New wsireader #4147

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Merged

bhashemian merged 33 commits into Project-MONAI:dev from bhashemian:new-wsireader

Apr 20, 2022

Member

bhashemian commented Apr 19, 2022

Fixes #4071
Fixes #4098

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.

bhashemian and others added 30 commits

April 12, 2022 01:18


          Redesign BaseWSIReader, WSIReader, CuCIMWSIReader

2baa344

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>


          Add unittests for WSIReader

e46fea0

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>


          Add image mode for output validation

f946a63

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>


          Merge branch 'dev' into new-wsireader

9b41019


          Update docs

9c15ea3

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>


          Update references to new WSIReader

e004538

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>


          Remove legacy WSIReader

df0a61e

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>


          Update unittests

b64c087

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>


          Update docs

7f09e73

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>


          sort imports

d95e1c2

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>


          Clean up imports

025376b

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>


          Update docstrings

3e6fb27

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>


          Update docs and docstrings

b8a2444

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>


          [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 <3968947+drbeh@users.noreply.github.com>


          Remove redundant checking

aed0ac5

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>


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

272d11f

…ader


          Update read and other methods

ae4ff17

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>


          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 <3968947+drbeh@users.noreply.github.com>


          Make workaround for CuImage objects

da6b675

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>


          Add unittests for multi image reading

1ed8154

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>


          Update a note about cucim

77f8747

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>


          Update type hints and docstrings

36e5b17

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>


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

0328fe6

…sireader


          Redesign whole slide image reading (Project-MONAI#4107)

78340a9

* Redesign BaseWSIReader,  WSIReader, CuCIMWSIReader

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Add unittests for WSIReader

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Add image mode for output validation

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Update docs

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Update references to new WSIReader

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Remove legacy WSIReader

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Update unittests

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Update docs

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* sort imports

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Clean up imports

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Update docstrings

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Update docs and docstrings

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* [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 <3968947+drbeh@users.noreply.github.com>

* Remove redundant checking

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Update read and other methods

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Update wsireader to support multi image and update docstrings

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Make workaround for CuImage objects

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Add unittests for multi image reading

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Update a note about cucim

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Update type hints and docstrings

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>


          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 <3968947+drbeh@users.noreply.github.com>


          Revert to legacy WSIReader

41337db

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>


          Rename test files

daec9c7

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

bhashemian added 2 commits

April 19, 2022 22:28


          Rename test files

124477e

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>


          Merge branch 'dev' into new-wsireader

5aa59b3

Member Author

bhashemian commented Apr 19, 2022 •

edited

Loading

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.

bhashemian requested a review from Nic-Ma

April 19, 2022 22:33

Nic-Ma approved these changes

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Contributor

Nic-Ma left a comment

Looks good to me.
Thanks for the quick update.

bhashemian enabled auto-merge (squash)

April 19, 2022 22:36


          Merge branch 'dev' into new-wsireader

f848288

Contributor

Nic-Ma commented Apr 19, 2022

/build

bhashemian merged commit cb9040e into Project-MONAI:dev

Can-Zhao added a commit to Can-Zhao/MONAI that referenced this pull request


          Add comments

4379e90

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 <vennw@nvidia.com>

* remove duplicate places

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

4105 drops pt16 support (Project-MONAI#4106)

* update sys req

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* temp test

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update code for torch>=1.7

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* temp tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* autofix

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes import

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* clear cache

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update based on comments

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* remove temp cmd

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Make `pixelshuffle` scriptable (Project-MONAI#4109)

* Update the existing functionality to comply with the `torchscript.jit.script` function.

Signed-off-by: Ramon Emiliani <ramon@afxmedical.com>

meta tensor (Project-MONAI#4077)

* meta tensor

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

4084 Add kwargs for `Tensor.to()` in engines (Project-MONAI#4112)

* [DLMED] add kwargs for to() API

Signed-off-by: Nic Ma <nma@nvidia.com>

* [MONAI] python code formatting

Signed-off-by: monai-bot <monai.miccai2019@gmail.com>

* [DLMED] fix typo

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix flake8

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>

Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

fixes pytorch version tests (Project-MONAI#4127)

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

update meta tensor api (Project-MONAI#4131)

* update meta tensor api

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update based on comments

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

runtests.sh isort (Project-MONAI#4134)

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

update citation (Project-MONAI#4133)

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

`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 <33289025+rijobro@users.noreply.github.com>

* fix

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* fix

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

[DLMED] fix file name in meta (Project-MONAI#4145)

Signed-off-by: Nic Ma <nma@nvidia.com>

4116 Add support for advanced args of AMP (Project-MONAI#4132)

* [DLMED] fix typo in bundle scripts

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] add support for AMP args

Signed-off-by: Nic Ma <nma@nvidia.com>

* [MONAI] python code formatting

Signed-off-by: monai-bot <monai.miccai2019@gmail.com>

* [DLMED] fix flake8

Signed-off-by: Nic Ma <nma@nvidia.com>

Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

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 deleted the new-wsireader branch

February 22, 2023 15:30

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