AttributeError: 'NoneType' object has no attribute 'max_time' when initializing .tiff files

[mheydasch]

When trying to initialize .tiff (double f) files the Morpho_segmentation notebook will throw the error:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
~/opt/anaconda3/envs/morphodynamics/lib/python3.7/site-packages/morphodynamics/morpho_segmentation.py in initialize(self, b)
    298             )
    299 
--> 300         self.max_time_ipw.max = self.data.max_time
    301         self.max_time_ipw.min = 0
    302         self.param.max_time = self.data.max_time

AttributeError: 'NoneType' object has no attribute 'max_time'

When the same images are converted to .tif (single f) the notebook can correctly initialize them.

[guiwitz]

This should be fixed now for the tif files of the data. I added 'tiff' to the possible tif extensions 'tif' and 'TIF' here: ea4b290. You can just upgrade with:

pip install --upgrade git+https://github.com/guiwitz/MorphoDynamics.git@master#egg=morphodynamics

Beware that if you use Ilastik to generate a segmentation, those files should still be called 'segmented_k_0.tif' and not 'segmented_k_0.tiff'.

[mheydasch]

I updated and made sure that the appropriate line in the code is indeed updated to include 'tiff', but the same error is still thrown, while just changing the extension solves it.

[guiwitz]

Can you update again with
pip install --upgrade git+https://github.com/guiwitz/MorphoDynamics.git@master#egg=morphodynamics

then open a notebook (or directly in the terminal) check the version and tell me the output:

import morphodynamics
morphodynamics.__version__

[mheydasch]

If I use that command in the terminal, I do get the error 'command not found'
If I use the command in the morphodynamics notebook I get version '0.0.0'
If I use the command in Spyder I get output '0.2.0'
edit: after again running the update comment you suggested, the error still persists but now version output is:
'0.2.1.dev4+g847ec3b'

I completely deleted the morphodynamics folder, removed the morphodynamics environment and redownloaded everything.
Saving the .csv files from the Morphodynamic segmentation works, too. But neither 'tiff', not 'TIF' files work currently. Only 'tif' works.

[guiwitz]

Ok this is strange, can you also upload the problematic data so that I can check. Regarding the versions, the last one is the correct one. I guess you were using the "local" cloned version instead of the one installed with pip.