X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=bc28cd19ea484773535b420a477dc7439d6fb4a9;hb=4beda181275414e5cba990113f8d16424b2c09e6;hp=9d7f6a115672e8ae28a2315c33709727dadc2f8c;hpb=4f48626ba6d2dc26d40f07b780b0fdb5fcc04911;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index 9d7f6a11..bc28cd19 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -1,34 +1,42 @@ -// gdcmHeader.cxx -//----------------------------------------------------------------------------- -#include -#include -#include // for isalpha -#include +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmHeader.cxx,v $ + Language: C++ + Date: $Date: 2005/01/06 15:36:48 $ + Version: $Revision: 1.220 $ + + 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.html 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 //sscanf + +#include +namespace gdcm +{ //----------------------------------------------------------------------------- // Constructor / Destructor /** * \brief Constructor - * @param InFilename name of the file whose header we want to analyze - * @param exception_on_error whether we want to throw an exception or not - * @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 - */ -gdcmHeader::gdcmHeader(const char *InFilename, - bool exception_on_error, - bool enable_sequences, - bool ignore_shadow): - gdcmParser(InFilename,exception_on_error,enable_sequences,ignore_shadow) -{ - + * @param filename name of the file whose header we want to analyze + */ +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 // (Image Location") . This Element contains the number of @@ -37,358 +45,952 @@ 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; + // Image Location + const 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; + } + + // 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 - NumPixel = 0x0010; + PixelVR = "OW"; - TagKey key = gdcmDictEntry::TranslateToKey(GrPixel, NumPixel); - countGrPixel = GetEntry().count(key); + 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) : - gdcmParser(exception_on_error) +Header::Header() + :Document() { + InitializeDefaultHeader(); } /** - * \ingroup gdcmHeader * \brief Canonical destructor. */ -gdcmHeader::~gdcmHeader (void) { +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 filetype Type of the File to be written + * (ACR-NEMA, ExplicitVR, ImplicitVR) + */ +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") + { + 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 + 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 + + 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; } //----------------------------------------------------------------------------- // 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 Header 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 Header is the one of a reasonable Dicom/Acr file, * false otherwise. */ -bool gdcmHeader::IsReadable(void) { - if(!gdcmParser::IsReadable()) { - return(false); +bool Header::IsReadable() +{ + if( !Document::IsReadable() ) + { + return false; } - std::string res = GetEntryByNumber(0x0028, 0x0005); - if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) + + const std::string &res = GetEntryByNumber(0x0028, 0x0005); + 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) ) + } + 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 Header::GetXSize() +{ + const std::string &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 Header::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 Header::GetYSize() +{ + const 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 Header::GetZSize() +{ + // Both DicomV3 and ACR/Nema consider the "Number of Frames" + // as the third dimension. + const std::string &strSize = GetEntryByNumber(0x0028,0x0008); + 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; + // We then consider the "Planes" entry as the third dimension + const std::string &strSize2 = GetEntryByNumber(0x0028,0x0012); + if ( strSize2 != GDCM_UNFOUND ) + { + return atoi( strSize2.c_str() ); + } + + return 1; +} + +/** + * \brief gets the info from 0028,0030 : Pixel Spacing + * else 1.0 + * @return X dimension of a pixel + */ +float Header::GetXSpacing() +{ + float xspacing, yspacing; + const std::string &strSpacing = GetEntryByNumber(0x0028,0x0030); + + if ( strSpacing == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::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 ) + { + xspacing = yspacing; + } + + if ( xspacing == 0.0 ) + xspacing = 1.0; + + return xspacing; + + } + + // to avoid troubles with David Clunie's-like images + if ( xspacing == 0. && yspacing == 0.) + return 1.; + + if ( xspacing == 0.) + { + dbg.Verbose(0, "Header::GetXSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem"); + // seems to be a bug in the header ... + nbValues = sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing); + assert( nbValues == 2 ); + } + + return xspacing; } /** - * \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. + * \brief gets the info from 0028,0030 : Pixel Spacing + * else 1.0 + * @return Y dimension of a pixel + */ +float Header::GetYSpacing() +{ + float yspacing = 1.; + std::string strSpacing = GetEntryByNumber(0x0028,0x0030); + + if ( strSpacing == GDCM_UNFOUND ) + { + 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; +} + +/** + * \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 */ -bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) { - gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadHeaderEntrySafe(Element); +float Header::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 + + const std::string &strSpacingBSlices = GetEntryByNumber(0x0018,0x0088); - std::string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.4.53" ) - return true; - return false; + if ( strSpacingBSlices == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::GetZSpacing: unfound StrSpacingBSlices"); + const 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 (float)atof( strSliceThickness.c_str() ); + } + } + //else + return (float)atof( strSpacingBSlices.c_str() ); } /** - * \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. + *\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 Header::GetRescaleIntercept() +{ + float resInter = 0.; + /// 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, "Header::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. + *\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 Header::GetRescaleSlope() +{ + float resSlope = 1.; + //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, "Header::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; +} - return false; +/** + * \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 ) + { + 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 || + Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME1") || + Util::DicomStringEqual(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 JPEG2000 one - * @return True when JPEG2000 (Lossly or LossLess) found. False in all - * other cases. + * \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' -) */ -bool gdcmHeader::IsJPEG2000(void) { - gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadHeaderEntrySafe(Element); +int Header::GetNumberOfScalarComponentsRaw() +{ + // 0028 0100 US IMG Bits Allocated + // (in order no to be messed up by old RGB images) + if ( Header::GetEntryByNumber(0x0028,0x0100) == "24" ) + { + 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. + * \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 */ -bool gdcmHeader::IsDicomV3(void) { - // Checking if Transfert Syntax exists is enough - // Anyway, it's to late check if the 'Preamble' was found ... - // And ... would it be a rich idea to check ? - // (some 'no Preamble' DICOM images exist !) - return (GetHeaderEntryByNumber(0x0002, 0x0010) != NULL); +float Header::GetXOrigin() +{ + float xImPos, yImPos, zImPos; + std::string strImPos = GetEntryByNumber(0x0020,0x0032); + + if ( strImPos == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::GetXImagePosition: unfound Image " + "Position Patient (0020,0032)"); + strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images + if ( strImPos == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::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 + * \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 */ -int gdcmHeader::GetXSize(void) { - std::string StrSize; - StrSize = GetEntryByNumber(0x0028,0x0011); - if (StrSize == GDCM_UNFOUND) - return 0; - return atoi(StrSize.c_str()); +float Header::GetYOrigin() +{ + float xImPos, yImPos, zImPos; + std::string strImPos = GetEntryByNumber(0x0020,0x0032); + + if ( strImPos == GDCM_UNFOUND) + { + dbg.Verbose(0, "Header::GetYImagePosition: unfound Image " + "Position Patient (0020,0032)"); + strImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images + if ( strImPos == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::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 ACR-MEMA file contains a Signal, not an Image). + * \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 */ -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; +float Header::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, "Header::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, "Header::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, "Header::GetZImagePosition: wrong Slice Location (0020,1041)"); + return 0.; // bug in the element 0x0020,0x1041 + } + else + { + return zImPos; + } + } + 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, "Header::GetZImagePosition: wrong Location (0020,0050)"); + return 0.; // bug in the element 0x0020,0x0050 + } + else + { + return zImPos; + } + } + 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 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 + // 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. + //0020 0013 IS REL Image Number + std::string strImNumber = GetEntryByNumber(0x0020,0x0013); + if ( strImNumber != GDCM_UNFOUND ) + { + return atoi( strImNumber.c_str() ); + } + 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 ACR-NEMA "Planes" tag content. - * @return The encountered size when found, 1 by default (single image). + * \brief gets the info from 0008,0060 : Modality + * @return Modality Type */ -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()); +ModalityType Header::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; - // 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; + 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 Header::GetBitsStored() +{ + std::string strSize = GetEntryByNumber( 0x0028, 0x0101 ); + if ( strSize == GDCM_UNFOUND ) + { + 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()); + } + 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() ); +} + +/** + * \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; } /** - * \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) { - std::string StrSize = GetEntryByNumber(0x0028,0x0100); - if (StrSize == GDCM_UNFOUND) +int Header::GetBitsAllocated() +{ + std::string strSize = GetEntryByNumber(0x0028,0x0100); + if ( strSize == GDCM_UNFOUND ) + { + 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()); + } + 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) { - std::string StrSize = GetEntryByNumber(0x0028,0x0002); - if (StrSize == GDCM_UNFOUND) +int Header::GetSamplesPerPixel() +{ + const std::string& strSize = GetEntryByNumber(0x0028,0x0002); + if ( strSize == GDCM_UNFOUND ) + { + 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()); + } + return atoi( strSize.c_str() ); +} + +/** + * \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; } /** - * \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 Header::GetPlanarConfiguration() +{ + std::string strSize = GetEntryByNumber(0x0028,0x0006); + if ( strSize == GDCM_UNFOUND ) + { return 0; - return atoi(StrSize.c_str()); + } + 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(void) { - std::string PixelType = GetPixelType(); - if (PixelType == "8U" || PixelType == "8S") +int Header::GetPixelSize() +{ + // 0028 0100 US IMG Bits Allocated + // (in order no to be messed up by old RGB images) + // if (Header::GetEntryByNumber(0x0028,0x0100) == "24") + // 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"); + } + if ( pixelType == "FD" ) + { + return 8; + } + 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, @@ -402,98 +1004,99 @@ int gdcmHeader::GetPixelSize(void) { * 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) { - dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated"); - BitsAlloc = std::string("16"); - } - if (BitsAlloc == "64") // ) - return ("FD"); - 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) { - dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation"); - BitsAlloc = std::string("0"); - } - if (Signed == "0") - Signed = std::string("U"); - else - Signed = std::string("S"); +std::string Header::GetPixelType() +{ + std::string bitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated + if ( bitsAlloc == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::GetPixelType: unfound Bits Allocated"); + bitsAlloc = "16"; + } + + if ( bitsAlloc == "64" ) + { + return "FD"; + } + else 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" - return( BitsAlloc + Signed); + if (sign == GDCM_UNFOUND ) + { + dbg.Verbose(0, "Header::GetPixelType: unfound Pixel Representation"); + bitsAlloc = "0"; + } + else 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(void) { - // - // 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 ... - - //std::string icone = GetEntryByNumber(0x0088,0x0200); //icone image sequence - - IterHT it = GetHeaderEntrySameNumber(GrPixel,NumPixel); - TagKey key = gdcmDictEntry::TranslateToKey(GrPixel,NumPixel); - gdcmHeaderEntry* PixelElement; - if (countGrPixel == 1) - PixelElement = (it.first)->second; - else { - PixelElement = (++it.first)->second; // hope there are no more than 2 ! - } - if (PixelElement) { - return PixelElement->GetOffset(); - } else { -/* std::cout << "Big trouble : Pixel Element (" +size_t Header::GetPixelOffset() +{ + DocEntry* 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; */ + << std::endl; +#endif //GDCM_DEBUG return 0; - } + } } -// 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(void) { - - IterHT it = GetHeaderEntrySameNumber(GrPixel,NumPixel); - TagKey key = gdcmDictEntry::TranslateToKey(GrPixel,NumPixel); - gdcmHeaderEntry* PixelElement; - - if (countGrPixel==1) - PixelElement = (it.first)->second; +size_t Header::GetPixelAreaLength() +{ + DocEntry* pxlElement = GetDocEntryByNumber(GrPixel,NumPixel); + if ( pxlElement ) + { + return pxlElement->GetLength(); + } else - PixelElement = (++it.first)->second; - - if (PixelElement) { - return PixelElement->GetLength(); - } else { -/* std::cout << "Big trouble : Pixel Element (" + { +#ifdef GDCM_DEBUG + std::cout << "Big trouble : Pixel Element (" << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" - << std::endl;*/ + << 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 @@ -501,344 +1104,145 @@ size_t gdcmHeader::GetPixelAreaLength(void) { * 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) { - +bool Header::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) ) - return false; + if ( !GetDocEntryByNumber(0x0028,0x1103) ) + { + return false; + } // 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 * @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(void) { +int Header::GetLUTNbits() +{ std::vector tokens; - //int LutLength; - //int LutDepth; - int LutNbits; - //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red = Lookup Table Desc-Blue + 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, "\\"); - //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 - */ -unsigned char * gdcmHeader::GetLUTRGBA(void) { -// 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; - - 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(); - - 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(); - - // 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; - } - // 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) { - 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) - unsigned char *a; - int i; - - a = LUTRGBA+0; - for(i=0;iGetValue(TransfertSyntax); - //delete ts; // Seg Fault when deleted ?! - return tsName; -} -/** - * \ingroup gdcmHeader - * \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]; + tokens.clear(); // clean any previous value + Util::Tokenize ( lutDescription, tokens, "\\" ); + //LutLength=atoi(tokens[0].c_str()); + //LutDepth=atoi(tokens[1].c_str()); - // Assumes HeaderEntry (GrPixel, NumPixel) is unique ... - // TODO deal with multiplicity (see gdcmData/icone.dcm) - sprintf(car,"%d",ImageDataSize); - - gdcmHeaderEntry *a = GetHeaderEntryByNumber(GrPixel, NumPixel); - a->SetLength(ImageDataSize); + lutNbits = atoi( tokens[2].c_str() ); + tokens.clear(); - ImageDataSize+=8; - sprintf(car,"%d",ImageDataSize); - content1=car; - SetEntryByNumber(content1, GrPixel, NumPixel); + return lutNbits; } - /** - * \ingroup gdcmHeader - * \brief compares 2 Headers, according to DICOMDIR rules - * --> not-for-rats function - * \warning does NOT work with ACR-NEMA files - * \todo find a trick to solve the pb (use RET fields ?) - * @param header - * @return true if 'smaller' + * \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) */ - bool gdcmHeader::operator<(gdcmHeader &header){ - std::string s1,s2; +std::string Header::GetTransfertSyntaxName() +{ + // use the TS (TS : Transfert Syntax) + std::string transfertSyntax = GetEntryByNumber(0x0002,0x0010); - // Patient Name - s1=this->GetEntryByNumber(0x0010,0x0010); - s2=header.GetEntryByNumber(0x0010,0x0010); - if(s1 < s2) - return(true); - else if(s1 > s2) - return(false); - else + if ( transfertSyntax == GDCM_NOTLOADED ) { - // Patient ID - s1=this->GetEntryByNumber(0x0010,0x0020); - s2=header.GetEntryByNumber(0x0010,0x0020); - if (s1 < s2) - return(true); - else if (s1 > s2) - return(1); - else - { - // Study Instance UID - s1=this->GetEntryByNumber(0x0020,0x000d); - s2=header.GetEntryByNumber(0x0020,0x000d); - if (s1 < s2) - return(true); - else if(s1 > s2) - return(false); - else - { - // Serie Instance UID - s1=this->GetEntryByNumber(0x0020,0x000e); - s2=header.GetEntryByNumber(0x0020,0x000e); - if (s1 < s2) - return(true); - else if(s1 > s2) - return(false); - } - } + std::cout << "Transfert Syntax not loaded. " << std::endl + << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE" + << std::endl; + return "Uncompressed ACR-NEMA"; } - return(false); -} - -bool gdcmHeader::WriteEntry(gdcmHeaderEntry *tag, FILE *_fp,FileType type) -{ - guint32 length = tag->GetLength(); - - // The value of a tag MUST (see the DICOM norm) be an odd number of - // bytes. When this is not the case, pad with an additional byte: - if(length%2==1) + if ( transfertSyntax == GDCM_UNFOUND ) { - tag->SetValue(tag->GetValue()+"\0"); - tag->SetLength(tag->GetReadLength()+1); + dbg.Verbose(0, "Header::GetTransfertSyntaxName:" + " unfound Transfert Syntax (0002,0010)"); + return "Uncompressed ACR-NEMA"; } - - WriteEntryTagVRLength(tag, _fp, type); - - // Pixels are never loaded in the element ! - // we stop writting when Pixel are processed - // FIX : we loose trailing elements (RAB, right now) - guint16 el = tag->GetElement(); - guint16 group = tag->GetGroup(); - int compte =0; - if ((group == GrPixel) && (el == NumPixel) ) { - compte++; - if (compte == countGrPixel) {// we passed *all* the GrPixel,NumPixel - return false; - } + + while ( ! isdigit((unsigned char)transfertSyntax[transfertSyntax.length()-1]) ) + { + transfertSyntax.erase(transfertSyntax.length()-1, 1); } - WriteEntryValue(tag, _fp, type); - return true; + // we do it only when we need it + TS* ts = Global::GetTS(); + std::string tsName = ts->GetValue( transfertSyntax ); + + //delete ts; /// \todo Seg Fault when deleted ?! + return tsName; } //----------------------------------------------------------------------------- // Protected /** - * \ingroup gdcmHeader * \brief anonymize a Header (removes Patient's personal info) * (read the code to see which ones ...) */ -bool gdcmHeader::anonymizeHeader() { +bool Header::AnonymizeHeader() +{ + // If exist, replace by spaces + SetEntryByNumber (" ",0x0010, 0x2154); // Telephone + SetEntryByNumber (" ",0x0010, 0x1040); // Adress + SetEntryByNumber (" ",0x0010, 0x0020); // Patient ID - gdcmHeaderEntry *patientNameHE = GetHeaderEntryByNumber (0x0010, 0x0010); - // gdcmHeaderEntry *patientIDHE = GetHeaderEntryByNumber (0x0010, 0x0020); - - 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); - } + DocEntry* 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("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 @@ -887,9 +1291,123 @@ bool gdcmHeader::anonymizeHeader() { //300a 0006 DA RT RT Plan Date //300a 022c DA RT Air Kerma Rate Reference Date //300e 0004 DA RT Review Date - return true; + + 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 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.; + + // 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, "Header::GetImageOrientationPatient: " + "wrong Image Orientation Patient (0020,0037)"); + } + } + //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, "Header::GetImageOrientationPatient: " + "wrong Image Orientation Patient (0020,0035)"); + } + } +} + +/** + * \brief Initialize a default DICOM header that should contain all the + * field require by other reader. DICOM standard does not + * explicitely defines those fields, heuristic has been choosen. + * This is not perfect as we are writting a CT image... + */ +void Header::InitializeDefaultHeader() +{ + typedef struct + { + const char *value; + uint16_t group; + uint16_t elem; + } DICOM_DEFAULT_VALUE; + + std::string date = Util::GetCurrentDate(); + std::string time = Util::GetCurrentTime(); + std::string uid = Util::CreateUniqueUID(); + std::string uidMedia = uid; + std::string uidClass = uid + ".1"; + std::string uidInst = uid + ".10"; + std::string uidStudy = uid + ".100"; + std::string uidSerie = uid + ".1000"; + + static DICOM_DEFAULT_VALUE defaultvalue[] = { + { "146 ", 0x0002, 0x0000}, // Meta Element Group Length // FIXME: how to recompute ? + { "1.2.840.10008.5.1.4.1.1.2", 0x0002, 0x0002}, // Media Storage SOP Class UID (CT Image Storage) + { uidClass.c_str(), 0x0002, 0x0003}, // Media Storage SOP Instance UID + { uidClass.c_str(), 0x0002, 0x0012}, // META Implementation Class UID + { "GDCM", 0x0002, 0x0016}, // Source Application Entity Title + + { date.c_str(), 0x0008, 0x0012}, // Instance Creation Date + { time.c_str(), 0x0008, 0x0013}, // Instance Creation Time + { "1.2.840.10008.5.1.4.1.1.2", 0x0008, 0x0016}, // SOP Class UID + { uidInst.c_str(), 0x0008, 0x0018}, // SOP Instance UID + { "CT", 0x0008, 0x0060}, // Modality + { "GDCM", 0x0008, 0x0070}, // Manufacturer + { "GDCM", 0x0008, 0x0080}, // Institution Name + { "http://www-creatis.insa-lyon.fr/Public/Gdcm", 0x0008, 0x0081}, // Institution Address + + { "GDCM", 0x0010, 0x0010}, // Patient's Name + { "GDCMID", 0x0010, 0x0020}, // Patient ID + + { uidStudy.c_str(), 0x0020, 0x000d}, // Study Instance UID + { uidSerie.c_str(), 0x0020, 0x000e}, // Series Instance UID + { "1", 0x0020, 0x0010}, // StudyID + { "1", 0x0020, 0x0011}, // SeriesNumber + + { "1", 0x0028, 0x0002}, // Samples per pixel 1 or 3 + { "MONOCHROME1", 0x0028, 0x0004}, // photochromatic interpretation + { "0", 0x0028, 0x0010}, // nbRows + { "0", 0x0028, 0x0011}, // nbCols + { "8", 0x0028, 0x0100}, // BitsAllocated 8 or 12 or 16 + { "8", 0x0028, 0x0101}, // BitsStored <= BitsAllocated + { "7", 0x0028, 0x0102}, // HighBit <= BitsAllocated - 1 + { "0", 0x0028, 0x0103}, // Pixel Representation 0(unsigned) or 1(signed) + { 0, 0, 0 } + }; + + // default value + // Special case this is the image (not a string) + GrPixel = 0x7fe0; + NumPixel = 0x0010; + ReplaceOrCreateByNumber(0, 0, GrPixel, NumPixel); + + // All remaining strings: + unsigned int i = 0; + DICOM_DEFAULT_VALUE current = defaultvalue[i]; + while( current.value ) + { + ReplaceOrCreateByNumber(current.value, current.group, current.elem); + current = defaultvalue[++i]; + } } + + //----------------------------------------------------------------------------- // Private //----------------------------------------------------------------------------- + +} // end namespace gdcm