Type checking issues

[blakedewey]

Hi Nibabel community,

Great job on getting some type checking into this package! I wanted to point out two scenarios that I use frequently that have run me into type checking issues based on 5.1.0.

1. nb.load shows a return type of FileBasedImage. This is all well and good, but unfortunately FileBasedImage does not define get_fdata(). A common code example that I use (and see around) is:

obj = nb.load(filepath)
data = obj.get_fdata()

2. nb.Nifti1Image doesn't want to take None for the affine. I previously saw this code used frequently:

nb.Nifti1Image(data_array, None, header)

Just bringing these to your attention. I'm also flexible to change up my code, if better patterns are recommended.

[blakedewey]

Just saw this comment #1109 (comment). I think this change to SpatialImage would fix my first issue.

[effigies]

Have you seen #1220 (comment)?

[blakedewey]

Ah. I had not. Good resource. I was wondering if that would have to be the case. It honestly is smarter code anyways, even if it is more verbose.

[effigies]

2. nb.Nifti1Image doesn't want to take None for the affine. I previously saw this code used frequently:

nb.Nifti1Image(data_array, None, header)

I'm a bit surprised by this. We haven't typed the __init__ method at this point, so I would expect it to be Any. What type checker are you using, and what error do you see?

[blakedewey]

This is in my IDE. I use PyCharm from JetBrains. The error I get is Expected type 'ndarray', got 'None' instead. I'm assuming it's doing some kind of inspection of how it's assigned somewhere in lieu of a known type.

[effigies]

Ah, I bet it's picking up on the SpatialImage.__init__:

nibabel/nibabel/spatialimages.py

Lines 481 to 488 in 1843355

	def __init__(
	self,
	dataobj: ArrayLike,
	affine: np.ndarray,
	header: FileBasedHeader | ty.Mapping | None = None,
	extra: ty.Mapping | None = None,
	file_map: FileMap | None = None,
	):

affine should be np.ndarray | None.

[blakedewey]

Is that as easy of a PR as I think? I can submit fix, if so.

[effigies]

I think it should be, yes. Please go ahead.

[blakedewey]

#1253 is open. Closing this issue as both concerns have been addressed.