merge master by Nic-Ma · Pull Request #124 · Nic-Ma/MONAI

Nic-Ma · 2021-06-07T15:55:18Z

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.

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

* [DLMED] add MapLabelValue Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] add missing doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]>

* Add unittests for SmartCachePatchWSIDataset Signed-off-by: Behrooz <[email protected]> * Turn off shuffle for SmartCachePatchWSIDataset Signed-off-by: Behrooz <[email protected]>

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

* fixes #1848 Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit 563e7ea. Signed-off-by: Wenqi Li <[email protected]>

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

Allowing the choice of epoch and iteration interval. Signed-off-by: Petru-Daniel Tudosiu <[email protected]>

* [DLMED] enhance list_collate Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] update based on comments Co-authored-by: Wenqi Li <[email protected]> Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

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

* [DLMED] add slicing support in datasets Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests 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] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update doc-strings and typehints Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue 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]>

* download_if_not_exist Signed-off-by: Behrooz <[email protected]> * Update cuimage reader tests Signed-off-by: Behrooz <[email protected]> * Update openslide reader tests Signed-off-by: Behrooz <[email protected]> * Update the file path to be relative to the test file Signed-off-by: Behrooz <[email protected]> * Update patch wsi dataset tests Signed-off-by: Behrooz <[email protected]> * Update smartcache patch wsi dataset tests Signed-off-by: Behrooz <[email protected]> * Revert "download_if_not_exist" This reverts commit a4c65f3. Signed-off-by: Behrooz <[email protected]> * Update with download_url Signed-off-by: Behrooz <[email protected]> * [MONAI] python code formatting

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]>

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

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

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

* additional deepgrow workflow events Signed-off-by: Wenqi Li <[email protected]> * remove the attach method Signed-off-by: Wenqi Li <[email protected]>

* 2304 enhance image dataset to handle meta Signed-off-by: Wenqi Li <[email protected]> * fixes typo Signed-off-by: Wenqi Li <[email protected]>

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

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

* [DLMED] update affine data Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix doc-build issue Signed-off-by: Nic Ma <[email protected]>

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

* [DLMED] fix endian issue of nibabel header Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

rijobro and others added 30 commits March 23, 2021 17:21

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

Update SmartCachePatchWSIDataset and add unittests (#1853)

c157fb8

* Add unittests for SmartCachePatchWSIDataset Signed-off-by: Behrooz <[email protected]> * Turn off shuffle for SmartCachePatchWSIDataset Signed-off-by: Behrooz <[email protected]>

adds-bicubic-option (#1850)

61a2a21

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

1848 - testing with pytorch 1.8.1 (#1856)

76beeb2

* fixes #1848 Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit 563e7ea. Signed-off-by: Wenqi Li <[email protected]>

[DLMED] support single item (#1884)

a1f938a

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

Epoch/Iteration interval (#1870)

9f6ceeb

Allowing the choice of epoch and iteration interval. Signed-off-by: Petru-Daniel Tudosiu <[email protected]>

[DLMED] add data_root_dir arg (#1890)

f3ccbac

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

rijobro and others added 29 commits May 27, 2021 10:36

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]>

[DLMED] move IterationEvents into workflow (#2299)

63a3c78

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

Use reshape to replace view in loss function (#2298)

4defcdf

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

[DLMED] update persistent dataset (#2307)

be87f31

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

2056 additional deepgrow workflow events (#2305)

c1e06f5

* additional deepgrow workflow events Signed-off-by: Wenqi Li <[email protected]> * remove the attach method Signed-off-by: Wenqi Li <[email protected]>

2304 enhances image dataset to handle meta (#2308)

2ff528e

* 2304 enhance image dataset to handle meta Signed-off-by: Wenqi Li <[email protected]> * fixes typo Signed-off-by: Wenqi Li <[email protected]>

fixes integration test (#2312)

316449b

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

optional strict check (#2309)

509c2c1

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

2316 Make saved affine match data content (#2322)

27e64e0

* [DLMED] update affine data Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix doc-build issue Signed-off-by: Nic Ma <[email protected]>

Modify initialize function (#2324)

a961918

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

Nic-Ma merged commit c52d484 into Nic-Ma:2310-csv-datalist Jun 7, 2021

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merge master#124

merge master#124
Nic-Ma merged 337 commits intoNic-Ma:2310-csv-datalistfrom
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Nic-Ma commented Jun 7, 2021

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