beam = (ch['BMAJ']*ch['BMIN'] * np.pi * u.deg**2)
cont_offset = (2.73*u.K).to(u.Jy,u.brightness_temperature(beam,14.488*u.GHz))
extra_cont_offset = 0.05
contlev = cont_offset.value + extra_cont_offset + noisefloor
#spec2 = f2[0].data[0,350:600,:,:] + 0.03
spec2 = f2[0].data[190:293,:,:] + contlev + cont2
# try to "subtract out" the negative continuum...
#spec2[:,cont2<0] -= cont2[cont2<0]
dosmooth = False
if dosmooth:
spec2s = cube_regrid.spatial_smooth_cube(spec2,kernelwidth=1.5)
cont2s = agpy.smooth(cont2+contlev,kernelwidth=1.5)
else:
spec2s = spec2
cont2s = cont2
spec2s[:,cont2s<0] -= cont2s[cont2s<0]
#cont2s[cont2s<contlev]=contlev
#cont2 += contlev
#cont2[cont2<contlev+noisefloor]=contlev+noisefloor
# "noise floor" (not really)
#spec2[spec2<0.01] = 0.01
#tau2 = -np.log((spec2/cont2))
def extract_subcube(cubefilename, outfilename, linefreq=218.22219*u.GHz,
debug=False, smooth=False, vsmooth=False):
ffile = fits.open(cubefilename)
# I don't know why this is necessary, but there were weird bugs showing up
# if I did not add this (some parts of the cube defaulted to 3e-319)
ffile[0].data = ffile[0].data.astype('float32')
hdr = ffile[0].header
cdk = 'CD3_3' if 'CD3_3' in hdr else 'CDELT3'
if debug:
xarr = (np.arange(hdr['NAXIS3'])+1-hdr['CRPIX3']) * hdr[cdk] + hdr['CRVAL3']
print xarr.min(),xarr.max()
hdr['CTYPE3'] = 'VELO'
cdfrq = hdr[cdk]
crvfreq = hdr['CRVAL3']
crpixf = hdr['CRPIX3']
hdr[cdk] = -((cdfrq/crvfreq)*constants.c).to(u.km/u.s).value
hdr['CRVAL3'] = 0.0
hdr['CRPIX3'] = (linefreq.to(u.Hz).value-crvfreq)/cdfrq + crpixf
hdr['CUNIT3'] = 'km/s'
if debug:
xarr = (np.arange(hdr['NAXIS3'])+1-hdr['CRPIX3']) * hdr[cdk] + hdr['CRVAL3']
print xarr.min(),xarr.max()
for k in ['CTYPE3','CRVAL3',cdk,'CRPIX3','CUNIT3']:
assert ffile[0].header[k] == hdr[k]
outhdr = hdr.copy()
outhdr[cdk] = 1.0
outhdr['RESTFREQ'] = linefreq.to(u.Hz).value
outhdr['RESTFRQ'] = linefreq.to(u.Hz).value
outhdr['CRVAL3'] = 50
outhdr['CRPIX3'] = 199.5
outhdr['NAXIS3'] = 400
if smooth:
#cubesm = gsmooth_cube(ffile[0].data, [3,2,2], use_fft=True,
# psf_pad=False, fft_pad=False)
# smoothed with 2 pixels -> sigma=10", fwhm=23"
# this is an "optimal smooth", boosting s/n and smoothing to 36"
# resolution.
kw = 2 if not vsmooth else 4
cubesm = cube_regrid.spatial_smooth_cube(ffile[0].data, kw,
use_fft=False,
numcores=4)
cubesm = cube_regrid.spectral_smooth_cube(cubesm, 3/2.35,
use_fft=False,
numcores=4)
ffile[0].data = cubesm
outhdr[cdk] = 3.0
outhdr['CRVAL3'] = 50
outhdr['CRPIX3'] = 70
outhdr['NAXIS3'] = 140
if debug:
xarr = (np.arange(outhdr['NAXIS3'])+1-outhdr['CRPIX3']) * outhdr[cdk] + outhdr['CRVAL3']
print xarr.min(),xarr.max()
xarr = (-xarr/3e5) * linefreq + linefreq
print xarr.min(),xarr.max()
return hdr,outhdr
newhdu = cube_regrid.regrid_cube_hdu(ffile[0], outhdr, order=1,
prefilter=False)
newhdu.writeto(outfilename, clobber=True)
return newhdu
makecube.make_flats(cubename,vrange=[-20,60],noisevrange=[150,200])
#import FITS_tools
from astropy.io import fits
from FITS_tools.cube_regrid import gsmooth_cube,spatial_smooth_cube
for cubename in ('LimaBean_H2CO33_cube', 'LimaBean_H213CO33_cube', 'LimaBean_H2C18O33_cube'):
cubename = os.path.join(outpath,cubename)
cube = fits.open(cubename+"_sub.fits")
# OUT OF DATE: for 2-2....
# kernel = ((2.5*60)**2 - 50.**2)**0.5 / sqrt(8*log(2)) = 60 arcsec
# 60 arcsec / 15 "/pixel = 4
cubesm2 = gsmooth_cube(cube[0].data, [5,4,4], use_fft=True, psf_pad=False, fft_pad=False)
cubesm = spatial_smooth_cube(cube[0].data, kernelwidth=4, interpolate_nan=True)
cube[0].data = cubesm
cube.writeto(cubename+"_sub_smoothtoCband.fits",clobber=True)
cube[0].data = cubesm2
cube.writeto(cubename+"_sub_smoothtoCband_vsmooth.fits",clobber=True)
# etamb = 56-64% * 1.37 from GTBpg
makecube.make_taucube(cubename,
cubename+"_continuum.fits",
etamb=1.37*0.6,
tex=2.0,
suffix="_sub_smoothtoCband_vsmooth.fits",
outsuffix="_smoothtoCband_vsmooth.fits",
TCMB=2.7315+0.4)
makecube.make_taucube(cubename,
