skimage/imageio fails to read grayscale images

Question

I have been reading images using (Python) skimage.imread (or imageio.imread) for months successfully, but now, without changing the code, I get failures when reading grayscale images. My collaborators can read the files. The image properties are:

 identify  test/resources/biosynth1_cropped/text_removed.png 
test/resources/biosynth1_cropped/text_removed.png PNG 1512x315 1512x315+0+0 8-bit sRGB 48c 10094B 0.000u 0:00.005

and some properties with --verbose

 Type: Grayscale
  Base type: Undefined
  Endianness: Undefined
  Depth: 8-bit
  Channel depth:
    Red: 8-bit
    Green: 8-bit
    Blue: 8-bit
  Channel statistics:
    Pixels: 476280

The code (run in repl) is:

from skimage import io
import imageio
file="/Users/pm286/workspace/pyamiimage/test/resources/biosynth1_cropped/arrows_removed.png" 
img = imageio.imread(file)

and gives errors:

(base) pm286macbook:pyamiimage pm286$ python test_load.py 
Traceback (most recent call last):
  File "test_load.py", line 9, in <module>
    img = imageio.imread(file)
  File "/opt/anaconda3/lib/python3.8/site-packages/imageio/core/functions.py", line 265, in imread
    reader = read(uri, format, "i", **kwargs)
  File "/opt/anaconda3/lib/python3.8/site-packages/imageio/core/functions.py", line 186, in get_reader
    return format.get_reader(request)
  File "/opt/anaconda3/lib/python3.8/site-packages/imageio/core/format.py", line 170, in get_reader
    return self.Reader(self, request)
  File "/opt/anaconda3/lib/python3.8/site-packages/imageio/core/format.py", line 221, in __init__
    self._open(**self.request.kwargs.copy())
  File "/opt/anaconda3/lib/python3.8/site-packages/imageio/plugins/pillow.py", line 298, in _open
    return PillowFormat.Reader._open(self, pilmode=pilmode, as_gray=as_gray)
  File "/opt/anaconda3/lib/python3.8/site-packages/imageio/plugins/pillow.py", line 138, in _open
    as_gray=as_gray, is_gray=_palette_is_grayscale(self._im)
  File "/opt/anaconda3/lib/python3.8/site-packages/imageio/plugins/pillow.py", line 689, in _palette_is_grayscale
    palette = np.asarray(pil_image.getpalette()).reshape((256, 3))
ValueError: cannot reshape array of size 144 into shape (256,3)

I have (un/re)installed skimage, imageio, and pillow.

(The code seems to read coloured images satisfactorily.)

I’d be grateful for pointers to solutions.

EDIT.The comment from @Nick ODell seems to have identified the problem.
Has the dimensionality of the output changed from (x, y)to (x, y, 3)?

Asked By: peter.murray.rust

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Source

Answer 1

This is a bug which was fixed in imageio version 2.16.2. The issue is caused by Pillow returning image palettes with less than 256 colors.

To fix it, upgrade to imageio version 2.16.2 or later.

More information:

Answered By: Nick ODell

skimage/imageio fails to read grayscale images

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