def test_get_local_s2n():
spec = XSpectrum1D.from_file(data_path('UM184_nF.fits'))
wv0 = 4000 * u.AA
s2n, sig_s2n = spec.get_local_s2n(wv0, 20, flux_th=0.9)
np.testing.assert_allclose(s2n, 9.30119800567627, rtol=1e-5)
np.testing.assert_allclose(sig_s2n, 1.0349911451339722, rtol=1e-5)
# test with continuum
spec.co = np.ones_like(spec.flux)
s2n, sig_s2n = spec.get_local_s2n(wv0, 20, flux_th=0.9)
np.testing.assert_allclose(s2n, 10.330545425415039, rtol=1e-5)
np.testing.assert_allclose(sig_s2n, 0.4250050187110901, rtol=1e-5)
# test errors
# out of range
with pytest.raises(IOError):
spec.get_local_s2n(1215*u.AA, 20)
# sig not defined
spec = XSpectrum1D.from_tuple((spec.wavelength, spec.flux))
with pytest.raises(ValueError):
spec.get_local_s2n(wv0, 20)
# bad shape for flux_th
with pytest.raises(ValueError):
spec.get_local_s2n(wv0, 20, flux_th=np.array([1,2,3,4,5]))
# npix too big
with pytest.raises(ValueError):
spec.get_local_s2n(wv0, 1 + len(spec.wavelength))
def test_from_tuple():
tmp = ascii.read(data_path('UM184.dat.gz'), names=['wave', 'flux', 'sig'])
idl = dict(wave=np.array(tmp['wave']),
flux=np.array(tmp['flux']),
sig=np.array(tmp['sig']))
spec = XSpectrum1D.from_tuple((idl['wave'], idl['flux'], idl['sig']))
#
np.testing.assert_allclose(spec.data['wave'][spec.select], idl['wave'])
np.testing.assert_allclose(spec.data['sig'][spec.select],
idl['sig'],
atol=2e-3,
rtol=0)
assert spec.wavelength.unit == u.Unit('AA')
#
spec = XSpectrum1D.from_tuple((idl['wave'], idl['flux']))
np.testing.assert_allclose(spec.data['wave'][spec.select], idl['wave'])
# continuum
co = np.ones_like(idl['flux'])
spec = XSpectrum1D.from_tuple((idl['wave'], idl['flux'], idl['sig'], co))
np.testing.assert_allclose(spec.data['wave'][spec.select], idl['wave'])
co = None
spec = XSpectrum1D.from_tuple((idl['wave'], idl['flux'], idl['sig'], co))
np.testing.assert_allclose(spec.data['wave'][spec.select], idl['wave'])
def test_get_local_s2n():
spec = XSpectrum1D.from_file(data_path('UM184_nF.fits'))
wv0 = 4000 * u.AA
s2n, sig_s2n = spec.get_local_s2n(wv0, 20, flux_th=0.9)
np.testing.assert_allclose(s2n, 9.30119800567627, rtol=1e-5)
np.testing.assert_allclose(sig_s2n, 1.0349911451339722, rtol=1e-5)
# test with continuum
spec.co = np.ones_like(spec.flux)
s2n, sig_s2n = spec.get_local_s2n(wv0, 20, flux_th=0.9)
np.testing.assert_allclose(s2n, 10.330545425415039, rtol=1e-5)
np.testing.assert_allclose(sig_s2n, 0.4250050187110901, rtol=1e-5)
# test errors
# out of range
with pytest.raises(IOError):
spec.get_local_s2n(1215 * u.AA, 20)
# sig not defined
spec = XSpectrum1D.from_tuple((spec.wavelength, spec.flux))
with pytest.raises(ValueError):
spec.get_local_s2n(wv0, 20)
# bad shape for flux_th
with pytest.raises(ValueError):
spec.get_local_s2n(wv0, 20, flux_th=np.array([1, 2, 3, 4, 5]))
# npix too big
with pytest.raises(ValueError):
spec.get_local_s2n(wv0, 1 + len(spec.wavelength))
def init_conti_full(self):
print("Initializing the continuum")
spec = self.spec_widg.orig_spec
spec.select = self.model_spec # Just in case, but this should already be the case
# Full Model (LLS+continuum)
self.full_model = XSpectrum1D.from_tuple(
(spec.wavelength, np.ones(len(spec.wavelength))))
self.conti_dict = pycc.init_conti_dict(
Norm=float(np.median(spec.flux.value)),
piv_wv=1215. * (1 + self.zqso),
#piv_wv2=915.*(1+zqso),
igm='True')
# Read Telfer and apply IGM
if self.template is not None:
tspec = lsi.readspec(self.template)
# assume wavelengths
tspec = XSpectrum1D.from_tuple(
(tspec.wavelength.value * (1 + self.zqso), tspec.flux.value))
else:
tspec = pycq.get_telfer_spec(
zqso=self.zqso, igm=(self.conti_dict['igm'] == 'True'))
# Rebin
self.continuum = tspec.rebin(spec.wavelength)
# Reset pivot wave
self.conti_dict['piv_wv'] = 915. * (1 + self.zqso)
#self.conti_dict['piv_wv'] = 1215.*(1+zqso)
#self.conti_dict['piv_wv2'] = 915.*(1+zqso)
self.base_continuum = self.continuum.flux
self.update_conti()
self.spec_widg.continuum = self.continuum
def load_spectrum(spec_fil):
'''Load X-Shooter spectra'''
# Load Spectrum
uvb_spec = XSpectrum1D.from_file(spec_fil)
vis_specfil = spec_fil.replace('uvb', 'vis')
vis_spec = XSpectrum1D.from_file(vis_specfil)
comb_spec = uvb_spec.splice(vis_spec)
comb_spec.filename = spec_fil
# Return
return comb_spec
def insert_dlas(sightline,
overlap=False,
rstate=None,
slls=False,
mix=False,
high=False,
noise=False):
""" Insert a DLA into input spectrum
Also adjusts the noise
Will also add noise 'everywhere' if requested
Parameters
----------
sightline:dla_cnn.data_model.sightline.Sightline object
overlap: bool
noise: bool, optional
Returns
-------
None
"""
#init
if rstate is None:
rstate = np.random.RandomState()
spec = XSpectrum1D.from_tuple(
(10**sightline.loglam, sightline.flux)) #generate xspectrum1d
# Generate DLAs
dlas = []
spec_dlas = []
zabslist = init_zabs(sightline, overlap)
for zabs in zabslist:
# Random NHI
NHI = uniform_NHI(slls=slls, mix=mix, high=high)
spec_dla = Dla((1 + zabs) * 1215.6701, NHI, '00' + str(jj))
if (slls or mix):
dla = LLSSystem((sightline.ra, sightline.dec), zabs, None, NHI=NHI)
else:
dla = DLASystem((sightline.ra, sightline.dec), zabs, None, NHI)
dlas.append(dla)
spec_dlas.append(spec_dla)
# Insert dlas to one sightline
vmodel, _ = hi_model(dlas, spec, fwhm=3.)
#add noise
if noise:
rand = rstate.randn(len(sightline.flux))
noise = rand * sightline.error * np.sqrt(1 - vmodel.flux.value**2)
else:
noise = 0
final_spec = XSpectrum1D.from_tuple(
(vmodel.wavelength, spec.flux.value * vmodel.flux.value + noise))
#generate new sightline
sightline.flux = final_spec.flux.value
sightline.dlas = spec_dlas
sightline.s2n = estimate_s2n(sightline)
def test_wvmnx():
npix = 1000
# Without sig
spec = XSpectrum1D.from_tuple((np.linspace(5000.,6000,npix), np.ones(npix)))
assert spec.wvmin.value == 5000.
assert spec.wvmax.value == 6000.
# With sig
spec = XSpectrum1D.from_tuple((np.linspace(5000.,6000,npix), np.ones(npix),
np.ones(npix)*0.1))
assert spec.wvmin.value == 5000.
assert spec.wvmax.value == 6000.
def xspectrum1d_from_mpdaf_spec(sp, airvac='air'):
"""Gets a XSpectrum1D object in vacuum from an MPDAF Spectrum"""
nomask = ~sp.mask
fl = sp.data[nomask]
er = np.sqrt(sp.var[nomask])
wv = sp.wave.coord()[nomask]
meta = dict(airvac=airvac)
spec = XSpectrum1D.from_tuple((wv, fl, er), meta=meta)
spec.airtovac()
spec2 = XSpectrum1D.from_tuple((spec.wavelength, fl, er))
return spec2
def test_wvmnx():
npix = 1000
# Without sig
spec = XSpectrum1D.from_tuple((np.linspace(5000.,6000,npix), np.ones(npix)))
assert spec.wvmin.value == 5000.
assert spec.wvmax.value == 6000.
# With sig
spec = XSpectrum1D.from_tuple((np.linspace(5000.,6000,npix), np.ones(npix),
np.ones(npix)*0.1))
assert spec.wvmin.value == 5000.
assert spec.wvmax.value == 6000.
def test_mask_edge():
wave = 3000. + np.arange(1000)
flux = np.ones_like(wave)
sig = 0.1*np.ones_like(wave)
sig[900:] = 0.
sig[800:825] = 0.
wave[900:] = 0. # WARNING, the data are sorted first!
#
spec = XSpectrum1D.from_tuple((wave,flux,sig), masking='edges')
assert len(spec.wavelength) == 900
spec2 = XSpectrum1D.from_tuple((wave,flux,sig), masking='all')
assert len(spec2.wavelength) == 875
def test_errors():
# from_tuple
try:
spec = XSpectrum1D.from_tuple('this_is_not_a_tuple')
except IOError:
pass
try:
n_tuple = np.array([np.ones(5), np.ones(5)]), np.ones(5)
spec = XSpectrum1D.from_tuple(n_tuple)
except IOError:
pass
# wrong instances
flux = [1,2,3]
wave = [1,2,3]
try:
spec = XSpectrum1D(wave, flux)
except IOError:
pass
#wrong shapes
flux = np.ones(5)
wave = np.array([1,2,3])
try:
spec = XSpectrum1D(wave, flux)
except IOError:
pass
try:
spec = XSpectrum1D(wave, np.ones(len(wave)), sig=np.ones(2))
except IOError:
pass
try:
spec = XSpectrum1D(wave, np.ones(len(wave)), co=np.ones(2), verbose = True) # test verbose here too
except IOError:
pass
# wrong masking
try:
spec = XSpectrum1D(wave, np.ones(len(wave)), masking = 'wrong_masking')
except IOError:
pass
#wrong units input
try:
spec = XSpectrum1D(wave, np.ones(len(wave)), units = 'not_a_dict')
except IOError:
pass
try:
spec = XSpectrum1D(wave, np.ones(len(wave)), units =dict(wrong_key=2))
except IOError:
pass
def test_masking():
wave = 3000. + np.arange(1000)
flux = np.ones_like(wave)
sig = 0.1 * np.ones_like(wave)
sig[900:] = 0.
sig[800:825] = 0.
wave[900:] = 0. # WARNING, the data are sorted first!
#
spec = XSpectrum1D.from_tuple((wave, flux, sig), masking='edges')
assert len(spec.wavelength) == 900
spec2 = XSpectrum1D.from_tuple((wave, flux, sig), masking='all')
assert len(spec2.wavelength) == 875
spec3 = XSpectrum1D.from_tuple((wave, flux, sig), masking='none')
assert len(spec3.wavelength) == len(wave)
def test_errors():
# from_tuple
try:
spec = XSpectrum1D.from_tuple('this_is_not_a_tuple')
except IOError:
pass
try:
n_tuple = np.array([np.ones(5), np.ones(5)]), np.ones(5)
spec = XSpectrum1D.from_tuple(n_tuple)
except IOError:
pass
# wrong instances
flux = [1, 2, 3]
wave = [1, 2, 3]
try:
spec = XSpectrum1D(wave, flux)
except IOError:
pass
#wrong shapes
flux = np.ones(5)
wave = np.array([1, 2, 3])
try:
spec = XSpectrum1D(wave, flux)
except IOError:
pass
try:
spec = XSpectrum1D(wave, np.ones(len(wave)), sig=np.ones(2))
except IOError:
pass
try:
spec = XSpectrum1D(wave,
np.ones(len(wave)),
co=np.ones(2),
verbose=True) # test verbose here too
except IOError:
pass
# wrong masking
try:
spec = XSpectrum1D(wave, np.ones(len(wave)), masking='wrong_masking')
except IOError:
pass
#wrong units input
try:
spec = XSpectrum1D(wave, np.ones(len(wave)), units='not_a_dict')
except IOError:
pass
try:
spec = XSpectrum1D(wave, np.ones(len(wave)), units=dict(wrong_key=2))
except IOError:
pass
def load_1dspec(fname, exten=None, extract='OPT', objname=None, flux=False):
"""
Parameters
----------
fname : str
Name of the file
exten : int, optional
Extension of the spectrum
If not given, all spectra in the file are loaded
extract : str, optional
Extraction type ('opt', 'box')
objname : str, optional
Identify extension based on input object name
flux : bool, optional
Return fluxed spectra?
Returns
-------
spec : XSpectrum1D
"""
# Identify extension from objname?
if objname is not None:
hdulist = fits.open(fname)
hdu_names = [hdu.name for hdu in hdulist]
exten = hdu_names.index(objname)
if exten < 0:
msgs.error("Bad input object name: {:s}".format(objname))
# Keywords for Table
rsp_kwargs = {}
if flux:
rsp_kwargs['flux_tag'] = '{:s}_FLAM'.format(extract)
rsp_kwargs['sig_tag'] = '{:s}_FLAM_SIG'.format(extract)
else:
rsp_kwargs['flux_tag'] = '{:s}_COUNTS'.format(extract)
rsp_kwargs['sig_tag'] = '{:s}_COUNTS_SIG'.format(extract)
# Use the WAVE_GRID (for 2d coadds) if it exists, otherwise use WAVE
rsp_kwargs['wave_tag'] = '{:s}_WAVE_GRID'.format(extract)
# Load
try:
spec = XSpectrum1D.from_file(fname, exten=exten, **rsp_kwargs)
except ValueError:
rsp_kwargs['wave_tag'] = '{:s}_WAVE'.format(extract)
spec = XSpectrum1D.from_file(fname, exten=exten, **rsp_kwargs)
# Return
return spec
def xspectrum1d_from_mpdaf_spec(sp, airvac='air'):
"""Gets a XSpectrum1D object in vacuum from an MPDAF Spectrum
It does not take into account whether the wv is in air or vac anymore
"""
nomask = ~sp.mask
fl = sp.data[nomask]
er = np.sqrt(sp.var[nomask])
wv = sp.wave.coord()[nomask]
meta = dict(airvac=airvac)
spec = XSpectrum1D.from_tuple((wv, fl, er), meta=meta)
#spec.airtovac()
# print("\t Hola!!!!!!!!!!!!!!1")
spec2 = XSpectrum1D.from_tuple((spec.wavelength, fl, er))
return spec2
def test_readwrite_meta_as_dicts(spec):
sp = XSpectrum1D.from_tuple((np.array([5,6,7]), np.ones(3), np.ones(3)*0.1))
sp.meta['headers'][0] = dict(a=1, b='abc')
sp2 = XSpectrum1D.from_tuple((np.array([8,9,10]), np.ones(3), np.ones(3)*0.1))
sp2.meta['headers'][0] = dict(c=2, d='efg')
spec = ltsu.collate([sp,sp2])
# Write
spec.write_to_fits(data_path('tmp.fits'))
spec.write_to_hdf5(data_path('tmp.hdf5'))
# Read and test
newspec = io.readspec(data_path('tmp.hdf5'))
assert newspec.meta['headers'][0]['a'] == 1
assert newspec.meta['headers'][0]['b'] == 'abc'
newspec2 = io.readspec(data_path('tmp.fits'))
assert 'METADATA' in newspec2.meta['headers'][0].keys()
def test_from_tuple():
idl = ascii.read(data_path('UM184.dat.gz'), names=['wave', 'flux', 'sig'])
spec = XSpectrum1D.from_tuple((idl['wave'],idl['flux'],idl['sig']))
#
np.testing.assert_allclose(spec.dispersion.value, idl['wave'])
np.testing.assert_allclose(spec.sig, idl['sig'], atol=2e-3, rtol=0)
assert spec.dispersion.unit == u.Unit('AA')
#
spec = XSpectrum1D.from_tuple((idl['wave'],idl['flux']))
np.testing.assert_allclose(spec.dispersion.value, idl['wave'])
# continuum
co = np.ones_like(idl['flux'])
spec = XSpectrum1D.from_tuple((idl['wave'],idl['flux'],idl['sig'], co))
np.testing.assert_allclose(spec.dispersion.value, idl['wave'])
def dummy_spectrum(s2n=10., rstate=None, seed=1234, wave=None):
"""
Parameters
----------
s2n
seed
wave
Returns
-------
spec : XSpectrum1D
"""
if rstate is None:
rstate=np.random.RandomState(seed)
if wave is None:
wave = np.linspace(4000., 5000., 2000)
# Create
flux = np.ones_like(wave)
sig = np.ones_like(wave) / s2n
ispec = XSpectrum1D.from_tuple((wave,flux,sig))
# Noise and append
spec = ispec.add_noise(rstate=rstate)
flux, sig, mask = spec.data['flux'], spec.data['sig'], spec.data['flux'].mask
ivar = utils.inverse(sig**2)
return flux, ivar, mask
def parse_DESI_brick(hdulist, select=0, **kwargs):
""" Read a spectrum from a DESI brick format HDU list
Parameters
----------
hdulist : FITS HDU list
select : int, optional
Spectrum selected. Default is 0
Returns
-------
xspec1d : XSpectrum1D
Parsed spectrum
"""
fx = hdulist[0].data
# Sig
if hdulist[1].name in ['ERROR', 'SIG']:
sig = hdulist[1].data
else:
ivar = hdulist[1].data
sig = np.zeros_like(ivar)
gdi = ivar > 0.
sig[gdi] = np.sqrt(1. / ivar[gdi])
# Wave
wave = hdulist[2].data
wave = give_wv_units(wave)
if wave.shape != fx.shape:
wave = np.tile(wave, (fx.shape[0], 1))
# Finish
xspec1d = XSpectrum1D(wave, fx, sig, select=select, **kwargs)
return xspec1d
def spec_from_array(wave, flux, sig, **kwargs):
"""
Make an XSpectrum1D from numpy arrays of wave, flux and sig
Parameters
----------
If wave is unitless, Angstroms are assumed
If flux is unitless, it is made dimensionless
The units for sig and co are taken from flux.
Return spectrum from arrays of wave, flux and sigma
"""
# Get rid of 0 wavelength
good_wave = (wave > 1.0 * units.AA)
wave, flux, sig = wave[good_wave], flux[good_wave], sig[good_wave]
ituple = (wave, flux, sig)
spectrum = XSpectrum1D.from_tuple(ituple, **kwargs)
# Polish a bit -- Deal with NAN, inf, and *very* large values that will exceed
# the floating point precision of float32 for var which is sig**2 (i.e. 1e38)
bad_flux = np.any([
np.isnan(spectrum.flux),
np.isinf(spectrum.flux),
np.abs(spectrum.flux) > 1e30,
spectrum.sig**2 > 1e10,
],
axis=0)
if np.sum(bad_flux):
msgs.warn(
"There are some bad flux values in this spectrum. Will zero them out and mask them (not ideal)"
)
spectrum.data['flux'][spectrum.select][bad_flux] = 0.
spectrum.data['sig'][spectrum.select][bad_flux] = 0.
return spectrum
def get_telfer_spec(zqso=0., igm=False, fN_gamma=None, LL_flatten=True):
'''Generate a Telfer QSO composite spectrum
Parameters:
----------
zqso: float, optional
Redshift of the QSO
igm: bool, optional
Include IGM opacity? [False]
fN_gamma: float, optional
Power-law evolution in f(N,X)
LL_flatten: bool, optional
Set Telfer to a constant below the LL?
Returns:
--------
telfer_spec: XSpectrum1D
Spectrum
'''
# Read
telfer = ascii.read(
xa_path+'/data/quasar/telfer_hst_comp01_rq.ascii', comment='#')
scale = telfer['flux'][(telfer['wrest'] == 1450.)]
telfer_spec = XSpectrum1D.from_tuple((telfer['wrest']*(1+zqso),
telfer['flux']/scale[0])) # Observer frame
# IGM?
if igm is True:
'''The following is quite experimental.
Use at your own risk.
'''
import multiprocessing
from xastropy.igm.fN import model as xifm
from xastropy.igm import tau_eff as xit
fN_model = xifm.default_model()
# Expanding range of zmnx (risky)
fN_model.zmnx = (0.,5.)
if fN_gamma is not None:
fN_model.gamma = fN_gamma
# Parallel
igm_wv = np.where(telfer['wrest']<1220.)[0]
adict = []
for wrest in telfer_spec.dispersion[igm_wv].value:
tdict = dict(ilambda=wrest, zem=zqso, fN_model=fN_model)
adict.append(tdict)
# Run
#xdb.set_trace()
pool = multiprocessing.Pool(4) # initialize thread pool N threads
ateff = pool.map(xit.map_etl, adict)
# Apply
telfer_spec.flux[igm_wv] *= np.exp(-1.*np.array(ateff))
# Flatten?
if LL_flatten:
wv_LL = np.where(np.abs(telfer_spec.dispersion/(1+zqso)-914.*u.AA)<3.*u.AA)[0]
f_LL = np.median(telfer_spec.flux[wv_LL])
wv_low = np.where(telfer_spec.dispersion/(1+zqso)<911.7*u.AA)[0]
telfer_spec.flux[wv_low] = f_LL
# Return
return telfer_spec
def __init__(self):
super().__init__()
self.setWindowTitle('My simple dialog app')
button = QPushButton('Press me for a dialog!')
button.clicked.connect(self.button_clicked)
self.setCentralWidget(button)
#Add your flux extraction code in here
sp = XSpectrum1D.from_file('./example-data/test.fits')
wave = sp.wavelength.value
flux = sp.flux.value
error = sp.sig.value
q = np.where((wave > 1330) & (wave < 1340))
self.wave = wave[q]
self.flux = flux[q]
self.error = error[q]
sizeObj = QDesktopWidget().screenGeometry(-1)
print('Screen size:' + str(sizeObj.height()) + 'x' +
str(sizeObj.width()))
availObj = QDesktopWidget().availableGeometry(-1)
print('Availble size:' + str(availObj.height()) + 'x' +
str(availObj.width()))
self.move(sizeObj.width() // 2, sizeObj.height() // 2)
def fit_cont(filename):
from linetools.spectra.xspectrum1d import XSpectrum1D
import re
from astropy.coordinates import SkyCoord
from linetools.isgm import abssystem as lt_absys
from linetools.spectralline import AbsLine
from linetools.isgm.abscomponent import AbsComponent
from linetools import line_utils as ltlu
from linetools.spectralline import AbsLine, SpectralLine
import numpy
from astropy.io import fits
from glob import glob
from astropy import units as u
from linetools.lists.linelist import LineList
import warnings
warnings.filterwarnings('ignore')
# Create a spectrum class object from the fits file
sp = XSpectrum1D.from_file(filename)
data, radec = get_prop(filename)
# Call the GUI to interactively fit the continuum
sp.fit_continuum(kind='QSO', redshift=data['zq'])
# Normalize the Continuum
sp.normalize(co=sp.co)
# Write the Normalized Continuum to a new fits file
sp.write_to_fits('n_' + filename)
return print(filename + ' has been normalized and written to ' + 'n_' +
filename)
def compare_s2n(pp,lrdx_sciobj,pypit_boxfile, iso):
'''Compare boxcar S/N
'''
# Read/Load
pypit_boxspec = lsio.readspec(pypit_boxfile)
# Read LowRedux
sig = np.sqrt(lrdx_sciobj['MASK_BOX']/(lrdx_sciobj['SIVAR_BOX'] + (lrdx_sciobj['MASK_BOX']==0)))
lwrdx_boxspec = XSpectrum1D.from_tuple( (lrdx_sciobj['WAVE_BOX'], lrdx_sciobj['FLUX_BOX'], sig) )
# Plot
plt.clf()
fig = plt.figure(figsize=(16,7))
fig.suptitle("Instr={:s}, Setup={:s} :: Boxcar S/N for {:s} :: PYPIT ({:s})".format(iso[0], iso[1], iso[2], pypit.version), fontsize=18.)
ax = plt.gca()
ymax = np.median(pypit_boxspec.flux)*2.
# PYPIT
gdpy = pypit_boxspec.sig > 0.
pys2n = pypit_boxspec.flux[gdpy]/pypit_boxspec.sig[gdpy]
ax.plot(pypit_boxspec.dispersion[gdpy],pys2n, 'k-', drawstyle='steps', label='PYPIT')
# LowRedux
gdlx = lwrdx_boxspec.sig > 0.
ax.plot(lwrdx_boxspec.dispersion[gdlx], lwrdx_boxspec.flux[gdlx]/lwrdx_boxspec.sig[gdlx],
'-', color='blue', label='LowRedux')
# Axes
ax.set_xlim(np.min(pypit_boxspec.dispersion.value), np.max(pypit_boxspec.dispersion.value))
ax.set_ylim(0.,np.median(pys2n)*2.)
ax.set_xlabel('Wavelength',fontsize=17.)
ax.set_ylabel('S/N per pixel',fontsize=17.)
# Legend
legend = plt.legend(loc='upper right', borderpad=0.3,
handletextpad=0.3, fontsize='x-large')
# Finish
plt.tight_layout(pad=0.2,h_pad=0.,w_pad=0.1,rect=[0, 0.03, 1, 0.95])
pp.savefig(bbox_inches='tight')
plt.close()
def dump_bestfit(ppfit, outfile=None, z=0.):
"""
Create the bestfit in the observer frame and with vacuum wavelengths
Parameters
----------
ppfit
outfile
Returns
-------
bestfit: XSpectrum1D
"""
meta = dict(airvac='air', headers=[None])
# Spectrum
bestfit = XSpectrum1D.from_tuple(
(ppfit.lam * (1 + z), ppfit.bestfit / (1 + z)), meta=meta)
# Convert to vacuum
bestfit.airtovac()
# Write
if outfile is not None:
bestfit.write(outfile)
# Return
return bestfit
def extract_spectrum(cube,pixels,wvslice=None):
from linetools.spectra.xspectrum1d import XSpectrum1D
if isinstance(cube,str):
cube = DataCube(cube)
if wvslice is not None:
cube = kt.slice_cube(cube,wvslice[0],wvslice[1])
dat = cube.data
# Get rid of NaNs
dc = dat.copy()
nans = np.where(np.isnan(dc))
dc[nans]=0
# Perform the extraction
spaxels = []
for i,px in enumerate(pixels):
thisspec = dc[:,px[0],px[1]]
spaxels.append(thisspec)
spaxels=np.array(spaxels)
medspec = np.median(spaxels, axis=0)
# Get the wavelength array
newwavearr = cube.wavelength
# Create the spectrum
try:
spec = XSpectrum1D(wave = newwavearr,flux=medspec)
except:
import pdb; pdb.set_trace()
return spec
def grab_specmeta(self,
rows,
verbose=None,
masking='edges',
use_XSpec=True,
**kwargs):
""" Grab the spectra and meta data for an input set of rows
Aligned to the rows input
Parameters
----------
rows : int or ndarray
verbose
kwargs
Returns
-------
spec : XSpectrum1D or ndarray
Spectra requested, ordered by the input rows
meta : Table -- THIS MAY BE DEPRECATED
Meta table, ordered by the input rows
"""
if isinstance(rows, (int, np.int64)):
rows = np.array([rows]) # Insures meta and other arrays are proper
if verbose is None:
verbose = self.verbose
# Check spectra even exist! (can be only meta data)
if 'spec' not in list(self.hdf[self.group].keys()):
warnings.warn("No spectra in group: {:s}".format(self.group))
return None, None
# Check memory
if self.stage_data(rows, **kwargs):
if verbose:
print("Loaded spectra")
# Load
msk = np.array([False] * len(self.meta))
msk[rows] = True
tmp_data = self.hdf[self.group]['spec'][msk]
# Replicate and sort according to input rows
idx = match_ids(rows, np.where(msk)[0])
data = tmp_data[idx]
else:
print("Staging failed.. Not returning spectra")
return
# Generate XSpectrum1D
if 'co' in data.dtype.names:
co = data['co']
else:
co = None
if use_XSpec:
spec = XSpectrum1D(data['wave'],
data['flux'],
sig=data['sig'],
co=co,
masking=masking)
else:
spec = data
# Return
return spec, self.meta[rows]
def test_readwrite_meta_as_dicts(spec):
sp = XSpectrum1D.from_tuple((np.array([5, 6,
7]), np.ones(3), np.ones(3) * 0.1))
sp.meta['headers'][0] = dict(a=1, b='abc')
sp2 = XSpectrum1D.from_tuple(
(np.array([8, 9, 10]), np.ones(3), np.ones(3) * 0.1))
sp2.meta['headers'][0] = dict(c=2, d='efg')
spec = ltsu.collate([sp, sp2])
# Write
spec.write_to_fits(data_path('tmp.fits'))
spec.write_to_hdf5(data_path('tmp.hdf5'))
# Read and test
newspec = io.readspec(data_path('tmp.hdf5'))
assert newspec.meta['headers'][0]['a'] == 1
assert newspec.meta['headers'][0]['b'] == 'abc'
newspec2 = io.readspec(data_path('tmp.fits'))
assert 'METADATA' in newspec2.meta['headers'][0].keys()
def parse_linetools_spectrum_format(hdulist):
""" Parse an old linetools-format spectrum from an hdulist
Parameters
----------
hdulist : FITS HDU list
Returns
-------
xspec1d : XSpectrum1D
Parsed spectrum
"""
if 'WAVELENGTH' not in hdulist:
pdb.set_trace()
#spec1d = spec_read_fits.read_fits_spectrum1d(
# os.path.expanduser(datfil), dispersion_unit='AA')
xspec1d = XSpectrum1D.from_spec1d(spec1d)
else:
wave = hdulist['WAVELENGTH'].data * u.AA
fx = hdulist['FLUX'].data
# Error array
if 'ERROR' in hdulist:
sig = hdulist['ERROR'].data
else:
sig = None
if 'CONTINUUM' in hdulist:
co = hdulist['CONTINUUM'].data
else:
co = None
xspec1d = XSpectrum1D.from_tuple((wave, fx, sig, co))
if 'METADATA' in hdulist[0].header:
# import pdb; pdb.set_trace()
# patch for reading continuum metadata; todo: should be fixed properly!!!
if "contpoints" in hdulist[0].header['METADATA']:
aux_s = hdulist[0].header['METADATA']
if aux_s.endswith("}\' /"):
aux_s = aux_s[:-3] # delete these extra characters
hdulist[0].header['METADATA'] = aux_s
xspec1d.meta.update(json.loads(hdulist[0].header['METADATA']))
return xspec1d
def test_from_file():
spec = XSpectrum1D.from_file(data_path('UM184_nF.fits'))
idl = ascii.read(data_path('UM184.dat.gz'), names=['wave', 'flux', 'sig'])
np.testing.assert_allclose(spec.dispersion.value, idl['wave'])
np.testing.assert_allclose(spec.sig, idl['sig'], atol=2e-3, rtol=0)
assert spec.dispersion.unit == u.Unit('AA')
def wfc3_continuum(wfc3_indx=None, zqso=0., wave=None, smooth=3., NHI_max=17.5, rstate=None):
'''Use the WFC3 data + models from O'Meara+13 to generate a continuum
Parameters
----------
wfc3_indx : int, optional
Index of WFC3 data to use
zqso : float, optional
Redshift of the QSO
wave : Quantity array, optional
Wavelengths to rebin on
smooth : float, optional
Number of pixels to smooth on
NHI_max : float, optional
Maximum NHI for the sightline
Returns
-------
wfc3_continuum : XSpectrum1D
of the continuum
idx : int
Index of the WFC3 spectrum used
'''
# Random number
if rstate is None:
rstate = np.random.RandomState()
# Open
wfc3_models_hdu = fits.open(os.getenv('DROPBOX_DIR')+'XQ-100/LLS/wfc3_conti_models.fits')
nwfc3 = len(wfc3_models_hdu)-1
# Load up models
wfc_models = []
for ii in range(1,nwfc3-1):
wfc_models.append( Table(wfc3_models_hdu[ii].data) )
# Grab a random one
if wfc3_indx is None:
need_c = True
while(need_c):
idx = rstate.randint(0,nwfc3-1)
if wfc_models[idx]['TOTNHI'] > NHI_max:
continue
if wfc_models[idx]['QSO'] in ['J122836.05+510746.2', 'J122015.50+460802.4']:
continue # These QSOs are NG
need_c=False
else:
idx = wfc3_indx
# Generate spectrum
wfc_spec = XSpectrum1D.from_tuple( (wfc_models[idx]['WREST'].flatten()*(1+zqso),
wfc_models[idx]['FLUX'].flatten()) )
# Smooth
wfc_smooth = wfc_spec.gauss_smooth(fwhm=smooth)
# Rebin?
if wave is not None:
wfc_rebin = wfc_smooth.rebin(wave)
return wfc_rebin, idx
else:
return wfc_smooth, idx
def wfc3_continuum(wfc3_indx=None, zqso=0., wave=None, smooth=3., NHI_max=17.5, rstate=None):
'''Use the WFC3 data + models from O'Meara+13 to generate a continuum
Parameters
----------
wfc3_indx : int, optional
Index of WFC3 data to use
zqso : float, optional
Redshift of the QSO
wave : Quantity array, optional
Wavelengths to rebin on
smooth : float, optional
Number of pixels to smooth on
NHI_max : float, optional
Maximum NHI for the sightline
Returns
-------
wfc3_continuum : XSpectrum1D
of the continuum
idx : int
Index of the WFC3 spectrum used
'''
# Random number
if rstate is None:
rstate = np.random.RandomState()
# Open
wfc3_models_hdu = fits.open(os.getenv('DROPBOX_DIR')+'XQ-100/LLS/wfc3_conti_models.fits')
nwfc3 = len(wfc3_models_hdu)-1
# Load up models
wfc_models = []
for ii in range(1,nwfc3-1):
wfc_models.append( Table(wfc3_models_hdu[ii].data) )
# Grab a random one
if wfc3_indx is None:
need_c = True
while(need_c):
idx = rstate.randint(0,nwfc3-1)
if wfc_models[idx]['TOTNHI'] > NHI_max:
continue
if wfc_models[idx]['QSO'] in ['J122836.05+510746.2', 'J122015.50+460802.4']:
continue # These QSOs are NG
need_c=False
else:
idx = wfc3_indx
# Generate spectrum
wfc_spec = XSpectrum1D.from_tuple( (wfc_models[idx]['WREST'].flatten()*(1+zqso),
wfc_models[idx]['FLUX'].flatten()) )
# Smooth
wfc_smooth = wfc_spec.gauss_smooth(fwhm=smooth)
# Rebin?
if wave is not None:
wfc_rebin = wfc_smooth.rebin(wave)
return wfc_rebin, idx
else:
return wfc_smooth, idx
def __init__(self, filepath=''):
self.fitsobj = FitsObj(wave=[])
self.filepath = filepath
self.warning = ''
try:
self.sp = XSpectrum1D.from_file(self.filepath)
except (OSError, KeyError, AttributeError):
self.warning += 'XSpectrum1D cannot read this file.'
def loop_grab_spec(self, survey, IDs, verbose=None, **kwargs):
""" Grab spectra using staged IDs
All IDs must occur in each of the surveys listed
Order of spectra and meta tables will match the input IDs
Parameters
----------
survey : str or list
IDs : int or intarr
Returns
-------
spec : XSpectrum1D
Spectra requested, ordered by the IDs
meta : Table
Meta table, ordered by the IDs
"""
if verbose is None:
verbose = self.verbose
if isinstance(survey, list):
all_spec = []
all_meta = []
for isurvey in survey:
spec, meta = self.grab_spec(isurvey, IDs, **kwargs)
if spec is not None:
all_spec.append(spec.copy())
all_meta.append(meta.copy())
return all_spec, all_meta
# Grab IDs
if self.stage_data(survey, IDs, **kwargs):
if np.sum(self.survey_bool) == 0:
if verbose:
print("No spectra matching in survey {:s}".format(survey))
return None, None
else:
if verbose:
print("Loaded spectra")
tmp_data = self.hdf[survey]['spec'][self.survey_bool]
# Replicate and sort according to input IDs
data = tmp_data[self.indices]
else:
print("Staging failed.. Not returning spectra")
return
# Generate XSpectrum1D
if 'co' in data.dtype.names:
co = data['co']
else:
co = None
spec = XSpectrum1D(data['wave'],
data['flux'],
sig=data['sig'],
co=co,
masking='edges')
# Return
return spec, self.meta
def parse_hdf5(inp, close=True, **kwargs):
""" Read a spectrum from HDF5 written in XSpectrum1D format
Expects: meta, data, units
Parameters
----------
inp : str or hdf5
Returns
-------
"""
import json
import h5py
# Path
path = kwargs.pop('path', '/')
# Open
if isinstance(inp, basestring):
hdf5 = h5py.File(inp, 'r')
else:
hdf5 = inp
# Data
data = hdf5[path+'data'].value
# Meta
if 'meta' in hdf5[path].keys():
meta = json.loads(hdf5[path+'meta'].value)
# Headers
for jj,heads in enumerate(meta['headers']):
try:
meta['headers'][jj] = fits.Header.fromstring(meta['headers'][jj])
except TypeError: # dict
if not isinstance(meta['headers'][jj], dict):
raise IOError("Bad meta type")
else:
meta = None
# Units
units = json.loads(hdf5[path+'units'].value)
for key,item in units.items():
if item == 'dimensionless_unit':
units[key] = u.dimensionless_unscaled
else:
units[key] = getattr(u, item)
# Other arrays
try:
sig = data['sig']
except (NameError, IndexError):
sig = None
try:
co = data['co']
except (NameError, IndexError):
co = None
# Finish
if close:
hdf5.close()
return XSpectrum1D(data['wave'], data['flux'], sig=sig, co=co,
meta=meta, units=units, **kwargs)
def main(args):
from scipy.io.idl import readsav
from linetools.spectra.xspectrum1d import XSpectrum1D
# Read
lrdx_sky = readsav(args.lowrdx_sky)
# Generate
xspec = XSpectrum1D.from_tuple((lrdx_sky['wave_calib'], lrdx_sky['sky_calib']))
# Write
xspec.write_to_fits(args.new_file)
def load_spec(self):
'''Input the Spectrum
'''
from linetools.spectra.xspectrum1d import XSpectrum1D
if self._specfil is None:
self.get_specfil()
#
if self.verbose:
print('SdssQso: Loading spectrum from {:s}'.format(self._specfil))
self.spec = XSpectrum1D.from_file(self._specfil)
def main(args):
from scipy.io.idl import readsav
from linetools.spectra.xspectrum1d import XSpectrum1D
# Read
lrdx_sky = readsav(args.lowrdx_sky)
# Generate
xspec = XSpectrum1D.from_tuple((lrdx_sky['wave_calib'], lrdx_sky['sky_calib']))
# Write
xspec.write_to_fits(args.new_file)
def calculate_empirical_rms(spec, test=False):
fl = spec.flux.value
wv = spec.wavelength.value
min_cond = ltu.is_local_minima(fl)
max_cond = ltu.is_local_maxima(fl)
min_local_inds = np.where(min_cond)[0]
max_local_inds = np.where(max_cond)[0]
interpolated_max = interp1d(wv[max_local_inds],
fl[max_local_inds],
kind='linear',
bounds_error=False,
fill_value=0)
interpolated_min = interp1d(wv[min_local_inds],
fl[min_local_inds],
kind='linear',
bounds_error=False,
fill_value=0)
# these are the envelopes
fl_max = interpolated_max(wv)
fl_min = interpolated_min(wv)
# take the mid value
fl_mid = 0.5 * (fl_max + fl_min) # reference flux
# the idea here is that these will be the intrinsic rms per pixel (both are the same though)
max_mean_diff = np.abs(fl_mid - fl_max)
min_mean_diff = np.abs(fl_mid - fl_min)
sigma = 0.5 * (
max_mean_diff + min_mean_diff
) # anyways these two differences are the same by definition
if test:
# fluxes
wv_mins = wv[min_local_inds]
wv_maxs = wv[max_local_inds]
plt.figure()
plt.plot(wv, fl, drawstyle='steps-mid')
plt.plot(wv_mins,
fl[min_local_inds],
marker='o',
color='r',
label='Local minimum')
plt.plot(wv_maxs,
fl[max_local_inds],
marker='o',
color='green',
label='Local maximum')
plt.plot(wv, fl_mid, color='black', label='flux_mid')
# sigmas
plt.plot(wv, sigma, marker='o-', color='pink', label='Empirical sigma')
plt.plot(wv, spec.sig.value, color='yellow', label='Original sigma')
plt.legend()
plt.show()
return XSpectrum1D.from_tuple((wv, fl, sigma))
def test_addmask():
spec = XSpectrum1D.from_file(data_path('UM184_nF.fits'))
assert not spec.data['flux'][0].mask[100]
mask = spec.data['flux'][0].mask.copy()
mask[100:110] = True
spec.add_to_mask(mask)
assert spec.data['flux'][0].mask[100]
# Compressed
badp = spec.flux < 0.1
spec.add_to_mask(badp, compressed=True)
assert np.sum(spec.data['flux'][0].mask) > 3000
def writeVPmodel(outfile, wave, fitpars, normflux, normsig): from astropy.table import Table model = voigtfunc(wave, fitpars) modeltab = Table([wave, model, normflux, normsig], names=['wavelength', 'model', 'normflux', 'normsig']) # modeltab.write(outfile, format='fits', overwrite=True) dummycont = np.ones(len(wave)) spec = XSpectrum1D.from_tuple((modeltab['wavelength'], modeltab['model'], modeltab['normsig'], dummycont)) spec.write_to_fits(outfile) print 'Voigt profile model written to:' print outfile
def test_copy(spec):
# From existing
spec2 = spec.copy()
assert spec.wavelength[0] == spec2.wavelength[0]
assert spec.flux[-1] == spec2.flux[-1]
#
wave = np.arange(3000., 6500)
npix = len(wave)
spect = XSpectrum1D.from_tuple((wave*u.AA,np.ones(npix)))
specf = spect.copy()
assert specf.sig_is_set is False
def dumb_spec():
""" Generate a dummy spectrum
Returns
-------
"""
npix = 1000
dspec = XSpectrum1D.from_tuple((np.arange(npix)+5000., np.ones(npix),
np.ones(npix)))
#
return dspec
def test_copy(spec):
# From existing
spec2 = spec.copy()
assert spec.wavelength[0] == spec2.wavelength[0]
assert spec.flux[-1] == spec2.flux[-1]
#
wave = np.arange(3000., 6500)
npix = len(wave)
spect = XSpectrum1D.from_tuple((wave * u.AA, np.ones(npix)))
specf = spect.copy()
assert specf.sig_is_set is False
def test_addmask():
spec = XSpectrum1D.from_file(data_path('UM184_nF.fits'))
assert not spec.data['flux'][0].mask[100]
mask = spec.data['flux'][0].mask.copy()
mask[100:110] = True
spec.add_to_mask(mask)
assert spec.data['flux'][0].mask[100]
# Compressed
badp = spec.flux < 0.1
spec.add_to_mask(badp, compressed=True)
assert np.sum(spec.data['flux'][0].mask) > 3000
def test_from_tuple():
tmp = ascii.read(data_path('UM184.dat.gz'), names=['wave', 'flux', 'sig'])
idl = dict(wave=np.array(tmp['wave']), flux=np.array(tmp['flux']),
sig=np.array(tmp['sig']))
spec = XSpectrum1D.from_tuple((idl['wave'],idl['flux'], idl['sig']))
#
np.testing.assert_allclose(spec.data['wave'][spec.select], idl['wave'])
np.testing.assert_allclose(spec.data['sig'][spec.select], idl['sig'], atol=2e-3, rtol=0)
assert spec.wavelength.unit == u.Unit('AA')
#
spec = XSpectrum1D.from_tuple((idl['wave'],idl['flux']))
np.testing.assert_allclose(spec.data['wave'][spec.select], idl['wave'])
# continuum
co = np.ones_like(idl['flux'])
spec = XSpectrum1D.from_tuple((idl['wave'],idl['flux'],idl['sig'], co))
np.testing.assert_allclose(spec.data['wave'][spec.select], idl['wave'])
co = None
spec = XSpectrum1D.from_tuple((idl['wave'],idl['flux'],idl['sig'], co))
np.testing.assert_allclose(spec.data['wave'][spec.select], idl['wave'])
def test_fluxmodel():
# Init
lls = LLSSystem((0.*u.deg, 0.*u.deg), 2.5, None, NHI=17.9)
# Fill LLS lines
lls.fill_lls_lines()
# Generate a spectrum
wave = np.arange(3000., 6500)
npix = len(wave)
spec = XSpectrum1D.from_tuple((wave*u.AA,np.ones(npix)))
# Model
model = lls.flux_model(spec)
np.testing.assert_allclose(model.flux[100].value,0.009424664763760516)
def parse_linetools_spectrum_format(hdulist, **kwargs):
""" Parse an old linetools-format spectrum from an hdulist
Parameters
----------
hdulist : FITS HDU list
Returns
-------
xspec1d : XSpectrum1D
Parsed spectrum
"""
if 'WAVELENGTH' not in hdulist:
pdb.set_trace()
xspec1d = XSpectrum1D.from_spec1d(spec1d)
else:
wave = hdulist['WAVELENGTH'].data * u.AA
fx = hdulist['FLUX'].data
# Error array
if 'ERROR' in hdulist:
sig = hdulist['ERROR'].data
else:
sig = None
if 'CONTINUUM' in hdulist:
co = hdulist['CONTINUUM'].data
else:
co = None
xspec1d = XSpectrum1D.from_tuple((wave, fx, sig, co), **kwargs)
if 'METADATA' in hdulist[0].header:
# Prepare for JSON (bug fix of sorts)
metas = hdulist[0].header['METADATA']
ipos = metas.rfind('}')
xspec1d.meta.update(json.loads(metas[:ipos+1]))
return xspec1d
def load_spec_order(fname,objid=None,order=None,extract='OPT',flux=True):
"""
Loading single order spectrum from a PypeIt 1D specctrum fits file
:param file:
:param objid:
:param order:
:param extract:
:param flux:
:return:
"""
if objid is None:
objid = 0
if order is None:
msgs.error('Please specify which order you want to load')
# read extension name into a list
primary_header = fits.getheader(fname, 0)
nspec = primary_header['NSPEC']
extnames = [primary_header['EXT0001']] * nspec
for kk in range(nspec):
extnames[kk] = primary_header['EXT' + '{0:04}'.format(kk + 1)]
extnameroot = extnames[0]
# Figure out which extension is the required data
ordername = '{0:04}'.format(order)
extname = extnameroot.replace('OBJ0000', objid)
extname = extname.replace('ORDER0000', 'ORDER' + ordername)
try:
exten = extnames.index(extname) + 1
msgs.info("Loading extension {:s} of spectrum {:s}".format(extname, fname))
except:
msgs.error("Spectrum {:s} does not contain {:s} extension".format(fname, extname))
spectrum = load.load_1dspec(fname, exten=exten, extract=extract, flux=flux)
# Polish a bit -- Deal with NAN, inf, and *very* large values that will exceed
# the floating point precision of float32 for var which is sig**2 (i.e. 1e38)
bad_flux = np.any([np.isnan(spectrum.flux), np.isinf(spectrum.flux),
np.abs(spectrum.flux) > 1e30,
spectrum.sig ** 2 > 1e10,
], axis=0)
# Sometimes Echelle spectra have zero wavelength
bad_wave = spectrum.wavelength < 1000.0*units.AA
bad_all = bad_flux + bad_wave
## trim bad part
wave_out,flux_out,sig_out = spectrum.wavelength[~bad_all],spectrum.flux[~bad_all],spectrum.sig[~bad_all]
spectrum_out = XSpectrum1D.from_tuple((wave_out,flux_out,sig_out), verbose=False)
#if np.sum(bad_flux):
# msgs.warn("There are some bad flux values in this spectrum. Will zero them out and mask them (not ideal)")
# spectrum.data['flux'][spectrum.select][bad_flux] = 0.
# spectrum.data['sig'][spectrum.select][bad_flux] = 0.
return spectrum_out
def test_airtovac_andback(spec):
npix = 1000
spec = XSpectrum1D.from_tuple((np.linspace(5000.,6000,npix), np.ones(npix)))
# Airtovac
spec.meta['airvac'] = 'air'
spec.airtovac()
# Test
np.testing.assert_allclose(spec.wavelength[0].value, 5001.394869990007, rtol=1e-5)
assert spec.meta['airvac'] == 'vac'
# Vactoair
spec.vactoair()
np.testing.assert_allclose(spec.wavelength[0].value, 5000., rtol=1e-5)
assert spec.meta['airvac'] == 'air'
def parse_UVES_popler(hdulist):
""" Read a spectrum from a UVES_popler-style fits file.
"""
from linetools.spectra.xspectrum1d import XSpectrum1D
hd = hdulist[0].header
uwave = setwave(hd) * u.Angstrom
co = hdulist[0].data[3]
fx = hdulist[0].data[0] * co # Flux
sig = hdulist[0].data[1] * co
xspec1d = XSpectrum1D.from_tuple((uwave, fx, sig))
xspec1d.co = co
return xspec1d
def parse_linetools_spectrum_format(hdulist):
""" Parse an old linetools-format spectrum from an hdulist
Parameters
----------
hdulist : FITS HDU list
Returns
-------
xspec1d : XSpectrum1D
Parsed spectrum
"""
if 'WAVELENGTH' not in hdulist:
pdb.set_trace()
#spec1d = spec_read_fits.read_fits_spectrum1d(
# os.path.expanduser(datfil), dispersion_unit='AA')
xspec1d = XSpectrum1D.from_spec1d(spec1d)
else:
wave = hdulist['WAVELENGTH'].data * u.AA
fx = hdulist['FLUX'].data
# Error array
if 'ERROR' in hdulist:
sig = hdulist['ERROR'].data
else:
sig = None
if 'CONTINUUM' in hdulist:
co = hdulist['CONTINUUM'].data
else:
co = None
xspec1d = XSpectrum1D.from_tuple((wave, fx, sig, co))
if 'METADATA' in hdulist[0].header:
xspec1d.meta.update(json.loads(hdulist[0].header['METADATA']))
return xspec1d
def parse_UVES_popler(hdulist):
""" Read a spectrum from a UVES_popler-style fits file.
"""
from linetools.spectra.xspectrum1d import XSpectrum1D
hd = hdulist[0].header
uwave = setwave(hd) * u.Angstrom
co = hdulist[0].data[3]
fx = hdulist[0].data[0] * co # Flux
sig = hdulist[0].data[1] * co
xspec1d = XSpectrum1D.from_array(uwave, u.Quantity(fx),
uncertainty=StdDevUncertainty(sig))
xspec1d.co = co
return xspec1d
def test_rebin(spec):
# Add units
funit = u.erg/u.s/u.cm**2
spec.units['flux'] = funit
# Rebin
new_wv = np.arange(3000., 9000., 5) * u.AA
newspec = spec.rebin(new_wv, do_sig=True)
# Test
np.testing.assert_allclose(newspec.flux[1000].value, 1.0192499, rtol=1e-5)
assert newspec.flux.unit == funit
# Without sig
spec_nosig = XSpectrum1D.from_tuple((spec.wavelength, spec.flux))
newspec = spec.rebin(new_wv)
assert newspec.sig_is_set is False
def get_telfer_spec(zqso=0., igm=False):
'''Generate a Telfer QSO composite spectrum
Paraemters:
----------
zqso: float, optional
Redshift of the QSO
igm: bool, optional
Include IGM opacity? [False]
Returns:
--------
telfer_spec: XSpectrum1D
Spectrum
'''
# Read
telfer = ascii.read(
xa_path+'/data/quasar/telfer_hst_comp01_rq.ascii', comment='#')
scale = telfer['flux'][(telfer['wrest'] == 1450.)]
telfer_spec = XSpectrum1D.from_tuple((telfer['wrest']*(1+zqso),
telfer['flux']/scale[0])) # Observer frame
# IGM?
if igm is True:
'''The following is quite experimental.
Use at your own risk.
'''
import multiprocessing
from xastropy.igm.fN import model as xifm
from xastropy.igm import tau_eff as xit
fN_model = xifm.default_model()
# Expanding range of zmnx (risky)
fN_model.zmnx = (0.,5.)
# Parallel
igm_wv = np.where(telfer['wrest']<1220.)[0]
adict = []
for wrest in telfer_spec.dispersion[igm_wv].value:
tdict = dict(ilambda=wrest, zem=zqso, fN_model=fN_model)
adict.append(tdict)
# Run
#xdb.set_trace()
pool = multiprocessing.Pool(4) # initialize thread pool N threads
ateff = pool.map(xit.map_etl, adict)
# Apply
telfer_spec.flux[igm_wv] *= np.exp(-1.*np.array(ateff))
# Return
return telfer_spec
def main() :
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('lowrdx_sky', type = str, default = None,
help = 'LowRedux Sky Spectrum (IDL save file)')
parser.add_argument('new_file', type = str, default = None, help = 'PYPIT FITS sky spectrum')
args = parser.parse_args()
# Read
lrdx_sky = readsav(args.lowrdx_sky)
# Generate
xspec = XSpectrum1D.from_tuple((lrdx_sky['wave_calib'], lrdx_sky['sky_calib']))
# Write
xspec.write_to_fits(args.new_file)
def spec_from_array(wave,flux,sig,**kwargs):
"""
return spectrum from arrays of wave, flux and sigma
"""
ituple = (wave, flux, sig)
spectrum = XSpectrum1D.from_tuple(ituple, **kwargs)
# Polish a bit -- Deal with NAN, inf, and *very* large values that will exceed
# the floating point precision of float32 for var which is sig**2 (i.e. 1e38)
bad_flux = np.any([np.isnan(spectrum.flux), np.isinf(spectrum.flux),
np.abs(spectrum.flux) > 1e30,
spectrum.sig ** 2 > 1e10,
], axis=0)
if np.sum(bad_flux):
msgs.warn("There are some bad flux values in this spectrum. Will zero them out and mask them (not ideal)")
spectrum.data['flux'][spectrum.select][bad_flux] = 0.
spectrum.data['sig'][spectrum.select][bad_flux] = 0.
return spectrum
def compare_boxcar(pp,lrdx_sciobj,pypit_boxfile, iso):
'''Compare boxcar extractions
'''
# Read/Load
pypit_boxspec = lsio.readspec(pypit_boxfile)
# Read LowRedux
sig = np.sqrt(lrdx_sciobj['MASK_BOX']/(lrdx_sciobj['SIVAR_BOX'] + (lrdx_sciobj['MASK_BOX']==0)))
lwrdx_boxspec = XSpectrum1D.from_tuple( (lrdx_sciobj['WAVE_BOX'], lrdx_sciobj['FLUX_BOX'], sig) )
# Plot
plt.clf()
fig = plt.figure(figsize=(16,11))
gs = gridspec.GridSpec(2, 1)
fig.suptitle("Instr={:s}, Setup={:s} :: Boxcar Extractions for {:s} :: PYPIT ({:s})".format(iso[0], iso[1], iso[2], pypit.version), fontsize=18.)
for qq in range(2):
ax = plt.subplot(gs[qq])
if qq == 0:
xlim = None
else:
xlim = (6700,7000)
ymax = np.median(pypit_boxspec.flux)*2.
# PYPIT
ax.plot(pypit_boxspec.dispersion, pypit_boxspec.flux, 'k-', drawstyle='steps',label='PYPIT')
ax.plot(pypit_boxspec.dispersion, pypit_boxspec.sig, 'g-', drawstyle='steps')
# LowRedux
ax.plot(lwrdx_boxspec.dispersion, lwrdx_boxspec.flux, '-', color='blue',label='LowRedux')
ax.plot(lwrdx_boxspec.dispersion, lwrdx_boxspec.sig, '-', color='gray')
# Axes
if xlim is None:
ax.set_xlim(np.min(pypit_boxspec.dispersion.value), np.max(pypit_boxspec.dispersion.value))
else:
ax.set_xlim(xlim)
ax.set_ylim(0.,ymax)
ax.set_xlabel('Wavelength',fontsize=19.)
ax.set_ylabel('electrons',fontsize=19.)
# Legend
legend = plt.legend(loc='upper right', borderpad=0.3,
handletextpad=0.3, fontsize='x-large')
# Finish
plt.tight_layout(pad=0.2,h_pad=0.,w_pad=0.1,rect=[0, 0.03, 1, 0.95])
pp.savefig(bbox_inches='tight')
plt.close()
