merge master by Nic-Ma · Pull Request #153 · Nic-Ma/MONAI

Nic-Ma · 2021-06-30T09:23:16Z

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.

* refactor docker building Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update docs deps. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes https://github.com/Project-MONAI/MONAI/runs/2283148095\?check_suite_focus\=true\#step:7:8972 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "fixes https://github.com/Project-MONAI/MONAI/runs/2283148095\?check_suite_focus\=true\#step:7:8972" This reverts commit 1407400. Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* Update garbage collection assertion to a more reliable one Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove print Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

* Working ParameterScheduler Added a new ParameterScheduler handler and the required tests. Signed-off-by: Petru-Daniel Tudosiu <petru.daniel@tudosiu.com>

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

* [DLMED] add support for addtional events Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typehints Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * fixes typos Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* fixes #1965 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] enhance doc-strings 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>

* adding init efficientnet support Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * fixing flake8 and further refactoring Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * adding unittests for efficiennet Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * making unittests backwards compatible python<3.8 Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * fixed kitty unittests file path Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * adding docstrings and minor refactoring Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * fix flake8-py3 failing test Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * generalize drop_connect for n-dim, fix/add unittests, remove assert Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * fix failing unittest, CC0-license image for test Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * refactoring code for review Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * WIP fix mypy type hint errors Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * fix cuda test error Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * WIP fix test errors Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * adding non-default shape tests Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * remove 3d case from non-default shape test Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> * refactoring and updating docs Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk> Co-authored-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add TransformInverter handler Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add support in SegmentationSaver handler Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CI test 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>

* changelog for 0.5.0 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update changelog Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add TransformInverter handler Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add support in SegmentationSaver handler Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CI test Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] save mode into inverse dict Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix ToTensor inverse issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] change the replacement logic into util function Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 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>

* [DLMED] update highlights for 0.5 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add invert transforms Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more highlights Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add checkpointloader Signed-off-by: Nic Ma <nma@nvidia.com> * downscale image Signed-off-by: Wenqi Li <wenqil@nvidia.com> * downscale image Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update desc Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* update convs docstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com> * increase tol for cuda crf Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update requirements according to docs/requirements Signed-off-by: Wenqi Li <wenqil@nvidia.com> * prune image Signed-off-by: Wenqi Li <wenqil@nvidia.com>

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

* [DLMED] metrics support a list of tensor Signed-off-by: Nic Ma <nma@nvidia.com> * update workflow test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [DLMED] fix engine.state.output dict copy issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add num_workers Signed-off-by: Nic Ma <nma@nvidia.com> * fixes typos Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com> * tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

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

* handling error Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "temp test" This reverts commit 60661ae. Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update dev version Signed-off-by: Wenqi Li <wenqil@nvidia.com> * typo fix Signed-off-by: Wenqi Li <wenqil@nvidia.com>

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

TTA progress bar, use torch for mode, add label meta_data

* follow up of #1992 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update spacing inverse Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] update TransformInverter Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix deepcopy 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>

* [DLMED] add more tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add nearest test cases Signed-off-by: Nic Ma <nma@nvidia.com>

* adds a what's new page Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add SaliencyInferer Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance CAM logic Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com> Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* [DLMED] enhance unit tests 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>

* [DLMED] add warning 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>

* Jupyter and other additions Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

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

* added spikes transform Signed-off-by: Yaniel Cabrera <yaniel.cabrera@gmail.com>

* [DLMED] add image_only and unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com>

* add json config model support Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add -1 support for pixdim Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add scale_np = scale_np[:d] Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update accortding to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove image_only in Spacing and Orientation Signed-off-by: Nic Ma <nma@nvidia.com>

Signed-off-by: am <am>

Signed-off-by: Dong Yang <dongy@nvidia.com>

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

* [DLMED] add TorchVisionClassificationModel Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* Add parameter unpacking for transforms Signed-off-by: Sebastian Penhouet <sebastian.penhouet@airamed.de>

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

* [DLMED] add copy logic Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com>

* Add query to NGC to get matched model URL and version. Allow mmar download with latest version or a specific version. Signed-off-by: Isaac Yang <isaacy@nvidia.com>

no need for default orig_size stored for invertible transforms

Signed-off-by: Can Zhao <canz@nvidia.com>

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

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

#2455) * add clara_train_covid19_3d_ct_classification and clara_train_covid19_annotation_ct_lung_1 point to pt version of covid19 lung annotation model Signed-off-by: Holger Roth <hroth@nvidia.com>

* [DLMED] add pad options Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add to dict transforms 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> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

Signed-off-by: ahatamizadeh <ahatamizadeh@nvidia.com>

* [DLMED] update ignite to 0.4.5 Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] add dynamic data list in CacheDataset Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add support to PersistentDataset Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CI tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance dataset 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_data -> set_data Signed-off-by: Nic Ma <nma@nvidia.com>

Signed-off-by: Holger Roth <hroth@nvidia.com>

…grow (#2442) Signed-off-by: vnath <vnath@nvidia.com>

…2315) * [WIP] 2220 Decollate batch into list of tensors after model forward (#2244) * [DLMED] add support for Activation transform Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] change all the array level post transforms to channel-first Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update all the IO, utility, post transforms Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update engines for list of dict Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update all the event handlers Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] support non-batch data 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> * [DLMED] update based on the latest APIs Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix all the unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issues Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove unused import Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix integration test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix integration tests Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix integration 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] add support to copy scalar Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix wrong unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix doc issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix broken tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] simplify CSV saver Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add copy_scalar_to_batch util Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] change to preprocessing and postprocessing Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] change file name to postprocessing Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo in doc-string Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add Decollated back 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> * [DLMED] update to use ignite v0.4.5 metrics API Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix conflicts Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * fixes #2452 Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

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

wyli and others added 30 commits April 7, 2021 01:12

1956 - docker image building pipelines (#1957)

5c411d1

* refactor docker building Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Update garbage collection assertion (#1959)

d6ed956

* Update garbage collection assertion to a more reliable one Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove print Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Working ParameterScheduler (#1949)

7581255

* Working ParameterScheduler Added a new ParameterScheduler handler and the required tests. Signed-off-by: Petru-Daniel Tudosiu <petru.daniel@tudosiu.com>

[DLMED] remove warning (#1962)

baca6e0

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

1965 - register_backward_hook (#1966)

8cbd59a

* fixes #1965 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com>

1968 Enhance meta data doc-string in SegmentationSaver (#1969)

d56c002

* [DLMED] enhance doc-strings 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>

1889 - changelog for v0.5.0 (#1923)

3a7cd46

* changelog for 0.5.0 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update changelog Signed-off-by: Wenqi Li <wenqil@nvidia.com>

test runner (#1986)

a625d38

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

add timeout (#1989)

f5d5737

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

1889 update preview version number (#1991)

b4d8780

* update dev version Signed-off-by: Wenqi Li <wenqil@nvidia.com> * typo fix Signed-off-by: Wenqi Li <wenqil@nvidia.com>

fix comprehension error (#1995)

d1f4e6f

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

TTA progress bar, use torch for mode, add label meta_data (#1992)

b3eb73a

TTA progress bar, use torch for mode, add label meta_data

include meta when inverting (#1997)

d72f61e

* follow up of #1992 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update spacing inverse Signed-off-by: Wenqi Li <wenqil@nvidia.com>

update (#2000)

2707407

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

Add more test for nearest interpolation in TransformInverter (#2001)

583e35b

* [DLMED] add more tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add nearest test cases Signed-off-by: Nic Ma <nma@nvidia.com>

2003 - adds a what's new page (#2005)

2c6d688

* adds a what's new page Signed-off-by: Wenqi Li <wenqil@nvidia.com>

2007 Enhance the unit tests of MapLabelValue transform (#2008)

5f47407

* [DLMED] enhance unit tests 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>

2011 Add warning for resample in SegnmentationSaver (#2013)

88806e1

* [DLMED] add warning 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>

Plot engine fix (#2015)

357e6d4

* Jupyter and other additions Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

wyli and others added 29 commits June 22, 2021 20:16

fixes concurrency group (#2409)

0bd312a

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

Spike (Herringbone) artifact transform (#2337)

88fe0fc

* added spikes transform Signed-off-by: Yaniel Cabrera <yaniel.cabrera@gmail.com>

2420 Add image_only option to several spatial transforms (#2421)

a0afa60

* [DLMED] add image_only and unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com>

2415 - add json config model support for mmar loading (#2416)

ea028f5

* add json config model support Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Brain MMAR pretrained examples (#2406)

855a025

Signed-off-by: am <am>

add model desc for liver and pancreas seg (#2431)

5ff1bba

Signed-off-by: Dong Yang <dongy@nvidia.com>

[DLMED] enhance docs (#2429)

c20f70b

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

Fix permissions for blossom CI (#2438)

0662ed2

2407 Add support to set number classes for TorchVision models (#2408)

79b83d9

* [DLMED] add TorchVisionClassificationModel Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

Add parameter unpacking for transforms (#2437)

38403bb

* Add parameter unpacking for transforms Signed-off-by: Sebastian Penhouet <sebastian.penhouet@airamed.de>

[DLMED] enhance assert (#2444)

05b2da6

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

2445 Fix inplace modification issue of SmartCacheDataset (#2446)

eec33b6

* [DLMED] add copy logic Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com>

Add query to NGC to get matched model URL and version. (#2433)

43aba96

* Add query to NGC to get matched model URL and version. Allow mmar download with latest version or a specific version. Signed-off-by: Isaac Yang <isaacy@nvidia.com>

no need for default orig_size stored for invertible transforms (#2441)

6401c5e

no need for default orig_size stored for invertible transforms

add annotation for brain and spleen (#2448)

079fcd4

Signed-off-by: Can Zhao <canz@nvidia.com>

Fix docstring error (#2461)

eb29e99

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

2453 Enhance ToTensor transform to support data with no dim (#2454)

9f9b63a

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

add clara_train_covid19_3d_ct_classification and clara_train_covid19_… (

1a707f0

#2455) * add clara_train_covid19_3d_ct_classification and clara_train_covid19_annotation_ct_lung_1 point to pt version of covid19 lung annotation model Signed-off-by: Holger Roth <hroth@nvidia.com>

update_model_desc_prostate_spleen (#2466)

7b08d40

Signed-off-by: ahatamizadeh <ahatamizadeh@nvidia.com>

2399 update ignite to v0.4.5 (#2451)

91ea1b6

* [DLMED] update ignite to 0.4.5 Signed-off-by: Nic Ma <nma@nvidia.com>

update clara_pt_covid19_3d_ct_classification model description (#2472)

cdf05b0

Signed-off-by: Holger Roth <hroth@nvidia.com>

Model Description in apps/mmars updated with NGC description for Deep…

0aa936f

…grow (#2442) Signed-off-by: vnath <vnath@nvidia.com>

2273 update model items (#2473)

f831c7f

Update blossom-ci.yml (#2484)

50d8391

Nic-Ma merged commit 59a04da into Nic-Ma:2467-enhance-score-func Jun 30, 2021

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merge master#153

merge master#153
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