MATLAB: A problem in TIFF reading

tiff_reading; tiff_short; tiff_long

Hi,Everybody.

I have a problem in TIFF reading. The matlab gave me a warning when I read a TIFF file:

WARNING: The datatype for tag SamplesPerPixel should be TIFF_SHORT instead of
TIFF_LONG.  This may cause data corruption.

the code I used is given as follows:

FileTif=filename;
InfoImage=imfinfo(FileTif);
mImage=InfoImage(1).Width;
nImage=InfoImage(1).Height;
NumberImages=length(InfoImage);
FinalImage=zeros(nImage,mImage,NumberImages,'uint16');

How can I overcome this problem? Thanks a lot

Best Answer

The TIFF file you are reading does not have proper headers, and MATLAB is warning you about it. However, SamplesPerPixel is going to be a very small number, 1 for grayscale and 3 for RGB. If you were happening to use a TIFF with more than 32767 channels per pixel then you would encounter problems. For normal images it is just a warning about an improper file.

You could fix the file by opening it with some random image utility and asking to save it again.

Related Solutions

MATLAB: Efficiently saving multislice tiff using Tifflib

Does this help?

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.

Best Answer

Related Solutions

MATLAB: Efficiently saving multislice tiff using Tifflib

MATLAB: How to update Tiff object in ImageAdapter class

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