Fix computational issues across analyses, stats, prep and utils#252
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deep-introspection wants to merge 2 commits intomasterfrom
Open
Fix computational issues across analyses, stats, prep and utils#252deep-introspection wants to merge 2 commits intomasterfrom
deep-introspection wants to merge 2 commits intomasterfrom
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analyses.py: - compute_conn_mvar: counter += counter -> counter += 1 (was always 0) - compute_nmPLV: use phase exponentiation for n:m PLV instead of scalar multiplication which doesn't change phase angles - compute_nmPLV: remove **filter_options passed to compute_single_freq which doesn't accept them stats.py: - statscluster: fix undefined variable 'args' -> 'arg' in f_mway_rm call - statscluster: compute proper t/F critical values as cluster thresholds instead of using alpha (a p-value) as a test statistic threshold - statscluster: use alpha parameter instead of hardcoded 0.05 in f_threshold_mway_rm - statscondCluster: use alpha instead of alpha/2 for F-test threshold - statsCond: use boolean mask from fdr_correction instead of fragile float equality comparison on p-values prep.py: - AR_local: fix clean_epochs_subj[subject_id].info to clean_epochs_subj.info (was indexing epoch not subject) utils.py: - generate_virtual_epoch: use n_chan//2 instead of n_chan/2 to avoid TypeError from float index
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Summary
Systematic audit and correction of computational issues across the codebase.
WTC mode in
xwt()(analyses.py)|W1×W2*|/(|W1|×|W2|)trivially 1.0WTC = |S(W1×W2*)|² / (S(|W1|²) × S(|W2|²))n:m PLV in
compute_nmPLV()(analyses.py)k * exp(iφ)) which changes magnitude, not phaseexp(iφ)^n = exp(inφ)) for correct n:m phase coupling**filter_optionspassed tocompute_single_freq()which doesn't accept themCluster statistics (stats.py)
statscluster: threshold was set toalpha(e.g. 0.05), a p-value, but MNE expects a test statistic (e.g. t≈2.02). This made nearly all values form one cluster.statscluster:args→argtypo causedNameErroronf multiplewaypathstatscluster: hardcodedpvalue=0.05→ usesalphaparameterstatscondCluster: F-threshold usedalpha/2(too conservative for one-tailed F-test) → usesalphastatsCond: replaced fragile float equality on p-values with boolean mask fromfdr_correctionOther fixes
compute_conn_mvar(analyses.py):counter += counter→counter += 1(was always 0, making retry logic dead code)AR_local(prep.py):clean_epochs_subj[subject_id].info→clean_epochs_subj.info(was indexing into epochs, not subjects)generate_virtual_epoch(utils.py):n_chan/2→n_chan//2(float division causedTypeError)Impact on existing pipelines
statscondClusterandstatsclusterwere overly conservative or broken; may detect previously missed effectscompute_nmPLVoutput changes fundamentally — previous results were not measuring n:m phase couplingTest plan