protocol-bicorder/analysis/scripts/review_analysis.py

#!/usr/bin/env python3
"""
Comprehensive review of the analysis for errors and inconsistencies.

Usage:
  python3 scripts/review_analysis.py data/synthetic_20251116.csv
  python3 scripts/review_analysis.py data/manual_20260101.csv --results-dir analysis_results/manual_20260101
"""

import argparse
import pandas as pd
import numpy as np
from pathlib import Path


def main():
    parser = argparse.ArgumentParser(
        description='Check analysis results for errors and inconsistencies',
        formatter_class=argparse.RawDescriptionHelpFormatter,
        epilog="""
Example usage:
  python3 scripts/review_analysis.py data/synthetic_20251116/readings.csv
  python3 scripts/review_analysis.py data/manual_20260101/readings.csv --analysis-dir data/manual_20260101/analysis
        """
    )
    parser.add_argument('input_csv', help='Diagnostic readings CSV (e.g. data/synthetic_20251116/readings.csv)')
    parser.add_argument('--analysis-dir', default=None,
                        help='Analysis directory (default: <dataset_dir>/analysis)')
    args = parser.parse_args()

    dataset_dir = Path(args.input_csv).parent
    results_dir = Path(args.analysis_dir) if args.analysis_dir else dataset_dir / 'analysis'

    print("=" * 80)
    print("ANALYSIS REVIEW - ERROR CHECKING")
    print("=" * 80)
    print(f"Dataset: {args.input_csv}")
    print(f"Results: {results_dir}")

    # Load data
    df = pd.read_csv(args.input_csv)
    clusters = pd.read_csv(results_dir / 'data' / 'kmeans_clusters.csv')
    pca_coords = pd.read_csv(results_dir / 'data' / 'pca_coordinates.csv')

    # Identify dimension columns
    design_cols = [c for c in df.columns if c.startswith('Design_')]
    entanglement_cols = [c for c in df.columns if c.startswith('Entanglement_')]
    experience_cols = [c for c in df.columns if c.startswith('Experience_')]
    dimension_cols = design_cols + entanglement_cols + experience_cols

    errors_found = []
    warnings_found = []

    print("\n1. DATA COMPLETENESS CHECK")
    print("-" * 80)

    missing_count = df[dimension_cols].isna().sum().sum()
    rows_with_missing = df[dimension_cols].isna().any(axis=1).sum()

    print(f"✓ Total protocols in source data: {len(df)}")
    print(f"✓ Protocols with complete data: {len(df) - rows_with_missing}")
    print(f"✓ Protocols with missing values: {rows_with_missing}")
    print(f"✓ Protocols in cluster analysis: {len(clusters)}")

    if rows_with_missing > 0:
        warnings_found.append(f"{rows_with_missing} protocols excluded due to missing values")
        missing_protocols = df[df[dimension_cols].isna().any(axis=1)]['Descriptor'].tolist()
        print(f"\n  Excluded protocols: {', '.join(missing_protocols)}")

    merged = df.merge(clusters, on='Descriptor', how='inner')
    if len(merged) != len(clusters):
        errors_found.append(f"Descriptor mismatch: {len(merged)} matched vs {len(clusters)} expected")
    else:
        print(f"✓ All cluster descriptors match source data")

    print("\n2. DATA QUALITY CHECK")
    print("-" * 80)

    for col in dimension_cols:
        values = df[col].dropna()
        if values.min() < 1 or values.max() > 9:
            errors_found.append(f"Column {col} has out-of-range values: [{values.min()}, {values.max()}]")

    print(f"✓ All dimension values within expected range [1, 9]")

    df_clean = df.dropna(subset=dimension_cols)
    variances = df_clean[dimension_cols].var()
    low_var_dims = variances[variances < 1.0]
    if len(low_var_dims) > 0:
        warnings_found.append(f"{len(low_var_dims)} dimensions have very low variance (< 1.0)")
        print(f"\n  Low variance dimensions:")
        for dim, var in low_var_dims.items():
            print(f"    - {dim}: {var:.3f}")
    else:
        print(f"✓ All dimensions have reasonable variance")

    print("\n3. CLUSTERING VALIDATION")
    print("-" * 80)

    cluster_sizes = clusters['cluster'].value_counts().sort_index()
    print(f"✓ Cluster 1: {cluster_sizes[1]} protocols ({cluster_sizes[1]/len(clusters)*100:.1f}%)")
    print(f"✓ Cluster 2: {cluster_sizes[2]} protocols ({cluster_sizes[2]/len(clusters)*100:.1f}%)")

    imbalance_ratio = max(cluster_sizes) / min(cluster_sizes)
    if imbalance_ratio > 2.0:
        warnings_found.append(f"Cluster imbalance ratio is {imbalance_ratio:.2f} (ideally < 2.0)")

    if len(pca_coords) != len(clusters):
        errors_found.append(f"PCA coordinates count ({len(pca_coords)}) != cluster count ({len(clusters)})")
    else:
        print(f"✓ PCA coordinates match cluster count")

    pca_loadings = pd.read_csv(results_dir / 'data' / 'pca_loadings.csv', index_col=0)
    if pca_loadings.shape[0] != 23:
        errors_found.append(f"PCA loadings have {pca_loadings.shape[0]} rows, expected 23")
    else:
        print(f"✓ PCA loadings have correct dimensions")

    print("\n4. STATISTICAL VALIDITY")
    print("-" * 80)

    corr_matrix = pd.read_csv(results_dir / 'data' / 'correlation_matrix.csv', index_col=0)

    np.fill_diagonal(corr_matrix.values, 0)
    perfect_corrs = np.where(np.abs(corr_matrix.values) > 0.99)
    if len(perfect_corrs[0]) > 0:
        warnings_found.append(f"Found {len(perfect_corrs[0])} near-perfect correlations between dimensions")
    else:
        print(f"✓ No perfect correlations found (multicollinearity check)")

    try:
        if corr_matrix.shape[0] == corr_matrix.shape[1]:
            if not np.allclose(corr_matrix.values, corr_matrix.values.T, equal_nan=True):
                errors_found.append("Correlation matrix is not symmetric")
            else:
                print(f"✓ Correlation matrix is symmetric")
        else:
            errors_found.append(f"Correlation matrix is not square: {corr_matrix.shape}")
    except Exception as e:
        warnings_found.append(f"Could not verify correlation matrix symmetry: {e}")

    print("\n5. AVERAGE VALUES CHECK")
    print("-" * 80)

    df_clean = df.dropna(subset=dimension_cols)
    calculated_averages = df_clean[dimension_cols].mean(axis=1)
    print(f"✓ Average values range: [{calculated_averages.min():.2f}, {calculated_averages.max():.2f}]")
    print(f"✓ Mean of averages: {calculated_averages.mean():.2f}")
    print(f"✓ Std of averages: {calculated_averages.std():.2f}")

    from scipy import stats
    bins = np.arange(int(calculated_averages.min()), int(calculated_averages.max()) + 1, 0.5)
    observed_counts, _ = np.histogram(calculated_averages, bins=bins)
    expected_count = len(calculated_averages) / len(bins[:-1])
    chi2_stat = np.sum((observed_counts - expected_count)**2 / expected_count)
    p_value = 1 - stats.chi2.cdf(chi2_stat, len(bins) - 2)

    print(f"✓ Distribution uniformity test p-value: {p_value:.4f}")
    if p_value < 0.05:
        print(f"  (Distribution is significantly non-uniform, as expected for real data)")
    else:
        warnings_found.append("Average values may be too uniformly distributed (p > 0.05)")

    print("\n6. CLUSTER SEPARATION CHECK")
    print("-" * 80)

    merged = df_clean.merge(clusters, on='Descriptor')
    cluster1_means = merged[merged['cluster'] == 1][dimension_cols].mean()
    cluster2_means = merged[merged['cluster'] == 2][dimension_cols].mean()

    differences = (cluster1_means - cluster2_means).abs()
    significant_diffs = differences[differences > 0.5]
    print(f"✓ Dimensions with meaningful difference (>0.5) between clusters: {len(significant_diffs)}/23")

    if len(significant_diffs) < 5:
        warnings_found.append(f"Only {len(significant_diffs)} dimensions show meaningful separation between clusters")

    print(f"\n  Top 5 differentiating dimensions:")
    for dim in differences.nlargest(5).index:
        print(f"    - {dim}: {differences[dim]:.3f}")

    print("\n" + "=" * 80)
    print("SUMMARY")
    print("=" * 80)

    if len(errors_found) == 0:
        print("✓ No critical errors found!")
    else:
        print(f"✗ {len(errors_found)} CRITICAL ERROR(S) FOUND:")
        for i, error in enumerate(errors_found, 1):
            print(f"  {i}. {error}")

    if len(warnings_found) == 0:
        print("✓ No warnings!")
    else:
        print(f"\n⚠ {len(warnings_found)} WARNING(S):")
        for i, warning in enumerate(warnings_found, 1):
            print(f"  {i}. {warning}")

    print("\n" + "=" * 80)
    print("REVIEW COMPLETE")
    print("=" * 80)


if __name__ == '__main__':
    main()