def test_plotting():
sc.heading('Testing plotting')
fig_path = 'plotting_test.png'
# Create sim with data and interventions
ce = cv.clip_edges(**{'start_day': 10, 'change': 0.5})
sim = cv.Sim(pop_size=100,
n_days=60,
datafile=csv_file,
interventions=ce,
verbose=verbose)
sim.run(do_plot=True)
# Handle lesser-used plotting options
sim.plot(to_plot=['cum_deaths', 'new_infections'],
sep_figs=True,
font_family='Arial',
log_scale=['Number of new infections'],
interval=5,
do_save=True,
fig_path=fig_path)
print('↑ May print a warning about zero values')
# Handle Plotly functions
cv.plotly_sim(sim)
cv.plotly_people(sim)
cv.plotly_animate(sim)
# Tidy up
remove_files(fig_path)
return
def test_plotting():
sc.heading('Testing plotting')
fig_paths = ['plotting_test1.png', 'plotting_test2.png']
# Create sim with data and interventions
ce = cv.clip_edges(**{'days': 10, 'changes': 0.5})
sim = cv.Sim(pop_size=100,
n_days=60,
datafile=csv_file,
interventions=ce,
verbose=verbose)
sim.run(do_plot=True)
# Handle lesser-used plotting options
sim.plot(to_plot=['cum_deaths', 'new_infections'],
sep_figs=True,
log_scale=['Number of new infections'],
do_save=True,
fig_path=fig_paths)
# Handle Plotly functions
try:
cv.plotly_sim(sim)
cv.plotly_people(sim)
cv.plotly_animate(sim)
except Exception as E:
print(
f'Plotly plotting failed ({str(E)}), but not essential so continuing'
)
# Tidy up
remove_files(*fig_paths)
return
'''
Test Plotly plotting outside of the webapp.
'''
import plotly.io as pio
import covasim as cv
pio.renderers.default = "browser" # Or can use a Jupyter notebook
ce = cv.clip_edges(**{'start_day': 10, 'change': 0.5})
sim = cv.Sim(pop_size=100, n_days=60, datafile='../example_data.csv', interventions=ce, verbose=0)
sim.run()
f1list = cv.plotly_sim(sim, do_show=True)
f2 = cv.plotly_people(sim, do_show=True)
f3 = cv.plotly_animate(sim, do_show=True)
def run_sim(sim_pars=None,
epi_pars=None,
int_pars=None,
datafile=None,
show_animation=False,
n_days=90,
location=None,
verbose=True,
die=die):
''' Create, run, and plot everything '''
errs = []
try:
web_pars = parse_parameters(sim_pars=sim_pars,
epi_pars=epi_pars,
int_pars=int_pars,
n_days=n_days,
location=location,
verbose=verbose,
errs=errs,
die=die)
if verbose:
print('Input parameters:')
print(web_pars)
except Exception as E:
errs.append(log_err('Parameter conversion failed!', E))
if die: raise
# Create the sim and update the parameters
try:
extra_pars = dict(pop_type='hybrid')
pars = sc.mergedicts(extra_pars, web_pars)
sim = cv.Sim(pars=pars, datafile=datafile)
except Exception as E:
errs.append(log_err('Sim creation failed!', E))
if die: raise
# Core algorithm
try:
sim.run(do_plot=False)
except TimeoutError as TE:
err = f"The simulation stopped on day {sim.t} because run time limit ({sim['timelimit']} seconds) was exceeded. Please reduce the population size and/or number of days simulated."
errs.append(log_err(err, TE))
if die: raise
except Exception as E:
errs.append(log_err('Sim run failed!', E))
if die: raise
# Core plotting
def process_graphs(figs):
jsons = []
for fig in sc.promotetolist(figs):
fig.update_layout(paper_bgcolor=bgcolor, plot_bgcolor=plotbg)
output = {'json': fig.to_json(), 'id': str(sc.uuid())}
d = json.loads(output['json'])
d['config'] = {'responsive': True}
output['json'] = json.dumps(d)
jsons.append(output)
return jsons
graphs = []
try:
graphs += process_graphs(cv.plotly_sim(sim))
graphs += process_graphs(cv.plotly_people(sim))
if show_animation:
graphs += process_graphs(cv.plotly_animate(sim))
except Exception as E:
errs.append(log_err('Plotting failed!', E))
if die: raise
# Create and send output files (base64 encoded content)
try:
files, summary = get_output_files(sim)
except Exception as E:
files = {}
summary = {}
errs.append(log_err('Unable to save output files!', E))
if die: raise
output = {}
output['errs'] = errs
output['sim_pars'] = sim_pars
output['epi_pars'] = epi_pars
output['int_pars'] = int_pars
output['graphs'] = graphs
output['files'] = files
output['summary'] = summary
return output