How to use the morphio.vasculature.Vasculature function in morphio

To help you get started, we’ve selected a few morphio examples, based on popular ways it is used in public projects.

Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.

github BlueBrain / MorphIO / tests / test_10_vasculature.py View on Github external
def test_section_types():
    morphology = vasculature.Vasculature(os.path.join(_path, "h5/vasculature1.h5"))
    assert_equal(morphology.section(0).type, VasculatureSectionType.vein)
    assert_equal(morphology.section(1).type, VasculatureSectionType.artery)
    assert_equal(morphology.section(2).type, VasculatureSectionType.venule)
    assert_equal(morphology.section(3).type, VasculatureSectionType.arteriole)
    assert_equal(morphology.section(4).type, VasculatureSectionType.venous_capillary)
    assert_equal(morphology.section(5).type, VasculatureSectionType.arterial_capillary)

    assert_raises(RawDataError, vasculature.Vasculature, os.path.join(_path, "h5/vasculature-broken-section-type.h5"))
github BlueBrain / MorphIO / tests / test_10_vasculature.py View on Github external
def test_empty_vasculature():
    assert_raises(RawDataError, vasculature.Vasculature, os.path.join(_path, "h5/empty_vasculature.h5"))
github BlueBrain / MorphIO / tests / test_10_vasculature.py View on Github external
def test_components_vasculature():
    morphology = vasculature.Vasculature(os.path.join(_path, "h5/vasculature1.h5"))
    assert_array_almost_equal(morphology.section(0).points,
                              np.array([[1265.47399902,  335.42364502, 1869.19274902],
                                        [1266.26647949,  335.57000732, 1869.74914551],
                                        [1267.09082031,  335.68869019, 1870.31469727],
                                        [1267.89404297,  335.78134155, 1870.91418457],
                                        [1268.67077637,  335.85733032, 1871.54992676],
                                        [1269.42773438,  335.92602539, 1872.21008301],
                                        [1270.17431641,  335.99368286, 1872.88195801],
                                        [1270.92016602,  336.06558228, 1873.55395508],
                                        [1271.6739502 ,  336.14227295, 1874.21740723],
                                        [1272.44091797,  336.23706055, 1874.86047363],
                                        [1273.22216797,  336.31613159, 1875.49523926],
                                        [1274.        ,  336.70001221, 1876.        ]]))

    assert_array_almost_equal(morphology.section(0).diameters,
                              np.array([1.96932483, 1.96932483, 1.96932483, 1.96932483, 1.96932483,
github BlueBrain / MorphIO / tests / test_10_vasculature.py View on Github external
def test_section_types():
    morphology = vasculature.Vasculature(os.path.join(_path, "h5/vasculature1.h5"))
    assert_equal(morphology.section(0).type, VasculatureSectionType.vein)
    assert_equal(morphology.section(1).type, VasculatureSectionType.artery)
    assert_equal(morphology.section(2).type, VasculatureSectionType.venule)
    assert_equal(morphology.section(3).type, VasculatureSectionType.arteriole)
    assert_equal(morphology.section(4).type, VasculatureSectionType.venous_capillary)
    assert_equal(morphology.section(5).type, VasculatureSectionType.arterial_capillary)

    assert_raises(RawDataError, vasculature.Vasculature, os.path.join(_path, "h5/vasculature-broken-section-type.h5"))
github BlueBrain / MorphIO / tests / test_10_vasculature.py View on Github external
def test_iterators_vasculature():
    morphology = vasculature.Vasculature(os.path.join(_path, "h5/vasculature1.h5"))
    assert_array_equal([sec.id for sec in morphology.sections], range(3080))
    assert_equal(len([section.id for section in morphology.iter()]), 3080)
    all_sections = set([sec.id for sec in morphology.sections])
    for sec in morphology.iter():
        all_sections.remove(sec.id)
    assert_equal(len(all_sections), 0)
github BlueBrain / MorphIO / tests / test_10_vasculature.py View on Github external
def test_from_pathlib():
    vasc = vasculature.Vasculature(Path(_path, "h5/vasculature1.h5"))
    assert_equal(len(vasc.sections), 3080)