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Refactor, test and optimize compute_synchrony_metrics #2528

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Refactor, test and optimize compute_synchrony_metrics #2528

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Commits on Feb 27, 2024

  1. Refactored synthesize_random_firings and synthesize_poisson_spike_vec… 

    …tor to match structured array spike trains. And added option of manual insertions. Will be used for testing.
    @chrishalcrow
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  2. Added test for insertion structuring

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Commits on Feb 29, 2024

  1. Refactor compute_synchrony_metrics into two functions

    @chrishalcrow
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  2. compute_synchrony_metrics outputs dict, as documented

    @chrishalcrow
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  3. fix compute_synchrony_metrics return value

    @chrishalcrow
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  4. Update test for dict output of compute_synchrony_metrics

    @chrishalcrow
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  5. Add test for no sync counts

    @chrishalcrow
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  6. Add tests for get_synchrony_counts

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  7. Concatenate spike segments into one spike train

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  8. Make synchrony_counts a numpy array

    @chrishalcrow
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  9. Optimise get_synchrony_counts

    @chrishalcrow
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  10. Fix bugs related to dict -> numpy array change

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  11. Add tests for compute_synchrony_metrics

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  12. Rearrange and format

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  13. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  14. Merge branch 'dev' into quality_metrics_dev

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Commits on Mar 20, 2024

  1. Added round option to recording.astype

    @DradeAW @chrishalcrow
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  2. Fixed import

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  3. Fixed bug

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  4. Rounding by default

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  5. add shell note for Windows

    @zm711 @chrishalcrow
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  6. Fix scaling of inject templates with copy

    @alejoe91 @chrishalcrow
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  7. Fix mutually exclusive keys in job_kwargs

    @samuelgarcia @chrishalcrow
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  9. Oups

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  10. WIP: kilosort4 wrapper

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  11. Add extensive tests

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  12. handle_multi_segment=False

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  13. Add to DOCKER_MAP

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  14. Update src/spikeinterface/sorters/external/kilosort4.py 

    Co-authored-by: Zach McKenzie <92116279+zm711@users.noreply.github.com>
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  15. Update description

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  16. Cleanup params, add installation and singularity tests

    @alejoe91 @chrishalcrow
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  17. Fix sparsity check for old waveform extractor

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  18. WIP

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  19. WIP

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  20. Fix test peak localization

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  21. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  23. Fix a bug in Silence_period

    @yger @chrishalcrow
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  24. Fix in benchmarks

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  25. WIP

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  27. WIP

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  28. Default no cache for Windows

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  29. typos

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  31. Conflict

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  32. Conflict

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  33. Conflict

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  34. WIP

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  35. Playing with simple sorter

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  37. WIP

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  39. WIP

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  40. Cleaning

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  42. Add the cache for simple sorter

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  44. Fixes in benchmarks

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  45. Plots for detection

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  48. analyzer in howto analyze_neuropixel

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  49. oups

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  51. revert cache_preprocessing in simple_sorter

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  52. Make pandas weak import for pandas in core

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  54. oups

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  55. oups

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  56. more fix in dev

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  57. Fixes after Pierre remove many features methods!!!

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  58. oups remove file push by accident some time ago. Sorry.

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  60. Handle negative gain for neo rawio to make smarter user eperience.

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  62. Fixes bug in SortingAnalyzer 

    Fixes a bug where `self.folder / "something"` crashes if the given
folder was a str to begin with.
Need to cast it to a Path.
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  63. sortinganalyzer doc cleanup

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  64. add xarray to docs instead + couple more typos

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  65. Update yaml files for installation + add a new one

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  67. Apply suggestions from code review 

    Co-authored-by: Zach McKenzie <92116279+zm711@users.noreply.github.com>
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  69. Update check_your_install.py and yaml

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  70. oups

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  71. Add strict_gap_mode in read_neuralynx to reflect neo.

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  73. Apply suggestions from code review 

    Co-authored-by: Zach McKenzie <92116279+zm711@users.noreply.github.com>
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  74. Split by recording first commit.

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  75. Reword and tidy up, currently fixing recording issue.

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  76. Update example to be neuropixels-like.

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  77. Tidy up and check.

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  78. Update doc/how_to/process_by_channel_group.rst 

    Co-authored-by: Heberto Mayorquin <h.mayorquin@gmail.com>
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  79. Remove execution times .rst

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  80. Integrate the end section of the page into the text.

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  81. Update doc/how_to/process_by_channel_group.rst 

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  82. add check_json to zarr

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  83. fix bug in zarr sparsity mask (self->cls)

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  84. add SelectRandomSpikes to init for registration

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  85. Added doc for astype rounding

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  86. Put SortingAnalyzer in get_started

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  87. Add SortingAnalyzer first draft

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  88. Update get started to have SortingAnalyzer

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  89. Add compute options and change to compute(quality_metrics)

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  90. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  91. Update examples/how_to/get_started.py 

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  92. Update examples/how_to/get_started.py 

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  93. Delete quality metrics NaN warnings

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  94. Add set_probe comment in get_started.rst

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  95. Add set_probe comment in get_started.py

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  96. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  97. Make filepaths clearer and delete duplication

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  98. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  99. Fix

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  100. add import os for read_binary

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  101. Clarify status of main and Sortinganalyzer

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  102. Typos

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  103. Use GPU in Kilosort4Sorter

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  104. Use nvidia-optional instead of nvidia-required for Kilosort4 

    Co-authored-by: Alessio Buccino <alejoe9187@gmail.com>
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  105. gpu_compatibility -> gpu_capability in Kilosort4Sorter

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  106. wip

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  107. wip2

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  108. wip

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  109. Add loading instructions

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  110. typos

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  111. Apply suggestions from code review 

    Suggestions from Zach

Co-authored-by: Zach McKenzie <92116279+zm711@users.noreply.github.com>
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  112. fix typo in __repr__

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  113. fix typo in rsts

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  114. Update doc/modules/core.rst

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  115. Merci Zach 

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  116. Apply suggestions from code review

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  117. Add batch size to KS4 wrapper

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  118. Update exclude_sweep_ms for SimpleSortersimplesorter

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  119. Fix

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  120. Patch

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  121. fix broken link

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  122. switch links to main

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  123. [pre-commit.ci] pre-commit autoupdate 

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  124. Proposal for auto load extensions.

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  125. better error

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  126. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  127. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  128. CHange strategy for get_saved_extension_names

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  129. oups

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  130. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  131. Thanks you Zach and Alessio 

    Co-authored-by: Zach McKenzie <92116279+zm711@users.noreply.github.com>
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  132. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  133. WIP

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  134. Fix test peak localization

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  135. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  136. wip

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  137. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  138. Fix in benchmarks

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  139. WIP

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  140. Conflict

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  141. Conflict

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  142. WIP

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  143. WIP

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  144. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  145. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  146. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  147. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  148. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  149. Update examples/how_to/get_started.py 

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  150. Update examples/how_to/get_started.py 

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  151. Make filepaths clearer and delete duplication

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  152. wip

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  153. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  154. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  155. WIP

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  156. Fix test peak localization

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  157. Fix in benchmarks

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  158. WIP

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  159. WIP

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  160. WIP

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  161. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  162. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  163. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  164. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  165. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  166. Make filepaths clearer and delete duplication

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  167. wip

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  168. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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