def main():
parser = argparse.ArgumentParser()
parser.add_argument('filename')
options = parser.parse_args()
results = collections.defaultdict(list)
with open(options.filename) as f:
for line in f:
for pattern in patterns:
m = pattern.search(line)
if m:
gd = m.groupdict()
iteration = gd['iter']
del gd['iter']
key, val = list(gd.items())[0]
results[key].append((float(iteration), float(val)))
fig, ax = util.make_figure()
for key, data in sorted(results.items()):
x, y = list(zip(*data))
ax.loglog(x, y, label=key)
util.save_columns(options.filename + '-' + key + '.tsv', x, y)
ax.set_xlabel('Conjugate Gradient Iteration')
ax.set_ylabel('Spinor Norms')
ax.set_title(options.filename)
util.save_figure(fig, options.filename)
def plot_num_cases_over_period(output_dir, fig_name, all_num_cases,
display_scenario_names, y_label):
plt.violinplot(all_num_cases)
plt.plot(range(1,
len(all_num_cases) + 1),
[np.mean(scen) for scen in all_num_cases],
marker="o",
linestyle="None")
plt.xticks(range(1,
len(all_num_cases) + 1),
scenario_display_names,
rotation=25)
plt.ylabel(y_label)
save_figure(output_dir, fig_name, extension="png")
def io_extract_mass(paths_in, path_out):
twopts_orig = correlators.loader.folded_list_loader(paths_in)
sample_count = 3 * len(twopts_orig)
b_twopts = bootstrap.Boot(
bootstrap.make_dist_draw(twopts_orig, sample_count))
b_corr_matrix = bootstrap.Boot([
correlators.corrfit.correlation_matrix(twopts)
for twopts in b_twopts.dist
])
omit_pre = 7
b_inv_corr_mat = bootstrap.Boot([
corr_matrix[omit_pre:, omit_pre:].getI()
for corr_matrix in b_corr_matrix.dist
])
time_extent = len(b_twopts.dist[0][0])
time = np.arange(time_extent)
fit_function = correlators.fit.cosh_fit_decorator(2 * (time_extent - 1))
b_fit_param = bootstrap.Boot([
perform_fits(time, bootstrap.average_arrays(twopts),
bootstrap.std_arrays(twopts), inv_corr_mat, fit_function,
(0.4, 1.0, 0.0), omit_pre)
for twopts, inv_corr_mat in zip(b_twopts.dist, b_inv_corr_mat.dist)
])
fig, ax = util.make_figure()
ax.errorbar(time, bootstrap.average_arrays(b_twopts.cen),
bootstrap.std_arrays(b_twopts.cen))
ax.plot(time, fit_function(time, *b_fit_param.cen))
ax.set_yscale('log')
util.save_figure(fig, 'test-corr.pdf')
print('cen', b_fit_param.cen[0])
print('val', b_fit_param.val[0])
print('err', b_fit_param.err[0])
print('len', len(twopts_orig), len(b_fit_param.dist))
np.savetxt(
path_out,
np.column_stack(
[b_fit_param.cen[0], b_fit_param.val[0], b_fit_param.err[0]]))
def main():
options = _parse_args()
fig, ax = util.make_figure()
t, e = util.load_columns(
'/home/mu/Dokumente/Studium/Master_Science_Physik/Masterarbeit//Runs/0106-bmw-rho011/shard-wflow.config-100.out.xml.e.tsv'
)
t, w = util.load_columns(
'/home/mu/Dokumente/Studium/Master_Science_Physik/Masterarbeit//Runs/0106-bmw-rho011/shard-wflow.config-100.out.xml.w.tsv'
)
data = np.loadtxt('gradflow.000100', skiprows=1)
tm_traj = data[:, 0]
tm_t = data[:, 1]
tm_P = data[:, 2]
tm_Eplaq = data[:, 3]
tm_Esym = data[:, 4]
tm_tsqEplaq = data[:, 5]
tm_tsqEsym = data[:, 6]
tm_Wsym = data[:, 7]
for i, method in enumerate(
['gradient', 'chain-gradient', 'explicit-sym', 'explicit-asym']):
tm_my_w = wflow.derive_w(tm_t, tm_Esym, method=method)
ax.plot(tm_t + 0.1 * i, np.abs(tm_Wsym - tm_my_w), label=method)
ax.set_yscale('log')
ax.set_xlabel('$t/a^2$ (shifted)')
ax.set_ylabel(
r'$\left|(w/a)^\mathrm{tmLQCD} - (w/a)^\mathrm{Method}\right|$')
util.save_figure(fig, 'plot-wflow-norm')
x = np.linspace(0, 4, 1000)
y = np.sin(x)
z = x * (x**2 * np.cos(x) + 2 * x * np.sin(x))
fig, ax = util.make_figure()
for i, method in enumerate(
['gradient', 'chain-gradient', 'explicit-sym', 'explicit-asym']):
w = wflow.derive_w(x, y, method=method)
ax.plot(x + 0.1 * i, np.abs(z - w), label=method)
ax.set_xlabel('$x$ (shifted)')
ax.set_ylabel('absolute deviation from analytic $w(x)$')
ax.set_yscale('log')
util.save_figure(fig, 'plot-gradient-check')
def plot_resurgence_probabilities(output_dir, fig_name,
all_num_case_after_release,
display_scenario_names,
extinction_threshold):
resurgence_probs = []
for scenario in all_num_case_after_release:
resurgence_probs.append(
len([run for run in scenario if run >= extinction_threshold]) /
len(scenario))
plt.bar(range(len(resurgence_probs)), resurgence_probs)
plt.xticks(range(len(resurgence_probs)),
display_scenario_names,
rotation=25)
plt.ylabel("Resurgence probability")
plt.ylim((0, 1))
save_figure(output_dir, fig_name)
def plot_extinction_probabilities(output_dir,
fig_name,
display_scenario_names,
all_total_cases,
extinction_threshold=0):
extinction_probabilities = []
for scenario_total_cases in all_total_cases:
extinction_probabilities.append(
len([x
for x in scenario_total_cases if x < extinction_threshold]) /
len(scenario_total_cases))
plt.bar(range(len(all_total_cases)), extinction_probabilities)
plt.xticks(range(len(display_scenario_names)),
display_scenario_names,
rotation=25)
plt.ylabel("Extinction probability (threshold = {} cases)".format(
extinction_threshold))
plt.ylim(0, 1.1)
save_figure(output_dir, fig_name)
def plot_effective_r_by_day(output_dir,
fig_name,
scenario_name,
rt_by_day,
num_days,
fraction=False):
mean = []
lower = []
upper = []
for day in range(num_days):
er_on_day = [run[day] for run in rt_by_day]
er_on_day = [result for result in er_on_day if not np.isnan(result)]
mean.append(np.mean(er_on_day) if len(er_on_day) > 0 else np.nan)
lower.append(
np.percentile(er_on_day, 2.5) if len(er_on_day) > 0 else np.nan)
upper.append(
np.percentile(er_on_day, 97.5) if len(er_on_day) > 0 else np.nan)
plt.plot(range(num_days), mean)
plt.fill_between(range(num_days), lower, upper, color="lightgrey")
if not fraction: # If looking at mean Rt per day, add reference line at Rt = 1
plt.plot(range(num_days), [1] * num_days)
plt.xlabel("Simulation day")
plt.xlim(0, num_days)
if fraction:
plt.ylabel("Fraction of Rt >= 1")
plt.ylim(-0.1, 1.1)
else:
plt.ylabel("Mean Rt")
plt.ylim(-0.5, 22)
save_figure(output_dir, fig_name + "_" + scenario_name)
def plot_herd_immunity_threshold(output_dir,
fig_name,
display_scenario_names,
all_herd_immunity_thresholds,
show_day=False):
means = [
np.mean(scenario_results)
for scenario_results in all_herd_immunity_thresholds
]
plt.violinplot(all_herd_immunity_thresholds)
plt.plot(range(1, len(means) + 1), means, linestyle="None", marker="o")
plt.xticks(range(1,
len(scenario_display_names) + 1),
display_scenario_names,
rotation=25)
if show_day:
plt.ylabel("Day on which Rt >= 1 for the last time")
else:
plt.ylabel("Herd immunity threshold")
save_figure(output_dir, fig_name, extension="png"
) # Use png extension to accurately save opaqueness in figure
def main():
options = _parse_args()
pattern = re.compile(
r'0105-perf_nodes=(?P<A_nodes>\d+)_ntasks=(?P<B_ntasks>\d+)_cpus=(?P<C_cpus>\d+)_affinity=(?P<E_affinity>\w+?)/'
)
pattern_total_time = re.compile('HMC: total time = ([\d.]+) secs')
rows = []
for run in options.run:
print(run)
m = pattern.match(run)
if not m:
continue
cols1 = m.groupdict()
nodes = int(cols1['A_nodes'])
tasks = int(cols1['B_ntasks'])
cpus = int(cols1['C_cpus'])
cols1['D_SMT'] = tasks * cpus // 24
try:
cols2 = {
'QPhiX CG Perf':
np.loadtxt(
os.path.join(
run,
'extract-solver-QPhiX_Clover_CG-gflops_per_node.tsv'))
[1],
'QPhiX M-Shift Perf':
np.loadtxt(
os.path.join(
run,
'extract-solver-QPhiX_Clover_M-Shift_CG-gflops_per_node.tsv'
))[1],
}
except FileNotFoundError as e:
print(e)
continue
logfile = glob.glob(os.path.join(run, 'slurm-*.out'))[0]
with open(logfile) as f:
lines = f.readlines()
m = pattern_total_time.match(lines[-1])
if m:
cols2['minutes'] = float(m.group(1)) / 60
else:
cols2['minutes'] = 0
print(cols2.values())
rows.append((cols1, cols2))
print()
print()
for key in itertools.chain(sorted(cols1.keys()), sorted(cols2.keys())):
print('{:15s}'.format(str(key)[:13]), end='')
print()
for cols1, cols2 in rows:
for key, value in itertools.chain(sorted(cols1.items()),
sorted(cols2.items())):
print('{:15s}'.format(str(value)[:13]), end='')
print()
for x in cols1.keys():
for y in cols2.keys():
fig, ax = util.make_figure()
data = collections.defaultdict(list)
for c1, c2 in rows:
data[c1[x]].append(c2[y])
d = [value for key, value in sorted(data.items())]
l = [key for key, value in sorted(data.items())]
ax.boxplot(d, labels=l)
ax.set_xlabel(x)
ax.set_ylabel(y)
util.save_figure(fig, 'boxplot-{}-{}'.format(x, y))
def main():
options = _parse_args()
R = 300
# Read in the data from the paper.
a_inv_val = 1616
a_inv_err = 20
a_inv_dist = bootstrap.make_dist(a_inv_val, a_inv_err, n=R)
aml, ams, l, t, trajectories, ampi_val, ampi_err, amk_val, amk_err, f_k_f_pi_val, f_k_f_pi_err = util.load_columns(
'physical_point/gmor.txt')
ampi_dist = bootstrap.make_dist(ampi_val, ampi_err, n=R)
amk_dist = bootstrap.make_dist(amk_val, amk_err, n=R)
mpi_dist = [ampi * a_inv for ampi, a_inv in zip(ampi_dist, a_inv_dist)]
mk_dist = [amk * a_inv for amk, a_inv in zip(amk_dist, a_inv_dist)]
# Convert the data in lattice units into physical units.
mpi_dist = [a_inv * ampi for ampi, a_inv in zip(ampi_dist, a_inv_dist)]
mpi_val, mpi_avg, mpi_err = bootstrap.average_and_std_arrays(mpi_dist)
mpi_sq_dist = [mpi**2 for mpi in mpi_dist]
mpi_sq_val, mpi_sq_avg, mpi_sq_err = bootstrap.average_and_std_arrays(
mpi_sq_dist)
ampi_sq_dist = [ampi**2 for ampi in ampi_dist]
ampi_sq_val, ampi_sq_avg, ampi_sq_err = bootstrap.average_and_std_arrays(
ampi_sq_dist)
# Do a GMOR fit in order to extract `a B` and `a m_cr`.
popt_dist = [
op.curve_fit(gmor_pion, aml, ampi_sq)[0] for ampi_sq in ampi_sq_dist
]
aB_dist = [popt[0] for popt in popt_dist]
amcr_dist = [popt[1] for popt in popt_dist]
aB_val, aB_avg, aB_err = bootstrap.average_and_std_arrays(aB_dist)
amcr_val, amcr_avg, amcr_err = bootstrap.average_and_std_arrays(amcr_dist)
print('aB =', siunitx(aB_val, aB_err))
print('am_cr =', siunitx(amcr_val, amcr_err))
ams_paper = -0.057
ams_phys = ams_paper - amcr_val
ams_red = 0.9 * ams_phys
ams_bare_red = ams_red + amcr_val
print(ams_paper, ams_phys, ams_red, ams_bare_red)
print()
print('Mass preconditioning masses:')
amlq = aml - amcr_val
for i in range(3):
amprec = amlq * 10**i + amcr_val
kappa = 1 / (amprec * 2 + 8)
print('a m_prec:', amprec)
print('κ', kappa)
exit()
diff_dist = [
np.sqrt(2) * np.sqrt(mk**2 - 0.5 * mpi**2)
for mpi, mk in zip(mpi_dist, mk_dist)
]
diff_val, diff_avg, diff_err = bootstrap.average_and_std_arrays(diff_dist)
popt_dist = [
op.curve_fit(linear, mpi, diff)[0]
for mpi, diff in zip(mpi_dist, diff_dist)
]
fit_x = np.linspace(np.min(mpi_dist), np.max(mpi_dist), 100)
fit_y_dist = [linear(fit_x, *popt) for popt in popt_dist]
fit_y_val, fit_y_avg, fit_y_err = bootstrap.average_and_std_arrays(
fit_y_dist)
# Physical meson masses from FLAG paper.
mpi_phys_dist = bootstrap.make_dist(134.8, 0.3, R)
mk_phys_dist = bootstrap.make_dist(494.2, 0.3, R)
mpi_phys_val, mpi_phys_avg, mpi_phys_err = bootstrap.average_and_std_arrays(
mpi_phys_dist)
ampi_phys_dist = [
mpi_phys / a_inv for a_inv, mpi_phys in zip(a_inv_dist, mpi_phys_dist)
]
amk_phys_dist = [
mk_phys / a_inv for a_inv, mk_phys in zip(a_inv_dist, mk_phys_dist)
]
ampi_phys_val, ampi_phys_avg, ampi_phys_err = bootstrap.average_and_std_arrays(
ampi_phys_dist)
amk_phys_val, amk_phys_avg, amk_phys_err = bootstrap.average_and_std_arrays(
amk_phys_dist)
print('aM_pi phys =', siunitx(ampi_phys_val, ampi_phys_err))
print('aM_k phys =', siunitx(amk_phys_val, amk_phys_err))
new_b_dist = [
np.sqrt(mk_phys**2 - 0.5 * mpi_phys**2) - popt[0] * mpi_phys for
mpi_phys, mk_phys, popt in zip(mpi_phys_dist, mk_phys_dist, popt_dist)
]
diff_sqrt_phys_dist = [
np.sqrt(mk_phys**2 - 0.5 * mpi_phys**2)
for mpi_phys, mk_phys in zip(mpi_phys_dist, mk_phys_dist)
]
diff_sqrt_phys_val, diff_sqrt_phys_avg, diff_sqrt_phys_err = bootstrap.average_and_std_arrays(
diff_sqrt_phys_dist)
ex_x = np.linspace(120, 700, 100)
ex_y_dist = [
linear(ex_x, popt[0], b) for popt, b in zip(popt_dist, new_b_dist)
]
ex_y_val, ex_y_avg, ex_y_err = bootstrap.average_and_std_arrays(ex_y_dist)
ams_art_dist = [
linear(mpi, popt[0], b)**2 / a_inv**2 / aB - amcr
for mpi, popt, b, a_inv, aB, amcr in zip(
mpi_dist, popt_dist, new_b_dist, a_inv_dist, aB_dist, amcr_dist)
]
ams_art_val, ams_art_avg, ams_art_err = bootstrap.average_and_std_arrays(
ams_art_dist)
print('a m_s with artifacts', siunitx(ams_art_val, ams_art_err))
fig, ax = util.make_figure()
ax.fill_between(fit_x,
fit_y_val + fit_y_err,
fit_y_val - fit_y_err,
color='red',
alpha=0.2)
ax.plot(fit_x, fit_y_val, label='Fit', color='red')
ax.fill_between(ex_x,
ex_y_val + ex_y_err,
ex_y_val - ex_y_err,
color='orange',
alpha=0.2)
ax.plot(ex_x, ex_y_val, label='Extrapolation', color='orange')
ax.errorbar(mpi_val,
diff_val,
xerr=mpi_err,
yerr=diff_err,
linestyle='none',
label='Data (Dürr 2010)')
ax.errorbar([mpi_phys_val], [diff_sqrt_phys_val],
xerr=[mpi_phys_err],
yerr=[diff_sqrt_phys_err],
label='Physical Point (Aoki)')
util.save_figure(fig, 'test')
np.savetxt('artifact-bmw-data.tsv',
np.column_stack([mpi_val, diff_val, mpi_err, diff_err]))
np.savetxt('artifact-bmw-fit.tsv', np.column_stack([fit_x, fit_y_val]))
np.savetxt('artifact-bmw-band.tsv',
bootstrap.pgfplots_error_band(fit_x, fit_y_val, fit_y_err))
np.savetxt(
'artifact-phys-data.tsv',
np.column_stack([[mpi_phys_val], [diff_sqrt_phys_val], [mpi_phys_err],
[diff_sqrt_phys_err]]))
np.savetxt('artifact-phys-fit.tsv', np.column_stack([ex_x, ex_y_val]))
np.savetxt('artifact-phys-band.tsv',
bootstrap.pgfplots_error_band(ex_x, ex_y_val, ex_y_err))
np.savetxt('artifact-ms.tsv',
np.column_stack([mpi_val, ams_art_val, mpi_err, ams_art_err]))
# Compute the strange quark mass that is needed to obtain a physical meson
# mass difference, ignoring lattice artifacts.
ams_phys_dist = [(amk_phys**2 - 0.5 * ampi_phys**2) / aB - amcr
for ampi_phys, amk_phys, aB, amcr in zip(
ampi_phys_dist, amk_phys_dist, aB_dist, amcr_dist)]
ams_phys_cen, ams_phys_val, ams_phys_err = bootstrap.average_and_std_arrays(
ams_phys_dist)
print('M_K = {} MeV <== am_s ='.format(siunitx(494.2, 0.3)),
siunitx(ams_phys_cen, ams_phys_err))
aml_phys_dist = [
op.newton(lambda aml: gmor_pion(aml, *popt) - ampi_phys**2,
np.min(aml))
for popt, ampi_phys in zip(popt_dist, ampi_phys_dist)
]
fit_x = np.linspace(np.min(aml_phys_dist), np.max(aml), 100)
fit_y_dist = [
np.sqrt(gmor_pion(fit_x, *popt)) * a_inv
for popt, a_inv in zip(popt_dist, a_inv_dist)
]
fit_y_cen, fit_y_val, fit_y_err = bootstrap.average_and_std_arrays(
fit_y_dist)
np.savetxt('physical_point/mpi-vs-aml-data.tsv',
np.column_stack([aml, mpi_val, mpi_err]))
np.savetxt('physical_point/mpi-vs-aml-fit.tsv',
np.column_stack([fit_x, fit_y_cen]))
np.savetxt('physical_point/mpi-vs-aml-band.tsv',
bootstrap.pgfplots_error_band(fit_x, fit_y_cen, fit_y_err))
aml_phys_val, aml_phys_avg, aml_phys_err = bootstrap.average_and_std_arrays(
aml_phys_dist)
mpi_cen, mpi_val, mpi_err = bootstrap.average_and_std_arrays(mpi_dist)
#aml_240_val, aml_240_avg, aml_240_err = bootstrap.average_and_std_arrays(aml_240_dist)
print('M_pi = {} MeV <== am_l ='.format(siunitx(134.8, 0.3)),
siunitx(aml_phys_val, aml_phys_err))
#print('M_pi = 240 MeV <== am_l =', siunitx(aml_240_val, aml_240_err))
fig = pl.figure()
ax = fig.add_subplot(2, 1, 1)
ax.fill_between(fit_x,
fit_y_val - fit_y_err,
fit_y_val + fit_y_err,
color='0.8')
ax.plot(fit_x, fit_y_val, color='black', label='GMOR Fit')
ax.errorbar(aml,
mpi_val,
yerr=mpi_err,
color='blue',
marker='+',
linestyle='none',
label='Data')
ax.errorbar([aml_phys_val], [135],
xerr=[aml_phys_err],
marker='+',
color='red',
label='Extrapolation')
#ax.errorbar([aml_240_val], [240], xerr=[aml_240_err], marker='+', color='red')
ax.set_title('Extrapolation to the Physical Point')
ax.set_xlabel(r'$a m_\mathrm{ud}$')
ax.set_ylabel(r'$M_\pi / \mathrm{MeV}$')
util.dandify_axes(ax)
ax = fig.add_subplot(2, 1, 2)
ax.hist(aml_phys_dist - aml_phys_val, bins=50)
ax.locator_params(nbins=6)
ax.set_title('Bootstrap Bias')
ax.set_xlabel(
r'$(a m_\mathrm{ud}^\mathrm{phys})^* - a m_\mathrm{ud}^\mathrm{phys}$')
util.dandify_axes(ax)
util.dandify_figure(fig)
fig.savefig('physical_point/GMOR.pdf')
np.savetxt('physical_point/ampi-sq-vs-aml.tsv',
np.column_stack([aml, ampi_sq_val, ampi_sq_err]))
np.savetxt('physical_point/mpi-sq-vs-aml.tsv',
np.column_stack([aml, mpi_sq_val, mpi_sq_err]))
def plot_p80s(output_dir, fig_name, display_scenario_names, all_p80s):
plt.boxplot(all_p80s, labels=display_scenario_names)
plt.xticks(rotation=25)
plt.ylabel("P80")
save_figure(output_dir, fig_name)
def main(output_dir, scenario_names, overdispersion_params, population_file, contact_matrix_file):
infectious_period_length = 7 # FIXME This probably should not be hard-coded here...
for scenario_i in range(len(scenario_names)):
print(scenario_names[scenario_i])
# Get transmission probability per experiment
experiments = get_trans_prob_by_exp(output_dir, scenario)
secondary_cases = []
index_case_ids = []
with multiprocessing.Pool(processes=4) as pool:
secondary_cases = pool.starmap(get_secondary_cases_per_index_case,
[(output_dir, scenario_names[scenario_i], exp_id) for exp_id in experiments.keys()])
index_case_ids = pool.starmap(get_index_case_ids,
[(output_dir, scenario_names[scenario_i], exp_id) for exp_id in experiments.keys()])
# Group by transmission probability
secondary_cases_by_tp = {}
for experiment_id, cases in secondary_cases:
tp = experiments[experiment_id]
if tp in secondary_cases_by_tp:
secondary_cases_by_tp[tp].append(cases)
else:
secondary_cases_by_tp[tp] = [cases]
tps_sorted = list(secondary_cases_by_tp.keys())
tps_sorted.sort()
# Estimate mean + variance number of effective contacts for index cases
person_ids = list(set([x[1][0] for x in index_case_ids]))
means_theoretical_by_tp, var_theoretical_by_tp = estimate_effective_contacts(population_file, contact_matrix_file,
tps_sorted, infectious_period_length,
overdispersion=overdispersion_vals[scenario_i],
person_ids=person_ids)
# Plot theoretical estimate of mean number of secondary cases per index case
# VS mean and 95% interval of number of secondary cases per index case from simulations
means = [np.mean(secondary_cases_by_tp[tp]) for tp in tps_sorted]
lower = [np.percentile(secondary_cases_by_tp[tp], 2.5) for tp in tps_sorted]
upper = [np.percentile(secondary_cases_by_tp[tp], 97.5) for tp in tps_sorted]
plt.plot(tps_sorted, means, marker="o", label="Simulations")
plt.fill_between(tps_sorted, lower, upper, color="lightgrey")
plt.plot(tps_sorted, [means_theoretical_by_tp[tp] for tp in tps_sorted], linestyle="None", marker="^", label="Theoretical")
plt.xlabel("Mean transmission probality")
plt.ylabel("Secondary cases caused by index case")
plt.ylim(-2, 100)
plt.legend()
save_figure(output_dir, "mean_ibrn_comparison_" + scenario_names[scenario_i], extension="png")
# Plot theoretical estimate of variance for number of secondary cases per index case
# VS variance for number of secondary cases per index case from simulations
variances = [np.var(secondary_cases_by_tp[tp]) for tp in tps_sorted]
plt.plot(tps_sorted, variances, linestyle="None", marker="o")
plt.plot(tps_sorted, [var_theoretical_by_tp[tp] for tp in tps_sorted], linestyle="None", marker="^")
plt.legend(["Simulations", "Theoretical"])
plt.xlabel("Mean transmission probality")
plt.ylabel("Variance of secondary cases caused by index case")
save_figure(output_dir, "var_" + scenario_names[scenario_i], extension="png")
def load_average_corr(paths):
t = util.load_columns(paths[0])[0]
reals = [util.load_columns(path)[1] for path in paths]
a = np.row_stack(reals)
return t, np.mean(a, axis=0), np.std(a, axis=0) / np.sqrt(len(reals))
source_0 = load_average_corr(
glob.glob(
'/home/mu/Dokumente/Studium/Master_Science_Physik/Masterarbeit/Runs/0120-Mpi270-L24-T96/corr/T=0/extract/corr/*.tsv'
))
source_20 = load_average_corr(
glob.glob(
'/home/mu/Dokumente/Studium/Master_Science_Physik/Masterarbeit/Runs/0120-Mpi270-L24-T96/corr/extract/corr/*.tsv'
))
fig, ax = util.make_figure()
print([x.shape for x in source_0])
ax.errorbar(source_0[0], source_0[1], source_0[2], label='T = 0')
ax.errorbar(source_20[0], source_20[1], source_20[2], label='T = 20')
ax.set_title('Different Source time with Chroma')
ax.set_xlabel(r'$t$')
ax.set_ylabel(r'$C(t)$')
ax.set_yscale('log')
util.save_figure(fig, 'chroma-source_t20')
def main(output_dir, scenario_names, overdispersion_params, display_scenario_names):
if len(display_scenario_names) < len(scenario_names):
display_scenario_names = scenario_names
all_means = []
all_means_exclude_extinction = []
for scenario_i in range(len(scenario_names)):
print(scenario_names[scenario_i])
experiments = get_trans_prob_by_exp(output_dir, scenario)
secondary_cases = []
with multiprocessing.Pool(processes=4) as pool:
secondary_cases = pool.starmap(get_secondary_cases_per_index_case,
[(output_dir, scenario_names[scenario_i], exp_id) for exp_id in experiments.keys()])
# Group by transmission probability
secondary_cases_by_tp = {}
for experiment_id, cases in secondary_cases:
tp = experiments[experiment_id]
if tp in secondary_cases_by_tp:
secondary_cases_by_tp[tp].append(cases)
else:
secondary_cases_by_tp[tp] = [cases]
tps_sorted = list(secondary_cases_by_tp.keys())
tps_sorted.sort()
# Mean secondary cases per index case
mean_secondary_cases_by_tp = [np.mean(secondary_cases_by_tp[tp]) for tp in tps_sorted]
all_means.append(mean_secondary_cases_by_tp)
# Mean secondary cases per index case,
# excluding runs where index case makes 0 secondary cases
mean_secondary_cases_by_tp_exclude_extinction = []
for tp in tps_sorted:
if tp == 0:
mean_secondary_cases_by_tp_exclude_extinction.append(np.nan)
else:
mean_secondary_cases_by_tp_exclude_extinction.append(np.mean([x for x in secondary_cases_by_tp[tp] if x > 0]))
all_means_exclude_extinction.append(mean_secondary_cases_by_tp_exclude_extinction)
# Create QQ-plots to compare offspring distribution
# to negative binomial distribution
tp_i = 0
for tp in tps_sorted:
k = overdispersion_params[scenario_i]
if k is None:
k = np.inf
res = probplot(secondary_cases_by_tp[tp], dist=nbinom, sparams=(k, k / (mean_secondary_cases_by_tp[tp_i] + k)), fit=False, plot=plt)
save_figure(output_dir, "QQplot_" + scenario + "_tp_" + str(tp))
tp_i += 1
# Plot mean secondary cases per index case
for scenario_i in scenario_names:
plt.plot([0.0, 0.025, 0.05, 0.075, 0.10], all_means[scenario_i])
plt.xlabel("Mean individual transmission probability")
plt.xticks([0.00, 0.02, 0.04, 0.06, 0.08, 0.10])
plt.ylabel("Mean number of secondary cases per index case")
plt.legend(display_scenario_names)
save_figure(output_dir, "mean_secondary_cases_by_tp")
# Plot mean secondary cases per index case, excluding runs where index case had 0 secondary cases
for scenario_i in scenario_names:
plt.plot([0.0, 0.025, 0.05, 0.075, 0.10], all_means_exclude_extinction[scenario_i])
plt.xlabel("Mean individual transmission probability")
plt.xticks([0.00, 0.02, 0.04, 0.06, 0.08, 0.10])
plt.ylabel("Mean number of secondary cases per index case")
plt.legend(display_scenario_names)
save_figure(output_dir, "mean_secondary_cases_by_tp_exclude_extinction")