merge master by Nic-Ma · Pull Request #381 · Nic-Ma/MONAI

Nic-Ma · 2022-02-28T16:17:56Z

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 <nma@nvidia.com>

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

* drop pytorch 1.5.x Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update premerge gpu Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] optimize astype Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] improve astype Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] simiplify AsDiscrete transform Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add examples Signed-off-by: Nic Ma <nma@nvidia.com>

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

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

* [DLMED] add wrap_sequence Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update default value Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more tests Signed-off-by: Nic Ma <nma@nvidia.com>

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

* Add tiffile and imagecodes to build option dependencies Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * update optional dep Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: myron <amyronenko@nvidia.com>

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

* Adding smooth field transforms Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Adding smooth field transforms Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * [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 <eric.kerfoot@kcl.ac.uk> * Adding smooth field transforms Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Updates to smooth field transforms Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Updates to smooth field transforms Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Updates to smooth field transforms Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Updates to smooth field transforms Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

Co-authored-by: dongy <dongy@nvidia.com>

* fixes typos in docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes type errors Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes the docstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typo Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* option to zip_longest Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds a pad option Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes batch size Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* Refactor some variable names Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Fix SplitOnGrid issue with numpy backend Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add unittest to cover the fixed issue Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Rename c_image to n_channels Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* [DLMED] fix threshold issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

* Adding repeats option to ThreadDataLoader Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * [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 <eric.kerfoot@kcl.ac.uk> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * 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 <eric.kerfoot@kcl.ac.uk> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

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

* [DLMED] fix None value Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com>

* add dints model Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * rename scripts Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * rename scripts Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * 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 <dongy@nvidia.com> * adds doc; update test_factorized_reduce.py Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring of mixops Signed-off-by: Wenqi Li <wenqil@nvidia.com> * ReLU -> Acti Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update mixops cell Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove forward() Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * 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 <wenqil@nvidia.com> * fix docstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fix docstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update mixop and cell Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * 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 <dongy@nvidia.com> * 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 <wenqil@nvidia.com> * [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 <wenqil@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <dongy@nvidia.com> * [DLMED] add TorchScript Signed-off-by: Nic Ma <nma@nvidia.com> * 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 <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update docstrings; remoted `is_search` Signed-off-by: Wenqi Li <wenqil@nvidia.com> * torchscript dints inference Signed-off-by: Wenqi Li <wenqil@nvidia.com> * test fixes Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes gpu tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes dints cell tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * skip for previous torch versions Signed-off-by: Wenqi Li <wenqil@nvidia.com> * inplace grads Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove warning msg Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: dongy <dongy@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Yufan He <heyufan1995@gmail.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Nic Ma <nma@nvidia.com>

* [DLMED] add frame_dim Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CI test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove doc-string of args "currently not used" Signed-off-by: Nic Ma <nma@nvidia.com>

* whats new in 0.8 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * updated based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [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 <nma@nvidia.com>

* update changelog for v0.8.0 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Nic Ma <nma@nvidia.com>

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

* make vit support torchscript Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add torch version restriction Signed-off-by: Yiheng Wang <vennw@nvidia.com> * change skip decorator order Signed-off-by: Yiheng Wang <vennw@nvidia.com> * remove extra cls Signed-off-by: Yiheng Wang <vennw@nvidia.com>

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

Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

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

* [DLMED] add ensure_channel_first 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>

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

* fixes #3791 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring of invertd, update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typo Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: Peixin Li <pxli@nyu.edu> Co-authored-by: Nic Ma <nma@nvidia.com>

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

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

* fixes #3791 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring of invertd, update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typo Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

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

…tes (#3489) * update changelog for v0.8.1 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * rc4 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * prepare for mmar verion updates Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update for 0.8.1 Signed-off-by: Wenqi Li <wenqil@nvidia.com>

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

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

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

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

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

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

* ResampleToMatch Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * mypy Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * safe get, fixes min test Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* update contrib guide Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update testing data Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typos Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* intensity augmentation transforms Signed-off-by: yc7620 <yaniel.cabrera20@imperial.ac.uk> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * mapping via bitbucket operation Signed-off-by: yc7620 <yaniel.cabrera20@imperial.ac.uk> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: yc7620 <yaniel.cabrera20@imperial.ac.uk> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] fix margin region in crop Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add to other transforms Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update arg name Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* Add failing test Signed-off-by: Sven Koitka <sven.koitka@uk-essen.de> * Fix reshape after ViT Signed-off-by: Sven Koitka <sven.koitka@uk-essen.de> * Remove unused import Signed-off-by: Sven Koitka <sven.koitka@uk-essen.de>

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

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

[DLMED] refine doc (#3349)

0a7a4f1

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

fixes mednist dataset (#3348)

b86d751

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

close file (#3342)

33b6d61

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

3350 drops pytorch 1.5.x support (#3353)

2e83cd2

* drop pytorch 1.5.x Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update premerge gpu Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Fix casting for tile step (#3355)

c3fd5a9

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

remove dynunetv1 blocks (#3360)

f7e4cc3

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

[DLMED] enhance doc-string (#3363)

d89807f

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

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

a4e7ba0

* Add tiffile and imagecodes to build option dependencies Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * update optional dep Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

unit tests for step (#3361)

9048166

Signed-off-by: myron <amyronenko@nvidia.com>

backward compatible as discrete (#3367)

e36fbd3

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

adds dints blocks (#3372)

73d9afa

Co-authored-by: dongy <dongy@nvidia.com>

[DLMED] add frame_dim (#3369)

d0e72fb

Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

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

fixes readme links (#3380)

839f7ef

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

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

721f6f7

* [DLMED] fix None value Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com>

3368 add frame_dim to TensorBoard plot utility (#3385)

a640dde

* [DLMED] add frame_dim Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CI test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove doc-string of args "currently not used" Signed-off-by: Nic Ma <nma@nvidia.com>

update changelog for v0.8.0 (#3382)

d4c1bbe

* update changelog for v0.8.0 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Nic Ma <nma@nvidia.com>

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

[DLMED] add default value (#3785)

e3a9730

Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

3795 Add ensure_channel_first to LoadImage (#3796)

2d35301

* [DLMED] add ensure_channel_first 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>

adds alias check (#3794)

eb947e8

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

3791 orientation xform warning spatial dims (#3792)

42603b3

* fixes #3791 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring of invertd, update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typo Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Update blossom-ci allow list (#3800)

817c1cf

Signed-off-by: Peixin Li <pxli@nyu.edu> Co-authored-by: Nic Ma <nma@nvidia.com>

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

b39e7fa

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

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

e21e6ee

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

3791 orientation xform warning spatial dims (#3792)

b2bd500

* fixes #3791 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring of invertd, update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typo Signed-off-by: Wenqi Li <wenqil@nvidia.com>

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

4e09627

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

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

3a08450

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

Merge branch 'dev' into releasing/0.8.1

046e625

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

fixes #3708 (#3814)

bcbfbdd

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

calculate min/max foreground (#3826)

c3db337

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

fixes #3788 according to the suggestions (#3824)

b0f70e2

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

3708 update testing data contrib (#3835)

2770092

* update contrib guide Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update testing data Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typos Signed-off-by: Wenqi Li <wenqil@nvidia.com>

update link in MedNISTDataset (#3840)

fd63af4

Signed-off-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

Fix reshape in ViTAutoEnc (#3841)

2cfb896

* Add failing test Signed-off-by: Sven Koitka <sven.koitka@uk-essen.de> * Fix reshape after ViT Signed-off-by: Sven Koitka <sven.koitka@uk-essen.de> * Remove unused import Signed-off-by: Sven Koitka <sven.koitka@uk-essen.de>

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

3af9d73

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

add status check (#3846)

d6327a7

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

Nic-Ma merged commit 28f2a0d into Nic-Ma:3864-update-docker Feb 28, 2022

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merge master#381

merge master#381
Nic-Ma merged 440 commits intoNic-Ma:3864-update-dockerfrom
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Nic-Ma commented Feb 28, 2022

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