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Make bending energy loss invariant to resolution #3493

Merged
merged 2 commits into from
Dec 15, 2021
Merged

Make bending energy loss invariant to resolution #3493

merged 2 commits into from
Dec 15, 2021

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ebrahimebrahim
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@ebrahimebrahim ebrahimebrahim commented Dec 15, 2021 •
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Fixes #3485

Description

See #3485 for a complete description.

  • Introduce normalize parameter to BendingEnergyLoss constructor, which defaults to True. This makes loss computation robust to different image resolutions. Setting normalize to False explicitly provides the old behavior, which follows the "bending energy" formula as it appears in publications.
  • Raise error when number of vector components does not match the number of spatial dimensions.
  • Add test cases for the new error.
  • Adjust old test cases to expect the new bending loss behavior, and add test cases to test both behaviors
  • Adjust tensor shapes in old test cases so that the number of vector components always matches the number of spatial dimensions.

Feedback wanted: Should normalize=True be the default? I preferred this because I felt that the default behavior should be resolution-invariant... but this is also the reason it's a breaking change. If BendingEnergyLoss is already used in some project, then a revision would be needed in that project. If I set normalize=False by default, it's not a breaking change.

Status

Ready

  • Run some less trivial tests
  • Get feedback to my question above

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.

wyli
wyli approved these changes Dec 15, 2021
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It looks good to me. Thanks for the additional input validation I was thinking about the same.

I'm inclined to default to False as that's the basic formulation described in the literature.

@wyli wyli requested a review from kate-sann5100 December 15, 2021 09:12
kate-sann5100
kate-sann5100 approved these changes Dec 15, 2021
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Nice work! Looks good to me as well. You can merge after setting the default option to False if you wish.

@ebrahimebrahim
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I think I agree with setting default to False. Maybe it's more important that the default behavior match usage of the term elsewhere, rather than being the most convenient behavior. Also it's nice to have it be non-breaking. I will make that change now.

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wyli commented Dec 15, 2021

thank you, could you merge the latest dev branch into this PR?

@ebrahimebrahim
make bending energy loss invariant to resolution
79de4e1 
fixes Project-MONAI#3485

Signed-off-by: Ebrahim Ebrahim <ebrahim.ebrahim@kitware.com>
@ebrahimebrahim
set BendingEnergyLoss default normalize to False
bb2366f 
Maybe it's more important that the default behavior match usage of the
term "bending energy" elsewhere, rather than that it be the most
convenient behavior.

Signed-off-by: Ebrahim Ebrahim <ebrahim.ebrahim@kitware.com>
@ebrahimebrahim
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@wyli should be ready now!

@wyli
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wyli commented Dec 15, 2021

/build

@wyli wyli enabled auto-merge (squash) December 15, 2021 20:04
@wyli wyli merged commit 88d91d6 into Project-MONAI:dev Dec 15, 2021
wyli pushed a commit that referenced this pull request Jan 4, 2022
@ebrahimebrahim @wyli
Make bending energy loss invariant to resolution (#3493)
2615ead 
* make bending energy loss invariant to resolution

fixes #3485

Signed-off-by: Ebrahim Ebrahim <ebrahim.ebrahim@kitware.com>

* set BendingEnergyLoss default normalize to False

Maybe it's more important that the default behavior match usage of the
term "bending energy" elsewhere, rather than that it be the most
convenient behavior.

Signed-off-by: Ebrahim Ebrahim <ebrahim.ebrahim@kitware.com>
Can-Zhao added a commit that referenced this pull request Jan 5, 2022
@Can-Zhao @drbeh
@Nic-Ma @wyli @monai-bot @yiheng-wang-nv @rijobro @ebrahimebrahim @ericspod @pre-commit-ci
rebase dev and add box utils (#3586)
dd74c59 
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* Make bending energy loss invariant to resolution (#3493)

* make bending energy loss invariant to resolution

fixes #3485

Signed-off-by: Ebrahim Ebrahim <ebrahim.ebrahim@kitware.com>

* set BendingEnergyLoss default normalize to False

Maybe it's more important that the default behavior match usage of the
term "bending energy" elsewhere, rather than that it be the most
convenient behavior.

Signed-off-by: Ebrahim Ebrahim <ebrahim.ebrahim@kitware.com>

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Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes timed tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update based on comments

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* 3580 - create codeql-analysis.yml (#3579)

* Create codeql-analysis.yml

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* build cpp

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes Multiplication result converted to larger type

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes url parsing

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* 498 Add logger_handler to LrScheduleHandler (#3570)

* [DLMED] add log handler

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix CI tests

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix CI test

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] test CI

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix logging

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] temp test

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix wrong unit test

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix wrong test cases

Signed-off-by: Nic Ma <nma@nvidia.com>

Co-authored-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Co-authored-by: Nic Ma <nma@nvidia.com>
Co-authored-by: Wenqi Li <wenqil@nvidia.com>
Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
Co-authored-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com>
Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
Co-authored-by: Ebrahim Ebrahim <ebrahim.mt@gmail.com>
Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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@kate-sann5100 kate-sann5100 kate-sann5100 approved these changes

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Bending energy loss is not scale invariant
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@ebrahimebrahim @wyli @kate-sann5100