def spectrum_aperture_technical():
"""
Compute residual corrected spectrum. Plot spectra extracted from various maps for comparison.
Also plot clean-to-dirty beam ratio epsilon.
"""
filename = "./data/Pisco.cube.50kms.image.fits"
ra, dec = (205.533741, 9.477317341) # [degrees] we know where the source is
radius = 1.3 # [arcsec] we know the size of the aperture we want
scale = 1e3 # map units are Jy/beam, will use to scale fluxes to mJy
# load the cube and perform residual scaling spectrum extraction
mcub = MultiCube(filename) # because the cubes follow a naming convention, will open several present cubes
spectrum, err, tab = mcub.spectrum_corrected(ra=ra, dec=dec, radius=radius, calc_error=True)
freqs = mcub.freqs # this will be the x-axis
# tab.write("spectrum.txt", format="ascii.fixed_width", overwrite=True) # save results in a human readable format
# plot the spectrum, fill around the fitted continuum value
fig, axes = plt.subplots(figsize=(4.8, 4.8), nrows=2, ncols=1, sharex=True, gridspec_kw={'height_ratios': [3, 1]})
ax = axes[0]
ax.set_title("Spectrum with and without correction")
# the table returned from spectrum_corrected contains fluxes measured in different map
# as well as clean-to-dirty beam ratios
spectrum_dirty = tab["flux_dirty"]
ax.plot(freqs, spectrum_dirty * scale, color="black", drawstyle='steps-mid', lw=0.75)
ax.fill_between(freqs, spectrum_dirty * scale, 0, color="firebrick", step='mid', lw=0, alpha=1, label="Dirty")
spectrum_uncorrected = tab["flux_image"]
ax.plot(freqs, spectrum_uncorrected * scale, color="black", drawstyle='steps-mid', lw=0.75)
ax.fill_between(freqs, spectrum_uncorrected * scale, 0, color="forestgreen", step='mid', lw=0, alpha=1,
label="Uncorrected")
ax.plot(freqs, spectrum * scale, color="black", drawstyle='steps-mid', lw=0.75)
ax.fill_between(freqs, spectrum * scale, 0, color="skyblue", step='mid', lw=0, alpha=1, label="Corrected")
ax.set_xlim(freqs[0], freqs[-1])
ax.tick_params(direction='in', which="both")
ax.set_ylabel("Aperture flux density (mJy)")
ax.legend(frameon=False) # loc="upper right"
ax2 = axes[1]
# epsilon_fix was estimated from higher S/N channels and applied on all channels
ax2.axhline(tab["epsilon_fix"][0], color="skyblue", lw=1)
ax2.plot(freqs, tab["epsilon"], lw=0, marker="o", ms=1, color="black")
ax2.tick_params(direction='in', which="both")
ax2.set_xlabel("Frequency (GHz)")
ax2.set_ylabel("Clean-to-dirty\nbeam ratio: " + r"$\epsilon$")
ax2.set_ylim(-1.5, 1.5)
plt.savefig("./plots/spectrum_aperture_technical.pdf", bbox_inches="tight") # save plot
plt.savefig("./thumbnails/spectrum_aperture_technical.png", bbox_inches="tight", dpi=72) # web raster version
plt.show()
def spectrum_aperture_paper():
"""
Compute residual corrected spectrum. Fit a Gaussian plus a continuum.
Generate paper quality plot.
"""
filename = "./data/Pisco.cube.50kms.image.fits"
ra, dec = (205.533741, 9.477317341) # [degrees] we know where the source is
radius = 1.3 # [arcsec] we know the size of the aperture we want
scale = 1e3 # map units are Jy/beam, will use to scale fluxes to mJy
# load the cube and perform residual scaling spectrum extraction
mcub = MultiCube(filename) # because the cubes follow a naming convention, will open several present cubes
spectrum, err, tab = mcub.spectrum_corrected(ra=ra, dec=dec, radius=radius, calc_error=True)
freqs = mcub.freqs # this will be the x-axis
# fit the spectrum with a Gaussian on top of a constant continuum, initial fit parameters (p0) must be set manually
popt, pcov = curve_fit(iftools.gausscont, freqs, spectrum, p0=(1, 5, 222.5, 0.2), sigma=err, absolute_sigma=True)
cont, amp, nu, sigma = popt
cont_err, amp_err, nu_err, sigma_err = np.sqrt(np.diagonal(pcov))
# compute some further numbers from the fit
sigma_kms = iftools.ghz2kms(sigma, nu)
fwhm_kms = iftools.sig2fwhm(sigma_kms)
fwhm_err_kms = iftools.sig2fwhm(iftools.ghz2kms(sigma_err, nu))
integral_fit = amp * sigma_kms * np.sqrt(2 * np.pi)
integral_err = integral_fit * np.sqrt((sigma_err / sigma) ** 2 + (nu_err / nu) ** 2 + (amp_err / amp) ** 2)
txt = "[CII] Flux = " + str(iftools.sigfig(integral_fit, 2)) \
+ r" $\pm$ " + str(iftools.sigfig(integral_err, 1)) + " Jy km/s\n" \
+ "[CII] FWHM = " + str(iftools.sigfig(int(fwhm_kms), 2)) \
+ r" $\pm$ " + str(iftools.sigfig(int(fwhm_err_kms), 1)) + " km/s\n" \
+ "Freq = " + str(iftools.sigfig(nu, 6)) \
+ r" $\pm$ " + str(iftools.sigfig(nu_err, 1)) + " GHz\n" \
+ "Continuum = " + str(iftools.sigfig(cont * scale, 2)) \
+ r" $\pm$ " + str(iftools.sigfig(cont_err * scale, 1)) + " mJy\n"
# print("Gaussian fit:")
# print("Flux = " + str(iftools.sigfig(integral_fit, 2)) + " +- " + str(iftools.sigfig(integral_err, 1)) + " Jy.km/s")
# print("FWHM = " + str(iftools.sigfig(fwhm_kms, 2)) + " +- " + str(iftools.sigfig(fwhm_err_kms, 1)) + " km/s")
# print("Freq = " + str(iftools.sigfig(nu, 7)) + " +- " + str(iftools.sigfig(nu_err, 1)) + " GHz")
# plot the spectrum, fill around the fitted continuum value
fig, ax = plt.subplots(figsize=(4.8, 3))
ax.plot(freqs, spectrum * scale, color="black", drawstyle='steps-mid', lw=0.75)
ax.fill_between(freqs, spectrum * scale, cont * scale, color="skyblue", step='mid', lw=0, alpha=0.3)
ax.text(0.98, 0.95, txt, va='top', ha='right', transform=ax.transAxes)
# Plot the uncorrected specturum as well
# ax.plot(freqs, tab["flux_image"] * scale, color="black", drawstyle='steps-mid', lw=0.5, ls="--")
# plot Gaussian fit
x_gauss = np.linspace(freqs[0], freqs[-1], 1000)
y_gauss = iftools.gausscont(x_gauss, *popt)
ax.plot(x_gauss, y_gauss * scale, color="firebrick")
# add velocity axis based around the fitted peak
vels = mcub.cubes["image"].vels(nu)
ax2 = ax.twiny()
# match ranges of the two axes
ax.set_xlim(freqs[0], freqs[-1])
ax2.set_xlim(vels[0], vels[-1])
# add axis labels
ax.tick_params(direction='in', which="both")
ax.set_xlabel("Frequency (GHz)")
ax.set_ylabel("Aperture flux density (mJy)")
ax2.tick_params(direction='in', which="both")
ax2.set_xlabel(r"Velocity (km s$^{-1}$)")
# add the zero line
ax.axhline(0, color="gray", lw=0.5, ls=":")
plt.savefig("./plots/spectrum_aperture_paper.pdf", bbox_inches="tight") # save plot
plt.savefig("./thumbnails/spectrum_aperture_paper.png", bbox_inches="tight", dpi=72) # web raster version
plt.show()