batch_processing.py does not recognize tiff files in some cases about aics-segmentation

[jxchen01]

Are you running within a conda environment as the installation guide suggested? If so, can you copy and paste the console output after running pip show aicssegmentation and pip show pip show aicsimageio`?

[gewitterblitz]

Yes, running this in a conda environment. Here's the output for pip show aicssegmentation

Name: aicssegmentation
Version: 0.1.16.dev4
Summary: Scripts for structure segmentation.
Home-page: UNKNOWN
Author: AICS
Author-email: [email protected]
License: Allen Institute Software License
Location: /Users/sharm261/Documents/aics-segmentation
Requires: numpy, scipy, scikit-image, pandas, aicsimageio, aicsimageprocessing, numba, itk
Required-by:

and pip show aicsimageio

Name: aicsimageio
Version: 0.6.4
Summary: A generalized scientific image processing module from the Allen Institute for Cell Science.
Home-page: UNKNOWN
Author: AICS
Author-email: [email protected]
License: Allen Institute Software License
Location: /anaconda3/envs/segmentation/lib/python3.6/site-packages
Requires: matplotlib, scipy, numpy, scikit-image, Pillow, imageio, tifffile
Required-by: aicssegmentation

[jxchen01]

The packages look correct to me. There are a couple to easy/quick things to try.

(1) If you simply add print(filenames) in https://github.com/AllenInstitute/aics-segmentation/blob/master/aicssegmentation/bin/batch_processing.py#L216

The detected files should be printed out to your screen console. Then, you can make sure they are exactly what you are trying to run on.

(2) If the filenames shown in the test above are different from what you are expecting, you can try insert print(os.listdir(args.input_dir)) as you did above. This is kind of making sure the program is getting the correct directory.