7047 simplify resnet pretrained by vgrau98 · Pull Request #7095 · Project-MONAI/MONAI

vgrau98 · 2023-10-06T15:01:07Z

Description

Resnet did not support True value (not implemented ) for its pretrained flag.
2 implemented behavior:

When pretrained is True, download weights from https://huggingface.co/TencentMedicalNet
When pretrained is a string, loads weights from the path defined by the string

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.

Fixes: Project-MONAI#7047 Original behaviour did not support True pretrained flag. Signed-off-by: vgrau98 <[email protected]>

Signed-off-by: vgrau98 <[email protected]>

vgrau98 · 2023-10-06T15:02:23Z

Not sure about good practices in added test

vgrau98 · 2023-10-06T15:22:05Z

Documentation should be updated too

Signed-off-by: vgrau98 <[email protected]>

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

monai/networks/nets/resnet.py

Signed-off-by: vgrau98 <[email protected]>

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

monai/networks/nets/resnet.py

Signed-off-by: vgrau98 <[email protected]>

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

Signed-off-by: vgrau98 <[email protected]>

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

vgrau98 · 2023-10-08T22:05:35Z

test_resnet gives errors, all the tests i wrote don't seem to be unitary, there's an integration part with the huggingface api. I'll try to fix this quickly by creating integration tests in the dedicated test_integration_resnet.py file. Maybe the test environment is not the same between unit and integration tests ?

wyli · 2023-10-09T09:20:55Z

/black

test_resnet gives errors, all the tests i wrote don't seem to be unitary, there's an integration part with the huggingface api. I'll try to fix this quickly by creating integration tests in the dedicated test_integration_resnet.py file. Maybe the test environment is not the same between unit and integration tests ?

thanks, please follow this guide for adding new dep https://github.com/Project-MONAI/MONAI/blob/dev/CONTRIBUTING.md#adding-new-optional-dependencies

I think the current unit test looks great, we just need to somehow pin down a specific commit hash of the model version, then I don't see much risk of regression.

Signed-off-by: vgrau98 <[email protected]>

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

vgrau98 · 2023-10-09T22:01:19Z

test_resnet gives errors, all the tests i wrote don't seem to be unitary, there's an integration part with the huggingface api. I'll try to fix this quickly by creating integration tests in the dedicated test_integration_resnet.py file. Maybe the test environment is not the same between unit and integration tests ?

thanks, please follow this guide for adding new dep https://github.com/Project-MONAI/MONAI/blob/dev/CONTRIBUTING.md#adding-new-optional-dependencies

I think the current unit test looks great, we just need to somehow pin down a specific commit hash of the model version, then I don't see much risk of regression.

Yes sorry my bad, didn't read the doc carefully enough, should be fixed now

Signed-off-by: monai-bot <[email protected]>

Signed-off-by: vgrau98 <[email protected]>

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

KumoLiu

Looks good to me, several minor comments inline.
Could you please also fix the format ci error?
https://github.com/Project-MONAI/MONAI/blob/dev/CONTRIBUTING.md#checking-the-coding-style

monai/networks/utils.py

monai/networks/nets/resnet.py

Signed-off-by: vgrau98 <[email protected]>

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

Signed-off-by: vgrau98 <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

wyli · 2023-10-18T17:49:51Z

/build

wyli · 2023-10-18T18:53:31Z

/build

wyli

thanks! trying to merge this pr for more integration tests

Signed-off-by: Wenqi Li <[email protected]>

wyli · 2023-10-18T19:46:47Z

/build

vgrau98 added 2 commits October 6, 2023 10:49

Simplify resnet pretrained flag

0613c2f

Fixes: Project-MONAI#7047 Original behaviour did not support True pretrained flag. Signed-off-by: vgrau98 <[email protected]>

add tests + typos

1005fe8

Signed-off-by: vgrau98 <[email protected]>

add MedicalNet resnet 3D pretrained models support

8b75095

Signed-off-by: vgrau98 <[email protected]>

vgrau98 force-pushed the 7047-simplify-resnet-pretrained branch from e6a29e5 to 8b75095 Compare October 6, 2023 16:26

[pre-commit.ci] auto fixes from pre-commit.com hooks

00ec022

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KumoLiu reviewed Oct 7, 2023

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KumoLiu reviewed Oct 7, 2023

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vgrau98 and others added 5 commits October 7, 2023 13:38

add optional import

f5e09b1

Signed-off-by: vgrau98 <[email protected]>

simplify user pretrained weights loading

c7a827b

Signed-off-by: vgrau98 <[email protected]>

Manage MedicalNet resnet model validation with pretrained flag

fa60fad

Signed-off-by: vgrau98 <[email protected]>

update resnet tests

e9ba99d

Signed-off-by: vgrau98 <[email protected]>

[pre-commit.ci] auto fixes from pre-commit.com hooks

0ddfb04

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KumoLiu reviewed Oct 8, 2023

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vgrau98 and others added 6 commits October 8, 2023 17:57

update resnet unit tests

06ed8b0

Signed-off-by: vgrau98 <[email protected]>

fix incorrect optional import

955dcf1

Signed-off-by: vgrau98 <[email protected]>

[pre-commit.ci] auto fixes from pre-commit.com hooks

ff7f6d3

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Merge branch 'dev' into 7047-simplify-resnet-pretrained

a707d1c

Line shortening

bb6830f

Signed-off-by: vgrau98 <[email protected]>

[pre-commit.ci] auto fixes from pre-commit.com hooks

d21a022

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vgrau98 and others added 3 commits October 9, 2023 23:10

Merge branch 'dev' into 7047-simplify-resnet-pretrained

5ac3627

update resnet tests and deployment files

3735733

Signed-off-by: vgrau98 <[email protected]>

[pre-commit.ci] auto fixes from pre-commit.com hooks

8b6782a

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wyli and others added 3 commits October 10, 2023 10:44

Merge branch 'dev' into 7047-simplify-resnet-pretrained

801edf6

[MONAI] code formatting

02a360a

Signed-off-by: monai-bot <[email protected]>

Update utils.py

1993f04

Signed-off-by: vgrau98 <[email protected]>

vgrau98 and others added 6 commits October 10, 2023 23:56

Update utils.py

e344771

Signed-off-by: vgrau98 <[email protected]>

Merge branch 'dev' into 7047-simplify-resnet-pretrained

0ea682b

Update resnet.py

be516c0

Signed-off-by: vgrau98 <[email protected]>

Update utils.py

3dd89de

Signed-off-by: vgrau98 <[email protected]>

[pre-commit.ci] auto fixes from pre-commit.com hooks

b74d48a

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

Merge branch 'dev' into 7047-simplify-resnet-pretrained

46e7acc

vgrau98 marked this pull request as ready for review October 11, 2023 22:40

KumoLiu approved these changes Oct 16, 2023

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vgrau98 and others added 11 commits October 16, 2023 09:28

fix lint error

6896216

Signed-off-by: vgrau98 <[email protected]>

minor refactos

b30ea73

Signed-off-by: vgrau98 <[email protected]>

Merge branch 'dev' into 7047-simplify-resnet-pretrained

9ee9e45

fix lint error

2945704

Signed-off-by: vgrau98 <[email protected]>

fix typo

7a01bb5

Signed-off-by: vgrau98 <[email protected]>

Merge branch 'dev' into 7047-simplify-resnet-pretrained

1a29bb2

fix mypy error

8198203

Signed-off-by: vgrau98 <[email protected]>

[pre-commit.ci] auto fixes from pre-commit.com hooks

2930f97

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

fix lint error

7a0a2c3

Signed-off-by: vgrau98 <[email protected]>

Merge branch 'dev' into 7047-simplify-resnet-pretrained

5b279b6

update unit test

741970d

Signed-off-by: Wenqi Li <[email protected]>

wyli enabled auto-merge (squash) October 18, 2023 19:20

wyli approved these changes Oct 18, 2023

View reviewed changes

local torch.cuda check

89eda2c

Signed-off-by: Wenqi Li <[email protected]>

wyli merged commit 9f1168f into Project-MONAI:dev Oct 18, 2023

vgrau98 deleted the 7047-simplify-resnet-pretrained branch October 18, 2023 21:06

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