Covid_19_DINN/plot_results.py

import numpy as np
import pandas as pd
from src.plotter import Plotter

SRC_DIR = './results/'
I_PRED_SRC_DIR = SRC_DIR + 'I_predictions/'
SIM_DIR = './visualizations/'

def get_error(y, y_ref):
    err = []
    for i in range(len(y)):
        diff = y[i] - y_ref
        err.append(np.linalg.norm(diff) / np.linalg.norm(y_ref))
    return np.array(err).mean(axis=0)

STATE_LOOKUP = {'Schleswig_Holstein' : (79.5,0.0849),
                'Hamburg' : (84.5, 0.0948),
                'Niedersachsen' : (77.6, 0.0774),
                'Bremen' : (88.3,0.0933),
                'Nordrhein_Westfalen' : (79.5,0.0777),
                'Hessen' : (75.8,0.1017),
                'Rheinland_Pfalz' : (75.6,0.0895),
                'Baden_Wuerttemberg' : (74.5,0.0796),
                'Bayern' : (75.1,0.0952),
                'Saarland' : (82.4,0.1080),
                'Berlin' : (78.1,0.0667),
                'Brandenburg' : (68.1,0.0724),
                'Mecklenburg_Vorpommern' : (74.7,0.0540),
                'Sachsen' : (65.1,0.1109),
                'Sachsen_Anhalt' : (74.1,0.0785),
                'Thueringen' : (70.3,0.0837),
                'Germany' : (76.4, 0.0804)}

state_names = ['Schleswig-Holstein',
                'Hamburg', 
                'Lower Saxony', 
                'Bremen',
                'North Rhine-Westphalia',
                'Hesse',
                'Rhineland-Palatinate',
                'Baden-Württemberg',
                'Bavaria',
                'Saarland',
                'Berlin',
                'Brandenburg',
                'Mecklenburg-Western Pomerania',
                'Saxony',
                'Saxony-Anhalt',
                'Thuringia', 
                'Germany']

plotter = Plotter(additional_colors=['yellow', 'cyan', 'magenta', ])

# plot results for alpha and beta

print("Visualizing Alpha and Beta results")

# synth
param_matrix = np.genfromtxt(SRC_DIR + f'synthetic_parameters.csv', delimiter=',')
mean = param_matrix.mean(axis=0)
std = param_matrix.std(axis=0)

print("States Table form:")
print('{0:.4f}'.format(1/3), "&", '{0:.4f}'.format(mean[0]), "&", '{0:.4f}'.format(std[0]), "&", '{0:.4f}'.format(1/2), "&", '{0:.4f}'.format(mean[1]), "&", '{0:.4f}'.format(std[1]), "\\\ ")

plotter.scatter(np.arange(1, 6, 1), [param_matrix[:,0], param_matrix[:,1]], [r"$\alpha$", r"$\beta$"], (7,3.5), 'reproducability', '', true_values=[1/3, 1/2], xlabel='iteration')

vaccination_ratios = []
mean_std_parameters = {}
for state in STATE_LOOKUP.keys():
    state_matrix = np.genfromtxt(SRC_DIR + f'{state}_parameters.csv', delimiter=',')
    mean = state_matrix.mean(axis=0)
    std = state_matrix.std(axis=0)
    mean_std_parameters.update({state : (mean, std)})
    vaccination_ratios.append(STATE_LOOKUP[state][0])

values = np.array(list(mean_std_parameters.values()))
means = values[:,0]
stds = values[:,1]
alpha_means = means[:,0]
beta_means = means[:,1]
alpha_stds = stds[:,0]
beta_stds = stds[:,1]

print(f"Vaccination corr: {np.corrcoef(beta_means, vaccination_ratios)[0, 1]}")
vaccination_ratios = vaccination_ratios[:-1]
sn = np.array(state_names[:-1]).copy()
sn[12] = "MWP"
plotter.scatter(sn, 
                [alpha_means[:-1], beta_means[:-1]], 
                [r'$\alpha$', r'$\beta$', ],
                (12, 6), 
                'mean_std_alpha_beta_res',
                '',
                std=[alpha_stds[:-1], beta_stds[:-1]],
                true_values=[alpha_means[-1], beta_means[-1]],
                true_label='Germany',
                xlabel_rotation=60,
                plot_legend=True,
                legend_loc="lower right")

print("States Table form:")
for i, state in enumerate(STATE_LOOKUP.keys()):
    print(state_names[i], "&", '{0:.3f}'.format(alpha_means[i]), "{\\tiny $\\pm",'{0:.3f}'.format(alpha_stds[i]), "$}", "&", '{0:.3f}'.format(beta_means[i]), "{\\tiny $\\pm", '{0:.3f}'.format(beta_stds[i]), "$}", "&", STATE_LOOKUP[state][1], "&", '{0:.3f}'.format(beta_means[i]-beta_means[16]), "&", '{0:.1f}'.format(STATE_LOOKUP[state][0]), "\\\ ")

print()
# plot results for reproduction number

# synth
synth_iterations = []
for i in range(10):   
    synth_iterations.append(np.genfromtxt(SRC_DIR + f'synthetic_{i}.csv', delimiter=','))

synth_matrix = np.array(synth_iterations)
t = np.arange(0, len(synth_matrix[0]), 1)
synth_r_t = np.zeros(150, dtype=np.float64)
for i, time in enumerate(range(150)):
    synth_r_t[i] = -np.tanh(time * 0.05 - 2) * 0.4 + 1.35

print(f"Synthetic error R_t: {get_error(synth_matrix.mean(axis=0), synth_r_t)}")
plotter.plot(t, 
             [synth_matrix.mean(axis=0), synth_r_t],
             [r'$\mathcal{R}_t$', r'true $\mathcal{R}_t$'], 
             f"synthetic_R_t_statistics", 
             r"Synthetic data $\mathcal{R}_t$", 
             (9, 6),
             fill_between=[synth_matrix.std(axis=0)],
             xlabel="time / days")

pred_synth = np.genfromtxt(I_PRED_SRC_DIR + f'synthetic_0_I_prediction.csv', delimiter=',')

print(f"Synthetic error I: {get_error(pred_synth[2], pred_synth[1])}")

plotter.plot(pred_synth[0], 
             [pred_synth[2], pred_synth[1]],
             [r'prediction $I$', r'true $I$'], 
             f"synthetic_I_prediction", 
             r"Synthetic data $I$ prediction", 
             (9, 6),
             xlabel="time / days",
             ylabel='amount of people')

EVENT_LOOKUP = {'start of vaccination' : 455,
                'alpha variant' : 357,
                'delta variant' : 473,
                'omicron variant' : 663}


ALPHA = [1 / 14, 1 / 5]


cluster_counter = 1
cluster_idx = 0

in_text_r_t_mean = []
in_text_r_t_std = []
in_text_I = []
in_text_I_std = []

cluster_r_t_mean = []
cluster_r_t_std = []
cluster_I = []
cluster_I_std = []
cluster_states = []

for k, state in enumerate(STATE_LOOKUP.keys()):

    if state == "Thueringen":
        l = 1
    elif state == "Bremen":
        l = 0
    # data fetch arrays
    r_t = []
    pred_i = []
    true_i = []
    cluster_states.append(state_names[k])
    cluster_r_t_mean.append([])
    cluster_r_t_std.append([])
    cluster_I.append([])
    cluster_I_std.append([np.zeros(1200), np.zeros(1200)])
    if state == "Thueringen" or state == "Bremen":
        in_text_r_t_mean.append([])
        in_text_r_t_std.append([])   
        in_text_I.append([])
        in_text_I_std.append([np.zeros(1200), np.zeros(1200)])
    for i, alpha in enumerate(ALPHA):
        iterations = []
        predictions = []
        true = []
        for j in range(10): 
            iterations.append(np.genfromtxt(SRC_DIR + f'{state}_{i}_{j}.csv', delimiter=','))
            if (k >= 3 and j == 3) or j > 3:
                data = np.genfromtxt(I_PRED_SRC_DIR + f'{state}_{i}_{j}_I_prediction.csv', delimiter=',')
                predictions.append(data[2])
                true = data[1]
        iterations = np.array(iterations)
        r_t.append(iterations)

        predictions = np.array(predictions)
        pred_i.append(predictions)
        true_i.append(true)

        cluster_r_t_mean[cluster_counter-1].append(iterations.mean(axis=0))
        cluster_r_t_std[cluster_counter-1].append(iterations.std(axis=0))
        if state == "Thueringen" or state == "Bremen":
            in_text_r_t_mean[l].append(iterations.mean(axis=0))
            in_text_r_t_std[l].append(iterations.std(axis=0))
    if state == "Thueringen" or state == "Bremen":
        in_text_I[l].append(true_i[0])
        in_text_I[l].append(true_i[1])
        in_text_I[l].append(pred_i[0].mean(axis=0))
        in_text_I[l].append(pred_i[1].mean(axis=0))
        in_text_I_std[l].append(pred_i[0].std(axis=0))
        in_text_I_std[l].append(pred_i[1].std(axis=0))

    cluster_I[cluster_counter-1].append(true_i[0])
    cluster_I[cluster_counter-1].append(true_i[1])
    cluster_I[cluster_counter-1].append(pred_i[0].mean(axis=0))
    cluster_I[cluster_counter-1].append(pred_i[1].mean(axis=0))
    cluster_I_std[cluster_counter-1].append(pred_i[0].std(axis=0))
    cluster_I_std[cluster_counter-1].append(pred_i[1].std(axis=0))

    # plot
    print(f"{state_names[k]} & {'{0:.3f}'.format(get_error(pred_i[0], true_i[0]))} & {'{0:.3f}'.format(get_error(pred_i[1], true_i[1]))} & \phantom{{0}} & {(r_t[0] > 1).sum(axis=1).mean()} & {(r_t[1] > 1).sum(axis=1).mean()} & {'{0:.3f}'.format(r_t[0].max(axis=1).mean())} & {'{0:.3f}'.format(r_t[1].max(axis=1).mean())}\\\ ")
    if len(cluster_states) == 4 and state != "Thueringen" or len(cluster_states) == 5 and state == "Germany":
        t = np.arange(0, 1200, 1)
        if len(cluster_states) == 5:
            y_lim_exception = 4
        else:
            y_lim_exception = None
        plotter.cluster_plot(t,
                            cluster_r_t_mean,
                            [r"$\alpha=\frac{1}{14}$", r"$\alpha=\frac{1}{5}$"],
                            (len(cluster_states), 1),
                            (9, 6),
                            f'r_t_cluster_{cluster_idx}',
                            [state + r"  $\mathcal{R}_t$" for state in cluster_states],
                            fill_between=cluster_r_t_std,
                            event_lookup=EVENT_LOOKUP,
                            xlabel='time / days',
                            ylim=(0.3, 2.0),
                            legend_loc=(0.53, 0.992),
                            number_of_legend_columns=3)
        plotter.cluster_plot(t,
                             cluster_I,
                             [r"true $I$ $\alpha=\frac{1}{14}$", 
                             r"true $I$ $\alpha=\frac{1}{5}$", 
                             r"prediction $I$ $\alpha=\frac{1}{14}$", 
                             r"prediction $I$ $\alpha=\frac{1}{5}$"],
                             (len(cluster_states), 1),
                             (9, 6),
                             f'I_cluster_{cluster_idx}',
                             [state + r" $I$ prediction" for state in cluster_states],
                             fill_between=cluster_I_std,
                             xlabel='time / days',
                             ylabel='amount of people',
                             same_axes=False,
                             ylim=(0, 600000),
                             legend_loc=(0.55, 0.992),
                             number_of_legend_columns=2,
                             y_lim_exception=y_lim_exception)
        cluster_counter = 0
        cluster_idx += 1
        cluster_r_t_mean = []
        cluster_r_t_std = []
        cluster_I = []
        cluster_I_std = []
        cluster_states = []
    cluster_counter += 1

plotter.cluster_plot(t,
                    in_text_r_t_mean,
                    [r"$\alpha=\frac{1}{14}$", r"$\alpha=\frac{1}{5}$"],
                    (2, 1),
                    (9, 6),
                    f'r_t_cluster_intext',
                    [state + r"  $\mathcal{R}_t$" for state in ['Bremen', 'Thuringia']],
                    fill_between=in_text_r_t_std,
                    event_lookup=EVENT_LOOKUP,
                    xlabel='time / days',
                    ylim=(0.3, 2.0),
                    legend_loc=(0.53, 0.999),
                    add_y_space=0.08,
                    number_of_legend_columns=3)
plotter.cluster_plot(t,
                     in_text_I,
                     [r"true $I$ $\alpha=\frac{1}{14}$", 
                     r"true $I$ $\alpha=\frac{1}{5}$", 
                     r"prediction $I$ $\alpha=\frac{1}{14}$", 
                     r"prediction $I$ $\alpha=\frac{1}{5}$"],
                     (2, 1),
                     (9, 6),
                     f'I_cluster_intext',
                     [state + r" $I$ prediction" for state in ['Bremen', 'Thuringia']],
                     fill_between=in_text_I_std,
                     xlabel='time / days',
                     ylabel='amount of people',
                     ylim=(0, 600000),
                     legend_loc=(0.55, 0.999),
                     add_y_space=0.08,
                     number_of_legend_columns=2)