sorting analyzer - waveform computation warnings

Open
#4,056 1 comment 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
30/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Tech stack
python
Domain
data

Research direction

Reproduce waveform extraction with the analyzer and inspect the estimate_sparsity, noise_level, and compute_waveforms stages. Trace the warnings reported from scipy.stats._stats_py.py and establish which SciPy versions are supported. The work is complete when the warning cause and supported version are documented or the warning behavior is corrected.

Written by the indexing model from the issue text.

Description

question

dear Devs,
whenever i try to use the analyzer to extract waveforms, regardless of sorter used, i get warnings from scipy.
what version of scipy is currently supported?

estimate_sparsity
engine=thread - n_jobs=8 - samples_per_chunk=30,000 - chunk_memory=21.97 MiB - total_memory=175.78 MiB - chunk_duration=1.00s (999.99 ms)
estimate_sparsity (workers: 8 threads): 0%| | 0/5304 [00:00<?, ?it/s]
noise_level (workers: 8 threads): 0%| | 0/20 [00:00<?, ?it/s]
compute_waveforms (workers: 8 threads): 0%| | 0/5304 [00:00<?, ?it/s]
C:\Users\su-weisss\AppData\Roaming\Python\Python311\site-packages\scipy\stats_stats_py.py:10730: RuntimeWarning: invalid value encountered in scalar divide
slope = ssxym / ssxm
C:\Users\su-weisss\AppData\Roaming\Python\Python311\site-packages\scipy\stats_stats_py.py:10744: RuntimeWarning: invalid value encountered in sqrt
t = r * np.sqrt(df / ((1.0 - r + TINY)*(1.0 + r + TINY)))
C:\Users\su-weisss\AppData\Roaming\Python\Python311\site-packages\scipy\stats_stats_py.py:10750: RuntimeWarning: invalid value encountered in scalar divide
slope_stderr = np.sqrt((1 - r**2) * ssym / ssxm / df)

Dominant language
Python
Stars
847
Forks
280
Avg merge
3d 9h
Merged PRs (30d)
29

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

More from SpikeInterface/spikeinterface

All issues in SpikeInterface/spikeinterface

Similar issues

More Python issues

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.