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support GPU tensor for GridPatch and GridPatchDataset#6246

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wyli merged 10 commits intoProject-MONAI:devfrom
qingpeng9802:support_GPUTensor_gridpatch
Mar 29, 2023
Merged

support GPU tensor for GridPatch and GridPatchDataset#6246
wyli merged 10 commits intoProject-MONAI:devfrom
qingpeng9802:support_GPUTensor_gridpatch

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@qingpeng9802 qingpeng9802 commented Mar 27, 2023

Fixes #6245 .

Description

support GPU tensor for

  • GridPatch, GridPatchd, RandGridPatch and RandGridPatchd
  • GridPatchDataset, PatchIter, PatchIterd and iter_patch

Changes

Need to Notice

  • Default padding mode of PatchIter, PatchIterd and iter_patch are kept as NumpyPadMode.WRAP. However, GridPatch defaults to None. (might be inconsistent?)

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.

qingpeng9802 and others added 2 commits March 27, 2023 21:56
@qingpeng9802
support GPU tensor for
4d178e2 
* `GridPatch`, `GridPatchd`, `RandGridPatch` and `RandGridPatchd`
* `GridPatchDataset`, `PatchIter`, `PatchIterd` and `iter_patch`
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wyli commented Mar 28, 2023

/black

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[MONAI] code formatting
537f6c2 
Signed-off-by: monai-bot <[email protected]>
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qingpeng9802 commented Mar 28, 2023

By checking the tests in CI, it seems torch.argwhere has some compatibility issues. From pytorch/pytorch#64257, would it be better to replace torch.argwhere with torch.nonzero or a version-specified solution?

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wyli commented Mar 28, 2023

By checking the tests in CI, it seems torch.argwhere has some compatibility issues. From pytorch/pytorch#64257, would it be better to replace torch.argwhere with torch.nonzero or a version-specified solution?

thanks, let me skip the tests for this new feature for torch<1.11...

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update to skip test
b926426 
Signed-off-by: Wenqi Li <[email protected]>
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wyli commented Mar 28, 2023

there are still some typing issues, I think you can debug with ./runtests.sh --mypy locally. also please follow this page to sign the commit https://github.com/Project-MONAI/MONAI/pull/6246/checks

qingpeng9802 and others added 2 commits March 29, 2023 18:16
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fix type check
27721d5 
DCO Remediation Commit for Qingpeng Li <[email protected]>

I, Qingpeng Li <[email protected]>, hereby add my Signed-off-by to this commit: 4d178e2

Signed-off-by: Qingpeng Li <[email protected]>
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qingpeng9802 commented Mar 29, 2023

/black

monai-bot and others added 2 commits March 29, 2023 10:33
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[MONAI] code formatting
8f64c3d 
Signed-off-by: monai-bot <[email protected]>
@qingpeng9802
fix type check
b546d28 
Signed-off-by: Qingpeng Li <[email protected]>
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wyli commented Mar 29, 2023

/build

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wyli commented Mar 29, 2023

/build

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update
3aa7879 
Signed-off-by: Wenqi Li <[email protected]>
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wyli commented Mar 29, 2023

/build

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thanks, it looks good to me. @ericspod @Nic-Ma @KumoLiu if you have further comments I can create followup PRs.

@wyli wyli merged commit e2f9d51 into Project-MONAI:dev Mar 29, 2023
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@wyli wyli wyli approved these changes

@yiheng-wang-nv yiheng-wang-nv Awaiting requested review from yiheng-wang-nv

@KumoLiu KumoLiu Awaiting requested review from KumoLiu KumoLiu is a code owner

@ericspod ericspod Awaiting requested review from ericspod ericspod is a code owner

@Nic-Ma Nic-Ma Awaiting requested review from Nic-Ma Nic-Ma is a code owner

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GridPatchDataset does not support GPU tensor as the data source

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@qingpeng9802 @wyli @monai-bot