2025 11 15 96o6 91a92

[seqasim]

accidental branch - merge

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Note

Add comprehensive type hints and docstrings plus a suite of LFP analysis utilities (preprocessing/baseline, BOSC/eBOSC, connectivity incl. GC/GCMI and amp coupling, FOOOF, synchronization, NLX/IOWA parsing, and permutation/mixed-effects stats).

• analysis_utils:
  • Add type hints/docstrings and utilities: ROI/channel selection, LFP STA, TFR plotting, fast burst detection, FOOOF per-epoch and parallel wrappers, catch22 features.
• iowa_utils:
  • Add parsers for connection/electrode tables; channel renaming stub with typing/docstring.
• lfp_preprocess_utils:
  • Add baseline functions (time-series/TFR, trialwise and permutation), referencing (white matter, bipolar; laplacian stub), channel name matching, bad-electrode/artifact/IED detection, electrode loading, MNE builders (scalp/NLX/EDF), re-referencing, epoching, electrode DF renaming, and TFR compute+baseline pipeline.
• nlx_utils:
  • Add typed, documented IO helpers for headers, records, NCS/NEV loading, record checks, subject parsing, and NCS merge scaffold.
• oscillation_utils:
  • Implement surrogate generators; connectivity metrics (phase GCMI, amp-amp, time-resolved and epoch GC); seed-target mapping; BOSC/eBOSC libraries and parallel wrapper; helpers with typing/docs.
• statistics_utils:
  • Add permutation OLS z-scoring, hierarchical shuffling and surrogate generation, time-resolved single-channel regression, and parallel time-resolved mixed-effects with empirical/z p-values.
• sync_utils:
  • Add photodiode/TTL timestamp extraction, pulse alignment, robust synchronization, and typed/docs across functions.

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Bug: NameError: Variable from Unquoted String

The condition elif entorhinal in roi: references an undefined variable entorhinal (missing quotes). This should be the string 'entorhinal' to check if the string is in the roi list. This will cause a NameError at runtime when this branch is executed.

LFPAnalysis/analysis_utils.py#L154-L155

LFPAnalysis/LFPAnalysis/analysis_utils.py

Lines 154 to 155 in 473232a

	roi += ['cingulate gyrus a', 'cingulate gyrus b', 'cingulate gyrus c']
	elif entorhinal in roi:

 

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[cursor]

Bug: Scope Error: Variable Name Mismatch

The variable elec_df is used but the function parameter is named elec_data. This causes a NameError since elec_df is not defined in the function scope. The code should use elec_data instead of elec_df.

 

[cursor]

Bug: Naming Error Prevents Code Execution

The variable elec_df is used but the function parameter is named elec_data. This causes a NameError since elec_df is not defined in the function scope. The code should use elec_data instead of elec_df.