Skip to content
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

Multithread batch sampler for PatchInferer #6139

Merged
merged 9 commits into from
Jul 15, 2023
Merged

Multithread batch sampler for PatchInferer #6139

merged 9 commits into from
Jul 15, 2023

Conversation

bhashemian
Copy link
Member

@bhashemian bhashemian commented Mar 13, 2023 •
edited
Loading

Fixes #6138

Description

This PR makes the batch sampling of PatchInferer multi-threaded so that WSI inference (using WSI splitters) can leverage this to enhance performance.

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.

@bhashemian bhashemian marked this pull request as ready for review June 6, 2023 18:36
@bhashemian bhashemian mentioned this pull request Jun 28, 2023
Merged
6 tasks
@bhashemian bhashemian marked this pull request as draft July 6, 2023 16:49
@bhashemian
implement multithread buffer for batch sampling
2b9ec31 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
add unittests for multithread buffer
a40b29a 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian bhashemian force-pushed the multithread-patch-inference branch from 3fe72ed to a40b29a Compare July 10, 2023 18:12
@bhashemian bhashemian marked this pull request as ready for review July 10, 2023 18:41
@bhashemian bhashemian mentioned this pull request Jul 10, 2023
Merged
5 tasks
KumoLiu
KumoLiu reviewed Jul 11, 2023
View reviewed changes
monai/inferers/inferer.py Show resolved Hide resolved
monai/inferers/inferer.py Outdated Show resolved Hide resolved
@bhashemian bhashemian requested a review from KumoLiu July 13, 2023 15:00
KumoLiu
KumoLiu approved these changes Jul 14, 2023
View reviewed changes
Copy link
Contributor

@KumoLiu KumoLiu 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 update, LGTM.

@bhashemian
Copy link
Member Author

@ericspod any more comments here? Otherwise, we can merge it. Thanks

ericspod
ericspod approved these changes Jul 14, 2023
View reviewed changes
Copy link
Member

@ericspod ericspod left a comment

Choose a reason for hiding this comment

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

@drbeh I'm good here!

@wyli
Copy link
Contributor

wyli commented Jul 14, 2023

/build

@bhashemian bhashemian enabled auto-merge (squash) July 15, 2023 02:57
@bhashemian bhashemian disabled auto-merge July 15, 2023 02:58
@bhashemian bhashemian enabled auto-merge (squash) July 15, 2023 02:59
@bhashemian bhashemian merged commit dc1bc77 into Project-MONAI:dev Jul 15, 2023
@bhashemian bhashemian deleted the multithread-patch-inference branch July 15, 2023 15:14
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@KumoLiu KumoLiu KumoLiu approved these changes

@ericspod ericspod ericspod approved these changes

@Nic-Ma Nic-Ma Awaiting requested review from Nic-Ma

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Multi-threaded patch inference
4 participants
@bhashemian @wyli @ericspod @KumoLiu