https://github.com/Project-MONAI/MONAI/
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| Revision | Author | Date | Message | Commit Date |
|---|---|---|---|---|
| 865972f | YunLiu | 12 October 2023, 10:51:53 UTC | Fix unsuitable default value to bundle_root in ckpt_export (#7124) Fixes #7123 ### 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> | 12 October 2023, 10:51:53 UTC |
| e36982b | Wenqi Li | 12 October 2023, 09:02:23 UTC | update validation epoch (#7121) - this allows for validation epoch at the very beginning of training - fixes #7122 ### 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> | 12 October 2023, 09:02:23 UTC |
| 4743945 | Wenqi Li | 11 October 2023, 14:36:14 UTC | update changelog and docs for v1.3 (#7110) part of https://github.com/Project-MONAI/MONAI/issues/7017 fixes #7112 ### 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> | 11 October 2023, 14:36:14 UTC |
| 2b1e3d0 | YunLiu | 11 October 2023, 12:03:45 UTC | Add support for metatensor in AddGuidanceFromPointsDeepEditd and ResizeGuidanceMultipleLabelDeepEditd (#7115) Fixes #7114 ### 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> | 11 October 2023, 12:03:45 UTC |
| 8d730cd | Wenqi Li | 10 October 2023, 20:47:10 UTC | 6387 update_kwargs for merging multiple configs (#7109) Fixes #6387 Fixes #5899 ### Description - add api for update_kwargs - add support of merging multiple configs files and dictionaries - remove warning message of directory in `runtests.sh` ### 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> | 10 October 2023, 20:47:10 UTC |
| fc1350a | Nic Ma | 10 October 2023, 06:14:18 UTC | 7107 Add support to validate at training start (#7108) Fixes #7107 . ### Description This PR added support to optionally execute validation at training start first, this is useful for transfer learning to validate the initial model. ### 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: Nic Ma <nma@nvidia.com> | 10 October 2023, 06:14:18 UTC |
| 5c6d199 | YunLiu | 09 October 2023, 19:08:10 UTC | Code formatting for user specified directories (#7106) Fixes #7099 ### 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> | 09 October 2023, 19:08:10 UTC |
| 825021d | YunLiu | 09 October 2023, 09:02:14 UTC | `EnsureTyped` flexible dtype (#7104) Fixes #7102 ### Description Make dtype in `EnsureTyped` configurable as different dtypes for difference 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: KumoLiu <yunl@nvidia.com> | 09 October 2023, 09:02:14 UTC |
| 2b0a95e | monai-bot | 09 October 2023, 07:33:25 UTC | auto updates (#7105) Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> | 09 October 2023, 07:33:25 UTC |
| 7930f85 | YunLiu | 08 October 2023, 10:40:56 UTC | Add weight in `DiceLoss` (#7098) Fixes #7065. ### Description - standardize the naming to be simply "weight". - add this "weight" parameter to `DiceLoss`. ### 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. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: KumoLiu <yunl@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 08 October 2023, 10:40:56 UTC |
| e8edc2e | Wenqi Li | 08 October 2023, 06:56:34 UTC | fixes releasing pipeline (#7103) Fixes https://github.com/Project-MONAI/MONAI/actions/runs/6443867275/job/17496241665 ### 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> | 08 October 2023, 06:56:34 UTC |
| 112e431 | Matthias Hadlich | 07 October 2023, 15:49:46 UTC | Add distance_transform_edt to transforms.__init__ (#7100) Forgot the import of the helper function `distance_transform_edt` in `transforms.__init__` ### 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: Matthias Hadlich <matthiashadlich@posteo.de> | 07 October 2023, 15:49:46 UTC |
| f239825 | john-zielke-snkeos | 06 October 2023, 17:45:59 UTC | SwinUNETR refactored img_size parameter and removed checkpointing dep… (#7093) ### Description Make two changes for the SwinUNETR network: - The image_size parameter does not seem to have an effect apart from checking shape compatibility in the beginning. This is now expressed in the docstring and the parameter will be deprecated in the future. Instead the shape compatibility is checked during the forward pass on the actual shape - newer pytorch versions accept a parameter [use_reentrant](https://pytorch.org/docs/2.1/checkpoint.html). The old default of True is deprecated in favor of True. This PR sets the parameter to true and therefore adopts the recommended value and removes the warning. ### 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. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: John Zielke <john.zielke@snkeos.com> | 06 October 2023, 17:45:59 UTC |
| 100db27 | Matthias Hadlich | 05 October 2023, 19:54:56 UTC | Signalfillempty set track_meta to True (#7089) Related to #7011. I was using the `Signalfillemptyd` (based on `Signalfillempty`) transform in monailabel and found out, it currently allows no inversion. When digging deeper I realized that SignalFillEmpty just throws away the meta information. With the simple addition of `track_meta=True` it works as expected. I hope it has no other impact, but I honestly don't know. @wyli would be cool if we can add this to MONAI 1.3.0, thanks! I can also rework `Signalfillempty` to just accept any datatype, if that would the more appropriate approach. ### 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. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. - [ ] 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. Signed-off-by: Matthias Hadlich <matthiashadlich@posteo.de> | 05 October 2023, 19:54:56 UTC |
| 4cb7bb2 | Wenqi Li | 05 October 2023, 15:19:20 UTC | 7088 compatible metric util torch inf nan (#7080) Fixes #7088 ### 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> | 05 October 2023, 15:19:20 UTC |
| 141bcf0 | monai-bot | 04 October 2023, 22:05:10 UTC | Auto3DSeg algo_template hash update (#7087) Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> | 04 October 2023, 22:05:10 UTC |
| e8b79f7 | vgrau98 | 04 October 2023, 20:01:04 UTC | Unify env vars access (#7084) Fixes #6879. ### Description Some environment variable called using `os.get.environ("MONAI_VAR")` instead of `monai.utils.MONAIEnvVars`. Can't use `monai.utils.MONAIEnvVars` in `monai.utils.module.py` due to circular imports. ### 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`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: vgrau98 <victor.grau93@gmail.com> | 04 October 2023, 20:01:04 UTC |
| 65e8f5b | vgrau98 | 03 October 2023, 21:29:37 UTC | add shape check for arbitrary types for DataStats (#7082) Fixes #6844. ### Description DataStats was breaking for arbitrary types (other than tensor or array) because of shape attribute. Changes are made in order to be consistent with other DataStats attributes management like `data_type`. ### 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: vgrau98 <victor.grau93@gmail.com> | 03 October 2023, 21:29:37 UTC |
| 31040c8 | monai-bot | 02 October 2023, 14:40:00 UTC | auto updates (#7077) | 02 October 2023, 14:40:00 UTC |
| 8b7effd | vgrau98 | 02 October 2023, 11:43:20 UTC | update saveImaged docstrings (#7076) Fixes #6884 . ### Description Documentation didn't indicate dcm files support. After checking dcm seems to be the only extension whose doc was missing. ### 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: vgrau98 <victor.grau93@gmail.com> | 02 October 2023, 11:43:20 UTC |
| 8f356a4 | YunLiu | 02 October 2023, 10:45:27 UTC | 7017 update changelog for v1.3 (#7048) Part of #7017 ### Description - update changelog - fixes documentation typos ### 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: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> | 02 October 2023, 10:45:27 UTC |
| f140e06 | john-zielke-snkeos | 01 October 2023, 16:13:24 UTC | Cucim support for `get_mask_edges` and `get_surface_distance` (#7008) ### Description Add support for cucim for `get_mask_edges` and `get_surface_distance`. This provides significant speedup in surface related metrics. Profiling on my system gave 3-20x speedups depending on the input shape: [---------------- (250, 250, 250) -----------------] | cpu | cuda 1 threads: ----------------------------------------- random()>0.2 | 26400.8 | 1306.3 random()>0.5 | 26411.8 | 1399.1 random()>0.8 | 29993.2 | 1009.5 create_spherical_seg_3d | 623.8 | 45.0 Times are in milliseconds (ms). [--------------- (100, 100, 100) ----------------] | cpu | cuda 1 threads: --------------------------------------- random()>0.2 | 1332.5 | 140.2 random()>0.5 | 1276.3 | 128.1 random()>0.8 | 1179.2 | 89.1 create_spherical_seg_3d | 111.7 | 44.0 Times are in milliseconds (ms). [---------------- (50, 50, 50) ----------------] | cpu | cuda 1 threads: ------------------------------------- random()>0.2 | 154.5 | 47.4 random()>0.5 | 166.7 | 39.3 random()>0.8 | 165.0 | 38.0 create_spherical_seg_3d | 77.2 | 44.4 Times are in milliseconds (ms). where create_spherical_seg_3d uses the same function from test_hausdorff_distance, and binarizes random array using `random(shape)>ratio`. ### 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`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: John Zielke <john.zielke@snkeos.com> | 01 October 2023, 16:13:24 UTC |
| 21028ee | monai-bot | 01 October 2023, 14:38:23 UTC | auto updates (#7073) | 01 October 2023, 14:38:23 UTC |
| 93fbea7 | dependabot[bot] | 01 October 2023, 13:05:47 UTC | Bump actions/checkout from 3 to 4 (#7072) 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/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. 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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> | 01 October 2023, 13:05:47 UTC |
| 2b39067 | Jupy | 30 September 2023, 16:36:45 UTC | Adding padding option to autoencoder (#7068) Fixes #7045 . ### Description Added "padding" option to `monai/network/nets/autoencoder.py` such that the conv and residual units will be passed the padding option. ### 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). - [ ] 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. ### Notes I haven't been able to run the `./runtests.sh`, even tried running `./runtests.sh -h` and got no output (no error or anything). I guess I don't have permissions to run `.sh` files on this machine. However the changes are very small and default to previous functionality so unless somebody passes a padding argument, this should not break existing usage of the function. --------- Signed-off-by: Jupilogy <j.dick@lboro.ac.uk> | 30 September 2023, 16:36:45 UTC |
| 317ef1f | myron | 29 September 2023, 07:25:34 UTC | segresnet_ds lower peak GPU mem (#7066) Reduces peak GPU mem usage of segresnet_ds(), by releasing buffers earlier. Signed-off-by: myron <amyronenko@nvidia.com> | 29 September 2023, 07:25:34 UTC |
| 14fcf72 | YunLiu | 28 September 2023, 08:11:23 UTC | Improve `ConfigParser` documentation (#7058) Fixes #7057 ### Description Improve the usage of `ConfigParser` methods `read_config`, `load_config_file`, `load_config_files`. ### 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> | 28 September 2023, 08:11:23 UTC |
| 84566d1 | Matthias Hadlich | 27 September 2023, 15:28:31 UTC | Implement distance_transform_edt and the DistanceTransformEDT transform (#6981) Related to https://github.com/Project-MONAI/MONAI/discussions/6845, this commits adds an EDT distance transform to MONAI. Most importantly this enables GPU based distance transforms which lead to a huge speedup. ### 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`. - [ ] In-line docstrings updated. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Matthias Hadlich <matthiashadlich@posteo.de> | 27 September 2023, 15:28:31 UTC |
| a29ab04 | Wenqi Li | 27 September 2023, 08:51:31 UTC | 7042 collate common meta dictionary keys (#7054) Fixes #7042 - handling inconsistent meta keys when collating metatensor ### 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`. - [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: Wenqi Li <wenqil@nvidia.com> | 27 September 2023, 08:51:31 UTC |
| f214b27 | Wenqi Li | 26 September 2023, 17:12:24 UTC | 7017 update highlights page for v1.3 (#7051) part of #7017 ### 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> | 26 September 2023, 17:12:24 UTC |
| d652774 | monai-bot | 26 September 2023, 13:27:13 UTC | Auto3DSeg algo_template hash update (#7050) Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> | 26 September 2023, 13:27:13 UTC |
| fabc198 | YunLiu | 25 September 2023, 18:33:54 UTC | Default downloading bundles from `monaihosting` (#7046) Fixes #7044 ### Description Update to checking versions and downloading bundles from "monaihosting" as "hosting_storage_v1" is no longer being updated. ### 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. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: KumoLiu <yunl@nvidia.com> | 25 September 2023, 18:33:54 UTC |
| 18a671a | Wenqi Li | 25 September 2023, 13:14:11 UTC | 7039 deprecating some self-hosted test (#7041) Fixes #7039 ### 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> | 25 September 2023, 13:14:11 UTC |
| e4dbfde | monai-bot | 25 September 2023, 11:58:52 UTC | auto updates (#7038) Signed-off-by: monai-bot <monai.miccai2019@gmail.com> | 25 September 2023, 11:58:52 UTC |
| cc3faa3 | YunLiu | 25 September 2023, 09:19:54 UTC | Add LICENSE requirement in spec (#7014) Fixes #6964. ### Description Add LICENSE requirement in specification. https://github.com/Project-MONAI/model-zoo/blob/bdd183ebc113a70d50db4e4fb2ebd9a7c8c7532b/ci/verify_bundle.py#L28 ### 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> | 25 September 2023, 09:19:54 UTC |
| 3bea5cf | Mikael Brudfors | 22 September 2023, 17:34:58 UTC | Allow for defining reference grid on non-integer coordinates (#7032) This is a non-breaking change that is disabled by default. It allows for defining the reference identity grid on non-integer values. This can be beneficial for registration applications as shown in: B. Likar and F. Pernus. A heirarchical approach to elastic registration based on mutual information. Image and Vision Computing, 19:33-44, 2001. cc: @nvahmadi --------- Signed-off-by: Mikael Brudfors <mbrudfors@nvidia.com> | 22 September 2023, 17:34:58 UTC |
| bfabad7 | Wenqi Li | 22 September 2023, 14:37:46 UTC | 7030 Fixes docker release (#7031) Fixes #7030 and typos ### 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> | 22 September 2023, 14:37:46 UTC |
| 7dfa0b9 | YunLiu | 22 September 2023, 11:55:46 UTC | Remove deprecated args and class for v1.3 (#7019) Fixes #7018. ### Description - Remove `compute_meaniou` - Remove `AsChannelFirst`, `AddChannel` and `SplitChannel` - Remove `create_multigpu_supervised_trainer` and `create_multigpu_supervised_evaluator` - deprecated `data_src_cfg_filename` in `AlgoEnsembleBuilder` - deprecated `runner_id` in `run` - deprecated `epoch_interval` and `iteration_interval` in `TensorBoardStatsHandler` - deprecated `get_validation_stats` in `Evaluator` - deprecated `get_train_stats` in `Trainer` - update the default value of `name` to `StatsHandler` in `StatsHandler` - update the default value of `random_size` to `False` in `RandSpatialCrop`, `RandScaleCrop`, `RandSpatialCropSamples` - update the default value of `image_only` to `True` in `LoadImage` and `SaveImage` - update `MetaTenor` related deprecation ### 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. - [x] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: KumoLiu <yunl@nvidia.com> | 22 September 2023, 11:55:46 UTC |
| 0d1337e | YunLiu | 22 September 2023, 10:52:47 UTC | Update docstring and typehint for `epoch_log` and `iteration_log` in `TensorBoardStatsHandler` (#7027) Fixes #7026. ### Description Update docstring and type-hint for `epoch_log` and `iteration_log` in `TensorBoardStatsHandler` ### 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> | 22 September 2023, 10:52:47 UTC |
| 9b81f10 | deepsource-autofix[bot] | 22 September 2023, 09:43:19 UTC | refactor: remove assert statement from non-test files (#7029) Usage of `assert` statement in application logic is discouraged. `assert` is removed with compiling to optimized byte code. Consider raising an exception instead. Ideally, `assert` statement should be used only in tests. --------- Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> | 22 September 2023, 09:43:19 UTC |
| c21df49 | YunLiu | 22 September 2023, 08:37:56 UTC | Add `channel_wise` in `RandShiftIntensity` (#7025) Fixes #6629. ### Description Add `channel_wise` in `RandShiftIntensity` and `RandShiftIntensityd`. ### 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> | 22 September 2023, 08:37:56 UTC |
| 2539266 | YunLiu | 22 September 2023, 07:48:58 UTC | Add `SlidingWindowInfererAdapt` in docs (#7024) Fixes #7023. ### Description Add `SlidingWindowInfererAdapt` in https://docs.monai.io/en/latest/inferers.html. ### 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> | 22 September 2023, 07:48:58 UTC |
| def73cf | Matthias Hadlich | 21 September 2023, 18:50:27 UTC | Add SignalFillEmptyd tranform (#7011) As mentioned here https://github.com/Project-MONAI/MONAI/discussions/2637#discussioncomment-7038045 , this transform helps to fix NaN values after the input transforms. It is basically only a wrapper around `SignalFillEmpty`. ### 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`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Matthias Hadlich <matthiashadlich@posteo.de> | 21 September 2023, 18:50:27 UTC |
| f7e46dd | YunLiu | 21 September 2023, 15:23:47 UTC | Add auto-generated data during tests into gitignore (#7020) Fixes #7010 ### Description Add auto-generated data during tests into gitignore ### 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> | 21 September 2023, 15:23:47 UTC |
| f3200b9 | Wenqi Li | 21 September 2023, 07:25:42 UTC | 6794 optionally pass coordinates to predictor during sliding window (#6795) Fixes #6794 ### 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> | 21 September 2023, 07:25:42 UTC |
| 2a0ed97 | YunLiu | 20 September 2023, 10:46:23 UTC | Change deprecated since="1.3" to since="1.2" (#7016) Fixes #7015. ### Description Change deprecated since="1.3" to since="1.2" before 1.3 is released and tagged. ### 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). - [ ] 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> | 20 September 2023, 10:46:23 UTC |
| e5f9337 | Imad Toubal | 19 September 2023, 07:39:02 UTC | Add Hausdorff loss (#6994) Integrating an existing implementation publicly available on GitHub by Patryk Rygiel into the MONAI framework. Fixes #6993. ### Description Hausdorff distance is widely used in evaluating medical image segmentation methods. Adding an objective/loss function directly to optimize this distance can be instrumental in optimizing this score [1]. <center><img src="https://upload.wikimedia.org/wikipedia/commons/2/21/Hausdorff_distance_sample.svg" alt="Hausdorff Distance"></center> An existing implementation is [publicly available on GitHub](https://github.com/PatRyg99/HausdorffLoss) by [Patryk Rygiel](https://github.com/PatRyg99), although it might take some engineering work to integrate within the MONAI framework. I was able to train a 3D segmentation model successfully using MONAI's SwinUNETR with this implementation and I would like to contribute the code for this loss so that it's more widely available and easier to integrate with MONAI-based repositories. **References**: [1] Karimi, D., & Salcudean, S. E. (2019). [Reducing the Hausdorff distance in medical image segmentation with convolutional neural networks](https://ieeexplore.ieee.org/abstract/document/8767031?casa_token=OGugo3jEuXQAAAAA:y5fp0CuZiEWlbx8FS4XKHu43Wi_W7albLeIAjsnZ1c-IlTpJmEFJUgoMlKl_taSYuBpcPyCvtTMe). IEEE Transactions on medical imaging, 39(2), 499-513. ### 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. - [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: Imad Toubal <imad.toubal@gmail.com> | 19 September 2023, 07:39:02 UTC |
| 73a7601 | YunLiu | 18 September 2023, 14:44:08 UTC | Enhancing `get_all_bundles_list` under monai.bundle to support model zoo NGC hosting (#6997) Fixes #6833 ### Description Add `model_info_url` in `get_all_bundles_list`, `get_bundle_versions`, and `get_bundle_info`. ### 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] 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: KumoLiu <yunl@nvidia.com> | 18 September 2023, 14:44:08 UTC |
| b31367f | Wenqi Li | 18 September 2023, 13:42:02 UTC | 6985 metatensor_to_itk_image compatible space (#7000) Fixes #6985 ### Description - update `metatensor_to_itk_image` to accept RAS metatensor - nrrdreader default 'space' from empty/"left-posterior-superior" to `SpaceKeys.LPS` - more tests ### 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`. - [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> | 18 September 2023, 13:42:02 UTC |
| 5a644e4 | YunLiu | 18 September 2023, 12:07:11 UTC | Fix unused `kernel_size` in `ResBlock` (#6999) Fixes #6998 ### Description Fixed unused `kernel_size` in `ResBlock`. Fixed untested `norm` in unit tests. ### 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] 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`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: KumoLiu <yunl@nvidia.com> | 18 September 2023, 12:07:11 UTC |
| 281cb01 | NoTody | 16 September 2023, 17:05:52 UTC | 6973 sincos pos embed (#6986) Fixes #6973 ### Description Adding support for sincos positional embedding for monai.networks.blocks.patchembedding.PatchEmbedding class. This pull request corresponds to this opened issue https://github.com/Project-MONAI/MONAI/issues/6973 ### 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] 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: NoTody <howardwong1780@gmail.com> | 16 September 2023, 17:05:52 UTC |
| 56ca224 | Yiheng Wang | 15 September 2023, 08:13:33 UTC | 6989 Enhance EarlyStopHandler docstring (#6990) Fixes #6989 . ### Description This PR enhances the handler's docstring, and adds an example of how to define a suitable score function when using distributed training. ### 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: Yiheng Wang <vennw@nvidia.com> | 15 September 2023, 08:13:33 UTC |
| 6dfe17a | nvkevlu | 13 September 2023, 21:35:16 UTC | Add stats_sender to MonaiAlgo for FL stats (#6984) PR #6220 was closed and NVFlareStatsHandler has now been implemented in NVFlare in https://github.com/NVIDIA/NVFlare/pull/1925. However, there is still the piece in MonaiAlgo to attach the stats_sender in initialize, so this PR adds that missing piece. ### 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: Kevin <kevlu@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 13 September 2023, 21:35:16 UTC |
| c22a2bd | Wenqi Li | 13 September 2023, 11:04:07 UTC | 6976 improve config expr error msg (#6977) Fixes #6976 ### 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`. - [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: Wenqi Li <wenqil@nvidia.com> | 13 September 2023, 11:04:07 UTC |
| d4dc055 | YunLiu | 13 September 2023, 08:45:15 UTC | Fix `Lazy=True` ignored when using `Dataset` call (#6975) Fixes #6974. ### Description Change default value of `lazy` in `apply_transform` to None. ### 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> | 13 September 2023, 08:45:15 UTC |
| 392c5c1 | YunLiu | 12 September 2023, 20:15:13 UTC | Support regular expression in the mapping arg of `copy_model_state` (#6917) Part of #6552. ### Description After PR #6835, we have added `copy_model_args` in the `load` API which can help us update the state_dict flexibly. https://github.com/KumoLiu/MONAI/blob/93a149a611b66153cf804b31a7b36a939e2e593a/monai/bundle/scripts.py#L397 Given this [issue](https://github.com/Project-MONAI/MONAI/issues/6552), we need to be able to filter the model's weights flexibly. In `copy_model_state`, we already have a "mapping" arg, the filter will be more flexible if we can support regular expression in the mapping. This PR mainly added the support for regular expression for "mapping" arg. In the [example](https://github.com/Project-MONAI/MONAI/issues/6552#issuecomment-1587582734) in this [issue](https://github.com/Project-MONAI/MONAI/issues/6552), after this PR, we can do something like: ``` exclude_vars = "encoder.mask_token|encoder.norm.weight|encoder.norm.bias|out.conv.conv.weight|out.conv.conv.bias" mapping={"encoder.layers(.*).0.0.": "swinViT.layers(.*).0."} dst_dict, updated_keys, unchanged_keys = copy_model_state( model, ssl_weights, exclude_vars=exclude_vars, mapping=mapping ) ``` Additionally, based on the comments of Eric [here](https://github.com/Project-MONAI/MONAI/issues/6552#issuecomment-1697404590), I totally agree, we could add a handler to make the pipeline easier to implement, but perhaps this task is no need to set as a "BundleTodo" for MONAIv1.3 but as an enhancement for MONAI near future. What do you think? @ericspod @wyli @Nic-Ma ### 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> | 12 September 2023, 20:15:13 UTC |
| 66f42c1 | YunLiu | 12 September 2023, 15:48:04 UTC | Add `freeze_layers` (#6970) Part of #6552. ### Description Add `freeze_layers`. ### 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] 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: KumoLiu <yunl@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 12 September 2023, 15:48:04 UTC |
| 5fd23b8 | YunLiu | 11 September 2023, 14:28:01 UTC | Improve `ckpt_export ` (#6965) Fixes #6953 ### Description ### 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: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> | 11 September 2023, 14:28:01 UTC |
| 5b9d24e | Yiheng Wang | 11 September 2023, 06:58:49 UTC | 6962 Fix bundle download naming issue (#6969) Fixes #6962 . ### Description This PR is used to fix the bundle download issue if using monaihosting source. Detailed information is attached in #6962 . ### 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] 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: Yiheng Wang <vennw@nvidia.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 11 September 2023, 06:58:49 UTC |
| 339292c | YunLiu | 08 September 2023, 11:32:12 UTC | Fix error in download bundle from ngc (#6963) Fixes #6962. ### 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> | 08 September 2023, 11:32:12 UTC |
| 8040aa2 | Wenqi Li | 08 September 2023, 10:19:42 UTC | 6721 bundle syntax # as alias of :: (#6955) fixes #6721 ### Description compatible syntax by normalising any `#` in ids to `::` ```py from monai.bundle import ConfigParser config = { "my_dims": 2, "dims_1": "$@my_dims + 1", "my_net": {"_target_": "BasicUNet", "spatial_dims": "@dims_1", "in_channels": 1, "out_channels": 4}, } # in the example $@my_dims + 1 is an expression, which adds 1 to the value of @my_dims parser = ConfigParser(config) print(parser.get_parsed_content("my_net::spatial_dims")) # returns 3 print(parser.get_parsed_content("my_net#spatial_dims")) # returns 3 ``` new test cases: https://github.com/Project-MONAI/MONAI/blob/66b50fb8384ae2dc3c76b39de673ce76908f94f2/tests/test_config_parser.py#L317-L321 ### 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. - [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: Wenqi Li <wenqil@nvidia.com> | 08 September 2023, 10:19:42 UTC |
| ef7debe | YunLiu | 07 September 2023, 12:36:17 UTC | Add `download_large_files` in `monai/bundle/scripts.py` (#6958) Fixes #6362 . ### Description Add `download_large_files` in `monai/bundle/scripts.py`. Refer to the one in https://github.com/Project-MONAI/model-zoo/blob/131b0da3f540ed13a8a1c02d8395e92a682d47cf/ci/utils.py#L93. ### 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> | 07 September 2023, 12:36:17 UTC |
| 6f13b8d | YunLiu | 07 September 2023, 08:06:19 UTC | Avoid breaking change in creating `BundleWorkflow` (#6950) Fixes # . ### Description Avoid breaking changes introduced by https://github.com/Project-MONAI/MONAI/pull/6835 - when creating `BundleWorkflow` - when using `load` API, add `return_state_dict` when `model` and `net_name` are both `None`. ### 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> | 07 September 2023, 08:06:19 UTC |
| 8ccde11 | YunLiu | 07 September 2023, 05:48:53 UTC | optional import cucim.skimage directly (#6957) Fixes #6956 . ### Description Looks like an error which introduced by this [PR](https://github.com/rapidsai/cucim/pull/575). The submodule in cucim.skimage can import correctly, so change to directly import cucim.skimage. ### 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> | 07 September 2023, 05:48:53 UTC |
| c4ed1f8 | YunLiu | 05 September 2023, 14:45:11 UTC | Fix KeyError in `PydicomReader` (#6946) Fixes #6945 . ### Description Try get "00280030" (PixelSpacing) first. ### 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> | 05 September 2023, 14:45:11 UTC |
| 8e77e03 | YunLiu | 05 September 2023, 11:52:20 UTC | Fix reading dicom series error in `ITKReader` (#6943) Fixes #6942 fixes #6944. ### Description When using itk backend reading dicom series and there is only one file in the folder, return the first name since itk assuming that there must be more than one file in the tuple. https://github.com/InsightSoftwareConsortium/ITK/blob/452cb3f9716e95532200de3196d51cd705a0ec5e/Wrapping/Generators/Python/itk/support/extras.py#L1275-L1284 ### 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> | 05 September 2023, 11:52:20 UTC |
| 02e7b79 | Wenqi Li | 04 September 2023, 17:32:03 UTC | 6728 enhance bundle config docs (#6939) Fixes #6728 ### 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> | 04 September 2023, 17:32:03 UTC |
| d876c3f | YunLiu | 04 September 2023, 14:25:37 UTC | Fix missing `SegmentDescription` in `PydicomReader` (#6937) Fixes #6928. ### Description `SegmentDescription` is optional, https://dicom.innolitics.com/ciods/segmentation/segmentation-image/00620002/00620006, so try [`SegmentLabel`](https://dicom.innolitics.com/ciods/segmentation/segmentation-image/00620002/00620005) first. ### 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> | 04 September 2023, 14:25:37 UTC |
| 37b58fc | monai-bot | 04 September 2023, 10:35:34 UTC | auto updates (#6938) | 04 September 2023, 10:35:34 UTC |
| 4ea40cf | YunLiu | 04 September 2023, 09:33:50 UTC | Fix test error in tests.ngc_bundle_download (#6935) Fixes #6932. ### Description Add `remove_ngc_prefix` for ngc source download ### 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> | 04 September 2023, 09:33:50 UTC |
| cb4f517 | YunLiu | 04 September 2023, 08:44:03 UTC | Avoid FutureWarning in `CropForeground` (#6934) Fixes #6685 . ### Description Change the default value of `allow_smaller` to `False` where `CropForeground` is used to avoid FutureWarning. ### 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> | 04 September 2023, 08:44:03 UTC |
| 50e66fa | YunLiu | 02 September 2023, 09:13:06 UTC | Add support for `BCEWithLogitsLoss` in `DiceCELoss` (#6924) Fixes #6923. ### Description Add support for `BCEWithLogitsLoss` for single-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: KumoLiu <yunl@nvidia.com> | 02 September 2023, 09:13:06 UTC |
| 3b27bb6 | Wenqi Li | 02 September 2023, 07:19:05 UTC | 6920 update base image 23.08 (#6921) Fixes #6920 ### 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: Wenqi Li <wenqil@nvidia.com> | 02 September 2023, 07:19:05 UTC |
| e48c3e2 | Wenqi Li | 01 September 2023, 06:46:45 UTC | 6725 generate properties for bundle docs (#6918) Fixes #6725 - adding the bundle properties to https://monai-dev.readthedocs.io/en/fixes-sphinx/mb_properties.html ### 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. - [x] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> | 01 September 2023, 06:46:45 UTC |
| df1779b | Anish Rajan | 31 August 2023, 23:50:19 UTC | Robust Username Masking in print_config (#6922) Fixes #6914. ### 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: anishrajan25 <anishrajan2708@gmail.com> | 31 August 2023, 23:50:19 UTC |
| be4e1f5 | YunLiu | 31 August 2023, 07:12:11 UTC | Add bundle root directory to Python search directories automatically (#6910) Fixes #6722 . ### Description Add scripts directory to Python search directories automatically in the `run` function in `ConfigWorkflow`. ### 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> | 31 August 2023, 07:12:11 UTC |
| a4e4894 | YunLiu | 30 August 2023, 13:47:11 UTC | 6834 Add `MetaProterties` and update `load` API (#6835) Fixes #6834. ### Description This PR introduces the idea of `BundleManager`, with `get` as one of the methods, to avoid repeatedly instantiating `ConfigWorkflow`. **usage** ``` bundle = BundleManager("spleen_ct_segmentation") bundle.get("network_data_format") or bundle.get(property="train_preprocessing") ``` ### 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> | 30 August 2023, 13:47:11 UTC |
| 6f5005f | YunLiu | 30 August 2023, 10:04:59 UTC | Fix `Spacing` (#6912) Fixes #6911. ### 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`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: KumoLiu <yunl@nvidia.com> | 30 August 2023, 10:04:59 UTC |
| 2862f53 | Anudeep Adiraju | 29 August 2023, 22:52:53 UTC | Mask usernames in print_config function (#6471) (#6913) Fixes #6471 ### 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: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 29 August 2023, 22:52:53 UTC |
| 40048d7 | Wenqi Li | 28 August 2023, 11:29:56 UTC | 6907 TORCH_ALLOW_TF32_CUBLAS_OVERRIDE warning and update print (#6909) Fixes #6907 ### Description - removes the default warning on `TORCH_ALLOW_TF32_CUBLAS_OVERRIDE` - add debug print info and documentation ### 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: Wenqi Li <wenqil@nvidia.com> | 28 August 2023, 11:29:56 UTC |
| 2daabf9 | Wenqi Li | 21 August 2023, 19:02:19 UTC | 6894 update rank filter (#6895) Fixes #6894 ### 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. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 21 August 2023, 19:02:19 UTC |
| 59bcad4 | monai-bot | 21 August 2023, 07:35:33 UTC | auto updates (#6893) Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> | 21 August 2023, 07:35:33 UTC |
| 8aabdc9 | john-zielke-snkeos | 18 August 2023, 14:44:34 UTC | Improve performance for NormalizeIntensity (#6887) ### Description In order to implement the "nonzero" functionality of the NormalizeIntensity transform a mask is used. In case nonzero is False, the mask is still used, but is initialized to all True/1. This unecessary masking causes a considerable performance hit. The changed implementation forgoes using the mask in case nonzero is False. I ran a quick benchmark on my system comparing the old implementation, the new implementation and the normalization using the wrapper around the torchvision normalize transform. The results were the following, showing a more than 10x performance improvement (notice the times for the old normalize are in milliseconds, the other times are in microseconds): > [-------------- torchvision ---------------] > | cpu | cuda > 1 threads: --------------------------------- > (250, 250, 250) | 18847.2 | 1440.5 > (100, 100, 100) | 484.6 | 395.5 > > Times are in microseconds (us). > > [--------------- monai ----------------] > | cpu | cuda > 1 threads: ----------------------------- > (250, 250, 250) | 603.7 | 11.5 > (100, 100, 100) | 39.9 | 1.5 > > Times are in milliseconds (ms). > > [------------- monai_improved ------------] > | cpu | cuda > 1 threads: -------------------------------- > (250, 250, 250) | 17763.2 | 720.0 > (100, 100, 100) | 938.0 | 185.2 > > Times are in microseconds (us). The benchmarks were created with the following code (the ImprovedNormalizeIntensity class does not exist in the PR, this was my quick fix to have both the old and the new implementation available) ```python import torch.utils.benchmark as benchmark import torch from monai.transforms import TorchVision from monai.transforms.intensity.array import ImprovedNormalizeIntensity, NormalizeIntensity shapes = [ (250, 250, 250), (100,100,100) ] normalizers = { 'torchvision': TorchVision(name="Normalize", mean=1000, std=333), 'monai': NormalizeIntensity(subtrahend=1000, divisor=333), 'monai_improved': ImprovedNormalizeIntensity(subtrahend=1000, divisor=333), } results = [] for shape in shapes: for device in ['cpu', 'cuda']: torch_tensor = torch.rand((1,1)+shape).to(device) for name, normalizer in normalizers.items(): t = benchmark.Timer( stmt='normalizer(x)', globals={'normalizer': normalizer , 'x': torch_tensor}, label=name, sub_label=str(shape), description=device, num_threads=1, ) results.append(t.blocked_autorange(min_run_time=10)) compare = benchmark.Compare(results) compare.print() ``` ### 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: John Zielke <john.zielke@snkeos.com> | 18 August 2023, 14:44:34 UTC |
| 6e47140 | Amirreza Aflakparast | 18 August 2023, 08:56:03 UTC | remove: shuffle=False option (#6886) Fixes #6885 ### Description ### 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: Amirreza Aflakparast <84932095+AmirAflak@users.noreply.github.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 18 August 2023, 08:56:03 UTC |
| 4cd717c | elitap | 17 August 2023, 15:54:32 UTC | 6841 follow up tests and upgrades (#6878) Followup to #6841 ### Description Added testcases to catch bug found in #6841. For consistency Compose implements LazyTransform. Probably there is a better option to test... ### 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] New tests added to cover the changes. - [x] Fix tests failing due to compose beeing of type LazyTransform, mocked compose did not consider lazy option --------- Signed-off-by: elitap <elias.tappeiner@gmx.at> | 17 August 2023, 15:54:32 UTC |
| 2a41e98 | elitap | 17 August 2023, 14:45:00 UTC | 6804 enhance compose input check (#6882) Fixes case mentioned in #6804 by checking type of second 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). - [x] New tests added to cover the changes. --------- Signed-off-by: elitap <elias.tappeiner@gmx.at> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 17 August 2023, 14:45:00 UTC |
| 9ae72e4 | Mark Graham | 16 August 2023, 22:38:43 UTC | 6676 port generative metrics (#6836) Work towards addressing #6676. Ports all metrics to MONAI. ### 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. - [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: Mark Graham <markgraham539@gmail.com> | 16 August 2023, 22:38:43 UTC |
| baa6485 | Qingpeng Li | 16 August 2023, 14:33:53 UTC | optimize doc img urls (#6877) ### Description Current doc imgs' url cause HTTP 302 redirect and decrease the rendering performance of the online doc.  In vscode extension community, we usually use `raw.githubusercontent.com` directly, see https://github.com/microsoft/vscode-python/blob/v2023.14.0/README.md?plain=1#L28-L36 ### Also 1. the urls `RandSmoothDeform.png` and `RandSmoothDeformd.png` are invalid. There is no img in `Project-MONAI/DocImages/` 2. `Project-MONAI/DocImages/` uses [Calibre](https://calibreapp.com/)'s [image-actions](https://github.com/marketplace/actions/image-actions), maybe this repo also needs one? There are some imgs in this repo can be optimized, see https://github.com/qingpeng9802/MONAI/pull/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: Qingpeng Li <qingpeng9802@gmail.com> | 16 August 2023, 14:33:53 UTC |
| 617c1be | Wenqi Li | 16 August 2023, 13:02:54 UTC | 6873 data analyzer histogram_only=True fix (#6874) Fixes #6873 ### Description - fixes data analyzer - replace `"image_stats"` with `DataStatsKeys.IMAGE_STATS` ### 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`. - [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: Wenqi Li <wenqil@nvidia.com> | 16 August 2023, 13:02:54 UTC |
| e24b969 | Wenqi Li | 15 August 2023, 16:31:20 UTC | MapLabelValue support tensor/gpu backend (#6872) ### Description - adding pytorch backend support for `MapLabelValue` - fixes #6869 ### 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`. - [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: Wenqi Li <wenqil@nvidia.com> | 15 August 2023, 16:31:20 UTC |
| 5833b1c | Matthias Hadlich | 15 August 2023, 14:25:53 UTC | Update Checkpoint Loader docs with an example (#6871) Related to #6687, this adds some documentation how to resume a network. I did not find this documented anywhere in MONAI and it's rather important imo. Please shortly check doc the syntax, I don't have any experience with it. The code itself is from my own repository and working. What is potentially still missing here is some information on when to use the Checkpoint Loader. As far I understood the docs, this shall mostly be used to resume interrupted training runs. But what is 1) with pure inference runs where the state of the trainer does not matter, only the evaluator 2) Resuming the training at epoch 200 but with a learning rate reset (e.g. DeepEdit train without clicks first for 200 epochs, then 200 epochs with clicks on top). 1 works well in my experience, 2 as well if you modify the state_dict to exclude e.g. the learning rate scheduler. ### 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: Matthias Hadlich <matthiashadlich@posteo.de> | 15 August 2023, 14:25:53 UTC |
| a01a726 | Matthias Hadlich | 15 August 2023, 12:17:03 UTC | Add use_subvoxels to Surface Dice (#6870) fixes #6866. It makes the `use_subvoxels` in class `SurfaceDiceMetric` usable as a paramter for Ignite based code. Changes previous behaviour, where `use_subvoxels` was drawn from kwargs on the function call. ### 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). - [x] 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: Matthias Hadlich <matthiashadlich@posteo.de> | 15 August 2023, 12:17:03 UTC |
| 0247672 | monai-bot | 14 August 2023, 09:43:49 UTC | auto updates (#6865) Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> | 14 August 2023, 09:43:49 UTC |
| faf6f74 | elitap | 13 August 2023, 20:12:24 UTC | fix for #6841 lazy argument has no effect in Compose.__call__ (#6862) Fixes #6841 ### Description added check if lazy flag is set, then use it! ### 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). No tests added yet, will do asp. However unsure where. I think something similar as TestComposeExecuteWithLogging would work as the results of the flag could be made visible there. I dont like the string compares, but applying the flag is not changing the output, so thats probalby the best option anyway. Signed-off-by: elitap <elias.tappeiner@gmx.at> | 13 August 2023, 20:12:24 UTC |
| a86c0e0 | Suraj Pai | 10 August 2023, 21:22:49 UTC | Remove hard coding of `bias_downsample` in `resnet` methods (#6848) Fixes #6811 . ### Description Remove hard coding of `bias_downsample` in `resnet` methods. This allows for loading `MedicalNet` models. ### 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 <bspai@bwh.harvard.edu> | 10 August 2023, 21:22:49 UTC |
| 7a760e6 | Wenqi Li | 10 August 2023, 11:41:51 UTC | 6766 data analyser label argmax (#6852) Fixes #6766 ### Description the label might have been processed during the GPU transform, in the retry on CPU, the argmax should be skipped in this case. ### 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> | 10 August 2023, 11:41:51 UTC |
| 3990cd4 | Wenqi Li | 10 August 2023, 09:04:57 UTC | 6846 convert to contiguous seq type (#6849) Fixes #6846 ### 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`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 10 August 2023, 09:04:57 UTC |
| 8e99af5 | Qingpeng Li | 08 August 2023, 10:33:12 UTC | make `is_tf32_env()` safer (#6839) Following #6816 ### Description make `is_tf32_env()` safer. check `cuda` to prevent fallthrough case when `pynvml` is not found ### 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: Qingpeng Li <qingpeng9802@gmail.com> | 08 August 2023, 10:33:12 UTC |
| ca96867 | Qingpeng Li | 07 August 2023, 18:07:39 UTC | Tf32 warnings (#6816) about #6754 . ### Description show a warning if any thing may enable tf32 is detected ### 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. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Qingpeng Li <qingpeng9802@gmail.com> | 07 August 2023, 18:07:39 UTC |
| cb257d2 | Matthias Hadlich | 07 August 2023, 15:19:17 UTC | Add warning in a multiprocessing special case (#6830) Related to discussion https://github.com/Project-MONAI/MONAI/discussions/6657 This code at least adds a warning if `set_track_meta(False)` and `multiprocessing_context='spawn'` are used in the same code. However this warning only triggers if `set_track_meta(False)` has been called before the DataLoader has been initialized. I will append some example code where this is not True, still the bug is triggered. Imo this is still a MONAI bug even though in the discussion it was claimed otherwise. The multiprocessing_context='spawn' has unintended consequences and this is only true for MONAI and not for torch. (I believe the problem is that with 'spawn' Python and all the libs get reinitialized and thus _TRACK_META is reset to being True). ### 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: Matthias Hadlich <matthiashadlich@posteo.de> | 07 August 2023, 15:19:17 UTC |
