X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=c46ddb0f91c78decda2c1e17121b5c7d911625d7;hb=3ba8c03aa6cb08add6599a1ec7b2b693a967db62;hp=ca880becce9229520286b4bd35610cf959dd5dfd;hpb=689f929ff0f35aabd30d81ffa75eb66fdf1a3c16;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index ca880bec..c46ddb0f 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmHeader.cxx,v $ Language: C++ - Date: $Date: 2004/09/29 17:33:17 $ - Version: $Revision: 1.190 $ + Date: $Date: 2004/11/30 16:24:31 $ + Version: $Revision: 1.209 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -22,17 +22,20 @@ #include "gdcmDebug.h" #include "gdcmTS.h" #include "gdcmValEntry.h" +#include //sscanf #include +namespace gdcm +{ //----------------------------------------------------------------------------- // Constructor / Destructor /** * \brief Constructor * @param filename name of the file whose header we want to analyze */ -gdcmHeader::gdcmHeader( std::string const & filename ): - gdcmDocument( filename ) +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 @@ -45,7 +48,7 @@ gdcmHeader::gdcmHeader( std::string const & filename ): // Note: this IS the right place for the code // Image Location - std::string imgLocation = GetEntryByNumber(0x0028, 0x0200); + const std::string &imgLocation = GetEntryByNumber(0x0028, 0x0200); if ( imgLocation == GDCM_UNFOUND ) { // default value @@ -76,21 +79,21 @@ gdcmHeader::gdcmHeader( std::string const & filename ): } /** - * \brief Constructor + * \brief Constructor used when we want to generate dicom files from scratch */ -gdcmHeader::gdcmHeader() - :gdcmDocument() +Header::Header() + :Document() { + InitializeDefaultHeader(); } /** * \brief Canonical destructor. */ -gdcmHeader::~gdcmHeader () +Header::~Header () { } - /** * \brief Performs some consistency checking on various 'File related' * (as opposed to 'DicomDir related') entries @@ -99,8 +102,16 @@ gdcmHeader::~gdcmHeader () * @param filetype Type of the File to be written * (ACR-NEMA, ExplicitVR, ImplicitVR) */ -void gdcmHeader::Write(FILE* fp,FileType filetype) +bool Header::Write(std::string fileName,FileType filetype) { + std::ofstream* fp = new std::ofstream(fileName.c_str(), + std::ios::out | std::ios::binary); + if (fp == NULL) + { + dbg.Verbose(2, "Failed to open (write) File: " , fileName.c_str()); + return false; + } + // Bits Allocated if ( GetEntryByNumber(0x0028,0x0100) == "12") { @@ -113,14 +124,12 @@ void gdcmHeader::Write(FILE* fp,FileType filetype) 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; + std::string s_lgPix = Util::Format("%d", i_lgPix+12); + s_lgPix = Util::DicomString( s_lgPix.c_str() ); ReplaceOrCreateByNumber(s_lgPix,GrPixel, 0x0000); } - // FIXME : should be nice if we could move it to gdcmFile + // FIXME : should be nice if we could move it to File // (or in future gdcmPixelData class) // Drop Palette Color, if necessary @@ -131,7 +140,7 @@ void gdcmHeader::Write(FILE* fp,FileType filetype) // Drop 0028|1101, 0028|1102, 0028|1103 // Drop 0028|1201, 0028|1202, 0028|1203 - gdcmDocEntry* e = GetDocEntryByNumber(0x0028,0x01101); + DocEntry* e = GetDocEntryByNumber(0x0028,0x01101); if (e) { RemoveEntryNoDestroy(e); @@ -162,7 +171,12 @@ void gdcmHeader::Write(FILE* fp,FileType filetype) RemoveEntryNoDestroy(e); } } - gdcmDocument::Write(fp,filetype); + Document::WriteContent(fp,filetype); + + fp->close(); + delete fp; + + return true; } //----------------------------------------------------------------------------- @@ -174,20 +188,20 @@ 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; } - std::string res = GetEntryByNumber(0x0028, 0x0005); + const std::string &res = GetEntryByNumber(0x0028, 0x0005); if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) { return false; // Image Dimensions @@ -217,10 +231,9 @@ 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); + const std::string &strSize = GetEntryByNumber(0x0028,0x0011); if ( strSize == GDCM_UNFOUND ) { return 0; @@ -231,13 +244,13 @@ int gdcmHeader::GetXSize() /** * \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); + const std::string &strSize = GetEntryByNumber(0x0028,0x0010); if ( strSize != GDCM_UNFOUND ) { return atoi( strSize.c_str() ); @@ -260,21 +273,21 @@ 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. - std::string strSize = GetEntryByNumber(0x0028,0x0008); + const 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 ) + const std::string &strSize2 = GetEntryByNumber(0x0028,0x0012); + if ( strSize2 != GDCM_UNFOUND ) { - return atoi( strSize.c_str() ); + return atoi( strSize2.c_str() ); } return 1; @@ -285,14 +298,14 @@ int gdcmHeader::GetZSize() * else 1.0 * @return X dimension of a pixel */ -float gdcmHeader::GetXSpacing() +float Header::GetXSpacing() { float xspacing, yspacing; - std::string strSpacing = GetEntryByNumber(0x0028,0x0030); + const 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 +321,7 @@ 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); } @@ -321,14 +334,14 @@ float gdcmHeader::GetXSpacing() * 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.; } @@ -344,7 +357,7 @@ float gdcmHeader::GetYSpacing() * else 1.0 * @return Z dimension of a voxel-to be */ -float gdcmHeader::GetZSpacing() +float Header::GetZSpacing() { // Spacing Between Slices : distance entre le milieu de chaque coupe // Les coupes peuvent etre : @@ -360,7 +373,7 @@ 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 ) { @@ -372,20 +385,21 @@ float gdcmHeader::GetZSpacing() // we assume slices join together // (no overlapping, no interslice gap) // if they don't, we're fucked up - return atof( strSliceThickness.c_str() ); + return (float)atof( strSliceThickness.c_str() ); } } else { - return atof( strSpacingBSlices.c_str() ); + return (float)atof( strSpacingBSlices.c_str() ); } + return 1.; } /** *\brief gets the info from 0028,1052 : Rescale Intercept * @return Rescale Intercept */ -float gdcmHeader::GetRescaleIntercept() +float Header::GetRescaleIntercept() { float resInter = 0.; /// 0028 1052 DS IMG Rescale Intercept @@ -395,7 +409,7 @@ float gdcmHeader::GetRescaleIntercept() if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 ) { // bug in the element 0x0028,0x1052 - dbg.Verbose(0, "gdcmHeader::GetRescaleIntercept: Rescale Slope " + dbg.Verbose(0, "Header::GetRescaleIntercept: Rescale Slope " "is empty"); } } @@ -407,7 +421,7 @@ float gdcmHeader::GetRescaleIntercept() *\brief gets the info from 0028,1053 : Rescale Slope * @return Rescale Slope */ -float gdcmHeader::GetRescaleSlope() +float Header::GetRescaleSlope() { float resSlope = 1.; //0028 1053 DS IMG Rescale Slope @@ -417,7 +431,7 @@ float gdcmHeader::GetRescaleSlope() 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"); } } @@ -431,7 +445,7 @@ float gdcmHeader::GetRescaleSlope() * \warning to be used with GetImagePixels() * @return 1 if Gray level, 3 if Color (RGB, YBR or PALETTE COLOR) */ -int gdcmHeader::GetNumberOfScalarComponents() +int Header::GetNumberOfScalarComponents() { if ( GetSamplesPerPixel() == 3 ) { @@ -462,8 +476,8 @@ int gdcmHeader::GetNumberOfScalarComponents() // beware of trailing space at end of string // DICOM tags are never of odd length if ( strPhotometricInterpretation == GDCM_UNFOUND || - strPhotometricInterpretation == "MONOCHROME1 " || - strPhotometricInterpretation == "MONOCHROME2 " ) + Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME1") || + Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME2") ) { return 1; } @@ -481,11 +495,11 @@ 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() +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; } @@ -516,19 +530,19 @@ int gdcmHeader::GetNumberOfScalarComponentsRaw() * else 0. * @return up-left image corner X position */ -float gdcmHeader::GetXOrigin() +float Header::GetXOrigin() { float xImPos, yImPos, zImPos; std::string strImPos = GetEntryByNumber(0x0020,0x0032); if ( strImPos == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image " + 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 " + dbg.Verbose(0, "Header::GetXImagePosition: unfound Image " "Position (RET) (0020,0030)"); /// \todo How to tell the caller nothing was found ? return 0.; @@ -549,19 +563,19 @@ float gdcmHeader::GetXOrigin() * else 0. * @return up-left image corner Y position */ -float gdcmHeader::GetYOrigin() +float Header::GetYOrigin() { float xImPos, yImPos, zImPos; std::string strImPos = GetEntryByNumber(0x0020,0x0032); if ( strImPos == GDCM_UNFOUND) { - dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image " + 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 " + dbg.Verbose(0, "Header::GetYImagePosition: unfound Image " "Position (RET) (0020,0030)"); /// \todo How to tell the caller nothing was found ? return 0.; @@ -584,7 +598,7 @@ float gdcmHeader::GetYOrigin() * else 0. * @return up-left image corner Z position */ -float gdcmHeader::GetZOrigin() +float Header::GetZOrigin() { float xImPos, yImPos, zImPos; std::string strImPos = GetEntryByNumber(0x0020,0x0032); @@ -593,7 +607,7 @@ float gdcmHeader::GetZOrigin() { if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) { - dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image " + dbg.Verbose(0, "Header::GetZImagePosition: wrong Image " "Position Patient (0020,0032)"); return 0.; // bug in the element 0x0020,0x0032 } @@ -609,7 +623,7 @@ 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 @@ -623,7 +637,7 @@ 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 @@ -631,14 +645,14 @@ 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 @@ -646,7 +660,7 @@ 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 } @@ -655,7 +669,7 @@ float gdcmHeader::GetZOrigin() * \brief gets the info from 0020,0013 : Image Number else 0. * @return image number */ -int gdcmHeader::GetImageNumber() +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 @@ -676,7 +690,7 @@ int gdcmHeader::GetImageNumber() * \brief gets the info from 0008,0060 : Modality * @return Modality Type */ -ModalityType gdcmHeader::GetModality() +ModalityType Header::GetModality() { // 0008 0060 CS ID Modality std::string strModality = GetEntryByNumber(0x0008,0x0060); @@ -740,12 +754,12 @@ 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() +int Header::GetBitsStored() { std::string strSize = GetEntryByNumber( 0x0028, 0x0101 ); if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetBitsStored: this is supposed to " + 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 @@ -759,12 +773,12 @@ int gdcmHeader::GetBitsStored() * The responsability of checking this value is left to the caller. * @return The high bit positin when present. 0 when absent. */ -int gdcmHeader::GetHighBitPosition() +int Header::GetHighBitPosition() { std::string strSize = GetEntryByNumber( 0x0028, 0x0102 ); if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetHighBitPosition: this is supposed " + dbg.Verbose(0, "Header::GetHighBitPosition: this is supposed " "to be mandatory"); return 0; } @@ -777,12 +791,12 @@ int gdcmHeader::GetHighBitPosition() * The responsability of checking this value is left to the caller. * @return True when signed, false when UNsigned */ -bool gdcmHeader::IsSignedPixelData() +bool Header::IsSignedPixelData() { std::string strSize = GetEntryByNumber( 0x0028, 0x0103 ); if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::IsSignedPixelData: this is supposed " + dbg.Verbose(0, "Header::IsSignedPixelData: this is supposed " "to be mandatory"); return false; } @@ -800,12 +814,12 @@ bool gdcmHeader::IsSignedPixelData() * @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 " + 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 @@ -819,12 +833,12 @@ int gdcmHeader::GetBitsAllocated() * @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); + const std::string& strSize = GetEntryByNumber(0x0028,0x0002); if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetBitsStored: this is supposed to " + 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 @@ -837,17 +851,17 @@ int gdcmHeader::GetSamplesPerPixel() * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise. */ -bool gdcmHeader::IsMonochrome() +bool Header::IsMonochrome() { - std::string PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 ); - if ( PhotometricInterp == "MONOCHROME1 " - || PhotometricInterp == "MONOCHROME2 " ) + const std::string& PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 ); + if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") + || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") ) { return true; } if ( PhotometricInterp == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::IsMonochrome: absent Photometric " + dbg.Verbose(0, "Header::IsMonochrome: absent Photometric " "Interpretation"); } return false; @@ -858,7 +872,7 @@ bool gdcmHeader::IsMonochrome() * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). * @return true when "PALETTE COLOR". False otherwise. */ -bool gdcmHeader::IsPaletteColor() +bool Header::IsPaletteColor() { std::string PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 ); if ( PhotometricInterp == "PALETTE COLOR " ) @@ -867,7 +881,7 @@ bool gdcmHeader::IsPaletteColor() } if ( PhotometricInterp == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::IsPaletteColor: absent Photometric " + dbg.Verbose(0, "Header::IsPaletteColor: absent Photometric " "Interpretation"); } return false; @@ -878,7 +892,7 @@ bool gdcmHeader::IsPaletteColor() * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). * @return true when "YBR_FULL". False otherwise. */ -bool gdcmHeader::IsYBRFull() +bool Header::IsYBRFull() { std::string PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 ); if ( PhotometricInterp == "YBR_FULL" ) @@ -887,7 +901,7 @@ bool gdcmHeader::IsYBRFull() } if ( PhotometricInterp == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::IsYBRFull: absent Photometric " + dbg.Verbose(0, "Header::IsYBRFull: absent Photometric " "Interpretation"); } return false; @@ -898,7 +912,7 @@ bool gdcmHeader::IsYBRFull() * (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 ) @@ -913,11 +927,11 @@ 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() +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(); @@ -937,7 +951,7 @@ int gdcmHeader::GetPixelSize() { return 8; } - dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type"); + dbg.Verbose(0, "Header::GetPixelSize: Unknown pixel type"); return 0; } @@ -955,12 +969,12 @@ 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"; } @@ -983,7 +997,7 @@ std::string gdcmHeader::GetPixelType() 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" ) @@ -1003,9 +1017,9 @@ std::string gdcmHeader::GetPixelType() * 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(); @@ -1029,9 +1043,9 @@ size_t gdcmHeader::GetPixelOffset() * -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(); @@ -1055,7 +1069,7 @@ 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 @@ -1101,7 +1115,7 @@ bool gdcmHeader::HasLUT() * 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; @@ -1116,7 +1130,7 @@ 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()); @@ -1127,176 +1141,13 @@ int gdcmHeader::GetLUTNbits() } /** - * \brief builts Red/Green/Blue/Alpha LUT from Header - * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] - * and (0028,1101),(0028,1102),(0028,1102) - * - xxx Palette Color Lookup Table Descriptor - are found - * and (0028,1201),(0028,1202),(0028,1202) - * - xxx Palette Color Lookup Table Data - are found - * \warning does NOT deal with : - * 0028 1100 Gray Lookup Table Descriptor (Retired) - * 0028 1221 Segmented Red Palette Color Lookup Table Data - * 0028 1222 Segmented Green Palette Color Lookup Table Data - * 0028 1223 Segmented Blue Palette Color Lookup Table Data - * no known Dicom reader deals with them :-( - * @return a RGBA Lookup Table - */ -uint8_t* gdcmHeader::GetLUTRGBA() -{ - // Not so easy : see - // http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables - -// if Photometric Interpretation # PALETTE COLOR, no LUT to be done - if ( GetEntryByNumber(0x0028,0x0004) != "PALETTE COLOR " ) - { - return NULL; - } - - int lengthR, debR, nbitsR; - int lengthG, debG, nbitsG; - int lengthB, debB, nbitsB; - - // Get info from Lut Descriptors - // (the 3 LUT descriptors may be different) - std::string lutDescriptionR = GetEntryByNumber(0x0028,0x1101); - if ( lutDescriptionR == GDCM_UNFOUND ) - { - return NULL; - } - - std::string lutDescriptionG = GetEntryByNumber(0x0028,0x1102); - if ( lutDescriptionG == GDCM_UNFOUND ) - { - return NULL; - } - - std::string lutDescriptionB = GetEntryByNumber(0x0028,0x1103); - if ( lutDescriptionB == GDCM_UNFOUND ) - { - return NULL; - } - - // lengthR: Red LUT length in Bytes - // debR: subscript of the first Lut Value - // nbitsR: Lut item size (in Bits) - int nbRead = sscanf( lutDescriptionR.c_str(), "%d\\%d\\%d", - &lengthR, &debR, &nbitsR ); - if( nbRead != 3 ) - { - dbg.Verbose(0, "gdcmHeader::GetLUTRGBA: trouble reading red LUT"); - } - - // lengthG: Green LUT length in Bytes - // debG: subscript of the first Lut Value - // nbitsG: Lut item size (in Bits) - nbRead = sscanf( lutDescriptionG.c_str(), "%d\\%d\\%d", - &lengthG, &debG, &nbitsG ); - if( nbRead != 3 ) - { - dbg.Verbose(0, "gdcmHeader::GetLUTRGBA: trouble reading green LUT"); - } - - // lengthB: Blue LUT length in Bytes - // debB: subscript of the first Lut Value - // nbitsB: Lut item size (in Bits) - nbRead = sscanf( lutDescriptionB.c_str(), "%d\\%d\\%d", - &lengthB, &debB, &nbitsB ); - if( nbRead != 3 ) - { - dbg.Verbose(0, "gdcmHeader::GetLUTRGBA: trouble reading blue LUT"); - } - - // Load LUTs into memory, (as they were stored on disk) - uint8_t* lutR = (uint8_t*) 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"); - return NULL; - } - // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT - - uint8_t* LUTRGBA = new uint8_t[1024]; // 256 * 4 (R, G, B, Alpha) - if ( !LUTRGBA ) - { - return NULL; - } - memset(LUTRGBA, 0, 1024); - - // Bits Allocated - int nb; - std::string str_nb = GetEntryByNumber(0x0028,0x0100); - if ( str_nb == GDCM_UNFOUND ) - { - nb = 16; - } - else - { - nb = atoi( str_nb.c_str() ); - } - int mult; - - if ( nbitsR == 16 && nb == 8) - { - // when LUT item size is different than pixel size - mult = 2; // high byte must be = low byte - } - else - { - // See PS 3.3-2003 C.11.1.1.2 p 619 - mult = 1; - } - - // if we get a black image, let's just remove the '+1' - // from 'i*mult+1' and check again - // if it works, we shall have to check the 3 Palettes - // to see which byte is ==0 (first one, or second one) - // and fix the code - // We give up the checking to avoid some (useless ?)overhead - // (optimistic asumption) - uint8_t* a; - int i; - - a = LUTRGBA + 0; - for( i=0; i < lengthR; ++i) - { - *a = lutR[i*mult+1]; - a += 4; - } - - a = LUTRGBA + 1; - for( i=0; i < lengthG; ++i) - { - *a = lutG[i*mult+1]; - a += 4; - } - - a = LUTRGBA + 2; - for(i=0; i < lengthB; ++i) - { - *a = lutB[i*mult+1]; - a += 4; - } - - a = LUTRGBA + 3; - for(i=0; i < 256; ++i) - { - *a = 1; // Alpha component - a += 4; - } - return LUTRGBA; -} - -/** - * \brief Accesses the info from 0002,0010 : Transfert Syntax and gdcmTS + * \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 ) @@ -1308,44 +1159,23 @@ std::string gdcmHeader::GetTransfertSyntaxName() } if ( transfertSyntax == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetTransfertSyntaxName:" + dbg.Verbose(0, "Header::GetTransfertSyntaxName:" " unfound Transfert Syntax (0002,0010)"); return "Uncompressed ACR-NEMA"; } - while ( ! isdigit(transfertSyntax[transfertSyntax.length()-1]) ) + while ( ! isdigit((unsigned char)transfertSyntax[transfertSyntax.length()-1]) ) { 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 ?! return tsName; } -/** - * \brief Sets the Pixel Area size in the Header - * --> not-for-rats function - * @param ImageDataSize new Pixel Area Size - * warning : nothing else is checked - */ -void gdcmHeader::SetImageDataSize(size_t ImageDataSize) -{ - char car[20]; - sprintf(car,"%d",ImageDataSize); - - gdcmDocEntry *a = GetDocEntryByNumber(GrPixel, NumPixel); - a->SetLength(ImageDataSize); - - ImageDataSize += 8; - sprintf(car,"%d",ImageDataSize); - - const std::string content1 = car; - SetEntryByNumber(content1, GrPixel, NumPixel); -} - //----------------------------------------------------------------------------- // Protected @@ -1353,14 +1183,14 @@ 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() { // If exist, replace by spaces SetEntryByNumber (" ",0x0010, 0x2154); // Telephone SetEntryByNumber (" ",0x0010, 0x1040); // Adress SetEntryByNumber (" ",0x0010, 0x0020); // Patient ID - gdcmDocEntry* patientNameHE = GetDocEntryByNumber (0x0010, 0x0010); + DocEntry* patientNameHE = GetDocEntryByNumber (0x0010, 0x0010); if ( patientNameHE ) // we replace it by Study Instance UID (why not) { @@ -1371,7 +1201,7 @@ bool gdcmHeader::AnonymizeHeader() } else { - ReplaceOrCreateByNumber(std::string("anonymised"), 0x0010, 0x0010); + ReplaceOrCreateByNumber("anonymised", 0x0010, 0x0010); } } @@ -1435,7 +1265,7 @@ 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[6] ) +void Header::GetImageOrientationPatient( float iop[6] ) { std::string strImOriPat; //iop is supposed to be float[6] @@ -1447,7 +1277,7 @@ void gdcmHeader::GetImageOrientationPatient( float iop[6] ) 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: " + dbg.Verbose(0, "Header::GetImageOrientationPatient: " "wrong Image Orientation Patient (0020,0037)"); } } @@ -1458,13 +1288,101 @@ void gdcmHeader::GetImageOrientationPatient( float iop[6] ) 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: " + dbg.Verbose(0, "Header::GetImageOrientationPatient: " "wrong Image Orientation Patient (0020,0035)"); } } } +/** + * \brief Initialize a default DICOM header that should contain all the + * field require by other reader. DICOM standart does not + * explicitely defines thoses fields, heuristic has been choosen. + * This is not perfect as we are writting a CT image... + */ +void Header::InitializeDefaultHeader() +{ + typedef struct + { + const char *value; + uint16_t group; + uint16_t elem; + } DICOM_DEFAULT_VALUE; + + const char *date = Util::GetCurrentDate().c_str(); + const char *time = Util::GetCurrentTime().c_str(); + const char *uid = Util::CreateUniqueUID().c_str(); + + static DICOM_DEFAULT_VALUE defaultvalue[] = { + "76", 0x0002, 0x0000, // MetaElementGroup Length // FIXME: how to recompute ? + "1.2.840.10008.5.1.4.1.1.2", 0x0002, 0x0002, // MediaStorageSOPInstanceUID (CT Image Storage) + uid, 0x0002, 0x0012, // META Implementation Class UID + "ISO_IR 100", 0x0008, 0x0005, // Specific Character Set + "DERIVED\\SECONDARY\\OTHER\\GDCM", 0x0008, 0x0008, // Image Type + "1.2.840.10008.5.1.4.1.1.2", 0x0008, 0x0016, // SOP Class UID + "", 0x0008, 0x0050, // Accession Number + "GDCM", 0x0008, 0x0070, // Manufacturer + "GDCM", 0x0008, 0x0080, // Institution Name + "http://www-creatis.insa-lyon.fr/Public/Gdcm/", 0x0008, 0x0081, // Institution Address + "", 0x0008, 0x0090, // Refering Physician Name + "", 0x0008, 0x1030, // Study Description + "", 0x0008, 0x1050, // Performing Physician's Name + "", 0x0008, 0x1060, // Name of Physician(s) Reading Study + "", 0x0010, 0x0040, // Patient's Sex + uid, 0x0020, 0x000d, // StudyInstanceUID + uid, 0x0020, 0x000e, // SeriesInstanceUID + "", 0x0020, 0x0011, // AcquisitionNumber + "1\\0\\0\\0\\1\\0", 0x0020, 0x0037, // Image Orientation Patient + "1", 0x0028, 0x0002, // Samples per pixel 1 or 3 + "MONOCHROME2", 0x0028, 0x0004, // photochromatic interpretation + +// Date and time + + date, 0x0008, 0x0012, // Instance Creation Date + time, 0x0008, 0x0013, // Instance Creation Time + date, 0x0008, 0x0020, // Study Date + date, 0x0008, 0x0022, // Acquisition Date + date, 0x0008, 0x0023, // Content Date + time, 0x0008, 0x0030, // Study Time + "CT", 0x0008, 0x0060, // Modality + "GDCM", 0x0010, 0x0010, // Patient's Name + "GDCMID", 0x0010, 0x0020, // Patient ID + "1", 0x0020, 0x0010, // StudyID + "1", 0x0020, 0x0011, // SeriesNumber + "1.0", 0x0018, 0x0050, // slice Thickness + "1.0", 0x0018, 0x0088, // space between slices + "1.0\\1.0", 0x0028, 0x0030, // pixelSpacing + "64", 0x0028, 0x0010, // nbRows + "64", 0x0028, 0x0011, // nbCols + "16", 0x0028, 0x0100, // BitsAllocated 8 or 16 + "12", 0x0028, 0x0101, // BitsStored 8 or 12 + "11", 0x0028, 0x0102, // HighBit 7 or 11 + "0", 0x0028, 0x0103, // Pixel Representation 0(unsigned) or 1(signed) + "1000.0", 0x0028, 0x1051, // Window Width + "500.0", 0x0028, 0x1050, // Window Center + 0, 0, 0 + }; + + // default value + // Special case this is the image (not a string) + GrPixel = 0x7fe0; + NumPixel = 0x0010; + ReplaceOrCreateByNumber(0, 0, GrPixel, NumPixel); + + // All remaining strings: + unsigned int i = 0; + DICOM_DEFAULT_VALUE current = defaultvalue[i]; + while( current.value ) + { + std::string value = Util::DicomString( current.value ); //pad the string properly + ReplaceOrCreateByNumber(value, current.group, current.elem); + current = defaultvalue[++i]; + } +} + //----------------------------------------------------------------------------- // Private //----------------------------------------------------------------------------- + +} // end namespace gdcm