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_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)): print p print 'Initial segment IDs:', init_seg_ids nrn = neuron.Neuron(soma, trees) print 'Neuron soma raw data', [r for r in nrn.soma.iter()] print 'Neuron soma points', [as_point(p) for p in nrn.soma.iter()] print 'Neuron tree init points, types' for tt in nrn.neurites: print tt.value[COLS.ID], tt.value[COLS.TYPE]
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_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) for p in nrn.soma.iter()]) LOG.info('Neuron tree init points, types') for tt in nrn.neurites:
def test_get_soma_ids(): for i, d in enumerate(RAW_DATA): nt.ok_(utils.get_soma_ids(d) == SOMA_IDS[i])