enable gpu load nifti

[yiheng-wang-nv]

Related to #8241 .

Description

A few sentences describing the changes proposed in this pull request.

Types of changes

• Non-breaking change (fix or new feature that would not break existing functionality).
• Breaking change (fix or new feature that would cause existing functionality to change).
• New tests added to cover the changes.
• Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
• Quick tests passed locally by running ./runtests.sh --quick --unittests --disttests.
• In-line docstrings updated.
• Documentation updated, tested make html command in the docs/ folder.

[yiheng-wang-nv]

related topic in: nipy/nibabel#1385

Will modify my draft PR accordingly.

[yiheng-wang-nv]

Hi @Nic-Ma @KumoLiu @ericspod , here I added a TODO, and later after finishing an acceleration tutorial, I will submit a separate PR to update the docstrings. What do you think?

[ericspod]

Is there any way to do that warm up call in some other way, such as in the constructor?

[yiheng-wang-nv]

Hi @ericspod , thanks for the suggestions.
Yes, we can do in the constructor, and trigger if to_gpu=True. However, there is no standard warm up way according to kvikio team's information. My current method is:

def warm_up():
    a = cp.arange(100)
    with tempfile.NamedTemporaryFile(delete=False) as tmp_file:
        tmp_file_name = tmp_file.name
        f = kvikio.CuFile(tmp_file_name, "w")
        # Write whole array to file
        f.write(a)
        f.close()

        b = cp.empty_like(a)
        f = kvikio.CuFile(tmp_file_name, "r")
        f.read(b)

I think it can be used in practical, or in a tutorial, but I'm not sure if it's formal to add this kind of code in our reader. What do you think?

[ericspod]

This is the probably only way if there's nothing to explicitly init things, so it's up to you if avoiding the slow initial call is worth adding this. I would add a comment about why this is here and set delete_on_close to False instead of delete in the context manager.

[KumoLiu]

Thank you for your contribution!

I have a question about this enhancement: Will it load NIfTI/DICOM files to the GPU faster compared to caching all the data on the GPU? If not, does this option use less GPU memory since the metadata is stored on the CPU? Thanks.

[yiheng-wang-nv]

Thank you for your contribution!

I have a question about this enhancement: Will it load NIfTI/DICOM files to the GPU faster compared to caching all the data on the GPU? If not, does this option use less GPU memory since the metadata is stored on the CPU? Thanks.

Hi @KumoLiu , these are two different things. The enhanced reader can load nii images from disk to GPU directly (the old way is to load from disk to cpu, and then convert from cpu to gpu), and the loaded data can do other things, like cache as you mentioned.

[yiheng-wang-nv]

Hi @KumoLiu , do you know what is the root cause of the doc error: https://github.com/Project-MONAI/MONAI/actions/runs/12311294929/job/34361260922?pr=8188#step:7:247
cupy and kvikio are only imported optionally, I'm not sure why we have the error. Do I need to modify some other places?

[KumoLiu]

Hi @KumoLiu , do you know what is the root cause of the doc error: https://github.com/Project-MONAI/MONAI/actions/runs/12311294929/job/34361260922?pr=8188#step:7:247 cupy and kvikio are only imported optionally, I'm not sure why we have the error. Do I need to modify some other places?

Yes, you may need include cupy here: https://github.com/Project-MONAI/MONAI/blob/dev/docs/requirements.txt

[ericspod]

Does the typing work if CuPy isn't installed? I don't know if our CICD tests are going to catch when it's not.

[yiheng-wang-nv]

Thanks @ericspod . TYPE_CHECKING requires the library is installed, but install cupy and kvikio in our CI/CD machine seems not easy (cannot simply add in requirements.txt)
Therefore, I remove this type hint and remove the import from TYPE_CHECKING. Do you think it's fine?

[ericspod]

I think we have to be pragmatic so if that works let's do it for now. Users who don't have Cupy installed would have issues too. I'd suggest later looking at defining some sort of placeholder type for Cupy so we can type things as either sort of ndarray.