training_code/utils/plots.py

import numpy as np
import matplotlib.pyplot as plt
from sklearn.metrics import balanced_accuracy_score, roc_auc_score, roc_curve, confusion_matrix, auc

    
def moving_average(data, window_size=5):
    """
    Compute moving average over specified window size.
    """
    
    if len(data) < window_size:
        return data
    
    return np.convolve(data, np.ones(window_size)/window_size, mode='valid')


def plot_training_progress_classification(all_train_loss, all_val_loss, all_train_acc, all_val_acc, 
                          all_train_auc, all_val_auc, save_path, window_size=5):
    """
    Plot training progress with both raw epoch-by-epoch data and moving averages.
    
    Args:
        all_train_loss: List of training losses per epoch
        all_val_loss: List of validation losses per epoch  
        all_train_acc: List of training accuracies per epoch
        all_val_acc: List of validation accuracies per epoch
        all_train_auc: List of training AUCs per epoch
        all_val_auc: List of validation AUCs per epoch
        save_path: Path to save the plot
        window_size: Window size for moving average (default: 5)
    """
    
    plt.figure(figsize=(10, 5))
    epochs = np.arange(1, len(all_train_loss) + 1)
    
    # Loss subplot
    plt.subplot(1, 3, 1)
    train_loss_line = plt.plot(epochs, all_train_loss, '--', alpha=0.6, label="Train Loss (raw)")[0]
    val_loss_line = plt.plot(epochs, all_val_loss, '--', alpha=0.6, label="Val Loss (raw)")[0]
    if len(all_train_loss) >= window_size:
        ma_epochs = np.arange(window_size, len(all_train_loss) + 1)
        plt.plot(ma_epochs, moving_average(all_train_loss, window_size), '-', 
                color=train_loss_line.get_color(), label=f"Train Loss (MA-{window_size})")
        plt.plot(ma_epochs, moving_average(all_val_loss, window_size), '-', 
                color=val_loss_line.get_color(), label=f"Val Loss (MA-{window_size})")
    plt.legend()
    plt.xlabel("Epoch")
    plt.ylabel("Loss")
    
    # Accuracy subplot
    plt.subplot(1, 3, 2)
    train_acc_line = plt.plot(epochs, all_train_acc, '--', alpha=0.6, label="Train Acc (raw)")[0]
    val_acc_line = plt.plot(epochs, all_val_acc, '--', alpha=0.6, label="Val Acc (raw)")[0]
    if len(all_train_acc) >= window_size:
        ma_epochs = np.arange(window_size, len(all_train_acc) + 1)
        plt.plot(ma_epochs, moving_average(all_train_acc, window_size), '-', 
                color=train_acc_line.get_color(), label=f"Train Acc (MA-{window_size})")
        plt.plot(ma_epochs, moving_average(all_val_acc, window_size), '-', 
                color=val_acc_line.get_color(), label=f"Val Acc (MA-{window_size})")
    plt.legend()
    plt.xlabel("Epoch")
    plt.ylabel("Accuracy")
    
    # AUC subplot
    plt.subplot(1, 3, 3)
    train_auc_line = plt.plot(epochs, all_train_auc, '--', alpha=0.6, label="Train AUC (raw)")[0]
    val_auc_line = plt.plot(epochs, all_val_auc, '--', alpha=0.6, label="Val AUC (raw)")[0]
    if len(all_train_auc) >= window_size:
        ma_epochs = np.arange(window_size, len(all_train_auc) + 1)
        plt.plot(ma_epochs, moving_average(all_train_auc, window_size), '-', 
                color=train_auc_line.get_color(), label=f"Train AUC (MA-{window_size})")
        plt.plot(ma_epochs, moving_average(all_val_auc, window_size), '-', 
                color=val_auc_line.get_color(), label=f"Val AUC (MA-{window_size})")
    plt.legend()
    plt.xlabel("Epoch")
    plt.ylabel("AUC")
    
    plt.tight_layout()
    plt.savefig(save_path)
    plt.close() 
    
    return


def plot_pred_summary_bc(preds, probs, gts, save_path):
    """
    Plot predictions for binary classification with confusion matrix, performance metrics, and ROC curve.
    """
    
    probs = np.array(probs)
    preds = np.array(preds)
    gts = np.array(gts)
    
    # Compute metrics
    balanced_accuracy = balanced_accuracy_score(gts, preds)
    auc = roc_auc_score(gts, probs)
    
    # Confusion matrix
    cm = confusion_matrix(gts, preds)
    tn, fp, fn, tp = cm.ravel()
    
    # Additional metrics
    sensitivity = tp / (tp + fn) if (tp + fn) > 0 else 0
    specificity = tn / (tn + fp) if (tn + fp) > 0 else 0
    ppv = tp / (tp + fp) if (tp + fp) > 0 else 0
    npv = tn / (tn + fn) if (tn + fn) > 0 else 0
    
    # ROC curve
    fpr, tpr, _ = roc_curve(gts, probs[:, 1] if probs.ndim == 2 else probs)
    
    # Create figure with 3 subplots
    fig, (ax1, ax2, ax3) = plt.subplots(1, 3, figsize=(15, 5))
    
    # Confusion matrix
    im = ax1.imshow(cm, interpolation='nearest', cmap=plt.cm.Blues)
    ax1.set_title('Confusion Matrix')
    ax1.set_xlabel('Predicted')
    ax1.set_ylabel('Actual')
    ax1.set_xticks([0, 1])
    ax1.set_yticks([0, 1])
    ax1.set_xticklabels(['Negative', 'Positive'])
    ax1.set_yticklabels(['Negative', 'Positive'])
    
    # Add text annotations
    thresh = cm.max() / 2
    for i in range(2):
        for j in range(2):
            ax1.text(j, i, format(cm[i, j], 'd'),
                    ha="center", va="center",
                    color="white" if cm[i, j] > thresh else "black")
    
    # Performance metrics bar chart
    metrics = ['Sensitivity', 'Specificity', 'PPV', 'NPV', 'Balanced Accuracy']
    values = [sensitivity, specificity, ppv, npv, balanced_accuracy]
    bars = ax2.bar(metrics, values, color=['skyblue', 'lightcoral', 'lightgreen', 'gold', 'lightpink'])
    ax2.set_title('Performance Metrics')
    ax2.set_ylabel('Value')
    ax2.set_ylim(0, 1)
    
    # Add value labels on bars
    for bar, value in zip(bars, values):
        height = bar.get_height()
        ax2.text(bar.get_x() + bar.get_width()/2., height + 0.01,
                f'{value:.3f}', ha='center', va='bottom')
    
    # ROC curve
    ax3.plot(fpr, tpr, color='darkorange', lw=2, label=f'ROC curve (AUC = {auc:.3f})')
    ax3.plot([0, 1], [0, 1], color='navy', lw=2, linestyle='--')
    ax3.set_xlim([0.0, 1.0])
    ax3.set_ylim([0.0, 1.05])
    ax3.set_xlabel('False Positive Rate')
    ax3.set_ylabel('True Positive Rate')
    ax3.set_title('ROC Curve')
    ax3.legend(loc="lower right")
    ax3.grid(True)
    
    plt.tight_layout()
    plt.savefig(save_path, dpi=150, bbox_inches='tight')
    plt.close()
    
    return


def plot_pred_summary_mc(preds, probs, gts, n_classes, save_path):
    """
    Plot predictions for multiclass classification with confusion matrix and performance metrics.
    """
    
    # Normalize probabilities to handle floating point precision errors from mixed precision training
    probs = np.array(probs)
    probs = probs / probs.sum(axis=1, keepdims=True)
    
    preds = np.array(preds)
    gts = np.array(gts)
    
    # Compute metrics
    balanced_accuracy = balanced_accuracy_score(gts, preds)
    auc = roc_auc_score(gts, probs, multi_class='ovo', average='macro', labels=list(range(n_classes)))
    
    # Confusion matrix
    cm = confusion_matrix(gts, preds, labels=list(range(n_classes)))
    
    # Create figure with 2 subplots for multiclass
    fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(12, 5))
    
    # Confusion matrix
    im = ax1.imshow(cm, interpolation='nearest', cmap=plt.cm.Blues)
    ax1.set_title('Confusion Matrix')
    ax1.set_xlabel('Predicted Class')
    ax1.set_ylabel('True Class')
    ax1.set_xticks(range(n_classes))
    ax1.set_yticks(range(n_classes))
    ax1.set_xticklabels([f'Class {i}' for i in range(n_classes)])
    ax1.set_yticklabels([f'Class {i}' for i in range(n_classes)])
    
    # Add text annotations
    thresh = cm.max() / 2
    for i in range(n_classes):
        for j in range(n_classes):
            ax1.text(j, i, format(cm[i, j], 'd'),
                    ha="center", va="center",
                    color="white" if cm[i, j] > thresh else "black")
    
    # Performance metrics bar chart
    metrics = ['Balanced Accuracy', 'Macro AUC']
    values = [balanced_accuracy, auc]
    bars = ax2.bar(metrics, values, color=['lightpink', 'lightblue'])
    ax2.set_title('Performance Metrics')
    ax2.set_ylabel('Value')
    ax2.set_ylim(0, 1)
    
    # Add value labels on bars
    for bar, value in zip(bars, values):
        height = bar.get_height()
        ax2.text(bar.get_x() + bar.get_width()/2., height + 0.01,
                f'{value:.3f}', ha='center', va='bottom')
    
    plt.tight_layout()
    plt.savefig(save_path, dpi=150, bbox_inches='tight')
    plt.close()
    
    return


def plot_multiclass_roc_curve(roc_curve_data, save_path=None):
    """
    Plot the ROC curve for multiclass classification.
    """

    n_classes = len(roc_curve_data)
    plt.figure(figsize=(n_classes * 5, 5))

    for c, (fpr, tpr, _) in enumerate(roc_curve_data):
        plt.subplot(1, n_classes, c + 1)
        plt.plot(fpr, tpr, label=f'ROC curve of class {c}')
        plt.plot([0, 1], [0, 1], color='navy', lw=2, linestyle='--')
        plt.xlim([0.0, 1.0])
        plt.ylim([0.0, 1.0])
        auc_val = auc(fpr, tpr)
        plt.legend([f"AUC = {auc_val:.2f}"])
        plt.xlabel("False Positive Rate")
        plt.ylabel("True Positive Rate")
        plt.title(f"ROC Curve of Class {c}")
        plt.grid(True)

    plt.savefig(save_path, dpi=150, bbox_inches="tight")
    plt.close()

    return
    
def plot_multiclass_confusion_matrix(cm, save_path=None):
    """
    Plot the confusion matrix.
    """
    
    n_classes = cm.shape[0]
    fig, ax1 = plt.subplots(1, 1, figsize=(n_classes * 3, n_classes * 3))
    
    # Confusion matrix
    im = ax1.imshow(cm, interpolation='nearest', cmap=plt.cm.Blues)
    ax1.set_title('Confusion Matrix')
    ax1.set_xlabel('Predicted Class')
    ax1.set_ylabel('True Class')
    ax1.set_xticks(range(n_classes))
    ax1.set_yticks(range(n_classes))
    ax1.set_xticklabels([f'Class {i}' for i in range(n_classes)])
    ax1.set_yticklabels([f'Class {i}' for i in range(n_classes)])
    
    # Add text annotations
    thresh = cm.max() / 2
    for i in range(n_classes):
        for j in range(n_classes):
            ax1.text(j, i, format(cm[i, j], 'd'),
                    ha="center", va="center",
                    color="white" if cm[i, j] > thresh else "black")
    
    plt.tight_layout()
    plt.savefig(save_path, dpi=150, bbox_inches='tight')
    plt.close()
    
    return