def combinespectfiles(spfile_a, spfile_b, file_ab):
""" Coadd two spectra, and write output in a file
Parameters
----------
spfile_a : str
spfile_b : str
.fits files with spectra
file_ab : str
output .fits file with combined spectra
Returns
-------
"""
from linetools.spectra import io as tio
from linetools.spectra import utils as spltu
file_a = tio.readspec(spfile_a)
file_b = tio.readspec(spfile_b)
spliced_sp = spltu.splice_two(file_b, file_a, chk_units=False)
spliced_sp.write(file_ab)
def load_gal_spec(self, inp):
""" Load the galaxy spectrum
Parameters
----------
inp : int or tuple
int -- Index of the cgm_abs list
tuple -- (field,gal_id)
Returns
----------
spec : XSpectrum1D
Splices the blue and red side for LRIS
JXP on 12 Oct 2015
"""
from linetools.spectra import utils as ltsu
# Init
cgm_abs = self[inp]
# Directories
galdir = self.cdir+'/Galaxies/'
#fielddir = 'fields/'+cgm_abs.field+'/'
#sysdir = cgm_abs.gal_id+'/spec1d/'
sysname = cgm_abs.galaxy.field+'_'+cgm_abs.galaxy.gal_id
# Find files
lris_files = glob.glob(galdir+sysname+'*corr.fits.gz')
if len(lris_files) == 0:
raise ValueError('No LRIS files! {:s}'.format(galdir+sysname))
elif len(lris_files) == 2:
lris_files.sort()
specb = lsio.readspec(lris_files[0])
specr = lsio.readspec(lris_files[1])
spec = ltsu.splice_two(specb, specr)
else:
raise ValueError('Not sure what happened')
# Return
return spec
def load_gal_spec(self, inp):
""" Load the galaxy spectrum
Parameters
----------
inp : int or tuple
int -- Index of the cgm_abs list
tuple -- (field,gal_id)
Returns
----------
spec : XSpectrum1D
Splices the blue and red side for LRIS
"""
from linetools.spectra import utils as ltsu
# Init
cgm_abs = self[inp]
# Directories
galdir = self.cdir + '/Galaxies/'
#fielddir = 'fields/'+cgm_abs.field+'/'
#sysdir = cgm_abs.gal_id+'/spec1d/'
sysname = cgm_abs.galaxy.field + '_' + cgm_abs.galaxy.gal_id
# Find files
lris_files = glob.glob(galdir + sysname + '*corr.fits.gz')
if len(lris_files) == 0:
raise ValueError('No LRIS files! {:s}'.format(galdir + sysname))
elif len(lris_files) == 2:
lris_files.sort()
specb = lsio.readspec(lris_files[0])
specr = lsio.readspec(lris_files[1])
spec = ltsu.splice_two(specb, specr)
else:
raise ValueError('Not sure what happened')
# Return
return spec
def test_splice_two(spec, spec2):
spec3 = ltsu.splice_two(spec, spec2)
assert spec3.npix == 18390
def read_spec(ispec, exten=None, norm=True, **kwargs):
"""Parse spectrum out of the input
If 2 spectra are given, the 2nd is scaled to the first
Parameters
----------
ispec : XSpectrum1D, str, list of files (ordered blue to red),
or tuple of arrays
exten : int, optional
FITS extension
Returns
-------
spec : XSpectrum1D
spec_file : str
"""
from linetools.spectra import xspectrum1d as lsx
from linetools.spectra import utils as ltsu
from astropy.utils.misc import isiterable
#
if isinstance(ispec,basestring):
spec_fil = ispec
if 'rsp_kwargs' in kwargs.keys():
spec = lsx.XSpectrum1D.from_file(spec_fil, exten=exten, **kwargs['rsp_kwargs'])
else:
spec = lsx.XSpectrum1D.from_file(spec_fil, exten=exten)
elif isinstance(ispec, lsx.XSpectrum1D):
spec = ispec
spec_fil = spec.filename # Grab from Spectrum1D
elif isinstance(ispec,tuple):
spec = lsx.XSpectrum1D.from_tuple(ispec)
spec_fil = 'none'
elif isinstance(ispec,list): # Multiple file names
# Loop on the files
for kk,ispecf in enumerate(ispec):
if isiterable(exten):
iexten = exten[kk]
else:
iexten = exten
jspec = lsx.XSpectrum1D.from_file(ispecf, exten=iexten)
if kk == 0:
spec = jspec
_, xper1 = ltsp.get_flux_plotrange(spec.flux, perc=0.9)
else:
# Scale flux for convenience of plotting (sig is not scaled)
_, xper2 = ltsp.get_flux_plotrange(jspec.flux, perc=0.9)
scl = xper1/xper2
# Splice
#from PyQt4 import QtCore
#QtCore.pyqtRemoveInputHook()
#pdb.set_trace()
#QtCore.pyqtRestoreInputHook()
spec = ltsu.splice_two(spec, jspec)#, scale=scl)
# Filename
spec_fil = ispec[0]
spec.filename=spec_fil
else:
raise ValueError('Bad input to read_spec: {}'.format(type(ispec)))
# Normalize?
if norm:
if spec.co_is_set:
spec.normed=True
# Demand AA for wavelength unit (unless over-ridden)
if spec.wavelength.unit != u.AA:
wvAA = spec.wavelength.to('AA')
spec.wavelength = wvAA
#from PyQt4 import QtCore
#QtCore.pyqtRemoveInputHook()
#pdb.set_trace()
#QtCore.pyqtRestoreInputHook()
# Return
return spec, spec_fil
def test_splice_two(spec, spec2):
spec3 = ltsu.splice_two(spec, spec2)
assert spec3.npix == 18390