fix: failing to measure diameter of nonexistent compartment

neuron_morphology/features/size.py

@@ -13,15 +13,15 @@
 
 @marked(Geometric)
 def total_length(
-    data: MorphologyLike, 
+    data: MorphologyLike,
     node_types: Optional[List[int]] = None
 ) -> float:
     """ Calculate the total length across all compartments in a reconstruction
 
     Parameters
     ----------
     data : the input reconstruction
-    node_types : if provided, restrict the calculation to compartments 
+    node_types : if provided, restrict the calculation to compartments
         involving these types
 
     Returns
@@ -33,8 +33,8 @@ def total_length(
     Excludes compartments where the parent is:
         1. the soma
         2. a root of the reconstruction
-    The logic here is that the soma root is likely to substantially overlap any 
-    of its compartments, while non-root soma nodes will be closer to the soma 
+    The logic here is that the soma root is likely to substantially overlap any
+    of its compartments, while non-root soma nodes will be closer to the soma
     surface.
 
     """
@@ -58,18 +58,18 @@ def total_length(
 @marked(RequiresRadii)
 @marked(Geometric)
 def total_surface_area(
-    data: MorphologyLike, 
+    data: MorphologyLike,
     node_types: Optional[List[int]] = None
 ) -> float:
-    """ Calculates the sum of lateral surface areas across all comparments 
-    (linked pairs of nodes) in a reconstruction. This approximates the total 
-    surface area of the reconstruction. See 
+    """ Calculates the sum of lateral surface areas across all comparments
+    (linked pairs of nodes) in a reconstruction. This approximates the total
+    surface area of the reconstruction. See
     Morphology.get_compartment_surface_area for details.
 
     Parameters
     ----------
     data : The reconstruction whose surface area will be computed
-    node_types : restrict the calculation to compartments involving these node 
+    node_types : restrict the calculation to compartments involving these node
         types
 
     Returns
@@ -88,25 +88,25 @@ def total_surface_area(
 @marked(RequiresRadii)
 @marked(Geometric)
 def total_volume(
-    data: MorphologyLike, 
+    data: MorphologyLike,
     node_types: Optional[List[int]] = None
 ) -> float:
-    """ Calculates the sum of volumes across all comparments (linked pairs of 
-    nodes) in a reconstruction. This approximates the total volume of the 
+    """ Calculates the sum of volumes across all comparments (linked pairs of
+    nodes) in a reconstruction. This approximates the total volume of the
     reconstruction. See Morphology.get_compartment_volume for details.
 
     Parameters
     ----------
     data : The reconstruction whose volume will be computed
-    node_types : restrict the calculation to compartments involving these node 
+    node_types : restrict the calculation to compartments involving these node
         types
 
     Returns
     -------
     The sum of compartment volumes across this reconstruction
 
     """
-    
+
     morphology = get_morphology(data)
     nodes = morphology.get_node_by_types(node_types)
     compartments = morphology.get_compartments(nodes, node_types)
@@ -116,15 +116,15 @@ def total_volume(
 
 @marked(RequiresRadii)
 def mean_diameter(
-    data: MorphologyLike, 
+    data: MorphologyLike,
     node_types: Optional[List[int]] = None
 ) -> float:
     """ Calculates the mean diameter of all nodes
-    
+
     Parameters
     ----------
     morphology : The reconstruction whose mean diameter
-    node_types : restrict the calculation to compartments involving these node 
+    node_types : restrict the calculation to compartments involving these node
         types
 
     Returns
@@ -134,20 +134,21 @@ def mean_diameter(
     """
 
     morphology = get_morphology(data)
-
-    return 2 * mean(
-        node["radius"] for node in morphology.get_node_by_types(node_types)
-    )
+    radii = [node["radius"] for node in morphology.get_node_by_types(node_types)]
+    if radii:
+        return 2 * mean(radii)
+    else:
+        return float('nan')
 
 
 
 def parent_daughter_ratio_visitor(
-    node: Dict[str, Any], 
-    morphology: Morphology, 
+    node: Dict[str, Any],
+    morphology: Morphology,
     counters: Dict[str, Union[int, float]],
     node_types: Optional[List[int]] = None
 ):
-    """ Calculates for a single node the ratio of the node's parent's radius to 
+    """ Calculates for a single node the ratio of the node's parent's radius to
     the node's radius. Stores these values in a provided dictionary.
 
     Parameters
@@ -164,7 +165,7 @@ def parent_daughter_ratio_visitor(
     """
 
     parent = morphology.parent_of(node)
-    
+
     if parent is None:
         return
 
@@ -174,45 +175,45 @@ def parent_daughter_ratio_visitor(
 
     counters["ratio_sum"] += parent["radius"] / node["radius"]
     counters["ratio_count"] += 1
-    
+
 
 @marked(RequiresRadii)
 def mean_parent_daughter_ratio(
     data: MorphologyLike,
     node_types: Optional[List[int]] = None
 ) -> float:
-    """ Calculate the average ratio of parent radii to child radii across a 
+    """ Calculate the average ratio of parent radii to child radii across a
     reconstruction.
 
     Parameters
     ----------
     data : The reconstruction whose mean parent daugther ratio will be computed
-    node_types : restrict the calculation to compartments involving these node 
+    node_types : restrict the calculation to compartments involving these node
         types
 
     Notes
     -----
-    Note that this function differs from the L-measure parent daughter ratio, 
-    which calculates the ratio of the child node size to the parent. Note also 
+    Note that this function differs from the L-measure parent daughter ratio,
+    which calculates the ratio of the child node size to the parent. Note also
     that both the parent and child must be in node_types in order for a
     compartment to be included in the calculation
 
     """
 
     morphology = get_morphology(data)
     roots = morphology.get_roots()
-    
+
     counters: Dict[str, int] = defaultdict(lambda *a, **k: 0)
     visitor = partial(
-        parent_daughter_ratio_visitor, 
-        morphology=morphology, 
+        parent_daughter_ratio_visitor,
+        morphology=morphology,
         counters=counters,
         node_types=node_types
     )
-    
+
     for root in roots:
         morphology.breadth_first_traversal(
-            visitor, 
+            visitor,
             start_id=morphology.node_id_cb(root)
         )
 
@@ -225,18 +226,18 @@ def max_euclidean_distance(
     data: MorphologyLike,
     node_types: Optional[List[int]] = None
 ) -> float:
-    """Calculate the furthest distance, in 3-space, of a compartment's end from 
+    """Calculate the furthest distance, in 3-space, of a compartment's end from
     the soma. This is equivalent to the distance to the furthest SWC node.
 
     Parameters
     ----------
-    data: The reconstruction whose max euclidean distance will be 
+    data: The reconstruction whose max euclidean distance will be
         calculated
     node_types: restrict consideration to these types
 
     Returns
     -------
-    The distance between the soma and the farthest-from-soma node in this 
+    The distance between the soma and the farthest-from-soma node in this
     morphology.
 
     """

tests/feature_extractor/test_size_features.py

@@ -106,7 +106,7 @@ class TestMeanDiameter(unittest.TestCase):
     def setUp(self):
         nodes = basic_nodes()
         self.sizes = np.random.rand(len(nodes))
-        
+
         for sz, node in zip(self.sizes, nodes):
             node["radius"] = sz
 
@@ -118,12 +118,34 @@ def setUp(self):
 
         self.mean_diameter = np.mean(self.sizes) * 2
 
+        self.mean_diameter_by_compartment = {}
+        compartments = [APICAL_DENDRITE, BASAL_DENDRITE, AXON]
+        for c in compartments:
+            radii = [n['radius'] for n in nodes if n['type']==c]
+            diam = float('nan')
+            if radii:
+                diam = 2*np.mean(radii)
+            self.mean_diameter_by_compartment[c] = diam
+
+
     def test_generic(self):
         self.assertAlmostEqual(
             size.mean_diameter(self.morphology),
             self.mean_diameter
         )
 
+    def test_restricted(self):
+        for compartment, expected_value in self.mean_diameter_by_compartment.items():
+            if np.math.isnan(expected_value):
+                self.assertTrue(np.math.isnan(size.mean_diameter(self.morphology, [compartment])))
+            else:
+                self.assertAlmostEqual(
+                    size.mean_diameter(self.morphology, [compartment]),
+                    expected_value
+                )
+
+
+
 
 class TestMeanParentDaughterRatio(unittest.TestCase):
 
@@ -204,4 +226,4 @@ def test_restricted(self):
         self.assertAlmostEqual(
             size.max_euclidean_distance(self.morphology, [APICAL_DENDRITE]),
             6
-        )
+        )