X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=31263819c3b7ea2cace0232fb4eee99965e04bc1;hb=327dfe7647e3720b0f3125f9b19397cb9afc0ed3;hp=5e01a8f37ecdc30f4a940207709bfb3ac9fd108c;hpb=4c8c80589b3770976ea27fc03b290b97db5da3e6;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index 5e01a8f3..31263819 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -3,12 +3,12 @@ Program: gdcm Module: $RCSfile: gdcmHeader.cxx,v $ Language: C++ - Date: $Date: 2004/07/30 11:40:13 $ - Version: $Revision: 1.179 $ + Date: $Date: 2005/01/06 20:03:28 $ + Version: $Revision: 1.222 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or - http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details. + http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR @@ -22,24 +22,20 @@ #include "gdcmDebug.h" #include "gdcmTS.h" #include "gdcmValEntry.h" +#include //sscanf #include +namespace gdcm +{ //----------------------------------------------------------------------------- // Constructor / Destructor /** * \brief Constructor * @param filename name of the file whose header we want to analyze - * @param exception_on_error whether we want to throw an exception or not - * @param ignore_shadow = true if user wants to skip shadow groups - * during parsing, to save memory space */ -gdcmHeader::gdcmHeader( std::string const & filename, - bool exception_on_error, - bool ignore_shadow ): - gdcmDocument( filename, - exception_on_error, - ignore_shadow ) +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 @@ -49,11 +45,10 @@ gdcmHeader::gdcmHeader( std::string const & filename, // 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. - - // This IS the right place for the code + // 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 @@ -81,85 +76,130 @@ gdcmHeader::gdcmHeader( std::string const & filename, { NumPixel = 0x0010; } + + // Now, we know GrPixel and NumPixel. + // Let's create a VirtualDictEntry to allow a further VR modification + // and force VR to match with BitsAllocated. + + DocEntry *entry = GetDocEntryByNumber(GrPixel, NumPixel); + if ( entry != 0 ) + { + + std::string PixelVR; + // 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB) + // more than 8 (i.e 12, 16) is a 'O Words' + if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 ) + PixelVR = "OB"; + else + PixelVR = "OW"; + + DictEntry* newEntry = NewVirtualDictEntry( + GrPixel, NumPixel, + PixelVR, "PXL", "Pixel Data"); + + entry->SetDictEntry( newEntry ); + } } /** - * \brief Constructor - * @param exception_on_error whether we want to throw an exception or not + * \brief Constructor used when we want to generate dicom files from scratch */ -gdcmHeader::gdcmHeader(bool exception_on_error) : - gdcmDocument( exception_on_error ) +Header::Header() + :Document() { + InitializeDefaultHeader(); } /** - * \ingroup gdcmHeader * \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) + { + dbg.Verbose(2, "Failed to open (write) File: " , fileName.c_str()); + return false; + } + // Bits Allocated - if ( GetEntryByNumber(0x0028,0x0100) == "12") { + if ( GetEntryByNumber(0x0028,0x0100) == "12") + { SetEntryByNumber("16", 0x0028,0x0100); } - // correct Pixel group Length if necessary - - // TODO : create a gdcmHeader::Write method and move this part. - // (only gdcmHeader knows GrPixel, NumPixel) + /// \todo correct 'Pixel group' Length if necessary int i_lgPix = GetEntryLengthByNumber(GrPixel, NumPixel); - if (i_lgPix != -2) { // no (GrPixel, NumPixel) element - char * dumm = new char[20]; - sprintf(dumm ,"%d", i_lgPix+12); - std::string s_lgPix = dumm; - delete dumm; + 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); } - + + // 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 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; - e=GetDocEntryByNumber(0x0028,0x01101); - if (e) - RemoveEntry(e); - e=GetDocEntryByNumber(0x0028,0x1102); - if (e) - RemoveEntry(e); - e=GetDocEntryByNumber(0x0028,0x1103); - - if (e) - RemoveEntry(e); - e=GetDocEntryByNumber(0x0028,0x01201); - if (e) - RemoveEntry(e); - e=GetDocEntryByNumber(0x0028,0x1202); - if (e) - RemoveEntry(e); - e=GetDocEntryByNumber(0x0028,0x1203); - if (e) - RemoveEntry(e); - } - - gdcmDocument::Write(fp,filetype); + if ( GetEntryByNumber(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); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntryByNumber(0x0028,0x1102); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntryByNumber(0x0028,0x1103); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntryByNumber(0x0028,0x01201); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntryByNumber(0x0028,0x1202); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntryByNumber(0x0028,0x1203); + if (e) + { + RemoveEntryNoDestroy(e); + } + } + Document::WriteContent(fp,filetype); + + fp->close(); + delete fp; + + return true; } //----------------------------------------------------------------------------- @@ -171,20 +211,20 @@ void gdcmHeader::Write(FILE* fp,FileType filetype) { /** * \brief This predicate, based on hopefully reasonable heuristics, - * decides whether or not the current gdcmHeader was properly parsed + * decides whether or not the current Header was properly parsed * and contains the mandatory information for being considered as * a well formed and usable Dicom/Acr File. - * @return true when gdcmHeader is the one of a reasonable Dicom/Acr file, + * @return true when Header is the one of a reasonable Dicom/Acr file, * false otherwise. */ -bool gdcmHeader::IsReadable() +bool Header::IsReadable() { - if( !gdcmDocument::IsReadable() ) + if( !Document::IsReadable() ) { return false; } - std::string res = GetEntryByNumber(0x0028, 0x0005); + const std::string &res = GetEntryByNumber(0x0028, 0x0005); if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) { return false; // Image Dimensions @@ -214,10 +254,9 @@ bool gdcmHeader::IsReadable() * @return The encountered size when found, 0 by default. * 0 means the file is NOT USABLE. The caller will have to check */ -int gdcmHeader::GetXSize() +int Header::GetXSize() { - std::string strSize; - strSize = GetEntryByNumber(0x0028,0x0011); + const std::string &strSize = GetEntryByNumber(0x0028,0x0011); if ( strSize == GDCM_UNFOUND ) { return 0; @@ -227,15 +266,14 @@ int gdcmHeader::GetXSize() } /** - * \ingroup gdcmHeader * \brief Retrieve the number of lines of image. - * \warning The defaulted value is 1 as opposed to gdcmHeader::GetXSize() + * \warning The defaulted value is 1 as opposed to Header::GetXSize() * @return The encountered size when found, 1 by default * (The ACR-NEMA file contains a Signal, not an Image). */ -int gdcmHeader::GetYSize() +int Header::GetYSize() { - std::string strSize = GetEntryByNumber(0x0028,0x0010); + const std::string &strSize = GetEntryByNumber(0x0028,0x0010); if ( strSize != GDCM_UNFOUND ) { return atoi( strSize.c_str() ); @@ -246,12 +284,11 @@ 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; } /** - * \ingroup gdcmHeader * \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 @@ -259,40 +296,39 @@ int gdcmHeader::GetYSize() * being the ACR-NEMA "Planes" tag content. * @return The encountered size when found, 1 by default (single image). */ -int gdcmHeader::GetZSize() +int Header::GetZSize() { // Both DicomV3 and ACR/Nema consider the "Number of Frames" // as the third dimension. - std::string strSize = GetEntryByNumber(0x0028,0x0008); + const std::string &strSize = GetEntryByNumber(0x0028,0x0008); if ( strSize != GDCM_UNFOUND ) { return atoi( strSize.c_str() ); } // We then consider the "Planes" entry as the third dimension - strSize = GetEntryByNumber(0x0028,0x0012); - if ( strSize != GDCM_UNFOUND ) + const std::string &strSize2 = GetEntryByNumber(0x0028,0x0012); + if ( strSize2 != GDCM_UNFOUND ) { - return atoi( strSize.c_str() ); + return atoi( strSize2.c_str() ); } return 1; } /** - * \ingroup gdcmHeader * \brief gets the info from 0028,0030 : Pixel Spacing * else 1.0 * @return X dimension of a pixel */ -float gdcmHeader::GetXSpacing() +float Header::GetXSpacing() { float xspacing, yspacing; - std::string strSpacing = GetEntryByNumber(0x0028,0x0030); + const std::string &strSpacing = GetEntryByNumber(0x0028,0x0030); if ( strSpacing == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetXSpacing: unfound Pixel Spacing (0028,0030)"); + dbg.Verbose(0, "Header::GetXSpacing: unfound Pixel Spacing (0028,0030)"); return 1.; } @@ -303,50 +339,63 @@ float gdcmHeader::GetXSpacing() // if single value is found, xspacing is defaulted to yspacing if ( nbValues == 1 ) { - return yspacing; + xspacing = yspacing; } + + if ( xspacing == 0.0 ) + xspacing = 1.0; + + return xspacing; + } + + // to avoid troubles with David Clunie's-like images + if ( xspacing == 0. && yspacing == 0.) + return 1.; + if ( xspacing == 0.) { - dbg.Verbose(0, "gdcmHeader::GetYSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem"); + dbg.Verbose(0, "Header::GetXSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem"); // seems to be a bug in the header ... - sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing); + nbValues = sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing); + assert( nbValues == 2 ); } return xspacing; } /** - * \ingroup gdcmHeader * \brief gets the info from 0028,0030 : Pixel Spacing * else 1.0 * @return Y dimension of a pixel */ -float gdcmHeader::GetYSpacing() +float Header::GetYSpacing() { - float yspacing = 0; + float yspacing = 1.; std::string strSpacing = GetEntryByNumber(0x0028,0x0030); if ( strSpacing == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetYSpacing: unfound Pixel Spacing (0028,0030)"); + dbg.Verbose(0, "Header::GetYSpacing: unfound Pixel Spacing (0028,0030)"); return 1.; } // if sscanf cannot read any float value, it won't affect yspacing sscanf( strSpacing.c_str(), "%f", &yspacing); + if ( yspacing == 0.0 ) + yspacing = 1.0; + return yspacing; } /** - *\ingroup gdcmHeader - *\brief gets the info from 0018,0088 : Space Between Slices - * else from 0018,0050 : Slice Thickness - * else 1.0 - * @return Z dimension of a voxel-to be - */ -float gdcmHeader::GetZSpacing() + * \brief gets the info from 0018,0088 : Space Between Slices + * else from 0018,0050 : Slice Thickness + * else 1.0 + * @return Z dimension of a voxel-to be + */ +float Header::GetZSpacing() { // Spacing Between Slices : distance entre le milieu de chaque coupe // Les coupes peuvent etre : @@ -358,12 +407,12 @@ float gdcmHeader::GetZSpacing() // Si le Spacing Between Slices est absent, // on suppose que les coupes sont jointives - std::string strSpacingBSlices = GetEntryByNumber(0x0018,0x0088); + const std::string &strSpacingBSlices = GetEntryByNumber(0x0018,0x0088); if ( strSpacingBSlices == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetZSpacing: unfound StrSpacingBSlices"); - std::string strSliceThickness = GetEntryByNumber(0x0018,0x0050); + dbg.Verbose(0, "Header::GetZSpacing: unfound StrSpacingBSlices"); + const std::string &strSliceThickness = GetEntryByNumber(0x0018,0x0050); if ( strSliceThickness == GDCM_UNFOUND ) { return 1.; @@ -374,51 +423,50 @@ 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() ); } /** - *\ingroup gdcmHeader - *\brief gets the info from 0028,1052 : Rescale Intercept - * @return Rescale Intercept + *\brief gets the info from 0028,1052 : Rescale Intercept + * @return Rescale Intercept */ -float gdcmHeader::GetRescaleIntercept() +float Header::GetRescaleIntercept() { float resInter = 0.; - std::string strRescInter = GetEntryByNumber(0x0028,0x1052); //0028 1052 DS IMG Rescale Intercept + /// 0028 1052 DS IMG Rescale Intercept + const std::string &strRescInter = GetEntryByNumber(0x0028,0x1052); if ( strRescInter != GDCM_UNFOUND ) { if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 ) { // bug in the element 0x0028,0x1052 - dbg.Verbose(0, "gdcmHeader::GetRescaleIntercept: Rescale Slope is empty"); + dbg.Verbose(0, "Header::GetRescaleIntercept: Rescale Slope " + "is empty"); } } - return resInter; + return resInter; } /** - *\ingroup gdcmHeader - *\brief gets the info from 0028,1053 : Rescale Slope - * @return Rescale Slope + *\brief gets the info from 0028,1053 : Rescale Slope + * @return Rescale Slope */ -float gdcmHeader::GetRescaleSlope() +float Header::GetRescaleSlope() { float resSlope = 1.; - std::string strRescSlope = GetEntryByNumber(0x0028,0x1053); //0028 1053 DS IMG Rescale Slope + //0028 1053 DS IMG Rescale Slope + std::string strRescSlope = GetEntryByNumber(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"); + dbg.Verbose(0, "Header::GetRescaleSlope: Rescale Slope is empty"); } } @@ -426,14 +474,13 @@ float gdcmHeader::GetRescaleSlope() } /** - * \ingroup gdcmHeader - * \brief This function is intended to user who doesn't want - * to have to manage a LUT and expects to get an RBG Pixel image - * (or a monochrome one ...) - * \warning to be used with GetImagePixels() - * @return 1 if Gray level, 3 if Color (RGB, YBR or PALETTE COLOR) - */ -int gdcmHeader::GetNumberOfScalarComponents() + * \brief This function is intended to user who doesn't want + * to have to manage a LUT and expects to get an RBG Pixel image + * (or a monochrome one ...) + * \warning to be used with GetImagePixels() + * @return 1 if Gray level, 3 if Color (RGB, YBR or PALETTE COLOR) + */ +int Header::GetNumberOfScalarComponents() { if ( GetSamplesPerPixel() == 3 ) { @@ -464,8 +511,8 @@ int gdcmHeader::GetNumberOfScalarComponents() // beware of trailing space at end of string // DICOM tags are never of odd length if ( strPhotometricInterpretation == GDCM_UNFOUND || - strPhotometricInterpretation == "MONOCHROME1 " || - strPhotometricInterpretation == "MONOCHROME2 " ) + Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME1") || + Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME2") ) { return 1; } @@ -477,18 +524,17 @@ int gdcmHeader::GetNumberOfScalarComponents() } /** - * \ingroup gdcmHeader - * \brief This function is intended to user that DOESN'T want - * to get RGB pixels image when it's stored as a PALETTE COLOR image - * - the (vtk) user is supposed to know how deal with LUTs - - * \warning to be used with GetImagePixelsRaw() - * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -) - */ -int gdcmHeader::GetNumberOfScalarComponentsRaw() + * \brief This function is intended to user that DOESN'T want + * to get RGB pixels image when it's stored as a PALETTE COLOR image + * - the (vtk) user is supposed to know how deal with LUTs - + * \warning to be used with GetImagePixelsRaw() + * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -) + */ +int Header::GetNumberOfScalarComponentsRaw() { // 0028 0100 US IMG Bits Allocated // (in order no to be messed up by old RGB images) - if ( gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24" ) + if ( Header::GetEntryByNumber(0x0028,0x0100) == "24" ) { return 3; } @@ -514,24 +560,25 @@ int gdcmHeader::GetNumberOfScalarComponentsRaw() // /** - * \brief gets the info from 0020,0032 : Image Position Patient - * else from 0020,0030 : Image Position (RET) - * else 0. - * @return up-left image corner X position - */ - -float gdcmHeader::GetXOrigin() + * \brief gets the info from 0020,0032 : Image Position Patient + * else from 0020,0030 : Image Position (RET) + * else 0. + * @return up-left image corner X position + */ +float Header::GetXOrigin() { float xImPos, yImPos, zImPos; std::string strImPos = GetEntryByNumber(0x0020,0x0032); if ( strImPos == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position Patient (0020,0032)"); + dbg.Verbose(0, "Header::GetXImagePosition: unfound Image " + "Position Patient (0020,0032)"); strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images if ( strImPos == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position (RET) (0020,0030)"); + dbg.Verbose(0, "Header::GetXImagePosition: unfound Image " + "Position (RET) (0020,0030)"); /// \todo How to tell the caller nothing was found ? return 0.; } @@ -539,30 +586,32 @@ float gdcmHeader::GetXOrigin() if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 ) { - return 0.; + return 0.; } return xImPos; } /** - * \brief gets the info from 0020,0032 : Image Position Patient - * else from 0020,0030 : Image Position (RET) - * else 0. - * @return up-left image corner Y position - */ -float gdcmHeader::GetYOrigin() + * \brief gets the info from 0020,0032 : Image Position Patient + * else from 0020,0030 : Image Position (RET) + * else 0. + * @return up-left image corner Y position + */ +float Header::GetYOrigin() { float xImPos, yImPos, zImPos; std::string strImPos = GetEntryByNumber(0x0020,0x0032); if ( strImPos == GDCM_UNFOUND) { - dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position Patient (0020,0032)"); + dbg.Verbose(0, "Header::GetYImagePosition: unfound Image " + "Position Patient (0020,0032)"); strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images if ( strImPos == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position (RET) (0020,0030)"); + dbg.Verbose(0, "Header::GetYImagePosition: unfound Image " + "Position (RET) (0020,0030)"); /// \todo How to tell the caller nothing was found ? return 0.; } @@ -577,14 +626,14 @@ float gdcmHeader::GetYOrigin() } /** - * \brief gets the info from 0020,0032 : Image Position Patient - * \ else from 0020,0030 : Image Position (RET) - * \ else from 0020,1041 : Slice Location - * \ else from 0020,0050 : Location - * \ else 0. - * @return up-left image corner Z position - */ -float gdcmHeader::GetZOrigin() + * \brief gets the info from 0020,0032 : Image Position Patient + * else from 0020,0030 : Image Position (RET) + * else from 0020,1041 : Slice Location + * else from 0020,0050 : Location + * else 0. + * @return up-left image corner Z position + */ +float Header::GetZOrigin() { float xImPos, yImPos, zImPos; std::string strImPos = GetEntryByNumber(0x0020,0x0032); @@ -593,7 +642,8 @@ float gdcmHeader::GetZOrigin() { if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) { - dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position Patient (0020,0032)"); + dbg.Verbose(0, "Header::GetZImagePosition: wrong Image " + "Position Patient (0020,0032)"); return 0.; // bug in the element 0x0020,0x0032 } else @@ -608,7 +658,7 @@ float gdcmHeader::GetZOrigin() if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos ) != 3 ) { - dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position (RET) (0020,0030)"); + dbg.Verbose(0, "Header::GetZImagePosition: wrong Image Position (RET) (0020,0030)"); return 0.; // bug in the element 0x0020,0x0032 } else @@ -622,7 +672,7 @@ float gdcmHeader::GetZOrigin() { if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1) { - dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Slice Location (0020,1041)"); + dbg.Verbose(0, "Header::GetZImagePosition: wrong Slice Location (0020,1041)"); return 0.; // bug in the element 0x0020,0x1041 } else @@ -630,14 +680,14 @@ float gdcmHeader::GetZOrigin() return zImPos; } } - dbg.Verbose(0, "gdcmHeader::GetZImagePosition: unfound Slice Location (0020,1041)"); + dbg.Verbose(0, "Header::GetZImagePosition: unfound Slice Location (0020,1041)"); std::string strLocation = GetEntryByNumber(0x0020,0x0050); if ( strLocation != GDCM_UNFOUND ) { if( sscanf( strLocation.c_str(), "%f", &zImPos) != 1) { - dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Location (0020,0050)"); + dbg.Verbose(0, "Header::GetZImagePosition: wrong Location (0020,0050)"); return 0.; // bug in the element 0x0020,0x0050 } else @@ -645,17 +695,16 @@ float gdcmHeader::GetZOrigin() return zImPos; } } - dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Location (0020,0050)"); + dbg.Verbose(0, "Header::GetYImagePosition: unfound Location (0020,0050)"); return 0.; // Hopeless } /** - * \brief gets the info from 0020,0013 : Image Number - * \ else 0. - * @return image number - */ -int gdcmHeader::GetImageNumber() + * \brief gets the info from 0020,0013 : Image Number else 0. + * @return image number + */ +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 @@ -663,7 +712,8 @@ int gdcmHeader::GetImageNumber() // be preferable to sscanf() since atoi() is a much smaller, simpler and // faster function. sscanf() can do all possible conversions whereas // atoi() can only do single decimal integer conversions. - std::string strImNumber = GetEntryByNumber(0x0020,0x0013); //0020 0013 IS REL Image Number + //0020 0013 IS REL Image Number + std::string strImNumber = GetEntryByNumber(0x0020,0x0013); if ( strImNumber != GDCM_UNFOUND ) { return atoi( strImNumber.c_str() ); @@ -672,10 +722,10 @@ int gdcmHeader::GetImageNumber() } /** - * \brief gets the info from 0008,0060 : Modality - * @return Modality Type - */ -ModalityType gdcmHeader::GetModality() + * \brief gets the info from 0008,0060 : Modality + * @return Modality Type + */ +ModalityType Header::GetModality() { // 0008 0060 CS ID Modality std::string strModality = GetEntryByNumber(0x0008,0x0060); @@ -734,93 +784,189 @@ ModalityType gdcmHeader::GetModality() } /** - * \ingroup gdcmHeader * \brief Retrieve the number of Bits Stored (actually used) * (as opposite to number of Bits Allocated) * @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 = GetEntryByNumber( 0x0028, 0x0101 ); if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetBitsStored: this is supposed to be mandatory"); + dbg.Verbose(0, "Header::GetBitsStored: this is supposed to " + "be mandatory"); return 0; // It's supposed to be mandatory // the caller will have to check } + return atoi( strSize.c_str() ); +} +/** + * \brief Retrieve the high bit position. + * \warning The method defaults to 0 when information is absent. + * The responsability of checking this value is left to the caller. + * @return The high bit positin when present. 0 when absent. + */ +int Header::GetHighBitPosition() +{ + std::string strSize = GetEntryByNumber( 0x0028, 0x0102 ); + if ( strSize == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::GetHighBitPosition: this is supposed " + "to be mandatory"); + return 0; + } return atoi( strSize.c_str() ); } /** - * \ingroup gdcmHeader + * \brief Check wether the pixels are signed or UNsigned data. + * \warning The method defaults to false (UNsigned) when information is absent. + * 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 ); + if ( strSize == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::IsSignedPixelData: this is supposed " + "to be mandatory"); + return false; + } + int sign = atoi( strSize.c_str() ); + if ( sign == 0 ) + { + return false; + } + return true; +} + +/** * \brief Retrieve the number of Bits Allocated * (8, 12 -compacted ACR-NEMA files, 16, ...) * @return The encountered number of Bits Allocated, 0 by default. * 0 means the file is NOT USABLE. The caller has to check it ! */ -int gdcmHeader::GetBitsAllocated() +int Header::GetBitsAllocated() { std::string strSize = GetEntryByNumber(0x0028,0x0100); if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetBitsStored: this is supposed to be mandatory"); + dbg.Verbose(0, "Header::GetBitsStored: this is supposed to " + "be mandatory"); return 0; // It's supposed to be mandatory // the caller will have to check } - return atoi( strSize.c_str() ); } /** - * \ingroup gdcmHeader * \brief Retrieve the number of Samples Per Pixel * (1 : gray level, 3 : RGB -1 or 3 Planes-) * @return The encountered number of Samples Per Pixel, 1 by default. * (Gray level Pixels) */ -int gdcmHeader::GetSamplesPerPixel() +int Header::GetSamplesPerPixel() { - std::string strSize = GetEntryByNumber(0x0028,0x0002); + const std::string& strSize = GetEntryByNumber(0x0028,0x0002); if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetBitsStored: this is supposed to be mandatory"); + dbg.Verbose(0, "Header::GetBitsStored: this is supposed to " + "be mandatory"); return 1; // Well, it's supposed to be mandatory ... // but sometimes it's missing : *we* assume Gray pixels } - return atoi( strSize.c_str() ); } /** - * \ingroup gdcmHeader + * \brief Check wether 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 ); + if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") + || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") ) + { + return true; + } + if ( PhotometricInterp == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::IsMonochrome: absent Photometric " + "Interpretation"); + } + return false; +} + +/** + * \brief Check wether 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 ); + if ( PhotometricInterp == "PALETTE COLOR " ) + { + return true; + } + if ( PhotometricInterp == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::IsPaletteColor: absent Photometric " + "Interpretation"); + } + return false; +} + +/** + * \brief Check wether 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 ); + if ( PhotometricInterp == "YBR_FULL" ) + { + return true; + } + if ( PhotometricInterp == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::IsYBRFull: absent Photometric " + "Interpretation"); + } + return false; +} + +/** * \brief Retrieve the Planar Configuration for RGB images * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane) * @return The encountered Planar Configuration, 0 by default. */ -int gdcmHeader::GetPlanarConfiguration() +int Header::GetPlanarConfiguration() { std::string strSize = GetEntryByNumber(0x0028,0x0006); if ( strSize == GDCM_UNFOUND ) { return 0; } - return atoi( strSize.c_str() ); } /** - * \ingroup gdcmHeader * \brief Return the size (in bytes) of a single pixel of data. * @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 + * 0 means the file is NOT USABLE; the caller will have to check */ -int gdcmHeader::GetPixelSize() +int Header::GetPixelSize() { // 0028 0100 US IMG Bits Allocated // (in order no to be messed up by old RGB images) - // if (gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24") + // if (Header::GetEntryByNumber(0x0028,0x0100) == "24") // return 3; std::string pixelType = GetPixelType(); @@ -840,13 +986,11 @@ int gdcmHeader::GetPixelSize() { return 8; } - - dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type"); + dbg.Verbose(0, "Header::GetPixelSize: Unknown pixel type"); return 0; } /** - * \ingroup gdcmHeader * \brief Build the Pixel Type of the image. * Possible values are: * - 8U unsigned 8 bit, @@ -860,12 +1004,12 @@ int gdcmHeader::GetPixelSize() * 24 bit images appear as 8 bit * @return 0S if nothing found. NOT USABLE file. The caller has to check */ -std::string gdcmHeader::GetPixelType() +std::string Header::GetPixelType() { std::string bitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated if ( bitsAlloc == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated"); + dbg.Verbose(0, "Header::GetPixelType: unfound Bits Allocated"); bitsAlloc = "16"; } @@ -873,7 +1017,7 @@ std::string gdcmHeader::GetPixelType() { return "FD"; } - if ( bitsAlloc == "12" ) + else if ( bitsAlloc == "12" ) { // It will be unpacked bitsAlloc = "16"; @@ -884,14 +1028,14 @@ std::string gdcmHeader::GetPixelType() bitsAlloc = "8"; // by old RGB images) } - std::string sign = GetEntryByNumber(0x0028, 0x0103); // "Pixel Representation" + std::string sign = GetEntryByNumber(0x0028, 0x0103);//"Pixel Representation" if (sign == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation"); + dbg.Verbose(0, "Header::GetPixelType: unfound Pixel Representation"); bitsAlloc = "0"; } - if ( sign == "0" ) + else if ( sign == "0" ) { sign = "U"; } @@ -899,20 +1043,18 @@ std::string gdcmHeader::GetPixelType() { sign = "S"; } - return bitsAlloc + sign; } /** - * \ingroup gdcmHeader * \brief Recover the offset (from the beginning of the file) * of *image* pixels (not *icone image* pixels, if any !) * @return Pixel Offset */ -size_t gdcmHeader::GetPixelOffset() +size_t Header::GetPixelOffset() { - gdcmDocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel); + DocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel); if ( pxlElement ) { return pxlElement->GetOffset(); @@ -928,18 +1070,17 @@ size_t gdcmHeader::GetPixelOffset() } } -// TODO : unify those two (previous one and next one) +/// \todo TODO : unify those two (previous one and next one) /** - * \ingroup gdcmHeader * \brief Recover the pixel area length (in Bytes) * @return Pixel Element Length, as stored in the header * (NOT the memory space necessary to hold the Pixels * -in case of embeded compressed image-) * 0 : NOT USABLE file. The caller has to check. */ -size_t gdcmHeader::GetPixelAreaLength() +size_t Header::GetPixelAreaLength() { - gdcmDocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel); + DocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel); if ( pxlElement ) { return pxlElement->GetLength(); @@ -956,7 +1097,6 @@ size_t gdcmHeader::GetPixelAreaLength() } /** - * \ingroup gdcmHeader * \brief tells us if LUT are used * \warning Right now, 'Segmented xxx Palette Color Lookup Table Data' * are NOT considered as LUT, since nobody knows @@ -964,7 +1104,7 @@ size_t gdcmHeader::GetPixelAreaLength() * Please warn me if you know sbdy that *does* know ... jprx * @return true if LUT Descriptors and LUT Tables were found */ -bool gdcmHeader::HasLUT() +bool Header::HasLUT() { // Check the presence of the LUT Descriptors, and LUT Tables // LutDescriptorRed @@ -1004,19 +1144,19 @@ bool gdcmHeader::HasLUT() } /** - * \ingroup gdcmHeader * \brief gets the info from 0028,1101 : Lookup Table Desc-Red * else 0 * @return Lookup Table number of Bits , 0 by default * 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; - //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red = Lookup Table Desc-Blue + //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); if ( lutDescription == GDCM_UNFOUND ) @@ -1025,7 +1165,7 @@ int gdcmHeader::GetLUTNbits() } tokens.clear(); // clean any previous value - Tokenize ( lutDescription, tokens, "\\" ); + Util::Tokenize ( lutDescription, tokens, "\\" ); //LutLength=atoi(tokens[0].c_str()); //LutDepth=atoi(tokens[1].c_str()); @@ -1036,221 +1176,41 @@ int gdcmHeader::GetLUTNbits() } /** - * \ingroup gdcmHeader - * \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*) GetEntryVoidAreaByNumber(0x0028,0x1201); - uint8_t* lutG = (uint8_t*) GetEntryVoidAreaByNumber(0x0028,0x1202); - uint8_t* lutB = (uint8_t*) GetEntryVoidAreaByNumber(0x0028,0x1203); - - if ( !lutR || !lutG || !lutB ) - { - dbg.Verbose(0, "gdcmHeader::GetLUTRGBA: trouble with one of the LUT"); - return NULL; - } - // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT - - uint8_t* LUTRGBA = new uint8_t[1024]; // 256 * 4 (R, G, B, Alpha) - if ( !LUTRGBA ) - { - return NULL; - } - memset(LUTRGBA, 0, 1024); - - // Bits Allocated - int nb; - std::string str_nb = GetEntryByNumber(0x0028,0x0100); - if ( str_nb == GDCM_UNFOUND ) - { - nb = 16; - } - else - { - nb = atoi( str_nb.c_str() ); - } - int mult; - - if ( nbitsR == 16 && nb == 8) - { - // when LUT item size is different than pixel size - mult = 2; // high byte must be = low byte - } - else - { - // See PS 3.3-2003 C.11.1.1.2 p 619 - mult = 1; - } - - // if we get a black image, let's just remove the '+1' - // from 'i*mult+1' and check again - // if it works, we shall have to check the 3 Palettes - // to see which byte is ==0 (first one, or second one) - // and fix the code - // We give up the checking to avoid some (useless ?)overhead - // (optimistic asumption) - uint8_t* a; - int i; - - a = LUTRGBA + 0; - for( i=0; i < lengthR; ++i) - { - *a = lutR[i*mult+1]; - a += 4; - } - - a = LUTRGBA + 1; - for( i=0; i < lengthG; ++i) - { - *a = lutG[i*mult+1]; - a += 4; - } - - a = LUTRGBA + 2; - for(i=0; i < lengthB; ++i) - { - *a = lutB[i*mult+1]; - a += 4; - } - - a = LUTRGBA + 3; - for(i=0; i < 256; ++i) - { - *a = 1; // Alpha component - a += 4; - } - - return LUTRGBA; -} - -/** - * \brief Accesses the info from 0002,0010 : Transfert Syntax and gdcmTS + * \brief Accesses the info from 0002,0010 : Transfert Syntax and TS * else 1. * @return The full Transfert Syntax Name (as opposed to Transfert Syntax UID) */ -std::string gdcmHeader::GetTransfertSyntaxName() +std::string Header::GetTransfertSyntaxName() { - // use the gdcmTS (TS : Transfert Syntax) + // use the TS (TS : Transfert Syntax) std::string transfertSyntax = GetEntryByNumber(0x0002,0x0010); + if ( transfertSyntax == GDCM_NOTLOADED ) + { + 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:" + dbg.Verbose(0, "Header::GetTransfertSyntaxName:" " unfound Transfert Syntax (0002,0010)"); return "Uncompressed ACR-NEMA"; } - while ( ! isdigit(transfertSyntax[transfertSyntax.length()-1]) ) + while ( ! isdigit((unsigned char)transfertSyntax[transfertSyntax.length()-1]) ) { transfertSyntax.erase(transfertSyntax.length()-1, 1); } // we do it only when we need it - gdcmTS* ts = gdcmGlobal::GetTS(); + TS* ts = Global::GetTS(); std::string tsName = ts->GetValue( transfertSyntax ); //delete ts; /// \todo Seg Fault when deleted ?! return tsName; } -/** - * \brief Sets the Pixel Area size in the Header - * --> not-for-rats function - * @param ImageDataSize new Pixel Area Size - * warning : nothing else is checked - */ -void gdcmHeader::SetImageDataSize(size_t ImageDataSize) -{ - std::string content1; - char car[20]; - - sprintf(car,"%d",ImageDataSize); - - gdcmDocEntry *a = GetDocEntryByNumber(GrPixel, NumPixel); - a->SetLength(ImageDataSize); - - ImageDataSize+=8; - sprintf(car,"%d",ImageDataSize); - content1=car; - SetEntryByNumber(content1, GrPixel, NumPixel); -} - //----------------------------------------------------------------------------- // Protected @@ -1258,15 +1218,16 @@ 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() { - gdcmDocEntry* patientNameHE = GetDocEntryByNumber (0x0010, 0x0010); + // If exist, replace by spaces + SetEntryByNumber (" ",0x0010, 0x2154); // Telephone + SetEntryByNumber (" ",0x0010, 0x1040); // Adress + SetEntryByNumber (" ",0x0010, 0x0020); // Patient ID - ReplaceIfExistByNumber (" ",0x0010, 0x2154); // Telephone - ReplaceIfExistByNumber (" ",0x0010, 0x1040); // Adress - ReplaceIfExistByNumber (" ",0x0010, 0x0020); // Patient ID + DocEntry* patientNameHE = GetDocEntryByNumber (0x0010, 0x0010); - if ( patientNameHE ) + if ( patientNameHE ) // we replace it by Study Instance UID (why not) { std::string studyInstanceUID = GetEntryByNumber (0x0020, 0x000d); if ( studyInstanceUID != GDCM_UNFOUND ) @@ -1275,7 +1236,7 @@ bool gdcmHeader::AnonymizeHeader() } else { - ReplaceOrCreateByNumber(std::string("anonymised"), 0x0010, 0x0010); + ReplaceOrCreateByNumber("anonymised", 0x0010, 0x0010); } } @@ -1339,46 +1300,114 @@ 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 ) +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; + iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.; // 0020 0037 DS REL Image Orientation (Patient) - std::string strImOriPat = GetEntryByNumber(0x0020,0x0037); - if ( strImOriPat != GDCM_UNFOUND ) + if ( (strImOriPat = GetEntryByNumber(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)"); - return ; // bug in the element 0x0020,0x0037 - } - else - { - return ; + dbg.Verbose(0, "Header::GetImageOrientationPatient: " + "wrong Image Orientation Patient (0020,0037)"); } } - //For ACR-NEMA // 0020 0035 DS REL Image Orientation (RET) - strImOriPat = GetEntryByNumber(0x0020,0x0035); - if ( strImOriPat != GDCM_UNFOUND ) + else if ( (strImOriPat = GetEntryByNumber(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)"); - return ; // bug in the element 0x0020,0x0035 + dbg.Verbose(0, "Header::GetImageOrientationPatient: " + "wrong Image Orientation Patient (0020,0035)"); } } - else - { - return; +} + +/** + * \brief Initialize a default DICOM header that should contain all the + * field require by other reader. DICOM standard does not + * explicitely defines those fields, heuristic has been choosen. + * This is not perfect as we are writting a CT image... + */ +void Header::InitializeDefaultHeader() +{ + typedef struct + { + const char *value; + uint16_t group; + uint16_t elem; + } DICOM_DEFAULT_VALUE; + + std::string date = Util::GetCurrentDate(); + std::string time = Util::GetCurrentTime(); + std::string uid = Util::CreateUniqueUID(); + std::string uidMedia = uid; + std::string uidClass = uid + ".1"; + std::string uidInst = uid + ".10"; + std::string uidStudy = uid + ".100"; + std::string uidSerie = uid + ".1000"; + + static DICOM_DEFAULT_VALUE defaultvalue[] = { + { "146 ", 0x0002, 0x0000}, // Meta Element Group Length // FIXME: how to recompute ? + { "1.2.840.10008.5.1.4.1.1.2", 0x0002, 0x0002}, // Media Storage SOP Class UID (CT Image Storage) + { uidClass.c_str(), 0x0002, 0x0003}, // Media Storage SOP Instance UID + { uidClass.c_str(), 0x0002, 0x0012}, // META Implementation Class UID + { "GDCM", 0x0002, 0x0016}, // Source Application Entity Title + + { date.c_str(), 0x0008, 0x0012}, // Instance Creation Date + { time.c_str(), 0x0008, 0x0013}, // Instance Creation Time + { "1.2.840.10008.5.1.4.1.1.2", 0x0008, 0x0016}, // SOP Class UID + { uidInst.c_str(), 0x0008, 0x0018}, // SOP Instance UID + { "CT", 0x0008, 0x0060}, // Modality + { "GDCM", 0x0008, 0x0070}, // Manufacturer + { "GDCM", 0x0008, 0x0080}, // Institution Name + { "http://www-creatis.insa-lyon.fr/Public/Gdcm", 0x0008, 0x0081}, // Institution Address + + { "GDCM", 0x0010, 0x0010}, // Patient's Name + { "GDCMID", 0x0010, 0x0020}, // Patient ID + + { uidStudy.c_str(), 0x0020, 0x000d}, // Study Instance UID + { uidSerie.c_str(), 0x0020, 0x000e}, // Series Instance UID + { "1", 0x0020, 0x0010}, // StudyID + { "1", 0x0020, 0x0011}, // SeriesNumber + + { "1", 0x0028, 0x0002}, // Samples per pixel 1 or 3 + { "MONOCHROME1", 0x0028, 0x0004}, // photochromatic interpretation + { "0", 0x0028, 0x0010}, // nbRows + { "0", 0x0028, 0x0011}, // nbCols + { "8", 0x0028, 0x0100}, // BitsAllocated 8 or 12 or 16 + { "8", 0x0028, 0x0101}, // BitsStored <= BitsAllocated + { "7", 0x0028, 0x0102}, // HighBit <= BitsAllocated - 1 + { "0", 0x0028, 0x0103}, // Pixel Representation 0(unsigned) or 1(signed) + { 0, 0, 0 } + }; + + // default value + // Special case this is the image (not a string) + GrPixel = 0x7fe0; + NumPixel = 0x0010; + ReplaceOrCreateByNumber(0, 0, GrPixel, NumPixel); + + // All remaining strings: + unsigned int i = 0; + DICOM_DEFAULT_VALUE current = defaultvalue[i]; + while( current.value ) + { + ReplaceOrCreateByNumber(current.value, current.group, current.elem); + current = defaultvalue[++i]; } } + //----------------------------------------------------------------------------- // Private //----------------------------------------------------------------------------- + +} // end namespace gdcm