X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=1c5bebc48f7a4571e12a4ecb82b8e37e0aa575d5;hb=15cdc6738aa1efbcb1444b6cae04f24d2de977df;hp=189987accea4fe82f10ee617dc004136775a3ac2;hpb=4f189b7cd8d7aff962887245b7b30ede39b7856c;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 189987ac..1c5bebc4 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2005/10/24 16:00:48 $ - Version: $Revision: 1.290 $ + Date: $Date: 2005/12/21 14:52:12 $ + Version: $Revision: 1.313 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -19,21 +19,21 @@ // // -------------- Remember ! ---------------------------------- // -// Image Position Patient (0020,0032): +// 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 // -// Image Position (Patient) (0020,0032) VM=3 What is it used for? +// Image Position (Patient) (0020,0032) VM=3 // --> // The attribute Patient Orientation (0020,0020) from the General Image Module // is of type 2C and has the condition Required if image does not require // Image Orientation (0020,0037) and Image Position (0020,0032). // However, if the image does require the attributes // - Image Orientation (Patient) (0020,0037), VM=6 -// - Image Position Patient (0020,0032), VM=3 +// - Image Position (Patient) (0020,0032), VM=3 // then attribute Patient Orientation (0020,0020) should not be present // in the images. // @@ -65,7 +65,7 @@ // FFDR = Feet First-Decubitus Right // FFDL = Feet First-Decubitus Left -// we can also find +// we can also find (non standard!) // SEMIERECT // SUPINE @@ -155,7 +155,6 @@ bool File::Load( ) */ 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 @@ -469,9 +468,13 @@ float File::GetXSpacing() { nbValue = entry->GetValueCount(); // Can't use IsValueCountValid because of the complex heuristic. + if( nbValue !=2 ) + gdcmWarningMacro("ImagerPixelSpacing (0x0018,0x1164) " + << "has a wrong number of values :" << nbValue); + if( nbValue >= 3 ) xspacing = (float)entry->GetValue(2); - if( nbValue >= 2 ) + else if( nbValue >= 2 ) xspacing = (float)entry->GetValue(1); else xspacing = (float)entry->GetValue(0); @@ -489,9 +492,13 @@ float File::GetXSpacing() if( entry ) { nbValue = entry->GetValueCount(); + if( nbValue !=2 ) + gdcmWarningMacro("PixelSpacing (0x0018,0x0030) " + << "has a wrong number of values :" << nbValue); + if( nbValue >= 3 ) xspacing = (float)entry->GetValue(2); - if( nbValue >= 2 ) + else if( nbValue >= 2 ) xspacing = (float)entry->GetValue(1); else xspacing = (float)entry->GetValue(0); @@ -554,18 +561,18 @@ float File::GetYSpacing() * \brief gets the info from 0018,0088 : Space Between Slices * else from 0018,0050 : Slice Thickness * else 1.0 + * + * When an element is missing, we suppose slices join together + * (no overlapping, no interslice gap) but we have no way to check it ! + * For *Dicom* images, ZSpacing *should be* calculated using + * XOrigin, YOrigin, ZOrigin (of the top left image corner) + * of 2 consecutive images, and the Orientation + * Computing ZSpacing on a single image is not really meaningfull ! + * @return Z dimension of a voxel-to be */ float File::GetZSpacing() { - // ---> - // ---> Warning : - // ---> - // For *Dicom* images, ZSpacing should be calculated using - // XOrigin, YOrigin, ZOrigin (of the top left image corner) - // of 2 consecutive images, and the Orientation - // - // Computing ZSpacing on a single image is not really meaningfull ! float zspacing = 1.0f; @@ -593,7 +600,6 @@ float File::GetZSpacing() // if no 'Spacing Between Slices' is found, // we assume slices join together // (no overlapping, no interslice gap) - // if they don't, we're fucked up entry = GetDataEntry(0x0018,0x0050); if( entry ) { @@ -606,6 +612,21 @@ float File::GetZSpacing() else gdcmWarningMacro("Unfound Slice Thickness (0018,0050)"); + // if no 'Spacing Between Slices' is found, + // we assume slices join together + // (no overlapping, no interslice gap) + entry = GetDataEntry(0x3004,0x000c); + if( entry ) + { + float z1 = (float)entry->GetValue(0); + float z2 = (float)entry->GetValue(1); + zspacing = z2 - z1; // can be negative... + + if ( zspacing == 0.0 ) + zspacing = 1.0; + return zspacing; + } + return zspacing; } @@ -631,7 +652,10 @@ float File::GetXOrigin() if( entry->GetValueCount() == 3 ) { - gdcmErrorMacro( entry->IsValueCountValid() ); + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } return (float)entry->GetValue(0); } return 0.0f; @@ -659,7 +683,10 @@ float File::GetYOrigin() if( entry->GetValueCount() == 3 ) { - gdcmErrorMacro( entry->IsValueCountValid() ); + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } return (float)entry->GetValue(1); } return 0.0f; @@ -680,7 +707,10 @@ float File::GetZOrigin() { if( entry->GetValueCount() == 3 ) { - gdcmErrorMacro( entry->IsValueCountValid() ); + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } return (float)entry->GetValue(2); } gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)"); @@ -692,7 +722,10 @@ float File::GetZOrigin() { if( entry->GetValueCount() == 3 ) { - gdcmErrorMacro( entry->IsValueCountValid() ); + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } return (float)entry->GetValue(2); } gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)"); @@ -705,7 +738,10 @@ float File::GetZOrigin() { if( entry->GetValueCount() == 1 ) { - gdcmErrorMacro( entry->IsValueCountValid() ); + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } return (float)entry->GetValue(0); // VM=1 ! } gdcmWarningMacro( "Wrong Slice Location (0020,1041)"); @@ -717,7 +753,10 @@ float File::GetZOrigin() { if( entry->GetValueCount() == 1 ) { - gdcmErrorMacro( entry->IsValueCountValid() ); + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } return (float)entry->GetValue(0); } gdcmWarningMacro( "Wrong Location (0020,0050)"); @@ -729,16 +768,19 @@ float File::GetZOrigin() /** * \brief gets the info from 0020,0037 : Image Orientation Patient * or from 0020 0035 : Image Orientation (RET) + * * (needed to organize DICOM files based on their x,y,z position) - * @param iop adress of the (6)float array to receive values - * @return true when one of the tag is found - * false when nothing is found + * + * @param iop adress of the (6)float array to receive values. + * (defaulted as 1.,0.,0.,0.,1.,0. if nothing -or inconsistent stuff- + * is found. + * @return true when one of the tag -with consistent values- is found + * false when nothing or inconsistent stuff - is found */ bool 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.; // 0020 0037 DS REL Image Orientation (Patient) if ( (strImOriPat = GetEntryString(0x0020,0x0037)) != GDCM_UNFOUND ) @@ -746,10 +788,14 @@ bool File::GetImageOrientationPatient( float iop[6] ) if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ", &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) { + iop[0] = iop[4] = 1.; + iop[1] = iop[2] = iop[3] = iop[5] = 0.; gdcmWarningMacro( "Wrong Image Orientation Patient (0020,0037)." << " Less than 6 values were found." ); return false; } + else + return true; } //For ACR-NEMA // 0020 0035 DS REL Image Orientation (RET) @@ -758,12 +804,16 @@ bool File::GetImageOrientationPatient( float iop[6] ) if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ", &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) { + iop[0] = iop[4] = 1.; + iop[1] = iop[2] = iop[3] = iop[5] = 0.; gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). " << "Less than 6 values were found." ); return false; } + else + return true; } - return true; + return false; } /** @@ -777,7 +827,7 @@ int File::GetBitsStored() DataEntry *entry = GetDataEntry(0x0028,0x0101); if( !entry ) { - gdcmWarningMacro("(0028,0101) is supposed to be mandatory"); + gdcmWarningMacro("BitsStored (0028,0101) is supposed to be mandatory"); return 0; } return (int)entry->GetValue(0); @@ -794,7 +844,7 @@ int File::GetBitsAllocated() DataEntry *entry = GetDataEntry(0x0028,0x0100); if( !entry ) { - gdcmWarningMacro("(0028,0100) is supposed to be mandatory"); + gdcmWarningMacro("BitsAllocated (0028,0100) is supposed to be mandatory"); return 0; } return (int)entry->GetValue(0); @@ -811,7 +861,7 @@ int File::GetHighBitPosition() DataEntry *entry = GetDataEntry(0x0028,0x0102); if( !entry ) { - gdcmWarningMacro("(0028,0102) is supposed to be mandatory"); + gdcmWarningMacro("HighBitPosition (0028,0102) is supposed to be mandatory"); return 0; } return (int)entry->GetValue(0); @@ -828,7 +878,7 @@ int File::GetSamplesPerPixel() DataEntry *entry = GetDataEntry(0x0028,0x0002); if( !entry ) { - gdcmWarningMacro("(0028,0002) is supposed to be mandatory"); + gdcmWarningMacro("SamplesPerPixel (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 } @@ -845,7 +895,6 @@ int File::GetPlanarConfiguration() DataEntry *entry = GetDataEntry(0x0028,0x0006); if( !entry ) { - gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)"); return 0; } return (int)entry->GetValue(0); @@ -903,7 +952,7 @@ std::string File::GetPixelType() std::string bitsAlloc = GetEntryString(0x0028, 0x0100); // Bits Allocated if ( bitsAlloc == GDCM_UNFOUND ) { - gdcmWarningMacro( "Missing Bits Allocated (0028,0100)"); + gdcmWarningMacro( "Bits Allocated (0028,0100) supposed to be mandatory"); bitsAlloc = "16"; // default and arbitrary value, not to polute the output } @@ -947,7 +996,8 @@ bool File::IsSignedPixelData() DataEntry *entry = GetDataEntry(0x0028, 0x0103);//"Pixel Representation" if( !entry ) { - gdcmWarningMacro( "Missing Pixel Representation (0028,0103)"); + gdcmWarningMacro( "Pixel Representation (0028,0103) supposed to be " + << "mandatory"); return false; } return entry->GetValue(0) != 0; @@ -968,7 +1018,8 @@ bool File::IsMonochrome() } if ( PhotometricInterp == GDCM_UNFOUND ) { - gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)"); + gdcmWarningMacro( "Photometric Interpretation (0028,0004) supposed to be " + << "mandatory"); } return false; } @@ -987,7 +1038,8 @@ bool File::IsMonochrome1() } if ( PhotometricInterp == GDCM_UNFOUND ) { - gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)"); + gdcmWarningMacro( "Photometric Interpretation (0028,0004) : supposed to" + << " be mandatory! "); } return false; } @@ -1006,7 +1058,7 @@ bool File::IsPaletteColor() } if ( PhotometricInterp == GDCM_UNFOUND ) { - gdcmWarningMacro( "Not found : Palette color (0028,0004)"); + gdcmDebugMacro( "Not found : Palette color (0028,0004)"); } return false; } @@ -1025,7 +1077,7 @@ bool File::IsYBRFull() } if ( PhotometricInterp == GDCM_UNFOUND ) { - gdcmWarningMacro( "Not found : YBR Full (0028,0004)"); + gdcmDebugMacro( "Not found : YBR Full (0028,0004)"); } return false; } @@ -1111,7 +1163,7 @@ int File::GetLUTNbits() /** *\brief gets the info from 0028,1052 : Rescale Intercept - * @return Rescale Intercept + * @return Rescale Intercept. defaulted to 0.0 is not found or empty */ float File::GetRescaleIntercept() { @@ -1128,7 +1180,7 @@ float File::GetRescaleIntercept() /** *\brief gets the info from 0028,1053 : Rescale Slope - * @return Rescale Slope + * @return Rescale Slope. defaulted to 0.0 is not found or empty */ float File::GetRescaleSlope() { @@ -1136,7 +1188,7 @@ float File::GetRescaleSlope() DataEntry *entry = GetDataEntry(0x0028, 0x1053); if( !entry ) { - gdcmWarningMacro( "Missing Rescale Slope (0028,1053)"); + gdcmDebugMacro( "Missing Rescale Slope (0028,1053)"); return 1.0f; } return (float)entry->GetValue(0); @@ -1226,7 +1278,7 @@ size_t File::GetPixelOffset() } else { - gdcmDebugMacro( "Big trouble : Pixel Element (" + gdcmWarningMacro( "Big trouble : Pixel Element (" << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" ); return 0; } @@ -1248,7 +1300,7 @@ size_t File::GetPixelAreaLength() } else { - gdcmDebugMacro( "Big trouble : Pixel Element (" + gdcmWarningMacro( "Big trouble : Pixel Element (" << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" ); return 0; } @@ -1454,19 +1506,18 @@ bool File::Write(std::string fileName, FileType writetype) e0000->SetString(sLen.str()); } - // Derma?.dcm does not have it...let's remove it FIXME FIXME + /// \todo FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx if( writetype != JPEG ) - { - 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() ); - InsertEntryString(s_lgPix,GrPixel, 0x0000); - } - } - + { + 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() ); + InsertEntryString(s_lgPix,GrPixel, 0x0000); + } + } Document::WriteContent(fp, writetype); fp->close(); @@ -1475,6 +1526,7 @@ bool File::Write(std::string fileName, FileType writetype) return true; } + //----------------------------------------------------------------------------- // Protected @@ -1659,7 +1711,7 @@ void File::ComputeJPEGFragmentInfo() /** * \brief Assuming the internal file pointer \ref Document::Fp - * is placed at the beginning of a tag check whether this + * is placed at the beginning of a tag, check whether this * tag is (TestGroup, TestElem). * \warning On success the internal file pointer \ref Document::Fp * is modified to point after the tag. @@ -1694,15 +1746,17 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElem) return false; } if ( itemTagGroup != testGroup || itemTagElem != testElem ) - { - gdcmErrorMacro( "Wrong Item Tag found:" - << " We should have found tag (" - << DictEntry::TranslateToKey(testGroup,testElem) << ")" << std::endl - << " but instead we encountered tag (" - << DictEntry::TranslateToKey(itemTagGroup,itemTagElem) << ")" - << " at address: " << " 0x(" << std::hex - << (unsigned int)currentPosition << std::dec << ")" - ) ; + { + // in order not to pollute output we don't warn on 'delimitors' + if (itemTagGroup != 0xfffe || testGroup != 0xfffe ) + gdcmWarningMacro( "Wrong Item Tag found:" + << " We should have found tag (" + << DictEntry::TranslateToKey(testGroup,testElem) << ")" << std::endl + << " but instead we encountered tag (" + << DictEntry::TranslateToKey(itemTagGroup,itemTagElem) << ")" + << " at address: " << " 0x(" << std::hex + << (unsigned int)currentPosition << std::dec << ")" + ) ; Fp->seekg(positionOnEntry, std::ios::beg); return false; @@ -1729,7 +1783,9 @@ uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElem) if ( !ReadTag(testGroup, testElem) ) { - gdcmErrorMacro( "ReadTag did not succeed for (" + // Avoid polutting output + if ( testGroup != 0xfffe ) + gdcmErrorMacro( "ReadTag did not succeed for (" << DictEntry::TranslateToKey(testGroup,testElem) << ")..." ); return 0; @@ -1773,9 +1829,9 @@ void File::ReadEncapsulatedBasicOffsetTable() uint32_t val = BasicOffsetTableItemValue[i]; BasicOffsetTableItemValue[i] = ( (val<<24) | ((val<<8) & 0x00ff0000) | - ((val>>8) & 0x0000ff00) | (val>>24) ); + ( (val>>8) & 0x0000ff00) | (val>>24) ); #endif - gdcmWarningMacro( "Read one length for: " << + gdcmDebugMacro( "Read one length for: " << std::hex << BasicOffsetTableItemValue[i] ); } @@ -1785,22 +1841,7 @@ void File::ReadEncapsulatedBasicOffsetTable() // These are the deprecated method that one day should be removed (after the next release) -#ifndef GDCM_LEGACY_REMOVE -/* - * brief Constructor (DEPRECATED : temporaryly kept not to break the API) - * param filename name of the file whose header we want to analyze - * deprecated do not use any longer - */ -File::File( std::string const &filename ) - :Document( ) -{ - RLEInfo = new RLEFramesInfo; - JPEGInfo = new JPEGFragmentsInfo; - - SetFileName( filename ); - Load( ); // gdcm::Document is first Loaded, then the 'File part' -} - +//#ifndef GDCM_LEGACY_REMOVE /* * \ brief Loader. (DEPRECATED : temporaryly kept not to break the API) * @ param fileName file to be open for parsing @@ -1808,6 +1849,7 @@ File::File( std::string const &filename ) * or no tag was found. * @ deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead */ + /* bool File::Load( std::string const &fileName ) { GDCM_LEGACY_REPLACED_BODY(File::Load(std::string), "1.2", @@ -1818,7 +1860,8 @@ bool File::Load( std::string const &fileName ) return DoTheLoadingJob( ); } -#endif +*/ +//#endif //----------------------------------------------------------------------------- // Print