def analyse(name):
data = genfromtxt('data/%s.tsv' % name, delimiter='\t', dtype=None,
names=['ext_timestamp', 'time_delta'])
time_delta = data['time_delta']
# Plot distribution
counts, bins = histogram(time_delta, bins=arange(-10.5, 11.5, 1))
plot = Plot()
plot.histogram(counts, bins)
plot.set_ylimits(min=0)
plot.set_ylabel('counts')
plot.set_xlabel(r'time delta [\si{\nano\second}]')
plot.save_as_pdf(name)
# Plot moving average
n = 300
skip = 20
moving_average = convolve(time_delta, ones((n,)) / n, mode='valid')
plot = Plot()
timestamps = (data['ext_timestamp'][:-n + 1:skip] -
data['ext_timestamp'][0]) / 1e9 / 3600.
plot.plot(timestamps, moving_average[::skip], mark=None)
plot.set_xlimits(min=0)
plot.set_ylabel(r'time delta [\si{\nano\second}]')
plot.set_xlabel('timestamp [\si{\hour}]')
plot.save_as_pdf('moving_average_%s' % name)
def plot_raw(raw_traces):
length = 2.5 * len(raw_traces[0])
plot = Plot()
max_signal = max(chain.from_iterable(raw_traces))
plot.add_pin_at_xy(500,
max_signal,
'pre-trigger',
location='above',
use_arrow=False)
plot.draw_vertical_line(1000, 'gray')
plot.add_pin_at_xy(1750,
max_signal,
'trigger',
location='above',
use_arrow=False)
plot.draw_vertical_line(2500, 'gray')
plot.add_pin_at_xy(4250,
max_signal,
'post-trigger',
location='above',
use_arrow=False)
for i, raw_trace in enumerate(raw_traces):
plot.plot(arange(0, length, 2.5),
raw_trace,
mark=None,
linestyle=COLORS[i])
plot.set_ylimits(min=0)
plot.set_xlimits(min=0, max=length)
plot.set_ylabel(r'Signal strength [ADC counts]')
plot.set_xlabel(r'Sample [\si{\nano\second}]')
plot.save_as_pdf('raw')
def plot_comparison_501_510(stats, field_name):
plot = Plot()
bins = arange(0, 1, .02)
ref_stat = stats[501][field_name][0]
stat = stats[510][field_name][0]
tmp_stat = stat.compress((ref_stat > 0) & (stat > 0))
tmp_ref_stat = ref_stat.compress((ref_stat > 0) & (stat > 0))
counts, xbin, ybin = histogram2d(tmp_stat, tmp_ref_stat, bins=bins)
plot.histogram2d(counts, xbin, ybin, type='reverse_bw', bitmap=True)
plot.plot([0, 1.2], [0, 1.2], mark=None, linestyle='red, very thin')
if field_name == 'event_rate':
label = r'Event rate [\si{\hertz}]'
elif field_name == 'mpv':
label = r'MPV [ADC.ns]'
else:
label = (r'Fraction of bad %s data [\si{\percent}]' %
field_name.replace('_', ' '))
plot.set_ylabel(label)
plot.set_xlabel(label)
if field_name in ['event_rate', 'mpv']:
plot.save_as_pdf('plots_501_510/compare_%s' % field_name)
else:
plot.save_as_pdf('plots_501_510/compare_bad_fraction_%s' % field_name)
def plot_E_d_P(ldf):
energies = linspace(13, 21, 100)
sizes = energy_to_size(energies, 13.3, 1.07)
core_distances = logspace(-1, 4.5, 100)
probabilities = []
for size in sizes:
prob_temp = []
for distance in core_distances:
prob_temp.append(P_2(ldf, distance, size))
probabilities.append(prob_temp)
probabilities = array(probabilities)
plot = Plot('semilogx')
low = []
mid = []
high = []
for p in probabilities:
# Using `1 -` to ensure x (i.e. p) is increasing.
low.append(interp(1 - 0.10, 1 - p, core_distances))
mid.append(interp(1 - 0.50, 1 - p, core_distances))
high.append(interp(1 - 0.90, 1 - p, core_distances))
plot.plot(low, energies, linestyle='densely dotted', mark=None)
plot.plot(mid, energies, linestyle='densely dashed', mark=None)
plot.plot(high, energies, mark=None)
plot.set_ylimits(13, 20)
plot.set_xlimits(1., 1e4)
plot.set_xlabel(r'Core distance [\si{\meter}]')
plot.set_ylabel(r'Energy [log10(E/\si{\eV})]')
plot.save_as_pdf('efficiency_distance_energy_' + ldf.__class__.__name__)
def main(ts, ns):
station = Station(501)
traces = station.event_trace(ts, ns, True)
dr = DataReduction()
reduced_traces, o = dr.reduce_traces(array(traces).T, return_offset=True)
reduced_traces = reduced_traces.T
plot = Plot()
t = arange(len(traces[0])) * 2.5
for i, trace in enumerate(traces):
plot.plot(t, trace, linestyle='%s, thin' % COLORS[i], mark=None)
plot.draw_vertical_line(o * 2.5, 'gray')
plot.draw_vertical_line((o + len(reduced_traces[0])) * 2.5, 'gray')
plot.set_axis_options('line join=round')
plot.set_xlabel(r'Event time [\si{\ns}]')
plot.set_ylabel(r'Signal strength [ADCcounts]')
plot.set_xlimits(t[0], t[-1])
plot.save_as_pdf('raw_traces_%d_%d' % (ts, ns))
t = arange(o, o + len(reduced_traces[0])) * 2.5
for i, trace in enumerate(reduced_traces):
plot.plot(t, trace, linestyle='%s, thin' % COLORS[i], mark=None)
plot.set_axis_options('line join=round')
plot.set_xlabel(r'Event time [\si{\ns}]')
plot.set_ylabel(r'Signal strength [ADCcounts]')
plot.set_xlimits(t[0], t[-1])
plot.save_as_pdf('reduced_traces_%d_%d' % (ts, ns))
def plot_shower_size(leptons=['electron', 'muon']):
plot = Plot(axis='semilogy')
cq = CorsikaQuery(OVERVIEW)
p = 'proton'
for e in sorted(cq.available_parameters('energy', particle=p)):
median_size = []
min_size = []
max_size = []
zeniths = sorted(cq.available_parameters('zenith', energy=e, particle=p))
for z in zeniths:
selection = cq.simulations(zenith=z, energy=e, particle=p)
n_leptons = selection['n_%s' % leptons[0]]
for lepton in leptons[1:]:
n_leptons += selection['n_%s' % lepton]
sizes = percentile(n_leptons, [16, 50, 84])
min_size.append(sizes[0] if sizes[0] else 0.1)
median_size.append(sizes[1] if sizes[1] else 0.1)
max_size.append(sizes[2] if sizes[2] else 0.1)
if len(zeniths):
plot.plot(zeniths, median_size, linestyle='very thin')
plot.shade_region(zeniths, min_size, max_size,
color='lightgray, semitransparent')
plot.add_pin('%.1f' % e, relative_position=0)
plot.set_xticks([t for t in arange(0, 60.1, 7.5)])
plot.set_ylimits(1, 1e9)
plot.set_ylabel(r'Shower size (leptons)')
plot.set_xlabel(r'Zenith [\si{\degree}]')
plot.save_as_pdf('shower_sizes_%s' % '_'.join(leptons))
cq.finish()
def plot_coincidence_rate_distance(data, sim_data):
"""Plot results
:param distances: dictionary with occuring distances for different
combinations of number of detectors.
:param coincidence_rates: dictionary of occuring coincidence rates for
different combinations of number of detectors.
:param rate_errors: errors on the coincidence rates.
"""
(distances, coincidence_rates, interval_rates, distance_errors,
rate_errors, pairs) = data
sim_distances, sim_energies, sim_areas = sim_data
markers = {4: 'o', 6: 'triangle', 8: 'square'}
colors = {4: 'red', 6: 'black!50!green', 8: 'black!20!blue'}
coincidence_window = 10e-6 # seconds
freq_2 = 0.3
freq_4 = 0.6
background = {
4: 2 * freq_2 * freq_2 * coincidence_window,
6: 2 * freq_2 * freq_4 * coincidence_window,
8: 2 * freq_4 * freq_4 * coincidence_window
}
for rates, name in [(coincidence_rates, 'coincidence'),
(interval_rates, 'interval')]:
plot = Plot('loglog')
for n in distances.keys():
plot.draw_horizontal_line(background[n], 'dashed,' + colors[n])
# for n in distances.keys():
for n in [4, 8]:
expected_rates = expected_rate(distances[n],
rates[n],
background[n],
sim_distances,
sim_energies,
sim_areas[n],
n=n)
plot.plot(sim_distances,
expected_rates,
linestyle=colors[n],
mark=None,
markstyle='mark size=0.5pt')
for n in distances.keys():
plot.scatter(distances[n],
rates[n],
xerr=distance_errors[n],
yerr=rate_errors[n],
mark=markers[n],
markstyle='%s, mark size=.75pt' % colors[n])
plot.set_xlabel(r'Distance between stations [\si{\meter}]')
plot.set_ylabel(r'%s rate [\si{\hertz}]' % name.title())
plot.set_axis_options('log origin y=infty')
plot.set_xlimits(min=1, max=20e3)
plot.set_ylimits(min=1e-7, max=5e-1)
plot.save_as_pdf('distance_v_%s_rate' % name)
def plot_interaction_height(cq):
plot = Plot()
p = 'proton'
for e in sorted(cq.available_parameters('energy', particle=p)):
median_altitude = []
min_altitude = []
max_altitude = []
zeniths = []
for z in sorted(cq.available_parameters('zenith', particle=p,
energy=e)):
selection = cq.simulations(particle=p, energy=e, zenith=z)
if len(selection) > 50:
interaction_altitudes = selection[
'first_interaction_altitude'] / 1e3
median_altitude.append(median(interaction_altitudes))
min_altitude.append(percentile(interaction_altitudes, 2))
max_altitude.append(percentile(interaction_altitudes, 98))
zeniths.append(z)
if len(zeniths):
plot.plot(zeniths + (e - 12) / 3., median_altitude)
# plot.shade_region(zeniths, min_altitude, max_altitude,
# color='lightgray,semitransparent')
plot.add_pin('%.1f' % e, relative_position=0)
plot.set_ylabel(r'First interaction altitude [\si{\kilo\meter}]')
plot.set_xlabel(r'Zenith [\si{\radian}]')
plot.save_as_pdf('plots/interaction_altitude')
def plot_coincidence_v_interval_rate(data):
"""Plot results
:param distances: dictionary with occuring distances for different
combinations of number of detectors.
:param coincidence_rates: dictionary of occuring coincidence rates for
different combinations of number of detectors.
:param rate_errors: errors on the coincidence rates.
"""
(distances, coincidence_rates, interval_rates, distance_errors,
rate_errors, pairs) = data
markers = {4: 'o', 6: 'triangle', 8: 'square'}
colors = {4: 'red', 6: 'black!50!green', 8: 'black!20!blue'}
plot = Plot('loglog')
plot.plot([1e-7, 1e-1], [1e-7, 1e-1], mark=None)
for n in distances.keys():
plot.scatter(interval_rates[n],
coincidence_rates[n],
yerr=rate_errors[n],
mark=markers[n],
markstyle='%s, thin, mark size=.75pt' % colors[n])
plot.set_xlabel(r'Rate based on coincidence intervals [\si{\hertz}]')
plot.set_ylabel(r'Rate based on coincidences and exposure [\si{\hertz}]')
plot.set_axis_options('log origin y=infty')
plot.set_xlimits(min=1e-7, max=1e-1)
plot.set_ylimits(min=1e-7, max=1e-1)
plot.save_as_pdf('interval_v_coincidence_rate')
def main():
# data series
x = [0, 40, 60, 69, 80, 90, 100]
y = [0, 0, 0.5, 2.96, 2, 1, .5]
# make graph
graph = Plot()
# make Plot
graph.plot(x, y, mark=None, linestyle='smooth,very thick')
# set labels and limits
graph.set_xlabel(r"$f [\si{\mega\hertz}]$")
graph.set_ylabel("signal strength")
graph.set_xlimits(0, 100)
graph.set_ylimits(0, 5)
# set scale: 1cm equals 10 units along the x-axis
graph.set_xscale(cm=10)
# set scale: 1cm equals 1 unit along the y-axis
graph.set_yscale(cm=1)
# set ticks at every unit along the y axis
graph.set_yticks(range(6))
# set graph paper
graph.use_graph_paper()
# save graph to file
graph.save('mm_paper')
def plot_traces():
with tables.open_file(DATA, 'r') as data:
for i, pre, coin, post in TIME_WINDOWS:
test_node = data.get_node('/t%d' % i)
events = test_node.events.read()
events.sort(order='ext_timestamp')
blobs = test_node.blobs
for e_idx in [0, 1]:
t_idx = events[e_idx]['traces'][1]
extts = events[e_idx]['ext_timestamp']
try:
trace = zlib.decompress(blobs[t_idx]).split(',')
except zlib.error:
trace = zlib.decompress(blobs[t_idx][1:-1]).split(',')
if trace[-1] == '':
del trace[-1]
trace = [int(x) for x in trace]
plot = Plot()
plot.plot(range(len(trace)), trace, mark=None)
plot.set_label('%d' % extts)
microsec_to_sample = 400
plot.draw_vertical_line(pre * microsec_to_sample,
linestyle='thick,red,semitransparent')
plot.draw_vertical_line((pre + coin) * microsec_to_sample,
linestyle='thick,blue,semitransparent')
plot.set_ylabel('Signal strength [ADCcounts]')
plot.set_xlabel('Sample [2.5ns]')
plot.set_ylimits(min=150, max=1500)
plot.set_xlimits(min=0, max=len(trace))
plot.save_as_pdf('trace_%d_%d' % (i, e_idx))
def analyse(name):
data = genfromtxt('data/%s.tsv' % name, delimiter='\t', dtype=None,
names=['ext_timestamp', 'time_delta'])
time_delta = data['time_delta']
# Plot distribution
counts, bins = histogram(time_delta, bins=arange(-10.5, 11.5, 1))
plot = Plot()
plot.histogram(counts, bins)
x = (bins[1:] + bins[:-1]) / 2.
popt, pcov = curve_fit(gauss, x, counts, p0=(sum(counts), 0., 2.5))
plot.plot(x, gauss(x, *popt), mark=None)
print popt
plot.set_ylimits(min=0)
plot.set_ylabel('Counts')
plot.set_xlabel(r'Time delta [\si{\nano\second}]')
plot.save_as_pdf(name)
# Plot moving average
n = 5000
skip = 100
moving_average = convolve(time_delta, ones((n,)) / n, mode='valid')
plot = Plot()
timestamps = (data['ext_timestamp'][:-n + 1:skip] -
data['ext_timestamp'][0]) / 1e9 / 3600.
plot.plot(timestamps, moving_average[::skip], mark=None)
plot.set_xlimits(min=0)
plot.set_ylabel(r'time delta [\si{\nano\second}]')
plot.set_xlabel('timestamp [\si{\hour}]')
plot.save_as_pdf('moving_average_%s' % name)
def plot_pulseheight_histogram(data):
events = data.root.hisparc.cluster_kascade.station_601.events
ph = events.col('n1')
s = landau.Scintillator()
mev_scale = 3.38 / 1.
count_scale = 6e3 / .32
n, bins = histogram(ph, bins=arange(0, 9, 0.025))
x = linspace(0, 9, 1500)
plot = Plot()
n_trunc = where(n <= 100000, n, 100000)
plot.histogram(n_trunc, bins, linestyle='gray')
plot.plot(x,
s.conv_landau_for_x(x,
mev_scale=mev_scale,
count_scale=count_scale,
gauss_scale=.68),
mark=None)
# plot.add_pin('convolved Landau', x=1.1, location='above right',
# use_arrow=True)
plot.plot(x,
count_scale * s.landau_pdf(x * mev_scale),
mark=None,
linestyle='black')
# plot.add_pin('Landau', x=1., location='above right', use_arrow=True)
plot.set_xlabel(r"Number of particles")
plot.set_ylabel(r"Number of events")
plot.set_xlimits(0, 9)
plot.set_ylimits(0, 21000)
plot.save_as_pdf("plot_pulseheight_histogram_pylandau")
def plot_fit(x, data, slope, intercept, pair):
plot = Plot()
plot.scatter(x, log(c))
plot.plot(x, x * slope + intercept, mark=None)
plot.set_ylimits(min=0)
plot.set_label(r'%.1e \si{\hertz}' % rate)
plot.save_as_pdf('intervals/intervals_%d_%d_r' % pair)
def plot_offset_timeline(ref_station, station):
ref_s = Station(ref_station)
s = Station(station)
# ref_gps = ref_s.gps_locations
# ref_voltages = ref_s.voltages
# ref_n = get_n_events(ref_station)
# gps = s.gps_locations
# voltages = s.voltages
# n = get_n_events(station)
# Determine offsets for first day of each month
# d_off = s.detector_timing_offsets
s_off = get_station_offsets(ref_station, station)
graph = Plot(width=r'.6\textwidth')
# graph.scatter(ref_gps['timestamp'], [95] * len(ref_gps), mark='square', markstyle='purple,mark size=.5pt')
# graph.scatter(ref_voltages['timestamp'], [90] * len(ref_voltages), mark='triangle', markstyle='purple,mark size=.5pt')
# graph.scatter(gps['timestamp'], [85] * len(gps), mark='square', markstyle='gray,mark size=.5pt')
# graph.scatter(voltages['timestamp'], [80] * len(voltages), mark='triangle', markstyle='gray,mark size=.5pt')
# graph.shade_region(n['timestamp'], -ref_n['n'] / 1000, n['n'] / 1000, color='lightgray,const plot')
# graph.plot(d_off['timestamp'], d_off['d0'], markstyle='mark size=.5pt')
# graph.plot(d_off['timestamp'], d_off['d2'], markstyle='mark size=.5pt', linestyle='green')
# graph.plot(d_off['timestamp'], d_off['d3'], markstyle='mark size=.5pt', linestyle='blue')
graph.plot(s_off['timestamp'],
s_off['offset'],
mark='*',
markstyle='mark size=1.25pt',
linestyle=None)
graph.set_ylabel('$\Delta t$ [ns]')
graph.set_xlabel('Date')
graph.set_xticks(
[datetime_to_gps(date(y, 1, 1)) for y in range(2010, 2016)])
graph.set_xtick_labels(['%d' % y for y in range(2010, 2016)])
graph.set_xlimits(1.25e9, 1.45e9)
graph.set_ylimits(-150, 150)
graph.save_as_pdf('plots/offsets/offsets_ref%d_%d' %
(ref_station, station))
def plot_min_max(variable_pairs):
plot = Plot()
variable_pairs = sorted(variable_pairs)
for i, minmax_d in enumerate(variable_pairs):
plot.plot([i, i], minmax_d, mark=None)
plot.set_xlabel('Station pair')
plot.set_xtick_labels([' '])
plot.set_ylabel(r'Distance between stations [\si{\meter}]')
plot.save_as_pdf('min_max_distances')
def plot_filtered(filtered_trace):
plot = Plot()
time = arange(0, len(filtered_trace) * 2.5, 2.5)
plot.plot(time, filtered_trace, mark=None, linestyle='const plot')
plot.set_xlabel(r'Trace time [\si{\ns}]')
plot.set_ylabel(r'Signal strength [ADC]')
plot.save_as_pdf('mean_filter')
def plot_derrivative_pmt(self):
plot = Plot()
plot.plot(self.lin_bins, self.dvindvout, mark=None)
plot.set_xlimits(min=self.lin_bins[0], max=self.lin_bins[-1])
plot.set_xlabel(r'Particle density [\si{\per\meter\squared}]')
plot.set_ylabel(
r'$\sigma V_{\mathrm{in}}\frac{\mathrm{d}V_{\mathrm{out}}}'
r'{\mathrm{d}V_{\mathrm{in}}}$')
plot.save_as_pdf('plots/derrivative_pmt_saturation')
def main():
x, t25, t50, t75 = np.loadtxt('data/DIR-boxplot_arrival_times-1.txt')
graph = Plot()
graph.plot(x, t50, mark='*')
graph.shade_region(x, t25, t75)
graph.set_xlabel(r"Core distance [\si{\meter}]")
graph.set_ylabel(r"Arrival time delay [\si{\nano\second}]")
graph.set_ylimits(min=0)
graph.save('shower-front')
def make_logo():
size = '.02\linewidth'
x = arange(0, 2*pi, .01)
y = sin(x)
plot = Plot(width=size, height=size)
plot.set_ylimits(-1.3, 1.3)
plot.set_yticks([-1, 0, 1])
plot.set_ytick_labels(['', '', ''])
plot.set_xticks([0, pi, 2*pi])
plot.set_xtick_labels(['', '', ''])
plot.plot(x, y, mark=None, linestyle='thick')
plot.set_axis_options("axis line style=thick, major tick length=.04cm")
plot.save_as_pdf('logo')
def plot_traces(traces, label='', raw=False):
"""Plot traces
Does not take different mV/ADC for HiSPARC II-III into account!
:param traces: list of lists of trace values.
:param label: name (suffix) for the output pdf.
"""
colors = ['black', 'red', 'black!40!green', 'blue']
plot = Plot(width=r'.6\textwidth')
times = arange(0, len(traces[0]) * 2.5, 2.5)
for i, trace in enumerate(traces):
if not raw:
if max(trace) * 0.57 < 500:
use_milli = True
trace = [t * -0.57 for t in trace]
else:
use_milli = False
trace = [t * -0.57 / 1e3 for t in trace]
plot.plot(times, trace, linestyle='%s, thin' % colors[i], mark=None)
if len(traces[0]) == 2400 and raw:
plot.add_pin_at_xy(500,
10,
'pre-trigger',
location='below',
use_arrow=False)
plot.add_pin_at_xy(1750,
10,
'trigger',
location='below',
use_arrow=False)
plot.add_pin_at_xy(4250,
10,
'post-trigger',
location='below',
use_arrow=False)
plot.draw_vertical_line(1000, 'gray')
plot.draw_vertical_line(2500, 'gray')
if raw:
plot.set_ylabel(r'Signal strength [ADCcounts]')
elif use_milli:
plot.set_ylabel(r'Signal strength [\si{\milli\volt}]')
else:
plot.set_ylabel(r'Signal strength [\si{\volt}]')
plot.set_xlabel(r'Event time [\si{\ns}]')
plot.set_xlimits(0, times[-1])
plot.set_axis_options('line join=round')
plot.save_as_pdf('trace_' + label)
def plot_front_shapes():
r = [20, 29, 41, 58, 84, 120, 171, 245, 350, 501]
fit_r = arange(0, 510, 5)
for particle in ['gamma', 'proton', 'iron']:
for energy in ['15.0', '15.5', '16.0', '16.5', '17.0']:
files = glob(PATH + '%s_E_%s*' % (particle, energy))
if not len(files):
continue
t = zeros((len(r), len(files)))
for i, file in enumerate(files):
detected_t = loadtxt(file, usecols=(1, ))
t[:, i][:len(detected_t)] = detected_t
t_src = t.copy()
for j in range(1, len(t)):
t[j] -= t[0]
t[0] -= t[0]
mean_t = t.mean(axis=1)
try:
min_limit = 3
min_efficiency = 0.9
limit = min_limit + next(
i for i, ti in enumerate(t_src[min_limit:])
if not count_nonzero(ti) > min_efficiency * len(files))
except:
limit = len(r)
plot = Plot()
plot.scatter(r[:limit],
mean_t[:limit],
yerr=t.std(axis=1)[:limit],
xerr=[10] * limit)
plot.scatter(r[:limit], median(t, axis=1)[:limit], mark='x')
popt, pcov = curve_fit(front_shape, r[:limit], mean_t[:limit])
plot.plot(fit_r,
front_shape(fit_r, *popt),
linestyle='gray',
mark=None)
print particle, energy, popt
plot.set_ylimits(-10, 130)
plot.set_xlimits(-10, 510)
plot.set_ylabel(r'Delay [\si{\ns}]')
plot.set_xlabel(r'Core distance [\si{\meter}]')
plot.save_as_pdf('plots/front_shape/%s_%s.pdf' %
(particle, energy))
def plot_contributions():
colors = ['red', 'blue', 'green', 'purple', 'gray', 'brown', 'cyan',
'magenta', 'orange', 'teal']
lamb = arange(MIN, MAX, 0.1)
plot = Plot('semilogy')
for j, k in enumerate(range(1, 8) + [15] + [20]):
ks = [k] # arange(k - 0.5, k + 0.5, 0.2)
p = sum(density_probability(lamb, ki) for ki in ks) / len(ks)
plot.plot(lamb, p, linestyle=colors[j % len(colors)], mark=None)
plot.set_ylimits(min=0.01)
plot.set_xlimits(0, 20)
plot.set_xlabel('Expected actual number of particles')
plot.set_ylabel('Probability')
plot.save_as_pdf('plots/poisson_distributions')
def plot_compared():
popt, perr = fit_curve(senstech_m_ph, senstech_e_ph)
fit = FIT % (popt[0], P1, popt[1])
plot = Plot(width=r'.67\linewidth', height=r'.67\linewidth')
plot.set_label(fit, location='upper left')
plot.scatter(senstech_e_ph, senstech_m_ph, mark='*')
plot.scatter(nikhef_e_ph, nikhef_m_ph, mark='o')
inputs = linspace(min(senstech_m_ph), max(senstech_m_ph), 500)
plot.plot(ice_cube_pmt_p1(inputs, *popt), inputs, mark=None)
plot.plot([0, 6], [0, 6], mark=None, linestyle='gray')
plot.set_xlimits(0, 6)
plot.set_ylimits(0, 6)
plot.set_axis_equal()
plot.set_xlabel(r'Sum individual LED pulseheights [\si{\volt}]')
plot.set_ylabel(r'Multiple-LED pulseheight [\si{\volt}]')
plot.save_as_pdf('plots/linearity_compared')
def scatter_n():
r = 420
with tables.open_file(RESULT_PATH, 'r') as data:
cluster = data.root.coincidences._v_attrs.cluster
coincidences = data.root.coincidences.coincidences
graph = Plot()
for n in range(0, len(cluster.stations) + 1):
c = coincidences.read_where('N == n')
if len(c) == 0:
continue
graph.plot(c['x'],
c['y'],
mark='*',
linestyle=None,
markstyle='mark size=.2pt,color=%s' %
COLORS[n % len(COLORS)])
graph1 = Plot()
graph1.plot(c['x'],
c['y'],
mark='*',
linestyle=None,
markstyle='mark size=.2pt')
plot_cluster(graph1, cluster)
graph1.set_axis_equal()
graph1.set_ylimits(-r, r)
graph1.set_xlimits(-r, r)
graph1.set_ylabel('y [m]')
graph1.set_xlabel('x [m]')
graph1.set_title('Showers that caused triggers in %d stations' % n)
graph1.save_as_pdf('N_%d' % n)
graph_azi = PolarPlot(use_radians=True)
plot_azimuth(graph_azi, c['azimuth'])
graph_azi.set_label('N = %d' % n)
graph_azi.save('azi_%d' % n)
graph_azi.save_as_pdf('azi_%d' % n)
plot_cluster(graph, cluster)
graph.set_axis_equal()
graph.set_ylimits(-r, r)
graph.set_xlimits(-r, r)
graph.set_ylabel('y [m]')
graph.set_xlabel('x [m]')
graph.set_title('Color indicates the number triggered stations by '
'a shower.')
graph.save_as_pdf('N')
def plot_delta_histogram(ids, **kwargs):
""" Plot a histogram of the deltas
"""
if type(ids) is int:
ids = [ids]
# Bin width
bin_size = 1 # 2.5*n
# Begin Figure
plot = Plot()
for id in ids:
ext_timestamps, deltas = get(id)
low = floor(min(deltas))
high = ceil(max(deltas))
bins = np.arange(low - .5 * bin_size, high + bin_size, bin_size)
n, bins = np.histogram(deltas, bins)
bin_centers = (bins[:-1] + bins[1:]) / 2
popt, pcov = curve_fit(gauss,
bin_centers,
n,
p0=[.15, np.mean(deltas),
np.std(deltas)])
plot.histogram(n, bins)
plot.plot(bin_centers,
gauss(bin_centers, *popt),
mark=None,
linestyle='gray')
if kwargs.keys():
plot.set_title('Tijdtest ' + kwargs[kwargs.keys()[0]])
plot.set_label(r'$\mu={1:.1f}$, $\sigma={2:.1f}$'.format(*popt))
plot.set_xlabel(r'Time difference [ns]')
plot.set_ylabel(r'Counts')
plot.set_xlimits(low, high)
plot.set_ylimits(min=0.)
# Save Figure
if len(ids) == 1:
name = 'delta_histogram/tt_delta_hist_%03d' % ids[0]
elif kwargs.keys():
name = 'delta_histogram/tt_delta_hist_' + kwargs[kwargs.keys()[0]]
plot.save_as_pdf(PLOT_PATH + name)
print 'tt_analyse: Plotted histogram'
def main():
plot = Plot()
size = 20
x = np.linspace(1, 20, size)
y = np.linspace(10, 50, size)
y_random = y + np.random.uniform(-3, 1, size)
err_l = np.random.uniform(0, 2, size)
err_h = np.random.uniform(1, 5, size)
err_x = [0.4] * size
plot.plot(x, y, mark=None)
plot.scatter(x, y_random, xerr=err_x, yerr=list(zip(err_l, err_h)))
plot.set_xlabel("Value with symmetric error")
plot.set_ylabel("Other value with asymmetric errors")
plot.save("error_bars")
def plot_luminosity(timestamp, aligned_data, aligned_data_all, i):
n_active_aligned = (aligned_data != 0).sum(axis=0)
cumsummed_data_all = aligned_data_all.sum(axis=0).cumsum()
summed_data = aligned_data.sum(axis=0)
cumsummed_data = summed_data.cumsum()
plot = Plot(width=r'.5\textwidth')
# plot.plot([t / 1e9 for t in timestamp[::100]], cumsummed_data_all[::100],
# linestyle='black!50!green, thick', mark=None)
plot.plot([t / 1e9 for t in timestamp[::100]],
cumsummed_data[::100],
linestyle='thick',
mark=None)
plot.set_xticks([datetime_to_gps(date(y, 1, 1)) / 1e9 for y in YEARS[::3]])
plot.set_xtick_labels(['%d' % y for y in YEARS[::3]])
plot.set_ylabel('Cummulative number of events')
plot.set_xlabel('Date')
plot.save_as_pdf('luminosity_%s' % ['network', 'spa'][i])
def plot_ranges():
k = arange(26)
p_low = [percentile_low_density_for_n(ki) for ki in k]
p_median = [median_density_for_n(ki) for ki in k]
p_mean = [mean_density_for_n(ki) for ki in k]
# p_mpv = [most_probable_density_for_n(ki) for ki in k]
p_high = [percentile_high_density_for_n(ki) for ki in k]
plot = Plot(height=r'\defaultwidth')
plot.plot([0, 1.5 * max(k)], [0, 1.5 * max(k)], mark=None, linestyle='dashed')
plot.scatter(k, p_median)
# plot.plot(k, p_mean, mark=None, linestyle='green')
# plot.plot(k, p_mpv, mark=None, linestyle='red')
plot.shade_region(k, p_low, p_high)
plot.set_xlimits(min(k) - 0.05 * max(k), 1.05 * max(k))
plot.set_ylimits(min(k) - 0.05 * max(k), 1.05 * max(k))
plot.set_axis_equal()
plot.set_xlabel('Detected number of particles')
plot.set_ylabel('Expected actual number of particles')
plot.save_as_pdf('plots/poisson_ranges')
def plot_effiencies():
efficiencies, errors = collect_efficiencies()
for energy in efficiencies.keys():
plot = Plot('semilogx')
for i, zenith in enumerate(sorted(efficiencies[energy].keys())):
if any(abs(zenith - z) < 0.1 for z in [0, 22.5, 37.5]):
plot.plot(CORE_DISTANCES, efficiencies[energy][zenith],
# yerr=errors[energy][zenith],
markstyle='mark size=1pt', linestyle='blue')
plot.add_pin(str(zenith), x=15, use_arrow=True)
else:
plot.plot(CORE_DISTANCES, efficiencies[energy][zenith], mark=None)
plot_david_data(plot)
plot.set_ylabel('Efficiency')
plot.set_ylimits(min=0, max=1.02)
plot.set_xlimits(min=2, max=500)
plot.set_xlabel('Core distance')
plot.save_as_pdf('efficiency_%s_%.1f.pdf' % (STATION_TYPE[STATION_NUMBER], energy))
def plot_integral(trace, baseline):
plot = Plot()
time = arange(0, len(trace) * 2.5, 2.5)
plot.plot(time, trace, mark=None, linestyle='const plot')
integral_trace = where(trace > baseline + BASELINE_THRESHOLD, trace,
baseline)
plot.shade_region(time + 2.5, [baseline] * len(trace),
integral_trace,
color='lightgray, const plot')
plot.draw_horizontal_line(baseline, linestyle='densely dashed, gray')
plot.draw_horizontal_line(baseline + BASELINE_THRESHOLD,
linestyle='densely dotted, gray')
plot.draw_horizontal_line(max(trace), linestyle='densely dashed, gray')
# plot.set_ylimits(0)
plot.set_xlabel(r'Trace time [\si{\ns}]')
plot.set_ylabel(r'Signal strength [ADC]')
plot.save_as_pdf('integral')
def plot_detector_offsets(offsets, type='month'):
d1, d2, d3, d4 = zip(*offsets)
x = range(len(d1))
graph = Plot()
graph.plot(x, d1, markstyle='mark size=.5pt')
graph.plot(x, d2, markstyle='mark size=.5pt', linestyle='red')
graph.plot(x, d3, markstyle='mark size=.5pt', linestyle='green')
graph.plot(x, d4, markstyle='mark size=.5pt', linestyle='blue')
graph.set_ylabel('$\Delta t$ [ns]')
graph.set_xlabel('Date')
graph.set_xlimits(0, max(x))
graph.set_ylimits(-LIMITS, LIMITS)
graph.save_as_pdf('detector_offset_drift_%s_%d' % (type, station))
def plot_pmt_curves(self):
plot = Plot('loglog')
filter = self.ref_out < 50
for i in range(4):
filter2 = self.ref_in_i[:, i] < 500
pin = self.ref_in_i[:, i].compress(filter & filter2)
pout = self.ref_out.compress(filter & filter2)
plot.plot(pout, pin, linestyle=COLORS[i], mark=None)
filter2 = self.ref_in < 500
pin = self.ref_in.compress(filter & filter2)
pout = self.ref_out.compress(filter & filter2)
plot.plot(pout, pin, linestyle='pink', mark=None)
plot.set_ylimits(min=min(self.lin_bins), max=max(self.lin_bins))
plot.set_xlimits(min=min(self.lin_bins), max=max(self.lin_bins))
plot.set_ylabel(r'Input signal')
plot.set_xlabel(r'Output signal')
plot.save_as_pdf('plots/pmt_curves')
def scatter_n():
with tables.open_file(RESULT_PATH, 'r') as data:
cluster = data.root.coincidences._v_attrs.cluster
coincidences = data.root.coincidences.coincidences
for n in range(0, len(cluster.stations) + 1):
graph = Plot()
c = coincidences.read_where('N == n')
print 'N = %d: %d' % (n, len(c))
graph.plot(c['x'],
c['y'],
mark='*',
linestyle=None,
markstyle='mark size=.3pt')
plot_cluster(graph, cluster)
r = 520
graph.set_ylimits(-r, r)
graph.set_xlimits(-r, r)
graph.set_ylabel('y (m)')
graph.set_xlabel('x (m)')
graph.save_as_pdf('N_%d' % n)
def main():
locations = np.genfromtxt(
'data/SP-DIR-plot_sciencepark_cluster-detectors.txt',
names=['x', 'y'])
stations = np.genfromtxt(
'data/SP-DIR-plot_sciencepark_cluster-stations.txt',
names=['id', 'x', 'y'])
graph = Plot()
graph.scatter(locations['x'], locations['y'])
graph.set_axis_equal()
locations = ['right'] * len(stations)
locations[0] = 'left'
locations[5] = 'above right'
locations = iter(locations)
for num, x, y in stations:
graph.add_pin_at_xy(x, y, int(num), location=next(locations),
use_arrow=False, style='gray,label distance=1ex')
x = [stations['x'][u] for u in [0, 2, 5]]
y = [stations['y'][u] for u in [0, 2, 5]]
x.append(x[0])
y.append(y[0])
graph.plot(x, y, mark=None, linestyle='dashed')
graph.add_pin_at_xy([x[0], x[1]], [y[0], y[1]], r'\SI{128}{\meter}',
relative_position=.4, location='below right',
use_arrow=False)
graph.add_pin_at_xy([x[0], x[2]], [y[0], y[2]], r'\SI{151}{\meter}',
relative_position=.5, location='left',
use_arrow=False)
graph.add_pin_at_xy([x[2], x[1]], [y[2], y[1]], r'\SI{122}{\meter}',
relative_position=.5, location='above right',
use_arrow=False)
graph.set_xlabel(r"Distance [\si{\meter}]")
graph.set_ylabel(r"Distance [\si{\meter}]")
graph.save('sciencepark')
def main():
x = np.arange(10)
y = (x / 2.0) - 3.0
colors = ["black", "red", "blue", "yellow", "purple"]
plot = Plot()
for i in range(5):
plot.plot(x, y - i, mark="", linestyle=colors[i])
plot.set_axis_options(
"yticklabel pos=right,\n"
"grid=major,\n"
"legend entries={$a$,[red]$b$,[green]$c$,$d$,$a^2$},\n"
"legend pos=north west"
)
plot.set_xlabel("Something important")
plot.set_ylabel("A related thing")
plot.save("any_option")
x = np.linspace(0.6 * np.pi, 10 * np.pi, 150)
y = np.sin(x) / x
plot = MultiPlot(1, 2, width=r".4\linewidth", height=r".25\linewidth")
subplot = plot.get_subplot_at(0, 0)
subplot.plot(x, y, mark=None)
subplot = plot.get_subplot_at(0, 1)
subplot.plot(x, y, mark=None)
plot.show_xticklabels_for_all([(0, 0), (0, 1)])
plot.show_yticklabels(0, 1)
plot.set_axis_options(0, 1, "yticklabel pos=right, grid=major")
plot.set_axis_options_for_all(None, r"enlargelimits=false")
plot.set_xlabel("Something important")
plot.set_ylabel("A related thing")
plot.save("multi_any_option")
def main():
# Draw random numbers from the normal distribution
np.random.seed(1)
N = np.random.normal(size=2000)
# define bin edges
edge = 5
bin_width = .1
bins = np.arange(-edge, edge + .5 * bin_width, bin_width)
# build histogram and x, y values at the center of the bins
n, bins = np.histogram(N, bins=bins)
x = (bins[:-1] + bins[1:]) / 2
y = n
# fit normal distribution pdf to data
f = lambda x, N, mu, sigma: N * scipy.stats.norm.pdf(x, mu, sigma)
popt, pcov = scipy.optimize.curve_fit(f, x, y)
print("Parameters from fit (N, mu, sigma):", popt)
# make graph
graph = Plot()
# graph histogram
graph.histogram(n, bins)
# graph model with fit parameters
x = np.linspace(-edge, edge, 100)
graph.plot(x, f(x, *popt), mark=None)
# set labels and limits
graph.set_xlabel("value")
graph.set_ylabel("count")
graph.set_label("Fit to data")
graph.set_xlimits(-6, 6)
# save graph to file
graph.save('histogram-fit')
def main():
gamma = np.genfromtxt('data/showere15-proton.t2001', usecols=(1, 2))
e = np.genfromtxt('data/showere15-proton.t2205', usecols=(1, 2))
mu = np.genfromtxt('data/showere15-proton.t2207', usecols=(1, 2))
graph = Plot(axis='loglog')
graph.plot(gamma[:, 0], gamma[:, 1], mark=None)
graph.add_pin(r'$\gamma$')
graph.plot(e[:, 0], e[:, 1], mark=None)
graph.add_pin('e')
graph.plot(mu[:, 0], mu[:, 1], mark=None)
graph.add_pin(r'$\mu$')
graph.set_xlabel(r"Core distance [\si{\meter}]")
graph.set_ylabel(r"Particle density [\si{\per\square\meter}]")
graph.set_logyticks(range(-6, 3, 2))
graph.save('eas-lateral')
def main():
leap = np.genfromtxt('data/leap-prot.dat', delimiter=',',
usecols=(0, 1), names=['E', 'F'])
leap['E'] *= 1e6
leap['F'] *= 1e3 * 2
proton = read_data('data/proton', 1, 0)
akeno_new_lo = read_data('data/akeno-new-lo', 0, 1)
flys_eye = read_data('data/fe-new', 0, 1)
yakutsk = read_data('data/yakustk', 1, 0)
haverah = read_data('data/haverah', 1, 0)
graph = Plot(axis='loglog', width=r'.5\linewidth', height=r'.65\linewidth')
graph.plot(leap['E'], leap['F'], mark=None)
graph.add_pin('LEAP', 'above right', use_arrow=True,
relative_position=.5)
graph.plot(proton['E'], proton['F'], mark=None)
graph.add_pin('PROTON', 'above right', use_arrow=True,
relative_position=.5)
graph.plot(akeno_new_lo['E'], akeno_new_lo['F'], mark=None)
graph.add_pin('AGASA', 'above right', use_arrow=True,
relative_position=.5)
graph.plot(yakutsk['E'], yakutsk['F'], mark=None)
graph.add_pin('Yakutsk', 'below left', use_arrow=True,
relative_position=.55)
graph.plot(haverah['E'], haverah['F'], mark=None)
graph.add_pin('Haverah Park', 'below left', use_arrow=True,
relative_position=.85)
graph.plot(flys_eye['E'], flys_eye['F'], mark=None)
graph.add_pin("Fly's Eye", 'below left', use_arrow=True,
relative_position=1.0)
graph.set_xlabel(r"Energy [\si{\electronvolt}]")
graph.set_ylabel(r"Flux [\si{\per\square\meter\per\steradian"
"\per\second\per\giga\electronvolt}]")
x = np.logspace(11, 17)
graph.plot(x, 1.5e29 * x ** -2.75, mark=None, linestyle='dashed')
graph.set_logxticks(range(6, 22, 3))
graph.save('spectrum')
if x > 0.0:
return 1.0
return 2 * (H(x / L) - H(x / L - 1)) - 1
def fourier(x, N):
''' fourier approximation with N terms'''
term = 0.0
for n in range(1, N, 2):
term += (1.0 / n) * math.sin(n * math.pi * x / L)
return (4.0 / (math.pi)) * term
X = npy.linspace(0.0, 2 * L, num=1000)
Y_sqr = [square(x) for x in X]
Y = lambda n: [fourier(x, n) for x in X]
graph = Plot()
graph.set_title("Fourier approximation")
graph.plot(x=X, y=Y( 3), linestyle='red' , mark=None, legend='n=3' )
graph.plot(x=X, y=Y( 5), linestyle='yellow', mark=None, legend='n=5' )
graph.plot(x=X, y=Y( 8), linestyle='green' , mark=None, legend='n=8' )
graph.plot(x=X, y=Y(13), linestyle='blue' , mark=None, legend='n=13')
#graph.plot(x=X, y=Y(21), linestyle='violet', mark=None, legend='n=21')
#graph.plot(x=X, y=Y(34), linestyle='violet', mark=None, legend='n=34')
graph.plot(x=X, y=Y(55), linestyle='cyan' , mark=None, legend='n=55')
graph.plot(x=X, y=Y_sqr, linestyle='black' , mark=None, legend='square')
graph.save_as_pdf('plot')
q = int(0.25 * len(y))
y = y[q:2*q]
max_index = q + np.argmax(y)
max_x = x[max_index]
plot.add_pin(label, x=max_x, location='above', use_arrow=True,
style='pin distance=%s' % distance)
X = np.linspace(0., 2 * L, num=1000)
Y_sqr = [square(x) for x in X]
Y = lambda n: [fourier(x, n) for x in X]
graph = Plot()
graph.set_title("Fourier approximation")
graph.plot(x=X, y=Y(3), linestyle='red', mark=None, legend='n=3')
graph.plot(x=X, y=Y(5), linestyle='yellow', mark=None, legend='n=5')
graph.plot(x=X, y=Y(8), linestyle='green', mark=None, legend='n=8')
graph.plot(x=X, y=Y(13), linestyle='blue', mark=None, legend='n=13')
graph.plot(x=X, y=Y(55), linestyle='cyan', mark=None, legend='n=55')
graph.plot(x=X, y=Y_sqr, linestyle='black', mark=None, legend='square')
graph.save('fourier_with_legend')
graph = Plot()
graph.set_title("Fourier approximation")
graph.plot(x=X, y=Y(3), mark=None, linestyle='black!20')
add_custom_pin(graph, X, Y(3), 3)
graph.plot(x=X, y=Y(5), mark=None, linestyle='black!30')
add_custom_pin(graph, X, Y(5), 5)
def main():
plot = Plot(width=r'.5\linewidth', height=r'.5\linewidth')
r = linspace(1, 5, 100)
phi = linspace(0, 4.5 * pi, 100)
x = r * cos(phi)
y = r * sin(phi)
plot.plot(x, y, mark=None)
plot.add_pin('start', relative_position=0, use_arrow=True)
plot.add_pin('half', relative_position=.5, use_arrow=True)
plot.add_pin('46\%', relative_position=.46, use_arrow=True,
location='above')
plot.add_pin('end', relative_position=1, use_arrow=True, location='below')
phi = linspace(0, 2 * pi, 10)
x = 6 * cos(phi)
y = 6 * sin(phi)
plot.plot(x, y, mark=None, linestyle='thick, gray')
plot.add_pin('start', relative_position=0, use_arrow=True,
location='above right')
plot.add_pin('half', relative_position=.5, use_arrow=True,
location='above left')
plot.add_pin('70\%', relative_position=.7, use_arrow=True,
location='below')
plot.add_pin('end', relative_position=1, use_arrow=True,
location='below right')
plot.plot([-5, 2, 5], [-7.5, -7.5, -7.5], linestyle='lightgray')
plot.add_pin('50\%', relative_position=.5, use_arrow=True,
location='above right')
plot.set_xlimits(-8, 8)
plot.set_ylimits(-8, 8)
plot.save('relative_pin')
# With one logarithmic axis
plot = Plot(axis='semilogy')
x = [2, 2, 2]
y = [1, 10, 100]
plot.plot(x, y)
for xi, yi in zip(x, y):
plot.add_pin_at_xy(xi, yi, '(%d,%d)' % (xi, yi),
location='below right')
plot.add_pin('half', relative_position=.5, use_arrow=True,
location='right')
x = [4, 5, 6]
y = [3, 3, 3]
plot.plot(x, y)
for xi, yi in zip(x, y):
plot.add_pin_at_xy(xi, yi, '(%d,%d)' % (xi, yi), location='below')
plot.add_pin('half', relative_position=.5, use_arrow=True,
location='above')
x = [3, 4, 5]
y = [1, 10, 100]
plot.plot(x, y)
for xi, yi in zip(x, y):
plot.add_pin_at_xy(xi, yi, '(%d,%d)' % (xi, yi), location='above left')
plot.add_pin('half', relative_position=.5, use_arrow=True,
location='right')
plot.save('relative_pin_log')