"""
Statistical analysis tools for morphology and spatial metrics.
"""
from typing import Optional
from google.adk.tools.tool_context import ToolContext

from ..services import analysis


def compute_comprehensive_stats(
    cell_file: Optional[str] = None,
    nuc_file: Optional[str] = None,
    tool_context: ToolContext = None
) -> dict:
    """
    Calculate morphology, spatial, and relational statistics in a single pass.
    
    Args:
        cell_file: Path to the .npz mask file for Cells (optional)
        nuc_file: Path to the .npz mask file for Nuclei (optional)
        tool_context: Automatically injected by ADK
    
    Returns:
        Nested dict containing 'cell_stats', 'nuc_stats', 'spatial_stats', 
        and 'relational_stats' where applicable.
    """
    pixel_scale = tool_context.state.get("app:pixel_size_microns")
    results = {}

    # 1. Analyze Cells (Morphology + Spatial)
    if cell_file:
        # Basic stats
        results["cell_stats"] = analysis.get_basic_stats(
            cell_file, pixel_scale=pixel_scale
        )
        # Spatial stats (only relevant for cells usually, but can be adapted)
        results["spatial_stats"] = analysis.get_spatial_stats(
            cell_file, pixel_scale=pixel_scale
        )
    
    # 2. Analyze Nuclei (Morphology only)
    if nuc_file:
        results["nuc_stats"] = analysis.get_basic_stats(
            nuc_file, pixel_scale=pixel_scale
        )

    # 3. Analyze Relationships (Overlap)
    # Only possible if we have both files
    if cell_file and nuc_file:
        results["relational_stats"] = analysis.analyze_relationships(
            cell_file, nuc_file
        )

    return results