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[WIP] Adding Stain Normalization Transform for Pathology #1912

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nsrivathsa
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Fixes # .

Description

Added a Transform for CuPy-based Stain Normalization for Pathology.

Status

Work in progress

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 -f -u --net --coverage.
  • Quick tests passed locally by running ./runtests.sh --quick --unittests.
  • In-line docstrings updated.
  • Documentation updated, tested make html command in the docs/ folder.

@nsrivathsa nsrivathsa changed the title [Draft] Adding Stain Normalization Transform for Pathology [WIP] Adding Stain Normalization Transform for Pathology Mar 31, 2021
@bhashemian bhashemian self-requested a review April 1, 2021 00:17
bhashemian
bhashemian reviewed Apr 7, 2021
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Well done! It's a great job!
I left few comments but once you add the unittests, I will review it again. Thanks

bhashemian
bhashemian reviewed Apr 7, 2021
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I left few comments on cupy. Please let me know if you have any question on that.

bhashemian
bhashemian reviewed Apr 12, 2021
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Hi @nsrivathsa, thanks for addressing all the comments. So far so good! Have you had a chance to work on the test cases?

bhashemian and others added 25 commits April 12, 2021 15:42
@bhashemian @nsrivathsa
Update CuCIM (Project-MONAI#1909)
63ad63c 
Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@bhashemian @nsrivathsa
Update pathology unittests (Project-MONAI#1910)
e761433 
Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@nsrivathsa
added stain norm transform
8337cd2 
Signed-off-by: Neha Srivathsa <[email protected]>
@bhashemian @nsrivathsa
Update prob map handler (Project-MONAI#1911)
71ce959 
* Rename the prob map producer unittest to match the module

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

* Change probs_map to prob_map

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

* Prepend image_inference_outputs with temp to be ignored

Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@yiheng-wang-nv @nsrivathsa
Implement dice_focal loss (Project-MONAI#1914)
40afac8 
Signed-off-by: Yiheng Wang <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@wyli @bhashemian @nsrivathsa
followup of Project-MONAI#1878 (Project-MONAI#1913)
5113396 
* followup of Project-MONAI#1878, fixes tests, remove json loading

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

* Update test ordinal numbers

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

Co-authored-by: Behrooz <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@kate-sann5100 @wyli @nsrivathsa
1868-fix-potential-inf-in-lncc-loss (Project-MONAI#1915)
7552279 
* clip variance to be >= 0

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

* max for torch1.6

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

Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@wyli @nsrivathsa
1919 - test pt 2103 (Project-MONAI#1920)
47a3069 
* update to use pytorch2103

Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@wyli @nsrivathsa
fixes typos (Project-MONAI#1924)
89447c4 
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@Nic-Ma @wyli @nsrivathsa
1900 Add support to save patch data into NIfTI or PNG files (Project-…
26749ff 
…MONAI#1922)

* [DLMED] SaveImage supports patch data

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]>

* [DLMED] fix flake8 issue

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

Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@wyli @Nic-Ma @nsrivathsa
Revert "1919 - test pt 2103 (Project-MONAI#1920)" (Project-MONAI#1925)
7300b92 
This reverts commit 4bd26f9.

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

Co-authored-by: Nic Ma <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@wyli @nsrivathsa
skip warp tests before torch 18 (Project-MONAI#1927)
11e6a81 
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@wyli @nsrivathsa
update docstrings (Project-MONAI#1931)
d5afef3 
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@wyli @nsrivathsa
update get_package_version (Project-MONAI#1930)
7a2ac8a 
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@Nic-Ma @monai-bot
@wyli @nsrivathsa
1904 Add early stop handler (Project-MONAI#1921)
f602cdc 
* [DLMED] add EarlyStop handler

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

* [MONAI] python code formatting

Signed-off-by: monai-bot <[email protected]>

* [DLMED] enhance validation handler

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

* [DLMED] add set_trainer support

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

* [DLMED] add more check

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

* [DLMED] fix flake8 issue

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]>

Co-authored-by: monai-bot <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@Nic-Ma @monai-bot @nsrivathsa
1900 Change to save patch_index in the meta_dict (Project-MONAI#1933)
b67aed7 
* [DLMED] change to save patch_index in meta_dict

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

* [DLMED] remove error import

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]>

Co-authored-by: monai-bot <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@wyli @nsrivathsa
enhance min/exact version check (Project-MONAI#1937)
b5dbcbe 
Signed-off-by: Neha Srivathsa <[email protected]>
@danieltudosiu @monai-bot
@Nic-Ma @nsrivathsa
Enabled partial checkpoint loading (Project-MONAI#1936)
18b50a5 
* Enabled partial checkpoint loading

Allowing partial loading of a model via strict=False.

Signed-off-by: Petru-Daniel Tudosiu <[email protected]>

* [MONAI] python code formatting

Signed-off-by: monai-bot <[email protected]>

* [DLMED] simplify strict arg

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

Co-authored-by: monai-bot <[email protected]>
Co-authored-by: Nic Ma <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@wyli @nsrivathsa
fixes issue of typing with py3.6 (Project-MONAI#1942)
4c2894d 
* less warning msg; remove PILImage types

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

* remove engine type

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

* temp tests

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

* add quick py36 37 tests

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

* temp tests

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

* Revert "temp tests"

This reverts commit deaed40.

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

* Revert "temp tests"

This reverts commit 3e8d8f4.

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

* min test exclude senet test

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

* update

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

* temp test

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

* Revert "temp test"

This reverts commit 31f40a0.

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

* update get gpu id

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

* update docsstrings

Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@bhashemian @wyli @nsrivathsa
Make ProbNMS a Transform (Project-MONAI#1941)
fc547d3 
* Add ProbNMS to transforts/post/array

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

* Implement ProbNMSDict

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

* Update the usage and add unittests

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

* Update docs

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

* Correct docs

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

* Correct test case

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

Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@wyli @nsrivathsa
fixes ThreadDataLoader (Project-MONAI#1945)
29d3ae5 
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@wyli @nsrivathsa
fixes itk dep. version (Project-MONAI#1944)
a5c631d 
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@bhashemian @nsrivathsa
Garbage Collector Handler (Project-MONAI#1940)
ec0b5ad 
* Implement garbage collector handler

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

* Make trigger_event lower case

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

* Add unittest for garbage collector

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

* Update docs

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

* Exclude from min test

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

* Fix a typo

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

* Fix a bug

Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@nsrivathsa
style and api changes
a5ed4a4 
Signed-off-by: Neha Srivathsa <[email protected]>
@Nic-Ma @wyli @nsrivathsa
1939 Add strict_shape option in CheckpointLoader (Project-MONAI#1946)
5e7be9b 
* [DLMED] add strict_shape option

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

* [DLMED] add unit tests

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

* update test case

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

* fixes test config

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

Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
wyli and others added 27 commits April 12, 2021 15:42
@wyli @nsrivathsa
remove unused RandomizableTransform (Project-MONAI#1952)
4aad0cf 
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@wyli @nsrivathsa
1956 - docker image building pipelines (Project-MONAI#1957)
4456604 
* refactor docker building

Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@wyli @nsrivathsa
1955 style issue (Project-MONAI#1958)
1c4dcd9 
* update docs deps.

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

* fixes https://github.com/Project-MONAI/MONAI/runs/2283148095\?check_suite_focus\=true\#step:7:8972

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

* 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 <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@bhashemian @nsrivathsa
Update garbage collection assertion (Project-MONAI#1959)
6e39205 
* Update garbage collection assertion to a more reliable one

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

* Remove print

Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@danieltudosiu @nsrivathsa
Working ParameterScheduler (Project-MONAI#1949)
2fdee25 
* Working ParameterScheduler 

Added a new ParameterScheduler handler and the required tests.

Signed-off-by: Petru-Daniel Tudosiu <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@Nic-Ma @nsrivathsa
[DLMED] remove warning (Project-MONAI#1962)
4803f9d 
Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@Nic-Ma @monai-bot
@wyli @nsrivathsa
1916 Add support for custom events in workflows (Project-MONAI#1961)
08dfbeb 
* [DLMED] add support for addtional events

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

* [DLMED] add unit tests

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

* [DLMED] fix typehints

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

* [MONAI] python code formatting

Signed-off-by: monai-bot <[email protected]>

* fixes typos

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

Co-authored-by: monai-bot <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@nsrivathsa
added cupy requirement
b1703b2 
Signed-off-by: Neha Srivathsa <[email protected]>
@wyli @nsrivathsa
1965 - register_backward_hook (Project-MONAI#1966)
f965d49 
* fixes Project-MONAI#1965

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

* adds docstring

Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@Nic-Ma @monai-bot @nsrivathsa
1968 Enhance meta data doc-string in SegmentationSaver (Project-MONAI…
06c9720 
…#1969)

* [DLMED] enhance doc-strings

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: Neha Srivathsa <[email protected]>
@nsrivathsa
made cupy an optional import
43acc44 
Signed-off-by: Alvin Ihsani <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@nsrivathsa
minor changes per comments
c18f20c 
Signed-off-by: Neha Srivathsa <[email protected]>
@masadcv @yiheng-wang-nv
@wyli @nsrivathsa
Adding EfficientNetsB0-B7 support (Project-MONAI#1938)
5bd8a83 
* adding init efficientnet support

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

* fixing flake8 and further refactoring

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

* adding unittests for efficiennet

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

* making unittests backwards compatible python<3.8

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

* fixed kitty unittests file path

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

* adding docstrings and minor refactoring

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

* fix flake8-py3 failing test

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

* generalize drop_connect for n-dim, fix/add unittests, remove assert

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

* fix failing unittest, CC0-license image for test

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

* refactoring code for review

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

* WIP fix mypy type hint errors

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

* fix cuda test error

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

* WIP fix test errors

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

* adding non-default shape tests

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

* remove 3d case from non-default shape test

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

* refactoring and updating docs

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

Co-authored-by: Yiheng Wang <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@Nic-Ma @monai-bot @nsrivathsa
1866 Add TransformInverter handler (Project-MONAI#1970)
b5b89c6 
* [DLMED] add TransformInverter handler

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

* [DLMED] fix typo

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

* [DLMED] add support in SegmentationSaver handler

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]>

* [DLMED] fix CI test

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: Neha Srivathsa <[email protected]>
@wyli @nsrivathsa
1889 - changelog for v0.5.0 (Project-MONAI#1923)
66c78ab 
* changelog for 0.5.0

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

* update changelog

Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@Nic-Ma @monai-bot @nsrivathsa
1977 Support different inverse interpolation mode (Project-MONAI#1978)
4487a53 
* [DLMED] add TransformInverter handler

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

* [DLMED] fix typo

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

* [DLMED] add support in SegmentationSaver handler

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]>

* [DLMED] fix CI test

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

* [MONAI] python code formatting

Signed-off-by: monai-bot <[email protected]>

* [DLMED] save mode into inverse dict

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

* [DLMED] add unit tests

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

* [DLMED] fix ToTensor inverse issue

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

* [DLMED] change the replacement logic into util function

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

* [DLMED] add more tests

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

* [DLMED] fix flake8

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: Neha Srivathsa <[email protected]>
@Nic-Ma @wyli @nsrivathsa
Update technical highlights for v0.5 (Project-MONAI#1981)
997e6a1 
* [DLMED] update highlights for 0.5

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

* [DLMED] add invert transforms

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

* [DLMED] add more highlights

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

* [DLMED] add checkpointloader

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

* downscale image

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

* downscale image

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

* update docs

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

* update desc

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

* update

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

Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@wyli @nsrivathsa
1973 - docstring update convs example (Project-MONAI#1980)
cb58c96 
* update convs docstrings

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

* increase tol for cuda crf

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

* update requirements according to docs/requirements

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

* prune image

Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@kate-sann5100 @wyli @nsrivathsa
test runner (Project-MONAI#1986)
9b3dd3f 
Signed-off-by: Wenqi Li <[email protected]>

Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@Nic-Ma @wyli @nsrivathsa
1987 Add support for a list of Tensor in metrics handlers (Project-MO…
8bbc607 
…NAI#1988)

* [DLMED] metrics support a list of tensor

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

* update workflow test

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

* [DLMED] fix engine.state.output dict copy issue

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

* [DLMED] add num_workers

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

* fixes typos

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

* update tests

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

* update docstrings

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

* tests

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

Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@wyli @nsrivathsa
add timeout (Project-MONAI#1989)
daf6730 
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@wyli @nsrivathsa
fixes ci error handling (Project-MONAI#1990)
f39bed4 
* handling error

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

* temp test

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

* fixes tests

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

* Revert "temp test"

This reverts commit 60661ae.

Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@wyli @nsrivathsa
1889 update preview version number (Project-MONAI#1991)
b71b607 
* update dev version

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

* typo fix

Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@nsrivathsa
minor formatting change
875bcab 
Signed-off-by: Neha Srivathsa <[email protected]>
@rijobro @nsrivathsa
fix comprehension error (Project-MONAI#1995)
f319c27 
Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@bhashemian @nsrivathsa
Import cupy for type checking
be632aa 
Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Neha Srivathsa <[email protected]>
@nsrivathsa
added unit tests
060421b 
Signed-off-by: Neha Srivathsa <[email protected]>
@bhashemian
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closing in favor of #1998

@bhashemian bhashemian closed this Apr 13, 2021
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@nsrivathsa @bhashemian @yiheng-wang-nv @wyli @kate-sann5100 @Nic-Ma @danieltudosiu @masadcv @rijobro