def test_plot_phaseogram_direct(self):
import matplotlib.pyplot as plt
phaseogr, phases, times, additional_info = \
phaseogram(self.event_times, self.pulse_frequency)
plot_phaseogram(phaseogr, phases, times)
plt.savefig('phaseogram_direct.png')
plt.close(plt.gcf())
def test_phaseogram_mjdref_pepoch(self):
phaseogr, phases, times, additional_info = \
phaseogram(self.event_times, self.pulse_frequency,
mjdref=57000, out_filename='phaseogram_mjdref.png',
pepoch=57000)
assert np.all(times >= 57000)
assert np.all((phases >= 0) & (phases <= 2))
def test_phaseogram_mjdref_pepoch(self):
phaseogr, phases, times, additional_info = \
phaseogram(self.event_times, self.pulse_frequency,
mjdref=57000, out_filename='phaseogram_mjdref.png',
pepoch=57000)
assert np.all(times >= 57000)
assert np.all((phases >= 0) & (phases <= 2))
def test_plot_phaseogram_direct(self):
import matplotlib.pyplot as plt
phaseogr, phases, times, additional_info = \
phaseogram(self.event_times, self.pulse_frequency)
plot_phaseogram(phaseogr, phases, times)
plt.savefig('phaseogram_direct.png')
plt.close(plt.gcf())
def test_plot_phaseogram_fromfunc(self):
import matplotlib.pyplot as plt
fig = plt.figure('Phaseogram from func')
ax = plt.subplot()
phaseogr, phases, times, additional_info = \
phaseogram(self.event_times, self.pulse_frequency, mjdref=57000,
pepoch=57000, phaseogram_ax=ax, plot=True)
plt.savefig('phaseogram_fromfunc.png')
plt.close(fig)
def test_plot_phaseogram_fromfunc(self):
import matplotlib.pyplot as plt
fig = plt.figure('Phaseogram from func')
ax = plt.subplot()
phaseogr, phases, times, additional_info = \
phaseogram(self.event_times, self.pulse_frequency, mjdref=57000,
pepoch=57000, phaseogram_ax=ax, plot=True)
plt.savefig('phaseogram_fromfunc.png')
plt.close(fig)
def test_phaseogram_weights(self):
phaseogr, phases, times, additional_info = \
phaseogram(self.times, self.pulse_frequency, weights=self.counts,
nph=16)
assert np.all(times < 25.6)
assert np.any(times > 25)
assert np.all((phases >= 0) & (phases <= 2))
import matplotlib.pyplot as plt
fig = plt.figure('Phaseogram direct weights')
plot_phaseogram(phaseogr, phases, times)
plt.savefig('phaseogram_weights.png')
plt.close(fig)
def test_phaseogram_weights(self):
phaseogr, phases, times, additional_info = \
phaseogram(self.times, self.pulse_frequency, weights=self.counts,
nph=16)
assert np.all(times < 25.6)
assert np.any(times > 25)
assert np.all((phases >= 0) & (phases <= 2))
import matplotlib.pyplot as plt
fig = plt.figure('Phaseogram direct weights')
plot_phaseogram(phaseogr, phases, times)
plt.savefig('phaseogram_weights.png')
plt.close(fig)
def normalized_phaseogram(norm, *args, **kwargs):
phas, phases, times, additional_info = phaseogram(*args, **kwargs)
if norm is None:
pass
elif norm == 'to1':
minarr = np.min(phas, axis=0)
maxarr = np.max(phas, axis=0)
for i in range(phas.shape[0]):
phas[i][:] -= minarr
phas[i][:] /= (maxarr - minarr)
elif norm == 'mediansub':
medarr = np.median(phas, axis=0)
for i in range(phas.shape[0]):
phas -= medarr
else:
warnings.warn('Profile normalization '
'{} not known. Using default'.format(norm))
return phas, phases, times, additional_info
def recalculate(self, event):
dfreq, dfdot, dfddot = self._read_sliders()
pepoch = self.pepoch
self.fddot = self.fddot - dfddot
self.fdot = self.fdot - dfdot
self.freq = self.freq - dfreq
self.phaseogr, _, _, _ = \
phaseogram(self.ev_times, self.freq, fdot=self.fdot, plot=False,
nph=self.nph, nt=self.nt, pepoch=pepoch,
fddot=self.fddot)
self.reset(1)
self.fig.canvas.draw()
print("------------------------")
print("PEPOCH {} + MJDREF".format(self.pepoch / 86400))
print("F0 {}".format(self.freq))
print("F1 {}".format(self.fdot))
print("F2 {}".format(self.fddot))
print("------------------------")
def stingphase(evt_data,
freq,
figsize=(10, 10),
nbins=32,
save=False,
pname='stingphase',
mjd=False):
'''
Plots Stingray phaseogram.
Inputs:
-------
evt_data
freq
figsize
nbins: number of bins for histogram and phaseogram
save: bool for whether or not to save plot as png
pname: string of path and name of output png file to save
TO DO:
add option to put MJD referencce time
'''
plt.figure(figsize=figsize)
gs = GridSpec(2, 1, height_ratios=(1, 3))
ax0 = plt.subplot(gs[0])
ax1 = plt.subplot(gs[1], sharex=ax0)
plt.subplots_adjust(wspace=0, hspace=0)
phaseogr, phases, times, additional_info = \
phaseogram(evt_data['TIME'], freq, return_plot=True,nt=nbins,nph=nbins)
mean_phases = (phases[:-1] + phases[1:]) / 2
plot_profile(mean_phases, np.sum(phaseogr, axis=1), ax=ax0)
_ = plot_phaseogram(phaseogr,
phases,
times,
ax=ax1,
vmin=np.median(phaseogr))
if save:
plt.savefig(pname + '.png', dpi=200, bbox_inches='tight')
def recalculate(self, event):
self.orbital_period, self.asini, self.t0 = self._read_sliders()
corrected_times = self.ev_times - self._delay_fun(self.ev_times)
self.phaseogr, _, _, _ = \
phaseogram(corrected_times, self.freq, fdot=self.fdot, plot=False,
nph=self.nph, nt=self.nt, pepoch=self.pepoch,
fddot=self.fddot)
self._set_lines(False)
self.pcolor.set_array(self.phaseogr.T.ravel())
self.sasini.valinit = self.asini
self.speriod.valinit = self.orbital_period
self.st0.valinit = self.t0
self.st0.valmin = self.t0 - self.orbital_period
self.st0.valmax = self.t0 + self.orbital_period
self.fig.canvas.draw()
print("------------------------")
print("PB (s) {} ({} d)".format(self.orbital_period,
self.orbital_period / 86400))
print("A1 (l-s) {}".format(self.asini))
print("T0 (MET) {}".format(self.t0))
print("------------------------")
def test_phaseogram(self):
phaseogr, phases, times, additional_info = \
phaseogram(self.event_times, self.pulse_frequency)
assert np.all(times < 25.6)
assert np.any(times > 25)
assert np.all((phases >= 0) & (phases <= 2))
def test_phaseogram_bad_weights(self):
with pytest.raises(ValueError) as excinfo:
phaseogr, phases, times, additional_info = \
phaseogram(self.event_times, self.pulse_frequency,
weights=[0, 2])
assert 'must match' in str(excinfo)
def test_phaseogram_bad_weights(self):
with pytest.raises(ValueError) as excinfo:
phaseogr, phases, times, additional_info = \
phaseogram(self.event_times, self.pulse_frequency,
weights=[0, 2])
assert 'must match' in str(excinfo)
def __init__(self,
ev_times,
freq,
nph=128,
nt=128,
test=False,
pepoch=None,
fdot=0,
fddot=0,
**kwargs):
self.fdot = fdot
self.fddot = fddot
self.nt = nt
self.nph = nph
self.pepoch = assign_value_if_none(pepoch, ev_times[0])
self.ev_times = ev_times
self.freq = freq
self.fig, ax = plt.subplots()
plt.subplots_adjust(left=0.25, bottom=0.30)
corrected_times = self.ev_times - self._delay_fun(self.ev_times)
self.phaseogr, phases, times, additional_info = \
phaseogram(corrected_times, freq, return_plot=True, nph=nph, nt=nt,
fdot=fdot, fddot=fddot, plot=False, pepoch=pepoch)
self.phases, self.times = phases, times
self.pcolor = plt.pcolormesh(phases,
times,
self.phaseogr.T,
cmap='magma')
plt.xlabel('Phase')
plt.ylabel('Time')
plt.colorbar()
self.lines = []
self.line_phases = np.arange(-2, 3, 0.5)
for ph0 in self.line_phases:
newline, = plt.plot(np.zeros_like(times) + ph0,
times,
zorder=10,
lw=2,
color='w')
self.lines.append(newline)
plt.xlim([0, 2])
axcolor = '#ff8888'
self.slider_axes = []
self.slider_axes.append(
plt.axes([0.25, 0.1, 0.5, 0.03], facecolor=axcolor))
self.slider_axes.append(
plt.axes([0.25, 0.15, 0.5, 0.03], facecolor=axcolor))
self.slider_axes.append(
plt.axes([0.25, 0.2, 0.5, 0.03], facecolor=axcolor))
self._construct_widgets(**kwargs)
self.closeax = plt.axes([0.15, 0.020, 0.15, 0.04])
self.button_close = Button(self.closeax,
'Quit',
color=axcolor,
hovercolor='0.8')
self.recalcax = plt.axes([0.3, 0.020, 0.15, 0.04])
self.button_recalc = Button(self.recalcax,
'Recalculate',
color=axcolor,
hovercolor='0.975')
self.resetax = plt.axes([0.45, 0.020, 0.15, 0.04])
self.button_reset = Button(self.resetax,
'Reset',
color=axcolor,
hovercolor='0.975')
self.zoominax = plt.axes([0.6, 0.020, 0.15, 0.04])
self.button_zoomin = Button(self.zoominax,
'Zoom in',
color=axcolor,
hovercolor='0.975')
self.zoomoutax = plt.axes([0.75, 0.020, 0.15, 0.04])
self.button_zoomout = Button(self.zoomoutax,
'Zoom out',
color=axcolor,
hovercolor='0.975')
self.button_reset.on_clicked(self.reset)
self.button_zoomin.on_clicked(self.zoom_in)
self.button_zoomout.on_clicked(self.zoom_out)
self.button_recalc.on_clicked(self.recalculate)
self.button_close.on_clicked(self.quit)
if not test:
plt.show()
def test_phaseogram(self):
phaseogr, phases, times, additional_info = \
phaseogram(self.event_times, self.pulse_frequency)
assert np.all(times < 25.6)
assert np.any(times > 25)
assert np.all((phases >= 0) & (phases <= 2))
