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Add `correct_inter_session_displacement` function - #3126

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JoeZiminski wants to merge 124 commits into

SpikeInterface:mainfrom

JoeZiminski:inter_session_displacement

Open

Add `correct_inter_session_displacement` function#3126
JoeZiminski wants to merge 124 commits into
SpikeInterface:mainfrom
JoeZiminski:inter_session_displacement

Commits on Mar 14, 2025
- drifting_generator.py - factor out get probe
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  5a61b9f
- drifting_generator.py - factor out fixing of 'generate_templates_kwargs'.
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  c5c1a0b
- Factor out unit_factor calculation, fix wrong unit_locations dim in docstring.
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  b010f8f
- generate.py - factor out setup InjectTemplatesRecording setup.
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  3a6300c
- generate.py - add extra outputs.
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  62d5755
- Add a debugging script.
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  89ebe2b
- Add session displacement generator.
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  08c6ae3
- Add tests for session displacement generator.
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  1f9ed1a
- Remove debugging script.
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  f5c7e49
- Update docstring on 'calculate_displacement_unit_factor.
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  7aeec39
- Remove print.
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  8bceeaa
- Add units to recording durations
  
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  and
  chrishalcrow
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  2d0b93b
- Remove uncessary changes to generate.py
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  040d1ca
- Merge branch 'add_session_displacement_generation' of github.com:JoeZiminski/spikeinterface into add_session_displacement_generation
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  77f8c89
- Additional removal on generate.py
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  27a67bb
- typo fix (double ".")
  
  JoeZiminski
  and
  chrishalcrow
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  6d36da1
- Allow
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  d66d636
- Merge branch 'add_session_displacement_generation' of github.com:JoeZiminski/spikeinterface into add_session_displacement_generation
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  050e22a
- Make small adjustment to threshold for macOS.
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  263f0d7
- Begin adding rough implementation.
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  e35b2e3
- Doing some basic alignment.
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  6590e0b
- Finish naive alignment to first session.
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  a5eec8f
- Play around with slope drift for generate_drifting_recording.
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  d3356b3
- Very minimal first working version.
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  68525b2
- Start playing around with histogram estimation.
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  6ce724f
- Continue playing with estimation.
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  d26f6fd
- Continue playing around with estimation.
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  b95e932
- Add rough time estimatino.
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  1a5402e
- To some refactoring.
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  2355fd4
- Add in alignment and interpolation functions.
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  bd49361
- Fix scaling on histograms and bin_s estimation, add benchmarking initial function.
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  ed3071e
- Adding some mp benchmarking.
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  bf49924
- Small fixes for hpc.
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  2777398
- Add arg input for SLURM.
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  2b11de3
- sbatch file.
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  66cc1be
- small fixes to other methods.
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  4d46f29
- Start adding widgets.
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  44921aa
- Add first rough nonrigid.
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  55c26fd
- Try a recursive nonrigid alignment, doesn't really work.
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  53ddf57
- Revert "Try a recursive nonrigid alignment, doesn't really work."
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  eb8a736
- Adding a few more options.
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  66e6466
- small changes prior to refactoring.
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  ad5ed88
- Small changes.
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  d641bae
- Remove old and benchmarking scripts.
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  3334e14
- Begin tidying up.
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  c7eb654
- Major refactor, add smoothing, interpolation, better spatial binning.
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  958e0b9
- Update some notes.
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  756c534
- Tidy up, expose aling to session X.
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  23ef544
- Thinking about trimmed versions and robust xcorr, leave until later.
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  cf4aca9
- PLaying with large shifts.
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  1558950
- Playing with alignment algorithm, completely fails when rigid shift leads to empty regions.
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  1bc19a2
- some small tidying up
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  d5d5ab1
- Lots of tidying up, need to look into nonrigid more something has regressed.
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  committed
  1746df9
- Look further into rigid, it was working well, but the parameters chosen make a huge difference.
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  committed
  1bec728
- Fix corrected histogram to use same method as compute.
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  committed
  cde7faa
- Big refactor, getting close to first draft.
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  committed
  be44468
- Begin typing and documentation.
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  committed
  aad90cf
- Fix from motion correction function, adding typing and docstrings.
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  0bce36a
- Docstrings and typing for session_alignment.
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  d7fb138
- Continue adding docstring / types.
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  3e705b7
- Continue with docstrings.
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  a06c62c
- Small fixes
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  e651018
- Remove a TODO.
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  975802a
- Add recording shifts argument.
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  8809f0f
- Update time estimate method.
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  committed
  cd77308
- Fix time estimate, other tidy ups.
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  committed
  9aa1bfb
- gaussian process first draft.
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  committed
  3fd72fc
- remove some debug stuff from gp first draft.
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  ccf6d6d
- Very rough introduce 2D versions.
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  8c444f9
- Add scaling to GP, beter convergence.
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  06de591
- Tidy up.
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  016e6b9
- Tidy up and fixes for 'session_alignment.py'
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  committed
  202ab6c
- Tidying up, begin fixing alignment alg.
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  committed
  e49b6cb
- Remove pickle files.
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  committed
  565ede3
- [pre-commit.ci] auto fixes from pre-commit.com hooks
  
  pre-commit-ci[bot]
  authored and
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  committed
  a3c35b7
- Reformatting alignment methods and add 2D, need to tidy up.
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  955451e
- delete big files.
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  9eb80e6
- Trying different alg
  JoeZiminski
  committed
  b11ce7f
- [pre-commit.ci] auto fixes from pre-commit.com hooks
  
  pre-commit-ci[bot]
  authored and
  JoeZiminski
  committed
  e5dcdc6
- Playing with alg rigid shift but scales for better rigid shift, okay but errors obviously
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  committed
  41f4b50
- Testing on the session_alignment side.
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  27faccd
- playing with nonrigid.
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  committed
  1c3c3d0
- Save.
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  549f6d0
- With additional windowing.
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  ca79a66
- Doing some tidying, use amplitudes much more TODO!
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  150c2a3
- Remove additional improvements on alignment alg to work on later.
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  f0ffa99
- First draft add plotting 2D histograms.
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  62f9b2c
- Tidying up, checking alignment function.
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  committed
  96a977c
- Add 2d histogram plot, move plots to SI widgets.
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  967e863
- Update playing.py
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  committed
  1eec363
- Start adding tests.
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  c6e9f06
- Continue working on tests.
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  71ca388
- Continue adding tests.
  JoeZiminski
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  d231e9b
- Continue! working on tests.
  JoeZiminski
  committed
  b4b9e28
- [pre-commit.ci] auto fixes from pre-commit.com hooks
  
  pre-commit-ci[bot]
  authored and
  JoeZiminski
  committed
  42fb3de
- Tidy up tests and (slightly) improve num_iter handling.
  JoeZiminski
  committed
  2e77036
- Add how-to doc.
  JoeZiminski
  committed
  9bb06ec
- Small changes to docs.
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  committed
  3c9593b
- Tidying up tests.
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  committed
  7e35574
- fix rebase.
  JoeZiminski
  committed
  4bdc45c
- Fixing after rebase.
  JoeZiminski
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  7e9b039
- Remove files.
  JoeZiminski
  committed
  140a8c7
- Fix tests.
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  committed
  74d4f9e
- Fix bad import.
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  committed
  4542ec5
- Fix tests, tidy up.
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  committed
  03fdf1f
Commits on Mar 15, 2025
- Some more test tidying and documentation.
  JoeZiminski
  committed
  47882a4
- Speed up tests.
  JoeZiminski
  committed
  96ce603
Commits on Mar 16, 2025
- Continue fixing tests.
  JoeZiminski
  committed
  ad3b6ad
- Finalise tidying up tests.
  JoeZiminski
  committed
  0f8a3d4
- rework the docs to tutorial, add final TODOs.
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  committed
  5a2bd1b
Commits on Mar 19, 2025
- Add a few more examples.
  JoeZiminski
  committed
  9d06801
Commits on Mar 20, 2025
- Add documentation.
  JoeZiminski
  committed
  caee4c8
- Fix import, remove debugging.
  JoeZiminski
  committed
  20a5bfd
- Compute log transform after mean / median taken. Tidy up, fix tests.
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  committed
  cf2c6c8
Commits on Jan 19, 2026
- Merge branch 'main' into add_session_displacement_generation
  JoeZiminski
  committed
  ad4779d
- Update probe name to Neuropixels1-128.
  JoeZiminski
  committed
  45feaf3
Commits on Feb 6, 2026
Commits on Mar 30, 2026
- Quick fix.
  JoeZiminski
  committed
  b3f0e39

Commits

Commits on Mar 14, 2025

Commits on Mar 15, 2025

Commits on Mar 16, 2025

Commits on Mar 19, 2025

Commits on Mar 20, 2025

Commits on Jan 19, 2026

Commits on Feb 6, 2026

Commits on Mar 30, 2026