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Improve the speed of some post-cluster calculations #932

Merged
merged 30 commits into from
Jan 18, 2022
Merged

Improve the speed of some post-cluster calculations #932

merged 30 commits into from
Jan 18, 2022

Commits on Jan 13, 2022

  1. Start adding scripts for benchmarking clustering

    @drroe
    drroe committed Jan 13, 2022
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  2. Determine number of trajin needed

    @drroe
    drroe committed Jan 13, 2022
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  3. Finish up cluster script

    @drroe
    drroe committed Jan 13, 2022
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  4. Add script to extract timings

    @drroe
    drroe committed Jan 13, 2022
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  5. Move to correct dir

    @drroe
    drroe committed Jan 13, 2022
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  6. Reduce # frames for initial testing

    @drroe
    drroe committed Jan 13, 2022
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Commits on Jan 14, 2022

  1. Dramatically improve cluster Summary execution time by creating an array 

    with sieve status of each frame
    @drroe
    drroe committed Jan 14, 2022
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  2. Have ClusterDist take boolean array of frame is present

    @drroe
    drroe committed Jan 14, 2022
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Commits on Jan 17, 2022

  1. Remove some debug info

    @drroe
    drroe committed Jan 17, 2022
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  2. Benchmark silhouette

    @drroe
    drroe committed Jan 17, 2022
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  3. Use frameIsPresent arrays in silhouette calc

    @drroe
    drroe committed Jan 17, 2022
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  4. Clean up and better-document the Sieve class

    @drroe
    drroe committed Jan 17, 2022
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  5. Rewrite the frame is present array as being present inside Sieve, this 

    way it only needs to be generated once. It may be better to just have it
generated all the time.
    @drroe
    drroe committed Jan 17, 2022
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  6. Benchmark the bestreps calc

    @drroe
    drroe committed Jan 17, 2022
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Commits on Jan 18, 2022

  1. Add a debug number of frames

    @drroe
    drroe committed Jan 18, 2022
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  2. Add some debug print, commented out

    @drroe
    drroe committed Jan 18, 2022
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  3. Use frameIsPresent array instead of HasFrame. Make it a warning if no 

    rep found when doing best rep search for cluster by parts and all
frames just happen to be sieved out
    @drroe
    drroe committed Jan 18, 2022
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  4. Pass in the FrameIsPresent array for bestreps calc. Add part to Node for 

    bookkeeping
    @drroe
    drroe committed Jan 18, 2022
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  5. Get rid of FIXME, fixed

    @drroe
    drroe committed Jan 18, 2022
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  6. Start new Silhouette class

    @drroe
    drroe committed Jan 18, 2022
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  7. Add Silhouette class

    @drroe
    drroe committed Jan 18, 2022
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  8. Silhouette calc is now in a separate class

    @drroe
    drroe committed Jan 18, 2022
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  9. Silhouette write moved to Silhouette

    @drroe
    drroe committed Jan 18, 2022
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  10. Use new Silhouette calc

    @drroe
    drroe committed Jan 18, 2022
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  11. Add missing depend for <list>

    @drroe
    drroe committed Jan 18, 2022
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  12. Write out actual frame numbers for cluster silhouette for each frame. 

    Not sure why I wasn't doing this already...
    @drroe
    drroe committed Jan 18, 2022
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  13. Add option to choose either the sorted silhouette index or frame number 

    for cluster silhouette frame output.
    @drroe
    drroe committed Jan 18, 2022
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  14. Sorted frame indices have been fixed for silhouette

    @drroe
    drroe committed Jan 18, 2022
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  15. Minor bump to 6.2.0. Fixes for post-clustering speed (summary etc), fix 

    best reps for split, fix frame index in silhouette calc.
    @drroe
    drroe committed Jan 18, 2022
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  16. Add Silhouette.cpp to CMakeLists.txt

    @drroe
    drroe committed Jan 18, 2022
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