compile SparseKernelInserter event loop with numba - #34
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
SparseKernelInserter._processlooped over every event in Python and, perevent, re-evaluated the kernel (allocating a mask + zeros + fancy-index) and
did a sliced add. The cost scaled with channels × firing rate, making it a top
stage in the velocity→ecephys encoder.
This pre-samples every kernel once into a zero-padded table (one row per
distinct kernel, cached in state and rebuilt on stream reset) and scatters it
onto the dense buffer in a numba
njitloop. Event value → table row isresolved vectorized via
np.uniqueover the (typically tiny) set of distinctvalues.
The rewrite stays fully general — it works for any
Kernelsubclass(
ArrayKernelwaveforms,FunctionalKernel, unit impulses) and preservesscale_by_value, acausalpre_samples, and the chunk-boundarypendingtail.Results
Per-stage encoder benchmark (
bench_cosine_encoder.py, 256ch @ 30 kHz):kernel_insertbeforeEnd-to-end (simulator over LSL, 50 Hz, 256ch):
WAVEFORMSat 0.097 ms/msg,flat-to-better despite each message now carrying 2× the samples.
Correctness
0.0) — kernel insertion is pure indexed addition, no reduction reassociation.
paths —
scale_by_valuewith a real kernel and with a MultiKernel, unknownvalues falling back to the default key, and an explicit
default_key.Dependency
Declares
numbaexplicitly. It was already imported bypoissonevents.pybutnever declared — this fixes that latent gap.