MATLAB: Loading in raw image data using the Tiff class: Images return as all zeros, multiple warnings

.dnggettagImage Processing Toolboxnefraw image formatsetsubdirectorytifftiff library warning

I have image data in the Nikon .NEF raw format that I would like to open in MATLAB for some image processing. To accomplish this, I have followed Steve Eddins' blog post on the subject. Specifically, I am converting my .NEF files to digital negative (.dng) files using the Adobe DNG Converter, then using the Tiff class to read in the data.

I should also note that I am able to view my converted .dng files externally to MATLAB, and there are no apparent problems with the conversion.

My images are 4288×2848 px, and simply calling the imread() function on them returns a smaller thumbnail, which seems consistent with the blog post. Since I would like to view them in full resolution, I run the following lines, copied from the blog:

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

However, the data read into cfa returns as a 2868×4310 uint16 of zeros. I suspect this has something to do with my offsets, but I don't know enough about .tiff and SubIFDs in particular to really know where to go from here.

A few relevant warnings that appear in the code are copy+pasted below:

The following appears after calling Tiff() and getTag():

Warning: TIFF library warning: TIFFReadDirectory: [full path of .dng redacted]: unknown field with tag 37393 (0x9211) encountered..

This warning appears numerous times with numerous tags listed.

The following appears after attempting to read in the data into cfa:

Warning: TIFF library warning: JPEGPreDecode: Improper JPEG strip/tile size, expected 256x240, got 128x240.. 
Warning: TIFF library warning: JPEGLib: Must downscale data from 16 bits to 8..

Apologies if it sounds like I am just dumping this on the forum and saying "fix this," as that is not my intention. As I said, I know next to nothing about .tiff files, so if my problem is one that could be solved simply by reading up on them, relevant sources in lieu of a line-by-line solution would be appreciated.

Best Answer

It looks as if my problems stemmed not from the Matlab code, but from Adobe's DNG converter. The below settings in the DNG converter solved my problem:

Preferences > Compatability > Custom > Backward Version > DNG 1.3
Preferences > Compatability > Custom > Uncompressed

Related Solutions

MATLAB: How to update Tiff object in ImageAdapter class

I found something that fixes the issue, but I'm not 100% sure why it works. In any case, I have included the solution below. I will also be reporting this as a bug/documentation problem, as it is definitely not clear in the documentation of the TIFF class.

To fix this, I modified the changePage() function as follows:

function [] = changePage(obj, imageSize, tileSize)
    % get tags from last page, before we switch
    bitsPerSample = obj.TiffObject.getTag('BitsPerSample');
    sFormat = obj.TiffObject.getTag('SampleFormat');
    compression = obj.TiffObject.getTag('Compression');
    
    % increments to next directory, so next time we call blockproc
    % it will write to the next page
    obj.TiffObject.writeDirectory();
    
    % now write out new metadata for the new page
    obj.ImageSize  = [imageSize(1), imageSize(2), 1]; %length first
    obj.TileLength = tileSize(1);
    obj.TileWidth  = tileSize(2);
    obj.TiffObject.setTag('ImageLength',   obj.ImageSize(1));
    obj.TiffObject.setTag('ImageWidth',    obj.ImageSize(2));
    obj.TiffObject.setTag('TileLength',    obj.TileLength);
    obj.TiffObject.setTag('TileWidth',     obj.TileWidth);
    obj.TiffObject.setTag('Photometric',   Tiff.Photometric.MinIsBlack);
    obj.TiffObject.setTag('BitsPerSample', bitsPerSample);
    obj.TiffObject.setTag('SampleFormat',  sFormat);
    obj.TiffObject.setTag('SamplesPerPixel', 1);
    obj.TiffObject.setTag('PlanarConfiguration', Tiff.PlanarConfiguration.Chunky);
    obj.TiffObject.setTag('Compression',compression);
end

Essentially, I added the rest of the tags that came from the first page. As soon as call to setTag() for Photometric is called, the TiffObject magically contains the entries of previous setTag calls. At first I thought it was because Photometric makes another call to the Tiff class within it, so I rearranged the setTag calls like this:

    obj.TiffObject.setTag('Photometric',   Tiff.Photometric.MinIsBlack);
    obj.TiffObject.setTag('BitsPerSample', bitsPerSample);
    obj.TiffObject.setTag('SampleFormat',  sFormat);
    obj.TiffObject.setTag('SamplesPerPixel', 1);
    obj.TiffObject.setTag('PlanarConfiguration', Tiff.PlanarConfiguration.Chunky);
    obj.TiffObject.setTag('Compression',compression);
    obj.TiffObject.setTag('ImageLength',   obj.ImageSize(1));
    obj.TiffObject.setTag('ImageWidth',    obj.ImageSize(2));
    obj.TiffObject.setTag('TileLength',    obj.TileLength);
    obj.TiffObject.setTag('TileWidth',     obj.TileWidth);

Here, the TiffObject did not update until the setTag for ImageLength was called. What this tells me is that in order to update the TiffObject, a certain number of bytes must be written to the metadata. This is not at all clear in the documentation. I thought that rewriteDirectory() would work, but it does not update the TiffObject. It may actually write out to file like it says, but without the corresponding update to the TiffObject the code will crash the next time a tile is written, because it thinks the TileLength/TileWidth have not been set.

I am still open to answers on better ways to do my multi-resolution file writing, as this seems a bit haphazard, so feel free to add.

MATLAB: Reading camera raw file

I had the same problem, but fixed by making sure the image was uncompressed. If you are using Adobe DNG converter make sure the "compatibility" is set to custom, with "Uncompressed" ticked.

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