Closed hermancollin closed 2 years ago
I'm looking at the section of code that starts here.
It's a bit hard to follow how variables with paths are used. I admit I haven't tested the -i
option when implementing the index images.
Ok so the main reason why this was confusing is because of this except block: https://github.com/axondeepseg/axondeepseg/blob/443c0579f417f8b1d0046e3904f9d54220b6091e/AxonDeepSeg/morphometrics/launch_morphometrics_computation.py#L237-L239
where the error is caught but not re-raised again. This should be fixed.
Describe the bug Using the
axondeepseg_morphometrics
script and specifying folders with the-i
option produces an unwanted behavior.The first point was reported by @mathieuboudreau last week when he tried to run morphometrics via the CLI with subfolders, similar to what is described here.
When running the script directly in the folder containing the segmentation, we do not encounter this problem and the index files are generated as expected.
Platform (please complete the following information):