Test possible bugs with --overwrite flag & possibly default to clearing old outputs until this is resolved

[LuciMoore]

What happened?

I was debugging by running the application and had produced all of the prebibsnet outputs up until the point that the prebibsnet output anatomicals are copied into the bibsnet input folder. I ran the application again using the --overwrite flag (for reasons that aren't relevant here) and it errored at https://github.com/DCAN-Labs/CABINET/blob/main/run.py#L666 because the output file didn't exist yet from the prior run, so when it tries to remove it there is a file not found error

I would suggest that we only run the copy command whether the file exists or not (if it doesn't exist, it will create it and if it does exist from a prior run, it will be overwritten).

So replace:

        if j_args["common"]["overwrite"]:  # TODO Should --overwrite delete old image file(s)?
            os.remove(out_nii_fpath)
        if not os.path.exists(out_nii_fpath): 
            shutil.copy2(transformed_images[f"T{t}w"], out_nii_fpath)

with:

        if j_args["common"]["overwrite"]:  # TODO Should --overwrite delete old image file(s)?
            shutil.copy2(transformed_images[f"T{t}w"], out_nii_fpath)        

We'll also want to look through the rest of the code base to make sure this issue doesn't exist elsewhere

What command did you use?

not relevant - logic is apparent in code

What version of CABINET are you using?

2.4.0

Relevant log output

No response

Add any additional information or context about the problem here.

No response

[kellyhi08]

I believe I ran into a similar problem when using the overwrite flag. My command worked without it, but failed with the overwrite flag.

Command that works
singularity run --nv --cleanenv --no-home -B $path/BIBSnet_inputs/:/input -B $path/BIBSnet_outputs:/output $path/infant/BIBSnet/bibsnet.sif /input /output participant -v --participant-label $subnum -z

Command that does not work
singularity run --nv --cleanenv --no-home -B $path/BIBSnet_inputs/:/input -B $path/BIBSnet_outputs:/output $path/infant/BIBSnet/bibsnet.sif /input /output participant -v --participant-label $subnum -z --overwrite
Error
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/bibsnet/bibsnet/sub-019/ses-01/input/sub-019_ses-01_optimal_resized_0000.nii.gz'

[LuciMoore]

adding info from related issue #46: in prebibsnet, if the crop2full.mat files exist, it skips cropping with robustfov. we should also look for the presence of the cropped T1 and T2 (eg cropped/T1w/sub-_ses-_0000.nii.gz) before skipping robustfov

[LuciMoore]

see relevant issue #137 - might be best to default to clearing old outputs and/or update documentation to help with triage