New wsireader #4147

bhashemian · 2022-04-19T22:24:57Z

Description

This PR is a re-design and re-implementation of WSIReader with similar API but not provide full backward compatibility. This PR implements BaseWSIReader, WSIReader, and CuCIMWSIReader. It also make sure that the current dependencies on the legacy WSIReader is correctly satisfied.

Status

Ready

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 --disttests.
In-line docstrings updated.
Documentation updated, tested make html command in the docs/ folder.

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

for more information, see https://pre-commit.ci

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

…ader

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

…sireader

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

…sireader

* Redesign BaseWSIReader, WSIReader, CuCIMWSIReader Signed-off-by: Behrooz <[email protected]> * Add unittests for WSIReader Signed-off-by: Behrooz <[email protected]> * Add image mode for output validation Signed-off-by: Behrooz <[email protected]> * Update docs Signed-off-by: Behrooz <[email protected]> * Update references to new WSIReader Signed-off-by: Behrooz <[email protected]> * Remove legacy WSIReader Signed-off-by: Behrooz <[email protected]> * Update unittests Signed-off-by: Behrooz <[email protected]> * Update docs Signed-off-by: Behrooz <[email protected]> * sort imports Signed-off-by: Behrooz <[email protected]> * Clean up imports Signed-off-by: Behrooz <[email protected]> * Update docstrings Signed-off-by: Behrooz <[email protected]> * Update docs and docstrings Signed-off-by: Behrooz <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix a typo Signed-off-by: Behrooz <[email protected]> * Remove redundant checking Signed-off-by: Behrooz <[email protected]> * Update read and other methods Signed-off-by: Behrooz <[email protected]> * Update wsireader to support multi image and update docstrings Signed-off-by: Behrooz <[email protected]> * Make workaround for CuImage objects Signed-off-by: Behrooz <[email protected]> * Add unittests for multi image reading Signed-off-by: Behrooz <[email protected]> * Update a note about cucim Signed-off-by: Behrooz <[email protected]> * Update type hints and docstrings Signed-off-by: Behrooz <[email protected]>

…sireader

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

bhashemian · 2022-04-19T22:33:48Z

Hi @Nic-Ma, This PR is the same as the PR #4107 that you reviewed except that I brought back the legacy WSIReader to have backward compatibility. Later, once we have all the component ready we can deprecate the legacy components.

Nic-Ma

Looks good to me.
Thanks for the quick update.

Nic-Ma · 2022-04-19T23:58:58Z

/build

Add padding to filter to ensure same size after anti-aliasing Use replicate padding insteadof zero padding to avoid artifacts for non-zero boundary Reuse GaussianSmooth 4073 Enhance DynUNet doc-strings (Project-MONAI#4102) * Fix doc strings error Signed-off-by: Yiheng Wang <[email protected]> * remove duplicate places Signed-off-by: Yiheng Wang <[email protected]> 4105 drops pt16 support (Project-MONAI#4106) * update sys req Signed-off-by: Wenqi Li <[email protected]> * temp test Signed-off-by: Wenqi Li <[email protected]> * update code for torch>=1.7 Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * autofix Signed-off-by: Wenqi Li <[email protected]> * fixes import Signed-off-by: Wenqi Li <[email protected]> * clear cache Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * remove temp cmd Signed-off-by: Wenqi Li <[email protected]> Make `pixelshuffle` scriptable (Project-MONAI#4109) * Update the existing functionality to comply with the `torchscript.jit.script` function. Signed-off-by: Ramon Emiliani <[email protected]> meta tensor (Project-MONAI#4077) * meta tensor Signed-off-by: Richard Brown <[email protected]> 4084 Add kwargs for `Tensor.to()` in engines (Project-MONAI#4112) * [DLMED] add kwargs for to() API 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 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]> fixes pytorch version tests (Project-MONAI#4127) Signed-off-by: Wenqi Li <[email protected]> update meta tensor api (Project-MONAI#4131) * update meta tensor api Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> runtests.sh isort (Project-MONAI#4134) Signed-off-by: Richard Brown <[email protected]> update citation (Project-MONAI#4133) Signed-off-by: Wenqi Li <[email protected]> `ToMetaTensor` and `FromMetaTensor` transforms (Project-MONAI#4115) to and from meta no skip if before pytorch 1.7 (Project-MONAI#4139) * no skip if before pytorch 1.7 Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> [DLMED] fix file name in meta (Project-MONAI#4145) Signed-off-by: Nic Ma <[email protected]> 4116 Add support for advanced args of AMP (Project-MONAI#4132) * [DLMED] fix typo in bundle scripts Signed-off-by: Nic Ma <[email protected]> * [DLMED] add support for AMP args 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]> Co-authored-by: monai-bot <[email protected]> New wsireader (Project-MONAI#4147) `MetaTensor`: collate; decollate; dataset; dataloader; out=; indexing and iterating across batches (Project-MONAI#4137) `MetaTensor`: collate; decollate; dataset; dataloader; out=; indexing and iterating across batches (Project-MONAI#4137)

bhashemian and others added 30 commits April 12, 2022 01:18

Redesign BaseWSIReader, WSIReader, CuCIMWSIReader

2baa344

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

Add unittests for WSIReader

e46fea0

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

Add image mode for output validation

f946a63

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

Merge branch 'dev' into new-wsireader

9b41019

Update docs

9c15ea3

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

Update references to new WSIReader

e004538

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

Remove legacy WSIReader

df0a61e

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

Update unittests

b64c087

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

Update docs

7f09e73

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

sort imports

d95e1c2

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

Clean up imports

025376b

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

Update docstrings

3e6fb27

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

Update docs and docstrings

b8a2444

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

[pre-commit.ci] auto fixes from pre-commit.com hooks

0268a03

for more information, see https://pre-commit.ci

Fix a typo

f2b14aa

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

Remove redundant checking

aed0ac5

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

Merge branch 'new-wsireader' of github.com:drbeh/MONAI into new-wsire…

272d11f

…ader

Update read and other methods

ae4ff17

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

Merge branch 'pathology' of github.com:Project-MONAI/MONAI into new-w…

e0bad98

…sireader

Update wsireader to support multi image and update docstrings

e5a7a18

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

Make workaround for CuImage objects

da6b675

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

Add unittests for multi image reading

1ed8154

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

Update a note about cucim

77f8747

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

Update type hints and docstrings

36e5b17

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

Merge branch 'pathology' of github.com:Project-MONAI/MONAI into new-w…

0328fe6

…sireader

Merge branch 'pathology' of github.com:Project-MONAI/MONAI into new-w…

a0ddd3f

…sireader

Bring back previous WSIReader for backward compatibility

a592482

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

Revert to legacy WSIReader

41337db

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

Rename test files

daec9c7

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

bhashemian added 2 commits April 19, 2022 22:28

Rename test files

124477e

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

Merge branch 'dev' into new-wsireader

5aa59b3

bhashemian requested a review from Nic-Ma April 19, 2022 22:33

Nic-Ma approved these changes Apr 19, 2022

View reviewed changes

bhashemian enabled auto-merge (squash) April 19, 2022 22:36

Merge branch 'dev' into new-wsireader

f848288

bhashemian merged commit cb9040e into Project-MONAI:dev Apr 20, 2022

bhashemian deleted the new-wsireader branch February 22, 2023 15:30

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New wsireader #4147

New wsireader #4147

bhashemian commented Apr 19, 2022

bhashemian commented Apr 19, 2022 •

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Nic-Ma left a comment

Nic-Ma commented Apr 19, 2022

New wsireader #4147

New wsireader #4147

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bhashemian commented Apr 19, 2022

Status

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Nic-Ma commented Apr 19, 2022

bhashemian commented Apr 19, 2022 •

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