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 <[email protected]> * [DLMED] add more random test Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

…gLabel (#3129) Signed-off-by: Richard Brown <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

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

* upgrade torch image to 2109 Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * more time for fast training Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit a5b4447. Signed-off-by: Wenqi Li <[email protected]>

* add griddistortion Signed-off-by: Yiheng Wang <[email protected]> * [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 <[email protected]> * add unittest Signed-off-by: Yiheng Wang <[email protected]> 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 <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

* update rand grid distortion Signed-off-by: Wenqi Li <[email protected]> * update docs Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * fixes formatting and errors Signed-off-by: Wenqi Li <[email protected]>

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

Signed-off-by: Nic Ma <[email protected]>

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

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

* temp tests Signed-off-by: Wenqi Li <[email protected]> * adds doker Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * check branches Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * fixes cmp Signed-off-by: Wenqi Li <[email protected]> * remove temp tests Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] add tutorial link Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] update spacing and orientation transforms Signed-off-by: Nic Ma <[email protected]> * [DLMED] update others Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix test Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

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

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

* revise docstrings Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * fixes windows tests Signed-off-by: Wenqi Li <[email protected]>

* adds util logger Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add scale_datalist Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* [DLMED] add utitlity Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI for old PyTorch Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI issue Signed-off-by: Nic Ma <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

) * Torch `BoundingRect`, `FillHoles`, VoteEnsemble` Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * skip test_fill_holesd Signed-off-by: Richard Brown <[email protected]> * merge fix Signed-off-by: Richard Brown <[email protected]> * fixes Signed-off-by: Richard Brown <[email protected]> * np->np/pt->pt Signed-off-by: Richard Brown <[email protected]> * no type check Signed-off-by: Richard Brown <[email protected]> * return ndarrayortensor Signed-off-by: Richard Brown <[email protected]> * MeanEnsemble Signed-off-by: Richard Brown <[email protected]>

* [DLMED] add preparebatch Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix min tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix min tests Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add backend Signed-off-by: Nic Ma <[email protected]> * [DLMED] add backend Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix PyTorch 1.5.1 test Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more tests Signed-off-by: Nic Ma <[email protected]> * [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 <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* squeeze non-spatial dims in nib-reader Signed-off-by: Bryn Lloyd <[email protected]> * fix: add squeeze_non_spatial_dims=False option Signed-off-by: Bryn Lloyd <[email protected]> * fix: add docstring for arg Signed-off-by: Bryn Lloyd <[email protected]> * fix: add docstring for arg Signed-off-by: Bryn Lloyd <[email protected]> * fix: typos Signed-off-by: Bryn Lloyd <[email protected]> Co-authored-by: Bryn Lloyd <[email protected]>

* support stack of images with channels Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

… is 0 (#3690) * [DLMED] check 0 length Signed-off-by: Nic Ma <[email protected]> * [DLMED] add dist tests Signed-off-by: Nic Ma <[email protected]>

* remove tensor-array convertions Signed-off-by: Wenqi Li <[email protected]> * update backend Signed-off-by: Wenqi Li <[email protected]> * update tests, remove meshgrid warnings Signed-off-by: Wenqi Li <[email protected]> * fixes typing issue Signed-off-by: Wenqi Li <[email protected]> * fixes import Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] update ignite to 0.4.8 Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix format issue Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

* add dev mode collate Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

* add benchmarking warp against python itk Signed-off-by: kate-sann5100 <[email protected]>

* fix differentiability of generalized Dice loss Signed-off-by: Josafat-Mattias Burmeister <[email protected]> * fix weight clamping for the case that is True Signed-off-by: Josafat-Mattias Burmeister <[email protected]> * add test case for batch mode Co-authored-by: Wenqi Li <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

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

Signed-off-by: Nic Ma <[email protected]>

* fixes grid_sample, interpolate URLs Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

* add non-determinism tips Signed-off-by: Yiheng Wang <[email protected]> * fix the name error Signed-off-by: Yiheng Wang <[email protected]>

Signed-off-by: Richard Brown <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

* fixes test Signed-off-by: Wenqi Li <[email protected]> * skip when downloading fails Signed-off-by: Wenqi Li <[email protected]>

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

* ignore 60.6.0 Signed-off-by: Wenqi Li <[email protected]> * workaround #3752 Signed-off-by: Wenqi Li <[email protected]> * fixes windows issue Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] update to 22.01 Signed-off-by: Nic Ma <[email protected]> * [DLMED] update environment Signed-off-by: Nic Ma <[email protected]>

* update unit tests intensity range percentiles Signed-off-by: Wenqi Li <[email protected]> * fixes channel wise tests Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] add HashCacheDataset Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more test Signed-off-by: Nic Ma <[email protected]> * [DLMED] skip min test Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* [DLMED] refine TTA Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance TTA Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] refine example in doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * add to optimize tta Signed-off-by: Richard Brown <[email protected]> * update Signed-off-by: Richard Brown <[email protected]> * .item for np.ndarray too Signed-off-by: Richard Brown <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Richard Brown <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* [DLMED] enhance missing key error Signed-off-by: Nic Ma <[email protected]> * [DLMED] update doc Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

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

* [DLMED] fix PadListCollate issue Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

* update based on comments Signed-off-by: Wenqi Li <[email protected]> * -Wmaybe-uninitialized Signed-off-by: Wenqi Li <[email protected]>

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

* [DLMED] add check for devices Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

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 <[email protected]>

skip tests for torch 1.5 (#3131)

ff08334

Signed-off-by: Wenqi Li <[email protected]>

senet tests with testing data (#3136)

1259042

Signed-off-by: Wenqi Li <[email protected]>

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

467138f

* [DLMED] add metric example Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

[DLMED] fix data type issue (#3143)

2920dd3

Signed-off-by: Nic Ma <[email protected]>

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

4785ede

* [DLMED] add tutorial link Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]>

update based on comments (#3156)

e641722

Signed-off-by: Wenqi Li <[email protected]>

fixes #3165 (#3166)

536e056

Signed-off-by: Wenqi Li <[email protected]>

2929 revise docstrings (#3170)

ee8b981

* revise docstrings Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * fixes windows tests Signed-off-by: Wenqi Li <[email protected]>

3159 adds a default util logger (#3160)

7964d45

* adds util logger Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

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

299367e

Signed-off-by: Nic Ma <[email protected]>

3174 Add support to scale datalist (#3175)

a2027ec

* [DLMED] add scale_datalist Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

fixes url (#3183)

53b98ac

Signed-off-by: Wenqi Li <[email protected]>

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 <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

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 <[email protected]> * [DLMED] add dist tests Signed-off-by: Nic Ma <[email protected]>

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

32a045d

* add dev mode collate Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

add benchmarking warp against python itk (#3692)

3907cb4

* add benchmarking warp against python itk Signed-off-by: kate-sann5100 <[email protected]>

compiler warnings (#3698)

c2018cf

Signed-off-by: Wenqi Li <[email protected]>

try to fix #3621 (#3673)

3180c27

Signed-off-by: Wenqi Li <[email protected]>

[DLMED] fix mode issue (#3715)

927483b

Signed-off-by: Nic Ma <[email protected]>

fixes grid_sample, interpolate URLs (#3712)

0996aab

* fixes grid_sample, interpolate URLs Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

3716 enhance doc-strings of DenseNet (#3717)

8227cae

* add non-determinism tips Signed-off-by: Yiheng Wang <[email protected]> * fix the name error Signed-off-by: Yiheng Wang <[email protected]>

pip mypy (#3722)

4aa3596

Signed-off-by: Richard Brown <[email protected]>

update bbox docstring (#3724)

b1a96c5

Signed-off-by: Wenqi Li <[email protected]>

3725 fixes download test (#3728)

db61a08

* fixes test Signed-off-by: Wenqi Li <[email protected]> * skip when downloading fails Signed-off-by: Wenqi Li <[email protected]>

3750 skip setuptool 60.6 (#3751)

ba9cd45

* ignore 60.6.0 Signed-off-by: Wenqi Li <[email protected]> * workaround #3752 Signed-off-by: Wenqi Li <[email protected]> * fixes windows issue Signed-off-by: Wenqi Li <[email protected]>

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 <[email protected]> * [DLMED] update environment Signed-off-by: Nic Ma <[email protected]>

3620 intensity range percentiles (#3685)

ec5c9d5

* update unit tests intensity range percentiles Signed-off-by: Wenqi Li <[email protected]> * fixes channel wise tests Signed-off-by: Wenqi Li <[email protected]>

Update offset assign (#3764)

d050ea5

* update based on comments Signed-off-by: Wenqi Li <[email protected]> * -Wmaybe-uninitialized Signed-off-by: Wenqi Li <[email protected]>

3765 Enhance create_multigpu_supervised_XXX for distributed (#3768)

62b3f6e

* [DLMED] add check for devices Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

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

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merge master#367

merge master#367
Nic-Ma merged 352 commits intoNic-Ma:3763-enhance-num-workersfrom
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Nic-Ma commented Feb 5, 2022

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