[Bug] Loading .tif image produces image artifact

[KronosTheLate]

The original image looks like this:

I then load the image with the following command:
Images.load(joinpath(pwd(), "above_focal_sum", "113mm.tif"))

The resulting image looks like this (imprecise cropping, color and lines are of interest)

, where the image is displayed in a pluto notebook

There is now an artifact in the image, with vertical lines across the entire thing. The artifact is very visible in a plot of the values of two slices of the image, where the RGB values have been converted to Gray and then to float:

As can be seen from the path, the image is a .tif file. The original image is grayscale, whereas the read in image has RGB values and visually a warmer tone.
The original image file can be found at https://drive.google.com/file/d/1dIhkYY5C7EumgCZaLI0TqPlorRjL1BX0/view?usp=sharing

Can anyone help me on how to correctly read the image?

[timholy]

CC @tlnagy as the TIFF expert

[KronosTheLate]

The fix for me ended up being using ImageMagick's convert function to convert the images to .jpg, and to load those. That worked fine. That could be a good temporary fix I suppose - at least vastly superior to a silent incorrectness bug. Something like making the .jpg file, loading it into Julia, and then deleting the file.

Just to provide a starting point, here is the code I used to convert all images to .jpg. My proposed solution would obviously entail doing this behind the scenes, with cleanup, one picture at a time, when the Images.load method is called.

begin
	function convert_tif_to_jpg()
		for folder in folder_names
		try
			cd(folder)
			files = readdir()
			tif_files = filter(x->occursin(".tif", x), files)
			tif_filenames = getindex.(split.(tif_files, '.'), 1)
			for filename in tif_filenames
				tif_filename = string(filename, ".tif")
				jpg_filename = string(filename, ".jpg")
				isfile(jpg_filename)  && continue
				run(`convert $tif_filename $jpg_filename`)
			end
			
			finally cd("..")
		end
		end
	end
	#convert_tif_to_jpg()
	md"Converting tif to jpg"
end

[tlnagy]

Huh, initially I was worried that this was a bug in TiffImages.jl, but the file is LZW compressed so it hits tlnagy/TiffImages.jl#8 (I don't yet support LZW compression), which causes TiffImages.jl to error out on load and then FileIO switches to ImageMagick.jl and that loads the image incorrectly.

So this is a missing feature in TiffImages.jl and a bug in ImageMagick.jl. Your solution is a pragmatic one, but LZW support would be very nice to have in TiffImages.jl longer term.

[KronosTheLate]

It seems strange that ImageMagick can not load the image correctly, while I used ImageMagick to correctly convert the image to jpg...

[tlnagy]

I don't know the ImageMagick.jl codebase well but my guess is that the raw type isn't properly mapped to the Julian type so not a bug in imagemagick itself, but in the Julia conversion. The bug looks like it's potentially a RGB vs RGBA problem.

[KronosTheLate]

Oscar Smith said on discourse that it looked like an issue with alpha values....
So this issue should be reproduced purely in ImageMagick, and an issue should be opened up over there?

[tlnagy]

Oscar Smith said on discourse that it looked like an issue with alpha values....

Yeah, that was my guess too.

So this issue should be reproduced purely in ImageMagick, and an issue should be opened up over there?

I would do that (+ link to the discussion here) and close this issue.

[KronosTheLate]

I made JuliaIO/ImageMagick.jl#211.
When someone reproduces the image without Images.jl, we can close this issue.

[KronosTheLate]

I more refined workaround, as I encountered this again:

let  #! Converting image type
    original_dir = pwd()
    input_dir = "/home/dennishb/Uni/Semester/8. Sem/Advanced Physical Optics/Lab excercise 2/Pictures"
    cd(input_dir)
    
    input_extension = ".tif"
    output_extension = ".bmp"

    files = readdir()
    input_files = filter(x->occursin(input_extension, x), files)
    filenames = getindex.(split.(input_files, '.'), 1)
    for filename in filenames
        input_filename = string(filename, input_extension)
        output_filename = string(filename, output_extension)
        isfile(output_filename)  && continue
        try
            run(`convert $input_filename $output_filename`)
            @info "Converted $filename from $input_extension to $output_extension."
        catch e
            @warn "Error occured in converting $filename from $input_extension to $output_extension.
            Continuing to next file."
        end
    end
    cd(original_dir)
end

[KronosTheLate]

This could be related to tlnagy/TiffImages.jl#8, as loading the image with TiffImages results in Compression COMPRESSION_LZW is not implemented.

[tlnagy]

Yes, TiffImages doesn't yet support LZW compressed images so it will complain. It on my list of things to do, but I don't have the bandwidth to fix this for the next couple months at least.

[ashwanirathee]

Can this issue be moved to TiffImages.jl?

[timholy]

I'm not sure you can transfer across orgs; at any rate, I don't have the requisite permissions.

[tlnagy]

AFAICT this is a dupe of tlnagy/TiffImages.jl#8 for the TiffImsges side of things. So it can be closed in lieu of that issue.