merge master by Nic-Ma · Pull Request #374 · Nic-Ma/MONAI

Nic-Ma · 2022-02-21T09:33:42Z

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 affine to dict transform Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]>

* torch version check Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * additional cases Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * update unit test names Signed-off-by: Wenqi Li <[email protected]> * remove temp tests Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * fixes codeformat Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]>

* update clang-format download Signed-off-by: Wenqi Li <[email protected]> * fixes unit test Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

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

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

* MIL component to extract patches Signed-off-by: myron <[email protected]> * MIL component to extract patches Signed-off-by: myron <[email protected]> * random flag, minor fixes Signed-off-by: myron <[email protected]> * minor fixes for padding Signed-off-by: myron <[email protected]> * improve tests Signed-off-by: myron <[email protected]> Co-authored-by: Behrooz <[email protected]>

* 3251 Add dependency check in WSIReader (#3312) * [DLMED] add dep check 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: myron <[email protected]> * [DLMED] MILmodel PR Signed-off-by: myron <[email protected]> * small updates Signed-off-by: myron <[email protected]> * fix jit issues Signed-off-by: myron <[email protected]> * jit fix attempt Signed-off-by: myron <[email protected]> * removing Enum Signed-off-by: myron <[email protected]> Co-authored-by: Nic Ma <[email protected]> Co-authored-by: Behrooz <[email protected]>

* update pathlike obj Signed-off-by: Wenqi Li <[email protected]> * support of pathlike obj Signed-off-by: Wenqi Li <[email protected]> * review path obj Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]> * autofix Signed-off-by: Wenqi Li <[email protected]> * fixes unit test Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * fixes dep issue Signed-off-by: Wenqi Li <[email protected]>

…_keys is True (#3325) * [DLMED] enhance no keys for allow_missing_keys 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] update according to comments Signed-off-by: Nic Ma <[email protected]>

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

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

* drop pytorch 1.5.x Signed-off-by: Wenqi Li <[email protected]> * update premerge gpu Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] optimize astype Signed-off-by: Nic Ma <[email protected]> * [DLMED] improve astype 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]> * [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] update according to comments Signed-off-by: Nic Ma <[email protected]>

* [DLMED] simiplify AsDiscrete transform Signed-off-by: Nic Ma <[email protected]> * [DLMED] update tests 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] add examples Signed-off-by: Nic Ma <[email protected]>

Signed-off-by: Behrooz <[email protected]>

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

* [DLMED] add wrap_sequence Signed-off-by: Nic Ma <[email protected]> * [DLMED] update default value Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more tests Signed-off-by: Nic Ma <[email protected]>

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

* Add tiffile and imagecodes to build option dependencies Signed-off-by: Behrooz <[email protected]> * update optional dep Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

Signed-off-by: myron <[email protected]>

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

* Adding smooth field transforms Signed-off-by: Eric Kerfoot <[email protected]> * Adding smooth field transforms Signed-off-by: Eric Kerfoot <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Adding smooth field transforms Signed-off-by: Eric Kerfoot <[email protected]> * Adding smooth field transforms Signed-off-by: Eric Kerfoot <[email protected]> * Updates to smooth field transforms Signed-off-by: Eric Kerfoot <[email protected]> * Updates to smooth field transforms Signed-off-by: Eric Kerfoot <[email protected]> * Updates to smooth field transforms Signed-off-by: Eric Kerfoot <[email protected]> * Updates to smooth field transforms Signed-off-by: Eric Kerfoot <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <[email protected]>

Co-authored-by: dongy <[email protected]>

* fixes typos in docstring Signed-off-by: Wenqi Li <[email protected]> * fixes type errors Signed-off-by: Wenqi Li <[email protected]> * fixes the docstrings Signed-off-by: Wenqi Li <[email protected]> * fixes typo Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* option to zip_longest Signed-off-by: Wenqi Li <[email protected]> * adds a pad option Signed-off-by: Wenqi Li <[email protected]> * fixes batch size Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

* Refactor some variable names Signed-off-by: Behrooz <[email protected]> * Fix SplitOnGrid issue with numpy backend Signed-off-by: Behrooz <[email protected]> * Add unittest to cover the fixed issue Signed-off-by: Behrooz <[email protected]> * Rename c_image to n_channels Signed-off-by: Behrooz <[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]>

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

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

* 3616 test downloading issues Signed-off-by: Wenqi Li <[email protected]> * update based on comments 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]>

* [DLMED] add save_state utility 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] add atomic and func Signed-off-by: Nic Ma <[email protected]> * [DLMED] refactor saving logic Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] restore persistent dataset Signed-off-by: Nic Ma <[email protected]> * [DLMED] simplify kwargs Signed-off-by: Nic Ma <[email protected]>

* make vit support torchscript Signed-off-by: Yiheng Wang <[email protected]> * add torch version restriction Signed-off-by: Yiheng Wang <[email protected]> * change skip decorator order Signed-off-by: Yiheng Wang <[email protected]> * remove extra cls Signed-off-by: Yiheng Wang <[email protected]>

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

Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* update largest cc function Signed-off-by: Dong Yang <[email protected]> * update largest cc function Signed-off-by: Dong Yang <[email protected]> * [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 <[email protected]> * update largest cc function Signed-off-by: Dong Yang <[email protected]> * update largest cc function Signed-off-by: Dong Yang <[email protected]> * update largest cc function Signed-off-by: Dong Yang <[email protected]> * [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 <[email protected]> * [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 <[email protected]> * update largest cc function Signed-off-by: Dong Yang <[email protected]> * update largest cc function Signed-off-by: Dong Yang <[email protected]> * update largest cc function Signed-off-by: Dong Yang <[email protected]> * update largest cc function Signed-off-by: Dong Yang <[email protected]> * update repo Signed-off-by: dongy <[email protected]> Co-authored-by: Dong Yang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: dongy <[email protected]>

* [DLMED] add ensure_channel_first Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>

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

* fixes #3791 Signed-off-by: Wenqi Li <[email protected]> * update docstring of invertd, update based on comments Signed-off-by: Wenqi Li <[email protected]> * fixes typo Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Peixin Li <[email protected]> Co-authored-by: Nic Ma <[email protected]>

Signed-off-by: Yiheng Wang <[email protected]>

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

* fixes #3791 Signed-off-by: Wenqi Li <[email protected]> * update docstring of invertd, update based on comments Signed-off-by: Wenqi Li <[email protected]> * fixes typo Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Yiheng Wang <[email protected]>

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

…tes (#3489) * update changelog for v0.8.1 Signed-off-by: Wenqi Li <[email protected]> * rc4 Signed-off-by: Wenqi Li <[email protected]> * prepare for mmar verion updates Signed-off-by: Wenqi Li <[email protected]> * update for 0.8.1 Signed-off-by: Wenqi Li <[email protected]>

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

* [DLMED] add ConfigComponent Signed-off-by: Nic Ma <[email protected]> * [DLMED] totally update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] add excludes Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update ComponentScanner Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance doc Signed-off-by: Nic Ma <[email protected]> * [DLMED] use load_submodules Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove locate Signed-off-by: Nic Ma <[email protected]> * [DLMED] add test to ensure all components support `locate` Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix min_tests 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] add more doc-strings Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] extract ConfigItem base class Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments 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]> * update instantiate util Signed-off-by: Wenqi Li <[email protected]> * [DLMED] optimize design Signed-off-by: Nic Ma <[email protected]> * update docstring Signed-off-by: Wenqi Li <[email protected]> * updating ConfigComponent Signed-off-by: Wenqi Li <[email protected]> * revise confi* Signed-off-by: Wenqi Li <[email protected]> * [DLMED] fix unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] update function name Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

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

* [DLMED] add ReferenceResolver Signed-off-by: Nic Ma <[email protected]> * [DLMED] refine docs Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] simplify Instantiable interface Signed-off-by: Nic Ma <[email protected]> * update docstring (wip) Signed-off-by: Wenqi Li <[email protected]> * [DLMED] update id Signed-off-by: Nic Ma <[email protected]> * nonbreaking updates Signed-off-by: Wenqi Li <[email protected]> * [DLMED] simplify code Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

Signed-off-by: Yiheng Wang <[email protected]>

Nic-Ma and others added 30 commits November 12, 2021 21:44

3313 Add affine arg to the dict transform (#3326)

9ddc9e6

* [DLMED] add affine to dict transform Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]>

3335 update clang-format download (#3340)

af21f11

* update clang-format download Signed-off-by: Wenqi Li <[email protected]> * fixes unit test Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

fixes #3331 (#3334)

8a454bd

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

[DLMED] enhance metrics in workflow (#3341)

4d83fc0

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

[DLMED] refine doc (#3349)

0a7a4f1

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

fixes mednist dataset (#3348)

b86d751

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

close file (#3342)

33b6d61

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

3350 drops pytorch 1.5.x support (#3353)

2e83cd2

* drop pytorch 1.5.x Signed-off-by: Wenqi Li <[email protected]> * update premerge gpu Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

Fix casting for tile step (#3355)

c3fd5a9

Signed-off-by: Behrooz <[email protected]>

remove dynunetv1 blocks (#3360)

f7e4cc3

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

[DLMED] enhance doc-string (#3363)

d89807f

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

Update setup.cfg with tifffile and imagecodes (#3362)

a4e7ba0

* Add tiffile and imagecodes to build option dependencies Signed-off-by: Behrooz <[email protected]> * update optional dep Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

unit tests for step (#3361)

9048166

Signed-off-by: myron <[email protected]>

backward compatible as discrete (#3367)

e36fbd3

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

adds dints blocks (#3372)

73d9afa

Co-authored-by: dongy <[email protected]>

[DLMED] add frame_dim (#3369)

d0e72fb

Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

Numpy Implementation of SplitOnGrid (#3378)

5adf30b

TileOnGrid support for Tensor input (#3384)

5d87b23

Nic-Ma and others added 29 commits February 9, 2022 12:40

3765 Enhance create_multigpu_supervised_XXX for distributed (#3768)

227bad0

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

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

0dbf06c

autoformatting

f9e68d2

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

tests workaround

4826824

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

3616 test downloading issues (#3617)

d391b16

* 3616 test downloading issues Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

3725 fixes download test (#3728)

d27ab6c

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

[DLMED] add default value (#3785)

e3a9730

Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

3795 Add ensure_channel_first to LoadImage (#3796)

2d35301

* [DLMED] add ensure_channel_first Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>

adds alias check (#3794)

eb947e8

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

3791 orientation xform warning spatial dims (#3792)

42603b3

* fixes #3791 Signed-off-by: Wenqi Li <[email protected]> * update docstring of invertd, update based on comments Signed-off-by: Wenqi Li <[email protected]> * fixes typo Signed-off-by: Wenqi Li <[email protected]>

Update blossom-ci allow list (#3800)

817c1cf

Signed-off-by: Peixin Li <[email protected]> Co-authored-by: Nic Ma <[email protected]>

change raise error to warnings for some metrics (#3804)

b39e7fa

Signed-off-by: Yiheng Wang <[email protected]>

following Project-MONAI/tutorials#545 (#3802)

e21e6ee

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

3791 orientation xform warning spatial dims (#3792)

b2bd500

* fixes #3791 Signed-off-by: Wenqi Li <[email protected]> * update docstring of invertd, update based on comments Signed-off-by: Wenqi Li <[email protected]> * fixes typo Signed-off-by: Wenqi Li <[email protected]>

change raise error to warnings for some metrics (#3804)

4e09627

Signed-off-by: Yiheng Wang <[email protected]>

following Project-MONAI/tutorials#545 (#3802)

3a08450

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

Merge branch 'dev' into releasing/0.8.1

046e625

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

fixes #3708 (#3814)

bcbfbdd

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

calculate min/max foreground (#3826)

c3db337

Signed-off-by: Yiheng Wang <[email protected]>

Nic-Ma merged commit 2ab8fd5 into Nic-Ma:3482-add-config-reader Feb 21, 2022

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merge master#374

merge master#374
Nic-Ma merged 431 commits intoNic-Ma:3482-add-config-readerfrom
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Nic-Ma commented Feb 21, 2022

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