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Allow user to dynamically set batch size of pixel SOM assignments #1069

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Merged
merged 8 commits into from
Oct 30, 2023
Merged

Allow user to dynamically set batch size of pixel SOM assignments #1069

merged 8 commits into from
Oct 30, 2023

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alex-l-kong
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What is the purpose of this PR?

The current hard-coded batch size of 100 makes pixel SOM cluster assignment extremely slow. For a powerful machine (and even modern-day M1's and M2's), it can handle a much larger batch size and offer a 100x+ speedup.

How did you implement your changes

Pass an argument through the PixelSOMCluster process called num_parallel_pixels, which controls how many SOM clusters get assigned at once.

@alex-l-kong
Ensure default batch size is efficient for big machines and large coh…
466cd27 
…orts, and also that users can change if necessary
@alex-l-kong alex-l-kong self-assigned this Sep 28, 2023
@alex-l-kong alex-l-kong requested a review from cliu72 October 3, 2023 20:15
cliu72
cliu72 reviewed Oct 13, 2023
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cliu72
cliu72 reviewed Oct 13, 2023
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cliu72
cliu72 requested changes Oct 13, 2023
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Sorry for the late review! Just some small requests.

@alex-l-kong alex-l-kong requested a review from cliu72 October 19, 2023 22:34
cliu72
cliu72 requested changes Oct 23, 2023
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Can we add the same functionality to assign_som_clusters in the CellSOMCluster class in cluster_helpers.py (and cell_som_clustering.py respectively)?

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Can we add the same functionality to assign_som_clusters in the CellSOMCluster class in cluster_helpers.py (and cell_som_clustering.py respectively)?

Sure, same batch size work?

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cliu72 commented Oct 25, 2023

Can we add the same functionality to assign_som_clusters in the CellSOMCluster class in cluster_helpers.py (and cell_som_clustering.py respectively)?

Sure, same batch size work?

Yup, that works.

@alex-l-kong alex-l-kong requested a review from cliu72 October 25, 2023 23:15
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cliu72 approved these changes Oct 27, 2023
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Looks good!

@alex-l-kong alex-l-kong added this pull request to the merge queue Oct 27, 2023
@github-merge-queue github-merge-queue bot removed this pull request from the merge queue due to no response for status checks Oct 27, 2023
@alex-l-kong alex-l-kong added this pull request to the merge queue Oct 30, 2023
Merged via the queue into main with commit bfc53b7 Oct 30, 2023
@alex-l-kong alex-l-kong deleted the pixie_som_batch branch October 30, 2023 19:54
@cliu72 cliu72 mentioned this pull request Nov 10, 2023
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@alex-l-kong @cliu72