Add `correct_inter_session_displacement`function#3126

Draft

JoeZiminski wants to merge 81 commits intoSpikeInterface:mainfrom JoeZiminski:inter_session_displacement

+4,169-68

Commits on Dec 17, 2024

Add debugging.
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Factor out get probe from generate drifting recording.
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Add start of session_displacement_generator, generate probe.
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Factor out fixing of 'generate_templates_kwargs'.
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Factor out unit_factor calculation, fix wrong unit_locations dim in docstring.
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Factor out setup for InjectTemplatesRecording.
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Add first draft session_displacement_generator.py
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Start adding tests.
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Add annotations to hopefully fix tests.
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Add return extra outputs.
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Add tests.
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Improve tests and test documentation.
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Add optional return to 'generate_sorting' to get extra outputs, firing_rates.
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Start adding scaling of template amplitudes across recordings.
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Finalising amplitude scalings.
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Add input checks.
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Add documentation.
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Start finalising tests.
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Finalise and tidy up tests.
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Temporarily fix the mutable defaults so tests path.
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Fix string formatting, remove breakpoint.
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Add shift_units_outside_probe.
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Begin adding rough implementation.
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Doing some basic alignment.
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Finish naive alignment to first session.
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Play around with slope drift for generate_drifting_recording.
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Very minimal first working version.
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Start playing around with histogram estimation.
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Continue playing with estimation.
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Continue playing around with estimation.
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Add rough time estimatino.
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To some refactoring.
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Add in alignment and interpolation functions.
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Fix scaling on histograms and bin_s estimation, add benchmarking initial function.
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Adding some mp benchmarking.
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Small fixes for hpc.
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Add arg input for SLURM.
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sbatch file.
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small fixes to other methods.
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Start adding widgets.
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Add first rough nonrigid.
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Try a recursive nonrigid alignment, doesn't really work.
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Revert "Try a recursive nonrigid alignment, doesn't really work."
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Adding a few more options.
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small changes prior to refactoring.
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Small changes.
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Remove old and benchmarking scripts.
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Begin tidying up.
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Major refactor, add smoothing, interpolation, better spatial binning.
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Update some notes.
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Tidy up, expose aling to session X.
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Thinking about trimmed versions and robust xcorr, leave until later.
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PLaying with large shifts.
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Playing with alignment algorithm, completely fails when rigid shift leads to empty regions.
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some small tidying up
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Lots of tidying up, need to look into nonrigid more something has regressed.
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Look further into rigid, it was working well, but the parameters chosen make a huge difference.
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Fix corrected histogram to use same method as compute.
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Big refactor, getting close to first draft.
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Begin typing and documentation.
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Fix from motion correction function, adding typing and docstrings.
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Docstrings and typing for session_alignment.
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Continue adding docstring / types.
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Continue with docstrings.
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Small fixes
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Remove a TODO.
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Add recording shifts argument.
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Update time estimate method.
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Fix time estimate, other tidy ups.
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gaussian process first draft.
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remove some debug stuff from gp first draft.
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Very rough introduce 2D versions.
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Add scaling to GP, beter convergence.
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Tidy up.
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Handle the 1-bin case in Motion objects __repre__
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Tidy up and fixes for 'session_alignment.py'
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Tidying up, begin fixing alignment alg.
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Remove pickle files.
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[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot]
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Reformatting alignment methods and add 2D, need to tidy up.
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delete big files.
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