scitex 2.14.0__py3-none-any.whl → 2.16.0__py3-none-any.whl

scitex/ai/classification/reporters/_SingleClassificationReporter.py

@@ -1,120 +1,58 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# Timestamp: "2025-10-04 04:38:23 (ywatanabe)"
-# File: /ssh:sp:/home/ywatanabe/proj/scitex_repo/src/scitex/ml/classification/reporters/_SingleClassificationReporter.py
-# ----------------------------------------
-from __future__ import annotations
-import os
-
-__FILE__ = "./src/scitex/ml/classification/reporters/_SingleClassificationReporter.py"
-__DIR__ = os.path.dirname(__FILE__)
-# ----------------------------------------
-
-__FILE__ = __file__
-
-from pprint import pprint
+# Timestamp: "2026-01-24 (ywatanabe)"
+# File: /home/ywatanabe/proj/scitex-python/src/scitex/ai/classification/reporters/_SingleClassificationReporter.py
 
 """
 Improved Single Classification Reporter with unified API.
 
-Enhanced version that addresses all identified issues:
-- Unified API interface
-- Lazy directory creation
-- Numerical precision control
-- Graceful plotting with error handling
-- Consistent parameter names
+This module provides a comprehensive classification reporter that:
+- Uses unified API interface
+- Supports lazy directory creation
+- Provides numerical precision control
+- Creates visualizations with proper error handling
+- Maintains consistent parameter naming
+
+The main class inherits from multiple mixins for modular functionality:
+- MetricsMixin: Metrics calculation and aggregation
+- StorageMixin: File storage and organization
+- PlottingMixin: Visualization generation
+- FeatureImportanceMixin: Feature importance analysis
+- CVSummaryMixin: Cross-validation summary generation
+- ReportsMixin: Multi-format report generation
 """
 
+from __future__ import annotations
+
 from pathlib import Path
+from pprint import pprint
 from typing import Any, Dict, List, Optional, Union
 
-import numpy as np
-import pandas as pd
 from scitex.logging import getLogger
 
-# Import base class and utilities
 from ._BaseClassificationReporter import BaseClassificationReporter, ReporterConfig
-
-# Import original metric calculation functions (these are good)
-from .reporter_utils import (
-    calc_bacc,
-    calc_clf_report,
-    calc_conf_mat,
-    calc_mcc,
-    calc_pre_rec_auc,
-    calc_roc_auc,
+from ._mixins import (
+    CVSummaryMixin,
+    FeatureImportanceMixin,
+    MetricsMixin,
+    PlottingMixin,
+    ReportsMixin,
+    StorageMixin,
 )
 from .reporter_utils._Plotter import Plotter
-from .reporter_utils.reporting import (
-    create_summary_statistics,
-    generate_latex_report,
-    generate_markdown_report,
-    generate_org_report,
-)
-from .reporter_utils.storage import MetricStorage, save_metric
+from .reporter_utils.storage import MetricStorage
 
 logger = getLogger(__name__)
 
 
-# Fold directory and filename prefixes for consistent naming
-FOLD_DIR_PREFIX_PATTERN = "fold_{fold:02d}"  # Directory: fold_00, fold_01, ...
-FOLD_FILE_PREFIX_PATTERN = "fold-{fold:02d}"  # Filename prefix: fold-00_, fold-01_, ...
-
-# Filename patterns for consistent naming across the reporter
-# Note: fold-{fold:02d} comes first to group files by fold when sorted
-# Convention: hyphens within chunks, underscores between chunks
-FILENAME_PATTERNS = {
-    # Individual fold metrics (with metric value in filename)
-    "fold_metric_with_value": f"{FOLD_FILE_PREFIX_PATTERN}_{{metric_name}}-{{value:.3f}}.json",
-    "fold_metric": f"{FOLD_FILE_PREFIX_PATTERN}_{{metric_name}}.json",
-    # Confusion matrix
-    "confusion_matrix_csv": f"{FOLD_FILE_PREFIX_PATTERN}_confusion-matrix_bacc-{{bacc:.3f}}.csv",
-    "confusion_matrix_csv_no_bacc": f"{FOLD_FILE_PREFIX_PATTERN}_confusion-matrix.csv",
-    "confusion_matrix_jpg": f"{FOLD_FILE_PREFIX_PATTERN}_confusion-matrix_bacc-{{bacc:.3f}}.jpg",
-    "confusion_matrix_jpg_no_bacc": f"{FOLD_FILE_PREFIX_PATTERN}_confusion-matrix.jpg",
-    # Classification report
-    "classification_report": f"{FOLD_FILE_PREFIX_PATTERN}_classification-report.csv",
-    # ROC curve
-    "roc_curve_csv": f"{FOLD_FILE_PREFIX_PATTERN}_roc-curve_auc-{{auc:.3f}}.csv",
-    "roc_curve_csv_no_auc": f"{FOLD_FILE_PREFIX_PATTERN}_roc-curve.csv",
-    "roc_curve_jpg": f"{FOLD_FILE_PREFIX_PATTERN}_roc-curve_auc-{{auc:.3f}}.jpg",
-    "roc_curve_jpg_no_auc": f"{FOLD_FILE_PREFIX_PATTERN}_roc-curve.jpg",
-    # PR curve
-    "pr_curve_csv": f"{FOLD_FILE_PREFIX_PATTERN}_pr-curve_ap-{{ap:.3f}}.csv",
-    "pr_curve_csv_no_ap": f"{FOLD_FILE_PREFIX_PATTERN}_pr-curve.csv",
-    "pr_curve_jpg": f"{FOLD_FILE_PREFIX_PATTERN}_pr-curve_ap-{{ap:.3f}}.jpg",
-    "pr_curve_jpg_no_ap": f"{FOLD_FILE_PREFIX_PATTERN}_pr-curve.jpg",
-    # Raw prediction data (optional, enabled via calculate_metrics parameters)
-    "y_true": f"{FOLD_FILE_PREFIX_PATTERN}_y-true.csv",
-    "y_pred": f"{FOLD_FILE_PREFIX_PATTERN}_y-pred.csv",
-    "y_proba": f"{FOLD_FILE_PREFIX_PATTERN}_y-proba.csv",
-    # Metrics dashboard
-    "metrics_summary": f"{FOLD_FILE_PREFIX_PATTERN}_metrics-summary.jpg",
-    # Feature importance
-    "feature_importance_json": f"{FOLD_FILE_PREFIX_PATTERN}_feature-importance.json",
-    "feature_importance_jpg": f"{FOLD_FILE_PREFIX_PATTERN}_feature-importance.jpg",
-    # Classification report edge cases (when CSV conversion fails)
-    "classification_report_json": f"{FOLD_FILE_PREFIX_PATTERN}_classification-report.json",
-    "classification_report_txt": f"{FOLD_FILE_PREFIX_PATTERN}_classification-report.txt",
-    # Folds all (CV summary)
-    "cv_summary_metric": "cv-summary_{metric_name}_mean-{mean:.3f}_std-{std:.3f}_n-{n_folds}.json",
-    "cv_summary_confusion_matrix_csv": "cv-summary_confusion-matrix_bacc-{mean:.3f}_{std:.3f}_n-{n_folds}.csv",
-    "cv_summary_confusion_matrix_jpg": "cv-summary_confusion-matrix_bacc-{mean:.3f}_{std:.3f}_n-{n_folds}.jpg",
-    "cv_summary_classification_report": "cv-summary_classification-report_n-{n_folds}.csv",
-    "cv_summary_roc_curve_csv": "cv-summary_roc-curve_auc-{mean:.3f}_{std:.3f}_n-{n_folds}.csv",
-    "cv_summary_roc_curve_jpg": "cv-summary_roc-curve_auc-{mean:.3f}_{std:.3f}_n-{n_folds}.jpg",
-    "cv_summary_pr_curve_csv": "cv-summary_pr-curve_ap-{mean:.3f}_{std:.3f}_n-{n_folds}.csv",
-    "cv_summary_pr_curve_jpg": "cv-summary_pr-curve_ap-{mean:.3f}_{std:.3f}_n-{n_folds}.jpg",
-    "cv_summary_feature_importance_json": "cv-summary_feature-importance_n-{n_folds}.json",
-    "cv_summary_feature_importance_jpg": "cv-summary_feature-importance_n-{n_folds}.jpg",
-    "cv_summary_summary": "cv-summary_summary.json",
-    # Folds all edge cases (when balanced_acc is None)
-    "cv_summary_confusion_matrix_csv_no_bacc": "cv-summary_confusion-matrix_n-{n_folds}.csv",
-    "cv_summary_confusion_matrix_jpg_no_bacc": "cv-summary_confusion-matrix_n-{n_folds}.jpg",
-}
-
-
-class SingleTaskClassificationReporter(BaseClassificationReporter):
+class SingleTaskClassificationReporter(
+    MetricsMixin,
+    StorageMixin,
+    PlottingMixin,
+    FeatureImportanceMixin,
+    CVSummaryMixin,
+    ReportsMixin,
+    BaseClassificationReporter,
+):
     """
     Improved single-task classification reporter with unified API.
 
@@ -142,6 +80,8 @@ class SingleTaskClassificationReporter(BaseClassificationReporter):
         Base directory for outputs. If None, creates timestamped directory.
     config : ReporterConfig, optional
         Configuration object for advanced settings
+    verbose : bool, default True
+        Print initialization message
     **kwargs
         Additional arguments passed to base class
 
@@ -174,11 +114,9 @@ class SingleTaskClassificationReporter(BaseClassificationReporter):
         verbose: bool = True,
         **kwargs,
     ):
-        # Use config or create default
         if config is None:
             config = ReporterConfig()
 
-        # Initialize base class with config settings
         super().__init__(
             output_dir=output_dir,
             precision=config.precision,
@@ -186,14 +124,11 @@ class SingleTaskClassificationReporter(BaseClassificationReporter):
         )
 
         self.config = config
-        self.session_config = None  # Will store SciTeX session CONFIG if provided
+        self.session_config = None
         self.storage = MetricStorage(self.output_dir, precision=self.precision)
         self.plotter = Plotter(enable_plotting=True)
 
-        # Track calculated metrics for summary
         self.fold_metrics: Dict[int, Dict[str, Any]] = {}
-
-        # Store all predictions for overall curves
         self.all_predictions: List[Dict[str, Any]] = []
 
         if verbose:
@@ -212,1252 +147,6 @@ class SingleTaskClassificationReporter(BaseClassificationReporter):
         """
         self.session_config = config
 
-    def calculate_metrics(
-        self,
-        y_true: np.ndarray,
-        y_pred: np.ndarray,
-        y_proba: Optional[np.ndarray] = None,
-        labels: Optional[List[str]] = None,
-        fold: Optional[int] = None,
-        verbose=True,
-        store_y_true: bool = True,
-        store_y_pred: bool = True,
-        store_y_proba: bool = True,
-        model=None,
-        feature_names: Optional[List[str]] = None,
-    ) -> Dict[str, Any]:
-        """
-        Calculate and save classification metrics using unified API.
-
-        Parameters
-        ----------
-        y_true : np.ndarray
-            True class labels
-        y_pred : np.ndarray
-            Predicted class labels
-        y_proba : np.ndarray, optional
-            Prediction probabilities (required for AUC metrics)
-        labels : List[str], optional
-            Class labels for display
-        fold : int, optional
-            Fold index for cross-validation
-        verbose : bool, default True
-            Print progress messages
-        store_y_true : bool, default True
-            Save y_true as CSV with sample_index and fold columns
-        store_y_pred : bool, default True
-            Save y_pred as CSV with sample_index and fold columns
-        store_y_proba : bool, default True
-            Save y_proba as CSV with sample_index and fold columns
-        model : object, optional
-            Trained model for feature importance extraction
-        feature_names : List[str], optional
-            Feature names for feature importance (required if model is provided)
-
-        Returns
-        -------
-        Dict[str, Any]
-            Dictionary of calculated metrics
-        """
-
-        if verbose:
-            if fold:
-                print()
-                logger.info(f"Calculating metrics for fold #{fold:02d}...")
-            else:
-                logger.info(f"Calculating metrics...")
-
-        # Validate inputs
-        if len(y_true) != len(y_pred):
-            raise ValueError("y_true and y_pred must have same length")
-
-        if y_proba is not None and len(y_true) != len(y_proba):
-            raise ValueError("y_true and y_proba must have same length")
-
-        # Set default fold index
-        if fold is None:
-            fold = 0
-
-        # Set default labels if not provided
-        if labels is None:
-            unique_labels = sorted(np.unique(np.concatenate([y_true, y_pred])))
-            labels = [f"Class_{i}" for i in unique_labels]
-
-        # Calculate all metrics
-        metrics = {}
-
-        # Core metrics (always calculated) - pass fold to all metrics
-        metrics["balanced-accuracy"] = calc_bacc(y_true, y_pred, fold=fold)
-        metrics["mcc"] = calc_mcc(y_true, y_pred, fold=fold)
-
-        metrics["confusion_matrix"] = calc_conf_mat(
-            y_true=y_true, y_pred=y_pred, labels=labels, fold=fold
-        )
-        metrics["classification_report"] = calc_clf_report(
-            y_true, y_pred, labels, fold=fold
-        )
-
-        # AUC metrics (only if probabilities available)
-        if y_proba is not None:
-            try:
-                from scitex.ai.metrics import calc_pre_rec_auc, calc_roc_auc
-
-                metrics["roc-auc"] = calc_roc_auc(
-                    y_true,
-                    y_proba,
-                    labels=labels,
-                    fold=fold,
-                    return_curve=False,
-                )
-                metrics["pr-auc"] = calc_pre_rec_auc(
-                    y_true,
-                    y_proba,
-                    labels=labels,
-                    fold=fold,
-                    return_curve=False,
-                )
-            except Exception as e:
-                logger.warning(f"Could not calculate AUC metrics: {e}")
-
-        # Round all numerical values
-        metrics = self._round_numeric(metrics)
-
-        # Add labels to metrics for later use
-        metrics["labels"] = labels
-
-        if verbose:
-            logger.info(f"Metrics calculated:")
-            pprint(metrics)
-
-        # Store metrics for summary
-        self.fold_metrics[fold] = metrics.copy()
-
-        # Store predictions for overall curves
-        if y_proba is not None:
-            self.all_predictions.append(
-                {
-                    "fold": fold,
-                    "y_true": y_true.copy(),
-                    "y_proba": y_proba.copy(),
-                }
-            )
-
-        # Save metrics if requested
-        self._save_fold_metrics(metrics, fold, labels)
-
-        # Generate plots if requested
-        self._create_plots(y_true, y_pred, y_proba, labels, fold, metrics)
-
-        # Handle feature importance automatically if model provided
-        if model is not None and feature_names is not None:
-            try:
-                from scitex.ai.feature_selection import extract_feature_importance
-
-                importance_dict = extract_feature_importance(
-                    model, feature_names, method="auto"
-                )
-                if importance_dict:
-                    # Store in fold metrics for cross-fold aggregation
-                    metrics["feature-importance"] = importance_dict
-                    self.fold_metrics[fold]["feature-importance"] = importance_dict
-
-                    # Save feature importance
-                    fold_dir = FOLD_DIR_PREFIX_PATTERN.format(fold=fold)
-                    filename = FILENAME_PATTERNS["feature_importance_json"].format(
-                        fold=fold
-                    )
-                    self.storage.save(importance_dict, f"{fold_dir}/{filename}")
-
-                    if verbose:
-                        logger.info(f"  Feature importance extracted and saved")
-            except Exception as e:
-                logger.warning(f"Could not extract feature importance: {e}")
-
-        # Save raw predictions if requested (as CSV using DataFrames)
-        # Include sample_index for easy concatenation across folds
-        if store_y_true or store_y_pred or store_y_proba:
-            fold_dir = FOLD_DIR_PREFIX_PATTERN.format(fold=fold)
-            sample_indices = np.arange(len(y_true))
-
-            # Warn if file size will be large (>10MB estimated)
-            n_samples = len(y_true)
-            estimated_size_mb = 0
-            if store_y_true:
-                estimated_size_mb += n_samples * 0.0001  # ~100 bytes per row
-            if store_y_pred:
-                estimated_size_mb += n_samples * 0.0001
-            if store_y_proba and y_proba is not None:
-                n_classes = 1 if y_proba.ndim == 1 else y_proba.shape[1]
-                estimated_size_mb += n_samples * n_classes * 0.0001
-
-            if estimated_size_mb > 10:
-                logger.warning(
-                    f"Storing raw predictions for fold {fold} will create ~{estimated_size_mb:.1f}MB of CSV files. "
-                    f"Set store_y_true/store_y_pred/store_y_proba=False to disable."
-                )
-
-            if store_y_true:
-                filename = FILENAME_PATTERNS["y_true"].format(fold=fold)
-                # Convert to DataFrame for CSV format with index
-                df_y_true = pd.DataFrame(
-                    {"sample_index": sample_indices, "fold": fold, "y_true": y_true}
-                )
-                self.storage.save(df_y_true, f"{fold_dir}/{filename}")
-
-            if store_y_pred:
-                filename = FILENAME_PATTERNS["y_pred"].format(fold=fold)
-                # Convert to DataFrame for CSV format with index
-                df_y_pred = pd.DataFrame(
-                    {"sample_index": sample_indices, "fold": fold, "y_pred": y_pred}
-                )
-                self.storage.save(df_y_pred, f"{fold_dir}/{filename}")
-
-            if store_y_proba and y_proba is not None:
-                filename = FILENAME_PATTERNS["y_proba"].format(fold=fold)
-                # Convert to DataFrame for CSV format with index
-                # Handle both 1D (binary) and 2D (multiclass) probability arrays
-                if y_proba.ndim == 1:
-                    df_y_proba = pd.DataFrame(
-                        {
-                            "sample_index": sample_indices,
-                            "fold": fold,
-                            "y_proba": y_proba,
-                        }
-                    )
-                else:
-                    # Create column names for each class
-                    data = {"sample_index": sample_indices, "fold": fold}
-                    for i in range(y_proba.shape[1]):
-                        data[f"proba_class_{i}"] = y_proba[:, i]
-                    df_y_proba = pd.DataFrame(data)
-                self.storage.save(df_y_proba, f"{fold_dir}/{filename}")
-
-        return metrics
-
-    def _save_fold_metrics(
-        self, metrics: Dict[str, Any], fold: int, labels: List[str]
-    ) -> None:
-        """Save metrics for a specific fold in shallow directory structure."""
-        fold_dir = FOLD_DIR_PREFIX_PATTERN.format(fold=fold)
-
-        # Extract metric values for filenames
-        balanced_acc = self._extract_metric_value(metrics.get("balanced-accuracy"))
-        mcc_value = self._extract_metric_value(metrics.get("mcc"))
-        roc_auc_value = self._extract_metric_value(metrics.get("roc-auc"))
-        pr_auc_value = self._extract_metric_value(metrics.get("pr-auc"))
-
-        # Save individual metrics with values in filenames
-        for metric_name, metric_value in metrics.items():
-            # Extract actual value if it's a wrapped dict with 'value' key
-            if isinstance(metric_value, dict) and "value" in metric_value:
-                actual_value = metric_value["value"]
-            else:
-                actual_value = metric_value
-
-            if metric_name == "confusion_matrix":
-                # Save confusion matrix as CSV with proper formatting
-                try:
-                    # actual_value is already a DataFrame from calc_conf_mat
-                    # Just rename the index and columns
-                    if isinstance(actual_value, pd.DataFrame):
-                        cm_df = actual_value.copy()
-                        cm_df.index = [f"True_{label}" for label in labels]
-                        cm_df.columns = [f"Pred_{label}" for label in labels]
-                    else:
-                        # Fallback for numpy array
-                        cm_df = pd.DataFrame(
-                            actual_value,
-                            index=[f"True_{label}" for label in labels],
-                            columns=[f"Pred_{label}" for label in labels],
-                        )
-                except Exception as e:
-                    logger.error(f"Error formatting confusion matrix: {e}")
-                    cm_df = None
-
-                # Save if cm_df was created successfully
-                if cm_df is not None:
-                    # Create filename with balanced accuracy
-                    if balanced_acc is not None:
-                        cm_filename = FILENAME_PATTERNS["confusion_matrix_csv"].format(
-                            fold=fold, bacc=balanced_acc
-                        )
-                    else:
-                        cm_filename = FILENAME_PATTERNS[
-                            "confusion_matrix_csv_no_bacc"
-                        ].format(fold=fold)
-
-                    # Save with index=True to preserve row labels
-                    self.storage.save(cm_df, f"{fold_dir}/{cm_filename}", index=True)
-
-            elif metric_name == "classification_report":
-                # Save classification report with consistent naming
-                report_filename = FILENAME_PATTERNS["classification_report"].format(
-                    fold=fold
-                )
-                if isinstance(actual_value, pd.DataFrame):
-                    # Reset index to make it an ordinary column with name
-                    report_df = actual_value.reset_index()
-                    report_df = report_df.rename(columns={"index": "class"})
-                    self.storage.save(report_df, f"{fold_dir}/{report_filename}")
-                elif isinstance(actual_value, dict):
-                    # Try to create DataFrame from dict
-                    try:
-                        report_df = pd.DataFrame(actual_value).transpose()
-                        self.storage.save(report_df, f"{fold_dir}/{report_filename}")
-                    except:
-                        # Save as JSON if DataFrame conversion fails
-                        report_filename = FILENAME_PATTERNS[
-                            "classification_report_json"
-                        ].format(fold=fold)
-                        self.storage.save(
-                            actual_value,
-                            f"{fold_dir}/{report_filename}",
-                        )
-                else:
-                    # String or other format
-                    report_filename = FILENAME_PATTERNS[
-                        "classification_report_txt"
-                    ].format(fold=fold)
-                    self.storage.save(actual_value, f"{fold_dir}/{report_filename}")
-
-            elif metric_name == "balanced-accuracy" and balanced_acc is not None:
-                # Save with value in filename
-                filename = FILENAME_PATTERNS["fold_metric_with_value"].format(
-                    fold=fold,
-                    metric_name="balanced-accuracy",
-                    value=balanced_acc,
-                )
-                save_metric(
-                    actual_value,
-                    self.output_dir / f"{fold_dir}/{filename}",
-                    fold=fold,
-                    precision=self.precision,
-                )
-            elif metric_name == "mcc" and mcc_value is not None:
-                # Save with value in filename
-                filename = FILENAME_PATTERNS["fold_metric_with_value"].format(
-                    fold=fold, metric_name="mcc", value=mcc_value
-                )
-                save_metric(
-                    actual_value,
-                    self.output_dir / f"{fold_dir}/{filename}",
-                    fold=fold,
-                    precision=self.precision,
-                )
-            elif metric_name == "roc-auc" and roc_auc_value is not None:
-                # Save with value in filename
-                filename = FILENAME_PATTERNS["fold_metric_with_value"].format(
-                    fold=fold, metric_name="roc-auc", value=roc_auc_value
-                )
-                save_metric(
-                    actual_value,
-                    self.output_dir / f"{fold_dir}/{filename}",
-                    fold=fold,
-                    precision=self.precision,
-                )
-            elif metric_name == "pr-auc" and pr_auc_value is not None:
-                # Save with value in filename
-                filename = FILENAME_PATTERNS["fold_metric_with_value"].format(
-                    fold=fold, metric_name="pr-auc", value=pr_auc_value
-                )
-                save_metric(
-                    actual_value,
-                    self.output_dir / f"{fold_dir}/{filename}",
-                    fold=fold,
-                    precision=self.precision,
-                )
-
-    def _extract_metric_value(self, metric_data: Any) -> Optional[float]:
-        """Extract numeric value from metric data."""
-        if metric_data is None:
-            return None
-        if isinstance(metric_data, dict) and "value" in metric_data:
-            return float(metric_data["value"])
-        if isinstance(metric_data, (int, float, np.number)):
-            return float(metric_data)
-        return None
-
-    def _save_curve_data(
-        self,
-        y_true: np.ndarray,
-        y_proba: Optional[np.ndarray],
-        fold: int,
-        metrics: Dict[str, Any],
-    ) -> None:
-        """Save ROC and PR curve data as CSV files with metric values in filenames."""
-        if y_proba is None:
-            return
-
-        from sklearn.metrics import (
-            auc,
-            average_precision_score,
-            precision_recall_curve,
-            roc_curve,
-        )
-
-        fold_dir = FOLD_DIR_PREFIX_PATTERN.format(fold=fold)
-
-        # Handle binary vs multiclass
-        if y_proba.ndim == 1 or y_proba.shape[1] == 2:
-            # Binary classification
-            if y_proba.ndim == 2:
-                y_proba_pos = y_proba[:, 1]
-            else:
-                y_proba_pos = y_proba
-
-            # Normalize labels to integers for sklearn curve functions
-            from scitex.ai.metrics import _normalize_labels
-
-            y_true_norm, _, _, _ = _normalize_labels(y_true, y_true)
-
-            # ROC curve data
-            fpr, tpr, _ = roc_curve(y_true_norm, y_proba_pos)
-            roc_auc = auc(fpr, tpr)
-
-            # Create ROC curve DataFrame with just FPR and TPR columns
-            roc_df = pd.DataFrame({"FPR": fpr, "TPR": tpr})
-
-            # Save with AUC value in filename
-            roc_filename = FILENAME_PATTERNS["roc_curve_csv"].format(
-                fold=fold, auc=roc_auc
-            )
-            self.storage.save(roc_df, f"{fold_dir}/{roc_filename}")
-
-            # PR curve data
-            precision, recall, _ = precision_recall_curve(y_true_norm, y_proba_pos)
-            avg_precision = average_precision_score(y_true_norm, y_proba_pos)
-
-            # Create PR curve DataFrame with Recall and Precision columns
-            pr_df = pd.DataFrame({"Recall": recall, "Precision": precision})
-
-            # Save with AP value in filename
-            pr_filename = FILENAME_PATTERNS["pr_curve_csv"].format(
-                fold=fold, ap=avg_precision
-            )
-            self.storage.save(pr_df, f"{fold_dir}/{pr_filename}")
-
-    def _create_plots(
-        self,
-        y_true: np.ndarray,
-        y_pred: np.ndarray,
-        y_proba: Optional[np.ndarray],
-        labels: List[str],
-        fold: int,
-        metrics: Dict[str, Any],
-    ) -> None:
-        """Create and save plots with metric-based filenames in unified structure."""
-        # Use unified fold directory
-        fold_dir = self._create_subdir_if_needed(
-            FOLD_DIR_PREFIX_PATTERN.format(fold=fold)
-        )
-        fold_dir.mkdir(parents=True, exist_ok=True)
-
-        # # Save curve data for external plotting
-        # self._save_curve_data(y_true, y_proba, fold, metrics)
-
-        # Confusion matrix plot with metric in filename
-        if "confusion_matrix" in metrics:
-            # Extract actual confusion matrix value if wrapped in dict
-            cm_data = metrics["confusion_matrix"]
-            if isinstance(cm_data, dict) and "value" in cm_data:
-                cm_data = cm_data["value"]
-
-            # Get balanced accuracy for title and filename
-            balanced_acc = metrics.get("balanced-accuracy", {})
-            if isinstance(balanced_acc, dict) and "value" in balanced_acc:
-                balanced_acc = balanced_acc["value"]
-            elif isinstance(balanced_acc, (float, np.floating)):
-                balanced_acc = float(balanced_acc)
-            else:
-                balanced_acc = None
-
-            # Create title with balanced accuracy and filename with fold and metric
-            if balanced_acc is not None:
-                title = f"Confusion Matrix (Fold {fold:02d}) - Balanced Acc: {balanced_acc:.3f}"
-                filename = FILENAME_PATTERNS["confusion_matrix_jpg"].format(
-                    fold=fold, bacc=balanced_acc
-                )
-            else:
-                title = f"Confusion Matrix (Fold {fold:02d})"
-                filename = FILENAME_PATTERNS["confusion_matrix_jpg_no_bacc"].format(
-                    fold=fold
-                )
-
-            self.plotter.create_confusion_matrix_plot(
-                cm_data,
-                labels=labels,
-                save_path=fold_dir / filename,
-                title=title,
-            )
-
-        # ROC curve with AUC in filename (if probabilities available)
-        if y_proba is not None:
-            # Get AUC for filename
-            roc_auc = metrics.get("roc-auc", {})
-            if isinstance(roc_auc, dict) and "value" in roc_auc:
-                roc_auc_val = roc_auc["value"]
-                roc_filename = FILENAME_PATTERNS["roc_curve_jpg"].format(
-                    fold=fold, auc=roc_auc_val
-                )
-            else:
-                roc_filename = FILENAME_PATTERNS["roc_curve_jpg_no_auc"].format(
-                    fold=fold
-                )
-
-            self.plotter.create_roc_curve(
-                y_true,
-                y_proba,
-                labels=labels,
-                save_path=fold_dir / roc_filename,
-                title=f"ROC Curve (Fold {fold:02d})",
-            )
-
-            # PR curve with AP in filename
-            pr_auc = metrics.get("pr-auc", {})
-            if isinstance(pr_auc, dict) and "value" in pr_auc:
-                pr_auc_val = pr_auc["value"]
-                pr_filename = FILENAME_PATTERNS["pr_curve_jpg"].format(
-                    fold=fold, ap=pr_auc_val
-                )
-            else:
-                pr_filename = FILENAME_PATTERNS["pr_curve_jpg_no_ap"].format(fold=fold)
-
-            self.plotter.create_precision_recall_curve(
-                y_true,
-                y_proba,
-                labels=labels,
-                save_path=fold_dir / pr_filename,
-                title=f"Precision-Recall Curve (Fold {fold:02d})",
-            )
-
-        # NEW: Create comprehensive metrics visualization dashboard
-        # This automatically creates a 4-panel figure with confusion matrix, ROC, PR curve, and metrics table
-        summary_filename = FILENAME_PATTERNS["metrics_summary"].format(fold=fold)
-        self.plotter.create_metrics_visualization(
-            metrics=metrics,
-            y_true=y_true,
-            y_pred=y_pred,
-            y_proba=y_proba,
-            labels=labels,
-            save_path=fold_dir / summary_filename,
-            title="Classification Metrics Dashboard",
-            fold=fold,
-            verbose=False,  # Already have verbose output from individual plots
-        )
-
-    def get_summary(self) -> Dict[str, Any]:
-        """
-        Get summary of all calculated metrics across folds.
-
-        Returns
-        -------
-        Dict[str, Any]
-            Summary statistics across all folds
-        """
-        if not self.fold_metrics:
-            return {"error": "No metrics calculated yet"}
-
-        summary = {
-            "output_dir": str(self.output_dir),
-            "total_folds": len(self.fold_metrics),
-            "metrics_summary": {},
-        }
-
-        # Aggregate confusion matrices across all folds
-        confusion_matrices = []
-        for fold_metrics in self.fold_metrics.values():
-            if "confusion_matrix" in fold_metrics:
-                cm_data = fold_metrics["confusion_matrix"]
-                # Extract actual value if wrapped in dict
-                if isinstance(cm_data, dict) and "value" in cm_data:
-                    cm_data = cm_data["value"]
-                if cm_data is not None:
-                    confusion_matrices.append(cm_data)
-
-        if confusion_matrices:
-            # Sum all confusion matrices to get overall counts
-            overall_cm = np.sum(confusion_matrices, axis=0)
-            summary["overall_confusion_matrix"] = overall_cm.tolist()
-
-            # Also calculate normalized version (as percentages)
-            overall_cm_normalized = overall_cm / overall_cm.sum()
-            summary["overall_confusion_matrix_normalized"] = self._round_numeric(
-                overall_cm_normalized.tolist()
-            )
-
-        # Calculate summary statistics for scalar metrics
-        scalar_metrics = ["balanced-accuracy", "mcc", "roc-auc", "pr-auc"]
-
-        for metric_name in scalar_metrics:
-            values = []
-            for fold_metrics in self.fold_metrics.values():
-                if metric_name in fold_metrics:
-                    # Extract actual value if it's wrapped in dict
-                    metric_val = fold_metrics[metric_name]
-                    if isinstance(metric_val, dict) and "value" in metric_val:
-                        values.append(metric_val["value"])
-                    else:
-                        values.append(metric_val)
-
-            if values:
-                values = np.array(values)
-                summary["metrics_summary"][metric_name] = {
-                    "mean": self._round_numeric(np.mean(values)),
-                    "std": self._round_numeric(np.std(values)),
-                    "min": self._round_numeric(np.min(values)),
-                    "max": self._round_numeric(np.max(values)),
-                    "values": self._round_numeric(values.tolist()),
-                }
-
-        # Aggregate feature importance across folds
-        feature_importances_list = []
-        for fold_metrics in self.fold_metrics.values():
-            if "feature-importance" in fold_metrics:
-                feature_importances_list.append(fold_metrics["feature-importance"])
-
-        if feature_importances_list:
-            from scitex.ai.feature_selection import (
-                aggregate_feature_importances,
-                create_feature_importance_dataframe,
-            )
-
-            aggregated_importances = aggregate_feature_importances(
-                feature_importances_list
-            )
-            summary["feature-importance"] = aggregated_importances
-
-        return summary
-
-    def create_cv_aggregation_visualizations(
-        self,
-        output_dir: Optional[Path] = None,
-        show_individual_folds: bool = True,
-        fold_alpha: float = 0.15,
-    ) -> None:
-        """
-        Create CV aggregation visualizations with faded individual fold lines.
-
-        This creates publication-quality cross-validation plots showing:
-        - Individual fold curves (faded/transparent)
-        - Mean curve across folds (bold)
-        - Confidence intervals (± 1 std. dev.)
-
-        Parameters
-        ----------
-        output_dir : Path, optional
-            Directory to save plots (defaults to cv_summary)
-        show_individual_folds : bool, default True
-            Whether to show individual fold curves
-        fold_alpha : float, default 0.15
-            Transparency for individual fold curves (0-1)
-        """
-        if not self.all_predictions:
-            logger.warning("No predictions stored for CV aggregation visualizations")
-            return
-
-        if output_dir is None:
-            output_dir = self._create_subdir_if_needed("cv_summary")
-            output_dir.mkdir(parents=True, exist_ok=True)
-
-        n_folds = len(self.all_predictions)
-
-        # ROC curve with faded fold lines
-        roc_save_path = output_dir / f"roc_cv_aggregation_n{n_folds}.jpg"
-        self.plotter.create_cv_aggregation_plot(
-            fold_predictions=self.all_predictions,
-            curve_type="roc",
-            save_path=roc_save_path,
-            show_individual_folds=show_individual_folds,
-            fold_alpha=fold_alpha,
-            title=f"ROC Curves - Cross Validation (n={n_folds} folds)",
-            verbose=True,
-        )
-        logger.info(f"Created CV aggregation ROC plot with faded fold lines")
-
-        # PR curve with faded fold lines
-        pr_save_path = output_dir / f"pr_cv_aggregation_n{n_folds}.jpg"
-        self.plotter.create_cv_aggregation_plot(
-            fold_predictions=self.all_predictions,
-            curve_type="pr",
-            save_path=pr_save_path,
-            show_individual_folds=show_individual_folds,
-            fold_alpha=fold_alpha,
-            title=f"Precision-Recall Curves - Cross Validation (n={n_folds} folds)",
-            verbose=True,
-        )
-        logger.info(f"Created CV aggregation PR plot with faded fold lines")
-
-    def save_feature_importance(
-        self,
-        model,
-        feature_names: List[str],
-        fold: Optional[int] = None,
-    ) -> Dict[str, float]:
-        """
-        Calculate and save feature importance for tree-based models.
-
-        Parameters
-        ----------
-        model : object
-            Fitted classifier (must have feature_importances_ or coef_)
-        feature_names : List[str]
-            Names of features
-        fold : int, optional
-            Fold number for tracking
-
-        Returns
-        -------
-        Dict[str, float]
-            Dictionary of feature importances {feature_name: importance}
-        """
-        # Use centralized metric calculation
-        from scitex.ai.metrics import calc_feature_importance
-
-        try:
-            importance_dict, importances = calc_feature_importance(model, feature_names)
-        except ValueError as e:
-            logger.warning(f"Could not extract feature importance: {e}")
-            return {}
-
-        # Already sorted by calc_feature_importance
-        sorted_importances = list(importance_dict.items())
-
-        # Save as JSON using FILENAME_PATTERNS
-        fold_subdir = (
-            FOLD_DIR_PREFIX_PATTERN.format(fold=fold)
-            if fold is not None
-            else "cv_summary"
-        )
-        json_filename = FILENAME_PATTERNS["feature_importance_json"].format(fold=fold)
-        self.storage.save(dict(sorted_importances), f"{fold_subdir}/{json_filename}")
-
-        # Create visualization using FILENAME_PATTERNS
-        jpg_filename = FILENAME_PATTERNS["feature_importance_jpg"].format(fold=fold)
-        save_path = self.output_dir / fold_subdir / jpg_filename
-        save_path.parent.mkdir(parents=True, exist_ok=True)
-
-        self.plotter.create_feature_importance_plot(
-            feature_importance=importances,
-            feature_names=feature_names,
-            save_path=save_path,
-            title=(
-                f"Feature Importance (Fold {fold:02d})"
-                if fold is not None
-                else "Feature Importance (CV Summary)"
-            ),
-        )
-
-        logger.info(
-            f"Saved feature importance"
-            + (f" for fold {fold}" if fold is not None else "")
-        )
-
-        return importance_dict
-
-    def save_feature_importance_summary(
-        self,
-        all_importances: List[Dict[str, float]],
-    ) -> None:
-        """
-        Create summary visualization of feature importances across all folds.
-
-        Parameters
-        ----------
-        all_importances : List[Dict[str, float]]
-            List of feature importance dicts from each fold
-        """
-        if not all_importances:
-            return
-
-        # Aggregate importances across folds
-        all_features = set()
-        for imp_dict in all_importances:
-            all_features.update(imp_dict.keys())
-
-        # Calculate mean and std for each feature
-        feature_stats = {}
-        for feature in all_features:
-            values = [imp_dict.get(feature, 0) for imp_dict in all_importances]
-            feature_stats[feature] = {
-                "mean": float(np.mean(values)),
-                "std": float(np.std(values)),
-                "values": [float(v) for v in values],
-            }
-
-        # Sort by mean importance
-        sorted_features = sorted(
-            feature_stats.items(), key=lambda x: x[1]["mean"], reverse=True
-        )
-
-        # Save as JSON using FILENAME_PATTERNS
-        n_folds = len(all_importances)
-        json_filename = FILENAME_PATTERNS["cv_summary_feature_importance_json"].format(
-            n_folds=n_folds
-        )
-        self.storage.save(
-            dict(sorted_features),
-            f"cv_summary/{json_filename}",
-        )
-
-        # Create visualization using centralized plotting function
-        from scitex.ai.plt import plot_feature_importance_cv_summary
-
-        jpg_filename = FILENAME_PATTERNS["cv_summary_feature_importance_jpg"].format(
-            n_folds=n_folds
-        )
-        save_path = self.output_dir / "cv_summary" / jpg_filename
-        save_path.parent.mkdir(parents=True, exist_ok=True)
-
-        fig = plot_feature_importance_cv_summary(
-            all_importances=all_importances,
-            spath=save_path,
-        )
-
-        logger.info("Saved feature importance summary")
-
-    def create_cv_summary_curves(self, summary: Dict[str, Any]) -> None:
-        """
-        Create CV summary ROC and PR curves from aggregated predictions.
-        """
-        if not self.all_predictions:
-            logger.warning("No predictions stored for CV summary curves")
-            return
-
-        # Aggregate all predictions
-        all_y_true = np.concatenate([p["y_true"] for p in self.all_predictions])
-        all_y_proba = np.concatenate([p["y_proba"] for p in self.all_predictions])
-
-        # Get per-fold metrics for mean and std
-        roc_values = []
-        pr_values = []
-        for metrics in self.fold_metrics.values():
-            if "roc-auc" in metrics:
-                val = metrics["roc-auc"]
-                if isinstance(val, dict) and "value" in val:
-                    roc_values.append(val["value"])
-                else:
-                    roc_values.append(val)
-            if "pr-auc" in metrics:
-                val = metrics["pr-auc"]
-                if isinstance(val, dict) and "value" in val:
-                    pr_values.append(val["value"])
-                else:
-                    pr_values.append(val)
-
-        # Calculate mean and std
-        n_folds = len(self.fold_metrics)
-        if roc_values:
-            roc_mean = np.mean(roc_values)
-            roc_std = np.std(roc_values)
-        else:
-            from .reporter_utils.metrics import calc_roc_auc
-
-            overall_roc = calc_roc_auc(all_y_true, all_y_proba)
-            roc_mean = overall_roc["value"]
-            roc_std = 0.0
-
-        if pr_values:
-            pr_mean = np.mean(pr_values)
-            pr_std = np.std(pr_values)
-        else:
-            from .reporter_utils.metrics import calc_pre_rec_auc
-
-            overall_pr = calc_pre_rec_auc(all_y_true, all_y_proba)
-            pr_mean = overall_pr["value"]
-            pr_std = 0.0
-
-        # Create cv_summary directory
-        cv_summary_dir = self._create_subdir_if_needed("cv_summary")
-        cv_summary_dir.mkdir(parents=True, exist_ok=True)
-
-        # Save CV summary curve data
-        self._save_cv_summary_curve_data(
-            all_y_true,
-            all_y_proba,
-            roc_mean,
-            roc_std,
-            pr_mean,
-            pr_std,
-            n_folds,
-        )
-
-        # Normalize labels to integers for sklearn curve functions in plotter
-        from scitex.ai.metrics import _normalize_labels
-
-        all_y_true_norm, _, label_names, _ = _normalize_labels(all_y_true, all_y_true)
-
-        # ROC Curve with mean±std and n_folds in filename
-        roc_title = f"ROC Curve (CV Summary) - AUC: {roc_mean:.3f} ± {roc_std:.3f} (n={n_folds})"
-        roc_filename = FILENAME_PATTERNS["cv_summary_roc_curve_jpg"].format(
-            mean=roc_mean, std=roc_std, n_folds=n_folds
-        )
-        self.plotter.create_overall_roc_curve(
-            all_y_true_norm,
-            all_y_proba,
-            labels=label_names,
-            save_path=cv_summary_dir / roc_filename,
-            title=roc_title,
-            auc_mean=roc_mean,
-            auc_std=roc_std,
-            verbose=True,
-        )
-
-        # PR Curve with mean±std and n_folds in filename
-        pr_title = f"Precision-Recall Curve (CV Summary) - AP: {pr_mean:.3f} ± {pr_std:.3f} (n={n_folds})"
-        pr_filename = FILENAME_PATTERNS["cv_summary_pr_curve_jpg"].format(
-            mean=pr_mean, std=pr_std, n_folds=n_folds
-        )
-        self.plotter.create_overall_pr_curve(
-            all_y_true_norm,
-            all_y_proba,
-            labels=label_names,
-            save_path=cv_summary_dir / pr_filename,
-            title=pr_title,
-            ap_mean=pr_mean,
-            ap_std=pr_std,
-            verbose=True,
-        )
-
-        logger.info(
-            f"Created CV summary ROC curve: AUC = {roc_mean:.3f} ± {roc_std:.3f} (n={n_folds})"
-        )
-        logger.info(
-            f"Created CV summary PR curve: AP = {pr_mean:.3f} ± {pr_std:.3f} (n={n_folds})"
-        )
-
-    def _save_cv_summary_curve_data(
-        self,
-        y_true: np.ndarray,
-        y_proba: np.ndarray,
-        roc_mean: float,
-        roc_std: float,
-        pr_mean: float,
-        pr_std: float,
-        n_folds: int,
-    ) -> None:
-        """Save CV summary ROC and PR curve data as CSV files with metric values in filenames."""
-        from sklearn.metrics import (
-            auc,
-            average_precision_score,
-            precision_recall_curve,
-            roc_curve,
-        )
-
-        cv_summary_dir = "cv_summary"
-
-        # Handle binary vs multiclass
-        if y_proba.ndim == 1 or y_proba.shape[1] == 2:
-            # Binary classification
-            if y_proba.ndim == 2:
-                y_proba_pos = y_proba[:, 1]
-            else:
-                y_proba_pos = y_proba
-
-            # Normalize labels to integers for sklearn curve functions
-            from scitex.ai.metrics import _normalize_labels
-
-            y_true_norm, _, _, _ = _normalize_labels(y_true, y_true)
-
-            # ROC curve data
-            fpr, tpr, _ = roc_curve(y_true_norm, y_proba_pos)
-            roc_auc = auc(fpr, tpr)
-
-            # Create ROC curve DataFrame with just FPR and TPR columns
-            roc_df = pd.DataFrame({"FPR": fpr, "TPR": tpr})
-
-            # Save with mean±std and n_folds in filename
-            roc_filename = FILENAME_PATTERNS["cv_summary_roc_curve_csv"].format(
-                mean=roc_mean, std=roc_std, n_folds=n_folds
-            )
-            self.storage.save(roc_df, f"{cv_summary_dir}/{roc_filename}")
-
-            # PR curve data
-            precision, recall, _ = precision_recall_curve(y_true_norm, y_proba_pos)
-            avg_precision = average_precision_score(y_true_norm, y_proba_pos)
-
-            # Create PR curve DataFrame with Recall and Precision columns
-            pr_df = pd.DataFrame({"Recall": recall, "Precision": precision})
-
-            # Save with mean±std and n_folds in filename
-            pr_filename = FILENAME_PATTERNS["cv_summary_pr_curve_csv"].format(
-                mean=pr_mean, std=pr_std, n_folds=n_folds
-            )
-            self.storage.save(pr_df, f"{cv_summary_dir}/{pr_filename}")
-
-    def save_cv_summary_confusion_matrix(self, summary: Dict[str, Any]) -> None:
-        """
-        Save and plot the CV summary confusion matrix.
-
-        Parameters
-        ----------
-        summary : Dict[str, Any]
-            Summary dictionary containing overall_confusion_matrix
-        """
-        # Aggregate confusion matrices across all folds
-        confusion_matrices = []
-        for fold_metrics in self.fold_metrics.values():
-            if "confusion_matrix" in fold_metrics:
-                cm_data = fold_metrics["confusion_matrix"]
-                # Extract actual value if wrapped in dict
-                if isinstance(cm_data, dict) and "value" in cm_data:
-                    cm_data = cm_data["value"]
-                if cm_data is not None:
-                    confusion_matrices.append(cm_data)
-
-        if not confusion_matrices:
-            return
-
-        # Sum all confusion matrices to get overall counts
-        overall_cm = np.sum(confusion_matrices, axis=0)
-
-        # Get labels from one of the folds
-        labels = None
-        for fold_metrics in self.fold_metrics.values():
-            # Labels are stored directly in fold_metrics now
-            if "labels" in fold_metrics:
-                labels = fold_metrics["labels"]
-                break
-            # Fallback: check if labels are in confusion_matrix dict
-            elif "confusion_matrix" in fold_metrics:
-                cm_data = fold_metrics["confusion_matrix"]
-                if isinstance(cm_data, dict) and "labels" in cm_data:
-                    labels = cm_data["labels"]
-                    break
-
-        # Save as CSV with labels in cv_summary directory
-        cv_summary_dir = self._create_subdir_if_needed("cv_summary")
-        cv_summary_dir.mkdir(parents=True, exist_ok=True)
-
-        # Get balanced accuracy stats for filename
-        balanced_acc_mean = None
-        balanced_acc_std = None
-        n_folds = len(self.fold_metrics)
-        if "metrics_summary" in summary:
-            if "balanced-accuracy" in summary["metrics_summary"]:
-                balanced_acc_stats = summary["metrics_summary"]["balanced-accuracy"]
-                balanced_acc_mean = balanced_acc_stats.get("mean")
-                balanced_acc_std = balanced_acc_stats.get("std")
-
-        # Create filename with mean±std and n_folds
-        if balanced_acc_mean is not None and balanced_acc_std is not None:
-            cm_filename = FILENAME_PATTERNS["cv_summary_confusion_matrix_csv"].format(
-                mean=balanced_acc_mean, std=balanced_acc_std, n_folds=n_folds
-            )
-        else:
-            cm_filename = FILENAME_PATTERNS[
-                "cv_summary_confusion_matrix_csv_no_bacc"
-            ].format(n_folds=n_folds)
-
-        if labels:
-            cm_df = pd.DataFrame(
-                overall_cm,
-                index=[f"True_{label}" for label in labels],
-                columns=[f"Pred_{label}" for label in labels],
-            )
-        else:
-            cm_df = pd.DataFrame(overall_cm)
-
-        # Save with proper filename (with index=True to preserve row labels)
-        self.storage.save(cm_df, f"cv_summary/{cm_filename}", index=True)
-
-        # Create plot for CV summary confusion matrix
-        cv_summary_dir = self._create_subdir_if_needed("cv_summary")
-        cv_summary_dir.mkdir(parents=True, exist_ok=True)
-
-        # Calculate balanced accuracy mean and std for overall confusion matrix title
-        balanced_acc_mean = None
-        balanced_acc_std = None
-        if "metrics_summary" in self.get_summary():
-            metrics_summary = self.get_summary()["metrics_summary"]
-            if "balanced-accuracy" in metrics_summary:
-                balanced_acc_stats = metrics_summary["balanced-accuracy"]
-                balanced_acc_mean = balanced_acc_stats.get("mean")
-                balanced_acc_std = balanced_acc_stats.get("std")
-
-        # Create title with balanced accuracy stats and filename with mean±std and n_folds
-        if balanced_acc_mean is not None and balanced_acc_std is not None:
-            title = f"Confusion Matrix (CV Summary) - Balanced Acc: {balanced_acc_mean:.3f} ± {balanced_acc_std:.3f} (n={n_folds})"
-            filename = FILENAME_PATTERNS["cv_summary_confusion_matrix_jpg"].format(
-                mean=balanced_acc_mean, std=balanced_acc_std, n_folds=n_folds
-            )
-        else:
-            title = f"Confusion Matrix (CV Summary) (n={n_folds})"
-            filename = FILENAME_PATTERNS[
-                "cv_summary_confusion_matrix_jpg_no_bacc"
-            ].format(n_folds=n_folds)
-
-        # Create the plot with enhanced title
-        self.plotter.create_confusion_matrix_plot(
-            overall_cm,
-            labels=labels,
-            save_path=cv_summary_dir / filename,
-            title=title,
-        )
-
-    def generate_reports(self) -> Dict[str, Path]:
-        """
-        Generate comprehensive reports in multiple formats.
-
-        Returns
-        -------
-        Dict[str, Path]
-            Paths to generated report files
-        """
-        # Prepare results dictionary for report generation
-        results = {
-            "config": {
-                "n_folds": len(self.fold_metrics),
-                "output_dir": str(self.output_dir),
-            },
-            "session_config": self.session_config,  # Pass the SciTeX CONFIG
-            "summary": {},
-            "folds": [],
-            "plots": {},
-        }
-
-        # Get summary statistics
-        summary = self.get_summary()
-
-        # Extract summary statistics for reporting
-        if "metrics_summary" in summary:
-            results["summary"] = summary["metrics_summary"]
-
-        # Add feature importance if available
-        if "feature-importance" in summary:
-            results["summary"]["feature-importance"] = summary["feature-importance"]
-
-        # Add per-fold results
-        for fold, fold_data in self.fold_metrics.items():
-            fold_result = {"fold_id": fold}
-            fold_result.update(fold_data)
-
-            # Try to load sample size info from features.json
-            # scitex.io.save transforms relative paths: adds storage_out to calling file's dir
-            try:
-                import json
-
-                # Construct the storage_out path where scitex.io.save actually saves files
-                # Pattern: {calling_file_dir}/storage_out/{relative_path}
-                calling_file_dir = Path(__file__).parent / "reporter_utils"
-                storage_out_path = (
-                    calling_file_dir
-                    / "storage_out"
-                    / self.output_dir
-                    / FOLD_DIR_PREFIX_PATTERN.format(fold=fold)
-                    / "features.json"
-                )
-
-                # Also try regular path in case storage behavior changes
-                regular_path = (
-                    self.output_dir
-                    / FOLD_DIR_PREFIX_PATTERN.format(fold=fold)
-                    / "features.json"
-                )
-
-                features_json = None
-                if storage_out_path.exists():
-                    features_json = storage_out_path
-                elif regular_path.exists():
-                    features_json = regular_path
-
-                if features_json:
-                    with open(features_json, "r") as f:
-                        features_data = json.load(f)
-                        # Add sample size info if available
-                        for key in [
-                            "n_train",
-                            "n_test",
-                            "n_train_seizure",
-                            "n_train_interictal",
-                            "n_test_seizure",
-                            "n_test_interictal",
-                        ]:
-                            if key in features_data:
-                                fold_result[key] = int(features_data[key])
-            except Exception:
-                pass
-
-            results["folds"].append(fold_result)
-
-        # Add plot references with unified structure
-        # CV summary plots in cv_summary directory
-        cv_summary_dir = self.output_dir / "cv_summary"
-        if cv_summary_dir.exists():
-            for plot_file in cv_summary_dir.glob("*.jpg"):
-                plot_key = f"cv_summary_{plot_file.stem}"
-                results["plots"][plot_key] = str(plot_file.relative_to(self.output_dir))
-
-        # Per-fold plots in fold directories
-        for fold_dir in sorted(self.output_dir.glob("fold_*")):
-            # Extract fold number (directory is fold_XX, filename starts with fold-XX)
-            fold_num = fold_dir.name.replace("fold_", "")
-            for plot_file in fold_dir.glob("*.jpg"):
-                # Use just the stem as the plot key since filename already contains fold info
-                # e.g., "fold-00_confusion-matrix_bacc-0.500" becomes plot key "fold_00_confusion-matrix"
-                plot_key = f"fold_{fold_num}_{plot_file.stem}"
-                results["plots"][plot_key] = str(plot_file.relative_to(self.output_dir))
-
-        # Generate reports
-        reports_dir = self._create_subdir_if_needed("reports")
-        generated_files = {}
-
-        # Org-mode report (primary format) - will generate other formats via pandoc
-        org_path = reports_dir / "classification_report.org"
-        generate_org_report(results, org_path, include_plots=True, convert_formats=True)
-        generated_files["org"] = org_path
-        logger.info(f"Generated org-mode report: {org_path}")
-
-        # Note: Markdown, HTML, LaTeX, and DOCX are now generated via pandoc from org
-        # This ensures consistency across all formats
-
-        # Try to compile LaTeX to PDF
-        try:
-            import shutil
-            import subprocess
-
-            if shutil.which("pdflatex"):
-                # Change to reports directory for compilation
-                original_dir = Path.cwd()
-                try:
-                    import os
-
-                    os.chdir(reports_dir)
-
-                    # Run pdflatex twice for proper references
-                    for _ in range(2):
-                        result = subprocess.run(
-                            [
-                                "pdflatex",
-                                "-interaction=nonstopmode",
-                                "classification_report.tex",
-                            ],
-                            capture_output=True,
-                            text=True,
-                            timeout=30,
-                        )
-
-                    pdf_path = reports_dir / "classification_report.pdf"
-                    if pdf_path.exists():
-                        generated_files["pdf"] = pdf_path
-                        logger.info(f"Generated PDF report: {pdf_path}")
-
-                        # Clean up LaTeX auxiliary files
-                        for ext in [".aux", ".log", ".out", ".toc"]:
-                            aux_file = reports_dir / f"classification_report{ext}"
-                            if aux_file.exists():
-                                aux_file.unlink()
-                finally:
-                    os.chdir(original_dir)
-            else:
-                logger.warning("pdflatex not found. Skipping PDF generation.")
-        except Exception as e:
-            logger.warning(f"Could not generate PDF report: {e}")
-
-        # Skip paper_exports - all data is already available in fold_XX/ and cv_summary/
-        # with descriptive filenames perfect for sharing
-
-        return generated_files
-
     def save_summary(
         self, filename: str = "cv_summary/summary.json", verbose: bool = True
     ) -> Path:
@@ -1468,6 +157,8 @@ class SingleTaskClassificationReporter(BaseClassificationReporter):
         ----------
         filename : str, default "cv_summary/summary.json"
             Filename for summary (now in cv_summary directory)
+        verbose : bool, default True
+            Print summary to console
 
         Returns
         -------
@@ -1476,17 +167,11 @@ class SingleTaskClassificationReporter(BaseClassificationReporter):
         """
         summary = self.get_summary()
 
-        # Try to load and include configuration
         try:
-            # Try different possible locations for CONFIG.yaml
             possible_paths = [
-                self.output_dir.parent
-                / "CONFIGS"
-                / "CONFIG.yaml",  # ../CONFIGS/CONFIG.yaml
-                self.output_dir.parent.parent
-                / "CONFIGS"
-                / "CONFIG.yaml",  # ../../CONFIGS/CONFIG.yaml
-                self.output_dir / "CONFIGS" / "CONFIG.yaml",  # ./CONFIGS/CONFIG.yaml
+                self.output_dir.parent / "CONFIGS" / "CONFIG.yaml",
+                self.output_dir.parent.parent / "CONFIGS" / "CONFIG.yaml",
+                self.output_dir / "CONFIGS" / "CONFIG.yaml",
             ]
 
             config_path = None
@@ -1498,33 +183,21 @@ class SingleTaskClassificationReporter(BaseClassificationReporter):
             if config_path and config_path.exists():
                 import yaml
 
-                with open(config_path, "r") as config_file:
+                with open(config_path) as config_file:
                     config_data = yaml.safe_load(config_file)
                     summary["experiment_configuration"] = config_data
         except Exception as e:
             logger.warning(f"Could not load CONFIG.yaml: {e}")
 
-        # Save CV summary metrics with proper filenames
         self._save_cv_summary_metrics(summary)
-
-        # Save and plot CV summary confusion matrix
         self.save_cv_summary_confusion_matrix(summary)
-
-        # Create CV summary ROC and PR curves
         self.create_cv_summary_curves(summary)
-
-        # Create CV aggregation visualizations with faded fold lines
         self.create_cv_aggregation_visualizations(
             show_individual_folds=True, fold_alpha=0.15
         )
-
-        # Save CV summary classification report
         self._save_cv_summary_classification_report(summary)
-
-        # Generate comprehensive reports in multiple formats
         self.generate_reports()
 
-        # Ensure cv_summary directory exists
         cv_summary_dir = self._create_subdir_if_needed("cv_summary")
         cv_summary_dir.mkdir(parents=True, exist_ok=True)
 
@@ -1533,239 +206,8 @@ class SingleTaskClassificationReporter(BaseClassificationReporter):
             logger.info("Summary:")
             pprint(summary)
 
-        # Save summary in cv_summary directory
         return self.storage.save(summary, "cv_summary/summary.json")
 
-    def _save_cv_summary_metrics(self, summary: Dict[str, Any]) -> None:
-        """
-        Save individual CV summary metrics with mean/std/n_folds in filenames.
-        """
-        if "metrics_summary" not in summary:
-            return
-
-        n_folds = len(self.fold_metrics)
-        cv_summary_dir = "cv_summary"
-
-        for metric_name, stats in summary["metrics_summary"].items():
-            if isinstance(stats, dict) and "mean" in stats:
-                mean_val = stats.get("mean", 0)
-                std_val = stats.get("std", 0)
-
-                # Create filename with mean_std_n format
-                filename = FILENAME_PATTERNS["cv_summary_metric"].format(
-                    metric_name=metric_name,
-                    mean=mean_val,
-                    std=std_val,
-                    n_folds=n_folds,
-                )
-
-                # Save metric statistics
-                self.storage.save(stats, f"{cv_summary_dir}/{filename}")
-
-    def _save_cv_summary_classification_report(self, summary: Dict[str, Any]) -> None:
-        """
-        Save CV summary classification report with mean ± std (n_folds=X) format.
-        """
-        n_folds = len(self.fold_metrics)
-        cv_summary_dir = "cv_summary"
-
-        # Collect classification reports from all folds
-        all_reports = []
-        for fold_num, fold_metrics in self.fold_metrics.items():
-            if "classification_report" in fold_metrics:
-                report = fold_metrics["classification_report"]
-                if isinstance(report, dict) and "value" in report:
-                    report = report["value"]
-
-                # Convert DataFrame to dict if needed
-                if isinstance(report, pd.DataFrame):
-                    # Convert DataFrame to dict format expected by aggregation
-                    # Assumes DataFrame has 'class' column and metric columns
-                    if "class" in report.columns:
-                        report_dict = {}
-                        for _, row in report.iterrows():
-                            class_name = row["class"]
-                            report_dict[class_name] = {
-                                col: row[col]
-                                for col in report.columns
-                                if col != "class"
-                            }
-                        report = report_dict
-                    else:
-                        # DataFrame with class names as index
-                        report = report.to_dict("index")
-
-                if isinstance(report, dict):
-                    all_reports.append(report)
-
-        if not all_reports:
-            return
-
-        # Calculate mean and std for each metric in the classification report
-        summary_report = {}
-
-        # Get all class labels (excluding summary rows)
-        all_classes = set()
-        for report in all_reports:
-            all_classes.update(
-                [
-                    k
-                    for k in report.keys()
-                    if k not in ["accuracy", "macro avg", "weighted avg"]
-                ]
-            )
-
-        # Process each class
-        for cls in sorted(all_classes):
-            cls_metrics = {
-                "precision": [],
-                "recall": [],
-                "f1-score": [],
-                "support": [],
-            }
-
-            for report in all_reports:
-                if cls in report:
-                    for metric in [
-                        "precision",
-                        "recall",
-                        "f1-score",
-                        "support",
-                    ]:
-                        if metric in report[cls]:
-                            cls_metrics[metric].append(report[cls][metric])
-
-            summary_report[cls] = {}
-            for metric, values in cls_metrics.items():
-                if values:
-                    if metric == "support":
-                        # For support, show total and mean±std to capture variability
-                        total_support = int(np.sum(values))
-                        mean_support = np.mean(values)
-                        std_support = np.std(values)
-                        if std_support > 0:
-                            # Show mean±std if there's variability across folds
-                            summary_report[cls][metric] = (
-                                f"{mean_support:.1f} ± {std_support:.1f} (total={total_support})"
-                            )
-                        else:
-                            # If constant across folds, just show the value
-                            summary_report[cls][metric] = (
-                                f"{int(mean_support)} per fold (total={total_support})"
-                            )
-                    else:
-                        mean_val = np.mean(values)
-                        std_val = np.std(values)
-                        summary_report[cls][metric] = (
-                            f"{mean_val:.3f} ± {std_val:.3f} (n={n_folds})"
-                        )
-
-        # Process summary rows (macro avg, weighted avg)
-        for avg_type in ["macro avg", "weighted avg"]:
-            avg_metrics = {"precision": [], "recall": [], "f1-score": []}
-
-            for report in all_reports:
-                if avg_type in report:
-                    for metric in ["precision", "recall", "f1-score"]:
-                        if metric in report[avg_type]:
-                            avg_metrics[metric].append(report[avg_type][metric])
-
-            if any(avg_metrics.values()):
-                summary_report[avg_type] = {}
-                for metric, values in avg_metrics.items():
-                    if values:
-                        mean_val = np.mean(values)
-                        std_val = np.std(values)
-                        summary_report[avg_type][metric] = (
-                            f"{mean_val:.3f} ± {std_val:.3f} (n={n_folds})"
-                        )
-
-        # Convert to DataFrame for better visualization
-        if summary_report:
-            report_df = pd.DataFrame(summary_report).T
-            # Reset index to make it an ordinary column with name
-            report_df = report_df.reset_index()
-            report_df = report_df.rename(columns={"index": "class"})
-
-            # Save as CSV
-            filename = FILENAME_PATTERNS["cv_summary_classification_report"].format(
-                n_folds=n_folds
-            )
-            self.storage.save(
-                report_df,
-                f"{cv_summary_dir}/{filename}",
-            )
-
-    def save(
-        self,
-        data: Any,
-        relative_path: Union[str, Path],
-        fold: Optional[int] = None,
-    ) -> Path:
-        """
-        Save custom data with automatic fold organization and filename prefixing.
-
-        Parameters
-        ----------
-        data : Any
-            Custom data to save (any format supported by stx.io.save)
-        relative_path : Union[str, Path]
-            Relative path from output_dir or fold directory. Examples:
-            - When fold is provided: "custom_metrics.json" → "fold_00/fold-00_custom_metrics.json"
-            - When fold is None: "cv_summary/results.csv" → "cv_summary/results.csv"
-        fold : Optional[int], default None
-            If provided, automatically prepends "fold_{fold:02d}/" to the path
-            and adds "fold-{fold:02d}_" prefix to the filename
-
-        Returns
-        -------
-        Path
-            Absolute path to the saved file
-
-        Examples
-        --------
-        >>> # Save custom metrics for fold 0 (automatic fold directory and prefix)
-        >>> reporter.save(
-        ...     {"metric1": 0.95, "metric2": 0.87},
-        ...     "custom_metrics.json",
-        ...     fold=0
-        ... )  # Saves to: fold_00/fold-00_custom_metrics.json
-
-        >>> # Save to cv_summary (no fold, no prefix)
-        >>> reporter.save(
-        ...     df_results,
-        ...     "cv_summary/final_analysis.csv"
-        ... )
-
-        >>> # Save to reports directory
-        >>> reporter.save(
-        ...     report_content,
-        ...     "reports/analysis.md"
-        ... )
-        """
-        # Automatically prepend fold directory and prefix filename if fold is provided
-        if fold is not None:
-            # Parse the path to add prefix to filename only
-            path_obj = Path(relative_path)
-            filename = path_obj.name
-            parent = path_obj.parent
-
-            # Add fold prefix to filename (e.g., "fold-00_custom_metrics.json")
-            prefixed_filename = (
-                f"{FOLD_FILE_PREFIX_PATTERN.format(fold=fold)}_{filename}"
-            )
-
-            # Construct full path: fold_00/fold-00_filename.ext
-            if parent and str(parent) != ".":
-                relative_path = f"{FOLD_DIR_PREFIX_PATTERN.format(fold=fold)}/{parent}/{prefixed_filename}"
-            else:
-                relative_path = (
-                    f"{FOLD_DIR_PREFIX_PATTERN.format(fold=fold)}/{prefixed_filename}"
-                )
-
-        # Use the existing storage.save method which already handles everything
-        return self.storage.save(data, relative_path)
-
     def __repr__(self) -> str:
         fold_count = len(self.fold_metrics)
         return (