def plotMgb(spectrum_array, template, ax, teff, logg, feh, vsini=12, vshift=0):
spec = []
for order in range(len(spectrum_array)):
if max(spectrum_array[order][:, 0]) > 5100 and min(
spectrum_array[order][:, 0]) < 5300:
print order
spec_normed = spectrum_array[order].copy()
#spec_normed[:,1] = normalise(spec_normed[:,1],niter=5,sigma_low = 0.05,deg=5)
spec_normed = normalise_with_template(spec_normed,
template.copy(),
vsini=vsini,
vshift=vshift)
plt.plot(spec_normed[:, 0], spec_normed[:, 1], color="b", lw=2)
template_mask = template[:, 0] > 5000
template_mask *= template[:, 0] < 5400
vaxis = template[:, 0][template_mask]
vaxis = c * (vaxis - median(vaxis)) / vaxis
vprof = spectype.make_rot_prof(vaxis,
vsini=vsini,
epsilon=0.5,
scale=1,
vshift=vshift)
vprof = spectype.vgauss(vaxis, vprof, macro=13.04 / 2.355, scale=1)
vprof /= sum(vprof)
template_f = convolve(template[:, 1][template_mask], vprof, mode="same")
plt.plot(template[:, 0][template_mask], template_f, color="r")
plt.xlim(5100, 5300)
plt.ylim(0.02, 1.2)
[i.set_linewidth(2.) for i in ax.spines.itervalues()]
plt.xlabel("Wavelength $(\AA)$", fontsize=15, weight="black")
plt.text(0.99,
0.05,
"$v\sin i = " + str(round(vsini, 1)) + "$ km/s",
transform=ax.transAxes,
ha="right",
fontsize=14)
plt.text(0.99,
0.2,
"$T_\mathrm{eff} = " + str(teff) + "$ K",
transform=ax.transAxes,
ha="right",
fontsize=14)
plt.text(0.99,
0.15,
"$\log g = " + str(logg) + "$",
transform=ax.transAxes,
ha="right",
fontsize=14)
plt.text(0.99,
0.1,
"[Fe/H]$ = " + str(feh) + "$",
transform=ax.transAxes,
ha="right",
fontsize=14)
def measure_telluric_rv(spectrum, stellar_template, vsini, vshift):
spectrum_hdulist = pyfits.open(spectrum)
stellar_template = loadtxt(stellar_template)
template = loadtxt("transmission.dat")
template[:, 0] *= 10.
epos = 0
for order in range(0, len(spectrum_hdulist[0].data)):
try:
wave = spectrum_hdulist[5].data[order][20:-20]
flux = spectrum_hdulist[0].data[order][20:-20]
except IndexError:
wave = spectrum_hdulist[3].data[order][20:-20]
flux = spectrum_hdulist[0].data[order][20:-20]
if min(wave) < 6270 and max(wave) > 6330:
mask = wave > 6270
mask *= wave < 6330
vel = arange(-300, 300, 0.01)
lsd_interp = spectype.make_rot_prof(vel,
vsini=vsini,
scale=1.,
vshift=vshift)
lsd_interp = spectype.vgauss(vel,
lsd_interp,
macro=13.04 / 2.355,
scale=1.)
lsd_interp = transpose(array([vel, lsd_interp]))
#epos,drv,cc = cross_correlate_order(wave[mask],flux[mask],template,ap=10)
#print epos
flux = remove_stellar_template(stellar_template,
transpose(array([wave, flux])),
lsd_interp)
#runlsd(transpose(array([wave,flux])),template)
#sys.exit()
epos, drv, cc = cross_correlate_order(wave, flux, template, ap=10)
# print "telluric rv",epos
# plt.plot(drv,cc)
# plt.axvline(x=epos)
# plt.show()
break
return epos
def normalise_with_template(spectrum, template, vsini=10, vshift=0):
spectrum[:, 1] = normalise(spectrum[:, 1], deg=5)
template_mask = template[:, 0] > min(spectrum[:, 0]) - 10
template_mask *= template[:, 0] < max(spectrum[:, 0]) + 10
template = template[template_mask]
vaxis = template[:, 0]
vaxis = c * (vaxis - median(vaxis)) / vaxis
if vsini < 1:
vsini = 1.
vprof = spectype.make_rot_prof(vaxis,
vsini=vsini,
epsilon=0.5,
scale=1,
vshift=vshift)
vprof = spectype.vgauss(vaxis, vprof, macro=13.04 / 2.355, scale=1)
vprof /= sum(vprof)
template[:, 1] = convolve(template[:, 1], vprof, mode="same")
### Now fit template continuum to spectrum
fit = interpolate.splrep(template[:, 0], template[:, 1])
fit = interpolate.splev(spectrum[:, 0], fit)
diff = spectrum[:, 1] / fit
mask = diff - median(diff) < 1
mask *= diff - median(diff) > -1
fit = polyfit(spectrum[:, 0][mask], diff[mask], 20)
fit = polyval(fit, spectrum[:, 0])
spectrum[:, 1] /= fit
return spectrum
def measure_telluric_rv(spectrum,stellar_template,vsini,vshift):
spectrum_hdulist = pyfits.open(spectrum)
stellar_template = loadtxt(stellar_template)
template = loadtxt("transmission.dat")
template[:,0] *= 10.
epos = 0
for order in range(1,len(spectrum_hdulist[0].data)):
#s = read_spec.read_spec(spectrum,order=order)[20:-20]
#wave,flux = s[:,0],s[:,1]
wave = spectrum_hdulist[0].data[order,:,0][20:-20]
flux = spectrum_hdulist[0].data[order,:,2][20:-20]
mask = flux != flux
flux[mask] = 1
if min(wave) < 6270 and max(wave) > 6320:
mask = wave > 6270
mask *= wave < 6320
vel = arange(-300,300,0.01)
lsd_interp = spectype.make_rot_prof(vel,vsini=vsini,scale=1.,vshift=vshift)
lsd_interp = spectype.vgauss(vel,lsd_interp,macro=5.66/2.355,scale=1.)
lsd_interp = transpose(array([vel,lsd_interp]))
#epos,drv,cc = cross_correlate_order(wave[mask],flux[mask],template,ap=10)
#print epos
flux = remove_stellar_template(stellar_template,transpose(array([wave,flux])),lsd_interp)
ccf = runlsd(transpose(array([wave,flux])),template)
ccfmask = abs(ccf[:,0]) < 60
ccf = ccf[ccfmask]
ccfmask = abs(ccf[:,0]) > 30
fit = polyfit(ccf[:,0][ccfmask],ccf[:,1][ccfmask],1)
fit = polyval(fit,ccf[:,0])
ccf[:,1] -= fit
# plt.plot(ccf[:,0],ccf[:,1])
# plt.show()
x0 = spectype.fitlsd_mcmc(ccf,vsini_init=12.0,nrun=500)
epos = x0[2]
#runlsd(transpose(array([wave,flux])),template)
#sys.exit()
#epos,drv,cc = cross_correlate_order(wave,flux,template,ap=10)
# print "telluric rv",epos
# plt.plot(drv,cc)
# plt.axvline(x=epos)
# plt.show()
break
return epos
