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WSI sliding window splitter#6107

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Nic-Ma merged 104 commits intoProject-MONAI:devfrom
bhashemian:wsi-sliding-window
May 26, 2023
Merged

WSI sliding window splitter#6107
Nic-Ma merged 104 commits intoProject-MONAI:devfrom
bhashemian:wsi-sliding-window

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@bhashemian bhashemian commented Mar 6, 2023 •
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Fixes #5871

Description

This PR:

  • implements a WSISlidingWindowSplitter a splitter for whole slide imaging,
  • refactors SlidingWindowSplitter to make it inheritable for wsi version (backward incompatible arguments),
  • adds new feature to AvgMerger to crop the output (backward compatible), and
  • updates PatchInference to set cropping shape for new feature in AvgMerger (backward compatible)

Types of changes

  • Non-breaking change (fix or new feature that would not break existing functionality).
  • 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 11 commits March 1, 2023 15:29
@bhashemian
implement wsi sliding window splitter
ebb8ca6 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
add unittests
0b9b817 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
add unittests
dd0224d 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Merge branch 'dev' of github.com:Project-MONAI/MONAI into wsi-sliding…
52d1aa4 
…-window
@bhashemian
Merge branch 'dev' of github.com:Project-MONAI/MONAI into wsi-sliding…
1efcbea 
…-window
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
acd2bb8 
for more information, see https://pre-commit.ci
@bhashemian
formatting and typing
0441b2b 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Merge branch 'wsi-sliding-window' of github.com:drbeh/MONAI into wsi-…
65883f6 
…sliding-window
@bhashemian
formatting
31646cc 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Merge branch 'dev' into wsi-sliding-window
0608934
@bhashemian
Add several unittests
5c4d415 
Signed-off-by: Behrooz <[email protected]>
@bhashemian bhashemian marked this pull request as ready for review March 9, 2023 18:05
@bhashemian bhashemian requested a review from KumoLiu March 9, 2023 18:05
@bhashemian
add docs
a1a3852 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
update docs
630b76b 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
add test case for filter
c0fdd69 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
fomatting
3fc350c 
Signed-off-by: Behrooz <[email protected]>
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bhashemian commented Mar 9, 2023

@Nic-Ma @wyli do you know why flake8 is failing here?
I cannot reproduce it locally. All checks of ./runtests.sh --build --codeformat are being passed on my machine.

@wyli wyli enabled auto-merge (squash) March 9, 2023 19:55
@wyli wyli disabled auto-merge March 9, 2023 19:55
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Nic-Ma commented Mar 10, 2023

/black

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Nic-Ma commented Mar 10, 2023

Hi @drbeh ,

You can use /black or --autofix command to format the code, refer to:
https://github.com/Project-MONAI/MONAI/blob/dev/runtests.sh#L77

Thanks.

@monai-bot
[MONAI] code formatting
4d51cd1 
Signed-off-by: monai-bot <[email protected]>
@bhashemian bhashemian requested a review from Nic-Ma March 10, 2023 14:35
KumoLiu
KumoLiu reviewed Mar 13, 2023
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@bhashemian bhashemian marked this pull request as draft March 14, 2023 19:44
@bhashemian bhashemian requested a review from KumoLiu May 19, 2023 14:13
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bhashemian commented May 22, 2023

Hi @Nic-Ma @KumoLiu, could you please check if all your comments are addressed and if you have any other feedback. Thanks

@Nic-Ma Nic-Ma requested a review from ericspod May 23, 2023 08:47
ericspod
ericspod reviewed May 23, 2023
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ericspod reviewed May 23, 2023
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ericspod reviewed May 24, 2023
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ericspod commented May 24, 2023

Hi @drbeh I was asked to review as @KumoLiu may not be available. I had a few minor comments I've given above but otherwise it looks good to me.

bhashemian and others added 7 commits May 24, 2023 15:46
@bhashemian @ericspod
Update monai/inferers/inferer.py
202e538 
Co-authored-by: Eric Kerfoot <[email protected]>
Signed-off-by: Dr. Behrooz Hashemian <[email protected]>
@bhashemian @ericspod
Update monai/inferers/splitter.py
276524a 
Co-authored-by: Eric Kerfoot <[email protected]>
Signed-off-by: Dr. Behrooz Hashemian <[email protected]>
@bhashemian
Merge branch 'dev' into wsi-sliding-window
c8865f9
@bhashemian
Update monai/inferers/splitter.py
11db54a 
Signed-off-by: Behrooz <[email protected]>
@bhashemian @ericspod
Update monai/inferers/splitter.py
9237596 
Co-authored-by: Eric Kerfoot <[email protected]>
Signed-off-by: Dr. Behrooz Hashemian <[email protected]>
@bhashemian
Update monai/inferers/splitter.py
9915305 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Update monai/inferers/splitter.py
66181e1 
Signed-off-by: Behrooz <[email protected]>
KumoLiu
KumoLiu approved these changes May 25, 2023
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I have no other comments, thanks for the update.

ericspod
ericspod approved these changes May 25, 2023
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Looks good!

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Nic-Ma commented May 25, 2023

/build

@Nic-Ma Nic-Ma enabled auto-merge (squash) May 25, 2023 15:57
@Nic-Ma Nic-Ma merged commit 4bd93c0 into Project-MONAI:dev May 26, 2023
@bhashemian bhashemian deleted the wsi-sliding-window branch June 9, 2023 15:41
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@ericspod ericspod ericspod approved these changes

@Nic-Ma Nic-Ma Nic-Ma approved these changes

@KumoLiu KumoLiu KumoLiu approved these changes

@wyli wyli Awaiting requested review from wyli

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Implement a sliding window Splitter for whole slide images

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@bhashemian @Nic-Ma @wyli @KumoLiu @ericspod @monai-bot