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 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
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')