How to use the morphio.PointLevel function in morphio

def test_child_section():
    m = Morphology()
    section = m.append_root_section(PointLevel([[1, 2, 3]], [2], [20]),
                                    SectionType.axon)

    ok_(section.is_root)

    section.append_section(PointLevel([[1, 2, 3], [4, 5, 6]],
                                      [2, 3],
                                      [20, 30]))

    children = m.root_sections[0].children

    assert_equal(len(children),
                 1)

    assert_array_equal(children[0].points,
                       [[1, 2, 3], [4, 5, 6]])
    assert_array_equal(children[0].diameters,
                       [2, 3])
    assert_array_equal(children[0].perimeters,
                       [20, 30])

    children[0].points = [[7, 8, 9], [10, 11, 12]]

def test_single_neurite():
    m = Morphology()
    m.append_root_section(PointLevel([[1, 2, 3]], [2], [20]),
                          SectionType.axon)

    assert_array_equal(m.root_sections[0].points,
                       [[1, 2, 3]])
    assert_equal(m.root_sections[0].diameters,
                 [2])
    assert_equal(m.root_sections[0].perimeters,
                 [20])

    m.root_sections[0].points = [[10, 20, 30]]
    assert_array_equal(m.root_sections[0].points,
                       [[10, 20, 30]],
                       'Points array should have been mutated')

    m.root_sections[0].diameters = [7]

def test_child_section():
    m = Morphology()
    section = m.append_root_section(PointLevel([[1, 2, 3]], [2], [20]),
                                    SectionType.axon)

    ok_(section.is_root)

    section.append_section(PointLevel([[1, 2, 3], [4, 5, 6]],
                                      [2, 3],
                                      [20, 30]))

    children = m.root_sections[0].children

    assert_equal(len(children),
                 1)

    assert_array_equal(children[0].points,
                       [[1, 2, 3], [4, 5, 6]])
    assert_array_equal(children[0].diameters,

def test_duplicate_different_diameter():
    '''Test that starting a child section with a different diamete
    work as expected'''
    morpho = Morphology()
    morpho.soma.points = [[0, 0, 0], [1, 1, 1]]
    morpho.soma.diameters = [1, 1]

    section = morpho.append_root_section(PointLevel([[2, 2, 2], [3, 3, 3]],
                                                       [4, 4]),
                                         SectionType.axon,)

    section.append_section(PointLevel([[3, 3, 3], [4, 4, 4]], [10, 12]))
    section.append_section(PointLevel([[3, 3, 3], [5, 5, 5]], [11, 12]))


    with setup_tempdir('test_write_duplicate_different_diameter', no_cleanup=True) as tmp_folder:
        for ext in ['asc', 'h5', 'swc']:
            with captured_output() as (_, err):
                with ostream_redirect(stdout=True, stderr=True):
                    outfile = os.path.join(tmp_folder, 'tmp.' + ext)
                    morpho.write(outfile)

                    read = Morphology(outfile)

            assert_equal(len(read.root_sections[0].children), 2)
            child1, child2 = read.root_sections[0].children
            assert_array_equal(child1.points, [[3, 3, 3], [4, 4, 4]])
            assert_array_equal(child2.points, [[3, 3, 3], [5, 5, 5]])
            assert_array_equal(child1.diameters, [10, 12])

def test_duplicate_different_diameter():
    '''Test that starting a child section with a different diamete
    work as expected'''
    morpho = Morphology()
    morpho.soma.points = [[0, 0, 0], [1, 1, 1]]
    morpho.soma.diameters = [1, 1]

    section = morpho.append_root_section(PointLevel([[2, 2, 2], [3, 3, 3]],
                                                       [4, 4]),
                                         SectionType.axon,)

    section.append_section(PointLevel([[3, 3, 3], [4, 4, 4]], [10, 12]))
    section.append_section(PointLevel([[3, 3, 3], [5, 5, 5]], [11, 12]))


    with setup_tempdir('test_write_duplicate_different_diameter', no_cleanup=True) as tmp_folder:
        for ext in ['asc', 'h5', 'swc']:
            with captured_output() as (_, err):
                with ostream_redirect(stdout=True, stderr=True):
                    outfile = os.path.join(tmp_folder, 'tmp.' + ext)
                    morpho.write(outfile)

                    read = Morphology(outfile)

def test_point_level():
    a = PointLevel([[1, 2, 3]], [2], [])
    assert_equal(a.points, [[1, 2, 3]])
    assert_equal(a.diameters, [2])

    with assert_raises(SectionBuilderError) as obj:
        a = PointLevel([[1, 2, 3],
                        [1, 2, 3]],
                       [2],
                       [])

    assert_substring("Point vector have size: 2 while Diameter vector has size: 1",
                     str(obj.exception))

    with assert_raises(SectionBuilderError) as obj:
        a = PointLevel([[1, 2, 3],
                        [1, 2, 3]],
                       [2, 3],
                       [4])

    assert_substring("Point vector have size: 2 while Perimeter vector has size: 1",
                     str(obj.exception))

def test_empty_neurite():
    m = Morphology()
    with captured_output() as (_, err):
        with ostream_redirect(stdout=True, stderr=True):
            root = m.append_root_section(PointLevel(), SectionType.axon)
            assert_equal(err.getvalue().strip(),
                         'Warning: appending empty section with id: 0')

    assert_equal(len(m.root_sections), 1)
    assert_equal(m.root_sections[0].type,
                 SectionType.axon)

    with captured_output() as (_, err):
        with ostream_redirect(stdout=True, stderr=True):
            root.append_section(PointLevel(), SectionType.axon)
            assert_equal(err.getvalue().strip(),
                         'Warning: appending empty section with id: 1')

dendrite = morpho.append_root_section(
                                     PointLevel([[0, 0, 0],
                                                 [0, 5, 0]],
                                                [2, 2],
                                                [5, 6]),
                                     SectionType.basal_dendrite)

    dendrite.append_section(
                          PointLevel([[0, 5, 0],
                                      [-5, 5, 0]],
                                     [2, 3],
                                     [6, 7]))

    dendrite.append_section(
                          PointLevel([[0, 5, 0],
                                      [6, 5, 0]],
                                     [2, 3],
                                     [6, 8]))

    with setup_tempdir('test_write_perimeter') as tmp_folder:
        morpho.write(os.path.join(tmp_folder, "test_write.h5"))

        assert_array_equal(ImmutMorphology(os.path.join(tmp_folder, "test_write.h5")).perimeters,
                           [5., 6., 6., 7., 6., 8.])

def test_write_basic():
    morpho = Morphology()
    morpho.soma.points = [[0, 0, 0]]
    morpho.soma.diameters = [2]

    dendrite = morpho.append_root_section(PointLevel([[0, 0, 0], [0, 5, 0]], [2, 2]),
                                          SectionType.basal_dendrite)

    dendrite.append_section(PointLevel([[0, 5, 0], [-5, 5, 0]], [2, 3]))
    dendrite.append_section(PointLevel([[0, 5, 0], [6, 5, 0]], [2, 3]))

    axon = morpho.append_root_section(
                                 PointLevel([[0, 0, 0],
                                             [0, -4, 0]],
                                            [2, 2]),
                                 SectionType.axon)

    axon.append_section(PointLevel([[0, -4, 0],
                                      [6, -4, 0]],
                                     [2, 4]))

    axon = axon.append_section(PointLevel([[0, -4, 0],
                                             [-5, -4, 0]],
                                            [2, 4]))

    with setup_tempdir('test_write_basic') as tmp_folder: