Fix: Raise clear errors for empty angles

neurots/extract_input/from_TMD.py

@@ -17,6 +17,8 @@
 
 import tmd
 
+from neurots.utils import NeuroTSError
+
 
 def persistent_homology_angles(
     pop, threshold=2, neurite_type="basal_dendrite", feature="radial_distances"
@@ -35,10 +37,17 @@ def persistent_homology_angles(
     ph_ang = [
         tmd.methods.get_ph_angles(tree, feature=feature) for tree in getattr(pop, neurite_type)
     ]
+    if not ph_ang:
+        raise NeuroTSError(f"The given population does contain any tree of {neurite_type} type.")
 
     # Keep only the trees whose number of terminations is above the threshold
     # Saves the list of persistence diagrams for the selected neurite_type
     phs = [p for p in ph_ang if len(p) > threshold]
+    if not phs:
+        raise NeuroTSError(
+            "The given threshold excluded all bars of the persistence diagram, please use a "
+            "lower threshold value."
+        )
     min_bar_length = min(min(tmd.analysis.get_lengths(ph)) for ph in phs)
 
     return {"persistence_diagram": phs, "min_bar_length": min_bar_length}

setup.py

@@ -22,13 +22,13 @@
 
 reqs = [
     "jsonschema>=3.0.1",
-    "matplotlib>=3.2.1",
-    "morphio>=3.3.3,<4.0",
+    "matplotlib>=3.4",
+    "morphio>=3.3.4,<4.0",
     "neurom>=3.0,<4.0",
     "numpy>=1.22.0",
     "scipy>=1.6",
-    "tmd>=2.2.0",
-    "diameter-synthesis>=0.5.2",
+    "tmd>=2.3.0",
+    "diameter-synthesis>=0.5.4",
 ]
 
 doc_reqs = [
@@ -40,7 +40,6 @@
 ]
 
 test_reqs = [
-    "diameter-synthesis>=0.5.0",
     "dictdiffer>=0.5",
     "mock>=3",
     "morph-tool>=2.9",

tests/test_extract_input.py

@@ -305,6 +305,28 @@ def test_path_distances(self, filename):
         assert_equal(distr["basal_dendrite"]["filtration_metric"], "path_distances")
         validator.validate_neuron_distribs(distr)
 
+    def test_threshold_too_small(self):
+        with pytest.raises(
+            NeuroTSError,
+            match=(
+                "The given threshold excluded all bars of the persistence diagram, please use a "
+                "lower threshold value."
+            ),
+        ):
+            extract_input.distributions(
+                os.path.join(_PATH, "diam_simple.swc"),
+                feature="path_distances",
+                neurite_types=["basal_dendrite"],
+            )
+
+    def test_missing_neurite_type(self):
+        with pytest.raises(NeuroTSError):
+            extract_input.distributions(
+                os.path.join(_PATH, "diam_simple.swc"),
+                feature="path_distances",
+                neurite_types=["basal_dendrite", "apical_dendrite"],
+            )
+
     def test_trunk_length(self, filename):
         distr = extract_input.distributions(filename, feature="trunk_length")
         assert "persistence_diagram" not in distr["basal_dendrite"]