add example script to plot branching simulation

Author: jonaspleyer

examples/plot.py

@@ -0,0 +1,36 @@
+import cr_bayesian_optim as crb
+import matplotlib.pyplot as plt
+import numpy as np
+
+if __name__ == "__main__":
+    # Define Parameters for Simulation
+    options = crb.Options(show_progressbar=True)
+    options.domain.domain_size = 2000
+    options.time.t_max = 2000
+
+    # Load Results or Run new Simulation if needed
+    cells, out_path = crb.sim_branching.load_or_compute_full(options)
+
+    # Specify bounds for visualizing the intracellular
+    # and extracellular concentrations
+    intra_bounds = (0.5, 1)
+    extra_bounds = (0, 10.0)
+
+    # Plots the last iteration of the simulation
+    last_iter = sorted(cells.keys())[-1]
+    crb.plotting.plot_iteration(
+        last_iter,
+        intra_bounds,
+        extra_bounds,
+        out_path,
+    )
+
+    # Simple Plot to visualize the Growth Curve
+    x = np.array(sorted(cells.keys())) * options.time.dt / 60
+    y = [len(cells[i]) for i in cells.keys()]
+
+    fig, ax = plt.subplots()
+    ax.set_title("Number of Cells")
+    ax.plot(x, y, color=crb.plotting.COLOR1)
+    ax.set_xlabel("Time [min]")
+    plt.show()