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')
cx = meshes_val['x'][xi, yi, zi]
cy = meshes_val['y'][xi, yi, zi]
cz = meshes_val['z'][xi, yi, zi]
positions = np.array([
[cx, cy, cz],
[cx - input_shape[0]/2, cy - input_shape[1]/2, cz],
[cx - input_shape[0]/2, cy + input_shape[1]/2, cz],
[cx + input_shape[0]/2, cy - input_shape[1]/2, cz],
[cx + input_shape[0]/2, cy + input_shape[1]/2, cz],
[cx + input_shape[0]/2, cy + input_shape[1]/2 - 1, cz]
])
max_id = min_id + positions.shape[0] - 1
# nodes = skel.define_nodes_from_positions(positions)
nodes = skel.define_nodes(
position_x=positions[:, 0].tolist(),
position_y=positions[:, 1].tolist(),
position_z=positions[:, 2].tolist(),
id=list(range(min_id, max_id + 1))
)
edges = np.array([
[1, 2],
[1, 3],
[1, 4],
[1, 5],
[2, 3],
[2, 4],
[3, 5],
[4, 6]
]) + skel.max_node_id()
if zi not in skel.group_ids:
skel.add_group(id=zi, name='plane{:03d}:X'.format(zi))