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2499 adds 2d/3d support of patchembedding, ViT, and unetr model #2698

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ahatamiz merged 8 commits into from
Aug 6, 2021
Merged

2499 adds 2d/3d support of patchembedding, ViT, and unetr model #2698

ahatamiz merged 8 commits into from
Aug 6, 2021

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@wyli
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@wyli wyli commented Aug 5, 2021 •
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Signed-off-by: Wenqi Li wenqil@nvidia.com

part of #2499

Description

the current patchembedding/vit model only supports 3d input,
this PR extends them for 2d

Status

Ready

Types of changes

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

@wyli wyli requested review from Nic-Ma and ahatamiz August 5, 2021 16:07
@wyli
2d/3d patchembedding
363e574 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli wyli force-pushed the 2499-2d-patchembedding branch from d2722a7 to 363e574 Compare August 5, 2021 16:10
@wyli wyli changed the title adds support of 2d patchembedding adds support of 2d/3d patchembedding Aug 5, 2021
@ahatamiz
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ahatamiz commented Aug 5, 2021 •
edited by wyli
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/black

wyli added 4 commits August 5, 2021 18:04
@wyli
minor updates for selfattention
3d72d08 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
Merge branch '2499-2d-patchembedding' into 2499-self-attention
fb3157a
@wyli
2d vit
a41bdfd 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
fixes type hint
e248698 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli wyli changed the title adds support of 2d/3d patchembedding adds support of 2d/3d patchembedding and the ViT model Aug 5, 2021
@wyli
update unetr
f822f67 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli wyli changed the title adds support of 2d/3d patchembedding and the ViT model adds 2d/3d support of patchembedding, ViT, and unetr model Aug 5, 2021
@wyli wyli changed the title adds 2d/3d support of patchembedding, ViT, and unetr model 2499 adds 2d/3d support of patchembedding, ViT, and unetr model Aug 5, 2021
@wyli
fixes unit test
10d6117 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Nic-Ma
Nic-Ma approved these changes Aug 6, 2021
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Thanks for the enhancement.
PR looks good to me.
@ahatamiz could you please help double confirm as you are expert on the UNETR, I may missed to check some computation theory.

Thanks in advance.

ahatamiz
ahatamiz approved these changes Aug 6, 2021
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Thanks @wyli for the great work.

This PR looks good to me.

@ahatamiz ahatamiz merged commit 62425d7 into Project-MONAI:dev Aug 6, 2021
@wyli wyli deleted the 2499-2d-patchembedding branch August 6, 2021 14:20
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ahatamiz commented Aug 6, 2021

Thanks for the enhancement.
PR looks good to me.
@ahatamiz could you please help double confirm as you are expert on the UNETR, I may missed to check some computation theory.

Thanks in advance.

Thanks @Nic-Ma for your review.

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@Nic-Ma Nic-Ma Nic-Ma approved these changes

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@ahatamiz ahatamiz ahatamiz approved these changes

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3 participants

@wyli @ahatamiz @Nic-Ma