basic

basic#

An example of the most basic way to use elements from FIESpipe.

Illustrated here for a single order for a single spectrum.

The star here is \(\gamma\) Cephei A, which is a slow rotator, so it has nice sharp lines.

Normalization and outlier rejection#

>>> import FIESpipe as fp
>>> import matplotlib.pyplot as plt
>>> import numpy as np

>>> ## Sort the FIES files into science and ThAr spectra
>>> spec = 'your_path/gamCep/'
>>> filenames, tharnames = fp.sortFIES(spec)
>>> filenames.sort()
>>> ## Run the standard reduction on the science spectra
>>> file = filenames[0]
>>> ## Extract the data from the FITS file
>>> wave, flux, ferr, hdr = fp.extractFIES(file)
>>> order = 45 #+1 # 0-indexed
>>> w, f, e = wave[order], flux[order], ferr[order]
>>> ## Relative error
>>> re = e/f

>>> ## Plot the spectrum
>>> fig = plt.figure()
>>> ax = fig.add_subplot(111)
>>> ax.set_xlabel(r'$\rm \lambda \ (\AA)$')
>>> ax.set_ylabel(r'$\rm F_{\lambda}$')
>>> ax.errorbar(w,f,yerr=e)
../_images/raw_spec.png 
>>> ## Normalize the spectrum
>>> pdeg = 2 # Polynomial degree
>>> wl, nfl = fp.normalize(w,f,poly=pdeg)
>>> ## Scaled error
>>> nfle = re*nfl
>>> ## Cosmic ray removal/outlier rejection
>>> wlo, flo, eflo, idxs = fp.crm(wl,nfl,nfle)

>>> ## Plot the normalized, cleansed spectrum
>>> fig = plt.figure()
>>> ax = fig.add_subplot(111)
>>> ax.set_xlabel(r'$\rm \lambda \ (\AA)$')
>>> ax.set_ylabel(r'$\rm F_{\lambda}$')
>>> ax.plot(wl[idxs],nfl[idxs],'rx',zorder=5)
>>> ## Plot the cleaned spectrum
>>> ax.errorbar(wlo,flo,yerr=eflo)

>>> ## Load Kurucz template
>>> temp = 'your_path/4750_30_p02p00.ms.fits'
>>> tw, tf = fp.readKurucz(temp)
>>> ## Plot the template in an interval around the order
>>> show = (tw > wlo.min()-5) & (tw < wlo.max()+5)
>>> ax.plot(tw[show],tf[show],'k-')

>>> ## For this star, I know the systemic velocity is around -40 km/s
>>> rvsys = -40 # km/s
>>> ## Shift the template to the systemic velocity,
>>> ### to center the grid around 0 km/s
>>> ### not important, but easier to work with
>>> sw = tw*(1.0 + rvsys*1e3/fp.const.c.value)
>>> ## Plot the shifted template
>>> ax.plot(sw[show],tf[show],'--',color='C7')
../_images/norm_spec.png

Cross-correlation function#

>>> ## Resample the template and the wavelength grid of the spectrum
>>> dv = fp.velRes(R=67000,s=2.1) # km/s, velocity resolution of the FIES spectrograph using fibre 4
>>> ccfs, ccferrs, arvr, _, _, _ = fp.grids(rvr=51,R=67000,s=2.1) # velocity grid, range from 101 km/s
>>> lam, resamp_fl, resamp_tfl, resamp_fle = fp.resample(wl,nfl,nfle,sw,tf,dv=dv)
>>> rvs, ccf, errs = fp.getCCF(resamp_fl,resamp_tfl,resamp_fle,rvr=arvr,dv=dv)
>>> ## Plot the CCF
>>> fig = plt.figure()
>>> ax = fig.add_subplot(111)
>>> ax.set_xlabel(r'$\rm RV \ (km\,s^{-1})$')
>>> ax.set_ylabel(r'$\rm CCF$')
>>> ax.errorbar(rvs,ccf,yerr=errs)
../_images/ccf.png 
>>> ## Shift the CCF to the systemic velocity
>>> rvs += rvsys

>>> ## Fit the CCF with a Gaussian
>>> ## RV, FWHM, contrast
>>> rv, erv, fw, efw, co, eco, pars, cov = fp.getRV(rvs,ccf,flipped=1,return_pars=1)

>>> ## Plot the CCF with the Gaussian fit
>>> fig = plt.figure()
>>> ax = fig.add_subplot(111)
>>> ax.set_xlabel(r'$\rm RV \ (km\,s^{-1})$')
>>> ax.set_ylabel(r'$\rm CCF$')
>>> ax.errorbar(rvs,ccf,yerr=errs)
>>> xx = np.linspace(rvs.min(),rvs.max(),1000)
>>> ax.plot(xx,fp.Gauss(xx,*pars),'k--')
>>> ax.plot([rv-fw/2,rv+fw/2],[pars[0]*0.5+pars[3],pars[0]*0.5+pars[3]],label='FWHM',color='C3')
>>> ax.plot([rv,rv],[pars[3],pars[3]+pars[0]],label='Contrast',color='C1')
>>> ## Calculate BIS
>>> ## First estimate error on RV grid/x-axis
>>> errt, d, xerr = fp.getxError(rvs,ccf,errs)
>>> ## BIS, BIS error
>>> bis, bx, by, biserr = fp.getBIS(rvs,ccf,xerr)
>>> ax.errorbar(rvs,ccf,yerr=errs,xerr=xerr)
>>> ax.plot(bx,by,label='BIS',color='C2')
>>> ax.legend()
../_images/ccf_fit.png 
>>> ## Get the barycentric correction and BJD in TDB
>>> bjd, bvc = fp.getBarycorrs(file,rvmeas=rv)
>>> rv += bvc
>>> print('RV measured: {0:.3f} +/- {1:.3f} km/s'.format(rv,erv))

RV measured: -44.372 +/- 0.121 km/s
basic.basic(fpath='data/spectra/gamCep/', tpath='/4750_30_p02p00.ms.fits', save=False, width=15, height=6)#

Basic example of the FIESpipe package.

Used for testing.

Parameters:

  • fpath (str) – Path to the FIES data. Default is data/spectra/gamCep/.

  • tpath (str) – Path to the Kurucz template. Default is /4750_30_p02p00.ms.fits.

  • save (bool) – Save the figures. Default is False.

  • width (float) – Width of the figures. Default is 15 (inches).

  • height (float) – Height of the figures. Default is 6 (inches).

Returns:

RV, RV error, BJD, BVC, FWHM, FWHM error, contrast, contrast error

Return type:

float, float, float, float, float, float, float, float

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