/*========================================================================= Program: gdcm Module: $RCSfile: gdcmHeader.cxx,v $ Language: C++ Date: $Date: 2004/09/20 18:14:23 $ Version: $Revision: 1.187 $ 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. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "gdcmHeader.h" #include "gdcmGlobal.h" #include "gdcmUtil.h" #include "gdcmDebug.h" #include "gdcmTS.h" #include "gdcmValEntry.h" #include //----------------------------------------------------------------------------- // Constructor / Destructor /** * \brief Constructor * @param filename name of the file whose header we want to analyze */ gdcmHeader::gdcmHeader( std::string const & filename ): gdcmDocument( filename ) { // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010 // We may encounter the 'RETired' (0x0028, 0x0200) tag // (Image Location") . This Element contains the number of // the group that contains the pixel data (hence the "Pixel Data" // 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. // Note: this IS the right place for the code // Image Location std::string imgLocation = GetEntryByNumber(0x0028, 0x0200); if ( imgLocation == GDCM_UNFOUND ) { // default value GrPixel = 0x7fe0; } else { GrPixel = (uint16_t) atoi( imgLocation.c_str() ); } // sometimes Image Location value doesn't follow // the supposed processor endianity. // see gdcmData/cr172241.dcm if ( GrPixel == 0xe07f ) { GrPixel = 0x7fe0; } if ( GrPixel != 0x7fe0 ) { // This is a kludge for old dirty Philips imager. NumPixel = 0x1010; } else { NumPixel = 0x0010; } } /** * \brief Constructor */ gdcmHeader::gdcmHeader() :gdcmDocument() { } /** * \ingroup gdcmHeader * \brief Canonical destructor. */ gdcmHeader::~gdcmHeader () { } /** * \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 filetype Type of the File to be written * (ACR-NEMA, ExplicitVR, ImplicitVR) */ void gdcmHeader::Write(FILE* fp,FileType filetype) { // Bits Allocated if ( GetEntryByNumber(0x0028,0x0100) == "12") { SetEntryByNumber("16", 0x0028,0x0100); } // 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; ReplaceOrCreateByNumber(s_lgPix,GrPixel, 0x0000); } // FIXME : should be nice if we could move it to gdcmFile // (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 = 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); } } gdcmDocument::Write(fp,filetype); } //----------------------------------------------------------------------------- // Print //----------------------------------------------------------------------------- // Public /** * \brief This predicate, based on hopefully reasonable heuristics, * decides whether or not the current gdcmHeader 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, * false otherwise. */ bool gdcmHeader::IsReadable() { if( !gdcmDocument::IsReadable() ) { return false; } std::string res = GetEntryByNumber(0x0028, 0x0005); if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) { return false; // Image Dimensions } if ( !GetDocEntryByNumber(0x0028, 0x0100) ) { return false; // "Bits Allocated" } if ( !GetDocEntryByNumber(0x0028, 0x0101) ) { return false; // "Bits Stored" } if ( !GetDocEntryByNumber(0x0028, 0x0102) ) { return false; // "High Bit" } if ( !GetDocEntryByNumber(0x0028, 0x0103) ) { return false; // "Pixel Representation" i.e. 'Sign' } return true; } /** * \brief Retrieve the number of columns of image. * @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() { std::string strSize; strSize = GetEntryByNumber(0x0028,0x0011); if ( strSize == GDCM_UNFOUND ) { return 0; } return atoi( strSize.c_str() ); } /** * \ingroup gdcmHeader * \brief Retrieve the number of lines of image. * \warning The defaulted value is 1 as opposed to gdcmHeader::GetXSize() * @return The encountered size when found, 1 by default * (The ACR-NEMA file contains a Signal, not an Image). */ int gdcmHeader::GetYSize() { std::string strSize = GetEntryByNumber(0x0028,0x0010); if ( strSize != GDCM_UNFOUND ) { return atoi( strSize.c_str() ); } if ( IsDicomV3() ) { return 0; } // The Rows (0028,0010) entry was optional for ACR/NEMA. It might // 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 * dimension. When absent we consider the third dimension as * being the ACR-NEMA "Planes" tag content. * @return The encountered size when found, 1 by default (single image). */ int gdcmHeader::GetZSize() { // Both DicomV3 and ACR/Nema consider the "Number of Frames" // as the third dimension. 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 ) { return atoi( strSize.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 xspacing, yspacing; std::string strSpacing = GetEntryByNumber(0x0028,0x0030); if ( strSpacing == GDCM_UNFOUND ) { dbg.Verbose(0, "gdcmHeader::GetXSpacing: unfound Pixel Spacing (0028,0030)"); return 1.; } int nbValues; if( ( nbValues = sscanf( strSpacing.c_str(), "%f\\%f", &yspacing, &xspacing)) != 2 ) { // if single value is found, xspacing is defaulted to yspacing if ( nbValues == 1 ) { return yspacing; } } if ( xspacing == 0.) { dbg.Verbose(0, "gdcmHeader::GetYSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem"); // seems to be a bug in the header ... sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing); } 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 yspacing = 0; std::string strSpacing = GetEntryByNumber(0x0028,0x0030); if ( strSpacing == GDCM_UNFOUND ) { dbg.Verbose(0, "gdcmHeader::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); 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() { // Spacing Between Slices : distance entre le milieu de chaque coupe // Les coupes peuvent etre : // jointives (Spacing between Slices = Slice Thickness) // chevauchantes (Spacing between Slices < Slice Thickness) // 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, // on suppose que les coupes sont jointives std::string strSpacingBSlices = GetEntryByNumber(0x0018,0x0088); if ( strSpacingBSlices == GDCM_UNFOUND ) { dbg.Verbose(0, "gdcmHeader::GetZSpacing: unfound StrSpacingBSlices"); std::string strSliceThickness = GetEntryByNumber(0x0018,0x0050); if ( strSliceThickness == GDCM_UNFOUND ) { return 1.; } else { // if no 'Spacing Between Slices' is found, // we assume slices join together // (no overlapping, no interslice gap) // if they don't, we're fucked up return atof( strSliceThickness.c_str() ); } } else { return atof( strSpacingBSlices.c_str() ); } } /** *\ingroup gdcmHeader *\brief gets the info from 0028,1052 : Rescale Intercept * @return Rescale Intercept */ float gdcmHeader::GetRescaleIntercept() { float resInter = 0.; std::string strRescInter = GetEntryByNumber(0x0028,0x1052); //0028 1052 DS IMG Rescale Intercept 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"); } } return resInter; } /** *\ingroup gdcmHeader *\brief gets the info from 0028,1053 : Rescale Slope * @return Rescale Slope */ float gdcmHeader::GetRescaleSlope() { float resSlope = 1.; std::string strRescSlope = GetEntryByNumber(0x0028,0x1053); //0028 1053 DS IMG Rescale Slope 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"); } } return resSlope; } /** * \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() { if ( GetSamplesPerPixel() == 3 ) { return 3; } // 0028 0100 US IMG Bits Allocated // (in order no to be messed up by old RGB images) if ( GetEntryByNumber(0x0028,0x0100) == "24" ) { return 3; } std::string strPhotometricInterpretation = GetEntryByNumber(0x0028,0x0004); if ( ( strPhotometricInterpretation == "PALETTE COLOR ") ) { if ( HasLUT() )// PALETTE COLOR is NOT enough { return 3; } else { return 1; } } // beware of trailing space at end of string // DICOM tags are never of odd length if ( strPhotometricInterpretation == GDCM_UNFOUND || strPhotometricInterpretation == "MONOCHROME1 " || strPhotometricInterpretation == "MONOCHROME2 " ) { return 1; } else { // we assume that *all* kinds of YBR are dealt with return 3; } } /** * \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() { // 0028 0100 US IMG Bits Allocated // (in order no to be messed up by old RGB images) if ( gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24" ) { return 3; } // we assume that *all* kinds of YBR are dealt with return GetSamplesPerPixel(); } // // -------------- Remember ! ---------------------------------- // // Image Position Patient (0020,0032): // If not found (ACR_NEMA) we try Image Position (0020,0030) // If not found (ACR-NEMA), we consider Slice Location (0020,1041) // or Location (0020,0050) // as the Z coordinate, // 0. for all the coordinates if nothing is found // \todo find a way to inform the caller nothing was found // \todo How to tell the caller a wrong number of values was found? // // --------------------------------------------------------------- // /** * \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() { 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)"); strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images if ( strImPos == GDCM_UNFOUND ) { dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position (RET) (0020,0030)"); /// \todo How to tell the caller nothing was found ? return 0.; } } if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 ) { 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() { 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)"); strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images if ( strImPos == GDCM_UNFOUND ) { dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position (RET) (0020,0030)"); /// \todo How to tell the caller nothing was found ? return 0.; } } if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 ) { return 0.; } return yImPos; } /** * \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() { float xImPos, yImPos, zImPos; std::string strImPos = GetEntryByNumber(0x0020,0x0032); if ( strImPos != GDCM_UNFOUND ) { if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) { dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position Patient (0020,0032)"); return 0.; // bug in the element 0x0020,0x0032 } else { return zImPos; } } strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images if ( strImPos != GDCM_UNFOUND ) { if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos ) != 3 ) { dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position (RET) (0020,0030)"); return 0.; // bug in the element 0x0020,0x0032 } else { return zImPos; } } std::string strSliceLocation = GetEntryByNumber(0x0020,0x1041); // for *very* old ACR-NEMA images if ( strSliceLocation != GDCM_UNFOUND ) { if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1) { dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Slice Location (0020,1041)"); return 0.; // bug in the element 0x0020,0x1041 } else { return zImPos; } } dbg.Verbose(0, "gdcmHeader::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)"); return 0.; // bug in the element 0x0020,0x0050 } else { return zImPos; } } dbg.Verbose(0, "gdcmHeader::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() { // 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 // using the external decimal to internal binary conversion rules. This may // 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 if ( strImNumber != GDCM_UNFOUND ) { return atoi( strImNumber.c_str() ); } return 0; //Hopeless } /** * \brief gets the info from 0008,0060 : Modality * @return Modality Type */ ModalityType gdcmHeader::GetModality() { // 0008 0060 CS ID Modality std::string strModality = GetEntryByNumber(0x0008,0x0060); if ( strModality != GDCM_UNFOUND ) { if ( strModality.find("AU") < strModality.length()) return AU; else if ( strModality.find("AS") < strModality.length()) return AS; else if ( strModality.find("BI") < strModality.length()) return BI; else if ( strModality.find("CF") < strModality.length()) return CF; else if ( strModality.find("CP") < strModality.length()) return CP; else if ( strModality.find("CR") < strModality.length()) return CR; else if ( strModality.find("CT") < strModality.length()) return CT; else if ( strModality.find("CS") < strModality.length()) return CS; else if ( strModality.find("DD") < strModality.length()) return DD; else if ( strModality.find("DF") < strModality.length()) return DF; else if ( strModality.find("DG") < strModality.length()) return DG; else if ( strModality.find("DM") < strModality.length()) return DM; else if ( strModality.find("DS") < strModality.length()) return DS; else if ( strModality.find("DX") < strModality.length()) return DX; else if ( strModality.find("ECG") < strModality.length()) return ECG; else if ( strModality.find("EPS") < strModality.length()) return EPS; else if ( strModality.find("FA") < strModality.length()) return FA; else if ( strModality.find("FS") < strModality.length()) return FS; else if ( strModality.find("HC") < strModality.length()) return HC; else if ( strModality.find("HD") < strModality.length()) return HD; else if ( strModality.find("LP") < strModality.length()) return LP; else if ( strModality.find("LS") < strModality.length()) return LS; else if ( strModality.find("MA") < strModality.length()) return MA; else if ( strModality.find("MR") < strModality.length()) return MR; else if ( strModality.find("NM") < strModality.length()) return NM; else if ( strModality.find("OT") < strModality.length()) return OT; else if ( strModality.find("PT") < strModality.length()) return PT; else if ( strModality.find("RF") < strModality.length()) return RF; else if ( strModality.find("RG") < strModality.length()) return RG; else if ( strModality.find("RTDOSE") < strModality.length()) return RTDOSE; else if ( strModality.find("RTIMAGE") < strModality.length()) return RTIMAGE; else if ( strModality.find("RTPLAN") < strModality.length()) return RTPLAN; else if ( strModality.find("RTSTRUCT") < strModality.length()) return RTSTRUCT; else if ( strModality.find("SM") < strModality.length()) return SM; else if ( strModality.find("ST") < strModality.length()) return ST; else if ( strModality.find("TG") < strModality.length()) return TG; else if ( strModality.find("US") < strModality.length()) return US; else if ( strModality.find("VF") < strModality.length()) return VF; else if ( strModality.find("XA") < strModality.length()) return XA; else if ( strModality.find("XC") < strModality.length()) return XC; else { /// \todo throw error return value ??? /// specified <> unknow in our database return Unknow; } } return Unknow; } /** * \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() { std::string strSize = GetEntryByNumber(0x0028,0x0101); if ( strSize == GDCM_UNFOUND ) { dbg.Verbose(0, "gdcmHeader::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 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() { std::string strSize = GetEntryByNumber(0x0028,0x0100); if ( strSize == GDCM_UNFOUND ) { dbg.Verbose(0, "gdcmHeader::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() { std::string strSize = GetEntryByNumber(0x0028,0x0002); if ( strSize == GDCM_UNFOUND ) { dbg.Verbose(0, "gdcmHeader::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 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() { 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 */ int gdcmHeader::GetPixelSize() { // 0028 0100 US IMG Bits Allocated // (in order no to be messed up by old RGB images) // if (gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24") // return 3; std::string pixelType = GetPixelType(); if ( pixelType == "8U" || pixelType == "8S" ) { return 1; } if ( pixelType == "16U" || pixelType == "16S") { return 2; } if ( pixelType == "32U" || pixelType == "32S") { return 4; } if ( pixelType == "FD" ) { return 8; } dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type"); return 0; } /** * \ingroup gdcmHeader * \brief Build the Pixel Type of the image. * Possible values are: * - 8U unsigned 8 bit, * - 8S signed 8 bit, * - 16U unsigned 16 bit, * - 16S signed 16 bit, * - 32U unsigned 32 bit, * - 32S signed 32 bit, * - FD floating double 64 bits (Not kosher DICOM, but so usefull!) * \warning 12 bit images appear as 16 bit. * 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 bitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated if ( bitsAlloc == GDCM_UNFOUND ) { dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated"); bitsAlloc = "16"; } if ( bitsAlloc == "64" ) { return "FD"; } if ( bitsAlloc == "12" ) { // It will be unpacked bitsAlloc = "16"; } else if ( bitsAlloc == "24" ) { // (in order no to be messed up bitsAlloc = "8"; // by old RGB images) } std::string sign = GetEntryByNumber(0x0028, 0x0103); // "Pixel Representation" if (sign == GDCM_UNFOUND ) { dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation"); bitsAlloc = "0"; } if ( sign == "0" ) { sign = "U"; } else { 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() { gdcmDocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel); if ( pxlElement ) { return pxlElement->GetOffset(); } else { #ifdef GDCM_DEBUG std::cout << "Big trouble : Pixel Element (" << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" << std::endl; #endif //GDCM_DEBUG return 0; } } // 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() { gdcmDocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel); if ( pxlElement ) { return pxlElement->GetLength(); } else { #ifdef GDCM_DEBUG std::cout << "Big trouble : Pixel Element (" << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" << std::endl; #endif //GDCM_DEBUG return 0; } } /** * \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 * how to deal with them * Please warn me if you know sbdy that *does* know ... jprx * @return true if LUT Descriptors and LUT Tables were found */ bool gdcmHeader::HasLUT() { // Check the presence of the LUT Descriptors, and LUT Tables // LutDescriptorRed if ( !GetDocEntryByNumber(0x0028,0x1101) ) { return false; } // LutDescriptorGreen if ( !GetDocEntryByNumber(0x0028,0x1102) ) { return false; } // LutDescriptorBlue if ( !GetDocEntryByNumber(0x0028,0x1103) ) { return false; } // Red Palette Color Lookup Table Data if ( !GetDocEntryByNumber(0x0028,0x1201) ) { return false; } // Green Palette Color Lookup Table Data if ( !GetDocEntryByNumber(0x0028,0x1202) ) { return false; } // Blue Palette Color Lookup Table Data if ( !GetDocEntryByNumber(0x0028,0x1203) ) { return false; } // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent) // NOT taken into account, but we don't know how to use it ... return true; } /** * \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() { std::vector tokens; int lutNbits; //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 ) { return 0; } tokens.clear(); // clean any previous value Tokenize ( lutDescription, tokens, "\\" ); //LutLength=atoi(tokens[0].c_str()); //LutDepth=atoi(tokens[1].c_str()); lutNbits = atoi( tokens[2].c_str() ); tokens.clear(); return lutNbits; } /** * \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 * else 1. * @return The full Transfert Syntax Name (as opposed to Transfert Syntax UID) */ std::string gdcmHeader::GetTransfertSyntaxName() { // use the gdcmTS (TS : Transfert Syntax) std::string transfertSyntax = GetEntryByNumber(0x0002,0x0010); if ( transfertSyntax == GDCM_NOTLOADED ) { // fusible std::cout << "Transfert Syntax not loaded. " << std::endl << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE" << std::endl; return "Uncompressed ACR-NEMA"; } if ( transfertSyntax == GDCM_UNFOUND ) { dbg.Verbose(0, "gdcmHeader::GetTransfertSyntaxName:" " unfound Transfert Syntax (0002,0010)"); return "Uncompressed ACR-NEMA"; } while ( ! isdigit(transfertSyntax[transfertSyntax.length()-1]) ) { transfertSyntax.erase(transfertSyntax.length()-1, 1); } // we do it only when we need it gdcmTS* ts = gdcmGlobal::GetTS(); std::string tsName = ts->GetValue( transfertSyntax ); //delete ts; /// \todo Seg Fault when deleted ?! return tsName; } /** * \brief Sets the Pixel Area size in the Header * --> not-for-rats function * @param ImageDataSize new Pixel Area Size * warning : nothing else is checked */ void gdcmHeader::SetImageDataSize(size_t ImageDataSize) { char car[20]; sprintf(car,"%d",ImageDataSize); gdcmDocEntry *a = GetDocEntryByNumber(GrPixel, NumPixel); a->SetLength(ImageDataSize); ImageDataSize += 8; sprintf(car,"%d",ImageDataSize); const std::string content1 = car; SetEntryByNumber(content1, GrPixel, NumPixel); } //----------------------------------------------------------------------------- // Protected /** * \brief anonymize a Header (removes Patient's personal info) * (read the code to see which ones ...) */ bool gdcmHeader::AnonymizeHeader() { // If exist, replace by spaces SetEntryByNumber (" ",0x0010, 0x2154); // Telephone SetEntryByNumber (" ",0x0010, 0x1040); // Adress SetEntryByNumber (" ",0x0010, 0x0020); // Patient ID gdcmDocEntry* patientNameHE = GetDocEntryByNumber (0x0010, 0x0010); if ( patientNameHE ) // we replace it by Study Instance UID (why not) { std::string studyInstanceUID = GetEntryByNumber (0x0020, 0x000d); if ( studyInstanceUID != GDCM_UNFOUND ) { ReplaceOrCreateByNumber(studyInstanceUID, 0x0010, 0x0010); } else { ReplaceOrCreateByNumber(std::string("anonymised"), 0x0010, 0x0010); } } // Just for fun :-( // (if any) remove or replace all the stuff that contains a Date //0008 0012 DA ID Instance Creation Date //0008 0020 DA ID Study Date //0008 0021 DA ID Series Date //0008 0022 DA ID Acquisition Date //0008 0023 DA ID Content Date //0008 0024 DA ID Overlay Date //0008 0025 DA ID Curve Date //0008 002a DT ID Acquisition Datetime //0018 9074 DT ACQ Frame Acquisition Datetime //0018 9151 DT ACQ Frame Reference Datetime //0018 a002 DT ACQ Contribution Date Time //0020 3403 SH REL Modified Image Date (RET) //0032 0032 DA SDY Study Verified Date //0032 0034 DA SDY Study Read Date //0032 1000 DA SDY Scheduled Study Start Date //0032 1010 DA SDY Scheduled Study Stop Date //0032 1040 DA SDY Study Arrival Date //0032 1050 DA SDY Study Completion Date //0038 001a DA VIS Scheduled Admission Date //0038 001c DA VIS Scheduled Discharge Date //0038 0020 DA VIS Admitting Date //0038 0030 DA VIS Discharge Date //0040 0002 DA PRC Scheduled Procedure Step Start Date //0040 0004 DA PRC Scheduled Procedure Step End Date //0040 0244 DA PRC Performed Procedure Step Start Date //0040 0250 DA PRC Performed Procedure Step End Date //0040 2004 DA PRC Issue Date of Imaging Service Request //0040 4005 DT PRC Scheduled Procedure Step Start Date and Time //0040 4011 DT PRC Expected Completion Date and Time //0040 a030 DT PRC Verification Date Time //0040 a032 DT PRC Observation Date Time //0040 a120 DT PRC DateTime //0040 a121 DA PRC Date //0040 a13a DT PRC Referenced Datetime //0070 0082 DA ??? Presentation Creation Date //0100 0420 DT ??? SOP Autorization Date and Time //0400 0105 DT ??? Digital Signature DateTime //2100 0040 DA PJ Creation Date //3006 0008 DA SSET Structure Set Date //3008 0024 DA ??? Treatment Control Point Date //3008 0054 DA ??? First Treatment Date //3008 0056 DA ??? Most Recent Treatment Date //3008 0162 DA ??? Safe Position Exit Date //3008 0166 DA ??? Safe Position Return Date //3008 0250 DA ??? Treatment Date //300a 0006 DA RT RT Plan Date //300a 022c DA RT Air Kerma Rate Reference Date //300e 0004 DA RT Review Date return true; } /** * \brief gets the info from 0020,0037 : Image Orientation Patient * @param iop adress of the (6)float aray to receive values * @return cosines of image orientation patient */ void gdcmHeader::GetImageOrientationPatient( float iop[6] ) { std::string strImOriPat; //iop is supposed to be float[6] iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.; // 0020 0037 DS REL Image Orientation (Patient) if ( (strImOriPat = GetEntryByNumber(0x0020,0x0037)) != GDCM_UNFOUND ) { if( 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)"); // bug in the element 0x0020,0x0037 } } //For ACR-NEMA // 0020 0035 DS REL Image Orientation (RET) 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)"); // bug in the element 0x0020,0x0035 } } } //----------------------------------------------------------------------------- // Private //-----------------------------------------------------------------------------