X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=3fc1414adf560767ec1e8ec77e98bc0a5c81d16f;hb=34eec700805c1b9795aac2bfdc6fc84268517df9;hp=c1381c8621f169d66cc59927f4722cfa6b8607fa;hpb=3f99e798955f65c1b906ad65016d1b49bde25ef8;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index c1381c86..3fc1414a 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2005/02/17 11:02:47 $ - Version: $Revision: 1.225 $ + Date: $Date: 2005/06/03 16:08:16 $ + Version: $Revision: 1.241 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -46,12 +46,25 @@ namespace gdcm { //----------------------------------------------------------------------------- // Constructor / Destructor + +/** + * \brief Constructor used when we want to generate dicom files from scratch + */ +File::File(): + Document() +{ + RLEInfo = new RLEFramesInfo; + JPEGInfo = new JPEGFragmentsInfo; + GrPixel = 0x7fe0; + NumPixel = 0x0010; +} + /** * \brief Constructor * @param filename name of the file whose header we want to analyze */ File::File( std::string const &filename ) - :Document( filename ) + :Document(filename) { RLEInfo = new RLEFramesInfo; JPEGInfo = new JPEGFragmentsInfo; @@ -104,7 +117,7 @@ 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(); @@ -145,16 +158,6 @@ File::File( std::string const &filename ) } } -/** - * \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. @@ -169,6 +172,8 @@ File::~File () //----------------------------------------------------------------------------- // Public + + /** * \brief This predicate, based on hopefully reasonable heuristics, * decides whether or not the current File was properly parsed @@ -187,25 +192,35 @@ 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 } if ( !GetDocEntry(0x0028, 0x0100) ) { + gdcmWarningMacro("Bits Allocated (0028|0100) not found"); return false; // "Bits Allocated" } if ( !GetDocEntry(0x0028, 0x0101) ) { + gdcmWarningMacro("Bits Stored (0028|0101) not found"); return false; // "Bits Stored" } if ( !GetDocEntry(0x0028, 0x0102) ) { + gdcmWarningMacro("Hight Bit (0028|0102) not found"); return false; // "High Bit" } if ( !GetDocEntry(0x0028, 0x0103) ) { + gdcmWarningMacro("Pixel Representation (0028|0103) not found"); return false; // "Pixel Representation" i.e. 'Sign' } - + if ( !GetDocEntry(GrPixel, NumPixel) ) + { + gdcmWarningMacro("Pixel Dicom Element " << std::hex << + GrPixel << "|" << NumPixel << "not found"); + return false; // Pixel Dicom Element not found :-( + } return true; } @@ -263,10 +278,14 @@ ModalityType File::GetModality() 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("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; @@ -355,6 +374,7 @@ int File::GetZSize() /** * \brief gets the info from 0028,0030 : Pixel Spacing + * (first in 0018,1164 : ImagerPixelSpacing) * else 1.0 * @return X dimension of a pixel */ @@ -362,6 +382,32 @@ float File::GetXSpacing() { float xspacing = 1.0; float yspacing = 1.0; + int nbValues; + + // To follow David Clunie's advice, we first check ImagerPixelSpacing + // (never saw any image with that field :-( + + 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 ) @@ -370,9 +416,8 @@ float File::GetXSpacing() return 1.; } - int nbValues; if( ( nbValues = sscanf( strSpacing.c_str(), - "%f\\%f", &yspacing, &xspacing)) != 2 ) + "%f \\%f ", &yspacing, &xspacing)) != 2 ) { // if no values, xspacing is set to 1.0 if( nbValues == 0 ) @@ -396,7 +441,7 @@ float File::GetXSpacing() { 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 ); } @@ -405,14 +450,33 @@ float File::GetXSpacing() /** * \brief gets the info from 0028,0030 : Pixel Spacing + * (first in 0018,1164 : ImagerPixelSpacing) * 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 + // (never saw any image with that field :-( + + 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 ) { gdcmWarningMacro("Unfound Pixel Spacing (0028,0030)"); @@ -420,9 +484,9 @@ float File::GetYSpacing() } // if sscanf cannot read any float value, it won't affect yspacing - int nbValues = sscanf( strSpacing.c_str(), "%f", &yspacing); + nbValues = sscanf( strSpacing.c_str(), "%f", &yspacing); - // if no values, xspacing is set to 1.0 + // if no values, yspacing is set to 1.0 if( nbValues == 0 ) yspacing = 1.0; @@ -496,7 +560,7 @@ float File::GetXOrigin() } } - 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.; } @@ -526,7 +590,7 @@ float File::GetYOrigin() } } - 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.; } @@ -549,7 +613,7 @@ 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) { gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)"); return 0.; // bug in the element 0x0020,0x0032 @@ -564,7 +628,7 @@ float File::GetZOrigin() if ( strImPos != GDCM_UNFOUND ) { if( sscanf( strImPos.c_str(), - "%f\\%f\\%f", &xImPos, &yImPos, &zImPos ) != 3 ) + "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos ) != 3 ) { gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)"); return 0.; // bug in the element 0x0020,0x0032 @@ -578,7 +642,7 @@ float File::GetZOrigin() std::string strSliceLocation = GetEntryValue(0x0020,0x1041); // for *very* old ACR-NEMA images if ( strSliceLocation != GDCM_UNFOUND ) { - if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1) + if( sscanf( strSliceLocation.c_str(), "%f ", &zImPos) != 1) { gdcmWarningMacro( "Wrong Slice Location (0020,1041)"); return 0.; // bug in the element 0x0020,0x1041 @@ -593,7 +657,7 @@ float File::GetZOrigin() 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) { gdcmWarningMacro( "Wrong Location (0020,0050)"); return 0.; // bug in the element 0x0020,0x0050 @@ -623,7 +687,7 @@ 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 ) { gdcmWarningMacro( "Wrong Image Orientation Patient (0020,0037). Less than 6 values were found." ); @@ -633,7 +697,7 @@ void File::GetImageOrientationPatient( float iop[6] ) // 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 ) { gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). Less than 6 values were found." ); @@ -668,7 +732,7 @@ int File::GetBitsStored() int File::GetBitsAllocated() { std::string strSize = GetEntryValue(0x0028,0x0100); - if ( strSize == GDCM_UNFOUND ) + if ( strSize == GDCM_UNFOUND ) { gdcmWarningMacro( "(0028,0100) is supposed to be mandatory"); return 0; // It's supposed to be mandatory @@ -818,20 +882,21 @@ 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. + * \brief Check whether the pixels are signed (1) or UNsigned (0) data. + * \warning The method defaults to false (UNsigned) when tag 0028|0103 + * is missing. * The responsability of checking this value is left to the caller. * @return True when signed, false when UNsigned */ bool File::IsSignedPixelData() { - std::string strSize = GetEntryValue( 0x0028, 0x0103 ); - if ( strSize == GDCM_UNFOUND ) + std::string strSign = GetEntryValue( 0x0028, 0x0103 ); + if ( strSign == GDCM_UNFOUND ) { 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; @@ -1006,7 +1071,7 @@ 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 gdcmWarningMacro( "Rescale Intercept (0028,1052) is empty." ); @@ -1027,7 +1092,7 @@ 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 gdcmWarningMacro( "Rescale Slope (0028,1053) is empty."); @@ -1171,12 +1236,7 @@ void File::AddAnonymizeElement (uint16_t group, uint16_t elem, void File::AnonymizeNoLoad() { 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 ? - - + std::ios::in | std::ios::out | std::ios::binary); gdcm::DocEntry *d; uint32_t offset; uint32_t lgth; @@ -1342,12 +1402,6 @@ bool File::Write(std::string fileName, FileType writetype) e0000->SetValue(sLen.str()); } - // Bits Allocated - if ( GetEntryValue(0x0028,0x0100) == "12") - { - SetValEntry("16", 0x0028,0x0100); - } - int i_lgPix = GetEntryLength(GrPixel, NumPixel); if (i_lgPix != -2) { @@ -1357,48 +1411,6 @@ bool File::Write(std::string fileName, FileType writetype) 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, writetype); fp->close(); @@ -1409,90 +1421,7 @@ bool File::Write(std::string fileName, FileType writetype) //----------------------------------------------------------------------------- // 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 Secondary Capture image... - */ -void File::InitializeDefaultFile() -{ - 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(); - - // Meta Element Group Length - InsertValEntry("146 ", 0x0002, 0x0000); - // Media Storage SOP Class UID (Secondary Capture Image Storage) - InsertValEntry("1.2.840.10008.5.1.4.1.1.7", 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); -} + //----------------------------------------------------------------------------- // Private @@ -1532,7 +1461,7 @@ 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. @@ -1611,7 +1540,7 @@ 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();