When using the relative paths for ${IO_DIRECTORY} (see README.md) to execute inference using inference.py, there's a duplication of the ${IO_DIRECTORY} in the args.dir and all subsequent dependent variables -- most notably options['test_folder]. First reported by @creativedoctor via email
Expected Behavior
When executing inference using either
./inference.py FCD_001 t1.nii.gz t2.nii.gz ./data cuda0 1 1 or ./inference.py FCD_001 t1.nii.gz t2.nii.gz /home/user/deepFCD/app/data cuda0 1 1, ./data/FCD_001 should map to /home/user/deepFCD/app/data/FCD_001
Actual Behavior
Instead, ./data maps to ./data/FCD_001/./data/FCD_001/
Possible Fix
Convert all relative path instances of args.dir to absolute paths
Steps to Reproduce
See Expected Behaviour
Context
${IO_DIRECTORY} was placed inside the deepFCD root folder. Untested whether this affects absolute paths outside the deepFCD root folder
Your Environment
Version used (e.g. v1.1.1 or commit hash): NOEL-MNI/deepFCD@d13c903
Environment name and version: Linux (Conda 4.11 w/ Python 3.7.13)
Description
When using the relative paths for
${IO_DIRECTORY}(seeREADME.md) to execute inference usinginference.py, there's a duplication of the${IO_DIRECTORY}in theargs.dirand all subsequent dependent variables -- most notablyoptions['test_folder]. First reported by @creativedoctor via emailExpected Behavior
When executing inference using either
./inference.py FCD_001 t1.nii.gz t2.nii.gz ./data cuda0 1 1or./inference.py FCD_001 t1.nii.gz t2.nii.gz /home/user/deepFCD/app/data cuda0 1 1, ./data/FCD_001 should map to/home/user/deepFCD/app/data/FCD_001Actual Behavior
Instead,
./datamaps to./data/FCD_001/./data/FCD_001/Possible Fix
Convert all relative path instances of
args.dirto absolute pathsSteps to Reproduce
See Expected Behaviour
Context
${IO_DIRECTORY}was placed inside thedeepFCDroot folder. Untested whether this affects absolute paths outside thedeepFCDroot folderYour Environment