Closed
Conversation
Fixes Project-MONAI#8157 . ### Description Fixed some typos in README.md ### 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: Smoothengineer <160827599+Smoothengineer@users.noreply.github.com>
Fixes Project-MONAI#8160 ### Description A few sentences describing the changes proposed in this pull request. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Fixes # . ### Description Added a top button because of file length as it improves readibility 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: ANUSHKA KATHARE <anushkakathare07@gmail.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
The Rearrange code failed dynamo export in 24.09 container: pytorch/pytorch#137629 While we can't still use dynamo export with TRT in 23.09, I also noticed that my workaround improved runtime by about 1 second end-to-end for 100 seconds run. ### Description Replaced einops Rearrange with reshape/transpose ### 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: Boris Fomitchev <bfomitchev@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Fixes Project-MONAI#8122 . ### Description As shown in [this PR](Project-MONAI/model-zoo#671), the memory malloc and mask embedding for-loop are the bottlenecks that caused the vista3d slow inference. Therefore, this PR fixed them by adding the logic for malloc and replacing the for-loop with a tensor multiplication. ### 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> Co-authored-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
…roject-MONAI#8165) Fixes # . ### Description related bug pytorch/pytorch#138674 ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
… the bundle (Project-MONAI#8142) Fix Project-MONAI/model-zoo#658, part of Project-MONAI#7513 ### Description Enable redirection of all loggers by configuring a FileHandler within the bundle ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
### Description Included is a commit here applying pyupgrade changes for Python 3.8+ syntax. This should have been included in Project-MONAI@104a360 when Python 3.7 support was dropped. Also included is a commit here apply pyupgrade changes for Python 3.9+ syntax. This should have been included in Project-MONAI@14b086b when Python 3.8 support was dropped. I've also run the pre-commit autoupdate command to use the latest versions of the various pre-commit hook repos. It appears that pre-commit.ci bot has not been doing this on the quarterly schedule as expected? It appears the last time it submitted the PR to update the pre-commit hook repos was back in Project-MONAI#6286 from April 2023. ### 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: James Butler <james.butler@revvity.com>
### Description This addresses expired numpy deprecations that happened with the numpy 2 release. This code is compatible with numpy 1 and 2 to support future enablement of numpy2 for monai. See https://docs.astral.sh/ruff/rules/numpy2-deprecation/ ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). --------- Signed-off-by: James Butler <james.butler@revvity.com>
) ### Description Frequently getting warning massage in a newer Pytorch version (2.4.1 in my case): "_You are using `torch.load` with `weights_only=False` (the current default value), which uses the default pickle module implicitly. It is possible to construct malicious pickle data which will execute arbitrary code during unpickling (See https://github.com/pytorch/pytorch/blob/main/SECURITY.md#untrusted-models for more details). In a future release, the default value for `weights_only` will be flipped to `True`. This limits the functions that could be executed during unpickling. Arbitrary objects will no longer be allowed to be loaded via this mode unless they are explicitly allowlisted by the user via `torch.serialization.add_safe_globals`. We recommend you start setting `weights_only=True` for any use case where you don't have full control of the loaded file. Please open an issue on GitHub for any issues related to this experimental feature._" This pull request fixes an issue with the `torch.load()` function in the `PersistentDataset` and `GDSDataset` classes by adding `weights_only=False`. The fix ensures that the `torch.load()` function maintains load consistency in future versions of PyTorch. ### 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: bnbqq8 <bnbqq8@i.smu.edu.cn>
…I#8169) Fix Project-MONAI/model-zoo#697 ### Description Flatten the metric dict when the metric is a nested dictionary. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…-MONAI#8184) Fixes # . ### Description A few sentences describing the changes proposed in this pull request. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
…-MONAI#8189) Fixes Project-MONAI#8127 Update `ImageFilter` to handle Gaussian filter without requiring `filter_size`. * Modify `monai/transforms/utility/array.py` to allow Gaussian filter without `filter_size`. - Adjust `_check_filter_format` method to skip `filter_size` check for Gaussian filter. Indeed Gauss filter is the only one in the list that doesn't require a filter_size. * Add unit test in `tests/test_image_filter.py` for Gaussian filter without `filter_size`. - Verify output shape matches input shape. Note that this method is compliant with the dictionnary version since this one load the fixed version. Signed-off-by: Eloi <eloi.navet@gmail.com> --------- Signed-off-by: Eloi Navet <eloi.navet@labri.fr> Signed-off-by: Eloi <eloi.navet@gmail.com> Signed-off-by: Eloi eloi.navet@gmail.com
Fixes # . ### Description A few sentences describing the changes proposed in this pull request. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Fixes Project-MONAI#8198 NVIDIA Volta support (GPUs with compute capability 7.0) has been removed starting with TensorRT 10.5. Review the [TensorRT Support Matrix](https://docs.nvidia.com/deeplearning/tensorrt/support-matrix/index.html) for which GPUs are supported by this release. Add SM architecture version check to skip trt test before 7.0. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Fixes Project-MONAI#7786 ### Description Added MedNext architectures implementation for MONAI. Since a lot of the code is heavily sourced from the original MedNext repo, https://github.com/MIC-DKFZ/MedNeXt, I wanted to check if there is an attribution policy with regarded to borrowed source code. I've added a derivative notice bellow the monai copyright comment. Let me know if this needs to be changed. The blocks have been taken almost as is but the network implementation has been changed largely to allow flexible blocks and follow MONAI segresnet styling. ### 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: Suraj Pai <bspai@bwh.harvard.edu> Signed-off-by: Robin CREMESE <robin.cremese@pasteur.fr> Co-authored-by: Robin CREMESE <robin.cremese@pasteur.fr> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
### Description
Added trt_compile() support for Lists and Tuples in arguments for
forward() - needed for MAISI.
Did not add support for grouping return results yet - MAISI worked with
explicit workaround unrolling the return results.
### Notes
To successfully export MAISI, either latest Torch nightly is needed, or
this patch needs to be applied to 24.09-based container:
```
--- /usr/local/lib/python3.10/dist-packages/torch/onnx/symbolic_opset14.bak 2024-10-09 01:38:04.920316673 +0000
+++ /usr/local/lib/python3.10/dist-packages/torch/onnx/symbolic_opset14.py 2024-10-09 01:38:25.228053951 +0000
@@ -148,7 +148,6 @@
is_causal and symbolic_helper._is_none(attn_mask)
), "is_causal and attn_mask cannot be set at the same time"
- scale = symbolic_helper._maybe_get_const(scale, "f")
if symbolic_helper._is_none(scale):
scale = _attention_scale(g, query)
```
### 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: Boris Fomitchev <bfomitchev@nvidia.com>
Signed-off-by: Yiheng Wang <vennw@nvidia.com>
Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Co-authored-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com>
Co-authored-by: Yiheng Wang <vennw@nvidia.com>
Co-authored-by: binliunls <107988372+binliunls@users.noreply.github.com>
Fixed fold_constants: the result was not saved. test_handler switched to onnx as torch-tensorrt is causing issues with CI on various Torch versions and is not used anyway. ### 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: Boris Fomitchev <bfomitchev@nvidia.com>
### Description There is a minor bug in a test which causes a second fail to occur when one does. In `test_module_list.py`, there is a list of classes to check which must have aliases removed from it. This must be done before the test assert so that in the event the assert fails this removal isn't skipped. ### 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>
Fixes Project-MONAI#8134 . ### Description This PR added unit test to cover the realtime inference with bundles. And updated `BundleWorkflow` to support cyclically calling the `run` function with all components instantiated. ### 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
### 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. - [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: Eloi Navet eloi.navet@labri.fr Signed-off-by: Eloi Navet <eloi.navet@labri.fr> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
…AI#8235) ### Description The aim of this PR is to enable the use of an arbitrary mask in the self attention module, which is very useful in the case of missing data or masked modeling. Official torch implementations allow the use of an arbitrary mask, and in MONAI the use of a mask is also made possible with the `causal` argument. Here, it's just a generalization directly in the forward pass. In the `SABlock` and `TransformerBlock`, it is now possible to input a boolean mask of size `(BS, Seq_length)`. Only the columns of the masked token are set to `-inf` and not the rows, as is rarely the case in common implementations. Masked tokens don't contribute to the gradient anyway. In cases where causal attention is required, inputting a mask is not supported to avoid masks overlapping. I haven't implemented the addition mask to the attention matrix, which allows you to use values other than `-inf` in certain cases, as may be the case here: https://pytorch.org/docs/stable/generated/torch.nn.functional.scaled_dot_product_attention.html If you think it's relevant, it could be added. ### 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`. - [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: Lucas Robinet <robinet.lucas@iuct-oncopole.fr> Signed-off-by: Lucas Robinet <luca.robinet@gmail.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Fixes # . ### Description Add PythonicWorkflow ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Boris Fomitchev <bfomitchev@nvidia.com> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Boris Fomitchev <bfomitchev@nvidia.com> Co-authored-by: Boris Fomitchev <borisfom@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
…roject-MONAI#8152) This follows a previous PR (Project-MONAI#7598). In the previous PR, the official implementation was under a non-compatible license. This is a clean-sheet implementation I developed. The code is fairly straightforward, involving a transformer, encoder, and decoder. The primary changes are in how masks are selected and how patches are organized as they pass through the model. In the official masked autoencoder implementation, noise is first generated and then sorted twice using `torch.argsort`. This rearranges the tokens and identifies which ones are retained, ultimately selecting only a subset of the shuffled indices. In our implementation, we use `torch.multinomial` to generate mask indices, followed by simple boolean indexing to manage the sub-selection of patches for encoding and the reordering with mask tokens in the decoder. **Let me know if you need a detailed, line-by-line explanation of the new code, including how it works and how it differs from the previous version.** ### Description Implementation of the Masked Autoencoder as described in the paper: [Masked Autoencoders Are Scalable Vision Learners](https://arxiv.org/pdf/2111.06377.pdf) from Kaiming et al. Its effectiveness has already been demonstrated in the literature for medical tasks in the paper [Self Pre-training with Masked Autoencoders for Medical Image Classification and Segmentation](https://arxiv.org/abs/2203.05573). The PR contains the architecture and associated unit tests. **Note:** The output includes the prediction, which is a tensor of size: ($BS$, $N_{tokens}$, $D$), and the associated mask ($BS$, $N_{tokens}$). The mask is used to apply loss only to masked patches, but I'm not sure it's the “best” output format, what do you think? ### 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: Lucas Robinet <robinet.lucas@iuct-oncopole.fr> Signed-off-by: Lucas Robinet <luca.robinet@gmail.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Project-MONAI#7579) …rms wrapper and test case Fixes Project-MONAI#7499 . ### Description As discussed in the issue, this PR implements a wrapper class for TorchIO transforms, analogous to the TorchVision transforms wrapper. The test cases just check that transforms are callable and that after applying a transform, the result is different from the inputs. ### 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: Fabian Klopfer <fabian.klopfer@ieee.org> Signed-off-by: Fabian Klopfer <fabian.klopfer@ibm.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Fabian Klopfer <fabian.klopfer@ibm.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/codecov/codecov-action/releases">codecov/codecov-action's releases</a>.</em></p> <blockquote> <h2>v5.0.0</h2> <h2>v5 Release</h2> <p><code>v5</code> of the Codecov GitHub Action will use the <a href="https://github.com/codecov/wrapper">Codecov Wrapper</a> to encapsulate the <a href="https://github.com/codecov/codecov-cli">CLI</a>. This will help ensure that the Action gets updates quicker.</p> <h3>Migration Guide</h3> <p>The <code>v5</code> release also coincides with the opt-out feature for tokens for public repositories. In the <code>Global Upload Token</code> section of the settings page of an organization in codecov.io, you can set the ability for Codecov to receive a coverage reports from any source. This will allow contributors or other members of a repository to upload without needing access to the Codecov token. For more details see <a href="https://docs.codecov.com/docs/codecov-tokens#uploading-without-a-token">how to upload without a token</a>.</p> <blockquote> <p>[!WARNING]<br /> <strong>The following arguments have been changed</strong></p> <ul> <li><code>file</code> (this has been deprecated in favor of <code>files</code>)</li> <li><code>plugin</code> (this has been deprecated in favor of <code>plugins</code>)</li> </ul> </blockquote> <p>The following arguments have been added:</p> <ul> <li><code>binary</code></li> <li><code>gcov_args</code></li> <li><code>gcov_executable</code></li> <li><code>gcov_ignore</code></li> <li><code>gcov_include</code></li> <li><code>report_type</code></li> <li><code>skip_validation</code></li> <li><code>swift_project</code></li> </ul> <p>You can see their usage in the <code>action.yml</code> <a href="https://github.com/codecov/codecov-action/blob/main/action.yml">file</a>.</p> <h2>What's Changed</h2> <ul> <li>chore(deps): bump to eslint9+ and remove eslint-config-google by <a href="https://github.com/thomasrockhu-codecov"><code>@thomasrockhu-codecov</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1591">codecov/codecov-action#1591</a></li> <li>build(deps-dev): bump <code>@octokit/webhooks-types</code> from 7.5.1 to 7.6.1 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1595">codecov/codecov-action#1595</a></li> <li>build(deps-dev): bump typescript from 5.6.2 to 5.6.3 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1604">codecov/codecov-action#1604</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/parser</code> from 8.8.0 to 8.8.1 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1601">codecov/codecov-action#1601</a></li> <li>build(deps): bump <code>@actions/core</code> from 1.11.0 to 1.11.1 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1597">codecov/codecov-action#1597</a></li> <li>build(deps): bump github/codeql-action from 3.26.9 to 3.26.11 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1596">codecov/codecov-action#1596</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/eslint-plugin</code> from 8.8.0 to 8.8.1 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1600">codecov/codecov-action#1600</a></li> <li>build(deps-dev): bump eslint from 9.11.1 to 9.12.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1598">codecov/codecov-action#1598</a></li> <li>build(deps): bump github/codeql-action from 3.26.11 to 3.26.12 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1609">codecov/codecov-action#1609</a></li> <li>build(deps): bump actions/checkout from 4.2.0 to 4.2.1 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1608">codecov/codecov-action#1608</a></li> <li>build(deps): bump actions/upload-artifact from 4.4.0 to 4.4.3 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1607">codecov/codecov-action#1607</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/parser</code> from 8.8.1 to 8.9.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1612">codecov/codecov-action#1612</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/eslint-plugin</code> from 8.8.1 to 8.9.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1611">codecov/codecov-action#1611</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/eslint-plugin</code> from 8.9.0 to 8.10.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1615">codecov/codecov-action#1615</a></li> <li>build(deps-dev): bump eslint from 9.12.0 to 9.13.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1618">codecov/codecov-action#1618</a></li> <li>build(deps): bump github/codeql-action from 3.26.12 to 3.26.13 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1617">codecov/codecov-action#1617</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/parser</code> from 8.9.0 to 8.10.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1614">codecov/codecov-action#1614</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/eslint-plugin</code> from 8.10.0 to 8.11.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1620">codecov/codecov-action#1620</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/parser</code> from 8.10.0 to 8.11.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1619">codecov/codecov-action#1619</a></li> <li>build(deps-dev): bump <code>@types/jest</code> from 29.5.13 to 29.5.14 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1622">codecov/codecov-action#1622</a></li> <li>build(deps): bump actions/checkout from 4.2.1 to 4.2.2 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1625">codecov/codecov-action#1625</a></li> <li>build(deps): bump github/codeql-action from 3.26.13 to 3.27.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1624">codecov/codecov-action#1624</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/eslint-plugin</code> from 8.11.0 to 8.12.1 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1626">codecov/codecov-action#1626</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/eslint-plugin</code> from 8.12.1 to 8.12.2 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1629">codecov/codecov-action#1629</a></li> </ul> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md">codecov/codecov-action's changelog</a>.</em></p> <blockquote> <h3>v5 Release</h3> <p><code>v5</code> of the Codecov GitHub Action will use the <a href="https://github.com/codecov/wrapper">Codecov Wrapper</a> to encapsulate the <a href="https://github.com/codecov/codecov-cli">CLI</a>. This will help ensure that the Action gets updates quicker.</p> <h3>Migration Guide</h3> <p>The <code>v5</code> release also coincides with the opt-out feature for tokens for public repositories. In the <code>Global Upload Token</code> section of the settings page of an organization in codecov.io, you can set the ability for Codecov to receive a coverage reports from any source. This will allow contributors or other members of a repository to upload without needing access to the Codecov token. For more details see <a href="https://docs.codecov.com/docs/codecov-tokens#uploading-without-a-token">how to upload without a token</a>.</p> <blockquote> <p>[!WARNING] <strong>The following arguments have been changed</strong></p> <ul> <li><code>file</code> (this has been deprecated in favor of <code>files</code>)</li> <li><code>plugin</code> (this has been deprecated in favor of <code>plugins</code>)</li> </ul> </blockquote> <p>The following arguments have been added:</p> <ul> <li><code>binary</code></li> <li><code>gcov_args</code></li> <li><code>gcov_executable</code></li> <li><code>gcov_ignore</code></li> <li><code>gcov_include</code></li> <li><code>report_type</code></li> <li><code>skip_validation</code></li> <li><code>swift_project</code></li> </ul> <p>You can see their usage in the <code>action.yml</code> <a href="https://github.com/codecov/codecov-action/blob/main/action.yml">file</a>.</p> <h2>What's Changed</h2> <ul> <li>chore(deps): bump to eslint9+ and remove eslint-config-google by <a href="https://github.com/thomasrockhu-codecov"><code>@thomasrockhu-codecov</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1591">codecov/codecov-action#1591</a></li> <li>build(deps-dev): bump <code>@octokit/webhooks-types</code> from 7.5.1 to 7.6.1 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1595">codecov/codecov-action#1595</a></li> <li>build(deps-dev): bump typescript from 5.6.2 to 5.6.3 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1604">codecov/codecov-action#1604</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/parser</code> from 8.8.0 to 8.8.1 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1601">codecov/codecov-action#1601</a></li> <li>build(deps): bump <code>@actions/core</code> from 1.11.0 to 1.11.1 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1597">codecov/codecov-action#1597</a></li> <li>build(deps): bump github/codeql-action from 3.26.9 to 3.26.11 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1596">codecov/codecov-action#1596</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/eslint-plugin</code> from 8.8.0 to 8.8.1 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1600">codecov/codecov-action#1600</a></li> <li>build(deps-dev): bump eslint from 9.11.1 to 9.12.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1598">codecov/codecov-action#1598</a></li> <li>build(deps): bump github/codeql-action from 3.26.11 to 3.26.12 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1609">codecov/codecov-action#1609</a></li> <li>build(deps): bump actions/checkout from 4.2.0 to 4.2.1 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1608">codecov/codecov-action#1608</a></li> <li>build(deps): bump actions/upload-artifact from 4.4.0 to 4.4.3 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1607">codecov/codecov-action#1607</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/parser</code> from 8.8.1 to 8.9.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1612">codecov/codecov-action#1612</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/eslint-plugin</code> from 8.8.1 to 8.9.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1611">codecov/codecov-action#1611</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/eslint-plugin</code> from 8.9.0 to 8.10.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1615">codecov/codecov-action#1615</a></li> <li>build(deps-dev): bump eslint from 9.12.0 to 9.13.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1618">codecov/codecov-action#1618</a></li> <li>build(deps): bump github/codeql-action from 3.26.12 to 3.26.13 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1617">codecov/codecov-action#1617</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/parser</code> from 8.9.0 to 8.10.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1614">codecov/codecov-action#1614</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/eslint-plugin</code> from 8.10.0 to 8.11.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1620">codecov/codecov-action#1620</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/parser</code> from 8.10.0 to 8.11.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1619">codecov/codecov-action#1619</a></li> <li>build(deps-dev): bump <code>@types/jest</code> from 29.5.13 to 29.5.14 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1622">codecov/codecov-action#1622</a></li> <li>build(deps): bump actions/checkout from 4.2.1 to 4.2.2 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1625">codecov/codecov-action#1625</a></li> <li>build(deps): bump github/codeql-action from 3.26.13 to 3.27.0 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1624">codecov/codecov-action#1624</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/eslint-plugin</code> from 8.11.0 to 8.12.1 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1626">codecov/codecov-action#1626</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/eslint-plugin</code> from 8.12.1 to 8.12.2 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1629">codecov/codecov-action#1629</a></li> <li>build(deps-dev): bump <code>@typescript-eslint/parser</code> from 8.11.0 to 8.12.2 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/codecov/codecov-action/pull/1628">codecov/codecov-action#1628</a></li> </ul> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/codecov/codecov-action/commit/015f24e6818733317a2da2edd6290ab26238649a"><code>015f24e</code></a> chore(release): 5.0.7 (<a href="https://redirect.github.com/codecov/codecov-action/issues/1691">#1691</a>)</li> <li><a href="https://github.com/codecov/codecov-action/commit/a76271d95946adc3b90b6bab0bb870368626d618"><code>a76271d</code></a> fix: use HEAD_REPO (<a href="https://redirect.github.com/codecov/codecov-action/issues/1690">#1690</a>)</li> <li><a href="https://github.com/codecov/codecov-action/commit/d168679d447a7d9f9917d4b26caf2cfbf080cfb4"><code>d168679</code></a> chore(release): 5.0.6 (<a href="https://redirect.github.com/codecov/codecov-action/issues/1689">#1689</a>)</li> <li><a href="https://github.com/codecov/codecov-action/commit/373fd71a645bc4bb6a527a2225d0db67206bf786"><code>373fd71</code></a> fix: update CODECOV_TOKEN and fix tokenless (<a href="https://redirect.github.com/codecov/codecov-action/issues/1688">#1688</a>)</li> <li><a href="https://github.com/codecov/codecov-action/commit/288befbd1044bd1756afb0bdae077549e0ddb31f"><code>288befb</code></a> chore(release): 5.0.5 (<a href="https://redirect.github.com/codecov/codecov-action/issues/1686">#1686</a>)</li> <li><a href="https://github.com/codecov/codecov-action/commit/7e69d37f7e784d6f57e82f0ad50ad9b1f7993974"><code>7e69d37</code></a> chore(release): wrapper-0.0.27 (<a href="https://redirect.github.com/codecov/codecov-action/issues/1685">#1685</a>)</li> <li><a href="https://github.com/codecov/codecov-action/commit/985343d70564a82044c1b7fcb84c2fa05405c1a2"><code>985343d</code></a> chore(release): 5.0.4 (<a href="https://redirect.github.com/codecov/codecov-action/issues/1682">#1682</a>)</li> <li><a href="https://github.com/codecov/codecov-action/commit/31d19009808eced04a37b82636957c08462c8a27"><code>31d1900</code></a> chore(deps): bump wrapper to 0.0.26 (<a href="https://redirect.github.com/codecov/codecov-action/issues/1681">#1681</a>)</li> <li><a href="https://github.com/codecov/codecov-action/commit/095cfe09c682a0e3d0a2d2ed15de74b77b568f20"><code>095cfe0</code></a> fix: strip out a trailing /n from input tokens (<a href="https://redirect.github.com/codecov/codecov-action/issues/1679">#1679</a>)</li> <li><a href="https://github.com/codecov/codecov-action/commit/b542d5a35cdb78f4b6ee83df70403b7fa1508ff0"><code>b542d5a</code></a> fix: add action version (<a href="https://redirect.github.com/codecov/codecov-action/issues/1678">#1678</a>)</li> <li>Additional commits viewable in <a href="https://github.com/codecov/codecov-action/compare/v4...v5">compare view</a></li> </ul> </details> <br /> [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot show <dependency name> ignore conditions` will show all of the ignore conditions of the specified dependency - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) </details> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Resolves Project-MONAI#8225. ### Description Updated brats18 classes description. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [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: Vladislav Tumko <56307628+vectorvp@users.noreply.github.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
…-MONAI#8249) Fixes Project-MONAI#8248 ### Description Update the default value of `patch_norm` to False in `SwinUNETR` to align with the default value in `SwinTransformer`. This [change](Project-MONAI@3ee4cd2#diff-04583cc0f4aed09787775eec8cece2b1fd70290799a7a3a2671353f2a3cf9af3R105) modifies the default behavior of the model https://github.com/Project-MONAI/MONAI/blob/e6cae1ced23f32feb2f42943d15b7dd49481c794/monai/networks/nets/swin_unetr.py#L960 ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Fixes Project-MONAI#8094. ### Description The Dice, Jaccard and Tversky losses in `monai.losses.dice` and `monai.losses.tversky` are modified based on [JDTLoss](https://github.com/zifuwanggg/JDTLosses/blob/master/losses/jdt_loss.py) and [segmentation_models.pytorch](https://github.com/qubvel-org/segmentation_models.pytorch/blob/main/segmentation_models_pytorch/losses/_functional.py). In the original versions, when `squared_pred=False`, the loss functions are incompatible with soft labels. For example, with a ground truth value of 0.5 for a single pixel, the Dice loss is minimized when the predicted value is 1, which is clearly erroneous. To address this, the intersection term is rewritten as $\frac{\|x\|_p^p + \|y\|_p^p - \|x-y\|_p^p}{2}$. When $p$ is 2 (`squared_pred=True`), this reformulation becomes the classical inner product: $\langle x,y \rangle$. When $p$ is 1 (`squared_pred=False`), the reformulation has been proven to retain equivalence with the original versions when the ground truth is binary (i.e. one-hot hard labels). Moreover, since the new versions are minimized if and only if the prediction is identical to the ground truth, even when the ground truth include fractional numbers, they resolves the issue with soft labels [1, 2]. In summary, there are three scenarios: * [Scenario 1] $x$ is nonnegative and $y$ is binary: The new versions are the same as the original versions. * [Scenario 2] Both $x$ and $y$ are nonnegative: The new versions differ from the original versions. The new versions are minimized if and only if $x=y$, while the original versions may not, making them incorrect. * [Scenario 3] Either $x$ or $y$ is negative: The new versions differ from the original versions. The new versions are minimized if and only if $x=y$, while the original versions may not, making them incorrect. Due to these differences, particularly in Scenarios 2 and 3, some tests fail with the new versions: * The target is non-binary: `test_multi_scale` * The input is negative: `test_dice_loss`, `test_tversky_loss`, `test_generalized_dice_loss`, `test_masked_loss`, `test_seg_loss_integration` The failures in `test_multi_scale` are expected since the original versions are incorrectly defined for non-binary targets. Furthermore, because Dice, Jaccard, and Tversky losses are fundamentally defined over probabilities—which should be nonnegative—the new versions should not be tested against negative input or target values. ### Example ``` import torch import torch.linalg as LA import torch.nn.functional as F torch.manual_seed(0) b, c, h, w = 4, 3, 32, 32 dims = (0, 2, 3) pred = torch.rand(b, c, h, w).softmax(dim=1) soft_label = torch.rand(b, c, h, w).softmax(dim=1) hard_label = torch.randint(low=0, high=c, size=(b, h, w)) one_hot_label = F.one_hot(hard_label, c).permute(0, 3, 1, 2).float() def dice_old(x, y, ord, dims): cardinality = LA.vector_norm(x, ord=ord, dim=dims) ** ord + LA.vector_norm(y, ord=ord, dim=dims) ** ord intersection = torch.sum(x * y, dim=dims) return 2 * intersection / cardinality def dice_new(x, y, ord, dims): cardinality = LA.vector_norm(x, ord=ord, dim=dims) ** ord + LA.vector_norm(y, ord=ord, dim=dims) ** ord difference = LA.vector_norm(x - y, ord=ord, dim=dims) ** ord intersection = (cardinality - difference) / 2 return 2 * intersection / cardinality print(dice_old(pred, one_hot_label, 1, dims), dice_new(pred, one_hot_label, 1, dims)) print(dice_old(pred, soft_label, 1, dims), dice_new(pred, soft_label, 1, dims)) print(dice_old(pred, pred, 1, dims), dice_new(pred, pred, 1, dims)) print(dice_old(pred, one_hot_label, 2, dims), dice_new(pred, one_hot_label, 2, dims)) print(dice_old(pred, soft_label, 2, dims), dice_new(pred, soft_label, 2, dims)) print(dice_old(pred, pred, 2, dims), dice_new(pred, pred, 2, dims)) # tensor([0.3345, 0.3310, 0.3317]) tensor([0.3345, 0.3310, 0.3317]) # tensor([0.3321, 0.3333, 0.3350]) tensor([0.8680, 0.8690, 0.8700]) # tensor([0.3487, 0.3502, 0.3544]) tensor([1., 1., 1.]) # tensor([0.4921, 0.4904, 0.4935]) tensor([0.4921, 0.4904, 0.4935]) # tensor([0.9489, 0.9499, 0.9503]) tensor([0.9489, 0.9499, 0.9503]) # tensor([1., 1., 1.]) tensor([1., 1., 1.]) ``` ### References [1] Dice Semimetric Losses: Optimizing the Dice Score with Soft Labels. Zifu Wang, Teodora Popordanoska, Jeroen Bertels, Robin Lemmens, Matthew B. Blaschko. *MICCAI 2023*. [2] Jaccard Metric Losses: Optimizing the Jaccard Index with Soft Labels. Zifu Wang, Xuefei Ning, Matthew B. Blaschko. *NeurIPS 2023*. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [x] In-line docstrings updated. - [x] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Zifu Wang <zifuwang94@gmail.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Fixes Project-MONAI#8251 Remove `indexing="ij"` will not affect anything since it's default behavior in torch. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Project-MONAI#8419) The full error message was: `monai.utils.module.OptionalImportError: required package `openslide` is not installed or the version doesn't match requirement.` More details in: Project-MONAI/tutorials#1949 ### 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).
### Description Based on the changes in: Project-MONAI/model-zoo#739 All model zoo bundles are updated a new version in HuggingFace. Therefore, `_get_latest_bundle_version_monaihosting` should be updated accordingly ### 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>
Fixes Project-MONAI#8056. ### Description This fixes a race condition where the `tracing` member may be toggled in multiple threads. This is turned into a thread-local value that removes this 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). - [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: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…oject-MONAI#8325) ### Description when include_fc = False, the nn.Linear layer is unused. This leads to errors and warning when training with the pytorch Distributed Data Parallel infrastructure, since the parameters for the nn.Linear layer will not have gradients attached. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: John Zielke <j.l.zielke@gmail.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
workaround for Project-MONAI#8439 ### Description This PR temporarily restricts the setuptools version to 79.0.1 to maintain compatibility with our current setup. In future updates, we need to review and update our setup configurations to accommodate later versions of setuptools. ### 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> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
Fixes: Update cosine noise scheduling
### Description
In the current DDPMScheduler implementation, using the `cosine` noise
schedule results in a division-by-zero issue during sampling.
Specifically, `scheduler.alphas_cumprod[0] == 1.0`, which causes NaN
values in the output image.
You can reproduce the issue with the following snippet:
```python
from monai.inferers import DiffusionInferer
from monai.networks.nets import DiffusionModelUNet
from monai.networks.schedulers import DDPMScheduler
import torch
N = 250
device = 'cuda'
model = DiffusionModelUNet(
spatial_dims=3,
in_channels=1,
out_channels=1,
channels=[64, 64, 128],
attention_levels=[False, False, True],
num_head_channels=[0, 0, 128],
num_res_blocks=2,
).to(device)
scheduler = DDPMScheduler(num_train_timesteps=N, schedule="cosine").to(device)
print(scheduler.alphas_cumprod[0])
inferer = DiffusionInferer(scheduler)
scheduler.set_timesteps(num_inference_steps=N)
noise = torch.randn((1, 1, 32, 40, 32))
noise = noise.to(device)
image = inferer.sample(input_noise=noise, diffusion_model=model, scheduler=scheduler)
assert torch.isfinite(image).any(), "Image has NaN values"
```
### Fix
This PR applies clipping to the beta values first and re-computes
alphas_cumprod accordingly before returning in
`monai/networks/schedulers/scheduler.py: 112`. This ensures numerical
stability during sampling and prevents NaNs in the output.
### 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: Slava Shen <shen9910@gmail.com>
Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
remove deprecated functionality Part of Project-MONAI#8421 ### Description Removed Functionality: - metrics: Removed `compute_percent_hausdorff_distance`. Use `compute_hausdorff_distance` with the `percentile` argument instead. - bundle: Removed `net_name`, `net_kwargs`, and `return_state_dict` arguments from `load()`. Use the `model` argument for network instantiation. - bundle: Removed `workflow` argument from `BundleWorkflow` and `ConfigWorkflow`. Use `workflow_type` instead. - networks: Removed `img_size` argument from `SwinUNETR`. Input size checks are now performed during `forward()`. Default Value Changes: - `GeneralizedDiceScore`: Changed default `reduction` from `MEAN_BATCH` to `MEAN`. - `CropForeground` / `CropForegroundd`: Changed default `allow_smaller` from `True` to `False`. - `get_mask_edges`: Changed default `always_return_as_numpy` from `True` to `False`. - `generate_spatial_bounding_box`: Changed default `allow_smaller` from `True` to `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`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: 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>
…-MONAI#8446) Fixes # . ### Description The current default overlap (0.25) in OcclusionSensitivity produces severe grid artifacts that render visualizations unusable in most cases（Project-MONAI#8428,the 3d_classification/densenet_training_array.ipynb were created with the previous implementation(0.7.0) using stride=1 but not sliding_window）.The current default prioritizes performance at the expense of basic functionality. Since a visualization tool with unusable default output fails its primary purpose, changing the default is more appropriate than requiring users to modify tutorials or discover the correct parameter values. refernce in tutorials（v.0.7.0):  0.25 overleap (v.1.4):  0.6 overleap:  0.9 overleap:  I think a setting of 0.99 is closer to the paper and the previous implementation of stride=1, but a setting of 0.6 would be able to have a nice visual effect with a relatively small amount of computation I couldn't find a machine that could run version 0.7, so the reference images are the ones that came with the notes rather than the ones I ran, so the heatmaps may not look 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). - [ ] 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: Tiexin Li <Tiexin.Li21@student.xjtlu.edu.cn>
Fixes Project-MONAI#8444 ### Description Some of the docstrings in AutoencoderKL, Encoder and Decoder within autoencoderkl.py and some of the errors related to argument "channels" make reference to "num_channels" instead. ### 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. - [X] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Virginia Fernandez <virginia.fernandez@kcl.ac.uk> Co-authored-by: Virginia Fernandez <virginia.fernandez@kcl.ac.uk> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
…I#8454) Fixes Project-MONAI#8453 ### Description Remove deprecated `return_state_dict ` in bundle `load` ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
…t-MONAI#8402) Fixes Project-MONAI#7290. ### Description Enable code coverage on PR checks on file diff. ### 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: Christopher Le <locvicvn1234@gmail.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
### Description This PR resolves the deprecation warnings of the `logger` library: ```python DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead ``` ### 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: Emmanuel Ferdman <emmanuelferdman@gmail.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Addresses Project-MONAI#8303. ### Description This adds language in the README.md file stating the support policy. There's a few things needing updating in documents that I've added as well. I've explicitly not mentioned versions of libraries in the README.md so that this doesn't go out of date, and just stated the update policy time window of support. ### 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: Eric Kerfoot <eric.kerfoot@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Fixes Project-MONAI#8453 ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Fixes Project-MONAI#8448 ### Description Classifier-free guidance scale can be used in the sampling methods of diffusion models to strengthen the conditioning. It's been used in one of the generative MONAI tutorials, but the actual Inferers (DiffusionInferer, and ControlNetDiffusionInferer) do not support this feature. This means that, whenever users want to use CFG, they have to either copy the Inferer object or write their own sampling method. This PR incorporates classifier-free guidance into the inferer objects by modifying their sampling method and adding an argument cfg to the sampling method to control this. This should not change the default behaviour (cfg=None), although some rewriting has been necessary. ### 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 (to test_controlnet_inferers.py, test_diffusion_inferer.py and test_latent_diffusion_inferer.py). - [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. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Virginia Fernandez <virginia.fernandez@kcl.ac.uk> Co-authored-by: Virginia Fernandez <virginia.fernandez@kcl.ac.uk> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Virginia Fernandez <virginia.fernandez.kcl.ac.uk>
Fixes Project-MONAI#8453 ### Description Remove unused test cases in bundle load. https://github.com/Project-MONAI/MONAI/pull/8454/files#diff-5ad63db6f47bac69cb323c9d466ac0d8b86c9614cb7a96b9d69235feaa1c83d7 ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
### Description This adds the CODEOWNERS file to the repo to automatically requests reviews from people who are responsible for parts of MONAI. This is currently just the code team but others who have had a hand in specific parts should be added so that it's clear who could be requested to comment or review on specialised topics. ### 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@gmail.com> Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Adresses the changelog item in Project-MONAI#8421. ### Description This adds information to the changelog about what was done for 1.5. ### 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: Eric Kerfoot <eric.kerfoot@gmail.com> 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>
Addresses Project-MONAI#8421. ### Description This updates Colab links and adds a LinkedIn link for the MONAI page. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
Fixes Project-MONAI#8479 ### Description A few sentences describing the changes proposed in this pull request. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Fixes Project-MONAI#8482. ### Description This replaces broken URLs or removes them entirely. Two URLs which are not fixed relate to the `RandSmoothDeform` images in the `DocImages` repository, these aren't present so need to be generated later. ### 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: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
This PR fixes the issue with ZarrAvgMerger when using zarr v3, where the compressor argument is not supported. Changes: - Added deprecated_arg decorator for compressor, value_compressor, and count_compressor (since 1.5.0, to be removed in 1.7.0) - Added codecs, value_codecs, and count_codecs support for zarr format 3 - Updated tests to handle both zarr v2 and zarr v3 compatibility - Fixed issue where tests would fail with zarr v3 due to compressor usage This addresses the issue reported in Project-MONAI#8476 where using compressor with zarr v3 causes ValueError. Signed-off-by: kolasaniv1996 <kolasaniv1996@github.com> --------- Signed-off-by: kolasaniv1996 <kolasaniv1996@users.noreply.github.com> Signed-off-by: vivek kolasani <92003218+kolasaniv1996@users.noreply.github.com> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: kolasaniv1996 <kolasaniv1996@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Part of Project-MONAI#8421 ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
…MONAI#8504) Fixes Project-MONAI#8503. ### Description Added custom timeout for `cron-conda` job of the `cron-conda` workflow based on historical data. ### More details Over the last 633 successful runs, the `cron-conda` job has a maximum runtime of 40 minutes (mean=23, std=2) across all matrix combinations. However, there are failed runs that fail after reaching the threshold of 6 hours that GitHub imposes. In other words, these jobs seem to get stuck, possibly for external or random reasons. One such example is [this](https://github.com/Project-MONAI/MONAI/actions/runs/14507295168/job/40698965737) job run, that failed after 6 hours. More stuck jobs have been observed over the last six months, the first one on 11-Jan-2025 and the last one one on 17-Apr-2025, while more recent occurences are also possible because our dataset has a cutoff date around late May. With the proposed changes, a total of **145 hours would have been saved** over the last six months retrospectively, clearing the queue for other workflows and **speeding up the CI** of the project, while also **saving resources** in general 🌱. The idea is to set a timeout to stop jobs that run much longer than their historical maximum, because such jobs are probably stuck and will simply fail with a timeout at 6 hours. Our PR proposes to set the timeout to `max + 3*std = 46 minutes` where `max` and `std` (standard deviation) are derived from the history of 633 successful runs. This will provide sufficient margin if the workflow gets naturally slower in the future, but if you would prefer lower/higher threshold we would be happy to do it. Note that the timeout applies to all the matrix jobs, and not to their sum, overriding the default 6-hour timeout of github. ### Context Hi, We are a team of [researchers](https://www.ifi.uzh.ch/en/zest.html) from University of Zurich and we are currently working on energy optimizations in GitHub Actions workflows. Thanks for your time on this. Feel free to let us know (here or in the email below) if you have any questions, and thanks for putting in the time to read this. Best regards, [Konstantinos Kitsios](https://www.ifi.uzh.ch/en/zest/team/konstantinos_kitsios.html) konstantinos.kitsios@uzh.ch A few sentences describing the changes proposed in this pull request. ### Types of changes - [x] Non-breaking change (fix or new feature that would not break existing functionality). <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Chores** * Set a 46-minute timeout for the scheduled Conda workflow to improve reliability. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Signed-off-by: Konstantinos <konstantinos.kitsios@uzh.ch>
Fixes Project-MONAI#8492 ### Description This PR adds support for `**kwargs` in the `ResizeWithPadOrCrop` transform to fix the issue where extra keyword arguments were ignored, causing errors in some workflows. ### 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. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **New Features** * Enhanced zoom functionality to support additional parameters, allowing for greater flexibility in image transformation operations. * **Refactor** * Improved handling of optional arguments in zoom-related transformations for more customizable behavior. <!-- end of auto-generated comment: release notes by coderabbit.ai --> Signed-off-by: IamTingTing <6121smile@gmail.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
…MONAI#8494) ### Description This PR adds a very aesthetic number of citations (_that updates dynamically according to the research paper_) to the README.md of the repo. See how it looks below: - Before:  [](https://opensource.org/licenses/Apache-2.0) [](https://badge.fury.io/py/monai) [](https://hub.docker.com/r/projectmonai/monai) [](https://anaconda.org/conda-forge/monai) - After:  [](https://opensource.org/licenses/Apache-2.0) [](https://arxiv.org/abs/2211.02701) [](https://badge.fury.io/py/monai) [](https://hub.docker.com/r/projectmonai/monai) [](https://anaconda.org/conda-forge/monai) ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] 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: Mauro I. Dominguez <mau_igna_06@hotmail.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
### Description This adds the configuration file for CodeRabbit for us to look at and decide what to enable/disable. ### 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> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Mingxin Zheng <mingxinz@nvidia.com>
](https://opensource.org/licenses/Apache-2.0){kind=link}
](https://badge.fury.io/py/monai){kind=link}
](https://hub.docker.com/r/projectmonai/monai){kind=link}
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
20 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Fixes # .
Description
A few sentences describing the changes proposed in this pull request.
Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests --disttests.make htmlcommand in thedocs/folder.