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Allow for subsampling of featured trajectories #232

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Justin-J-Miller opened this issue Jun 27, 2024 · 2 comments
Open

Allow for subsampling of featured trajectories #232

Justin-J-Miller opened this issue Jun 27, 2024 · 2 comments
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enhancement good-first-issue this issue would be a good first commit

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@Justin-J-Miller
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Clustering on subsampled data is useful for both memory efficiency but also time to compute kmedoids updates. Would be nice to add the option to subsample featurized datasets at the point of clustering.

@Justin-J-Miller Justin-J-Miller added enhancement good-first-issue this issue would be a good first commit labels Jun 27, 2024
@justinrporter
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Is this really not available?

It looks like cluster.py at least theoretically has an option for this:
https://github.com/bowman-lab/enspara/blob/735a3fb52b61a30268f07375376edfb5859ad99a/enspara/apps/cluster.py#L148C30-L153C1

@Justin-J-Miller
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It's supported for trajectories, but for features/h5 files it is currently disallowed:

https://github.com/bowman-lab/enspara/blob/735a3fb52b61a30268f07375376edfb5859ad99a/enspara/apps/cluster.py#L185C1-L187C67

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