BIDS App preparation and serial/parallel behavior #21
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Made the code work for my data.
Adds stable parallel/serial processing and BIDS-App style inputs.
Updated the CLI display block
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Thanks for the PR @ericearl ! I'll test out the branch sometime mid-next week and add comments here. I'm working on a few issues on integrate-into-bids-tree branch, and I don't want to make new changes until I've resolved functional issues pertaining to running the pipeline on HPC and visualizing on TurboVNC. |
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@Arshitha You're welcome! If you want to point me to data that I didn't curate I can continue testing and iterate through usage and non-usage of flags, etc. I've been testing on curium with the C11 data and it's really easy to launch concurrently (I'm re-running tests since my last tests were before the merge). Let me know if you want another set of eyes or hands on the HPC and viz issues on TurboVNC. |
- Update shutil.move() to use absolute paths - Update the afni refacer cmd to use only one core, OMP_NUM_THREADS=1
Trying the pathlib Path.rename() function
Finally fixed the little shutil.move command
First attempt ayt parllelizing the renders with a -n argument
Update generate_renders.py
Broke a variable name during the last merge, fixed here
Hefty bunch of mini-edits to the README for this branch.
| subj_id = os.path.basename(subj_input_dir) | ||
| sess_id = os.path.basename(sess_dir) if sess_dir else None |
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This is a minor comment/question. Is there a reason you're using os.path.basename() instead of the pathlib function which does the same thing?
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I forgot the correct command and didn't want to look it up, so I used what I knew, which you're right does the same job. Also, if I remember right the subj_input_dir and sess_dir variables are strings coming into those arguments and not Path objects.
Wonderful additions! Co-authored-by: Arshitha Basavaraj <[email protected]>
Accepting per suggestion. Co-authored-by: Arshitha Basavaraj <[email protected]>
Accepting more per previous suggestion. Co-authored-by: Arshitha Basavaraj <[email protected]>
- change participant_label and session_id to default to None - add accompanying flow control logic for using None as the default
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@ericearl Thank you for you patience while I tested and reviewed this! PR has been to |
I started to move away from the "BIDS-App-like" behavior and started moving toward "BIDS-App" behavior like this:
https://github.com/bids-apps/example/blob/master/run.py
This involved changing the CLI. I also updated the serial and parallel behavior to rely on a
--n-cpusor-nargument provided an integer. I also recognize the README still needs an overhaul here, but the functionality is solid and tested in all four cases of:All "Local" runs were performed on curium. I'm happy to talk about this at your convenience.
Full disclosure, I have not tested the latest changes to the VisualQC prep'ed files. But I can quickly now if you'd prefer.