X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=c26b4bc6a5bf1ae93e62a7f878891e4ce5faa655;hb=c4eae790a08d862201d509f1224409358562b5f0;hp=2ccd0ac183d4a798164a298af7bf0be47e76c2ed;hpb=af698856153f426a4d852b6645e238f669d42276;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index 2ccd0ac1..c26b4bc6 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmHeader.cxx,v $ Language: C++ - Date: $Date: 2004/11/26 10:55:04 $ - Version: $Revision: 1.208 $ + Date: $Date: 2005/01/18 16:23:52 $ + Version: $Revision: 1.234 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -22,7 +22,8 @@ #include "gdcmDebug.h" #include "gdcmTS.h" #include "gdcmValEntry.h" -#include +#include "gdcmBinEntry.h" +#include //sscanf #include @@ -34,7 +35,7 @@ namespace gdcm * \brief Constructor * @param filename name of the file whose header we want to analyze */ -Header::Header( std::string const & filename ): +Header::Header( std::string const &filename ): Document( filename ) { // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010 @@ -44,11 +45,11 @@ Header::Header( 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 - const std::string &imgLocation = GetEntryByNumber(0x0028, 0x0200); + const std::string &imgLocation = GetEntry(0x0028, 0x0200); if ( imgLocation == GDCM_UNFOUND ) { // default value @@ -60,7 +61,7 @@ Header::Header( std::string const & filename ): } // sometimes Image Location value doesn't follow - // the supposed processor endianity. + // the supposed processor endianness. // see gdcmData/cr172241.dcm if ( GrPixel == 0xe07f ) { @@ -76,6 +77,29 @@ Header::Header( 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 ); + } } /** @@ -98,35 +122,35 @@ 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) */ -bool Header::Write(std::string fileName,FileType filetype) +bool Header::Write(std::string fileName, FileType filetype) { - std::ofstream* fp = new std::ofstream(fileName.c_str(), + std::ofstream *fp = new std::ofstream(fileName.c_str(), std::ios::out | std::ios::binary); - if (fp == NULL) + if (*fp == NULL) { - dbg.Verbose(2, "Failed to open (write) File: " , fileName.c_str()); + 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 = Util::Format("%d", i_lgPix+12); s_lgPix = Util::DicomString( s_lgPix.c_str() ); - ReplaceOrCreateByNumber(s_lgPix,GrPixel, 0x0000); + ReplaceOrCreate(s_lgPix,GrPixel, 0x0000); } // FIXME : should be nice if we could move it to File @@ -134,45 +158,78 @@ bool Header::Write(std::string fileName,FileType filetype) // 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 - DocEntry* 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); } } + +/* +#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; @@ -201,24 +258,24 @@ bool Header::IsReadable() return false; } - const 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' } @@ -233,7 +290,7 @@ bool Header::IsReadable() */ int Header::GetXSize() { - const std::string &strSize = GetEntryByNumber(0x0028,0x0011); + const std::string &strSize = GetEntry(0x0028,0x0011); if ( strSize == GDCM_UNFOUND ) { return 0; @@ -250,7 +307,7 @@ int Header::GetXSize() */ int Header::GetYSize() { - const std::string &strSize = GetEntryByNumber(0x0028,0x0010); + const std::string &strSize = GetEntry(0x0028,0x0010); if ( strSize != GDCM_UNFOUND ) { return atoi( strSize.c_str() ); @@ -261,7 +318,7 @@ int Header::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; } @@ -269,7 +326,7 @@ int Header::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). */ @@ -277,14 +334,14 @@ int Header::GetZSize() { // Both DicomV3 and ACR/Nema consider the "Number of Frames" // as the third dimension. - const 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 - const std::string &strSize2 = GetEntryByNumber(0x0028,0x0012); + const std::string &strSize2 = GetEntry(0x0028,0x0012); if ( strSize2 != GDCM_UNFOUND ) { return atoi( strSize2.c_str() ); @@ -301,11 +358,11 @@ int Header::GetZSize() float Header::GetXSpacing() { float xspacing, yspacing; - const std::string &strSpacing = GetEntryByNumber(0x0028,0x0030); + const std::string &strSpacing = GetEntry(0x0028,0x0030); if ( strSpacing == GDCM_UNFOUND ) { - dbg.Verbose(0, "Header::GetXSpacing: unfound Pixel Spacing (0028,0030)"); + gdcmVerboseMacro( "Unfound Pixel Spacing (0028,0030)" ); return 1.; } @@ -316,14 +373,26 @@ float Header::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, "Header::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; @@ -336,25 +405,28 @@ float Header::GetXSpacing() */ 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, "Header::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 Header::GetZSpacing() @@ -366,17 +438,18 @@ float Header::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, "Header::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 @@ -388,11 +461,8 @@ float Header::GetZSpacing() return (float)atof( strSliceThickness.c_str() ); } } - else - { - return (float)atof( strSpacingBSlices.c_str() ); - } - return 1.; + //else + return (float)atof( strSpacingBSlices.c_str() ); } /** @@ -403,14 +473,13 @@ 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, "Header::GetRescaleIntercept: Rescale Slope " - "is empty"); + gdcmVerboseMacro( "Rescale Intercept (0028,1052) is empty." ); } } @@ -425,13 +494,13 @@ 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, "Header::GetRescaleSlope: Rescale Slope is empty"); + gdcmVerboseMacro( "Rescale Slope (0028,1053) is empty."); } } @@ -454,12 +523,12 @@ int Header::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 ") ) { @@ -499,7 +568,7 @@ int Header::GetNumberOfScalarComponentsRaw() { // 0028 0100 US IMG Bits Allocated // (in order no to be messed up by old RGB images) - if ( Header::GetEntryByNumber(0x0028,0x0100) == "24" ) + if ( Header::GetEntry(0x0028,0x0100) == "24" ) { return 3; } @@ -533,17 +602,15 @@ int Header::GetNumberOfScalarComponentsRaw() 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, "Header::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, "Header::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.; } @@ -566,17 +633,15 @@ float Header::GetXOrigin() 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, "Header::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, "Header::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.; } @@ -601,14 +666,13 @@ float Header::GetYOrigin() 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, "Header::GetZImagePosition: wrong Image " - "Position Patient (0020,0032)"); + gdcmVerboseMacro( "Wrong Image Position Patient (0020,0032)"); return 0.; // bug in the element 0x0020,0x0032 } else @@ -617,13 +681,13 @@ float Header::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, "Header::GetZImagePosition: wrong Image Position (RET) (0020,0030)"); + gdcmVerboseMacro( "Wrong Image Position (RET) (0020,0030)"); return 0.; // bug in the element 0x0020,0x0032 } else @@ -632,12 +696,12 @@ float Header::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, "Header::GetZImagePosition: wrong Slice Location (0020,1041)"); + gdcmVerboseMacro( "Wrong Slice Location (0020,1041)"); return 0.; // bug in the element 0x0020,0x1041 } else @@ -645,14 +709,14 @@ float Header::GetZOrigin() return zImPos; } } - dbg.Verbose(0, "Header::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, "Header::GetZImagePosition: wrong Location (0020,0050)"); + gdcmVerboseMacro( "Wrong Location (0020,0050)"); return 0.; // bug in the element 0x0020,0x0050 } else @@ -660,7 +724,7 @@ float Header::GetZOrigin() return zImPos; } } - dbg.Verbose(0, "Header::GetYImagePosition: unfound Location (0020,0050)"); + gdcmVerboseMacro( "Unfound Location (0020,0050)"); return 0.; // Hopeless } @@ -678,7 +742,7 @@ int Header::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() ); @@ -693,7 +757,7 @@ int Header::GetImageNumber() 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; @@ -740,7 +804,7 @@ ModalityType Header::GetModality() else { /// \todo throw error return value ??? - /// specified <> unknow in our database + /// specified <> unknown in our database return Unknow; } } @@ -756,11 +820,10 @@ ModalityType Header::GetModality() */ int Header::GetBitsStored() { - std::string strSize = GetEntryByNumber( 0x0028, 0x0101 ); + std::string strSize = GetEntry( 0x0028, 0x0101 ); if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(0, "Header::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 } @@ -769,35 +832,33 @@ int Header::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 Header::GetHighBitPosition() { - std::string strSize = GetEntryByNumber( 0x0028, 0x0102 ); + std::string strSize = GetEntry( 0x0028, 0x0102 ); if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(0, "Header::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 Header::IsSignedPixelData() { - std::string strSize = GetEntryByNumber( 0x0028, 0x0103 ); + std::string strSize = GetEntry( 0x0028, 0x0103 ); if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(0, "Header::IsSignedPixelData: this is supposed " - "to be mandatory"); + gdcmVerboseMacro( "(0028,0103) is supposed to be mandatory"); return false; } int sign = atoi( strSize.c_str() ); @@ -816,11 +877,10 @@ bool Header::IsSignedPixelData() */ int Header::GetBitsAllocated() { - std::string strSize = GetEntryByNumber(0x0028,0x0100); + std::string strSize = GetEntry(0x0028,0x0100); if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(0, "Header::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 } @@ -835,11 +895,10 @@ int Header::GetBitsAllocated() */ int Header::GetSamplesPerPixel() { - const std::string& strSize = GetEntryByNumber(0x0028,0x0002); + const std::string& strSize = GetEntry(0x0028,0x0002); if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(0, "Header::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 } @@ -847,13 +906,13 @@ int Header::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 Header::IsMonochrome() { - const std::string& PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 ); + const std::string& PhotometricInterp = GetEntry( 0x0028, 0x0004 ); if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") ) { @@ -861,48 +920,45 @@ bool Header::IsMonochrome() } if ( PhotometricInterp == GDCM_UNFOUND ) { - dbg.Verbose(0, "Header::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 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, "Header::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 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, "Header::IsYBRFull: absent Photometric " - "Interpretation"); + gdcmVerboseMacro( "Not found : YBR Full (0028,0004)"); } return false; } @@ -914,9 +970,10 @@ bool Header::IsYBRFull() */ 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() ); @@ -931,7 +988,7 @@ int Header::GetPixelSize() { // 0028 0100 US IMG Bits Allocated // (in order no to be messed up by old RGB images) - // if (Header::GetEntryByNumber(0x0028,0x0100) == "24") + // if (Header::GetEntry(0x0028,0x0100) == "24") // return 3; std::string pixelType = GetPixelType(); @@ -951,7 +1008,7 @@ int Header::GetPixelSize() { return 8; } - dbg.Verbose(0, "Header::GetPixelSize: Unknown pixel type"); + gdcmVerboseMacro( "Unknown pixel type"); return 0; } @@ -971,18 +1028,18 @@ int Header::GetPixelSize() */ 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, "Header::GetPixelType: unfound Bits Allocated"); - bitsAlloc = "16"; + gdcmVerboseMacro( "Missing Bits Allocated (0028,0100)"); + bitsAlloc = "16"; // default and arbitrary value, not to polute the output } if ( bitsAlloc == "64" ) { return "FD"; } - if ( bitsAlloc == "12" ) + else if ( bitsAlloc == "12" ) { // It will be unpacked bitsAlloc = "16"; @@ -993,14 +1050,14 @@ std::string Header::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, "Header::GetPixelType: unfound Pixel Representation"); - bitsAlloc = "0"; + gdcmVerboseMacro( "Missing Pixel Representation (0028,0103)"); + sign = "U"; // default and arbitrary value, not to polute the output } - if ( sign == "0" ) + else if ( sign == "0" ) { sign = "U"; } @@ -1019,7 +1076,7 @@ std::string Header::GetPixelType() */ size_t Header::GetPixelOffset() { - DocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel); + DocEntry* pxlElement = GetDocEntry(GrPixel,NumPixel); if ( pxlElement ) { return pxlElement->GetOffset(); @@ -1045,7 +1102,7 @@ size_t Header::GetPixelOffset() */ size_t Header::GetPixelAreaLength() { - DocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel); + DocEntry* pxlElement = GetDocEntry(GrPixel,NumPixel); if ( pxlElement ) { return pxlElement->GetLength(); @@ -1073,32 +1130,32 @@ 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; } @@ -1123,7 +1180,7 @@ int Header::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; @@ -1140,41 +1197,6 @@ int Header::GetLUTNbits() return lutNbits; } -/** - * \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 Header::GetTransfertSyntaxName() -{ - // use the TS (TS : Transfert Syntax) - std::string transfertSyntax = GetEntryByNumber(0x0002,0x0010); - - if ( transfertSyntax == GDCM_NOTLOADED ) - { - std::cout << "Transfert Syntax not loaded. " << std::endl - << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE" - << std::endl; - return "Uncompressed ACR-NEMA"; - } - if ( transfertSyntax == GDCM_UNFOUND ) - { - dbg.Verbose(0, "Header::GetTransfertSyntaxName:" - " unfound Transfert Syntax (0002,0010)"); - return "Uncompressed ACR-NEMA"; - } - - while ( ! isdigit((unsigned char)transfertSyntax[transfertSyntax.length()-1]) ) - { - transfertSyntax.erase(transfertSyntax.length()-1, 1); - } - // we do it only when we need it - TS* ts = Global::GetTS(); - std::string tsName = ts->GetValue( transfertSyntax ); - - //delete ts; /// \todo Seg Fault when deleted ?! - return tsName; -} //----------------------------------------------------------------------------- // Protected @@ -1186,22 +1208,22 @@ std::string Header::GetTransfertSyntaxName() 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 - DocEntry* 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("anonymised", 0x0010, 0x0010); + ReplaceOrCreate("anonymised", 0x0010, 0x0010); } } @@ -1272,32 +1294,30 @@ void Header::GetImageOrientationPatient( float iop[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, "Header::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, "Header::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 standart does not - * explicitely defines thoses fields, heuristic has been choosen. + * 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() @@ -1309,77 +1329,67 @@ void Header::InitializeDefaultHeader() 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(); + 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[] = { - "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 + { "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); + ReplaceOrCreate(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); + ReplaceOrCreate(current.value, current.group, current.elem); current = defaultvalue[++i]; } } + //----------------------------------------------------------------------------- // Private