X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=2830ff3ceffeb003fe128bc124f6017863e84185;hb=cfd7023dd0efe6d0cf17cdc1b31bbf17ac8a9ade;hp=afe5e6d0ccac7cd5483e4a00654ff7cf72eb42d5;hpb=d1722eb98897b805be46612057abdcda1bd4bdaa;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index afe5e6d0..2830ff3c 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmHeader.cxx,v $ Language: C++ - Date: $Date: 2004/10/09 03:42:51 $ - Version: $Revision: 1.191 $ + Date: $Date: 2005/01/17 11:13:21 $ + Version: $Revision: 1.233 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -22,17 +22,21 @@ #include "gdcmDebug.h" #include "gdcmTS.h" #include "gdcmValEntry.h" +#include "gdcmBinEntry.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 @@ -41,11 +45,11 @@ gdcmHeader::gdcmHeader( std::string const & filename ): // is found by indirection through the "Image Location"). // Inside the group pointed by "Image Location" the searched element // is conventionally the element 0x0010 (when the norm is respected). - // When the "Image Location" is absent we default to group 0x7fe0. + // When the "Image Location" is Missing we default to group 0x7fe0. // Note: this IS the right place for the code // Image Location - std::string imgLocation = GetEntryByNumber(0x0028, 0x0200); + const std::string &imgLocation = GetEntry(0x0028, 0x0200); if ( imgLocation == GDCM_UNFOUND ) { // default value @@ -73,94 +77,163 @@ 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 = GetDocEntry(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 * then writes in a file all the (Dicom Elements) included the Pixels - * @param fp file pointer on an already open file + * @param fileName file name to write to * @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) + { + gdcmVerboseMacro("Failed to open (write) File: " << fileName.c_str()); + return false; + } + // Bits Allocated - if ( GetEntryByNumber(0x0028,0x0100) == "12") + if ( GetEntry(0x0028,0x0100) == "12") { - SetEntryByNumber("16", 0x0028,0x0100); + SetEntry("16", 0x0028,0x0100); } /// \todo correct 'Pixel group' Length if necessary - int i_lgPix = GetEntryLengthByNumber(GrPixel, NumPixel); + int i_lgPix = GetEntryLength(GrPixel, NumPixel); if (i_lgPix != -2) { // no (GrPixel, NumPixel) element - std::string s_lgPix; - s_lgPix = Format("%d", i_lgPix+12); - ReplaceOrCreateByNumber(s_lgPix,GrPixel, 0x0000); + std::string s_lgPix = Util::Format("%d", i_lgPix+12); + s_lgPix = Util::DicomString( s_lgPix.c_str() ); + ReplaceOrCreate(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 - if ( GetEntryByNumber(0x0028,0x0002).c_str()[0] == '3' ) + if ( GetEntry(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); + DocEntry *e = GetDocEntry(0x0028,0x01101); if (e) { RemoveEntryNoDestroy(e); } - e = GetDocEntryByNumber(0x0028,0x1102); + e = GetDocEntry(0x0028,0x1102); if (e) { RemoveEntryNoDestroy(e); } - e = GetDocEntryByNumber(0x0028,0x1103); + e = GetDocEntry(0x0028,0x1103); if (e) { RemoveEntryNoDestroy(e); } - e = GetDocEntryByNumber(0x0028,0x01201); + e = GetDocEntry(0x0028,0x01201); if (e) { RemoveEntryNoDestroy(e); } - e = GetDocEntryByNumber(0x0028,0x1202); + e = GetDocEntry(0x0028,0x1202); if (e) { RemoveEntryNoDestroy(e); } - e = GetDocEntryByNumber(0x0028,0x1203); + e = GetDocEntry(0x0028,0x1203); if (e) { RemoveEntryNoDestroy(e); } } - gdcmDocument::Write(fp,filetype); + +/* +#ifdef GDCM_WORDS_BIGENDIAN + // Super Super hack that will make gdcm a BOMB ! but should + // Fix temporarily the dashboard + BinEntry *b = GetBinEntry(GrPixel,NumPixel); + if ( GetPixelSize() == 16 ) + { + uint16_t *im16 = (uint16_t*)b->GetBinArea(); + int lgr = b->GetLength(); + for( int i = 0; i < lgr / 2; i++ ) + { + im16[i]= (im16[i] >> 8) | (im16[i] << 8 ); + } + } +#endif //GDCM_WORDS_BIGENDIAN +*/ + + Document::WriteContent(fp,filetype); + +/* +#ifdef GDCM_WORDS_BIGENDIAN + // Flip back the pixel ... I told you this is a hack + if ( GetPixelSize() == 16 ) + { + uint16_t *im16 = (uint16_t*)b->GetBinArea(); + int lgr = b->GetLength(); + for( int i = 0; i < lgr / 2; i++ ) + { + im16[i]= (im16[i] >> 8) | (im16[i] << 8 ); + } + } +#endif //GDCM_WORDS_BIGENDIAN +*/ + + fp->close(); + delete fp; + + return true; } //----------------------------------------------------------------------------- @@ -172,37 +245,37 @@ 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 = GetEntry(0x0028, 0x0005); if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) { return false; // Image Dimensions } - if ( !GetDocEntryByNumber(0x0028, 0x0100) ) + if ( !GetDocEntry(0x0028, 0x0100) ) { return false; // "Bits Allocated" } - if ( !GetDocEntryByNumber(0x0028, 0x0101) ) + if ( !GetDocEntry(0x0028, 0x0101) ) { return false; // "Bits Stored" } - if ( !GetDocEntryByNumber(0x0028, 0x0102) ) + if ( !GetDocEntry(0x0028, 0x0102) ) { return false; // "High Bit" } - if ( !GetDocEntryByNumber(0x0028, 0x0103) ) + if ( !GetDocEntry(0x0028, 0x0103) ) { return false; // "Pixel Representation" i.e. 'Sign' } @@ -215,10 +288,9 @@ 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 = GetEntry(0x0028,0x0011); if ( strSize == GDCM_UNFOUND ) { return 0; @@ -229,13 +301,13 @@ 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 = GetEntry(0x0028,0x0010); if ( strSize != GDCM_UNFOUND ) { return atoi( strSize.c_str() ); @@ -246,7 +318,7 @@ 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; } @@ -254,25 +326,25 @@ int gdcmHeader::GetYSize() * \brief Retrieve the number of planes of volume or the number * of frames of a multiframe. * \warning When present we consider the "Number of Frames" as the third - * dimension. When absent we consider the third dimension as + * dimension. When Missing we consider the third dimension as * 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 = GetEntry(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 = GetEntry(0x0028,0x0012); + if ( strSize2 != GDCM_UNFOUND ) { - return atoi( strSize.c_str() ); + return atoi( strSize2.c_str() ); } return 1; @@ -283,14 +355,14 @@ 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 = GetEntry(0x0028,0x0030); if ( strSpacing == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetXSpacing: unfound Pixel Spacing (0028,0030)"); + gdcmVerboseMacro( "Unfound Pixel Spacing (0028,0030)" ); return 1.; } @@ -301,14 +373,26 @@ 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"); + gdcmVerboseMacro("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); + gdcmAssertMacro( nbValues == 2 ); } return xspacing; @@ -319,30 +403,33 @@ 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); + float yspacing = 1.; + std::string strSpacing = GetEntry(0x0028,0x0030); if ( strSpacing == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetYSpacing: unfound Pixel Spacing (0028,0030)"); + gdcmVerboseMacro("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 : @@ -351,17 +438,18 @@ float gdcmHeader::GetZSpacing() // disjointes (Spacing between Slices > Slice Thickness) // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal // ca interesse le physicien de l'IRM, pas le visualisateur de volumes ... - // Si le Spacing Between Slices est absent, + // Si le Spacing Between Slices est Missing, // on suppose que les coupes sont jointives - std::string strSpacingBSlices = GetEntryByNumber(0x0018,0x0088); + const std::string &strSpacingBSlices = GetEntry(0x0018,0x0088); if ( strSpacingBSlices == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetZSpacing: unfound StrSpacingBSlices"); - std::string strSliceThickness = GetEntryByNumber(0x0018,0x0050); + gdcmVerboseMacro("Unfound Spacing Between Slices (0018,0088)"); + const std::string &strSliceThickness = GetEntry(0x0018,0x0050); if ( strSliceThickness == GDCM_UNFOUND ) { + gdcmVerboseMacro("Unfound Slice Thickness (0018,0050)"); return 1.; } else @@ -370,31 +458,28 @@ 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 = GetEntry(0x0028,0x1052); if ( strRescInter != GDCM_UNFOUND ) { if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 ) { // bug in the element 0x0028,0x1052 - dbg.Verbose(0, "gdcmHeader::GetRescaleIntercept: Rescale Slope " - "is empty"); + gdcmVerboseMacro( "Rescale Intercept (0028,1052) is empty." ); } } @@ -405,17 +490,17 @@ 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 - std::string strRescSlope = GetEntryByNumber(0x0028,0x1053); + std::string strRescSlope = GetEntry(0x0028,0x1053); if ( strRescSlope != GDCM_UNFOUND ) { if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1) { // bug in the element 0x0028,0x1053 - dbg.Verbose(0, "gdcmHeader::GetRescaleSlope: Rescale Slope is empty"); + gdcmVerboseMacro( "Rescale Slope (0028,1053) is empty."); } } @@ -429,7 +514,7 @@ 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 ) { @@ -438,12 +523,12 @@ int gdcmHeader::GetNumberOfScalarComponents() // 0028 0100 US IMG Bits Allocated // (in order no to be messed up by old RGB images) - if ( GetEntryByNumber(0x0028,0x0100) == "24" ) + if ( GetEntry(0x0028,0x0100) == "24" ) { return 3; } - std::string strPhotometricInterpretation = GetEntryByNumber(0x0028,0x0004); + std::string strPhotometricInterpretation = GetEntry(0x0028,0x0004); if ( ( strPhotometricInterpretation == "PALETTE COLOR ") ) { @@ -460,8 +545,8 @@ 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 +564,11 @@ 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::GetEntry(0x0028,0x0100) == "24" ) { return 3; } @@ -514,20 +599,18 @@ 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); + std::string strImPos = GetEntry(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 + gdcmVerboseMacro( "Unfound Image Position Patient (0020,0032)"); + strImPos = GetEntry(0x0020,0x0030); // For ACR-NEMA images if ( strImPos == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image " - "Position (RET) (0020,0030)"); + gdcmVerboseMacro( "Unfound Image Position (RET) (0020,0030)"); /// \todo How to tell the caller nothing was found ? return 0.; } @@ -547,20 +630,18 @@ 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); + std::string strImPos = GetEntry(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 + gdcmVerboseMacro( "Unfound Image Position Patient (0020,0032)"); + strImPos = GetEntry(0x0020,0x0030); // For ACR-NEMA images if ( strImPos == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image " - "Position (RET) (0020,0030)"); + gdcmVerboseMacro( "Unfound Image Position (RET) (0020,0030)"); /// \todo How to tell the caller nothing was found ? return 0.; } @@ -582,17 +663,16 @@ 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); + std::string strImPos = GetEntry(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)"); + gdcmVerboseMacro( "Wrong Image Position Patient (0020,0032)"); return 0.; // bug in the element 0x0020,0x0032 } else @@ -601,13 +681,13 @@ float gdcmHeader::GetZOrigin() } } - strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images + strImPos = GetEntry(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)"); + gdcmVerboseMacro( "Wrong Image Position (RET) (0020,0030)"); return 0.; // bug in the element 0x0020,0x0032 } else @@ -616,12 +696,12 @@ float gdcmHeader::GetZOrigin() } } - std::string strSliceLocation = GetEntryByNumber(0x0020,0x1041); // for *very* old ACR-NEMA images + std::string strSliceLocation = GetEntry(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)"); + gdcmVerboseMacro( "Wrong Slice Location (0020,1041)"); return 0.; // bug in the element 0x0020,0x1041 } else @@ -629,14 +709,14 @@ float gdcmHeader::GetZOrigin() return zImPos; } } - dbg.Verbose(0, "gdcmHeader::GetZImagePosition: unfound Slice Location (0020,1041)"); + gdcmVerboseMacro( "Unfound Slice Location (0020,1041)"); - std::string strLocation = GetEntryByNumber(0x0020,0x0050); + std::string strLocation = GetEntry(0x0020,0x0050); if ( strLocation != GDCM_UNFOUND ) { if( sscanf( strLocation.c_str(), "%f", &zImPos) != 1) { - dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Location (0020,0050)"); + gdcmVerboseMacro( "Wrong Location (0020,0050)"); return 0.; // bug in the element 0x0020,0x0050 } else @@ -644,7 +724,7 @@ float gdcmHeader::GetZOrigin() return zImPos; } } - dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Location (0020,0050)"); + gdcmVerboseMacro( "Unfound Location (0020,0050)"); return 0.; // Hopeless } @@ -653,7 +733,7 @@ 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 @@ -662,7 +742,7 @@ int gdcmHeader::GetImageNumber() // faster function. sscanf() can do all possible conversions whereas // atoi() can only do single decimal integer conversions. //0020 0013 IS REL Image Number - std::string strImNumber = GetEntryByNumber(0x0020,0x0013); + std::string strImNumber = GetEntry(0x0020,0x0013); if ( strImNumber != GDCM_UNFOUND ) { return atoi( strImNumber.c_str() ); @@ -674,10 +754,10 @@ 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); + std::string strModality = GetEntry(0x0008,0x0060); if ( strModality != GDCM_UNFOUND ) { if ( strModality.find("AU") < strModality.length()) return AU; @@ -738,13 +818,12 @@ 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 ); + std::string strSize = GetEntry( 0x0028, 0x0101 ); if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetBitsStored: this is supposed to " - "be mandatory"); + gdcmVerboseMacro("(0028,0101) is supposed to be mandatory"); return 0; // It's supposed to be mandatory // the caller will have to check } @@ -753,35 +832,33 @@ int gdcmHeader::GetBitsStored() /** * \brief Retrieve the high bit position. - * \warning The method defaults to 0 when information is absent. + * \warning The method defaults to 0 when information is Missing. * The responsability of checking this value is left to the caller. - * @return The high bit positin when present. 0 when absent. + * @return The high bit positin when present. 0 when Missing. */ -int gdcmHeader::GetHighBitPosition() +int Header::GetHighBitPosition() { - std::string strSize = GetEntryByNumber( 0x0028, 0x0102 ); + std::string strSize = GetEntry( 0x0028, 0x0102 ); if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetHighBitPosition: this is supposed " - "to be mandatory"); + gdcmVerboseMacro( "(0028,0102) is supposed to be mandatory"); return 0; } return atoi( strSize.c_str() ); } /** - * \brief Check wether the pixels are signed or UNsigned data. - * \warning The method defaults to false (UNsigned) when information is absent. + * \brief Check whether the pixels are signed or UNsigned data. + * \warning The method defaults to false (UNsigned) when information is Missing. * 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 ); + std::string strSize = GetEntry( 0x0028, 0x0103 ); if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::IsSignedPixelData: this is supposed " - "to be mandatory"); + gdcmVerboseMacro( "(0028,0103) is supposed to be mandatory"); return false; } int sign = atoi( strSize.c_str() ); @@ -798,13 +875,12 @@ 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); + std::string strSize = GetEntry(0x0028,0x0100); if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetBitsStored: this is supposed to " - "be mandatory"); + gdcmVerboseMacro( "(0028,0100) is supposed to be mandatory"); return 0; // It's supposed to be mandatory // the caller will have to check } @@ -817,13 +893,12 @@ 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 = GetEntry(0x0028,0x0002); if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetBitsStored: this is supposed to " - "be mandatory"); + gdcmVerboseMacro( "(0028,0002) is supposed to be mandatory"); return 1; // Well, it's supposed to be mandatory ... // but sometimes it's missing : *we* assume Gray pixels } @@ -831,62 +906,59 @@ int gdcmHeader::GetSamplesPerPixel() } /** - * \brief Check wether this a monochrome picture or not by accessing + * \brief Check whether this a monochrome picture or not by accessing * 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 = GetEntry( 0x0028, 0x0004 ); + if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") + || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") ) { return true; } if ( PhotometricInterp == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::IsMonochrome: absent Photometric " - "Interpretation"); + gdcmVerboseMacro( "Not found : Photometric Interpretation (0028,0004)"); } return false; } /** - * \brief Check wether this a "PALETTE COLOR" picture or not by accessing + * \brief Check whether this a "PALETTE COLOR" picture or not by accessing * 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 ); + std::string PhotometricInterp = GetEntry( 0x0028, 0x0004 ); if ( PhotometricInterp == "PALETTE COLOR " ) { return true; } if ( PhotometricInterp == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::IsPaletteColor: absent Photometric " - "Interpretation"); + gdcmVerboseMacro( "Not found : Palette color (0028,0004)"); } return false; } /** - * \brief Check wether this a "YBR_FULL" color picture or not by accessing + * \brief Check whether this a "YBR_FULL" color picture or not by accessing * 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 ); + std::string PhotometricInterp = GetEntry( 0x0028, 0x0004 ); if ( PhotometricInterp == "YBR_FULL" ) { return true; } if ( PhotometricInterp == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::IsYBRFull: absent Photometric " - "Interpretation"); + gdcmVerboseMacro( "Not found : YBR Full (0028,0004)"); } return false; } @@ -896,11 +968,12 @@ 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); + std::string strSize = GetEntry(0x0028,0x0006); if ( strSize == GDCM_UNFOUND ) { + gdcmVerboseMacro( "Not found : Planar Configuration (0028,0006)"); return 0; } return atoi( strSize.c_str() ); @@ -911,11 +984,11 @@ 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::GetEntry(0x0028,0x0100) == "24") // return 3; std::string pixelType = GetPixelType(); @@ -935,7 +1008,7 @@ int gdcmHeader::GetPixelSize() { return 8; } - dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type"); + gdcmVerboseMacro( "Unknown pixel type"); return 0; } @@ -953,12 +1026,12 @@ 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 + std::string bitsAlloc = GetEntry(0x0028, 0x0100); // Bits Allocated if ( bitsAlloc == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated"); + gdcmVerboseMacro( "Missing Bits Allocated (0028,0100)"); bitsAlloc = "16"; } @@ -966,7 +1039,7 @@ std::string gdcmHeader::GetPixelType() { return "FD"; } - if ( bitsAlloc == "12" ) + else if ( bitsAlloc == "12" ) { // It will be unpacked bitsAlloc = "16"; @@ -977,14 +1050,14 @@ std::string gdcmHeader::GetPixelType() bitsAlloc = "8"; // by old RGB images) } - std::string sign = GetEntryByNumber(0x0028, 0x0103);//"Pixel Representation" + std::string sign = GetEntry(0x0028, 0x0103);//"Pixel Representation" if (sign == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation"); + gdcmVerboseMacro( "Missing Pixel Representation (0028,0103)"); bitsAlloc = "0"; } - if ( sign == "0" ) + else if ( sign == "0" ) { sign = "U"; } @@ -1001,9 +1074,9 @@ 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 = GetDocEntry(GrPixel,NumPixel); if ( pxlElement ) { return pxlElement->GetOffset(); @@ -1027,9 +1100,9 @@ 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 = GetDocEntry(GrPixel,NumPixel); if ( pxlElement ) { return pxlElement->GetLength(); @@ -1053,36 +1126,36 @@ 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 - if ( !GetDocEntryByNumber(0x0028,0x1101) ) + if ( !GetDocEntry(0x0028,0x1101) ) { return false; } // LutDescriptorGreen - if ( !GetDocEntryByNumber(0x0028,0x1102) ) + if ( !GetDocEntry(0x0028,0x1102) ) { return false; } // LutDescriptorBlue - if ( !GetDocEntryByNumber(0x0028,0x1103) ) + if ( !GetDocEntry(0x0028,0x1103) ) { return false; } // Red Palette Color Lookup Table Data - if ( !GetDocEntryByNumber(0x0028,0x1201) ) + if ( !GetDocEntry(0x0028,0x1201) ) { return false; } // Green Palette Color Lookup Table Data - if ( !GetDocEntryByNumber(0x0028,0x1202) ) + if ( !GetDocEntry(0x0028,0x1202) ) { return false; } // Blue Palette Color Lookup Table Data - if ( !GetDocEntryByNumber(0x0028,0x1203) ) + if ( !GetDocEntry(0x0028,0x1203) ) { return false; } @@ -1099,7 +1172,7 @@ 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; @@ -1107,14 +1180,14 @@ int gdcmHeader::GetLUTNbits() //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); + std::string lutDescription = GetEntry(0x0028,0x1101); if ( lutDescription == GDCM_UNFOUND ) { return 0; } 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()); @@ -1124,224 +1197,6 @@ int gdcmHeader::GetLUTNbits() return lutNbits; } -/** - * \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 - * else 1. - * @return The full Transfert Syntax Name (as opposed to Transfert Syntax UID) - */ -std::string gdcmHeader::GetTransfertSyntaxName() -{ - // use the gdcmTS (TS : Transfert Syntax) - std::string transfertSyntax = GetEntryByNumber(0x0002,0x0010); - - if ( transfertSyntax == GDCM_NOTLOADED ) - { - std::cout << "Transfert Syntax not loaded. " << std::endl - << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE" - << std::endl; - return "Uncompressed ACR-NEMA"; - } - if ( transfertSyntax == GDCM_UNFOUND ) - { - dbg.Verbose(0, "gdcmHeader::GetTransfertSyntaxName:" - " unfound Transfert Syntax (0002,0010)"); - return "Uncompressed ACR-NEMA"; - } - - while ( ! isdigit(transfertSyntax[transfertSyntax.length()-1]) ) - { - transfertSyntax.erase(transfertSyntax.length()-1, 1); - } - // we do it only when we need it - gdcmTS* ts = gdcmGlobal::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 = Format("%d", ImageDataSize); - - gdcmDocEntry *a = GetDocEntryByNumber(GrPixel, NumPixel); - a->SetLength(ImageDataSize); - - ImageDataSize += 8; - car = Format("%d", ImageDataSize); - - SetEntryByNumber(car, GrPixel, NumPixel); -} //----------------------------------------------------------------------------- // Protected @@ -1350,25 +1205,25 @@ 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 + SetEntry (" ",0x0010, 0x2154); // Telephone + SetEntry (" ",0x0010, 0x1040); // Adress + SetEntry (" ",0x0010, 0x0020); // Patient ID - gdcmDocEntry* patientNameHE = GetDocEntryByNumber (0x0010, 0x0010); + DocEntry* patientNameHE = GetDocEntry (0x0010, 0x0010); if ( patientNameHE ) // we replace it by Study Instance UID (why not) { - std::string studyInstanceUID = GetEntryByNumber (0x0020, 0x000d); + std::string studyInstanceUID = GetEntry (0x0020, 0x000d); if ( studyInstanceUID != GDCM_UNFOUND ) { - ReplaceOrCreateByNumber(studyInstanceUID, 0x0010, 0x0010); + ReplaceOrCreate(studyInstanceUID, 0x0010, 0x0010); } else { - ReplaceOrCreateByNumber(std::string("anonymised"), 0x0010, 0x0010); + ReplaceOrCreate("anonymised", 0x0010, 0x0010); } } @@ -1432,36 +1287,112 @@ 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] 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 ( (strImOriPat = GetEntry(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)"); + gdcmVerboseMacro( "Wrong Image Orientation Patient (0020,0037). Less than 6 values were found." ); } } //For ACR-NEMA // 0020 0035 DS REL Image Orientation (RET) - else if ( (strImOriPat = GetEntryByNumber(0x0020,0x0035)) != GDCM_UNFOUND ) + else if ( (strImOriPat = GetEntry(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)"); + gdcmVerboseMacro( "wrong Image Orientation Patient (0020,0035). Less than 6 values were found." ); } } } +/** + * \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; + ReplaceOrCreate(0, 0, GrPixel, NumPixel); + + // All remaining strings: + unsigned int i = 0; + DICOM_DEFAULT_VALUE current = defaultvalue[i]; + while( current.value ) + { + ReplaceOrCreate(current.value, current.group, current.elem); + current = defaultvalue[++i]; + } +} + + //----------------------------------------------------------------------------- // Private //----------------------------------------------------------------------------- + +} // end namespace gdcm