def make_blanks(gal, header, cubefilename, clobber=True):
lrange = gal.l.deg.min()+15/3600.,gal.l.deg.max()+15/3600.
brange = gal.b.deg.min()+15/3600.,gal.b.deg.max()+15/3600.
print "Map extent: %0.2f < l < %0.2f, %0.2f < b < %0.2f" % (lrange[0],
lrange[1],
brange[0],
brange[1])
pixsize = 5*u.arcsec
naxis1 = (lrange[1]-lrange[0])/(pixsize.to(u.deg).value)
naxis2 = (brange[1]-brange[0])/(pixsize.to(u.deg).value)
restfreq = (header['RESTF']*u.MHz)
bmaj = (1.22*10*u.m / restfreq.to(u.m,u.spectral()))*u.radian
makecube.generate_header(np.mean(lrange), np.mean(brange), naxis1=naxis1,
naxis2=naxis2, naxis3=4096, coordsys='galactic',
ctype3='VELO-LSR',
bmaj=bmaj.to(u.deg).value,
bmin=bmaj.to(u.deg).value,
pixsize=pixsize.to(u.arcsec).value,
cunit3='km/s',
output_flatheader='header.txt',
output_cubeheader='cubeheader.txt',
cd3=header['VRES'],
crval3=-1*header['VRES']*header['RCHAN'],
crpix3=1,
clobber=True, bunit="K",
restfreq=restfreq.to(u.Hz).value, radio=True)
makecube.make_blank_images(cubefilename, clobber=clobber)
def make_blanks_merge(cubefilename, lowhigh='low', clobber=True):
pixsize = 5*u.arcsec
naxis1 = 950
naxis2 = 300
restfreq = 218222.192*u.MHz
bmaj = (1.22*10*u.m / restfreq.to(u.m,u.spectral()))**-1*u.radian
cd3 = ((1*u.km/u.s)/constants.c * 218.2*u.GHz).to(u.Hz).value
naxis3 = int(np.ceil(((1.0*u.GHz / (218.2*u.GHz) * constants.c) / (u.km/u.s)).decompose().value))
makecube.generate_header(0.35, -0.075, naxis1=naxis1,
naxis2=naxis2, naxis3=naxis3, coordsys='galactic',
bmaj=bmaj.to(u.deg).value,
bmin=bmaj.to(u.deg).value,
pixsize=pixsize.to(u.arcsec).value,
cunit3='Hz',
ctype3='FREQ',
output_flatheader='header.txt',
output_cubeheader='cubeheader.txt',
cd3=cd3,
crval3=216.8e9 if lowhigh=='low' else 218e9,
crpix3=1,
clobber=True, bunit="K",
restfreq=restfreq.to(u.Hz).value, radio=True)
makecube.make_blank_images(cubefilename, clobber=clobber)
def make_blanks_freq(gal, header, cubefilename, clobber=True):
""" complete freq covg """
lrange = gal.l.deg.min()+15/3600.,gal.l.deg.max()+15/3600.
brange = gal.b.deg.min()+15/3600.,gal.b.deg.max()+15/3600.
print "Map extent: %0.2f < l < %0.2f, %0.2f < b < %0.2f" % (lrange[0],
lrange[1],
brange[0],
brange[1])
pixsize = 5*u.arcsec
naxis1 = int((lrange[1]-lrange[0])/(pixsize.to(u.deg).value)+10)
naxis2 = int((brange[1]-brange[0])/(pixsize.to(u.deg).value)+10)
restfreq = (header['RESTF']*u.MHz)
bmaj = (1.22*10*u.m / restfreq.to(u.m,u.spectral()))*u.radian
rchan = header['RCHAN']
#scalefactor = 1./downsample_factor
#crpix3 = (rchan-1)*scalefactor+0.5+scalefactor/2.
makecube.generate_header(np.mean(lrange), np.mean(brange), naxis1=naxis1,
naxis2=naxis2, naxis3=header['NCHAN'],
coordsys='galactic',
bmaj=bmaj.to(u.deg).value,
bmin=bmaj.to(u.deg).value,
pixsize=pixsize.to(u.arcsec).value,
cunit3='Hz',
ctype3='FREQ',
output_flatheader='header.txt',
output_cubeheader='cubeheader.txt',
cd3=header['FRES']*1e6,
crval3=restfreq.to(u.Hz).value,
crpix3=rchan,
clobber=True, bunit="K",
restfreq=restfreq.to(u.Hz).value, radio=True)
makecube.make_blank_images(cubefilename, clobber=clobber)
import astropy.io.fits as pyfits
from astropy import units as u
import itertools
import sys
from sdpy import makecube,make_off_template,calibrate_map_scans
import numpy as np
from paths import outpath
# to ignore div-by-zero errors?
np.seterr(all='ignore')
cubename = os.path.join(outpath,'CMZ_East_H2CO22_cube')
# 0.5x0.2 deg = 30x12'
makecube.generate_header(0.466, -0.025, naxis1=200, naxis2=150, pixsize=15,
naxis3=800, cd3=0.5, clobber=True,
cunit3='km/s', crval3=0.0, restfreq=14.48848e9)
makecube.make_blank_images(cubename,clobber=True)
files = [os.path.join(outpath,x) for x in
(
'15B_129_1_19to76_H1_5_F2.fits',
'15B_129_1_77to134_H1_5_F2.fits',
'15B_129_1_149to194_H1_5_F2.fits',
'15B_129_1_196to242_H1_5_F2.fits',
'15B_129_1_248to305_H1_5_F2.fits',
'15B_129_1_306to352_H1_5_F2.fits',
'15B_129_1_19to76_H2_5_F2.fits',
'15B_129_1_77to134_H2_5_F2.fits',
'15B_129_1_149to194_H2_5_F2.fits',
'15B_129_1_196to242_H2_5_F2.fits',
'15B_129_1_248to305_H2_5_F2.fits',
'15B_129_1_306to352_H2_5_F2.fits',
for species in all_species:
for name,shape in zip(names,shapes):
cubename = os.path.join(outpath,'cube_{name}_{species}'.format(name=name, species=species))
print name,shape,cubename
naxis3 = (max(velocityrange)-min(velocityrange)) / cd3
crval3 = (max(velocityrange)+min(velocityrange)) / 2.
makecube.generate_header(shape[0], shape[1], naxis1=shape[2], naxis2=shape[3], pixsize=15,
naxis3=naxis3, cd3=cd3, clobber=True, restfreq=all_species[species],
crpix3=naxis3/2.,
crval3=crval3, cunit3='km/s',
output_cubeheader="{name}_{species}_cubeheader.txt".format(name=name, species=species),
output_flatheader="{name}_{species}_header.txt".format(name=name, species=species),
bmaj=28/3600., bmin=28/3600.)
makecube.make_blank_images(cubename,clobber=True,
cubeheader="{name}_{species}_cubeheader.txt".format(name=name, species=species),
flatheader="{name}_{species}_header.txt".format(name=name, species=species),
)
log.info("Completed blank making {0}".format(species))
for scan,name,session in zip(scans,names,sessions):
cubename = os.path.join(outpath,'cube_{name}_{species}'.format(name=name, species=species))
for sm,fd in samplers_feeds_mapping.items():
if sampler_lines[sm] != species:
print "Skipping {0} because it's not in this map. ({1},{2}): {3}".format(species, sm, fd, sampler_lines[sm])
continue
else:
print name,cubename
fn = os.path.join(outpath,
"{prefix}_{scan1}to{scan2}_{sampler}_{feed}.fits".format(scan1=scan[0],
-0.025,
naxis1=200,
naxis2=150,
pixsize=15,
naxis3=naxis3,
cd3=cdelt3,
cunit3=cunit3,
clobber=True,
ctype3=ctype3,
crval3=restfreq if ctype3 == "FREQ" else 0.0,
output_flatheader=cubename + "flatheader.txt",
output_cubeheader=cubename + "cubeheader.txt",
restfreq=restfreq,
)
makecube.make_blank_images(
cubename, flatheader=cubename + "flatheader.txt", cubeheader=cubename + "cubeheader.txt", clobber=True
)
files = [
x
for obsrun in scanranges
for scan1, scan2 in scanranges[obsrun]
for x in [
os.path.join(
outpath, fntemplate.format(scan1, scan2, samplers[ii], sampler_feeds[samplers[ii][0]], obsrun=obsrun)
)
for ii in range(len(samplers))
]
]
iterator = makecube.freq_iterator if ctype3 == "FREQ" else makecube.velo_iterator
cubename_supersampled = "/Users/adam/work/h2co/maps/w51/W51_H213CO11_cube_supersampled"
makecube.generate_header(
glon,
glat,
naxis1=naxis1,
naxis2=naxis2,
pixsize=15,
naxis3=int(naxis3),
cd3=cd3,
crval3=crval3,
clobber=True,
restfreq=linefreq,
author="Adam Ginsburg",
)
makecube.make_blank_images(cubename_supersampled, clobber=True)
files = [
"W51_h213coW_spectra_0910.fits",
"W51_h213coW_spectra_0911.fits",
"W51_h213coW_spectra_0912.fits",
"W51_h213coW_spectra_0915.fits",
]
for fn in files:
fullfn = fix_TDIM_in_header(prefix + fn)
makecube.add_file_to_cube(
fullfn,
cubename_supersampled + ".fits",
add_with_kernel=True,
kernel_fwhm=20.0 / 3600.0,
# dumb debug stuff
vels = crval3 + cd3 * (np.arange(naxis3) + 1 - naxis3 / 2 - 1)
# this will probably cause an error but I must insist..
#if velocityrange[0]<=vels.min() or velocityrange[1]>=vels.max():
# raise ValueError("Add more points. Something's going to be out of range for stupid star stupid link")
makecube.generate_header(49.209553,
-0.277137,
naxis1=192,
naxis2=128,
pixsize=24,
naxis3=naxis3,
cd3=cd3,
crval3=crval3,
clobber=True,
restfreq=14.488479e9)
makecube.make_blank_images(cubename_lores, clobber=True)
for fn in [filename]:
print "Adding file %s" % fn
fullfn = fn
makecube.add_file_to_cube(fullfn,
cubename_lores + ".fits",
add_with_kernel=True,
kernel_fwhm=50. / 3600.,
nhits=cubename_lores + "_nhits.fits",
diagnostic_plot_name=fullfn.replace(
'.fits', '_data_scrubbed.png'),
velocityrange=velocityrange,
excludefitrange=[40, 75],
noisecut=1.0)
# more aggressive noisecut
