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Merged
merged 86 commits into from
Jul 30, 2025
Merged

475 decode generalisation #480

merged 86 commits into from
Jul 30, 2025

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wulfdewolf
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@wulfdewolf wulfdewolf commented Jul 10, 2025 •
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This combines:

  • decode_1d
  • decode_2d

into a generalised n-dimensional decode_bayes, which takes as input an xarray.DataArray (the new output of compute_tuning_curves).

Since occupancy is now an attribute of the tuning curves, decode_bayes uses that directly, if a new argument use_occupancy is set to True, it is False by default.

(this builds on the generalised tuning curves PR)

The old functions (and tests) are still available but they throw a DeprecationWarning.

wulfdewolf added 30 commits June 30, 2025 16:49
@wulfdewolf
start of general decode
6a513fa
@wulfdewolf
general decoding tests
b760a8c
@wulfdewolf
start of general tuning curve computatio
1abad76
@wulfdewolf
continuous addition
1b4c3de
@wulfdewolf
changing inputs to bins&range, matching numpy
29a4ad8
@wulfdewolf
tests for general tuning curve + wrappers for the old function
8c0af2c
@wulfdewolf
1/dt = fs
6bf94ee
@wulfdewolf
fix tests
18b0868 
note as to why I changed some original tests:
the old compute_2d_tuning_curves_continuous used np.digitize, which does
not include the last edge
the new implementation does, so I had to reflect that in the expected
values
@wulfdewolf
re-add tests for deprecated functions
12285a6
@wulfdewolf
corrected isinstance to older way
b59e9cf
@wulfdewolf
use histogramdd only
7b9583b
@wulfdewolf
cleaning
e7a1468
@wulfdewolf
hard-coded tc tests
e873d2f
@wulfdewolf
fixed implementation with histgramdd + hard-coded tests
3b9905e 
also changed f0 -> feature0
@wulfdewolf
remove epochs warning as it is not neccessary
359f92e
@wulfdewolf
update tutorial_calcium_imaging
3c7c9fe
@wulfdewolf
input_output notebook
f8c3a0a
@wulfdewolf
update HD tutorial for new tuning curve function
52b7f87
@wulfdewolf
more doc updates for tuning curves
4bdf81a
@wulfdewolf
fix minimal working example path
cfeabac
@wulfdewolf
cleaner to pandas for old 1d function
d67b2c2
@wulfdewolf
more doc updates
16971be
@wulfdewolf
decoding notebook
39a9f62
@wulfdewolf
tutorial phase pref doc
13fbae3
@wulfdewolf
more generalising docs for tuning curves
b82dd3a
@wulfdewolf
dandi tutorial
2b1398f
@wulfdewolf
allow passing a tuple range when 1D
a50eb99
@wulfdewolf
Merge branch '477-tc-generalisation' into 475-decode-generalisation
0e279d9
@wulfdewolf
Merge branch 'dev' into 477-tc-generalisation
45093dc
@wulfdewolf
Merge branch '477-tc-generalisation' into 475-decode-generalisation
3d4a410
sjvenditto
sjvenditto requested changes Jul 21, 2025
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Great PR so far! I've added some suggestions for a first round of review

@wulfdewolf wulfdewolf requested a review from sjvenditto July 22, 2025 20:24
sjvenditto
sjvenditto requested changes Jul 25, 2025
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I noted a few minor fixes. Also I'm realizing now that the way the code is structured assumes that a dictionary of Tsd objects is spike times - this is probably fine, but see the comment for more detail/discussion!

@wulfdewolf wulfdewolf requested a review from sjvenditto July 29, 2025 15:23
sjvenditto
sjvenditto approved these changes Jul 29, 2025
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Everything looks good to me!

@gviejo gviejo merged commit 1c440bc into dev Jul 30, 2025
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@wulfdewolf wulfdewolf mentioned this pull request Jul 30, 2025
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@gviejo gviejo gviejo approved these changes

@sjvenditto sjvenditto sjvenditto approved these changes

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Generalising decode_1d and decode_2d to decode

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@wulfdewolf @gviejo @sjvenditto