Skip to content

GridPatch to Extract Tiles/Patches #4321

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Merged
bhashemian merged 72 commits into from
May 31, 2022
Merged

GridPatch to Extract Tiles/Patches #4321

bhashemian merged 72 commits into from
May 31, 2022

Conversation

@bhashemian
Copy link
Member

@bhashemian bhashemian commented May 23, 2022 •
edited
Loading

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 added 6 commits May 22, 2022 18:28
@bhashemian
Implement GridPatch and RandGridPatch
c96dd21 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Add unittests for GridPatch
3df8dbb 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Update pad mode
ec2e6cd 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Add several test cases
8cae266 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Implement GridPatchd
232fd6e 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Update module imports
d66377a 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian bhashemian linked an issue May 23, 2022 that may be closed by this pull request
Including tiles coordinates in TileOnGrid transform #4090
Closed
bhashemian added 11 commits May 23, 2022 13:14
@bhashemian
Add docs
cf6c72a 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Deprecate SplitOnGrid and TileOnGrid
a01faa7 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Merge branch 'dev' into grid-patch
f5bf4bf
@bhashemian
Fix formatting
c2afba0 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Update WSIReader value error message
a8e68cc 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Implement RandGridPatchd
13fbd8d 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Update init
4a1b8da 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Add unittests for GridPatchd
0b6fe58 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Add unittests for RandGridPatch
4105006 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Add unittests for RandGridPatchd
b7e2259 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Merge branch 'dev' into grid-patch
e7d8d25
@bhashemian
Copy link
Member Author

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 <3968947+drbeh@users.noreply.github.com>
@bhashemian
Fix List
3600bf0 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Convert lambda to method
55cf543 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
change array to patch
65a3a15 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Remove first patch_size dim
f948afd 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Remove first patch size dim and return gen
60deeea 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Separate overlap for each dimension
69c6e79 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Remove trailing comma
2b506a5 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Add num_patches
35c747e 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Remove trailing comma
770fa11 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Add seed and update docstring
fe04994 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Nic-Ma
Nic-Ma reviewed May 30, 2022
View reviewed changes
Copy link
Contributor

@Nic-Ma Nic-Ma left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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
View reviewed changes
ericspod
ericspod reviewed May 30, 2022
View reviewed changes
ericspod
ericspod reviewed May 30, 2022
View reviewed changes
ericspod
ericspod reviewed May 30, 2022
View reviewed changes
ericspod
ericspod reviewed May 30, 2022
View reviewed changes
bhashemian added 6 commits May 30, 2022 15:27
@bhashemian
Address reviews
dfb15b3 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Merge branch 'grid-patch' of github.com:behxyz/MONAI into grid-patch
337ca76
@bhashemian
Merge branch 'dev' into grid-patch
1ba9022
@bhashemian
Update additional patches
3d00f87 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Merge branch 'grid-patch' of github.com:behxyz/MONAI into grid-patch
a4a531f
@bhashemian
Add GridPatchSort
46b2069 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Copy link
Member Author

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.

@Nic-Ma
Copy link
Contributor

Nic-Ma commented May 31, 2022

/black

@Nic-Ma
Copy link
Contributor

Nic-Ma commented May 31, 2022

/build

Nic-Ma
Nic-Ma approved these changes May 31, 2022
View reviewed changes
Copy link
Contributor

@Nic-Ma Nic-Ma left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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

Thanks.

@ericspod
Copy link
Member

ericspod commented May 31, 2022

I'm good here!

@Nic-Ma
Copy link
Contributor

Nic-Ma commented May 31, 2022

/black

@Nic-Ma
Copy link
Contributor

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
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@ericspod ericspod ericspod left review comments

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

@wyli wyli Awaiting requested review from wyli

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

Including tiles coordinates in TileOnGrid transform Refactor and Simplify Tile transform

3 participants

@bhashemian @Nic-Ma @ericspod