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Subset pixel channel averaging to remove bottleneck #823

Merged
merged 31 commits into from
Dec 7, 2022
Merged

Subset pixel channel averaging to remove bottleneck #823

merged 31 commits into from
Dec 7, 2022

Commits on Nov 10, 2022

  1. Initial implementation of pixel subsetting for channel averaging

    @alex-l-kong
    alex-l-kong committed Nov 10, 2022
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  2. Polish up remaining tests that rely on count checks for channel avera… 

    …ging
    @alex-l-kong
    alex-l-kong committed Nov 10, 2022
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  3. Add comment in compute_pixel_cluster_channel_avg documentation to cla… 

    …rify we're subsetting prior to averaging
    @alex-l-kong
    alex-l-kong committed Nov 10, 2022
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Commits on Nov 11, 2022

  1. Merge branch 'main' into subset_channel_avg

    @alex-l-kong
    alex-l-kong authored Nov 11, 2022
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Commits on Nov 15, 2022

  1. Merge branch 'main' into subset_channel_avg

    @alex-l-kong
    alex-l-kong authored Nov 15, 2022
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  2. Update FOV subset logic

    @alex-l-kong
    alex-l-kong committed Nov 15, 2022
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  3. Merge remote-tracking branch 'origin/subset_channel_avg' into subset_… 

    …channel_avg
    @alex-l-kong
    alex-l-kong committed Nov 15, 2022
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  4. Include check for fov_subset_proportion too low

    @alex-l-kong
    alex-l-kong committed Nov 15, 2022
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  5. Final checks

    @alex-l-kong
    alex-l-kong committed Nov 15, 2022
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  6. Fix test for remapping

    @alex-l-kong
    alex-l-kong committed Nov 15, 2022
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  7. Increase FOV subset proportion

    @alex-l-kong
    alex-l-kong committed Nov 15, 2022
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  8. Add random seed to pytest

    @alex-l-kong
    alex-l-kong committed Nov 15, 2022
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Commits on Nov 17, 2022

  1. Merge branch 'main' into subset_channel_avg

    @alex-l-kong
    alex-l-kong authored Nov 17, 2022
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Commits on Nov 21, 2022

  1. Update pixel channel average function to take max subset of FOVs and … 

    …verify final number of pixel clusters included
    @alex-l-kong
    alex-l-kong committed Nov 21, 2022
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  2. Add tests for subsetting more FOVs than there exist

    @alex-l-kong
    alex-l-kong committed Nov 21, 2022
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  3. Add test to verify warning is thrown if final number of clusters is l… 

    …ess than desired value
    @alex-l-kong
    alex-l-kong committed Nov 21, 2022
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  4. Merge branch 'main' into subset_channel_avg

    @alex-l-kong
    alex-l-kong authored Nov 21, 2022
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  5. Fix fov_subset_proportion to num_fovs_subset

    @alex-l-kong
    alex-l-kong committed Nov 21, 2022
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Commits on Nov 22, 2022

  1. Clarify the warning message

    @alex-l-kong
    alex-l-kong committed Nov 22, 2022
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Commits on Nov 28, 2022

  1. Merge branch 'main' into subset_channel_avg

    @alex-l-kong
    alex-l-kong authored Nov 28, 2022
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Commits on Nov 29, 2022

  1. Initial commit of updated notebook process with summary file generati… 

    …on separated into separate functiona
    @alex-l-kong
    alex-l-kong committed Nov 29, 2022
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  2. Merge branch 'subset_channel_avg' of https://github.com/angelolab/ark… 

    …-analysis into subset_channel_avg
    @alex-l-kong
    alex-l-kong committed Nov 29, 2022
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  3. Purge new pipeline of bugs

    @alex-l-kong
    alex-l-kong committed Nov 29, 2022
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Commits on Nov 30, 2022

  1. Define stubs of new functions

    @alex-l-kong
    alex-l-kong committed Nov 30, 2022
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  2. Get tests for the broken up pixel clustering functions in

    @alex-l-kong
    alex-l-kong committed Nov 30, 2022
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  3. Adjust existing meta cluster remapping tests so they don't include av… 

    …erage summary file tests
    @alex-l-kong
    alex-l-kong committed Nov 30, 2022
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  4. Documentation fix

    @alex-l-kong
    alex-l-kong committed Nov 30, 2022
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  5. PYCODESTYLE

    @alex-l-kong
    alex-l-kong committed Nov 30, 2022
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  6. Adjust test in notebooks_test.py for broken up pixel remapping function

    @alex-l-kong
    alex-l-kong committed Nov 30, 2022
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Commits on Dec 6, 2022

  1. Update error message for lost clusters in channel subsetting

    @alex-l-kong
    alex-l-kong committed Dec 6, 2022
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  2. Merge branch 'main' into subset_channel_avg

    @alex-l-kong
    alex-l-kong authored Dec 6, 2022
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