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Add correct_inter_session_displacementfunction #3126

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4f3b748
Add debugging.
JoeZiminski Jul 18, 2024
4f76bb8
Factor out get probe from generate drifting recording.
JoeZiminski Jul 18, 2024
fb313bc
Add start of session_displacement_generator, generate probe.
JoeZiminski Jul 18, 2024
bc35c21
Factor out fixing of 'generate_templates_kwargs'.
JoeZiminski Jul 18, 2024
428d860
Factor out unit_factor calculation, fix wrong unit_locations dim in d…
JoeZiminski Jul 18, 2024
daedcf9
Factor out setup for InjectTemplatesRecording.
JoeZiminski Jul 18, 2024
1777938
Add first draft session_displacement_generator.py
JoeZiminski Jul 18, 2024
189fdbf
Start adding tests.
JoeZiminski Jul 18, 2024
6126cfa
Add annotations to hopefully fix tests.
JoeZiminski Jul 18, 2024
9be3016
Add return extra outputs.
JoeZiminski Jul 19, 2024
d946074
Add tests.
JoeZiminski Jul 19, 2024
c1a387b
Improve tests and test documentation.
JoeZiminski Jul 22, 2024
d362a1e
Add optional return to 'generate_sorting' to get extra outputs, firin…
JoeZiminski Jul 23, 2024
616184d
Start adding scaling of template amplitudes across recordings.
JoeZiminski Jul 23, 2024
b616bb2
Finalising amplitude scalings.
JoeZiminski Jul 24, 2024
c8a4d06
Add input checks.
JoeZiminski Jul 24, 2024
53794af
Add documentation.
JoeZiminski Jul 24, 2024
522108d
Start finalising tests.
JoeZiminski Jul 24, 2024
bf24f3b
Finalise and tidy up tests.
JoeZiminski Jul 25, 2024
06ab2de
Temporarily fix the mutable defaults so tests path.
JoeZiminski Jul 29, 2024
2568d88
Fix string formatting, remove breakpoint.
JoeZiminski Aug 28, 2024
c79b383
Add `shift_units_outside_probe`.
JoeZiminski Aug 28, 2024
08fc1dc
Begin adding rough implementation.
JoeZiminski Jul 2, 2024
392b118
Doing some basic alignment.
JoeZiminski Jul 9, 2024
61b357c
Finish naive alignment to first session.
JoeZiminski Jul 9, 2024
2a023db
Play around with slope drift for generate_drifting_recording.
JoeZiminski Jul 15, 2024
b932a54
Very minimal first working version.
JoeZiminski Jul 16, 2024
5ce20f7
Start playing around with histogram estimation.
JoeZiminski Jul 30, 2024
6c02a29
Continue playing with estimation.
JoeZiminski Jul 30, 2024
c749f48
Continue playing around with estimation.
JoeZiminski Jul 31, 2024
151fe5e
Add rough time estimatino.
JoeZiminski Aug 1, 2024
d4146b7
To some refactoring.
JoeZiminski Aug 12, 2024
b7a0f59
Add in alignment and interpolation functions.
JoeZiminski Aug 13, 2024
8a7c632
Fix scaling on histograms and bin_s estimation, add benchmarking init…
JoeZiminski Aug 14, 2024
515bb82
Adding some mp benchmarking.
JoeZiminski Aug 15, 2024
9744b06
Small fixes for hpc.
JoeZiminski Aug 15, 2024
c6caedc
Add arg input for SLURM.
JoeZiminski Aug 15, 2024
650ab8b
sbatch file.
JoeZiminski Aug 15, 2024
942a836
small fixes to other methods.
JoeZiminski Aug 15, 2024
2d22b89
Start adding widgets.
JoeZiminski Aug 21, 2024
88f3dd3
Add first rough nonrigid.
JoeZiminski Aug 23, 2024
78fcf80
Try a recursive nonrigid alignment, doesn't really work.
JoeZiminski Aug 27, 2024
cee8281
Revert "Try a recursive nonrigid alignment, doesn't really work."
JoeZiminski Aug 27, 2024
574d77f
Adding a few more options.
JoeZiminski Aug 27, 2024
14a8ed1
small changes prior to refactoring.
JoeZiminski Aug 28, 2024
9f18ad6
Small changes.
JoeZiminski Aug 28, 2024
3fc06b5
Remove old and benchmarking scripts.
JoeZiminski Aug 28, 2024
d08b51a
Begin tidying up.
JoeZiminski Aug 28, 2024
a9c9be0
Major refactor, add smoothing, interpolation, better spatial binning.
JoeZiminski Aug 30, 2024
66b61af
Update some notes.
JoeZiminski Aug 30, 2024
385589f
Tidy up, expose aling to session X.
JoeZiminski Sep 2, 2024
b75fefe
Thinking about trimmed versions and robust xcorr, leave until later.
JoeZiminski Sep 2, 2024
1aa2fe1
PLaying with large shifts.
JoeZiminski Sep 3, 2024
1e0e01b
Playing with alignment algorithm, completely fails when rigid shift l…
JoeZiminski Sep 3, 2024
fc0e7ad
some small tidying up
JoeZiminski Sep 4, 2024
523f94e
Lots of tidying up, need to look into nonrigid more something has reg…
JoeZiminski Sep 5, 2024
5f0165c
Look further into rigid, it was working well, but the parameters chos…
JoeZiminski Sep 6, 2024
fad9c65
Fix corrected histogram to use same method as compute.
JoeZiminski Sep 6, 2024
d1476cc
Big refactor, getting close to first draft.
JoeZiminski Sep 6, 2024
e33ea18
Begin typing and documentation.
JoeZiminski Sep 12, 2024
67546f7
Fix from motion correction function, adding typing and docstrings.
JoeZiminski Sep 13, 2024
6af5a3c
Docstrings and typing for session_alignment.
JoeZiminski Sep 17, 2024
46926bd
Continue adding docstring / types.
JoeZiminski Sep 27, 2024
ec72bd0
Continue with docstrings.
JoeZiminski Sep 30, 2024
b3eb95a
Small fixes
JoeZiminski Nov 21, 2024
87f6f70
Remove a TODO.
JoeZiminski Nov 21, 2024
a3aa475
Add recording shifts argument.
JoeZiminski Nov 21, 2024
059d962
Update time estimate method.
JoeZiminski Nov 22, 2024
12fd165
Fix time estimate, other tidy ups.
JoeZiminski Nov 27, 2024
0f12494
gaussian process first draft.
JoeZiminski Nov 29, 2024
b6b2a21
remove some debug stuff from gp first draft.
JoeZiminski Nov 29, 2024
24c8d7e
Very rough introduce 2D versions.
JoeZiminski Nov 29, 2024
4ce584b
Add scaling to GP, beter convergence.
JoeZiminski Dec 6, 2024
12b46c9
Tidy up.
JoeZiminski Dec 16, 2024
dec83be
Handle the 1-bin case in Motion objects __repre__
JoeZiminski Dec 16, 2024
e91e9d4
Tidy up and fixes for 'session_alignment.py'
JoeZiminski Dec 16, 2024
4ce7035
Tidying up, begin fixing alignment alg.
JoeZiminski Dec 16, 2024
74d6c45
Remove pickle files.
JoeZiminski Dec 17, 2024
e7435ec
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 17, 2024
62010d8
Reformatting alignment methods and add 2D, need to tidy up.
JoeZiminski Dec 17, 2024
300b781
delete big files.
JoeZiminski Dec 17, 2024
8e5ba68
Trying different alg
JoeZiminski Dec 19, 2024
62407b1
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 19, 2024
ede589b
Playing with alg rigid shift but scales for better rigid shift, okay …
JoeZiminski Dec 19, 2024
45502ce
Testing on the session_alignment side.
JoeZiminski Dec 19, 2024
cf16e06
playing with nonrigid.
JoeZiminski Dec 20, 2024
70db8e2
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 20, 2024
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Add annotations to hopefully fix tests.
  • Loading branch information
JoeZiminski committed Dec 17, 2024
commit 6126cfa5e293535ef0b97c941b20144531e509f9
4 changes: 2 additions & 2 deletions debugging/debugging_session_displacement.py
Original file line number Diff line number Diff line change
@@ -40,12 +40,12 @@
rec_durations=(25, 25, 25), # TODO: checks on inputs
rec_shifts=(
(0, 0),
(0, 0),
(0, 200),
(50, 200),
),
generate_sorting_kwargs=dict(firing_rates=(149, 150), refractory_period_ms=4.0),
generate_templates_kwargs=dict(unit_params=default_unit_params_range, ms_before=1.5, ms_after=3),
seed=None,
seed=44,
generate_unit_locations_kwargs=dict(
margin_um=0.0, # if this is say 20, then units go off the edge of the probe and are such low amplitude they are not picked up.
minimum_z=5.0,
1 change: 1 addition & 0 deletions src/spikeinterface/generation/drifting_generator.py
Original file line number Diff line number Diff line change
@@ -8,6 +8,7 @@

"""

from __future__ import annotations
import numpy as np

from probeinterface import generate_multi_columns_probe