merge master by Nic-Ma · Pull Request #367 · Nic-Ma/MONAI

Nic-Ma · 2022-02-05T01:01:01Z

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.

* [DLMED] add integration test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more random test 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>

…gLabel (#3129) Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

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

* add alias tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * monai.losses.dice Signed-off-by: Wenqi Li <wenqil@nvidia.com> * monai.utils.deprecated Signed-off-by: Wenqi Li <wenqil@nvidia.com> * monai.networks.nets.senet Signed-off-by: Wenqi Li <wenqil@nvidia.com> * monai.networks.nets.dynunet Signed-off-by: Wenqi Li <wenqil@nvidia.com> * monai.networks.nets.unet Signed-off-by: Wenqi Li <wenqil@nvidia.com> * monai.networks.nets.densenet Signed-off-by: Wenqi Li <wenqil@nvidia.com> * monai.networks.nets.ahnet Signed-off-by: Wenqi Li <wenqil@nvidia.com> * only check for the existing modules Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes docs Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* upgrade torch image to 2109 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * more time for fast training Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "temp tests" This reverts commit a5b4447. Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* add griddistortion Signed-off-by: Yiheng Wang <vennw@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix pre-commit ci black error Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add unittest Signed-off-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

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

* update rand grid distortion Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes formatting and errors Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add Tensor to CropForegroundd transform Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance data conversion Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more tests and fix convert tensor issue Signed-off-by: Nic Ma <nma@nvidia.com>

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

…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>

* support stack of images with channels Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

… is 0 (#3690) * [DLMED] check 0 length Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add dist tests Signed-off-by: Nic Ma <nma@nvidia.com>

* remove tensor-array convertions Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update backend Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update tests, remove meshgrid warnings Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typing issue Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes import 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> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] update ignite to 0.4.8 Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix format issue Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* add dev mode collate Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* add benchmarking warp against python itk Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>

* fix differentiability of generalized Dice loss Signed-off-by: Josafat-Mattias Burmeister <josafat-mattias.burmeister@student.hpi.de> * fix weight clamping for the case that is True Signed-off-by: Josafat-Mattias Burmeister <josafat-mattias.burmeister@student.hpi.de> * add test case for batch mode Co-authored-by: Wenqi Li <wenqil@nvidia.com>

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

… comma (#3711) * [DLMED] add support to config delimiter Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

Signed-off-by: Nic Ma <nma@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>

Nic-Ma and others added 30 commits October 14, 2021 23:01

allow ROIs bigger than im for RandCropByLabelClasses, RandCropByPosNe…

6155724

…gLabel (#3129) Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

skip tests for torch 1.5 (#3131)

ff08334

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

senet tests with testing data (#3136)

1259042

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

400 Add example in the doc-string of Metric (#3139)

467138f

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

[DLMED] fix data type issue (#3143)

2920dd3

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

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>

wyli and others added 29 commits January 20, 2022 01:08

support stack of images with channels (#3680)

50c201c

* support stack of images with channels Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

3686 Skip workflow run if data is empty or the specified epoch_length…

e96dcca

… is 0 (#3690) * [DLMED] check 0 length Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add dist tests Signed-off-by: Nic Ma <nma@nvidia.com>

adds a dev mode collate for diagnostic info (#3684)

32a045d

* add dev mode collate Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

add benchmarking warp against python itk (#3692)

3907cb4

* add benchmarking warp against python itk Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>

compiler warnings (#3698)

c2018cf

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

try to fix #3621 (#3673)

3180c27

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

[DLMED] fix mode issue (#3715)

927483b

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

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>

Nic-Ma merged commit 0a8dda6 into Nic-Ma:3763-enhance-num-workers Feb 5, 2022

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Nic-Ma merged 352 commits intoNic-Ma:3763-enhance-num-workersfrom
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