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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

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drbeh
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@drbeh drbeh commented Mar 13, 2023 •
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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.

@drbeh drbeh marked this pull request as ready for review June 6, 2023 18:36
@drbeh drbeh mentioned this pull request Jun 28, 2023
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@drbeh drbeh marked this pull request as draft July 6, 2023 16:49
drbeh added 2 commits July 10, 2023 14:11
@drbeh
implement multithread buffer for batch sampling
2b9ec31 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@drbeh
add unittests for multithread buffer
a40b29a 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@drbeh drbeh force-pushed the multithread-patch-inference branch from 3fe72ed to a40b29a Compare July 10, 2023 18:12
@drbeh drbeh marked this pull request as ready for review July 10, 2023 18:41
@drbeh drbeh requested review from Nic-Ma, ericspod and KumoLiu July 10, 2023 18:41
@drbeh drbeh mentioned this pull request Jul 10, 2023
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5 tasks
KumoLiu
KumoLiu reviewed Jul 11, 2023
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@drbeh drbeh requested a review from KumoLiu July 13, 2023 15:00
KumoLiu
KumoLiu approved these changes Jul 14, 2023
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Thanks for update, LGTM.

@drbeh
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drbeh commented Jul 14, 2023

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

ericspod
ericspod approved these changes Jul 14, 2023
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@drbeh I'm good here!

@wyli
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wyli commented Jul 14, 2023

/build

@drbeh drbeh enabled auto-merge (squash) July 15, 2023 02:57
@drbeh drbeh disabled auto-merge July 15, 2023 02:58
@drbeh drbeh enabled auto-merge (squash) July 15, 2023 02:59
@drbeh drbeh merged commit dc1bc77 into Project-MONAI:dev Jul 15, 2023
@drbeh drbeh deleted the multithread-patch-inference branch July 15, 2023 15:14
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@KumoLiu KumoLiu KumoLiu approved these changes

@ericspod ericspod ericspod approved these changes

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

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