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Given the following text description, write Python code to implement the functionality described below step by step
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Description:
 Spectrum Continuum Normalization
Aim
Step1:  The obeservatios were originally automatically continuum normalized in the iraf extraction pipeline. 
I believe the continuum is not quite at 1 here anymore due to the divsion by the telluric spectra.
Step2:  The two PHOENIX ACES spectra here are the first best guess of the two spectral components.
Step5:  Current Normalization
I then continuum normalize the Phoenix spectrum locally around my observations 
by fitting an exponenital to the continuum like so.
Split the spectrum into 50 bins
Take median of 20 highest points in each bin.
Fix an exponetial
Evaulate at the orginal wavelength values
Divide original by the fit
Step6:  Above the top is the unnormalize spectra, with the median points in orangeand the green line the continuum fit. The bottom plot is the contiuum normalized result
Step7:  Combining Spectra
I then mix the models using a combination of the two spectra.
In this case with NO RV shifts.
Step8:  The companion is cooler there are many more deeper lines present in the spectra.
Even a small contribution of the companion spectra reduce the continuum of the mixed spectra considerably.
When I compare these mixed spectra to my observations
Step9:  As you can see here my observations are above the continuum most of the time.
What I have noticed is this drastically affects the chisquared result as the mix model is the one with the least amount of alpha.
I am thinking of renormalizing my observations by implementing equation (1) from Passegger 2016 (Fundamental M-dwarf parameters from high-resolution spectra using PHOENIX ACES modesl)
        F_obs = F_obs * (continuum_fit model / continuum_fit observation)
They fit a linear function to the continuum of the observation and computed spectra to account for "slight differences in the continuum level and possible linear trends between the already noramlized spectra." 
One difference is that they say they normalize the average flux of the spectra to unity. Would this make a difference in this method.
Questions
Would this be the correct approach to take to solve this? 
Should I renomalize the observations first as well?
Am I treating the cooler M-dwarf spectra correctly in this approach? 
Attempting the Passegger method
Step10:  In this example for the 5% companion spectra there is a bit of difference between the linear and scalar normalizations. With a larger difference at the longer wavelength. (more orange visible above the red.)  Faint blue is the spectrum before the renormalization.
Range of phoenix spectra
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Python Code:
import copy
import numpy as np
from astropy.io import fits
import matplotlib.pyplot as plt
% matplotlib inline
#%matplotlib auto
Explanation: Spectrum Continuum Normalization
Aim:
To perform Chi^2 comparision between PHOENIX ACES spectra and my CRIRES observations.
Problem:
The nomalization of the observed spectra
Differences in the continuum normalization affect the chi^2 comparison when using mixed models of two different spectra. 
Proposed Solution:
equation (1) from Passegger 2016 
          Fobs = F obs * (cont_fit model / cont_fit observation) where con_fit is a linear fit to the spectra.
To take out and linear trends in the continuums and correct the amplitude of the continuum.
In this notebook I outline what I do currently showing an example.
End of explanation
# Observation
obs = fits.getdata("/home/jneal/.handy_spectra/HD211847-1-mixavg-tellcorr_1.fits")
plt.plot(obs["wavelength"], obs["flux"])
plt.hlines(1, 2111, 2124, linestyle="--")
plt.title("CRIRES spectra")
plt.xlabel("Wavelength (nm)")
plt.show()
Explanation: The obeservatios were originally automatically continuum normalized in the iraf extraction pipeline. 
I believe the continuum is not quite at 1 here anymore due to the divsion by the telluric spectra.
End of explanation
# Models
wav_model = fits.getdata("/home/jneal/Phd/data/PHOENIX-ALL/PHOENIX/WAVE_PHOENIX-ACES-AGSS-COND-2011.fits")
wav_model /= 10   # nm
host = "/home/jneal/Phd/data/PHOENIX-ALL/PHOENIX/Z-0.0/lte05700-4.50-0.0.PHOENIX-ACES-AGSS-COND-2011-HiRes.fits"
old_companion = "/home/jneal/Phd/data/PHOENIX-ALL/PHOENIX/Z-0.0/lte02600-4.50-0.0.PHOENIX-ACES-AGSS-COND-2011-HiRes.fits"
companion = "/home/jneal/Phd/data/PHOENIX-ALL/PHOENIX/Z-0.0/lte02300-4.50-0.0.PHOENIX-ACES-AGSS-COND-2011-HiRes.fits"
host_f = fits.getdata(host)
comp_f = fits.getdata(companion)
plt.plot(wav_model, host_f, label="Host")
plt.plot(wav_model, comp_f, label="Companion")
plt.title("Phoenix spectra")
plt.xlabel("Wavelength (nm)")
plt.legend()
plt.show()
mask = (2000 < wav_model) & (wav_model < 2200)
wav_model = wav_model[mask] 
host_f = host_f[mask] 
comp_f = comp_f[mask] 
plt.plot(wav_model, host_f, label="Host")
plt.plot(wav_model, comp_f, label="Companion")
plt.title("Phoenix spectra")
plt.legend()
plt.xlabel("Wavelength (nm)")
plt.show()
Explanation: The two PHOENIX ACES spectra here are the first best guess of the two spectral components.
End of explanation
def get_continuum_points(wave, flux, splits=50, top=20):
    Get continuum points along a spectrum.
    This splits a spectrum into "splits" number of bins and calculates
    the medain wavelength and flux of the upper "top" number of flux
    values.
    
    # Shorten array until can be evenly split up.
    remainder = len(flux) % splits
    if remainder:
        # Nozero reainder needs this slicing
        wave = wave[:-remainder]
        flux = flux[:-remainder]
    wave_shaped = wave.reshape((splits, -1))
    flux_shaped = flux.reshape((splits, -1))
    s = np.argsort(flux_shaped, axis=-1)[:, -top:]
    s_flux = np.array([ar1[s1] for ar1, s1 in zip(flux_shaped, s)])
    s_wave = np.array([ar1[s1] for ar1, s1 in zip(wave_shaped, s)])
    wave_points = np.median(s_wave, axis=-1)
    flux_points = np.median(s_flux, axis=-1)
    assert len(flux_points) == splits
    return wave_points, flux_points
def continuum(wave, flux, splits=50, method='scalar', plot=False, top=20):
    Fit continuum of flux.
    top: is number of top points to take median of continuum.
    
    org_wave = wave[:]
    org_flux = flux[:]
    # Get continuum value in chunked sections of spectrum.
    wave_points, flux_points = get_continuum_points(wave, flux, splits=splits, top=top)
    poly_num = {"scalar": 0, "linear": 1, "quadratic": 2, "cubic": 3}
    if method == "exponential":
        z = np.polyfit(wave_points, np.log(flux_points), deg=1, w=np.sqrt(flux_points))
        p = np.poly1d(z)
        norm_flux = np.exp(p(org_wave))   # Un-log the y values.
    else:
        z = np.polyfit(wave_points, flux_points, poly_num[method])
        p = np.poly1d(z)
        norm_flux = p(org_wave)
    if plot:
        plt.subplot(211)
        plt.plot(wave, flux)
        plt.plot(wave_points, flux_points, "x-", label="points")
        plt.plot(org_wave, norm_flux, label='norm_flux')
        plt.legend()
        plt.subplot(212)
        plt.plot(org_wave, org_flux / norm_flux)
        plt.title("Normalization")
        plt.xlabel("Wavelength (nm)")
        plt.show()
    return norm_flux
#host_cont = local_normalization(wav_model, host_f, splits=50, method="exponential", plot=True)
host_continuum = continuum(wav_model, host_f, splits=50, method="exponential", plot=True)
host_cont = host_f / host_continuum
#comp_cont = local_normalization(wav_model, comp_f, splits=50, method="exponential", plot=True)
comp_continuum = continuum(wav_model, comp_f, splits=50, method="exponential", plot=True)
comp_cont = comp_f / comp_continuum
Explanation: Current Normalization
I then continuum normalize the Phoenix spectrum locally around my observations 
by fitting an exponenital to the continuum like so.
Split the spectrum into 50 bins
Take median of 20 highest points in each bin.
Fix an exponetial
Evaulate at the orginal wavelength values
Divide original by the fit
End of explanation
plt.plot(wav_model, comp_cont, label="Companion")
plt.plot(wav_model, host_cont-0.3, label="Host")
plt.title("Continuum Normalized (with -0.3 offset)")
plt.xlabel("Wavelength (nm)")
plt.legend()
plt.show()
plt.plot(wav_model[20:200], comp_cont[20:200], label="Companion")
plt.plot(wav_model[20:200], host_cont[20:200], label="Host")
plt.title("Continuum Normalized - close up")
plt.xlabel("Wavelength (nm)")
ax = plt.gca()
ax.get_xaxis().get_major_formatter().set_useOffset(False)
plt.legend()
plt.show()
Explanation: Above the top is the unnormalize spectra, with the median points in orangeand the green line the continuum fit. The bottom plot is the contiuum normalized result
End of explanation
def mix(h, c, alpha):
    return (h + c * alpha) / (1 + alpha)
mix1 = mix(host_cont, comp_cont, 0.01)   # 1% of the companion spectra  
mix2 = mix(host_cont, comp_cont, 0.05)   # 5% of the companion spectra  
# plt.plot(wav_model[20:100], comp_cont[20:100], label="comp")
plt.plot(wav_model[20:100], host_cont[20:100], label="host")
plt.plot(wav_model[20:100], mix1[20:100], label="mix 1%")
plt.plot(wav_model[20:100], mix2[20:100], label="mix 5%")
plt.xlabel("Wavelength (nm)")
plt.legend()
plt.show()
Explanation: Combining Spectra
I then mix the models using a combination of the two spectra.
In this case with NO RV shifts.
End of explanation
mask = (wav_model > np.min(obs["wavelength"])) & (wav_model < np.max(obs["wavelength"]))
plt.plot(wav_model[mask], mix1[mask], label="mix 1%")
plt.plot(wav_model[mask], mix2[mask], label="mix 5%")
plt.plot(obs["wavelength"], obs["flux"], label="obs")
#plt.xlabel("Wavelength (nm)")
plt.legend()
plt.show()
# Zoomed in
plt.plot(wav_model[mask], mix2[mask], label="mix 5%")
plt.plot(wav_model[mask], mix1[mask], label="mix 1%")
plt.plot(obs["wavelength"], obs["flux"], label="obs")
plt.xlabel("Wavelength (nm)")
plt.legend()
plt.xlim([2112, 2117])
plt.ylim([0.9, 1.1])
plt.title("Zoomed")
plt.show()
Explanation: The companion is cooler there are many more deeper lines present in the spectra.
Even a small contribution of the companion spectra reduce the continuum of the mixed spectra considerably.
When I compare these mixed spectra to my observations
End of explanation
from scipy.interpolate import interp1d
# mix1_norm = continuum(wav_model, mix1, splits=50, method="linear", plot=False)
# mix2_norm = local_normalization(wav_model, mix2, splits=50, method="linear", plot=False)
obs_continuum = continuum(obs["wavelength"], obs["flux"], splits=20, method="linear", plot=True)
linear1 = continuum(wav_model, mix1, splits=50, method="linear", plot=True)
linear2 = continuum(wav_model, mix2, splits=50, method="linear", plot=False)
obs_renorm1 = obs["flux"]  * (interp1d(wav_model, linear1)(obs["wavelength"]) / obs_continuum)
obs_renorm2 = obs["flux"]  * (interp1d(wav_model, linear2)(obs["wavelength"]) / obs_continuum)
# Just a scalar
# mix1_norm = local_normalization(wav_model, mix1, splits=50, method="scalar", plot=False)
# mix2_norm = local_normalization(wav_model, mix2, splits=50, method="scalar", plot=False)
obs_scalar = continuum(obs["wavelength"], obs["flux"], splits=20, method="scalar", plot=False)
scalar1 = continuum(wav_model, mix1, splits=50, method="scalar", plot=True)
scalar2 = continuum(wav_model, mix2, splits=50, method="scalar", plot=False)
print(scalar2)
obs_renorm_scalar1 = obs["flux"] * (interp1d(wav_model, scalar1)(obs["wavelength"]) / obs_scalar)
obs_renorm_scalar2 = obs["flux"] * (interp1d(wav_model, scalar2)(obs["wavelength"]) / obs_scalar)
plt.plot(obs["wavelength"], obs_scalar, label="scalar observed")
plt.plot(obs["wavelength"], obs_continuum, label="linear observed")
plt.plot(obs["wavelength"], interp1d(wav_model, scalar1)(obs["wavelength"]), label="scalar 1%")
plt.plot(obs["wavelength"], interp1d(wav_model, linear1)(obs["wavelength"]), label="linear 1%")
plt.plot(obs["wavelength"], interp1d(wav_model, scalar2)(obs["wavelength"]), label="scalar 5%")
plt.plot(obs["wavelength"], interp1d(wav_model, linear2)(obs["wavelength"]), label="linear 5%")
plt.title("Linear and Scalar continuum renormalizations.")
plt.legend()
plt.show()
plt.plot(obs["wavelength"], obs["flux"],  label="obs", alpha =0.6)
plt.plot(obs["wavelength"], obs_renorm1, label="linear norm")
plt.plot(obs["wavelength"], obs_renorm_scalar1, label="scalar norm")
plt.plot(wav_model[mask], mix1[mask], label="mix 1%")
plt.legend()
plt.title("1% model")
plt.hlines(1, 2111, 2124, linestyle="--", alpha=0.2)
plt.show()
plt.plot(obs["wavelength"], obs["flux"],  label="obs", alpha =0.6)
plt.plot(obs["wavelength"], obs_renorm1, label="linear norm")
plt.plot(obs["wavelength"], obs_renorm_scalar1, label="scalar norm")
plt.plot(wav_model[mask], mix1[mask], label="mix 1%")
plt.legend()
plt.title("1% model, zoom")
plt.xlim([2120, 2122])
plt.hlines(1, 2111, 2124, linestyle="--", alpha=0.2)
plt.show()
plt.plot(obs["wavelength"], obs["flux"],  label="obs", alpha =0.6)
plt.plot(obs["wavelength"], obs_renorm2, label="linear norm")
plt.plot(obs["wavelength"], obs_renorm_scalar2, label="scalar norm")
plt.plot(wav_model[mask], mix2[mask], label="mix 5%")
plt.legend()
plt.title("5% model")
plt.hlines(1, 2111, 2124, linestyle="--", alpha=0.2)
plt.show()
plt.plot(obs["wavelength"], obs["flux"],  label="obs", alpha =0.6)
plt.plot(obs["wavelength"], obs_renorm2, label="linear norm")
plt.plot(obs["wavelength"], obs_renorm_scalar2, label="scalar norm")
plt.plot(wav_model[mask], mix2[mask], label="mix 5%")
plt.legend()
plt.title("5% model zoomed")
plt.xlim([2120, 2122])
plt.hlines(1, 2111, 2124, linestyle="--", alpha=0.2)
plt.show()
Explanation: As you can see here my observations are above the continuum most of the time.
What I have noticed is this drastically affects the chisquared result as the mix model is the one with the least amount of alpha.
I am thinking of renormalizing my observations by implementing equation (1) from Passegger 2016 (Fundamental M-dwarf parameters from high-resolution spectra using PHOENIX ACES modesl)
        F_obs = F_obs * (continuum_fit model / continuum_fit observation)
They fit a linear function to the continuum of the observation and computed spectra to account for "slight differences in the continuum level and possible linear trends between the already noramlized spectra." 
One difference is that they say they normalize the average flux of the spectra to unity. Would this make a difference in this method.
Questions
Would this be the correct approach to take to solve this? 
Should I renomalize the observations first as well?
Am I treating the cooler M-dwarf spectra correctly in this approach? 
Attempting the Passegger method
End of explanation
wav_model = fits.getdata("/home/jneal/Phd/data/PHOENIX-ALL/PHOENIX/WAVE_PHOENIX-ACES-AGSS-COND-2011.fits")
wav_model /= 10   # nm
temps = [2300, 3000, 4000, 5000]
mask1 = (1000 < wav_model) & (wav_model < 3300)
masked_wav1 = wav_model[mask1] 
for temp in temps[::-1]:
    file = "/home/jneal/Phd/data/PHOENIX-ALL/PHOENIX/Z-0.0/lte0{0}-4.50-0.0.PHOENIX-ACES-AGSS-COND-2011-HiRes.fits".format(temp)
    host_f = fits.getdata(file)
    
    plt.plot(masked_wav1, host_f[mask1], label="Teff={}".format(temp))
    
plt.title("Phoenix spectra")
plt.xlabel("Wavelength (nm)")
plt.legend()
plt.show()
mask = (2000 < wav_model) & (wav_model < 2300)
masked_wav = wav_model[mask] 
for temp in temps[::-1]:
    file = "/home/jneal/Phd/data/PHOENIX-ALL/PHOENIX/Z-0.0/lte0{0}-4.50-0.0.PHOENIX-ACES-AGSS-COND-2011-HiRes.fits".format(temp)
    host_f = fits.getdata(file)
    host_f = host_f[mask] 
    plt.plot(masked_wav, host_f, label="Teff={}".format(temp))
    
plt.title("Phoenix spectra")
plt.xlabel("Wavelength (nm)")
plt.legend()
plt.show()
# Observations
for chip in range(1,5):
    obs = fits.getdata("/home/jneal/.handy_spectra/HD211847-1-mixavg-tellcorr_{}.fits".format(chip))
    plt.plot(obs["wavelength"], obs["flux"], label="chip {}".format(chip))
plt.hlines(1, 2111, 2165, linestyle="--")
plt.title("CRIRES spectrum HD211847")
plt.xlabel("Wavelength (nm)")
plt.legend()
plt.show()
# Observations
for chip in range(1,5):
    obs = fits.getdata("/home/jneal/.handy_spectra/HD30501-1-mixavg-tellcorr_{}.fits".format(chip))
    plt.plot(obs["wavelength"], obs["flux"], label="chip {}".format(chip))
plt.hlines(1, 2111, 2165, linestyle="--")
plt.title("CRIRES spectrum HD30501")
plt.xlabel("Wavelength (nm)")
plt.legend()
plt.show()
Explanation: In this example for the 5% companion spectra there is a bit of difference between the linear and scalar normalizations. With a larger difference at the longer wavelength. (more orange visible above the red.)  Faint blue is the spectrum before the renormalization.
Range of phoenix spectra
End of explanation
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