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Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
* bc nonbreaking tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> * compatible collate Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds flag Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes min tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * integration Signed-off-by: Wenqi Li <wenqil@nvidia.com> * default to metatensor Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update baesd on comments, refactoring, more tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * debug typing Signed-off-by: Wenqi Li <wenqil@nvidia.com> * debug typing Signed-off-by: Wenqi Li <wenqil@nvidia.com> * debug typing Signed-off-by: Wenqi Li <wenqil@nvidia.com> * simplify, more tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * multisamples cropping Signed-off-by: Wenqi Li <wenqil@nvidia.com> * simplified utilities, docstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * exclude in min Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* Create meaniou.py Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * Create test_compute_meaniou.py Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * Update __init__.py Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * Update metrics.rst Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * Update test_compute_meaniou.py Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * Update meaniou.py Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * Update metrics.rst Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * Update __init__.py Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * Update meaniou.py Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * Update test_compute_meaniou.py Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * Update metrics.rst Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * Update test_compute_meaniou.py Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * Update test_compute_meaniou.py Signed-off-by: Yashika Jain <yashikajain201@gmail.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>
* fixes shape fallback Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes #4655 Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* [DLMED] enhance metrics doc with example Signed-off-by: Nic Ma <nma@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* fixes pad-collate Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* blend_images: voxel-wise alpha Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * linting is wrong Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fixes Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
* enhance verify metadata and dynunet docstring Signed-off-by: Yiheng Wang <vennw@nvidia.com> * reverse dynunet changes and fix flake8 error Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix flake8 error Signed-off-by: Yiheng Wang <vennw@nvidia.com>
[DLMED] fix collate issue Signed-off-by: Nic Ma <nma@nvidia.com>
* adds __array_function__ impl. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update ufunc Signed-off-by: Wenqi Li <wenqil@nvidia.com> * pt1.7 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typo Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * more checking Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* mri utils added Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fft_utils with its unit test added Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fft_utils updated with monai data converter Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * updated fft_util's docstring Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * apps.rst updated with fft_utils docstrings under the reconstruction module Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fft_utils docstring updated by adding dimension hins Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fft_utils docstring updated by removing redundant output type Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * test_fft_utils.py moved to the tests folder Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * created fft_utils_t, the torch-only version of fft_utils Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fft_utils_t updated with type ignore for mypy Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * docs/source/networks.rst updated with fft_utils_t Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * manual fix for fft_utils_t output data types Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * initial mri_transforms added under apps/reconstruction Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * with PR1 files to avoid error Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * PR1 included Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * PR1 files finally removed Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * putting test_mri_transforms under apps for now Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * isort fixed Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * ignore this commit, still in progress Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * created utils, array, and dictionary; still a very early-stage commit Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * completing transform arrays and dicts plus mri_utils and the unit tests Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * move tests under apps for now Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed docs and tests Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * added unittests for DetailedNormalizeIntensityd and TargetBasedSpatialCropd and fixed unbiased issue of torch.std Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed random seed; added enum keys; corrected docs format; corrected typos Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * rss name corrected Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * minor issues fixed; todos are __init__ and decide upon randomize Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * added __init__ Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed file names Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * added more notes to InputTargetNormalizeIntensity Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * added more clarifications to InputTargetNormalizeIntensityd Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * made ReferenceBasedNormalizeIntensityd and ReferenceBasedSpatialCropd consistent with other monai transforms Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * minor updates to kspace masks Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * new utils added: complex_mul and complex_conj Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * mypy issue with mri_utils unittest resolved Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * a separate PR for mri_utils Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * minor update to enum keys Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * minor docstring fix Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * separated complex utils Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * docs updated Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * docs updated Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * compelx_utils docstring updated Signed-off-by: mersad95zd <m.zalbagi@gmail.com> Co-authored-by: Can Zhao <69829124+Can-Zhao@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>
* mri utils added Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fft_utils with its unit test added Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fft_utils updated with monai data converter Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * updated fft_util's docstring Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * apps.rst updated with fft_utils docstrings under the reconstruction module Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fft_utils docstring updated by adding dimension hins Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fft_utils docstring updated by removing redundant output type Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * test_fft_utils.py moved to the tests folder Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * created fft_utils_t, the torch-only version of fft_utils Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fft_utils_t updated with type ignore for mypy Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * docs/source/networks.rst updated with fft_utils_t Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * manual fix for fft_utils_t output data types Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * initial mri_transforms added under apps/reconstruction Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * with PR1 files to avoid error Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * PR1 included Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * PR1 files finally removed Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * putting test_mri_transforms under apps for now Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * isort fixed Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * ignore this commit, still in progress Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * created utils, array, and dictionary; still a very early-stage commit Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * completing transform arrays and dicts plus mri_utils and the unit tests Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * move tests under apps for now Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed docs and tests Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fast-mri-reader initial commit; todo is the unittest Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * unittest added Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * remove unncessary packages from the reader Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * manual installation of h5py added Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * enum keys added Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * h5py added to requirements-dev.txt Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * optional import of h5py Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed h5py dependency Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed h5py dependency again Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed docstring; fixed import issue Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * added h5py to relevant requirement files; updated fastmri_reader Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * docs updated Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed os.path.basename Signed-off-by: mersad95zd <m.zalbagi@gmail.com> Co-authored-by: Can Zhao <69829124+Can-Zhao@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* get/set array Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes flake8 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com> * more tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes flake8 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update according to comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes #4699 Signed-off-by: Wenqi Li <wenqil@nvidia.com>
…support 0.9.1* (#4692) * Fix nuclick transform for meta tensor Signed-off-by: SACHIDANAND ALLE <sachidanand.alle@gmail.com> * Fix deepgrow transform for metatensor Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com>
* fixes swinunetr Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * less changes Signed-off-by: Wenqi Li <wenqil@nvidia.com> * review docs Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* preserve key order Signed-off-by: KumoLiu <yunl@nvidia.com> * fixes integration Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>
* fixes #4708 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * shallow copy Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update device affine Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update copy Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* update indexing methods Signed-off-by: Wenqi Li <wenqil@nvidia.com> * review attributes Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* using copy() Signed-off-by: Wenqi Li <wenqil@nvidia.com> * simple copy attr Signed-off-by: Wenqi Li <wenqil@nvidia.com> * simple copy Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update util Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update default Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update data converting to have is_batch Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update attr copying Signed-off-by: Wenqi Li <wenqil@nvidia.com> * refactoring Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typo Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove deepcopy Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * shape different assign Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* fix deepedit/nuclick transforms for metatensor Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com>
[DLMED] add update API for config parser Signed-off-by: Nic Ma <nma@nvidia.com>
* Add TCIA dataset Signed-off-by: Yiheng Wang <vennw@nvidia.com>
* dataset summary for metatensor Signed-off-by: Wenqi Li <wenqil@nvidia.com> * dataset summary support metatensor Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* fix metatensor for detection Signed-off-by: Can Zhao <canz@nvidia.com> * fix mypy Signed-off-by: Can Zhao <canz@nvidia.com>
* update detection transforms for metatensor Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes mypy Signed-off-by: Wenqi Li <wenqil@nvidia.com> * more tests about applied operations Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* optional final Tanh Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update param name Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* add user warnings in AsChannelFirst and AddChannel Signed-off-by: KumoLiu <yunl@nvidia.com> * change warning to deprecated Signed-off-by: KumoLiu <yunl@nvidia.com> * change since0.9 to 0.8 Signed-off-by: KumoLiu <yunl@nvidia.com> * add use MetaTensor data type Signed-off-by: KumoLiu <yunl@nvidia.com> * fix pep8 Signed-off-by: KumoLiu <yunl@nvidia.com>
* support block type string in resnet, senet Signed-off-by: KumoLiu <yunl@nvidia.com> * fix docstring Signed-off-by: KumoLiu <yunl@nvidia.com> * fix docstring in resnet Signed-off-by: KumoLiu <yunl@nvidia.com> Co-authored-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com>
* [DLMED] add track_meta option Signed-off-by: Nic Ma <nma@nvidia.com>
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>
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>
Signed-off-by: Wenqi Li <wenqil@nvidia.com> part of #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>
Fixes #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>
…ai.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>
### 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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
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>
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>
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>
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>
…5208) Signed-off-by: Wenqi Li <wenqil@nvidia.com> Fixes #5206 ### Description changes to `EnsureChannelFirst` so that the input `channel_dim` has a higher priority than `metatensor.meta['original_channel_dim']` ### Types of changes <!--- Put an `x` in all 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>
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>
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>
…ey()` 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>
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>
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>
…les (#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>
### 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>
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Fixes # .
Description
A few sentences describing the changes proposed in this pull request.
Status
Ready/Work in progress/Hold
Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests --disttests.make htmlcommand in thedocs/folder.