Implementing UNet++ by yashika-git · Pull Request #5084 · Project-MONAI/MONAI

yashika-git · 2022-09-03T13:53:26Z

Fixes #896.

Description

Added Unet++.

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

Signed-off-by: Yashika Jain <yashikajain201@gmail.com>

yashika-git · 2022-09-03T14:51:22Z

Hi @Nic-Ma, @KumoLiu,
I've resolved the Flake8 issues. Could you please review it?
Thanks.

Signed-off-by: Yashika Jain <yashikajain201@gmail.com>

ericspod · 2022-09-04T19:17:25Z

/black

Signed-off-by: monai-bot <monai.miccai2019@gmail.com>

KumoLiu

I think it overall looks good to me. Thanks!

yashika-git · 2022-09-05T08:58:18Z

I think it overall looks good to me. Thanks!

Thank you, @KumoLiu

Signed-off-by: Yashika Jain <yashikajain201@gmail.com>

for more information, see https://pre-commit.ci Signed-off-by: Yashika Jain <yashikajain201@gmail.com>

Signed-off-by: Yashika Jain <yashikajain201@gmail.com>

for more information, see https://pre-commit.ci Signed-off-by: Yashika Jain <yashikajain201@gmail.com>

Signed-off-by: monai-bot <monai.miccai2019@gmail.com>

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> ### Description Adds a handler for directing logging information to a file once an `Engine` object starts and then doing the cleanup when it completes. ### Status **Ready** ### 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). - [x] 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`. - [x] In-line docstrings updated. - [x] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

### Description This allows `default_prepare_batch` to handle batches containing a single tensor or a pair of tensors. Normally if one uses array transforms you'll get an error saying the default batch function needs dictionaries so this will allow such transform sequences to be used without modification. ### Status **Work in progress** ### 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). - [x] 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`. - [x] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Fixes Project-MONAI#4909 ### Status **Ready** ### 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: Wenqi Li <wenqil@nvidia.com>

Fixes Project-MONAI#4554. Requires latest Ignite RC. Also improves ClientAlgo docstrings formatting. ### Description A few sentences describing the changes proposed in this pull request. ### Status **Ready** ### 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: Holger Roth <hroth@nvidia.com> Signed-off-by: Nic Ma <nma@nvidia.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Nic Ma <nma@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> ### Description Numpy arrays with type uint16, uint32, and uint64 need to be converted to signed versions before conversion to Pytorch tensors. This is relevant because MR data is often stored in uint16 format. ### Status **Ready** ### 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). - [x] 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: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> ### Description Using `view` to avoid copying doesn't actually work as intended in the type conversion to use `astype`. ### Status **Ready** ### 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: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

…roject-MONAI#5087) ### Description Part of the requested improvements Project-MONAI#5085 Planned fixes - [x] fold number is not being updated in generate() - [x] put absolute paths in the bundle configs - [x] break the auto-generated auto_config into multiple files. ### Status WIP ### 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: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Nic Ma <nma@nvidia.com>

### Description This PR remove "Status" from PR template. The Status was very useful before GitHub introduced *Draft* PR. I believe right now it is redundant to have this and sometimes conflicting (e.g., Status Ready <> Draft PR), so I believe it is time to remove the "Status" from PR template. ### Types of changes  - [x] Non-breaking change (fix or new feature that would not break existing functionality). Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

Signed-off-by: KumoLiu <yunl@nvidia.com> Fixes # . ### Description Fix docstring in auto3dseg ### Status **Work in progress** ### 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: KumoLiu <yunl@nvidia.com> Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com>

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

Fixes Project-MONAI#5070 . ### Description The batch size for the contrastive loss is estimated automatically ### 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). - [x] 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`. - [x] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: a-parida12 <abhijeet.parida@tum.de> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

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

wyli · 2022-09-06T22:59:31Z

/build

wyli · 2022-09-06T23:12:38Z

/build

wyli · 2022-09-07T05:39:36Z

/build

yashika-git added 4 commits September 3, 2022 19:21

Create basic_unetplusplus.py

b61e288

Signed-off-by: Yashika Jain <yashikajain201@gmail.com>

Update __init__.py

13f1c6f

Signed-off-by: Yashika Jain <yashikajain201@gmail.com>

Add files via upload

601b9c5

Signed-off-by: Yashika Jain <yashikajain201@gmail.com>

Update networks.rst

49dea4c

Signed-off-by: Yashika Jain <yashikajain201@gmail.com>

yashika-git changed the title ~~Patch 3~~ Implementing UNet++ Sep 3, 2022

yashika-git marked this pull request as draft September 3, 2022 13:59

yashika-git added 2 commits September 3, 2022 20:16

Update basic_unetplusplus.py

35ce07e

Signed-off-by: Yashika Jain <yashikajain201@gmail.com>

Update __init__.py

342b076

Signed-off-by: Yashika Jain <yashikajain201@gmail.com>

yashika-git force-pushed the patch-3 branch from 5baf72c to 342b076 Compare September 3, 2022 14:46

yashika-git marked this pull request as ready for review September 3, 2022 14:47

Nic-Ma requested review from KumoLiu, ericspod, rijobro and wyli September 3, 2022 15:01

ericspod reviewed Sep 4, 2022

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Comment thread monai/networks/nets/basic_unetplusplus.py Outdated

Update basic_unetplusplus.py

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Signed-off-by: Yashika Jain <yashikajain201@gmail.com>

yashika-git force-pushed the patch-3 branch from 40711e2 to 6f4fbec Compare September 4, 2022 17:44

[MONAI] code formatting

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Signed-off-by: monai-bot <monai.miccai2019@gmail.com>

KumoLiu approved these changes Sep 5, 2022

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wyli reviewed Sep 6, 2022

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Comment thread monai/networks/nets/basic_unetplusplus.py Outdated

yashika-git and others added 5 commits September 6, 2022 23:31

Update basic_unetplusplus.py

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Signed-off-by: Yashika Jain <yashikajain201@gmail.com>

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

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for more information, see https://pre-commit.ci Signed-off-by: Yashika Jain <yashikajain201@gmail.com>

Update basic_unetplusplus.py

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Signed-off-by: Yashika Jain <yashikajain201@gmail.com>

Update basic_unetplusplus.py

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Signed-off-by: Yashika Jain <yashikajain201@gmail.com>

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

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for more information, see https://pre-commit.ci Signed-off-by: Yashika Jain <yashikajain201@gmail.com>

yashika-git force-pushed the patch-3 branch from e273fa1 to 3408ed7 Compare September 6, 2022 18:02

[MONAI] code formatting

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ericspod and others added 12 commits September 6, 2022 23:55

fixes docs

21129e5

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

Merge remote-tracking branch 'upstream/dev' into patch-3

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wyli force-pushed the patch-3 branch from 0a96bc5 to 24e8fb7 Compare September 6, 2022 22:58

wyli enabled auto-merge (squash) September 6, 2022 23:00

wyli merged commit fb6d950 into Project-MONAI:dev Sep 7, 2022

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Implementing UNet++#5084

Implementing UNet++#5084
wyli merged 26 commits into
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yashika-git commented Sep 3, 2022

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