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Experimental Python port of Kilosort 2 #200

Merged
merged 94 commits into from
Apr 30, 2020
Merged

Experimental Python port of Kilosort 2 #200

merged 94 commits into from
Apr 30, 2020

Commits on Oct 28, 2019

  1. Initial commit

    @rossant
    rossant authored Oct 28, 2019
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  2. First commit

    @rossant
    rossant committed Oct 28, 2019
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  3. WIP

    @rossant
    rossant committed Oct 28, 2019
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  4. WIP

    @rossant
    rossant committed Oct 28, 2019
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Commits on Oct 29, 2019

  1. bug fix in find_merges

    @kushbanga
    kushbanga committed Oct 29, 2019
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  2. Move Context to utils

    @rossant
    rossant committed Oct 29, 2019
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Commits on Oct 30, 2019

  1. Merge pull request #1 from kushbanga/master 

    bug fix in find_merges
    @rossant
    rossant authored Oct 30, 2019
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  2. Add CUDA files

    @rossant
    rossant committed Oct 30, 2019
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  3. WIP

    @rossant
    rossant committed Oct 30, 2019
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  4. WIP: testing postprocess

    @rossant
    rossant committed Oct 30, 2019
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Commits on Oct 31, 2019

  1. WIP: new pass on postprocess

    @rossant
    rossant committed Oct 31, 2019
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  2. Fixes in cptools

    @rossant
    rossant committed Oct 31, 2019
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  3. WIP: fixes in postprocessing

    @rossant
    rossant committed Oct 31, 2019
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Commits on Nov 2, 2019

  1. Bug fix

    @rossant
    rossant committed Nov 2, 2019
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  2. All steps pass. Todo: debug intermediate results

    @rossant
    rossant committed Nov 2, 2019
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Commits on Nov 8, 2019

  1. Update .gitignore

    @rossant
    rossant committed Nov 8, 2019
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  2. Add _extend() utility function

    @rossant
    rossant committed Nov 8, 2019
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  3. More robust replacement to cp.mean()

    @rossant
    rossant committed Nov 8, 2019
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  4. Fixes in cluster.py

    @rossant
    rossant committed Nov 8, 2019
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  5. Fixes in learn.py

    @rossant
    rossant committed Nov 8, 2019
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  6. Fixes in postprocess.py

    @rossant
    rossant committed Nov 8, 2019
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  7. A bit more comments in main.py

    @rossant
    rossant committed Nov 8, 2019
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  8. Fixes in phy export

    @rossant
    rossant committed Nov 8, 2019
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  9. Update comments in main function

    @rossant
    rossant committed Nov 8, 2019
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  10. Fix saving of similar_templates.npy

    @rossant
    rossant committed Nov 8, 2019
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  11. Classify not good units as unsorted instead

    @rossant
    rossant committed Nov 8, 2019
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  12. Fix bug in lfilter() with out-of-bounds access in custom CUDA kernel

    @rossant
    rossant committed Nov 8, 2019
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  13. Flakify

    @rossant
    rossant committed Nov 8, 2019
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Commits on Nov 10, 2019

  1. Update README

    @rossant
    rossant committed Nov 10, 2019
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  2. Update README

    @rossant
    rossant committed Nov 10, 2019
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Commits on Nov 11, 2019

  1. Update README

    @rossant
    rossant committed Nov 11, 2019
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  2. Update README

    @rossant
    rossant committed Nov 11, 2019
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  3. WIP: bug fixes in postprocess

    @rossant
    rossant committed Nov 11, 2019
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  4. WIP: fixing postprocess bugs

    @rossant
    rossant committed Nov 11, 2019
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  5. Fix in lfilter()

    @rossant
    rossant committed Nov 11, 2019
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  6. Fix bugs in ccg()

    @rossant
    rossant committed Nov 11, 2019
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Commits on Nov 12, 2019

  1. WIP: minor refactor of context arrays

    @rossant
    rossant committed Nov 12, 2019
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Commits on Nov 13, 2019

  1. Update README

    @rossant
    rossant committed Nov 13, 2019
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Commits on Nov 15, 2019

  1. Fix amplitudes.npy saving

    @rossant
    rossant committed Nov 15, 2019
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  2. Add timer in Context

    @rossant
    rossant committed Nov 15, 2019
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  3. Bug fix

    @rossant
    rossant committed Nov 15, 2019
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  4. Flakify

    @rossant
    rossant committed Nov 15, 2019
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Commits on Nov 18, 2019

  1. Proc file now in context subdir

    @rossant
    rossant committed Nov 18, 2019
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  2. Cache lfilter kernel creation

    @rossant
    rossant committed Nov 18, 2019
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Commits on Nov 20, 2019

  1. bug fix

    @kushbanga
    kushbanga committed Nov 20, 2019
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  2. Merge pull request #2 from kushbanga/master 

    bug fix
    @rossant
    rossant authored Nov 20, 2019
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Commits on Dec 9, 2019

  1. Faster splitting by replacing custom GPU lfilter by GPU FFT-based con… 

    …volution in my_conv2()
    @rossant
    rossant committed Dec 9, 2019
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Commits on Dec 17, 2019

  1. Optimization in preprocessing: dtype conversion on GPU and write filt… 

    …ered data directly to disk
    @rossant
    rossant committed Dec 17, 2019
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Commits on Dec 23, 2019

  1. Separate the temporary arrays saved by both splitting steps

    @rossant
    rossant committed Dec 23, 2019
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  2. Add LargeArrayWriter to fix out of memory problems during learning step

    @rossant
    rossant committed Dec 23, 2019
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  3. Fixing out-of-memory

    @rossant
    rossant committed Dec 23, 2019
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Commits on Jan 10, 2020

  1. WIP: spike sorting GUI

    @rossant
    rossant committed Jan 10, 2020
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Commits on Jan 13, 2020

  1. Add load_probe()

    @rossant
    rossant committed Jan 13, 2020
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  2. Add stop_after option

    @rossant
    rossant committed Jan 13, 2020
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  3. Add Parameters view in GUI

    @rossant
    rossant committed Jan 13, 2020
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Commits on Jan 20, 2020

  1. Fix an out-of-memory issue

    @rossant
    rossant committed Jan 20, 2020
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Commits on Jan 22, 2020

  1. Add npy writer

    @rossant
    rossant committed Jan 22, 2020
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  2. Minor fixes in postprocess

    @rossant
    rossant committed Jan 22, 2020
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  3. Fixing out of memory issues when saving the files for phy

    @rossant
    rossant committed Jan 22, 2020
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Commits on Jan 31, 2020

  1. Minor fix in usage instructions 

    Currently the probe variable is in the wrong argument position of the run function
    @kushbanga
    kushbanga committed Jan 31, 2020
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  2. Merge pull request #3 from kushbanga/master 

    Minor fix in usage instructions
    @rossant
    rossant authored Jan 31, 2020
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Commits on Feb 7, 2020

  1. Avoid out of GPU memory errors in convolve()

    @rossant
    rossant committed Feb 7, 2020
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  2. Fixing out of memory issues on large datasets

    @rossant
    rossant committed Feb 7, 2020
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  3. Merge branch 'master' of github.com:rossant/pykilosort

    @rossant
    rossant committed Feb 7, 2020
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Commits on Feb 21, 2020

  1. edited params handling in main + force-cast numpy arrays in int64

    @m-beau
    m-beau committed Feb 21, 2020
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Commits on Feb 26, 2020

  1. Merge pull request MouseLand#5 from m-beau/master 

    edited params handling in main + force-cast numpy arrays in int64
    @rossant
    rossant authored Feb 26, 2020
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Commits on Feb 28, 2020

  1. wip conv

    @oliche
    oliche committed Feb 28, 2020
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  2. full convolution on GPU test passing - before memory management

    @oliche
    oliche committed Feb 28, 2020
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Commits on Feb 29, 2020

  1. wip fir gpu

    @oliche
    oliche committed Feb 29, 2020
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  2. wip fir gpu

    @oliche
    oliche committed Feb 29, 2020
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Commits on Mar 4, 2020

  1. move convolution to cptools.py

    @oliche
    oliche committed Mar 4, 2020
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  2. tapering convolution

    @oliche
    oliche committed Mar 4, 2020
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  3. unit tests convolution

    @oliche
    oliche committed Mar 4, 2020
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  4. flake

    @oliche
    oliche committed Mar 4, 2020
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Commits on Mar 5, 2020

  1. added 'checkClusters'

    Jai Bhagat committed Mar 5, 2020
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Commits on Mar 6, 2020

  1. Refactor GPU convolve

    @rossant
    rossant committed Mar 6, 2020
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  2. Minor update in convolution code

    @rossant
    rossant committed Mar 6, 2020
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  3. Update my_conv2() with the new convolution code

    @rossant
    rossant committed Mar 6, 2020
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  4. change cluster ids in 'st3'

    Jai Bhagat committed Mar 6, 2020
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  5. added environment .yml

    Jai Bhagat committed Mar 6, 2020
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Commits on Mar 7, 2020

  1. Merge pull request MouseLand#7 from cortex-lab/add_yml 

    added environment .yml
    @rossant
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Commits on Mar 8, 2020

  1. WIP

    @rossant
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Commits on Mar 9, 2020

  1. Revert "WIP" 

    This reverts commit 85873b5.
    @rossant
    rossant committed Mar 9, 2020
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  2. WIP: refactor preprocessing with EphysReader

    @rossant
    rossant committed Mar 9, 2020
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Commits on Mar 10, 2020

  1. WIP: more memory-efficient export of features

    @rossant
    rossant committed Mar 10, 2020
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Commits on Mar 13, 2020

  1. Merge pull request MouseLand#6 from cortex-lab/rm_empty_cl 

    added 'checkClusters'
    @rossant
    rossant authored Mar 13, 2020
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  2. Add option to add log file

    @rossant
    rossant committed Mar 13, 2020
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  3. bug fix

    @kushbanga
    kushbanga committed Mar 13, 2020
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Commits on Apr 6, 2020

  1. Merge branch 'optim'

    @rossant
    rossant committed Apr 6, 2020
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Commits on Apr 7, 2020

  1. Add **kwargs to run()

    @rossant
    rossant committed Apr 7, 2020
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  2. Update README

    @rossant
    rossant committed Apr 7, 2020
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Commits on Apr 22, 2020

  1. bug fix

    @kushbanga
    kushbanga committed Apr 22, 2020
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  2. Output thresholds

    @kushbanga
    kushbanga committed Apr 22, 2020
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Commits on Apr 30, 2020

  1. Merge remote-tracking branch 'pyks2/master' into pyks2

    @rossant
    rossant committed Apr 30, 2020
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