def mkfluxstar(fluxfile, gratcode):
import pdb
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.widgets import Cursor
from astropy.io import fits
from tmath.wombat.get_screen_size import get_screen_size
from tmath.wombat.getmswave import getmswave
from tmath.wombat.inputter_single import inputter_single
from tmath.wombat.inputter import inputter
from tmath.wombat.womscipyrebin import womscipyrebin
from tmath.pydux.obs_extinction import obs_extinction
from tmath.pydux.wave_telluric import wave_telluric
from tmath.pydux.fitspl import fitspl
from tmath.pydux.finalscaler import finalscaler
from tmath.pydux.abcalc import abcalc
from tmath.pydux.pacheck import pacheck
screen_width, screen_height = get_screen_size()
plt.ion()
screenpos = '+{}+{}'.format(int(screen_width * 0.2),
int(screen_height * 0.05))
fig = plt.figure()
fig.canvas.manager.window.wm_geometry(screenpos)
fig.canvas.set_window_title('Flux Star')
fig.set_size_inches(18, 12)
# turns off key stroke interaction
fig.canvas.mpl_disconnect(fig.canvas.manager.key_press_handler_id)
# this should bring the window to the top, but it doesn't
wm = plt.get_current_fig_manager()
#fig.canvas.manager.window.attributes('-topmost', 1)
blah = wm.window.attributes('-topmost', 1)
#plt.pause(0.2)
#fig.canvas.manager.window.attributes('-topmost', 0)
blah = wm.window.attributes('-topmost', 0)
#extinction terms from Allen, 3rd edition
extwave= [2400.,2600.,2800.,3000.,3200.,3400.,3600.,3800., \
4000.,4500.,5000.,5500.,6000.,6500.,7000.,8000., \
9000.,10000.,12000.,14000.]
extvals=[68.0,89.0,36.0,4.5,1.30,0.84,0.68,0.55,0.46,0.31, \
0.23,0.195,0.170,0.126,0.092,0.062,0.048,0.039, \
0.028,0.021]
fitsfile = fits.open(fluxfile)
rawdata = fitsfile[0].data
head = fitsfile[0].header
num_apertures = rawdata.shape[1]
wavearr = np.zeros((rawdata.shape[2], rawdata.shape[1]))
objectname = head['OBJECT']
airmass = float(head['AIRMASS'])
exptime = float(head['EXPTIME'])
head = pacheck(head)
if (exptime < 1):
exptime = 1.
observat = head['OBSERVAT'].strip().lower()
sitefactor = obs_extinction(observat)
for i in range(0, num_apertures):
wavearr[:, i] = getmswave(head, i)
if (wavearr[-1, 0] < 3000):
print('************************************************')
print('Spectrum not wavelength calibrated---bailing out')
print('************************************************')
sys.exit(1)
ap_choice = -1
if (num_apertures != 1):
axarr = fig.subplots(num_apertures, sharex=True)
fig.subplots_adjust(hspace=0)
for i in range(0, num_apertures):
x = wavearr[:, i]
y = rawdata[0, i, :]
axarr[i].clear()
plt.pause(0.01)
axarr[i].plot(x, y, drawstyle='steps-mid')
axarr[i].set_ylabel('Aperture {}'.format(i))
plt.pause(0.01)
while (ap_choice < 0) or (ap_choice > num_apertures - 1):
ap_choice = inputter(
'Which aperture do you want to use for the flux star? ', 'int',
False)
fig.clf()
else:
ap_choice = 0
ymin, ymax = finalscaler(rawdata[0, ap_choice, :])
fig.clf()
x1 = wavearr[:, ap_choice]
y1 = rawdata[1, ap_choice, :]
y0 = rawdata[0, ap_choice, :]
plt.plot(x1, y1, drawstyle='steps-mid', color='r')
plt.plot(x1, y0, drawstyle='steps-mid', color='k')
plt.pause(0.01)
plt.ylim([ymin, ymax])
plt.pause(0.01)
print('\nPlotting optimal as black, normal as red')
extract = inputter_single(
'Do you want to use (n)ormal or (o)ptimal extraction? ', 'no')
if (extract == 'o'):
star = rawdata[0, ap_choice, :]
else:
star = rawdata[1, ap_choice, :]
# fix IRAF weirdness where data can go negative in dispcor interpolation
star[np.where(star < 0)] = 0.01
wave = wavearr[:, ap_choice]
extinction = womscipyrebin(extwave, extvals, wave)
extfactor = np.exp(extinction * sitefactor * airmass)
star = star * extfactor
abcurve = abcalc(wave, objectname)
wdata = 10.0**(0.4 * abcurve)
fstar = star * wdata / exptime
print('Now fit the continuum manually\n')
plt.clf()
ax = fig.add_subplot(111)
cursor = Cursor(ax, useblit=True, color='k', linewidth=1)
airlimit = 1.5
splineresult = fitspl(wave, np.log10(fstar), (airmass > airlimit), fig)
splineresult = 10**(splineresult)
plt.cla()
plt.plot(wave, splineresult, drawstyle='steps-mid')
plt.pause(0.01)
delkeylist=['WAT0_001', 'WAT1_001', 'WAT2_001', 'WAT0_002', \
'WAT1_002', 'WAT2_002', 'WAT3_001', 'WAT2_003', \
'CTYPE1', 'CTYPE2', 'CTYPE3', 'CD1_1', 'CD2_2', \
'CD3_3', 'LTM1_1', 'LTM2_2', 'LTM3_3', 'WCSDIM']
for k in delkeylist:
try:
head.remove(k)
except KeyError:
pass
head.set('CRPIX1', 1)
head.set('CRVAL1', wave[0])
head.set('CDELT1', wave[1] - wave[0])
head.set('CTYPE1', 'LINEAR')
head.set('FLUXFILE', fluxfile)
outfile = 'fluxstar' + gratcode + '.fits'
print('Writing data to {}'.format(outfile))
outhdu = fits.PrimaryHDU(splineresult)
hdul = fits.HDUList([outhdu])
hdul[0].header = head.copy()
hdul.writeto(outfile, overwrite=True)
print('mkfluxstar')
print(fluxfile, gratcode)
return
def calibrate(objectlist, gratcode, secondord, gratcode2):
from astropy.io import fits
import numpy as np
from tmath.wombat.getmswave import getmswave
from tmath.wombat.womscipyrebin import womscipyrebin
from tmath.pydux.obs_extinction import obs_extinction
#extinction terms from Allen, 3rd edition
extwave= [2400.,2600.,2800.,3000.,3200.,3400.,3600.,3800., \
4000.,4500.,5000.,5500.,6000.,6500.,7000.,8000., \
9000.,10000.,12000.,14000.]
extvals=[68.0,89.0,36.0,4.5,1.30,0.84,0.68,0.55,0.46,0.31, \
0.23,0.195,0.170,0.126,0.092,0.062,0.048,0.039, \
0.028,0.021]
fluxfits = fits.open('fluxstar' + gratcode + '.fits')
fluxstar = fluxfits[0].data
fluxhead = fluxfits[0].header
fluxwavezero = float(fluxhead['CRVAL1'])
fluxwavedelt = float(fluxhead['CDELT1'])
fluxwave = np.arange(len(fluxstar)) * fluxwavedelt + fluxwavezero
fluxairmass = float(fluxhead['AIRMASS'])
fluxname = fluxhead['OBJECT']
try:
fluxnum = int(fluxhead['OBSNUM'])
except KeyError:
fluxnum = 0
if (secondord):
fluxfits2 = fits.open('fluxstar' + gratcode2 + '.fits')
fluxstar2 = fluxfits[0].data
fluxhead2 = fluxfits[0].header
fluxwavezero2 = float(fluxhead2['CRVAL1'])
fluxwavedelt2 = float(fluxhead2['CDELT1'])
fluxwave2 = np.arange(len(fluxstar2)) * fluxwavedelt2 + fluxwavezero2
fluxairmass2 = float(fluxhead2['AIRMASS'])
fluxname2 = fluxhead2['OBJECT']
try:
fluxnum2 = int(fluxhead2['OBSNUM'])
except KeyError:
fluxnum2 = 0
observat = fluxhead['OBSERVAT'].strip().lower()
sitefactor = obs_extinction(observat)
infile = open(objectlist, 'r')
for msfile in infile:
msfile = msfile.strip()
if ('.fits' not in msfile):
msfile = msfile + '.fits'
multifits = fits.open(msfile)
multispec = multifits[0].data
mshead = multifits[0].header
objectname = mshead['OBJECT']
print('The object is: {}'.format(objectname))
airmass = float(mshead['AIRMASS'])
exptime = float(mshead['EXPTIME'])
if (exptime < 1):
exptime = 1.0
num_apertures = multispec.shape[1]
num_bands = multispec.shape[0]
wavearr = np.zeros((multispec.shape[2], multispec.shape[1]))
if (secondord):
multispec2 = multispec.copy()
mshead2 = mshead.copy()
for i in range(0, num_apertures):
print('\nAperture {}:'.format(i + 1))
wave = getmswave(mshead, i)
extinction = womscipyrebin(extwave, extvals, wave)
extfactor = np.exp(extinction * sitefactor * airmass)
fluxstartmp = womscipyrebin(fluxwave, fluxstar, wave)
wdelt = wave[1] - wave[0]
for j in range(0, num_bands):
multispec[j,
i, :] = multispec[j, i, :] * extfactor #extinction
multispec[j, i, :] = multispec[j, i, :] / fluxstartmp #flux
multispec[j,
i, :] = multispec[j, i, :] / exptime #adjust to time
multispec[j,
i, :] = multispec[j, i, :] * 10**(-19.44) #AB->fnu
multispec[j, i, :] = multispec[
j, i, :] * 2.99792458e18 / wave / wave #fnu->flm
if (secondord):
fluxstartmp2 = womscipyrebin(fluxwave2, fluxstar2, wave)
for j in range(0, num_bands):
multispec2[
j, i, :] = multispec2[j, i, :] * extfactor #extinction
multispec2[j,
i, :] = multispec2[j, i, :] / fluxstartmp #flux
multispec2[
j,
i, :] = multispec2[j, i, :] / exptime #adjust to time
multispec2[j, i, :] = multispec2[j, i, :] * 10**(
-19.44) #AB->fnu
multispec2[j, i, :] = multispec2[
j, i, :] * 2.99792458e18 / wave / wave #fnu->flm
msfile = 'c' + gratcode + msfile
mshead.set('FLUX_Z', fluxairmass, 'airmass of flux standard')
mshead.set('FLUX_NUM', fluxnum, 'obsnum of flux standard')
mshead.set('FLUX_OBJ', fluxname, 'id of flux standard')
outhdu = fits.PrimaryHDU(multispec)
hdul = fits.HDUList([outhdu])
hdul[0].header = mshead.copy()
hdul.writeto(msfile, overwrite=True)
hdul.close()
if (secondord):
msfile = 'c' + gratcode2 + msfile
mshead2.set('FLX2_Z', fluxairmass,
'airmass of flux second ord. standard')
mshead2.set('FLX2_NUM', fluxnum,
'obsnum of flux second ord. standard')
mshead2.set('FLX2_OBJ', fluxname,
'id of flux second ord. standard')
outhdu = fits.PrimaryHDU(multispec2)
hdul = fits.HDUList([outhdu])
hdul[0].header = mshead2.copy()
hdul.writeto(msfile2, overwrite=True)
hdul.close()
infile.close()
fluxfits.close()
if (secondord):
fluxfits2.close()
print('calibrate')
print(objectlist, gratcode, secondord, gratcode2)
return
def mkbstar(bfile, gratcode):
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.widgets import Cursor
from astropy.io import fits
from tmath.wombat.get_screen_size import get_screen_size
from tmath.wombat.getmswave import getmswave
from tmath.wombat.inputter_single import inputter_single
from tmath.wombat.inputter import inputter
from tmath.wombat.yesno import yesno
from tmath.pydux.obs_extinction import obs_extinction
from tmath.pydux.wave_telluric import wave_telluric
from tmath.pydux.fitspl import fitspl
from tmath.pydux.bblo import bblo
from tmath.pydux.finalscaler import finalscaler
from tmath.pydux.pacheck import pacheck
screen_width, screen_height = get_screen_size()
plt.ion()
screenpos = '+{}+{}'.format(int(screen_width * 0.2),
int(screen_height * 0.05))
fig = plt.figure()
fig.canvas.manager.window.wm_geometry(screenpos)
fig.canvas.set_window_title('B Star')
fig.set_size_inches(18, 12)
# turns off key stroke interaction
fig.canvas.mpl_disconnect(fig.canvas.manager.key_press_handler_id)
# this should bring the window to the top, but it doesn't
wm = plt.get_current_fig_manager()
#fig.canvas.manager.window.attributes('-topmost', 1)
blah = wm.window.attributes('-topmost', 1)
#plt.pause(0.2)
#fig.canvas.manager.window.attributes('-topmost', 0)
blah = wm.window.attributes('-topmost', 0)
fitsfile = fits.open(bfile)
rawdata = fitsfile[0].data
head = fitsfile[0].header
num_apertures = rawdata.shape[1]
wavearr = np.zeros((rawdata.shape[2], rawdata.shape[1]))
objectname = head['OBJECT']
airmass = float(head['AIRMASS'])
exptime = float(head['EXPTIME'])
if (exptime < 1):
exptime = 1.
head = pacheck(head)
observat = head['OBSERVAT'].strip().lower()
sitefactor = obs_extinction(observat)
for i in range(0, num_apertures):
wavearr[:, i] = getmswave(head, i)
if (wavearr[-1, 0] < 3000):
print('************************************************')
print('Spectrum not wavelength calibrated---bailing out')
print('************************************************')
sys.exit(1)
ap_choice = -1
if (np.mean(rawdata[0, 0, :]) < 1e-7):
rawdata = rawdata * 1e15
# scale to rational numbers for fit (rational as in sane,
# not opposed to irrational)
if (num_apertures != 1):
axarr = fig.subplots(num_apertures, sharex=True)
fig.subplots_adjust(hspace=0)
for i in range(0, num_apertures):
x = wavearr[:, i]
y = rawdata[0, i, :]
axarr[i].clear()
plt.pause(0.01)
axarr[i].plot(x, y, drawstyle='steps-mid')
axarr[i].set_ylabel('Aperture {}'.format(i))
plt.pause(0.01)
while (ap_choice < 0) or (ap_choice > num_apertures - 1):
ap_choice = inputter(
'Which aperture do you want to use for the B star? ', 'int',
False)
fig.clf()
else:
ap_choice = 0
ymin, ymax = finalscaler(rawdata[0, ap_choice, :])
fig.clf()
x1 = wavearr[:, ap_choice]
y1 = rawdata[1, ap_choice, :]
y0 = rawdata[0, ap_choice, :]
plt.plot(x1, y1, drawstyle='steps-mid', color='r')
plt.plot(x1, y0, drawstyle='steps-mid', color='k')
plt.pause(0.01)
plt.ylim([ymin, ymax])
plt.pause(0.01)
print('\nPlotting optimal as black, normal as red')
extract = inputter_single(
'Do you want to use (n)ormal or (o)ptimal extraction? ', 'no')
if (extract == 'o'):
bstar = rawdata[0, ap_choice, :]
else:
bstar = rawdata[1, ap_choice, :]
# fix IRAF weirdness where data can go negative in dispcor interpolation
bstar[np.where(bstar < 0)] = 0.01
wave = wavearr[:, ap_choice]
print('\nAirmass: {}\n'.format(airmass))
airlimit = 0.5
while (airlimit < 1.0) or (airlimit > 10.):
airlimit = inputter('Above what airmass is considered high? ', 'float',
False)
print('\nNow fit the continuum manually\n')
plt.clf()
ax = fig.add_subplot(111)
cursor = Cursor(ax, useblit=True, color='k', linewidth=1)
airlimit = 1.5
splineresult = fitspl(wave, np.log10(bstar), (airmass > airlimit), fig)
splineresult = 10**(splineresult)
plt.cla()
plt.plot(wave, splineresult, drawstyle='steps-mid')
plt.pause(0.01)
bstar = bstar / splineresult
if (airmass > airlimit):
loc = wave_telluric(wave, 'high')
else:
loc = wave_telluric(wave, 'low')
#invert loc and convert all good sections to np.nan so they won't plot
loc = np.invert(loc)
bstar[loc] = 1.0
bstar[np.where(bstar > 1.)] = 1.0
bstar[np.where(bstar <= 0.)] = 0.01
plt.cla()
plt.plot(wave, bstar, drawstyle='steps-mid')
plt.pause(0.01)
print('\nDo you want to blotch the B-star?')
blotch = yesno('n')
if (blotch == 'y'):
bstar = bblo(wave, bstar, (airmass > airlimit), fig)
delkeylist=['WAT0_001', 'WAT1_001', 'WAT2_001', 'WAT0_002', \
'WAT1_002', 'WAT2_002', 'WAT3_001', 'WAT2_003', \
'CTYPE1', 'CTYPE2', 'CTYPE3', 'CD1_1', 'CD2_2', \
'CD3_3', 'LTM1_1', 'LTM2_2', 'LTM3_3', 'WCSDIM']
for k in delkeylist:
try:
head.remove(k)
except KeyError:
pass
plt.cla()
plt.plot(wave, bstar, drawstyle='steps-mid')
plt.pause(0.01)
head.set('CRPIX1', 1)
head.set('CRVAL1', wave[0])
head.set('CDELT1', wave[1] - wave[0])
head.set('CTYPE1', 'LINEAR')
outfile = 'bstar' + gratcode + '.fits'
print('Writing data to {}'.format(outfile))
outhdu = fits.PrimaryHDU(bstar)
hdul = fits.HDUList([outhdu])
hdul[0].header = head.copy()
hdul.writeto(outfile, overwrite=True)
print('mkbstar')
print(bfile, gratcode)
return
def calibrate(objectlist, gratcode, secondord, gratcode2, answer_flux='y'):
from astropy.io import fits
import numpy as np
import matplotlib.pyplot as plt
import inspect
from tmath.pydux.xcor import xcor
from tmath.pydux.envelope import envelope
from tmath.pydux.congrid import congrid
from tmath.wombat.getmswave import getmswave
from tmath.wombat.womscipyrebin import womscipyrebin
from tmath.pydux.scipyrebinsky import scipyrebinsky
from tmath.pydux.obs_extinction import obs_extinction
from tmath.wombat.yesno import yesno
from tmath.wombat.inputter import inputter
from tmath.wombat.womget_element import womget_element
from tmath.wombat.get_screen_size import get_screen_size
#extinction terms from Allen, 3rd edition
extwave= [2400.,2600.,2800.,3000.,3200.,3400.,3600.,3800., \
4000.,4500.,5000.,5500.,6000.,6500.,7000.,8000., \
9000.,10000.,12000.,14000.]
extvals=[68.0,89.0,36.0,4.5,1.30,0.84,0.68,0.55,0.46,0.31, \
0.23,0.195,0.170,0.126,0.092,0.062,0.048,0.039, \
0.028,0.021]
fluxfits = fits.open('fluxstar' + gratcode + '.fits')
fluxstar = fluxfits[0].data
fluxhead = fluxfits[0].header
fluxwavezero = float(fluxhead['CRVAL1'])
fluxwavedelt = float(fluxhead['CDELT1'])
fluxwave = np.arange(len(fluxstar)) * fluxwavedelt + fluxwavezero
fluxairmass = float(fluxhead['AIRMASS'])
fluxname = fluxhead['OBJECT']
try:
fluxnum = int(fluxhead['OBSNUM'])
except KeyError:
fluxnum = 0
if (secondord):
fluxfits2 = fits.open('fluxstar' + gratcode2 + '.fits')
fluxstar2 = fluxfits[0].data
fluxhead2 = fluxfits[0].header
fluxwavezero2 = float(fluxhead2['CRVAL1'])
fluxwavedelt2 = float(fluxhead2['CDELT1'])
fluxwave2 = np.arange(len(fluxstar2)) * fluxwavedelt2 + fluxwavezero2
fluxairmass2 = float(fluxhead2['AIRMASS'])
fluxname2 = fluxhead2['OBJECT']
try:
fluxnum2 = int(fluxhead2['OBSNUM'])
except KeyError:
fluxnum2 = 0
observat = fluxhead['OBSERVAT'].strip().lower()
sitefactor = obs_extinction(observat)
infile = open(objectlist, 'r')
for msfile in infile:
msfile = msfile.strip()
if ('.fits' not in msfile):
msfile = msfile + '.fits'
multifits = fits.open(msfile)
multispec = multifits[0].data
mshead = multifits[0].header
objectname = mshead['OBJECT']
print('The object is: {}'.format(objectname))
airmass = float(mshead['AIRMASS'])
exptime = float(mshead['EXPTIME'])
if (exptime < 1):
exptime = 1.0
num_apertures = multispec.shape[1]
num_bands = multispec.shape[0]
wavearr = np.zeros((multispec.shape[2], multispec.shape[1]))
if (secondord):
multispec2 = multispec.copy()
mshead2 = mshead.copy()
for i in range(0, num_apertures):
print('\nAperture {}:'.format(i + 1))
wave = getmswave(mshead, i)
extinction = womscipyrebin(extwave, extvals, wave)
extfactor = np.exp(extinction * sitefactor * airmass)
fluxstartmp = womscipyrebin(fluxwave, fluxstar, wave)
wdelt = wave[1] - wave[0]
#TESTING applying shift before flux cal
reduxdir = inspect.getfile(xcor)
reduxdir = reduxdir.rsplit('/', 1)[0] + '/'
kecksky=['keck','gemini-north','gemini-n','gemini-south','gemini-s', \
'soar','ctio','vlt','lco','lco-imacs','lapalma']
licksky = ['lick', 'kpno', 'flwo', 'mmto', 'sso']
if (observat in kecksky):
mskyfile = reduxdir + 'kecksky.fits'
elif (observat in licksky):
mskyfile = reduxdir + 'licksky.fits'
else:
print('\nCannot find mastersky file and observatory unknown\n')
mskyfile = getfitsfile('master sky', '.fits')
print('Using {} as PRELIMINARY master sky'.format(
mskyfile.split('/')[-1]))
mskyfits = fits.open(mskyfile)
mskydata = mskyfits[0].data
mskyhead = mskyfits[0].header
mskywavezero = float(mskyhead['CRVAL1'])
mskywavedelt = float(mskyhead['CDELT1'])
mskywave = np.arange(len(mskydata)) * mskywavedelt + mskywavezero
if (np.abs(np.mean(mskydata)) < 1e-7):
mskydata = mskydata * 1e15
num_bands = multispec.shape[0]
skyband = 2
if (num_bands == 2):
skyband = 1
sky = multispec[skyband, i, :]
envelope_size = 25
mx, mn = envelope(sky, envelope_size)
skycont = congrid(mn, (len(sky), ), minusone=True)
sky = sky - skycont
if (np.abs(np.mean(sky)) < 1.e-7):
sky = sky * 1.e15
# print(len(mskywave),len(mskydata))
msky = scipyrebinsky(mskywave, mskydata, wave)
xfactor = 10
maxlag = 200
# shift=xcor(msky[50:-50],sky[50:-50],xfactor,maxlag)
if 'kast' in fluxhead.get('VERSION', ''):
shift = xcor(msky[50:-50], sky[50:-50], xfactor, maxlag)
else:
shift = xcor(msky, sky, xfactor, maxlag)
angshift = shift * wdelt
print(
'Potential preliminary shift of {} angstroms'.format(angshift))
print('Obj wave without shift: ', wave[0])
#The following code applies the calculated shift prior to fitting the flux star
#If the target is an object then the object is shifted prior to applying the flux star
# answer_flux = input('Is this a master standard star? y/[n]: ') or 'n'
# if answer_flux == 'y':
# fluxwave=fluxwave+angshift
# wave = wave+angshift
# #Testing only for standard star
# skyshiftdone=False
# while (not skyshiftdone):
# print('Is this ok?')
# answer=yesno('y')
# if (answer == 'n'):
# #undo shifts
# if answer_flux == 'y':
# fluxwave=fluxwave-angshift
# wave = wave-angshift
# angshift=inputter('Enter desired shift in Angstroms: ','float',False)
# if answer_flux == 'y':
# fluxwave=fluxwave+angshift
# wave = wave+angshift
# else:
# skyshiftdone = True
##
# skyshiftdone=False
# npixsky2=len(sky)//2
# screen_width, screen_height=get_screen_size()
# screenpos='+{}+{}'.format(int(screen_width*0.2),int(screen_height*0.05))
# fig=plt.figure()
# fig.canvas.manager.window.wm_geometry(screenpos)
# fig.canvas.set_window_title('Final Reductions')
# fig.set_size_inches(8,5)
# fig.canvas.mpl_disconnect(fig.canvas.manager.key_press_handler_id)
# msky_max = np.max(msky[npixsky2-1:])
# sky_max = np.max(sky[npixsky2-1:])
# scale = sky_max/msky_max
# while (not skyshiftdone):
# plt.clf()
# axarr=fig.subplots(2)
# # fig.subplots_adjust(hspace=0)
# waveplus=wave-angshift
# axarr[0].plot(waveplus[0:npixsky2],scale*msky[0:npixsky2], \
# drawstyle='steps-mid',color='k')
# axarr[0].plot(wave[0:npixsky2],sky[0:npixsky2], \
# drawstyle='steps-mid',color='r')
# axarr[1].plot(waveplus[npixsky2-1:],scale*msky[npixsky2-1:], \
# drawstyle='steps-mid',color='k')
# axarr[1].plot(wave[npixsky2-1:],sky[npixsky2-1:], \
# drawstyle='steps-mid',color='r')
# plt.pause(0.01)
# print('\nBlack spectrum = master sky')
# print('Red spectrum = object sky shifted to match master sky')
# print('Is this ok?')
# answer=yesno('y')
# if (answer == 'n'):
# if answer_flux == 'y':
# fluxwave=fluxwave-angshift
# wave=wave- angshift
# angshift=inputter('Enter desired shift in Angstroms: ','float',False)
# if answer_flux == 'y':
# fluxwave=fluxwave+angshift
# wave=wave+angshift
# else:
# skyshiftdone = True
# plt.close()
# print ('Obj wave with shift: ', wave[0])
# mshead.set('CRVAL1', wave[0])
# mshead.set('CDELT1', wave[1] - wave[0])
# print ('Fluxwave start', fluxwave[0])
if answer_flux == 'y':
print('Changing Flux Star Wavelength')
fluxhead.set('CRVAL1', fluxwave[0])
fluxhead.set('CDELT1', fluxwave[1] - fluxwave[0])
outfile = 'fluxstar' + gratcode + '.fits'
print('Updating wavelength data to {}'.format(outfile))
outhdu = fits.PrimaryHDU(fluxstar)
hdul = fits.HDUList([outhdu])
hdul[0].header = fluxhead.copy()
hdul.writeto(outfile, overwrite=True)
# fluxfits=fits.open(outfile)
# fluxstar=fluxfits[0].data
# fluxhead=fluxfits[0].header
# fluxwavezero=float(fluxhead['CRVAL1'])
# print (fluxwavezero)
fluxstartmp = womscipyrebin(fluxwave, fluxstar, wave)
########################################
#testing
# mx1=womget_element(wave,5500)
# mx2=womget_element(wave,6050)
# fx1=womget_element(fluxwave,5500)
# fx2=womget_element(fluxwave,5050)
mx1 = 0
mx2 = 300
fx1 = 0
fx2 = 300
# mx1=-1000
# mx2=-50
# fx1=-1000
# fx2=-50
test = extfactor[mx1:mx2] * multispec[0, i, :][mx1:mx2]
scale1 = 1. / np.median(test)
scale2 = 1. / np.median(fluxstartmp[fx1:fx2])
# print (xcor(scale1*multispec[0,i,:][mx1:mx2],scale2*fluxstar[fx1:fx2],10,200))
fig = plt.figure()
plt.clf()
plt.plot(wave[mx1:mx2],
scale1 * test,
drawstyle='steps-mid',
color='r')
plt.plot(fluxwave[fx1:fx2],
scale2 * fluxstar[fx1:fx2],
drawstyle='steps-mid',
color='k')
plt.pause(0.01)
check = inputter('Check plot [enter when done]: ', 'string', False)
plt.close()
#
for j in range(0, num_bands):
multispec[j,
i, :] = multispec[j, i, :] * extfactor #extinction
multispec[j, i, :] = multispec[j, i, :] / fluxstartmp #flux
multispec[j,
i, :] = multispec[j, i, :] / exptime #adjust to time
multispec[j,
i, :] = multispec[j, i, :] * 10**(-19.44) #AB->fnu
multispec[j, i, :] = multispec[
j, i, :] * 2.99792458e18 / wave / wave #fnu->flm
if (secondord):
fluxstartmp2 = womscipyrebin(fluxwave2, fluxstar2, wave)
for j in range(0, num_bands):
multispec2[
j, i, :] = multispec2[j, i, :] * extfactor #extinction
multispec2[j,
i, :] = multispec2[j, i, :] / fluxstartmp #flux
multispec2[
j,
i, :] = multispec2[j, i, :] / exptime #adjust to time
multispec2[j, i, :] = multispec2[j, i, :] * 10**(
-19.44) #AB->fnu
multispec2[j, i, :] = multispec2[
j, i, :] * 2.99792458e18 / wave / wave #fnu->flm
msfile = 'c' + gratcode + msfile
mshead.set('FLUX_Z', fluxairmass, 'airmass of flux standard')
mshead.set('FLUX_NUM', fluxnum, 'obsnum of flux standard')
mshead.set('FLUX_OBJ', fluxname, 'id of flux standard')
outhdu = fits.PrimaryHDU(multispec)
hdul = fits.HDUList([outhdu])
hdul[0].header = mshead.copy()
hdul.writeto(msfile, overwrite=True)
hdul.close()
if (secondord):
msfile = 'c' + gratcode2 + msfile
mshead2.set('FLX2_Z', fluxairmass,
'airmass of flux second ord. standard')
mshead2.set('FLX2_NUM', fluxnum,
'obsnum of flux second ord. standard')
mshead2.set('FLX2_OBJ', fluxname,
'id of flux second ord. standard')
outhdu = fits.PrimaryHDU(multispec2)
hdul = fits.HDUList([outhdu])
hdul[0].header = mshead2.copy()
hdul.writeto(msfile2, overwrite=True)
hdul.close()
infile.close()
fluxfits.close()
if (secondord):
fluxfits2.close()
print('calibrate')
print(objectlist, gratcode, secondord, gratcode2)
return