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merge master#403

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Nic-Ma merged 21 commits intoNic-Ma:4144-fix-resample-matchfrom
Project-MONAI:dev
Apr 19, 2022
Merged

merge master#403
Nic-Ma merged 21 commits intoNic-Ma:4144-fix-resample-matchfrom
Project-MONAI:dev

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@Nic-Ma Nic-Ma commented Apr 19, 2022

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 --disttests.
  • In-line docstrings updated.
  • Documentation updated, tested make html command in the docs/ folder.

ericspod and others added 21 commits April 4, 2022 19:38
@ericspod @pre-commit-ci
Adding discussion on format to bundle specification (#4047)
dc7a5b2 
* Adding discussion on format to bundle specification

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

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@pre-commit-ci
[pre-commit.ci] pre-commit suggestions (#4072)
c5bf120 
updates:
- [github.com/asottile/pyupgrade: v2.31.0 → v2.31.1](asottile/pyupgrade@v2.31.0...v2.31.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@Nic-Ma @pre-commit-ci
4060 Add PatchIter and PatchIterd transform (#4061)
c51d85e 
* [DLMED] change PatchIter to be a transform

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

* [DLMED] add dict transform

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

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* [DLMED] add unit tests

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

* [DLMED] store coords in dict

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

* [DLMED] update according to comments

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

* [DLMED] restore the doc-string

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

* [DLMED] store more info

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

* [DLMED] update according to comments

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

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@bhashemian
Fix a logical error in level verification (#4075)
b229e9c 
* Fix a logical error in level verification

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@Nic-Ma
[DLMED] add allow_missing_reference (#4079)
b5e7fe1 
Signed-off-by: Nic Ma <nma@nvidia.com>
@deepsource-autofix @monai-bot
autofixes: Refactor if expression and clangformat (#4081)
e8146e9 
* Refactor `if` expression

* update clang format

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

* [MONAI] python code formatting

Signed-off-by: monai-bot <monai.miccai2019@gmail.com>

Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
@rijobro @wyli
SplitDim (#3884)
b6b2cfb 
* SplitDim

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

* fix

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

* fixes

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

* fix update meta

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

* update docs

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

Co-authored-by: Wenqi Li <wenqil@nvidia.com>
@wyli @pre-commit-ci
update mmar tests (#4091)
d68554e 
* update mmar tests

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

* fixes pylint error

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

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@wyli
extending the mlp module (#4089)
17529e7 
* extend mlp

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

* 0 mlp_dim

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

* update based on comments

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@SilviaSeidlitz
added 2D (normalized) surface dice metric (#4050)
6602303 
* added 2D (normalized) surface dice metric

Signed-off-by: Silvia Seidlitz <s.seidlitz@dkfz-heidelberg.de>

* exclude from min tests

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

* more detailled docstring

Signed-off-by: Silvia Seidlitz <s.seidlitz@dkfz-heidelberg.de>
@yiheng-wang-nv
4073 Enhance DynUNet doc-strings (#4102)
af6560a 
* Fix doc strings error

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

* remove duplicate places

Signed-off-by: Yiheng Wang <vennw@nvidia.com>
@wyli
4105 drops pt16 support (#4106)
9c0a538 
* update sys req

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

* temp test

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

* update code for torch>=1.7

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

* temp tests

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

* fixes tests

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

* autofix

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

* fixes import

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

* clear cache

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

* update based on comments

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

* remove temp cmd

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@ramonemiliani93
Make pixelshuffle scriptable (#4109)
4e7ca44 
* Update the existing functionality to comply with the `torchscript.jit.script` function.

Signed-off-by: Ramon Emiliani <ramon@afxmedical.com>
@rijobro
meta tensor (#4077)
1880d38 
* meta tensor

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@Nic-Ma @monai-bot
4084 Add kwargs for Tensor.to() in engines (#4112)
f8c2655 
* [DLMED] add kwargs for to() API

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] fix flake8

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

* [DLMED] update according to comments

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

Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
@wyli
fixes pytorch version tests (#4127)
ccac5ff 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
update meta tensor api (#4131)
137164d 
* update meta tensor api

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

* update based on comments

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@rijobro
runtests.sh isort (#4134)
5e180c6 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@wyli
update citation (#4133)
8544d9e 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@rijobro
ToMetaTensor and FromMetaTensor transforms (#4115)
443fc0c 
to and from meta
@rijobro
no skip if before pytorch 1.7 (#4139)
cc9c066 
* no skip if before pytorch 1.7

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

* fix

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

* fix

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@Nic-Ma Nic-Ma merged commit d51ff4a into Nic-Ma:4144-fix-resample-match Apr 19, 2022
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8 participants

@Nic-Ma @ericspod @bhashemian @rijobro @wyli @SilviaSeidlitz @yiheng-wang-nv @ramonemiliani93