X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=945f2885fc7abb10ff0e76c222323aea86d2fa86;hb=9ca4fd0ccbfea12ed7760856de3a8faf41625869;hp=b6801f8b88955802c6ee3ac9e19aa0aee749e7ef;hpb=1d69b92978803204089d270599133917d944c651;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index b6801f8b..945f2885 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmHeader.cxx,v $ Language: C++ - Date: $Date: 2004/10/12 04:35:46 $ - Version: $Revision: 1.193 $ + Date: $Date: 2005/01/07 16:26:13 $ + Version: $Revision: 1.223 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -22,19 +22,19 @@ #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 */ -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 @@ -48,7 +48,7 @@ Header::Header( std::string const & filename ): // Note: this IS the right place for the code // Image Location - std::string imgLocation = GetEntryByNumber(0x0028, 0x0200); + const std::string &imgLocation = GetEntryByNumber(0x0028, 0x0200); if ( imgLocation == GDCM_UNFOUND ) { // default value @@ -76,14 +76,38 @@ 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 = 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 */ Header::Header() :Document() { + InitializeDefaultHeader(); } /** @@ -93,17 +117,24 @@ 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 Header::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) + { + Debug::Verbose(2, "Failed to open (write) File: " , fileName.c_str()); + return false; + } + // Bits Allocated if ( GetEntryByNumber(0x0028,0x0100) == "12") { @@ -116,8 +147,8 @@ void Header::Write(FILE* fp,FileType filetype) if (i_lgPix != -2) { // no (GrPixel, NumPixel) element - std::string s_lgPix; - s_lgPix = Util::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); } @@ -132,7 +163,7 @@ void Header::Write(FILE* fp,FileType filetype) // Drop 0028|1101, 0028|1102, 0028|1103 // Drop 0028|1201, 0028|1202, 0028|1203 - DocEntry* e = GetDocEntryByNumber(0x0028,0x01101); + DocEntry *e = GetDocEntryByNumber(0x0028,0x01101); if (e) { RemoveEntryNoDestroy(e); @@ -163,7 +194,12 @@ void Header::Write(FILE* fp,FileType filetype) RemoveEntryNoDestroy(e); } } - Document::Write(fp,filetype); + Document::WriteContent(fp,filetype); + + fp->close(); + delete fp; + + return true; } //----------------------------------------------------------------------------- @@ -188,7 +224,7 @@ bool Header::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 @@ -220,8 +256,7 @@ bool Header::IsReadable() */ int Header::GetXSize() { - std::string strSize; - strSize = GetEntryByNumber(0x0028,0x0011); + const std::string &strSize = GetEntryByNumber(0x0028,0x0011); if ( strSize == GDCM_UNFOUND ) { return 0; @@ -238,7 +273,7 @@ int Header::GetXSize() */ 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() ); @@ -249,7 +284,7 @@ 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; } @@ -265,17 +300,17 @@ 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; @@ -289,11 +324,11 @@ int Header::GetZSize() 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, "Header::GetXSpacing: unfound Pixel Spacing (0028,0030)"); + Debug::Verbose(0, "Header::GetXSpacing: unfound Pixel Spacing (0028,0030)"); return 1.; } @@ -304,14 +339,26 @@ 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"); + Debug::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; @@ -324,25 +371,28 @@ float Header::GetXSpacing() */ float Header::GetYSpacing() { - float yspacing = 0; + float yspacing = 1.; std::string strSpacing = GetEntryByNumber(0x0028,0x0030); if ( strSpacing == GDCM_UNFOUND ) { - dbg.Verbose(0, "Header::GetYSpacing: unfound Pixel Spacing (0028,0030)"); + Debug::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 Header::GetZSpacing() @@ -357,12 +407,12 @@ float Header::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, "Header::GetZSpacing: unfound StrSpacingBSlices"); - std::string strSliceThickness = GetEntryByNumber(0x0018,0x0050); + Debug::Verbose(0, "Header::GetZSpacing: unfound StrSpacingBSlices"); + const std::string &strSliceThickness = GetEntryByNumber(0x0018,0x0050); if ( strSliceThickness == GDCM_UNFOUND ) { return 1.; @@ -373,13 +423,11 @@ float Header::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() ); } /** @@ -390,13 +438,13 @@ 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, "Header::GetRescaleIntercept: Rescale Slope " + Debug::Verbose(0, "Header::GetRescaleIntercept: Rescale Slope " "is empty"); } } @@ -418,7 +466,7 @@ float Header::GetRescaleSlope() if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1) { // bug in the element 0x0028,0x1053 - dbg.Verbose(0, "Header::GetRescaleSlope: Rescale Slope is empty"); + Debug::Verbose(0, "Header::GetRescaleSlope: Rescale Slope is empty"); } } @@ -463,8 +511,8 @@ int Header::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; } @@ -524,12 +572,12 @@ float Header::GetXOrigin() if ( strImPos == GDCM_UNFOUND ) { - dbg.Verbose(0, "Header::GetXImagePosition: unfound Image " + Debug::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, "Header::GetXImagePosition: unfound Image " + Debug::Verbose(0, "Header::GetXImagePosition: unfound Image " "Position (RET) (0020,0030)"); /// \todo How to tell the caller nothing was found ? return 0.; @@ -557,12 +605,12 @@ float Header::GetYOrigin() if ( strImPos == GDCM_UNFOUND) { - dbg.Verbose(0, "Header::GetYImagePosition: unfound Image " + Debug::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, "Header::GetYImagePosition: unfound Image " + Debug::Verbose(0, "Header::GetYImagePosition: unfound Image " "Position (RET) (0020,0030)"); /// \todo How to tell the caller nothing was found ? return 0.; @@ -594,7 +642,7 @@ float Header::GetZOrigin() { if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) { - dbg.Verbose(0, "Header::GetZImagePosition: wrong Image " + Debug::Verbose(0, "Header::GetZImagePosition: wrong Image " "Position Patient (0020,0032)"); return 0.; // bug in the element 0x0020,0x0032 } @@ -610,7 +658,7 @@ float Header::GetZOrigin() if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos ) != 3 ) { - dbg.Verbose(0, "Header::GetZImagePosition: wrong Image Position (RET) (0020,0030)"); + Debug::Verbose(0, "Header::GetZImagePosition: wrong Image Position (RET) (0020,0030)"); return 0.; // bug in the element 0x0020,0x0032 } else @@ -624,7 +672,7 @@ float Header::GetZOrigin() { if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1) { - dbg.Verbose(0, "Header::GetZImagePosition: wrong Slice Location (0020,1041)"); + Debug::Verbose(0, "Header::GetZImagePosition: wrong Slice Location (0020,1041)"); return 0.; // bug in the element 0x0020,0x1041 } else @@ -632,14 +680,14 @@ float Header::GetZOrigin() return zImPos; } } - dbg.Verbose(0, "Header::GetZImagePosition: unfound Slice Location (0020,1041)"); + Debug::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, "Header::GetZImagePosition: wrong Location (0020,0050)"); + Debug::Verbose(0, "Header::GetZImagePosition: wrong Location (0020,0050)"); return 0.; // bug in the element 0x0020,0x0050 } else @@ -647,7 +695,7 @@ float Header::GetZOrigin() return zImPos; } } - dbg.Verbose(0, "Header::GetYImagePosition: unfound Location (0020,0050)"); + Debug::Verbose(0, "Header::GetYImagePosition: unfound Location (0020,0050)"); return 0.; // Hopeless } @@ -746,7 +794,7 @@ int Header::GetBitsStored() std::string strSize = GetEntryByNumber( 0x0028, 0x0101 ); if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(0, "Header::GetBitsStored: this is supposed to " + Debug::Verbose(0, "Header::GetBitsStored: this is supposed to " "be mandatory"); return 0; // It's supposed to be mandatory // the caller will have to check @@ -765,7 +813,7 @@ int Header::GetHighBitPosition() std::string strSize = GetEntryByNumber( 0x0028, 0x0102 ); if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(0, "Header::GetHighBitPosition: this is supposed " + Debug::Verbose(0, "Header::GetHighBitPosition: this is supposed " "to be mandatory"); return 0; } @@ -783,7 +831,7 @@ bool Header::IsSignedPixelData() std::string strSize = GetEntryByNumber( 0x0028, 0x0103 ); if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(0, "Header::IsSignedPixelData: this is supposed " + Debug::Verbose(0, "Header::IsSignedPixelData: this is supposed " "to be mandatory"); return false; } @@ -806,7 +854,7 @@ int Header::GetBitsAllocated() std::string strSize = GetEntryByNumber(0x0028,0x0100); if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(0, "Header::GetBitsStored: this is supposed to " + Debug::Verbose(0, "Header::GetBitsStored: this is supposed to " "be mandatory"); return 0; // It's supposed to be mandatory // the caller will have to check @@ -822,10 +870,10 @@ int Header::GetBitsAllocated() */ int Header::GetSamplesPerPixel() { - std::string strSize = GetEntryByNumber(0x0028,0x0002); + const std::string& strSize = GetEntryByNumber(0x0028,0x0002); if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(0, "Header::GetBitsStored: this is supposed to " + Debug::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 @@ -840,15 +888,15 @@ int Header::GetSamplesPerPixel() */ 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, "Header::IsMonochrome: absent Photometric " + Debug::Verbose(0, "Header::IsMonochrome: absent Photometric " "Interpretation"); } return false; @@ -868,7 +916,7 @@ bool Header::IsPaletteColor() } if ( PhotometricInterp == GDCM_UNFOUND ) { - dbg.Verbose(0, "Header::IsPaletteColor: absent Photometric " + Debug::Verbose(0, "Header::IsPaletteColor: absent Photometric " "Interpretation"); } return false; @@ -888,7 +936,7 @@ bool Header::IsYBRFull() } if ( PhotometricInterp == GDCM_UNFOUND ) { - dbg.Verbose(0, "Header::IsYBRFull: absent Photometric " + Debug::Verbose(0, "Header::IsYBRFull: absent Photometric " "Interpretation"); } return false; @@ -938,7 +986,7 @@ int Header::GetPixelSize() { return 8; } - dbg.Verbose(0, "Header::GetPixelSize: Unknown pixel type"); + Debug::Verbose(0, "Header::GetPixelSize: Unknown pixel type"); return 0; } @@ -961,7 +1009,7 @@ std::string Header::GetPixelType() std::string bitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated if ( bitsAlloc == GDCM_UNFOUND ) { - dbg.Verbose(0, "Header::GetPixelType: unfound Bits Allocated"); + Debug::Verbose(0, "Header::GetPixelType: unfound Bits Allocated"); bitsAlloc = "16"; } @@ -969,7 +1017,7 @@ std::string Header::GetPixelType() { return "FD"; } - if ( bitsAlloc == "12" ) + else if ( bitsAlloc == "12" ) { // It will be unpacked bitsAlloc = "16"; @@ -984,10 +1032,10 @@ std::string Header::GetPixelType() if (sign == GDCM_UNFOUND ) { - dbg.Verbose(0, "Header::GetPixelType: unfound Pixel Representation"); + Debug::Verbose(0, "Header::GetPixelType: unfound Pixel Representation"); bitsAlloc = "0"; } - if ( sign == "0" ) + else if ( sign == "0" ) { sign = "U"; } @@ -1127,169 +1175,6 @@ int Header::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* Header::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, "Header::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, "Header::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, "Header::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, "Header::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 TS * else 1. @@ -1309,12 +1194,12 @@ std::string Header::GetTransfertSyntaxName() } if ( transfertSyntax == GDCM_UNFOUND ) { - dbg.Verbose(0, "Header::GetTransfertSyntaxName:" + Debug::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); } @@ -1326,26 +1211,6 @@ std::string Header::GetTransfertSyntaxName() 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 Header::SetImageDataSize(size_t ImageDataSize) -{ - ///FIXME I don't understand this code wh ydo we set two times 'car' ? - std::string car = Util::Format("%d", ImageDataSize); - - DocEntry *a = GetDocEntryByNumber(GrPixel, NumPixel); - a->SetLength(ImageDataSize); - - ImageDataSize += 8; - car = Util::Format("%d", ImageDataSize); - - SetEntryByNumber(car, GrPixel, NumPixel); -} - //----------------------------------------------------------------------------- // Protected @@ -1371,7 +1236,7 @@ bool Header::AnonymizeHeader() } else { - ReplaceOrCreateByNumber(std::string("anonymised"), 0x0010, 0x0010); + ReplaceOrCreateByNumber("anonymised", 0x0010, 0x0010); } } @@ -1447,7 +1312,7 @@ void Header::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, "Header::GetImageOrientationPatient: " + Debug::Verbose(0, "Header::GetImageOrientationPatient: " "wrong Image Orientation Patient (0020,0037)"); } } @@ -1458,12 +1323,88 @@ void Header::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, "Header::GetImageOrientationPatient: " + Debug::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