merge master by Nic-Ma · Pull Request #118 · Nic-Ma/MONAI

Nic-Ma · 2021-06-03T04:06:15Z

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.

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

* Jupyter and other additions Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Jupyter utilities update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Jupyter utilities update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Jupyter utilities update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Jupyter utilities update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Jupyter utilities update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Jupyter utilities update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Jupyter utilities update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Jupyter utilities update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Jupyter utilities update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> Co-authored-by: Nic Ma <nma@nvidia.com> Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

batch inverse

* add pretrain options Signed-off-by: Yiheng Wang <vennw@nvidia.com> * rewrite error message add test cases Signed-off-by: Yiheng Wang <vennw@nvidia.com>

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

* cron tutorial notebooks Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

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

* allow None for switch endianness Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * add PIL testing Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.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> * Jupyter utilities update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

* [DLMED] update ROCAUC Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix CI 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>

test time augmentations

* fixes tutorial issue 150 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * revise based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* [DLMED] enhance transform logging 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 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] ignore type warning Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* [DLMED] add eval mode in Evaluators 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> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>

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

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

* 1837--collating Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes transform device Signed-off-by: Wenqi Li <wenqil@nvidia.com> * reverting self.affine Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* conditional random field implementation Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* [DLMED] fix affine error and thread-safe issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update CI tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update typehints Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.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] make cachedataset to be thread-safe Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove inverse ID check Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] restore CacheDataset and inverse transform Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* Implement PatchWSIDataset and SmartCachePathWSIDataset Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove label preprocessing and adopt new type of inputs Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update type hints Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add init file Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Change grid_size to grid_shape Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add a unittest for PatchWSIDataset Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add more unittests Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update docstrings and make minor changes Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Convert labels to numpy to match the change in dataset Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update location from center to corner Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update unittests locations from center to corner Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update docs for pathology datasets Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update type hint and doc Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update docstrings Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Format docstring Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update length of the smartcache dataset Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add unittest for SmartCachePatchWSIDataset Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Minor changes and fixes Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add unnittest for OpenSlide option Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add new line Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove SmartCachePatchWSIDataset test to fix it Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * move init docstring to class docstring Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* Implement fully convolutional version of torchvision models Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update networks init with TorchVisionFullyConvModel Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add unittests for TorchVisionFullyConvModel Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add another test case Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Upate docs for TorchVisionFullyConvModel Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Make torchvision import optional Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Skip the tests if torchvision not available Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Improve the model based on comments Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update and add test cases Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

* Add label dimensions to be compatible with changes in model output Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update test case outputs and add new test case Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

* fixes init affinehead Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>

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

* fixes #1857, SpatialCrop is compatible with tensors Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update val comparisons Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* Optimize speed and support any dimensions Signed-off-by: Yiheng Wang <vennw@nvidia.com> * Fix black issue Signed-off-by: Yiheng Wang <vennw@nvidia.com> * Add unittest and docstrings Signed-off-by: Yiheng Wang <vennw@nvidia.com> * Modify box size and others Signed-off-by: Yiheng Wang <vennw@nvidia.com> * Add pathology nms Signed-off-by: Yiheng Wang <vennw@nvidia.com> * Update docs Signed-off-by: Yiheng Wang <vennw@nvidia.com> * Update pathology nms Signed-off-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: Behrooz <3968947+behxyz@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] fix read permission issue Signed-off-by: Nic Ma <nma@nvidia.com>

* fix lr finder

* better way of managing Cache Signed-off-by: Coen <coengruijt@gmail.com> * Update test_smartcachedataset.py Signed-off-by: Coen <coengruijt@gmail.com>

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

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

)

Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

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

* cache grid Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds cache tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: ambroslins <ambros.lins@gmail.com>

* add pypi quick tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update Signed-off-by: Wenqi Li <wenqil@nvidia.com> * cron pypi tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "temp tests" This reverts commit b6d86d6. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update Signed-off-by: Wenqi Li <wenqil@nvidia.com> * revise cron Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "temp tests" This reverts commit 44cddc0. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update setup.cfg Signed-off-by: Wenqi Li <wenqil@nvidia.com>

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

* [DLMED] fix CopyItemsd transform 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>

* enhance downloading APIs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* removing convolutional compatability kernel for an optional matric multiplication Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * change to identity test against None Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com> Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * updating tests, non-determanism should be solved Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * moving compatability matrix to gpu in test to prevent errors when running without cuda Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * removing unused imports Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * pytyping fix for optional arg Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* removing convolutional compatability kernel for an optional matric multiplication Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * change to identity test against None Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com> Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * updating tests, non-determanism should be solved Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * moving compatability matrix to gpu in test to prevent errors when running without cuda Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * removing unused imports Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * pytyping fix for optional arg Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * moving back to permissive testing sue to cuda non determanism Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

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

* skip resampling if possible Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] enhance doc-string of CacheDataset 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>

* revise cron-pip Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes pythonpath Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update path Signed-off-by: Wenqi Li <wenqil@nvidia.com>

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

* skip resampling if possible Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* Started on a ResNet for classification from 1D, 2D, 3D images Signed-off-by: Douwe Spaanderman <dspaanderman@gmail.com>

* release note v0.5.3 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update changelog Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add more type to decollate 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 CI tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix pickle issue 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>

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

* update ci/cd to remove duplicated jobs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Isaac Yang <isaacy@nvidia.com> Co-authored-by: Nic Ma <nma@nvidia.com>

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

rijobro and others added 30 commits March 19, 2021 21:44

PadListDataCollate transform (#1813)

3e313d2

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

Batch inverse (#1795)

a2aeb40

batch inverse

1804 add pretrain for densenet senet by using subclass (#1812)

b6f213e

* add pretrain options Signed-off-by: Yiheng Wang <vennw@nvidia.com> * rewrite error message add test cases Signed-off-by: Yiheng Wang <vennw@nvidia.com>

remove .value from InverseKeys enum (#1817)

5151b15

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

cron tutorial notebooks (#1783)

06e1e99

* cron tutorial notebooks Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

refactor CommonKeys (#1825)

a8f83e1

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

Jupyter followup (#1826)

c4bb4cb

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

Test time augmentations (#1794)

83855b9

test time augmentations

fixes tutorial issue 150 (#1830)

8ddd09f

* fixes tutorial issue 150 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * revise based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

1807 Enhance SmartCacheDataset with shuffle and exception (#1832)

e8e2f3e

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

fix device bug (#1841)

f8c3901

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

truncate plot title string (#1843)

c3f1e02

Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Conditional Random Field (#1806)

b6d1cea

* conditional random field implementation Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

identity init. for global net (#1849)

126768f

* fixes init affinehead Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>

[DLMED] fix SmartCache warning (#1855)

e0feb53

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

1857 - SpatialCrop supports with tensors (#1858)

149216e

* fixes #1857, SpatialCrop is compatible with tensors Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update val comparisons Signed-off-by: Wenqi Li <wenqil@nvidia.com>

infer spatial dims from input (#1860)

83a6ad8

1862 Fix checkpoint read permission (#1863)

28e000d

* [DLMED] fix read permission issue Signed-off-by: Nic Ma <nma@nvidia.com>

[1859] fix lr finder (#1865)

32e6b12

* fix lr finder

cgrain and others added 29 commits May 27, 2021 10:35

More efficient SmartCacheLoader (#2181)

82936eb

* better way of managing Cache Signed-off-by: Coen <coengruijt@gmail.com> * Update test_smartcachedataset.py Signed-off-by: Coen <coengruijt@gmail.com>

tested (#2192)

c2b364b

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

fixes logo link (#2202)

381330c

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

Add warnings for inf/nan surface distance (#2205)

969bbb7

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

2041 - fixing main/releasing branch CI/CD; update contributing.md (#2123

7d36d8a

)

cleaning allocated memory (#2216)

5bae730

Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

improve error msg (#2229)

4377c4e

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

2172 caching grid for randaffine (#2228)

bb88eb2

* cache grid Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds cache tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>

fix type for margin argument in CropForegroundd (#2234)

d21038c

Signed-off-by: ambroslins <ambros.lins@gmail.com>

SaveImage print_log (#2237)

84b41d9

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

2236 Fix the duplicated key issue in CopyItemsd transform (#2238)

405975c

* [DLMED] fix CopyItemsd transform 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>

enhance downloading APIs (#2242)

8255973

* enhance downloading APIs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com>

move mednist to gdrive (#2276)

2b13246

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

skip resampling for randaffine(d) if possible (#2264)

2aec103

* skip resampling if possible Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Enhance the doc-string of CacheDataset (#2279)

70f9fd1

* [DLMED] enhance doc-string of CacheDataset 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>

Fixes cron tests (#2277)

7ee7989

* revise cron-pip Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes pythonpath Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update path Signed-off-by: Wenqi Li <wenqil@nvidia.com>

move mednist to gdrive (#2276)

9638a56

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

skip resampling for randaffine(d) if possible (#2264)

385ce70

* skip resampling if possible Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com>

[WIP] ResNet (#2253)

2f60799

* Started on a ResNet for classification from 1D, 2D, 3D images Signed-off-by: Douwe Spaanderman <dspaanderman@gmail.com>

updates changelog v0.5.3 (#2271)

d78c669

* release note v0.5.3 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update changelog Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Merge commit '385ce7059be16e8476d0c1b56fe251d8894241a5' into dev

37545b4

Merge branch 'releasing/0.5.3' into dev

51e4790

update contrib doc (#2293)

9af0e27

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

update ci/cd to remove duplicated jobs (#2285)

e442051

* update ci/cd to remove duplicated jobs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Isaac Yang <isaacy@nvidia.com> Co-authored-by: Nic Ma <nma@nvidia.com>

inverse one-to-many transforms (#2230)

d4d1733

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

Nic-Ma merged commit 405ef89 into Nic-Ma:adjust-engines Jun 3, 2021

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merge master#118

merge master#118
Nic-Ma merged 327 commits into
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Nic-Ma commented Jun 3, 2021

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