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__sanitize_config():
# fails if missing 'checks'
nt.assert_raises(ConfigError, CheckRunner._sanitize_config, {})
# creates minimal config
new_config = CheckRunner._sanitize_config({'checks': {}})
nt.eq_(new_config, {'checks':
{'structural_checks': [],
'neuron_checks': [],
},
'options': {},
'color': False,
})
# makes no changes to already filled out config
new_config = CheckRunner._sanitize_config(CONFIG)
nt.eq_(CONFIG, new_config)
def test__sanitize_config():
# fails if missing 'checks'
with pytest.raises(ConfigError):
CheckRunner._sanitize_config({})
# creates minimal config
new_config = CheckRunner._sanitize_config({'checks': {}})
assert new_config == {
'checks': {
'neuron_checks': [],
},
'options': {},
'color': False,
}
# makes no changes to already filled out config
new_config = CheckRunner._sanitize_config(CONFIG)
assert CONFIG == new_config
def test__sanitize_config():
# fails if missing 'checks'
nt.assert_raises(ConfigError, CheckRunner._sanitize_config, {})
# creates minimal config
new_config = CheckRunner._sanitize_config({'checks': {}})
nt.eq_(
new_config, {
'checks': {
'structural_checks': [],
'neuron_checks': [],
},
'options': {},
'color': False,
})
# makes no changes to already filled out config
new_config = CheckRunner._sanitize_config(CONFIG)
nt.eq_(CONFIG, new_config)
def test_invalid_data_path_raises_IOError():
checker = CheckRunner(CONFIG)
_ = checker.run('foo/bar/baz')
def test_directory_input():
checker = CheckRunner(CONFIG)
summ = checker.run(SWC_PATH)
nt.eq_(summ['files'][NRN_PATH_0]['Has axon'], True)
nt.eq_(summ['files'][NRN_PATH_2]['Has axon'], False)
def test_single_apical_no_soma():
checker = CheckRunner(CONFIG)
summ = checker.run(NRN_PATH_5)
nt.assert_equal(summ, REF_5)
def test_directory_input():
checker = CheckRunner(CONFIG)
summ = checker.run(SWC_PATH)
nt.eq_(summ['files'][NRN_PATH_0]['Has axon'], True)
nt.eq_(summ['files'][NRN_PATH_2]['Has axon'], False)
def test_zero_length_sections_neuron():
checker = CheckRunner(CONFIG)
summ = checker.run(NRN_PATH_1)
nt.assert_equal(summ, REF_1)
def test_single_axon_neuron():
checker = CheckRunner(CONFIG)
summ = checker.run(NRN_PATH_4)
nt.assert_equal(summ, REF_4)
def _run_test(path, ref, config=CONFIG, should_pass=False):
"""Run checkers with the passed "config" on file "path"
and compare the results to 'ref'"""
results = CheckRunner(config).run(path)
assert dict(results['files'][str(path)]) == ref
assert (results['STATUS'] == ("PASS" if should_pass else "FAIL"))
def test_ok_neuron_color():
checker = CheckRunner(CONFIG_COLOR)
summ = checker.run(NRN_PATH_0)
nt.assert_equal(summ, REF_0)
def test_directory_input():
checker = CheckRunner(CONFIG)
summ = checker.run(SWC_PATH)
assert summ['files'][str(SWC_PATH / 'Single_axon.swc')]['Has axon']
assert not summ['files'][str(SWC_PATH / 'Single_apical.swc')]['Has axon']
def test_invalid_data_path_raises_IOError():
checker = CheckRunner(CONFIG)
_ = checker.run('foo/bar/baz')
def test_single_apical_no_soma():
checker = CheckRunner(CONFIG)
summ = checker.run(NRN_PATH_5)
nt.assert_equal(summ, REF_5)
def test_single_axon_neuron():
checker = CheckRunner(CONFIG)
summ = checker.run(NRN_PATH_4)
nt.assert_equal(summ, REF_4)
def test_zero_length_sections_neuron():
checker = CheckRunner(CONFIG)
summ = checker.run(NRN_PATH_1)
nt.assert_equal(summ, REF_1)
def test_ok_neuron_color():
checker = CheckRunner(CONFIG_COLOR)
summ = checker.run(NRN_PATH_0)
nt.assert_equal(summ, REF_0)
def test_directory_input():
checker = CheckRunner(CONFIG)
summ = checker.run(SWC_PATH)
