Example #1
0
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)
Example #2
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def test_invalid_data_path_raises_IOError():
    checker = CheckRunner(CONFIG)
    _ = checker.run('foo/bar/baz')
Example #3
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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)
Example #4
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def test_single_apical_no_soma():
    checker = CheckRunner(CONFIG)
    summ = checker.run(NRN_PATH_5)
    nt.assert_equal(summ, REF_5)
Example #5
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def test_single_axon_neuron():
    checker = CheckRunner(CONFIG)
    summ = checker.run(NRN_PATH_4)
    nt.assert_equal(summ, REF_4)
Example #6
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def test_zero_length_sections_neuron():
    checker = CheckRunner(CONFIG)
    summ = checker.run(NRN_PATH_1)
    nt.assert_equal(summ, REF_1)
Example #7
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def test_ok_neuron_color():
    checker = CheckRunner(CONFIG_COLOR)
    summ = checker.run(NRN_PATH_0)
    nt.assert_equal(summ, REF_0)
Example #8
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def test_invalid_data_path_raises_IOError():
    checker = CheckRunner(CONFIG)
    _ = checker.run('foo/bar/baz')
Example #9
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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)
Example #10
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def test_single_apical_no_soma():
    checker = CheckRunner(CONFIG)
    summ = checker.run(NRN_PATH_5)
    nt.assert_equal(summ, REF_5)
Example #11
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def test_single_axon_neuron():
    checker = CheckRunner(CONFIG)
    summ = checker.run(NRN_PATH_4)
    nt.assert_equal(summ, REF_4)
Example #12
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def test_zero_length_sections_neuron():
    checker = CheckRunner(CONFIG)
    summ = checker.run(NRN_PATH_1)
    nt.assert_equal(summ, REF_1)
Example #13
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def test_ok_neuron_color():
    checker = CheckRunner(CONFIG_COLOR)
    summ = checker.run(NRN_PATH_0)
    nt.assert_equal(summ, REF_0)
Example #14
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def test_directory_input():
    checker = CheckRunner(CONFIG)
    summ = checker.run(SWC_PATH)
Example #15
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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']