def setUp(self):
self.morphology = Morphology(
basic_nodes(),
node_id_cb=lambda node: node["id"],
parent_id_cb=lambda node: node["parent_id"],
)
self.data = Data(self.morphology, relative_soma_depth=0.25)
def test_select_features_only(self):
run = (FeatureExtractionRun(Data(
self.morphology, a=2,
b=4)).select_marks([self.amark, self.bmark
]).select_features([self.foo, self.baz],
only_marks={self.bmark}))
self.assertEqual(set(run.selected_features), set())
def test_extract(self):
run = FeatureExtractionRun(Data(self.morphology, a=2, b=4))
run.selected_features = [self.foo]
run.extract()
self.assertEqual(run.results["foo"], True)
self.assertEqual(len(run.results), 1)
def test_normalized_depth_histograms_across_layers(self):
_data = Data(self.morphology,
reference_layer_depths=self.reference_depths,
layered_point_depths=self.point_depths)
obtained = layer.normalized_depth_histogram(_data, bin_size=10)
expected = {
"1":
layer.LayerHistogram(counts=np.array(
[0, 0, 0, 0, 1, 0, 1, 0, 1, 0]),
bin_edges=np.arange(0, 110, 10)),
"2":
layer.LayerHistogram(counts=np.array(
[1, 0, 0, 0, 0, 0, 0, 1, 0, 1]),
bin_edges=np.arange(100, 210, 10)),
"wm":
layer.LayerHistogram(counts=np.array(
[0, 1, 0, 0, 1, 0, 0, 0, 0, 0]),
bin_edges=np.arange(200, 310, 10))
}
self.assertEqual(set(expected.keys()), set(obtained.keys()))
for key, obt in obtained.items():
expt = expected[key]
print(key, expt.counts, obt.counts)
assert np.allclose(expt.counts, obt.counts)
assert np.allclose(expt.bin_edges, obt.bin_edges)
def setup_data(
reconstruction: Dict[str, Any],
global_parameters: Dict[str, Any]
) -> Tuple[str, Data]:
""" Construct a Data for extracting features from a single reconstruction.
Parameters
----------
reconstruction : The reconstruction to be setup. Must specify an swc_path
global_parameters : any cross-reconstruction feature parameters
Returns
-------
identifier : a label for this reconstruction
data suitable for feature extraction
"""
parameters: Dict[str, Any] = {}
identifier = reconstruction.get("identifier", reconstruction.get("swc_path"))
swc_path = reconstruction.pop("swc_path")
morphology = morphology_from_swc(swc_path)
parameters.update(hydrate_parameters(global_parameters))
parameters.update(hydrate_parameters(reconstruction))
return identifier, Data(morphology, **parameters)
def setUp(self):
# 180 deg at soma
# axon - 90 deg local, 60 deg remote
# basal - 90 deg local, 90 deg remote
self.morphology = (
MorphologyBuilder()
.root(0, 0, 0)
.axon(0, 0, 1)
.axon(0, 1, 2)
.axon(0, 1, 1 + np.sqrt(3)).up(2)
.axon(0, -1, 2)
.axon(0, -1, 1 + np.sqrt(3)).up(3)
.basal_dendrite(0, 0, -1)
.basal_dendrite(0, 1, -2).up()
.basal_dendrite(0, -1, -2)
.build()
)
nodes = self.morphology.nodes()
for node in nodes:
print(node)
self.data = Data(self.morphology)
self.local_specialized = specialize(
bf.mean_bifurcation_angle_local,
{AxonSpec, ApicalDendriteSpec, BasalDendriteSpec}
)
self.remote_specialized = specialize(
bf.mean_bifurcation_angle_remote,
{AxonSpec, ApicalDendriteSpec, BasalDendriteSpec}
)
def setUp(self):
# morphology with 3/4 axons below soma in z
self.morphology = Morphology(
[
{
"id": 0,
"parent_id": -1,
"type": SOMA,
"x": 0,
"y": 0,
"z": 100,
"radius": 5
},
{
"id": 1,
"parent_id": 0,
"type": AXON,
"x": 0,
"y": 0,
"z": 110,
"radius": 1
},
{
"id": 2,
"parent_id": 1,
"type": AXON,
"x": 0,
"y": 0,
"z": 90,
"radius": 1
},
{
"id": 3,
"parent_id": 2,
"type": AXON,
"x": 0,
"y": 0,
"z": 80,
"radius": 1
},
{
"id": 4,
"parent_id": 3,
"type": AXON,
"x": 0,
"y": 0,
"z": 70,
"radius": 1
},
],
node_id_cb=lambda node: node["id"],
parent_id_cb=lambda node: node["parent_id"],
)
self.data = Data(self.morphology)
def test_earth_movers_distance(self):
_data = Data(self.morphology,
reference_layer_depths=self.reference_depths,
layered_point_depths=self.point_depths)
obtained = layer.earth_movers_distance(_data, [AXON],
[APICAL_DENDRITE])
self.assertEqual(set(obtained.keys()), {"2"})
self.assertEqual(obtained["2"].result, 17)
class TestDefault(unittest.TestCase):
fe = FeatureExtractor()
for feature in default_features:
fe.register_features([feature])
data = Data(test_morphology_large())
feature_extraction_run = fe.extract(data)
results = feature_extraction_run.results
pass
def setUp(self):
# Create an axon that branches once,
# and a basal dendrite that has a bifurcation and a trifurcation
self.morphology = (MorphologyBuilder(
).root().axon().axon().axon().axon().up().axon().up(4).basal_dendrite(
).basal_dendrite().basal_dendrite().up().basal_dendrite(
).basal_dendrite().up().basal_dendrite().up().basal_dendrite().build())
self.data = Data(self.morphology)
self.num_nodes = specialize(ic.num_nodes, NEURITE_SPECIALIZATIONS)
self.num_tips = specialize(ic.num_tips, NEURITE_SPECIALIZATIONS)
self.num_branches = specialize(ic.num_branches,
NEURITE_SPECIALIZATIONS)
self.mean_fragmentation = specialize(ic.mean_fragmentation,
NEURITE_SPECIALIZATIONS)
self.max_branch_order = specialize(ic.max_branch_order,
NEURITE_SPECIALIZATIONS)
def test_additional_data(self):
obt = Data(self.morphology, a=1, b=2)
self.assertEqual(obt.a, 1)
self.assertEqual(obt.b, 2)
self.assertEqual(len(obt.morphology.nodes()), 4)
def setUp(self):
# Create an axon that extends positively,
# and a basal dendrite that extends negatively
self.one_dim_neuron = Morphology(
[
{
"id": 0,
"parent_id": -1,
"type": SOMA,
"x": 0,
"y": 100,
"z": 0,
"radius": 10
},
# Axon node [100, 125, 150, 175, 200]
{
"id": 1,
"parent_id": 0,
"type": AXON,
"x": 0,
"y": 100,
"z": 0,
"radius": 3
},
{
"id": 2,
"parent_id": 1,
"type": AXON,
"x": 0,
"y": 125,
"z": 0,
"radius": 3
},
{
"id": 3,
"parent_id": 2,
"type": AXON,
"x": 0,
"y": 150,
"z": 0,
"radius": 3
},
{
"id": 4,
"parent_id": 3,
"type": AXON,
"x": 0,
"y": 175,
"z": 0,
"radius": 3
},
{
"id": 5,
"parent_id": 4,
"type": AXON,
"x": 0,
"y": 200,
"z": 0,
"radius": 3
},
# Basal node [100, 75, 50]
{
"id": 11,
"parent_id": 0,
"type": BASAL_DENDRITE,
"x": 0,
"y": 100,
"z": 0,
"radius": 3
},
{
"id": 12,
"parent_id": 11,
"type": BASAL_DENDRITE,
"x": 0,
"y": 75,
"z": 0,
"radius": 3
},
{
"id": 13,
"parent_id": 12,
"type": BASAL_DENDRITE,
"x": 0,
"y": 50,
"z": 0,
"radius": 3
},
],
node_id_cb=lambda node: node["id"],
parent_id_cb=lambda node: node["parent_id"],
)
self.one_dim_neuron_data = Data(self.one_dim_neuron)
self.dimension_features = nested_specialize(
di.dimension,
[COORD_TYPE_SPECIALIZATIONS, NEURITE_SPECIALIZATIONS])
def setUp(self):
self.one_dim_neuron = Morphology([
{
"id": 0,
"parent_id": -1,
"type": SOMA,
"x": 0,
"y": 0,
"z": 100,
"radius": 1
},
{
"id": 1,
"parent_id": 0,
"type": AXON,
"x": 0,
"y": 0,
"z": 101,
"radius": 1
},
{
"id": 2,
"parent_id": 0,
"type": APICAL_DENDRITE,
"x": 0,
"y": 0,
"z": 102,
"radius": 1
},
{ # bifurcates and is within 120
"id": 3,
"parent_id": 1,
"type": AXON,
"x": 0,
"y": 0,
"z": 110,
"radius": 1
},
{ # This is the farthest node from the root
"id": 4,
"parent_id": 3,
"type": AXON,
"x": 0,
"y": 0,
"z": 140,
"radius": 1
},
{ # bifurcates, and is beyond 120
"id": 5,
"parent_id": 3,
"type": AXON,
"x": 0,
"y": 0,
"z": 130,
"radius": 1
},
{
"id": 6,
"parent_id": 5,
"type": AXON,
"x": 0,
"y": 0,
"z": 135,
"radius": 1
},
{
"id": 7,
"parent_id": 5,
"type": AXON,
"x": 0,
"y": 0,
"z": 136,
"radius": 1
},
{ # bifurcates and is beyond 120
"id": 8,
"parent_id": 2,
"type": APICAL_DENDRITE,
"x": 0,
"y": 0,
"z": 125,
"radius": 1
},
{
"id": 9,
"parent_id": 8,
"type": APICAL_DENDRITE,
"x": 0,
"y": 0,
"z": 126,
"radius": 1
},
{
"id": 10,
"parent_id": 8,
"type": APICAL_DENDRITE,
"x": 0,
"y": 0,
"z": 127,
"radius": 1
},
],
node_id_cb=lambda node: node["id"],
parent_id_cb=lambda node: node["parent_id"],
)
self.one_dim_neuron_data = Data(self.one_dim_neuron)
self.neurite_features = specialize(
bf.num_outer_bifurcations,
{AxonSpec, ApicalDendriteSpec, BasalDendriteSpec}
)
def test_get_morphology(self):
aa = get_morphology(Data(self.morphology))
bb = get_morphology(self.morphology)
self.assertEqual(aa.__class__.__name__, "Morphology")
self.assertEqual(bb.__class__.__name__, "Morphology")
def test_select_marks(self):
run = (FeatureExtractionRun(Data(
self.morphology, a=2, b=4)).select_marks([self.amark, self.bmark]))
self.assertEqual(run.selected_marks, {self.amark})
def test_hash(self):
dat = Data(self.morphology)
self.assertEqual({dat}, {dat})
def setUp(self):
# Create an Axon that extends y 100 to 120
# and Basal Dendrite that extends y 100 to 110 and 100 to 80
# So that 3/4 axon nodes overlap, 1/4 are above basal
# and that 3/6 basal are below, and 3/6 overlap
self.one_dim_neuron = Morphology(
[
{
"id": 0,
"parent_id": -1,
"type": SOMA,
"x": 0,
"y": 100,
"z": 0,
"radius": 10
},
# Axon y 100 to 150
{
"id": 1,
"parent_id": 0,
"type": AXON,
"x": 0,
"y": 101,
"z": 0,
"radius": 3
},
{
"id": 2,
"parent_id": 1,
"type": AXON,
"x": 0,
"y": 102,
"z": 0,
"radius": 3
},
{
"id": 3,
"parent_id": 2,
"type": AXON,
"x": 0,
"y": 110,
"z": 0,
"radius": 3
},
{
"id": 4,
"parent_id": 3,
"type": AXON,
"x": 0,
"y": 120,
"z": 0,
"radius": 3
},
{
"id": 11,
"parent_id": 0,
"type": BASAL_DENDRITE,
"x": 0,
"y": 101,
"z": 0,
"radius": 3
},
{
"id": 12,
"parent_id": 11,
"type": BASAL_DENDRITE,
"x": 0,
"y": 102,
"z": 0,
"radius": 3
},
{
"id": 13,
"parent_id": 12,
"type": BASAL_DENDRITE,
"x": 0,
"y": 110,
"z": 0,
"radius": 3
},
# Basal Dendrite y 100 to 80
{
"id": 14,
"parent_id": 12,
"type": BASAL_DENDRITE,
"x": 0,
"y": 99,
"z": 0,
"radius": 3
},
{
"id": 15,
"parent_id": 14,
"type": BASAL_DENDRITE,
"x": 0,
"y": 90,
"z": 0,
"radius": 3
},
{
"id": 16,
"parent_id": 15,
"type": BASAL_DENDRITE,
"x": 0,
"y": 80,
"z": 0,
"radius": 3
},
],
node_id_cb=lambda node: node["id"],
parent_id_cb=lambda node: node["parent_id"],
)
self.one_dim_neuron_data = Data(self.one_dim_neuron)
self.overlap_features = nested_specialize(
ol.overlap,
[
NEURITE_SPECIALIZATIONS, #.remove(AllNeuriteSpec),
NEURITE_COMPARISON_SPECIALIZATIONS
] #.remove(AllNeuriteCompareSpec)]
)
