perf(create_disrnn_dataset): group by session once instead of per-session df.query#29
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perf(create_disrnn_dataset): group by session once instead of per-session df.query#29hanhou wants to merge 1 commit into
hanhou wants to merge 1 commit into
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…sion df.query
create_disrnn_dataset looped df_trials["ses_idx"].unique() twice (xs then ys),
calling df.query("ses_idx == @ses_idx") per session. df.query re-parses the
expression string and re-scans the frame on every call, so for cohorts with many
sessions this dominated dataset construction (~107s of a profiled 441s
multisubject load). Replace both loops with a single groupby("ses_idx",
sort=False) pass; sort=False preserves the first-appearance session order that
defines the column index, matching unique(). xs/ys output is identical (verified).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Summary
create_disrnn_datasetloopeddf_trials["ses_idx"].unique()twice (once forxs, once forys), callingdf_trials.query("ses_idx == @ses_idx")per session.df.queryre-parses the expression string and re-scans the whole frame on every call, so on cohorts with many sessions this dominated dataset construction (it was ~24% of a profiled 441s multisubjectload()).Change
Replace both loops with a single
groupby("ses_idx", sort=False)pass.sort=Falsepreserves the first-appearance session order that defines the column indexdex(matchingdf_trials["ses_idx"].unique()), soxs/ysare identical.Measured performance (real cohort: 878 subjects, 23,569 sessions, 11.3M trials)
Per-subject
xs/ysbuild, summed over all subjects (onprem H200 node, CPU):df.query)groupby,sort=False)Verification
xs/ysbit-identical to the old query-loop output for all 878 subjects (identical=True).sort=True, which is whysort=Falseis required.create_disrnn_datasetreturns a validDatasetRNNwith correct shapes.🤖 Generated with Claude Code