Python utils.load_neuron函数代码示例

def test_load_neuron_mixed_tree_swc():
    nrn_mix =  utils.load_neuron(os.path.join(SWC_ORD_PATH, 'sample_mixed_tree_sections.swc'))
    nt.assert_items_equal(get('number_of_sections_per_neurite', nrn_mix), [5, 3])

    nt.assert_items_equal(get('number_of_sections_per_neurite', nrn_mix),
                          get('number_of_sections_per_neurite', SWC_ORD_REF))

    nt.assert_items_equal(get('number_of_segments', nrn_mix),
                          get('number_of_segments', SWC_ORD_REF))

    nt.assert_items_equal(get('total_length', nrn_mix),
                          get('total_length', SWC_ORD_REF))

def test_load_neuron_section_order_break_swc():
    nrn_mix =  utils.load_neuron(os.path.join(SWC_ORD_PATH, 'sample_disordered.swc'))

    assert_items_equal(get('number_of_sections_per_neurite', nrn_mix), [5, 3])

    assert_items_equal(get('number_of_sections_per_neurite', nrn_mix),
                       get('number_of_sections_per_neurite', SWC_ORD_REF))

    assert_items_equal(get('number_of_segments', nrn_mix),
                       get('number_of_segments', SWC_ORD_REF))

    assert_items_equal(get('total_length', nrn_mix),
                       get('total_length', SWC_ORD_REF))

def test_load_h5_trunk_points_regression():
    # regression test for issue encoutnered wile
    # implementing PR #479, related to H5 unpacking
    # of files with non-standard soma structure.
    # See #480.
    nrn = utils.load_neuron(os.path.join(DATA_PATH, 'h5', 'v1', 'Neuron.h5'))
    nt.ok_(np.allclose(nrn.neurites[0].root_node.points[1],
                       [0., 0. , 0.1, 0.31646374, 4., 4., 3.]))

    nt.ok_(np.allclose(nrn.neurites[1].root_node.points[1],
                       [0., 0., 0.1, 1.84130445e-01, 3.0, 235., 234.]))

    nt.ok_(np.allclose(nrn.neurites[2].root_node.points[1],
                       [0., 0., 0.1, 5.62225521e-01, 3., 466, 465]))

    nt.ok_(np.allclose(nrn.neurites[3].root_node.points[1],
                       [0., 0., 0.1, 7.28555262e-01, 2., 697, 696]))

def test_load_trees_good_neuron():
    '''Check trees in good neuron are the same as trees from loaded neuron'''
    filepath = os.path.join(SWC_PATH, 'Neuron.swc')
    nrn = utils.load_neuron(filepath)
    trees = utils.load_trees(filepath)
    nt.eq_(len(nrn.neurites), 4)
    nt.eq_(len(nrn.neurites), len(trees))

    nrn2 = MockNeuron(trees)

    @pts.point_function(as_tree=False)
    def elem(point):
        return point

    # Check data are the same in tree collection and neuron's neurites
    for a, b in izip(iter_neurites(nrn, elem), iter_neurites(nrn2, elem)):
        nt.ok_(np.all(a == b))

def test_load_neuron_deep_neuron():
    '''make sure that neurons with deep (ie: larger than the python
       recursion limit can be loaded)
    '''
    deep_neuron = os.path.join(DATA_PATH, 'h5/v1/deep_neuron.h5')
    utils.load_neuron(deep_neuron)

def test_load_neuron():
    nrn = utils.load_neuron(FILES[0])
    nt.ok_(nrn.name == FILES[0].strip('.swc').split('/')[-1])

def _load_neuron(name):
    if name.endswith('.swc'):
        path = os.path.join(SWC_PATH, name)
    elif name.endswith('.h5'):
        path = os.path.join(H5V1_PATH, name)
    return name, load_neuron(path)

def test_load_neuron_invalid_id_sequence_raises():
    utils.load_neuron(INVALID_ID_SEQUENCE_FILE);

def test_load_neuron_missing_parents_raises():
    utils.load_neuron(MISSING_PARENTS_FILE)

def test_load_bifurcating_soma_points_raises_SomaError():
    utils.load_neuron(os.path.join(SWC_PATH, 'soma', 'bifurcating_soma.swc'))

def test_load_neuromorpho_3pt_soma():
    nrn = utils.load_neuron(os.path.join(SWC_PATH, 'soma', 'three_pt_soma.swc'))
    nt.eq_(len(nrn.neurites), 4)
    nt.eq_(len(nrn.soma.points), 3)
    nt.eq_(nrn.soma.radius, 2)
    _check_neurites_have_no_parent(nrn)

def test_load_contour_split_1st_soma_neuron():
    nrn = utils.load_neuron(os.path.join(SWC_PATH, 'soma', 'contour_split_1st_soma_neuron.swc'))
    nt.eq_(len(nrn.neurites), 3)
    nt.eq_(len(nrn.soma.points), 6)
    nt.eq_(nrn.soma.radius, 2.0)
    _check_neurites_have_no_parent(nrn)

def test_neuron_name():

    for fn, nn in zip(FILENAMES, NRN_NAMES):
        nrn = utils.load_neuron(fn)
        nt.eq_(nrn.name, nn)

def test_load_neuron():

    nrn = utils.load_neuron(FILENAMES[0])
    nt.assert_true(isinstance(NRN, Neuron))
    nt.assert_equal(NRN.name, 'Neuron')
    _check_neurites_have_no_parent(nrn)

def test_load_neuron_no_consecutive_ids_raises_NonConsecutiveIDsError():
    utils.load_neuron(NON_CONSECUTIVE_ID_FILE);