def hstfos_readspec(obj, channel):
"""Read in an HST FOS quasar spectrum
"""
path = datapath.hstfos_path()
subpath = ((obj['NAME'].strip()).replace('+', 'p')).replace('-', 'm')
filename = channel + '.fits'
infile = join(path, subpath, filename)
if not isfile(infile):
raise IOError("{0} not found.")
# print "Reading {0}.".format(infile)
return fitsio.read(infile)
def starburst_filename():
path = datapath.hstfos_path()
return join(path, _subpath, _starburstfile)
outstr['flux'] = hstfos_obj['flux']
outstr['error'] = hstfos_obj['error']
# write out output
fits = fitsio.FITS(outfile, 'rw', clobber=True)
fits.write(outstr)
fits.close()
#
return
else:
warnings.warn("Can't find the file: " + repr(infile))
return
# Main Program
# read in qso list
catfile = starburst_filename()
gal = np.genfromtxt(catfile, dtype=[('gal', 'S15')])
path = datapath.hstfos_path()
for thisgal in gal:
specfile = thisgal['gal'] + '.txt'
infile = join(path, _subpath, specfile)
txt2fits(infile)
#print "I'm done! Some quick check by looking at the file Numbers."
#print "There are ", (subprocess.check_output("ls -l */*.txt | wc -l", shell=True)).split()[0], " .txt files"
#print "and ", (subprocess.check_output("ls -l */*.fits | wc -l", shell=True)).split()[0], ".fits files"
def hstfos_qso_filename():
path = datapath.hstfos_path()
filename = 'hstfos_master_visual.fits'
return join(path, filename)
def rest_allspec(overwrite=False):
"""Load and interpolate *ALL* HST FOS/GHRS starburst spectra
on to the same rest-frame wavelength grid
"""
path = join(datapath.hstfos_path(), _subpath, 'corrected')
# check output files
bands = _allinone_rest_bands
for thisband in bands:
# check outfiles
outfile = allinone_rest_filename(thisband)
if isfile(outfile) and not overwrite:
print "File {0} exists. Use overwrite to overwrite it.".format(outfile)
return -1
# print "Will write into these files: {0}".format(outfile)
# read in the starburst catalog
objs_ori = starburst_readin()
nobj = objs_ori.size
# make a temporary new catalog
objs_dtype = [('RA', 'f8'),
('DEC', 'f8'),
('Z', 'f8'),
('gal', 'S15')]
objs = np.zeros(nobj, dtype=objs_dtype)
objs['RA'] = 0.
objs['DEC'] = 0.
objs['Z'] = 0.
objs['gal'] = objs_ori['gal']
# read in master wavelength grid
master_wave = (aio.allinone_wave_readin())[0]['WAVE']
master_loglam = np.log10(master_wave)
nwave = master_wave.size
# initialization, nobj second dimension because of NMF traditions
rest_allflux = np.zeros((nwave, nobj))
rest_allivar = np.zeros((nwave, nobj))
# Wavelength
wave_pos = np.array([1000., 3300.])
rest_loc = np.searchsorted(master_wave, wave_pos)
newloglam = master_loglam[rest_loc[0]:rest_loc[1]]
flux = np.zeros((objs.size, newloglam.size))
ivar = np.zeros((objs.size, newloglam.size))
pbar = ProgressBar(maxval=nobj).start()
# Progress bar
for (iobj, thisobj) in zip(np.arange(objs.size), objs):
pbar.update(iobj)
thisdata = readspec_rest(thisobj)
inloglam = np.log10(thisdata['wave'])
influx = thisdata['flux']
inivar = 1./np.power(thisdata['error'], 2)
(rest_allflux[rest_loc[0]:rest_loc[1], iobj], rest_allivar[rest_loc[0]:rest_loc[1], iobj]) = specutils.interpol_spec(inloglam, influx, inivar, newloglam)
#Progress bar
pbar.finish()
# write out
print "Now I am writing everything out..."
allinone_rest_writeout(objs, master_wave, rest_allflux, rest_allivar, overwrite=overwrite)
def readspec_obs(obj):
obspath = join(datapath.hstfos_path(), _subpath, 'observed')
obsfile = join(obspath, obj['gal']+'.fits')
return (fitsio.read(obsfile))[0]
def readspec_rest(obj):
restpath = join(datapath.hstfos_path(), _subpath, 'corrected')
specfile = obj['gal']+'.fits'
restfile = join(restpath, specfile)
return (fitsio.read(restfile))[0]
def mgii_composite_filename():
path = datapath.hstfos_path()
return join(path, _subpath, _mgiicompositefile)