https://github.com/Project-MONAI/MONAI/
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Revision | Author | Date | Message | Commit Date |
---|---|---|---|---|
59fb2c3 | Holger Roth | 15 October 2022, 10:48:04 UTC | MonaiAlgo FedStats (#5240) Fixes #5196, #5316. ### Description Add api function that allows FL systems to request summary statistics, i.e. `get_data_stats` in new `ClientStats` class. `MonaiStats` is added to provide implementation based on Monai bundle. Utilizes DataAnalyzer functions from Auto3DSeg. Changes to DataAnalyzer are supposed to not change the behavior. ### 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: Holger Roth <hroth@nvidia.com> | 15 October 2022, 11:00:25 UTC |
50749ec | myron | 15 October 2022, 09:00:55 UTC | Dicece check for float target (#5326) Fixes https://github.com/Project-MONAI/tutorials/issues/987 ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: myron <amyronenko@nvidia.com> | 15 October 2022, 09:30:19 UTC |
7c3e838 | Wenqi Li | 14 October 2022, 18:46:03 UTC | adding a multigpu test of TestFLMonaiAlgo (#5327) Signed-off-by: Wenqi Li <wenqil@nvidia.com> Fixes https://github.com/Project-MONAI/MONAI/issues/5133 ### Description adds a 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). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [x] New tests added to cover the changes. - [x] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [x] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Wenqi Li <wenqil@nvidia.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 15 October 2022, 09:29:43 UTC |
fe5a3bf | Maxime-Perret | 14 October 2022, 06:36:03 UTC | Command format fix with backslashes on Windows System (#5280) Fixes MONAI/apps/Auto3DSeg/bundle_gen.py ### Description Commands ran in subprocess currently cause issues with string formatting and backslashes not being escaped properly. Changing from Back Flash to Forward Slash solves the issue. ### 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: Maxime <maxime.perret@epfl.ch> Signed-off-by: Mingxin Zheng <mingxinz@nvidia.com> Signed-off-by: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com> Co-authored-by: Maxime <maxime.perret@epfl.ch> Co-authored-by: Mingxin Zheng <mingxin.zheng@philips.com> Co-authored-by: Mingxin Zheng <mingxinz@nvidia.com> Co-authored-by: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com | 15 October 2022, 09:29:36 UTC |
9d43d19 | myron | 13 October 2022, 22:06:15 UTC | SlidingWindowInferer: option to adaptively stitch in cpu memory for large images (#5297) SlidingWindowInferer: option to adaptively stitch in cpu memory for large images. This adds an option to provide maximum input image volume (number of elements) to dynamically change stitching to cpu memory (to avoid gpu memory crashes). For example with `cpu_thresh=400*400*400`, all input images with large volume will be stitched on cpu. At the moment, a user must decide beforehand, to stitch ALL images on cpu or gpu (by specifying the 'device' parameter). But in many datasets, only a few large images require device==cpu, and running inference on cpu for ALL will be unnecessary slow. It's related to https://github.com/Project-MONAI/MONAI/discussions/4625 https://github.com/Project-MONAI/MONAI/discussions/4495 https://github.com/Project-MONAI/MONAI/discussions/3497 https://github.com/Project-MONAI/MONAI/discussions/4726 https://github.com/Project-MONAI/MONAI/discussions/4588 ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: myron <amyronenko@nvidia.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com> | 15 October 2022, 09:29:15 UTC |
258f3ca | myron | 13 October 2022, 20:03:31 UTC | Segresnet improvements (#5281) This adds improvements to SegResNet semantic segmentation to include deep supervision feature (among other things). I've decided to add a new network named SegResnetDS instead of replacing the existing SegResNet, because it would have broken all previously pretrained model checkpoints. Please take a look, and if it looks good, I can add unit tests. All the helper functions, and blocks are inside of the same file (which I prefer, since it's easier to read) instead of spreading it among other files (e.g segresnet_ds_block or segresnet_utils). ### Description A few sentences describing the changes proposed in this pull request. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: myron <amyronenko@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 15 October 2022, 09:29:06 UTC |
2b455e3 | Dženan Zukić | 13 October 2022, 19:21:10 UTC | Fix installation verification command (#5328) Current command did not work on my machine: ```batch M:\Dev\MONAI>python -c 'import monai; monai.config.print_config()' File "<string>", line 1 'import ^ SyntaxError: EOL while scanning string literal M:\Dev\MONAI>python -c "import monai; monai.config.print_config()" MONAI version: 1.0.0+39.g9355f1c2 Numpy version: 1.23.4 Pytorch version: 1.12.1+cu113 MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False MONAI rev id: 9355f1c264c7e69e28b005b8e8eb65c26e0c4ab0 MONAI __file__: M:\Dev\MONAI\monai\__init__.py Optional dependencies: Pytorch Ignite version: NOT INSTALLED or UNKNOWN VERSION. Nibabel version: NOT INSTALLED or UNKNOWN VERSION. scikit-image version: NOT INSTALLED or UNKNOWN VERSION. Pillow version: 9.2.0 Tensorboard version: NOT INSTALLED or UNKNOWN VERSION. gdown version: NOT INSTALLED or UNKNOWN VERSION. TorchVision version: 0.13.1+cu113 tqdm version: NOT INSTALLED or UNKNOWN VERSION. lmdb version: NOT INSTALLED or UNKNOWN VERSION. psutil version: NOT INSTALLED or UNKNOWN VERSION. pandas version: NOT INSTALLED or UNKNOWN VERSION. einops version: NOT INSTALLED or UNKNOWN VERSION. transformers version: NOT INSTALLED or UNKNOWN VERSION. mlflow version: NOT INSTALLED or UNKNOWN VERSION. pynrrd version: NOT INSTALLED or UNKNOWN VERSION. For details about installing the optional dependencies, please visit: https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies M:\Dev\MONAI> ``` | 15 October 2022, 09:28:56 UTC |
dd49e37 | Wenqi Li | 13 October 2022, 13:22:37 UTC | tutorial 982 984 fixes occ sens, 987 ce loss (#5323) Signed-off-by: Wenqi Li <wenqil@nvidia.com> fixes https://github.com/Project-MONAI/tutorials/issues/982 fixes https://github.com/Project-MONAI/tutorials/issues/984 fixes https://github.com/Project-MONAI/tutorials/issues/987 ### Description robust mask size and grid ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [x] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [x] In-line docstrings updated. - [x] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 13 October 2022, 14:59:11 UTC |
1e74bd6 | monai-bot | 13 October 2022, 09:47:02 UTC | auto updates (#5322) Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> | 13 October 2022, 14:59:02 UTC |
ef6fe38 | monai-bot | 13 October 2022, 06:45:22 UTC | auto updates (#5321) Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 13 October 2022, 14:57:24 UTC |
a215ea6 | myron | 12 October 2022, 19:02:12 UTC | fixes DiceCELoss for multichannel targets (#5292) Fixes DiceCELoss for multichannel targets. Currently if "target" (ground truth label) is provided as a multichannel data (each channel is binary or float), then current DiceCELoss attempts to convert it to 1-channel using argmax (which could be impossible with overlapping labels). There is no need for argmax, since pytorch's cross entropy can handle multi-channel targets already. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: myron <amyronenko@nvidia.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 12 October 2022, 19:25:56 UTC |
c77521e | myron | 12 October 2022, 09:49:24 UTC | updates to Gaussian map for sliding window inference (#5302) This updates the calculation of Gaussian map (weights) during sliding window inference with "gaussian" Current version had multiple small issues - it computed Gaussian weight map (image) via nn.Conv1d sequence with an empty image (with a single 1 in the middle). We don't need to run any convolutions, it's much simpler to directly calculate the Gaussian map (it's also faster and takes less memory) - For patch_sizes of even size (e.g. 128x128) it centered Gaussian on patch_size//2 which is 0.5 pixel off-center (I'm not sure why we did it. - Finally the Gaussian 1d convolutions were done approximately (with 'erf' internal approximation and truncated to sigma=4). I'm not sure why we need any approximations here at all, it's trivial to compute the Gaussian weight map directly ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: myron <amyronenko@nvidia.com> | 12 October 2022, 11:45:43 UTC |
d1fafc4 | Mingxin Zheng | 11 October 2022, 12:13:46 UTC | [ReadyForReview] Auto3DSeg DataAnalyzer OOM and other minor issue (#5278) Fixes #5277 . ### Updated results In my local test env, I have the following results: - The change of GPU memory before/after DataAnalyzer is less than 5MB after the fix. Previously, there are lots of cached PyTorch tensors and CuPy variables that are not released for trainings that takes up to several GBs of GPU mem. - DataAnalyzer can also process larger images now because leaks are fix (3D image with a size 512x512x512 passed for 12GB RTX 3080Ti) ### Description Auto3DSeg DataAnalyzer occupied a large trunk of memory and was unable to release them during the training. The reasons behind are possibly due to: - Training are done by subprocess call, and PyTorch in the subprocess is unable to find the memory pool allocated by the main process - GPU memory leakage ( DataAnalyzer math operations uses torch functions and CuPy) plus test functions need improvements and AutoRunner needs to expose the API call to change device of DataAnalyzer ### 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: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com> | 11 October 2022, 12:50:01 UTC |
f040ec0 | Nic Ma | 11 October 2022, 11:02:45 UTC | 5269 5291 Update PyTorch base docker to 22.09 (#5293) Fixes #5269 #5291 . ### Description This PR updated the PyTorch base docker to 22.09. ### 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> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> | 11 October 2022, 12:49:53 UTC |
9fa35cc | Yiheng Wang | 10 October 2022, 18:32:31 UTC | 5304 Add authenticated option for bundle api (#5306) Signed-off-by: Yiheng Wang <vennw@nvidia.com> Fixes #5304 . ### Description This PR adds the authenticated option for bundle api, which the authenticated token, users can increase their rate limits when using our bundle APIs. ### 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`. - [x] In-line docstrings updated. - [] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Yiheng Wang <vennw@nvidia.com> | 11 October 2022, 12:49:44 UTC |
f6f6529 | Wenqi Li | 10 October 2022, 17:08:26 UTC | fixes cherrypicking issues of spacing Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 10 October 2022, 17:08:26 UTC |
b61b21e | Wenqi Li | 09 October 2022, 15:08:50 UTC | 4206 adds ext tests and deps (#4207) Signed-off-by: Wenqi Li <wenqil@nvidia.com> Fixes #4206 ### Description Currently ninja+jit is not tested on the cpu-only cases, this adds ninja (optional dep.) and premerge tests on ubuntu for ninja + jit extension. ### Status **Ready** ### 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: Wenqi Li <wenqil@nvidia.com> | 10 October 2022, 12:58:01 UTC |
9b09863 | binliunls | 08 October 2022, 18:51:57 UTC | 5187 update the docstring of the is_pad parameter (#5296) Signed-off-by: binliu <binliu@nvidia.com> Fixes #5187 . ### Description Updated the docstring of the is_pad parameter in flexible-unet. ### 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: binliu <binliu@nvidia.com> | 10 October 2022, 12:58:01 UTC |
5a517fb | myron | 08 October 2022, 18:08:18 UTC | Upsample mode deconvgroup (#5282) This adds an additional UpSample mode DECONVGROUP to upsample with groupwise convolution transpose. Unit tests are passed too. A few sentences describing the changes proposed in this pull request. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: myron <amyronenko@nvidia.com> | 10 October 2022, 12:58:01 UTC |
eb0795e | TrellixVulnTeam | 06 October 2022, 07:56:23 UTC | CVE-2007-4559 Patch (#5274) # Patching CVE-2007-4559 Hi, we are security researchers from the Advanced Research Center at [Trellix](https://www.trellix.com). We have began a campaign to patch a widespread bug named CVE-2007-4559. CVE-2007-4559 is a 15 year old bug in the Python tarfile package. By using extract() or extractall() on a tarfile object without sanitizing input, a maliciously crafted .tar file could perform a directory path traversal attack. We found at least one unsantized extractall() in your codebase and are providing a patch for you via pull request. The patch essentially checks to see if all tarfile members will be extracted safely and throws an exception otherwise. We encourage you to use this patch or your own solution to secure against CVE-2007-4559. Further technical information about the vulnerability can be found in this [blog](https://www.trellix.com/en-us/about/newsroom/stories/research/tarfile-exploiting-the-world.html). If you have further questions you may contact us through this projects lead researcher [Kasimir Schulz](mailto:kasimir.schulz@trellix.com). Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 10 October 2022, 12:58:01 UTC |
c9d1a71 | Wenqi Li | 05 October 2022, 11:24:54 UTC | 4320 update docstrings for gradient based saliency (#5268) Signed-off-by: Wenqi Li <wenqil@nvidia.com> Fixes #4320 it seems we also have sufficient modules to close #3542 ### 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. - [x] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 10 October 2022, 12:58:01 UTC |
d76adc7 | Wenqi Li | 04 October 2022, 13:58:30 UTC | 5253 fixes output offset - spacing (#5254) Signed-off-by: Wenqi Li <wenqil@nvidia.com> Fixes #5253 ### Description enhance computing offset for spacing ### 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> | 10 October 2022, 12:58:00 UTC |
94673a9 | pre-commit-ci[bot] | 04 October 2022, 11:47:29 UTC | [pre-commit.ci] pre-commit suggestions/consolidate autofixes (#5256) <!--pre-commit.ci start--> updates: - [github.com/asottile/pyupgrade: v2.34.0 → v2.38.2](https://github.com/asottile/pyupgrade/compare/v2.34.0...v2.38.2) - [github.com/asottile/yesqa: v1.3.0 → v1.4.0](https://github.com/asottile/yesqa/compare/v1.3.0...v1.4.0) - [github.com/hadialqattan/pycln: v1.3.5 → v2.1.1](https://github.com/hadialqattan/pycln/compare/v1.3.5...v2.1.1) <!--pre-commit.ci end--> Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> | 10 October 2022, 12:58:00 UTC |
1ee8ba0 | Can Zhao | 03 October 2022, 20:02:16 UTC | fix bug in retina detector (#5255) Signed-off-by: Can Zhao <canz@nvidia.com> Fixes #5250. ### Description Fixed bug that allow_low_quality_matches in set_regular_matcher was always set to True and it's not using value from the argument, in retinanet. ### 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: Can Zhao <canz@nvidia.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 10 October 2022, 12:58:00 UTC |
6e63284 | Wenqi Li | 03 October 2022, 15:30:33 UTC | 5251 replace None type metadict content with 'none' (#5252) Signed-off-by: Wenqi Li <wenqil@nvidia.com> Fixes #5251 ### Description replace `None` with `"none"` in the readers ### 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> | 10 October 2022, 12:58:00 UTC |
2687b72 | myron | 01 October 2022, 15:04:05 UTC | UpSample optional kernel_size for deconv mode (#5221) ### Description Adds (optional) kernel_size parameter to UpSample, used for deconv (convolution transpose up-sampling). This allows to upsample, e.g to upscale to 2x with a kernel_size 3. (currently the default is to upscale to 2x with a kernel size 2) if this parameter is not set, the behavior is the same as before ### 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. - [x] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: myron <amyronenko@nvidia.com> | 10 October 2022, 12:58:00 UTC |
68d1b34 | Richard Brown | 30 September 2022, 16:29:27 UTC | Occlusion sensitivity to use slidiing_window_inference (#5230) ### Description Occlusion sensitivity currently works by setting the logits at the center of the occluded region. Even though neighbouring voxels are occluded at the same time, this is not recorded. A better way to do it would be to do an average each time a voxel is occluded. This is taken care of by switching to using `sliding_window_inference`. We had to do a bit of hacking to get this to work. `sliding_window_inference` normally takes a subset of the whole image and infers that. We want `sliding_window_inference` to tell us which part of the image we should occlude, then we occlude it and infer the **whole** image. To that end, we use a meshgrid to tell us the coordinates of the region `sliding_window_inference` wants us to occlude. We occlude, infer and then crop back to the size of the region that was requested by `sliding_window_inference`. This PR also allows for different occlusion kernels. We currently have: - gaussian (actually inverse gaussian): the center of the occluded region is zero, and towards the edge of the image is unchanged. This doesn't introduce hard edges into the image, which might undermine the visualisation process. - mean_patch: the occluded region is replaced with the mean of the patch it is occluding. - mean_img: the occluded region is replaced with the mean of the whole image (current implementation). ## Changes to input arguments This PR is backwards incompatible, as using `sliding_window_inference` means changing the API significantly. - pad_val: now determined by `mode` - stride: `overlap` used instead - per_channel: all channels are done simultaneously - upsampler: image is no longer downsampled ## Changes to output Output previously had the shape `B,C,H,W,[D],N` where `C` and `N` were the number of input and output channels of the network, respectively. Now, we output the shape `B,N,H,W,[D]` as the `per_channel` feature is no longer present. Columns 2-4 are occlusion sensitivity done with Gaussian, mean of patch and mean of image: ![vis](https://user-images.githubusercontent.com/33289025/193261000-b879bce8-3aab-433b-af6c-cbb9c885d0a3.png) ### 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: Richard Brown <33289025+rijobro@users.noreply.github.com> | 10 October 2022, 12:57:59 UTC |
e8879a0 | Behrooz Hashemian | 30 September 2022, 15:24:44 UTC | HoVerNet Mode and Branch to independent StrEnum (#5219) Fixes #5218 ### Description This PR moves `HoVerNet` Mode and Branch outside of the module and make them independent `StrEnums`. ### 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] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [x] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [x] In-line docstrings updated. Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 10 October 2022, 12:57:59 UTC |
21e0ad5 | Holger Roth | 30 September 2022, 14:25:10 UTC | Add multi-gpu support to MonaiAlgo (#5228) Signed-off-by: Holger Roth <hroth@nvidia.com> Fixes #5195. ### Description Add support for MonaiAlgo to be run with torchrun for multi-gpu 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: Holger Roth <hroth@nvidia.com> | 10 October 2022, 12:57:59 UTC |
06aee55 | macdavid | 30 September 2022, 12:44:38 UTC | Solve LoadImage issue when track_meta is False (#5239) 1. Fix the issue #5227 2. fix a small code flaw Signed-off-by: David <dyq.004@gmail.com> | 10 October 2022, 12:57:59 UTC |
df84c3d | YunLiu | 30 September 2022, 10:13:51 UTC | Fix 1D data error in `VarAutoEncoder` (#5236) Signed-off-by: KumoLiu <yunl@nvidia.com> Fixes #5225 . ### Description 1. fix 1d data error in `VarAutoEncoder` 2. add `use_sigmoid` flag ### 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: KumoLiu <yunl@nvidia.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com> | 10 October 2022, 12:57:58 UTC |
b862c75 | Nic Ma | 30 September 2022, 08:07:42 UTC | 5233 Add file check for the logging config (#5235) Fixes #5233 . ### Description This PR added file existing check for the logging config, requested by @holgerroth . ### 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> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com> | 10 October 2022, 12:57:58 UTC |
0cf3088 | Wenqi Li | 30 September 2022, 07:00:15 UTC | 5163 metatensor support for `OneOf` (#5217) Signed-off-by: Wenqi Li <wenqil@nvidia.com> Fixes #5163 ### Description enhance metatensor compatibility for `OneOf` ### 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> | 10 October 2022, 12:57:58 UTC |
4026c5e | Nic Ma | 30 September 2022, 05:46:53 UTC | 5232 Enhance bundle page with more information (#5234) Fixes #5232 . ### Description According to user's feedback, this PR enhanced the MONAI bundle doc page to include tutorial examples and model-zoo 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). - [ ] 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 2022, 12:57:58 UTC |
3d493ea | Richard Brown | 29 September 2022, 17:37:34 UTC | protobuf should use PYEXE not pip (#5231) ### Description We should be using `PY_EXE` in runtests as opposed to raw `pip`. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> | 10 October 2022, 12:57:58 UTC |
a7e62d7 | Richard Brown | 29 September 2022, 12:16:57 UTC | Visualisation classes to allow kwargs. combine GradCAM and ++ test files (#5224) ### Description Some users may have models that take adjoint information. This PR allows the adjoint information to be passed through the visualisation classes to the model via `**kwargs`. Also combined the test files of GradCAM and GradCAM++ as they were the same. ### 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] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [x] In-line docstrings updated. Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> | 10 October 2022, 12:57:57 UTC |
bacc6bb | Yiheng Wang | 29 September 2022, 10:36:47 UTC | 4264 Add antialiasing option for `Resized` (#5223) Signed-off-by: Yiheng Wang <vennw@nvidia.com> Fixes #4264 . ### Description This PR adds the antialiasing option for `Resized` transform. ### 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> | 10 October 2022, 12:57:57 UTC |
e672b70 | Wenqi Li | 27 September 2022, 11:43:51 UTC | 3844 flexible min/max_pixdim options for Spacing (#5212) Signed-off-by: Wenqi Li <wenqil@nvidia.com> Fixes #3844 ### Description adding the flexibility for skipping the transform if the pixdim is in the specified range ### 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> | 10 October 2022, 12:57:57 UTC |
c71df93 | Wenqi Li | 27 September 2022, 08:53:32 UTC | 5211 5214 infer device from first item RandElastic, simplify `first_key()` default (#5213) Signed-off-by: Wenqi Li <wenqil@nvidia.com> Fixes #5211 Fixes #5214 ### Description - set device based on the first item: ```py device = self.rand_2d_elastic.device if device is None and isinstance(d[first_key], torch.Tensor): device = d[first_key].device # type: ignore self.rand_2d_elastic.set_device(device) ``` - simplied transform `first_key()` default to a tuple ### 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> | 10 October 2022, 12:57:57 UTC |
b9f5dd8 | Wenqi Li | 26 September 2022, 11:26:27 UTC | 5193 5204 import error msg/warnings (#5205) fixes #5193 fixes #5204 ### Description revise the import error messages and ignore a torchaudio 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`. - [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> | 10 October 2022, 12:57:57 UTC |
6a4dd92 | YunLiu | 26 September 2022, 09:33:35 UTC | Fix typo in `RandScaleIntensityd` (#5210) Signed-off-by: KumoLiu <yunl@nvidia.com> Fixes #5209. ### Description Fix typo in `RandScaleIntensityd` ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [x] In-line docstrings updated. Signed-off-by: KumoLiu <yunl@nvidia.com> | 10 October 2022, 12:57:56 UTC |
ed5fd2d | Holger Roth | 22 September 2022, 16:26:50 UTC | update federated learning figure (#5194) Fixes #5031. ### Description Update federated learning figure. Using SVG format. Also removes from svg from 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. - [x] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Holger Roth <hroth@nvidia.com> | 10 October 2022, 12:57:56 UTC |
1c1815c | YunLiu | 21 September 2022, 15:18:06 UTC | Add channel dim in `ComputeHoVerMaps` and `ComputeHoVerMapsd` (#5183) Signed-off-by: KumoLiu <yunl@nvidia.com> Fixes #5177. ### Description Add channel dim in `ComputeHoVerMaps` and `ComputeHoVerMapsd` to make it consistent with other transforms. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: KumoLiu <yunl@nvidia.com> Co-authored-by: Behrooz Hashemian <3968947+drbeh@users.noreply.github.com> | 10 October 2022, 12:57:56 UTC |
0a4b085 | YunLiu | 20 September 2022, 16:18:14 UTC | Remove batch dim in `SobelGradients` and `SobelGradientsd` (#5182) Signed-off-by: KumoLiu <yunl@nvidia.com> Fixes #5176. ### Description Remove batch dim in `SobelGradients` and `SobelGradientsd` to make it consistent with other post transforms. ### 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> | 10 October 2022, 12:57:56 UTC |
8de4af1 | Wenqi Li | 16 September 2022, 16:33:45 UTC | 5090 releasing 1.0.0 (#5170) Signed-off-by: Wenqi Li <wenqil@nvidia.com> Fixes #5090 ### Description update version numbers ### 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 2022, 12:57:55 UTC |
1700933 | Wenqi Li | 16 September 2022, 13:41:22 UTC | Update URLs Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 16 September 2022, 13:42:25 UTC |
f8ad6c6 | Wenqi Li | 16 September 2022, 13:08:45 UTC | 5164 fixes wsireader test (#5165) Fixes #5164 ### Description fixes file path 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] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 16 September 2022, 13:08:45 UTC |
70c0443 | Wenqi Li | 16 September 2022, 11:34:05 UTC | 5090 5161 minor doc/env fixes (#5162) Fixes #5161 part of #5090 ### 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: Wenqi Li <wenqil@nvidia.com> | 16 September 2022, 11:34:05 UTC |
ca90628 | Wenqi Li | 15 September 2022, 21:08:36 UTC | 5090 Update highlight and whats new (#5128) Signed-off-by: Wenqi Li <wenqil@nvidia.com> part of #5090 ### 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: Wenqi Li <wenqil@nvidia.com> | 15 September 2022, 21:08:36 UTC |
d844caf | Wenqi Li | 15 September 2022, 13:37:50 UTC | 5150 fixes integration error reading stdout visible devices (#5154) Signed-off-by: Wenqi Li <wenqil@nvidia.com> Fixes #5150 ### Description `python -m tests.utils` may print additional contents from 3rd party packages, only the last line for the stdout should be used ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [x] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [x] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 15 September 2022, 13:37:50 UTC |
d763ca2 | Mingxin Zheng | 15 September 2022, 00:18:18 UTC | update template hash (#5146) Signed-off-by: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com> Fixes # . ### 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: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com> Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com> | 15 September 2022, 00:18:18 UTC |
57d4609 | Abhijeet Parida | 14 September 2022, 22:43:31 UTC | fix(UNETR): access Bias term in SAB block (#5149) Fixes #5148 . ### 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: a-parida12 <abhijeet.parida@tum.de> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 14 September 2022, 22:43:31 UTC |
a1e1af5 | Wenqi Li | 14 September 2022, 21:55:38 UTC | 5090 update changelog for v1.0.0 (#5139) Signed-off-by: Wenqi Li <wenqil@nvidia.com> part of #5090 ### Description update the changelog please see also the backward compatibility guide: https://github.com/Project-MONAI/MONAI/blob/dev/CONTRIBUTING.md#backwards-compatibility ### 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> | 14 September 2022, 21:55:38 UTC |
4a38e11 | Mingxin Zheng | 14 September 2022, 10:24:17 UTC | json loader -> ConfigParser in template zip (#5143) Signed-off-by: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com> Fixes datalist loader ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). Signed-off-by: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com> | 14 September 2022, 10:24:17 UTC |
548160a | Yiheng Wang | 14 September 2022, 09:36:20 UTC | 5140 Add update time information for bundle API (#5141) Signed-off-by: Yiheng Wang <vennw@nvidia.com> Fixes #5140 ### Description This PR is used to add `created_at` (the create time of a bundle) and `update_at` (the update time of a bundle) information in bundle API. It is helpful for showing the corresponding information in model zoo website. ### 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: Yiheng Wang <vennw@nvidia.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com> | 14 September 2022, 09:36:20 UTC |
50c30c1 | Mingxin Zheng | 14 September 2022, 03:26:16 UTC | Add Optuna and Improve Doc-strings for Auto3Dseg (#5137) ### Description Improve docstring and Optuna Integration(#5136 ) ### 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] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com> Signed-off-by: Mingxin Zheng <mingxin.zheng@philips.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Mingxin Zheng <mingxin.zheng@philips.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com> | 14 September 2022, 03:26:16 UTC |
02fb954 | Wenqi Li | 13 September 2022, 21:40:31 UTC | 4456 optional import issue on top-level modules -- monai.handlers/monai.engines (#5132) Fixes #4456 ### Description make sure that if the top-level modules miss dependencies, the optional import error raises properly. ### 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: Wenqi Li <wenqil@nvidia.com> | 13 September 2022, 21:40:31 UTC |
d64c6d2 | Richard Brown | 13 September 2022, 12:37:21 UTC | Keep n components (#5138) Fixes https://github.com/Project-MONAI/MONAI/issues/3809. ### Description Adds num_components argument. Defaults to 1 for backwards compatibility. ### 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] 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: Richard Brown <33289025+rijobro@users.noreply.github.com> | 13 September 2022, 12:37:21 UTC |
8700fee | Wenqi Li | 13 September 2022, 08:23:23 UTC | review the transform.backend variable (#5126) Signed-off-by: Wenqi Li <wenqil@nvidia.com> part of https://github.com/Project-MONAI/MONAI/issues/4974 ### Description mostly documentation updates and non functional changes ### 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> | 13 September 2022, 08:23:23 UTC |
53088c0 | Behrooz Hashemian | 13 September 2022, 06:40:00 UTC | MetaTensor support in `ProbMapProducer` (#5117) Fixes #4954 ### Description This PR updates `ProbMapProducer` to works with `MetaTensors`. It will cause a backward incompatibility when used with the older version (non-MetaTensor versions) of `MaskedPatchWSIDataset` and `SlidingPatchWSIDataset`. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [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`. Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> | 13 September 2022, 06:40:00 UTC |
af536ff | Yiheng Wang | 12 September 2022, 17:12:16 UTC | 4948 Enhance bundle API for getting model zoo info (#4994) Signed-off-by: Yiheng Wang <vennw@nvidia.com> Fixes #4948 . ### Description This PR is used to enhance the bundle API, and enable to get: 1. a list of all bundles as well as their latest versions (by function `get_all_bundles_list`) 2. a bundle's latest version, and all existing verions (by function `get_bundle_versions`) 3. a bundle's information, include "id", "name", "size", "download_count", "browser_download_url". The information are achieved from github API directly (by function `get_bundle_info`) ### Status **Ready** ### 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: Yiheng Wang <vennw@nvidia.com> | 12 September 2022, 17:12:16 UTC |
5375a74 | Wenqi Li | 12 September 2022, 16:16:30 UTC | 5127 fixes dtypes in randomized transforms (#5129) Signed-off-by: Wenqi Li <wenqil@nvidia.com> Fixes #5127 ### Description still does the dtype converting if self._do_transform is False ### 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. - [x] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 12 September 2022, 16:16:30 UTC |
3908131 | Mingxin Zheng | 12 September 2022, 06:43:21 UTC | Add Auto3Dseg AutoRunner (#5112) Signed-off-by: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com> ### Description The all-in-one minimal runner for auto3dseg pipeline. HPO is not included because PR is still WIP. ### 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: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 12 September 2022, 06:43:21 UTC |
d39ac50 | Wenqi Li | 11 September 2022, 09:27:15 UTC | fixes typos and integration tests (#5121) Signed-off-by: Wenqi Li <wenqil@nvidia.com> ### Description run integration 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). - [ ] New tests added to cover the changes. - [x] 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 September 2022, 09:27:15 UTC |
7f7aff8 | Mingxin Zheng | 11 September 2022, 01:03:52 UTC | Integrating HPO into Auto3Dseg (#5101) ### Description This is part of effort of Auto3D development. The goal of the PR is to address #4912. ### 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: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Nic Ma <nma@nvidia.com> | 11 September 2022, 01:03:52 UTC |
c1b4dac | Wenqi Li | 10 September 2022, 17:34:10 UTC | 5061 align corners and recompute_affine for spacing (#5075) Signed-off-by: Wenqi Li <wenqil@nvidia.com> Fixes #5061 ### Description computing output shape considering `align_corners`, recompute the output affine based on output shapes. a new `scale_extent` parameter is included to choose between the two resampling coordinate conventions. ### Status **Ready** ### 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> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 10 September 2022, 17:34:10 UTC |
ea2502f | Nic Ma | 10 September 2022, 10:26:46 UTC | Enhance BundleAlgo to support different template structures and download link (#5099) ### Description This PR enhanced the `BundleAlgo` base class to support different `sections` in the subclasses, for example DiNTS may need to save more config sections. And also enhanced the `BundleGen` to support other download link for the templates. ### 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> Signed-off-by: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com> Co-authored-by: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com> | 10 September 2022, 10:26:46 UTC |
81d2b30 | Holger Roth | 09 September 2022, 22:10:39 UTC | 5118 monai algo multi configs support (#5119) Fixes #5118. ### Description Change config file parsing logic to support multiple files. Also separate the logic of parsing training and eval files and opted to not automatically merge both configs. The default will be to keep the same behavior as before. ``` config_train_filename = "configs/train.json" config_evaluate_filename = ["configs/train.json", "configs/evaluate.json"] ``` ### 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: Holger Roth <hroth@nvidia.com> | 09 September 2022, 22:10:39 UTC |
59aeab0 | Behrooz Hashemian | 09 September 2022, 20:19:35 UTC | MetaTensor for `GridPatch` and `RandGridPatch` (#5107) Fixes #4955 ### Description This PR makes `GridPatch`, `GridPatchd`, `RandGridPatch` and `RandGridPatchd` to create outputs as MetaTensors and return them as a single MetaTensor with `is_batch=True`. It also makes `get_default_affine()` a static method, similar to `get_default_meta()`, to be able to it in other places. ### 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: Behrooz <3968947+drbeh@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 09 September 2022, 20:19:35 UTC |
15e15c6 | Vishwesh | 09 September 2022, 15:27:51 UTC | Label Quality Assessment for Active Learning (#5065) Signed-off-by: Vishwesh Nath <vnath@nvidia.com> ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [x] New tests added to cover the changes. - [x] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [x] In-line docstrings updated. - [x] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Vishwesh Nath <vnath@nvidia.com> | 09 September 2022, 15:27:51 UTC |
05de740 | Wenqi Li | 09 September 2022, 13:18:38 UTC | adds a debugging flag for bundle parser (#5104) Signed-off-by: Wenqi Li <wenqil@nvidia.com> ### Description adds a `_debug_` keyword, so that when it's set to true, the program stops at the component init stage and enter the debug mode , usage: ```yaml inferer: _target_: SlidingWindowInferer _debug_: true roi_size: [96, 96, 96] sw_batch_size: 4 overlap: 0.5 ``` alternatively at the CLI set `MONAI_DEBUG_CONFIG=1`, for example: ```bash MONAI_DEBUG_CONFIG=1 python -m my_test_5 run --config_file=my_test_5.yaml ``` ### 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> | 09 September 2022, 13:18:38 UTC |
e98226d | Behrooz Hashemian | 08 September 2022, 16:02:22 UTC | Metadata in WSIReader and MetaTensor in WSIDatasets (#5077) Fixes #4956 and #4674 ### Description This PR implements micron-per-pixel (mpp) resolution calculation for `WSIReader` and all its backend, and adds `mpp` to the metadata to support the requested metadata from pathology WG. To be consistent with other image readers, `WSIReader` continue to return (image, metadata) pair instead of a MetaTensor (but it would be nice to reconsider it for all the image readers). It also updates WSIDatasets to return a MetaTensor and reference the required metadata via image.meta. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [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: Behrooz <3968947+drbeh@users.noreply.github.com> Co-authored-by: Nic Ma <nma@nvidia.com> | 08 September 2022, 16:02:22 UTC |
c71b0eb | SACHIDANAND ALLE | 07 September 2022, 23:00:34 UTC | Fix deepgrow prepare data for 2D/3D (#5103) Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> Fixes # Fix data preparation for Deepgrow 2D/3D training ### Description Removing deprecated transform caused incorrect functionality for data-preparation step. ### 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: Sachidanand Alle <sachidanand.alle@gmail.com> | 07 September 2022, 23:00:34 UTC |
f4b6544 | Mohammad Zalbagi Darestani | 07 September 2022, 19:32:35 UTC | Disable weight sharing for VarNet model (#5102) Signed-off-by: mersad95zd <m.zalbagi@gmail.com> Fixes # . ### Description Disable weight sharing in VarNet 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: mersad95zd <m.zalbagi@gmail.com> | 07 September 2022, 19:32:35 UTC |
36200de | Mohammad Zalbagi Darestani | 07 September 2022, 14:55:49 UTC | Edit varnet model (#5096) Signed-off-by: mersad95zd <m.zalbagi@gmail.com> Fixes #5095 ### Description Minor fixes to varnet model (its unit 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). - [ ] 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: mersad95zd <m.zalbagi@gmail.com> | 07 September 2022, 14:55:49 UTC |
f23077d | Wenqi Li | 07 September 2022, 11:59:38 UTC | 4571 4616 remove deprecated api calls (#5089) fixes #4571 fixes #4616 fixes #5094 ### Description remove the deprecated calls ### 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> | 07 September 2022, 11:59:38 UTC |
fb6d950 | Yashika | 07 September 2022, 06:40:55 UTC | Implementing UNet++ (#5084) Fixes #896. ### Description Added Unet++. ### Status **Ready ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [ ] Non-breaking change (fix or new feature that would not break existing functionality). - [x] Breaking change (fix or new feature that would cause existing functionality to change). - [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: Yashika Jain <yashikajain201@gmail.com> | 07 September 2022, 06:40:55 UTC |
91a58ed | Abhijeet Parida | 06 September 2022, 22:33:59 UTC | Updated Contrastive Loss batch Size (#5093) Fixes #5070 . ### Description The batch size for the contrastive loss is estimated automatically ### 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: a-parida12 <abhijeet.parida@tum.de> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 06 September 2022, 22:33:59 UTC |
0af5e18 | YunLiu | 06 September 2022, 17:12:36 UTC | [WIP]Update auto3dseg docstring (#5083) Signed-off-by: KumoLiu <yunl@nvidia.com> Fixes # . ### Description Fix docstring in auto3dseg ### Status **Work in progress** ### 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 <wenqil@nvidia.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com> | 06 September 2022, 17:12:36 UTC |
658089b | Behrooz Hashemian | 06 September 2022, 16:06:10 UTC | Remove Status from PR Template (#5092) ### Description This PR remove "Status" from PR template. The Status was very useful before GitHub introduced *Draft* PR. I believe right now it is redundant to have this and sometimes conflicting (e.g., Status Ready <> Draft PR), so I believe it is time to remove the "Status" from PR template. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> | 06 September 2022, 16:06:10 UTC |
4105299 | Mingxin Zheng | 06 September 2022, 14:57:58 UTC | [Ready for review] Auto3D functional fixes in the BundleGen module (#5087) ### Description Part of the requested improvements #5085 Planned fixes - [x] fold number is not being updated in generate() - [x] put absolute paths in the bundle configs - [x] break the auto-generated auto_config into multiple files. ### Status WIP ### Types of changes <!--- 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: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Nic Ma <nma@nvidia.com> | 06 September 2022, 14:57:58 UTC |
8c4127b | Eric Kerfoot | 06 September 2022, 13:49:21 UTC | Slight Fix For Type Conversion (#5091) Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> ### Description Using `view` to avoid copying doesn't actually work as intended in the type conversion to use `astype`. ### Status **Ready** ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 06 September 2022, 13:49:21 UTC |
7fc5cf8 | Eric Kerfoot | 06 September 2022, 11:58:45 UTC | Fix for Numpy Unsigned Array Conversion (#5082) Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> ### Description Numpy arrays with type uint16, uint32, and uint64 need to be converted to signed versions before conversion to Pytorch tensors. This is relevant because MR data is often stored in uint16 format. ### Status **Ready** ### Types of changes <!--- 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: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> | 06 September 2022, 11:58:45 UTC |
b6016a9 | Holger Roth | 06 September 2022, 09:58:33 UTC | Use Ignite's interrupt api in MonaiAlgo (#5071) Fixes #4554. Requires latest Ignite RC. Also improves ClientAlgo docstrings formatting. ### Description A few sentences describing the changes proposed in this pull request. ### Status **Ready** ### Types of changes <!--- 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: Holger Roth <hroth@nvidia.com> Signed-off-by: Nic Ma <nma@nvidia.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Nic Ma <nma@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 06 September 2022, 09:58:33 UTC |
05856ef | Wenqi Li | 05 September 2022, 23:22:26 UTC | 4909 remove deprecated args since v0.6 and v0.7 (#5055) Fixes #4909 ### Status **Ready** ### 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 September 2022, 23:22:26 UTC |
2ed44aa | Eric Kerfoot | 05 September 2022, 15:01:10 UTC | Default prepare batch update (#5079) ### Description This allows `default_prepare_batch` to handle batches containing a single tensor or a pair of tensors. Normally if one uses array transforms you'll get an error saying the default batch function needs dictionaries so this will allow such transform sequences to be used without modification. ### Status **Work in progress** ### Types of changes <!--- 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: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 05 September 2022, 15:01:10 UTC |
b1aa40d | Eric Kerfoot | 05 September 2022, 07:17:57 UTC | LogfileHandler (#5064) Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> ### Description Adds a handler for directing logging information to a file once an `Engine` object starts and then doing the cleanup when it completes. ### Status **Ready** ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [x] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [x] In-line docstrings updated. - [x] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 05 September 2022, 07:17:57 UTC |
66df2b2 | Mingxin Zheng | 02 September 2022, 20:29:02 UTC | Ensemble 5008 (#5012) Initial draft for #5008 . ### Description Ensemble models for Auto3Dseg and external algorithm ### Status **Ready** ### 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: Mingxin Zheng <mingxinz@nvidia.com> | 02 September 2022, 20:29:02 UTC |
52aed2b | Wenqi Li | 02 September 2022, 09:52:54 UTC | 4569 consistent rng for data loader (#5067) Signed-off-by: Wenqi Li <wenqil@nvidia.com> Fixes #4569 ### Description with different `num_workers` the batch sampler's rng should be consistent, this PR keeps the initial random seed to achieve it. ### Status **Ready** ### 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). # the previous results for num_wokers==0 might change - [x] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [x] In-line docstrings updated. - [x] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 02 September 2022, 09:52:54 UTC |
f9e8e10 | Vishwesh | 02 September 2022, 08:02:05 UTC | Variance as a Metric for Active Learning (#4915) Signed-off-by: Vishwesh Nath <vnath@nvidia.com> ### Description Add a metric function which will return either 2D/3D spatial map depending upon input's dimensions or a single scalar value of mean/sum of variance given user's choice ### Status **Ready/Work in progress/Hold** ### 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: Vishwesh Nath <vnath@nvidia.com> Co-authored-by: Vishwesh Nath <vnath@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 02 September 2022, 08:02:05 UTC |
4780efe | Wenqi Li | 01 September 2022, 22:32:57 UTC | Revert "4966 fix deepedit get clicks" (#5066) Reverts Project-MONAI/MONAI#4969 cc @SachidanandAlle | 01 September 2022, 22:32:57 UTC |
8087dc5 | Behrooz Hashemian | 01 September 2022, 18:10:27 UTC | Sobel Gradients Operator (#5015) Fixes #4997 ### Description Implements Sobel gradients operators for a given size of kernel. ### 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] 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: Behrooz <3968947+drbeh@users.noreply.github.com> | 01 September 2022, 18:10:27 UTC |
fdb16ac | Wenqi Li | 01 September 2022, 13:01:09 UTC | 4731 squeeze dim update meta (#5041) Signed-off-by: Wenqi Li <wenqil@nvidia.com> Fixes #4731 (additionally fixes https://github.com/Project-MONAI/tutorials/issues/569) ### Description squeeze dim drops a spatial axis should also update the affine ### Status **Ready** ### 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> | 01 September 2022, 13:01:09 UTC |
63a198a | wojiazaiyugang | 01 September 2022, 12:15:29 UTC | 4966 fix deepedit get clicks (#4969) Fixes https://github.com/Project-MONAI/MONAI/issues/4966 ### 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: wojiazaiyugang <wojiazaiyugang@outlook.com> | 01 September 2022, 12:15:29 UTC |
d3aeec3 | Nic Ma | 01 September 2022, 10:06:40 UTC | 5052 Fix bundle.load API (#5053) Fixes #5052 . ### Description This PR updated the `bundle.load` API to fix the wrong path issue. ### Status **Ready** ### 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> | 01 September 2022, 10:06:40 UTC |
857e92b | YunLiu | 01 September 2022, 07:00:49 UTC | update `cat_chns` arg's docstring (#5051) Signed-off-by: KumoLiu <yunl@nvidia.com> Fixes #5046 . ### Description update `cat_chns` arg's docstring in basic_unet. ### Status **Ready** ### 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> | 01 September 2022, 07:00:49 UTC |
a109d3a | Wenqi Li | 01 September 2022, 03:32:06 UTC | 4891 base class algo generator (#5042) ### Description part of #4891 with some misc fixes and tests. adds: - Algo class - AlgoGen class ### Status **Readyd** ### 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: Nic Ma <nma@nvidia.com> | 01 September 2022, 03:32:06 UTC |
3e79851 | Behrooz Hashemian | 31 August 2022, 22:18:42 UTC | Update HoVerNet model with enum keys (#5030) Fixes #5029 ### Description Add enums to define different branches of HoVerNet 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). Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> | 31 August 2022, 22:18:42 UTC |
aa12381 | Behrooz Hashemian | 31 August 2022, 21:18:11 UTC | Implement TiffFile backend for WSIReader (#4972) * Implement TiffFileWSIReader Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> | 31 August 2022, 21:18:11 UTC |
f49cc96 | Wenqi Li | 31 August 2022, 14:40:31 UTC | Fixes various typos and static analysis issues (#5039) ### Description mostly minor typo fixes ### Status **Ready** Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 31 August 2022, 14:40:31 UTC |