X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=214d8035162bb3cdb4828970230063a55e1cf02e;hb=fbd2698cb0545343abc2d8aefe92bab1f5b3eaa3;hp=cc5ff672592fbdb3aad3684e8cfcc8467441c69a;hpb=5b89bede4607999aeb8d5b45311e7ee82f9471ef;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index cc5ff672..214d8035 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2005/02/02 16:18:48 $ - Version: $Revision: 1.208 $ + Date: $Date: 2005/07/07 16:37:40 $ + Version: $Revision: 1.249 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -23,7 +23,7 @@ // 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, +// as the Z coordinate, // 0. for all the coordinates if nothing is found // // --------------------------------------------------------------- @@ -35,26 +35,92 @@ #include "gdcmTS.h" #include "gdcmValEntry.h" #include "gdcmBinEntry.h" +#include "gdcmSeqEntry.h" #include "gdcmRLEFramesInfo.h" #include "gdcmJPEGFragmentsInfo.h" -#include //sscanf #include +#include //sscanf +#include // for atoi 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; // to avoid further troubles + NumPixel = 0x0010; +} + /** * \brief Constructor * @param filename name of the file whose header we want to analyze */ File::File( std::string const &filename ) - :Document( filename ) + :Document( ) { RLEInfo = new RLEFramesInfo; JPEGInfo = new JPEGFragmentsInfo; + Load( filename ); // gdcm::Document is first Loaded, then the 'File part' +} + +/** + * \brief Canonical destructor. + */ +File::~File () +{ + if ( RLEInfo ) + delete RLEInfo; + if ( JPEGInfo ) + delete JPEGInfo; +} + +//----------------------------------------------------------------------------- +// Public +/** + * \brief Loader + * @return false if file cannot be open or no swap info was found, + * or no tag was found. + */ +bool File::Load( ) +{ + if ( ! this->Document::Load( ) ) + return false; + + return DoTheLoadingJob( ); +} +/** + * \brief Loader. (DEPRECATED : not to break the API) + * @param fileName file to be open for parsing + * @return false if file cannot be open or no swap info was found, + * or no tag was found. + */ +bool File::Load( std::string const &fileName ) +{ + SetFileName( fileName ); + if ( ! this->Document::Load( ) ) + return false; + + return DoTheLoadingJob( ); +} + +/** + * \brief Does the Loading Job (internal use only) + * @return false if file cannot be open or no swap info was found, + * or no tag was found. + */ +bool File::DoTheLoadingJob( ) +{ + // 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 @@ -103,7 +169,7 @@ File::File( std::string const &filename ) { // Compute the RLE or JPEG info OpenFile(); - std::string ts = GetTransferSyntax(); + const std::string &ts = GetTransferSyntax(); Fp->seekg( entry->GetOffset(), std::ios::beg ); if ( Global::GetTS()->IsRLELossless(ts) ) ComputeRLEInfo(); @@ -111,13 +177,12 @@ File::File( std::string const &filename ) ComputeJPEGFragmentInfo(); CloseFile(); - // Create a new BinEntry to change the the DictEntry + // Create a new BinEntry to change the DictEntry // The changed DictEntry will have // - a correct PixelVR OB or OW) - // - a VM to "PXL" // - the name to "Pixel Data" BinEntry *oldEntry = dynamic_cast(entry); - if(oldEntry) + if (oldEntry) { std::string PixelVR; // 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB) @@ -128,7 +193,7 @@ File::File( std::string const &filename ) PixelVR = "OW"; // Change only made if usefull - if( PixelVR != oldEntry->GetVR() ) + if ( PixelVR != oldEntry->GetVR() ) { DictEntry* newDict = NewVirtualDictEntry(GrPixel,NumPixel, PixelVR,"1","Pixel Data"); @@ -143,32 +208,8 @@ File::File( std::string const &filename ) } } } + return true; } - -/** - * \brief Constructor used when we want to generate dicom files from scratch - */ -File::File(): - Document() -{ - RLEInfo = new RLEFramesInfo; - JPEGInfo = new JPEGFragmentsInfo; - InitializeDefaultFile(); -} - -/** - * \brief Canonical destructor. - */ -File::~File () -{ - if( RLEInfo ) - delete RLEInfo; - if( JPEGInfo ) - delete JPEGInfo; -} - -//----------------------------------------------------------------------------- -// Public /** * \brief This predicate, based on hopefully reasonable heuristics, * decides whether or not the current File was properly parsed @@ -179,7 +220,7 @@ File::~File () */ bool File::IsReadable() { - if( !Document::IsReadable() ) + if ( !Document::IsReadable() ) { return false; } @@ -187,25 +228,50 @@ bool File::IsReadable() const std::string &res = GetEntryValue(0x0028, 0x0005); if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) { + gdcmWarningMacro("Wrong Image Dimensions" << res); return false; // Image Dimensions } + bool b0028_0100 = true; if ( !GetDocEntry(0x0028, 0x0100) ) { - return false; // "Bits Allocated" + gdcmWarningMacro("Bits Allocated (0028|0100) not found"); + //return false; // "Bits Allocated" + b0028_0100 = false; } + bool b0028_0101 = true; if ( !GetDocEntry(0x0028, 0x0101) ) { - return false; // "Bits Stored" + gdcmWarningMacro("Bits Stored (0028|0101) not found"); + //return false; // "Bits Stored" + b0028_0101 = false; } + bool b0028_0102 = true; if ( !GetDocEntry(0x0028, 0x0102) ) { - return false; // "High Bit" + gdcmWarningMacro("Hight Bit (0028|0102) not found"); + //return false; // "High Bit" + b0028_0102 = false; } + bool b0028_0103 = true; if ( !GetDocEntry(0x0028, 0x0103) ) { - return false; // "Pixel Representation" i.e. 'Sign' + gdcmWarningMacro("Pixel Representation (0028|0103) not found"); + //return false; // "Pixel Representation" i.e. 'Sign' ( 0 : unsigned, 1 : signed) + b0028_0103 = false; + } + + if ( !b0028_0100 && !b0028_0101 && !b0028_0102 && !b0028_0103) + { + gdcmWarningMacro("Too much mandatory Tags missing !"); + return false; } + if ( !GetDocEntry(GrPixel, NumPixel) ) + { + gdcmWarningMacro("Pixel Dicom Element " << std::hex << + GrPixel << "|" << NumPixel << "not found"); + return false; // Pixel Dicom Element not found :-( + } return true; } @@ -215,13 +281,7 @@ bool File::IsReadable() */ 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 + //0020 0013 : Image Number std::string strImNumber = GetEntryValue(0x0020,0x0013); if ( strImNumber != GDCM_UNFOUND ) { @@ -236,50 +296,54 @@ int File::GetImageNumber() */ ModalityType File::GetModality() { - // 0008 0060 CS ID Modality + // 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; + 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 ( 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 { @@ -288,7 +352,6 @@ ModalityType File::GetModality() return Unknow; } } - return Unknow; } @@ -304,7 +367,6 @@ int File::GetXSize() { return 0; } - return atoi( strSize.c_str() ); } @@ -326,8 +388,9 @@ int File::GetYSize() return 0; } - // The Rows (0028,0010) entry was optional for ACR/NEMA. It might - // hence be a signal (1D image). So we default to 1: + // The Rows (0028,0010) entry was optional for ACR/NEMA. + // (at least some images didn't have it.) + // It might hence be a signal (1D image). So we default to 1: return 1; } @@ -335,7 +398,7 @@ int File::GetYSize() * \brief Retrieve the number of planes of volume or the number * of frames of a multiframe. * \warning When present we consider the "Number of Frames" as the third - * dimension. When Missing we consider the third dimension as + * dimension. When missing we consider the third dimension as * being the ACR-NEMA "Planes" tag content. * @return The encountered size when found, 1 by default (single image). */ @@ -355,52 +418,76 @@ int File::GetZSize() { return atoi( strSize2.c_str() ); } - return 1; } /** - * \brief gets the info from 0028,0030 : Pixel Spacing + * \brief gets the info from 0018,1164 : ImagerPixelSpacing + * then 0028,0030 : Pixel Spacing * else 1.0 * @return X dimension of a pixel */ float File::GetXSpacing() { - float xspacing, yspacing; + float xspacing = 1.0; + float yspacing = 1.0; + int nbValues; + + // To follow David Clunie's advice, we first check ImagerPixelSpacing + + const std::string &strImagerPixelSpacing = GetEntryValue(0x0018,0x1164); + if ( strImagerPixelSpacing != GDCM_UNFOUND ) + { + if ( ( nbValues = sscanf( strImagerPixelSpacing.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 ) + xspacing = yspacing; + + if ( xspacing == 0.0 ) + xspacing = 1.0; + + return xspacing; + } + } + const std::string &strSpacing = GetEntryValue(0x0028,0x0030); if ( strSpacing == GDCM_UNFOUND ) { - gdcmVerboseMacro( "Unfound Pixel Spacing (0028,0030)" ); + gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); return 1.; } - int nbValues; - if( ( nbValues = sscanf( strSpacing.c_str(), - "%f\\%f", &yspacing, &xspacing)) != 2 ) + 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 ) - { xspacing = yspacing; - } if ( xspacing == 0.0 ) xspacing = 1.0; return xspacing; - } - // to avoid troubles with David Clunie's-like images + // to avoid troubles with David Clunie's-like images (at least one) if ( xspacing == 0. && yspacing == 0.) return 1.; 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); + nbValues = sscanf( strSpacing.c_str(), "%f \\0\\%f ", &yspacing, &xspacing); gdcmAssertMacro( nbValues == 2 ); } @@ -408,23 +495,45 @@ float File::GetXSpacing() } /** - * \brief gets the info from 0028,0030 : Pixel Spacing + * \brief gets the info from 0018,1164 : ImagerPixelSpacing + * then from 0028,0030 : Pixel Spacing * else 1.0 * @return Y dimension of a pixel */ float File::GetYSpacing() { float yspacing = 1.; - std::string strSpacing = GetEntryValue(0x0028,0x0030); - + int nbValues; + // To follow David Clunie's advice, we first check ImagerPixelSpacing + + const std::string &strImagerPixelSpacing = GetEntryValue(0x0018,0x1164); + if ( strImagerPixelSpacing != GDCM_UNFOUND ) + { + nbValues = sscanf( strImagerPixelSpacing.c_str(), "%f", &yspacing); + + // if sscanf cannot read any float value, it won't affect yspacing + if ( nbValues == 0 ) + yspacing = 1.0; + + if ( yspacing == 0.0 ) + yspacing = 1.0; + + return yspacing; + } + + std::string strSpacing = GetEntryValue(0x0028,0x0030); 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); + nbValues = sscanf( strSpacing.c_str(), "%f", &yspacing); + + // if no values, yspacing is set to 1.0 + if ( nbValues == 0 ) + yspacing = 1.0; if ( yspacing == 0.0 ) yspacing = 1.0; @@ -440,25 +549,25 @@ 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 volumes + // 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 @@ -487,16 +596,16 @@ float File::GetXOrigin() if ( strImPos == GDCM_UNFOUND ) { - gdcmVerboseMacro( "Unfound Image Position Patient (0020,0032)"); + gdcmWarningMacro( "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)"); + gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); return 0.; } } - if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 ) + if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3 ) { return 0.; } @@ -517,16 +626,16 @@ float File::GetYOrigin() if ( strImPos == GDCM_UNFOUND) { - gdcmVerboseMacro( "Unfound Image Position Patient (0020,0032)"); + gdcmWarningMacro( "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)"); + gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); return 0.; } } - if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 ) + if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3 ) { return 0.; } @@ -549,9 +658,9 @@ float File::GetZOrigin() if ( strImPos != GDCM_UNFOUND ) { - if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) + 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 @@ -563,10 +672,10 @@ float File::GetZOrigin() strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images if ( strImPos != GDCM_UNFOUND ) { - if( sscanf( strImPos.c_str(), - "%f\\%f\\%f", &xImPos, &yImPos, &zImPos ) != 3 ) + 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 @@ -575,12 +684,13 @@ float File::GetZOrigin() } } - std::string strSliceLocation = GetEntryValue(0x0020,0x1041); // for *very* old ACR-NEMA images + // for *very* old ACR-NEMA images + std::string strSliceLocation = GetEntryValue(0x0020,0x1041); if ( strSliceLocation != GDCM_UNFOUND ) { - if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1) + 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 @@ -588,14 +698,14 @@ 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) + 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 @@ -603,7 +713,7 @@ float File::GetZOrigin() return zImPos; } } - gdcmVerboseMacro( "Unfound Location (0020,0050)"); + gdcmWarningMacro( "Unfound Location (0020,0050)"); return 0.; // Hopeless } @@ -611,7 +721,7 @@ float File::GetZOrigin() /** * \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 + * @param iop adress of the (6)float array to receive values * @return cosines of image orientation patient */ void File::GetImageOrientationPatient( float iop[6] ) @@ -623,27 +733,27 @@ void File::GetImageOrientationPatient( float iop[6] ) // 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", + 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." ); + gdcmWarningMacro( "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", + 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 (0020,0035). Less than 6 values were found." ); + gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). Less than 6 values were found." ); } } } /** * \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 ! */ @@ -652,7 +762,7 @@ 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 } @@ -661,16 +771,16 @@ int File::GetBitsStored() /** * \brief Retrieve the number of Bits Allocated - * (8, 12 -compacted ACR-NEMA files, 16, ...) + * (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 ) + if ( strSize == GDCM_UNFOUND ) { - gdcmVerboseMacro( "(0028,0100) is supposed to be mandatory"); + gdcmWarningMacro( "(0028,0100) is supposed to be mandatory"); return 0; // It's supposed to be mandatory // the caller will have to check } @@ -679,16 +789,16 @@ int File::GetBitsAllocated() /** * \brief Retrieve the high bit position. - * \warning The method defaults to 0 when information is Missing. + * \warning The method defaults to 0 when information is missing. * The responsability of checking this value is left to the caller. - * @return The high bit positin when present. 0 when Missing. + * @return The high bit position when present. 0 when missing. */ 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() ); @@ -696,16 +806,16 @@ int File::GetHighBitPosition() /** * \brief Retrieve the number of Samples Per Pixel - * (1 : gray level, 3 : RGB -1 or 3 Planes-) + * (1 : gray level, 3 : RGB/YBR -1 or 3 Planes-) * @return The encountered number of Samples Per Pixel, 1 by default. - * (Gray level Pixels) + * (we assume 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"); + 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 } @@ -722,7 +832,7 @@ 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() ); @@ -736,7 +846,7 @@ int File::GetPlanarConfiguration() int File::GetPixelSize() { // 0028 0100 US IMG Bits Allocated - // (in order no to be messed up by old RGB images) + // (in order no to be messed up by old ACR-NEMA RGB images) // if (File::GetEntryValue(0x0028,0x0100) == "24") // return 3; @@ -757,7 +867,7 @@ int File::GetPixelSize() { return 8; } - gdcmVerboseMacro( "Unknown pixel type"); + gdcmWarningMacro( "Unknown pixel type"); return 0; } @@ -772,7 +882,8 @@ 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 " + * + Planar Configuration = 0 * @return 0S if nothing found. NOT USABLE file. The caller has to check */ std::string File::GetPixelType() @@ -780,7 +891,7 @@ 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 } @@ -803,7 +914,7 @@ 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" ) @@ -818,20 +929,22 @@ std::string File::GetPixelType() } /** - * \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. + * \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 + * (NO transformation is performed on the pixels to make then >0) * @return True when signed, false when UNsigned */ bool File::IsSignedPixelData() { - std::string strSize = GetEntryValue( 0x0028, 0x0103 ); - if ( strSize == GDCM_UNFOUND ) + std::string strSign = GetEntryValue( 0x0028, 0x0103 ); + if ( strSign == GDCM_UNFOUND ) { - gdcmVerboseMacro( "(0028,0103) is supposed to be mandatory"); + gdcmWarningMacro( "(0028,0103) is supposed to be mandatory"); return false; } - int sign = atoi( strSize.c_str() ); + int sign = atoi( strSign.c_str() ); if ( sign == 0 ) { return false; @@ -840,8 +953,8 @@ bool File::IsSignedPixelData() } /** - * \brief Check whether this a monochrome picture or not by accessing - * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). + * \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. */ bool File::IsMonochrome() @@ -854,7 +967,26 @@ bool File::IsMonochrome() } if ( PhotometricInterp == GDCM_UNFOUND ) { - gdcmVerboseMacro( "Not found : Photometric Interpretation (0028,0004)"); + gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)"); + } + return false; +} + +/** + * \brief Check whether this a MONOCHROME1 picture (high values = dark) + * or not using "Photometric Interpretation" tag (0x0028,0x0004). + * @return true when "MONOCHROME1" . False otherwise. + */ +bool File::IsMonochrome1() +{ + const std::string &PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") ) + { + return true; + } + if ( PhotometricInterp == GDCM_UNFOUND ) + { + gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)"); } return false; } @@ -873,7 +1005,7 @@ bool File::IsPaletteColor() } if ( PhotometricInterp == GDCM_UNFOUND ) { - gdcmVerboseMacro( "Not found : Palette color (0028,0004)"); + gdcmWarningMacro( "Not found : Palette color (0028,0004)"); } return false; } @@ -892,7 +1024,7 @@ bool File::IsYBRFull() } if ( PhotometricInterp == GDCM_UNFOUND ) { - gdcmVerboseMacro( "Not found : YBR Full (0028,0004)"); + gdcmWarningMacro( "Not found : YBR Full (0028,0004)"); } return false; } @@ -987,10 +1119,10 @@ float File::GetRescaleIntercept() const std::string &strRescInter = GetEntryValue(0x0028,0x1052); if ( strRescInter != GDCM_UNFOUND ) { - if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 ) + if ( sscanf( strRescInter.c_str(), "%f ", &resInter) != 1 ) { // bug in the element 0x0028,0x1052 - gdcmVerboseMacro( "Rescale Intercept (0028,1052) is empty." ); + gdcmWarningMacro( "Rescale Intercept (0028,1052) is empty." ); } } @@ -1008,10 +1140,10 @@ float File::GetRescaleSlope() std::string strRescSlope = GetEntryValue(0x0028,0x1053); if ( strRescSlope != GDCM_UNFOUND ) { - if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1) + if ( sscanf( strRescSlope.c_str(), "%f ", &resSlope) != 1 ) { // bug in the element 0x0028,0x1053 - gdcmVerboseMacro( "Rescale Slope (0028,1053) is empty."); + gdcmWarningMacro( "Rescale Slope (0028,1053) is empty."); } } @@ -1023,7 +1155,7 @@ float File::GetRescaleSlope() * 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) + * @return 1 if Gray level, 3 if Color (RGB, YBR, *or PALETTE COLOR*) */ int File::GetNumberOfScalarComponents() { @@ -1095,18 +1227,15 @@ int File::GetNumberOfScalarComponentsRaw() */ 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; } } @@ -1120,50 +1249,128 @@ 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 anonymize a File (removes Patient's personal info) - * (read the code to see which ones ...) + * \brief Adds the characteristics of a new element we want to anonymize + * @param group Group number of the target tag. + * @param elem Element number of the target tag. + * @param value new value (string) to substitute with */ -bool File::AnonymizeFile() +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() { - // If exist, replace by spaces - SetValEntry (" ",0x0010, 0x2154); // Telephone - SetValEntry (" ",0x0010, 0x1040); // Adress - SetValEntry (" ",0x0010, 0x0020); // Patient ID + 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); - 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 ( d == NULL) + continue; + + if ( dynamic_cast(d) + || dynamic_cast(d) ) + continue; + + offset = d->GetOffset(); + lgth = d->GetLength(); + if (valLgth < lgth) { - InsertValEntry(studyInstanceUID, 0x0010, 0x0010); + spaces = new std::string( lgth-valLgth, ' '); + (*it).Value = (*it).Value + *spaces; + delete spaces; } - else + fp->seekp( offset, std::ios::beg ); + fp->write( (*it).Value.c_str(), lgth ); + + } + fp->close(); + delete fp; +} + +/** + * \brief anonymize a File (remove 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 ?) { - 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; - // Just for fun :-( - // (if any) remove or replace all the stuff that contains a Date + 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 @@ -1222,32 +1429,26 @@ bool File::AnonymizeFile() * (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 + * @param writetype type of the file to be written * (ACR, ExplicitVR, ImplicitVR) */ -bool File::Write(std::string fileName, FileType filetype) +bool File::Write(std::string fileName, FileType writetype) { 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()); + gdcmWarningMacro("Failed to open (write) File: " << fileName.c_str()); return false; } // Entry : 0002|0000 = group length -> recalculated - ValEntry *e0002 = GetValEntry(0x0002,0x0000); - if( e0002 ) + ValEntry*e0000 = GetValEntry(0x0002,0x0000); + if ( e0000 ) { std::ostringstream sLen; - sLen << ComputeGroup0002Length(filetype); - e0002->SetValue(sLen.str()); - } - - // Bits Allocated - if ( GetEntryValue(0x0028,0x0100) == "12") - { - SetValEntry("16", 0x0028,0x0100); + sLen << ComputeGroup0002Length(writetype); + e0000->SetValue(sLen.str()); } int i_lgPix = GetEntryLength(GrPixel, NumPixel); @@ -1259,81 +1460,7 @@ bool File::Write(std::string fileName, FileType filetype) 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 -*/ + Document::WriteContent(fp, writetype); fp->close(); delete fp; @@ -1343,81 +1470,7 @@ bool File::Write(std::string fileName, FileType filetype) //----------------------------------------------------------------------------- // Protected -/** - * \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... - */ -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(); - std::string uidMedia = uid; - std::string uidInst = uid; - std::string uidClass = Util::CreateUniqueUID(); - 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 } - }; - - // 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]; - } -} //----------------------------------------------------------------------------- // Private @@ -1457,7 +1510,7 @@ void File::ComputeRLEInfo() // - 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)) ) + 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. @@ -1469,7 +1522,7 @@ 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]; @@ -1478,9 +1531,9 @@ void File::ComputeRLEInfo() rleSegmentOffsetTable[k] = ReadInt32(); } - // Deduce from both the RLE Header and the frameLength the - // fragment length, and again store this info in a - // RLEFramesInfo. + // Deduce from both RLE Header and frameLength + // the fragment length, and again store this info + // in a RLEFramesInfo. long rleSegmentLength[15]; // skipping (not reading) RLE Segments if ( nbRleSegments > 1) @@ -1508,11 +1561,11 @@ void File::ComputeRLEInfo() RLEInfo->AddFrame(newFrame); } - // Make sure that at the end of the item we encounter a 'Sequence - // Delimiter Item': + // Make sure that we encounter a 'Sequence Delimiter Item' + // at the end of the 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"); } } @@ -1536,7 +1589,7 @@ void File::ComputeJPEGFragmentInfo() // Loop on the fragments[s] and store the parsed information in a // JPEGInfo. long fragmentLength; - while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) ) + while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) != 0 ) { long fragmentOffset = Fp->tellg(); @@ -1549,53 +1602,53 @@ void File::ComputeJPEGFragmentInfo() SkipBytes(fragmentLength); } - // Make sure that at the end of the item we encounter a 'Sequence - // Delimiter Item': + // Make sure that we encounter a 'Sequence Delimiter Item' + // at the end of the 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"); } } /** * \brief Assuming the internal file pointer \ref Document::Fp * is placed at the beginning of a tag check whether this - * tag is (TestGroup, TestElement). + * tag is (TestGroup, TestElem). * \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 + * (TestGroup, TestElem) 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. + * @param testGroup The expected group of the tag. + * @param testElem The expected Element of the tag. * @return True on success, false otherwise. */ -bool File::ReadTag(uint16_t testGroup, uint16_t testElement) +bool File::ReadTag(uint16_t testGroup, uint16_t testElem) { 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; + uint16_t itemTagElem; try { - itemTagGroup = ReadInt16(); - itemTagElement = ReadInt16(); + itemTagGroup = ReadInt16(); + itemTagElem = ReadInt16(); } catch ( FormatError e ) { //std::cerr << e << std::endl; return false; } - if ( itemTagGroup != testGroup || itemTagElement != testElement ) + if ( itemTagGroup != testGroup || itemTagElem != testElem ) { - gdcmVerboseMacro( "Wrong Item Tag found:" + gdcmWarningMacro( "Wrong Item Tag found:" << " We should have found tag (" - << std::hex << testGroup << "," << testElement << ")" << std::endl + << std::hex << testGroup << "," << testElem << ")" << std::endl << " but instead we encountered tag (" - << std::hex << itemTagGroup << "," << itemTagElement << ")" + << std::hex << itemTagGroup << "," << itemTagElem << ")" << " at address: " << " 0x(" << (unsigned int)currentPosition << ")" ) ; Fp->seekg(positionOnEntry, std::ios::beg); @@ -1614,15 +1667,15 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElement) * 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. + * @param testGroup The expected Group of the tag. + * @param testElem 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) +uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElem) { - if ( !ReadTag(testGroup, testElement) ) + if ( !ReadTag(testGroup, testElem) ) { return 0; } @@ -1631,7 +1684,7 @@ 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); } @@ -1663,7 +1716,7 @@ 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