Anyone knows what is in Skimage TIfffile save, unknown error "type b".? - save

Question

I am getting a strange error saving a tiff file (stack grayscale), any idea?:
File
"C:\Users\ptyimg_np.MT00200169\Anaconda3\lib\site-packages\tifffile\tifffile.py",
line 1241, in save
sampleformat = {'u': 1, 'i': 2, 'f': 3, 'c': 6}[datadtype.kind] KeyError: 'b'
my code is
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from skimage.morphology import watershed
from skimage.feature import peak_local_max
from scipy import ndimage
from skimage import img_as_float
from skimage import exposure,io
from skimage import external
from skimage.color import rgb2gray
from skimage.filters import threshold_local , threshold_niblack
import numpy as np
import tifffile
from joblib import Parallel, delayed
import sys
# Load an example image
input_namefile = sys.argv[1]
output_namefile = 'seg_'+ input_namefile
#Settings
block_size = 25 #Size block of the local thresholding
img = io.imread(input_namefile, plugin='tifffile')
thresh = threshold_niblack(img, window_size=block_size , k=0.8) #
res = img > thresh
res = np.asanyarray(res)
print("saving segmentation")
tifffile.imsave(output_namefile, res , photometric='minisblack' )

Answer 1

It looks like the error is caused by a bug in writing boolean images in your installed version of tifffile. However, the bug has been fixed in more recent versions (I have 2020.2.16 in my current environment). On my machine, this works fine:
import numpy as np
import tifffile
tifffile.imsave('test.tiff', np.random.random((10, 10)) > 0.5)
and the line causing a crash in your version is never executed in the case of a boolean image.
So, long story short, use python -m pip install -U tifffile to upgrade your version of tifffile, and your program should work!

Answer 2

Some analysis first. The offending line:
sampleformat = {'u': 1, 'i': 2, 'f': 3, 'c': 6}[datadtype.kind]
is causing a KeyError exception because the value of datadtype.kind (the NumPy datatype) is set to b and there is no b in that dictionary. It only caters for types i, u, f, and c (respectively, signed integer, unsigned integer, floating-point, and complex floating-point). Type b is boolean.
This looks like a bug in the code that you're using. If it's something that's not supported, the code should really catch the exception and report on it in a more user-friendly manner rather than just dumping an exception for you to figure out.
My advice is to raise this as a bug with the author.
In terms of the root cause of the issue (this is speculation based on analysis, so could be wrong, I'm just providing it as a possible cause), an examination of your code shows:
img = io.imread(input_namefile, plugin='tifffile')
thresh = threshold_niblack(img, window_size=block_size , k=0.8) #
res = img > thresh
res = np.asanyarray(res)
tifffile.imsave(output_namefile, res , photometric='minisblack' )
That third line above will set res to a either a boolean value or a boolean array that depends on the respective values of each pixel in img and thresh (I don't know enough about NumPy to pontificate on this).
However, regardless of that, they are one or more booleans so, when you try to write them with the imsave() call, it complains about the type being used (as mentioned above, it appears to not cater for boolean values correrctly).
Based on some sample code found elsewhere:
image = data.coins()
mask = image > 128
masked_image = image * mask
I suspect that you should use something similar to that last line to apply the mask to the image, then write the resultant value:
img = io.imread(input_namefile, plugin='tifffile')
thresh = threshold_niblack(img, window_size=block_size , k=0.8)
mask = image > 128 # <-- unsure if this is needed.
res = img * thresh # <-- add this line.
res = np.asanyarray(res)
tifffile.imsave(output_namefile, res , photometric='minisblack' )
Applying the mask to the original image should give you an array of usable values that you can write back out to an image file. Note that I'm unsure whether you need the res > thresh line since it appears to me that the threshold already gives you a mask. I could be wrong on that point so my advice is still to raise it with the author.