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merge master #19

Merged
merged 67 commits into from
Feb 1, 2021
Merged

merge master #19

merged 67 commits into from
Feb 1, 2021

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Nic-Ma
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@Nic-Ma Nic-Ma commented Feb 1, 2021

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.

Nic-Ma and others added 30 commits December 17, 2020 11:59
@Nic-Ma
[DLMED] add missing import (#1376)
09638a7 
Signed-off-by: Nic Ma <nma@nvidia.com>
@wyli
adds jpeg (#1379)
1608b10 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
[DLMED] add missing arg in GANTrainer (#1383)
b7ecd7b 
Signed-off-by: Nic Ma <nma@nvidia.com>
@charliebudd
1198 efficient differentiable bilateral filter (#1375)
70be9ab 
* Initial cpu implementation

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* hue speed increase moving away from torch tensors

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* allowing generic channel dimension size

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* allowing generic dimensionality

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* manual testing script for bilateral filter

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* Initial commit of CRF using permutohedral lattice to optimise message passing, implementation from https://github.com/SamuelJoutard/Permutohedral_attention_module

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* temporary example scripts demonstrating the usage of crf and phl, and some data to process

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* alternate phl implementation using a more efficient cuda hashtable, code currently untested due to windows build issues, implementation from https://github.com/SamuelJoutard/Permutohedral_attention_module

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* c++ cpu permutohedral lattice implementation

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* comparison script

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* cleaning

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* backwards pass

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* initial cuda brute force kernel

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* reverting setup.py

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* working cuda kernel for brute force 2d kernel

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* fixing unresolved symbols when compiling without cuda

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* removing macros file

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* placeholder cuda phl implementation

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* changing test case color sigma

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* Initial import of reference cuda phl implementation

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* fixing cuda kernel color weight error

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* initial edits to cuda phl code

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* fixing errors in cuda phl implementation

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* removing logging from cuda phl

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* using template data_ptr function

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* fixed cpu phl implementation

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* updating cpu phl to run on arbitrary input dimensions and channles

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* 2d and 3d testing scripts

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* Generalising permutohedral implementation to remove independance on width and height

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* removing width and height from permutohedral filter function and implementing templated feature creation

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* fixed typo

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* exteneding 3d testing script

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* generalising bruteforce cuda implementation

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* updating testing scripts

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* file organisiation

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* fixing weight error in cpu bruteforce implementation, also inlineing functions

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* some refactoring and introducing proper batch handling

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* fixing indexing error at border

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* fixing some artifacts in cuda phl for high color sigmas

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* fixing gaussian kernel function for cpu and cuda bruteforce

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* ensuring kernel is an odd numbered size

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* adding tests for precised implementation

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* adding approximate imlpementation test

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* templating implementations based on scalar_type

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* cleaning up

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* code formatting

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* removing half precision implementation for permutohedral due to errors caused on windows

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* skipping cuda tests if cuda missing

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* reformating

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* adding unit test skip based on cpp extention availablility

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* removing unused import

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* changing to  use of THCatomic add

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* adding missing licenses

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* clang reformat

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>
@rijobro
update contributing and normalis* -> normaliz* (#1388)
36b8302 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@Nic-Ma
[DLMED] add output_dtype (#1394)
f20e132 
Signed-off-by: Nic Ma <nma@nvidia.com>
@rijobro
with eval_mode(net): (#1384)
a4b1144 
* eval_mode

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

* DynUnetSupervision unittest shouldnt use eval_mode

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

* move to device

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@Nic-Ma
1390 Enhance DynUNet with get_feature_maps API (#1393)
e2c0ed2 
* [DLMED] add get_feature_maps API to dynunet

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

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>
@wyli
adds missing desc (#1403)
0c2411e 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli @Nic-Ma @IsaacYangSLA
part of #926 (#1368)
1924b43 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Co-authored-by: Nic Ma <nma@nvidia.com>
Co-authored-by: Isaac Yang <isaacy@nvidia.com>
@yiheng-wang-nv
Implement dice cross entropy loss (#1409)
115f146 
Signed-off-by: yiheng-wang-nv <vennw@nvidia.com>
@rijobro
Unify visualisation (#1381)
a74fef9 
* unify visualisation
@kate-sann5100
1405 add bending energy loss (#1408)
5aa5e16 
* 1405 add bending energy loss

Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>
@danielschulz
Fix failures from many pulls from hub.docker.com (Done) (#1406)
db831ae 
* changed year 2020 in copyright to "2020 - 2021" for both occurences

Signed-off-by: Daniel Schulz danielschulz2005@hotmail.com <danielschulz2005@hotmail.com>

* added SHA256 check before unpacking downloaded artifacts
added list of Nvidia maintainers
resolves: "docker image tests failed due to dockerhub limitation #1380"

Signed-off-by: Daniel Schulz danielschulz2005@hotmail.com <danielschulz2005@hotmail.com>

* added danielschulz-specific changes for GitHu Actions to work properly

Signed-off-by: Daniel Schulz danielschulz2005@hotmail.com <danielschulz2005@hotmail.com>

* added test

Signed-off-by: Daniel Schulz danielschulz2005@hotmail.com <danielschulz2005@hotmail.com>

* revoked test line

Signed-off-by: Daniel Schulz danielschulz2005@hotmail.com <danielschulz2005@hotmail.com>

* migrated code to local registry instead of hub.docker.com to circumvent rate limiting on it
remark: do not use it as pull-through cache as this would not work with static labels and docker images would diverge from one another

Signed-off-by: Daniel Schulz danielschulz2005@hotmail.com <danielschulz2005@hotmail.com>

* reverted back local-only changes

Signed-off-by: Daniel Schulz danielschulz2005@hotmail.com <danielschulz2005@hotmail.com>

* improved checking integrity of NGC CLI

Signed-off-by: Daniel Schulz danielschulz2005@hotmail.com <danielschulz2005@hotmail.com>

* removed typo in GH repository variable

Signed-off-by: Daniel Schulz danielschulz2005@hotmail.com <danielschulz2005@hotmail.com>

* added remark

Signed-off-by: Daniel Schulz danielschulz2005@hotmail.com <danielschulz2005@hotmail.com>

* improved MAINTAINER label
got rid of "as base" extension in FROM -- seems not be be pickup downwards (is no multi-stage Docker build -- hence: removed)

Signed-off-by: Daniel Schulz danielschulz2005@hotmail.com <danielschulz2005@hotmail.com>
@wyli
fixes dockerfile (#1413)
db7bf89 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@rijobro
Wildcard import (#1411)
1f74ca2 
add `__all__` and `remove import *`. Update CONTRIBUTING.md
@wyli @IsaacYangSLA
Fixes ci (#1416)
53c145d 
* temp tests

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

* fixes typo

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

* temp tests

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

* fixes docker login warning

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

* Revert "temp tests"

This reverts commit 99c6d20.

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

* Revert "temp tests"

This reverts commit c529bf9.

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

Co-authored-by: Isaac Yang <isaacy@nvidia.com>
@IsaacYangSLA
Improve docker build process (#1419)
a4ef691 
* Improve docker build process, fixes #1276
@kate-sann5100
1412 local normalized cross correlation (#1415)
1544d0c 
* 1412 add local normalized cross correlation

Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>
@de-sh
1404 Fixing a few code performance issues (#1423)
3d5554f 
* Add .deepsource.toml

Signed-off-by: Devdutt Shenoi <devdutt@outlook.in>

* Remove unnecessary use of comprehension

Signed-off-by: Devdutt Shenoi <devdutt@outlook.in>

* Use literal syntax instead of function calls to create data structure

Signed-off-by: Devdutt Shenoi <devdutt@outlook.in>

* Pass string format arguments as logging method parameters

Signed-off-by: Devdutt Shenoi <devdutt@outlook.in>
@Nic-Ma
[DLMED] add more clear doc-string (#1425)
3ac6957 
Signed-off-by: Nic Ma <nma@nvidia.com>
@rijobro
Make master installation clearer (#1426)
d735103 
People are asking for 0.4.0+ functionality, so by making the master installation instructions a section, we can easily copy a link pointing to the relevant bit of code.

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@deepsource-autofix
Refactor the comparison involving not (#1427)
2e26a33 
Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
@wyli
ignore versioneer -- deepsource check (#1429)
27919e3 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@deepsource-autofix @wyli
Remove unnecessary lambda expression (#1428)
0d59289 
* Remove unnecessary lambda expression

* fixes compatible attributes in config printing

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

Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Co-authored-by: Wenqi Li <wenqil@nvidia.com>
@wyli
update hashes (#1431)
fe28bba 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
Enhance Rotate90 transform with more check (#1432)
50bcaf1 
* [DLMED] enhance the arg of rotate90 transform

Signed-off-by: Nic Ma <nma@nvidia.com>
@rijobro
Update occ sens (#1430)
70483b6 
* update

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

* use mask_size rather than margin

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

* use mask_size instead of margin

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

* fix index typo

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

* remove postprocessing and fix docstring

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

* update for code review

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

* autofix

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@deepsource-autofix
Remove methods with unnecessary super delegation. (#1437)
df9bc68 
Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
@deepsource-autofix
Refactor unnecessary else / elif when if block has a return s…
85f6283 
…tatement (#1434)

* Refactor unnecessary `else` / `elif` when `if` block has a `return` statement

* [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>
Nic-Ma and others added 29 commits January 14, 2021 14:15
@Nic-Ma
909 Drop deprecated APIs in IO transforms (#1448)
8084394 
* [DLMED] remove deprecated APIs in IO transforms

Signed-off-by: Nic Ma <nma@nvidia.com>
@deepsource-autofix @wyli
Remove length check in favour of truthiness of the object (#1445)
c0983c4 
* Remove length check in favour of truthiness of the object

* fixes The truth value of an array with more than one element is ambiguous

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

* fixes indices types

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

Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Co-authored-by: Wenqi Li <wenqil@nvidia.com>
@kate-sann5100
1442 add LocalNet (#1447)
e115d6c 
* 1442 add localnet

Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>

* 1442 add test

Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>

* 1442 add documentation

Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>

* 1442 add typing

Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>

* 1442 reformat

Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>

* 1442 reformat

Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>

* 1442 reformat

Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>

* 1442 remove initializsation

Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>

* 1442 update factory calls

Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>
@rijobro
faster amazon download (#1450)
f349180 
* faster amazon download

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

* remove unused imports

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@deepsource-autofix @monai-bot @wyli
Remove assert statement from non-test files (#1446)
5e020a8 
* Remove assert statement from non-test files

* [MONAI] python code formatting

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

* fixes assertion conditions

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

Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
Co-authored-by: Wenqi Li <wenqil@nvidia.com>
@crnbaker
New simplelayer SavitzkyGolayFilter() and transform SavitzkyGolaySmoo…
ec70d96 
…th() (#1418)

* Added new simplelayer SavitskyGolayFilter()

Signed-off-by: Christian Baker <christian.baker@kcl.ac.uk>

* Unit tests written for SavitskyGolayFilter()

Signed-off-by: Christian Baker <christian.baker@kcl.ac.uk>

* New array transform SavitskyGolaySmooth() written that wraps SavitskyGolayFilter() simplelayer

Signed-off-by: Christian Baker <christian.baker@kcl.ac.uk>

* Tests added for SavitskyGolaySmooth()

Signed-off-by: Christian Baker <christian.baker@kcl.ac.uk>

* Added to Sphinx .rst files and rebuilt docs

Signed-off-by: Christian Baker <christian.baker@kcl.ac.uk>
@charliebudd @monai-bot
Exposing c++ PHL Implementation in Python API (#1453)
bf8f8e2 
* exposing permutohedral lattice filter in python api

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* unit tests for phl filter

Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
@Nic-Ma
909 develop ImageDataset to replace NiftiDataset (#1461)
d2064e0 
* [DLMED] change NiftiDataset to ImageDataset

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

* [DLMED] update CI tests

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

* [MONAI] python code formatting

Signed-off-by: monai-bot <monai.miccai2019@gmail.com>
@kate-sann5100
1452 warp layer (#1463)
b26cc24 
* 1452 add Warp layer and test

Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>

* 1452 add documentation

Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>

* 1452 enforce same image and ddf size, add test case

Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>
@rijobro
enhance mednist dataset (#1466)
91cb8cd 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@kate-sann5100
[WIP]1442 add LocalNet initialization (#1460)
012cf62 
* 1442 add initialization

Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>

* 1442 fix typing and add test cases

Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>
@Nic-Ma
1478 Fix TorchScript issue in AHnet (#1479)
c9d15f1 
* [DLMED] fix TorchScript issue in AHNet

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

* [DLMED] add test cases

Signed-off-by: Nic Ma <nma@nvidia.com>
@ericspod @monai-bot @wyli
Fix for device config script (#1480)
edbad43 
* Fix for device config script

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

* [MONAI] python code formatting

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

Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
Co-authored-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
[DLMED] fix flake8 issue (#1493)
cb7a9a0 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma @monai-bot
886 Add IterationMetric refer to to the EpochMetric in ignite (#1488)
0b7e645 
* [DLMED] add IterationHandler refer to the EpochHandler in ignite

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] fix the multi-gpu issue

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

* [DLMED] fix typo

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

* [DLMED] fix distributed tests

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>
@IsaacYangSLA
Add some details on weekly preview build process (#1494)
2eada01 
Stop build if the tag format is wrong

Signed-off-by: Isaac Yang <isaacy@nvidia.com>
@rijobro
remove decorator double negative (#1490)
f840fc5 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@FMCalisto @wyli
Create CODE_OF_CONDUCT.md; update contact (#1495)
db8f787 
Co-authored-by: Wenqi Li <wenqil@nvidia.com>
@rijobro
1014 learning rate finder (#1454)
a2da8a1 
learning rate finder and corresponding test
@wyli
1501-enhance-PR-testing-workflow (#1502)
8fef0e1 
* test new action for quick test; add temp tests

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

* testing action

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

* remove temp test

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@rijobro
change email (#1510)
84826b9 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@wyli
1501 workflow cleanup (#1511)
3025e8d 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma @monai-bot
Add more Events for MONAI workflow engines (#1474)
8207e1e 
* [DLMED] add more Events

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

* [DLMED] add 3 Events

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

* [MONAI] python code formatting

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

* [DLMED] add tests

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

* [MONAI] python code formatting

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

* [DLMED] update according to comments

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>
@kate-sann5100
1452 adjust-warp-layer-grid-pull-user-case (#1470)
f75b67a 
* 1442 use pull-grid only for above linear interpolation

Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>
@Nic-Ma @ericspod
[DLMED] add overwrite option (#1513)
50c4659 
Signed-off-by: Nic Ma <nma@nvidia.com>

Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
@Nic-Ma
[DLMED] Enhance MaskIntensityd transform (#1521)
56c88f6 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma @monai-bot
886 add MetricsSaver handler to save metrics and details into files (#…
b3d063c 
…1497)

* [DLMED] add IterationHandler refer to the EpochHandler in ignite

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] fix the multi-gpu issue

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

* [DLMED] fix typo

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

* [DLMED] fix distributed tests

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

* [DLMED] fix flake8 issue

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

* [DLMED] add engine to metrics

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

* [DLMED] share metric details in engine

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

* [DLMED] add metrics report

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

* [DLMED] add average value to report

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

* [DLMED] add summary report

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

* [DLMED] add docs

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>

* [MONAI] python code formatting

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

* [DLMED] add unit tests and distributed tests

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] fix typo

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

* [DLMED] remove from min_tests

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

* [DLMED] remove useless var

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

* [DLMED] add skip flag

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

* [DLMED] update according to comments

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

* [DLMED] add dist tests

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] enhance some unit tests

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

* [MONAI] python code formatting

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

* [DLMED] remove from min_tests

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

* [DLMED] change to standlone APIs to write files

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

* [MONAI] python code formatting

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

* [DLMED] add file type check

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

* [DLMED] add output_type arg

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

* [DLMED] develop standlone API

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] fix flake8 error

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

* [DLMED] fix min test

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

Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
@rijobro
unify installation instructions (#1524)
c435327 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@wyli
1526-DiceCE (#1527)
a6cb37c 
* fixes #1526

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

* fixes Useless inheritance from object https://deepsource.io/gh/Project-MONAI/MONAI/issue/PYL-R0205

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

* fixes https://github.com/Project-MONAI/MONAI/pull/1527/checks?check_run_id=1794062607#step:10:7763

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma Nic-Ma merged commit 42a45e0 into Nic-Ma:master Feb 1, 2021
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