%run -i load_bromo.py

%run brownian.py

# Initialize the random seed to a fixed value (for notebook reproducibility)
np.random.seed(6)

# Simulation time step
t_step = 0.5e-6   # seconds

# Time duration of the simulation
t_max = .2 # seconds

# Particles definition
P = gen_particles(2, box)

# Particle simulation definition
S = ParticlesSimulation(D=D, t_step=t_step, t_max=t_max, particles=P, box=box, psf=psf)

S

S.print_RAM()

S.sim_motion_em(total_emission=True, delete_pos=False)

# This requires delete_pos=False in .sim_motion_em()
plot_tracks(S)

plot_emission(S)

S.sim_timetrace(max_em_rate=3e5, bg_rate=2e3)

plot_timetrace(S, scroll_gui=False)
plt.legend(['Emission rate', 'Emitted photons + BG'])

S.gen_ph_times()

print S.ph_times[:10], '...'

plt.hist(S.ph_times, bins=np.r_[:200]*1e-3, histtype='step');

# Binning of timestamps
timestamps_hist = np.histogram(S.ph_times, bins=np.r_[:201]*1e-3)

# Rebinning of timetrace
rebin = 2000
rebinned_timetrace = S.tt.reshape(-1, rebin).sum(axis=1)
rebinned_time = (np.arange(rebinned_timetrace.size)+1)*(S.t_step*rebin)

# Comparison plot
plt.plot(timestamps_hist[1][1:], timestamps_hist[0])
plt.plot(rebinned_time, rebinned_timetrace)

# Rigorous check
assert ((timestamps_hist[0] - rebinned_timetrace) == 0).all()

S.dump(dir_=SIM_DATA_DIR)

S2 = load_sim_id(ID=0, EID=0, glob_str='*0.2s*', dir_=SIM_DATA_DIR)

S2

S2.em

print id(S2.em), id(S.em)

(S.em == S2.em).all()













from IPython.core.display import HTML
def css_styling():
    styles = open("./styles/custom2.css", "r").read()
    return HTML(styles)
css_styling()