def plot_distance_matrix(param_dir: str, names: List[str], ages: List[float],
n_layers: int):
assert len(names) == len(ages)
roots = []
for name, age in zip(names, ages):
rs = RootSystem()
rs.readParameters(join(param_dir, f"{name}.xml"))
rs.initialize()
rs.simulate(age)
pyroot = Root(rs)
pyroot.rescale()
roots.append(pyroot)
n = len(roots)
dist_matrix = np.zeros((n, n))
for i, root_i in enumerate(roots):
for j, root_j in enumerate(roots[:i + 1]):
dist_matrix[i, j] = lw_wasserstein(root_i, root_j, n_layers)
cleaned_names = [" ".join(name.split("_")[:-2]) for name in names]
#cleaned_names = ages
heatmap = pd.DataFrame(dist_matrix,
columns=cleaned_names,
index=cleaned_names)
ax = sns.heatmap(heatmap, square=True, cmap="Greens")
ax.tick_params(axis='both', which='both', length=0)
ax.xaxis.set_ticks_position('bottom')
plt.xticks(rotation=45)
plt.yticks(rotation=0)
bottom, top = ax.get_ylim()
ax.set_ylim(bottom + 0.5, top - 0.5)
plt.savefig(join(os.environ["HOME"], "reportOTDendrit", "images",
f"distance_matrix_Anagallis.pdf"),
bbox_inches="tight")
def plot_barycenters(param_dir: str, names: List[str], ages: List[float]):
roots = []
for name, age in zip(names, ages):
rs = RootSystem()
rs.readParameters(join(param_dir, f"{name}.xml"))
rs.initialize()
rs.simulate(age)
pyroot = Root(rs)
pyroot.rescale()
roots.append(pyroot)
for root in roots:
print(root.n_nodes)
pt_bar = point_cloud_barycenter(roots)
fig = plot_barycenter_nodes(pt_bar)
fig.write_image(
join(os.environ["HOME"], "reportOTDendrit", "images",
f"ptbar_{names[0]}_{names[1]}.pdf"))
_, _, bar_nodes = lw_barycenter(roots, n_layers=100, reg=1e-1)
fig = plot_barycenter_nodes(bar_nodes)
fig.write_image(
join(os.environ["HOME"], "reportOTDendrit", "images",
f"lwbar_{names[0]}_{names[1]}.pdf"))
