X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=def9a2ba8bd8d53bbc5f7e4c4f92232d073eea79;hb=4331b970c740503e6827e72a172101a86d630907;hp=1c0db8127a5b61e298c83688d6385a9a2338cda7;hpb=e89b83f2446db523e16058e478887acfa9c37a7e;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 1c0db812..def9a2ba 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2005/10/10 22:25:05 $ - Version: $Revision: 1.274 $ + Date: $Date: 2005/10/21 14:09:41 $ + Version: $Revision: 1.286 $ 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 ) @@ -231,10 +230,11 @@ 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 = new DataEntry(newDict); + newDict->Delete(); newEntry->Copy(entry); newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea()); oldEntry->SetSelfArea(false); @@ -261,7 +261,7 @@ 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 +318,7 @@ 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 +333,7 @@ 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 +398,10 @@ 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 +412,10 @@ 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 +439,14 @@ 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; } @@ -466,12 +459,31 @@ 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); + DataEntry *entry = GetDataEntry(0x0018,0x1164); + if( entry ) + { + nbValue = entry->GetValueCount(); + 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; + } + else + { + gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" ); + } + +/* const std::string &strImagerPixelSpacing = GetEntryString(0x0018,0x1164); if ( strImagerPixelSpacing != GDCM_UNFOUND ) { if ( ( nbValues = sscanf( strImagerPixelSpacing.c_str(), @@ -486,13 +498,31 @@ float File::GetXSpacing() if ( xspacing == 0.0 ) xspacing = 1.0; - - return xspacing; } - } + return xspacing; + }*/ - const std::string &strSpacing = GetEntryValue(0x0028,0x0030); + entry = GetDataEntry(0x0028,0x0030); + if( entry ) + { + nbValue = entry->GetValueCount(); + 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; + } + else + { + gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); + } +/* const std::string &strSpacing = GetEntryString(0x0028,0x0030); if ( strSpacing == GDCM_UNFOUND ) { gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); @@ -511,22 +541,22 @@ float File::GetXSpacing() 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. && yspacing == 0.) - return 1.; +/* if ( xspacing == 0.0 && yspacing == 0.0) + return 1.0; - if ( xspacing == 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; } @@ -538,11 +568,23 @@ float File::GetXSpacing() */ float File::GetYSpacing() { - float yspacing = 1.; - int nbValues; + float yspacing = 1.0; // To follow David Clunie's advice, we first check ImagerPixelSpacing - const std::string &strImagerPixelSpacing = GetEntryValue(0x0018,0x1164); + DataEntry *entry = GetDataEntry(0x0018,0x1164); + if( entry ) + { + yspacing = (float)entry->GetValue(0); + + if ( yspacing == 0.0 ) + yspacing = 1.0; + return yspacing; + } + else + { + 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); @@ -555,9 +597,22 @@ float File::GetYSpacing() yspacing = 1.0; return yspacing; - } + }*/ + + entry = GetDataEntry(0x0028,0x0030); + if( entry ) + { + yspacing = (float)entry->GetValue(0); - std::string strSpacing = GetEntryValue(0x0028,0x0030); + if ( yspacing == 0.0 ) + yspacing = 1.0; + return yspacing; + } + else + { + gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); + } +/* std::string strSpacing = GetEntryString(0x0028,0x0030); if ( strSpacing == GDCM_UNFOUND ) { gdcmWarningMacro("Unfound Pixel Spacing (0028,0030)"); @@ -572,7 +627,7 @@ float File::GetYSpacing() yspacing = 1.0; if ( yspacing == 0.0 ) - yspacing = 1.0; + yspacing = 1.0;*/ return yspacing; } @@ -585,6 +640,17 @@ 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) @@ -594,17 +660,45 @@ 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 - - const std::string &strSpacingBSlices = GetEntryValue(0x0018,0x0088); + DataEntry *entry = GetDataEntry(0x0018,0x0088); + if( entry ) + { + zspacing = (float)entry->GetValue(0); + + if ( zspacing == 0.0 ) + zspacing = 1.0; + return zspacing; + } + else + gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)"); + + // 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 ) + { + zspacing = (float)entry->GetValue(0); + if ( zspacing == 0.0 ) + zspacing = 1.0; + return zspacing; + } + else + gdcmWarningMacro("Unfound Slice Thickness (0018,0050)"); + + return zspacing; + +/* const std::string &strSpacingBSlices = GetEntryString(0x0018,0x0088); if ( strSpacingBSlices == GDCM_UNFOUND ) { gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)"); - const std::string &strSliceThickness = GetEntryValue(0x0018,0x0050); + const std::string &strSliceThickness = GetEntryString(0x0018,0x0050); if ( strSliceThickness == GDCM_UNFOUND ) { gdcmWarningMacro("Unfound Slice Thickness (0018,0050)"); - return 1.; + return 1.0; } else { @@ -615,8 +709,11 @@ float File::GetZSpacing() return (float)atof( strSliceThickness.c_str() ); } } - //else - return (float)atof( strSpacingBSlices.c_str() ); + + float zsp = (float)atof( strSpacingBSlices.c_str()); + if (zsp == 0.0) // last change not to break further computations ... + zsp = 1.0; + return zsp;*/ } /** @@ -627,26 +724,40 @@ float File::GetZSpacing() */ float File::GetXOrigin() { - float xImPos, yImPos, zImPos; - std::string strImPos = GetEntryValue(0x0020,0x0032); + DataEntry *entry = GetDataEntry(0x0020,0x0032); + if( !entry ) + { + gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); + entry = GetDataEntry(0x0020,0x0030); + if( !entry ) + { + gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); + return 0.0f; + } + } + + 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 = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images + strImPos = GetEntryString(0x0020,0x0030); // For ACR-NEMA images if ( strImPos == GDCM_UNFOUND ) { gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); - return 0.; + return 0.0; } } if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &xImPos, &yImPos, &zImPos) != 3 ) { - return 0.; + return 0.0; } - return xImPos; + return xImPos;*/ } /** @@ -657,13 +768,28 @@ float File::GetXOrigin() */ float File::GetYOrigin() { - float xImPos, yImPos, zImPos; - std::string strImPos = GetEntryValue(0x0020,0x0032); + DataEntry *entry = GetDataEntry(0x0020,0x0032); + if( !entry ) + { + gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); + entry = GetDataEntry(0x0020,0x0030); + if( !entry ) + { + gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); + return 0.0f; + } + } + + 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 = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images + strImPos = GetEntryString(0x0020,0x0030); // For ACR-NEMA images if ( strImPos == GDCM_UNFOUND ) { gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); @@ -676,7 +802,7 @@ float File::GetYOrigin() return 0.; } - return yImPos; + return yImPos;*/ } /** @@ -689,8 +815,16 @@ float File::GetYOrigin() */ float File::GetZOrigin() { - float xImPos, yImPos, zImPos; - std::string strImPos = GetEntryValue(0x0020,0x0032); + DataEntry *entry = GetDataEntry(0x0020,0x0032); + if( entry ) + { + if( entry->GetValueCount() == 3 ) + return (float)entry->GetValue(0); + gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)"); + return 0.0f; + } +/* float xImPos, yImPos, zImPos; + std::string strImPos = GetEntryString(0x0020,0x0032); if ( strImPos != GDCM_UNFOUND ) { @@ -703,9 +837,17 @@ float File::GetZOrigin() { return zImPos; } - } + }*/ - strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images + entry = GetDataEntry(0x0020,0x0030); + if( entry ) + { + if( entry->GetValueCount() == 3 ) + return (float)entry->GetValue(0); + 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(), @@ -718,10 +860,18 @@ float File::GetZOrigin() { return zImPos; } - } + }*/ // for *very* old ACR-NEMA images - std::string strSliceLocation = GetEntryValue(0x0020,0x1041); + 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) @@ -734,9 +884,17 @@ float File::GetZOrigin() return zImPos; } } - gdcmWarningMacro( "Unfound Slice Location (0020,1041)"); + gdcmWarningMacro( "Unfound Slice Location (0020,1041)");*/ - std::string strLocation = GetEntryValue(0x0020,0x0050); + entry = GetDataEntry(0x0020,0x0050); + if( entry ) + { + if( entry->GetValueCount() == 1 ) + 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 ) @@ -749,7 +907,7 @@ float File::GetZOrigin() return zImPos; } } - gdcmWarningMacro( "Unfound Location (0020,0050)"); + gdcmWarningMacro( "Unfound Location (0020,0050)");*/ return 0.; // Hopeless } @@ -769,7 +927,7 @@ 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 ) @@ -781,7 +939,7 @@ 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 ) @@ -804,14 +962,22 @@ bool File::GetImageOrientationPatient( float iop[6] ) */ int File::GetBitsStored() { - std::string strSize = GetEntryValue( 0x0028, 0x0101 ); + DataEntry *entry = GetDataEntry(0x0028,0x0101); + if( !entry ) + { + gdcmWarningMacro("(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() ); + return atoi( strSize.c_str() );*/ } /** @@ -822,14 +988,22 @@ int File::GetBitsStored() */ int File::GetBitsAllocated() { - std::string strSize = GetEntryValue(0x0028,0x0100); + DataEntry *entry = GetDataEntry(0x0028,0x0100); + if( !entry ) + { + gdcmWarningMacro("(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() ); + return atoi( strSize.c_str() );*/ } /** @@ -840,13 +1014,21 @@ int File::GetBitsAllocated() */ int File::GetHighBitPosition() { - std::string strSize = GetEntryValue( 0x0028, 0x0102 ); + DataEntry *entry = GetDataEntry(0x0028,0x0102); + if( !entry ) + { + gdcmWarningMacro("(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() ); + return atoi( strSize.c_str() );*/ } /** @@ -857,14 +1039,23 @@ int File::GetHighBitPosition() */ int File::GetSamplesPerPixel() { - const std::string &strSize = GetEntryValue(0x0028,0x0002); + DataEntry *entry = GetDataEntry(0x0028,0x0002); + if( !entry ) + { + 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 (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() ); + return atoi( strSize.c_str() );*/ } /** @@ -874,13 +1065,21 @@ int File::GetSamplesPerPixel() */ int File::GetPlanarConfiguration() { - std::string strSize = GetEntryValue(0x0028,0x0006); + 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() ); + return atoi( strSize.c_str() );*/ } /** @@ -892,9 +1091,7 @@ 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" ) @@ -913,7 +1110,7 @@ int File::GetPixelSize() { return 8; } - gdcmWarningMacro( "Unknown pixel type"); + gdcmWarningMacro( "Unknown pixel type: " << pixelType); return 0; } @@ -934,7 +1131,7 @@ 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)"); @@ -956,7 +1153,39 @@ std::string File::GetPixelType() bitsAlloc = "8"; } - std::string sign = GetEntryValue(0x0028, 0x0103);//"Pixel Representation" + std::string sign; + if( IsSignedPixelData() ) + { + sign = "S"; + } + else + { + 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 ) { @@ -970,7 +1199,7 @@ std::string File::GetPixelType() else { sign = "S"; - } + }*/ return bitsAlloc + sign; } @@ -984,7 +1213,14 @@ std::string File::GetPixelType() */ bool File::IsSignedPixelData() { - std::string strSign = GetEntryValue( 0x0028, 0x0103 ); + DataEntry *entry = GetDataEntry(0x0028, 0x0103);//"Pixel Representation" + if( !entry ) + { + gdcmWarningMacro( "Missing Pixel Representation (0028,0103)"); + 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"); @@ -995,7 +1231,7 @@ bool File::IsSignedPixelData() { return false; } - return true; + return true;*/ } /** @@ -1005,7 +1241,7 @@ 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") ) { @@ -1025,7 +1261,7 @@ 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; @@ -1044,7 +1280,7 @@ bool File::IsMonochrome1() */ bool File::IsPaletteColor() { - std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); if ( PhotometricInterp == "PALETTE COLOR " ) { return true; @@ -1063,7 +1299,7 @@ bool File::IsPaletteColor() */ bool File::IsYBRFull() { - std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); if ( PhotometricInterp == "YBR_FULL" ) { return true; @@ -1137,7 +1373,7 @@ 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; @@ -1160,9 +1396,18 @@ int File::GetLUTNbits() */ float File::GetRescaleIntercept() { - float resInter = 0.; + // 0028 1052 DS IMG Rescale Intercept + DataEntry *entry = GetDataEntry(0x0028, 0x1052); + if( !entry ) + { + gdcmWarningMacro( "Missing Rescale Intercept (0028,1052)"); + return 0.0f; + } + return (float)entry->GetValue(0); + +/* float resInter = 0.; /// 0028 1052 DS IMG Rescale Intercept - const std::string &strRescInter = GetEntryValue(0x0028,0x1052); + const std::string &strRescInter = GetEntryString(0x0028,0x1052); if ( strRescInter != GDCM_UNFOUND ) { if ( sscanf( strRescInter.c_str(), "%f ", &resInter) != 1 ) @@ -1172,7 +1417,7 @@ float File::GetRescaleIntercept() } } - return resInter; + return resInter;*/ } /** @@ -1181,9 +1426,17 @@ float File::GetRescaleIntercept() */ float File::GetRescaleSlope() { - float resSlope = 1.; + // 0028 1053 DS IMG Rescale Slope + DataEntry *entry = GetDataEntry(0x0028, 0x1053); + if( !entry ) + { + gdcmWarningMacro( "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 = GetEntryValue(0x0028,0x1053); + std::string strRescSlope = GetEntryString(0x0028,0x1053); if ( strRescSlope != GDCM_UNFOUND ) { if ( sscanf( strRescSlope.c_str(), "%f ", &resSlope) != 1 ) @@ -1193,7 +1446,7 @@ float File::GetRescaleSlope() } } - return resSlope; + return resSlope;*/ } /** @@ -1209,15 +1462,15 @@ 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 ") ) { @@ -1257,7 +1510,7 @@ 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; } @@ -1317,7 +1570,7 @@ 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; @@ -1371,7 +1624,7 @@ 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() { @@ -1379,22 +1632,22 @@ 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); } } } @@ -1416,13 +1669,13 @@ 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); } } @@ -1500,22 +1753,26 @@ 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) - { - // 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); - } + // Derma?.dcm does not have it...let's remove it FIXME FIXME + 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); + } + } Document::WriteContent(fp, writetype); @@ -1734,19 +1991,24 @@ 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:" + gdcmErrorMacro( "Wrong Item Tag found:" << " We should have found tag (" - << std::hex << testGroup << "," << testElem << ")" << std::endl + << DictEntry::TranslateToKey(testGroup,testElem) << ")" << std::endl << " but instead we encountered tag (" - << std::hex << itemTagGroup << "," << itemTagElem << ")" - << " at address: " << " 0x(" << (unsigned int)currentPosition << ")" + << DictEntry::TranslateToKey(itemTagGroup,itemTagElem) << ")" + << " at address: " << " 0x(" << std::hex + << (unsigned int)currentPosition << std::dec << ")" ) ; Fp->seekg(positionOnEntry, std::ios::beg); @@ -1774,17 +2036,17 @@ uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElem) if ( !ReadTag(testGroup, testElem) ) { + 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; } @@ -1831,7 +2093,7 @@ 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 @@ -1846,7 +2108,7 @@ File::File( std::string const &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,