allow for morphologies without soma (#900)

neurom/check/neuron_checks.py

@@ -38,6 +38,7 @@
 from neurom.check.morphtree import get_flat_neurites
 from neurom.core.neuron import Section, iter_neurites, iter_sections, iter_segments
 from neurom.core.dataformat import COLS
+from neurom.exceptions import NeuroMError
 from neurom.features import neuritefunc as _nf
 from neurom.morphmath import section_length, segment_length
 
@@ -67,8 +68,7 @@ def has_apical_dendrite(neuron, min_number=1, treefun=_read_neurite_type):
     Arguments:
         neuron(Neuron): The neuron object to test
         min_number: minimum number of apical dendrites required
-        treefun: Optional function to calculate the tree type of neuron's
-        neurites
+        treefun: Optional function to calculate the tree type of neuron's neurites
 
     Returns:
         CheckResult with result
@@ -279,6 +279,8 @@ def has_no_dangling_branch(neuron):
     Returns:
         CheckResult with a list of all first segments of dangling neurites
     """
+    if len(neuron.soma.points) == 0:
+        raise NeuroMError('Can\'t check for dangling neurites if there is no soma')
     soma_center = neuron.soma.points[:, COLS.XYZ].mean(axis=0)
     recentered_soma = neuron.soma.points[:, COLS.XYZ] - soma_center
     radius = np.linalg.norm(recentered_soma, axis=1)

neurom/core/neuron.py

@@ -416,7 +416,9 @@ def __init__(self, filename, name=None):
             name (str): a option neuron name
         """
         try:
-            morphio.set_ignored_warning([morphio.Warning.wrong_root_point], True)
+            morphio.set_ignored_warning([morphio.Warning.wrong_root_point,
+                                         morphio.Warning.no_soma_found,
+                                         morphio.Warning.zero_diameter], True)
             morphio.set_raise_warnings(True)
             super().__init__(filename)
         finally:

setup.py

@@ -39,7 +39,7 @@
     install_requires=[
         'click>=7.0',
         'matplotlib>=3.2.1',
-        'morphio>=3.0.2',
+        'morphio>=3.1.1',
         'numpy>=1.8.0',
         'pandas>=1.0.5',
         'pyyaml>=3.10',

tests/check/test_neuron_checks.py

@@ -34,6 +34,8 @@
 from neurom.check import neuron_checks as nrn_chk
 from neurom.core.dataformat import COLS
 from neurom.core.types import dendrite_filter
+from neurom.exceptions import NeuroMError
+import pytest
 from numpy.testing import assert_array_equal
 
 DATA_PATH = Path(__file__).parent.parent / 'data'
@@ -403,6 +405,12 @@ def test_has_no_dangling_branch():
     assert res.status
 
 
+def test_dangling_branch_no_soma():
+    with pytest.raises(NeuroMError, match='Can\'t check for dangling neurites if there is no soma'):
+        nrn = load_neuron(SWC_PATH / 'Single_apical_no_soma.swc')
+        nrn_chk.has_no_dangling_branch(nrn)
+
+
 def test__bool__():
     c = check.CheckResult(status=True)
     assert c.__nonzero__()

tests/check/test_runner.py

@@ -151,7 +151,15 @@ def test_single_axon_neuron():
 
 
 def test_single_apical_no_soma():
-    _run_test(SWC_PATH / 'Single_apical_no_soma.swc', dict([('ALL', False)]))
+    expected = {'ALL': False,
+                'Has all nonzero neurite radii': True,
+                'Has all nonzero section lengths': True,
+                'Has all nonzero segment lengths': False,
+                'Has apical dendrite': True,
+                'Has axon': False,
+                'Has basal dendrite': False,
+                'Has nonzero soma radius': False}
+    _run_test(SWC_PATH / 'Single_apical_no_soma.swc', expected)
 
 
 def test_directory_input():

tests/io/test_swc_reader.py

@@ -47,7 +47,7 @@ def test_repeated_id():
 
 
 def test_neurite_followed_by_soma():
-    with pytest.raises(MorphioError, match='Warning: found a disconnected neurite'):
+    with pytest.raises(MorphioError, match='Found a soma point with a neurite as parent'):
         load_neuron(SWC_PATH / 'soma_with_neurite_parent.swc')