merge master #472
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merge master #472
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Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com>
Fixes #7167 ### Description Make all the setting methods in `AutoRunner` to return `self` to enable chaining in cli. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). --------- Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Towards completing #6676 . ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [x] In-line docstrings updated. - [x] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Mark Graham <markgraham539@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/actions/checkout/releases">actions/checkout's releases</a>.</em></p> <blockquote> <h2>v4.0.0</h2> <h2>What's Changed</h2> <ul> <li>Update default runtime to node20 by <a href="https://github.com/takost"><code>@takost</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/1436">actions/checkout#1436</a></li> <li>Support fetching without the --progress option by <a href="https://github.com/simonbaird"><code>@simonbaird</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/1067">actions/checkout#1067</a></li> <li>Release 4.0.0 by <a href="https://github.com/takost"><code>@takost</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/1447">actions/checkout#1447</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/checkout/pull/1436">actions/checkout#1436</a></li> <li><a href="https://github.com/simonbaird"><code>@simonbaird</code></a> made their first contribution in <a href="https://redirect.github.com/actions/checkout/pull/1067">actions/checkout#1067</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/checkout/compare/v3...v4.0.0">https://github.com/actions/checkout/compare/v3...v4.0.0</a></p> <h2>v3.6.0</h2> <h2>What's Changed</h2> <ul> <li>Mark test scripts with Bash'isms to be run via Bash by <a href="https://github.com/dscho"><code>@dscho</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/1377">actions/checkout#1377</a></li> <li>Add option to fetch tags even if fetch-depth > 0 by <a href="https://github.com/RobertWieczoreck"><code>@RobertWieczoreck</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/579">actions/checkout#579</a></li> <li>Release 3.6.0 by <a href="https://github.com/luketomlinson"><code>@luketomlinson</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/1437">actions/checkout#1437</a></li> </ul> <h2>New Contributors</h2> <ul> <li><a href="https://github.com/RobertWieczoreck"><code>@RobertWieczoreck</code></a> made their first contribution in <a href="https://redirect.github.com/actions/checkout/pull/579">actions/checkout#579</a></li> <li><a href="https://github.com/luketomlinson"><code>@luketomlinson</code></a> made their first contribution in <a href="https://redirect.github.com/actions/checkout/pull/1437">actions/checkout#1437</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/checkout/compare/v3.5.3...v3.6.0">https://github.com/actions/checkout/compare/v3.5.3...v3.6.0</a></p> <h2>v3.5.3</h2> <h2>What's Changed</h2> <ul> <li>Fix: Checkout Issue in self hosted runner due to faulty submodule check-ins by <a href="https://github.com/megamanics"><code>@megamanics</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/1196">actions/checkout#1196</a></li> <li>Fix typos found by codespell by <a href="https://github.com/DimitriPapadopoulos"><code>@DimitriPapadopoulos</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/1287">actions/checkout#1287</a></li> <li>Add support for sparse checkouts by <a href="https://github.com/dscho"><code>@dscho</code></a> and <a href="https://github.com/dfdez"><code>@dfdez</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/1369">actions/checkout#1369</a></li> <li>Release v3.5.3 by <a href="https://github.com/TingluoHuang"><code>@TingluoHuang</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/1376">actions/checkout#1376</a></li> </ul> <h2>New Contributors</h2> <ul> <li><a href="https://github.com/megamanics"><code>@megamanics</code></a> made their first contribution in <a href="https://redirect.github.com/actions/checkout/pull/1196">actions/checkout#1196</a></li> <li><a href="https://github.com/DimitriPapadopoulos"><code>@DimitriPapadopoulos</code></a> made their first contribution in <a href="https://redirect.github.com/actions/checkout/pull/1287">actions/checkout#1287</a></li> <li><a href="https://github.com/dfdez"><code>@dfdez</code></a> made their first contribution in <a href="https://redirect.github.com/actions/checkout/pull/1369">actions/checkout#1369</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/checkout/compare/v3...v3.5.3">https://github.com/actions/checkout/compare/v3...v3.5.3</a></p> <h2>v3.5.2</h2> <h2>What's Changed</h2> <ul> <li>Fix: Use correct API url / endpoint in GHES by <a href="https://github.com/fhammerl"><code>@fhammerl</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/1289">actions/checkout#1289</a> based on <a href="https://redirect.github.com/actions/checkout/issues/1286">#1286</a> by <a href="https://github.com/1newsr"><code>@1newsr</code></a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/checkout/compare/v3.5.1...v3.5.2">https://github.com/actions/checkout/compare/v3.5.1...v3.5.2</a></p> <h2>v3.5.1</h2> <h2>What's Changed</h2> <ul> <li>Improve checkout performance on Windows runners by upgrading <code>@actions/github</code> dependency by <a href="https://github.com/BrettDong"><code>@BrettDong</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/1246">actions/checkout#1246</a></li> </ul> <h2>New Contributors</h2> <ul> <li><a href="https://github.com/BrettDong"><code>@BrettDong</code></a> made their first contribution in <a href="https://redirect.github.com/actions/checkout/pull/1246">actions/checkout#1246</a></li> </ul> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/actions/checkout/blob/main/CHANGELOG.md">actions/checkout's changelog</a>.</em></p> <blockquote> <h1>Changelog</h1> <h2>v4.1.0</h2> <ul> <li><a href="https://redirect.github.com/actions/checkout/pull/1396">Add support for partial checkout filters</a></li> </ul> <h2>v4.0.0</h2> <ul> <li><a href="https://redirect.github.com/actions/checkout/pull/1067">Support fetching without the --progress option</a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/1436">Update to node20</a></li> </ul> <h2>v3.6.0</h2> <ul> <li><a href="https://redirect.github.com/actions/checkout/pull/1377">Fix: Mark test scripts with Bash'isms to be run via Bash</a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/579">Add option to fetch tags even if fetch-depth > 0</a></li> </ul> <h2>v3.5.3</h2> <ul> <li><a href="https://redirect.github.com/actions/checkout/pull/1196">Fix: Checkout fail in self-hosted runners when faulty submodule are checked-in</a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/1287">Fix typos found by codespell</a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/1369">Add support for sparse checkouts</a></li> </ul> <h2>v3.5.2</h2> <ul> <li><a href="https://redirect.github.com/actions/checkout/pull/1289">Fix api endpoint for GHES</a></li> </ul> <h2>v3.5.1</h2> <ul> <li><a href="https://redirect.github.com/actions/checkout/pull/1246">Fix slow checkout on Windows</a></li> </ul> <h2>v3.5.0</h2> <ul> <li><a href="https://redirect.github.com/actions/checkout/pull/1237">Add new public key for known_hosts</a></li> </ul> <h2>v3.4.0</h2> <ul> <li><a href="https://redirect.github.com/actions/checkout/pull/1209">Upgrade codeql actions to v2</a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/1210">Upgrade dependencies</a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/1225">Upgrade <code>@actions/io</code></a></li> </ul> <h2>v3.3.0</h2> <ul> <li><a href="https://redirect.github.com/actions/checkout/pull/1045">Implement branch list using callbacks from exec function</a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/1050">Add in explicit reference to private checkout options</a></li> <li>[Fix comment typos (that got added in <a href="https://redirect.github.com/actions/checkout/issues/770">#770</a>)](<a href="https://redirect.github.com/actions/checkout/pull/1057">actions/checkout#1057</a>)</li> </ul> <h2>v3.2.0</h2> <ul> <li><a href="https://redirect.github.com/actions/checkout/pull/942">Add GitHub Action to perform release</a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/967">Fix status badge</a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/1002">Replace datadog/squid with ubuntu/squid Docker image</a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/964">Wrap pipeline commands for submoduleForeach in quotes</a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/1029">Update <code>@actions/io</code> to 1.1.2</a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/1039">Upgrading version to 3.2.0</a></li> </ul> <h2>v3.1.0</h2> <ul> <li><a href="https://redirect.github.com/actions/checkout/pull/939">Use <code>@actions/core</code> <code>saveState</code> and <code>getState</code></a></li> <li><a href="https://redirect.github.com/actions/checkout/pull/922">Add <code>github-server-url</code> input</a></li> </ul> <h2>v3.0.2</h2> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/actions/checkout/commit/b4ffde65f46336ab88eb53be808477a3936bae11"><code>b4ffde6</code></a> Link to release page from what's new section (<a href="https://redirect.github.com/actions/checkout/issues/1514">#1514</a>)</li> <li><a href="https://github.com/actions/checkout/commit/8530928916aaef40f59e6f221989ccb31f5759e7"><code>8530928</code></a> Correct link to GitHub Docs (<a href="https://redirect.github.com/actions/checkout/issues/1511">#1511</a>)</li> <li><a href="https://github.com/actions/checkout/commit/7cdaf2fbc075e6f3b9ca94cfd6cec5adc8a75622"><code>7cdaf2f</code></a> Update CODEOWNERS to Launch team (<a href="https://redirect.github.com/actions/checkout/issues/1510">#1510</a>)</li> <li><a href="https://github.com/actions/checkout/commit/8ade135a41bc03ea155e62e844d188df1ea18608"><code>8ade135</code></a> Prepare 4.1.0 release (<a href="https://redirect.github.com/actions/checkout/issues/1496">#1496</a>)</li> <li><a href="https://github.com/actions/checkout/commit/c533a0a4cfc4962971818edcfac47a2899e69799"><code>c533a0a</code></a> Add support for partial checkout filters (<a href="https://redirect.github.com/actions/checkout/issues/1396">#1396</a>)</li> <li><a href="https://github.com/actions/checkout/commit/72f2cec99f417b1a1c5e2e88945068983b7965f9"><code>72f2cec</code></a> Update README.md for V4 (<a href="https://redirect.github.com/actions/checkout/issues/1452">#1452</a>)</li> <li><a href="https://github.com/actions/checkout/commit/3df4ab11eba7bda6032a0b82a6bb43b11571feac"><code>3df4ab1</code></a> Release 4.0.0 (<a href="https://redirect.github.com/actions/checkout/issues/1447">#1447</a>)</li> <li><a href="https://github.com/actions/checkout/commit/8b5e8b768746b50394015010d25e690bfab9dfbc"><code>8b5e8b7</code></a> Support fetching without the --progress option (<a href="https://redirect.github.com/actions/checkout/issues/1067">#1067</a>)</li> <li><a href="https://github.com/actions/checkout/commit/97a652b80035363df47baee5031ec8670b8878ac"><code>97a652b</code></a> Update default runtime to node20 (<a href="https://redirect.github.com/actions/checkout/issues/1436">#1436</a>)</li> <li>See full diff in <a href="https://github.com/actions/checkout/compare/v3...v4">compare view</a></li> </ul> </details> <br /> [](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>
Fixes #5394 ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Add MLflow support in AutoRunner Class. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: dongy <dongy@nvidia.com>
Fixes #6627 ### Description adding a `fname_regex` option to the pydicom reader ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [x] 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: Wenqi Li <wenqil@nvidia.com>
Fixes #7186 ### Description remove unnecessary float() ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: KumoLiu <yunl@nvidia.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com>
allows setting AutoRunner params from config allows specifying number of folds in config --------- Signed-off-by: myron <amyronenko@nvidia.com>
Fixes #5484. ### Description Implemented VoxelMorph and added some docstrings. Checked coding style locally. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [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>
Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@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>
Fixes #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>
Fixes # . ### Description A few sentences describing the changes proposed in this pull request. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Add new developer to blossom-ci trigger list Signed-off-by: YanxuanLiu <yanxuanl@nvidia.com>
#7234) … MONAI with all dependencies on Windows Fixes #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 <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: ytl0623 <david89062388@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
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.
Signed-off-by: Dženan Zukić <dzenan.zukic@kitware.com>
Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Part of #6904 ### Description - Fix inefficient patching in `PatchDataset` - Add cache option in `GridPatchDataset` ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: 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>
Fixes #7101 ### Description Added examples in the docstrings for `EnsureType` and `CastToType` transforms which show how they function under different circumstances. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [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>
Fixes #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 <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [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: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com>
#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 <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). --------- Signed-off-by: elitap <elias.tappeiner@gmx.at> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…7262) Fixes #7261 ### Description Remove star-arg unpacking before a keyword argument. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: KumoLiu <yunl@nvidia.com>
…n Bash (#7268) Fixes #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 <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: ytl0623 <david89062388@gmail.com>
…ion (#7271) Fixes #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 <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: 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>
Fixes #7265. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: KumoLiu <yunl@nvidia.com>
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 2 to 3. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/conda-incubator/setup-miniconda/releases">conda-incubator/setup-miniconda's releases</a>.</em></p> <blockquote> <h2>Version 3.0.0</h2> <h3>Features</h3> <ul> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/308">#308</a> Update to node20</li> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/291">#291</a> Add conda-solver option (defaults to libmamba)</li> </ul> <h3>Fixes</h3> <ul> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/299">#299</a> Fix condaBasePath when useBundled is false, and there's no pre-existing conda</li> </ul> <h3>Documentation</h3> <ul> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/309">#309</a> Switch to main branch based development</li> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/313">#313</a> Specify team conda-incubator/setup-miniconda as codeowners</li> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/318">#318</a> README: update actions in examples, add security section, similar actions</li> </ul> <h3>Tasks and Maintenance</h3> <ul> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/307">#307</a> Run dependabot against main branch and also update node packages</li> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/311">#311</a> Bump actions/checkout from 2 to 4</li> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/310">#310</a> Bump actions/cache from 1 to 3</li> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/314">#314</a> Strip/update dependencies</li> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/315">#315</a> Split lint into check and build, switch from <code>npm install</code> to <code>npm ci</code></li> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/317">#317</a> Bump normalize-url from 4.5.1 to 8.0.0</li> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/316">#316</a> Faster workflow response / saving resources via timeout/concurrency policy</li> </ul> <p><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/308">#308</a>: <a href="https://redirect.github.com/conda-incubator/setup-miniconda/pull/308">conda-incubator/setup-miniconda#308</a> <a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/291">#291</a>: <a href="https://redirect.github.com/conda-incubator/setup-miniconda/pull/291">conda-incubator/setup-miniconda#291</a> <a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/299">#299</a>: <a href="https://redirect.github.com/conda-incubator/setup-miniconda/pull/299">conda-incubator/setup-miniconda#299</a> <a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/309">#309</a>: <a href="https://redirect.github.com/conda-incubator/setup-miniconda/pull/309">conda-incubator/setup-miniconda#309</a> <a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/313">#313</a>: <a href="https://redirect.github.com/conda-incubator/setup-miniconda/pull/313">conda-incubator/setup-miniconda#313</a> <a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/318">#318</a>: <a href="https://redirect.github.com/conda-incubator/setup-miniconda/pull/318">conda-incubator/setup-miniconda#318</a> <a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/307">#307</a>: <a href="https://redirect.github.com/conda-incubator/setup-miniconda/pull/307">conda-incubator/setup-miniconda#307</a> <a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/311">#311</a>: <a href="https://redirect.github.com/conda-incubator/setup-miniconda/pull/311">conda-incubator/setup-miniconda#311</a> <a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/310">#310</a>: <a href="https://redirect.github.com/conda-incubator/setup-miniconda/pull/310">conda-incubator/setup-miniconda#310</a> <a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/314">#314</a>: <a href="https://redirect.github.com/conda-incubator/setup-miniconda/pull/314">conda-incubator/setup-miniconda#314</a> <a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/315">#315</a>: <a href="https://redirect.github.com/conda-incubator/setup-miniconda/pull/315">conda-incubator/setup-miniconda#315</a> <a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/317">#317</a>: <a href="https://redirect.github.com/conda-incubator/setup-miniconda/pull/317">conda-incubator/setup-miniconda#317</a> <a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/316">#316</a>: <a href="https://redirect.github.com/conda-incubator/setup-miniconda/pull/316">conda-incubator/setup-miniconda#316</a></p> <h2>New Contributors</h2> <ul> <li><a href="https://github.com/isuruf"><code>@isuruf</code></a> made their first contribution in <a href="https://redirect.github.com/conda-incubator/setup-miniconda/pull/299">conda-incubator/setup-miniconda#299</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/conda-incubator/setup-miniconda/compare/v2...v3.0.0">https://github.com/conda-incubator/setup-miniconda/compare/v2...v3.0.0</a></p> <h2>Version 2.3.0</h2> <h3>Documentation</h3> <ul> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/263">#263</a> Update links to GitHub shell docs</li> </ul> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md">conda-incubator/setup-miniconda's changelog</a>.</em></p> <blockquote> <h2><a href="https://github.com/conda-incubator/setup-miniconda/releases/tag/v3.0.1">v3.0.1</a> (2023-11-29)</h2> <h3>Fixes</h3> <ul> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/325">#325</a> Fix environment activation on windows (a v3 regression) due to hard-coded install PATH</li> </ul> <p><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/325">#325</a>: <a href="https://redirect.github.com/conda-incubator/setup-miniconda/pull/325">conda-incubator/setup-miniconda#325</a></p> <h2><a href="https://github.com/conda-incubator/setup-miniconda/releases/tag/v3.0.0">v3.0.0</a> (2023-11-27)</h2> <h3>Features</h3> <ul> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/308">#308</a> Update to node20</li> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/291">#291</a> Add conda-solver option (defaults to libmamba)</li> </ul> <h3>Fixes</h3> <ul> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/299">#299</a> Fix condaBasePath when useBundled is false, and there's no pre-existing conda</li> </ul> <h3>Documentation</h3> <ul> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/309">#309</a> Switch to main branch based development</li> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/313">#313</a> Specify team conda-incubator/setup-miniconda as codeowners</li> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/318">#318</a> README: update actions in examples, add security section, similar actions</li> </ul> <h3>Tasks and Maintenance</h3> <ul> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/307">#307</a> Run dependabot against main branch and also update node packages</li> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/311">#311</a> Bump actions/checkout from 2 to 4</li> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/310">#310</a> Bump actions/cache from 1 to 3</li> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/314">#314</a> Strip/update dependencies</li> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/315">#315</a> Split lint into check and build, switch from <code>npm install</code> to <code>npm ci</code></li> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/317">#317</a> Bump normalize-url from 4.5.1 to 8.0.0</li> <li><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/316">#316</a> Faster workflow response / saving resources via timeout/concurrency policy</li> </ul> <p><a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/308">#308</a>: <a href="https://redirect.github.com/conda-incubator/setup-miniconda/pull/308">conda-incubator/setup-miniconda#308</a> <a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/291">#291</a>: <a href="https://redirect.github.com/conda-incubator/setup-miniconda/pull/291">conda-incubator/setup-miniconda#291</a> <a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/299">#299</a>: <a href="https://redirect.github.com/conda-incubator/setup-miniconda/pull/299">conda-incubator/setup-miniconda#299</a> <a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/309">#309</a>: <a href="https://redirect.github.com/conda-incubator/setup-miniconda/pull/309">conda-incubator/setup-miniconda#309</a> <a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/313">#313</a>: <a href="https://redirect.github.com/conda-incubator/setup-miniconda/pull/313">conda-incubator/setup-miniconda#313</a> <a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/318">#318</a>: <a href="https://redirect.github.com/conda-incubator/setup-miniconda/pull/318">conda-incubator/setup-miniconda#318</a> <a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/307">#307</a>: <a href="https://redirect.github.com/conda-incubator/setup-miniconda/pull/307">conda-incubator/setup-miniconda#307</a> <a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/311">#311</a>: <a href="https://redirect.github.com/conda-incubator/setup-miniconda/pull/311">conda-incubator/setup-miniconda#311</a> <a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/310">#310</a>: <a href="https://redirect.github.com/conda-incubator/setup-miniconda/pull/310">conda-incubator/setup-miniconda#310</a></p> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/conda-incubator/setup-miniconda/commit/11b562958363ec5770fef326fe8ef0366f8cbf8a"><code>11b5629</code></a> Prepare 3.0.1 (<a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/326">#326</a>)</li> <li><a href="https://github.com/conda-incubator/setup-miniconda/commit/8706aa744e0162a2264dc938c759d2b51f9b5e10"><code>8706aa7</code></a> Fix env activation on win (a v3 regression) due to hard-coded install PATH (#...</li> <li><a href="https://github.com/conda-incubator/setup-miniconda/commit/c585a970973750f68d4d5c75284051b3f0167afe"><code>c585a97</code></a> Bump conda-incubator/setup-miniconda from 2.3.0 to 3.0.0 (<a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/321">#321</a>)</li> <li><a href="https://github.com/conda-incubator/setup-miniconda/commit/2defc80cc6f4028b1780c50faf08dd505d698976"><code>2defc80</code></a> Prepare release (<a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/320">#320</a>)</li> <li><a href="https://github.com/conda-incubator/setup-miniconda/commit/0d5a56b9eb002ebca917fd24dbbb168694a769e3"><code>0d5a56b</code></a> Bump actions/checkout from 2 to 4 (<a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/319">#319</a>)</li> <li><a href="https://github.com/conda-incubator/setup-miniconda/commit/45fd3f90899ca98b9fe9ed48921c9edbb341a570"><code>45fd3f9</code></a> Merge pull request <a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/316">#316</a> from dbast/timeout</li> <li><a href="https://github.com/conda-incubator/setup-miniconda/commit/d1e04fc2677b38349d15832651d5d3c485c8411a"><code>d1e04fc</code></a> Merge pull request <a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/299">#299</a> from isuruf/condaBasePath</li> <li><a href="https://github.com/conda-incubator/setup-miniconda/commit/fab00738406b3d3854b3b57791e274f16ac95ab4"><code>fab0073</code></a> Merge pull request <a href="https://redirect.github.com/conda-incubator/setup-miniconda/issues/318">#318</a> from dbast/readme</li> <li><a href="https://github.com/conda-incubator/setup-miniconda/commit/fa6bdf964307f648fedc0f07787e550f08eb2812"><code>fa6bdf9</code></a> Update with npm run build</li> <li><a href="https://github.com/conda-incubator/setup-miniconda/commit/d42f8b884a951a7e5af53888bd6101e0fd1dc916"><code>d42f8b8</code></a> Fix condaBasePath when useBundled is false, and there's no pre-existing conda</li> <li>Additional commits viewable in <a href="https://github.com/conda-incubator/setup-miniconda/compare/v2...v3">compare view</a></li> </ul> </details> <br /> [](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. 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Fixes model-zoo#537 ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: KumoLiu <yunl@nvidia.com>
Part of #7250. ### Description Fix the Python version for transformers smaller than 3.10. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: KumoLiu <yunl@nvidia.com>
Fixes #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 <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [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>
Fixes # . ### Description A few sentences describing the changes proposed in this pull request. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: heyufan1995 <heyufan1995@gmail.com>
Fixes # . ### Description A few sentences describing the changes proposed in this pull request. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: heyufan1995 <heyufan1995@gmail.com> Signed-off-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Fixes # . ### Description A few sentences describing the changes proposed in this pull request. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: mylapallilavanyaa <149993494+mylapallilavanyaa@users.noreply.github.com> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Fixes # . ### Description Fix the bug that causes wrong results in model zoo finetuning. Patch coords was not passed from sliding window to vista3d. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: heyufan1995 <heyufan1995@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>
Add a function to create a JSON file that maps input and output paths. Fixes #7557 . ### Description A few sentences describing the changes proposed in this pull request. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: staydelight <kevin295643815697236@gmail.com> Co-authored-by: staydelight <kevin295643815697236@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>
Fixes #8050 ### Description A few sentences describing the changes proposed in this pull request. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Fixes #8054 ### Description Add cuda sync after invoke cuda ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
…' (#8055) Fixes #6857 ### Description Added docstring to RandImageFilterd method which informs the user that they need to manually scale the result image when using this method. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [x] In-line docstrings updated. --------- Signed-off-by: dedeepyasai <dedeepyasai.sai@gmail.com> Signed-off-by: saelra <rasaelee@gmail.com> Signed-off-by: Kelvin R <kelvinrbNsc@gmail.com> Signed-off-by: ken-ni <kennett.vera@gmail.com> Signed-off-by: Dureti <98233210+DuretiShemsi@users.noreply.github.com> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: saelra <rasaelee@gmail.com> Co-authored-by: Kelvin R. <138339140+K-Rilla@users.noreply.github.com> Co-authored-by: Kelvin R <kelvinrbNsc@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: dedeepyasai <dedeepyasai.sai@gmail.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Ratanachat Saelee <146144408+Saelra@users.noreply.github.com> Co-authored-by: Dureti <98233210+DuretiShemsi@users.noreply.github.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Fixes #8048 ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
### Description Added alternative class to ONNX->TRT export and wrap TRT engines for inference. It encapsulates filesystem persistence and does not rely on torch-tensortrt for execution. Also can be used to run ONNX with onnxruntime. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Boris Fomitchev <bfomitchev@nvidia.com> Signed-off-by: Yiheng Wang <vennw@nvidia.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: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com> Co-authored-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: binliunls <107988372+binliunls@users.noreply.github.com>
Add box and points convert transform Cherrypick ApplyTransformToPoints ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: 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: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Co-authored-by: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com>
Fixes # . ### Description A few sentences describing the changes proposed in this pull request. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: heyufan1995 <heyufan1995@gmail.com> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Yiheng Wang <vennw@nvidia.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: Yiheng Wang <vennw@nvidia.com> Co-authored-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com>
Fixes #7911, which describes how the RandSimulateLowResolutiond dictionary transform produces non-deterministic outputs, yet the typical array transform RandSimulateLowResolution produces deterministic ones. ### Description Inside of `RandSimulateLowResolutiond`, added the line `self.sim_lowres_tfm.set_random_state(seed, state)` in `set_random_state` to ensure the helper function `sim_lowres_tfm` is seeded and the transform can be performed deterministically. Note: I also sifted through the other dictionary transforms with helper functions and did not find anything that looked problematic similar to this. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [ ] Non-breaking change (fix or new feature that would not break existing functionality). - [x] 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: BenjaminLi <25benjaminli@gmail.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
workaround for #8061 ### Description Ignore warning from nptyping as workaround ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Forced `Fourier` class to output contiguous tensors, which potentially fixes a performance bottleneck. ### Description Some transforms, such as `RandKSpaceSpikeNoise`, rely on the `Fourier` class. In its current state, the `Fourier` class returns non-contiguous tensors, which potentially limits performance. For example, when followed by `RandHistogramShift`, the following warning occurs: ``` <path_to_monai>/monai/transforms/intensity/array.py:1852: UserWarning: torch.searchsorted(): input value tensor is non-contiguous, this will lower the performance due to extra data copy when converting non-contiguous tensor to contiguous, please use contiguous input value tensor if possible. This message will only appear once per program. (Triggered internally at /opt/conda/conda-bld/pytorch_1716905975447/work/aten/src/ATen/native/BucketizationUtils.h:32.) indices = ns.searchsorted(xp.reshape(-1), x.reshape(-1)) - 1 ``` A straightforward fix is to force the `Fourier` class to output contiguous tensors (see commit). To reproduce, please run: ``` from monai.transforms import RandKSpaceSpikeNoise from monai.transforms.utils import Fourier import numpy as np ### TEST WITH TRANSFORMS ### t = RandKSpaceSpikeNoise(prob=1) # for torch tensors a_torch = torch.rand(1, 128, 128, 128) print(a_torch.is_contiguous()) a_torch_mod = t(a_torch) print(a_torch_mod.is_contiguous()) # for np arrays a_np = np.random.rand(1, 128, 128, 128) print(a_np.flags['C_CONTIGUOUS']) a_np_mod = t(a_np) # automatically transformed to torch.tensor print(a_np_mod.is_contiguous()) ### TEST DIRECTLY WITH FOURIER ### f = Fourier() # inv_shift_fourier # for torch tensors real_torch = torch.randn(1, 128, 128, 128) im_torch = torch.randn(1, 128, 128, 128) k_torch = torch.complex(real_torch, im_torch) print(k_torch.is_contiguous()) out_torch = f.inv_shift_fourier(k_torch, spatial_dims=3) print(out_torch.is_contiguous()) # for np arrays real_np = np.random.randn(1, 100, 100, 100) im_np = np.random.randn(1, 100, 100, 100) k_np = real_np + 1j * im_np print(k_np.flags['C_CONTIGUOUS']) out_np = f.inv_shift_fourier(k_np, spatial_dims=3) print(out_np.flags['C_CONTIGUOUS']) # shift_fourier # for torch tensors a_torch = torch.rand(1, 128, 128, 128) print(a_torch.is_contiguous()) out_torch = f.shift_fourier(a_torch, spatial_dims=3) print(out_torch.is_contiguous()) # for np arrays a_np = np.random.rand(1, 128, 128, 128) print(a_np.flags['C_CONTIGUOUS']) out_np = f.shift_fourier(a_np, spatial_dims=3) print(out_np.flags['C_CONTIGUOUS']) ``` ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Bastian Wittmann <bastian.wittmann@uzh.ch>. Signed-off-by: Bastian Wittmann <bastian.wittmann@uzh.ch> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Fixes #8061. ### Description Post-merge fixes for trt_compile() ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Boris Fomitchev <bfomitchev@nvidia.com> Signed-off-by: Yiheng Wang <vennw@nvidia.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: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com> Co-authored-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: binliunls <107988372+binliunls@users.noreply.github.com>
Enhance `ApplyTransformToPointsd` to receive a sequence of refer keys. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: 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>
…7814) Fixes #5905 ### Description We simply add one argument for DataStats and DataStatsd to make MetaTensor optional printed. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Wei_Chuan, Chiang <jamesis1356@gmail.com> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Suraj Pai <b.pai@maastrichtuniversity.nl> 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> Co-authored-by: Suraj Pai <b.pai@maastrichtuniversity.nl> Co-authored-by: Ben Murray <ben.murray@gmail.com>
- add packaging in setup.cfg - fix test_gdsdataset.py issue - add test_matshow3d to the skip list for min test - suppress deprecated warning when import monai (workaround for #8060) ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Fixes #7966 ### Description A few sentences describing the changes proposed in this pull request. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Suraj Pai <b.pai@maastrichtuniversity.nl> Signed-off-by: Suraj Pai <bspai@bwh.harvard.edu> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Fixes #8075 ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Move publish to test pypi to blossom ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
the vectors presented for space directions are column vectors ref: https://teem.sourceforge.net/nrrd/format.html#spacedirections ### Description A few sentences describing the changes proposed in this pull request. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [ ] 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: Christian Herz <christianherz1985@gmail.com>
### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Fixes #7949 . ### Description Regardless of the type of `weight map`, random numbers should be kept as floating-point numbers for calculating the sampling location. However, `searchsorted` requires matching data structures. I have modified `convert_to_dst_type` to control converting only the data structure while maintaining the original data type. Additionally, I have included an example with integer weight maps in the test file. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Han123su <popsmall212@gmail.com> Signed-off-by: Han123su <107395380+Han123su@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Fixes #8108 ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
### Description This removes some functions which aren't needed any more. These related to an early idea for doing importation to avoid defining `__all__` components to modules, but this is being done instead as it is more standard. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> 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>
### Description This restores load_modules for now to resolve importation issues. Doing a two-pass loading process seems to allow some references which normally Python wouldn't permit. The fact that these issues weren't caught in testing is rather strange, and only showed up when symbols in `monai.apps` were references in bundles. I'm not sure if this is all related to circular imports, if parts of MONAI aren't being tested properly, or the way the symbol resolution works within `monai.bundle` should be improved. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
Fixes #8120 . ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
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Fixes # .
Description
A few sentences describing the changes proposed in this pull request.
Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests --disttests.make htmlcommand in thedocs/folder.