def repair_all(input_dir,
output_dir,
seed=0,
axons=None,
cut_points_dir=None,
plots_dir=None):
'''Repair all morphologies in input folder'''
for inputfilename in iter_morphology_files(input_dir):
outfilename = Path(output_dir, inputfilename.name)
if cut_points_dir:
cut_points = pd.read_csv(
Path(cut_points_dir, inputfilename.name).with_suffix('.csv'))
else:
cut_points = None
if plots_dir is not None:
name = 'neuron_{}.html'.format(
Path(inputfilename).stem.replace(' ', '_'))
plot_file = str(Path(plots_dir, name))
else:
plot_file = None
try:
repair(inputfilename,
outfilename,
seed=seed,
axons=axons,
cut_leaves_coordinates=cut_points,
plot_file=plot_file)
except Exception as e: # noqa, pylint: disable=broad-except
L.warning('%s failed', inputfilename)
L.warning(e, exc_info=True)
def test_repair_axon():
filename = DATA_PATH / 'real-with-axon.asc'
with TemporaryDirectory('test-cli-axon') as tmp_folder:
outfilename = Path(tmp_folder, 'out.asc')
test_module.repair(filename, outfilename, axons=[filename])
neuron_in = load_neuron(filename)
neuron_out = load_neuron(outfilename)
axon = neuron_out.section(40)
ok_(axon.type == NeuriteType.axon)
assert_array_equal(
neuron_in.section(40).points[0],
neuron_out.section(40).points[0])
ok_(
len(neuron_out.section(40).points) > len(
neuron_in.section(40).points))
# Test disactivating the axon repair
repair_flags = {RepairType.axon: False}
test_module.repair(filename,
outfilename,
axons=[filename],
repair_flags=repair_flags)
neuron_out = load_neuron(outfilename)
axon = neuron_out.section(40)
ok_(axon.type == NeuriteType.axon)
assert_array_equal(
neuron_in.section(40).points[0],
neuron_out.section(40).points[0])
ok_(
len(neuron_out.section(40).points) == len(
neuron_in.section(40).points),
'The section should not have been regrown')
def file(input_file, output_file, plot_file, axon_donor, cut_file):
'''Repair dendrites of a cut neuron'''
from neuror.main import repair # pylint: disable=redefined-outer-name
import pandas
if cut_file:
cut_points = pandas.read_csv(Path(cut_file).with_suffix('.csv')).values
else:
cut_points = None
repair(input_file,
output_file,
axons=axon_donor,
cut_leaves_coordinates=cut_points,
plot_file=plot_file)
def test_repair_no_trunk():
'''Test repair when the morph has oblique sections but no trunk'''
filename = DATA_PATH / 'Fluo42_right.h5'
with TemporaryDirectory('test-no-trunk') as tmp_folder:
outfilename = Path(tmp_folder, 'out.asc')
test_module.repair(filename, outfilename, legacy_detection=True)
def test_repair_no_intact_axon():
filename = DATA_PATH / 'no-intact-basals.h5'
with TemporaryDirectory('test-cli-axon') as tmp_folder:
outfilename = Path(tmp_folder, 'out.asc')
test_module.repair(filename, outfilename, axons=[filename])