feat(viz): Add DSS/benchmark/zapline visualization modules and theme + enhance examples (closes #22)#24
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snesmaeili wants to merge 17 commits intomainfrom
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feat(viz): Add DSS/benchmark/zapline visualization modules and theme + enhance examples (closes #22)#24snesmaeili wants to merge 17 commits intomainfrom
snesmaeili wants to merge 17 commits intomainfrom
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BabaSanfour
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v0.0.2 - Stability, Documentation, and Benchmarks milestone
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…ess issues - Fix isinstance union-type calls to use X | Y syntax (Python 3.10+) - Replace garbled Unicode placeholders with proper characters - Add _PUB_RC dict, use_style() context manager, _apply_style(), _finalize_fig() - Add METHOD_COLORS dict and _get_color() helper - Centralize all hardcoded colors to COLORS/METHOD_COLORS refs - Standardize return types: zapline functions now return Figure (not Axes) - Add fname parameter to all public plot functions for file saving - Rename benchmark save_path to fname for MNE-like consistency - Export new public API: METHOD_COLORS, use_style, _apply_style, _finalize_fig - Fix syntax error (double comma) in dss.py - Update tests: fix Axes->Figure assertions, add theme/helper smoke tests
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #24 +/- ##
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- Coverage 90.27% 89.04% -1.23%
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Files 32 41 +9
Lines 2622 4894 +2272
Branches 465 884 +419
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+ Hits 2367 4358 +1991
- Misses 145 336 +191
- Partials 110 200 +90
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Bug fixes: - Export _get_color in viz/__init__.py - Fix string channel picks crash in plot_time_course_comparison - Handle above-Nyquist frequencies in peak_attenuation_db (return NaN) New modules: - mne_denoise/qa/__init__.py — QA metrics package - mne_denoise/qa/metrics.py — peak_attenuation_db function New scripts: - scripts/visual_qa.py — comprehensive QA testing all 37 viz functions on real Runabout data (36/37 pass; plot_dss_comparison needs future DSS n_select/smooth/segmented params)
Review fixes from Nature Methods-style audit: - comparison.py: replace hardcoded 'k'/'r'/'b' with COLORS['before']/COLORS['after'] - components.py: replace 'steelblue'/'gray' with COLORS['primary']/COLORS['muted'] - zapline.py: replace plt.cm.tab10 with Wong (2011) palette from COLORS dict - dss.py: add fname param to all 5 public plot functions, use _finalize_fig - zapline.py: add fname param to 4 dashboard functions, use _finalize_fig - _theme.py: _finalize_fig closes figure after save when show=False - __init__.py: remove private helpers from __all__ - qa/metrics.py: add TODO for 6 missing QA metric functions All 322 tests pass.
…lues\n\nNew module `mne_denoise.viz.erp` with 5 pub-quality ERP benchmark\nvisualizations:\n - plot_erp_signal_diagnostics: 3×2 QA dashboard (PSD / evoked / diff wave)\n - plot_condition_interaction: diff waves + Hedges' g interaction plot\n - plot_metric_violins: violin + swarm + paired lines (generic)\n - plot_endpoint_summary: multipanel violins + null CI + paired slopes\n - plot_pipeline_slopes: multi-metric subject-level trajectories\n\nAlso fixes:\n - components.py: handle 2-D eigenvalues in plot_narrowband_scan peak marker\n\nAll 322 tests pass."
- Add 12 cells (Section 11) to viz_showcase.ipynb demonstrating all 5 ERP benchmark functions with synthetic data - Fix seaborn FutureWarning: add hue='Group', legend=False to all violinplot/stripplot calls in plot_metric_violins & plot_endpoint_summary - Replace deprecated set_xticklabels with tick_params in both functions - Add module-level warnings.filterwarnings in erp.py for residual seaborn palette warnings - Update Summary table with ERP Benchmark row
New functions in mne_denoise/viz/erp.py: - plot_grand_average_erp: group-mean evoked +/- between-subject SEM - plot_grand_condition_interaction: condition x pipeline with group error bars - plot_null_distribution: permutation null histogram + observed statistic - plot_forest: per-subject effect-size forest plot with CI Updated __init__.py exports (9 ERP functions + 3 constants). Added Section 12 to viz_showcase.ipynb (10 cells, all demos pass).
…lize_fig to auto-create parent directories (mkdir -p)\n before saving figures, preventing FileNotFoundError\n- Add erp_io.py with deferred-group workflow:\n - save_subject_erp_results(): persist evokeds, diff waves,\n effect sizes, and metrics per subject\n - load_subject_erp_results(): read one subject's saved data\n - aggregate_erp_results(): collect all subjects from disk into\n ERPGroupData namedtuple ready for group plot functions\n- Export 4 new symbols from viz __init__.py\n- 322 tests pass, IO round-trip verified"
- tests/test_erp_viz.py: 92 comprehensive tests for erp.py (96% cov), erp_io.py (97% cov), and _theme.py mkdir fix - mne_denoise/viz/erp.py: fix B904 (raise ... from err), fix E402 (move relative import above warnings.filterwarnings calls), ruff format - mne_denoise/viz/erp_io.py: ruff format only (no logic changes) - docs/changes/devel/feature.rst: document ERP functions, erp_io, _finalize_fig fix, and test suite Full suite: 414 passed, 11 skipped
- tests/test_qa_metrics.py: peak_attenuation_db (8 tests) - tests/test_viz_metrics.py: suppression, distortion, variance (9 tests) - tests/test_benchmark_io.py: save/load/aggregate IO (22 tests) - tests/test_viz_benchmark.py: all 9 plot functions + helpers (36 tests) - tests/test_viz_dss.py: DSS helpers + dashboards (35 tests) - tests/test_viz_zapline_extended.py: adaptive/standard summary + helpers (42 tests) - tests/test_utils.py: extract/reconstruct MNE objects (13 tests) - tests/test_averaging.py: AverageBias._apply_datasets (7 tests) - docs/testing.rst: testing documentation page - docs/index.rst: add testing to toctree
- Make pandas imports lazy in benchmark_io.py, erp_io.py, erp.py so viz module can be imported without pandas (fixes docs build) - Add per-file-ignores for scripts/ and run_erp_benchmark.py (D, E402) - Add F404 ignore for examples (notebook __future__ import) - Auto-fix ruff issues: unused imports, sort imports, dict literals, dict comprehensions, set comprehensions, SIM114
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feat(viz): Add DSS/benchmark/zapline visualization modules and theme + enhance examples
(Recreated from #23 which was accidentally merged)