def test_existence_of_constriction_for_dendrite_multiple_children(self):
for dendrite_type in [BASAL_DENDRITE, APICAL_DENDRITE]:
try:
nodes = [
test_node(id=1, type=SOMA, radius=35.1, parent_node_id=-1),
test_node(id=2,
type=dendrite_type,
radius=2.0,
parent_node_id=1),
test_node(id=3,
type=dendrite_type,
radius=2.0,
parent_node_id=2),
test_node(id=4,
type=dendrite_type,
radius=1.5,
parent_node_id=3),
test_node(id=5,
type=dendrite_type,
radius=1.5,
parent_node_id=3)
]
test_tree(nodes, strict_validation=True)
self.fail("Morphology should have been rejected.")
except InvalidMorphology as e:
self.assertNodeErrors(
e.validation_errors,
"Constriction: The radius of types 3 and 4 should not be "
"less than 2.0px", [[5], [4]])
def test_multiple_axon_initiation_points_valid(self):
nodes = [
test_node(id=1, type=SOMA, parent_node_id=-1),
test_node(id=2, type=AXON, parent_node_id=1)
]
test_tree(nodes, strict_validation=True)
def test_children_of(self):
morphology = test_morphology_small()
node = test_node(id=1,
type=SOMA,
x=800,
y=610,
z=30,
radius=35,
parent_node_id=-1)
children = morphology.children_of(node)
expected_children = [
test_node(id=2,
type=BASAL_DENDRITE,
x=400,
y=600,
z=10,
radius=3,
parent_node_id=1),
test_node(id=4,
type=APICAL_DENDRITE,
x=600,
y=300,
z=20,
radius=3,
parent_node_id=1),
test_node(id=6,
type=AXON,
x=900,
y=600,
z=30,
radius=3,
parent_node_id=1)
]
self.assertEqual(children, expected_children)
def test_coordinate_corresponding_to_dendrite_tips_multiple_cut_dendrite_invalid(
self):
for dendrite_type in [BASAL_DENDRITE, APICAL_DENDRITE]:
nodes = [
test_node(id=1, type=SOMA, parent_node_id=-1),
test_node(id=2,
type=dendrite_type,
x=0,
y=0,
z=0,
parent_node_id=1),
test_node(id=2,
type=dendrite_type,
x=0,
y=0,
z=0,
parent_node_id=1)
]
errors = mv.validate([
test_marker(x=1, y=0, z=0, name=CUT_DENDRITE),
test_marker(x=1, y=0, z=0, name=TYPE_30)
], test_tree(nodes))
self.assertMarkerErrors(
errors,
"Coordinates for each dendrite (type 10) needs to correspond to "
"a tip of a dendrite type (type 3 or 4) in the related morphology",
[[{
'x': 1,
'y': 0,
'z': 0,
'name': CUT_DENDRITE
}]])
def test_apical_dendrite_traceable_back_to_soma_valid(self):
nodes = [
test_node(id=1, type=SOMA, parent_node_id=-1),
test_node(id=2, type=AXON, parent_node_id=1),
test_node(id=3, type=APICAL_DENDRITE, parent_node_id=1)
]
test_tree(nodes, strict_validation=True)
def test_axon_node_with_valid_parent_type(self):
for node_type in [SOMA, AXON]:
nodes = [
test_node(id=1, type=node_type, parent_node_id=-1),
test_node(id=2, type=AXON, parent_node_id=1)
]
test_tree(nodes, strict_validation=True)
def test_basal_dendrite_node_with_valid_parent_type(self):
for node_type in [SOMA]:
nodes = [
test_node(id=1, type=node_type, parent_node_id=-1),
test_node(id=2, type=BASAL_DENDRITE, parent_node_id=1)
]
test_tree(nodes, strict_validation=True)
def test_validate_expected_type_valid(self):
for node_type in [AXON, BASAL_DENDRITE, APICAL_DENDRITE]:
nodes = [
test_node(id=1, type=SOMA),
test_node(id=2, type=node_type, parent_node_id=1)
]
errors = tv.validate_expected_types(test_tree(nodes))
self.assertEqual(len(errors), 0)
def test_independent_axon_with_more_than_four_nodes_child_branch(self):
nodes = [
test_node(id=1, type=SOMA, parent_node_id=-1),
test_node(id=2, type=AXON, parent_node_id=-1),
test_node(id=3, type=AXON, parent_node_id=2),
test_node(id=4, type=AXON, parent_node_id=3),
test_node(id=5, type=AXON, parent_node_id=3)
]
test_tree(nodes, strict_validation=True)
def test_immediate_child_of_soma_doesnt_more_than_one_child(self):
nodes = [
test_node(id=1, type=SOMA, parent_node_id=-1),
test_node(id=2, type=APICAL_DENDRITE, parent_node_id=1),
test_node(id=3, type=APICAL_DENDRITE, parent_node_id=2),
test_node(id=4, type=APICAL_DENDRITE, parent_node_id=3),
test_node(id=5, type=APICAL_DENDRITE, parent_node_id=3)
]
test_tree(nodes, strict_validation=True)
def test_children_nodes_appear_before_parent_nodes_not_valid(self):
try:
nodes = [test_node(id=1, type=AXON, parent_node_id=2),
test_node(id=2, type=SOMA, parent_node_id=-1)]
test_tree(nodes, strict_validation=True)
self.fail("Morphology should have been rejected.")
except InvalidMorphology as e:
self.assertNodeErrors(e.validation_errors, "Child node needs to come before parent node",
[[1]])
def test_extreme_taper_less_than_eight_nodes_in_segment(self):
nodes = [
test_node(id=1, type=SOMA, radius=36.0, parent_node_id=-1),
test_node(id=2, type=BASAL_DENDRITE, radius=2.0, parent_node_id=1),
test_node(id=3, type=BASAL_DENDRITE, radius=2.0, parent_node_id=2),
test_node(id=4, type=BASAL_DENDRITE, radius=2.0, parent_node_id=3)
]
test_tree(nodes, strict_validation=True)
def test_decreasing_radius_when_going_away_from_soma_axon_valid(self):
nodes = [
test_node(id=1, type=SOMA, radius=36.0, parent_node_id=-1),
test_node(id=2, type=AXON, radius=4.0, parent_node_id=1),
test_node(id=3, type=AXON, radius=4.0, parent_node_id=2),
test_node(id=4, type=AXON, radius=4.0, parent_node_id=1),
test_node(id=5, type=AXON, radius=4.0, parent_node_id=4)
]
test_tree(nodes, strict_validation=True)
def test_decreasing_radius_when_going_away_from_soma_dendrite_valid(self):
nodes = [
test_node(id=1, type=SOMA, radius=36.0, parent_node_id=-1),
test_node(id=2, type=BASAL_DENDRITE, radius=4.0, parent_node_id=1),
test_node(id=3, type=BASAL_DENDRITE, radius=2.0, parent_node_id=2),
test_node(id=4, type=APICAL_DENDRITE, radius=4.0,
parent_node_id=1),
test_node(id=5, type=APICAL_DENDRITE, radius=2.0, parent_node_id=4)
]
test_tree(nodes, strict_validation=True)
def test_number_of_soma_nodes_invalid(self):
try:
nodes = [
test_node(id=1, type=SOMA, parent_node_id=-1),
test_node(id=2, type=SOMA, parent_node_id=-1)
]
test_tree(nodes, strict_validation=True)
self.fail("Morphology should have been rejected.")
except InvalidMorphology as e:
self.assertNodeErrors(
e.validation_errors,
"The morphology needs to have one soma node", [[1], [2]])
def test_independent_axon_count_zero(self):
nodes = [
test_node(id=1, type=SOMA, parent_node_id=-1),
test_node(id=2, type=AXON, parent_node_id=1)
]
test_morphology = Morphology(nodes,
node_id_cb=lambda node: node['id'],
parent_id_cb=lambda node: node['parent'])
test_morphology.validate(strict=False)
stat = morphology_statistics(test_morphology)
self.assertEqual(stat["Number of Independent Axons"], 0)
def test_independent_axon_with_less_than_four_nodes_no_children(self):
try:
nodes = [
test_node(id=1, type=SOMA, parent_node_id=-1),
test_node(id=2, type=AXON, parent_node_id=-1)
]
test_tree(nodes, strict_validation=True)
self.fail("Morphology should have been rejected.")
except InvalidMorphology as e:
self.assertNodeErrors(
e.validation_errors,
"There is an independent axon with less than 4 nodes", [[2]])
def test_soma_node_with_invalid_parent(self):
try:
nodes = [
test_node(id=1, type=SOMA, parent_node_id=-1),
test_node(id=2, type=SOMA, parent_node_id=1)
]
test_tree(nodes, strict_validation=True)
self.fail("Morphology should have been rejected.")
except InvalidMorphology as e:
self.assertNodeErrors(
e.validation_errors,
"Type 1 can only have a parent of the following types:", [[2]])
def test_basal_dendrite_traceable_back_to_soma_invalid(self):
try:
nodes = [
test_node(id=1, type=SOMA, parent_node_id=-1),
test_node(id=2, type=AXON, parent_node_id=1),
test_node(id=3, type=BASAL_DENDRITE, parent_node_id=-1)
]
test_tree(nodes, strict_validation=True)
self.fail("Morphology should have been rejected.")
except InvalidMorphology as e:
self.assertNodeErrors(e.validation_errors,
"must be traceable back to the soma", [[3]])
def test_any_radius_valid_for_axon(self):
for valid_radius in [-10, 0, 3, float('inf')]:
nodes = [
test_node(id=1, type=SOMA, radius=36, parent_node_id=-1),
test_node(id=2,
type=AXON,
radius=valid_radius,
parent_node_id=1)
]
errors = rv.validate_radius_threshold(
test_tree(nodes, strict_validation=False))
self.assertEqual(len(errors), 0)
def test_number_of_apical_dendrite_with_parent_of_soma_invalid(self):
try:
nodes = [
test_node(id=1, type=SOMA, parent_node_id=-1),
test_node(id=2, type=APICAL_DENDRITE, parent_node_id=1),
test_node(id=3, type=APICAL_DENDRITE, parent_node_id=1)
]
test_tree(nodes, strict_validation=True)
self.fail("Morphology should have been rejected.")
except InvalidMorphology as e:
self.assertNodeErrors(
e.validation_errors,
"Nodes of type 4 can only have 1 parent of type 1", [[2], [3]])
def test_invalid_radius_for_dendrite(self):
for valid_radius in [20.002, 35, 40, 100, 1000]:
for dendrite in [BASAL_DENDRITE, APICAL_DENDRITE]:
nodes = [
test_node(id=1, type=SOMA, radius=36, parent_node_id=-1),
test_node(id=2,
type=dendrite,
radius=valid_radius,
parent_node_id=1)
]
errors = rv.validate_radius_threshold(
test_tree(nodes, strict_validation=False))
self.assertNodeErrors(errors, "The radius must be", [[2]])
def test_valid_radius_for_dendrite(self):
for valid_radius in [-1, 0, 10, 16, 19.999]:
for dendrite in [BASAL_DENDRITE, APICAL_DENDRITE]:
nodes = [
test_node(id=1, type=SOMA, radius=36, parent_node_id=-1),
test_node(id=2,
type=dendrite,
radius=valid_radius,
parent_node_id=1)
]
errors = rv.validate_radius_threshold(
test_tree(nodes, strict_validation=False))
self.assertEqual(len(errors), 0)
def test_basal_dendrite_node_with_invalid_parent_type_independent(self):
try:
nodes = [
test_node(id=1, type=SOMA, parent_node_id=-1),
test_node(id=2, type=AXON, parent_node_id=1),
test_node(id=3, type=BASAL_DENDRITE, parent_node_id=-1)
]
test_tree(nodes, strict_validation=True)
self.fail("Morphology should have been rejected.")
except InvalidMorphology as e:
self.assertNodeErrors(
e.validation_errors,
"Type 3 can only have a parent of the following types:", [[3]])
def test_coordinate_corresponding_to_dendrite_tips_type_20_valid(self):
for dendrite_type in [BASAL_DENDRITE, APICAL_DENDRITE]:
nodes = [
test_node(id=1, type=SOMA, parent_node_id=-1),
test_node(id=2,
type=dendrite_type,
x=0,
y=0,
z=0,
parent_node_id=1)
]
mv.validate([test_marker(x=1, y=0, z=0, name=AXON)],
test_tree(nodes))
def test_immediate_child_of_soma_has_more_than_one_child(self):
try:
nodes = [
test_node(id=1, type=SOMA, parent_node_id=-1),
test_node(id=2, type=APICAL_DENDRITE, parent_node_id=1),
test_node(id=3, type=APICAL_DENDRITE, parent_node_id=2),
test_node(id=4, type=APICAL_DENDRITE, parent_node_id=2)
]
test_tree(nodes, strict_validation=True)
self.fail("Morphology should have been rejected.")
except InvalidMorphology as e:
self.assertNodeErrors(e.validation_errors,
"Immediate children of soma cannot branch",
[[2]])
def test_multiple_axon_initiation_points_not_valid(self):
try:
nodes = [
test_node(id=1, type=SOMA, parent_node_id=-1),
test_node(id=2, type=AXON, parent_node_id=1),
test_node(id=3, type=AXON, parent_node_id=1)
]
test_tree(nodes, strict_validation=True)
self.fail("Morphology should have been rejected.")
except InvalidMorphology as e:
self.assertNodeErrors(
e.validation_errors,
"Axon can only have one parent of type basal dendrite or soma",
[[2], [3]])
def test_decreasing_radius_when_going_away_from_soma_dendrite_one_branch_valid(
self):
for dendrite_type in [BASAL_DENDRITE, APICAL_DENDRITE]:
nodes = [
test_node(id=1, type=SOMA, radius=36.0, parent_node_id=-1),
test_node(id=2,
type=dendrite_type,
radius=2.0,
parent_node_id=1),
test_node(id=3,
type=dendrite_type,
radius=4.0,
parent_node_id=2)
]
test_tree(nodes, strict_validation=True)
def test_distance_between_connected_nodes_valid(self):
nodes = [
test_node(id=1, type=SOMA, parent_node_id=-1),
test_node(id=2,
type=AXON,
x=3188.34,
y=2891.57,
z=88.9906,
parent_node_id=1),
test_node(id=3,
type=AXON,
x=3198.34,
y=2888.57,
z=89.9906,
parent_node_id=2)
]
test_tree(nodes, strict_validation=True)
def test_invalid_radius_multiple_types(self):
try:
nodes = [
test_node(id=1, type=SOMA, radius=2.0, parent_node_id=-1),
test_node(id=2, type=AXON, radius=2.0, parent_node_id=-1),
test_node(id=3,
type=BASAL_DENDRITE,
radius=32.0,
parent_node_id=1),
test_node(id=4,
type=APICAL_DENDRITE,
radius=32.0,
parent_node_id=1)
]
test_tree(nodes, strict_validation=True)
self.fail("Morphology should have been rejected.")
except InvalidMorphology as e:
self.assertNodeErrors(e.validation_errors, "The radius must be",
[[1], [3], [4]])
