fig, [[ax1, ax2], [ax3, ax4]] = plt.subplots(2, 2, constrained_layout=True)
fig.set_size_inches(6.5, 6.5)
cube = SpectralCube.read(thisfile)
gal = os.path.split(thisfile)[-1].split('_')[0]
shortfile = os.path.split(thisfile)[-1]
try:
mask = SpectralCube.read(degas_data +
'/masks/{0}_mask.fits'.format(gal))
mask = mask.with_spectral_unit(u.km / u.s, velocity_convention='radio')
hdr = mask.header
hdr['CTYPE3'] = 'VRAD'
mask = SpectralCube(mask.filled_data[:], wcs.WCS(hdr), header=hdr)
mask = mask.with_mask(mask.filled_data[:] > 0)
mask = mask.spectral_interpolate(cube.spectral_axis)
mask = mask.reproject(cube.header)
except FileNotFoundError:
print('No mask for ' + thisfile)
mask = SpectralCube(np.ones(cube.shape),
wcs=cube.wcs,
header=cube.header)
rmsamplitude = scm.noise_cube(cube.filled_data[:].value,
box=5,
spec_box=5,
iterations=5,
bandpass_smooth_window=21)
s2n = cube.filled_data[:].value / rmsamplitude
s2n_in_mask = s2n[(mask.filled_data[:].value == 1)]
eta_mb = eta_mb_dict[molecule]
degas_cube_name = 'IR5/{0}_{1}_rebase3_smooth1.3_hanning1.fits'.format(gal, molecule)
if not os.path.exists(degas_data + degas_cube_name):
ax.set_title(gal)
ax.text(0.5, 0.5, 'No data',ha='center')
continue
cube_degas = SpectralCube.read(degas_data + degas_cube_name)
cube_degas = cube_degas / eta_mb
mask = SpectralCube.read(degas_data + '/masks/{0}_mask.fits'.format(gal))
mask = mask.with_spectral_unit(u.km/u.s, velocity_convention='radio')
hdr = mask.header
hdr['CTYPE3'] = 'VRAD'
mask = SpectralCube(mask.filled_data[:], wcs.WCS(hdr), header=hdr)
mask = mask.with_mask(mask.filled_data[:] > 0)
mask = mask.spectral_interpolate(cube_degas.spectral_axis)
mask = mask.reproject(cube_degas.header)
fl = glob.glob(empire_data + 'EMPIRE_{0}_{1}_*.fits'.format(gal.lower(),molecule.lower()))
hdulist = fits.open(fl[0])
hdu = sanitize(hdulist[0])
cube_empire = SpectralCube(data=hdu.data, header=hdu.header, wcs=wcs.WCS(hdu.header))
empire_mask = np.isfinite(hdu.data)
cube_empire = cube_empire.with_mask(empire_mask)
channel_ratio = ((cube_degas.spectral_axis[1]
- cube_degas.spectral_axis[0]) /
(cube_empire.spectral_axis[1]
- cube_empire.spectral_axis[0])).to(u.dimensionless_unscaled).value
kernel = Box1DKernel(channel_ratio)
cube_empire = cube_empire.spectral_smooth(kernel)
