def measure_MGPS(snr):
sourcedir = "/media/data/Dropbox/MWA/SNR_search/confirm_candidates/regrid_all/MGPS/"
fitsfile = sourcedir + snr.name + "_MGPS.fits"
final_flux, total_flux, bkg_flux, rms_flux, nbeam = find_fluxes(
snr.polygon, snr.sources, snr.exclude, fitsfile)
make_single_plot(snr.polygon, snr.sources, snr.exclude, fitsfile)
print "final flux, total flux, background flux, rms flux, number of beams"
print final_flux, total_flux, bkg_flux, rms_flux, nbeam
# In units of Jy
return final_flux, total_flux, bkg_flux, rms_flux, nbeam
def do_fit(colors, snr):
freqs = []
fluxes = []
bkg = []
rms = []
nbeams = []
for color in colors:
if color == "white":
fitsfile = color + "/" + snr.name + ".fits"
else:
fitsfile = color + "/rpj/" + snr.name + ".fits"
if os.path.exists(fitsfile):
hdu = fits.open(fitsfile)
freqs.append(hdu[0].header["FREQ"])
final_flux, total_flux, bkg_flux, rms_flux, nbeam = find_fluxes(
snr.polygon, snr.sources, snr.exclude, fitsfile)
fluxes.append(final_flux)
bkg.append(bkg_flux)
rms.append(rms_flux)
nbeams.append(nbeam)
else:
print "Unable to fit flux for {0} in {1}".format(snr.name, color)
fluxes = np.array(fluxes)
freqs = np.array(freqs)
logfreqs = np.log([f / normfreq for f in freqs])
logfluxes = np.log(fluxes)
fluxerrors = [
np.sqrt((0.02 * s)**2 + n * (r**2))
for s, r, n in zip(fluxes, rms, nbeams)
]
logfluxerrors = np.array([e / f for e, f in zip(fluxerrors, fluxes)])
alpha, err_alpha, amp, err_amp, chi2red = fit_spectrum(
logfreqs[np.where(fluxes > 0)], logfluxes[np.where(fluxes > 0)],
logfluxerrors[np.where(fluxes > 0)])
return snr, dict(zip(freqs, fluxes)), dict(zip(freqs, bkg)), dict(
zip(freqs,
rms)), dict(zip(freqs,
nbeams)), alpha, err_alpha, amp, err_amp, chi2red
def measure_E11(snr):
sourcedir = "/media/data/Dropbox/MWA/SNR_search/confirm_candidates/regrid_all/E11/"
fitsfile = sourcedir + snr.name + "_E11.fits"
final_flux, total_flux, bkg_flux, rms_flux, nbeam = find_fluxes(
snr.polygon, snr.sources, snr.exclude, fitsfile)
hdu = fits.open(fitsfile)
T = mK2K(final_flux)
nu = WL2freq(cm2m(11.)) # Effelsberg 11cm survey
bmaj = hdu[0].header["BMAJ"]
bmin = hdu[0].header["BMIN"]
make_single_plot(snr.polygon, snr.sources, snr.exclude, fitsfile)
print "final temperature, total temperature, background temperature, rms temperature (all in K), number of beams"
print mK2K(final_flux), mK2K(total_flux), mK2K(bkg_flux), mK2K(
rms_flux), nbeam
# In units of Jy
S_11 = T2PFD(T, nu, bmaj, bmin)
tot_11 = T2PFD(mK2K(total_flux), nu, bmaj, bmin)
bkg_11 = T2PFD(mK2K(bkg_flux), nu, bmaj, bmin)
rms_11 = T2PFD(mK2K(rms_flux), nu, bmaj, bmin)
print "final flux, total flux, background flux, rms flux, number of beams"
print S_11, tot_11, bkg_11, rms_11, nbeam
return S_11, tot_11, bkg_11, rms_11, nbeam
def poly_plot(fitsfile, makeplots):
print "Fitting polygons to " + fitsfile
hdu = fits.open(fitsfile)
data = hdu[0].data
xmax = hdu[0].header["NAXIS1"]
ymax = hdu[0].header["NAXIS2"]
w = wcs.WCS(hdu[0].header)
try:
pix2deg = hdu[0].header["CD2_2"]
except KeyError:
pix2deg = hdu[0].header["CDELT2"]
def update(val):
vmin = svmin.val
vmax = svmax.val
img.set_clim([svmin.val, svmax.val])
fig.canvas.draw()
fig = plt.figure(figsize=(5, 5))
ax = fig.add_axes([0.05, 0.15, 0.8, 0.8])
img = ax.imshow(data, cmap="gray")
cbaxes = fig.add_axes([0.85, 0.1, 0.03, 0.85])
cb = plt.colorbar(img, cax=cbaxes, orientation="vertical")
axcolor = 'white'
axmin = fig.add_axes([0.05, 0.05, 0.2, 0.02], axisbg=axcolor)
axmax = fig.add_axes([0.44, 0.05, 0.2, 0.02], axisbg=axcolor)
vmin0 = np.min(data)
vmax0 = np.max(data)
# include the slider: cribbed from https://stackoverflow.com/questions/5611805/using-matplotlib-slider-widget-to-change-clim-in-image
svmin = Slider(axmin, "vmin", -5.0, 1.0, valinit=vmin0)
svmax = Slider(axmax, "vmax", -1.0, 10.0, valinit=vmax0)
svmin.on_changed(update)
svmax.on_changed(update)
fig.suptitle(
'Left-click = select source, middle-click = source subtract, right-click = select region to exclude from background calculation'
)
# If you don't do this, it automatically zooms out when you first click on the plot
ax.set_xlim(0, xmax)
ax.set_ylim(0, ymax)
polypick = PolyPick(ax)
plt.show()
# Export pixel co-ordinates as WCS co-ordinates in order to use on any arbitrary image, and save for later
polygon = Coords()
sources = Coords()
exclude = Coords()
if len(polypick.points.x):
sources.x, sources.y = w.wcs_pix2world(
zip(polypick.points.x, polypick.points.y), 0).transpose()
if len(polypick.exclude.x):
exclude.x, exclude.y = w.wcs_pix2world(
zip(polypick.exclude.x, polypick.exclude.y), 0).transpose()
# Now I have the co-ordinates...
# Go measure the flux densities
if len(polypick.coords.x):
polygon.x, polygon.y = w.wcs_pix2world(
zip(polypick.coords.x, polypick.coords.y), 0).transpose()
find_fluxes(polygon, sources, exclude, fitsfile)
# And make nice plots
if makeplots is True:
make_single_plot(polygon, sources, exclude, fitsfile)
else:
print "Failed to draw any points; exiting."