An academic colleague asked me recently how to read the sensor data (in Bayer or color filter array form) from a Nikon raw camera file (an NEF file) into MATLAB. We figured out a way to do it, and I thought I'd pass it along.

I should caution you, though, that there are multiple steps involved, some of which are "advanced maneuvers."

First, I suggested that we try using the free Adobe DNG Converter program to convert the NEF file to a DNG (Digital Negative) file. After some trial-and-error we found that it's necessary to tell DNG Converter to do the conversion "uncompressed." Here are some screenshots of the relevant dialogs.

Under the covers, a DNG file is a very specialized kind of TIFF file. However, we can't read the raw sensor data using imread. If you call imread on the DNG file, it will just give you back the thumbnail image. Instead, we have to make use of the MATLAB Tiff class. This class offers low-level access to the "guts" of a TIFF file. To use it successfully, it helps to have some familiarity with how TIFF files work.

But first let's poke at a sample DNG file using imfinfo.

info = imfinfo('books.dng')

info = 

                     Filename: '\\mathworks\home\eddins\files\I\ipblog_material\2011\books.dng'
                  FileModDate: '08-Mar-2011 12:01:20'
                     FileSize: 25079002
                       Format: 'tif'
                FormatVersion: []
                        Width: 256
                       Height: 170
                     BitDepth: 24
                    ColorType: 'truecolor'
              FormatSignature: [73 73 42 0]
                    ByteOrder: 'little-endian'
               NewSubFileType: 1
                BitsPerSample: [8 8 8]
                  Compression: 'Uncompressed'
    PhotometricInterpretation: 'RGB'
                 StripOffsets: 133234
              SamplesPerPixel: 3
                 RowsPerStrip: 170
              StripByteCounts: 130560
                  XResolution: []
                  YResolution: []
               ResolutionUnit: 'None'
                     Colormap: []
          PlanarConfiguration: 'Chunky'
                    TileWidth: []
                   TileLength: []
                  TileOffsets: []
               TileByteCounts: []
                  Orientation: 1
                    FillOrder: 1
             GrayResponseUnit: 0.0100
               MaxSampleValue: [255 255 255]
               MinSampleValue: 0
                 Thresholding: 1
                       Offset: 8
                         Make: 'NIKON CORPORATION '
                        Model: 'NIKON D90 '
                     Software: 'Ver.1.00 '
                     DateTime: '2011:03:06 14:45:58 '
                      SubIFDs: {2x1 cell}
                          XMP: [1x7309 char]
                DigitalCamera: [1x1 struct]
                   DNGVersion: [4x1 double]
           DNGBackwardVersion: [4x1 double]
            UniqueCameraModel: 'Nikon D90 '
                 ColorMatrix1: [9x1 double]
                 ColorMatrix2: [9x1 double]
                AnalogBalance: [3x1 double]
                AsShotNeutral: [3x1 double]
             BaselineExposure: 0.2500
                BaselineNoise: 1
            BaselineSharpness: 1
           LinearResponseUnit: 1
           CameraSerialNumber: '3276464 '
                     LensInfo: [4x1 double]
                  ShadowScale: 1
               DNGPrivateData: [121588x1 double]
       CalibrationIlluminant1: 17
       CalibrationIlluminant2: 21
           AliasLayerMetadata: [16x1 double]
          OriginalRawFileName: 'books.NEF '
                  UnknownTags: [15x1 struct]

You can see that imfinfo thinks that this file is a 256-by-170 truecolor image. But as I mentioned above, that's just a thumbnail image. The data we want is hiding in something called a "SubIFD."

info.SubIFDs{1}

ans = 

                     Filename: '\\mathworks\home\eddins\files\I\ipblog_material\2011\books.dng'
                  FileModDate: '08-Mar-2011 12:01:20'
                     FileSize: 25079002
                       Format: 'tif'
                FormatVersion: []
                        Width: 4310
                       Height: 2868
                     BitDepth: 16
                    ColorType: 'CFA'
              FormatSignature: [73 73 42 0]
                    ByteOrder: 'little-endian'
               NewSubFileType: 0
                BitsPerSample: 16
                  Compression: 'Uncompressed'
    PhotometricInterpretation: 'CFA'
                 StripOffsets: 356842
              SamplesPerPixel: 1
                 RowsPerStrip: 2868
              StripByteCounts: 24722160
                  XResolution: []
                  YResolution: []
               ResolutionUnit: 'None'
                     Colormap: []
          PlanarConfiguration: 'Chunky'
                    TileWidth: []
                   TileLength: []
                  TileOffsets: []
               TileByteCounts: []
                  Orientation: 1
                    FillOrder: 1
             GrayResponseUnit: 0.0100
               MaxSampleValue: 65535
               MinSampleValue: 0
                 Thresholding: 1
                       Offset: 130252
                CFAPlaneColor: [3x1 double]
                    CFALayout: 1
           LinearizationTable: [772x1 double]
          BlackLevelRepeatDim: [2x1 double]
                   BlackLevel: 0
                   WhiteLevel: 3767
                 DefaultScale: [2x1 double]
            DefaultCropOrigin: [2x1 double]
              DefaultCropSize: [2x1 double]
              BayerGreenSplit: 0
            AntiAliasStrength: 1
             BestQualityScale: 1
                   ActiveArea: [4x1 double]
                  UnknownTags: [2x1 struct]

That's the good stuff! It's a 16-bit-per-sample 4310-by-2868 color filter array (CFA). Here's how to read it. I'm just going to give the steps without explanation and refer you to the documentation for the Tiff class for more information.

warning off MATLAB:tifflib:TIFFReadDirectory:libraryWarning
t = Tiff('books.dng','r');
offsets = getTag(t,'SubIFD');
setSubDirectory(t,offsets(1));
cfa = read(t);
close(t);

Here's a screen shot of imtool showing the resulting color filter array at 400% magnification. You can clearly see the Bayer array pattern.

We wondered why the maximum sensor value was 768. After some investigation, we found that Nikon appears to be storing a nonlinear quantization off the original 12-bit values. The linearization curve can be found in the DNG file as follows:

curve = info.SubIFDs{1}.LinearizationTable;
plot(curve)

So if you were going to do calculations based on this raw data, you'd probably want to linearize it back to the original 12-bit range first using this curve.

Have you used the MATLAB Tiff class to do advanced maneuvers with TIFF files? Let us know what you've done by posting a comment here.

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