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_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_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)
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']