wrapper.py

from pathlib import Path
from typing import Dict, Callable, Optional, Generator, Any
import shutil
from PIL import Image
import glob
import os

from sorghum_pipeline.pipeline import SorghumPipeline
from sorghum_pipeline.config import Config, Paths


def run_pipeline_on_image(input_image_path: str, work_dir: str, save_artifacts: bool = True, 
                          progress_callback: Optional[Callable[[str, Dict[str, Any]], None]] = None,
                          single_plant_mode: bool = False) -> Generator[Dict[str, str], None, None]:
    """
    Run sorghum pipeline on a single image (no instance segmentation).
    Yields dict[label -> image_path] progressively for gallery display.
    
    Args:
        input_image_path: Path to input image
        work_dir: Working directory for outputs
        save_artifacts: Whether to save artifacts
        progress_callback: Optional callback(stage_name, data) called after each pipeline stage
    
    Yields:
        Dictionary of output paths progressively as they become available
    """

    work = Path(work_dir)
    work.mkdir(parents=True, exist_ok=True)

    # Use input path directly (already in work_dir from app.py)
    input_path = Path(input_image_path)

    # Ensure demo env vars are set before pipeline construction
    os.environ['MINIMAL_DEMO'] = '1'
    os.environ['FAST_OUTPUT'] = '1'

    # Build in-memory config pointing input/output to the working directory
    cfg = Config()
    cfg.paths = Paths(
        input_folder=str(work),
        output_folder=str(work),
        boundingbox_dir=str(work)
    )
    pipeline = SorghumPipeline(config=cfg, single_plant_mode=single_plant_mode)

    # Run the pipeline with progress callback (generator)
    for stage_result in pipeline.run_with_progress(single_image_path=str(input_path), progress_callback=progress_callback, single_plant_mode=single_plant_mode):
        # Yield intermediate outputs as they become available
        outputs = _collect_outputs(work, stage_result.get('plants', {}))
        yield outputs
    
    # Final results
    results = stage_result


def _collect_outputs(work: Path, plants: Dict[str, Any]) -> Dict[str, str]:
    """Collect all available outputs from work directory and plants data."""
    outputs: Dict[str, str] = {}
    
    try:
        # Log immediate output directory contents for debugging
        for sub in ['results', 'Vegetation_indices_images', 'texture_output']:
            p = work / sub
            if p.exists():
                files = sorted([str(x.name) for x in p.iterdir() if x.is_file()])
                print(f"Artifacts in {sub}: {files}")
    except Exception:
        pass

    # Collect desired vegetation indices (replace ARI with SAVI)
    wanted = [
        work / 'Vegetation_indices_images/ndvi.png',
        work / 'Vegetation_indices_images/gndvi.png',
        work / 'Vegetation_indices_images/savi.png',
    ]
    labels = [
        'NDVI', 'GNDVI', 'SAVI',
    ]
    for label, path in zip(labels, wanted):
        if path.exists():
            outputs[label] = str(path)

    # Also include overlay and mask if present
    overlay_path = work / 'results/overlay.png'
    mask_path = work / 'results/mask.png'
    composite_path = work / 'results/composite.png'
    input_img_path = work / 'results/input_image.png'
    if overlay_path.exists():
        outputs['Overlay'] = str(overlay_path)
    if mask_path.exists():
        outputs['Mask'] = str(mask_path)
    if composite_path.exists():
        outputs['Composite'] = str(composite_path)
    if input_img_path.exists():
        outputs['InputImage'] = str(input_img_path)

    # Extract simple stats for display if present in pipeline results
    try:
        if plants:
            _, pdata = next(iter(plants.items()))
            veg = pdata.get('vegetation_indices', {})
            stats_lines = []
            for name in ['NDVI', 'GNDVI', 'SAVI']:
                entry = veg.get(name, {})
                st = entry.get('statistics', {}) if isinstance(entry, dict) else {}
                if st:
                    stats_lines.append(f"{name}: mean={st.get('mean', 0):.3f}, std={st.get('std', 0):.3f}")
            # Morphology stats (height - always show as single plant)
            morph = pdata.get('morphology_features', {}) if isinstance(pdata, dict) else {}
            traits = morph.get('traits', {}) if isinstance(morph, dict) else {}
            
            # Get plant height (system now filters to largest plant only)
            plant_heights = traits.get('plant_heights', {})
            num_plants = traits.get('num_plants', 0)
            
            # Display plant info based on mode
            if num_plants > 0 and isinstance(plant_heights, dict):
                if num_plants == 1 or len(plant_heights) == 1:
                    # Single plant display
                    height_cm = list(plant_heights.values())[0]
                    stats_lines.append(f"Number of plants: 1")
                    stats_lines.append(f"Plant height: {height_cm:.2f} cm")
                else:
                    # Multiple plants display
                    stats_lines.append(f"Number of plants: {num_plants}")
                    sorted_plants = sorted(plant_heights.items(), key=lambda x: int(x[0].split('_')[1]))
                    for plant_name, height_cm in sorted_plants:
                        plant_num = plant_name.split('_')[1]
                        stats_lines.append(f"  Plant {plant_num}: {height_cm:.2f} cm")
            else:
                # Fallback to old single height field
                height_cm = traits.get('plant_height_cm')
                if isinstance(height_cm, (int, float)) and height_cm > 0:
                    stats_lines.append(f"Number of plants: 1")
                    stats_lines.append(f"Plant height: {height_cm:.2f} cm")
            if stats_lines:
                outputs['StatsText'] = "\n".join(stats_lines)
    except Exception:
        pass

    return outputs