merge master by Nic-Ma · Pull Request #380 · Nic-Ma/MONAI

Nic-Ma · 2022-02-28T03:51:25Z

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.

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] fix threshold issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

* Adding repeats option to ThreadDataLoader 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 repeats option to ThreadDataLoader Signed-off-by: Eric Kerfoot <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * Update thread_buffer.py * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci 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: monai-bot <[email protected]>

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

* [DLMED] fix None value Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]>

* add dints model Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * rename scripts Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * rename scripts Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Move stem out of dints * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add test dints cell, mixop and dints bug fix * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Change dints.stem * update scripts Signed-off-by: dongy <[email protected]> * adds doc; update test_factorized_reduce.py Signed-off-by: Wenqi Li <[email protected]> * update docstring of mixops Signed-off-by: Wenqi Li <[email protected]> * ReLU -> Acti Signed-off-by: Wenqi Li <[email protected]> * update mixops cell Signed-off-by: Wenqi Li <[email protected]> * remove forward() Signed-off-by: Wenqi Li <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Add dints comments * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add device to dints and fix unit test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixes typos Signed-off-by: Wenqi Li <[email protected]> * fix docstrings Signed-off-by: Wenqi Li <[email protected]> * fix docstrings Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * update mixop and cell Signed-off-by: Wenqi Li <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Add dints comments * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Remove arch_codes in forward * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add Dints weight parameter function * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * Fix 2D Dints bugs, unit testing, and commenting * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * dints/dints_blocks updates Signed-off-by: Wenqi Li <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update ram cost Signed-off-by: Wenqi Li <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * [DLMED] add TorchScript Signed-off-by: Nic Ma <[email protected]> * Fix dints bug, add comments, torchscript support * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update docstrings; remoted `is_search` Signed-off-by: Wenqi Li <[email protected]> * torchscript dints inference Signed-off-by: Wenqi Li <[email protected]> * test fixes Signed-off-by: Wenqi Li <[email protected]> * fixes gpu tests Signed-off-by: Wenqi Li <[email protected]> * fixes dints cell tests Signed-off-by: Wenqi Li <[email protected]> * skip for previous torch versions Signed-off-by: Wenqi Li <[email protected]> * inplace grads Signed-off-by: Wenqi Li <[email protected]> * remove warning msg Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: dongy <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Yufan He <[email protected]> Co-authored-by: Wenqi Li <[email protected]> Co-authored-by: Nic Ma <[email protected]>

* [DLMED] add frame_dim Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI test Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove doc-string of args "currently not used" Signed-off-by: Nic Ma <[email protected]>

* whats new in 0.8 Signed-off-by: Wenqi Li <[email protected]> * updated based on comments Signed-off-by: Wenqi Li <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Nic Ma <[email protected]>

* update changelog for v0.8.0 Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Nic Ma <[email protected]>

* [DLMED] update highlights for v0.8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] add tutorial link Signed-off-by: Nic Ma <[email protected]> * [DLMED] add MLFlow related Signed-off-by: Nic Ma <[email protected]> * [DLMED] update description and charts Signed-off-by: Nic Ma <[email protected]> * [DLMED] update chart name Signed-off-by: Nic Ma <[email protected]> * update docs Signed-off-by: Wenqi Li <[email protected]> * update dints link Signed-off-by: Wenqi Li <[email protected]> * update highlights Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[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]>

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

* ResampleToMatch Signed-off-by: Richard Brown <[email protected]> * mypy Signed-off-by: Richard Brown <[email protected]> * safe get, fixes min test Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* update contrib guide Signed-off-by: Wenqi Li <[email protected]> * update testing data Signed-off-by: Wenqi Li <[email protected]> * fixes typos Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* intensity augmentation transforms Signed-off-by: yc7620 <[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]> * mapping via bitbucket operation Signed-off-by: yc7620 <[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: yc7620 <[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]>

* [DLMED] fix margin region in crop Signed-off-by: Nic Ma <[email protected]> * [DLMED] add to other transforms Signed-off-by: Nic Ma <[email protected]> * [DLMED] update arg name Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* Add failing test Signed-off-by: Sven Koitka <[email protected]> * Fix reshape after ViT Signed-off-by: Sven Koitka <[email protected]> * Remove unused import Signed-off-by: Sven Koitka <[email protected]>

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

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

Nic-Ma and others added 30 commits November 17, 2021 13:32

[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

3387 fix threshold value issue in AsDiscrete (#3388)

9cc339d

* [DLMED] fix threshold issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

fixes readme links (#3380)

839f7ef

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

3387 Fix 0.0 or None value in AsDiscrete (#3393)

721f6f7

* [DLMED] fix None value Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]>

3368 add frame_dim to TensorBoard plot utility (#3385)

a640dde

* [DLMED] add frame_dim Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI test Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove doc-string of args "currently not used" Signed-off-by: Nic Ma <[email protected]>

update changelog for v0.8.0 (#3382)

d4c1bbe

* update changelog for v0.8.0 Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Nic Ma <[email protected]>

yiheng-wang-nv and others added 29 commits February 10, 2022 09:13

[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]>

fixes #3788 according to the suggestions (#3824)

b0f70e2

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

[3823] ResampleToMatch (#3833)

05013c7

* ResampleToMatch Signed-off-by: Richard Brown <[email protected]> * mypy Signed-off-by: Richard Brown <[email protected]> * safe get, fixes min test Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

3708 update testing data contrib (#3835)

2770092

* update contrib guide Signed-off-by: Wenqi Li <[email protected]> * update testing data Signed-off-by: Wenqi Li <[email protected]> * fixes typos Signed-off-by: Wenqi Li <[email protected]>

update link in MedNISTDataset (#3840)

fd63af4

Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

Fix reshape in ViTAutoEnc (#3841)

2cfb896

* Add failing test Signed-off-by: Sven Koitka <[email protected]> * Fix reshape after ViT Signed-off-by: Sven Koitka <[email protected]> * Remove unused import Signed-off-by: Sven Koitka <[email protected]>

KeepLargest... by default use all labels (#3776)

3af9d73

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

add status check (#3846)

d6327a7

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

Nic-Ma merged commit 5aa5384 into Nic-Ma:3482-add-schema-verify Feb 28, 2022

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merge master#380

merge master#380
Nic-Ma merged 440 commits intoNic-Ma:3482-add-schema-verifyfrom
Project-MONAI:dev

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Nic-Ma commented Feb 28, 2022

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