コード例 #1
0
ファイル: test_utils.py プロジェクト: guozanhua/NeuroM
def test_load_trees_postaction():

    def post_action(t):
        t.foo = 'bar'

    filepath = os.path.join(SWC_PATH, 'Neuron.swc')
    trees = utils.load_trees(filepath, tree_action=post_action)
    nt.eq_(len(trees), 4)  # sanity check

    for t in trees:
        nt.ok_(hasattr(t, 'foo') and t.foo == 'bar')
コード例 #2
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ファイル: test_utils.py プロジェクト: guozanhua/NeuroM
def test_load_neuron_disconnected_components():

    filepath = DISCONNECTED_POINTS_FILE
    trees = utils.load_trees(filepath)
    nt.eq_(len(trees), 8)

    # tree ID - number of points map
    ref_ids_pts = {4: 1, 215: 1, 426: 1, 637: 1, 6: 209, 217: 209, 428: 209, 639: 209}

    ids_pts =  {}
    for t in trees:
        ids_pts[t.value[COLS.ID]] = pts.count(t)

    nt.eq_(ref_ids_pts, ids_pts)
コード例 #3
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ファイル: test_utils.py プロジェクト: Tsolmongerel/NeuroM
def test_load_neuron_disconnected_components():

    filepath = os.path.join(SWC_PATH, 'Neuron_disconnected_components.swc')
    trees = utils.load_trees(filepath)
    nt.eq_(len(trees), 8)

    # tree ID - number of points map
    ref_ids_pts = {4: 1, 215: 1, 426: 1, 637: 1, 6: 209, 217: 209, 428: 209, 639: 209}

    ids_pts =  {}
    for t in trees:
        ids_pts[t.value[COLS.ID]] = pts.count(t)

    nt.eq_(ref_ids_pts, ids_pts)
コード例 #4
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ファイル: test_utils.py プロジェクト: guozanhua/NeuroM
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))
コード例 #5
0
ファイル: test_utils.py プロジェクト: guozanhua/NeuroM
def test_load_trees_invalid_id_sequence_raises():
    utils.load_trees(INVALID_ID_SEQUENCE_FILE);
コード例 #6
0
ファイル: test_utils.py プロジェクト: guozanhua/NeuroM
def test_load_trees_no_soma():

    trees = utils.load_trees(NO_SOMA_FILE)
    nt.eq_(len(trees), 1)
コード例 #7
0
            pass
        stylize(ax, cell.name, feature)
    return fig


if __name__ == "__main__":
    import numpy as np
    import os

    args = parse_args()
    nrns = []

    for j, neuronFile in enumerate(get_morph_files(args.datapath)):
        _name = os.path.splitext(os.path.split(neuronFile)[-1])[0]
        nrn = None

        try:
            soma = make_soma([np.array([11, 22, 33, 44, 1, 1, -1])])
            trees = load_trees(neuronFile)
            cn = coreNeuron(soma, trees, name=_name)
            nrn = ezyNeuron(cn)
        except IDSequenceError:
            pass

        for i, _feature in enumerate(args.features):

            f = plot_feature(_feature, nrn)
            figname = "{0}_{1}_{2}.eps".format(i, j, _name)
            f.savefig(os.path.join(args.odir, figname))
            pl.close(f)