X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=bc28cd19ea484773535b420a477dc7439d6fb4a9;hb=4beda181275414e5cba990113f8d16424b2c09e6;hp=a623626f2efae27c0645295f9543749ec735acb6;hpb=c9dd24ae7aab3c9f32af740ebfce6dfb47bd855f;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index a623626f..bc28cd19 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmHeader.cxx,v $ Language: C++ - Date: $Date: 2004/10/10 00:42:54 $ - Version: $Revision: 1.192 $ + Date: $Date: 2005/01/06 15:36:48 $ + Version: $Revision: 1.220 $ 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 @@ -73,24 +76,47 @@ gdcmHeader::gdcmHeader( std::string const & filename ): { NumPixel = 0x0010; } + + // Now, we know GrPixel and NumPixel. + // Let's create a VirtualDictEntry to allow a further VR modification + // and force VR to match with BitsAllocated. + + DocEntry* entry = GetDocEntryByNumber(GrPixel, NumPixel); + if ( entry != 0 ) + { + + std::string PixelVR; + // 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB) + // more than 8 (i.e 12, 16) is a 'O Words' + if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 ) + PixelVR = "OB"; + else + PixelVR = "OW"; + + DictEntry* newEntry = NewVirtualDictEntry( + GrPixel, NumPixel, + PixelVR, "PXL", "Pixel Data"); + + entry->SetDictEntry( newEntry ); + } } /** - * \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 +125,16 @@ 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") { @@ -113,12 +147,12 @@ void gdcmHeader::Write(FILE* fp,FileType filetype) if (i_lgPix != -2) { // no (GrPixel, NumPixel) element - std::string s_lgPix; - s_lgPix = gdcmUtil::Format("%d", i_lgPix+12); + 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 @@ -129,7 +163,7 @@ 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); @@ -160,7 +194,12 @@ void gdcmHeader::Write(FILE* fp,FileType filetype) RemoveEntryNoDestroy(e); } } - gdcmDocument::Write(fp,filetype); + Document::WriteContent(fp,filetype); + + fp->close(); + delete fp; + + return true; } //----------------------------------------------------------------------------- @@ -172,20 +211,20 @@ 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 @@ -215,10 +254,9 @@ 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; @@ -229,13 +267,13 @@ 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() ); @@ -246,7 +284,7 @@ int gdcmHeader::GetYSize() } // The Rows (0028,0010) entry was optional for ACR/NEMA. It might - // hence be a signal (1d image). So we default to 1: + // hence be a signal (1D image). So we default to 1: return 1; } @@ -258,21 +296,21 @@ 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; @@ -283,14 +321,14 @@ 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.; } @@ -301,14 +339,26 @@ float gdcmHeader::GetXSpacing() // if single value is found, xspacing is defaulted to yspacing if ( nbValues == 1 ) { - return yspacing; + xspacing = yspacing; } + + if ( xspacing == 0.0 ) + xspacing = 1.0; + + return xspacing; + } + + // to avoid troubles with David Clunie's-like images + if ( xspacing == 0. && yspacing == 0.) + return 1.; + if ( xspacing == 0.) { - dbg.Verbose(0, "gdcmHeader::GetYSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem"); + dbg.Verbose(0, "Header::GetXSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem"); // seems to be a bug in the header ... - sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing); + nbValues = sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing); + assert( nbValues == 2 ); } return xspacing; @@ -319,30 +369,33 @@ float gdcmHeader::GetXSpacing() * else 1.0 * @return Y dimension of a pixel */ -float gdcmHeader::GetYSpacing() +float Header::GetYSpacing() { - float yspacing = 0; + float yspacing = 1.; 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.; } // if sscanf cannot read any float value, it won't affect yspacing sscanf( strSpacing.c_str(), "%f", &yspacing); + if ( yspacing == 0.0 ) + yspacing = 1.0; + return yspacing; } /** * \brief gets the info from 0018,0088 : Space Between Slices - * else from 0018,0050 : Slice Thickness - * else 1.0 + * else from 0018,0050 : Slice Thickness + * 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 : @@ -354,12 +407,12 @@ float gdcmHeader::GetZSpacing() // Si le Spacing Between Slices est absent, // on suppose que les coupes sont jointives - std::string strSpacingBSlices = GetEntryByNumber(0x0018,0x0088); + const std::string &strSpacingBSlices = GetEntryByNumber(0x0018,0x0088); if ( strSpacingBSlices == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetZSpacing: unfound StrSpacingBSlices"); - std::string strSliceThickness = GetEntryByNumber(0x0018,0x0050); + dbg.Verbose(0, "Header::GetZSpacing: unfound StrSpacingBSlices"); + const std::string &strSliceThickness = GetEntryByNumber(0x0018,0x0050); if ( strSliceThickness == GDCM_UNFOUND ) { return 1.; @@ -370,30 +423,28 @@ 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() ); - } + //else + return (float)atof( strSpacingBSlices.c_str() ); } /** *\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 - std::string strRescInter = GetEntryByNumber(0x0028,0x1052); + const 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 " + dbg.Verbose(0, "Header::GetRescaleIntercept: Rescale Slope " "is empty"); } } @@ -405,7 +456,7 @@ 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 @@ -415,7 +466,7 @@ 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"); } } @@ -429,7 +480,7 @@ 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 ) { @@ -460,8 +511,8 @@ 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; } @@ -479,11 +530,11 @@ 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; } @@ -514,19 +565,19 @@ 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.; @@ -547,19 +598,19 @@ 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.; @@ -582,7 +633,7 @@ 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); @@ -591,7 +642,7 @@ 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 } @@ -607,7 +658,7 @@ 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 @@ -621,7 +672,7 @@ 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 @@ -629,14 +680,14 @@ 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 @@ -644,7 +695,7 @@ 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 } @@ -653,7 +704,7 @@ 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 @@ -674,7 +725,7 @@ 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); @@ -738,12 +789,12 @@ 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 @@ -757,12 +808,12 @@ 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; } @@ -775,12 +826,12 @@ 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; } @@ -798,12 +849,12 @@ 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 @@ -817,12 +868,12 @@ 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 @@ -835,17 +886,17 @@ 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; @@ -856,7 +907,7 @@ 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 " ) @@ -865,7 +916,7 @@ bool gdcmHeader::IsPaletteColor() } if ( PhotometricInterp == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::IsPaletteColor: absent Photometric " + dbg.Verbose(0, "Header::IsPaletteColor: absent Photometric " "Interpretation"); } return false; @@ -876,7 +927,7 @@ 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" ) @@ -885,7 +936,7 @@ bool gdcmHeader::IsYBRFull() } if ( PhotometricInterp == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::IsYBRFull: absent Photometric " + dbg.Verbose(0, "Header::IsYBRFull: absent Photometric " "Interpretation"); } return false; @@ -896,7 +947,7 @@ 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 ) @@ -911,11 +962,11 @@ 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(); @@ -935,7 +986,7 @@ int gdcmHeader::GetPixelSize() { return 8; } - dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type"); + dbg.Verbose(0, "Header::GetPixelSize: Unknown pixel type"); return 0; } @@ -953,12 +1004,12 @@ 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"; } @@ -966,7 +1017,7 @@ std::string gdcmHeader::GetPixelType() { return "FD"; } - if ( bitsAlloc == "12" ) + else if ( bitsAlloc == "12" ) { // It will be unpacked bitsAlloc = "16"; @@ -981,10 +1032,10 @@ 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" ) + else if ( sign == "0" ) { sign = "U"; } @@ -1001,9 +1052,9 @@ 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(); @@ -1027,9 +1078,9 @@ 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(); @@ -1053,7 +1104,7 @@ 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 @@ -1099,7 +1150,7 @@ 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; @@ -1114,7 +1165,7 @@ int gdcmHeader::GetLUTNbits() } tokens.clear(); // clean any previous value - gdcmUtil::Tokenize ( lutDescription, tokens, "\\" ); + Util::Tokenize ( lutDescription, tokens, "\\" ); //LutLength=atoi(tokens[0].c_str()); //LutDepth=atoi(tokens[1].c_str()); @@ -1125,176 +1176,13 @@ 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 ) @@ -1306,43 +1194,23 @@ 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) -{ - ///FIXME I don't understand this code wh ydo we set two times 'car' ? - std::string car = gdcmUtil::Format("%d", ImageDataSize); - - gdcmDocEntry *a = GetDocEntryByNumber(GrPixel, NumPixel); - a->SetLength(ImageDataSize); - - ImageDataSize += 8; - car = gdcmUtil::Format("%d", ImageDataSize); - - SetEntryByNumber(car, GrPixel, NumPixel); -} - //----------------------------------------------------------------------------- // Protected @@ -1350,14 +1218,14 @@ 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) { @@ -1368,7 +1236,7 @@ bool gdcmHeader::AnonymizeHeader() } else { - ReplaceOrCreateByNumber(std::string("anonymised"), 0x0010, 0x0010); + ReplaceOrCreateByNumber("anonymised", 0x0010, 0x0010); } } @@ -1432,7 +1300,7 @@ 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] @@ -1444,7 +1312,7 @@ 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)"); } } @@ -1455,13 +1323,91 @@ 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 standard does not + * explicitely defines those 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; + + std::string date = Util::GetCurrentDate(); + std::string time = Util::GetCurrentTime(); + std::string uid = Util::CreateUniqueUID(); + std::string uidMedia = uid; + std::string uidClass = uid + ".1"; + std::string uidInst = uid + ".10"; + std::string uidStudy = uid + ".100"; + std::string uidSerie = uid + ".1000"; + + static DICOM_DEFAULT_VALUE defaultvalue[] = { + { "146 ", 0x0002, 0x0000}, // Meta Element Group Length // FIXME: how to recompute ? + { "1.2.840.10008.5.1.4.1.1.2", 0x0002, 0x0002}, // Media Storage SOP Class UID (CT Image Storage) + { uidClass.c_str(), 0x0002, 0x0003}, // Media Storage SOP Instance UID + { uidClass.c_str(), 0x0002, 0x0012}, // META Implementation Class UID + { "GDCM", 0x0002, 0x0016}, // Source Application Entity Title + + { date.c_str(), 0x0008, 0x0012}, // Instance Creation Date + { time.c_str(), 0x0008, 0x0013}, // Instance Creation Time + { "1.2.840.10008.5.1.4.1.1.2", 0x0008, 0x0016}, // SOP Class UID + { uidInst.c_str(), 0x0008, 0x0018}, // SOP Instance UID + { "CT", 0x0008, 0x0060}, // Modality + { "GDCM", 0x0008, 0x0070}, // Manufacturer + { "GDCM", 0x0008, 0x0080}, // Institution Name + { "http://www-creatis.insa-lyon.fr/Public/Gdcm", 0x0008, 0x0081}, // Institution Address + + { "GDCM", 0x0010, 0x0010}, // Patient's Name + { "GDCMID", 0x0010, 0x0020}, // Patient ID + + { uidStudy.c_str(), 0x0020, 0x000d}, // Study Instance UID + { uidSerie.c_str(), 0x0020, 0x000e}, // Series Instance UID + { "1", 0x0020, 0x0010}, // StudyID + { "1", 0x0020, 0x0011}, // SeriesNumber + + { "1", 0x0028, 0x0002}, // Samples per pixel 1 or 3 + { "MONOCHROME1", 0x0028, 0x0004}, // photochromatic interpretation + { "0", 0x0028, 0x0010}, // nbRows + { "0", 0x0028, 0x0011}, // nbCols + { "8", 0x0028, 0x0100}, // BitsAllocated 8 or 12 or 16 + { "8", 0x0028, 0x0101}, // BitsStored <= BitsAllocated + { "7", 0x0028, 0x0102}, // HighBit <= BitsAllocated - 1 + { "0", 0x0028, 0x0103}, // Pixel Representation 0(unsigned) or 1(signed) + { 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 ) + { + ReplaceOrCreateByNumber(current.value, current.group, current.elem); + current = defaultvalue[++i]; + } +} + + //----------------------------------------------------------------------------- // Private //----------------------------------------------------------------------------- + +} // end namespace gdcm