NACLLoss memory management #8020

Bala93 · 2024-08-15T04:53:55Z

Fixes # .

Description

Calling contiguous after applying the permute option to work with view operation in apply_filter (

MONAI/monai/networks/layers/simplelayers.py

Line 293 in 59a7211

x = x.view(1, kernel.shape[0], *spatials)

).

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.

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Fix the order of loss function in import statement

Fixed the formatting and minor issues.

Reorder import statements

Reorder system imports.

isort inferred one

Updated class name according to standard

Fixed the inline comment

Add datatype in functions and classes

Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Signed-off-by: Balamurali <balamuralim.1993@gmail.com>

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Add model description.

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Fixed the initialization issues with return types

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Use Any instead of tensor

Import typing

Fix return type formatting

Fix parameter datatype

DCO Remediation Commit for bala93 <balamuralim.1993@gmail.com> I, Balamurali <balamuralim.1993@gmail.com>, hereby add my Signed-off-by to this commit: c4f8283 I, bala93 <balamuralim.1993@gmail.com>, hereby add my Signed-off-by to this commit: 8fbec82 I, bala93 <balamuralim.1993@gmail.com>, hereby add my Signed-off-by to this commit: 7c121a0 I, bala93 <balamuralim.1993@gmail.com>, hereby add my Signed-off-by to this commit: dccde47 Signed-off-by: bala93 <balamuralim.1993@gmail.com>

DCO Remediation Commit for bala93 <balamuralim.1993@gmail.com> I, bala93 <balamuralim.1993@gmail.com>, hereby add my Signed-off-by to this commit: 8fbec82 I, bala93 <balamuralim.1993@gmail.com>, hereby add my Signed-off-by to this commit: 7c121a0 I, bala93 <balamuralim.1993@gmail.com>, hereby add my Signed-off-by to this commit: dccde47 Signed-off-by: bala93 <balamuralim.1993@gmail.com>

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Signed-off-by: Balamurali <balamuralim.1993@gmail.com>

I, bala93 <balamuralim.1993@gmail.com>, hereby add my Signed-off-by to this commit: 3a00aec Signed-off-by: bala93 <balamuralim.1993@gmail.com>

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Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Balamurali <balamuralim.1993@gmail.com>

* Modify the code with MeanFilter, and GaussianFilter of MONAI layers * Add Doc string explaining the mask preparation Signed-off-by: Balamurali <balamuralim.1993@gmail.com>

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Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Balamurali <balamuralim.1993@gmail.com>

Signed-off-by: Balamurali <balamuralim.1993@gmail.com>

…nto model-calibration

DCO Remediation Commit for Balamurali <balamuralim.1993@gmail.com> I, Balamurali <balamuralim.1993@gmail.com>, hereby add my Signed-off-by to this commit: 7deb2cc Signed-off-by: Balamurali <balamuralim.1993@gmail.com>

Call contiguous after permute to avoid reshaping issue.

Signed-off-by: Balamurali <balamuralim.1993@gmail.com>

KumoLiu · 2024-08-15T05:18:57Z

Hi @Bala93, please help sign off to fix the DCO issue, then I can help trigger more tests.
https://github.com/Project-MONAI/MONAI/pull/8020/checks?check_run_id=28797284498

I, Balamurali <balamuralim.1993@gmail.com>, hereby add my Signed-off-by to this commit: f579763 Signed-off-by: Balamurali <balamuralim.1993@gmail.com>

Bala93 · 2024-08-15T05:55:38Z

Hi @KumoLiu, thanks for the immediate response. I also added the test case for testing with batch size>1, which was failing in the previous version.

KumoLiu · 2024-08-15T06:51:06Z

/build

Fixes # . ### Description Calling contiguous after applying the permute option to work with view operation in apply_filter (https://github.com/Project-MONAI/MONAI/blob/59a7211070538586369afd4a01eca0a7fe2e742e/monai/networks/layers/simplelayers.py#L293). ### Types of changes  - [x] 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: Balamurali <balamuralim.1993@gmail.com> Signed-off-by: bala93 <balamuralim.1993@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>

Bala93 and others added 30 commits June 1, 2024 22:11

Initial commit -- Adding calibration loss specific to segmentation

8fbec82

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

23b897b

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Update __init__.py

b2ec62b

Fix the order of loss function in import statement

Update segcalib.py

93ee114

Fixed the formatting and minor issues.

Update segcalib.py

42e732b

Reorder import statements

Update segcalib.py

187053d

Reorder system imports.

Update segcalib.py

1d27ec5

isort inferred one

Update segcalib.py

d499134

Updated class name according to standard

Update segcalib.py

1e3f755

Fixed the inline comment

Update segcalib.py

9dedfba

Add datatype in functions and classes

Update monai/losses/segcalib.py

59959ce

Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Signed-off-by: Balamurali <balamuralim.1993@gmail.com>

Update monai/losses/segcalib.py

cf1d044

Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Signed-off-by: Balamurali <balamuralim.1993@gmail.com>

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

0926851

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Update segcalib.py

5317706

Add model description.

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

3155433

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Add specific to gaussian for both 2d and 3d

7c121a0

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

24efd85

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Merge branch 'Project-MONAI:dev' into model-calibration

0067953

Add mean loss and resolve formatting

dccde47

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

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Merge branch 'dev' into model-calibration

57686d7

Update segcalib.py

5cd9a33

Fixed the initialization issues with return types

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

b547c4e

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Update segcalib.py

42a0215

Use Any instead of tensor

Update segcalib.py

7e36ca1

Import typing

Update segcalib.py

6dbd53d

Update segcalib.py

354056c

Update segcalib.py

7eb911f

Fix return type formatting

Update segcalib.py

0b1209b

Update segcalib.py

035c92e

Fix parameter datatype

Bala93 and others added 21 commits August 5, 2024 14:25

Formatting check with monai

3a00aec

DCO Remediation Commit for Balamurali <balamuralim.1993@gmail.com> I, Balamurali <balamuralim.1993@gmail.com>, hereby add my Signed-off-by to this commit: bc6b995 Signed-off-by: Balamurali <balamuralim.1993@gmail.com>

Update test_nacl_loss.py

818b42b

DCO Remediation Commit for Balamurali <balamuralim.1993@gmail.com> I, Balamurali <balamuralim.1993@gmail.com>, hereby add my Signed-off-by to this commit: bc6b995 Signed-off-by: Balamurali <balamuralim.1993@gmail.com>

Added mypy fixes

6647708

Signed-off-by: Balamurali <balamuralim.1993@gmail.com>

DCO Remediation Commit for bala93 <balamuralim.1993@gmail.com>

7e579dd

I, bala93 <balamuralim.1993@gmail.com>, hereby add my Signed-off-by to this commit: 3a00aec Signed-off-by: bala93 <balamuralim.1993@gmail.com>

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

4f8abf1

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Update docs/source/losses.rst

b72e478

Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Balamurali <balamuralim.1993@gmail.com>

* Include test cases covering more cases

747681d

* Modify the code with MeanFilter, and GaussianFilter of MONAI layers * Add Doc string explaining the mask preparation Signed-off-by: Balamurali <balamuralim.1993@gmail.com>

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

3b15554

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Update monai/losses/nacl_loss.py

877139c

Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Balamurali <balamuralim.1993@gmail.com>

Update monai/losses/nacl_loss.py

4679456

Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Balamurali <balamuralim.1993@gmail.com>

* Add docstring with better explanations

7c5217e

Signed-off-by: Balamurali <balamuralim.1993@gmail.com>

* Maintain the dimension consistency.

d33f435

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Update nacl_loss.py

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Update nacl_loss.py

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Merge branch 'model-calibration' of https://github.com/Bala93/MONAI i…

7f87e0c

…nto model-calibration

Modify docstring

0e880a8

DCO Remediation Commit for Balamurali <balamuralim.1993@gmail.com> I, Balamurali <balamuralim.1993@gmail.com>, hereby add my Signed-off-by to this commit: 7deb2cc Signed-off-by: Balamurali <balamuralim.1993@gmail.com>

Merge branch 'dev' into model-calibration

db9daeb

Update nacl_loss.py

f579763

Call contiguous after permute to avoid reshaping issue.

Merge branch 'dev' into model-calibration

c579768

Signed-off-by: Balamurali <balamuralim.1993@gmail.com>

DCO Remediation Commit for Balamurali <balamuralim.1993@gmail.com>

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I, Balamurali <balamuralim.1993@gmail.com>, hereby add my Signed-off-by to this commit: f579763 Signed-off-by: Balamurali <balamuralim.1993@gmail.com>

Merge branch 'dev' into model-calibration

2469e14

KumoLiu enabled auto-merge (squash) August 15, 2024 07:54

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KumoLiu merged commit 7b9a523 into Project-MONAI:dev Aug 15, 2024
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NACLLoss memory management #8020

NACLLoss memory management #8020

Bala93 commented Aug 15, 2024 •

edited

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KumoLiu commented Aug 15, 2024

Bala93 commented Aug 15, 2024

KumoLiu commented Aug 15, 2024

NACLLoss memory management #8020

NACLLoss memory management #8020

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Bala93 commented Aug 15, 2024 • edited Loading

Description

Types of changes

KumoLiu commented Aug 15, 2024

Bala93 commented Aug 15, 2024

KumoLiu commented Aug 15, 2024

Bala93 commented Aug 15, 2024 •

edited

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