def multiBandCurves(star='gj832',
inst='cos_g130m',
trange=[24400, 24900],
n=100,
tref=24625.0,
bandnames=['NV', 'SiIV', 'SiIII', 'CII', 'cont1380'],
ax=None,
norms=None,
fluxed=False,
maxpts=500):
if ax is None: ax = plt.gca()
ph, p = io.readphotons(star, inst)
p['time'] -= tref
trange = np.array(trange) - tref
ax.set_xlabel('Time [s]')
ax.set_xlim(trange)
if fluxed:
wtkey = 'epera'
ax.set_ylabel(linefluxlabel)
else:
wtkey = 'epsilon'
ax.set_ylabel('Count Rate [s$^{-1}$]')
if norms is not None:
ax.set_ylabel('Normalized Flux')
lines, labels = [], []
for i, name in enumerate(bandnames):
bands = rc.stdbands.loc[name, 'bands']
label = rc.stdbands.loc[name, 'name txt']
Tform = rc.stdbands.loc[name, 'Tform']
# wavelbl = rc.stdbands.loc[name, 'wave lbl']
# label += ' ' + wavelbl
if not np.isnan(Tform):
label += ' ({:.1f})'.format(Tform)
t0, t1, rate, err = sp.smooth_curve(p['time'],
p['wavelength'],
p[wtkey],
n=n,
bands=bands)
t = (t0 + t1) / 2.0
keep = (t1 > trange[0]) & (t0 < trange[1])
t, rate, err = t[keep], rate[keep], err[keep]
if len(t) > maxpts:
keep = un.downsample_even(t, maxpts)
t, rate, err = t[keep], rate[keep], err[keep]
if norms is not None:
rate /= norms[i]
line, poly = pu.errorpoly(t, rate, err, ealpha=0.2, ax=ax)
lines.append(line)
labels.append(label)
ax.legend(lines, labels, loc='best', fontsize='small')
def flareCompare(inst='cos_g130m', band='SiIV', nflares=3, ax=None):
if ax is None: ax = plt.gca()
ax.set_xlabel('Time [s]')
ax.set_ylabel('Normalized Flux')
flares = reduce.combine_flarecats(band, inst)
flares = flares[:nflares]
bands, dt = flares.meta['BANDS'], flares.meta['DT']
groups = [range(len(bands))]
mxpeak = max(flares['pkratio'])
# plot all curves
lines, labels = [], []
for flare in flares:
star = flare['star']
label = starprops['name tex'][star]
# curve = reduce.auto_curve(star, inst, bands=bands, dt=dt, appx=False, groups=groups)
# t0, t1, cps, cpserr = zip(*curve)[0]
ph, p = io.readphotons(star, inst)
t0, t1, cps, cpserr = sp.smooth_curve(p['time'],
p['wavelength'],
p['epsilon'],
bands=bands,
n=100)
tmid = (t0 + t1) / 2.0
t = tmid - flare['peak rel']
qcps = fits.getval(rc.flarepath(star, inst, 'SiIV'), 'QSCTCPS', ext=1)
rate, err = cps / qcps, cpserr / qcps
fac = 10.0**np.floor(np.log10(mxpeak / flare['pkratio']))
if fac > 1.0:
label += ' $\\times$%i' % fac
rate = (rate - 1.0) * fac + 1.0
err = err * fac
# line = ax.plot(t, rate, '-')[0]
# ax.errorbar(t, rate, err, fmt='.', color=line.get_color(), capsize=0)
line, poly = pu.errorpoly(t, rate, err, ax=ax)
lines.append(line)
labels.append(label)
ax.legend(lines, labels, loc='best', fontsize='small')
starts, stops = flares['start rel'] - flares['peak rel'], flares[
'stop rel'] - flares['peak rel']
ax.set_xlim(min(starts) * 1.5, max(stops))
def specSnapshot(star,
inst,
trange,
wrange,
n=100,
ax=None,
vCen=None,
maxpts=500,
**kwargs):
if ax is None: ax = plt.gca()
ph, p = io.readphotons(star, inst)
keep = mnp.inranges(p['time'], trange)
p = p[keep]
gtis = np.array([ph['gti'].data['start'], ph['gti'].data['stop']]).T
gt = mnp.range_intersect([trange], gtis)
dt = np.sum(gt[:, 1] - gt[:, 0])
w0, w1, spec, err = sp.smooth_spec(p['wavelength'], p['epera'], n)
spec, err = spec / dt, err / dt
w = (w0 + w1) / 2.0
keep, = np.nonzero(mnp.inranges(w, wrange))
keep = np.insert(keep, [0, len(keep)], [keep[0] - 1, keep[-1] + 1])
w, spec, err = w[keep], spec[keep], err[keep]
if len(w) > maxpts:
keep = un.downsample_even(w, maxpts)
w, spec, err = w[keep], spec[keep], err[keep]
velocify = lambda w: (w - vCen) / vCen * 3e5
if vCen is not None:
w = velocify(w)
ax.set_xlabel('Doppler Velocity [km s$^{-1}$]')
ax.set_xlim(map(velocify, wrange))
else:
ax.set_xlabel('Wavelength [$\AA$]')
ax.set_xlim(wrange)
ax.set_ylabel(fluxlabel)
return pu.errorpoly(w, spec, err, **kwargs)
def spectrumMovieFrames(star,
inst,
band,
trange,
dt,
smoothfac,
axspec,
axcurve,
folder,
dpi=80,
velocityplot=False,
reftrange=None,
dryRun=False,
ylim=None):
ph, photons = io.readphotons(star, inst)
band, trange, reftrange = map(np.asarray, [band, trange, reftrange])
fig = axcurve.get_figure()
figwidth = fig.get_figwidth()
axwidth = axcurve.get_position().width * figwidth
axPix = axwidth * dpi
def goodN(Nphotons):
n = 100 # SN of 10
if Nphotons / n > axPix: # don't need to sample more finely than the pixel scale
n = Nphotons / axPix
elif Nphotons / n < 20: # want at least some resolution
n = max(Nphotons / 20, 9) # but no less than SN of 3ish
return n
# re-reference times to start of time range
tref = trange[0]
photons['time'] -= tref
if reftrange is not None: reftrange -= tref
trange -= tref
if velocityplot:
velocify = lambda w: (w - velocityplot) / velocityplot * 3e5
vband = velocify(band)
p = photons
tkeep = [
max(p['time'][0], -trange[1] * 0.5),
min(p['time'][-1], trange[1] * 1.5)
]
dw = band[1] - band[0]
wkeep = [band[0] - 5 * dw, band[1] + 5 * dw]
# get rid of superfluous counts
keep = mnp.inranges(p['time'], tkeep) & mnp.inranges(
p['wavelength'], wkeep)
p = p[keep]
## make lightcurve and set up initial plot
nlc = goodN(
np.sum(
mnp.inranges(p['wavelength'], band)
& mnp.inranges(p['time'], trange)))
t0, t1, lc, lcerr = sp.smooth_curve(p['time'],
p['wavelength'],
p['epera'],
nlc,
bands=[band],
trange=tkeep)
tlc = (t0 + t1) / 2.0
axcurve.set_xlim(trange)
axcurve.set_xlabel('Time [s]')
axcurve.set_ylabel('Integrated Flux \n[erg cm$^{-2}$ s$^{-1}$]')
inrange = mnp.inranges(tlc, trange)
pu.errorpoly(tlc[inrange],
lc[inrange],
lcerr[inrange],
'k-',
ax=axcurve,
alpha=0.3,
ealpha=0.15)
# make spectrum frames
T = dt * smoothfac
nframes = int(round((trange[1] - trange[0] - T) / dt))
t1s = np.linspace(trange[0] + T, trange[1], nframes)
t0s = t1s - T
wList, specList, errList = [], [], []
for t0, t1 in zip(t0s, t1s):
inInterval = mnp.inranges(p['time'], [t0, t1])
pt = p[inInterval]
n = goodN(np.sum(mnp.inranges(pt['wavelength'], band)))
w0, w1, spec, err = sp.smooth_spec(pt['wavelength'], pt['epera'], n,
wkeep)
wList.append((w0 + w1) / 2.0)
specList.append(spec / T)
errList.append(err / T)
## set up spectrum plot
if velocityplot:
axspec.set_xlabel('Doppler Velocity [km s$^{-1}$]')
axspec.set_xlim(vband)
else:
axspec.set_xlabel('Wavelength [$\AA$]')
axspec.set_xlim(band)
axspec.set_ylabel(fluxlabel)
if ylim is None:
ymin = min([np.min(s - e) for s, e in zip(specList, errList)])
ymax = max([np.max(s + e) for s, e in zip(specList, errList)])
axspec.set_ylim(ymin, ymax)
else:
axspec.set_ylim(ylim)
# compute and plot reference spectrum, if desired
if reftrange is not None:
gtis = np.array([ph['gti'].data['start'], ph['gti'].data['stop']
]).T - tref
gt = mnp.range_intersect([reftrange], gtis)
Tref = np.sum(gt[:, 1] - gt[:, 0])
keep = mnp.inranges(photons['time'], reftrange) & mnp.inranges(
photons['wavelength'], wkeep)
pt = photons[keep]
nref = goodN(np.sum(mnp.inranges(pt['wavelength'], band)))
w0, w1, spec, _ = sp.smooth_spec(pt['wavelength'], pt['epera'], nref,
wkeep)
w = (w0 + w1) / 2.0
if velocityplot:
w = velocify(w)
spec = spec / Tref
axspec.plot(w, spec, 'k-', alpha=0.3)
# make folder to save frames in if it doesn't exist
if not os.path.exists(folder):
os.mkdir(folder)
## loop through frames
if dryRun:
nframes = dryRun
for i in range(nframes):
# plot time range on lightcurve
span = axcurve.axvspan(t0s[i], t1s[i], color='k', alpha=0.2)
inrange = mnp.inranges(tlc, [t0s[i], t1s[i]])
linelc, polylc = pu.errorpoly(tlc[inrange],
lc[inrange],
lcerr[inrange],
'k-',
ax=axcurve,
ealpha=0.3)
# plot spectrum
w, spec, err = wList[i], specList[i], errList[i]
inrange = mnp.inranges(w, band)
inrange = np.nonzero(inrange)[0]
inrange = np.insert(inrange, [0, len(inrange)],
[inrange[0] - 1, inrange[-1] + 1])
ww, ss, ee = w[inrange], spec[inrange], err[inrange]
ss[[0, -1]] = np.interp(band, ww, spec[inrange])
ee[[0, -1]] = np.interp(band, ww, err[inrange])
ww[[0, -1]] = band
if velocityplot:
ww = velocify(ww)
linespec, polyspec = pu.errorpoly(ww,
ss,
ee,
'k-',
ax=axspec,
ealpha=0.2)
# save frame
path = os.path.join(folder, '{:04d}.png'.format(i))
fig.savefig(path, dpi=dpi)
# remove plots
[obj.remove() for obj in [span, linelc, polylc, linespec, polyspec]]