X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=90299a8a0ab45d4a08a4d685b8f7533b1390f508;hb=e6671b4378ba33a2cdf7c711e4e45250af74dbbc;hp=7b28ed4294e152e08fec80a0967471bd5b6116dc;hpb=cc65499518ef9cab0d2b3d348bc15cfc2990a31a;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index 7b28ed42..90299a8a 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -1,38 +1,42 @@ -// gdcmHeader.cxx -//----------------------------------------------------------------------------- -#include "gdcmHeader.h" - -#include -#include -#include // for isalpha +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmHeader.cxx,v $ + Language: C++ + Date: $Date: 2004/07/31 23:30:04 $ + Version: $Revision: 1.181 $ + + 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 /** - * \ingroup gdcmHeader - * \brief - * @param InFilename - * @param exception_on_error - * @param enable_sequences = true to allow the header - * to be parsed *inside* the SeQuences, - * when they have an actual length - * @param ignore_shadow = true if user wants to skip shadow groups - during parsing, to save memory space - *\TODO : may be we need one more bool, - * to allow skipping the private elements while parsing the header - * in order to save space + * \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 */ -gdcmHeader::gdcmHeader(const char *InFilename, - bool exception_on_error, - bool enable_sequences, - bool ignore_shadow): - gdcmParser(InFilename,exception_on_error,enable_sequences,ignore_shadow) -{ - +gdcmHeader::gdcmHeader( std::string const & filename, + bool exception_on_error ): + gdcmDocument( filename, + exception_on_error ) +{ // 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 @@ -41,35 +45,45 @@ gdcmHeader::gdcmHeader(const char *InFilename, // 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 - std::string ImageLocation = GetEntryByNumber(0x0028, 0x0200); - if ( ImageLocation == GDCM_UNFOUND ) { // Image Location - GrPixel = 0x7fe0; // default value - } else { - GrPixel = (guint16) atoi( ImageLocation.c_str() ); - } - if (GrPixel == 0xe07f) // sometimes Image Location value doesn't follow - GrPixel = 0x7fe0; // the supposed processor endianity. - // see gdcmData/cr172241.dcm - if (GrPixel != 0x7fe0) - // This is a kludge for old dirty Philips imager. - NumPixel = 0x1010; - else - NumPixel = 0x0010; - - TagKey key = gdcmDictEntry::TranslateToKey(GrPixel, NumPixel); - countGrPixel = GetEntry().count(key); + // 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; + } } /** - * \ingroup gdcmHeader - * \brief - * @param exception_on_error + * \brief Constructor + * @param exception_on_error whether we want to throw an exception or not */ gdcmHeader::gdcmHeader(bool exception_on_error) : - gdcmParser(exception_on_error) + gdcmDocument( exception_on_error ) { } @@ -77,308 +91,731 @@ gdcmHeader::gdcmHeader(bool exception_on_error) : * \ingroup gdcmHeader * \brief Canonical destructor. */ -gdcmHeader::~gdcmHeader (void) { +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); + } + + // correct Pixel group Length if necessary + + // TODO : create a gdcmHeader::Write method and move this part. + // (only gdcmHeader knows GrPixel, NumPixel) + + 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); + } + + // 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) + { + 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); } //----------------------------------------------------------------------------- // Print -// see gdcmParser.cxx + //----------------------------------------------------------------------------- // Public + /** - * \ingroup gdcmHeader * \brief This predicate, based on hopefully reasonable heuristics, - * decides whether or not the current gdcmParser was properly parsed + * 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 gdcmParser is the one of a reasonable Dicom/Acr file, + * @return true when gdcmHeader is the one of a reasonable Dicom/Acr file, * false otherwise. */ -bool gdcmHeader::IsReadable(void) { - if(!gdcmParser::IsReadable()) { - return(false); +bool gdcmHeader::IsReadable() +{ + if( !gdcmDocument::IsReadable() ) + { + return false; } + std::string res = GetEntryByNumber(0x0028, 0x0005); - if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) + if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) + { return false; // Image Dimensions - if ( !GetHeaderEntryByNumber(0x0028, 0x0100) ) + } + if ( !GetDocEntryByNumber(0x0028, 0x0100) ) + { return false; // "Bits Allocated" - if ( !GetHeaderEntryByNumber(0x0028, 0x0101) ) + } + if ( !GetDocEntryByNumber(0x0028, 0x0101) ) + { return false; // "Bits Stored" - if ( !GetHeaderEntryByNumber(0x0028, 0x0102) ) + } + if ( !GetDocEntryByNumber(0x0028, 0x0102) ) + { return false; // "High Bit" - if ( !GetHeaderEntryByNumber(0x0028, 0x0103) ) - return false; // "Pixel Representation" + } + if ( !GetDocEntryByNumber(0x0028, 0x0103) ) + { + return false; // "Pixel Representation" i.e. 'Sign' + } + return true; } /** - * \ingroup gdcmHeader - * \brief Determines if the Transfer Syntax was already encountered - * and if it corresponds to a JPEGBaseLineProcess1 one. - * - * @return True when JPEGBaseLineProcess1found. False in all other cases. + * \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 */ -bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) { - gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadHeaderEntrySafe(Element); +int gdcmHeader::GetXSize() +{ + std::string strSize; + strSize = GetEntryByNumber(0x0028,0x0011); + if ( strSize == GDCM_UNFOUND ) + { + return 0; + } - std::string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.4.50" ) - return true; - return false; + return atoi( strSize.c_str() ); } /** * \ingroup gdcmHeader - * \brief Determines if the Transfer Syntax was already encountered - * and if it corresponds to a JPEGExtendedProcess2-4 one. - * - * @return True when JPEGExtendedProcess2-4 found. False in all other cases. + * \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). */ -bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) { - gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadHeaderEntrySafe(Element); - return ( Element->GetValue() == "1.2.840.10008.1.2.4.51" ); +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 Determines if the Transfer Syntax was already encountered - * and if it corresponds to a JPEGExtendeProcess3-5 one. - * - * @return True when JPEGExtendedProcess3-5 found. False in all other cases. + * \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). */ -bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) { - gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadHeaderEntrySafe(Element); +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() ); + } - std::string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.4.52" ) - return true; - return false; + return 1; } /** - * \ingroup gdcmHeader - * \brief Determines if the Transfer Syntax was already encountered - * and if it corresponds to a JPEGSpectralSelectionProcess6-8 one. - * - * @return True when JPEGSpectralSelectionProcess6-8 found. False in all - * other cases. - */ -bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) { - gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadHeaderEntrySafe(Element); + * \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.; + } - std::string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.4.53" ) - return true; - return false; + 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 Determines if the Transfer Syntax was already encountered - * and if it corresponds to a RLE Lossless one. - * - * @return True when RLE Lossless found. False in all - * other cases. + * \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 */ -bool gdcmHeader::IsRLELossLessTransferSyntax(void) { - gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadHeaderEntrySafe(Element); +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"); + } + } - std::string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.5" ) { - return true; - } - return false; + return resInter; } /** - * \ingroup gdcmHeader - * \brief Determines if Transfer Syntax was already encountered - * and if it corresponds to a JPEG Lossless one. - * - * @return True when RLE Lossless found. False in all - * other cases. + *\ingroup gdcmHeader + *\brief gets the info from 0028,1053 : Rescale Slope + * @return Rescale Slope */ -bool gdcmHeader::IsJPEGLossless(void) { - gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); - // faire qq chose d'intelligent a la place de ça - if ( !Element ) - return false; - LoadHeaderEntrySafe(Element); +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"); + } + } - const char * Transfert = Element->GetValue().c_str(); - if ( memcmp(Transfert+strlen(Transfert)-2 ,"70",2)==0) return true; - if ( memcmp(Transfert+strlen(Transfert)-2 ,"55",2)==0) return true; - if (Element->GetValue() == "1.2.840.10008.1.2.4.57") return true; + 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); - return false; + 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 Determines if the Transfer Syntax was already encountered - * and if it corresponds to a JPEG200 one.0 - * - * @return True when JPEG2000 (Lossly or LossLess) found. False in all - * other cases. - */ -bool gdcmHeader::IsJPEG2000(void) { - gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadHeaderEntrySafe(Element); + * \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; + } - std::string Transfer = Element->GetValue(); - if ( (Transfer == "1.2.840.10008.1.2.4.90") - || (Transfer == "1.2.840.10008.1.2.4.91") ) - return true; - return false; + // 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? +// +// --------------------------------------------------------------- +// + /** - * \ingroup gdcmHeader - * \brief Predicate for dicom version 3 file. - * @return True when the file is a dicom version 3. - */ -bool gdcmHeader::IsDicomV3(void) { - // Checking if Transfert Syntax exists is enough - return (GetHeaderEntryByNumber(0x0002, 0x0010) != NULL); + * \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; } /** - * \ingroup gdcmHeader - * \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(void) { - std::string StrSize; - StrSize = GetEntryByNumber(0x0028,0x0011); - if (StrSize == GDCM_UNFOUND) - return 0; - return atoi(StrSize.c_str()); + * \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; } /** - * \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 file contains a Signal, not an Image). - */ -int gdcmHeader::GetYSize(void) { - std::string StrSize = GetEntryByNumber(0x0028,0x0010); - if (StrSize != GDCM_UNFOUND) - return atoi(StrSize.c_str()); - if ( IsDicomV3() ) - return 0; - else - // 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; + * \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 } /** - * \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 "Planes" tag content. - * @return The encountered size when found, 1 by default (single image). - */ -int gdcmHeader::GetZSize(void) { - // 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 [we - // cannot retrieve by name since "Planes tag is present both in - // IMG (0028,0012) and OLY (6000,0012) sections of the dictionary]. - StrSize = GetEntryByNumber(0x0028,0x0012); - if (StrSize != GDCM_UNFOUND) - return atoi(StrSize.c_str()); - return 1; + * \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(void) { - std::string StrSize = GetEntryByNumber(0x0028,0x0101); - if (StrSize == GDCM_UNFOUND) +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()); + } + + 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(void) { // TODO : move to gdcmFile - std::string StrSize = GetEntryByNumber(0x0028,0x0100); - if (StrSize == GDCM_UNFOUND) +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()); + } + + 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(void) { // TODO : move to gdcmFile - std::string StrSize = GetEntryByNumber(0x0028,0x0002); - if (StrSize == GDCM_UNFOUND) +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()); + // 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(void) { - std::string StrSize = GetEntryByNumber(0x0028,0x0006); - if (StrSize == GDCM_UNFOUND) +int gdcmHeader::GetPlanarConfiguration() +{ + std::string strSize = GetEntryByNumber(0x0028,0x0006); + if ( strSize == GDCM_UNFOUND ) + { return 0; - return atoi(StrSize.c_str()); + } + + return atoi( strSize.c_str() ); } /** @@ -387,14 +824,31 @@ int gdcmHeader::GetPlanarConfiguration(void) { * @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(void) { - std::string PixelType = GetPixelType(); - if (PixelType == "8U" || PixelType == "8S") +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") + } + if ( pixelType == "16U" || pixelType == "16S") + { return 2; - if (PixelType == "32U" || PixelType == "32S") + } + if ( pixelType == "32U" || pixelType == "32S") + { return 4; + } + if ( pixelType == "FD" ) + { + return 8; + } + dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type"); return 0; } @@ -409,142 +863,102 @@ int gdcmHeader::GetPixelSize(void) { * - 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 + * 24 bit images appear as 8 bit * @return 0S if nothing found. NOT USABLE file. The caller has to check */ -std::string gdcmHeader::GetPixelType(void) { - std::string BitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated - if (BitsAlloc == GDCM_UNFOUND) { +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 = std::string("16"); - } - if (BitsAlloc == "12") // It will be unpacked - BitsAlloc = std::string("16"); - else if (BitsAlloc == "24") // (in order no to be messed up - BitsAlloc = std::string("8"); // by old RGB images) - - std::string Signed = GetEntryByNumber(0x0028, 0x0103); // "Pixel Representation" - if (Signed == GDCM_UNFOUND) { + 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 = std::string("0"); + bitsAlloc = "0"; + } + if ( sign == "0" ) + { + sign = "U"; } - if (Signed == "0") - Signed = std::string("U"); else - Signed = std::string("S"); + { + sign = "S"; + } - return( BitsAlloc + Signed); + return bitsAlloc + sign; } /** * \ingroup gdcmHeader * \brief Recover the offset (from the beginning of the file) - * \ of *image* pixels (not *icone image* pixels, if any !) + * of *image* pixels (not *icone image* pixels, if any !) + * @return Pixel Offset */ -size_t gdcmHeader::GetPixelOffset(void) { // TODO : move to gdcmFile - - // - // If the element (0x0088,0x0200) 'icone image sequence' is found - // (grPixel,numPixel) is stored twice : the first one for the icon - // the second one for the image ... - // pb : sometimes , (0x0088,0x0200) exists, but doesn't contain *anything* - // see gdcmData/MxTwinLossLess.dcm ... - - - /* - guint16 grPixel = GrPixel; - guint16 numPixel= NumPixel; - std::string ImageLocation = GetEntryByNumber(0x0028, 0x0200); - - if ( ImageLocation == GDCM_UNFOUND ) { // Image Location - grPixel = 0x7fe0; // default value - } else { - grPixel = (guint16) atoi( ImageLocation.c_str() ); - } - - if (grPixel == 0xe07f) // sometimes Image Location value doesn't follow - grPixel = 0x7fe0; // the supposed processor endianity. - // see gdcmData/cr172241.dcm - - if (grPixel != 0x7fe0) - // This is a kludge for old dirty Philips imager. - numPixel = 0x1010; - else - numPixel = 0x0010; - */ - - IterHT it = GetHeaderEntrySameNumber(GrPixel,NumPixel); - //std::string icone = GetEntryByNumber(0x0088,0x0200); //icone image sequence - TagKey key = gdcmDictEntry::TranslateToKey(GrPixel,NumPixel); - gdcmHeaderEntry* PixelElement; - - //if (tagHT.count(key) == 1) - if (countGrPixel == 1) - PixelElement = (it.first)->second; - else - PixelElement = (++it.first)->second; - - if (PixelElement) { - return PixelElement->GetOffset(); +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 0 by default. NOT USABLE file. The caller has to check. + * @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(void) { - -/* - // If this file complies with the norm we should encounter the - // "Image Location" tag (0x0028, 0x0200). This tag contains the - // 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. - - - guint16 grPixel; - guint16 numPixel; - std::string ImageLocation = GetEntryByNumber(0x0028, 0x0200); - if ( ImageLocation == GDCM_UNFOUND ) { // Image Location - grPixel = 0x7fe0; // default value - } else { - grPixel = (guint16) atoi( ImageLocation.c_str() ); +size_t gdcmHeader::GetPixelAreaLength() +{ + gdcmDocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel); + if ( pxlElement ) + { + return pxlElement->GetLength(); } - if (grPixel == 0xe07f) // sometimes group doesn't follow - grPixel = 0x7fe0; // the supposed processor endianity. see cr172241.dcm - - if (grPixel != 0x7fe0) - // This is a kludge for old dirty Philips imager. - numPixel = 0x1010; - else - numPixel = 0x0010; - */ - - IterHT it = GetHeaderEntrySameNumber(GrPixel,NumPixel); - //std::string icone = GetEntryByNumber(0x0088,0x0200); //icone image sequence - TagKey key = gdcmDictEntry::TranslateToKey(GrPixel,NumPixel); - gdcmHeaderEntry* PixelElement; - - // if (tagHT.count(key) == 1) - if (countGrPixel) - PixelElement = (it.first)->second; else - PixelElement = (++it.first)->second; - - if (PixelElement) - return PixelElement->GetLength(); - else { + { +#ifdef GDCM_DEBUG std::cout << "Big trouble : Pixel Element (" - << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" + << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" << std::endl; +#endif //GDCM_DEBUG return 0; } } @@ -553,161 +967,206 @@ size_t gdcmHeader::GetPixelAreaLength(void) { * \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 - * @return a Boolean + * 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(void) { - - // Check the presence of the LUT Descriptors - +bool gdcmHeader::HasLUT() +{ + // Check the presence of the LUT Descriptors, and LUT Tables // LutDescriptorRed - if ( !GetHeaderEntryByNumber(0x0028,0x1101) ) + if ( !GetDocEntryByNumber(0x0028,0x1101) ) + { return false; + } // LutDescriptorGreen - if ( !GetHeaderEntryByNumber(0x0028,0x1102) ) + if ( !GetDocEntryByNumber(0x0028,0x1102) ) + { return false; + } // LutDescriptorBlue - if ( !GetHeaderEntryByNumber(0x0028,0x1103) ) + if ( !GetDocEntryByNumber(0x0028,0x1103) ) + { return false; - - // It is not enough : - // we check also - + } // Red Palette Color Lookup Table Data - if ( !GetHeaderEntryByNumber(0x0028,0x1201) ) - return false; + if ( !GetDocEntryByNumber(0x0028,0x1201) ) + { + return false; + } // Green Palette Color Lookup Table Data - if ( !GetHeaderEntryByNumber(0x0028,0x1202) ) + if ( !GetDocEntryByNumber(0x0028,0x1202) ) + { return false; + } // Blue Palette Color Lookup Table Data - if ( !GetHeaderEntryByNumber(0x0028,0x1203) ) - return false; + 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 + * else 0 * @return Lookup Table number of Bits , 0 by default - * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] + * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] + * @ return bit number of each LUT item */ -int gdcmHeader::GetLUTNbits(void) { +int gdcmHeader::GetLUTNbits() +{ std::vector tokens; - //int LutLength; - //int LutDepth; - int LutNbits; + 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) + std::string lutDescription = GetEntryByNumber(0x0028,0x1101); + if ( lutDescription == GDCM_UNFOUND ) + { return 0; - tokens.erase(tokens.begin(),tokens.end()); // clean any previous value - Tokenize (LutDescription, tokens, "\\"); + } + + 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()); + + lutNbits = atoi( tokens[2].c_str() ); tokens.clear(); - return LutNbits; + + 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 + * 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 :-( + * 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 */ -unsigned char * gdcmHeader::GetLUTRGBA(void) { -// Not so easy : see -// http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables +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; - } + 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) + // 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 LutDescriptionG = GetEntryByNumber(0x0028,0x1102); - if (LutDescriptionG == GDCM_UNFOUND) - return NULL; - std::string LutDescriptionB = GetEntryByNumber(0x0028,0x1103); - if (LutDescriptionB == GDCM_UNFOUND) + } + + std::string lutDescriptionB = GetEntryByNumber(0x0028,0x1103); + if ( lutDescriptionB == GDCM_UNFOUND ) + { return NULL; - - std::vector tokens; - - tokens.erase(tokens.begin(),tokens.end()); // clean any previous value - Tokenize (LutDescriptionR, tokens, "\\"); - lengthR=atoi(tokens[0].c_str()); // Red LUT length in Bytes - debR =atoi(tokens[1].c_str()); // subscript of the first Lut Value - nbitsR =atoi(tokens[2].c_str()); // Lut item size (in Bits) - tokens.clear(); - - tokens.erase(tokens.begin(),tokens.end()); // clean any previous value - Tokenize (LutDescriptionG, tokens, "\\"); - lengthG=atoi(tokens[0].c_str()); // Green LUT length in Bytes - debG =atoi(tokens[1].c_str()); // subscript of the first Lut Value - nbitsG =atoi(tokens[2].c_str()); // Lut item size (in Bits) - tokens.clear(); + } + + // 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"); + } - tokens.erase(tokens.begin(),tokens.end()); // clean any previous value - Tokenize (LutDescriptionB, tokens, "\\"); - lengthB=atoi(tokens[0].c_str()); // Blue LUT length in Bytes - debB =atoi(tokens[1].c_str()); // subscript of the first Lut Value - nbitsB =atoi(tokens[2].c_str()); // Lut item size (in Bits) - tokens.clear(); + // 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) - unsigned char *lutR = (unsigned char *) - GetEntryVoidAreaByNumber(0x0028,0x1201); - unsigned char *lutG = (unsigned char *) - GetEntryVoidAreaByNumber(0x0028,0x1202); - unsigned char *lutB = (unsigned char *) - GetEntryVoidAreaByNumber(0x0028,0x1203); - - if (!lutR || !lutG || !lutB ) { - return NULL; + 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 - - unsigned char *LUTRGBA = (unsigned char *)calloc(1024,1); // 256 * 4 (R, G, B, Alpha) - if (!LUTRGBA) { + + uint8_t* LUTRGBA = new uint8_t[1024]; // 256 * 4 (R, G, B, Alpha) + if ( !LUTRGBA ) + { return NULL; } memset(LUTRGBA, 0, 1024); - // Bits Allocated + + // Bits Allocated int nb; std::string str_nb = GetEntryByNumber(0x0028,0x0100); - if (str_nb == GDCM_UNFOUND ) { + if ( str_nb == GDCM_UNFOUND ) + { nb = 16; - } else { - nb = atoi(str_nb.c_str() ); - } + } + 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 ( 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 @@ -715,86 +1174,207 @@ unsigned char * gdcmHeader::GetLUTRGBA(void) { // and fix the code // We give up the checking to avoid some (useless ?)overhead // (optimistic asumption) - unsigned char *a; + uint8_t* a; int i; - a = LUTRGBA+0; - for(i=0;iGetValue(TransfertSyntax); - //delete ts; // Seg Fault when deleted ?! + gdcmTS* ts = gdcmGlobal::GetTS(); + std::string tsName = ts->GetValue( transfertSyntax ); + + //delete ts; /// \todo Seg Fault when deleted ?! return tsName; } /** - * \ingroup gdcmFile * \brief Sets the Pixel Area size in the Header * --> not-for-rats function - * - * \warning WARNING doit-etre etre publique ? - * TODO : y aurait il un inconvenient à fusionner ces 2 fonctions - * * @param ImageDataSize new Pixel Area Size * warning : nothing else is checked */ -void gdcmHeader::SetImageDataSize(size_t ImageDataSize) { - std::string content1; +void gdcmHeader::SetImageDataSize(size_t ImageDataSize) +{ char car[20]; - - // Assumes HeaderEntry (GrPixel, NumPixel) is unique ... - // TODO deal with multiplicity (see gdcmData/icone.dcm) sprintf(car,"%d",ImageDataSize); - gdcmHeaderEntry *a = GetHeaderEntryByNumber(GrPixel, NumPixel); + gdcmDocEntry *a = GetDocEntryByNumber(GrPixel, NumPixel); a->SetLength(ImageDataSize); - - ImageDataSize+=8; + + ImageDataSize += 8; sprintf(car,"%d",ImageDataSize); - content1=car; + + 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() +{ + gdcmDocEntry* patientNameHE = GetDocEntryByNumber (0x0010, 0x0010); + + ReplaceIfExistByNumber (" ",0x0010, 0x2154); // Telephone + ReplaceIfExistByNumber (" ",0x0010, 0x1040); // Adress + ReplaceIfExistByNumber (" ",0x0010, 0x0020); // Patient ID + + if ( patientNameHE ) + { + 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