import numpy as np import os from scipy.interpolate import InterpolatedUnivariateSpline, interp1d from scipy import interpolate, integrate from astropy.table import Table import galsim VC_A = 2.99792458e+18 # speed of light: A/s VC_M = 2.99792458e+8 # speed of light: m/s H_PLANK = 6.626196e-27 # Plank constant: erg s def comoving_dist(z, om_m=0.3111, om_L=0.6889, h=0.6766): # Return comving distance in pc H0 = h*100. # km / (s Mpc) def dist_int(z): return 1./np.sqrt(om_m*(1.+z)**3 + om_L) res, err = integrate.quad(dist_int, 0., z) return [res * (VC_M/1e3/H0) * 1e6, err * (VC_M/1e3/H0) * 1e6] def magToFlux(mag): """ flux of a given AB magnitude Parameters: mag: magnitude in unit of AB Return: flux: flux in unit of erg/s/cm^2/Hz """ flux = 10**(-0.4*(mag+48.6)) return flux def extAv(nav, seed=1212123): """ Generate random intrinsic extinction Av following the distribution from Holwerda et al, 2015 """ np.random.seed(seed) tau = 0.4 peak, a = 0.1, 0.5 b = a*(tau-peak) pav = lambda av: (a*av+b)*np.exp(-av/tau) avmin, avmax = 0., 3. avs = np.linspace(avmin, avmax, int((avmax-avmin)/0.001)+1) norm = np.trapz(pav(avs), avs) pav_base = pav(avs)/np.sum(pav(avs)) rav = np.random.choice(avs, nav, p=pav_base) return rav ########################################### def seds(sedlistn, seddir="./", unit="A"): """ read SEDs and save into Python dictionary Parameters: sedlistn: filename of the sed template list and corresponding intrinsic extinction model, see tmag_dz.py for detailes listdir: directory of the list unit: wavelength unit of the input templates Return: SED dictionary, the output wavelength unit is 'A' """ seds = {} reds = {} sedlist = seddir + sedlistn sedn = open(sedlist).read().splitlines() sedtype = range(1,len(sedn)+1) for i in range(len(sedn)): xxx = sedn[i].split() isedn = seddir+xxx[0] itype = sedtype[i] ised = np.loadtxt(isedn) if unit=="nm": ised[:,0] *= 10.0 seds[itype] = ised reds[itype] = int(xxx[1]) return seds, reds def sed_assign(phz, btt, rng): """ assign SED template to a galaxy. """ sedid = list(range(1, 34)) lzid = sedid[0:13] + sedid[23:28] hzid = sedid[13:23] if btt == 1.0: sedtype = rng.sample(sedid[0:5] + sedid[28:33], 1)[0] if phz > 2.0 and sedtype in sedid[0:5]: sedtype = rng.sample(sedid[28:33], 1)[0] elif btt > 0.3 and btt < 1.0: sedtype = rng.sample(sedid, 1)[0] if phz > 2.0 and sedtype in lzid: sedtype = rng.sample(hzid, 1)[0] elif btt >= 0.1 and btt < 0.3: sedtype = rng.sample(sedid[5:28], 1)[0] if phz > 1.5 and sedtype in lzid: sedtype = rng.sample(hzid, 1)[0] elif btt >= 0.0 and btt < 0.1: sedtype = rng.sample(sedid[5:23], 1)[0] if phz > 1.5 and sedtype in lzid: sedtype = rng.sample(hzid, 1)[0] else: sedtype = 0 return sedtype ########################################### def tflux(filt, sed, redshift=0.0, av=0.0, redden=0): """ calculate the theoretical SED for given filter set and template Only AB magnitude is support!!! Parameters: filt: 2d array fliter transmissions: lambda(A), T sed: 2d array sed templateL lambda (A), flux (erg s-1 cm-2 A-1) redshift: float redshift of the corresponding source, default is zero av: float extinction value for intrincal extinction redden: int reddening model, see Function 'reddening' for details return: tflux: float theoretical flux sedObs: array SED in observed frame """ z = redshift + 1.0 sw, sf = sed[:,0], sed[:,1] # reddening sf = reddening(sw, sf, av=av, model=redden) sw, sf = sw*z, sf*(z**3) # lyman forest correction sf = lyman_forest(sw, sf, redshift) sedxx = (sw.copy(), sf.copy()) sw = VC_A/sw sf = sf*(VC_A/sw**2) # convert flux unit to erg/s/cm^s/Hz sw, sf = sw[::-1], sf[::-1] sfun = interp1d(sw, sf, kind='linear') fwave, fresp = filt[:,0], filt[:,1] fwave = VC_A/fwave fwave, fresp = fwave[::-1], fresp[::-1] tflux = sfun(fwave) zpflux = 3.631*1.0e-20 tflux = np.trapz(tflux*fresp/fwave,fwave)/np.trapz(zpflux*fresp/fwave,fwave) #tflux = np.trapz(tflux*fresp,fwave)/np.trapz(zpflux*fresp,fwave) return tflux, sedxx ########################################### def lyman_forest(wavelen, flux, z): """ Compute the Lyman forest mean absorption of an input spectrum, according to D_A and D_B evolution from Madau (1995). The waveeln and flux are in observed frame """ if z<=0: flux0 = flux else: nw = 200 istep = np.linspace(0,nw-1,nw) w1a, w2a = 1050.0*(1.0+z), 1170.0*(1.0+z) w1b, w2b = 920.0*(1.0+z), 1015.0*(1.0+z) wstepa = (w2a-w1a)/float(nw) wstepb = (w2b-w1b)/float(nw) wtempa = w1a + istep*wstepa ptaua = np.exp(-3.6e-03*(wtempa/1216.0)**3.46) wtempb = w1b + istep*wstepb ptaub = np.exp(-1.7e-3*(wtempb/1026.0)**3.46\ -1.2e-3*(wtempb/972.50)**3.46\ -9.3e-4*(wtempb/950.00)**3.46) da = (1.0/(120.0*(1.0+z)))*np.trapz(ptaua, wtempa) db = (1.0/(95.0*(1.0+z)))*np.trapz(ptaub, wtempb) if da>1.0: da=1.0 if db>1.0: db=1.0 if da<0.0: da=0.0 if db<0.0: db=0.0 flux0 = flux.copy() id0 = wavelen<=1026.0*(1.0+z) id1 = np.logical_and(wavelen<1216.0*(1.0+z),wavelen>=1026.0*(1.0+z)) flux0[id0] = db*flux[id0] flux0[id1] = da*flux[id1] return flux0 ########################################### def reddening(sw, sf, av=0.0, model=0): """ calculate the intrinsic extinction of a given template Parameters: sw: array wavelength sf: array flux av: float or array model: int Five models will be used: 1: Allen (1976) for the Milky Way 2: Seaton (1979) fit by Fitzpatrick (1986) for the Milky Way 3: Fitzpatrick (1986) for the Large Magellanic Cloud (LMC) 4: Prevot et al (1984) and Bouchet (1985) for the Small Magellanic Cloud (SMC) 5: Calzetti et al (2000) for starburst galaxies 6: Reddy et al (2015) for star forming galaxies Return: reddening-corrected flux or observed flux """ if model==0 or av==0.0: flux=sf elif model==1: # Allen (1976) for the Milky Way lambda0 = np.array([1000, 1110, 1250, 1430, 1670, \ 2000, 2220, 2500, 2850, 3330, \ 3650, 4000, 4400, 5000, 5530, \ 6700, 9000, 10000, 20000, 100000], dtype=float) kR = np.array([4.20, 3.70, 3.30, 3.00, 2.70, \ 2.80, 2.90, 2.30, 1.97, 1.69, \ 1.58, 1.45, 1.32, 1.13, 1.00, \ 0.74, 0.46, 0.38, 0.11, 0.00],dtype=float) ext0 = InterpolatedUnivariateSpline(lambda0, kR, k=1) A_lambda = av*ext0(sw) A_lambda[A_lambda<0.0] = 0.0 flux = sf*10**(-0.4*A_lambda) elif model==2: # Seaton (1979) fit by Fitzpatrick (1986) for the Milky Way Rv=3.1 al0, ga, c1, c2, c3, c4 = 4.595, 1.051, -0.38, 0.74, 3.96, 0.26 ff11 = __red(1100.0,al0,ga,c1,c2,c3,c4) ff12 = __red(1200.0,al0,ga,c1,c2,c3,c4) slope=(ff12-ff11)/100.0 lambda0 = np.array([3650, 4000, 4400, 5000, 5530, \ 6700, 9000, 10000, 20000, 100000], dtype=float) kR = np.array([1.58, 1.45, 1.32, 1.13, 1.00, \ 0.74, 0.46, 0.38, 0.11, 0.00],dtype=float) fun = interp1d(lambda0, kR, kind='linear') sw0 = sw[sw<1200.0] A_lambda0 = (ff11+(sw0-1100.0)*slope)/Rv+1.0 sw1 = sw[np.logical_and(sw>=1200.0, sw<=3650.0)] ff = __red(sw1,al0,ga,c1,c2,c3,c4) A_lambda1 = ff/Rv+1.0 sw2 = sw[np.logical_and(sw>3650.0, sw<=100000.0)] A_lambda2 = fun(sw2) A_lambda3 = sw[sw>100000.0]*0.0 A_lambda = av*np.hstack([A_lambda0,A_lambda1,A_lambda2,A_lambda3]) A_lambda[A_lambda<0.0] = 0.0 flux = sf*10**(-0.4*A_lambda) elif model==3: # Fitzpatrick (1986) for the Large Magellanic Cloud (LMC) Rv=3.1 al0, ga, c1, c2, c3, c4 = 4.608, 0.994, -0.69, 0.89, 2.55, 0.50 ff11 = __red(1100.0,al0,ga,c1,c2,c3,c4) ff12 = __red(1200.0,al0,ga,c1,c2,c3,c4) slope=(ff12-ff11)/100.0 lambda0 = np.array([3330, 3650, 4000, 4400, 5000, 5530, \ 6700, 9000, 10000, 20000, 100000], dtype=float) kR = np.array([1.682, 1.58, 1.45, 1.32, 1.13, 1.00, \ 0.74, 0.46, 0.38, 0.11, 0.00],dtype=float) fun = interp1d(lambda0, kR, kind='linear') sw0 = sw[sw<1200.0] A_lambda0 = (ff11+(sw0-1100.0)*slope)/Rv+1.0 sw1 = sw[np.logical_and(sw>=1200.0, sw<=3330.0)] ff = __red(sw1,al0,ga,c1,c2,c3,c4) A_lambda1 = ff/Rv+1.0 sw2 = sw[np.logical_and(sw>3330.0, sw<=100000.0)] A_lambda2 = fun(sw2) A_lambda3 = sw[sw>100000.0]*0.0 A_lambda = av*np.hstack([A_lambda0,A_lambda1,A_lambda2,A_lambda3]) A_lambda[A_lambda<0.0] = 0.0 flux = sf*10**(-0.4*A_lambda) elif model==4: # Prevot et al (1984) and Bouchet (1985) for the Small Magellanic Cloud (SMC) Rv = 2.72 lambda0 = np.array([1275, 1330, 1385, 1435, 1490, 1545, \ 1595, 1647, 1700, 1755, 1810, 1860, \ 1910, 2000, 2115, 2220, 2335, 2445, \ 2550, 2665, 2778, 2890, 2995, 3105, \ 3704, 4255, 5291, 12500, 16500, 22000], dtype=float) kR = np.array([13.54, 12.52, 11.51, 10.80, 9.84, 9.28, \ 9.06, 8.49, 8.01, 7.71, 7.17, 6.90, 6.76, \ 6.38, 5.85, 5.30, 4.53, 4.24, 3.91, 3.49, \ 3.15, 3.00, 2.65, 2.29, 1.81, 1.00, 0.00, \ -2.02, -2.36, -2.47],dtype=float) kR = kR/Rv+1.0 ext0 = InterpolatedUnivariateSpline(lambda0, kR, k=1) A_lambda = av*ext0(sw) A_lambda[A_lambda<0.0] = 0.0 flux = sf*10**(-0.4*A_lambda) elif model==5: # Calzetti et al (2000) for starburst galaxies Rv = 4.05 sw = sw*1.0e-04 #wavelength in microns fun1 = lambda x: 2.659*(-2.156+1.509/x-0.198/x**2+0.011/x**3)+Rv fun2 = lambda x: 2.659*(-1.857+1.040/x)+Rv ff11, ff12 = fun1(0.11), fun1(0.12) slope1=(ff12-ff11)/0.01 ff99, ff100 = fun2(2.19), fun2(2.2) slope2=(ff100-ff99)/0.01 sw0 = sw[sw<0.12] sw1 = sw[np.logical_and(sw>=0.12, sw<=0.63)] sw2 = sw[np.logical_and(sw>0.63, sw<=2.2)] sw3 = sw[sw>2.2] k_lambda0 = ff11+(sw0-0.11)*slope1 k_lambda1, k_lambda2 = fun1(sw1), fun2(sw2) k_lambda3 = ff99+(sw3-2.19)*slope2 A_lambda = av*np.hstack([k_lambda0,k_lambda1,k_lambda2,k_lambda3])/Rv A_lambda[A_lambda<0.0] = 0.0 flux = sf*10**(-0.4*A_lambda) elif model==6: # Reddy et al (2015) for satr forming galaxies Rv = 2.505 sw = sw*1.0e-04 fun1 = lambda x: -5.726+4.004/x-0.525/x**2+0.029/x**3+Rv fun2 = lambda x: -2.672-0.010/x+1.532/x**2-0.412/x**3+Rv ff11, ff12 = fun1(0.14), fun1(0.15) slope1=(ff12-ff11)/0.01 ff99, ff100 = fun2(2.84), fun2(2.85) slope2=(ff100-ff99)/0.01 sw0 = sw[sw<0.15] sw1 = sw[np.logical_and(sw>=0.15, sw<0.60)] sw2 = sw[np.logical_and(sw>=0.60, sw<2.85)] sw3 = sw[sw>=2.85] k_lambda0 = ff11+(sw0-0.14)*slope1 k_lambda1, k_lambda2 = fun1(sw1), fun2(sw2) k_lambda3 = ff99+(sw3-2.84)*slope2 A_lambda = av*np.hstack([k_lambda0,k_lambda1,k_lambda2,k_lambda3])/Rv A_lambda[A_lambda<0.0] = 0.0 flux = sf*10**(-0.4*A_lambda) else: raise ValueError("!!! Please select a proper reddening model") return flux ########################################### def __red(alan,al0,ga,c1,c2,c3,c4): fun1 = lambda x: c3/(((x-(al0**2/x))**2)+ga*ga) fun2 = lambda x,cc: cc*(0.539*((x-5.9)**2)+0.0564*((x-5.9)**3)) fun = lambda x,cc: c1+c2*x+fun1(x)+fun2(x,cc) ala = alan*1.0e-04 #wavelength in microns p = 1.0/ala if np.size(p)>1: p1, p2 = p[p>=5.9], p[p<5.9] ff = np.append(fun(p1,c4), fun(p2,0.0)) elif np.size(p)==1: if p<5.9: c4 = 0.0 ff = fun(p, c4) else: return return ff ########################################### def sed2mag(mag_i, sedCat, filter_list, redshift=0.0, av=0.0, redden=0): # load the filters nfilt = len(filter_list) aflux = np.zeros(nfilt) nid = -1 for k in range(nfilt): if filter_list[k].filter_type == 'i': nid = k bandpass = filter_list[k].bandpass_full ktrans = np.transpose(np.array([bandpass.wave_list*10.0, bandpass.func(bandpass.wave_list)])) aflux[k], isedObs = tflux(ktrans, sedCat, redshift=redshift, av=av, redden=redden) # normalize to i-band aflux = aflux / aflux[nid] # magnitudes in all filters amag = -2.5*np.log10(aflux) + mag_i spec = galsim.LookupTable(x=np.array(isedObs[0]), f=np.array(isedObs[1]), interpolant='nearest') isedObs = galsim.SED(spec, wave_type='A', flux_type='1', fast=False) return amag, isedObs def eObs(e1,e2,g1,g2): """ Calculate the sheared (observed) ellipticity using the intrinsic ellipticity and cosmic shear components. Parameters: e1, e2: scalar or numpy array g1, g2: scalar or numpy array Return: Sheared (observed) ellipticity components, absolute value, and orientation in format of scalar or numpy array ** NOTE: e1, e2, g1, and g2 should have the same dimensions. """ if np.isscalar(e1): e1 = np.array([e1]) e2 = np.array([e2]) g1 = np.array([g1]) g2 = np.array([g2]) else: e1 = e1.flatten() e2 = e2.flatten() g1 = g1.flatten() g2 = g2.flatten() # calculate the sheared (observed) ellipticity using complex rule nobj = len(e1) e1obs, e2obs = [], [] eeobs, theta = [], [] for i in range(nobj): e = complex(e1[i], e2[i]) g = complex(g1[i], g2[i]) e, gg = abs(e), abs(g) if gg<=1.0: tt = e + g bb = 1.0 + e*g.conjugate() eobs = tt/bb else: tt = 1.0 + g*e.conjugate() bb = e.conjugate() + g.conjugate() eobs = tt/bb # derive the orientation dd = 0.5*np.arctan(abs(eobs.imag/eobs.real))*180.0/np.pi if eobs.imag>0 and eobs.real>0: dd = dd if eobs.imag>0 and eobs.real<0: dd = 90.0 - dd if eobs.imag<0 and eobs.real>0: dd = 0.0 - dd if eobs.imag<0 and eobs.real<0: dd = dd - 90.0 e1obs += [eobs.real] e2obs += [eobs.imag] eeobs += [abs(eobs)] theta += [dd] e1obs,e2obs,eeobs,theta = np.array(e1obs),np.array(e2obs),np.array(eeobs),np.array(theta) if nobj == 1: e1obs,e2obs,eeobs,theta = e1obs[0],e2obs[0],eeobs[0],theta[0] return e1obs, e2obs, eeobs, theta def getObservedSED(sedCat, redshift=0.0, av=0.0, redden=0): z = redshift + 1.0 sw, sf = sedCat[:,0], sedCat[:,1] # reddening sf = reddening(sw, sf, av=av, model=redden) # sw, sf = sw*z, sf*(z**3) sw, sf = sw*z, sf/z # sw, sf = sw*z, sf # lyman forest correction sf = lyman_forest(sw, sf, redshift) isedObs = (sw.copy(), sf.copy()) return isedObs def integrate_sed_bandpass(sed, bandpass): wave = np.linspace(bandpass.blue_limit, bandpass.red_limit, 1000) # in nm flux_normalized = sed(wave)*bandpass(wave) # print('in integrate_sed_bandpass', bandpass.blue_limit, bandpass.red_limit) int_flux = np.trapz(y=flux_normalized, x=wave) * 10. # convert to photons s-1 m-2 A-1 return int_flux def getABMAG(interFlux, bandpass): throughtput = Table(np.array(np.array([bandpass.wave_list*10.0, bandpass.func(bandpass.wave_list)])).T, names=(['WAVELENGTH', 'SENSITIVITY'])) sWave = bandpass.blue_limit*10.0 eWave = bandpass.red_limit*10.0 # print('in getABMAG', sWave, eWave) ABMAG_zero = getABMagAverageVal( ABmag=0, norm_thr=throughtput, sWave=sWave, eWave=eWave) flux_ave = interFlux / (eWave-sWave) ABMAG_spec = -2.5 * np.log10(flux_ave/ABMAG_zero) return ABMAG_spec def getABMagAverageVal(ABmag=20.,norm_thr=None, sWave=6840, eWave=8250): """ norm_thr: astropy.table, 2 colum, 'WAVELENGTH', 'SENSITIVITY' Return: the integerate flux of AB magnitude in the norm_thr(the throughtput of band), photos s-1 m-2 A-1 """ inverseLambda = norm_thr['SENSITIVITY']/norm_thr['WAVELENGTH'] norm_thr_i = interpolate.interp1d(norm_thr['WAVELENGTH'], inverseLambda) x = np.linspace(sWave,eWave, int(eWave)-int(sWave)+1) y = norm_thr_i(x) AverageLamdaInverse = np.trapz(y,x)/(eWave-sWave) norm = 54798696332.52474 * pow(10.0, -0.4 * ABmag) * AverageLamdaInverse # print('AverageLamdaInverse = ', AverageLamdaInverse) # print('norm = ', norm) return norm def getNormFactorForSpecWithABMAG(ABMag=20., spectrum=None, norm_thr=None, sWave=6840, eWave=8250): """ Use AB magnitude system (zero point, fv = 3631 janskys) in the normal band(norm_thr) normalize the spectrum by inpute ABMag Parameters ---------- spectrum: astropy.table, 2 colum, 'WAVELENGTH', 'FLUX' norm_thr: astropy.table, 2 colum, 'WAVELENGTH', 'SENSITIVITY' sWave: the start of norm_thr eWave: the end of norm_thr Return: the normalization factor flux of AB system(fix a band and magnitude ) /the flux of inpute spectrum(fix a band) """ spectrumi = interpolate.interp1d(spectrum['WAVELENGTH'], spectrum['FLUX']) norm_thri = interpolate.interp1d(norm_thr['WAVELENGTH'], norm_thr['SENSITIVITY']) x = np.linspace(sWave,eWave, int(eWave)-int(sWave)+1) y_spec = spectrumi(x) y_thr = norm_thri(x) y = y_spec*y_thr specAve = np.trapz(y,x)/(eWave-sWave) norm = getABMagAverageVal(ABmag=ABMag, norm_thr=norm_thr, sWave=sWave, eWave=eWave) if specAve == 0: return 0 # print('specAve = ', specAve) return norm / specAve def tag_sed(h5file, model_tag, teff=5000, logg=2, feh=0): model_tag_str = model_tag.decode("utf-8").strip() teff_grid = np.unique(h5file["teff"][model_tag_str]) logg_grid = np.unique(h5file["logg"][model_tag_str]) feh_grid = np.unique(h5file["feh"][model_tag_str]) close_teff = teff_grid[np.argmin(np.abs(teff_grid - teff))] close_logg = logg_grid[np.argmin(np.abs(logg_grid - logg))] if model_tag_str == "koester" or model_tag_str == "MC": close_feh = 99 else: close_feh = feh_grid[np.argmin(np.abs(feh_grid - feh))] path = model_tag_str + f"_teff_{close_teff:.1f}_logg_{close_logg:.2f}_feh_{close_feh:.1f}" wave = np.array(h5file["wave"][model_tag_str][()]).ravel() flux = np.array(h5file["sed"][path][()]).ravel() return path, wave, flux def convolveGaussXorders(img=None, sigma = 1): from astropy.modeling.models import Gaussian2D from scipy import signal offset = int(np.ceil(sigma*10)) g_size = 2*offset+1 m_cen = int(g_size/2) g_PSF_ = Gaussian2D(1, m_cen, m_cen, sigma, sigma) yp, xp = np.mgrid[0:g_size, 0:g_size] g_PSF = g_PSF_(xp, yp) psf = g_PSF/g_PSF.sum() convImg = signal.fftconvolve(img, psf, mode='full', axes=None) return convImg, offset def convolveImg(img=None, psf = None): from astropy.modeling.models import Gaussian2D from scipy import signal convImg = signal.fftconvolve(img, psf, mode='full', axes=None) offset_x = int(psf.shape[1]/2. + 0.5) - 1 offset_y = int(psf.shape[0]/2. + 0.5) - 1 offset = [offset_x,offset_y] return convImg, offset