Refine does not work

[Chris-Cooney]

I have recently installed taglab on and have everything function in a python 3.9 environment in GPU (CUDA toolkit 11.6) on a Windows 11 system. All features in taglab appear to be running except the refine tool, i outline a feature, hit R or select refine in the right-click menu and nothing happens. This is the output message in the terminal window:

gaussian() got an unexpected keyword argument 'multichannel'
C:\TagLab-main\source\QtTablePanel.py:239: FutureWarning: Series.getitem treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use ser.iloc[pos]
if row[0] == newblob.id:

Thanks,
Chris

[Chris-Cooney]

Just to clarify, the output in the terminal is similar to most tools/functions that have assigned keys, but they work (e.g. dilate, assign, merge etc.) whereas refine does not

[Jordan-Pierce]

@Chris-Cooney There's a line (44) in Coraline.py that uses skimage's gaussian function; it's currently using a parameter called multichannel. Because you are receiving that error, it means that you're using a newer version of skimage than what TagLab was originally using when written, and that parameter is now depreciated.

To be able to use Refine without downgrading your scikit image version, just remove that parameter value:

# Should be this
img = gaussian(img, sigma = 1.5)

This is only a hot fix; alternatively, it's probably better to use the version of skimage that TagLab was written with, that way you can ensure full functionality. Otherwise, TagLab will need to (potentially) update any functions that have been changed since new versions of skimage has been updated.