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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"))
def test_empty_vasculature():
assert_raises(RawDataError, vasculature.Vasculature, os.path.join(_path, "h5/empty_vasculature.h5"))
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,
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"))
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)
def test_from_pathlib():
vasc = vasculature.Vasculature(Path(_path, "h5/vasculature1.h5"))
assert_equal(len(vasc.sections), 3080)