def test_has_sequential_ids_bad_data():
f = os.path.join(SWC_PATH, 'Neuron_missing_ids.swc')
ok, ids = check.has_sequential_ids(load_data(f))
nt.ok_(not ok)
nt.ok_(ids == [6, 217, 428, 639])
def test_has_sequential_ids_bad_data():
f = os.path.join(SWC_PATH, 'Neuron_missing_ids.swc')
ok, ids = check.has_sequential_ids(load_data(f))
nt.ok_(not ok)
nt.ok_(ids == [6, 217, 428, 639])
def test_has_sequential_ids_good_data():
files = [
os.path.join(SWC_PATH, f) for f in [
'Neuron.swc', 'Single_apical_no_soma.swc', 'Single_apical.swc',
'Single_basal.swc', 'Single_axon.swc', 'Neuron_zero_radius.swc',
'sequential_trunk_off_0_16pt.swc',
'sequential_trunk_off_1_16pt.swc',
'sequential_trunk_off_42_16pt.swc',
'Neuron_no_missing_ids_no_zero_segs.swc'
]
]
for f in files:
ok, ids = check.has_sequential_ids(load_data(f))
nt.ok_(ok)
nt.ok_(len(ids) == 0)
def test_has_sequential_ids_good_data():
files = [os.path.join(SWC_PATH, f)
for f in ['Neuron.swc',
'Single_apical_no_soma.swc',
'Single_apical.swc',
'Single_basal.swc',
'Single_axon.swc',
'Neuron_zero_radius.swc',
'sequential_trunk_off_0_16pt.swc',
'sequential_trunk_off_1_16pt.swc',
'sequential_trunk_off_42_16pt.swc',
'Neuron_no_missing_ids_no_zero_segs.swc']
]
for f in files:
ok, ids = check.has_sequential_ids(load_data(f))
nt.ok_(ok)
nt.ok_(len(ids) == 0)
def load_neuron(filename, tree_action=None):
"""
Loads a neuron keeping a record of the filename.
Args:
filename: the path of the file storing morphology data
tree_action: optional function to run on each of the neuron's
neurite trees.
Raises: SomaError if no soma points in data.
Raises: NonConsecutiveIDsError if filename contains non-consecutive
point IDs
"""
data = load_data(filename)
if not has_sequential_ids(data)[0]:
raise NonConsecutiveIDsError('Non consecutive IDs found in raw data')
nrn = make_neuron(data, tree_action)
nrn.name = os.path.splitext(os.path.basename(filename))[0]
return nrn
def load_neuron(filename, tree_action=None):
"""
Loads a neuron keeping a record of the filename.
Args:
filename: the path of the file storing morphology data
tree_action: optional function to run on each of the neuron's
neurite trees.
Raises: SomaError if no soma points in data.
Raises: NonConsecutiveIDsError if filename contains non-consecutive
point IDs
"""
data = load_data(filename)
if not has_sequential_ids(data)[0]:
raise NonConsecutiveIDsError('Non consecutive IDs found in raw data')
nrn = make_neuron(data, tree_action)
nrn.name = os.path.splitext(os.path.basename(filename))[0]
return nrn