def __init__(self, wrest, z=0., N=0., fill=True, spec_file=None):
# Test for Unit
raise ValueError('DEPRECATED!! Use AbsLine in lines_utils.py') #xdb.set_trace() # DEPRECATED
try:
unit = wrest.unit
except AttributeError:
raise ValueError('wrest needs to be a Quantity with a Unit, e.g. Ang')
self.wrest = wrest
self.z = z
# Fill in atomic data from Table (default)
# Dict : fval, gamma, A, Elow, Eup, Ex, j, name, wrest
if fill is True:
self.atomic = abs_line_data(self.wrest) # Dict
self.name = self.atomic['name']
else: self.name = ''
# Attribute dict
self.attrib = {'N': 0., 'Nsig': 0., 'flgN': 0,
'b': 0., 'bsig': 0., 'vmin': 0., 'vmax': 0.,
'EW': 0., 'EWsig': 0., 'flgEW': 0}
# Spectrum info (optional)
if spec_file is None:
self.spec = None
else:
import xastropy.spec.readwrite as xspec_rw
self.spec = xspec_rw.readspec(spec_file)
def __init__(self, wrest, z=0., N=0., fill=True, spec_file=None):
# Test for Unit
raise ValueError('DEPRECATED!! Use AbsLine in lines_utils.py') #xdb.set_trace() # DEPRECATED
try:
unit = wrest.unit
except AttributeError:
raise ValueError('wrest needs to be a Quantity with a Unit, e.g. Ang')
self.wrest = wrest
self.z = z
# Fill in atomic data from Table (default)
# Dict : fval, gamma, A, Elow, Eup, Ex, j, name, wrest
if fill is True:
self.atomic = abs_line_data(self.wrest) # Dict
self.name = self.atomic['name']
else: self.name = ''
# Attribute dict
self.attrib = {'N': 0., 'Nsig': 0., 'flgN': 0,
'b': 0., 'bsig': 0., 'vmin': 0., 'vmax': 0.,
'EW': 0., 'EWsig': 0., 'flgEW': 0}
# Spectrum info (optional)
if spec_file is None:
self.spec = None
else:
import xastropy.spec.readwrite as xspec_rw
self.spec = xspec_rw.readspec(spec_file)
def x_contifit(specfil, outfil=None, savfil=None, redshift=0., divmult=1, forest_divmult=1):
import os
import barak.fitcont as bf
from barak.spec import read
from barak.io import saveobj, loadobj
import xastropy.spec.readwrite as xsr
reload(xsr)
reload(bf)
# Initialize
if savfil == None:
savfil = 'conti.sav'
if outfil == None:
outfil = 'conti.fits'
# Read spectrum + convert to Barak format
sp = xsr.readspec(specfil)
# Fit spline continuum:
if os.path.lexists(savfil): #'contfit_' + name + '.sav'):
option = raw_input('Adjust old continuum? (y)/n: ')
if option.lower() != 'n':
co_old, knots_old = loadobj(savfil) #'contfit_' + name + '.sav')
co, knots = bf.fitqsocont(sp.wa, sp.fl, sp.er, redshift,
oldco=co_old, knots=knots_old,
divmult=divmult,
forest_divmult=forest_divmult)
else:
co, knots = bf.fitqsocont(sp.wa, sp.fl, sp.er, redshift,
divmult=divmult,
forest_divmult=forest_divmult)
else:
co, knots = bf.fitqsocont(sp.wa, sp.fl, sp.er, redshift,
divmult=divmult,
forest_divmult=forest_divmult)
os.remove('_knots.sav')
# Save continuum:
saveobj(savfil, (co, knots), overwrite=1)
# Check continuum:
print('Plotting new continuum')
plt.clf()
plt.plot(sp.wa, sp.fl, drawstyle='steps-mid')
plt.plot(sp.wa, sp.co, color='r')
plt.show()
# Repeat?
confirm = raw_input('Keep continuum? (y)/n: ')
if confirm == 'y':
fits.writeto(outfil, sp, clobber=True)
else:
print('Writing to tmp.fits anyhow!')
fits.writeto('tmp.fits', sp, clobber=True)
def spec_plot(spec_fil, ID_path=None, ambig_fil=None, dwv=25., outfil='tmp.pdf'):
mpl.rcParams['font.family'] = 'stixgeneral'
from matplotlib.backends.backend_pdf import PdfPages
import matplotlib.gridspec as gridspec
'''
spec_fil: string
Filename of spectrum
outfil: string ('tmp.pdf')
Filename for output
dwv: float (25.)
Ang per window
'''
npx = 1
npy = 4
# Read spectrum
spec = xsr.readspec(spec_file)
# Start plot
pp = PdfPages(outfil)
def x_contifit(specfil,
outfil=None,
savfil=None,
redshift=0.,
divmult=1,
forest_divmult=1):
import os
import barak.fitcont as bf
from barak.spec import read
from barak.io import saveobj, loadobj
import xastropy.spec.readwrite as xsr
reload(xsr)
reload(bf)
# Initialize
if savfil == None:
savfil = 'conti.sav'
if outfil == None:
outfil = 'conti.fits'
# Read spectrum + convert to Barak format
sp = xsr.readspec(specfil)
# Fit spline continuum:
if os.path.lexists(savfil): #'contfit_' + name + '.sav'):
option = raw_input('Adjust old continuum? (y)/n: ')
if option.lower() != 'n':
co_old, knots_old = loadobj(savfil) #'contfit_' + name + '.sav')
co, knots = bf.fitqsocont(sp.wa,
sp.fl,
sp.er,
redshift,
oldco=co_old,
knots=knots_old,
divmult=divmult,
forest_divmult=forest_divmult)
else:
co, knots = bf.fitqsocont(sp.wa,
sp.fl,
sp.er,
redshift,
divmult=divmult,
forest_divmult=forest_divmult)
else:
co, knots = bf.fitqsocont(sp.wa,
sp.fl,
sp.er,
redshift,
divmult=divmult,
forest_divmult=forest_divmult)
os.remove('_knots.sav')
# Save continuum:
saveobj(savfil, (co, knots), overwrite=1)
# Check continuum:
print('Plotting new continuum')
plt.clf()
plt.plot(sp.wa, sp.fl, drawstyle='steps-mid')
plt.plot(sp.wa, sp.co, color='r')
plt.show()
# Repeat?
confirm = raw_input('Keep continuum? (y)/n: ')
if confirm == 'y':
fits.writeto(outfil, sp, clobber=True)
else:
print('Writing to tmp.fits anyhow!')
fits.writeto('tmp.fits', sp, clobber=True)
# ################
if __name__ == "__main__":
flg_test = 0
#flg_test += 2**0 # Test write (simple)
#flg_test += 2**1 # Test write with 3 arrays
#flg_test += 2**2 # Test boxcar
flg_test += 2**3 # Test rebin
from xastropy.spec import readwrite as xsr
if (flg_test % 2**1) >= 2**0:
# Standard log-linear read + write (MagE)
fil = '~/PROGETTI/LLSZ3/data/normalize/UM669_nF.fits'
myspec = xsr.readspec(fil)
# Write
myspec.write_to_fits('tmp.fits')
if (flg_test % 2**2) >= 2**1:
# Now 2D
fil = '/Users/xavier/Dropbox/QSOPairs/data/LRIS_redux/SDSSJ231254.65-025403.1_b400_F.fits.gz'
myspec = xsr.readspec(fil)
myspec.write_to_fits('tmp.fits')
if (flg_test % 2**3) >= 2**2: # Boxcar
fil = '~/PROGETTI/LLSZ3/data/normalize/UM669_nF.fits'
myspec = xsr.readspec(fil)
newspec = myspec.box_smooth(3)
#
newspec2 = myspec.box_smooth(3, preserve=True)
flg_test += 2**1 # AODM
#flg_test += 2**2 # EW
# Test Absorption Line creation
if (flg_test % 2**1) >= 2**0:
print('-------------------------')
aline = AbsLine(1215.6701*u.AA)
print(aline)
# Test AODM
if (flg_test % 2**2) >= 2**1:
print('------------ AODM -------------')
# Spectrum
fil = '~/PROGETTI/LLSZ3/data/normalize/UM669_nF.fits'
aline = AbsLine(1302.1685*u.AA)
aline.spec = xsr.readspec(fil)
# Line info
aline.analy['z'] = 2.92652
aline.analy['VLIM'] = const.c.to('km/s') * (
( np.array([5110.668, 5116.305])*u.AA/(
1+aline.analy['z']) - aline.wrest) / aline.wrest )
# Evaluate
N,sigN = aline.aodm(conti=np.ones(len(aline.spec.flux)))
logN, sig_logN = xsb.lin_to_log(N,sigN)
print('logN = {:g}, sig_logN = {:g}'.format(logN, sig_logN))
# Test EW
if (flg_test % 2**3) >= 2**2:
print('------------ EW -------------')
# Spectrum
fil = '~/PROGETTI/LLSZ3/data/normalize/UM669_nF.fits'
# ################
if __name__ == "__main__":
flg_test = 0
#flg_test += 2**0 # Test write (simple)
#flg_test += 2**1 # Test write with 3 arrays
#flg_test += 2**2 # Test boxcar
flg_test += 2**3 # Test rebin
from xastropy.spec import readwrite as xsr
if (flg_test % 2**1) >= 2**0:
# Standard log-linear read + write (MagE)
fil = '~/PROGETTI/LLSZ3/data/normalize/UM669_nF.fits'
myspec = xsr.readspec(fil)
# Write
myspec.write_to_fits('tmp.fits')
if (flg_test % 2**2) >= 2**1:
# Now 2D
fil = '/Users/xavier/Dropbox/QSOPairs/data/LRIS_redux/SDSSJ231254.65-025403.1_b400_F.fits.gz'
myspec = xsr.readspec(fil)
myspec.write_to_fits('tmp.fits')
if (flg_test % 2**3) >= 2**2: # Boxcar
fil = '~/PROGETTI/LLSZ3/data/normalize/UM669_nF.fits'
myspec = xsr.readspec(fil)
newspec = myspec.box_smooth(3)
#
newspec2 = myspec.box_smooth(3, preserve=True)
