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GridPatch to Extract Tiles/Patches#4321

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bhashemian merged 72 commits intoProject-MONAI:devfrom
bhashemian:grid-patch
May 31, 2022
Merged

GridPatch to Extract Tiles/Patches#4321
bhashemian merged 72 commits intoProject-MONAI:devfrom
bhashemian:grid-patch

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@bhashemian bhashemian commented May 23, 2022 •
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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
Including tiles coordinates in TileOnGrid transform #4090
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bhashemian added 11 commits May 23, 2022 13:14
@bhashemian
Add docs
cf6c72a 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Deprecate SplitOnGrid and TileOnGrid
a01faa7 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Merge branch 'dev' into grid-patch
f5bf4bf
@bhashemian
Fix formatting
c2afba0 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Update WSIReader value error message
a8e68cc 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Implement RandGridPatchd
13fbd8d 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Update init
4a1b8da 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Add unittests for GridPatchd
0b6fe58 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Add unittests for RandGridPatch
4105006 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Add unittests for RandGridPatchd
b7e2259 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Merge branch 'dev' into grid-patch
e7d8d25
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bhashemian commented May 23, 2022

@wyli @Nic-Ma This PR requires PR #4239 to be merged first. Thanks

bhashemian added 11 commits May 23, 2022 18:10
@bhashemian
Gen to list
173f616 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Fix List
3600bf0 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Convert lambda to method
55cf543 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
change array to patch
65a3a15 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Remove first patch_size dim
f948afd 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Remove first patch size dim and return gen
60deeea 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Separate overlap for each dimension
69c6e79 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Remove trailing comma
2b506a5 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Add num_patches
35c747e 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Remove trailing comma
770fa11 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Add seed and update docstring
fe04994 
Signed-off-by: Behrooz <[email protected]>
Nic-Ma
Nic-Ma reviewed May 30, 2022
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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.

ericspod
ericspod reviewed May 30, 2022
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ericspod
ericspod reviewed May 30, 2022
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ericspod
ericspod reviewed May 30, 2022
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ericspod
ericspod reviewed May 30, 2022
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ericspod
ericspod reviewed May 30, 2022
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bhashemian commented May 30, 2022

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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Nic-Ma approved these changes May 31, 2022
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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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ericspod commented May 31, 2022

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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@ericspod ericspod ericspod left review comments

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

@wyli wyli Awaiting requested review from wyli

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Successfully merging this pull request may close these issues.

Including tiles coordinates in TileOnGrid transform Refactor and Simplify Tile transform

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@bhashemian @Nic-Ma @ericspod