scripts/fat_filter.py

#!/usr/bin/env python3
"""
Fat filtering script - replace voxels with HU < -20 with label 10
Processes both manual labels and model predictions separately
"""

import os
from pathlib import Path
import numpy as np # type: ignore
import nibabel as nib # type: ignore

# Input directories
root_100_120 = Path("../100-120")
manual_labels_dir = root_100_120 / "labels_9_muscles"
model_pred_labels_dir = root_100_120 / "label_9_muscles_model_pred"
images_dir = root_100_120 / "images_100-120"

# Output directories
output_base = Path("../fat_filtered_100-120")
manual_output_dir = output_base / "labels_9_muscles_fat_filtered"
model_pred_output_dir = output_base / "label_9_muscles_model_pred_fat_filtered"

# Fat threshold
fat_hu_thresh = -20
fat_label = 10

def load_image_and_label(case_id: int, label_dir: Path):
    """Load CT image and label file for a specific case."""
    
    img_path = images_dir / f"{case_id}_0000.nii.gz"
    if not img_path.exists():
        print(f"Image not found: {img_path}")
        return None, None, None

    lab_path = label_dir / f"{case_id}.nii.gz"
    if not lab_path.exists():
        print(f"Label not found: {lab_path}")
        return None, None, None
    
    try:
        img_nib = nib.load(str(img_path))  # type: ignore
        lab_nib = nib.load(str(lab_path))  # type: ignore
        
        img_arr = img_nib.get_fdata()
        lab_arr = lab_nib.get_fdata()
        
        return img_arr, lab_arr, lab_nib
    except Exception as e:
        print(f"Error loading case {case_id}: {e}")
        return None, None, None

def apply_fat_filter(img_arr: np.ndarray, lab_arr: np.ndarray):
    """Apply fat filtering - replace muscle voxels with HU < -20 with label 10."""
    filtered_lab = lab_arr.copy()
    fat_mask = (img_arr <= fat_hu_thresh) & (lab_arr > 0)
    filtered_lab[fat_mask] = fat_label
    return filtered_lab

def process_labels(label_dir: Path, output_dir: Path, label_type: str):
    """Process all labels in a directory and save fat-filtered versions."""
    
    print(f"\nProcessing {label_type} labels...")
    print(f"Input directory: {label_dir}")
    print(f"Output directory: {output_dir}")
    
    output_dir.mkdir(parents=True, exist_ok=True)
    
    processed_count = 0
    failed_count = 0
    
    for case_id in range(100, 121):
        print(f"Processing case {case_id}...")
        
        img_arr, lab_arr, lab_nib = load_image_and_label(case_id, label_dir)
        
        if img_arr is not None and lab_arr is not None and lab_nib is not None:
            filtered_lab = apply_fat_filter(img_arr, lab_arr)
            
            filtered_nib = nib.Nifti1Image(
                filtered_lab.astype(np.uint8),  # type: ignore
                lab_nib.affine,
                lab_nib.header
            )
            
            output_path = output_dir / f"{case_id}.nii.gz"
            nib.save(filtered_nib, str(output_path))  # type: ignore
            
            original_muscle_voxels = np.count_nonzero((lab_arr > 0) & (lab_arr <= 9))  # type: ignore
            fat_voxels = np.count_nonzero(filtered_lab == fat_label)  # type: ignore
            total_muscle_voxels = np.count_nonzero(lab_arr > 0)  # type: ignore
            
            print(f"  Case {case_id}: {fat_voxels} fat voxels added (original muscle voxels: {original_muscle_voxels})")
            
            processed_count += 1
        else:
            print(f"  Case {case_id}: Failed to load")
            failed_count += 1
    
    print(f"\n{label_type} processing complete:")
    print(f"  Successfully processed: {processed_count} cases")
    print(f"  Failed: {failed_count} cases")
    print(f"  Output saved to: {output_dir}")

def main():
    """Main function to process both manual and model prediction labels."""
    
    print("="*80)
    print("FAT FILTERING SCRIPT")
    print("Replace voxels with HU < -20 with label 10")
    print("="*80)
    
    if not manual_labels_dir.exists():
        print(f"Error: Manual labels directory not found: {manual_labels_dir}")
        return
    
    if not model_pred_labels_dir.exists():
        print(f"Error: Model prediction labels directory not found: {model_pred_labels_dir}")
        return
    
    if not images_dir.exists():
        print(f"Error: Images directory not found: {images_dir}")
        return
    
    process_labels(
        label_dir=manual_labels_dir,
        output_dir=manual_output_dir,
        label_type="Manual"
    )
    
    process_labels(
        label_dir=model_pred_labels_dir,
        output_dir=model_pred_output_dir,
        label_type="Model Prediction"
    )
    
    print("\n" + "="*80)
    print("FAT FILTERING COMPLETE")
    print("="*80)
    print(f"Results saved to:")
    print(f"  - {manual_output_dir} (manual labels with fat filtering)")
    print(f"  - {model_pred_output_dir} (model predictions with fat filtering)")
    print(f"\nFat filtering details:")
    print(f"  - Threshold: HU < {fat_hu_thresh}")
    print(f"  - Fat label: {fat_label}")
    print(f"  - Original muscle labels preserved (1-9)")
    print(f"  - Fat voxels labeled as {fat_label}")

if __name__ == "__main__":
    main()