def test_get_config():
#get the default
default = {'default': 'config'}
config = get_config(None, default)
nt.eq_(config, default)
#load valid yaml
test_yaml = os.path.abspath(os.path.join(os.path.dirname(__file__),
'../../../apps/config/morph_stats.yaml'))
config = get_config(test_yaml, default)
def test_get_config():
#get the default
default = {'default': 'config'}
config = get_config(None, default)
nt.eq_(config, default)
#load valid yaml
test_yaml = os.path.abspath(
os.path.join(os.path.dirname(__file__),
'../../../apps/config/morph_stats.yaml'))
config = get_config(test_yaml, default)
def test_get_config():
# get the default
test_yaml = os.path.abspath(os.path.join(os.path.dirname(__file__),
'../../config/morph_stats.yaml'))
expected = {'neurite': {'section_lengths': ['max', 'total'], 'section_volumes': ['total'], 'section_branch_orders': ['max']}, 'neurite_type': ['AXON', 'APICAL_DENDRITE', 'BASAL_DENDRITE', 'ALL'], 'neuron': {'soma_radii': ['mean']}}
config = get_config(None, test_yaml)
nt.assert_equal(config, expected)
config = get_config(test_yaml, '')
nt.assert_equal(config, expected)
def main(datapath, config, output_file, is_full_config, as_population,
ignored_exceptions):
"""Main function that get statistics for morphologies.
Args:
datapath (str|Path): path to a morphology file or folder
config (str|Path): path to a statistics config file
output_file (str|Path): path to output the resulted statistics file
is_full_config (bool): should be statistics made over all possible features, modes, neurites
as_population (bool): treat ``datapath`` as directory of morphologies population
ignored_exceptions (list|tuple|None): exceptions to ignore when loading a morphology
"""
if is_full_config:
config = full_config()
else:
try:
config = get_config(config, EXAMPLE_CONFIG)
config = sanitize_config(config)
except ConfigError as e:
L.error(e)
raise
if ignored_exceptions is None:
ignored_exceptions = ()
ignored_exceptions = tuple(IGNORABLE_EXCEPTIONS[k]
for k in ignored_exceptions)
neurons = nm.load_neurons(get_files_by_path(datapath),
ignored_exceptions=ignored_exceptions)
results = {}
if as_population:
results[datapath] = extract_stats(neurons, config)
else:
for neuron in tqdm(neurons):
results[neuron.name] = extract_stats(neuron, config)
if not output_file:
print(
json.dumps(results,
indent=2,
separators=(',', ':'),
cls=NeuromJSON))
elif output_file.endswith('.json'):
with open(output_file, 'w') as f:
json.dump(results, f, cls=NeuromJSON)
else:
with open(output_file, 'w') as f:
csvwriter = csv.writer(f)
header = get_header(results)
csvwriter.writerow(header)
for line in generate_flattened_dict(header, dict(results)):
csvwriter.writerow(line)
def main(datapath, config, output):
"""Main function that checks morphologies.
Args:
datapath (str|Path): path to a morphology file or folder
config (str|Path): path to a statistics config file
output (str|Path): path to output the resulted checks file
"""
config = get_config(config, EXAMPLE_CONFIG)
checker = CheckRunner(config)
summary = checker.run(datapath)
with open(output, 'w') as json_output:
json.dump(summary, json_output, indent=4)
def test_get_config():
# get the default
test_yaml = Path(
__file__).parent.parent.parent / 'neurom/apps/config/morph_stats.yaml'
expected = {
'neurite': {
'section_lengths': ['max', 'total'],
'section_volumes': ['total'],
'section_branch_orders': ['max']
},
'neurite_type': ['AXON', 'APICAL_DENDRITE', 'BASAL_DENDRITE', 'ALL'],
'neuron': {
'soma_radii': ['mean']
}
}
config = get_config(None, test_yaml)
assert config == expected
config = get_config(test_yaml, '')
assert config == expected
def test_get_config_exception():
#current python file isn't a yaml file
get_config(__file__, {})
def test_get_config_exception():
#current python file isn't a yaml file
get_config(__file__, {})
def test_get_config_exception():
"""current python file isn't a yaml file."""
with pytest.raises(ConfigError):
get_config(__file__, {})
