2872 implementation of mixup, cutmix and cutout #7198

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

for more information, see https://pre-commit.ci Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

for more information, see https://pre-commit.ci Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

for more information, see https://pre-commit.ci Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes # fix useless error msg in nnunetv2runner ### Description ### Types of changes - [x] Non-breaking change (fix or new feature that would not break existing functionality). Signed-off-by: elitap <elias.tappeiner@gmx.at> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7230. ### Description Fix the typing issues and the deprecation. Also always run type checking with Linux environment, since ForkServerContext is not available on Windows. ### Types of changes - [x] Non-breaking change (fix or new feature that would not break existing functionality). --------- Signed-off-by: Felix Schnabel <f.schnabel@tum.de> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

…AI#7239) Fixes # . ### Description A few sentences describing the changes proposed in this pull request. ### 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. Add new developer to blossom-ci trigger list Signed-off-by: YanxuanLiu <yanxuanl@nvidia.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Project-MONAI#7234) … MONAI with all dependencies on Windows Fixes Project-MONAI#6118 ### Description The Windows shell doesn't recognize single quotes to delimit a string at all, so on Windows you'll need to use double quotes. It's the same command no matter which type of quotes you use; after the shell does its processing, the argument is passed to pip with the quotation marks already removed. ### 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: ytl0623 <david89062388@gmail.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Avoid syntax error on Windows ### Description ```log (.venv) C:\Dev\Kitware\python>python -c 'import monai; monai.config.print_debug_info()' File "<string>", line 1 'import ^ SyntaxError: unterminated string literal (detected at line 1) ``` ### 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: Dženan Zukić <dzenan.zukic@kitware.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Part of Project-MONAI#6904 ### Description - Fix inefficient patching in `PatchDataset` - Add cache option in `GridPatchDataset` ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.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> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

) Fixes Project-MONAI#7101 ### Description Added examples in the docstrings for `EnsureType` and `CastToType` transforms which show how they function under different circumstances. ### 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. - [x] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [x] 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: Ishan Dutta <ishandutta0098@gmail.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

…t-MONAI#7244) Fixes Project-MONAI#5723 ### Description Corrupted cached files in the PersistentDataset cause the exception: `RuntimeError: Invalid magic number; corrupt file?` With this PR we handle that case in the try-except block and continue the usual functionality if the cached file was absent. ### 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. - [x] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [x] 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: Ishan Dutta <ishandutta0098@gmail.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Project-MONAI#7249) add class label option to write metric report to improve readability, without that option in case of many classes the resulting report is very hard to interpret. ### Types of changes  - [x] Non-breaking change (fix or new feature that would not break existing functionality). --------- Signed-off-by: elitap <elias.tappeiner@gmx.at> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

…roject-MONAI#7262) Fixes Project-MONAI#7261 ### Description Remove star-arg unpacking before a keyword argument. ### 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: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

…n Bash (Project-MONAI#7268) Fixes Project-MONAI#5857. ### Description When dealing with paths that contain spaces in Bash, it's important to properly quote the variables to ensure that spaces are handled correctly. So, maybe we can replace all `$PY_EXE` variables to `"$PY_EXE"` in the `runtests.sh` file. ### 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: ytl0623 <david89062388@gmail.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

…ion (Project-MONAI#7271) Fixes Project-MONAI#7193 ### Description add SoftclDiceLoss and SoftDiceclDiceLoss loss function in documentation(https://github.com/Project-MONAI/MONAI/blob/dev/docs/source/losses.rst?plain=1) ### 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: ytl0623 <david89062388@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7265. ### 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: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes model-zoo#537 ### 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: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

…I#7275) Part of Project-MONAI#7250. ### Description Fix the Python version for transformers smaller than 3.10. ### 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: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7263. ### Description Add diffusion loss. I also made a [demo notebook](https://github.com/kvttt/deep-atlas/blob/main/diffusion_loss_scale_test.ipynb) to provide some explanations and analyses of diffusion loss. ### 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: kaibo <ktang@unc.edu> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes # . ### Description A few sentences describing the changes proposed in this pull request. ### 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: heyufan1995 <heyufan1995@gmail.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7309 ### Description `DataAnalyzer` only catch error when data is on GPU, add catching error when data is on CPU. ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7317 ### Description Add support specified filename for users to save like nibabel.save. ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fix typo. ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes # . ### Description A few sentences describing the changes proposed in this pull request. ### 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: binliu <binliu@nvidia.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7314 Project-MONAI#7315. ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Ben Murray <ben.murray@gmail.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7338 ### Description transformers' version is pinned to v4.22 since Project-MONAI#5157. Updated the version refer to huggingface/transformers#21678. ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 3 to 4. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/actions/upload-artifact/releases">actions/upload-artifact's releases</a>.</em></p> <blockquote> <h2>v4.0.0</h2> <h2>What's Changed</h2> <p>The release of upload-artifact@v4 and download-artifact@v4 are major changes to the backend architecture of Artifacts. They have numerous performance and behavioral improvements.</p> <p>For more information, see the <a href="https://github.com/actions/toolkit/tree/main/packages/artifact"><code>@actions/artifact</code></a> documentation.</p> <h2>New Contributors</h2> <ul> <li><a href="https://github.com/vmjoseph"><code>@vmjoseph</code></a> made their first contribution in <a href="https://redirect.github.com/actions/upload-artifact/pull/464">actions/upload-artifact#464</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/upload-artifact/compare/v3...v4.0.0">https://github.com/actions/upload-artifact/compare/v3...v4.0.0</a></p> <h2>v3.1.3</h2> <h2>What's Changed</h2> <ul> <li>chore(github): remove trailing whitespaces by <a href="https://github.com/ljmf00"><code>@ljmf00</code></a> in <a href="https://redirect.github.com/actions/upload-artifact/pull/313">actions/upload-artifact#313</a></li> <li>Bump <code>@actions/artifact</code> version to v1.1.2 by <a href="https://github.com/bethanyj28"><code>@bethanyj28</code></a> in <a href="https://redirect.github.com/actions/upload-artifact/pull/436">actions/upload-artifact#436</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/upload-artifact/compare/v3...v3.1.3">https://github.com/actions/upload-artifact/compare/v3...v3.1.3</a></p> <h2>v3.1.2</h2> <ul> <li>Update all <code>@actions/*</code> NPM packages to their latest versions- <a href="https://redirect.github.com/actions/upload-artifact/issues/374">#374</a></li> <li>Update all dev dependencies to their most recent versions - <a href="https://redirect.github.com/actions/upload-artifact/issues/375">#375</a></li> </ul> <h2>v3.1.1</h2> <ul> <li>Update actions/core package to latest version to remove <code>set-output</code> deprecation warning <a href="https://redirect.github.com/actions/upload-artifact/issues/351">#351</a></li> </ul> <h2>v3.1.0</h2> <h2>What's Changed</h2> <ul> <li>Bump <code>@actions/artifact</code> to v1.1.0 (<a href="https://redirect.github.com/actions/upload-artifact/pull/327">actions/upload-artifact#327</a>) <ul> <li>Adds checksum headers on artifact upload (<a href="https://redirect.github.com/actions/toolkit/pull/1095">actions/toolkit#1095</a>) (<a href="https://redirect.github.com/actions/toolkit/pull/1063">actions/toolkit#1063</a>)</li> </ul> </li> </ul> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/actions/upload-artifact/commit/c7d193f32edcb7bfad88892161225aeda64e9392"><code>c7d193f</code></a> Merge pull request <a href="https://redirect.github.com/actions/upload-artifact/issues/466">#466</a> from actions/v4-beta</li> <li><a href="https://github.com/actions/upload-artifact/commit/13131bb095770b4070a7477c3cd2d96e1c16d9f4"><code>13131bb</code></a> licensed cache</li> <li><a href="https://github.com/actions/upload-artifact/commit/4a6c273b9834f66a1d05c170dc3f80f9cdb9def1"><code>4a6c273</code></a> Merge branch 'main' into v4-beta</li> <li><a href="https://github.com/actions/upload-artifact/commit/f391bb91a3d3118aeca171c365bb319ece276b37"><code>f391bb9</code></a> Merge pull request <a href="https://redirect.github.com/actions/upload-artifact/issues/465">#465</a> from actions/robherley/v4-documentation</li> <li><a href="https://github.com/actions/upload-artifact/commit/9653d03c4b74c32144e02dae644fea70e079d4b3"><code>9653d03</code></a> Apply suggestions from code review</li> <li><a href="https://github.com/actions/upload-artifact/commit/875b63076402f25ef9d52c294c86ba4f97810575"><code>875b630</code></a> add limitations section</li> <li><a href="https://github.com/actions/upload-artifact/commit/ecb21463e93740a6be75c3116242169bfdbcb15a"><code>ecb2146</code></a> add compression example</li> <li><a href="https://github.com/actions/upload-artifact/commit/5e7604f84a055838f64ed68bb9904751523081ae"><code>5e7604f</code></a> trim some repeated info</li> <li><a href="https://github.com/actions/upload-artifact/commit/d6437d07581fe318a364512e6cf6b1dca6b4f92c"><code>d6437d0</code></a> naming</li> <li><a href="https://github.com/actions/upload-artifact/commit/1b561557037b4957d7d184e9aac02bec86c771eb"><code>1b56155</code></a> s/v4-beta/v4/g</li> <li>Additional commits viewable in <a href="https://github.com/actions/upload-artifact/compare/v3...v4">compare view</a></li> </ul> </details> <br /> [![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=actions/upload-artifact&package-manager=github_actions&previous-version=3&new-version=4)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot show <dependency name> ignore conditions` will show all of the ignore conditions of the specified dependency - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) </details> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 3 to 4. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/actions/download-artifact/releases">actions/download-artifact's releases</a>.</em></p> <blockquote> <h2>v4.0.0</h2> <h2>What's Changed</h2> <p>The release of upload-artifact@v4 and download-artifact@v4 are major changes to the backend architecture of Artifacts. They have numerous performance and behavioral improvements.</p> <p>For more information, see the <a href="https://github.com/actions/toolkit/tree/main/packages/artifact"><code>@actions/artifact</code></a> documentation.</p> <h2>New Contributors</h2> <ul> <li><a href="https://github.com/bflad"><code>@bflad</code></a> made their first contribution in <a href="https://redirect.github.com/actions/download-artifact/pull/194">actions/download-artifact#194</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/download-artifact/compare/v3...v4.0.0">https://github.com/actions/download-artifact/compare/v3...v4.0.0</a></p> <h2>v3.0.2</h2> <ul> <li>Bump <code>@actions/artifact</code> to v1.1.1 - <a href="https://redirect.github.com/actions/download-artifact/pull/195">actions/download-artifact#195</a></li> <li>Fixed a bug in Node16 where if an HTTP download finished too quickly (<1ms, e.g. when it's mocked) we attempt to delete a temp file that has not been created yet <a href="hhttps://redirect.github.com/actions/toolkit/pull/1278">actions/toolkit#1278</a></li> </ul> <h2>v3.0.1</h2> <ul> <li><a href="https://redirect.github.com/actions/download-artifact/pull/178">Bump <code>@actions/core</code> to 1.10.0</a></li> </ul> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/actions/download-artifact/commit/f44cd7b40bfd40b6aa1cc1b9b5b7bf03d3c67110"><code>f44cd7b</code></a> Merge pull request <a href="https://redirect.github.com/actions/download-artifact/issues/259">#259</a> from actions/robherley/glob-downloads</li> <li><a href="https://github.com/actions/download-artifact/commit/3181fe853d2c9a606cd326853bf4c5b8ced5df02"><code>3181fe8</code></a> add some migration docs</li> <li><a href="https://github.com/actions/download-artifact/commit/aaaac7b403f278b6b7eebdca69ca1658616f1c57"><code>aaaac7b</code></a> licensed cache</li> <li><a href="https://github.com/actions/download-artifact/commit/7c9182f0e18dadedfbca3189ab7a22a416aa6714"><code>7c9182f</code></a> update readme</li> <li><a href="https://github.com/actions/download-artifact/commit/b94e7015566b40b2de5eeeda514f239968da2dd7"><code>b94e701</code></a> licensed cache</li> <li><a href="https://github.com/actions/download-artifact/commit/0b55470e40ab7435f445813ebc18b1107ecf7e32"><code>0b55470</code></a> add test case for globbed downloads to same directory</li> <li><a href="https://github.com/actions/download-artifact/commit/0b51c2ef9042b581aded9711127e4a6d5f71c550"><code>0b51c2e</code></a> update prettier/eslint versions</li> <li><a href="https://github.com/actions/download-artifact/commit/c4c6db724f9510b2b3cff5ebcc417c87a2b2fa97"><code>c4c6db7</code></a> support globbing artifact list & merging download directory</li> <li><a href="https://github.com/actions/download-artifact/commit/1bd0606e08fcaa4c28afc1fc7d45830ab5482dac"><code>1bd0606</code></a> Merge pull request <a href="https://redirect.github.com/actions/download-artifact/issues/252">#252</a> from stchr/patch-1</li> <li><a href="https://github.com/actions/download-artifact/commit/eff4d42b1f6ff704c7a0f37152ed8793673560ef"><code>eff4d42</code></a> fix default for run-id</li> <li>Additional commits viewable in <a href="https://github.com/actions/download-artifact/compare/v3...v4">compare view</a></li> </ul> </details> <br /> [![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=actions/download-artifact&package-manager=github_actions&previous-version=3&new-version=4)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot show <dependency name> ignore conditions` will show all of the ignore conditions of the specified dependency - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) </details> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

…tiplication (Project-MONAI#7326) Fixes Project-MONAI#7323 ### Description Give more useful exception when batch is considered during matrix multiplication. ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7222 ### Description remove int convert here. https://github.com/Project-MONAI/MONAI/blob/8fa6931b14ba9617a595fff1d396ac44cc82e207/monai/auto3dseg/analyzer.py#L259 ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

…-MONAI#7381) Fixes Project-MONAI#7380. ### Description Mention [demo](https://github.com/Project-MONAI/tutorials/blob/main/modules/bending_energy_diffusion_loss_notes.ipynb) in bending energy and diffusion docstrings. ### 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. - [x] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: kaibo <ktang@unc.edu> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Workaround for Project-MONAI#7382 Project-MONAI#7383 ### Description Based on the comment [here](wkentaro/gdown#291 (comment)), pin the gdown version as a workaround. Will review this one once gdown has some update internal. ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7396 ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7394 ### Description When ImageFilter is in the transformation sequence it didn't pass the applied_operations. Now it is passed when present. ### 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: axel.vlaminck <axel.vlaminck@gmail.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Project-MONAI#7375) Fixes # . ### Description Add `compile` support in `SupervisedTrainer` and `SupervisedEvaluator`. Convert to `torch.Tensor` internally. ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.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> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7407 ### Description Move `optional import cucim` inside the function to avoid using all GPUs. ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

…`ITKReader` (Project-MONAI#7415) Fixes Project-MONAI#7414 Fixes Project-MONAI#7371 ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7421 ### Description https://pypi.org/project/black/24.1.1/ ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

…roject-MONAI#7424) Fixes Project-MONAI#7416 ### Description update `rm -rf /opt/hostedtoolcache` avoid change the python version ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Bumps [actions/cache](https://github.com/actions/cache) from 3 to 4. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/actions/cache/releases">actions/cache's releases</a>.</em></p> <blockquote> <h2>v4.0.0</h2> <h2>What's Changed</h2> <ul> <li>Update action to node20 by <a href="https://github.com/takost"><code>@takost</code></a> in <a href="https://redirect.github.com/actions/cache/pull/1284">actions/cache#1284</a></li> <li>feat: save-always flag by <a href="https://github.com/to-s"><code>@to-s</code></a> in <a href="https://redirect.github.com/actions/cache/pull/1242">actions/cache#1242</a></li> </ul> <h2>New Contributors</h2> <ul> <li><a href="https://github.com/takost"><code>@takost</code></a> made their first contribution in <a href="https://redirect.github.com/actions/cache/pull/1284">actions/cache#1284</a></li> <li><a href="https://github.com/to-s"><code>@to-s</code></a> made their first contribution in <a href="https://redirect.github.com/actions/cache/pull/1242">actions/cache#1242</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/cache/compare/v3...v4.0.0">https://github.com/actions/cache/compare/v3...v4.0.0</a></p> <h2>v3.3.3</h2> <h2>What's Changed</h2> <ul> <li>Cache v3.3.3 by <a href="https://github.com/robherley"><code>@robherley</code></a> in <a href="https://redirect.github.com/actions/cache/pull/1302">actions/cache#1302</a></li> </ul> <h2>New Contributors</h2> <ul> <li><a href="https://github.com/robherley"><code>@robherley</code></a> made their first contribution in <a href="https://redirect.github.com/actions/cache/pull/1302">actions/cache#1302</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/cache/compare/v3...v3.3.3">https://github.com/actions/cache/compare/v3...v3.3.3</a></p> <h2>v3.3.2</h2> <h2>What's Changed</h2> <ul> <li>Fixed readme with new segment timeout values by <a href="https://github.com/kotewar"><code>@kotewar</code></a> in <a href="https://redirect.github.com/actions/cache/pull/1133">actions/cache#1133</a></li> <li>Readme fixes by <a href="https://github.com/kotewar"><code>@kotewar</code></a> in <a href="https://redirect.github.com/actions/cache/pull/1134">actions/cache#1134</a></li> <li>Updated description of the lookup-only input for main action by <a href="https://github.com/kotewar"><code>@kotewar</code></a> in <a href="https://redirect.github.com/actions/cache/pull/1130">actions/cache#1130</a></li> <li>Change two new actions mention as quoted text by <a href="https://github.com/bishal-pdMSFT"><code>@bishal-pdMSFT</code></a> in <a href="https://redirect.github.com/actions/cache/pull/1131">actions/cache#1131</a></li> <li>Update Cross-OS Caching tips by <a href="https://github.com/pdotl"><code>@pdotl</code></a> in <a href="https://redirect.github.com/actions/cache/pull/1122">actions/cache#1122</a></li> <li>Bazel example (Take <a href="https://redirect.github.com/actions/cache/issues/2">#2</a>️⃣) by <a href="https://github.com/vorburger"><code>@vorburger</code></a> in <a href="https://redirect.github.com/actions/cache/pull/1132">actions/cache#1132</a></li> <li>Remove actions to add new PRs and issues to a project board by <a href="https://github.com/jorendorff"><code>@jorendorff</code></a> in <a href="https://redirect.github.com/actions/cache/pull/1187">actions/cache#1187</a></li> <li>Consume latest toolkit and fix dangling promise bug by <a href="https://github.com/chkimes"><code>@chkimes</code></a> in <a href="https://redirect.github.com/actions/cache/pull/1217">actions/cache#1217</a></li> <li>Bump action version to 3.3.2 by <a href="https://github.com/bethanyj28"><code>@bethanyj28</code></a> in <a href="https://redirect.github.com/actions/cache/pull/1236">actions/cache#1236</a></li> </ul> <h2>New Contributors</h2> <ul> <li><a href="https://github.com/vorburger"><code>@vorburger</code></a> made their first contribution in <a href="https://redirect.github.com/actions/cache/pull/1132">actions/cache#1132</a></li> <li><a href="https://github.com/jorendorff"><code>@jorendorff</code></a> made their first contribution in <a href="https://redirect.github.com/actions/cache/pull/1187">actions/cache#1187</a></li> <li><a href="https://github.com/chkimes"><code>@chkimes</code></a> made their first contribution in <a href="https://redirect.github.com/actions/cache/pull/1217">actions/cache#1217</a></li> <li><a href="https://github.com/bethanyj28"><code>@bethanyj28</code></a> made their first contribution in <a href="https://redirect.github.com/actions/cache/pull/1236">actions/cache#1236</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/cache/compare/v3...v3.3.2">https://github.com/actions/cache/compare/v3...v3.3.2</a></p> <h2>v3.3.1</h2> <h2>What's Changed</h2> <ul> <li>Reduced download segment size to 128 MB and timeout to 10 minutes by <a href="https://github.com/kotewar"><code>@kotewar</code></a> in <a href="https://redirect.github.com/actions/cache/pull/1129">actions/cache#1129</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/cache/compare/v3...v3.3.1">https://github.com/actions/cache/compare/v3...v3.3.1</a></p> <h2>v3.3.0</h2> <h2>What's Changed</h2> <ul> <li>Bug: Permission is missing in cache delete example by <a href="https://github.com/kotokaze"><code>@kotokaze</code></a> in <a href="https://redirect.github.com/actions/cache/pull/1123">actions/cache#1123</a></li> </ul>  </blockquote> <p>... (truncated)</p> </details> <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/actions/cache/blob/main/RELEASES.md">actions/cache's changelog</a>.</em></p> <blockquote> <h1>Releases</h1> <h3>3.0.0</h3> <ul> <li>Updated minimum runner version support from node 12 -> node 16</li> </ul> <h3>3.0.1</h3> <ul> <li>Added support for caching from GHES 3.5.</li> <li>Fixed download issue for files > 2GB during restore.</li> </ul> <h3>3.0.2</h3> <ul> <li>Added support for dynamic cache size cap on GHES.</li> </ul> <h3>3.0.3</h3> <ul> <li>Fixed avoiding empty cache save when no files are available for caching. (<a href="https://redirect.github.com/actions/cache/issues/624">issue</a>)</li> </ul> <h3>3.0.4</h3> <ul> <li>Fixed tar creation error while trying to create tar with path as <code>~/</code> home folder on <code>ubuntu-latest</code>. (<a href="https://redirect.github.com/actions/cache/issues/689">issue</a>)</li> </ul> <h3>3.0.5</h3> <ul> <li>Removed error handling by consuming actions/cache 3.0 toolkit, Now cache server error handling will be done by toolkit. (<a href="https://redirect.github.com/actions/cache/pull/834">PR</a>)</li> </ul> <h3>3.0.6</h3> <ul> <li>Fixed <a href="https://redirect.github.com/actions/cache/issues/809">#809</a> - zstd -d: no such file or directory error</li> <li>Fixed <a href="https://redirect.github.com/actions/cache/issues/833">#833</a> - cache doesn't work with github workspace directory</li> </ul> <h3>3.0.7</h3> <ul> <li>Fixed <a href="https://redirect.github.com/actions/cache/issues/810">#810</a> - download stuck issue. A new timeout is introduced in the download process to abort the download if it gets stuck and doesn't finish within an hour.</li> </ul> <h3>3.0.8</h3> <ul> <li>Fix zstd not working for windows on gnu tar in issues <a href="https://redirect.github.com/actions/cache/issues/888">#888</a> and <a href="https://redirect.github.com/actions/cache/issues/891">#891</a>.</li> <li>Allowing users to provide a custom timeout as input for aborting download of a cache segment using an environment variable <code>SEGMENT_DOWNLOAD_TIMEOUT_MINS</code>. Default is 60 minutes.</li> </ul> <h3>3.0.9</h3> <ul> <li>Enhanced the warning message for cache unavailablity in case of GHES.</li> </ul> <h3>3.0.10</h3> <ul> <li>Fix a bug with sorting inputs.</li> <li>Update definition for restore-keys in README.md</li> </ul>  </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/actions/cache/commit/13aacd865c20de90d75de3b17ebe84f7a17d57d2"><code>13aacd8</code></a> Merge pull request <a href="https://redirect.github.com/actions/cache/issues/1242">#1242</a> from to-s/main</li> <li><a href="https://github.com/actions/cache/commit/53b35c543921fe2e8b288765ff817de9de8d906f"><code>53b35c5</code></a> Merge branch 'main' into main</li> <li><a href="https://github.com/actions/cache/commit/65b8989fab3bb394817bdb845a453dff480c2b51"><code>65b8989</code></a> Merge pull request <a href="https://redirect.github.com/actions/cache/issues/1284">#1284</a> from takost/update-to-node-20</li> <li><a href="https://github.com/actions/cache/commit/d0be34d54485f31ca2ccbe66e6ea3d96544a807b"><code>d0be34d</code></a> Fix dist</li> <li><a href="https://github.com/actions/cache/commit/66cf064d47313d2cccf392d01bd10925da2bd072"><code>66cf064</code></a> Merge branch 'main' into update-to-node-20</li> <li><a href="https://github.com/actions/cache/commit/1326563738ddb735c5f2ce85cba8c79f33b728cd"><code>1326563</code></a> Merge branch 'main' into main</li> <li><a href="https://github.com/actions/cache/commit/e71876755e268d6cc25a5d3e3c46ae447e35290a"><code>e718767</code></a> Fix format</li> <li><a href="https://github.com/actions/cache/commit/01229828ffa049a8dee4db27bcb23ed33f2b451f"><code>0122982</code></a> Apply workaround for earlyExit</li> <li><a href="https://github.com/actions/cache/commit/3185ecfd6135856ca6d904ae032cff4f39b8b365"><code>3185ecf</code></a> Update "only-" actions to node20</li> <li><a href="https://github.com/actions/cache/commit/25618a0a675e8447e5ffc8ed9b7ddb2aaf927f65"><code>25618a0</code></a> Bump version</li> <li>Additional commits viewable in <a href="https://github.com/actions/cache/compare/v3...v4">compare view</a></li> </ul> </details> <br /> [![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=actions/cache&package-manager=github_actions&previous-version=3&new-version=4)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot show <dependency name> ignore conditions` will show all of the ignore conditions of the specified dependency - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) </details> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7434 ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

… component as-is when in `_mode_="callable"` and no kwargs are specified (Project-MONAI#7413) ### Description A `_target_` component with `_mode_="partial"` will still be wrapped in `functools.partial` even when no kwargs are passed: `functool.partial(component)`. In such cases, the component can just be returned as-is. If you agree with this, I will add tests for it. Thank you! ### 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: Ibrahim Hadzic <ibrahimhadzic45@gmail.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7441 This PR enable Auto3DSeg users to manage their runs and experiment more efficiently in MLFlow under arbitrary experiment names, by providing experiment name as an input parameter. ### Types of changes  - [x] Non-breaking change (fix or new feature that would not break existing functionality). change). - [x] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [x] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [x] In-line docstrings updated. --------- Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

gdown library has been updated to fix Project-MONAI#7383 since wkentaro/gdown#295 Update the gdown version for this PR Project-MONAI#7384 ### Description A few sentences describing the changes proposed in this pull request. ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

…ct-MONAI#7474) workaround for Project-MONAI#7445 ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

…7484) workaround for Project-MONAI#7445 ### Description `Resize` also uses `GaussianFilter` inside. https://github.com/Project-MONAI/MONAI/blob/50f9aea67fb1ea7967020ad613ce83409261f2de/monai/transforms/spatial/functional.py#L332 ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7458 ### Description https://github.com/python/cpython/blob/a21c0c7def9a8495f1166d9b434dfc301cb92bff/Lib/importlib/abc.py#L68 ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7013 Project-MONAI#7478 ### Description replace `predict_from_raw_data` with `nnUNetPredictor` in test_nnunetv2runner ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7449 ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Use uint8 instead of int8 in `LabelStats`. ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes issue Project-MONAI#7425 ### Description Add a `sample_std` parameter to `RandGaussianNoise` and `RandGaussianNoised`. When True, the Gaussian's standard deviation is sampled uniformly from 0 to std (i.e., what is currently done). When False, the noise's standard deviation is non-random and set to std. The default for sample_std would be True for backwards compatibility. Changes were based on RandRicianNoise which already has a `sample_std` parameter and is similar to RandGaussianNoise in concept and implementation. ### Types of changes  - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [x] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [x] 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: Timothy Baker <bakertim@umich.edu> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

### Description When training a model using MONAI metrics for experiment tracking, I tend to log which metrics I am using. Unfortunately, just sending the metrics objects to Tensorboard will result in a list like [CustomMetric1, CustomMetric2, <monai.metrics.Metric ...>, etc.] Adding `__repr__` and `__str__` methods to the base class will solve this small annoyance. The current implementation will only return the class name, but if a certain metric would wish to report more data for its `__repr__` string, this can be easily overridden in any subclass. ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Mathijs de Boer <m.deboer-41@umcutrecht.nl> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Mathijs de Boer <m.deboer-41@umcutrecht.nl> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

…#7510) Bumps [al-cheb/configure-pagefile-action](https://github.com/al-cheb/configure-pagefile-action) from 1.3 to 1.4. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/al-cheb/configure-pagefile-action/releases">al-cheb/configure-pagefile-action's releases</a>.</em></p> <blockquote> <h2>v1.4: Update task node version to 20</h2> <h1>configure-pagefile-action</h1> <p>This action is intended to configure Pagefile size and location for Windows images in GitHub Actions.</p> <h1>Available parameters</h1> <table> <thead> <tr> <th>Argument</th> <th>Description</th> <th>Format</th> <th>Default value</th> </tr> </thead> <tbody> <tr> <td><code>minimum-size</code></td> <td>Set minimum size of Pagefile</td> <td><code>2048MB</code>, <code>4GB</code>, <code>8GB</code> and etc</td> <td><code>8GB</code></td> </tr> <tr> <td><code>maximum-size</code></td> <td>Set maximum size of Pagefile</td> <td>The same like <code>minimum-size</code></td> <td><code>minimum-size</code></td> </tr> <tr> <td><code>disk-root</code></td> <td>Set disk root where Pagefile will be located</td> <td><code>C:</code> or <code>D:</code></td> <td><code>D:</code></td> </tr> </tbody> </table> <h1>Usage</h1> <pre><code>name: CI on: [push] jobs: build: runs-on: windows-latest steps: - name: configure Pagefile uses: al-cheb/configure-pagefile-action@v1.4 with: minimum-size: 8 <pre><code>- name: configure Pagefile uses: al-cheb/configure-pagefile-action@v1.4 with: minimum-size: 8 maximum-size: 16 disk-root: &quot;D:&quot; </code></pre> <p></code></pre></p> <h1>License</h1> <p>The scripts and documentation in this project are released under the <a href="https://github.com/al-cheb/configure-pagefile-action/blob/HEAD/LICENSE">MIT License</a></p> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/al-cheb/configure-pagefile-action/commit/a3b6ebd6b634da88790d9c58d4b37a7f4a7b8708"><code>a3b6ebd</code></a> Merge pull request <a href="https://redirect.github.com/al-cheb/configure-pagefile-action/issues/20">#20</a> from mikehardy/mikehardy-patch-1</li> <li><a href="https://github.com/al-cheb/configure-pagefile-action/commit/850626ff7d6f5665848a60cdc3b0ace19fa0b094"><code>850626f</code></a> build(deps): bump javascript dependencies / forward-port as needed</li> <li><a href="https://github.com/al-cheb/configure-pagefile-action/commit/e7aac1b891d29f440ea916231d51d085206f9106"><code>e7aac1b</code></a> fix: use node 20</li> <li><a href="https://github.com/al-cheb/configure-pagefile-action/commit/d940d2434c38e1a228580edc8f9421aafca9800d"><code>d940d24</code></a> build(deps): use v4 of setup-node action, use node 20</li> <li><a href="https://github.com/al-cheb/configure-pagefile-action/commit/dfdc038768fdb21f91ed75a5fa40890fb92f5919"><code>dfdc038</code></a> build(deps): bump actions/checkout from 3 to 4</li> <li>See full diff in <a href="https://github.com/al-cheb/configure-pagefile-action/compare/v1.3...v1.4">compare view</a></li> </ul> </details> <br /> [![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=al-cheb/configure-pagefile-action&package-manager=github_actions&previous-version=1.3&new-version=1.4)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot show <dependency name> ignore conditions` will show all of the ignore conditions of the specified dependency - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) </details> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes # . ### Description Add arm support ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7523 ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7547 ### Description Previously it was 'medical_resnet50_23datasets' for both identifier and string, which doesn't correspond to the name in the hubconf.py of Warvito's repo. Now it is the correct version (according to Warvitos repo) 'medicalnet_resnet50_23datasets'. The docs state it correctly already. ### 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. - [ x] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [x ] 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: Fabian Klopfer <fabian.klopfer@ieee.org> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7533 ### Description A few sentences describing the changes proposed in this pull request. ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

…NAI#7551) Fixes Project-MONAI#7550 ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

### Description Addition of the BarlowTwinsLoss class. This cost function is introduced in the http://proceedings.mlr.press/v139/zbontar21a/zbontar21a.pdf paper with the aim of disentangling the representations learned on two views of the same sample, making it a powerful tool for multimodal and unsupervised learning. This cost function is similar to the InfoNCE Loss function already implemented in MONAI (https://docs.monai.io/en/latest/_modules/monai/losses/contrastive.html#ContrastiveLoss). However, it differs in several respects: there is no l2-normalisation, but rather a z-normalisation. In addition, rather than working between pairs of embeddings, Barlow Twins seeks to decorrelate the components of the representations. ```math \mathcal{L}_{BT} := \sum_i (1 - \mathcal{C}_{ii})^2 + \lambda \sum_i \sum_{i\neq j} \mathcal{C}_{ij}^2 ``` with $\lambda$ a positive hyperparameters and $\mathcal{C}$ the cross-correlation matrix ### 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. - [x] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [x] 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: Lucas Robinet <robinet.lucas@iuct-oncopole.fr> Signed-off-by: Lucas Robinet <67736918+Lucas-rbnt@users.noreply.github.com> Co-authored-by: Lucas Robinet <robinet.lucas@iuct-oncopole.fr> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

…roject-MONAI#7308) ### Description Based on the discussion topic [here](Project-MONAI#7161 (comment)), we implemented the Conjugate-Gradient algorithm for linear operator inversion, and Stein's Unbiased Risk Estimator (SURE) [1] loss for ground-truth-date free diffusion process guidance that is proposed in [2] and illustrated in the algorithm below: <img width="650" alt="Screenshot 2023-12-10 at 10 19 25 PM" src="https://github.com/Project-MONAI/MONAI/assets/8581162/97069466-cbaf-44e0-b7a7-ae9deb8fd7f2"> The Conjugate-Gradient (CG) algorithm is used to solve for the inversion of the linear operator in Line-4 in the algorithm above, where the linear operator is too large to store explicitly as a matrix (such as FFT/IFFT of an image) and invert directly. Instead, we can solve for the linear inversion iteratively as in CG. The SURE loss is applied for Line-6 above. This is a differentiable loss function that can be used to train/giude an operator (e.g. neural network), where the pseudo ground truth is available but the reference ground truth is not. For example, in the MRI reconstruction, the pseudo ground truth is the zero-filled reconstruction and the reference ground truth is the fully sampled reconstruction. The reference ground truth is not available due to the lack of fully sampled. **Reference** [1] Stein, C.M.: Estimation of the mean of a multivariate normal distribution. Annals of Statistics 1981 [[paper link](https://projecteuclid.org/journals/annals-of-statistics/volume-9/issue-6/Estimation-of-the-Mean-of-a-Multivariate-Normal-Distribution/10.1214/aos/1176345632.full)] [2] B. Ozturkler et al. SMRD: SURE-based Robust MRI Reconstruction with Diffusion Models. MICCAI 2023 [[paper link](https://arxiv.org/pdf/2310.01799.pdf)] ### 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. - [x] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [x] 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: chaoliu <chaoliu@nvidia.com> Signed-off-by: cxlcl <chaoliucxl@gmail.com> Signed-off-by: chaoliu <chaoliucxl@gmail.com> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

…nics@gmail.com> I, Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>, hereby add my Signed-off-by to this commit: b899421 I, Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>, hereby add my Signed-off-by to this commit: aaa640f I, Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>, hereby add my Signed-off-by to this commit: c85976f I, Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>, hereby add my Signed-off-by to this commit: f2fe14e Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Commits on Mar 26, 2024

Merge branch 'dev' into 2872-mixup

KumoLiu authored Mar 26, 2024

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2872 implementation of mixup, cutmix and cutout #7198

2872 implementation of mixup, cutmix and cutout #7198

Commits on Mar 25, 2024

Commits on Mar 26, 2024