X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=4ccb1e7ae0b52a14856c7b130a601333be791600;hb=ea7eafb27b49a3d467d3d752af40db6e94ebdd13;hp=88986f539279d14b3a622de674fde247a40d9515;hpb=6a7c2fbcb5bfc240a3b9875ad4836f5dc058e069;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 88986f53..4ccb1e7a 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2005/10/20 15:24:09 $ - Version: $Revision: 1.284 $ + Date: $Date: 2006/04/11 16:03:26 $ + Version: $Revision: 1.318 $ 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 @@ -118,13 +118,14 @@ File::File(): GrPixel = 0x7fe0; // to avoid further troubles NumPixel = 0x0010; BasicOffsetTableItemValue = 0; + FourthDimensionLocation = TagKey(0,0); } /** * \brief Canonical destructor. */ -File::~File () +File::~File() { if ( RLEInfo ) delete RLEInfo; @@ -155,7 +156,6 @@ 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 @@ -216,6 +216,11 @@ bool File::DoTheLoadingJob( ) // The changed DictEntry will have // - a correct PixelVR OB or OW) // - the name to "Pixel Data" + + //==>Take it easy! + //==> Just change the VR ! + +/* DataEntry *oldEntry = dynamic_cast(entry); if (oldEntry) { @@ -229,23 +234,38 @@ bool File::DoTheLoadingJob( ) // Change only made if usefull if ( PixelVR != oldEntry->GetVR() ) - { - DictEntry* newDict = DictEntry::New(GrPixel,NumPixel, - PixelVR,"1","Pixel Data"); - - DataEntry *newEntry = new DataEntry(newDict); - newDict->Delete(); - newEntry->Copy(entry); - newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea()); - oldEntry->SetSelfArea(false); - - RemoveEntry(oldEntry); - AddEntry(newEntry); + { + //DictEntry* newDict = DictEntry::New(GrPixel,NumPixel, + // PixelVR,"1","Pixel Data"); + //DataEntry *newEntry = DataEntry::New(newDict); + //newDict->Delete(); + //newEntry->Copy(entry); + //newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea()); + //oldEntry->SetSelfArea(false); + + //RemoveEntry(oldEntry); + //AddEntry(newEntry); + //newEntry->Delete(); + } } +*/ + VRKey PixelVR; + // 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB) + // more than 8 (i.e 12, 16) is a 'O Words' + if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 ) + PixelVR = "OB"; + else + PixelVR = "OW"; + // Change only made if usefull + if ( PixelVR != entry->GetVR() ) + { + entry->SetVR(PixelVR); + } } return true; } + /** * \brief This predicate, based on hopefully reasonable heuristics, * decides whether or not the current File was properly parsed @@ -450,6 +470,34 @@ int File::GetZSize() return 1; } +/** + * \brief Retrieve the -unnormalized- number of 'times' of '4D image'. + * User has to tell gdcm the location of this '4th Dimension component' + * using SetFourthDimensionLocation() method before. + * \warning The defaulted value is 1. + * @return The encountered size when found, 1 by default + * (The file doesn't contain a '4D image'.). + */ +int File::GetTSize() +{ + if (FourthDimensionLocation == TagKey(0,0) )// 4D location is not set : not a 4D object + return 1; + + DataEntry *entry = GetDataEntry(FourthDimensionLocation.GetGroup(), + FourthDimensionLocation.GetElement() ); + if( !entry ) + { + gdcmWarningMacro( " FourthDimensionLocation not found at : " << + std::hex << FourthDimensionLocation.GetGroup() + << "|" << FourthDimensionLocation.GetElement()); + return 1; + } + else + { + return (int)entry->GetValue(0); + } +} + /** * \brief gets the info from 0018,1164 : ImagerPixelSpacing * then 0028,0030 : Pixel Spacing @@ -467,9 +515,14 @@ float File::GetXSpacing() if( entry ) { 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); @@ -483,32 +536,17 @@ float File::GetXSpacing() gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" ); } -/* const std::string &strImagerPixelSpacing = GetEntryString(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; - }*/ - entry = GetDataEntry(0x0028,0x0030); 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); @@ -521,42 +559,6 @@ float File::GetXSpacing() { gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); } - -/* const std::string &strSpacing = GetEntryString(0x0028,0x0030); - if ( strSpacing == GDCM_UNFOUND ) - { - gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); - return 1.; - } - - 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 (at least one) -/* if ( xspacing == 0.0 && yspacing == 0.0) - return 1.0; - - if ( xspacing == 0.0) - { - 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); - gdcmAssertMacro( nbValues == 2 ); - } -*/ return xspacing; } @@ -584,20 +586,6 @@ float File::GetYSpacing() { gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" ); } -/* const std::string &strImagerPixelSpacing = GetEntryString(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; - }*/ entry = GetDataEntry(0x0028,0x0030); if( entry ) @@ -612,22 +600,6 @@ float File::GetYSpacing() { gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); } -/* std::string strSpacing = GetEntryString(0x0028,0x0030); - if ( strSpacing == GDCM_UNFOUND ) - { - gdcmWarningMacro("Unfound Pixel Spacing (0028,0030)"); - return 1.; - } - - // if sscanf cannot read any float value, it won't affect 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;*/ return yspacing; } @@ -636,18 +608,17 @@ 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; @@ -675,7 +646,6 @@ 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 ) { @@ -688,32 +658,22 @@ float File::GetZSpacing() else gdcmWarningMacro("Unfound Slice Thickness (0018,0050)"); - return zspacing; - -/* const std::string &strSpacingBSlices = GetEntryString(0x0018,0x0088); - if ( strSpacingBSlices == GDCM_UNFOUND ) + // if no 'Spacing Between Slices' is found, + // we assume slices join together + // (no overlapping, no interslice gap) + entry = GetDataEntry(0x3004,0x000c); + if( entry ) { - gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)"); - const std::string &strSliceThickness = GetEntryString(0x0018,0x0050); - if ( strSliceThickness == GDCM_UNFOUND ) - { - gdcmWarningMacro("Unfound Slice Thickness (0018,0050)"); - return 1.0; - } - else - { - // 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 - return (float)atof( strSliceThickness.c_str() ); - } + 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; } - - float zsp = (float)atof( strSpacingBSlices.c_str()); - if (zsp == 0.0) // last change not to break further computations ... - zsp = 1.0; - return zsp;*/ + + return zspacing; } /** @@ -737,27 +697,14 @@ float File::GetXOrigin() } if( entry->GetValueCount() == 3 ) - return (float)entry->GetValue(0); - return 0.0f; - -/* std::string strImPos = GetEntryString(0x0020,0x0032); - if ( strImPos == GDCM_UNFOUND ) { - gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); - strImPos = GetEntryString(0x0020,0x0030); // For ACR-NEMA images - if ( strImPos == GDCM_UNFOUND ) + if (!entry->IsValueCountValid() ) { - gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); - return 0.0; + gdcmErrorMacro( "Invalid Value Count" ); } + return (float)entry->GetValue(0); } - - if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3 ) - { - return 0.0; - } - - return xImPos;*/ + return 0.0f; } /** @@ -781,28 +728,14 @@ float File::GetYOrigin() } if( entry->GetValueCount() == 3 ) - return (float)entry->GetValue(1); - return 0.0f; -/* float xImPos, yImPos, zImPos; - std::string strImPos = GetEntryString(0x0020,0x0032); - - if ( strImPos == GDCM_UNFOUND) { - gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); - strImPos = GetEntryString(0x0020,0x0030); // For ACR-NEMA images - if ( strImPos == GDCM_UNFOUND ) + if (!entry->IsValueCountValid() ) { - gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); - return 0.; - } - } - - if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3 ) - { - return 0.; + gdcmErrorMacro( "Invalid Value Count" ); + } + return (float)entry->GetValue(1); } - - return yImPos;*/ + return 0.0f; } /** @@ -819,113 +752,83 @@ float File::GetZOrigin() if( entry ) { if( entry->GetValueCount() == 3 ) - return (float)entry->GetValue(0); + { + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } + return (float)entry->GetValue(2); + } gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)"); return 0.0f; } -/* float xImPos, yImPos, zImPos; - std::string strImPos = GetEntryString(0x0020,0x0032); - - if ( strImPos != GDCM_UNFOUND ) - { - 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 - } - else - { - return zImPos; - } - }*/ entry = GetDataEntry(0x0020,0x0030); if( entry ) { if( entry->GetValueCount() == 3 ) - return (float)entry->GetValue(0); + { + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } + return (float)entry->GetValue(2); + } gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)"); return 0.0f; } -/* strImPos = GetEntryString(0x0020,0x0030); // For ACR-NEMA images - if ( strImPos != GDCM_UNFOUND ) - { - if ( sscanf( strImPos.c_str(), - "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos ) != 3 ) - { - gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)"); - return 0.; // bug in the element 0x0020,0x0032 - } - else - { - return zImPos; - } - }*/ // for *very* old ACR-NEMA images entry = GetDataEntry(0x0020,0x1041); if( entry ) { if( entry->GetValueCount() == 1 ) - return (float)entry->GetValue(0); - gdcmWarningMacro( "Wrong Slice Location (0020,1041)"); - return 0.0f; - } -/* std::string strSliceLocation = GetEntryString(0x0020,0x1041); - if ( strSliceLocation != GDCM_UNFOUND ) - { - if ( sscanf( strSliceLocation.c_str(), "%f ", &zImPos) != 1) - { - gdcmWarningMacro( "Wrong Slice Location (0020,1041)"); - return 0.; // bug in the element 0x0020,0x1041 - } - else { - return zImPos; + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } + return (float)entry->GetValue(0); // VM=1 ! } + gdcmWarningMacro( "Wrong Slice Location (0020,1041)"); + return 0.0f; } - gdcmWarningMacro( "Unfound Slice Location (0020,1041)");*/ entry = GetDataEntry(0x0020,0x0050); if( entry ) { - gdcmWarningMacro( "Unfound Location (0020,0050)"); if( entry->GetValueCount() == 1 ) + { + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } return (float)entry->GetValue(0); + } gdcmWarningMacro( "Wrong Location (0020,0050)"); return 0.0f; } -/* std::string strLocation = GetEntryString(0x0020,0x0050); - if ( strLocation != GDCM_UNFOUND ) - { - if ( sscanf( strLocation.c_str(), "%f ", &zImPos) != 1 ) - { - gdcmWarningMacro( "Wrong Location (0020,0050)"); - return 0.; // bug in the element 0x0020,0x0050 - } - else - { - return zImPos; - } - } - gdcmWarningMacro( "Unfound Location (0020,0050)");*/ - return 0.; // Hopeless } /** * \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.; + iop[0] = iop[4] = 1.; + iop[1] = iop[2] = iop[3] = iop[5] = 0.; // 0020 0037 DS REL Image Orientation (Patient) if ( (strImOriPat = GetEntryString(0x0020,0x0037)) != GDCM_UNFOUND ) @@ -937,6 +840,7 @@ bool File::GetImageOrientationPatient( float iop[6] ) << " Less than 6 values were found." ); return false; } + return true; } //For ACR-NEMA // 0020 0035 DS REL Image Orientation (RET) @@ -949,12 +853,11 @@ bool File::GetImageOrientationPatient( float iop[6] ) << "Less than 6 values were found." ); return false; } + return true; } - return true; + return false; } - - /** * \brief Retrieve the number of Bits Stored (actually used) * (as opposed to number of Bits Allocated) @@ -966,19 +869,10 @@ 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); - -/* std::string strSize = GetEntryString( 0x0028, 0x0101 ); - if ( strSize == GDCM_UNFOUND ) - { - gdcmWarningMacro("(0028,0101) is supposed to be mandatory"); - return 0; // It's supposed to be mandatory - // the caller will have to check - } - return atoi( strSize.c_str() );*/ } /** @@ -992,19 +886,10 @@ 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); - -/* std::string strSize = GetEntryString(0x0028,0x0100); - if ( strSize == GDCM_UNFOUND ) - { - gdcmWarningMacro( "(0028,0100) is supposed to be mandatory"); - return 0; // It's supposed to be mandatory - // the caller will have to check - } - return atoi( strSize.c_str() );*/ } /** @@ -1018,18 +903,10 @@ 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); - -/* std::string strSize = GetEntryString( 0x0028, 0x0102 ); - if ( strSize == GDCM_UNFOUND ) - { - gdcmWarningMacro( "(0028,0102) is supposed to be mandatory"); - return 0; - } - return atoi( strSize.c_str() );*/ } /** @@ -1043,20 +920,11 @@ 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 } return (int)entry->GetValue(0); - -/* const std::string &strSize = GetEntryString(0x0028,0x0002); - if ( strSize == GDCM_UNFOUND ) - { - gdcmWarningMacro( "(0028,0002) is supposed to be mandatory"); - return 1; // Well, it's supposed to be mandatory ... - // but sometimes it's missing : *we* assume Gray pixels - } - return atoi( strSize.c_str() );*/ } /** @@ -1069,18 +937,9 @@ int File::GetPlanarConfiguration() DataEntry *entry = GetDataEntry(0x0028,0x0006); if( !entry ) { - gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)"); return 0; } return (int)entry->GetValue(0); - -/* std::string strSize = GetEntryString(0x0028,0x0006); - if ( strSize == GDCM_UNFOUND ) - { - gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)"); - return 0; - } - return atoi( strSize.c_str() );*/ } /** @@ -1135,7 +994,7 @@ 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 } @@ -1163,44 +1022,6 @@ std::string File::GetPixelType() { sign = "U"; } - -/* std::string bitsAlloc = GetEntryString(0x0028, 0x0100); // Bits Allocated - if ( bitsAlloc == GDCM_UNFOUND ) - { - gdcmWarningMacro( "Missing Bits Allocated (0028,0100)"); - bitsAlloc = "16"; // default and arbitrary value, not to polute the output - } - - if ( bitsAlloc == "64" ) - { - return "FD"; - } - else if ( bitsAlloc == "12" ) - { - // It will be unpacked - bitsAlloc = "16"; - } - else if ( bitsAlloc == "24" ) - { - // (in order no to be messed up by old RGB images) - bitsAlloc = "8"; - } - - std::string sign = GetEntryString(0x0028, 0x0103);//"Pixel Representation" - - if (sign == GDCM_UNFOUND ) - { - gdcmWarningMacro( "Missing Pixel Representation (0028,0103)"); - sign = "U"; // default and arbitrary value, not to polute the output - } - else if ( sign == "0" ) - { - sign = "U"; - } - else - { - sign = "S"; - }*/ return bitsAlloc + sign; } @@ -1217,22 +1038,11 @@ 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; -/* std::string strSign = GetEntryString( 0x0028, 0x0103 ); - if ( strSign == GDCM_UNFOUND ) - { - gdcmWarningMacro( "(0028,0103) is supposed to be mandatory"); - return false; - } - int sign = atoi( strSign.c_str() ); - if ( sign == 0 ) - { - return false; - } - return true;*/ } /** @@ -1250,7 +1060,8 @@ 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; } @@ -1269,7 +1080,8 @@ 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; } @@ -1288,7 +1100,7 @@ bool File::IsPaletteColor() } if ( PhotometricInterp == GDCM_UNFOUND ) { - gdcmWarningMacro( "Not found : Palette color (0028,0004)"); + gdcmDebugMacro( "Not found : Palette color (0028,0004)"); } return false; } @@ -1307,7 +1119,7 @@ bool File::IsYBRFull() } if ( PhotometricInterp == GDCM_UNFOUND ) { - gdcmWarningMacro( "Not found : YBR Full (0028,0004)"); + gdcmDebugMacro( "Not found : YBR Full (0028,0004)"); } return false; } @@ -1393,7 +1205,7 @@ 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() { @@ -1406,24 +1218,11 @@ float File::GetRescaleIntercept() } return (float)entry->GetValue(0); -/* float resInter = 0.; - /// 0028 1052 DS IMG Rescale Intercept - const std::string &strRescInter = GetEntryString(0x0028,0x1052); - if ( strRescInter != GDCM_UNFOUND ) - { - if ( sscanf( strRescInter.c_str(), "%f ", &resInter) != 1 ) - { - // bug in the element 0x0028,0x1052 - gdcmWarningMacro( "Rescale Intercept (0028,1052) is empty." ); - } - } - - return resInter;*/ } /** *\brief gets the info from 0028,1053 : Rescale Slope - * @return Rescale Slope + * @return Rescale Slope. defaulted to 1.0 is not found or empty */ float File::GetRescaleSlope() { @@ -1431,29 +1230,16 @@ 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); -/* float resSlope = 1.; - //0028 1053 DS IMG Rescale Slope - std::string strRescSlope = GetEntryString(0x0028,0x1053); - if ( strRescSlope != GDCM_UNFOUND ) - { - if ( sscanf( strRescSlope.c_str(), "%f ", &resSlope) != 1 ) - { - // bug in the element 0x0028,0x1053 - gdcmWarningMacro( "Rescale Slope (0028,1053) is empty."); - } - } - - return resSlope;*/ } /** * \brief This function is intended to user who doesn't want * to have to manage a LUT and expects to get an RBG Pixel image - * (or a monochrome one ...) + * (or a monochrome one, if no LUT found ...) * \warning to be used with GetImagePixels() * @return 1 if Gray level, 3 if Color (RGB, YBR, *or PALETTE COLOR*) */ @@ -1534,7 +1320,7 @@ size_t File::GetPixelOffset() } else { - gdcmDebugMacro( "Big trouble : Pixel Element (" + gdcmWarningMacro( "Big trouble : Pixel Element (" << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" ); return 0; } @@ -1556,7 +1342,7 @@ size_t File::GetPixelAreaLength() } else { - gdcmDebugMacro( "Big trouble : Pixel Element (" + gdcmWarningMacro( "Big trouble : Pixel Element (" << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" ); return 0; } @@ -1762,19 +1548,18 @@ 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, "UL"); + } + } Document::WriteContent(fp, writetype); fp->close(); @@ -1847,7 +1632,7 @@ void File::ComputeRLEInfo() // Offset Table information on fragments of this current Frame. // Note that the fragment pixels themselves are not loaded // (but just skipped). - long frameOffset = Fp->tellg(); + long frameOffset = Fp->tellg(); // once per fragment uint32_t nbRleSegments = ReadInt32(); if ( nbRleSegments > 16 ) @@ -1894,7 +1679,7 @@ void File::ComputeRLEInfo() // Make sure that we encounter a 'Sequence Delimiter Item' // at the end of the item : - if ( !ReadTag(0xfffe, 0xe0dd) ) + if ( !ReadTag(0xfffe, 0xe0dd) ) // once per RLE File { gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence"); } @@ -1947,7 +1732,7 @@ void File::ComputeJPEGFragmentInfo() i++; } - long fragmentOffset = Fp->tellg(); + long fragmentOffset = Fp->tellg(); // Once per fragment // Store the collected info JPEGFragment *newFragment = new JPEGFragment; newFragment->SetOffset(fragmentOffset); @@ -1967,7 +1752,7 @@ 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. @@ -1980,8 +1765,8 @@ void File::ComputeJPEGFragmentInfo() */ bool File::ReadTag(uint16_t testGroup, uint16_t testElem) { - long positionOnEntry = Fp->tellg(); - long currentPosition = Fp->tellg(); // On debugging purposes + long positionOnEntry = Fp->tellg(); // Only when reading fragments + //long currentPosition = positionOnEntry; // On debugging purposes // Read the Item Tag group and element, and make // sure they are what we expected: @@ -2003,14 +1788,16 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElem) } 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)positionOnEntry << std::dec << ")" + ) ; Fp->seekg(positionOnEntry, std::ios::beg); return false; @@ -2037,17 +1824,21 @@ 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; } //// Then read the associated Item Length - long currentPosition = Fp->tellg(); + + // long currentPosition = Fp->tellg(); // save time // JPRx uint32_t itemLength = ReadInt32(); gdcmDebugMacro( "Basic Item Length is: " << itemLength - << " at address: " << std::hex << (unsigned int)currentPosition); +// << " at address: " << std::hex << (unsigned int)currentPosition + ); return itemLength; } @@ -2081,9 +1872,9 @@ 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] ); } @@ -2094,25 +1885,10 @@ 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' -} - -/** - * \brief Loader. (DEPRECATED : temporaryly kept 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, +/* + * \ brief Loader. (DEPRECATED : temporaryly kept 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. * @deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead */