def test_has_increasing_ids_bad_data(self):
f = Path(SWC_PATH, 'non_increasing_trunk_off_1_16pt.swc')
ok = chk.has_increasing_ids(self.load_data(f))
nt.ok_(not ok)
nt.eq_(list(ok.info), [6, 12])
def test_has_increasing_ids_bad_data(self):
f = os.path.join(SWC_PATH, 'non_increasing_trunk_off_1_16pt.swc')
ok = chk.has_increasing_ids(self.load_data(f))
nt.ok_(not ok)
nt.assert_items_equal(ok.info, [6, 12])
def test_has_increasing_ids_bad_data(self):
f = os.path.join(SWC_PATH, 'non_increasing_trunk_off_1_16pt.swc')
ok = chk.has_increasing_ids(self.load_data(f))
nt.ok_(not ok)
nt.eq_(list(ok.info), [6, 12])
def test_has_increasing_ids_good_data(self):
files = [
Path(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 = chk.has_increasing_ids(self.load_data(f))
nt.ok_(ok)
nt.ok_(len(ok.info) == 0)
def test_has_increasing_ids_good_data(self):
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 = chk.has_increasing_ids(self.load_data(f))
nt.ok_(ok)
nt.ok_(len(ok.info) == 0)
def load_trees(filename, tree_action=None):
"""Load all trees in an input file
Loads all trees, regardless of whether they are connected
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:
IDSequenceError if filename contains non-incremental ID sequence
"""
data = load_data(filename)
if not check.has_increasing_ids(data):
raise IDSequenceError('Invald ID sequence found in raw data')
_ids = get_initial_neurite_segment_ids(data)
_ids.extend(data.get_ids(lambda r: r[COLS.P] == -1 and r[COLS.TYPE] != POINT_TYPE.SOMA))
return [make_point_tree(data, i, tree_action) for i in _ids]
def load_neuron(filename, tree_action=set_tree_type):
"""
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.
IDSequenceError if filename contains invalid ID sequence
"""
data = load_data(filename)
if not check.has_increasing_ids(data):
raise IDSequenceError('Invald ID sequence found in raw data')
if not check.is_single_tree(data):
raise MultipleTrees('Multiple trees detected')
if not check.no_missing_parents(data):
raise MissingParentError('Missing parents detected')
nrn = make_neuron(data, tree_action)
nrn.name = os.path.splitext(os.path.basename(filename))[0]
return nrn
def time_has_increasing_ids(self):
sc.has_increasing_ids(self.data_wrapper)
def time_has_increasing_ids(self):
sc.has_increasing_ids(self.data_wrapper)
