load() on a TIFF image returns all 0xffff

kbarbary commented 7 years ago

I have a few images I'm trying to read where load() returns an array of all Grey{N0f16}(1.0), but this doesn't seem to be the true file contents when read with other tools. An example image is here: https://www.dropbox.com/s/lelfacepaxvaf6w/testcase.tif?dl=0

julia> using Images

julia> img = load("testcase.tif")
256×256 Array{Gray{N0f16},2}:
 Gray{N0f16}(1.0)  Gray{N0f16}(1.0)  …  Gray{N0f16}(1.0)  Gray{N0f16}(1.0)
 Gray{N0f16}(1.0)  Gray{N0f16}(1.0)     Gray{N0f16}(1.0)  Gray{N0f16}(1.0)

julia> all(img .== Gray{N0f16}(1.0))
true

julia> using ImageMagick

julia> ImageMagick.libversion
v"6.8.9"

julia> Pkg.installed("ImageMagick")
v"0.4.0"

julia> versioninfo()
Julia Version 0.6.0-rc2.0
Commit 68e911b (2017-05-18 02:31 UTC)
Platform Info:
  OS: Linux (x86_64-pc-linux-gnu)
  CPU: Intel(R) Core(TM) i7-4500U CPU @ 1.80GHz
  WORD_SIZE: 64
  BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Haswell)
  LAPACK: libopenblas64_
  LIBM: libopenlibm
  LLVM: libLLVM-3.9.1 (ORCJIT, haswell)

In Python, I can load the same image with cv2, and get the correct shape of (256, 256, 4) and non-constant data:

In [1]: import cv2

In [4]: img = cv2.imread("testcase.tif", -1)

In [5]: img.shape
Out[5]: (256, 256, 4)

In [6]: img[0:3, 0:3]
Out[6]: 
array([[[12181, 13224, 13839,  9250],
        [12251, 13337, 13836,  9279],
        [12312, 13407, 13951,  9316]],

       [[12033, 13128, 13720,  9271],
        [12060, 13093, 13628,  9350],
        [11967, 13088, 13505,  9414]],

       [[11627, 12659, 13098,  9057],
        [11770, 12823, 13210,  9163],
        [11796, 12774, 13330,  9244]]], dtype=uint16)

I suppose this might be a libmagickwand problem, but any advice would be appreciated!

timholy commented 7 years ago

I think it's mostly an ImageMagick issue, but TIFF is a pretty complicated format. I don't have any great ideas, but a couple of options I thought of:

see about resurrecting https://github.com/rephorm/TIFF.jl or otherwise create a pure-julia TIFF loader
use Bioformats. See https://discourse.julialang.org/t/bioformats-in-julia/2440. Not sure that anything ever got posted, but you could "bump" the discussion.

timholy commented 7 years ago

I should note that I tested several non-Julia applications, and only ImageJ handled the file properly.

bjarthur commented 7 years ago

i've heard libtiff is great. might be worth making a julia wrapper for it if one doesn't already exist.

kbarbary commented 7 years ago

Thanks for taking a look Tim, and thanks for the pointers!

JuliaIO / ImageMagick.jl

load() on a TIFF image returns all 0xffff #99