def synth_mag(band=None, datapath=None, wave=None, flux=None, error=None):
"""
Function to calculate synthetic AB magnitudes. Following Bessell & Murphy (2012) and Casagrande & VandenBerg (2014).
Args:
band (string): string value for the band. Must match .dat files for the transmission curves
datapath (string): Path to transmission curves
wave (np.array): Input wavelength array
flux (np.array) = Input flux array
error (np.array) = Input error array
Returns:
float: Calculated apparent magnitude
"""
import glob
import numpy as np
from astropy.cosmology import Planck13 as cosmo
from gen_methods import medfilt
from supersmoother import SuperSmoother
#Read file
filter = glob.glob(datapath+band+'.dat')[0]
filter = np.genfromtxt(filter)
filter_wave = np.array(filter[:,0])
filter_throughput = filter[:,1]
#Convert micron to Angstrom
if np.mean(filter_wave) < 10:
filter_wave *= 10000.0
#Interpolate filter to same sampling as target spectrum
filt_new = common_wavelength(filter_wave, filter_throughput, wave, fill_value=0.0)
#Smooth flux to reject noisy pixels:
sflux = medfilt(flux, 25)
#Calculate AB magnitude
f_nu = (np.sum(filt_new * sflux * wave)) / (3e18 * np.sum(filt_new/wave))
i_band_mag = -2.5 * np.log10((f_nu)) - 48.6
return i_band_mag
def main():
root_dir = '/Users/jselsing/Work/X-Shooter/CompositeRedQuasar/processed_data/'
data_file = np.genfromtxt(root_dir+'Composite.dat')
wl = data_file[:,0]
mean = data_file[:,1]
err_mean = data_file[:,2]
wmean = data_file[:,3]
err_wmean = data_file[:,4]
geo_mean = data_file[:,5]
median = data_file[:,6]
n_spec = data_file[:,7]
std = data_file[:,8]
std_norm = data_file[:,9]
wmean_cont = data_file[:,10]
#Fitting power laws
from scipy import optimize
def power_law(x_tmp, a_tmp, k_tmp):
tmp = a_tmp * x_tmp ** k_tmp
return tmp
def power_law2(x_tmp, a1_tmp, x_c, k1_tmp, k2_tmp):
tmp1 = power_law(x_tmp, a1_tmp,k1_tmp)[x_tmp<x_c]
scale2loc = np.argmin(np.abs(x_tmp - x_c))
a2_tmp = power_law(x_tmp[scale2loc], a1_tmp, (k1_tmp - k2_tmp))
tmp2 = power_law(x_tmp, a2_tmp,k2_tmp)[x_tmp>= x_c]
return np.concatenate((tmp1,tmp2))
def power_law3(x_tmp, a_tmp, k_tmp, b_tmp):
tmp = a_tmp * x_tmp ** (k_tmp + b_tmp * x_tmp)
return tmp
par_guess = [1, -1.70]
par_guess2 = [1, 5000, -1.7, -1.7]
wmean[np.where(np.isnan(wmean) == True)] = 0
mask = (wl > 1300) & (wl < 1350) | (wl > 1425) & (wl < 1475) | (wl > 5500) & (wl < 5800) | (wl > 7300) & (wl < 7500)
err = ((std)[std != 0])[mask]
popt, pcov = optimize.curve_fit(power_law, wl[mask], wmean_cont[mask], p0=par_guess, sigma=np.sqrt(err**2 + err_wmean[mask]**2), absolute_sigma=True, maxfev=5000)
popt2, pcov2 = optimize.curve_fit(power_law2, wl[mask], wmean_cont[mask], p0=par_guess2, sigma=np.sqrt(err**2 + err_wmean[mask]**2), absolute_sigma=True, maxfev=5000)
print(*popt)
print(*popt2)
par_guess = [1, -1.7]
wl_new = wl
wm = []
m = []
geo = []
med = []
#Fit
np.random.seed(12345)
mask = (wl_new > 1300) & (wl_new < 1350) | (wl_new > 1425) & (wl_new < 1475) | (wl_new > 5500) & (wl_new < 5800) | (wl_new > 7300) & (wl_new < 7500)
for i in np.arange(10):
print('Iteration: ', i)
err = ((std)[std != 0])[mask]
resampled_spec = np.random.normal((wmean_cont)[mask], np.sqrt(err**2 + err_wmean[mask]**2))
popt_wmean, pcov_wmean = optimize.curve_fit(power_law, wl_new[mask], resampled_spec, p0=par_guess,
sigma=np.sqrt(err**2 + err_wmean[mask]**2), absolute_sigma=True)
wm.append(popt_wmean)
err = ((std)[std != 0])[mask]
resampled_spec = np.random.normal((mean)[mask], np.sqrt(err**2 + err_mean[mask]**2))
popt_mean, pcov_mean = optimize.curve_fit(power_law, wl_new[mask], resampled_spec, p0=par_guess,
sigma=np.sqrt(err**2 + err_mean[mask]**2), absolute_sigma=True)
m.append(popt_mean)
err = ((std)[std != 0])[mask]
resampled_spec = np.random.normal((median[std != 0])[mask], err)
popt_median, pcov_median = optimize.curve_fit(power_law, wl_new[mask], resampled_spec, p0=par_guess,
sigma=err, absolute_sigma=True, maxfev=600)
med.append(popt_median)
err = ((std)[std != 0])[mask]
resampled_spec = np.random.normal((geo_mean[std != 0])[mask], err)
# pl.plot(wl_new[mask], resampled_spec)
popt_geo, pcov_geo = optimize.curve_fit(power_law, wl_new[mask], resampled_spec, p0=par_guess,
sigma=err, absolute_sigma=True, maxfev=600)
geo.append(popt_geo)
# pl.plot(wl, geo_mean)
# pl.show()
print("""Composite fit slope wmean...{0} +- {1}""".format(np.mean(wm, axis=0)[1],np.std(wm, axis=0)[1]))
print("""Composite fit slope mean...{0} +- {1}""".format(np.mean(m, axis=0)[1], np.std(m, axis=0)[1]))
print("""Composite fit slope median...{0} +- {1}""".format(np.mean(med, axis=0)[1], np.std(med, axis=0)[1]))
print("""Composite fit slope geo...{0} +- {1}""".format(np.mean(geo, axis=0)[1], np.std(geo, axis=0)[1]))
# Plotting
latexify(columns=2, fig_height=7)
import matplotlib.gridspec as gridspec
fig = pl.figure()
gs = gridspec.GridSpec(4, 1, height_ratios=[2,1,1,1])
ax1 = pl.subplot(gs[0])
ax2 = pl.subplot(gs[1])
ax3 = pl.subplot(gs[2])
ax4 = pl.subplot(gs[3])
#Plotting
# ax1.plot(wl, power_law2(wl, *popt2) , 'b--')
# ax1.plot(wl, power_law(wl, *popt) , 'b--')
ax1.plot(wl, wmean_cont, lw = 0.5, linestyle = 'steps-mid', label='X-shooter wmean composite')
nbins = len(wl)
from methods import hist
log_binned_wl = np.array(hist(wl,[min(wl),max(wl)], int(2*nbins),'log'))
from scipy.interpolate import InterpolatedUnivariateSpline
sps = InterpolatedUnivariateSpline(wl, std_norm)
std_plot = smooth(medfilt(sps(log_binned_wl) , 9), window='hanning', window_len=15)
wave_std = log_binned_wl
ax2.plot(wave_std, std_plot, lw = 0.5, linestyle = 'steps-mid', label='Normalised variability')
ax3.plot(wl, wmean_cont/medfilt(err_wmean, 5), lw = 0.5, linestyle = 'steps-mid', label = 'Signal-to-noise')
ax4.plot(wl,medfilt( n_spec, 1), label='Number of spectra', lw=0.5)
#Overplot lines
fit_line_positions = np.genfromtxt('data/plotlinelist.txt', dtype=None)
linelist = []
linenames = []
for n in fit_line_positions:
linelist.append(n[1])
linenames.append(n[0])
pl.xlabel(r'Rest Wavelength [$\AA$]')
ax1.set_ylabel(r'Normalised flux density F$_{\lambda}$')
ax2.set_ylabel(r'Normalised Variability $\delta$F$_{\lambda}$')
ax3.set_ylabel(r'S/N Ratio')
ax4.set_ylabel(r'Number of spectra')
ax1.semilogy()
ax1.semilogx()
ax1.set_xlim((1000, 11500 ))
ax1.set_ylim((0.1, 750))
ax2.semilogy()
ax2.semilogx()
ax2.set_xlim((1000, 11500 ))
ax2.set_ylim((0.001, 90))
ax3.semilogx()
ax3.set_xlim((1000, 11500 ))
ax4.semilogx()
ax4.set_xlim((1000, 11500 ))
ax4.set_ylim((0, 9))
# Formatting axes
import matplotlib as mpl
ax4.xaxis.set_major_formatter(mpl.ticker.ScalarFormatter())
ax4.set_xticks([1000, 2000, 3000, 5000, 9000])
ax1.xaxis.set_major_locator(mpl.ticker.NullLocator())
ax2.xaxis.set_major_locator(mpl.ticker.NullLocator())
ax3.xaxis.set_major_locator(mpl.ticker.NullLocator())
ax1.yaxis.set_minor_locator(mpl.ticker.NullLocator())
ax2.yaxis.set_minor_locator(mpl.ticker.NullLocator())
ax1.yaxis.set_major_formatter(mpl.ticker.ScalarFormatter())
ax1.set_yticks([0.2, 0.5, 1, 2, 5, 10, 20, 50, 100, 200, 500])
ax2.yaxis.set_major_formatter(mpl.ticker.ScalarFormatter())
ax2.set_yticks([0.01, 0.03, 0.1, 0.3, 1, 3, 10, 30])
ax3.yaxis.set_major_formatter(mpl.ticker.ScalarFormatter())
ax3.set_yticks([50, 100, 150, 200, 250, 300])
ax4.yaxis.set_major_formatter(mpl.ticker.ScalarFormatter())
ax4.set_yticks([0, 1, 2, 3, 4, 5, 6, 7, 8])
pl.tight_layout()
fig.subplots_adjust(hspace=0)
format_axes(ax1)
format_axes(ax2)
format_axes(ax3)
format_axes(ax4)
val = []
for p in range(len(linelist)):
xcoord = linelist[p]
mask = (wl > xcoord - 1) & (wl < xcoord + 1)
y_val = np.mean(wmean_cont[mask])
val.append(1.5 * y_val)
arrow_tips = val
lineid_plot.plot_line_ids(wl, wmean_cont, linelist, linenames, arrow_tip=arrow_tips, ax=ax1)
for i in ax1.lines:
if '$' in i.get_label():
i.set_alpha(0.3)
i.set_linewidth(0.75)
for p in range(len(linelist)):
xcoord = linelist[p]
mask = (wl > xcoord - 1) & (wl < xcoord + 1)
y_val = np.mean(wmean_cont[mask])
ax1.vlines(xcoord, ax1.get_ylim()[0], y_val, color='black',linestyle='dashed', lw=0.75, alpha=0.3)
ax2.axvline(x=xcoord, color='black',linestyle='dashed', lw=0.75, alpha=0.3)
ax3.axvline(x=xcoord, color='black',linestyle='dashed', lw=0.75, alpha=0.3)
ax4.axvline(x=xcoord, color='black',linestyle='dashed', lw=0.75, alpha=0.3)
a = ax1.findobj(mpl.text.Annotation)
for i in a:
if '$' in i.get_label():
i.set_size(10)
fig.savefig("../documents/figs/Combined.pdf", rasterized=True, dpi=600)
pl.show()
if obs != []:
for n in arms:
# print 'In arm: '+n
# ob = [k for k in obs if n in k]
ob = [k for k in obs]
# print(ob)
dat = np.genfromtxt(str(ob[0]), dtype = np.float64)
wave = dat[:,0]
flux = dat[:,1]
nbins = len(wave)
log_binned_wl = np.array(hist(wave,[min(wave),max(wave)], int(nbins/2.0),'log'))
from scipy.interpolate import InterpolatedUnivariateSpline
sps = InterpolatedUnivariateSpline(wave, flux)
flux = medfilt(sps(log_binned_wl) , 35)
wave = log_binned_wl
ax.plot(wave, flux/1e-16, label='Corrected', zorder=5, lw = 1.25, color = cmap[0], linestyle='steps-mid', rasterized=True)
dat = np.genfromtxt(str(ob[0]), dtype = np.float64)
wave = dat[:,0]
flux = dat[:,1]
nbins = len(wave)
log_binned_wl = np.array(hist(wave,[min(wave),max(wave)], int(2.0*nbins),'log'))
from scipy.interpolate import InterpolatedUnivariateSpline
sps = InterpolatedUnivariateSpline(wave, flux)
flux = medfilt(sps(log_binned_wl) , 5)
wave = log_binned_wl
ax.plot(wave, flux/1e-16, label='Corrected', zorder=3, lw = 0.25, color = cmap[2], linestyle='steps-mid', rasterized=True)
# pl.show()
# from methods import ConfInt
# y_op_lower, y_op_upper = ConfInt(wl_fit, model2, best_vals, covar, [16,84]) + cont
#Plotting
ratio = (1.0 + np.sqrt(5.0))/2.0
latexify(columns=2)
fig, ax = pl.subplots()
# latexify(fig_width=4*ratio, fig_height=4, columns=1)
# latexify(columns=1)
# fig, ax = pl.subplots()
from gen_methods import medfilt
# ax.plot(wl, medfilt(flux, 3)/norm, drawstyle='steps-mid', lw = 0.5, alpha=0.5)
ax.errorbar(wl[1::10], ((medfilt(flux, 3)/norm)/1e-16)[1::10], yerr=((fluxerror/norm)/1e-16)[1::10], fmt=".k", capsize=0, elinewidth=0.5, ms=3, rasterized=True)
ax.plot(wl_fit, (y_op/norm)/1e-16, lw=1, color = cmap[2], rasterized=True)
ax.fill_between(wl_fit, (y_op_lower/norm)/1e-16, (y_op_upper/norm)/1e-16, alpha = 0.5, color = cmap[2], rasterized=True)
ax.set_xlim((4700, 5100))
ax.set_ylim((5e-16/1e-16, 9e-16/1e-16))
# ax.set_xticks([4750, 4850, 4950, 5050, 5150])
norm_reg1 = (wave > 1425) & (wave < 1450)
norm1 = np.median(flux[norm_reg1])
norm_reg2 = (wave > 3850) & (wave < 3875)
norm2 = np.median(flux[norm_reg2])
from scipy.interpolate import InterpolatedUnivariateSpline as spline
f = spline(wave[np.where(flux != 0)], flux[np.where(flux != 0)])
flux = f(wave)
nbins = len(wave)
log_binned_wl = np.array(hist(wave,[min(wave),max(wave)], int(2*nbins),'log'))
from scipy.interpolate import InterpolatedUnivariateSpline
sps = InterpolatedUnivariateSpline(wave, flux)
flux = medfilt(sps(log_binned_wl) , 9)
sps = InterpolatedUnivariateSpline(wave, err)
err = medfilt(sps(log_binned_wl) , 9)
wave = log_binned_wl
wave = wave[np.where(wave <= 11400)]
flux = flux[np.where(wave <= 11400)]
err = err[np.where(wave <= 14000)]
positive = (flux - err > 0 )
ax.plot(wave[1::1], flux[1::1], label='This work', zorder=5, lw = 0.75, color = cmap[0], linestyle='steps-mid')
ax.fill_between(wave, flux - err, flux + err, alpha=0.2, where=positive, label=r'1 $\sigma$ confidence interval', color = cmap[0], rasterized=True)
ax2.plot(wave[1::1], flux[1::1], label = 'This work', zorder=5, lw = 0.75, color = cmap[0], linestyle='steps-mid')
ax2.fill_between(wave, flux - err, flux + err, alpha=0.2, where=positive, label=r'1 $\sigma$ confidence interval', color = cmap[0], rasterized=True)
#Lusso et al. 2015
filename = '/Users/jselsing/Work/Projects/QuasarComposite/py/data/templates/Lusso2015.dat'