3 add change detection events and trials table by arielleleon · Pull Request #5 · AllenNeuralDynamics/camstim-behavior-processing

arielleleon · 2026-07-17T21:36:16Z

packages change detection task into NWB file

… in a pipeline

…data structures.

build_events_table initialized lick_classification, bout_start, and reward_type with np.nan (float64), then _classify_rewards/_classify_licks assigned strings into them. Older pandas silently upcast to object; pandas 3.0 enforces the dtype and raises "Invalid value ... for dtype float64" when packaging a change-detection session. Initialize these three columns as object dtype up front, preserving the NaN sentinels the NWB layer reads via pd.notna. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

pynwb 4.0 moved events/HED support into core, so the native NWBFile `events` field collides with the one the standalone ndx-events adds via NdxEventsNWBFile, raising "NdxEventsNWBFile.__init__: names duplicated: ['events']". The library was declared with unbounded deps, so a plain pip install resolved pynwb 4 and broke. Add version bounds (pynwb <4, ndx-events <0.5, ndx-hed <0.3) matching the standalone-extension / pynwb 3.x line the code targets, and re-lock. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Extract encoder lookup into `_encoder_from_pkl` and add an `encoder_keys` argument to `compute_running_speed` (default `("behavior",)`, unchanged for change-detection). The passive SweepStim path passes `("foraging", "behavior")` so it can read the foraging-item encoder, falling back to behavior. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Port the capsule's `sweepstim_packaging` into the library, refactored into the two-layer architecture: - load_data/sweepstim.py: `classify_sweepstim_session`, `compute_sweepstim_timestamp_alignment`, and `build_sweepstim_session` returning a new `SweepStimData` (presentation + epoch DataFrames + timing). Pure numpy/pandas/h5py; HED is left to the nwb layer. - nwb/sweepstim.py: subject/file builder, `stimulus_presentations` and flat `intervals` TimeIntervals builders, sidecar, `assemble_sweepstim_nwbfile`, and the one-call `package_sweepstim_nwb` (NWB-Zarr + events.json), mirroring `package_nwb`. HED fragments/helpers for passive sessions live in nwb/hed_tags.py (single source of truth). Classification/session builders are re-exported eagerly; `package_sweepstim_nwb` is lazy (pynwb). Full synthetic pkl+sync fixtures and tests keep flake8, interrogate (100%), and coverage (100%) green. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

package_nwb is change-detection-only, so a passive SweepStim pkl (no items['behavior']) fails deep inside the Stage-1 extractor with a confusing KeyError. Add package_session, which loads the pkl, classifies it with classify_sweepstim_session, and dispatches to package_sweepstim_nwb (passive) or package_nwb (change-detection), forwarding all keyword arguments. This lets a mixed batch be packaged through one entry point without knowing each session's type up front. - nwb/__init__.py: new package_session + __all__/docstring updates. - __init__.py: lazy root re-export (pynwb stays off the eager import path). - tests/test_package_session.py: routing (both branches via the real classifier) + kwargs-forwarding. Gates green: flake8, interrogate 100%, 152 tests, coverage 100%. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

matchings

i noted a few places where task parameter descriptions could be changed but i dont think that needs to block merge of this PR, as long as they are noted for the future.

arielleleon and others added 10 commits July 9, 2026 18:10

feat: port over Marina's logic into a Claude assembled library to run…

bf26bda

… in a pipeline

tests: add tests for source code

0433f7d

docs: example instructions on how to use the library

6913e4d

build: library bulid file

efeac49

refactor: refactor to trim down code an reorganize into intermediate …

911d15b

…data structures.

arielleleon requested a review from matchings July 17, 2026 21:36

arielleleon linked an issue Jul 17, 2026 that may be closed by this pull request

add change detection events and trials table #3

Closed