def test_as_point(): p = as_point([1, 2, 3, 4, 5, 6, 7]) nt.ok_(p.x == 1) nt.ok_(p.y == 2) nt.ok_(p.z == 3) nt.ok_(p.r == 4) nt.ok_(p.t == 5)
def get_point(self, idx): '''Get point data for element idx''' idx = self._apply_offset(idx) p = as_point(self.data_block[idx]) if idx > ROOT_ID else None return p
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] print 'Making neuron 2' nrn2 = make_neuron(rd) print 'Neuron 2 soma points', [r for r in nrn2.soma.iter()] print 'Neuron 2 soma points', [as_point(p) for p in nrn2.soma.iter()] print 'Neuron 2 tree init points, types' for tt in nrn2.neurites: print tt.value[COLS.ID], tt.value[COLS.TYPE] print 'Print neuron leaves as points' for tt in nrn2.neurites:
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: LOG.info('%s, %s', tt.value[COLS.ID], tt.value[COLS.TYPE]) LOG.info('Making neuron 2') nrn2 = make_neuron(rd) LOG.debug('Neuron 2 soma points %s', [r for r in nrn2.soma.iter()]) LOG.debug('Neuron 2 soma points %s', [as_point(p) for p in nrn2.soma.iter()]) LOG.info('Neuron 2 tree init points, types') for tt in nrn2.neurites: LOG.info('%s %s', tt.value[COLS.ID], tt.value[COLS.TYPE])
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] print 'Making neuron 2' nrn2 = make_neuron(rd) print 'Neuron 2 soma points', [r for r in nrn2.soma.iter()] print 'Neuron 2 soma points', [as_point(p) for p in nrn2.soma.iter()] print 'Neuron 2 tree init points, types' for tt in nrn2.neurites: print tt.value[COLS.ID], tt.value[COLS.TYPE]
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: LOG.info('%s, %s', tt.value[COLS.ID], tt.value[COLS.TYPE]) LOG.info('Making neuron 2') nrn2 = make_neuron(rd) LOG.debug('Neuron 2 soma points %s', [r for r in nrn2.soma.iter()]) LOG.debug('Neuron 2 soma points %s', [as_point(p) for p in nrn2.soma.iter()]) LOG.info('Neuron 2 tree init points, types') for tt in nrn2.neurites: LOG.info('%s %s', tt.value[COLS.ID], tt.value[COLS.TYPE]) LOG.debug('Print neuron leaves as points')