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):
# 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)
num_outer_bifurcations, mean_bifurcation_angle_local,
mean_bifurcation_angle_remote)
from neuron_morphology.features.size import (total_length, total_surface_area,
total_volume, mean_diameter,
mean_parent_daughter_ratio,
max_euclidean_distance)
from neuron_morphology.features.path import (max_path_distance,
early_branch_path,
mean_contraction)
from neuron_morphology.features.statistics.overlap import overlap
from neuron_morphology.features.statistics.moments import moments
default_features = [
nested_specialize(dimension,
[COORD_TYPE_SPECIALIZATIONS, NEURITE_SPECIALIZATIONS]),
specialize(num_nodes, NEURITE_SPECIALIZATIONS),
specialize(num_branches, NEURITE_SPECIALIZATIONS),
specialize(num_tips, NEURITE_SPECIALIZATIONS),
specialize(mean_fragmentation, NEURITE_SPECIALIZATIONS),
specialize(max_branch_order, NEURITE_SPECIALIZATIONS),
specialize(num_outer_bifurcations, NEURITE_SPECIALIZATIONS),
specialize(mean_bifurcation_angle_local, NEURITE_SPECIALIZATIONS),
specialize(mean_bifurcation_angle_remote, NEURITE_SPECIALIZATIONS),
specialize(total_length, NEURITE_SPECIALIZATIONS),
specialize(total_surface_area, NEURITE_SPECIALIZATIONS),
specialize(total_volume, NEURITE_SPECIALIZATIONS),
specialize(mean_diameter, NEURITE_SPECIALIZATIONS),
specialize(mean_parent_daughter_ratio, NEURITE_SPECIALIZATIONS),
specialize(max_euclidean_distance, NEURITE_SPECIALIZATIONS),
max_path_distance, early_branch_path, mean_contraction,
nested_specialize(
def test_specialize_marked(self):
multiply = MarkedFeature({self.does_math}, self.multiply)
multiply_by_4 = specialize(multiply, {self.by4})["By4.multiply"]
self.assertEqual(multiply_by_4(2), 8)
self.assertEqual(multiply_by_4.marks, {self.uses_four, self.does_math})
def test_specialize_fn(self):
multipliers = specialize(self.multiply, {self.by4})
multiply_by_4 = multipliers["By4.multiply"]
self.assertEqual(multiply_by_4(2), 8)
self.assertEqual(multiply_by_4.marks, {self.uses_four})
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}
)