merge master by Nic-Ma · Pull Request #113 · Nic-Ma/MONAI

Nic-Ma · 2021-05-25T02:08:25Z

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.

* fixes data type in switching Signed-off-by: Wenqi Li <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>

* Implement CuImageReader and OpenSlideReader Signed-off-by: Behrooz <[email protected]> * Add unittests for CuImageReader Signed-off-by: Behrooz <[email protected]> * Add unittests for OpenSlideReader Signed-off-by: Behrooz <[email protected]> * Sort imports Signed-off-by: Behrooz <[email protected]> * Add correct boundaries Signed-off-by: Behrooz <[email protected]> * Add test cases for reading patches on a grid for CuImage Signed-off-by: Behrooz <[email protected]> * Add patch whole slide imaging dataset for pathology Signed-off-by: Behrooz <[email protected]> * Add test case for read patches for OpenSlide Signed-off-by: Behrooz <[email protected]> * flake8 and few minor changes Signed-off-by: Behrooz <[email protected]> * black Signed-off-by: Behrooz <[email protected]> * flake8 Signed-off-by: Behrooz <[email protected]> * Add kwargs to CuImageReader and OpenSlideReader's read method Signed-off-by: Behrooz <[email protected]> * Change the type hint from np.dtype to DTypeLike Signed-off-by: Behrooz <[email protected]> * Fix a bug Signed-off-by: Behrooz <[email protected]> * Implement WSIReader and unittests Signed-off-by: Behrooz <[email protected]> * Minor updates Signed-off-by: Behrooz <[email protected]> * Fix few typing issues Signed-off-by: Behrooz <[email protected]> * Revert datasets Signed-off-by: Behrooz <[email protected]> * Add shape property to openslide image object Reverse size to be compatible with output size (hxw) Signed-off-by: Behrooz <[email protected]> * Add untittest for loading the whole image Reverse the size accroding to the WSIReader Signed-off-by: Behrooz <[email protected]> * Update the whole image size Signed-off-by: Behrooz <[email protected]> * Remove optional size Signed-off-by: Behrooz <[email protected]> * Remove optional dtype Signed-off-by: Behrooz <[email protected]> * Remove _get_spatial_shape return type Signed-off-by: Behrooz <[email protected]> * Reverse the orders of dimensions of `location` to be compatible with image shape Signed-off-by: Behrooz <[email protected]> * Change test cases to use smaller image and revese location's dimensions Signed-off-by: Behrooz <[email protected]> * Replace the test TIFF and some upgrades Signed-off-by: Behrooz <[email protected]> * Update dependencies for OpenSlide Signed-off-by: Behrooz <[email protected]> * Update unittests for OpenSlide and CuImage Signed-off-by: Behrooz <[email protected]> * Fix openslide dependency Signed-off-by: Behrooz <[email protected]> * Fix doc dependencies Signed-off-by: Behrooz <[email protected]> * Minor changes Signed-off-by: Behrooz <[email protected]> * Few variable name changes Signed-off-by: Behrooz <[email protected]> * Add EnsureChannelFirst Signed-off-by: Behrooz <[email protected]> * Add metadata to WSIReader Signed-off-by: Behrooz <[email protected]>

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

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

* update docstring Signed-off-by: Wenqi Li <[email protected]> * revise docstring Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] add Affined 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]>

* update for torch 1.8.0 Signed-off-by: Wenqi Li <[email protected]> * mute codecov upload error Signed-off-by: Wenqi Li <[email protected]>

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

with allow_missing_keys_mode

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

* fixes #1500 update grid dataset to support patch level transforms Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] update type of arg in workflows 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 flake8 issue 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]>

* 1651 implement RegUNet Signed-off-by: kate-sann5100 <[email protected]>

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

* Update MONAI Docker with OpenSlide dependencies Signed-off-by: Behrooz <[email protected]> * Update cron job to install apt dependencies Signed-off-by: Behrooz <[email protected]>

* use eval for getting class_idx for gradcam

* fixes unit test Signed-off-by: Wenqi Li <[email protected]> * fixes timed call tests Signed-off-by: Wenqi Li <[email protected]>

basic inverse API

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

* addresses testing instance memory errors Signed-off-by: Wenqi Li <[email protected]>

* update coverage config Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * fixes https://github.com/Project-MONAI/MONAI/runs/2083800079?check_suite_focus=true#step:5:13886 Signed-off-by: Wenqi Li <[email protected]> * test cases matching in runner Signed-off-by: Wenqi Li <[email protected]> * fixes openslide tests Signed-off-by: Wenqi Li <[email protected]> * fixes https://github.com/Project-MONAI/MONAI/runs/2086767998?check_suite_focus=true#step:7:5955 Signed-off-by: Wenqi Li <[email protected]> * fixes print stats Signed-off-by: Wenqi Li <[email protected]> * remove temp tests Signed-off-by: Wenqi Li <[email protected]> * remove unused Signed-off-by: Wenqi Li <[email protected]> * remove global logging config Signed-off-by: Wenqi Li <[email protected]> * omit setup.py Signed-off-by: Wenqi Li <[email protected]>

* 1651 implement RegUNet Signed-off-by: kate-sann5100 <[email protected]>

* 1651 implement RegUNet Signed-off-by: kate-sann5100 <[email protected]> * 1651 reformat code Signed-off-by: kate-sann5100 <[email protected]> * 1651 reformat code Signed-off-by: kate-sann5100 <[email protected]> * 1651 add globalnet Signed-off-by: kate-sann5100 <[email protected]> * 1651 reformat code Signed-off-by: kate-sann5100 <[email protected]> * 1651 reformat code Signed-off-by: kate-sann5100 <[email protected]> * 1651 reformat code Signed-off-by: kate-sann5100 <[email protected]> * 1651 reformat code Signed-off-by: kate-sann5100 <[email protected]>

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

* [DLMED] add DistributedWeightedRandomSampler Signed-off-by: Nic Ma <[email protected]>

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

…seeds (#1761) * TEST: Check for identical MedNISTDataset length for different seeds Signed-off-by: Adam Aji <[email protected]> * BUG: MedNISTDataset returns differently sized datasets for diff seeds Signed-off-by: Adam Aji <[email protected]>

* [DLMED] add length API Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove replacement arg Signed-off-by: Nic Ma <[email protected]>

* reduce randomly cropped amount to appease CI Signed-off-by: Richard Brown <[email protected]> * fixes rand inverse Signed-off-by: Wenqi Li <[email protected]>

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

* fixes docstring Signed-off-by: Wenqi Li <[email protected]> * 2099 docstring updates Signed-off-by: Wenqi Li <[email protected]>

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

test network consistency

* enhance norm and act layers Signed-off-by: Yiheng Wang <[email protected]> * write generic norm and act layers Signed-off-by: Yiheng Wang <[email protected]> * Fix flake8 errors Signed-off-by: Yiheng Wang <[email protected]>

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

gibbs transform

* enhance get layers Signed-off-by: Wenqi Li <[email protected]> * codeformat/typo fixes Signed-off-by: Wenqi Li <[email protected]> * fixes type errors Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] add RandScaleCrop Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update for corner case Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo 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]>

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

* Add array and dictionary based CoordConv transforms Signed-off-by: Mark <[email protected]> * Add comments and input checks Signed-off-by: Mark Graham <[email protected]> * Add docs for CoordConv Signed-off-by: Mark Graham <[email protected]> * Add tests for CoordConv Signed-off-by: Mark Graham <[email protected]> * Renames to AddCoordinateChannels and simplifies transform code Signed-off-by: Mark Graham <[email protected]> * Test input channel is unchanged and shorten code more Signed-off-by: Mark Graham <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: Richard Brown <[email protected]> Co-authored-by: monai-bot <[email protected]>

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

* [DLMED] add CenterScaleCrop 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]> Co-authored-by: monai-bot <[email protected]>

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

* [DLMED] enhance CSVSaver Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix test errors Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] update accoring to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

)

* [DLMED] add meta_key arg to components Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI test Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] read-only transforms can share same meta data for keys Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more unit tests Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

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

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

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

* [DLMED] temp combine batch and output Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: Wenqi Li <[email protected]> Co-authored-by: monai-bot <[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]>

* thread safety impl. Signed-off-by: Wenqi Li <[email protected]> * fixes croppad Signed-off-by: Wenqi Li <[email protected]> * fixed intensity Signed-off-by: Wenqi Li <[email protected]> * fixes spatial Signed-off-by: Wenqi Li <[email protected]> * fixes util Signed-off-by: Wenqi Li <[email protected]> * autofix Signed-off-by: Wenqi Li <[email protected]> * update docstring Signed-off-by: Wenqi Li <[email protected]> * update datastats Signed-off-by: Wenqi Li <[email protected]> * fixes docstring Signed-off-by: Wenqi Li <[email protected]> * fixes torch 1.7 issue Signed-off-by: Wenqi Li <[email protected]> * fixes mac/win n_workers Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[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]>

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

wyli and others added 30 commits March 5, 2021 00:52

fixes data type in switching (#1694)

75b5772

* fixes data type in switching Signed-off-by: Wenqi Li <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>

[DLMED] add WSIReader to LoadImage (#1695)

232e8a5

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

Raise import error for openslide and cuimage (#1699)

66811fe

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

1604 Revise docstring cam (#1705)

b25b3d3

* update docstring Signed-off-by: Wenqi Li <[email protected]> * revise docstring Signed-off-by: Wenqi Li <[email protected]>

1704 Add Affined transform (#1709)

ce6628a

* [DLMED] add Affined 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]>

1693 update for pytorch 1.8 (#1700)

133f42a

* update for torch 1.8.0 Signed-off-by: Wenqi Li <[email protected]> * mute codecov upload error Signed-off-by: Wenqi Li <[email protected]>

[DLMED] update datasets (#1712)

634b32d

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

with allow_missing_keys_mode (#1714)

08af0cc

with allow_missing_keys_mode

update links (#1717)

f4560a1

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

1500-update grid dataset to support patch level transforms (#1679)

cbddce9

* fixes #1500 update grid dataset to support patch level transforms Signed-off-by: Wenqi Li <[email protected]>

1651 implement RegUNet (#1658)

78ec66f

* 1651 implement RegUNet Signed-off-by: kate-sann5100 <[email protected]>

remove print msg (#1730)

ea1d04b

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

Fix MONAI docker dependency (#1731)

a462714

* Update MONAI Docker with OpenSlide dependencies Signed-off-by: Behrooz <[email protected]> * Update cron job to install apt dependencies Signed-off-by: Behrooz <[email protected]>

[1710] Gradcam eval (#1734)

d4c201e

* use eval for getting class_idx for gradcam

fixes unit test (#1735)

c362beb

* fixes unit test Signed-off-by: Wenqi Li <[email protected]> * fixes timed call tests Signed-off-by: Wenqi Li <[email protected]>

basic inverse API (#1720)

0b1fc4e

basic inverse API

improve decollate test for set_determinism (#1736)

c3e5a69

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

1236 integration test memory (#1738)

6d3bf2f

* addresses testing instance memory errors Signed-off-by: Wenqi Li <[email protected]>

1665 adjust localnet (#1752)

ce8f92a

* 1651 implement RegUNet Signed-off-by: kate-sann5100 <[email protected]>

[DLMED] update WSIReader for typos and docs (#1758)

e001d2a

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

1742 Add DistributedWeightedRandomSampler (#1745)

21a3c16

* [DLMED] add DistributedWeightedRandomSampler Signed-off-by: Nic Ma <[email protected]>

Croppad inverse transform (#1737)

f56058d

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

TEST: Fix failing pytype check for predict_segmentation (#1762)

e17e158

Add __len__ for DistributedWeightedRandomSampler (#1766)

4670fd2

* [DLMED] add length API Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove replacement arg Signed-off-by: Nic Ma <[email protected]>

reduce randomly cropped amount to appease CI (#1769)

1badb41

* reduce randomly cropped amount to appease CI Signed-off-by: Richard Brown <[email protected]> * fixes rand inverse Signed-off-by: Wenqi Li <[email protected]>

cgrain and others added 29 commits May 12, 2021 17:30

More efficient SmartCacheLoader (#2181)

4ef7d22

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

2099 - enhances dataloader/randomizable docstrings (#2188)

a5cf253

* fixes docstring Signed-off-by: Wenqi Li <[email protected]> * 2099 docstring updates Signed-off-by: Wenqi Li <[email protected]>

tested (#2192)

b94fe25

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

initial network consistency test (#2171)

e68af74

test network consistency

enhance norm and act layers (#2166)

29a0373

* enhance norm and act layers Signed-off-by: Yiheng Wang <[email protected]> * write generic norm and act layers Signed-off-by: Yiheng Wang <[email protected]> * Fix flake8 errors Signed-off-by: Yiheng Wang <[email protected]>

update msg (#2197)

05e1ec2

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

Added Gibbs transform (#2163)

0e6f945

gibbs transform

enhance get layers API (#2199)

95726b0

* enhance get layers Signed-off-by: Wenqi Li <[email protected]> * codeformat/typo fixes Signed-off-by: Wenqi Li <[email protected]> * fixes type errors Signed-off-by: Wenqi Li <[email protected]>

fixes logo link (#2202)

bbca50d

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

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

ca0bda1

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

allow sequence for network consistency (#2209)

fed0136

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

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

e6258c9

)

cleaning allocated memory (#2216)

26ee695

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

array transforms inherit Transform (#2219)

ba03150

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

inverse adjust contrast (#2217)

4c6af53

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

improve error msg (#2229)

ebfd550

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

2172 caching grid for randaffine (#2228)

2fb4b21

* 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)

33539db

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

SaveImage print_log (#2237)

fac9350

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

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

81994d2

* [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]>

fixes network docs (#2240)

5d46589

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

Nic-Ma merged commit 44882b7 into Nic-Ma:2223-post-transform-handler May 25, 2021

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merge master#113

merge master#113
Nic-Ma merged 277 commits intoNic-Ma:2223-post-transform-handlerfrom
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Nic-Ma commented May 25, 2021

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