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add UNETR, ViT#2476

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wyli merged 8 commits intoProject-MONAI:devfrom
ahatamiz:2394-unetr-v2
Jul 1, 2021
Merged

add UNETR, ViT#2476
wyli merged 8 commits intoProject-MONAI:devfrom
ahatamiz:2394-unetr-v2

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@ahatamiz ahatamiz commented Jun 29, 2021 •
edited by wyli
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Signed-off-by: ahatamizadeh [email protected]

fixes #2403, part of #2394

Description

This pull request adds the following:

Status

Ready

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.
  • In-line docstrings updated.
  • Documentation updated, tested make html command in the docs/ folder.

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add UNETR, ViT
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Signed-off-by: ahatamizadeh <[email protected]>
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ahatamiz commented Jun 29, 2021

/black

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ahatamiz commented Jun 29, 2021

@wyli , @Nic-Ma

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wyli commented Jun 29, 2021

Looks nice! Could you help fix the style errors? https://github.com/Project-MONAI/MONAI/runs/2940634277

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add UNETR, ViT
d268f96 
Signed-off-by: ahatamizadeh <[email protected]>
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ahatamiz commented Jun 29, 2021

Looks nice! Could you help fix the style errors? https://github.com/Project-MONAI/MONAI/runs/2940634277

@wyli, fixed those issues. But there are further issues in lint and type checks which I will address.

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wyli reviewed Jun 29, 2021
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thanks, the networks mainly support 3d, would be great to add the 2d support. or we could file a separate feature request and address that later.

monai/networks/blocks/mlp.py
self.drop2 = nn.Dropout(dropout_rate)

def forward(self, x):
x = self.fn(self.linear1(x))
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might be more robust if there's a torch.flatten as the first step?

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wyli commented Jun 29, 2021

Looks nice! Could you help fix the style errors? https://github.com/Project-MONAI/MONAI/runs/2940634277

@wyli, fixed those issues. But there are further issues in lint and type checks which I will address.

sure, in many cases mypy is not smart enough to infer the types and can be difficult to fix... you can use # type: ignore to skip the checks if needed

ahatamiz added 4 commits June 30, 2021 00:32
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add UNETR, ViT
70674f7 
Signed-off-by: ahatamizadeh <[email protected]>
@ahatamiz
add UNETR, ViT
c49d9f5 
Signed-off-by: ahatamizadeh <[email protected]>
@ahatamiz
add UNETR, ViT
70c2a19 
Signed-off-by: ahatamizadeh <[email protected]>
@ahatamiz
add UNETR, ViT
4f864a4 
Signed-off-by: ahatamizadeh <[email protected]>
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wyli commented Jun 30, 2021

I think the unit tests took too long to finish on cpu-only testing machine, could you reduce the input size/model size in the unit tests? otherwise please add @skip_if_quick to the test cases, for example

MONAI/tests/test_ahnet.py

Lines 128 to 129 in 12f267c

@skip_if_quick
def test_fcn_shape(self, input_param, input_shape, expected_shape):

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ahatamiz commented Jul 1, 2021

I think the unit tests took too long to finish on cpu-only testing machine, could you reduce the input size/model size in the unit tests? otherwise please add @skip_if_quick to the test cases, for example

MONAI/tests/test_ahnet.py

Lines 128 to 129 in 12f267c

@skip_if_quick
def test_fcn_shape(self, input_param, input_shape, expected_shape):

Pushed another version with reduced input sizes. Tests seem to be done in reasonable amount of time on CPU.

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Thanks! It looks nice. Could you please help create a ticket about supporting 2d patch embedding and networks

@wyli wyli merged commit d41af7e into Project-MONAI:dev Jul 1, 2021
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ahatamiz commented Jul 1, 2021

Thanks! It looks nice. Could you please help create a ticket about supporting 2d patch embedding and networks

Thanks a lot ! I just created #2499 in response to this.

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generic image-based attention modules (6/July)

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