bitsAlloc == "24" ) + { + // (in order no to be messed up + bitsAlloc = "8"; // by old RGB images) + } + + std::string sign = GetEntryByNumber(0x0028, 0x0103); // "Pixel Representation" + + if (sign == GDCM_UNFOUND ) + { dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation"); - BitsAlloc = std::string("0"); + bitsAlloc = "0"; + } + if ( sign == "0" ) + { + sign = "U"; } - if (Signed == "0") - Signed = std::string("U"); else - Signed = std::string("S"); + { + sign = "S"; + } - return( BitsAlloc + Signed); + return bitsAlloc + sign; } @@ -718,21 +918,24 @@ std::string gdcmHeader::GetPixelType() { * of *image* pixels (not *icone image* pixels, if any !) * @return Pixel Offset */ -size_t gdcmHeader::GetPixelOffset() { - - gdcmDocEntry* PixelElement = GetDocEntryByNumber(GrPixel,NumPixel); - - if (PixelElement) { - return PixelElement->GetOffset(); - } else { +size_t gdcmHeader::GetPixelOffset() +{ + gdcmDocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel); + if ( pxlElement ) + { + return pxlElement->GetOffset(); + } + else + { #ifdef GDCM_DEBUG std::cout << "Big trouble : Pixel Element (" << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" << std::endl; #endif //GDCM_DEBUG return 0; - } + } } + // TODO : unify those two (previous one and next one) /** * \ingroup gdcmHeader @@ -742,13 +945,15 @@ size_t gdcmHeader::GetPixelOffset() { * -in case of embeded compressed image-) * 0 : NOT USABLE file. The caller has to check. */ -size_t gdcmHeader::GetPixelAreaLength() { - - gdcmDocEntry* PixelElement = GetDocEntryByNumber(GrPixel,NumPixel); - - if (PixelElement) { - return PixelElement->GetLength(); - } else { +size_t gdcmHeader::GetPixelAreaLength() +{ + gdcmDocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel); + if ( pxlElement ) + { + return pxlElement->GetLength(); + } + else + { #ifdef GDCM_DEBUG std::cout << "Big trouble : Pixel Element (" << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" @@ -767,27 +972,40 @@ 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 gdcmHeader::HasLUT() +{ // Check the presence of the LUT Descriptors, and LUT Tables // LutDescriptorRed if ( !GetDocEntryByNumber(0x0028,0x1101) ) + { return false; + } // LutDescriptorGreen if ( !GetDocEntryByNumber(0x0028,0x1102) ) + { return false; + } // LutDescriptorBlue if ( !GetDocEntryByNumber(0x0028,0x1103) ) - return false; + { + return false; + } // Red Palette Color Lookup Table Data if ( !GetDocEntryByNumber(0x0028,0x1201) ) - return false; + { + 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; @@ -801,23 +1019,28 @@ bool gdcmHeader::HasLUT() { * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] * @ return bit number of each LUT item */ -int gdcmHeader::GetLUTNbits() { +int gdcmHeader::GetLUTNbits() +{ std::vector tokens; - //int LutLength; - //int LutDepth; - int LutNbits; + int lutNbits; + //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red = Lookup Table Desc-Blue // Consistency already checked in GetLUTLength - std::string LutDescription = GetEntryByNumber(0x0028,0x1101); - if (LutDescription == GDCM_UNFOUND) + 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 + 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; } /** @@ -836,86 +1059,114 @@ int gdcmHeader::GetLUTNbits() { * no known Dicom reader deals with them :-( * @return a RGBA Lookup Table */ -unsigned char * gdcmHeader::GetLUTRGBA() { -// Not so easy : see -// http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables +uint8_t* gdcmHeader::GetLUTRGBA() +{ + // Not so easy : see + // http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables // if Photometric Interpretation # PALETTE COLOR, no LUT to be done - if (GetEntryByNumber(0x0028,0x0004) != "PALETTE COLOR ") { + if ( GetEntryByNumber(0x0028,0x0004) != "PALETTE COLOR " ) + { return NULL; - } + } + int lengthR, debR, nbitsR; int lengthG, debG, nbitsG; int lengthB, debB, nbitsB; -// Get info from Lut Descriptors -// (the 3 LUT descriptors may be different) - std::string LutDescriptionR = GetEntryByNumber(0x0028,0x1101); - if (LutDescriptionR == GDCM_UNFOUND) + // Get info from Lut Descriptors + // (the 3 LUT descriptors may be different) + std::string lutDescriptionR = GetEntryByNumber(0x0028,0x1101); + if ( lutDescriptionR == GDCM_UNFOUND ) + { return NULL; - std::string LutDescriptionG = GetEntryByNumber(0x0028,0x1102); - if (LutDescriptionG == GDCM_UNFOUND) - return NULL; - std::string LutDescriptionB = GetEntryByNumber(0x0028,0x1103); - if (LutDescriptionB == GDCM_UNFOUND) + } + + 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()); // subscript of the first Lut Value - nbitsG =atoi(tokens[2].c_str()); // Lut item size (in Bits) - 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, "gdcmHeader::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()); // subscript of the first Lut Value - nbitsB =atoi(tokens[2].c_str()); // Lut item size (in Bits) - 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, "gdcmHeader::GetLUTRGBA: trouble reading green LUT"); + } + + // lengthB: Blue LUT length in Bytes + // debB: subscript of the first Lut Value + // nbitsB: Lut item size (in Bits) + nbRead = sscanf( lutDescriptionB.c_str(), "%d\\%d\\%d", + &lengthB, &debB, &nbitsB ); + if( nbRead != 3 ) + { + dbg.Verbose(0, "gdcmHeader::GetLUTRGBA: trouble reading blue LUT"); + } // Load LUTs into memory, (as they were stored on disk) - unsigned char *lutR = (unsigned char *) - GetEntryVoidAreaByNumber(0x0028,0x1201); - unsigned char *lutG = (unsigned char *) - GetEntryVoidAreaByNumber(0x0028,0x1202); - unsigned char *lutB = (unsigned char *) - GetEntryVoidAreaByNumber(0x0028,0x1203); - - if (!lutR || !lutG || !lutB ) { + uint8_t* lutR = (uint8_t*) GetEntryVoidAreaByNumber(0x0028,0x1201); + uint8_t* lutG = (uint8_t*) GetEntryVoidAreaByNumber(0x0028,0x1202); + uint8_t* lutB = (uint8_t*) GetEntryVoidAreaByNumber(0x0028,0x1203); + + if ( !lutR || !lutG || !lutB ) + { + dbg.Verbose(0, "gdcmHeader::GetLUTRGBA: trouble with one of the LUT"); return NULL; } // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT - - unsigned char *LUTRGBA = new unsigned char[1024]; // 256 * 4 (R, G, B, Alpha) - if (!LUTRGBA) { + + uint8_t* LUTRGBA = new uint8_t[1024]; // 256 * 4 (R, G, B, Alpha) + if ( !LUTRGBA ) + { return NULL; } memset(LUTRGBA, 0, 1024); + // Bits Allocated int nb; std::string str_nb = GetEntryByNumber(0x0028,0x0100); - if (str_nb == GDCM_UNFOUND ) { + if ( str_nb == GDCM_UNFOUND ) + { nb = 16; - } else { - nb = atoi(str_nb.c_str() ); - } + } + 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 ( 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 @@ -923,33 +1174,38 @@ unsigned char * gdcmHeader::GetLUTRGBA() { // and fix the code // We give up the checking to avoid some (useless ?)overhead // (optimistic asumption) - unsigned char *a; + uint8_t* a; int i; - a = LUTRGBA+0; - for(i=0;iGetValue(TransfertSyntax); + gdcmTS* ts = gdcmGlobal::GetTS(); + std::string tsName = ts->GetValue( transfertSyntax ); + //delete ts; /// \todo Seg Fault when deleted ?! return tsName; } @@ -978,18 +1243,18 @@ std::string gdcmHeader::GetTransfertSyntaxName() { * @param ImageDataSize new Pixel Area Size * warning : nothing else is checked */ -void gdcmHeader::SetImageDataSize(size_t ImageDataSize) { - std::string content1; +void gdcmHeader::SetImageDataSize(size_t ImageDataSize) +{ char car[20]; - sprintf(car,"%d",ImageDataSize); gdcmDocEntry *a = GetDocEntryByNumber(GrPixel, NumPixel); a->SetLength(ImageDataSize); - ImageDataSize+=8; + ImageDataSize += 8; sprintf(car,"%d",ImageDataSize); - content1=car; + + const std::string content1 = car; SetEntryByNumber(content1, GrPixel, NumPixel); } @@ -1000,25 +1265,30 @@ 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 gdcmHeader::AnonymizeHeader() +{ + gdcmDocEntry* patientNameHE = GetDocEntryByNumber (0x0010, 0x0010); - gdcmDocEntry *patientNameHE = GetDocEntryByNumber (0x0010, 0x0010); - - ReplaceIfExistByNumber (" ",0x0010, 0x2154); // Telephone - ReplaceIfExistByNumber (" ",0x0010, 0x1040); // Adress - ReplaceIfExistByNumber (" ",0x0010, 0x0020); // Patient ID - - if (patientNameHE) { - std::string studyInstanceUID = GetEntryByNumber (0x0020, 0x000d); - if (studyInstanceUID !=GDCM_UNFOUND) - ReplaceOrCreateByNumber(studyInstanceUID, 0x0010, 0x0010); - else - ReplaceOrCreateByNumber(std::string("anonymised"), 0x0010, 0x0010); - } + ReplaceIfExistByNumber (" ",0x0010, 0x2154); // Telephone + ReplaceIfExistByNumber (" ",0x0010, 0x1040); // Adress + ReplaceIfExistByNumber (" ",0x0010, 0x0020); // Patient ID + if ( patientNameHE ) + { + std::string studyInstanceUID = GetEntryByNumber (0x0020, 0x000d); + if ( studyInstanceUID != GDCM_UNFOUND ) + { + ReplaceOrCreateByNumber(studyInstanceUID, 0x0010, 0x0010); + } + else + { + ReplaceOrCreateByNumber(std::string("anonymised"), 0x0010, 0x0010); + } + } + // Just for fun :-( // (if any) remove or replace all the stuff that contains a Date - + //0008 0012 DA ID Instance Creation Date //0008 0020 DA ID Study Date //0008 0021 DA ID Series Date @@ -1067,7 +1337,8 @@ bool gdcmHeader::AnonymizeHeader() { //300a 0006 DA RT RT Plan Date //300a 022c DA RT Air Kerma Rate Reference Date //300e 0004 DA RT Review Date - return true; + + return true; } /** @@ -1075,35 +1346,33 @@ 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 ) { - - //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) - std::string StrImOriPat = GetEntryByNumber(0x0020,0x0037); - if (StrImOriPat != 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) { +void gdcmHeader::GetImageOrientationPatient( float iop[6] ) +{ + std::string strImOriPat; + //iop is supposed to be float[6] + iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.; + + // 0020 0037 DS REL Image Orientation (Patient) + if ( (strImOriPat = GetEntryByNumber(0x0020,0x0037)) != GDCM_UNFOUND ) + { + if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f", + &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) + { dbg.Verbose(0, "gdcmHeader::GetImageOrientationPatient: wrong Image Orientation Patient (0020,0037)"); - return ; // bug in the element 0x0020,0x0037 - } - else - return ; - } - - //For ACR-NEMA - // 0020 0035 DS REL Image Orientation (RET) - StrImOriPat = GetEntryByNumber(0x0020,0x0035); - if (StrImOriPat != 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) { + // bug in the element 0x0020,0x0037 + } + } + //For ACR-NEMA + // 0020 0035 DS REL Image Orientation (RET) + else if ( (strImOriPat = GetEntryByNumber(0x0020,0x0035)) != GDCM_UNFOUND ) + { + if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f", + &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) + { dbg.Verbose(0, "gdcmHeader::GetImageOrientationPatient: wrong Image Orientation Patient (0020,0035)"); - return ; // bug in the element 0x0020,0x0035 - } - else - return ; - } + // bug in the element 0x0020,0x0035 + } + } } //-----------------------------------------------------------------------------