X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=94f5ca5b22b4895807937ffae513695655a7fc4c;hb=e51bf0565bbe4c0e269dd941cb4071ebde6012e4;hp=ffa7ae08bb998bb79502119382fcd58471e55adf;hpb=643a8d9fe7dc8470db4cf7a6de639beebb339076;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index ffa7ae08..94f5ca5b 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2005/01/28 15:10:56 $ - Version: $Revision: 1.205 $ + Date: $Date: 2005/02/10 20:53:23 $ + Version: $Revision: 1.223 $ 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" @@ -23,6 +35,7 @@ #include "gdcmTS.h" #include "gdcmValEntry.h" #include "gdcmBinEntry.h" +#include "gdcmSeqEntry.h" #include "gdcmRLEFramesInfo.h" #include "gdcmJPEGFragmentsInfo.h" @@ -37,8 +50,8 @@ namespace gdcm * \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; @@ -155,137 +168,8 @@ File::~File () 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; - } - - // Entry : 0002|0000 = group length -> recalculated - ValEntry *e0002 = GetValEntry(0x0002,0x0000); - if( e0002 ) - { - std::ostringstream sLen; - sLen << ComputeGroup0002Length(filetype); - e0002->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) - { - 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 @@ -326,6 +210,89 @@ bool File::IsReadable() return true; } +/** + * \brief gets the info from 0020,0013 : Image Number else 0. + * @return image number + */ +int File::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 = 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 CS ID 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. @@ -400,12 +367,13 @@ 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.; } @@ -413,11 +381,12 @@ 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; @@ -432,7 +401,7 @@ float File::GetXSpacing() if ( xspacing == 0.) { - gdcmVerboseMacro("gdcmData/CT-MONO2-8-abdo.dcm problem"); + gdcmWarningMacro("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); gdcmAssertMacro( nbValues == 2 ); @@ -453,12 +422,16 @@ 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; @@ -488,11 +461,11 @@ float File::GetZSpacing() 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 @@ -509,180 +482,55 @@ 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 -// -// --------------------------------------------------------------- -// - -/** - * \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)"); - 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)"); - return 0.; - } + gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); + return 0.; + } } if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 ) @@ -710,7 +558,7 @@ 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 @@ -725,7 +573,7 @@ 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 @@ -739,7 +587,7 @@ 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 @@ -747,14 +595,14 @@ 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 @@ -762,97 +610,47 @@ 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 ! */ @@ -861,13 +659,31 @@ 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. @@ -879,68 +695,155 @@ 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() +int File::GetPlanarConfiguration() { - std::string strSize = GetEntryValue(0x0028,0x0100); + std::string strSize = GetEntryValue(0x0028,0x0006); 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 + gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)"); + return 0; } 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) + * \brief Return the size (in bytes) of a single pixel of data. + * @return The size in bytes of a single pixel of data; 0 by default + * 0 means the file is NOT USABLE; the caller will have to check */ -int File::GetSamplesPerPixel() +int File::GetPixelSize() { - const std::string& strSize = GetEntryValue(0x0028,0x0002); + // 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; + + std::string pixelType = GetPixelType(); + if ( pixelType == "8U" || pixelType == "8S" ) + { + return 1; + } + if ( pixelType == "16U" || pixelType == "16S") + { + return 2; + } + if ( pixelType == "32U" || pixelType == "32S") + { + return 4; + } + if ( pixelType == "FD" ) + { + return 8; + } + gdcmWarningMacro( "Unknown pixel type"); + return 0; +} + +/** + * \brief Build the Pixel Type of the image. + * Possible values are: + * - 8U unsigned 8 bit, + * - 8S signed 8 bit, + * - 16U unsigned 16 bit, + * - 16S signed 16 bit, + * - 32U unsigned 32 bit, + * - 32S signed 32 bit, + * - FD floating double 64 bits (Not kosher DICOM, but so usefull!) + * \warning 12 bit images appear as 16 bit. + * 24 bit images appear as 8 bit + * @return 0S if nothing found. NOT USABLE file. The caller has to check + */ +std::string File::GetPixelType() +{ + std::string bitsAlloc = GetEntryValue(0x0028, 0x0100); // Bits Allocated + if ( bitsAlloc == GDCM_UNFOUND ) + { + gdcmWarningMacro( "Missing Bits Allocated (0028,0100)"); + bitsAlloc = "16"; // default and arbitrary value, not to polute the output + } + + 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 = GetEntryValue(0x0028, 0x0103);//"Pixel Representation" + + if (sign == GDCM_UNFOUND ) + { + gdcmWarningMacro( "Missing Pixel Representation (0028,0103)"); + sign = "U"; // default and arbitrary value, not to polute the output + } + else if ( sign == "0" ) + { + sign = "U"; + } + else + { + sign = "S"; + } + return bitsAlloc + sign; +} + +/** + * \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 + */ +bool File::IsSignedPixelData() +{ + std::string strSize = GetEntryValue( 0x0028, 0x0103 ); 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 + gdcmWarningMacro( "(0028,0103) is supposed to be mandatory"); + return false; } - return atoi( strSize.c_str() ); + int sign = atoi( strSize.c_str() ); + if ( sign == 0 ) + { + return false; + } + return true; } /** @@ -950,7 +853,7 @@ int File::GetSamplesPerPixel() */ bool File::IsMonochrome() { - const std::string& PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + const std::string &PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") ) { @@ -958,7 +861,7 @@ bool File::IsMonochrome() } if ( PhotometricInterp == GDCM_UNFOUND ) { - gdcmVerboseMacro( "Not found : Photometric Interpretation (0028,0004)"); + gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)"); } return false; } @@ -977,7 +880,7 @@ bool File::IsPaletteColor() } if ( PhotometricInterp == GDCM_UNFOUND ) { - gdcmVerboseMacro( "Not found : Palette color (0028,0004)"); + gdcmWarningMacro( "Not found : Palette color (0028,0004)"); } return false; } @@ -996,116 +899,201 @@ bool File::IsYBRFull() } if ( PhotometricInterp == GDCM_UNFOUND ) { - gdcmVerboseMacro( "Not found : YBR Full (0028,0004)"); + gdcmWarningMacro( "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() + * \brief tells us if LUT are used + * \warning Right now, 'Segmented xxx Palette Color Lookup Table Data' + * are NOT considered as LUT, since nobody knows + * how to deal with them + * Please warn me if you know sbdy that *does* know ... jprx + * @return true if LUT Descriptors and LUT Tables were found + */ +bool File::HasLUT() { - std::string strSize = GetEntryValue(0x0028,0x0006); - if ( strSize == GDCM_UNFOUND ) + // Check the presence of the LUT Descriptors, and LUT Tables + // LutDescriptorRed + if ( !GetDocEntry(0x0028,0x1101) ) { - gdcmVerboseMacro( "Not found : Planar Configuration (0028,0006)"); - return 0; + return false; } - return atoi( strSize.c_str() ); -} - -/** - * \brief Return the size (in bytes) of a single pixel of data. - * @return The size in bytes of a single pixel of data; 0 by default - * 0 means the file is NOT USABLE; the caller will have to check - */ -int File::GetPixelSize() -{ - // 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; - - std::string pixelType = GetPixelType(); - if ( pixelType == "8U" || pixelType == "8S" ) + // LutDescriptorGreen + if ( !GetDocEntry(0x0028,0x1102) ) { - return 1; + return false; } - if ( pixelType == "16U" || pixelType == "16S") + // LutDescriptorBlue + if ( !GetDocEntry(0x0028,0x1103) ) { - return 2; + return false; } - if ( pixelType == "32U" || pixelType == "32S") + // Red Palette Color Lookup Table Data + if ( !GetDocEntry(0x0028,0x1201) ) { - return 4; + return false; } - if ( pixelType == "FD" ) + // Green Palette Color Lookup Table Data + if ( !GetDocEntry(0x0028,0x1202) ) { - return 8; + return false; } - gdcmVerboseMacro( "Unknown pixel type"); - return 0; + // Blue Palette Color Lookup Table Data + if ( !GetDocEntry(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; } /** - * \brief Build the Pixel Type of the image. - * Possible values are: - * - 8U unsigned 8 bit, - * - 8S signed 8 bit, - * - 16U unsigned 16 bit, - * - 16S signed 16 bit, - * - 32U unsigned 32 bit, - * - 32S signed 32 bit, - * - FD floating double 64 bits (Not kosher DICOM, but so usefull!) - * \warning 12 bit images appear as 16 bit. - * 24 bit images appear as 8 bit - * @return 0S if nothing found. NOT USABLE file. The caller has to check + * \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 File::GetLUTNbits() +{ + std::vector tokens; + int lutNbits; + + //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red + // = Lookup Table Desc-Blue + // Consistency already checked in GetLUTLength + std::string lutDescription = GetEntryValue(0x0028,0x1101); + if ( lutDescription == GDCM_UNFOUND ) + { + return 0; + } + + tokens.clear(); // clean any previous value + Util::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; +} + +/** + *\brief gets the info from 0028,1052 : Rescale Intercept + * @return Rescale Intercept */ -std::string File::GetPixelType() +float File::GetRescaleIntercept() { - std::string bitsAlloc = GetEntryValue(0x0028, 0x0100); // Bits Allocated - if ( bitsAlloc == GDCM_UNFOUND ) + float resInter = 0.; + /// 0028 1052 DS IMG Rescale Intercept + const std::string &strRescInter = GetEntryValue(0x0028,0x1052); + if ( strRescInter != GDCM_UNFOUND ) { - gdcmVerboseMacro( "Missing Bits Allocated (0028,0100)"); - bitsAlloc = "16"; // default and arbitrary value, not to polute the output + if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 ) + { + // bug in the element 0x0028,0x1052 + gdcmWarningMacro( "Rescale Intercept (0028,1052) is empty." ); + } } - if ( bitsAlloc == "64" ) + return resInter; +} + +/** + *\brief gets the info from 0028,1053 : Rescale Slope + * @return Rescale Slope + */ +float File::GetRescaleSlope() +{ + float resSlope = 1.; + //0028 1053 DS IMG Rescale Slope + std::string strRescSlope = GetEntryValue(0x0028,0x1053); + if ( strRescSlope != GDCM_UNFOUND ) { - return "FD"; + if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1) + { + // bug in the element 0x0028,0x1053 + gdcmWarningMacro( "Rescale Slope (0028,1053) is empty."); + } } - else if ( bitsAlloc == "12" ) + + 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 ) { - // It will be unpacked - bitsAlloc = "16"; + return 3; } - else if ( bitsAlloc == "24" ) + + // 0028 0100 US IMG Bits Allocated + // (in order no to be messed up by old RGB images) + if ( GetEntryValue(0x0028,0x0100) == "24" ) { - // (in order no to be messed up - bitsAlloc = "8"; // by old RGB images) + return 3; } + + std::string strPhotometricInterpretation = GetEntryValue(0x0028,0x0004); - std::string sign = GetEntryValue(0x0028, 0x0103);//"Pixel Representation" - - if (sign == GDCM_UNFOUND ) + if ( ( strPhotometricInterpretation == "PALETTE COLOR ") ) { - gdcmVerboseMacro( "Missing Pixel Representation (0028,0103)"); - sign = "U"; // default and arbitrary value, not to polute the output + if ( HasLUT() )// PALETTE COLOR is NOT enough + { + return 3; + } + else + { + return 1; + } } - else if ( sign == "0" ) + + // 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") ) { - sign = "U"; + return 1; } else { - sign = "S"; + // we assume that *all* kinds of YBR are dealt with + return 3; } - return bitsAlloc + sign; } +/** + * \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) @@ -1114,18 +1102,15 @@ std::string File::GetPixelType() */ size_t File::GetPixelOffset() { - DocEntry* pxlElement = GetDocEntry(GrPixel,NumPixel); + DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel); if ( pxlElement ) { return pxlElement->GetOffset(); } else { -#ifdef GDCM_DEBUG - std::cout << "Big trouble : Pixel Element (" - << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" - << std::endl; -#endif //GDCM_DEBUG + gdcmDebugMacro( "Big trouble : Pixel Element (" + << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" ); return 0; } } @@ -1139,162 +1124,132 @@ size_t File::GetPixelOffset() */ size_t File::GetPixelAreaLength() { - DocEntry* pxlElement = GetDocEntry(GrPixel,NumPixel); + DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel); if ( pxlElement ) { return pxlElement->GetLength(); } else { -#ifdef GDCM_DEBUG - std::cout << "Big trouble : Pixel Element (" - << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" - << std::endl; -#endif //GDCM_DEBUG + gdcmDebugMacro( "Big trouble : Pixel Element (" + << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" ); return 0; } } /** - * \brief tells us if LUT are used - * \warning Right now, 'Segmented xxx Palette Color Lookup Table Data' - * are NOT considered as LUT, since nobody knows - * how to deal with them - * Please warn me if you know sbdy that *does* know ... jprx - * @return true if LUT Descriptors and LUT Tables were found - */ -bool File::HasLUT() -{ - // Check the presence of the LUT Descriptors, and LUT Tables - // LutDescriptorRed - if ( !GetDocEntry(0x0028,0x1101) ) - { - return false; - } - // LutDescriptorGreen - if ( !GetDocEntry(0x0028,0x1102) ) - { - return false; - } - // LutDescriptorBlue - if ( !GetDocEntry(0x0028,0x1103) ) - { - return false; - } - // Red Palette Color Lookup Table Data - if ( !GetDocEntry(0x0028,0x1201) ) - { - return false; - } - // Green Palette Color Lookup Table Data - if ( !GetDocEntry(0x0028,0x1202) ) - { - return false; - } - // Blue Palette Color Lookup Table Data - if ( !GetDocEntry(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; + * \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 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 File::GetLUTNbits() + * \brief Overwrites in the file the values of the DicomElements + * held in the list + */ +void File::AnonymizeNoLoad() { - std::vector tokens; - int lutNbits; - - //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red - // = Lookup Table Desc-Blue - // Consistency already checked in GetLUTLength - std::string lutDescription = GetEntryValue(0x0028,0x1101); - if ( lutDescription == GDCM_UNFOUND ) - { - return 0; - } - - tokens.clear(); // clean any previous value - Util::Tokenize ( lutDescription, tokens, "\\" ); - //LutLength=atoi(tokens[0].c_str()); - //LutDepth=atoi(tokens[1].c_str()); - - lutNbits = atoi( tokens[2].c_str() ); - tokens.clear(); + std::fstream *fp = new std::fstream(Filename.c_str(), + std::ios::in | std::ios::out | std::ios::binary); + + // TODO : FIXME + // how to white out disk space if longer than 50 ? + + + 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); - return lutNbits; -} + if ( d == NULL) + continue; -/** - * \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] ) -{ - std::string strImOriPat; - //iop is supposed to be float[6] - iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.; + if ( dynamic_cast(d) + || dynamic_cast(d) ) + continue; - // 0020 0037 DS REL Image Orientation (Patient) - if ( (strImOriPat = GetEntryValue(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 ) - { - gdcmVerboseMacro( "Wrong Image Orientation Patient (0020,0037). Less than 6 values were found." ); - } - } - //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 ) + offset = d->GetOffset(); + lgth = d->GetLength(); + if (valLgth < lgth) { - gdcmVerboseMacro( "wrong Image Orientation Patient (0020,0035). Less than 6 values were found." ); + 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; } /** - * \brief anonymize a File (removes Patient's personal info) - * (read the code to see which ones ...) + * \brief anonymize a File (removes Patient's personal info passed with + * AddAnonymizeElement() */ bool File::AnonymizeFile() { - // If exist, replace by spaces - SetValEntry (" ",0x0010, 0x2154); // Telephone - SetValEntry (" ",0x0010, 0x1040); // Adress - SetValEntry (" ",0x0010, 0x0020); // Patient ID + // 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); + 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 ) + if ( patientNameHE ) // we replace it by Study Instance UID (why not ?) { - InsertValEntry(studyInstanceUID, 0x0010, 0x0010); - } - else - { - InsertValEntry("anonymised", 0x0010, 0x0010); + 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; - // Just for fun :-( - // (if any) remove or replace all the stuff that contains a Date + 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 @@ -1348,6 +1303,98 @@ bool File::AnonymizeFile() return true; } +/** + * \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) + { + gdcmWarningMacro("Failed to open (write) File: " << fileName.c_str()); + return false; + } + + // Entry : 0002|0000 = group length -> recalculated + ValEntry *e0002 = GetValEntry(0x0002,0x0000); + if( e0002 ) + { + std::ostringstream sLen; + sLen << ComputeGroup0002Length(filetype); + e0002->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) + { + RemoveEntryNoDestroy(e); + } + } + + Document::WriteContent(fp, filetype); + + fp->close(); + delete fp; + + return true; +} + //----------------------------------------------------------------------------- // Protected /** @@ -1358,13 +1405,6 @@ bool File::AnonymizeFile() */ void File::InitializeDefaultFile() { - 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(); @@ -1374,56 +1414,72 @@ void File::InitializeDefaultFile() std::string uidStudy = Util::CreateUniqueUID(); std::string uidSerie = Util::CreateUniqueUID(); - 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 } - }; + // Meta Element Group Length + InsertValEntry("146 ", 0x0002, 0x0000); + // Media Storage SOP Class UID (CT Image Storage) + InsertValEntry("1.2.840.10008.5.1.4.1.1.2", 0x0002, 0x0002); + // Media Storage SOP Instance UID + InsertValEntry(uidMedia.c_str(), 0x0002, 0x0003); + // Transfer Syntax UID (Explicit VR Little Endian) + InsertValEntry("1.2.840.10008.1.2.1 ", 0x0002, 0x0010); + // META Implementation Class UID + InsertValEntry(uidClass.c_str(), 0x0002, 0x0012); + // Source Application Entity Title + InsertValEntry("GDCM", 0x0002, 0x0016); + + // Instance Creation Date + InsertValEntry(date.c_str(), 0x0008, 0x0012); + // Instance Creation Time + InsertValEntry(time.c_str(), 0x0008, 0x0013); + // SOP Class UID + InsertValEntry("1.2.840.10008.5.1.4.1.1.2", 0x0008, 0x0016); + // SOP Instance UID + InsertValEntry(uidInst.c_str(), 0x0008, 0x0018); + // Modality + InsertValEntry("CT", 0x0008, 0x0060); + // Manufacturer + InsertValEntry("GDCM", 0x0008, 0x0070); + // Institution Name + InsertValEntry("GDCM", 0x0008, 0x0080); + // Institution Address + InsertValEntry("http://www-creatis.insa-lyon.fr/Public/Gdcm", 0x0008, 0x0081); + + // Patient's Name + InsertValEntry("GDCM", 0x0010, 0x0010); + // Patient ID + InsertValEntry("GDCMID", 0x0010, 0x0020); + + // Study Instance UID + InsertValEntry(uidStudy.c_str(), 0x0020, 0x000d); + // Series Instance UID + InsertValEntry(uidSerie.c_str(), 0x0020, 0x000e); + // StudyID + InsertValEntry("1", 0x0020, 0x0010); + // SeriesNumber + InsertValEntry("1", 0x0020, 0x0011); + + // Samples per pixel 1 or 3 + InsertValEntry("1", 0x0028, 0x0002); + // photochromatic interpretation + InsertValEntry("MONOCHROME1", 0x0028, 0x0004); + // nbRows + InsertValEntry("0", 0x0028, 0x0010); + // nbCols + InsertValEntry("0", 0x0028, 0x0011); + // BitsAllocated 8 or 12 or 16 + InsertValEntry("8", 0x0028, 0x0100); + // BitsStored <= BitsAllocated + InsertValEntry("8", 0x0028, 0x0101); + // HighBit <= BitsAllocated - 1 + InsertValEntry("7", 0x0028, 0x0102); + // Pixel Representation 0(unsigned) or 1(signed) + InsertValEntry("0", 0x0028, 0x0103); // default value // Special case this is the image (not a string) GrPixel = 0x7fe0; NumPixel = 0x0010; InsertBinEntry(0, 0, GrPixel, NumPixel); - - // All remaining strings: - unsigned int i = 0; - DICOM_DEFAULT_VALUE current = defaultvalue[i]; - while( current.value ) - { - InsertValEntry(current.value, current.group, current.elem); - current = defaultvalue[++i]; - } } //----------------------------------------------------------------------------- @@ -1476,7 +1532,7 @@ void File::ComputeRLEInfo() if ( nbRleSegments > 16 ) { // There should be at most 15 segments (refer to RLEFrame class) - gdcmVerboseMacro( "Too many segments."); + gdcmWarningMacro( "Too many segments."); } uint32_t rleSegmentOffsetTable[16]; @@ -1519,7 +1575,7 @@ void File::ComputeRLEInfo() // Delimiter Item': if ( !ReadTag(0xfffe, 0xe0dd) ) { - gdcmVerboseMacro( "No sequence delimiter item at end of RLE item sequence"); + gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence"); } } @@ -1560,7 +1616,7 @@ void File::ComputeJPEGFragmentInfo() // Delimiter Item': if ( !ReadTag(0xfffe, 0xe0dd) ) { - gdcmVerboseMacro( "No sequence delimiter item at end of JPEG item sequence"); + gdcmWarningMacro( "No sequence delimiter item at end of JPEG item sequence"); } } @@ -1582,7 +1638,7 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElement) long positionOnEntry = Fp->tellg(); long currentPosition = Fp->tellg(); // On debugging purposes - //// Read the Item Tag group and element, and make + // Read the Item Tag group and element, and make // sure they are what we expected: uint16_t itemTagGroup; uint16_t itemTagElement; @@ -1598,7 +1654,7 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElement) } if ( itemTagGroup != testGroup || itemTagElement != testElement ) { - gdcmVerboseMacro( "Wrong Item Tag found:" + gdcmWarningMacro( "Wrong Item Tag found:" << " We should have found tag (" << std::hex << testGroup << "," << testElement << ")" << std::endl << " but instead we encountered tag (" @@ -1638,7 +1694,7 @@ uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElement) long currentPosition = Fp->tellg(); uint32_t itemLength = ReadInt32(); { - gdcmVerboseMacro( "Basic Item Length is: " + gdcmWarningMacro( "Basic Item Length is: " << itemLength << std::endl << " at address: " << std::hex << (unsigned int)currentPosition); } @@ -1670,7 +1726,7 @@ void File::ReadAndSkipEncapsulatedBasicOffsetTable() { uint32_t individualLength = str2num( &basicOffsetTableItemValue[i], uint32_t); - gdcmVerboseMacro( "Read one length: " << + gdcmWarningMacro( "Read one length: " << std::hex << individualLength ); } #endif //GDCM_DEBUG @@ -1680,5 +1736,7 @@ void File::ReadAndSkipEncapsulatedBasicOffsetTable() } //----------------------------------------------------------------------------- +// Print +//----------------------------------------------------------------------------- } // end namespace gdcm