filtration_steps=args.filtration_steps)
print "Decomp. took {}s.".format(time.time() - t0)
print "Number of loops:", dual.number_of_nodes()
print "Number of tree nodes:", tree.number_of_nodes()
if args.save != "":
print "Saving file."
SAVE_FORMAT_VERSION = 5
sav = {'version':SAVE_FORMAT_VERSION, \
'leaf':leaf, 'tree':tree, 'dual':dual, \
'filtration':filtr, 'pruned':pruned, \
'removed-edges':removed_edges}
storage.save(sav, args.save)
print "Done."
if args.plot:
plt.figure()
plot.draw_leaf(leaf, "Input leaf data")
plt.figure()
plot.draw_leaf(pruned, "Pruned leaf data and dual graph")
plot.draw_dual(dual)
plt.figure()
plot.draw_tree(tree)
plt.figure()
plot.draw_filtration(filtr)
plt.show()
print "Drawing hierarchical trees."
plot.draw_tree(marked_tree, pos=tree_pos, fname=fname, fext=fext)
plt.figure()
if args.tree_heights:
pos = tree_pos_h
else:
pos = tree_pos
plot.draw_tree(marked_tree_no_ext, pos=pos,
fname=fname_no_ext, fext=fext)
plt.figure()
print "Drawing filtration."
plot.draw_filtration(filt, fname=fname, fext=fext, dpi=600)
print "Calculating average asymmetries."
Delta = args.Delta*marked_tree.node[marked_tree.graph['root']
]['subtree-degree']
Delta_no_ext = args.Delta*marked_tree_no_ext.node[
marked_tree_no_ext.graph['root']]['subtree-degree']
avg_asymmetries_plot(marked_tree, Delta, fname=fname +
"_asym_{}".format(args.Delta), fext=fext)
avg_asymmetries_plot(marked_tree_no_ext, Delta_no_ext,
mode="no-external", fname=fname_no_ext +
"_asym_{}".format(args.Delta), fext=fext)
plot_low_level_avg_asymmetries(marked_tree,
0.75, Delta, fname=fname + "_asym_{}".format(args.Delta),
fext=fext)