Update cellemetry/tools/statistics.py

cellemetry/tools/statistics.py

@@ -1,61 +1,41 @@
 """
 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 get_basic_stats(
-    filename: str,
-    tool_context: ToolContext
+def compute_comprehensive_stats(
+    cell_file: Optional[str] = None,
+    nuc_file: Optional[str] = None,
+    tool_context: ToolContext = None
 ) -> dict:
     """
-    Calculate basic morphology stats (count, area mean/std).
+    Calculate morphology, spatial, and relational statistics in a single pass.
     
     Args:
-        filename: Path to the .npz mask file
+        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:
-        dict with count, area_mean, area_std, unit
+        Nested dict containing 'cell_stats', 'nuc_stats', 'spatial_stats', 
+        and 'relational_stats' where applicable.
     """
     pixel_scale = tool_context.state.get("app:pixel_size_microns")
-    return analysis.get_basic_stats(filename, pixel_scale=pixel_scale)
-
+    results = {}
 
-def get_spatial_stats(
-    filename: str,
-    tool_context: ToolContext
-) -> dict:
-    """
-    Calculate spatial distribution stats (NND, density, neighbor count).
+    # 1. Analyze Cells (Morphology + Spatial)
+    if cell_file:
+        results["cell_stats"] = analysis.get_basic_stats(cell_file, pixel_scale=pixel_scale)
+        results["spatial_stats"] = analysis.get_spatial_stats(cell_file, pixel_scale=pixel_scale)
     
-    Args:
-        filename: Path to the .npz mask file
-        tool_context: Automatically injected by ADK
-    
-    Returns:
-        dict with spatial metrics
-    """
-    pixel_scale = tool_context.state.get("app:pixel_size_microns")
-    return analysis.get_spatial_stats(filename, 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)
+    if cell_file and nuc_file:
+        results["relational_stats"] = analysis.analyze_relationships(cell_file, nuc_file)
 
-def get_relationship_stats(
-    cell_file: str,
-    nuc_file: str,
-    tool_context: ToolContext
-) -> dict:
-    """
-    Analyze cell-nucleus relationships (overlap ratios).
-    
-    Args:
-        cell_file: Path to cell masks .npz
-        nuc_file: Path to nucleus masks .npz
-        tool_context: Automatically injected by ADK
-    
-    Returns:
-        dict with matched_pairs, avg_ratio, std_ratio
-    """
-    return analysis.analyze_relationships(cell_file, nuc_file)
+    return results