merge master by Nic-Ma · Pull Request #119 · Nic-Ma/MONAI

Nic-Ma · 2021-06-03T04:25:55Z

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 <[email protected]>

* Jupyter and other additions Signed-off-by: Eric Kerfoot <[email protected]> * Jupyter utilities update Signed-off-by: Eric Kerfoot <[email protected]> * Jupyter utilities update Signed-off-by: Eric Kerfoot <[email protected]> * Jupyter utilities update Signed-off-by: Eric Kerfoot <[email protected]> * Jupyter utilities update Signed-off-by: Eric Kerfoot <[email protected]> * Jupyter utilities update Signed-off-by: Eric Kerfoot <[email protected]> * Jupyter utilities update Signed-off-by: Eric Kerfoot <[email protected]> * Jupyter utilities update Signed-off-by: Eric Kerfoot <[email protected]> * Jupyter utilities update Signed-off-by: Eric Kerfoot <[email protected]> * Jupyter utilities update Signed-off-by: Eric Kerfoot <[email protected]> * Update Signed-off-by: Eric Kerfoot <[email protected]> Co-authored-by: Nic Ma <[email protected]> Co-authored-by: Richard Brown <[email protected]>

batch inverse

* add pretrain options Signed-off-by: Yiheng Wang <[email protected]> * rewrite error message add test cases Signed-off-by: Yiheng Wang <[email protected]>

Signed-off-by: Richard Brown <[email protected]>

* cron tutorial notebooks Signed-off-by: Richard Brown <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

Signed-off-by: Richard Brown <[email protected]>

* allow None for switch endianness Signed-off-by: Richard Brown <[email protected]> * add PIL testing Signed-off-by: Richard Brown <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>

* Jupyter and other additions Signed-off-by: Eric Kerfoot <[email protected]> * Jupyter utilities update Signed-off-by: Eric Kerfoot <[email protected]>

* [DLMED] update ROCAUC Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix CI tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

test time augmentations

* fixes tutorial issue 150 Signed-off-by: Wenqi Li <[email protected]> * revise based on comments Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Richard Brown <[email protected]>

* [DLMED] enhance transform logging Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] ignore type warning Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

* [DLMED] add eval mode in Evaluators Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]>

* [DLMED] enhance SmartCache Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI test Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

Signed-off-by: kate-sann5100 <[email protected]>

* 1837--collating Signed-off-by: Wenqi Li <[email protected]> * fixes transform device Signed-off-by: Wenqi Li <[email protected]> * reverting self.affine Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Richard Brown <[email protected]>

Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Richard Brown <[email protected]>

* conditional random field implementation Signed-off-by: charliebudd <[email protected]>

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

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

* Implement fully convolutional version of torchvision models Signed-off-by: Behrooz <[email protected]> * Update networks init with TorchVisionFullyConvModel Signed-off-by: Behrooz <[email protected]> * Add unittests for TorchVisionFullyConvModel Signed-off-by: Behrooz <[email protected]> * Add another test case Signed-off-by: Behrooz <[email protected]> * Upate docs for TorchVisionFullyConvModel Signed-off-by: Behrooz <[email protected]> * Make torchvision import optional Signed-off-by: Behrooz <[email protected]> * Skip the tests if torchvision not available Signed-off-by: Behrooz <[email protected]> * Improve the model based on comments Signed-off-by: Behrooz <[email protected]> * Update and add test cases Signed-off-by: Behrooz <[email protected]>

* Add label dimensions to be compatible with changes in model output Signed-off-by: Behrooz <[email protected]> * Update test case outputs and add new test case Signed-off-by: Behrooz <[email protected]>

* fixes init affinehead Signed-off-by: Wenqi Li <[email protected]> * fixes unit tests Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Nic Ma <[email protected]>

* fixes #1857, SpatialCrop is compatible with tensors Signed-off-by: Wenqi Li <[email protected]> * update val comparisons Signed-off-by: Wenqi Li <[email protected]>

* Optimize speed and support any dimensions Signed-off-by: Yiheng Wang <[email protected]> * Fix black issue Signed-off-by: Yiheng Wang <[email protected]> * Add unittest and docstrings Signed-off-by: Yiheng Wang <[email protected]> * Modify box size and others Signed-off-by: Yiheng Wang <[email protected]> * Add pathology nms Signed-off-by: Yiheng Wang <[email protected]> * Update docs Signed-off-by: Yiheng Wang <[email protected]> * Update pathology nms Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: Behrooz <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* [DLMED] fix read permission issue Signed-off-by: Nic Ma <[email protected]>

* fix lr finder

* better way of managing Cache Signed-off-by: Coen <[email protected]> * Update test_smartcachedataset.py Signed-off-by: Coen <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Yiheng Wang <[email protected]>

)

Signed-off-by: chaliebudd <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

* cache grid Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * adds cache tests Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: ambroslins <[email protected]>

* add pypi quick tests Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * cron pypi tests Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit b6d86d6. Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * revise cron Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit 44cddc0. Signed-off-by: Wenqi Li <[email protected]> * docstring Signed-off-by: Wenqi Li <[email protected]> * update setup.cfg Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Richard Brown <[email protected]>

* [DLMED] fix CopyItemsd transform Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>

* enhance downloading APIs Signed-off-by: Wenqi Li <[email protected]> * update docstrings Signed-off-by: Wenqi Li <[email protected]>

* removing convolutional compatability kernel for an optional matric multiplication Signed-off-by: chaliebudd <[email protected]> * change to identity test against None Co-authored-by: Richard Brown <[email protected]> Signed-off-by: chaliebudd <[email protected]> * updating tests, non-determanism should be solved Signed-off-by: chaliebudd <[email protected]> * moving compatability matrix to gpu in test to prevent errors when running without cuda Signed-off-by: chaliebudd <[email protected]> * removing unused imports Signed-off-by: chaliebudd <[email protected]> * pytyping fix for optional arg Signed-off-by: chaliebudd <[email protected]> Co-authored-by: Richard Brown <[email protected]>

* removing convolutional compatability kernel for an optional matric multiplication Signed-off-by: chaliebudd <[email protected]> * change to identity test against None Co-authored-by: Richard Brown <[email protected]> Signed-off-by: chaliebudd <[email protected]> * updating tests, non-determanism should be solved Signed-off-by: chaliebudd <[email protected]> * moving compatability matrix to gpu in test to prevent errors when running without cuda Signed-off-by: chaliebudd <[email protected]> * removing unused imports Signed-off-by: chaliebudd <[email protected]> * pytyping fix for optional arg Signed-off-by: chaliebudd <[email protected]> * moving back to permissive testing sue to cuda non determanism Signed-off-by: chaliebudd <[email protected]> Co-authored-by: Richard Brown <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

* skip resampling if possible Signed-off-by: Wenqi Li <[email protected]> * update docstring Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] enhance doc-string of CacheDataset Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>

* revise cron-pip Signed-off-by: Wenqi Li <[email protected]> * fixes pythonpath Signed-off-by: Wenqi Li <[email protected]> * update path Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

* skip resampling if possible Signed-off-by: Wenqi Li <[email protected]> * update docstring Signed-off-by: Wenqi Li <[email protected]>

* Started on a ResNet for classification from 1D, 2D, 3D images Signed-off-by: Douwe Spaanderman <[email protected]>

* release note v0.5.3 Signed-off-by: Wenqi Li <[email protected]> * update changelog Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] add more type to decollate Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix pickle issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Isaac Yang <[email protected]>

* update ci/cd to remove duplicated jobs Signed-off-by: Wenqi Li <[email protected]> * update docstring Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Isaac Yang <[email protected]> Co-authored-by: Nic Ma <[email protected]>

Signed-off-by: Richard Brown <[email protected]>

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

PadListDataCollate transform (#1813)

3e313d2

Signed-off-by: Richard Brown <[email protected]>

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 <[email protected]> * rewrite error message add test cases Signed-off-by: Yiheng Wang <[email protected]>

remove .value from InverseKeys enum (#1817)

5151b15

Signed-off-by: Richard Brown <[email protected]>

cron tutorial notebooks (#1783)

06e1e99

* cron tutorial notebooks Signed-off-by: Richard Brown <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

refactor CommonKeys (#1825)

a8f83e1

Signed-off-by: Richard Brown <[email protected]>

Jupyter followup (#1826)

c4bb4cb

* Jupyter and other additions Signed-off-by: Eric Kerfoot <[email protected]> * Jupyter utilities update Signed-off-by: Eric Kerfoot <[email protected]>

Test time augmentations (#1794)

83855b9

test time augmentations

fixes tutorial issue 150 (#1830)

8ddd09f

* fixes tutorial issue 150 Signed-off-by: Wenqi Li <[email protected]> * revise based on comments Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Richard Brown <[email protected]>

1807 Enhance SmartCacheDataset with shuffle and exception (#1832)

e8e2f3e

* [DLMED] enhance SmartCache Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI test Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

fix device bug (#1841)

f8c3901

Signed-off-by: kate-sann5100 <[email protected]>

truncate plot title string (#1843)

c3f1e02

Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Richard Brown <[email protected]>

Conditional Random Field (#1806)

b6d1cea

* conditional random field implementation Signed-off-by: charliebudd <[email protected]>

Support multidimensional labels (#1851)

5e4a0ab

* Add label dimensions to be compatible with changes in model output Signed-off-by: Behrooz <[email protected]> * Update test case outputs and add new test case Signed-off-by: Behrooz <[email protected]>

identity init. for global net (#1849)

126768f

* fixes init affinehead Signed-off-by: Wenqi Li <[email protected]> * fixes unit tests Signed-off-by: Wenqi Li <[email protected]>

[DLMED] fix SmartCache warning (#1855)

e0feb53

Signed-off-by: Nic Ma <[email protected]>

1857 - SpatialCrop supports with tensors (#1858)

149216e

* fixes #1857, SpatialCrop is compatible with tensors Signed-off-by: Wenqi Li <[email protected]> * update val comparisons Signed-off-by: Wenqi Li <[email protected]>

infer spatial dims from input (#1860)

83a6ad8

1862 Fix checkpoint read permission (#1863)

28e000d

* [DLMED] fix read permission issue Signed-off-by: Nic Ma <[email protected]>

[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 <[email protected]> * Update test_smartcachedataset.py Signed-off-by: Coen <[email protected]>

tested (#2192)

c2b364b

Signed-off-by: Wenqi Li <[email protected]>

fixes logo link (#2202)

381330c

Signed-off-by: Wenqi Li <[email protected]>

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

969bbb7

Signed-off-by: Yiheng Wang <[email protected]>

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

7d36d8a

)

cleaning allocated memory (#2216)

5bae730

Signed-off-by: chaliebudd <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

improve error msg (#2229)

4377c4e

Signed-off-by: Wenqi Li <[email protected]>

2172 caching grid for randaffine (#2228)

bb88eb2

* cache grid Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * adds cache tests Signed-off-by: Wenqi Li <[email protected]>

fix type for margin argument in CropForegroundd (#2234)

d21038c

Signed-off-by: ambroslins <[email protected]>

SaveImage print_log (#2237)

84b41d9

Signed-off-by: Richard Brown <[email protected]>

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

405975c

* [DLMED] fix CopyItemsd transform Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>

enhance downloading APIs (#2242)

8255973

* enhance downloading APIs Signed-off-by: Wenqi Li <[email protected]> * update docstrings Signed-off-by: Wenqi Li <[email protected]>

move mednist to gdrive (#2276)

2b13246

Signed-off-by: Wenqi Li <[email protected]>

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

2aec103

* skip resampling if possible Signed-off-by: Wenqi Li <[email protected]> * update docstring Signed-off-by: Wenqi Li <[email protected]>

Enhance the doc-string of CacheDataset (#2279)

70f9fd1

* [DLMED] enhance doc-string of CacheDataset Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>

Fixes cron tests (#2277)

7ee7989

* revise cron-pip Signed-off-by: Wenqi Li <[email protected]> * fixes pythonpath Signed-off-by: Wenqi Li <[email protected]> * update path Signed-off-by: Wenqi Li <[email protected]>

move mednist to gdrive (#2276)

9638a56

Signed-off-by: Wenqi Li <[email protected]>

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

385ce70

* skip resampling if possible Signed-off-by: Wenqi Li <[email protected]> * update docstring Signed-off-by: Wenqi Li <[email protected]>

[WIP] ResNet (#2253)

2f60799

* Started on a ResNet for classification from 1D, 2D, 3D images Signed-off-by: Douwe Spaanderman <[email protected]>

updates changelog v0.5.3 (#2271)

d78c669

* release note v0.5.3 Signed-off-by: Wenqi Li <[email protected]> * update changelog Signed-off-by: Wenqi Li <[email protected]>

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 <[email protected]> Co-authored-by: Isaac Yang <[email protected]>

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

e442051

* update ci/cd to remove duplicated jobs Signed-off-by: Wenqi Li <[email protected]> * update docstring Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Isaac Yang <[email protected]> Co-authored-by: Nic Ma <[email protected]>

inverse one-to-many transforms (#2230)

d4d1733

Signed-off-by: Richard Brown <[email protected]>

Nic-Ma merged commit c73eb75 into Nic-Ma:2300-decollate-non-batch Jun 3, 2021

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merge master#119

merge master#119
Nic-Ma merged 327 commits intoNic-Ma:2300-decollate-non-batchfrom
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Nic-Ma commented Jun 3, 2021

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Nic-Ma commented Jun 3, 2021

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