X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=1c5bebc48f7a4571e12a4ecb82b8e37e0aa575d5;hb=98f703e9f1e8335c483a3ac7c161d6a984e3e242;hp=c8e0d9029a52d392d17de88395fbe562831634b1;hpb=e70a7e5ba954ce367c4b1bce03f6c7065cd45edf;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index c8e0d902..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: 2005/11/03 14:23:13 $ - Version: $Revision: 1.300 $ + 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 @@ -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); @@ -489,6 +492,10 @@ 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); else if( nbValue >= 2 ) @@ -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; } @@ -747,16 +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 ) @@ -764,10 +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) @@ -776,12 +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; } /** @@ -795,7 +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); @@ -812,7 +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); @@ -829,7 +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); @@ -846,7 +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 } @@ -920,7 +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 } @@ -964,7 +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; @@ -985,7 +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; } @@ -1004,7 +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; } @@ -1023,7 +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; } @@ -1042,7 +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; } @@ -1128,7 +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() { @@ -1145,7 +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() { @@ -1153,7 +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); @@ -1243,7 +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; } @@ -1265,7 +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; } @@ -1471,7 +1506,7 @@ bool File::Write(std::string fileName, FileType writetype) e0000->SetString(sLen.str()); } - // FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx + /// \todo FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx if( writetype != JPEG ) { int i_lgPix = GetEntryLength(GrPixel, NumPixel); @@ -1491,6 +1526,7 @@ bool File::Write(std::string fileName, FileType writetype) return true; } + //----------------------------------------------------------------------------- // Protected @@ -1713,7 +1749,7 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElem) { // in order not to pollute output we don't warn on 'delimitors' if (itemTagGroup != 0xfffe || testGroup != 0xfffe ) - gdcmErrorMacro( "Wrong Item Tag found:" + gdcmWarningMacro( "Wrong Item Tag found:" << " We should have found tag (" << DictEntry::TranslateToKey(testGroup,testElem) << ")" << std::endl << " but instead we encountered tag (" @@ -1793,9 +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] ); } @@ -1805,7 +1841,7 @@ void File::ReadEncapsulatedBasicOffsetTable() // These are the deprecated method that one day should be removed (after the next release) -#ifndef GDCM_LEGACY_REMOVE +//#ifndef GDCM_LEGACY_REMOVE /* * \ brief Loader. (DEPRECATED : temporaryly kept not to break the API) * @ param fileName file to be open for parsing @@ -1813,6 +1849,7 @@ void File::ReadEncapsulatedBasicOffsetTable() * 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", @@ -1823,7 +1860,8 @@ bool File::Load( std::string const &fileName ) return DoTheLoadingJob( ); } -#endif +*/ +//#endif //----------------------------------------------------------------------------- // Print