def add_nodes_as_trees():
# Test merging skeleton with multiple trees from nodes
skel = Skeleton('testdata/02_ref.nml')
nodes = skel.define_nodes([40000, 40100, 40200], [45000, 45100, 45200],
[1000, 1100, 1200])
skel.add_nodes_as_trees(nodes)
skel.write_nml('testdata/01_NT_merged_gen.nml')
def construct_from_parameters_add_tree():
parameters = Skeleton.define_parameters('2017-01-12_FD0156-2',
(11.24, 11.24, 32))
skel = Skeleton(parameters=parameters)
nodes = skel.define_nodes([40000, 40100, 40200], [45000, 45100, 45200],
[1000, 1100, 1200], [1, 2, 3])
edges = [(1, 3), (2, 3)]
skel.add_tree(nodes, edges)
skel.write_nml('testdata/PA_gen.nml')
def add_tree_from_skel():
# Test merging skeleton with multiple trees with a single tree from another skeleton
skel = Skeleton('testdata/01_ref.nml')
skel.add_tree_from_skel(Skeleton('testdata/02_ref.nml'),
tree_idx=1,
group_id=10)
# Test for unique node and tree ids in merged nml
_, c = np.unique(np.concatenate([nodes.id.values for nodes in skel.nodes]),
return_counts=True)
assert all(c < 2)
_, c = np.unique(skel.tree_ids, return_counts=True)
assert all(c < 2)
# Test writing
skel.write_nml('testdata/01_02_single_merged_gen.nml')
def add_trees_from_skel():
# Test merging skeletons both having both root and (nested) group trees
skel = Skeleton('testdata/01_ref.nml')
assert all([
Skeleton._num_conn_comp(Skeleton._get_graph(nodes, edges)) == 1
for nodes, edges in zip(skel.nodes, skel.edges)
])
skel.add_trees_from_skel(Skeleton('testdata/02_ref.nml'))
# Test for unique node and tree ids in merged nml
_, c = np.unique(np.concatenate([nodes.id.values for nodes in skel.nodes]),
return_counts=True)
assert all(c < 2)
_, c = np.unique(skel.tree_ids, return_counts=True)
assert all(c < 2)
# Test writing
assert all([
Skeleton._num_conn_comp(Skeleton._get_graph(nodes, edges)) == 1
for nodes, edges in zip(skel.nodes, skel.edges)
])
skel.write_nml('testdata/01_02_merged_gen.nml')
# Test reading
skel_gen = Skeleton('testdata/01_02_merged_gen.nml')
skel_ref = Skeleton('testdata/01_02_merged_ref.nml')
# Test for equal numbers of nodes and edges in both generated and reference merge nml
assert set([len(nodes) for nodes in skel_gen.nodes
]) == set([len(nodes) for nodes in skel_ref.nodes])
assert set([len(edges) for edges in skel_gen.edges
]) == set([len(edges) for edges in skel_ref.edges])
# Test merging skeleton having both root and group trees with one having only root trees
skel = Skeleton('testdata/02_ref.nml')
skel.add_trees_from_skel(Skeleton('testdata/03_ref.nml'))
skel.write_nml('testdata/02_03_merged_gen.nml')
# Test merging skeleton having only root trees with one having both root and group trees
skel = Skeleton('testdata/03_ref.nml')
skel.add_trees_from_skel(Skeleton('testdata/02_ref.nml'))
skel.write_nml('testdata/03_02_merged_gen.nml')
def construct_from_parameters_empty():
parameters = Skeleton.define_parameters('2017-01-12_FD0156-2',
(11.24, 11.24, 32))
skel = Skeleton(parameters=parameters)
skel.write_nml('testdata/PE_gen.nml')
def construct_from_nml():
skel = Skeleton('testdata/02_ref.nml')
skel.write_nml('testdata/02_gen.nml')