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GridPatch to Extract Tiles/Patches #4321

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merged 72 commits into from
May 31, 2022
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@bhashemian bhashemian commented May 23, 2022

Fixes #4012

Description

This PR implement GridPath and GridPatchd that extracts patches sweeping the entire image. It will return a list of patches (and not a generator) to have a priorly defined number of patches, which is useful for the subsequent transforms and handlers. This transform should be able to replace the functionality of TileOnGrid for pathology pipelines.

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 -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 bhashemian linked an issue May 23, 2022 that may be closed by this pull request
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@wyli @Nic-Ma This PR requires PR #4239 to be merged first. Thanks

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Thanks for the quick update.
It overall looks good to me, just some minor comments inline and several questions to @ericspod @rijobro .

Thanks.

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Hi @Nic-Ma @Ericspo, thank you very much for your comments. I have addressed them all. Please let me know if anything is missing.

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Nic-Ma commented May 31, 2022

/black

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Nic-Ma commented May 31, 2022

/build

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Thanks for the quick update.
Looks good to me.
@ericspod do you have any other comments?

Thanks.

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I'm good here!

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Nic-Ma commented May 31, 2022

/black

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Nic-Ma commented May 31, 2022

/build

@bhashemian bhashemian merged commit 2f589c6 into Project-MONAI:dev May 31, 2022
@bhashemian bhashemian deleted the grid-patch branch February 22, 2023 15:30
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Including tiles coordinates in TileOnGrid transform Refactor and Simplify Tile transform
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