X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=71e8a7782c480f78418d2a0f8eed787410a826f3;hb=de5fc413dc579fc61f7e04397efd1dc1087fe3cf;hp=17e4a80acc2099687a9720bf6555b3c09e1f61c1;hpb=ce8913daafe02955368fd2f07e777e86824467cc;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 17e4a80a..71e8a778 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2005/01/25 15:44:24 $ - Version: $Revision: 1.200 $ + Date: $Date: 2005/04/19 09:58:19 $ + Version: $Revision: 1.233 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -16,6 +16,18 @@ =========================================================================*/ +// +// -------------- 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 +// +// --------------------------------------------------------------- +// #include "gdcmFile.h" #include "gdcmGlobal.h" #include "gdcmUtil.h" @@ -23,21 +35,40 @@ #include "gdcmTS.h" #include "gdcmValEntry.h" #include "gdcmBinEntry.h" -#include //sscanf +#include "gdcmSeqEntry.h" +#include "gdcmRLEFramesInfo.h" +#include "gdcmJPEGFragmentsInfo.h" +#include //sscanf #include namespace gdcm { //----------------------------------------------------------------------------- // Constructor / Destructor + +/** + * \brief Constructor used when we want to generate dicom files from scratch + */ +File::File(): + Document() +{ + RLEInfo = new RLEFramesInfo; + JPEGInfo = new JPEGFragmentsInfo; + GrPixel = 0x7fe0; + NumPixel = 0x0010; +} + /** * \brief Constructor * @param filename name of the file whose header we want to analyze */ -File::File( std::string const &filename ): - Document( filename ) +File::File( std::string const &filename ) + :Document(filename) { + RLEInfo = new RLEFramesInfo; + JPEGInfo = new JPEGFragmentsInfo; + // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010 // We may encounter the 'RETired' (0x0028, 0x0200) tag // (Image Location") . This entry contains the number of @@ -60,9 +91,9 @@ File::File( std::string const &filename ): GrPixel = (uint16_t) atoi( imgLocation.c_str() ); } - // sometimes Image Location value doesn't follow - // the supposed processor endianness. - // see gdcmData/cr172241.dcm + // sometimes Image Location value doesn't follow + // the supposed processor endianness. + // see gdcmData/cr172241.dcm if ( GrPixel == 0xe07f ) { GrPixel = 0x7fe0; @@ -84,166 +115,65 @@ File::File( std::string const &filename ): DocEntry *entry = GetDocEntry(GrPixel, NumPixel); if ( entry != 0 ) { - - std::string PixelVR; - // 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB) - // more than 8 (i.e 12, 16) is a 'O Words' - if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 ) - PixelVR = "OB"; - else - PixelVR = "OW"; - - DictEntry* newEntry = NewVirtualDictEntry( - GrPixel, NumPixel, - PixelVR, "PXL", "Pixel Data"); - - // friend class hunting : should we *create* a new entry, - // instead of modifying its DictEntry,in order not to use 'friend' ? - entry->SetDictEntry( newEntry ); + // Compute the RLE or JPEG info + OpenFile(); + std::string ts = GetTransferSyntax(); + Fp->seekg( entry->GetOffset(), std::ios::beg ); + if ( Global::GetTS()->IsRLELossless(ts) ) + ComputeRLEInfo(); + else if ( Global::GetTS()->IsJPEG(ts) ) + ComputeJPEGFragmentInfo(); + CloseFile(); + + // Create a new BinEntry to change the the DictEntry + // The changed DictEntry will have + // - a correct PixelVR OB or OW) + // - the name to "Pixel Data" + BinEntry *oldEntry = dynamic_cast(entry); + if(oldEntry) + { + std::string PixelVR; + // 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB) + // more than 8 (i.e 12, 16) is a 'O Words' + if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 ) + PixelVR = "OB"; + else + PixelVR = "OW"; + + // Change only made if usefull + if( PixelVR != oldEntry->GetVR() ) + { + DictEntry* newDict = NewVirtualDictEntry(GrPixel,NumPixel, + PixelVR,"1","Pixel Data"); + + BinEntry *newEntry = new BinEntry(newDict); + newEntry->Copy(entry); + newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea()); + oldEntry->SetSelfArea(false); + + RemoveEntry(oldEntry); + AddEntry(newEntry); + } + } } } -/** - * \brief Constructor used when we want to generate dicom files from scratch - */ -File::File() - :Document() -{ - InitializeDefaultFile(); -} /** * \brief Canonical destructor. */ File::~File () { + if( RLEInfo ) + delete RLEInfo; + if( JPEGInfo ) + delete JPEGInfo; } -/** - * \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 fileName file name to write to - * @param filetype Type of the File to be written - * (ACR, ExplicitVR, ImplicitVR) - */ -bool File::Write(std::string fileName, FileType filetype) -{ - std::ofstream *fp = new std::ofstream(fileName.c_str(), - std::ios::out | std::ios::binary); - if (*fp == NULL) - { - gdcmVerboseMacro("Failed to open (write) File: " << fileName.c_str()); - return false; - } - - // Bits Allocated - if ( GetEntryValue(0x0028,0x0100) == "12") - { - SetValEntry("16", 0x0028,0x0100); - } - - /// \todo correct 'Pixel group' Length if necessary - - int i_lgPix = GetEntryLength(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() ); - InsertValEntry(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 ( GetEntryValue(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 = GetDocEntry(0x0028,0x01101); - if (e) - { - RemoveEntryNoDestroy(e); - } - e = GetDocEntry(0x0028,0x1102); - if (e) - { - RemoveEntryNoDestroy(e); - } - e = GetDocEntry(0x0028,0x1103); - if (e) - { - RemoveEntryNoDestroy(e); - } - e = GetDocEntry(0x0028,0x01201); - if (e) - { - RemoveEntryNoDestroy(e); - } - e = GetDocEntry(0x0028,0x1202); - if (e) - { - RemoveEntryNoDestroy(e); - } - e = GetDocEntry(0x0028,0x1203); - if (e) - { - RemoveEntryNoDestroy(e); - } - } - -/* -#ifdef GDCM_WORDS_BIGENDIAN - // Super Super hack that will make gdcm a BOMB ! but should - // Fix temporarily the dashboard - BinEntry *b = GetBinEntry(GrPixel,NumPixel); - if ( GetPixelSize() == 16 ) - { - uint16_t *im16 = (uint16_t*)b->GetBinArea(); - int lgr = b->GetLength(); - for( int i = 0; i < lgr / 2; i++ ) - { - im16[i]= (im16[i] >> 8) | (im16[i] << 8 ); - } - } -#endif //GDCM_WORDS_BIGENDIAN -*/ - - Document::WriteContent(fp,filetype); - -/* -#ifdef GDCM_WORDS_BIGENDIAN - // Flip back the pixel ... I told you this is a hack - if ( GetPixelSize() == 16 ) - { - uint16_t *im16 = (uint16_t*)b->GetBinArea(); - int lgr = b->GetLength(); - for( int i = 0; i < lgr / 2; i++ ) - { - im16[i]= (im16[i] >> 8) | (im16[i] << 8 ); - } - } -#endif //GDCM_WORDS_BIGENDIAN -*/ - - fp->close(); - delete fp; - - return true; -} - -//----------------------------------------------------------------------------- -// Print - - //----------------------------------------------------------------------------- // Public + /** * \brief This predicate, based on hopefully reasonable heuristics, * decides whether or not the current File was properly parsed @@ -284,6 +214,87 @@ bool File::IsReadable() return true; } +/** + * \brief gets the info from 0020,0013 : Image Number else 0. + * @return image number + */ +int File::GetImageNumber() +{ + //0020 0013 : Image Number + std::string strImNumber = GetEntryValue(0x0020,0x0013); + if ( strImNumber != GDCM_UNFOUND ) + { + return atoi( strImNumber.c_str() ); + } + return 0; //Hopeless +} + +/** + * \brief gets the info from 0008,0060 : Modality + * @return Modality Type + */ +ModalityType File::GetModality() +{ + // 0008 0060 : Modality + std::string strModality = GetEntryValue(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 <> unknown in our database + return Unknow; + } + } + + return Unknow; +} + /** * \brief Retrieve the number of columns of image. * @return The encountered size when found, 0 by default. @@ -358,12 +369,13 @@ int File::GetZSize() */ float File::GetXSpacing() { - float xspacing, yspacing; + float xspacing = 1.0; + float yspacing = 1.0; const std::string &strSpacing = GetEntryValue(0x0028,0x0030); - if ( strSpacing == GDCM_UNFOUND ) + if( strSpacing == GDCM_UNFOUND ) { - gdcmVerboseMacro( "Unfound Pixel Spacing (0028,0030)" ); + gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); return 1.; } @@ -371,11 +383,12 @@ float File::GetXSpacing() if( ( nbValues = sscanf( strSpacing.c_str(), "%f\\%f", &yspacing, &xspacing)) != 2 ) { + // if no values, xspacing is set to 1.0 + if( nbValues == 0 ) + xspacing = 1.0; // if single value is found, xspacing is defaulted to yspacing - if ( nbValues == 1 ) - { + if( nbValues == 1 ) xspacing = yspacing; - } if ( xspacing == 0.0 ) xspacing = 1.0; @@ -390,7 +403,7 @@ float File::GetXSpacing() if ( xspacing == 0.) { - gdcmVerboseMacro("gdcmData/CT-MONO2-8-abdo.dcm problem"); + gdcmWarningMacro("gdcmData/CT-MONO2-8-abdo.dcm-like problem"); // seems to be a bug in the header ... nbValues = sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing); gdcmAssertMacro( nbValues == 2 ); @@ -411,12 +424,16 @@ float File::GetYSpacing() if ( strSpacing == GDCM_UNFOUND ) { - gdcmVerboseMacro("Unfound Pixel Spacing (0028,0030)"); + gdcmWarningMacro("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); + int nbValues = sscanf( strSpacing.c_str(), "%f", &yspacing); + + // if no values, xspacing is set to 1.0 + if( nbValues == 0 ) + yspacing = 1.0; if ( yspacing == 0.0 ) yspacing = 1.0; @@ -432,25 +449,25 @@ float File::GetYSpacing() */ float File::GetZSpacing() { - // Spacing Between Slices : distance entre le milieu de chaque coupe - // Les coupes peuvent etre : + // Spacing Between Slices : distance between the middle of 2 slices + // Slices may be : // jointives (Spacing between Slices = Slice Thickness) - // chevauchantes (Spacing between Slices < Slice Thickness) + // overlapping (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 Missing, - // on suppose que les coupes sont jointives + // It only concerns the MRI guys, not people wanting to visualize volmues + // If Spacing Between Slices is Missing, + // we suppose slices joint together const std::string &strSpacingBSlices = GetEntryValue(0x0018,0x0088); if ( strSpacingBSlices == GDCM_UNFOUND ) { - gdcmVerboseMacro("Unfound Spacing Between Slices (0018,0088)"); + gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)"); const std::string &strSliceThickness = GetEntryValue(0x0018,0x0050); if ( strSliceThickness == GDCM_UNFOUND ) { - gdcmVerboseMacro("Unfound Slice Thickness (0018,0050)"); + gdcmWarningMacro("Unfound Slice Thickness (0018,0050)"); return 1.; } else @@ -467,183 +484,53 @@ float File::GetZSpacing() } /** - *\brief gets the info from 0028,1052 : Rescale Intercept - * @return Rescale Intercept + * \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 File::GetRescaleIntercept() +float File::GetXOrigin() { - float resInter = 0.; - /// 0028 1052 DS IMG Rescale Intercept - const std::string &strRescInter = GetEntryValue(0x0028,0x1052); - if ( strRescInter != GDCM_UNFOUND ) + float xImPos, yImPos, zImPos; + std::string strImPos = GetEntryValue(0x0020,0x0032); + + if ( strImPos == GDCM_UNFOUND ) { - if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 ) + gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); + strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images + if ( strImPos == GDCM_UNFOUND ) { - // bug in the element 0x0028,0x1052 - gdcmVerboseMacro( "Rescale Intercept (0028,1052) is empty." ); + gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); + return 0.; } } - return resInter; + if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 ) + { + return 0.; + } + + return xImPos; } /** - *\brief gets the info from 0028,1053 : Rescale Slope - * @return Rescale Slope + * \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 File::GetRescaleSlope() +float File::GetYOrigin() { - float resSlope = 1.; - //0028 1053 DS IMG Rescale Slope - std::string strRescSlope = GetEntryValue(0x0028,0x1053); - if ( strRescSlope != GDCM_UNFOUND ) + float xImPos, yImPos, zImPos; + std::string strImPos = GetEntryValue(0x0020,0x0032); + + if ( strImPos == GDCM_UNFOUND) { - if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1) + gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); + strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images + if ( strImPos == GDCM_UNFOUND ) { - // bug in the element 0x0028,0x1053 - gdcmVerboseMacro( "Rescale Slope (0028,1053) is empty."); - } - } - - return resSlope; -} - -/** - * \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 File::GetNumberOfScalarComponents() -{ - if ( GetSamplesPerPixel() == 3 ) - { - return 3; - } - - // 0028 0100 US IMG Bits Allocated - // (in order no to be messed up by old RGB images) - if ( GetEntryValue(0x0028,0x0100) == "24" ) - { - return 3; - } - - std::string strPhotometricInterpretation = GetEntryValue(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; - } -} - -/** - * \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 File::GetNumberOfScalarComponentsRaw() -{ - // 0028 0100 US IMG Bits Allocated - // (in order no to be messed up by old RGB images) - if ( File::GetEntryValue(0x0028,0x0100) == "24" ) - { - return 3; - } - - // we assume that *all* kinds of YBR are dealt with - return GetSamplesPerPixel(); -} - -// -// -------------- Remember ! ---------------------------------- -// -// Image Position Patient (0020,0032): -// If not found (ACR_NEMA) we try Image Position (0020,0030) -// If not found (ACR-NEMA), we consider Slice Location (0020,1041) -// or Location (0020,0050) -// as the Z coordinate, -// 0. for all the coordinates if nothing is found - -// \todo find a way to inform the caller nothing was found -// \todo How to tell the caller a wrong number of values was found? -// -// --------------------------------------------------------------- -// - -/** - * \brief gets the info from 0020,0032 : Image Position Patient - * else from 0020,0030 : Image Position (RET) - * else 0. - * @return up-left image corner X position - */ -float File::GetXOrigin() -{ - float xImPos, yImPos, zImPos; - std::string strImPos = GetEntryValue(0x0020,0x0032); - - if ( strImPos == GDCM_UNFOUND ) - { - gdcmVerboseMacro( "Unfound Image Position Patient (0020,0032)"); - strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images - if ( strImPos == GDCM_UNFOUND ) - { - gdcmVerboseMacro( "Unfound Image Position (RET) (0020,0030)"); - /// \todo How to tell the caller nothing was found ? - return 0.; - } - } - - if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 ) - { - return 0.; - } - - return xImPos; -} - -/** - * \brief gets the info from 0020,0032 : Image Position Patient - * else from 0020,0030 : Image Position (RET) - * else 0. - * @return up-left image corner Y position - */ -float File::GetYOrigin() -{ - float xImPos, yImPos, zImPos; - std::string strImPos = GetEntryValue(0x0020,0x0032); - - if ( strImPos == GDCM_UNFOUND) - { - gdcmVerboseMacro( "Unfound Image Position Patient (0020,0032)"); - strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images - if ( strImPos == GDCM_UNFOUND ) - { - gdcmVerboseMacro( "Unfound Image Position (RET) (0020,0030)"); - /// \todo How to tell the caller nothing was found ? + gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); return 0.; } } @@ -673,7 +560,7 @@ float File::GetZOrigin() { if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) { - gdcmVerboseMacro( "Wrong Image Position Patient (0020,0032)"); + gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)"); return 0.; // bug in the element 0x0020,0x0032 } else @@ -688,7 +575,7 @@ float File::GetZOrigin() if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos ) != 3 ) { - gdcmVerboseMacro( "Wrong Image Position (RET) (0020,0030)"); + gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)"); return 0.; // bug in the element 0x0020,0x0032 } else @@ -702,7 +589,7 @@ float File::GetZOrigin() { if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1) { - gdcmVerboseMacro( "Wrong Slice Location (0020,1041)"); + gdcmWarningMacro( "Wrong Slice Location (0020,1041)"); return 0.; // bug in the element 0x0020,0x1041 } else @@ -710,14 +597,14 @@ float File::GetZOrigin() return zImPos; } } - gdcmVerboseMacro( "Unfound Slice Location (0020,1041)"); + gdcmWarningMacro( "Unfound Slice Location (0020,1041)"); std::string strLocation = GetEntryValue(0x0020,0x0050); if ( strLocation != GDCM_UNFOUND ) { if( sscanf( strLocation.c_str(), "%f", &zImPos) != 1) { - gdcmVerboseMacro( "Wrong Location (0020,0050)"); + gdcmWarningMacro( "Wrong Location (0020,0050)"); return 0.; // bug in the element 0x0020,0x0050 } else @@ -725,97 +612,47 @@ float File::GetZOrigin() return zImPos; } } - gdcmVerboseMacro( "Unfound Location (0020,0050)"); + gdcmWarningMacro( "Unfound Location (0020,0050)"); return 0.; // Hopeless } /** - * \brief gets the info from 0020,0013 : Image Number else 0. - * @return image number - */ -int File::GetImageNumber() + * \brief gets the info from 0020,0037 : Image Orientation Patient + * (needed to organize DICOM files based on their x,y,z position) + * @param iop adress of the (6)float aray to receive values + * @return cosines of image orientation patient + */ +void File::GetImageOrientationPatient( float iop[6] ) { - // 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 = GetEntryValue(0x0020,0x0013); - if ( strImNumber != GDCM_UNFOUND ) + 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 = GetEntryValue(0x0020,0x0037)) != GDCM_UNFOUND ) { - return atoi( strImNumber.c_str() ); + if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f", + &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) + { + gdcmWarningMacro( "Wrong Image Orientation Patient (0020,0037). Less than 6 values were found." ); + } } - return 0; //Hopeless -} - -/** - * \brief gets the info from 0008,0060 : Modality - * @return Modality Type - */ -ModalityType File::GetModality() -{ - // 0008 0060 CS ID Modality - std::string strModality = GetEntryValue(0x0008,0x0060); - if ( strModality != GDCM_UNFOUND ) + //For ACR-NEMA + // 0020 0035 DS REL Image Orientation (RET) + else if ( (strImOriPat = GetEntryValue(0x0020,0x0035)) != 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 + if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f", + &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) { - /// \todo throw error return value ??? - /// specified <> unknown in our database - return Unknow; + gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). Less than 6 values were found." ); } } - - return Unknow; } /** * \brief Retrieve the number of Bits Stored (actually used) - * (as opposite to number of Bits Allocated) + * (as opposed 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 ! */ @@ -824,13 +661,31 @@ int File::GetBitsStored() std::string strSize = GetEntryValue( 0x0028, 0x0101 ); if ( strSize == GDCM_UNFOUND ) { - gdcmVerboseMacro("(0028,0101) is supposed to be mandatory"); + gdcmWarningMacro("(0028,0101) is supposed to be mandatory"); return 0; // It's supposed to be mandatory // the caller will have to check } return atoi( strSize.c_str() ); } +/** + * \brief Retrieve the 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 File::GetBitsAllocated() +{ + std::string strSize = GetEntryValue(0x0028,0x0100); + if ( strSize == GDCM_UNFOUND ) + { + gdcmWarningMacro( "(0028,0100) is supposed to be mandatory"); + return 0; // It's supposed to be mandatory + // the caller will have to check + } + return atoi( strSize.c_str() ); +} + /** * \brief Retrieve the high bit position. * \warning The method defaults to 0 when information is Missing. @@ -842,139 +697,41 @@ int File::GetHighBitPosition() std::string strSize = GetEntryValue( 0x0028, 0x0102 ); if ( strSize == GDCM_UNFOUND ) { - gdcmVerboseMacro( "(0028,0102) is supposed to be mandatory"); + gdcmWarningMacro( "(0028,0102) is supposed to be mandatory"); return 0; } return atoi( strSize.c_str() ); } /** - * \brief Check whether the pixels are signed or UNsigned data. - * \warning The method defaults to false (UNsigned) when information is Missing. - * The responsability of checking this value is left to the caller. - * @return True when signed, false when UNsigned + * \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) */ -bool File::IsSignedPixelData() +int File::GetSamplesPerPixel() { - std::string strSize = GetEntryValue( 0x0028, 0x0103 ); + const std::string &strSize = GetEntryValue(0x0028,0x0002); if ( strSize == GDCM_UNFOUND ) { - gdcmVerboseMacro( "(0028,0103) is supposed to be mandatory"); - return false; - } - int sign = atoi( strSize.c_str() ); - if ( sign == 0 ) - { - return false; + gdcmWarningMacro( "(0028,0002) is supposed to be mandatory"); + return 1; // Well, it's supposed to be mandatory ... + // but sometimes it's missing : *we* assume Gray pixels } - return true; + return atoi( strSize.c_str() ); } /** - * \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 ! + * \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 File::GetBitsAllocated() -{ - std::string strSize = GetEntryValue(0x0028,0x0100); - if ( strSize == GDCM_UNFOUND ) - { - gdcmVerboseMacro( "(0028,0100) is supposed to be mandatory"); - return 0; // It's supposed to be mandatory - // the caller will have to check - } - return atoi( strSize.c_str() ); -} - -/** - * \brief Retrieve the 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 File::GetSamplesPerPixel() -{ - const std::string& strSize = GetEntryValue(0x0028,0x0002); - if ( strSize == GDCM_UNFOUND ) - { - gdcmVerboseMacro( "(0028,0002) 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() ); -} - -/** - * \brief Check whether this a monochrome picture or not by accessing - * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). - * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise. - */ -bool File::IsMonochrome() -{ - const std::string& PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); - if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") - || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") ) - { - return true; - } - if ( PhotometricInterp == GDCM_UNFOUND ) - { - gdcmVerboseMacro( "Not found : Photometric Interpretation (0028,0004)"); - } - return false; -} - -/** - * \brief Check whether this a "PALETTE COLOR" picture or not by accessing - * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). - * @return true when "PALETTE COLOR". False otherwise. - */ -bool File::IsPaletteColor() -{ - std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); - if ( PhotometricInterp == "PALETTE COLOR " ) - { - return true; - } - if ( PhotometricInterp == GDCM_UNFOUND ) - { - gdcmVerboseMacro( "Not found : Palette color (0028,0004)"); - } - return false; -} - -/** - * \brief Check whether this a "YBR_FULL" color picture or not by accessing - * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). - * @return true when "YBR_FULL". False otherwise. - */ -bool File::IsYBRFull() -{ - std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); - if ( PhotometricInterp == "YBR_FULL" ) - { - return true; - } - if ( PhotometricInterp == GDCM_UNFOUND ) - { - gdcmVerboseMacro( "Not found : YBR Full (0028,0004)"); - } - return false; -} - -/** - * \brief Retrieve the Planar Configuration for RGB images - * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane) - * @return The encountered Planar Configuration, 0 by default. - */ -int File::GetPlanarConfiguration() +int File::GetPlanarConfiguration() { std::string strSize = GetEntryValue(0x0028,0x0006); if ( strSize == GDCM_UNFOUND ) { - gdcmVerboseMacro( "Not found : Planar Configuration (0028,0006)"); + gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)"); return 0; } return atoi( strSize.c_str() ); @@ -1009,7 +766,7 @@ int File::GetPixelSize() { return 8; } - gdcmVerboseMacro( "Unknown pixel type"); + gdcmWarningMacro( "Unknown pixel type"); return 0; } @@ -1024,7 +781,7 @@ int File::GetPixelSize() * - 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 + photochromatic interp ="RGB " * @return 0S if nothing found. NOT USABLE file. The caller has to check */ std::string File::GetPixelType() @@ -1032,7 +789,7 @@ std::string File::GetPixelType() std::string bitsAlloc = GetEntryValue(0x0028, 0x0100); // Bits Allocated if ( bitsAlloc == GDCM_UNFOUND ) { - gdcmVerboseMacro( "Missing Bits Allocated (0028,0100)"); + gdcmWarningMacro( "Missing Bits Allocated (0028,0100)"); bitsAlloc = "16"; // default and arbitrary value, not to polute the output } @@ -1055,7 +812,7 @@ std::string File::GetPixelType() if (sign == GDCM_UNFOUND ) { - gdcmVerboseMacro( "Missing Pixel Representation (0028,0103)"); + gdcmWarningMacro( "Missing Pixel Representation (0028,0103)"); sign = "U"; // default and arbitrary value, not to polute the output } else if ( sign == "0" ) @@ -1069,54 +826,104 @@ std::string File::GetPixelType() return bitsAlloc + sign; } +/** + * \brief Check whether the pixels are signed (1) or UNsigned (0) data. + * \warning The method defaults to false (UNsigned) when tag 0028|0103 + * is missing. + * The responsability of checking this value is left to the caller. + * @return True when signed, false when UNsigned + */ +bool File::IsSignedPixelData() +{ + std::string strSign = GetEntryValue( 0x0028, 0x0103 ); + if ( strSign == GDCM_UNFOUND ) + { + gdcmWarningMacro( "(0028,0103) is supposed to be mandatory"); + return false; + } + int sign = atoi( strSign.c_str() ); + if ( sign == 0 ) + { + return false; + } + return true; +} /** - * \brief Recover the offset (from the beginning of the file) - * of *image* pixels (not *icone image* pixels, if any !) - * @return Pixel Offset + * \brief Check whether this a monochrome picture (gray levels) or not, + * using "Photometric Interpretation" tag (0x0028,0x0004). + * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise. */ -size_t File::GetPixelOffset() +bool File::IsMonochrome() { - DocEntry* pxlElement = GetDocEntry(GrPixel,NumPixel); - if ( pxlElement ) + const std::string &PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") + || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") ) { - return pxlElement->GetOffset(); + return true; } - else + if ( PhotometricInterp == GDCM_UNFOUND ) { -#ifdef GDCM_DEBUG - std::cout << "Big trouble : Pixel Element (" - << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" - << std::endl; -#endif //GDCM_DEBUG - return 0; + gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)"); } + return false; } -/// \todo TODO : unify those two (previous one and next one) /** - * \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. + * \brief Check whether this a MONOCHROME1 picture (high values = dark) + * or not using "Photometric Interpretation" tag (0x0028,0x0004). + * @return true when "MONOCHROME1" . False otherwise. */ -size_t File::GetPixelAreaLength() +bool File::IsMonochrome1() { - DocEntry* pxlElement = GetDocEntry(GrPixel,NumPixel); - if ( pxlElement ) + const std::string &PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") ) { - return pxlElement->GetLength(); + return true; } - else + if ( PhotometricInterp == GDCM_UNFOUND ) { -#ifdef GDCM_DEBUG - std::cout << "Big trouble : Pixel Element (" - << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" - << std::endl; -#endif //GDCM_DEBUG - return 0; + gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)"); + } + return false; +} + +/** + * \brief Check whether this a "PALETTE COLOR" picture or not by accessing + * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). + * @return true when "PALETTE COLOR". False otherwise. + */ +bool File::IsPaletteColor() +{ + std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + if ( PhotometricInterp == "PALETTE COLOR " ) + { + return true; + } + if ( PhotometricInterp == GDCM_UNFOUND ) + { + gdcmWarningMacro( "Not found : Palette color (0028,0004)"); + } + return false; +} + +/** + * \brief Check whether this a "YBR_FULL" color picture or not by accessing + * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). + * @return true when "YBR_FULL". False otherwise. + */ +bool File::IsYBRFull() +{ + std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + if ( PhotometricInterp == "YBR_FULL" ) + { + return true; + } + if ( PhotometricInterp == GDCM_UNFOUND ) + { + gdcmWarningMacro( "Not found : YBR Full (0028,0004)"); } + return false; } /** @@ -1198,38 +1005,268 @@ int File::GetLUTNbits() return lutNbits; } +/** + *\brief gets the info from 0028,1052 : Rescale Intercept + * @return Rescale Intercept + */ +float File::GetRescaleIntercept() +{ + float resInter = 0.; + /// 0028 1052 DS IMG Rescale Intercept + const std::string &strRescInter = GetEntryValue(0x0028,0x1052); + if ( strRescInter != GDCM_UNFOUND ) + { + if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 ) + { + // bug in the element 0x0028,0x1052 + gdcmWarningMacro( "Rescale Intercept (0028,1052) is empty." ); + } + } -//----------------------------------------------------------------------------- -// Protected + return resInter; +} /** - * \brief anonymize a File (removes Patient's personal info) - * (read the code to see which ones ...) + *\brief gets the info from 0028,1053 : Rescale Slope + * @return Rescale Slope */ -bool File::AnonymizeFile() +float File::GetRescaleSlope() { - // If exist, replace by spaces - SetValEntry (" ",0x0010, 0x2154); // Telephone - SetValEntry (" ",0x0010, 0x1040); // Adress - SetValEntry (" ",0x0010, 0x0020); // Patient ID + float resSlope = 1.; + //0028 1053 DS IMG Rescale Slope + std::string strRescSlope = GetEntryValue(0x0028,0x1053); + if ( strRescSlope != GDCM_UNFOUND ) + { + if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1) + { + // bug in the element 0x0028,0x1053 + gdcmWarningMacro( "Rescale Slope (0028,1053) is empty."); + } + } - DocEntry* patientNameHE = GetDocEntry (0x0010, 0x0010); - - if ( patientNameHE ) // we replace it by Study Instance UID (why not) + return resSlope; +} + +/** + * \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 File::GetNumberOfScalarComponents() +{ + if ( GetSamplesPerPixel() == 3 ) + { + return 3; + } + + // 0028 0100 US IMG Bits Allocated + // (in order no to be messed up by old RGB images) + if ( GetEntryValue(0x0028,0x0100) == "24" ) + { + return 3; + } + + std::string strPhotometricInterpretation = GetEntryValue(0x0028,0x0004); + + if ( ( strPhotometricInterpretation == "PALETTE COLOR ") ) { - std::string studyInstanceUID = GetEntryValue (0x0020, 0x000d); - if ( studyInstanceUID != GDCM_UNFOUND ) + if ( HasLUT() )// PALETTE COLOR is NOT enough { - InsertValEntry(studyInstanceUID, 0x0010, 0x0010); + return 3; } else { - InsertValEntry("anonymised", 0x0010, 0x0010); + 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; + } +} + +/** + * \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 File::GetNumberOfScalarComponentsRaw() +{ + // 0028 0100 US IMG Bits Allocated + // (in order no to be messed up by old RGB images) + if ( File::GetEntryValue(0x0028,0x0100) == "24" ) + { + return 3; + } + + // we assume that *all* kinds of YBR are dealt with + return GetSamplesPerPixel(); +} + +/** + * \brief Recover the offset (from the beginning of the file) + * of *image* pixels (not *icone image* pixels, if any !) + * @return Pixel Offset + */ +size_t File::GetPixelOffset() +{ + DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel); + if ( pxlElement ) + { + return pxlElement->GetOffset(); + } + else + { + gdcmDebugMacro( "Big trouble : Pixel Element (" + << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" ); + return 0; + } +} + +/** + * \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 File::GetPixelAreaLength() +{ + DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel); + if ( pxlElement ) + { + return pxlElement->GetLength(); + } + else + { + gdcmDebugMacro( "Big trouble : Pixel Element (" + << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" ); + return 0; + } +} + +/** + * \brief Adds the characteristics of a new element we want to anonymize + * + */ +void File::AddAnonymizeElement (uint16_t group, uint16_t elem, + std::string const &value) + +{ + Element el; + el.Group = group; + el.Elem = elem; + el.Value = value; + AnonymizeList.push_back(el); +} + +/** + * \brief Overwrites in the file the values of the DicomElements + * held in the list + */ +void File::AnonymizeNoLoad() +{ + std::fstream *fp = new std::fstream(Filename.c_str(), + std::ios::in | std::ios::out | std::ios::binary); + gdcm::DocEntry *d; + uint32_t offset; + uint32_t lgth; + uint32_t valLgth = 0; + std::string *spaces; + for (ListElements::iterator it = AnonymizeList.begin(); + it != AnonymizeList.end(); + ++it) + { + d = GetDocEntry( (*it).Group, (*it).Elem); + + if ( d == NULL) + continue; + + if ( dynamic_cast(d) + || dynamic_cast(d) ) + continue; + + offset = d->GetOffset(); + lgth = d->GetLength(); + if (valLgth < lgth) + { + spaces = new std::string( lgth-valLgth, ' '); + (*it).Value = (*it).Value + *spaces; + delete spaces; } + fp->seekp( offset, std::ios::beg ); + fp->write( (*it).Value.c_str(), lgth ); + } + fp->close(); + delete fp; +} - // Just for fun :-( - // (if any) remove or replace all the stuff that contains a Date +/** + * \brief anonymize a File (removes Patient's personal info passed with + * AddAnonymizeElement() + */ +bool File::AnonymizeFile() +{ + // If Anonymisation list is empty, let's perform some basic anonymization + if ( AnonymizeList.begin() == AnonymizeList.end() ) + { + // If exist, replace by spaces + SetValEntry (" ",0x0010, 0x2154); // Telephone + SetValEntry (" ",0x0010, 0x1040); // Adress + SetValEntry (" ",0x0010, 0x0020); // Patient ID + + DocEntry* patientNameHE = GetDocEntry (0x0010, 0x0010); + + if ( patientNameHE ) // we replace it by Study Instance UID (why not ?) + { + std::string studyInstanceUID = GetEntryValue (0x0020, 0x000d); + if ( studyInstanceUID != GDCM_UNFOUND ) + { + SetValEntry(studyInstanceUID, 0x0010, 0x0010); + } + else + { + SetValEntry("anonymised", 0x0010, 0x0010); + } + } + } + else + { + gdcm::DocEntry *d; + for (ListElements::iterator it = AnonymizeList.begin(); + it != AnonymizeList.end(); + ++it) + { + d = GetDocEntry( (*it).Group, (*it).Elem); + + if ( d == NULL) + continue; + + if ( dynamic_cast(d) + || dynamic_cast(d) ) + continue; + + SetValEntry ((*it).Value, (*it).Group, (*it).Elem); + } +} + + // In order to make definitively impossible any further identification + // remove or replace all the stuff that contains a Date //0008 0012 DA ID Instance Creation Date //0008 0020 DA ID Study Date @@ -1284,118 +1321,356 @@ bool File::AnonymizeFile() } /** - * \brief gets the info from 0020,0037 : Image Orientation Patient - * (needed to organize DICOM files based on their x,y,z position) - * @param iop adress of the (6)float aray to receive values - * @return cosines of image orientation patient - */ -void File::GetImageOrientationPatient( float iop[6] ) + * \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 fileName file name to write to + * @param writetype Type of the File to be written + * (ACR, ExplicitVR, ImplicitVR) + */ +bool File::Write(std::string fileName, FileType writetype) { - std::string strImOriPat; - //iop is supposed to be float[6] - iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.; + std::ofstream *fp = new std::ofstream(fileName.c_str(), + std::ios::out | std::ios::binary); + if (*fp == NULL) + { + gdcmWarningMacro("Failed to open (write) File: " << fileName.c_str()); + return false; + } - // 0020 0037 DS REL Image Orientation (Patient) - if ( (strImOriPat = GetEntryValue(0x0020,0x0037)) != GDCM_UNFOUND ) + // Entry : 0002|0000 = group length -> recalculated + ValEntry*e0000 = GetValEntry(0x0002,0x0000); + if( e0000 ) { - if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f", - &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) + std::ostringstream sLen; + sLen << ComputeGroup0002Length(writetype); + e0000->SetValue(sLen.str()); + } + + // Bits Allocated + if ( GetEntryValue(0x0028,0x0100) == "12") + { + SetValEntry("16", 0x0028,0x0100); + } + + int i_lgPix = GetEntryLength(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() ); + InsertValEntry(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 ( GetEntryValue(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 = GetDocEntry(0x0028,0x01101); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntry(0x0028,0x1102); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntry(0x0028,0x1103); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntry(0x0028,0x01201); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntry(0x0028,0x1202); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntry(0x0028,0x1203); + if (e) { - gdcmVerboseMacro( "Wrong Image Orientation Patient (0020,0037). Less than 6 values were found." ); + RemoveEntryNoDestroy(e); } } - //For ACR-NEMA - // 0020 0035 DS REL Image Orientation (RET) - else if ( (strImOriPat = GetEntryValue(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 ) + + Document::WriteContent(fp, writetype); + + fp->close(); + delete fp; + + return true; +} + +//----------------------------------------------------------------------------- +// Protected + + +//----------------------------------------------------------------------------- +// Private +/** + * \brief Parse pixel data from disk of [multi-]fragment RLE encoding. + * Compute the RLE extra information and store it in \ref RLEInfo + * for later pixel retrieval usage. + */ +void File::ComputeRLEInfo() +{ + std::string ts = GetTransferSyntax(); + if ( !Global::GetTS()->IsRLELossless(ts) ) + { + return; + } + + // Encoded pixel data: for the time being we are only concerned with + // Jpeg or RLE Pixel data encodings. + // As stated in PS 3.5-2003, section 8.2 p44: + // "If sent in Encapsulated Format (i.e. other than the Native Format) the + // value representation OB is used". + // Hence we expect an OB value representation. Concerning OB VR, + // the section PS 3.5-2003, section A.4.c p 58-59, states: + // "For the Value Representations OB and OW, the encoding shall meet the + // following specifications depending on the Data element tag:" + // [...snip...] + // - the first item in the sequence of items before the encoded pixel + // data stream shall be basic offset table item. The basic offset table + // item value, however, is not required to be present" + ReadAndSkipEncapsulatedBasicOffsetTable(); + + // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G) + // Loop on the individual frame[s] and store the information + // on the RLE fragments in a RLEFramesInfo. + // Note: - when only a single frame is present, this is a + // classical image. + // - when more than one frame are present, then we are in + // the case of a multi-frame image. + long frameLength; + while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) != 0 ) + { + // Parse the RLE Header and store the corresponding RLE Segment + // Offset Table information on fragments of this current Frame. + // Note that the fragment pixels themselves are not loaded + // (but just skipped). + long frameOffset = Fp->tellg(); + + uint32_t nbRleSegments = ReadInt32(); + if ( nbRleSegments > 16 ) + { + // There should be at most 15 segments (refer to RLEFrame class) + gdcmWarningMacro( "Too many segments."); + } + + uint32_t rleSegmentOffsetTable[16]; + for( int k = 1; k <= 15; k++ ) { - gdcmVerboseMacro( "wrong Image Orientation Patient (0020,0035). Less than 6 values were found." ); + rleSegmentOffsetTable[k] = ReadInt32(); } + + // Deduce from both the RLE Header and the frameLength the + // fragment length, and again store this info in a + // RLEFramesInfo. + long rleSegmentLength[15]; + // skipping (not reading) RLE Segments + if ( nbRleSegments > 1) + { + for(unsigned int k = 1; k <= nbRleSegments-1; k++) + { + rleSegmentLength[k] = rleSegmentOffsetTable[k+1] + - rleSegmentOffsetTable[k]; + SkipBytes(rleSegmentLength[k]); + } + } + + rleSegmentLength[nbRleSegments] = frameLength + - rleSegmentOffsetTable[nbRleSegments]; + SkipBytes(rleSegmentLength[nbRleSegments]); + + // Store the collected info + RLEFrame *newFrame = new RLEFrame; + newFrame->SetNumberOfFragments(nbRleSegments); + for( unsigned int uk = 1; uk <= nbRleSegments; uk++ ) + { + newFrame->SetOffset(uk,frameOffset + rleSegmentOffsetTable[uk]); + newFrame->SetLength(uk,rleSegmentLength[uk]); + } + RLEInfo->AddFrame(newFrame); + } + + // Make sure that at the end of the item we encounter a 'Sequence + // Delimiter Item': + if ( !ReadTag(0xfffe, 0xe0dd) ) + { + gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence"); } } /** - * \brief Initialize a default DICOM File 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... + * \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding. + * Compute the jpeg extra information (fragment[s] offset[s] and + * length) and store it[them] in \ref JPEGInfo for later pixel + * retrieval usage. */ -void File::InitializeDefaultFile() +void File::ComputeJPEGFragmentInfo() { - 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 - { "1.2.840.10008.1.2.1 ", 0x0002, 0x0010}, // Transfer Syntax UID (Explicit VR Little Endian) - { 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; - InsertBinEntry(0, 0, GrPixel, NumPixel); + // If you need to, look for comments of ComputeRLEInfo(). + std::string ts = GetTransferSyntax(); + if ( ! Global::GetTS()->IsJPEG(ts) ) + { + return; + } + + ReadAndSkipEncapsulatedBasicOffsetTable(); + + // Loop on the fragments[s] and store the parsed information in a + // JPEGInfo. + long fragmentLength; + while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) != 0 ) + { + long fragmentOffset = Fp->tellg(); + + // Store the collected info + JPEGFragment *newFragment = new JPEGFragment; + newFragment->SetOffset(fragmentOffset); + newFragment->SetLength(fragmentLength); + JPEGInfo->AddFragment(newFragment); - // All remaining strings: - unsigned int i = 0; - DICOM_DEFAULT_VALUE current = defaultvalue[i]; - while( current.value ) + SkipBytes(fragmentLength); + } + + // Make sure that at the end of the item we encounter a 'Sequence + // Delimiter Item': + if ( !ReadTag(0xfffe, 0xe0dd) ) { - InsertValEntry(current.value, current.group, current.elem); - current = defaultvalue[++i]; + gdcmWarningMacro( "No sequence delimiter item at end of JPEG item sequence"); } } +/** + * \brief Assuming the internal file pointer \ref Document::Fp + * is placed at the beginning of a tag check whether this + * tag is (TestGroup, TestElement). + * \warning On success the internal file pointer \ref Document::Fp + * is modified to point after the tag. + * On failure (i.e. when the tag wasn't the expected tag + * (TestGroup, TestElement) the internal file pointer + * \ref Document::Fp is restored to it's original position. + * @param testGroup The expected group of the tag. + * @param testElement The expected Element of the tag. + * @return True on success, false otherwise. + */ +bool File::ReadTag(uint16_t testGroup, uint16_t testElement) +{ + long positionOnEntry = Fp->tellg(); + long currentPosition = Fp->tellg(); // On debugging purposes -//----------------------------------------------------------------------------- -// Private + // Read the Item Tag group and element, and make + // sure they are what we expected: + uint16_t itemTagGroup; + uint16_t itemTagElement; + try + { + itemTagGroup = ReadInt16(); + itemTagElement = ReadInt16(); + } + catch ( FormatError e ) + { + //std::cerr << e << std::endl; + return false; + } + if ( itemTagGroup != testGroup || itemTagElement != testElement ) + { + gdcmWarningMacro( "Wrong Item Tag found:" + << " We should have found tag (" + << std::hex << testGroup << "," << testElement << ")" << std::endl + << " but instead we encountered tag (" + << std::hex << itemTagGroup << "," << itemTagElement << ")" + << " at address: " << " 0x(" << (unsigned int)currentPosition << ")" + ) ; + Fp->seekg(positionOnEntry, std::ios::beg); + + return false; + } + return true; +} + +/** + * \brief Assuming the internal file pointer \ref Document::Fp + * is placed at the beginning of a tag (TestGroup, TestElement), + * read the length associated to the Tag. + * \warning On success the internal file pointer \ref Document::Fp + * is modified to point after the tag and it's length. + * On failure (i.e. when the tag wasn't the expected tag + * (TestGroup, TestElement) the internal file pointer + * \ref Document::Fp is restored to it's original position. + * @param testGroup The expected group of the tag. + * @param testElement The expected Element of the tag. + * @return On success returns the length associated to the tag. On failure + * returns 0. + */ +uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElement) +{ + + if ( !ReadTag(testGroup, testElement) ) + { + return 0; + } + + //// Then read the associated Item Length + long currentPosition = Fp->tellg(); + uint32_t itemLength = ReadInt32(); + { + gdcmWarningMacro( "Basic Item Length is: " + << itemLength << std::endl + << " at address: " << std::hex << (unsigned int)currentPosition); + } + return itemLength; +} + +/** + * \brief When parsing the Pixel Data of an encapsulated file, read + * the basic offset table (when present, and BTW dump it). + */ +void File::ReadAndSkipEncapsulatedBasicOffsetTable() +{ + //// Read the Basic Offset Table Item Tag length... + uint32_t itemLength = ReadTagLength(0xfffe, 0xe000); + + // When present, read the basic offset table itself. + // Notes: - since the presence of this basic offset table is optional + // we can't rely on it for the implementation, and we will simply + // trash it's content (when present). + // - still, when present, we could add some further checks on the + // lengths, but we won't bother with such fuses for the time being. + if ( itemLength != 0 ) + { + char *basicOffsetTableItemValue = new char[itemLength + 1]; + Fp->read(basicOffsetTableItemValue, itemLength); + +#ifdef GDCM_DEBUG + for (unsigned int i=0; i < itemLength; i += 4 ) + { + uint32_t individualLength = str2num( &basicOffsetTableItemValue[i], + uint32_t); + gdcmWarningMacro( "Read one length: " << + std::hex << individualLength ); + } +#endif //GDCM_DEBUG + + delete[] basicOffsetTableItemValue; + } +} //----------------------------------------------------------------------------- +// Print +//----------------------------------------------------------------------------- } // end namespace gdcm