def test_intact_branching_angles():
obj = Repair(SIMPLE_PATH)
obj._fill_repair_type_map()
branches = [neurite.root_node for neurite in obj.neuron.neurites]
angles = obj._intact_branching_angles(branches)
assert_array_almost_equal(angles[test_module.RepairType.basal][0],
[1.5707963267948966, 1.5707963267948966])
def test__compute_sholl_data():
obj = Repair(SIMPLE_PATH)
obj._fill_repair_type_map()
branches = [neurite.root_node for neurite in obj.neuron.neurites]
sholl_data = obj._compute_sholl_data(branches)
assert_dict_equal(sholl_data[RepairType.basal][0][0], {
Action.TERMINATION: 0,
Action.CONTINUATION: 0,
Action.BIFURCATION: 1
})
assert_dict_equal(sholl_data[RepairType.basal][0][1], {
Action.TERMINATION: 2,
Action.CONTINUATION: 0,
Action.BIFURCATION: 0
})
assert_dict_equal(sholl_data[RepairType.oblique], {})
assert_dict_equal(
sholl_data[RepairType.axon], {
0: {
0: {
Action.BIFURCATION: 1,
Action.CONTINUATION: 0,
Action.TERMINATION: 0
},
1: {
Action.BIFURCATION: 0,
Action.CONTINUATION: 0,
Action.TERMINATION: 2
}
}
})
def test__grow():
obj = Repair(SIMPLE_PATH, seed=1)
leaf = obj.neuron.sections[2]
obj.repair_type_map = {
section: RepairType.basal
for section in obj.neuron.sections
}
obj.info = {
'sholl': {
RepairType.basal: {
0: {
1: {
Action.BIFURCATION: 0.5,
Action.TERMINATION: 0,
Action.CONTINUATION: 0.5
}
}
}
},
'dendritic_sections': obj.neuron.sections,
'intact_branching_angles': {
RepairType.basal: {
1: [0.2]
}
}
}
obj.current_trunk_radius = 1.0
obj._grow(leaf, 0, obj.neuron.soma.center)
assert_equal(len(obj.neuron.sections), 8)
def test_best_case_angle_data():
obj = Repair(SIMPLE_PATH)
obj.info = {
'intact_branching_angles': {
SectionType.axon: {
0: [1, 2, 3],
1: [2, 2],
2: []
}
}
}
# Use exact data for this specific branching angle
assert_array_equal(obj._best_case_angle_data(SectionType.axon, 0),
[1, 2, 3])
# No info for this branching angle, use aggregate data
assert_array_equal(obj._best_case_angle_data(SectionType.axon, 2),
[1, 2, 3, 2, 2])
def test__fill_repair_type_map():
obj = Repair(DATA_PATH / 'repair_type.asc')
obj.apical_section = obj.neuron.sections[3]
# Pre check to be sure that the apical point is the one it should be
assert_array_almost_equal(
obj.apical_section.points,
np.array([[0., 0., 4., 1.], [0., 0., 0., 0.5], [1., 0., 0., 0.5]],
dtype=np.float32))
obj._fill_repair_type_map()
assert_dict_equal({sec.id: v
for sec, v in obj.repair_type_map.items()}, {
0: test_module.RepairType.axon,
1: test_module.RepairType.trunk,
2: test_module.RepairType.oblique,
3: test_module.RepairType.trunk,
4: test_module.RepairType.tuft,
5: test_module.RepairType.tuft,
6: test_module.RepairType.basal,
})
def test_get_order_offset():
obj = Repair(SIMPLE_PATH)
section = obj.neuron.neurites[0].root_node.children[0]
obj.repair_type_map = {section: RepairType.basal}
assert_equal(obj._get_order_offset(section), 0)
obj.repair_type_map = {section: RepairType.oblique}
assert_equal(obj._get_order_offset(section), 1)
def test_get_origin():
obj = Repair(SIMPLE)
section = obj.neuron.section(1)
obj.repair_type_map = {section: RepairType.basal}
assert_array_equal(obj._get_origin(section), [0, 0, 0])
obj.repair_type_map = {section: RepairType.oblique}
assert_array_equal(obj._get_origin(section), [0, 5, 0])
def test__compute_statistics_for_intact_subtrees():
input_file = DATA_PATH / 'neuron-slice.h5'
points = test_module.CutPlane.find(input_file,
bin_width=15).cut_leaves_coordinates
obj = Repair(input_file, cut_leaves_coordinates=points)
obj._fill_repair_type_map()
obj._fill_statistics_for_intact_subtrees()
with open(DATA_PATH / 'neuron-slice-sholl-data.json') as f:
expected = json.load(f)
basal_data = expected['SectionType.basal_dendrite']
actual = json_compatible_dict(obj.info['sholl'][RepairType.basal])
for layer in basal_data:
for order in basal_data[layer]:
for action in basal_data[layer][order]:
assert_equal(basal_data[layer][order][action],
actual[layer][order][action])
def test__find_intact_sub_trees():
obj = Repair(SIMPLE_PATH)
obj.cut_leaves = np.array([[2, 2, 2]])
obj._fill_repair_type_map()
assert_equal(len(obj._find_intact_sub_trees()), 2)
points = test_module.CutPlane.find(SLICE,
bin_width=15).cut_leaves_coordinates
obj = Repair(SLICE_PATH, cut_leaves_coordinates=points)
obj._fill_repair_type_map()
intact_sub_trees = obj._find_intact_sub_trees()
assert_array_equal([section.id for section in intact_sub_trees], [0, 34])
obj = Repair(DATA_PATH / 'test-cut-apical' / 'simple-apical-cut.swc',
cut_leaves_coordinates=[[1.0, 30.0, 0.0]])
obj._fill_repair_type_map()
intact_sub_trees = obj._find_intact_sub_trees()
assert_array_equal([section.id for section in intact_sub_trees], [1, 0, 3])
assert_array_equal(
[obj.repair_type_map[section] for section in intact_sub_trees],
[RepairType.basal, RepairType.axon, RepairType.tuft])
filename = DATA_PATH / 'no-intact-basals.h5'
points = test_module.CutPlane.find(filename,
bin_width=15).cut_leaves_coordinates
obj = Repair(filename, cut_leaves_coordinates=points)
obj._fill_repair_type_map()
intact_sub_trees = obj._find_intact_sub_trees()
basals = [
section for section in intact_sub_trees
if section.type == NeuriteType.basal_dendrite
]
assert_equal(len(basals), 78)
def test__external_apical_point():
obj = Repair(DATA_PATH / 'repair_type.asc', apical_point=[1.0, 0.0, 0.0])
assert_array_almost_equal(
obj.apical_section.points,
np.array([[0., 0., 4., 1.], [0., 0., 0., 0.5], [1., 0., 0., 0.5]],
dtype=np.float32))