X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=e65e2efa9d9537086791e84b58b77ae0cb40cc32;hb=01b8a6a38ef3eb36670dada5f3abc48b09692db4;hp=688489687a36c4b69f00fd305f276f0ad6ddf474;hpb=dd8cbfc8d87e3d6b00c3bf74691ab6d4a076b29a;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 68848968..e65e2efa 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2005/10/17 14:26:44 $ - Version: $Revision: 1.275 $ + Date: $Date: 2005/10/26 06:23:37 $ + Version: $Revision: 1.297 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -92,11 +92,10 @@ #include "gdcmUtil.h" #include "gdcmDebug.h" #include "gdcmTS.h" -#include "gdcmValEntry.h" -#include "gdcmBinEntry.h" #include "gdcmSeqEntry.h" #include "gdcmRLEFramesInfo.h" #include "gdcmJPEGFragmentsInfo.h" +#include "gdcmDataEntry.h" #include #include //sscanf @@ -168,7 +167,7 @@ bool File::DoTheLoadingJob( ) // Note: this IS the right place for the code // Image Location - const std::string &imgLocation = GetEntryValue(0x0028, 0x0200); + const std::string &imgLocation = GetEntryString(0x0028, 0x0200); if ( imgLocation == GDCM_UNFOUND ) { // default value @@ -213,14 +212,14 @@ bool File::DoTheLoadingJob( ) ComputeJPEGFragmentInfo(); CloseFile(); - // Create a new BinEntry to change the DictEntry + // Create a new DataEntry to change the DictEntry // The changed DictEntry will have // - a correct PixelVR OB or OW) // - the name to "Pixel Data" - BinEntry *oldEntry = dynamic_cast(entry); + DataEntry *oldEntry = dynamic_cast(entry); if (oldEntry) { - std::string PixelVR; + 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 ) @@ -231,16 +230,18 @@ bool File::DoTheLoadingJob( ) // Change only made if usefull if ( PixelVR != oldEntry->GetVR() ) { - DictEntry* newDict = NewVirtualDictEntry(GrPixel,NumPixel, - PixelVR,"1","Pixel Data"); + DictEntry* newDict = DictEntry::New(GrPixel,NumPixel, + PixelVR,"1","Pixel Data"); - BinEntry *newEntry = new BinEntry(newDict); + 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(); } } } @@ -261,7 +262,7 @@ bool File::IsReadable() return false; } - const std::string &res = GetEntryValue(0x0028, 0x0005); + const std::string &res = GetEntryString(0x0028, 0x0005); if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) { gdcmWarningMacro("Wrong Image Dimensions" << res); @@ -318,7 +319,7 @@ bool File::IsReadable() int File::GetImageNumber() { //0020 0013 : Image Number - std::string strImNumber = GetEntryValue(0x0020,0x0013); + std::string strImNumber = GetEntryString(0x0020,0x0013); if ( strImNumber != GDCM_UNFOUND ) { return atoi( strImNumber.c_str() ); @@ -333,7 +334,7 @@ int File::GetImageNumber() ModalityType File::GetModality() { // 0008 0060 : Modality - std::string strModality = GetEntryValue(0x0008,0x0060); + std::string strModality = GetEntryString(0x0008,0x0060); if ( strModality != GDCM_UNFOUND ) { if ( strModality.find("AU") < strModality.length()) return AU; @@ -398,12 +399,10 @@ ModalityType File::GetModality() */ int File::GetXSize() { - const std::string &strSize = GetEntryValue(0x0028,0x0011); - if ( strSize == GDCM_UNFOUND ) - { - return 0; - } - return atoi( strSize.c_str() ); + DataEntry *entry = GetDataEntry(0x0028,0x0011); + if( entry ) + return (int)entry->GetValue(0); + return 0; } /** @@ -414,11 +413,10 @@ int File::GetXSize() */ int File::GetYSize() { - const std::string &strSize = GetEntryValue(0x0028,0x0010); - if ( strSize != GDCM_UNFOUND ) - { - return atoi( strSize.c_str() ); - } + DataEntry *entry = GetDataEntry(0x0028,0x0010); + if( entry ) + return (int)entry->GetValue(0); + if ( IsDicomV3() ) { return 0; @@ -442,18 +440,14 @@ int File::GetZSize() { // Both DicomV3 and ACR/Nema consider the "Number of Frames" // as the third dimension. - const std::string &strSize = GetEntryValue(0x0028,0x0008); - if ( strSize != GDCM_UNFOUND ) - { - return atoi( strSize.c_str() ); - } + DataEntry *entry = GetDataEntry(0x0028,0x0008); + if( entry ) + return (int)entry->GetValue(0); // We then consider the "Planes" entry as the third dimension - const std::string &strSize2 = GetEntryValue(0x0028,0x0012); - if ( strSize2 != GDCM_UNFOUND ) - { - return atoi( strSize2.c_str() ); - } + entry = GetDataEntry(0x0028,0x0012); + if( entry ) + return (int)entry->GetValue(0); return 1; } @@ -466,63 +460,49 @@ int File::GetZSize() float File::GetXSpacing() { float xspacing = 1.0; - float yspacing = 1.0; - int nbValues; + uint32_t nbValue; // To follow David Clunie's advice, we first check ImagerPixelSpacing - const std::string &strImagerPixelSpacing = GetEntryValue(0x0018,0x1164); - if ( strImagerPixelSpacing != GDCM_UNFOUND ) + DataEntry *entry = GetDataEntry(0x0018,0x1164); + if( entry ) { - 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; - } + nbValue = entry->GetValueCount(); + // Can't use IsValueCountValid because of the complex heuristic. + if( nbValue >= 3 ) + xspacing = (float)entry->GetValue(2); + if( nbValue >= 2 ) + xspacing = (float)entry->GetValue(1); + else + xspacing = (float)entry->GetValue(0); + + if ( xspacing == 0.0 ) + xspacing = 1.0; return xspacing; } - - const std::string &strSpacing = GetEntryValue(0x0028,0x0030); - - if ( strSpacing == GDCM_UNFOUND ) + else { - gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); - return 1.; + gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" ); } - if ( ( nbValues = sscanf( strSpacing.c_str(), - "%f \\%f ", &yspacing, &xspacing)) != 2 ) + entry = GetDataEntry(0x0028,0x0030); + if( entry ) { - // 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; + nbValue = entry->GetValueCount(); + if( nbValue >= 3 ) + xspacing = (float)entry->GetValue(2); + else if( nbValue >= 2 ) + xspacing = (float)entry->GetValue(1); + else + xspacing = (float)entry->GetValue(0); if ( xspacing == 0.0 ) xspacing = 1.0; + return xspacing; } - 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) + else { - 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 ); + gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); } return xspacing; @@ -537,40 +517,35 @@ float File::GetXSpacing() float File::GetYSpacing() { 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 ) + DataEntry *entry = GetDataEntry(0x0018,0x1164); + if( entry ) { - 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; + yspacing = (float)entry->GetValue(0); if ( yspacing == 0.0 ) - yspacing = 1.0; - - return yspacing; + yspacing = 1.0; + return yspacing; } - - std::string strSpacing = GetEntryValue(0x0028,0x0030); - if ( strSpacing == GDCM_UNFOUND ) + else { - 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); + gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" ); + } - // if no values, yspacing is set to 1.0 - if ( nbValues == 0 ) - yspacing = 1.0; + entry = GetDataEntry(0x0028,0x0030); + if( entry ) + { + yspacing = (float)entry->GetValue(0); - if ( yspacing == 0.0 ) - yspacing = 1.0; + if ( yspacing == 0.0 ) + yspacing = 1.0; + return yspacing; + } + else + { + gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); + } return yspacing; } @@ -583,6 +558,17 @@ float File::GetYSpacing() */ 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; + // Spacing Between Slices : distance between the middle of 2 slices // Slices may be : // jointives (Spacing between Slices = Slice Thickness) @@ -592,44 +578,35 @@ float File::GetZSpacing() // It only concerns the MRI guys, not people wanting to visualize volumes // If Spacing Between Slices is missing, // we suppose slices joint together + DataEntry *entry = GetDataEntry(0x0018,0x0088); + if( entry ) + { + zspacing = (float)entry->GetValue(0); - // ---> - // ---> 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 ! - - const std::string &strSpacingBSlices = GetEntryValue(0x0018,0x0088); + if ( zspacing == 0.0 ) + zspacing = 1.0; + return zspacing; + } + else + gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)"); - if ( strSpacingBSlices == GDCM_UNFOUND ) + // 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 ) { - gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)"); - const std::string &strSliceThickness = GetEntryValue(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() ); - } + zspacing = (float)entry->GetValue(0); + + if ( zspacing == 0.0 ) + zspacing = 1.0; + return zspacing; } - //else - - float zsp = (float)atof( strSpacingBSlices.c_str()); - if (zsp == 0.0) // last change not to break further computations ... - zsp = 1.0; - return zsp; + else + gdcmWarningMacro("Unfound Slice Thickness (0018,0050)"); + + return zspacing; } /** @@ -640,26 +617,27 @@ float File::GetZSpacing() */ float File::GetXOrigin() { - float xImPos, yImPos, zImPos; - std::string strImPos = GetEntryValue(0x0020,0x0032); - - if ( strImPos == GDCM_UNFOUND ) + DataEntry *entry = GetDataEntry(0x0020,0x0032); + if( !entry ) { gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); - strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images - if ( strImPos == GDCM_UNFOUND ) + entry = GetDataEntry(0x0020,0x0030); + if( !entry ) { gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); - return 0.0; + return 0.0f; } } - if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3 ) + if( entry->GetValueCount() == 3 ) { - return 0.0; + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } + return (float)entry->GetValue(0); } - - return xImPos; + return 0.0f; } /** @@ -670,26 +648,27 @@ float File::GetXOrigin() */ float File::GetYOrigin() { - float xImPos, yImPos, zImPos; - std::string strImPos = GetEntryValue(0x0020,0x0032); - - if ( strImPos == GDCM_UNFOUND) + DataEntry *entry = GetDataEntry(0x0020,0x0032); + if( !entry ) { gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); - strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images - if ( strImPos == GDCM_UNFOUND ) + entry = GetDataEntry(0x0020,0x0030); + if( !entry ) { gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); - return 0.; - } + return 0.0f; + } } - if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3 ) + if( entry->GetValueCount() == 3 ) { - return 0.; + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } + return (float)entry->GetValue(1); } - - return yImPos; + return 0.0f; } /** @@ -702,68 +681,66 @@ float File::GetYOrigin() */ float File::GetZOrigin() { - float xImPos, yImPos, zImPos; - std::string strImPos = GetEntryValue(0x0020,0x0032); - - if ( strImPos != GDCM_UNFOUND ) + DataEntry *entry = GetDataEntry(0x0020,0x0032); + if( entry ) { - if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3) + if( entry->GetValueCount() == 3 ) { - gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)"); - return 0.; // bug in the element 0x0020,0x0032 - } - else - { - return zImPos; + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } + return (float)entry->GetValue(2); } + gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)"); + return 0.0f; } - strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images - if ( strImPos != GDCM_UNFOUND ) + entry = GetDataEntry(0x0020,0x0030); + if( entry ) { - if ( sscanf( strImPos.c_str(), - "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos ) != 3 ) + if( entry->GetValueCount() == 3 ) { - gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)"); - return 0.; // bug in the element 0x0020,0x0032 - } - else - { - return zImPos; + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } + return (float)entry->GetValue(2); } + gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)"); + return 0.0f; } // for *very* old ACR-NEMA images - std::string strSliceLocation = GetEntryValue(0x0020,0x1041); - if ( strSliceLocation != GDCM_UNFOUND ) + entry = GetDataEntry(0x0020,0x1041); + if( entry ) { - if ( sscanf( strSliceLocation.c_str(), "%f ", &zImPos) != 1) + if( entry->GetValueCount() == 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)"); - std::string strLocation = GetEntryValue(0x0020,0x0050); - if ( strLocation != GDCM_UNFOUND ) + entry = GetDataEntry(0x0020,0x0050); + if( entry ) { - if ( sscanf( strLocation.c_str(), "%f ", &zImPos) != 1 ) + if( entry->GetValueCount() == 1 ) { - gdcmWarningMacro( "Wrong Location (0020,0050)"); - return 0.; // bug in the element 0x0020,0x0050 - } - else - { - return zImPos; + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } + return (float)entry->GetValue(0); } + gdcmWarningMacro( "Wrong Location (0020,0050)"); + return 0.0f; } - gdcmWarningMacro( "Unfound Location (0020,0050)"); - return 0.; // Hopeless } @@ -782,7 +759,7 @@ bool File::GetImageOrientationPatient( float iop[6] ) iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.; // 0020 0037 DS REL Image Orientation (Patient) - if ( (strImOriPat = GetEntryValue(0x0020,0x0037)) != GDCM_UNFOUND ) + if ( (strImOriPat = GetEntryString(0x0020,0x0037)) != GDCM_UNFOUND ) { if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ", &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) @@ -794,7 +771,7 @@ bool File::GetImageOrientationPatient( float iop[6] ) } //For ACR-NEMA // 0020 0035 DS REL Image Orientation (RET) - else if ( (strImOriPat = GetEntryValue(0x0020,0x0035)) != GDCM_UNFOUND ) + else if ( (strImOriPat = GetEntryString(0x0020,0x0035)) != GDCM_UNFOUND ) { if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ", &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) @@ -807,8 +784,6 @@ bool File::GetImageOrientationPatient( float iop[6] ) return true; } - - /** * \brief Retrieve the number of Bits Stored (actually used) * (as opposed to number of Bits Allocated) @@ -817,14 +792,13 @@ bool File::GetImageOrientationPatient( float iop[6] ) */ int File::GetBitsStored() { - std::string strSize = GetEntryValue( 0x0028, 0x0101 ); - if ( strSize == GDCM_UNFOUND ) + DataEntry *entry = GetDataEntry(0x0028,0x0101); + if( !entry ) { gdcmWarningMacro("(0028,0101) is supposed to be mandatory"); - return 0; // It's supposed to be mandatory - // the caller will have to check + return 0; } - return atoi( strSize.c_str() ); + return (int)entry->GetValue(0); } /** @@ -835,14 +809,13 @@ int File::GetBitsStored() */ int File::GetBitsAllocated() { - std::string strSize = GetEntryValue(0x0028,0x0100); - if ( strSize == GDCM_UNFOUND ) + DataEntry *entry = GetDataEntry(0x0028,0x0100); + if( !entry ) { - gdcmWarningMacro( "(0028,0100) is supposed to be mandatory"); - return 0; // It's supposed to be mandatory - // the caller will have to check + gdcmWarningMacro("(0028,0100) is supposed to be mandatory"); + return 0; } - return atoi( strSize.c_str() ); + return (int)entry->GetValue(0); } /** @@ -853,13 +826,13 @@ int File::GetBitsAllocated() */ int File::GetHighBitPosition() { - std::string strSize = GetEntryValue( 0x0028, 0x0102 ); - if ( strSize == GDCM_UNFOUND ) + DataEntry *entry = GetDataEntry(0x0028,0x0102); + if( !entry ) { - gdcmWarningMacro( "(0028,0102) is supposed to be mandatory"); + gdcmWarningMacro("(0028,0102) is supposed to be mandatory"); return 0; } - return atoi( strSize.c_str() ); + return (int)entry->GetValue(0); } /** @@ -870,14 +843,14 @@ int File::GetHighBitPosition() */ int File::GetSamplesPerPixel() { - const std::string &strSize = GetEntryValue(0x0028,0x0002); - if ( strSize == GDCM_UNFOUND ) + DataEntry *entry = GetDataEntry(0x0028,0x0002); + if( !entry ) { - gdcmWarningMacro( "(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 } - return atoi( strSize.c_str() ); + return (int)entry->GetValue(0); } /** @@ -887,13 +860,13 @@ int File::GetSamplesPerPixel() */ int File::GetPlanarConfiguration() { - std::string strSize = GetEntryValue(0x0028,0x0006); - if ( strSize == GDCM_UNFOUND ) + DataEntry *entry = GetDataEntry(0x0028,0x0006); + if( !entry ) { gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)"); return 0; } - return atoi( strSize.c_str() ); + return (int)entry->GetValue(0); } /** @@ -905,9 +878,7 @@ int File::GetPixelSize() { // 0028 0100 US IMG Bits Allocated // (in order no to be messed up by old ACR-NEMA RGB images) - // if (File::GetEntryValue(0x0028,0x0100) == "24") - // return 3; - assert( !(GetEntryValue(0x0028,0x0100) == "24") ); + assert( !(GetEntryString(0x0028,0x0100) == "24") ); std::string pixelType = GetPixelType(); if ( pixelType == "8U" || pixelType == "8S" ) @@ -926,7 +897,7 @@ int File::GetPixelSize() { return 8; } - gdcmWarningMacro( "Unknown pixel type"); + gdcmWarningMacro( "Unknown pixel type: " << pixelType); return 0; } @@ -947,7 +918,7 @@ int File::GetPixelSize() */ std::string File::GetPixelType() { - std::string bitsAlloc = GetEntryValue(0x0028, 0x0100); // Bits Allocated + std::string bitsAlloc = GetEntryString(0x0028, 0x0100); // Bits Allocated if ( bitsAlloc == GDCM_UNFOUND ) { gdcmWarningMacro( "Missing Bits Allocated (0028,0100)"); @@ -969,20 +940,14 @@ std::string File::GetPixelType() bitsAlloc = "8"; } - std::string sign = GetEntryValue(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" ) + std::string sign; + if( IsSignedPixelData() ) { - sign = "U"; + sign = "S"; } else { - sign = "S"; + sign = "U"; } return bitsAlloc + sign; } @@ -997,18 +962,13 @@ std::string File::GetPixelType() */ bool File::IsSignedPixelData() { - std::string strSign = GetEntryValue( 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 ) + DataEntry *entry = GetDataEntry(0x0028, 0x0103);//"Pixel Representation" + if( !entry ) { + gdcmWarningMacro( "Missing Pixel Representation (0028,0103)"); return false; } - return true; + return entry->GetValue(0) != 0; } /** @@ -1018,7 +978,7 @@ bool File::IsSignedPixelData() */ bool File::IsMonochrome() { - const std::string &PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") ) { @@ -1038,7 +998,7 @@ bool File::IsMonochrome() */ bool File::IsMonochrome1() { - const std::string &PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") ) { return true; @@ -1057,7 +1017,7 @@ bool File::IsMonochrome1() */ bool File::IsPaletteColor() { - std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); if ( PhotometricInterp == "PALETTE COLOR " ) { return true; @@ -1076,7 +1036,7 @@ bool File::IsPaletteColor() */ bool File::IsYBRFull() { - std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); if ( PhotometricInterp == "YBR_FULL" ) { return true; @@ -1150,7 +1110,7 @@ int File::GetLUTNbits() //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red // = Lookup Table Desc-Blue // Consistency already checked in GetLUTLength - std::string lutDescription = GetEntryValue(0x0028,0x1101); + std::string lutDescription = GetEntryString(0x0028,0x1101); if ( lutDescription == GDCM_UNFOUND ) { return 0; @@ -1173,19 +1133,15 @@ int File::GetLUTNbits() */ float File::GetRescaleIntercept() { - float resInter = 0.; - /// 0028 1052 DS IMG Rescale Intercept - const std::string &strRescInter = GetEntryValue(0x0028,0x1052); - if ( strRescInter != GDCM_UNFOUND ) + // 0028 1052 DS IMG Rescale Intercept + DataEntry *entry = GetDataEntry(0x0028, 0x1052); + if( !entry ) { - if ( sscanf( strRescInter.c_str(), "%f ", &resInter) != 1 ) - { - // bug in the element 0x0028,0x1052 - gdcmWarningMacro( "Rescale Intercept (0028,1052) is empty." ); - } + gdcmWarningMacro( "Missing Rescale Intercept (0028,1052)"); + return 0.0f; } + return (float)entry->GetValue(0); - return resInter; } /** @@ -1194,19 +1150,14 @@ float File::GetRescaleIntercept() */ float File::GetRescaleSlope() { - float resSlope = 1.; - //0028 1053 DS IMG Rescale Slope - std::string strRescSlope = GetEntryValue(0x0028,0x1053); - if ( strRescSlope != GDCM_UNFOUND ) + // 0028 1053 DS IMG Rescale Slope + DataEntry *entry = GetDataEntry(0x0028, 0x1053); + if( !entry ) { - if ( sscanf( strRescSlope.c_str(), "%f ", &resSlope) != 1 ) - { - // bug in the element 0x0028,0x1053 - gdcmWarningMacro( "Rescale Slope (0028,1053) is empty."); - } + gdcmWarningMacro( "Missing Rescale Slope (0028,1053)"); + return 1.0f; } - - return resSlope; + return (float)entry->GetValue(0); } /** @@ -1222,15 +1173,15 @@ int File::GetNumberOfScalarComponents() { return 3; } - + // 0028 0100 US IMG Bits Allocated // (in order no to be messed up by old RGB images) - if ( GetEntryValue(0x0028,0x0100) == "24" ) + if ( GetEntryString(0x0028,0x0100) == "24" ) { return 3; } - - std::string strPhotometricInterpretation = GetEntryValue(0x0028,0x0004); + + std::string strPhotometricInterpretation = GetEntryString(0x0028,0x0004); if ( ( strPhotometricInterpretation == "PALETTE COLOR ") ) { @@ -1270,7 +1221,7 @@ int File::GetNumberOfScalarComponentsRaw() { // 0028 0100 US IMG Bits Allocated // (in order no to be messed up by old RGB images) - if ( File::GetEntryValue(0x0028,0x0100) == "24" ) + if ( File::GetEntryString(0x0028,0x0100) == "24" ) { return 3; } @@ -1330,7 +1281,7 @@ size_t File::GetPixelAreaLength() void File::AddAnonymizeElement (uint16_t group, uint16_t elem, std::string const &value) { - Element el; + DicomElement el; el.Group = group; el.Elem = elem; el.Value = value; @@ -1384,7 +1335,7 @@ void File::AnonymizeNoLoad() /** * \brief anonymize a File (remove Patient's personal info passed with * AddAnonymizeElement() - * \note You cannot Anonymize a BinEntry (to be fixed) + * \note You cannot Anonymize a DataEntry (to be fixed) */ bool File::AnonymizeFile() { @@ -1392,22 +1343,22 @@ bool File::AnonymizeFile() if ( UserAnonymizeList.begin() == UserAnonymizeList.end() ) { // If exist, replace by spaces - SetValEntry (" ",0x0010, 0x2154); // Telephone - SetValEntry (" ",0x0010, 0x1040); // Adress - SetValEntry (" ",0x0010, 0x0020); // Patient ID + SetEntryString(" ",0x0010, 0x2154); // Telephone + SetEntryString(" ",0x0010, 0x1040); // Adress + SetEntryString(" ",0x0010, 0x0020); // Patient ID - DocEntry* patientNameHE = GetDocEntry (0x0010, 0x0010); + DocEntry *patientNameHE = GetDocEntry (0x0010, 0x0010); if ( patientNameHE ) // we replace it by Study Instance UID (why not ?) { - std::string studyInstanceUID = GetEntryValue (0x0020, 0x000d); + std::string studyInstanceUID = GetEntryString (0x0020, 0x000d); if ( studyInstanceUID != GDCM_UNFOUND ) { - SetValEntry(studyInstanceUID, 0x0010, 0x0010); + SetEntryString(studyInstanceUID, 0x0010, 0x0010); } else { - SetValEntry("anonymized", 0x0010, 0x0010); + SetEntryString("anonymized", 0x0010, 0x0010); } } } @@ -1429,13 +1380,13 @@ bool File::AnonymizeFile() continue; } - if ( dynamic_cast(d) ) + if ( dynamic_cast(d) ) { - gdcmWarningMacro( "To 'Anonymize' a BinEntry, better use AnonymizeNoLoad (FIXME) "); + gdcmWarningMacro( "To 'Anonymize' a DataEntry, better use AnonymizeNoLoad (FIXME) "); continue; } else - SetValEntry ((*it).Value, (*it).Group, (*it).Elem); + SetEntryString ((*it).Value, (*it).Group, (*it).Elem); } } @@ -1513,22 +1464,26 @@ bool File::Write(std::string fileName, FileType writetype) } // Entry : 0002|0000 = group length -> recalculated - ValEntry*e0000 = GetValEntry(0x0002,0x0000); + DataEntry *e0000 = GetDataEntry(0x0002,0x0000); if ( e0000 ) { std::ostringstream sLen; sLen << ComputeGroup0002Length( ); - e0000->SetValue(sLen.str()); + e0000->SetString(sLen.str()); } - int i_lgPix = GetEntryLength(GrPixel, NumPixel); - if (i_lgPix != -2) + // Derma?.dcm does not have it...let's remove it FIXME FIXME + if( writetype != JPEG ) { - // no (GrPixel, NumPixel) element - std::string s_lgPix = Util::Format("%d", i_lgPix+12); - s_lgPix = Util::DicomString( s_lgPix.c_str() ); - InsertValEntry(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); @@ -1722,7 +1677,7 @@ 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. @@ -1747,20 +1702,27 @@ bool File::ReadTag(uint16_t testGroup, uint16_t testElem) itemTagGroup = ReadInt16(); itemTagElem = ReadInt16(); } - catch ( FormatError /*e*/ ) + catch ( FormatError ) { - //std::cerr << e << std::endl; + gdcmErrorMacro( "Can not read tag for " + << " We should have found tag (" + << DictEntry::TranslateToKey(testGroup,testElem) << ")" + ) ; + return false; } if ( itemTagGroup != testGroup || itemTagElem != testElem ) - { - gdcmWarningMacro( "Wrong Item Tag found:" - << " We should have found tag (" - << std::hex << testGroup << "," << testElem << ")" << std::endl - << " but instead we encountered tag (" - << std::hex << itemTagGroup << "," << itemTagElem << ")" - << " at address: " << " 0x(" << (unsigned int)currentPosition << ")" - ) ; + { + // in order not to pollute output we don't warn on 'delimitors' + if (itemTagGroup != 0xfffe || testGroup != 0xfffe ) + 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 << ")" + ) ; Fp->seekg(positionOnEntry, std::ios::beg); return false; @@ -1787,17 +1749,19 @@ uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElem) if ( !ReadTag(testGroup, testElem) ) { + // 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(); uint32_t itemLength = ReadInt32(); - { - gdcmWarningMacro( "Basic Item Length is: " - << itemLength << std::endl + gdcmDebugMacro( "Basic Item Length is: " << itemLength << " at address: " << std::hex << (unsigned int)currentPosition); - } return itemLength; } @@ -1844,27 +1808,12 @@ 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 + * @ deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead */ bool File::Load( std::string const &fileName ) {