enable gpu load nifti #8188

yiheng-wang-nv · 2024-11-02T00:11:44Z

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.

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

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yiheng-wang-nv · 2024-11-07T05:27:45Z

related topic in: nipy/nibabel#1385

Will modify my draft PR accordingly.

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

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monai/data/image_reader.py

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

for more information, see https://pre-commit.ci

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

for more information, see https://pre-commit.ci

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

monai/data/image_reader.py

KumoLiu · 2024-12-13T08:30:31Z

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 · 2024-12-13T08:56:27Z

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 · 2024-12-13T09:03:56Z

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 · 2024-12-13T09:14:39Z

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

monai/data/image_reader.py

Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Signed-off-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com>

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

monai/data/image_reader.py

Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Signed-off-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com>

KumoLiu · 2024-12-19T05:36:14Z

/build

KumoLiu · 2024-12-19T08:26:04Z

monai/data/meta_tensor.py

@@ -565,7 +572,7 @@ def ensure_torch_and_prune_meta(
        if simple_keys:
            # ensure affine is of type `torch.Tensor`
            if MetaKeys.AFFINE in meta:
-                meta[MetaKeys.AFFINE] = convert_to_tensor(meta[MetaKeys.AFFINE])  # bc-breaking
+                meta[MetaKeys.AFFINE] = convert_to_tensor(meta[MetaKeys.AFFINE], device=device)  # bc-breaking


May don't need move affine to device here.

Hi @KumoLiu , thanks for the comments, I removed the device arg, and re-tested the changes with decathlon Task03_Liver dataset.

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

KumoLiu · 2024-12-21T14:27:07Z

/build

yiheng-wang-nv added 2 commits November 2, 2024 08:11

enable gpu load nifti

84d8cf3

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

fix issue

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yiheng-wang-nv force-pushed the add-gds-support-on-niftireader branch from ed1de7e to ca1cfb8 Compare November 2, 2024 00:35

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update loadimage

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update filename

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update supported reader

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update load image call

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yiheng-wang-nv and others added 3 commits November 8, 2024 13:55

Merge branch 'dev' into add-gds-support-on-niftireader

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reformat to add gpu load support on nibabelreader

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Possible feature: add GPU Direct Storage Support for Nibabel nipy/nibabel#1401

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yiheng-wang-nv and others added 5 commits December 12, 2024 12:05

Merge branch 'dev' into add-gds-support-on-niftireader

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yiheng-wang-nv requested review from KumoLiu, Nic-Ma and ericspod December 13, 2024 06:51

add description on warm up

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yiheng-wang-nv and others added 4 commits December 16, 2024 15:08

Update monai/data/image_reader.py

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add doc string

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resolve comments

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Update monai/data/image_reader.py

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Update monai/data/image_reader.py

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Update monai/data/image_reader.py

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remove device set

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enable gpu load nifti #8188

enable gpu load nifti #8188

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KumoLiu commented Dec 21, 2024

enable gpu load nifti #8188

Are you sure you want to change the base?

enable gpu load nifti #8188

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