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Refactor, test and optimize compute_synchrony_metrics #2528

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ed11d9f
Refactored synthesize_random_firings and synthesize_poisson_spike_vec…
chrishalcrow Feb 27, 2024
da03c5e
Added test for insertion structuring
chrishalcrow Feb 27, 2024
f237cb8
Refactor compute_synchrony_metrics into two functions
chrishalcrow Feb 29, 2024
5dc4a63
compute_synchrony_metrics outputs dict, as documented
chrishalcrow Feb 29, 2024
a2e1368
fix compute_synchrony_metrics return value
chrishalcrow Feb 29, 2024
8c09499
Update test for dict output of compute_synchrony_metrics
chrishalcrow Feb 29, 2024
caff2a8
Add test for no sync counts
chrishalcrow Feb 29, 2024
c2f5e0e
Add tests for get_synchrony_counts
chrishalcrow Feb 29, 2024
74f995e
Concatenate spike segments into one spike train
chrishalcrow Feb 29, 2024
a79c3a3
Make synchrony_counts a numpy array
chrishalcrow Feb 29, 2024
a15270a
Optimise get_synchrony_counts
chrishalcrow Feb 29, 2024
0e2f941
Fix bugs related to dict -> numpy array change
chrishalcrow Feb 29, 2024
b0becd2
Add tests for compute_synchrony_metrics
chrishalcrow Feb 29, 2024
22ca26c
Rearrange and format
chrishalcrow Feb 29, 2024
e5534ab
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Feb 29, 2024
c376c26
Merge branch 'dev' into quality_metrics_dev
chrishalcrow Feb 29, 2024
ec0ece5
Added `round` option to `recording.astype`
DradeAW Feb 26, 2024
5fd2749
Fixed import
DradeAW Feb 26, 2024
8a8b77c
Fixed bug
DradeAW Feb 26, 2024
d90a63c
Rounding by default
DradeAW Feb 29, 2024
0fe3cb6
add shell note for Windows
zm711 Feb 16, 2024
978ecc8
Fix scaling of inject templates with copy
alejoe91 Feb 27, 2024
7cc82c1
Fix mutually exclusive keys in job_kwargs
samuelgarcia Feb 23, 2024
93536c1
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Feb 23, 2024
da01a5d
Oups
samuelgarcia Mar 4, 2024
7d37530
WIP: kilosort4 wrapper
alejoe91 Mar 1, 2024
b242eae
Add extensive tests
alejoe91 Mar 1, 2024
fa870cd
handle_multi_segment=False
alejoe91 Mar 1, 2024
9c6d003
Add to DOCKER_MAP
alejoe91 Mar 1, 2024
8bdf72c
Update src/spikeinterface/sorters/external/kilosort4.py
alejoe91 Mar 1, 2024
1c443ff
Update description
alejoe91 Mar 1, 2024
beff83e
Cleanup params, add installation and singularity tests
alejoe91 Mar 4, 2024
a948d11
Fix sparsity check for old waveform extractor
chrishalcrow Feb 29, 2024
12c22ac
WIP
yger Feb 26, 2024
f115085
WIP
yger Feb 26, 2024
77ceaf9
Fix test peak localization
yger Feb 26, 2024
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pre-commit-ci[bot] Feb 26, 2024
8a61175
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pre-commit-ci[bot] Feb 27, 2024
e4b7e4b
Fix a bug in Silence_period
yger Feb 27, 2024
826a83a
Fix in benchmarks
yger Feb 27, 2024
60703f5
WIP
yger Feb 28, 2024
7821f7d
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Feb 27, 2024
fa61b24
WIP
yger Feb 28, 2024
10ef204
Default no cache for Windows
yger Feb 28, 2024
75a5935
typos
yger Feb 28, 2024
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[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Feb 28, 2024
7bcb076
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yger Feb 28, 2024
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yger Feb 28, 2024
5fce2b9
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yger Feb 28, 2024
7f0bc8f
WIP
yger Feb 29, 2024
6218c43
Playing with simple sorter
yger Feb 29, 2024
ed5ceb8
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pre-commit-ci[bot] Feb 29, 2024
6214c9f
WIP
yger Feb 29, 2024
b66499e
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d1bccef
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yger Mar 1, 2024
4423216
Cleaning
yger Mar 1, 2024
966e48e
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 1, 2024
bc0d8e9
Add the cache for simple sorter
yger Mar 1, 2024
035c510
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 1, 2024
9481544
Fixes in benchmarks
yger Mar 1, 2024
3f75a55
Plots for detection
yger Mar 1, 2024
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5195ac4
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3c35637
analyzer in howto analyze_neuropixel
samuelgarcia Feb 27, 2024
6bcf651
oups
samuelgarcia Mar 4, 2024
57d28a8
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 4, 2024
bbb31da
revert cache_preprocessing in simple_sorter
samuelgarcia Mar 4, 2024
6ba2762
Make pandas weak import for pandas in core
samuelgarcia Mar 4, 2024
15b83d0
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pre-commit-ci[bot] Mar 4, 2024
10a21c9
oups
samuelgarcia Mar 4, 2024
301194b
oups
samuelgarcia Mar 4, 2024
a8792da
more fix in dev
samuelgarcia Mar 4, 2024
c44eb64
Fixes after Pierre remove many features methods!!!
samuelgarcia Mar 4, 2024
220927e
oups remove file push by accident some time ago. Sorry.
samuelgarcia Mar 4, 2024
b2d301b
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d47d095
Handle negative gain for neo rawio to make smarter user eperience.
samuelgarcia Mar 5, 2024
72c7488
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 5, 2024
26b009d
Fixes bug in SortingAnalyzer
DradeAW Mar 6, 2024
ccd3fb3
sortinganalyzer doc cleanup
zm711 Mar 6, 2024
e95205b
add xarray to docs instead + couple more typos
zm711 Mar 6, 2024
de15b67
Update yaml files for installation + add a new one
samuelgarcia Mar 6, 2024
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68eee95
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samuelgarcia Mar 6, 2024
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fbc4290
Update check_your_install.py and yaml
samuelgarcia Mar 6, 2024
dfe9d67
oups
samuelgarcia Mar 6, 2024
6a79d33
Add strict_gap_mode in read_neuralynx to reflect neo.
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98446dc
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samuelgarcia Mar 6, 2024
be47073
Split by recording first commit.
JoeZiminski Dec 7, 2023
b9ab17f
Reword and tidy up, currently fixing recording issue.
JoeZiminski Dec 8, 2023
809e3b4
Update example to be neuropixels-like.
JoeZiminski Dec 11, 2023
c974a7c
Tidy up and check.
JoeZiminski Dec 11, 2023
09834a7
Update doc/how_to/process_by_channel_group.rst
alejoe91 Jan 19, 2024
3739231
Remove execution times .rst
JoeZiminski Feb 13, 2024
46f98ce
Integrate the end section of the page into the text.
JoeZiminski Feb 13, 2024
ab139ab
Update doc/how_to/process_by_channel_group.rst
samuelgarcia Mar 8, 2024
a2697a7
add check_json to zarr
zm711 Mar 8, 2024
1105084
fix bug in zarr sparsity mask (self->cls)
zm711 Mar 8, 2024
8f5133a
add SelectRandomSpikes to init for registration
zm711 Mar 8, 2024
3ac60a0
Added doc for `astype` rounding
DradeAW Mar 12, 2024
52bd177
Put SortingAnalyzer in get_started
chrishalcrow Mar 13, 2024
eb90c99
Add SortingAnalyzer first draft
chrishalcrow Mar 13, 2024
67cd18f
Update get started to have SortingAnalyzer
chrishalcrow Mar 15, 2024
4694683
Add compute options and change to compute(quality_metrics)
chrishalcrow Mar 15, 2024
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pre-commit-ci[bot] Mar 15, 2024
4e96cfe
Update examples/how_to/get_started.py
chrishalcrow Mar 15, 2024
e1a6bbb
Update examples/how_to/get_started.py
chrishalcrow Mar 15, 2024
65de660
Delete quality metrics NaN warnings
chrishalcrow Mar 18, 2024
97f1e4e
Add set_probe comment in get_started.rst
chrishalcrow Mar 18, 2024
c163a2e
Add set_probe comment in get_started.py
chrishalcrow Mar 18, 2024
fb6cc38
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 18, 2024
c604f82
Make filepaths clearer and delete duplication
chrishalcrow Mar 19, 2024
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a7f6d01
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yger Mar 15, 2024
d56687c
add import os for read_binary
zm711 Mar 14, 2024
54e8af6
Clarify status of main and Sortinganalyzer
alejoe91 Mar 15, 2024
7a0cdf2
Typos
alejoe91 Mar 15, 2024
2f1730d
Use GPU in Kilosort4Sorter
bagibence Mar 14, 2024
a51e78e
Use nvidia-optional instead of nvidia-required for Kilosort4
bagibence Mar 15, 2024
5fc3590
gpu_compatibility -> gpu_capability in Kilosort4Sorter
bagibence Mar 15, 2024
8422356
wip
alejoe91 Feb 26, 2024
b72e8d5
wip2
alejoe91 Feb 27, 2024
062089d
wip
alejoe91 Feb 29, 2024
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Add loading instructions
alejoe91 Mar 11, 2024
d6b943b
typos
alejoe91 Mar 11, 2024
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94fe2bf
fix typo in __repr__
alejoe91 Mar 12, 2024
bf2c42f
fix typo in rsts
alejoe91 Mar 12, 2024
b470231
Update doc/modules/core.rst
samuelgarcia Mar 13, 2024
e33093d
Merci Zach
samuelgarcia Mar 13, 2024
90facf1
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alejoe91 Mar 15, 2024
830a6c7
Add batch size to KS4 wrapper
alejoe91 Mar 18, 2024
a844bde
Update exclude_sweep_ms for SimpleSortersimplesorter
samuelgarcia Mar 6, 2024
d658b35
Fix
yger Mar 18, 2024
afc2b73
Patch
yger Mar 18, 2024
e07d75c
fix broken link
zm711 Mar 18, 2024
873fafb
switch links to main
zm711 Mar 18, 2024
af74924
[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot] Mar 18, 2024
4bbc7cb
Proposal for auto load extensions.
samuelgarcia Mar 13, 2024
d48384d
better error
samuelgarcia Mar 13, 2024
957ac99
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samuelgarcia Mar 14, 2024
01d2ac6
oups
samuelgarcia Mar 14, 2024
c0f8bc6
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Thanks you Zach and Alessio
samuelgarcia Mar 18, 2024
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7593071
WIP
yger Feb 26, 2024
a4555d1
Fix test peak localization
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Fix in benchmarks
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Update examples/how_to/get_started.py
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Update examples/how_to/get_started.py
Co-authored-by: Zach McKenzie <92116279+zm711@users.noreply.github.com>
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chrishalcrow and zm711 committed Mar 20, 2024
commit faebae931bf03e96900b0902755b4af20eac0dff
5 changes: 3 additions & 2 deletions examples/how_to/get_started.py
Original file line number Diff line number Diff line change
Expand Up @@ -59,11 +59,12 @@
import spikeinterface.curation as scur
import spikeinterface.widgets as sw

# Alternatively, we can import all submodules at once with `import spikeinterface.full as si` which
# Alternatively, we can import all submodules at once with `import spikeinterface.full as si` which
# internally imports core+extractors+preprocessing+sorters+postprocessing+
# qualitymetrics+comparison+widgets+exporters. In this case all aliases in the following tutorial
# would be `si`.

# would be `si`
#
# This is useful for notebooks, but it is a heavier import because internally many more dependencies
# are imported (scipy/sklearn/networkx/matplotlib/h5py...)

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