merge master by Nic-Ma · Pull Request #371 · Nic-Ma/MONAI

Nic-Ma · 2022-02-12T15:24:39Z

Fixes # .

Description

A few sentences describing the changes proposed in this pull request.

Status

Ready/Work in progress/Hold

Types of changes

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.
In-line docstrings updated.
Documentation updated, tested make html command in the docs/ folder.

…tatement (#3147) * Refactor unnecessary `else` / `elif` when `if` block has a `return` statement * black --skip-magic-trailing-comma Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* update versioning Signed-off-by: Wenqi Li <wenqil@nvidia.com> * build docker Signed-off-by: Wenqi Li <wenqil@nvidia.com> * install docker Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove selfhosted Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * ubuntu cpu tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * full tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * test docker options Signed-off-by: Wenqi Li <wenqil@nvidia.com> * full tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * full tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * exclude open slide tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * full tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp checkout Signed-off-by: Wenqi Li <wenqil@nvidia.com> * full tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * full tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes flake8 error Signed-off-by: Wenqi Li <wenqil@nvidia.com> * skip weights downloading when http error out Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds doker Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update Signed-off-by: Wenqi Li <wenqil@nvidia.com> * check branches Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes cmp Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add tutorial link Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com>

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] update spacing and orientation transforms Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update others Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com>

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update to torch 1.10 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes for torch 1.10 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes coverage tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * type fixes Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "temp tests" This reverts commit cb3e0c7. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes for windows Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes integration Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes #3171 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp fix windows Signed-off-by: Wenqi Li <wenqil@nvidia.com>

…3158) * [DLMED] add example in doc-string Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add example about copy_cache Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* revise docstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes windows tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* adds util logger Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] add scale_datalist Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add utitlity Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CI for old PyTorch Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CI issue Signed-off-by: Nic Ma <nma@nvidia.com>

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

) * Torch `BoundingRect`, `FillHoles`, VoteEnsemble` Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * skip test_fill_holesd Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * merge fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fixes Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * np->np/pt->pt Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * no type check Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * return ndarrayortensor Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * MeanEnsemble Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* [DLMED] add preparebatch Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix min tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix min tests Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] add backend Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add backend Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix PyTorch 1.5.1 test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more tests 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 * [MONAI] python code formatting 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> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* squeeze non-spatial dims in nib-reader Signed-off-by: Bryn Lloyd <lloyd@itis.swiss> * fix: add squeeze_non_spatial_dims=False option Signed-off-by: Bryn Lloyd <lloyd@itis.swiss> * fix: add docstring for arg Signed-off-by: Bryn Lloyd <lloyd@itis.swiss> * fix: add docstring for arg Signed-off-by: Bryn Lloyd <lloyd@itis.swiss> * fix: typos Signed-off-by: Bryn Lloyd <lloyd@itis.swiss> Co-authored-by: Bryn Lloyd <lloyd@itis.swiss>

Signed-off-by: Nic Ma <nma@nvidia.com>

remove flooring

Signed-off-by: Nic Ma <nma@nvidia.com>

* Fixes focal loss when reduction=none Signed-off-by: joncrall <jon.crall@kitware.com> * Added doctest example, fixed mypy errors Signed-off-by: joncrall <jon.crall@kitware.com> * Linting and test fixes Signed-off-by: joncrall <jon.crall@kitware.com> * Change dice loss to return broadcastable reductions Signed-off-by: joncrall <jon.crall@kitware.com> * Fixed backwards compatibility issues Signed-off-by: joncrall <jon.crall@kitware.com> * Fix masked loss test Signed-off-by: joncrall <jon.crall@kitware.com>

* [DLMED] enhance document Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com>

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* Torch `ProbNMS`, `LabelFilter` Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix test_probnmsd Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix for older pt Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] enhance the doc-string Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add shuffle Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] change to ShuffleBuffer Signed-off-by: Nic Ma <nma@nvidia.com> * update according to discussions Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [DLMED] add multi-workers support Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix docs Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] improve perf Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add metrics check Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update workflow Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add reduction Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add reduction to metric handlers Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes grid_sample, interpolate URLs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* add non-determinism tips Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix the name error Signed-off-by: Yiheng Wang <vennw@nvidia.com>

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * skip when downloading fails Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* Remove assert statement from non-test files * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* ignore 60.6.0 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * workaround #3752 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes windows issue Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] update to 22.01 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update environment Signed-off-by: Nic Ma <nma@nvidia.com>

* update unit tests intensity range percentiles Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes channel wise tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add HashCacheDataset Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] skip min test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] refine TTA Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance TTA Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] refine example in doc-string Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * add to optimize tta Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * update Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * .item for np.ndarray too Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] enhance missing key error Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update doc Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

* temp spatial_resample Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes resampling Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes precisions Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update dict version Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds docs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * copy grid for resampling Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove normalize coordinates Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * try to fix #3621 (#3673) Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typing Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes grid_sample, interpolate URLs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * simplify norm_coords Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update moveaxis Signed-off-by: Wenqi Li <wenqil@nvidia.com> * spatial sample tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * additional tests spatial resample Signed-off-by: Wenqi Li <wenqil@nvidia.com> * test invert saptial resample Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * rtol assert close Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes TF32 tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * smaller tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * skip when quick testing Signed-off-by: Wenqi Li <wenqil@nvidia.com> * comp tensor and ndarray Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * try to use torch.solve Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "fixes tests" This reverts commit e532490. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes test_affined Signed-off-by: Wenqi Li <wenqil@nvidia.com> * default to float32 rotate/randrotate Signed-off-by: Wenqi Li <wenqil@nvidia.com> * workaround for #3752 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * default to float32 rotate/randrotate Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* [DLMED] fix PadListCollate issue Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * -Wmaybe-uninitialized Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* temp spatial_resample Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes resampling Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes precisions Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update dict version Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds docs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * copy grid for resampling Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove normalize coordinates Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * try to fix #3621 (#3673) Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typing Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes grid_sample, interpolate URLs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * simplify norm_coords Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update moveaxis Signed-off-by: Wenqi Li <wenqil@nvidia.com> * spatial sample tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * additional tests spatial resample Signed-off-by: Wenqi Li <wenqil@nvidia.com> * test invert saptial resample Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * rtol assert close Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes TF32 tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * smaller tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * skip when quick testing Signed-off-by: Wenqi Li <wenqil@nvidia.com> * comp tensor and ndarray Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * try to use torch.solve Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp updates Signed-off-by: Wenqi Li <wenqil@nvidia.com> * enhance typing Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "temp test" This reverts commit 6200a38. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * enhance types Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update util Signed-off-by: Wenqi Li <wenqil@nvidia.com> * reverse workaround Signed-off-by: Wenqi Li <wenqil@nvidia.com> * formatting Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update type def. Signed-off-by: Wenqi Li <wenqil@nvidia.com> Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * warn unused Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remote ignore Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "warn unused" This reverts commit e645807. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "temp test" This reverts commit ddc4770. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* [DLMED] add check for devices Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* temp spatial_resample Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes resampling Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes precisions Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update dict version Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds docs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * copy grid for resampling Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove normalize coordinates Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * try to fix #3621 (#3673) Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typing Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes grid_sample, interpolate URLs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * simplify norm_coords Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update moveaxis Signed-off-by: Wenqi Li <wenqil@nvidia.com> * spatial sample tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * additional tests spatial resample Signed-off-by: Wenqi Li <wenqil@nvidia.com> * test invert saptial resample Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds a base writer and an itk writer Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove return self Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds reorient_spatial_axes Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * sync 3701 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * try to fix #3766 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * revise docstring to be concise Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * 3765 Enhance `create_multigpu_supervised_XXX` for distributed (#3768) * [DLMED] add check for devices Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * update to support dynamic spatial_size Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] enhance logger Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update doc Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix packaging test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] totally update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update handlers Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update tutorial link Signed-off-by: Nic Ma <nma@nvidia.com>

* temp spatial_resample Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes resampling Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes precisions Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update dict version Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds docs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * copy grid for resampling Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove normalize coordinates Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * try to fix #3621 (#3673) Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typing Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes grid_sample, interpolate URLs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * simplify norm_coords Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update moveaxis Signed-off-by: Wenqi Li <wenqil@nvidia.com> * spatial sample tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * additional tests spatial resample Signed-off-by: Wenqi Li <wenqil@nvidia.com> * test invert saptial resample Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds a base writer and an itk writer Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove return self Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds reorient_spatial_axes Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * sync 3701 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * try to fix #3766 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * revise docstring to be concise Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * 3765 Enhance `create_multigpu_supervised_XXX` for distributed (#3768) * [DLMED] add check for devices Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * update to support dynamic spatial_size Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds nibabel pil writers Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove unused ignore Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add save_state utility Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add atomic and func Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] refactor saving logic Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] restore persistent dataset Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] simplify kwargs Signed-off-by: Nic Ma <nma@nvidia.com>

* make vit support torchscript Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add torch version restriction Signed-off-by: Yiheng Wang <vennw@nvidia.com> * change skip decorator order Signed-off-by: Yiheng Wang <vennw@nvidia.com> * remove extra cls Signed-off-by: Yiheng Wang <vennw@nvidia.com>

…g_saver/writer (#3773) * update saveimage and writer selector Signed-off-by: Wenqi Li <wenqil@nvidia.com> * more tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * more tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds saving loading tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes #3783 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * enhance import checks Signed-off-by: Wenqi Li <wenqil@nvidia.com> * warn to exception; int check Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes #3787 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * unit testing Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* update largest cc function Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * update largest cc function Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update largest cc function Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * update largest cc function Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * update largest cc function Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * update largest cc function Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update largest cc function Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update largest cc function Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * update largest cc function Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * update largest cc function Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * update largest cc function Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * update largest cc function Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * update repo Signed-off-by: dongy <dongy@nvidia.com> Co-authored-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: dongy <dongy@nvidia.com>

deepsource-autofix Bot and others added 30 commits October 19, 2021 17:26

Add tutorial link to doc-string of handlers (#3150)

4785ede

* [DLMED] add tutorial link Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com>

update based on comments (#3156)

e641722

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

fixes #3165 (#3166)

536e056

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

2929 revise docstrings (#3170)

ee8b981

* revise docstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes windows tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>

3159 adds a default util logger (#3160)

7964d45

* adds util logger Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

[DLMED] add link and update chart (#3179)

299367e

Signed-off-by: Nic Ma <nma@nvidia.com>

3174 Add support to scale datalist (#3175)

a2027ec

* [DLMED] add scale_datalist Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

fixes url (#3183)

53b98ac

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

[DLMED] fix iteration bug (#3202)

c877001

Signed-off-by: Nic Ma <nma@nvidia.com>

2755 fix bug (#3196)

95ed167

remove flooring

[DLMED] add param at runtime (#3205)

11ff52a

Signed-off-by: Nic Ma <nma@nvidia.com>

3210 Fix misleading document in the Torchvision netadapter (#3211)

d932c5a

* [DLMED] enhance document Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com>

minor typo fixes (#3209)

a7bc776

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

remove used param (#3206)

f43a927

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

fixes iterable tests (#3221)

ec479d5

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

wyli and others added 29 commits January 26, 2022 11:55

fixes grid_sample, interpolate URLs (#3712)

0996aab

* fixes grid_sample, interpolate URLs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

3716 enhance doc-strings of DenseNet (#3717)

8227cae

* add non-determinism tips Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix the name error Signed-off-by: Yiheng Wang <vennw@nvidia.com>

pip mypy (#3722)

4aa3596

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

update bbox docstring (#3724)

b1a96c5

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

3725 fixes download test (#3728)

db61a08

* fixes test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * skip when downloading fails Signed-off-by: Wenqi Li <wenqil@nvidia.com>

3750 skip setuptool 60.6 (#3751)

ba9cd45

* ignore 60.6.0 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * workaround #3752 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes windows issue Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Update installation.md (#3758)

19d5d8d

3753 Update PyTorch base docker to 22.01 (#3754)

e0643ab

* [DLMED] update to 22.01 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update environment Signed-off-by: Nic Ma <nma@nvidia.com>

3620 intensity range percentiles (#3685)

ec5c9d5

* update unit tests intensity range percentiles Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes channel wise tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>

3747 Enhance errors and docs according to Youtube feedback (#3759)

6c75550

* [DLMED] enhance missing key error Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update doc Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

Update offset assign (#3764)

d050ea5

* update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * -Wmaybe-uninitialized Signed-off-by: Wenqi Li <wenqil@nvidia.com>

3765 Enhance create_multigpu_supervised_XXX for distributed (#3768)

62b3f6e

* [DLMED] add check for devices Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

3763 Enhance the doc of ThreadDataLoader for num_workers (#3770)

b61db79

update blossom config (#3771)

fa066fb

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

revert workaround (#3778)

3c96cb8

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

[DLMED] add default value (#3785)

e3a9730

Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

Nic-Ma merged commit 419e9aa into Nic-Ma:3795-ensure-channel-first Feb 12, 2022

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Nic-Ma merged 363 commits intoNic-Ma:3795-ensure-channel-firstfrom
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