Add BIDS reading support and prepare input loading for pydra workflow by maestroque · Pull Request #7 · physiopy/physutils

maestroque · 2024-08-28T13:08:07Z

Closes #9

Proposed Changes

Add a transform_to_physio pydra task to be used in all worfklows

Change Type

Checklist before review

I added everything I wanted to add to this PR.
[Code or tests only] I wrote/updated the necessary docstrings.
[Code or tests only] I ran and passed tests locally.
[Documentation only] I built the docs locally.
My contribution is harmonious with the rest of the code: I'm not introducing repetitions.
My code respects the adopted style, especially linting conventions.
The title of this PR is explanatory on its own, enough to be understood as part of a changelog.
I added or indicated the right labels.

I added information regarding the timeline of completion for this PR.

Please, comment on my PR while it's a draft and give me feedback on the development!

physutils/physio.py

setup.cfg

smoia · 2024-08-28T14:22:55Z

physutils/tasks.py

@@ -0,0 +1,34 @@
+import logging
+
+import pydra


This definitely adds complexity, but since physutils might be used by modules that are not based in pydra, could we try to create a safe import and make it optional, like the one we have for duecredit?

https://github.com/physiopy/phys2denoise/blob/master/phys2denoise/due.py

The idea would then to try from pydra.mark import task, but if it is not found, import task from a stub submodule of physutils. That task would be a decorator that returns the function.
(like here: https://github.com/BMRRgroup/wfTFI/blob/ec5a62cf2ffb347c752293e6234b7c89cebe711d/QSM.py#L7C1-L13C1)

That task would be a decorator that returns the function

What do you mean here? I'm not sure I understand how you'd like this to be done (mostly given the duecredit example).

I tried doing smth like this, but it didn't really work out

def mark_task_wrapper(func): try: import pydra logger.debug("Pydra is installed and is currently enabled.") return pydra.mark.task(func) except ImportError: logger.warning("Pydra is not installed and is currently disabled. Please install it to use this module.") return func

@smoia feel free to check, I implemented it with just a wrapper and it seems to work

me-pic · 2024-08-28T15:08:18Z

Other than the changes requested by Stef, LGTM !

m-miedema · 2024-08-29T19:45:14Z

physutils/tasks.py

+
+@pydra.mark.task
+def transform_to_physio(
+    input_file: str, mode="physio", fs=None, bids_parameters=dict(), bids_channel=None


It makes a lot of sense to add this as a task, great addition to the phys2denoise workflow and to continue to build up physutils :)

I'd like to suggest changing the name of bids_channel to col_physio_type to increase consistency with the load_from_bids function - since there is not a lot of documentation within the code itself, I think it's important to try to maintain intuitive links!

Beyond that, I'm wondering why the task is named transform_to_physio when it can either transform to physio or read-in an existing physio object. Perhaps e.g. generate_physio would be more appropriate? At minimum I think it's helpful to describe the goal of this task and its potential use cases in the description for the PR. Also, please indicate the change type in the PR description :)

Other than these considerations and what Stef mentioned above regarding avoiding a dependency on pydra, this looks good to me!

Imo, it's ok as transform_to_physio, as even in case it reads a .phys file, it transforms a pickled Physio object file, into a Physio object instance to be used in further tasks.

Also maybe it'd be better to change the variable name in load_from_bids? It's not an interface variable (not used outside the function scope) so I don't think we should take this naming as a basis

Kudos on changing name to generate_physio or something similar.
Double kudos on adding a good docstring for explanations!

maestroque · 2024-09-03T14:25:13Z

I also added an auto mode, as per physiopy/phys2denoise#57 (comment)
@smoia @me-pic @m-miedema

smoia · 2024-09-03T16:49:48Z

physutils/tasks.py

+def mark_task(pydra_imported=pydra_imported):
+    def decorator(func):
+        if pydra_imported:
+            # If the decorator exists, apply it
+            @wraps(func)
+            def wrapped_func(*args, **kwargs):
+                logger.debug(f"Creating pydra task for {func.__name__}")
+                return pydra.mark.task(func)(*args, **kwargs)
+
+            return wrapped_func
+        # Otherwise, return the original function
+        return func
+
+    return decorator


That may work, but I honestly was thinking about something like:

def task(func): @functools.wraps(func) def wrapper(*args, **kwargs): return func(*args, **kwargs) return wrapper

In a utils module, and then here:.

try: from pydra.mark import task except ImportError: from .utils import task

smoia · 2024-09-03T16:51:19Z

physutils/tasks.py

+    input_file: str, mode="physio", fs=None, bids_parameters=dict(), bids_channel=None
+) -> Physio:
+    if not pydra_imported:
+        LGR.warning(


Suggested change

LGR.warning(

LGR.debug(

smoia · 2024-09-03T16:54:05Z

setup.cfg

    numpy >=1.9.3
-    scipy
    loguru
+    pydra


Move this to an extra

smoia · 2024-09-03T16:56:47Z

setup.cfg

-    scipy
    loguru
+    pydra
    pybids


Eventually, we need to move this to extras as well (it comes with SO MANY dependencies). Could you please open an issue to generically move as many dependencies as possible to extra dependencies? Not now, but it would be good to do so later.

m-miedema · 2024-09-26T18:22:30Z

@maestroque do you need any help addressing @smoia's comments?

smoia · 2024-10-09T15:52:17Z

@maestroque any progress on this side?

maestroque · 2024-10-09T17:15:30Z

@smoia @m-miedema I didnt have in mind that there was something pending for this sorry. As far as i can tell only the dependencies issue opening

smoia · 2024-10-09T18:43:05Z

physutils/tasks.py

+    if not fs:
+        fs = None


I'm a bit confused about these two lines, was there something you were trying to check?

…trings, rename transform_to_physio function

smoia · 2024-10-09T19:18:44Z

@maestroque @m-miedema @me-pic I opened a PR to @maestroque 's branch: ~~https://github.com/maestroque/physutils/pull/1/files~~ https://github.com/maestroque/physutils/pull/2/files

It should take care of most issues. Emphasis on should.

smoia · 2024-10-09T19:26:57Z

And I also made a mess out of it - sorry. I shoudl have fixed things now, but the PR is #2 not #1

smoia · 2024-10-09T19:28:46Z

The only thing is that logging is still a bit weird cause it uses logging on one side and loguru on the other. Maybe we should just use logging for the moment?

A few mods stemming from PR convo

smoia

LGTM!

me-pic · 2024-10-16T00:14:26Z

physutils/tests/test_tasks.py

+        input_file=bids_dir,
+        mode="bids",
+        bids_parameters=bids_parameters,
+        bids_channel="cardiac",


This is failing since bids_channel is not a valid argument in the generate_physio function

Ok just realized looking at the previous comments that bids_channel was changed to col_physio_type in generate_physio, but the test_tasks.py have not been update accordingly

physutils/tests/test_tasks.py

me-pic · 2024-10-16T00:28:08Z

physutils/tests/test_tasks.py

+    assert task.inputs.input_file == physio_file
+    assert task.inputs.mode == "physio"
+    assert task.inputs.fs is None


pytest is failing.. inputs is not an attribute included in the Physio class, nor input_file or mode...

inputs is a pydra task attribute specifying the input struct of the task, it may be that the new changes making pydra optional broke the tests. Before the tests were successful

physutils/tests/test_tasks.py

me-pic

All the tests in test_tasks.py are failing... Not sure I understand the inputs attribute. Also all the bids_channel need to be changed to col_physio_type

maestroque · 2024-10-16T07:37:21Z

@me-pic @smoia please check the comments, unfortunately I cannot look into this right now. Before the changes it was ready however.

me-pic · 2024-10-25T16:32:38Z

physutils/tasks.py

+# from loguru import logger
+
+try:
+    from pydra import task


@smoia Is it possible that here it should be from pydra.mark import task instead of from pydra import task ?

With that change test_generate_physio_bids_file and test_generate_physio_auto in test_tasks.py are now passing 🤔

Yes that could be it actually. Thank you for catching it!

smoia · 2024-10-25T17:50:48Z

🚀 PR was released in 0.3.0 🚀

maestroque added 6 commits July 22, 2024 16:05

Initial pydra transformation task

557513e

Update pydra task

52cc61e

Pull updates from master

9c224f0

Add BIDS loading option to transform_to_physio task

05d90ea

Working transform_to_physio pydra task and tests

cb67b7c

Verify transform_to_physio for BIDS files

e10c9b2

github-actions bot assigned maestroque Aug 28, 2024

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maestroque added Minormod and removed Testing Internal labels Aug 28, 2024

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maestroque requested review from m-miedema and me-pic August 28, 2024 14:16

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m-miedema mentioned this pull request Aug 29, 2024

Add pydra tasks, workflow and update CLI physiopy/phys2denoise#57

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18 tasks

maestroque added 3 commits September 3, 2024 16:53

Add wrapper for pydra tasks, in order to eliminate pydra requirement

67ee789

Add better logs for pydra package import handling

3a08510

Add transform_to_physio auto mode

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setup.cfg Outdated

numpy >=1.9.3

scipy

loguru

pydra

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Move this to an extra

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smoia added 2 commits October 9, 2024 21:13

Create utils and move there pydra checks and BIDS directory checks

a19bc19

Clean code, remove moved functions, remove pydra mask check, add docs…

34fc89d

…trings, rename transform_to_physio function

Remove extras

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smoia force-pushed the add-pydra branch from 94b711c to 1cd7539 Compare October 9, 2024 19:24

Merge pull request #2 from smoia/add-pydra

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A few mods stemming from PR convo

smoia changed the title ~~Add transform_to_physio pydra task~~ Add BIDS reading support and prepare input loading for pydra workflow Oct 12, 2024

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Fix test tasks

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me-pic merged commit ab85017 into physiopy:master Oct 25, 2024

smoia added the released label Oct 25, 2024

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