def test_segment_path_length():
leaves = [l for l in tr.ileaf(NEURON_TREE)]
for l in leaves:
nt.ok_(path_length(l) == 9)
leaves = [l for l in tr.ileaf(SIMPLE_TREE)]
for l in leaves:
nt.ok_(path_length(l) == 8)
def _check_trees(trees):
for t in trees:
nt.ok_(len(list(tree.ileaf(t))) == 11)
nt.ok_(len(list(tree.iforking_point(t))) == 10)
nt.ok_(len(list(tree.ipreorder(t))) == 211)
nt.ok_(len(list(tree.ipostorder(t))) == 211)
nt.ok_(len(list(tree.isegment(t))) == 210)
leaves = [l for l in tree.ileaf(t)]
# path length from each leaf to root node.
branch_order = [21, 31, 41, 51, 61, 71, 81, 91, 101, 111, 111]
for i, l in enumerate(leaves):
nt.ok_(len(list(tree.iupstream(l))) == branch_order[i])
def _check_trees(trees):
for t in trees:
nt.ok_(len(list(tree.ileaf(t))) == 11)
nt.ok_(len(list(tree.iforking_point(t))) == 10)
nt.ok_(len(list(tree.ipreorder(t))) == 211)
nt.ok_(len(list(tree.ipostorder(t))) == 211)
nt.ok_(len(list(tree.isegment(t))) == 210)
leaves = [l for l in tree.ileaf(t)]
# path length from each leaf to root node.
branch_order = [21, 31, 41, 51, 61, 71, 81, 91, 101, 111, 111]
for i, l in enumerate(leaves):
nt.ok_(len(list(tree.iupstream(l))) == branch_order[i])
def test_ibifurcation_point_upstream():
leaves = [l for l in ileaf(REF_TREE2)]
ref_paths = [[11, 0], [11, 0], [11, 0], [11, 0], [1211, 12, 0],
[1211, 12, 0], [12, 0]]
for l, ref in zip(leaves, ref_paths):
nt.assert_equal(
[s for s in val_iter(ibifurcation_point(l, iupstream))], ref)
def test_ibifurcation_point_upstream():
leaves = [l for l in ileaf(REF_TREE2)]
ref_paths = [
[11, 0], [11, 0], [11, 0], [11, 0],
[1211, 12, 0], [1211, 12, 0], [12, 0]
]
for l, ref in zip(leaves, ref_paths):
nt.assert_equal([s for s in val_iter(ibifurcation_point(l, iupstream))], ref)
def test_leaf_iteration():
nt.ok_(list(val_iter(ileaf(REF_TREE))) == [111, 112, 12111, 12112, 122])
nt.ok_(list(val_iter(ileaf(REF_TREE.children[0]))) == [111, 112])
nt.ok_(list(val_iter(ileaf(REF_TREE.children[1]))) == [12111, 12112, 122])
nt.ok_(list(val_iter(ileaf(REF_TREE.children[0].children[0]))) == [111])
nt.ok_(list(val_iter(ileaf(REF_TREE.children[0].children[1]))) == [112])
nt.ok_(list(val_iter(ileaf(REF_TREE.children[1].children[0]))) == [12111, 12112])
nt.ok_(list(val_iter(ileaf(REF_TREE.children[1].children[1]))) == [122])
def test_section_upstream_iteration():
leaves = [l for l in ileaf(REF_TREE2)]
ref_paths = [[(1111, 11111), (11, 111, 1111), (0, 11)],
[(1111, 11112), (11, 111, 1111), (0, 11)],
[(1111, 11113), (11, 111, 1111), (0, 11)], [(11, 112),
(0, 11)],
[(1211, 12111), (12, 121, 1211), (0, 12)],
[(1211, 12112), (12, 121, 1211), (0, 12)], [(12, 122),
(0, 12)]]
for l, ref in zip(leaves, ref_paths):
nt.assert_equal([s for s in val_iter(isection(l, iupstream))], ref)
def test_leaf_iteration():
nt.ok_(list(val_iter(ileaf(REF_TREE))) == [111, 112, 12111, 12112, 122])
nt.ok_(list(val_iter(ileaf(REF_TREE.children[0]))) == [111, 112])
nt.ok_(list(val_iter(ileaf(REF_TREE.children[1]))) == [12111, 12112, 122])
nt.ok_(list(val_iter(ileaf(REF_TREE.children[0].children[0]))) == [111])
nt.ok_(list(val_iter(ileaf(REF_TREE.children[0].children[1]))) == [112])
nt.ok_(
list(val_iter(ileaf(REF_TREE.children[1].children[0]))) ==
[12111, 12112])
nt.ok_(list(val_iter(ileaf(REF_TREE.children[1].children[1]))) == [122])
def test_section_upstream_iteration():
leaves = [l for l in ileaf(REF_TREE2)]
ref_paths = [
[(1111, 11111), (11, 111, 1111), (0, 11)],
[(1111, 11112), (11, 111, 1111), (0, 11)],
[(1111, 11113), (11, 111, 1111), (0, 11)],
[(11, 112), (0, 11)],
[(1211, 12111), (12, 121, 1211), (0, 12)],
[(1211, 12112), (12, 121, 1211), (0, 12)],
[(12, 122), (0, 12)]]
for l, ref in zip(leaves, ref_paths):
nt.assert_equal([s for s in val_iter(isection(l, iupstream))], ref)
def compare_trees(tree1, tree2):
'''
Comparison between all the nodes and their respective radii between two trees.
Ids are do not have to be identical between the trees, and swapping is allowed
Returns:
False if the trees are not identical. True otherwise.
'''
leaves1 = list(tr.ileaf(tree1))
leaves2 = list(tr.ileaf(tree2))
if len(leaves1) != len(leaves2):
return False
else:
nleaves = len(leaves1)
for leaf1, leaf2 in product(leaves1, leaves2):
is_equal = True
for node1, node2 in izip(tr.val_iter(tr.iupstream(leaf1)),
tr.val_iter(tr.iupstream(leaf2))):
if any(node1[0:5] != node2[0:5]):
is_equal = False
continue
if is_equal:
nleaves -= 1
return nleaves == 0
def n_terminations(tree):
"""
Return number of terminations in tree
"""
return sum(1 for _ in tr.ileaf(tree))
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:
for p in point_iter(tree.ileaf(tt)):
print p
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')
for tt in nrn2.neurites:
for p in point_iter(tree.ileaf(tt)):
LOG.debug(p)
def n_terminations(tree):
"""
Return number of terminations in tree
"""
return sum(1 for _ in tr.ileaf(tree))
def path_end_to_end_distance(path):
'''Calculate and return end-to-end-distance of a given path.'''
trunk = path.value
return max(morphmath.point_dist(l, trunk) for l in tree.val_iter(tree.ileaf(path)))
