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Add OptogenSIMLight: Monte Carlo–based light model - #74

Merged

kjohnsen merged 42 commits into

masterfrom

light-model-improvements

Oct 5, 2026

Merged

Add OptogenSIMLight: Monte Carlo–based light model#74
kjohnsen merged 42 commits into
masterfrom
light-model-improvements

Commits on Jul 11, 2026
- Add OptogenSIMLight prototype and compressed 4D dataset
  akhilsnarra-ui
  committed
  14aa1b8
Commits on Jul 15, 2026
- Store dataset as gzipped NetCDF3 (scipy backend, no new dependency)
  akhilsnarra-ui
  committed
  57bfebe
Commits on Jul 16, 2026
- Load packaged data via importlib.resources; include data file in Poetry build
  akhilsnarra-ui
  committed
  3d89dd8
Commits on Jul 18, 2026
- Add OptogenSIMLight to light visualization notebook
  akhilsnarra-ui
  committed
  3abb054
Commits on Jul 20, 2026
- Add dedicated OptogenSIMLight transmittance test and viz_params coverage; export from cleo.light
  akhilsnarra-ui
  committed
  3db06a3
Commits on Jul 21, 2026
- Add OptogenSIMLight demonstration to multi-opto tutorial
  akhilsnarra-ui
  committed
  9317a61
Commits on Jul 25, 2026
Commits on Aug 5, 2026
- Rename optogensim_light.py to optogensim.py per review
  akhilsnarra-ui
  committed
  e684943
- Clean notebooks: remove change markers, strip execution counts, fresh run
  akhilsnarra-ui
  committed
  80fb94e
Commits on Aug 6, 2026
Commits on Aug 7, 2026
- Move wavelength from Light to LightModel
  akhilsnarra-ui
  committed
  f88c835
Commits on Aug 8, 2026
- Fix two_photon call site missed in wavelength refactor
  akhilsnarra-ui
  committed
  56d081b
Commits on Aug 14, 2026
- Address review on optogensim.py + fix light_viz wavelength calls
  akhilsnarra-ui
  committed
  3cf2aec
Commits on Aug 17, 2026
- Extend beam-width transmittance test to fiber and GaussianEllipsoid
  akhilsnarra-ui
  committed
  d280664
Commits on Aug 18, 2026
- Apply ruff formatting to optogensim.py
  akhilsnarra-ui
  committed
  8b2fc0e
Commits on Aug 19, 2026
- Tune multi_opto amplitude to 0.45 and use np.ptp for trace spacing
  akhilsnarra-ui
  committed
  81dd5e5
Commits on Aug 21, 2026
- Use OptogenSIM LightModel in profile explorer; fix heatmap aspect ratio
  akhilsnarra-ui
  committed
  47a6540
Commits on Aug 26, 2026
- Add OptogenSIM fork link to data docstring
  akhilsnarra-ui
  committed
  838a676
Commits on Aug 28, 2026
- Silence brian2 warning for discarded light-source objects
  akhilsnarra-ui
  committed
  d6319a0
Commits on Aug 31, 2026
- tweak visualization
  kjohnsen
  committed
  9949c01
- format tests
  kjohnsen
  committed
  5e10b0e
Commits on Sep 5, 2026
- Merge remote-tracking branch 'origin/master' into light-model-improvements
  akhilsnarra-ui
  committed
  b42b63b
Commits on Sep 12, 2026
- Address final review comments
  akhilsnarra-ui
  committed
  3b60daf
Commits on Sep 19, 2026
- Warn when OptogenSIM targets fall outside the data range
  akhilsnarra-ui
  committed
  9b0e017
Commits on Oct 3, 2026
- Zero OptogenSIM transmittance outside data range
  kjohnsen
  committed
  24e74f1
- Fix CI: drop setup-python, let setup-uv provide Python
  kjohnsen
  committed
  5bdc7b4
- Test OptogenSIM packaged data is peak-normalized to 1
  kjohnsen
  committed
  8ff3df5
- Use setup-uv@v7 (no v10 major tag exists)
  kjohnsen
  committed
  e51e7ff
- CI: prefer uv-managed Python (runner Pythons are PEP 668 locked)
  kjohnsen
  committed
  3213f9e
- CI: setup-uv v7 cancels on all runners, use known-good v5
  kjohnsen
  committed
  4fc4657
- CI: install into uv venv instead of system python
  kjohnsen
  committed
  193d00e
- CI: drop empty env block (invalid workflow)
  kjohnsen
  committed
  69c46e4
- CI: setup-uv already provides .venv, drop manual uv venv
  kjohnsen
  committed
  6e8b96b

Commits

Commits on Jul 11, 2026

Commits on Jul 15, 2026

Commits on Jul 16, 2026

Commits on Jul 18, 2026

Commits on Jul 20, 2026

Commits on Jul 21, 2026

Commits on Jul 25, 2026

Commits on Aug 5, 2026

Commits on Aug 6, 2026

Commits on Aug 7, 2026

Commits on Aug 8, 2026

Commits on Aug 14, 2026

Commits on Aug 17, 2026

Commits on Aug 18, 2026

Commits on Aug 19, 2026

Commits on Aug 21, 2026

Commits on Aug 26, 2026

Commits on Aug 28, 2026

Commits on Aug 31, 2026

Commits on Sep 5, 2026

Commits on Sep 12, 2026

Commits on Sep 19, 2026

Commits on Oct 3, 2026