CODEWITHSUNDEEP
pythonimage-processing3dtiffscikit-image
Itzik walters
Itzik walters

Reputation: 1

TypeError: unexpected keyword argument: img_num

I have several 2D images, and want to convert these slices to a 3D image with python. i found the next code, and I don't not know what exactly I have done worng...

from skimage import io
im_collection = io.imread_collection('C:/Users/Itzik/Desktop/images/*.tiff')
im_3d = im_collection.concatenate()

This is the error message that I got:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)

~\anaconda3\envs\Segmentation 3D\lib\site-packages\skimage\io\collection.py in concatenate_images(ic)
     45         ar = np.concatenate(all_images)
     46     except ValueError:
---> 47         raise ValueError('Image dimensions must agree.')
     48     return ar
     49 

~\anaconda3\envs\Segmentation 3D\lib\site-packages\skimage\io\collection.py in <listcomp>(.0)
      45         ar = np.concatenate(all_images)
      46     except ValueError:
 ---> 47         raise ValueError('Image dimensions must agree.')
      48     return ar
      49

~\anaconda3\envs\Segmentation 3D\lib\site-packages\tifffile\tifffile.py in __init__(self, arg, name, 
offset, size, multifile, _useframes, **kwargs)
   2179                         setattr(self, key, bool(value))
   2180                 else:
-> 2181                     raise TypeError(f'unexpected keyword argument: {key}')
   2182 
   2183         fh = FileHandle(arg, mode='rb', name=name, offset=offset, size=size)

TypeError: unexpected keyword argument: img_num

Upvotes: 0

Views: 851

Answers (1)

Juan
Juan

Reputation: 5768

We finally figured this out on the scikit-image issue tracker. The fix is to specify the tifffile plugin:

from skimage import io
im_collection = io.imread_collection(
    'C:/Users/Itzik/Desktop/images/*.tiff', plugin='tifffile'
)
im_3d = im_collection.concatenate()

Upvotes: 1

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