imagej=True argument eats dimensions and complicates interpretation

[amsikking]

Hi there,

I've really enjoyed using tifffile for my microscope - thank you!

I often deal with data in a 'tzcyx' format and want to save with imagej=True. I've noticed a behavior that's tricky for me to deal with and I'm wondering if there's an easy fix to keep all dimensions?

Example script:

import numpy as np
from tifffile import imread, imwrite

def imwrite_imread(data):
    print('in :', data.shape)
    imwrite('data.tif', data, imagej=True)
    data_out = imread('data.tif')
    print('out:', data_out.shape)
    return data_out

data_1 = np.random.randint(0, 2**8, (1, 10, 1, 248, 260), 'uint8')
data_2 = np.random.randint(0, 2**8, (10, 1, 1, 248, 260), 'uint8')

imwrite_imread(data_1)
imwrite_imread(data_2)

Output:

in : (1, 10, 1, 248, 260)
out: (10, 248, 260)
in : (10, 1, 1, 248, 260)
out: (10, 248, 260)
>>> 

[cgohlke]

Hello,

this is a duplicate of #19. Please see the discussion there. I am trying to find a way to preserve singlet dimensions with an optional keyword (in imread) that works with ImageJ, LSM, OME-TIFF...

[amsikking]

Ah okay, thanks for getting back quickly. Yes a keyword argument for imread that supports singlet dimensions could work. It's kind of a deal breaker for my setup right now so I'd be very excited for a solution . Thanks for working on this!

[cgohlke]

Hi @amsikking,

would the squeeze=False option work for you? That would return the ImageJ hyperstack in 6 dimensions in TZCYXS order (S is for Samples). E.g.

import numpy as np
from tifffile import imread, imwrite

def imwrite_imread(data):
    print('in :', data.shape)
    imwrite('data.tif', data, imagej=True)
    data_out = imread('data.tif', squeeze=False)
    print('out:', data_out.shape)
    return data_out

data_1 = np.random.randint(0, 2**8, (1, 10, 1, 248, 260), 'uint8')
data_2 = np.random.randint(0, 2**8, (10, 1, 1, 248, 260), 'uint8')

imwrite_imread(data_1)
imwrite_imread(data_2)

in : (1, 10, 1, 248, 260)
out: (1, 10, 1, 248, 260, 1)
in : (10, 1, 1, 248, 260)
out: (10, 1, 1, 248, 260, 1)

[amsikking]

imread with squeeze=False is certainly more convenient than redefining imread with a call to transpose_axes each time. Could squeeze=False be the kwarg default? and with a default behavior of out.shape == in.shape?

(apologies in advance if these are silly questions, my knowledge of tiff's is very shallow so I'm just approaching this from a 'user' viewpoint!)

[cgohlke]

out.shape == in.shape cannot be achieved without extending the ImageJ format. Use the default tifffile format for that. squeeze=False as default will likely break most existing applications.

[cgohlke]

Closed in v2021.2.26.