def test_make_tree_postaction():
def post_action(t):
t.foo = 'bar'
rd = RAW_DATA[0]
seg_ids = utils.get_initial_neurite_segment_ids(rd)
trees = [utils.make_tree(rd, root_id=seg_id, post_action=post_action)
for seg_id in seg_ids]
for t in trees:
nt.ok_(hasattr(t, 'foo') and t.foo == 'bar')
def test_get_initial_neurite_segment_ids():
for i, d in enumerate(RAW_DATA):
nt.ok_(utils.get_initial_neurite_segment_ids(d) == INIT_IDS[i])
def test_make_tree():
rd = RAW_DATA[0]
seg_ids = utils.get_initial_neurite_segment_ids(rd)
trees = [utils.make_tree(rd, seg_id) for seg_id in seg_ids]
nt.ok_(len(trees) == len(INIT_IDS[0]))
_check_trees(trees)
def point_iter(iterator):
'''Transform tree iterator into a point iterator
Args:
iterator: tree iterator for a tree holding raw data rows.
'''
return imap(as_point, tree.val_iter(iterator))
if __name__ == '__main__':
filename = 'test_data/swc/Neuron.swc'
rd = load_data(filename)
init_seg_ids = get_initial_neurite_segment_ids(rd)
trees = [make_tree(rd, sg) for sg in init_seg_ids]
soma = neuron.make_soma([rd.get_row(si) for si in get_soma_ids(rd)])
for tr in trees:
for p in point_iter(tree.ipreorder(tr)):
LOG.debug(p)
LOG.info('Initial segment IDs: %s', init_seg_ids)
nrn = neuron.Neuron(soma, trees)
LOG.info('Neuron soma raw data % s', [r for r in nrn.soma.iter()])
LOG.info('Neuron soma points %s', [as_point(p)