integrating generate renders to pipeline #32
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and some code refactoring to reduce number of output files
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README has now been updated. |
| for p in args.participant_label: | ||
| to_deface.extend(glob(os.path.join(args.bids_dir, f'sub-{p}', "ses-*"))) | ||
| to_deface.extend(list(args.bids_dir.joinpath(f'sub-{p}').glob("ses-*"))) |
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glob 1. These comments are just making sure this was intentional.
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Yes, this was intentional just to stay consistent with usage of pathlib library coz all the other scripts use pathlib.Path objects. And I think it's a bit more readable too.
| if not to_deface: | ||
| to_deface = glob(os.path.join(args.bids_dir, f'sub-{p}')) | ||
| to_deface = list(args.bids_dir.glob(f'sub-{p}')) |
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glob 2. These comments are just making sure this was intentional.
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yes, and same reasoning as above.
| for s in args.session_id: | ||
| to_deface = glob(os.path.join(args.bids_dir, "sub-*", f'ses-{s}')) | ||
| to_deface = list(args.bids_dir.rglob(f'ses-{s}')) |
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rglob 1. These comments are just making sure this was intentional.
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yes, and same reasoning as above.
| if args.participant_label == None and args.session_id == None: | ||
| session_check = glob(os.path.join(args.bids_dir, "sub-*", "ses-*")) | ||
| if args.participant_label is None and args.session_id is None: | ||
| session_check = list(args.bids_dir.rglob("ses-*")) |
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rglob 2. These comments are just making sure this was intentional.
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yes, and same reasoning as above. Also, I tested each of these changes specifically to make sure it doesn't affect the functionality.
README fixes.
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I spoke too soon! I got a lot of:
I was testing over an SSH connection on curium from my VPN'ed PC. I don't know whether or not that should have worked... I will try direct on curium one more time and then I'm done. But this begs the question, "how can a user ONLY generate renders if they fail the first time and save all that defacing again?" we may want to file an issue to add |
ericearl
dismissed
their stale review
I was wrong, it did not work on my second test either in the generate renders portion.
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@ericearl I'll try this out on curium too but just to confirm, did you have fsleyes on your env? |
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Oy. I did forget to activate conda again. Testing over right now... |
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It was the conda environment, got me again. |
Co-authored-by: Eric Earl <[email protected]>
Co-authored-by: Eric Earl <[email protected]>
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@ericearl Great, thank you! I'll merge this to main and do some more testing with the main branch. |
This PR includes the following changes:
I've tested the code on two sample datasets from start to end, and its working as expected.
Things to do before it can be merged: