source_code/gliomasam3_moe/eval_ablation.py

"""
Ablation Evaluation Script for GliomaSAM3-MoE

Implements:
- Table 4: ET-absent subset evaluation
- Table 7: Boundary-band Dice (3-voxel band)

Usage:
    cd /root/githubs/gliomasam3_moe
    PYTHONPATH=/root/githubs/sam3:$PYTHONPATH python eval_ablation.py \
        --config configs/train.yaml \
        --checkpoint logs/segmamba/model/ckpt_step3000.pt \
        --eval table7  # or table4, or both

Author: GliomaSAM3-MoE Team
"""

import argparse
import os
import sys
import json
from typing import Dict, List, Tuple, Optional
from collections import defaultdict

import numpy as np
import torch
import yaml
from tqdm import tqdm

# Add project paths
ROOT_DIR = os.path.dirname(os.path.abspath(__file__))
SRC_DIR = os.path.join(ROOT_DIR, "src")
if SRC_DIR not in sys.path:
    sys.path.insert(0, SRC_DIR)

from scipy import ndimage as ndi
from scipy.ndimage import binary_dilation, binary_erosion
from sklearn.metrics import roc_auc_score, accuracy_score, roc_curve

# ============================================================================
# Configuration
# ============================================================================
DEFAULT_CONFIG = {
    "data_dir": "/data/yty/brats23_segmamba_processed",
    "seed": 20251225,  # Fixed seed as per spec
    "train_rate": 0.7,
    "val_rate": 0.1,
    "test_rate": 0.2,
    "threshold": 0.5,
    "et_cc_min_size": 50,
    "boundary_band_radius": 3,
    "hd95_empty_value": 50.0,
}


# ============================================================================
# Utility Functions
# ============================================================================
def load_yaml(path: str) -> Dict:
    with open(path, "r") as f:
        return yaml.safe_load(f)


def split_npz_paths(data_dir: str, train_rate: float, val_rate: float, 
                    test_rate: float, seed: int) -> Tuple[List[str], List[str], List[str]]:
    """Split data paths into train/val/test sets with fixed seed."""
    import glob
    import random
    
    all_paths = sorted(glob.glob(os.path.join(data_dir, "*.npz")))
    
    random.seed(seed)
    random.shuffle(all_paths)
    
    n = len(all_paths)
    n_train = int(n * train_rate)
    n_val = int(n * val_rate)
    
    train_paths = all_paths[:n_train]
    val_paths = all_paths[n_train:n_train + n_val]
    test_paths = all_paths[n_train + n_val:]
    
    return train_paths, val_paths, test_paths


def load_case(npz_path: str) -> Dict:
    """Load a single case from npz/npy files."""
    npy_path = npz_path[:-4] + ".npy"
    seg_path = npz_path[:-4] + "_seg.npy"
    
    # Load image
    if os.path.isfile(npy_path):
        image = np.load(npy_path, mmap_mode="r")
    else:
        data = np.load(npz_path)
        image = data["data"]
    
    image = np.asarray(image, dtype=np.float32)
    if image.ndim == 5 and image.shape[0] == 1:
        image = image[0]
    if image.ndim == 4 and image.shape[0] != 4 and image.shape[-1] == 4:
        image = image.transpose(3, 0, 1, 2)
    
    # Load label
    if os.path.isfile(seg_path):
        label = np.load(seg_path, mmap_mode="r")
    else:
        data = np.load(npz_path)
        label = data["seg"] if "seg" in data else None
    
    if label is not None:
        label = np.asarray(label, dtype=np.int16)
        if label.ndim == 4 and label.shape[0] == 1:
            label = label[0]
        # Map ET label 3 -> 4 if needed (BraTS convention)
        if label.max() == 3 and (label == 4).sum() == 0:
            label = label.copy()
            label[label == 3] = 4
    
    case_id = os.path.basename(npz_path)[:-4]
    return {"image": image, "label": label, "case_id": case_id}


def label_to_regions(label: np.ndarray) -> np.ndarray:
    """Convert BraTS label to [WT, TC, ET] regions."""
    label = np.asarray(label)
    wt = label > 0
    tc = (label == 1) | (label == 4)
    et = label == 4
    return np.stack([wt, tc, et], axis=0).astype(np.uint8)


def remove_small_components(mask: np.ndarray, min_size: int, connectivity: int = 3) -> np.ndarray:
    """Remove connected components smaller than min_size.
    
    Args:
        mask: Binary mask [D, H, W]
        min_size: Minimum voxel count to keep
        connectivity: 1 for 6-connectivity, 2 for 18, 3 for 26
    """
    struct = ndi.generate_binary_structure(3, connectivity)
    labeled, num = ndi.label(mask.astype(np.uint8), structure=struct)
    if num == 0:
        return mask.astype(np.uint8)
    
    sizes = ndi.sum(mask.astype(np.uint8), labeled, index=np.arange(1, num + 1))
    keep = np.zeros_like(mask, dtype=np.uint8)
    for i, s in enumerate(sizes, start=1):
        if s >= min_size:
            keep[labeled == i] = 1
    return keep


def count_connected_components(mask: np.ndarray, connectivity: int = 3) -> int:
    """Count number of connected components."""
    struct = ndi.generate_binary_structure(3, connectivity)
    _, num = ndi.label(mask.astype(np.uint8), structure=struct)
    return num


# ============================================================================
# Model Inference
# ============================================================================
class ModelPredictor:
    """Predictor for GliomaSAM3-MoE model."""
    
    def __init__(self, config_path: str, checkpoint_path: str, device: str = "cuda"):
        self.device = torch.device(device if torch.cuda.is_available() else "cpu")
        self.cfg = load_yaml(config_path)
        
        from gliomasam3_moe.models.gliomasam3_moe import GliomaSAM3_MoE
        
        self.model = GliomaSAM3_MoE(**self.cfg["model"]).to(self.device)
        ckpt = torch.load(checkpoint_path, map_location="cpu")
        state_dict = {k: v for k, v in ckpt["model"].items() if "freqs_cis" not in k}
        self.model.load_state_dict(state_dict, strict=False)
        self.model.eval()
        print(f"Loaded checkpoint: {checkpoint_path}")
    
    def predict(self, image: np.ndarray) -> Dict:
        """Run inference and return predictions with aux outputs.
        
        Returns:
            {
                "probs": np.ndarray [3, D, H, W] - raw probabilities before gating
                "probs_gated": np.ndarray [3, D, H, W] - probabilities after ET gating
                "pi_et": float - ET presence probability
                "regions_bin": np.ndarray [3, D, H, W] - binary predictions (after gating + threshold)
            }
        """
        if image.ndim == 4:
            x = torch.from_numpy(image.copy()).float().unsqueeze(0)
        else:
            raise ValueError(f"Invalid image shape: {image.shape}")
        
        x = x.to(self.device)
        
        with torch.no_grad():
            logits, aux = self.model(x)
            probs = torch.sigmoid(logits)
            
            # Get pi_et
            pi_et = aux["pi_et"]
            pi_et_value = float(pi_et.item())
            
            # Probs before gating
            probs_np = probs[0].cpu().numpy()
            
            # Apply ET gating
            probs_gated = probs.clone()
            probs_gated[:, 2:3] = probs[:, 2:3] * pi_et.view(-1, 1, 1, 1, 1)
            probs_gated_np = probs_gated[0].cpu().numpy()
            
            # Binary prediction with threshold
            threshold = self.cfg.get("infer", {}).get("threshold", 0.5)
            regions_bin = (probs_gated_np > threshold).astype(np.uint8)
        
        return {
            "probs": probs_np,
            "probs_gated": probs_gated_np,
            "pi_et": pi_et_value,
            "regions_bin": regions_bin,
        }


# ============================================================================
# Table 7: Boundary-band Dice
# ============================================================================
def compute_boundary_band(mask: np.ndarray, radius: int = 3) -> np.ndarray:
    """Compute 3D boundary band using morphological operations.
    
    Args:
        mask: Binary mask [D, H, W]
        radius: Dilation/erosion radius in voxels
        
    Returns:
        band: Binary mask of boundary band
    """
    struct = ndi.generate_binary_structure(3, 3)  # 26-connectivity
    
    mask_bool = mask.astype(bool)
    if mask_bool.sum() == 0:
        return np.zeros_like(mask, dtype=np.uint8)
    
    # Dilate and erode
    dilated = binary_dilation(mask_bool, structure=struct, iterations=radius)
    eroded = binary_erosion(mask_bool, structure=struct, iterations=radius)
    
    # Band = dilated XOR eroded
    band = np.logical_xor(dilated, eroded).astype(np.uint8)
    return band


def compute_boundary_band_dice(pred: np.ndarray, gt: np.ndarray, radius: int = 3) -> float:
    """Compute Boundary-band Dice score.
    
    Args:
        pred: Binary prediction [D, H, W]
        gt: Binary ground truth [D, H, W]
        radius: Band radius in voxels
        
    Returns:
        Dice score for boundary band region
    """
    eps = 1e-7
    
    pred = pred.astype(bool)
    gt = gt.astype(bool)
    
    # Handle empty cases
    if gt.sum() == 0 and pred.sum() == 0:
        return 1.0
    if gt.sum() == 0 and pred.sum() > 0:
        return 0.0
    
    # Compute boundary band from GT
    band = compute_boundary_band(gt, radius=radius)
    
    # Restrict pred and gt to band
    pred_band = pred & band.astype(bool)
    gt_band = gt & band.astype(bool)
    
    # Dice on band
    intersection = (pred_band & gt_band).sum()
    dice = 2 * intersection / (pred_band.sum() + gt_band.sum() + eps)
    
    return float(dice)


def eval_table7(predictor: ModelPredictor, val_paths: List[str], 
                config: Dict, output_dir: str) -> Dict:
    """Evaluate Table 7: Boundary-band Dice (3-voxel band).
    
    Returns:
        Results dict with per-region and mean boundary dice
    """
    print("\n" + "=" * 60)
    print("Table 7: Boundary-band Dice Evaluation")
    print("=" * 60)
    
    radius = config.get("boundary_band_radius", 3)
    min_size = config.get("et_cc_min_size", 50)
    
    results = {
        "WT": [], "TC": [], "ET": [],
        "config": {"radius": radius, "min_size": min_size}
    }
    
    for npz_path in tqdm(val_paths, desc="Evaluating"):
        case = load_case(npz_path)
        if case["label"] is None:
            continue
        
        # Get predictions
        pred_out = predictor.predict(case["image"])
        pred_regions = pred_out["regions_bin"].copy()
        
        # Post-process ET: remove small components
        pred_regions[2] = remove_small_components(pred_regions[2], min_size, connectivity=3)
        
        # Get GT regions
        gt_regions = label_to_regions(case["label"])
        
        # Compute boundary-band dice for each region
        for i, region in enumerate(["WT", "TC", "ET"]):
            dice = compute_boundary_band_dice(pred_regions[i], gt_regions[i], radius=radius)
            results[region].append(dice)
    
    # Compute statistics
    stats = {}
    for region in ["WT", "TC", "ET"]:
        scores = results[region]
        stats[region] = {
            "mean": float(np.mean(scores)),
            "std": float(np.std(scores)),
            "n": len(scores),
        }
    
    stats["Mean"] = {
        "mean": float(np.mean([stats[r]["mean"] for r in ["WT", "TC", "ET"]])),
    }
    
    # Print results
    print(f"\nBoundary-band Dice (radius={radius} voxels):")
    print("-" * 40)
    print(f"{'Region':<10} {'Mean':>10} {'Std':>10} {'N':>8}")
    print("-" * 40)
    for region in ["WT", "TC", "ET"]:
        s = stats[region]
        print(f"{region:<10} {s['mean']:>10.4f} {s['std']:>10.4f} {s['n']:>8}")
    print("-" * 40)
    print(f"{'Mean':<10} {stats['Mean']['mean']:>10.4f}")
    
    # Save results
    output_path = os.path.join(output_dir, "table7_boundary_dice.json")
    with open(output_path, "w") as f:
        json.dump({"stats": stats, "config": results["config"]}, f, indent=2)
    print(f"\nResults saved to: {output_path}")
    
    return stats


# ============================================================================
# Table 4: ET-absent Subset Evaluation
# ============================================================================
def eval_table4(predictor: ModelPredictor, val_paths: List[str], 
                config: Dict, output_dir: str) -> Dict:
    """Evaluate Table 4: ET-absent subset evaluation.
    
    Metrics:
    - ET-absent subset (n cases where GT ET voxels = 0):
        - FP volume (mm³)
        - FP components (count)
    - Full validation set:
        - ET presence classification: AUROC, Acc, Sens, Spec
    """
    print("\n" + "=" * 60)
    print("Table 4: ET-absent Subset Evaluation")
    print("=" * 60)
    
    min_size = config.get("et_cc_min_size", 50)
    threshold = config.get("threshold", 0.5)
    
    # Collect results
    et_absent_results = []  # For ET-absent subset
    classification_results = []  # For full validation set
    
    for npz_path in tqdm(val_paths, desc="Evaluating"):
        case = load_case(npz_path)
        if case["label"] is None:
            continue
        
        # Get predictions
        pred_out = predictor.predict(case["image"])
        
        # Get GT regions
        gt_regions = label_to_regions(case["label"])
        gt_et = gt_regions[2]
        gt_et_voxels = int(gt_et.sum())
        
        # Classification labels: y=1 if ET present, 0 otherwise
        y_true = 1 if gt_et_voxels > 0 else 0
        
        # Score for classification: pi_et
        s_score = pred_out["pi_et"]
        
        # Binary ET prediction (after gating + threshold + post-process)
        pred_et_prob = pred_out["probs_gated"][2]
        pred_et_bin = (pred_et_prob > threshold).astype(np.uint8)
        pred_et_bin = remove_small_components(pred_et_bin, min_size, connectivity=3)
        
        # Store classification data
        classification_results.append({
            "case_id": case["case_id"],
            "y_true": y_true,
            "s_score": s_score,
            "y_pred": 1 if s_score > 0.5 else 0,
        })
        
        # For ET-absent cases, compute FP metrics
        if gt_et_voxels == 0:
            fp_voxels = int(pred_et_bin.sum())
            fp_components = count_connected_components(pred_et_bin, connectivity=3)
            
            et_absent_results.append({
                "case_id": case["case_id"],
                "fp_volume_mm3": fp_voxels,  # spacing=1mm
                "fp_components": fp_components,
            })
    
    # -------------------------
    # ET-absent subset metrics
    # -------------------------
    n_et_absent = len(et_absent_results)
    if n_et_absent > 0:
        fp_volumes = [r["fp_volume_mm3"] for r in et_absent_results]
        fp_components = [r["fp_components"] for r in et_absent_results]
        
        et_absent_stats = {
            "n": n_et_absent,
            "fp_volume_mm3": {
                "mean": float(np.mean(fp_volumes)),
                "std": float(np.std(fp_volumes)),
                "min": float(np.min(fp_volumes)),
                "max": float(np.max(fp_volumes)),
            },
            "fp_components": {
                "mean": float(np.mean(fp_components)),
                "std": float(np.std(fp_components)),
                "min": int(np.min(fp_components)),
                "max": int(np.max(fp_components)),
            },
        }
    else:
        et_absent_stats = {"n": 0, "fp_volume_mm3": None, "fp_components": None}
    
    # -------------------------
    # Classification metrics (full validation set)
    # -------------------------
    y_true = np.array([r["y_true"] for r in classification_results])
    s_score = np.array([r["s_score"] for r in classification_results])
    
    # AUROC and optimal threshold using Youden's J statistic
    if len(np.unique(y_true)) > 1:
        auroc = roc_auc_score(y_true, s_score)
        
        # Find optimal threshold using Youden's J = Sens + Spec - 1
        fpr, tpr, thresholds = roc_curve(y_true, s_score)
        j_scores = tpr - fpr  # Youden's J statistic
        best_idx = np.argmax(j_scores)
        optimal_threshold = thresholds[best_idx]
        
        # Use optimal threshold for predictions
        y_pred_optimal = (s_score >= optimal_threshold).astype(int)
    else:
        auroc = float("nan")
        optimal_threshold = 0.5
        y_pred_optimal = (s_score >= 0.5).astype(int)
    
    # Compute metrics at optimal threshold
    tp = int(((y_true == 1) & (y_pred_optimal == 1)).sum())
    tn = int(((y_true == 0) & (y_pred_optimal == 0)).sum())
    fp = int(((y_true == 0) & (y_pred_optimal == 1)).sum())
    fn = int(((y_true == 1) & (y_pred_optimal == 0)).sum())
    
    acc_optimal = (tp + tn) / len(y_true) if len(y_true) > 0 else float("nan")
    sens_optimal = tp / (tp + fn) if (tp + fn) > 0 else float("nan")
    spec_optimal = tn / (tn + fp) if (tn + fp) > 0 else float("nan")
    
    classification_stats = {
        "n": len(classification_results),
        "n_et_present": int(y_true.sum()),
        "n_et_absent": int((1 - y_true).sum()),
        "auroc": float(auroc),
        "optimal_threshold": float(optimal_threshold),
        "accuracy_optimal": float(acc_optimal),
        "sensitivity_optimal": float(sens_optimal),
        "specificity_optimal": float(spec_optimal),
    }
    
    # Print results
    print(f"\nET Presence Classification (n={classification_stats['n']}):")
    print("-" * 50)
    print(f"ET-present: {classification_stats['n_et_present']}, "
          f"ET-absent: {classification_stats['n_et_absent']}")
    print(f"AUROC:              {classification_stats['auroc']:.4f}")
    print(f"Optimal Threshold:  {classification_stats['optimal_threshold']:.4f}")
    print(f"Accuracy:           {classification_stats['accuracy_optimal']:.4f}")
    print(f"Sensitivity:        {classification_stats['sensitivity_optimal']:.4f}")
    print(f"Specificity:        {classification_stats['specificity_optimal']:.4f}")
    
    # Save results
    results = {
        "et_absent_subset": et_absent_stats,
        "et_absent_cases": et_absent_results,
        "classification": classification_stats,
        "config": {"min_size": min_size, "threshold": threshold},
    }
    
    output_path = os.path.join(output_dir, "table4_et_absent.json")
    with open(output_path, "w") as f:
        json.dump(results, f, indent=2)
    print(f"\nResults saved to: {output_path}")
    
    return results


# ============================================================================
# Main
# ============================================================================
def main():
    parser = argparse.ArgumentParser(description="Ablation Evaluation for GliomaSAM3-MoE")
    parser.add_argument("--config", type=str, default="configs/train.yaml",
                        help="Model config path")
    parser.add_argument("--checkpoint", type=str, required=True,
                        help="Model checkpoint path")
    parser.add_argument("--eval", type=str, default="both",
                        choices=["table4", "table7", "both"],
                        help="Which evaluation to run")
    parser.add_argument("--seed", type=int, default=20251225,
                        help="Random seed for data split")
    parser.add_argument("--output_dir", type=str, default="./eval_results",
                        help="Output directory for results")
    parser.add_argument("--device", type=str, default="cuda",
                        help="Device to use")
    parser.add_argument("--data_dir", type=str, default=None,
                        help="Override data directory")
    parser.add_argument("--use_all", action="store_true",
                        help="Use all data instead of validation split only")
    args = parser.parse_args()
    
    # Setup
    os.makedirs(args.output_dir, exist_ok=True)
    
    # Load model config
    model_cfg = load_yaml(args.config)
    
    # Setup evaluation config
    config = DEFAULT_CONFIG.copy()
    config["seed"] = args.seed
    if args.data_dir:
        config["data_dir"] = args.data_dir
    else:
        config["data_dir"] = model_cfg.get("data", {}).get("root_dir", config["data_dir"])
    
    print("=" * 60)
    print("GliomaSAM3-MoE Ablation Evaluation")
    print("=" * 60)
    print(f"Config: {args.config}")
    print(f"Checkpoint: {args.checkpoint}")
    print(f"Data dir: {config['data_dir']}")
    print(f"Seed: {config['seed']}")
    print(f"Evaluation: {args.eval}")
    print(f"Use all data: {args.use_all}")
    
    # Get data paths
    import glob
    all_paths = sorted(glob.glob(os.path.join(config["data_dir"], "*.npz")))
    
    if args.use_all:
        # Use all data for evaluation
        val_paths = all_paths
        print(f"\nUsing all data: {len(val_paths)} cases")
    else:
        # Split data
        print("\nSplitting data...")
        train_paths, val_paths, test_paths = split_npz_paths(
            config["data_dir"],
            train_rate=config["train_rate"],
            val_rate=config["val_rate"],
            test_rate=config["test_rate"],
            seed=config["seed"],
        )
        print(f"Train: {len(train_paths)}, Val: {len(val_paths)}, Test: {len(test_paths)}")
    
    # Initialize predictor
    print("\nLoading model...")
    predictor = ModelPredictor(args.config, args.checkpoint, args.device)
    
    # Run evaluations
    results = {}
    
    if args.eval in ["table7", "both"]:
        results["table7"] = eval_table7(predictor, val_paths, config, args.output_dir)
    
    if args.eval in ["table4", "both"]:
        results["table4"] = eval_table4(predictor, val_paths, config, args.output_dir)
    
    print("\n" + "=" * 60)
    print("Evaluation Complete!")
    print("=" * 60)
    
    return results


if __name__ == "__main__":
    main()