def has_no_cycle(chain: Chain):
graph, _ = as_nx_graph(chain)
cycled = list(simple_cycles(graph))
if len(cycled) > 0:
raise ValueError(f'{ERROR_PREFIX} Chain has cycles')
return True
def has_no_isolated_components(chain: Chain):
graph, _ = as_nx_graph(chain)
ud_graph = nx.Graph()
ud_graph.add_nodes_from(graph)
ud_graph.add_edges_from(graph.edges)
if not nx.is_connected(ud_graph):
raise ValueError(f'{ERROR_PREFIX} Chain has isolated components')
return True
def visualise(chain: Chain):
try:
chain.sort_nodes()
graph, node_labels = as_nx_graph(chain=chain)
pos = node_positions(graph.to_undirected())
plt.figure(figsize=(10, 16))
nx.draw(graph,
pos=pos,
with_labels=True,
labels=node_labels,
font_size=12,
font_family='calibri',
font_weight='bold',
node_size=7000,
width=2.0,
node_color=colors_by_node_labels(node_labels),
cmap='Set3')
plt.show()
except Exception as ex:
print(f'Visualisation failed with {ex}')
def _visualise_chains(chains, fitnesses):
fitnesses = deepcopy(fitnesses)
last_best_chain = chains[0]
prev_fit = fitnesses[0]
for ch_id, chain in enumerate(chains):
graph, node_labels = as_nx_graph(chain=chain)
pos = node_positions(graph.to_undirected())
plt.rcParams['axes.titlesize'] = 20
plt.rcParams['axes.labelsize'] = 20
plt.rcParams['figure.figsize'] = [10, 10]
plt.title('Current chain')
nx.draw(graph,
pos=pos,
with_labels=True,
labels=node_labels,
font_size=12,
font_family='calibri',
font_weight='bold',
node_size=scaled_node_size(chain.length),
width=2.0,
node_color=colors_by_node_labels(node_labels),
cmap='Set3')
path = f'{ComposerVisualiser.temp_path}ch_{ch_id}.png'
plt.savefig(path, bbox_inches='tight')
plt.cla()
plt.clf()
plt.close('all')
path_best = f'{ComposerVisualiser.temp_path}best_ch_{ch_id}.png'
if fitnesses[ch_id] > prev_fit:
fitnesses[ch_id] = prev_fit
else:
last_best_chain = chain
prev_fit = fitnesses[ch_id]
best_graph, best_node_labels = as_nx_graph(chain=last_best_chain)
pos = node_positions(best_graph.to_undirected())
plt.rcParams['axes.titlesize'] = 20
plt.rcParams['axes.labelsize'] = 20
plt.rcParams['figure.figsize'] = [10, 10]
plt.title(f'Best chain after {round(ch_id)} evals')
nx.draw(best_graph,
pos=pos,
with_labels=True,
labels=best_node_labels,
font_size=12,
font_family='calibri',
font_weight='bold',
node_size=scaled_node_size(chain.length),
width=2.0,
node_color=colors_by_node_labels(best_node_labels),
cmap='Set3')
plt.savefig(path_best, bbox_inches='tight')
plt.cla()
plt.clf()
plt.close('all')
def has_no_isolated_nodes(chain: Chain):
graph, _ = as_nx_graph(chain)
isolated = list(isolates(graph))
if len(isolated) > 0:
raise ValueError(f'{ERROR_PREFIX} Chain has isolated nodes')
return True