def test__repair():
neuron = load_neuron(Path(DATA_PATH, 'valid.h5'))
axon = neuron.root_sections[0]
assert_equal(axon.type, SectionType.axon)
test_module.repair(neuron, axon, [axon], [axon], set(), y_extent=10000)
assert_equal(len(axon.children), 1)
assert_array_equal(axon.children[0].points[0], axon.points[-1])
ok_(not diff(neuron, DATA_PATH / 'axon-repair.h5'))
def test__repair_no_intact_axon():
filename = Path(DATA_PATH, 'valid.h5')
neuron = load_neuron(filename)
axon = neuron.root_sections[0]
used_axon_branches = set()
test_module.repair(neuron,
axon, [], [axon],
used_axon_branches,
y_extent=10000)
# There should not be any repair
ok_(not diff(neuron, filename))
def run(self, outputfile: Path, plot_file: Optional[Path] = None):
'''Run'''
if self.cut_leaves.size == 0:
L.warning('No cut leaves. Nothing to repair for morphology %s',
self.inputfile)
self.neuron.write(outputfile)
return
# See https://github.com/BlueBrain/MorphIO/issues/161
keep_axons_alive = list()
for axon_donor in self.axon_donors:
if self.legacy_detection:
plane = CutPlane.find_legacy(axon_donor, 'z')
else:
plane = CutPlane.find(axon_donor)
keep_axons_alive.append(plane)
self.donated_intact_axon_sections.extend([
section for section in iter_sections(plane.morphology)
if section.type == SectionType.axon
and is_branch_intact(section, plane.cut_leaves_coordinates)
])
self._fill_repair_type_map()
self._fill_statistics_for_intact_subtrees()
intact_axonal_sections = [
section for section in iter_sections(self.neuron)
if section.type == SectionType.axon
and is_branch_intact(section, self.cut_leaves)
]
# BlueRepairSDK used to have a bounding cylinder filter but
# I don't know what is it good at so I have commented
# the only relevant line
# bounding_cylinder_radius = 10000
cut_sections_in_bounding_cylinder = [
section for section in iter_sections(self.neuron) if
(is_cut_section(section, cut_points=self.cut_leaves)
# and np.linalg.norm(section.points[-1, COLS.XZ]) < bounding_cylinder_radius
)
]
used_axon_branches = set()
cut_leaves_ids = {
section: len(section.points)
for section in cut_sections_in_bounding_cylinder
}
for section in sorted(cut_sections_in_bounding_cylinder,
key=section_path_length):
type_ = self.repair_type_map[section]
if not self.repair_flags.get(type_, True):
continue
L.info('Repairing: %s, section id: %s', type_, section.id)
if type_ in {
RepairType.basal, RepairType.oblique, RepairType.tuft
}:
origin = self._get_origin(section)
if section.type == NeuriteType.basal_dendrite:
_continuation(section, origin)
self._grow(section, self._get_order_offset(section), origin)
elif type_ == RepairType.axon:
axon.repair(self.neuron, section, intact_axonal_sections,
self.donated_intact_axon_sections,
used_axon_branches, self.max_y_extent)
elif type_ == RepairType.trunk:
L.info('Trunk repair is not (nor has ever been) implemented')
else:
raise Exception('Unknown type: {}'.format(type_))
if plot_file is not None:
try:
from neuror.view import plot_repaired_neuron
plot_repaired_neuron(self.neuron, cut_leaves_ids, plot_file)
except ImportError:
L.warning(
'Skipping writing plots as [plotly] extra is not installed'
)
self.neuron.write(outputfile)
L.info('Repair successful for %s', self.inputfile)