def test_annotate():
correct_result = """
(Circle1 ; MUK_ANNOTATION
(Color Blue) ; MUK_ANNOTATION
(Name "narrow start") ; MUK_ANNOTATION
( 0.00 0.00 2.00 0.50) ; MUK_ANNOTATION
) ; MUK_ANNOTATION
"""
checkers = {has_no_narrow_start: {"name": "narrow start",
"label": "Circle1",
"color": "Blue"}}
neuron = load_neuron(SWC_PATH / 'narrow_start.swc')
results = [checker(neuron) for checker in checkers.keys()]
assert annotate(results, checkers.values()) == correct_result
def test_annotate():
correct_result = """
(Circle1 ; MUK_ANNOTATION
(Color Blue) ; MUK_ANNOTATION
(Name "narrow start") ; MUK_ANNOTATION
(0.0 0.0 0.0 0.50) ; MUK_ANNOTATION
(0.0 0.0 0.0 0.50) ; MUK_ANNOTATION
) ; MUK_ANNOTATION
"""
checkers = {
has_no_narrow_start: {
"name": "narrow start",
"label": "Circle1",
"color": "Blue"
}
}
neuron = load_neuron('test_data/swc/Neuron_zero_radius.swc')
results = [checker(neuron) for checker in checkers.keys()]
nt.assert_equal(annotate(results, checkers.values()), correct_result)
def annotate_neurolucida(morph_path, checkers=None):
"""Annotate errors on a morphology in neurolucida format.
Args:
morph_path (str): absolute path to an ascii morphology
checkers (dict): dict of checker functons from neurom with function as keys
and marker data in a dict as values, if None, default checkers are used
Default checkers include:
- fat ends
- z-jumps
- narrow start
- dangling branch
- multifurcation
Returns:
annotations to append to .asc file
dict of error summary
dict of error markers
"""
if checkers is None:
checkers = {
nc.has_no_fat_ends: {
"name": "fat end",
"label": "Circle3",
"color": "Blue"
},
partial(nc.has_no_jumps, axis="z"): {
"name": "zjump",
"label": "Circle2",
"color": "Green",
},
nc.has_no_narrow_start: {
"name": "narrow start",
"label": "Circle1",
"color": "Blue"
},
nc.has_no_dangling_branch: {
"name": "dangling",
"label": "Circle6",
"color": "Magenta"
},
nc.has_multifurcation: {
"name": "Multifurcation",
"label": "Circle8",
"color": "Yellow",
},
}
def _try(checker, neuron):
"""Try to apply a checker, returns True if exception raised, so the checker is bypassed."""
try:
return checker(neuron)
except Exception as e: # pylint: disable=broad-except
L.exception("%s failed on %s", checker, morph_path)
L.exception(e, exc_info=True)
return CheckResult(True)
neuron = load_neuron(morph_path)
results = [_try(checker, neuron) for checker in checkers]
markers = [
dict(setting, data=result.info)
for result, setting in zip(results, checkers.values())
if not result.status
]
summary = {
setting["name"]: len(result.info)
for result, setting in zip(results, checkers.values()) if result.info
}
return annotate(results, checkers.values()), summary, markers