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Segresnet improvements#5281

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wyli merged 12 commits intoProject-MONAI:devfrom
myron:segresnet2
Oct 13, 2022
Merged

Segresnet improvements#5281
wyli merged 12 commits intoProject-MONAI:devfrom
myron:segresnet2

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@myron myron commented Oct 6, 2022

This adds improvements to SegResNet semantic segmentation to include deep supervision feature (among other things).

I've decided to add a new network named SegResnetDS instead of replacing the existing SegResNet, because it would have broken all previously pretrained model checkpoints.

Please take a look, and if it looks good, I can add unit tests. All the helper functions, and blocks are inside of the same file (which I prefer, since it's easier to read) instead of spreading it among other files (e.g segresnet_ds_block or segresnet_utils).

Description

A few sentences describing the changes proposed in this pull request.

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.

@myron myron added this to the Auto3D Seg framework [P0 v1.0] milestone Oct 6, 2022
@myron myron requested a review from wyli October 6, 2022 20:55
myron added 2 commits October 6, 2022 15:48
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@myron myron changed the title Segresnet2 Segresnet improvements Oct 12, 2022
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myron commented Oct 12, 2022

@wyli I've updated the code to reuse shared get_norm_layer, get_act_layer, following your request.
I've also added unit tests. and internal blocks and components are inside of the same file (instead of creating extra files), which I very much prefer. Please check and merge.

@Nic-Ma Nic-Ma requested a review from ericspod October 13, 2022 05:16
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wyli commented Oct 13, 2022

thanks, this looks to me, please address these minor issues detected: https://deepsource.io/gh/Project-MONAI/MONAI/run/2c41e145-4caa-4a5d-b7b9-78fa88b415ee/python/

for the torchscript issues (https://github.com/Project-MONAI/MONAI/actions/runs/3237807871/), the test could be skipped with a decorator:

MONAI/tests/test_dints_network.py

Line 153 in 16a0614

@SkipIfBeforePyTorchVersion((1, 9))

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myron commented Oct 13, 2022

thanks, this looks to me, please address these minor issues detected: https://deepsource.io/gh/Project-MONAI/MONAI/run/2c41e145-4caa-4a5d-b7b9-78fa88b415ee/python/

for the torchscript issues (https://github.com/Project-MONAI/MONAI/actions/runs/3237807871/), the test could be skipped with a decorator:

MONAI/tests/test_dints_network.py

Line 153 in 16a0614

@SkipIfBeforePyTorchVersion((1, 9))

Thanks, I've addressed all those issues, and pushed. plz check

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wyli commented Oct 13, 2022

/build

@wyli wyli enabled auto-merge (squash) October 13, 2022 19:22
@wyli wyli merged commit 02a6a6d into Project-MONAI:dev Oct 13, 2022
wyli pushed a commit to wyli/MONAI that referenced this pull request Oct 15, 2022
@myron @pre-commit-ci @wyli
Segresnet improvements (Project-MONAI#5281)
258f3ca 
This adds improvements to SegResNet semantic segmentation to include
deep supervision feature (among other things).

I've decided to add a new network named SegResnetDS instead of replacing
the existing SegResNet, because it would have broken all previously
pretrained model checkpoints.

Please take a look, and if it looks good, I can add unit tests. All the
helper functions, and blocks are inside of the same file (which I
prefer, since it's easier to read) instead of spreading it among other
files (e.g segresnet_ds_block or segresnet_utils).


### Description

A few sentences describing the changes proposed in this pull request.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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: myron <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@myron myron deleted the segresnet2 branch October 22, 2022 18:50
KumoLiu pushed a commit that referenced this pull request Nov 2, 2022
@myron @pre-commit-ci @KumoLiu
Segresnet improvements (#5281)
deb8402 
This adds improvements to SegResNet semantic segmentation to include
deep supervision feature (among other things).

I've decided to add a new network named SegResnetDS instead of replacing
the existing SegResNet, because it would have broken all previously
pretrained model checkpoints.

Please take a look, and if it looks good, I can add unit tests. All the
helper functions, and blocks are inside of the same file (which I
prefer, since it's easier to read) instead of spreading it among other
files (e.g segresnet_ds_block or segresnet_utils).


### Description

A few sentences describing the changes proposed in this pull request.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [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: myron <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Signed-off-by: KumoLiu <[email protected]>
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nhhung1810 commented Aug 5, 2023 •
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Hi @myron , I'm working on a PR about writing tutorials on this module SegResNetDS, can I ask some details, about

  • Why this was an improvement compare to SegResnet and SegResNetVAE, because I can not find any papers that discuss about the SegResNet with deep supervision and non-isotropic kernel
  • I wonder if this deep-supervision is the same as deep-supervision as UNet++, as I found the implementation quite similar
  • It would be very helpful if you could point out some resources to non-isotropic/isotropic kernel, too, so that I can write the tutorials better

Thank for your help :D

Edit: I've found this publication, it's the right one?

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