merge master by Nic-Ma · Pull Request #148 · Nic-Ma/MONAI

Nic-Ma · 2021-06-25T03:41:37Z

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 --codeformat --coverage.
Quick tests passed locally by running ./runtests.sh --quick.
In-line docstrings updated.
Documentation updated, tested make html command in the docs/ folder.

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

* [DLMED] add EarlyStop handler Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] enhance validation handler Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add set_trainer support Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more check Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue 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] change to save patch_index in meta_dict Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove error import Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix CI tests Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* Enabled partial checkpoint loading Allowing partial loading of a model via strict=False. Signed-off-by: Petru-Daniel Tudosiu <petru.daniel@tudosiu.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] simplify strict arg Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Nic Ma <nma@nvidia.com>

* less warning msg; remove PILImage types Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove engine type Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * add quick py36 37 tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "temp tests" This reverts commit deaed40. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "temp tests" This reverts commit 3e8d8f4. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * min test exclude senet test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "temp test" This reverts commit 31f40a0. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update get gpu id Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docsstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* Add ProbNMS to transforts/post/array Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Implement ProbNMSDict Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update the usage and add unittests Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update docs Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Correct docs Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Correct test case Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

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

* Implement garbage collector handler Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Make trigger_event lower case Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add unittest for garbage collector Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update docs Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Exclude from min test Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Fix a typo Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Fix a bug Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

* [DLMED] add strict_shape option Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * update test case Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes test config Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] enhance decathlon datalist Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

* adds docker tag action Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds tag info Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update versioneer Signed-off-by: Wenqi Li <wenqil@nvidia.com>

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

* refactor docker building Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update docs deps. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes https://github.com/Project-MONAI/MONAI/runs/2283148095\?check_suite_focus\=true\#step:7:8972 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "fixes https://github.com/Project-MONAI/MONAI/runs/2283148095\?check_suite_focus\=true\#step:7:8972" This reverts commit 1407400. Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* Update garbage collection assertion to a more reliable one Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove print Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

* Working ParameterScheduler Added a new ParameterScheduler handler and the required tests. Signed-off-by: Petru-Daniel Tudosiu <petru.daniel@tudosiu.com>

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

* [DLMED] add support for addtional events Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typehints Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * fixes typos Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* fixes #1965 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] enhance doc-strings Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* adding init efficientnet support Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * fixing flake8 and further refactoring Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * adding unittests for efficiennet Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * making unittests backwards compatible python<3.8 Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * fixed kitty unittests file path Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * adding docstrings and minor refactoring Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * fix flake8-py3 failing test Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * generalize drop_connect for n-dim, fix/add unittests, remove assert Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * fix failing unittest, CC0-license image for test Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * refactoring code for review Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * WIP fix mypy type hint errors Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * fix cuda test error Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * WIP fix test errors Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * adding non-default shape tests Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * remove 3d case from non-default shape test Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * refactoring and updating docs Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> Co-authored-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add TransformInverter handler Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add support in SegmentationSaver handler Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CI test Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* changelog for 0.5.0 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update changelog Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add TransformInverter handler Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add support in SegmentationSaver handler Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CI test Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] save mode into inverse dict Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix ToTensor inverse issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] change the replacement logic into util function Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* [DLMED] update highlights for 0.5 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add invert transforms Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more highlights Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add checkpointloader Signed-off-by: Nic Ma <nma@nvidia.com> * downscale image Signed-off-by: Wenqi Li <wenqil@nvidia.com> * downscale image Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update desc Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* temp quick test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes basic unet tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * upgrade tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * upgrade cron Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update base Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update 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 condition Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update cuda Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "temp tests" This reverts commit 1e448f6. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "temp quick test" This reverts commit 6563e84. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "temp tests" This reverts commit e246bde. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "temp test" This reverts commit 794d517. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* adds partial weight util Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update coverage config Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes mypy Signed-off-by: Wenqi Li <wenqil@nvidia.com> * unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * tests, examples Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typo Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typos 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> * compatible_mod_state -> copy_model_state Signed-off-by: Wenqi Li <wenqil@nvidia.com> * tests/test_set_mod_state.py -> tests/test_copy_model_state.py Signed-off-by: Wenqi Li <wenqil@nvidia.com> * inplace False checkpoint loader Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

…t_transform` (#2384) * [DLMED] enhance all doc-string of 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: Nic Ma <nma@nvidia.com>

* refactoring decollate Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * more test cases and fixes Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes pytype error Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] enhance crop and pad doc-strings Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] add `the` Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add examples Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

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

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

* update not nan docstring Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix black error Signed-off-by: Yiheng Wang <vennw@nvidia.com> * Fix indentation errors Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* initial gmm commit Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

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

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

* Add blossom pre-merge pipeline Signed-off-by: Mohammad Adil <madil@nvidia.com>

* [DLMED] add min tests command Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update CI script Signed-off-by: Nic Ma <nma@nvidia.com>

* [DKMED] add CSV datalist Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add group feature Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add optional install Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add doc-strings Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add CSVDataset for non-iterable data Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix min test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add CSVIterableDataset base Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add CSVIterableDataset Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] support multiple processes Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix docs-build Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix min tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CI tests Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] change sys.platform Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] skip if windows Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] add col_types arg Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] test mypy fix Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] test commit Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix np.random Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix other numpy data type errors Signed-off-by: Nic Ma <nma@nvidia.com>

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

* added spikes transform Signed-off-by: Yaniel Cabrera <yaniel.cabrera@gmail.com>

* [DLMED] add image_only and unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com>

* add json config model support Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add -1 support for pixdim Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add scale_np = scale_np[:d] 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] update accortding to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove image_only in Spacing and Orientation Signed-off-by: Nic Ma <nma@nvidia.com>

Signed-off-by: am <am>

Signed-off-by: Dong Yang <dongy@nvidia.com>

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

* [DLMED] add TorchVisionClassificationModel Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* Add parameter unpacking for transforms Signed-off-by: Sebastian Penhouet <sebastian.penhouet@airamed.de>

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

wyli and others added 30 commits April 3, 2021 13:24

skip warp tests before torch 18 (#1927)

e871ee3

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

update docstrings (#1931)

e80cc4a

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

update get_package_version (#1930)

30523c0

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

enhance min/exact version check (#1937)

23f98f3

fixes ThreadDataLoader (#1945)

baf1bec

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

fixes itk dep. version (#1944)

a6b8f2a

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

Add progress bar to LesionFROC (#1951)

fbce3c2

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

pipeline for releasing the docker images (#1953)

501026b

* adds docker tag action Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds tag info Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update versioneer Signed-off-by: Wenqi Li <wenqil@nvidia.com>

remove unused RandomizableTransform (#1952)

81cfbf0

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

1956 - docker image building pipelines (#1957)

5c411d1

* refactor docker building Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Update garbage collection assertion (#1959)

d6ed956

* Update garbage collection assertion to a more reliable one Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove print Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Working ParameterScheduler (#1949)

7581255

* Working ParameterScheduler Added a new ParameterScheduler handler and the required tests. Signed-off-by: Petru-Daniel Tudosiu <petru.daniel@tudosiu.com>

[DLMED] remove warning (#1962)

baca6e0

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

1965 - register_backward_hook (#1966)

8cbd59a

* fixes #1965 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com>

1968 Enhance meta data doc-string in SegmentationSaver (#1969)

d56c002

* [DLMED] enhance doc-strings Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

1889 - changelog for v0.5.0 (#1923)

3a7cd46

* changelog for 0.5.0 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update changelog Signed-off-by: Wenqi Li <wenqil@nvidia.com>

wyli and others added 29 commits June 16, 2021 08:54

2380 fix inverse bug of CenterScaleCropd transform (#2383)

6e65fe6

* [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

Fix and enhance wrong doc-strings of all batch_transform and `outpu…

82fc4c1

…t_transform` (#2384) * [DLMED] enhance all doc-string of handlers Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] drop inheritance for future inverse feature (#2385)

4d9e8aa

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

temp. skip pytype on macos (#2392)

2f1afa8

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

[DLMED] add missing arg detach (#2393)

f3f9584

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

2390 Add docstring for not nans (#2395)

b829fe9

* update not nan docstring Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix black error Signed-off-by: Yiheng Wang <vennw@nvidia.com> * Fix indentation errors Signed-off-by: Yiheng Wang <vennw@nvidia.com>

JIT compiled gaussian mixture model (GMM) (#1802)

67e68f6

* initial gmm commit Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

fixes loader (#2398)

162b54a

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

fixes jit concurrent build (#2405)

b653799

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

Add blossom pre-merge pipeline (21/June) (#2382)

fb7d9f1

* Add blossom pre-merge pipeline Signed-off-by: Mohammad Adil <madil@nvidia.com>

Add min tests cmd to runtests script (#2400)

8cda6c1

* [DLMED] add min tests command Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update CI script Signed-off-by: Nic Ma <nma@nvidia.com>

fixes concurrency group (#2409)

0bd312a

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

Spike (Herringbone) artifact transform (#2337)

88fe0fc

* added spikes transform Signed-off-by: Yaniel Cabrera <yaniel.cabrera@gmail.com>

2420 Add image_only option to several spatial transforms (#2421)

a0afa60

* [DLMED] add image_only and unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com>

2415 - add json config model support for mmar loading (#2416)

ea028f5

* add json config model support Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Brain MMAR pretrained examples (#2406)

855a025

Signed-off-by: am <am>

add model desc for liver and pancreas seg (#2431)

5ff1bba

Signed-off-by: Dong Yang <dongy@nvidia.com>

[DLMED] enhance docs (#2429)

c20f70b

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

Fix permissions for blossom CI (#2438)

0662ed2

2407 Add support to set number classes for TorchVision models (#2408)

79b83d9

* [DLMED] add TorchVisionClassificationModel Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

Add parameter unpacking for transforms (#2437)

38403bb

* Add parameter unpacking for transforms Signed-off-by: Sebastian Penhouet <sebastian.penhouet@airamed.de>

[DLMED] enhance assert (#2444)

05b2da6

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

Nic-Ma merged commit bf4d7e5 into Nic-Ma:fix-inplace-shuffle-smartcache Jun 25, 2021

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merge master#148

merge master#148
Nic-Ma merged 388 commits into
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Nic-Ma commented Jun 25, 2021

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