I hit this error in formatting the log warning when I didn't provide min_sc and max_sc as inputs. I was expecting it to warn me, and then move on using some default choices, but instead the formatting error in the warning breaks the script.
The problem is that os.path.join() will only accept str, bytes or os.PathLike object, not a zarr group.
To get a string path from the zarr group, we can use rf.store.dir_path() instead of just rf. That is the suggestion in this PR.
File ~/...CNNectome/CNNectome/inference/unet_inference.py in get_contrast_adjustment(rf, raw_ds)
102 logging.warning(
103 ("min_sc and max_sc not specified and contrastAdjustment not found in attributes of {0:}, will "
104 "continue with default contrast (min {1:}, max{2:}").format(
---> 105 os.path.join(rf.store.dir_path(), raw_ds), min_sc, max_sc
106 )
107 )
---> os.path.join(rf, raw_ds), min_sc, max_sc
TypeError: expected str, bytes of os.Pathlike object, not Group
I hit this error in formatting the log warning when I didn't provide
min_scandmax_scas inputs. I was expecting it to warn me, and then move on using some default choices, but instead the formatting error in the warning breaks the script.The problem is that os.path.join() will only accept str, bytes or os.PathLike object, not a zarr group.
To get a string path from the zarr group, we can use
rf.store.dir_path()instead of justrf. That is the suggestion in this PR.