Esempio n. 1
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def test_multiple_soma():
    with assert_raises(SomaError) as obj:
        Morphology(os.path.join(_path, 'multiple_soma.swc'))
    assert_substring(
        ''.join([
            'Multiple somata found: \n\n',
            os.path.join(_path, 'multiple_soma.swc:2:error\n\n\n'),
            os.path.join(_path, 'multiple_soma.swc:11:error')
        ]), strip_color_codes(str(obj.exception)))
Esempio n. 2
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def test_unsupported_section_type():
    with tmp_swc_file('''1 1 0 4 0 3.0 -1
                         2 3 0 0 2 0.5 1
                         3 5 0 0 3 0.5 2  # <-- 5 is unsupported section type
                         ''') as tmp_file:

        with assert_raises(RawDataError) as obj:
            Morphology(tmp_file.name)
    assert_substring('.swc:3:error', strip_color_codes(str(obj.exception)))

    assert_substring('Unsupported section type: 5',
                     strip_color_codes(str(obj.exception)))
Esempio n. 3
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def test_single_children():
    '''Single children are merged with their parent'''
    with tmp_asc_file('''
                     ((Dendrite)
                      (3 -4 0 2)
                      (3 -6 0 2)
                      (3 -8 0 2)
                      (3 -10 0 2)
                      (
                        (3 -10 0 2)  ; merged with parent section
                        (0 -10 0 2)  ; merged with parent section
                        (-3 -10 0 2) ; merged with parent section
                        (
                          (-5 -5 5 5)
                          |
                          (-6 -6 6 6)
                        )
                       )
                      )
                 ''') as tmp_file:

        with captured_output() as (_, err):
            with ostream_redirect(stdout=True, stderr=True):
                n = Morphology(tmp_file.name)
                assert_substring('is the only child of section: 0 starting at:',
                                 err.getvalue().strip())
                assert_substring('It will be merged with the parent section',
                                 err.getvalue().strip())

        nt.assert_equal(len(n.soma.points), 0)
        nt.assert_equal(len(n.soma.points), 0)
        assert_equal(len(n.root_sections), 1)
        assert_array_equal(n.root_sections[0].points,
                           np.array([[3, -4, 0],
                                     [3, -6, 0],
                                     [3, -8, 0],
                                     [3, -10, 0],
                                     [0, -10, 0],
                                     [-3, -10, 0]],
                                    dtype=np.float32))

        assert_equal(len(n.root_sections[0].children), 2)

        assert_array_equal(n.root_sections[0].children[0].points,
                           np.array([[-3, -10, 0],
                                     [-5, -5, 5]]))

        assert_array_equal(n.root_sections[0].children[1].points,
                           np.array([[-3, -10, 0],
                                     [-6, -6, 6]]))
Esempio n. 4
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def test_non_C_nparray():
    m = Morphology(os.path.join(_path, "simple.swc"))
    section = m.root_sections[0]
    points = np.array([[1, 2, 3], [4, 5, 6]])
    section.points = points
    assert_array_equal(section.points, points)

    with assert_raises(MorphioError) as obj:
        section.points = points.T

    assert_substring("Wrong array shape. Expected: (X, 3), got: (3, 2)",
                     str(obj.exception))

    non_standard_stride = np.asfortranarray(points)
    section.points = non_standard_stride
    assert_array_equal(section.points, points)
Esempio n. 5
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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))
Esempio n. 6
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def test_empty_sibling():
    '''The empty sibling will be removed and the single child will be merged
    with its parent'''
    with captured_output() as (_, err):
        with ostream_redirect(stdout=True, stderr=True):
            with tmp_asc_file('''((Dendrite)
                      (3 -4 0 10)
                      (3 -6 0 9)
                      (3 -8 0 8)
                      (3 -10 0 7)
                      (
                        (3 -10 0 6)
                        (0 -10 0 5)
                        (-3 -10 0 4)
                        |       ; <-- empty sibling but still works !
                       )
                      )
                 ''') as tmp_file:
                n = Morphology(tmp_file.name)
                n.remove_unifurcations()
                assert_substring('is the only child of section: 0',
                                 err.getvalue().strip())
                assert_substring('It will be merged with the parent section',
                                 err.getvalue().strip())

    assert len(n.root_sections) == 1
    assert_array_equal(
        n.root_sections[0].points,
        np.array([[3, -4, 0], [3, -6, 0], [3, -8, 0], [3, -10, 0], [0, -10, 0],
                  [-3, -10, 0]],
                 dtype=np.float32))
    assert_array_equal(n.root_sections[0].diameters,
                       np.array([10, 9, 8, 7, 5, 4], dtype=np.float32))

    assert len(n.annotations) == 1
    annotation = n.annotations[0]
    assert annotation.type == morphio.AnnotationType.single_child
    assert annotation.line_number == -1
    assert_array_equal(annotation.points,
                       [[3, -10, 0], [0, -10, 0], [-3, -10, 0]])
    assert_array_equal(annotation.diameters, [6, 5, 4])
Esempio n. 7
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def test_empty_sibling():
    '''The empty sibling will be removed and the single child will be merged
    with its parent'''
    with captured_output() as (_, err):
        with ostream_redirect(stdout=True, stderr=True):
            with tmp_asc_file('''((Dendrite)
                      (3 -4 0 2)
                      (3 -6 0 2)
                      (3 -8 0 2)
                      (3 -10 0 2)
                      (
                        (3 -10 0 2)
                        (0 -10 0 2)
                        (-3 -10 0 2)
                        |       ; <-- empty sibling but still works !
                       )
                      )
                 ''') as tmp_file:
                n = Morphology(tmp_file.name)
                assert_substring('is the only child of section: 0 starting at:',
                                 err.getvalue().strip())
                assert_substring('It will be merged with the parent section',
                                 err.getvalue().strip())

    assert_equal(len(n.root_sections), 1)
    assert_array_equal(n.root_sections[0].points,
                       np.array([[3, -4, 0],
                                 [3, -6, 0],
                                 [3, -8, 0],
                                 [3, -10, 0],
                                 [0, -10, 0],
                                 [-3, -10, 0]],
                                dtype=np.float32))

    assert_equal(len(n.annotations), 1)
    annotation = n.annotations[0]
    assert_equal(annotation.type, morphio.AnnotationType.single_child)
    assert_equal(annotation.line_number, 6)
    assert_array_equal(annotation.points, [[3, -10, 0], [0, -10, 0], [-3, -10, 0]])
    assert_array_equal(annotation.diameters, [2, 2, 2])