Code

v0.16#54

Code

Merged

kjohnsen merged 85 commits intomastersiplab-gt/cleo:masterfrom v0.16siplab-gt/cleo:v0.16Copy head branch name to clipboardSep 18, 2024

+8,440-218,361

Commits

Commits on Jan 19, 2024

• Update t_ms and interval_ms

  arnavt2955

  committed
  ea3150e

• updates t in other files

  arnavt2955

  committed
  8892069

• updated t

  arnavt2955

  committed
  d4a7274

Commits on Feb 2, 2024

• changed more _ms

  arnavt2955

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  05978e0

• Merge remote-tracking branch 'origin' into UsingBrianUnits

  arnavt2955

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  d5c5f03

• added import

  arnavt2955

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  9f4add0

• addes imports

  arnavt2955

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  ee04625

Commits on Mar 15, 2024

• fixed base.py and made changes to lfp - still failing 10 cases

  arnavt2955

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  c77a52a

Commits on Apr 18, 2024

• Created jupyteer notebook for calculating ratios

  arnavt2955

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  288a286

• added ratio into opsin library and added 2p action spectra into spectrum variables for all opsins

  arnavt2955

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  efff6b6

Commits on May 8, 2024

• progress on all_optical fig

  kjohnsen

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  aa0609a

Commits on May 27, 2024

• improve action spectrum extrapolation

  kjohnsen

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  756bbf1

• start Newman 15 with alternate opsins

  kjohnsen

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  521ac34

• Merge remote-tracking branch 'origin' into validation2

  kjohnsen

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  23bf74b

• update Overview doc

  kjohnsen

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  18ac155

Commits on May 31, 2024

• finish newman15 validation w/ alternate opsins

  kjohnsen

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  e85ed03

• Update paper plot style

  kjohnsen

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  a66da8d

Commits on Jun 6, 2024

• style_plots_for_paper docstring

  kjohnsen

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  b6607b5

• Merge branch 'master' of https://github.com/Sensory-Information-Processing-Lab/Cleo into validation2

  kjohnsen

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  e7897c5

Commits on Jun 21, 2024

• change Jupyter to Python for linguist

  kjohnsen

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  9e3bd1a

• change OGB-1 name

  kjohnsen

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  7e4dd0f

• add warning to scope when sensor not injected

  kjohnsen

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  8e121f0

• add showcase to docs

  kjohnsen

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  f34b0b7

• implement LIOP reset in _base_reset

  kjohnsen

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  5d14096

• add showcase doc to index

  kjohnsen

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  1f67236

• add _base_reset to sim.reset

  kjohnsen

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  7173b74

• fresh run through of all-optical-fig notebook

  kjohnsen

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  4b32fb8

• add README to notebooks, env info to all_optical_fig.ipynb

  kjohnsen

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  689a0f8

• bump to v0.15.0

  kjohnsen

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  18e470d

• remove images [skip ci]

  kjohnsen

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  cda9382

• untrack images

  kjohnsen

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  1e2eaa0

• more organizing notebook images

  kjohnsen

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  023eb4e

• Merge branch 'UsingBrianUnits' of https://github.com/Sensory-Information-Processing-Lab/Cleo into v0.16

  kjohnsen

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  c7a79f7

• move Sridharan fig2

  kjohnsen

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  37ed3a1

Commits on Jun 24, 2024

• use Brian units everywhere

  kjohnsen

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  523e70e

• reorganize ioproc tests

  kjohnsen

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  5d904ae

• add firing_rate_estimate and pi_ctrl methods, revise PI_Ctrl notebook

  kjohnsen

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  ded4fde

• ax ioproc folder

  kjohnsen

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  6d33767

• ax ProcessingBlock

  kjohnsen

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  5c74e9f

Commits on Jun 25, 2024

• upgrade nptyping, make sim.remove() private

  kjohnsen

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  1928c01

• fix more unit problems

  kjohnsen

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  06c2d0f

Commits on Jun 27, 2024

• get overview working

  kjohnsen

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  be690c3

• get tutorials working

  kjohnsen

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  0933ffc

Commits on Jul 16, 2024

• use explicit units on Light

  kjohnsen

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  df3b507

• add units to SimpleOpsin gain

  kjohnsen

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  04fc0a8

• extend font stack

  kjohnsen

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  b552d23

Commits on Jul 18, 2024

• fix spike count problem

  kjohnsen

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  ddd7f60

Commits on Jul 20, 2024

• scope to_neo

  kjohnsen

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  7dc7375

Commits on Jul 21, 2024

• 2p light to_neo

  kjohnsen

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  bdf27b6

• fix spiking test fail

  kjohnsen

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  b1c7582

• Use utilities.rng

  kjohnsen

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  0b8b763

Commits on Aug 14, 2024

• units on Light.values and other small tweaks

  kjohnsen

  committed
  1db73f1

• add version note to newman15 notebooks

  kjohnsen

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  84f9452

• add version note to opto val notebook

  kjohnsen

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  30db678

• fix electrodes tutorial

  kjohnsen

  committed
  bd9a9fb

• fix opto tutorial

  kjohnsen

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  9b8a546

• fix multi_opto notebook, add range to plot_spectra

  kjohnsen

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  09723e3

Commits on Aug 15, 2024

• fix on_off_ctrl notebook

  kjohnsen

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  93d07ce

Commits on Aug 16, 2024

• update PI ctrl notebook

  kjohnsen

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  2c09a76

• fix all_optical tutorial

  kjohnsen

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  b65a154

• fix video viz tutorial

  kjohnsen

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  79de3bd

• fix Neo tutorial

  kjohnsen

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  8f58745

• fix advanced LFP notebook

  kjohnsen

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  26a933d

Commits on Sep 4, 2024

• rename firing_rate_estimate to exp_firing_rate_estimate

  kjohnsen

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  e0d81f9

Commits on Sep 12, 2024

• fix global set_seed

  kjohnsen

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  49a559a

• progress on lqr tutorial, before cutting adaptive control

  kjohnsen

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  2ad5ad1

• revamp ldsCtrlEst tutorial

  kjohnsen

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  0336931

• support numpy >= 2.0

  kjohnsen

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  bf66e87

• remove bug workaround (closes Remove bug workaround in tutorials #16)

  kjohnsen

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  f615489

Commits on Sep 13, 2024

• fix light.to_neo

  kjohnsen

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  41176c5

Commits on Sep 16, 2024

• replace nptyping with jaxtyping

  kjohnsen

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  6dd8dcb

• remove imported members from ioproc docs

  kjohnsen

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  ee25e92

• mark lfp tests as slow

  kjohnsen

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  63b50ca

Commits on Sep 17, 2024

• polish tutorial notebooks

  kjohnsen

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  f7f9db2

• tweak docstrings

  kjohnsen

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  4cb34d0

• add LatencyIOProcessor to base cleo import

  kjohnsen

  committed
  88836ac

• clean up imports

  kjohnsen

  committed
  4b34135

• Merge branch 'master' into v0.16

  kjohnsen

  committed
  84ee159

• fix lqr notebook, fresh rerun of all

  kjohnsen

  committed
  2852b72

Commits on Sep 18, 2024

• polish video tutorial, exit if no ffmpeg

  kjohnsen

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  646eaa6

• skip execution of video write cell

  kjohnsen

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  3566ac4

• tweak overview docs, increase test cell timeout

  kjohnsen

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  ede7deb

• simplify 4-state opsin model

  kjohnsen

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  fc73d86

• eliminate warnings

  kjohnsen

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  44b6f83

• rerun opto tutorial, increase timestep

  kjohnsen

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  23f1cbf