def rest_allspec_readin(version='DR7'):
''' Read in all All_in_One (AIO) files and make a gigantic AIO array
'''
# Read in the catalog
objs_ori = absorber_readin(version)
nobj = objs_ori.size
# 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 convention
rest_allflux = np.zeros((nwave, nobj))
rest_allivar = np.zeros((nwave, nobj))
bands = _allinone_rest_bands
for thisband in bands:
data = allinone_rest_readin_band(thisband, version)
index_wave = data['INDEX_WAVE']
index_obj = data['INDEX_OBJ']
rest_allflux[index_wave[0]:index_wave[1], index_obj] = data['FLUX']
rest_allivar[index_wave[0]:index_wave[1], index_obj] = data['IVAR']
return (master_wave, rest_allflux, rest_allivar)
def rest_allspec_readin():
# read in the elg catalog
objs_ori = elg_readin()
nobj = objs_ori.size
# 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))
bands = _allinone_rest_bands
for thisband in bands:
data = allinone_rest_readin_band(thisband)
index_wave = data['INDEX_WAVE']
index_obj = data['INDEX_OBJ']
rest_allflux[index_wave[0]:index_wave[1], index_obj] = data['FLUX']
rest_allivar[index_wave[0]:index_wave[1], index_obj] = data['IVAR']
master_wave = master_wave*(1.+_zcorr)
return (master_wave, rest_allflux, rest_allivar)
def rest_allspec(version='DR7', overwrite=False):
"""Make the All_in_One (AIO) file in the rest frame
Load and interpolate *ALL* Absorber spectra on to the same rest-frame wavelength grid
"""
# Spectra directory
path0 = join(datapath.nmf_path(), '107')
if version == 'DR7':
path = join(path0, 'Decompose')
elif version == 'DR12':
path = join(path0, 'Decompose_DR12')
else:
raise IOError(
"Please check the data release version and the path to the decomposed spectroscopic data."
)
# Check All_in_One (AIO) output files
bands = _allinone_rest_bands
for thisband in bands:
# Check outfiles
outfile = allinone_rest_filename(thisband, version)
if isfile(outfile) and not overwrite:
print("File {0} exists. Use overwrite to overwrite it.".format(
outfile))
return -1
# Read in the catalog
objs_ori = absorber_readin(version)
nobj = objs_ori.size
# Make a temporary new catalog, universal
objs_dtype = [('PLATE', 'i4'), ('MJD', 'i4'), ('FIBER', 'i4'),
('RA', 'f8'), ('DEC', 'f8'), ('Z', 'f8')]
objs = np.zeros(nobj, dtype=objs_dtype)
# Assign the right values
objs['PLATE'] = objs_ori['PLATE']
objs['MJD'] = objs_ori['MJD']
objs['FIBER'] = objs_ori['FIBER']
objs['RA'] = objs_ori['RA']
objs['DEC'] = objs_ori['DEC']
objs['Z'] = objs_ori['ZABS'] # This is very important
# 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 convention
rest_allflux = np.zeros((nwave, nobj))
rest_allivar = np.zeros((nwave, nobj))
# rest_allflux = np.zeros((nwave, 10)) # This is for testing
# rest_allivar = np.zeros((nwave, 10))
# Initialization of the progress bar
pbar = ProgressBar(maxval=nobj).start()
# for i in np.arange(10): # This is for testing
for i in np.arange(nobj):
# Progress bar
pbar.update(i)
tmpz = objs[i]['Z']
# Useful wavelength range in the observer frame
wave_pos = np.array([_minwave / (1. + tmpz), _maxwave / (1. + tmpz)])
rest_loc = np.searchsorted(master_wave, wave_pos)
tmp_loglam = master_loglam[rest_loc[0]:rest_loc[1]]
# Read in and interpolate
tmp_outflux, tmp_outivar = decompose_sdssspec.load_interp_spec(
objs[i], tmp_loglam, path, rest=True)
rest_allflux[rest_loc[0]:rest_loc[1], i] = tmp_outflux
rest_allivar[rest_loc[0]:rest_loc[1], i] = tmp_outivar
# Closing progress bar
pbar.finish()
# raise ValueError("Stop here")
# Write out
print "Now I am writing everything out..."
allinone_rest_writeout(objs,
master_wave,
rest_allflux,
rest_allivar,
version,
overwrite=overwrite)
def rest_allspec(overwrite=False):
"""Load and interpolate *ALL* eBOSS ELG spectra
on to the same rest-frame wavelength grid
"""
path1 = join(datapath.sdss_path(), 'v5_7_6')
path2 = join(datapath.sdss_path(), 'specDR12')
# 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 elg catalog
objs_ori = elg_readin()
nobj = objs_ori.size
# make a temporary new catalog
objs_dtype = [('PLATE', 'i4'),
('MJD', 'i4'),
('FIBER', 'i4'),
('RA', 'f8'),
('DEC', 'f8'),
('Z', 'f8')]
objs = np.zeros(nobj, dtype=objs_dtype)
objs['PLATE'] = objs_ori['PLATE_1']
objs['MJD'] = objs_ori['MJD']
objs['FIBER'] = objs_ori['FIBERID_1']
objs['RA'] = objs_ori['PLUG_RA']
objs['DEC'] = objs_ori['PLUG_DEC']
objs['Z'] = objs_ori['Z']
# 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))
#rest_allflux = np.zeros((nwave, 10))
#rest_allivar = np.zeros((nwave, 10))
# Progress bar
pbar = ProgressBar(maxval=nobj).start()
#for i in np.arange(10):
for i in np.arange(nobj):
# Progress bar
pbar.update(i)
tmpz = objs[i]['Z']
# Wavelength
wave_pos = np.array([3600./(1.+tmpz), 10400./(1.+tmpz)])
rest_loc = np.searchsorted(master_wave, wave_pos)
tmp_loglam = master_loglam[rest_loc[0]:rest_loc[1]]
# read and interpolate
try:
tmp_outflux, tmp_outivar = sdssspec.load_interp_spec(objs[i], tmp_loglam, path1, rest=True)
rest_allflux[rest_loc[0]:rest_loc[1],i] = tmp_outflux
rest_allivar[rest_loc[0]:rest_loc[1],i] = tmp_outivar
except (IndexError, TypeError, NameError, ValueError):
try:
tmp_outflux, tmp_outivar = sdssspec.load_interp_spec(objs[i], tmp_loglam, path2, rest=True)
rest_allflux[rest_loc[0]:rest_loc[1],i] = tmp_outflux
rest_allivar[rest_loc[0]:rest_loc[1],i] = tmp_outivar
except (IndexError, TypeError, NameError, ValueError):
print("Error reading plate {0} mjd {1} fiber {2}".format(objs[i]['PLATE'], objs[i]['MJD'], objs[i]['FIBER']))
# output
#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 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)