Leaf region will only trigger if the region exists

atlas_densities/densities/inhibitory_neuron_densities_optimization.py

@@ -491,11 +491,29 @@ def _check_variables_consistency(
             if np.isfinite(deltas.loc[region_name, cell_type]):
                 for desc_id in id_set:
                     if np.isnan(x_result.loc[desc_id, cell_type]):
-                        raise AtlasDensitiesError(
-                            f"Cell count estimate of region named '{region_name}' for cell type "
-                            f"{cell_type} was given for certain whereas the cell count of "
-                            f"descendant id {desc_id} is not certain."
-                        )
+                        if ((deltas.loc[region_name, cell_type] in [0.0, np.inf]) & 
+                           (x_result.loc[id_, cell_type] == 0.0) or 
+                           (np.isnan(x_result.loc[id_, cell_type]))):
+                            ''' 
+                            If the region's cell count value was set to 0 because the region does 
+                            not exist we don't have to raise an error. Instead of x_result
+                            volumes.loc[id_, 'volume'] == 0.0 would be a better condition.. '''
+                            deltas.loc[region_name, cell_type] = np.inf
+                            x_result.loc[id_, cell_type] = np.nan
+                            warnings.warn(
+                                f"Cell count estimate of region named "
+                                f"'{region_name}' for cell type {cell_type} was given 0 for "
+                                f"its volume is 0 whereas the cell count of descendant id {desc_id} "
+                                f"is not certain. Cell count estimate for this region is thus set "
+                                f"to np.nan to avoid inconsistency.",
+                                AtlasDensitiesWarning,
+                                )
+
+                        else:
+                            raise AtlasDensitiesError(
+                                f"Cell count estimate of region named '{region_name}' for cell type "
+                                f"{cell_type} was given for certain whereas the cell count of "
+                            )
             neuron_count = neuron_counts.loc[id_, "cell_count"]
             if (
                 not np.isnan(x_result.loc[id_, cell_type])