def womrebindriver(hop, mode):
"""input info to call womrebin functions"""
import matplotlib.pyplot as plt
import numpy as np
from tmath.wombat.inputter import inputter
from tmath.wombat.waveparse import waveparse
from tmath.wombat.yesno import yesno
from tmath.wombat.womashrebin import womashrebin
from tmath.wombat.womscipyrebin import womscipyrebin
print('Current A/pix is {}'.format(hop[0].wave[1] - hop[0].wave[0]))
print('Wavelength rage: {} to {}'.format(hop[0].wave[0], hop[0].wave[-1]))
plt.cla()
plt.plot(hop[0].wave, hop[0].flux, drawstyle='steps-mid')
plt.xlabel('Wavelength')
plt.ylabel('Flux')
plt.title(hop[0].obname)
done = False
while (not done):
newdelt=inputter('Rebin to how many Angstroms per pixel? ', \
'float',False)
waveb, waver = waveparse()
if (waveb > waver):
waveb, waver = waver, waveb
if (newdelt > 0):
newbin = (waver - waveb) / newdelt + 1.0
frac, whole = np.modf(newbin)
if (frac > 0.000001):
print('NON-INTEGER number of bins')
testwave = newdelt * whole + waveb
print('Closest match is: {} to {}'.format(waveb, testwave))
print('Would you like this wavelength range?')
answer = yesno('y')
if (answer == 'y'):
waver = testwave
done = True
else:
print('Rebinning to {} A/pix, {} to {}'.format(newdelt,waveb,\
waver))
print('Is this OK?')
answer = yesno('y')
if (answer == 'y'):
done = True
nwave = np.arange(0, whole) * newdelt + waveb
if (mode == 'ash'):
nflux = womashrebin(hop[0].wave, hop[0].flux, nwave)
nvar = womashrebin(hop[0].wave, hop[0].var, nwave)
else:
nflux = womscipyrebin(hop[0].wave, hop[0].flux, nwave)
nvar = womscipyrebin(hop[0].wave, hop[0].var, nwave)
print('Overplotting rebinned spectrum')
plt.cla()
plt.plot(hop[0].wave, hop[0].flux, drawstyle='steps-mid')
plt.plot(nwave, nflux, drawstyle='steps-mid')
#FIX header
hop[0].wave = nwave.copy()
hop[0].flux = nflux.copy()
hop[0].var = nvar.copy()
return hop
def womblueshift(hop):
"""add redshift to spectrum"""
import numpy as np
from tmath.wombat.yesno import yesno
from tmath.wombat.inputter_single import inputter_single
from tmath.wombat.inputter import inputter
from tmath.wombat.womrebindriver import womrebindriver
light_speed = 2.99792458e5
print('Current A/pix is {}'.format(hop[0].wave[1] - hop[0].wave[0]))
print('\nWavelength range: {} to {}\n'.format(hop[0].wave[0],
hop[0].wave[-1]))
answer = inputter_single('Remove redshift in (z) or (k)m/s? (z/k) ', 'zk')
z = inputter('Enter the desired blueshift (positive is away from us): ',
'float', False)
if (answer == 'k'):
z = np.sqrt((1.0 + z / c) / (1.0 - z / c)) - 1.0
hop[0].wave = hop[0].wave * (1.0 + z)
print('\nNew wavelength range: {} to {}\n'.format(hop[0].wave[0],
hop[0].wave[-1]))
print('Rebin spectrum?')
rebin = yesno('n')
if (rebin == 'y'):
hop = womrebindriver(hop, 'scipy')
else:
pass
#FIX header
return hop
def womreddening(hop):
"""redden or deredden with various reddening laws"""
import matplotlib.pyplot as plt
import extinction
from tmath.wombat.inputter_single import inputter_single
from tmath.wombat.inputter import inputter
from tmath.wombat.yesno import yesno
r_v=3.1
print('Redden or deredden a spectrum')
plt.cla()
plt.plot(hop[0].wave,hop[0].flux,drawstyle='steps-mid',color='k')
plt.xlabel('Wavelength')
plt.ylabel('Flux')
plt.title(hop[0].obname)
flux=hop[0].flux.copy()
action=inputter_single('(r)edden or (d)eredden the spectrum? (r/d) ', 'rd')
print(' ')
type=inputter_single('Do you want to enter the (c)olor excess, or (v)isual extinction? ','cv')
print(' ')
if (type == 'v'):
av=inputter('Enter A_V in magnitudes: ','float',False)
else:
ebv=inputter('Enter E(B-V) in magnitudes: ','float',False)
av=r_v*ebv
print(' ')
print('Do you want to use: ')
print('(c)ardelli, Clayton, Mathis 1989')
print("(o)'donnell 1994")
print('(f)itzpatrick 1999\n')
method=inputter_single('(c/o/f) ','cof')
if (action == 'r'):
if (method == 'c'):
newflux=extinction.apply(extinction.ccm89(hop[0].wave,av,r_v),flux)
elif (method == 'o'):
newflux=extinction.apply(extinction.odonnell94(hop[0].wave,av,r_v),flux)
else:
newflux=extinction.apply(extinction.fitzpatrick99(hop[0].wave,av,r_v),flux)
else:
if (method == 'c'):
ext=extinction.ccm89(hop[0].wave,av,r_v)
elif (method == 'o'):
ext=extinction.odonnell94(hop[0].wave,av,r_v)
else:
ext=extinction.fitzpatrick99(hop[0].wave,av,r_v)
newflux=flux*10**(0.4*ext)
plt.plot(hop[0].wave,newflux,drawstyle='steps-mid',color='r')
print('\nOriginal spectrum in black, red/dered in red\n')
print('Is this OK?\n')
answer=yesno('y')
if (answer == 'y'):
hop[0].flux=newflux.copy()
print('\nActive spectrum now changed')
else:
print('\nSorry to disappoint you, active spectrum unchanged')
return hop
def womplot(hop):
import matplotlib.pyplot as plt
from tmath.wombat.yesno import yesno
from tmath.wombat.wshow import wshow
plt.cla()
plt.plot(hop[0].wave, hop[0].flux, drawstyle='steps-mid')
plt.xlabel('Wavelength')
if (hop[0].wave[0] < 0):
plt.xlabel('Velocity')
plt.ylabel('Flux')
plt.title(hop[0].obname)
plt.pause(0.01)
wshow()
print('Change scale?')
answer = yesno('n')
if (answer == 'y'):
xmin, xmax = plt.xlim()
ymin, ymax = plt.ylim()
done = False
while (not done):
print('Click corners of box to change plot scale')
newlims = plt.ginput(2, timeout=-1)
xmin = newlims[0][0]
ymin = newlims[0][1]
xmax = newlims[1][0]
ymax = newlims[1][1]
plt.cla()
plt.plot(hop[0].wave, hop[0].flux, drawstyle='steps-mid')
plt.xlabel('Wavelength')
if (hop[0].wave[0] < 0):
plt.xlabel('Velocity')
plt.ylabel('Flux')
plt.title(hop[0].obname)
plt.xlim([xmin, xmax])
plt.ylim([ymin, ymax])
print('Is this OK?')
loopanswer = yesno('y')
if (loopanswer == 'y'):
done = True
return hop
def womwaverange(wave, flux, mode):
import matplotlib.pyplot as plt
from tmath.wombat.waveparse import waveparse
from tmath.wombat.womget_element import womget_element
from tmath.wombat.inputter_single import inputter_single
from tmath.wombat.yesno import yesno
from tmath.wombat.wshow import wshow
if (mode == 'none'):
print('Enter method to select wavelength range')
mode = inputter_single(
'Enter (w)avelengths or mark with the (m)ouse? (w/m) ', 'wm')
print(mode)
print('Spectrum runs from {} to {}.'.format(wave[0], wave[-1]))
plt.cla()
plt.plot(wave, flux, drawstyle='steps-mid')
plt.ylabel('Flux')
plt.xlabel('Wavelength')
wshow()
done = False
while (not done):
if (mode == 'w'):
waveb, waver = waveparse()
else:
pickpoints = plt.ginput(2, timeout=-1)
waveb = pickpoints[0][0]
waver = pickpoints[1][0]
if (waveb > waver):
waveb, waver = waver, waveb
indexblue = womget_element(wave, waveb)
indexred = womget_element(wave, waver)
print('Range selected: {} to {}'.format(wave[indexblue],
wave[indexred]))
plt.plot(wave[indexblue:indexred+1],flux[indexblue:indexred+1], \
drawstyle='steps-mid',color='r')
plt.pause(0.01)
print('Is this range correct?')
answer = yesno('y')
if (answer == 'n'):
plt.cla()
plt.plot(wave, flux, drawstyle='steps-mid')
plt.ylabel('Flux')
plt.xlabel('Wavelength')
wshow()
else:
done = True
return wave[indexblue:indexred + 1], flux[indexblue:indexred + 1], mode
def womexam(hop):
"""print spectrum bin values"""
from tmath.wombat.womwaverange import womwaverange
from tmath.wombat.womget_element import womget_element
from tmath.wombat.yesno import yesno
done = False
while (not done):
answer = 'y'
wave, flux, mode = womwaverange(hop[0].wave, hop[0].flux, 'none')
indexblue = womget_element(hop[0].wave, wave[0])
indexred = womget_element(hop[0].wave, wave[-1])
var = hop[0].var[indexblue:indexred + 1]
if (len(wave) > 30):
print('This will print out {} values'.format(len(wave)))
print('Do you really want to do that?')
answer = yesno('n')
if (answer == 'y'):
done = True
print('\nWave Flux')
for i, _ in enumerate(wave):
print('{} {} {}'.format(wave[i], flux[i], var[i]))
return hop
def final(objectlist, gratcode, secondord, gratcode2, user):
import matplotlib.pyplot as plt
from matplotlib import gridspec
import numpy as np
from datetime import datetime
import os, pdb
import inspect
import glob
import math
from astropy.io import fits
from astropy import units as u
from astropy.coordinates import SkyCoord
# from astropy.time import Time
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.womcatfinal import womcatfinal
from tmath.pydux.scipyrebinsky import scipyrebinsky
from tmath.wombat.yesno import yesno
from tmath.wombat.womashrebin import womashrebin
from tmath.wombat.wominterpofluxconserving import interpo_flux_conserving
from tmath.wombat.womspectres import spectres
from tmath.pydux.getfitsfile import getfitsfile
from tmath.pydux.pacheck import pacheck
from tmath.pydux.jdcnv import jdcnv
from tmath.pydux.baryvel import baryvel
from tmath.pydux.finalscaler import finalscaler
from tmath.pydux.envelope import envelope
from tmath.pydux.congrid import congrid
from tmath.pydux.xcor import xcor
from tmath.pydux.telluric_remove import telluric_remove
from tmath.pydux.waveparse import waveparse
from tmath.pydux.parsehourangle import parsehourangle
from tmath.pydux import RADEG
plt.ion()
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)
# 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)
bstarfits = fits.open('bstar' + gratcode + '.fits')
bstarstar = bstarfits[0].data
bstarhead = bstarfits[0].header
bstarwavezero = float(bstarhead['CRVAL1'])
bstarwavedelt = float(bstarhead['CDELT1'])
bstarwave = np.arange(len(bstarstar)) * bstarwavedelt + bstarwavezero
bstarairmass = float(bstarhead['AIRMASS'])
bstarname = bstarhead['OBJECT']
try:
bstarnum = int(bstarhead['OBSNUM'])
except KeyError:
bstarnum = 0
if (secondord):
bstarfits2 = fits.open('bstarstar' + gratcode2 + '.fits')
bstarstar2 = bstarfits[0].data
bstarhead2 = bstarfits[0].header
bstarwavezero2 = float(bstarhead2['CRVAL1'])
bstarwavedelt2 = float(bstarhead2['CDELT1'])
bstarwave2 = np.arange(
len(bstarstar2)) * bstarwavedelt2 + bstarwavezero2
bstarairmass2 = float(bstarhead2['AIRMASS'])
bstarname2 = bstarhead2['OBJECT']
try:
bstarnum2 = int(bstarhead2['OBSNUM'])
except KeyError:
bstarnum2 = 0
observat = bstarhead['OBSERVAT'].strip().lower()
#reduxdir=os.environ['PY_REDUX']
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 master sky'.format(mskyfile))
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
print('\nHello {}\n'.format(user))
lat_dict = {
'keck': 19.8283,
'gemini-north': 19.8238,
'gemini-south': -30.228,
'gemini-n': 19.8238,
'gemini-s': -30.228,
'soar': -30.228,
'kpno': 31.9633,
'lick': 37.3414,
'palomar': 33.35611,
'mcdonald': 30.6717,
'flwo': 31.681,
'mmto': 31.688,
'sso': -31.2734,
'vlt': -24.6254,
'lco': -29.01,
'lco-imacs': -29.01,
'lapalma': 28.75833,
'ctio': -30.16894
}
infile = open(objectlist, 'r')
objname = ''
secondtime = False
seconddone = False
for inputfile in infile:
inputfile = inputfile.strip()
if ('.fits' not in inputfile):
inputfile = inputfile + '.fits'
multifits = fits.open('c' + gratcode + inputfile)
multispec = multifits[0].data
mshead = multifits[0].header
num_apertures = multispec.shape[1]
num_bands = multispec.shape[0]
wavearr = np.zeros((multispec.shape[2], multispec.shape[1]))
if (secondord):
multifits2 = fits.open('c' + gratcode2 + inputfile)
multispec2 = multifits2[0].data
mshead2 = multifits2[0].header
pacheck(mshead)
objectname = mshead['OBJECT']
print('The object is: {}'.format(objectname))
observat = mshead['OBSERVAT'].strip().lower()
airmass = float(mshead['AIRMASS'])
if (airmass < 1):
airmass = 1.0
stringra = mshead['RA']
stringdec = mshead['DEC']
geminilist = ['gemini-north', 'gemini-south', 'gemini-n', 'gemini-s']
if (observat) in geminilist:
ra = float(stringra)
dec = float(stringdec)
else:
coords = SkyCoord(stringra, stringdec, unit=(u.hourangle, u.deg))
ra = coords.ra.deg
dec = coords.dec.deg
ra = ra / RADEG
dec = dec / RADEG
haheader = mshead['HA']
ha = parsehourangle(haheader)
ha = ha * (360. / 24.) / RADEG
if (observat in lat_dict):
latitude = lat_dict[observat]
else:
print('Observatory Unknown!!!!!!!')
latitude = 0.0
latitude = latitude / RADEG
# Get Julian date and Earth's velocity
#epoch=float(mshead['EPOCH'])
date = mshead['DATE-OBS'].strip()
# get year,month,day from ISO Y2K format YYYY-MM-DDThh:mm:ss.ssss
# the time following T is optional, so we get T from UTMIDDLE
if (date[4] == '-'):
year = int(date.split('-')[0])
month = int(date.split('-')[1])
day = int(date.split('-')[2].split('T')[0])
printdate = '{}{:02d}{:02d}'.format(year, month, day)
else:
# Old date format DD/MM/YY
year = int(date[6:8])
month = int(date[3:5])
day = int(date[0:2])
# try to catch old format written after 2000
# good until 2050, by which time no one should
# be doing this
if (year > 50):
year = year + 1900
else:
year = year + 2000
printdate = '{}{:02d}{:02d}'.format(year, month, day)
try:
ut = mshead['UTMIDDLE'].strip()
except KeyError:
ut = mshead['UT'].strip()
if ('T' in ut):
ut = ut.split('T')[1]
# some UT/UTMIDDLE values are ISO format
hour = int(ut.split(':')[0])
minute = int(ut.split(':')[1])
second = float(ut.split(':')[2])
julian = jdcnv(year, month, day,
(hour + (minute / 60.) + (second / 3600.)))
vh, vb = baryvel(julian)
# Earth's velocity toward object
v=vb[0]*np.cos(dec)*np.cos(ra) + vb[1]*np.cos(dec)*np.sin(ra) \
+ vb[2]*np.sin(dec)
# Correct for earth's rotation.
# Note that this isn't strictly correct because ha is set to
# the beginning of the observation, while it really should be
# the middle. But this is a small difference and doesn't affect
# the results in any way that we would notice...
v = v - (0.4651 * np.cos(latitude) * np.sin(ha) * np.cos(dec))
print(
'\nThe velocity of the Earth toward the target is {} km/s'.format(
v))
print('\nThere are {} apertures in the spectrum.\n'.format(
num_apertures))
# clean up header
""" 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:
mshead.remove(k)
except KeyError:
pass """
waveb = None
waver = None
bshift = None
for i in range(0, num_apertures):
# plt.close()
# fig=plt.figure()
# plt.plot(multispec[0,i,:], drawstyle='steps-mid',color='r')
# plt.plot(multispec[1,i,:], drawstyle='steps-mid',color='k')
# plt.xlim(1750,1900)
# plt.pause(0.01)
# print('Check plot')
# answer=yesno('y')
print('\nAperture {}:'.format(i + 1))
wave = getmswave(mshead, i)
print(wave[0], wave[-1])
wdelt = wave[1] - wave[0]
mean = np.mean(multispec[0, i, :])
ymin, ymax = finalscaler(multispec[0, i, :])
# plt.clf()
gs = gridspec.GridSpec(2, 1, height_ratios=[4, 1])
ax0 = plt.subplot(gs[0])
ax1 = plt.subplot(gs[1])
fig.subplots_adjust(hspace=0)
ax0.plot(wave,
multispec[1, i, :],
drawstyle='steps-mid',
color='r')
ax0.plot(wave,
multispec[0, i, :],
drawstyle='steps-mid',
color='k')
# ax0.plot(multispec[0,i,:],multispec[2,i,:],drawstyle='steps-mid',color='r')
# ax0.plot(multispec[0,i,:],multispec[1,i,:],drawstyle='steps-mid',color='k')
plt.pause(0.01)
ax0.set_ylim((ymin, ymax))
ax1.semilogy(wave,np.abs(multispec[1,i,:]-multispec[0,i,:])/mean, \
drawstyle='steps-mid',color='k')
ax0.set_ylabel('Flux')
ax1.set_ylabel('Log of fractional residuals')
ax1.set_xlabel('Wavelength')
plt.pause(0.01)
print('\nPlotting optimal as black, normal as red\n')
extract = inputter_single(
'Do you want to use the (n)ormal or the (o)ptimal extraction? ',
'no')
if (extract == 'o'):
object = multispec[0, i, :]
extractcode = 'optimal'
if (secondord):
object2 = multispec2[0, i, :]
else:
object = multispec[1, i, :]
extractcode = 'normal'
if (secondord):
object2 = multispec2[1, i, :]
skyband = 2
if (num_bands == 2):
skyband = 1
if (num_bands > 3):
sigma = multispec[3, i, :]
else:
sigma = np.sqrt(multispec[skyband, i, :])
if (np.abs(np.mean(object)) < 1e-7):
print('\nScaling data up by 10^15\n')
object = object * 1.e15
sigma = sigma * 1.e15
if (secondord):
if (num_bands > 3):
sigma2 = multispec2[3, i, :]
else:
sigma2 = np.sqrt(multispec2[skyband, i, :])
if (np.abs(np.mean(object)) < 1e-7):
object2 = object2 * 1.e15
sigma2 = sigma2 * 1.e15
nandslist = ['gemini-n', 'gemini-s', 'lco-imacs']
if (observat in nandslist):
skyfile = inputfile.replace('tot', 'sky')
skyfits = fits.open(skyfile)
sky = skyfits[0].data[2, 0, :]
else:
sky = multispec[skyband, i, :]
envelope_size = 25
mx, mn = envelope(sky, envelope_size)
skycont = congrid(mn, (len(sky), ), minusone=True)
test_sky = sky
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
if 'kast' in mshead.get('VERSION', ''):
shift = xcor(msky[50:-50], sky[50:-50], xfactor, maxlag)
else:
shift = xcor(msky, sky, xfactor, maxlag)
angshift = shift * wdelt
print('wdeltf', wdelt)
print('The x-cor shift in Angstroms is {}'.format(angshift))
wave = wave + angshift #check to make sure signs are right
skyshiftdone = False
npixsky2 = len(sky) // 2
msky_max = np.max(msky[npixsky2 - 1:])
sky_max = np.max(sky[npixsky2 - 1:])
scale = sky_max / msky_max
plt.close()
fig = plt.figure(figsize=[8, 5])
fig.subplots_adjust(hspace=0)
while (not skyshiftdone):
axarr = fig.subplots(2)
waveplus = wave - angshift
if not secondtime:
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'):
wave = wave - angshift
angshift = inputter(
'Enter desired shift in Angstroms: ', 'float',
False)
wave = wave + angshift
else:
skyshiftdone = True
else:
wave = wave + angshift
skyshiftdone = True
plt.close()
# B star removal
bstarpass = bstarstar
bobj, bsig, bangshift=telluric_remove(bstarwave,bstarpass, bstarairmass, wave, \
object, airmass, sigma, object, shift=bshift)
# bobj, bsig, bangshift=telluric_remove(bstarwave,bstarpass, bstarairmass, wave, \
# test_sky, airmass, sigma, object)
bshift = bangshift
if (secondord):
bobj2, bsig2, bangshift2 =telluric_remove(bstarwave2,bstarpass2, bstarairmass2, \
wave, object2, airmass, sigma2)
print('\nRemoving redshift due to motion of Earth...')
z = -1 * v / 2.99792458e5
wave = wave / (1 + z)
# rebin
fig = plt.figure()
axarr = fig.subplots(1, 2)
ymin, ymax = finalscaler(bobj[0:100])
axarr[0].plot(wave[0:100], bobj[0:100], drawstyle='steps-mid')
axarr[0].set_xlabel('Wavelength')
axarr[0].set_ylabel('Flux')
#axarr[0].set_ylim((ymin,ymax))
if (secondtime):
axarr[0].plot([wavesave0, wavesave0], [ymin, ymax], color='r')
plt.pause(0.01)
ymin, ymax = finalscaler(bobj[-100:])
axarr[1].plot(wave[-100:], bobj[-100:], drawstyle='steps-mid')
axarr[1].set_xlabel('Wavelength')
axarr[1].set_ylabel('Flux')
try:
axarr[1].set_ylim((ymin, ymax))
except ValueError:
bobj_median = np.nanmedian(bobj)
axarr[1].set_ylim((bobj_median / 10., bobj_median * 10.))
if (secondtime):
axarr[1].plot([wavesaven, wavesaven], [ymin, ymax], color='r')
newdelt = 0.0
plt.pause(0.01)
print('\nCurrent A/pix is {}'.format(wave[1] - wave[0]))
if (secondtime):
print('\nPrevious resolution choice: {}'.format(deltsave))
else:
deltsave = 0.0
newdelt = wave[1] - wave[0]
# while (newdelt <= 0) or (newdelt > wave[-1]):
# print('Rebin to how many Angstroms per pixel? ')
# newdelt=inputter(' <CR> selects previous choice: ','float',True,deltsave)
# if (newdelt <= 0) or (newdelt > wave[-1]):
# print('Need positive resoution and smaller than the')
# print('entire spectrum. Try again')
print('\nCurrent range: {} {}'.format(wave[0], wave[-1]))
if (secondtime):
print('\nPrevious selection was {} {} (marked in red on plot)'.
format(wavesave0, wavesaven))
print('\n<CR> selects previous choice\n')
else:
wavesave0 = 0.0
wavesaven = 0.0
print('Enter the new wavelength range desired: ')
waveb, waver = waveparse(wave, wavesave0, wavesaven)
newbin = (waver - waveb) / newdelt + 1.0 #should stay the same now
# frac,whole=np.modf(newbin)
# if (frac > 0.000001):
# testwave=newdelt*whole+waveb
# print('Closest match is: {} to {}'.format(waveb,testwave))
# print('Would you like this wavelength range?')
# answer=yesno('y')
# if (answer == 'y'):
# waver=testwave
wave_locs = np.where((wave > waveb) & (wave < waver))
# deltsave=newdelt
wavesave0 = waveb
wavesaven = waver
waverange = str(waveb) + ' ' + str(waver)
secondtime = True
# nwave=np.arange(0,whole)*newdelt + waveb
# vartmp=bsig*bsig
# olddeltvec=wave-np.roll(wave,1)
# olddelt=np.mean(olddeltvec)
# nwave = wave
# finalobj = bobj
# finalvar = bsig**2.
# finalsig = bsig
#NOT TESTED!!!
nwave = wave[wave_locs]
print(nwave[0], nwave[-1])
finalobj = bobj[wave_locs]
finalvar = bsig[wave_locs]**2.
finalsig = bsig[wave_locs]
# finalobj=womashrebin(wave,bobj,nwave)
# finalvar=womashrebin(wave,vartmp,nwave)
# finalsig=np.sqrt(finalvar)*np.sqrt(olddelt/newdelt)
#Matt's interpolation algorithm. womashrebin is an unreadable monstrosity.
# interp_data = interpo_flux_conserving(wave, bobj, 1./vartmp, waveb, waver, dw=newdelt, testing=False)
# interp_wave = np.arange(math.ceil(wave[0])+1., math.floor(wave[-1])-1., dtype=float, step=newdelt)
# spectres_data = spectres(interp_wave, wave, bobj, spec_errs=bsig)
# trim_range = (interp_data[0] > waveb) & (interp_data[0] < waver)
# nwave = interp_data[0][trim_range]
# finalobj = interp_data[1][trim_range]
# finalvar = 1./interp_data[2][trim_range]
# finalsig = np.sqrt(finalvar)
suffixes = {}
suffixes['ap' + str(i + 1)] = ''
if os.path.isfile('../HOST_AP_DATA.txt'):
with open('../HOST_AP_DATA.txt') as host_ap_data:
h_lines = host_ap_data.readlines()
for l in h_lines:
suffixes[l.split()[0]] = '_' + l.split()[1]
#gonna ignore the second order stuff for now
if (secondord):
vartmp2 = bsig2 * bsig2
finalobj2 = womashrebin(wave, bobj2, nwave)
finalvar2 = womashrebin(wave, vartmp2, nwave)
finalsig2 = np.sqrt(finalvar2) * np.sqrt(olddelt / newdelt)
if (secondord and not seconddone):
finalobj, finalsig, wavebeg, waveend, brscale = secondcat(
nwave, finalobj, finalobj2, finalsig, finalsig2,
secondtime, wavebeg, waveend, brscale)
seconddone = True
ymin, ymax = finalscaler(finalobj)
plt.close()
fig = plt.figure()
plt.plot(nwave, finalobj, drawstyle='steps-mid')
# plt.plot(spectres_data[0],spectres_data[1],drawstyle='steps-mid', color='green')
plt.xlabel('Wavelength')
plt.ylabel('Flux')
plt.title(objectname)
plt.savefig(objectname + '-' + gratcode + '_ap' + str(i + 1) +
suffixes['ap' + str(i + 1)] + '.png')
plt.show()
outputdone = False
while (not outputdone):
print('\nThe file is: {}'.format(inputfile))
print('The object is: {}'.format(objectname))
print('The DATE-OBS is: {}'.format(date))
print('The aperture is: {}'.format(i + 1))
print('The previous name was: {}'.format(objname))
print('\nEnter the object name for the final fits file: ')
# objname=inputter('(UT date and .fits will be added): ','string',False)
objname = objectname + '-' + gratcode
fname = objname + '-' + printdate + '_ap' + str(
i + 1) + suffixes['ap' + str(i + 1)] + '.fits'
sname = objname + '-' + printdate + '_ap' + str(
i + 1) + suffixes['ap' + str(i + 1)] + '-sigma.fits'
outputdone = True
if (os.path.isfile(fname)):
print('{} already exists!!!!'.format(fname))
print('Do you wish to overwrite it? ')
answer = yesno('y')
if (answer == 'y'):
outputdone = True
else:
outputdone = True
# add to header
new_mshead = mshead.copy()
new_mshead.set('CRPIX1', 1)
new_mshead.set('CRVAL1', nwave[0])
new_mshead.set('CDELT1', nwave[1] - nwave[0])
new_mshead.set('CTYPE1', 'LINEAR')
new_mshead.set('W_RANGE', waverange)
new_mshead.set('BSTAR_Z', bstarairmass)
new_mshead.set('BSTARNUM', bstarnum)
new_mshead.set('BSTAROBJ', bstarname)
new_mshead.set('BARYVEL', v)
new_mshead.set('SKYSHIFT', angshift)
new_mshead.set('ATMSHIFT', bangshift)
new_mshead.set('EXTRACT', extractcode)
new_mshead.set('REDUCER', user)
new_mshead.set('RED_DATE',
str(datetime.now()).split()[0],
'EPOCH OF REDUCTION')
new_mshead.set('OBJECT', objectname)
# if (secondord):
# new_mshead.set('SECOND', 'yes', 'Second order correction attempted')
# new_mshead.set('COMBRANGE',combrange)
# new_mshead.set('BSTAR_Z2',bstarairmass2)
# new_mshead.set('BSTARNU2', bstarnum2)
# new_mshead.set('BSTAROB2', bstarname2)
# fluxairmass2=mshead2['FLX2_Z']
# fluxnum2=mshead2['FLX2_NUM']
# fluxname2=mshead2['FLX2_OBJ']
# new_mshead.set('FLX2_Z',fluxairmass2)
# new_mshead.set('FLX2_NUM', fluxnum2)
# new_mshead.set('FLX2_OBJ', fluxname2)
outdata = np.zeros((len(finalobj), 2))
outdata[:, 0] = finalobj.copy()
outdata[:, 1] = finalsig.copy()
outhdu = fits.PrimaryHDU(outdata)
hdul = fits.HDUList([outhdu])
mshead.set('NAXIS2', 2)
hdul[0].header = new_mshead.copy()
hdul.writeto(fname, overwrite=True)
spectxt = objname + '-' + printdate + '_ap' + str(
i + 1) + suffixes['ap' + str(i + 1)] + '.flm'
spectxt = spectxt.strip()
np.savetxt(spectxt,
np.transpose([nwave,
finalobj.copy(),
finalsig.copy()]))
hdul.close()
print('Do you wish to combine with another spectrum? ')
answer = yesno('y')
fname_comb = None
if (answer == 'y'):
plt.close()
done = False
while (not done):
files = glob.glob(objname.split('-')[0] + '*.fits')
print(files)
for f in files:
if objname not in f and ('red' in f or 'blue' in f
) and '_ap' + str(i + 1) in f:
inputfile = f
inputfile = input(
'Name of fits file to be combined? [{}]: '.format(
inputfile)) or inputfile
print(inputfile)
inputfile = inputfile.strip()
if (inputfile == ''):
return hop
if ('.fits' not in inputfile):
inputfile = inputfile + '.fits'
try:
fitsdata = fits.open(inputfile)
except OSError:
print('File {} cannot be opened.'.format(inputfile))
else:
done = True
crval1 = fitsdata[0].header['CRVAL1']
try:
wdelt = fitsdata[0].header['CDELT1']
except KeyError:
wdelt = 0.0000001
if (wdelt < 0.000001):
wdelt = fitsdata[0].header['CD1_1']
try:
objectname = fitsdata[0].header['OBJECT']
if (not isinstance(objectname, str)):
objectname = inputfile
except KeyError:
objectname = inputfile
data_new = fitsdata[0].data
wave_new = np.arange(1, len(data_new) + 1) * wdelt + crval1
if (len(data_new.shape) == 2):
var_new = data_new[:, 1]
var_new = var_new.astype(float)
var_new = var_new * var_new
flux_new = data_new[:, 0]
flux_new = flux_new.astype(float)
else:
flux_new = data_new.astype(float)
var_new = np.ones(data_new.shape)
if 'red' in inputfile:
wavecomb, fluxcomb, varcomb = womcatfinal(
[nwave, finalobj, finalvar],
[wave_new, flux_new, var_new])
nwave = wavecomb
finalobj = fluxcomb
finalsig = np.sqrt(varcomb)
elif 'blue' in inputfile:
wavecomb, fluxcomb, varcomb = womcatfinal(
[wave_new, flux_new, var_new],
[nwave, finalobj, finalvar])
nwave = wavecomb
finalobj = fluxcomb
finalsig = np.sqrt(varcomb)
else:
print(
"Please include 'blue' or 'red' in filename of spectrum to combine"
)
plt.clf()
plt.plot(nwave, finalobj, drawstyle='steps-mid')
plt.xlabel('Wavelength')
plt.ylabel('Flux')
plt.title(objectname)
plt.savefig(objectname + '_combined_ap' + str(i + 1) +
suffixes['ap' + str(i + 1)] + '.png')
outputdone = False
while (not outputdone):
print('\nThe file is: {}'.format(inputfile))
print('The object is: {}'.format(objectname))
print('The DATE-OBS is: {}'.format(date))
print('The aperture is: {}'.format(i + 1))
print('The previous name was: {}'.format(objname))
print('\nEnter the object name for the final fits file: ')
# objname=inputter('(UT date and .fits will be added): ','string',False)
objname = objectname + '-combined'
fname_comb = objname + '-' + printdate + '_ap' + str(
i + 1) + suffixes['ap' + str(i + 1)] + '.fits'
sname_comb = objname + '-' + printdate + '_ap' + str(
i + 1) + suffixes['ap' + str(i + 1)] + '-sigma.fits'
outputdone = True
if (os.path.isfile(fname)):
print('{} already exists!!!!'.format(fname))
print('Do you wish to overwrite it? ')
answer = yesno('y')
if (answer == 'y'):
outputdone = True
else:
outputdone = True
# add to header
mshead_combined = new_mshead.copy()
mshead_combined.set('CRPIX1', 1)
mshead_combined.set('CRVAL1', nwave[0])
mshead_combined.set('CDELT1', nwave[1] - nwave[0])
mshead_combined.set('CTYPE1', 'LINEAR')
mshead_combined.set('W_RANGE', waverange)
mshead_combined.set('BSTAR_Z', bstarairmass)
mshead_combined.set('BSTARNUM', bstarnum)
mshead_combined.set('BSTAROBJ', bstarname)
mshead_combined.set('BARYVEL', v)
mshead_combined.set('SKYSHIFT', angshift)
mshead_combined.set('ATMSHIFT', bangshift)
mshead_combined.set('EXTRACT', extractcode)
mshead_combined.set('REDUCER', user)
mshead_combined.set(
'RED_DATE',
datetime.now().strftime("%Y-%M-%d %I:%M%p"),
'EPOCH OF REDUCTION')
mshead_combined.set('OBJECT', objectname)
if (secondord): #not implemented
mshead_combined.set('SECOND', 'yes',
'Second order correction attempted')
mshead_combined.set('COMBRANGE', combrange)
mshead_combined.set('BSTAR_Z2', bstarairmass2)
mshead_combined.set('BSTARNU2', bstarnum2)
mshead_combined.set('BSTAROB2', bstarname2)
fluxairmass2 = mshead2['FLX2_Z']
fluxnum2 = mshead2['FLX2_NUM']
fluxname2 = mshead2['FLX2_OBJ']
mshead_combined.set('FLX2_Z', fluxairmass2)
mshead_combined.set('FLX2_NUM', fluxnum2)
mshead_combined.set('FLX2_OBJ', fluxname2)
outdata = np.zeros((len(finalobj), 2))
outdata[:, 0] = finalobj.copy()
outdata[:, 1] = finalsig.copy()
outhdu = fits.PrimaryHDU(outdata)
hdul = fits.HDUList([outhdu])
mshead_combined.set('NAXIS2', 2)
hdul[0].header = mshead_combined.copy()
hdul.writeto(fname_comb, overwrite=True)
hdul.close()
spectxt = objname + '-' + printdate + '_ap' + str(
i + 1) + suffixes['ap' + str(i + 1)] + '.flm'
spectxt = spectxt.strip()
np.savetxt(
spectxt,
np.transpose([nwave,
finalobj.copy(),
finalsig.copy()]))
is_final = input('Is this a final reduction? [y]/n: ') or 'y'
if is_final:
if not os.path.isdir('../../final_reductions/'):
os.mkdir('../../final_reductions/')
os.system('cp ' + fname + ' ' + '../../final_reductions/' +
fname)
if fname_comb:
os.system('cp ' + fname_comb + ' ' +
'../../final_reductions/' + fname_comb)
print('final')
print(objectlist, gratcode, secondord, gratcode2)
plt.close()
return
def womblo(hop, fig):
"""blotch out bad data"""
import logging
import numpy as np
import matplotlib.pyplot as plt
from scipy.interpolate import splrep, splev
from tmath.wombat.inputter_single import inputter_single
from tmath.wombat.waveparse import waveparse
from tmath.wombat.womwaverange import womwaverange
from tmath.wombat.womget_element import womget_element
from tmath.wombat.yesno import yesno
global nsplinepoints, tmpsplptsx, tmpsplptsy, pflag
print('Select regions to blotch')
wave = hop[0].wave.copy()
flux = hop[0].flux.copy()
done = False
while (not done):
plt.cla()
plt.plot(wave, flux, drawstyle='steps-mid')
plt.xlabel('Wavelength')
plt.ylabel('Flux')
plt.title(hop[0].obname)
wavesub, fluxsub, mode = womwaverange(wave, flux, 'none')
wavebind = womget_element(wave, wavesub[0])
waverind = womget_element(wave, wavesub[-1])
plt.cla()
plt.plot(wave[wavebind:waverind+1],flux[wavebind:waverind+1], \
drawstyle='steps-mid')
plt.xlabel('Wavelength')
plt.ylabel('Flux')
plt.title(hop[0].obname)
plt.pause(0.01)
print('Do you want to enter blotch wavelengths by hand (w),')
print('mark points (m), fit a spline (s), or quit (q)?')
choice = inputter_single('(w/m/s/q): ', 'wmsq')
if (choice == 'w') or (choice == 'm'):
blotchgood = False
while (not blotchgood):
wavechoicedone = False
while (not wavechoicedone):
if (choice == 'w'):
waveselb, waveselr = waveparse()
else:
print('Mark the two endpoints of the blotch region')
endpoints = plt.ginput(2, timeout=-1)
waveselb = endpoints[0][0]
waveselr = endpoints[1][0]
if (waveselb > waveselr):
waveselb, waveselr = waveselr, waveselb
waveselbind = womget_element(wave, waveselb)
waveselrind = womget_element(wave, waveselr)
print(waveselb, waveselr, waveselbind, waveselrind)
if (waveselbind == 0) or (waveselrind == (len(wave) - 1)):
print('Wavelengths incorrect--too close to endpoints')
else:
wavechoicedone = True
contblue = flux[waveselbind - 1]
contred = flux[waveselrind + 1]
delta = (contred - contblue) / (waveselrind - waveselbind + 1)
fluxcor = flux.copy()
for i in range(waveselbind, waveselrind + 1):
fluxcor[i] = contblue + (i - waveselbind + 1) * delta
plt.plot(wave[wavebind:waverind+1],fluxcor[wavebind:waverind+1], \
drawstyle='steps-mid')
plt.pause(0.01)
print('Is this acceptable')
answer = yesno('y')
if (answer == 'y'):
flux = fluxcor.copy()
blotchgood = True
logging.info('File {} blotched from {} to {}'.format(
hop[0].obname, wave[waveselbind], wave[waveselrind]))
elif (choice == 's'):
xmin, xmax = plt.xlim()
ymin, ymax = plt.ylim()
plt.xlim([xmin, xmax])
plt.ylim([ymin, ymax])
nsplinepoints = 0
tmpsplptsx = []
tmpsplptsy = []
spldone = False
while (not spldone):
plt.cla()
plt.plot(wave[wavebind:waverind+1],flux[wavebind:waverind+1], \
drawstyle='steps-mid')
if (len(tmpsplptsx) > 0):
plt.plot(tmpsplptsx, tmpsplptsy, 'ro')
plt.xlabel('Wavelength')
plt.ylabel('Flux')
plt.title(hop[0].obname)
plt.xlim([xmin, xmax])
plt.ylim([ymin, ymax])
cid = fig.canvas.mpl_connect('button_press_event', onclick)
print('\nClick on continuum points for spline fit.')
print(
'Spline will replace values between first and last point')
print('Left button = add point')
print('Middle button = delete point')
print('Right button = done\n')
pflag = ''
while (pflag != 'done'):
plt.pause(0.01)
fig.canvas.mpl_disconnect(cid)
splptsy = [z for _, z in sorted(zip(tmpsplptsx, tmpsplptsy))]
splptsx = sorted(tmpsplptsx)
spline = splrep(splptsx, splptsy, k=3)
splblueindex = womget_element(wave, splptsx[0])
splredindex = womget_element(wave, splptsx[-1])
splwave = wave[splblueindex:splredindex + 1].copy()
splineresult = splev(splwave, spline)
fluxcor = flux.copy()
fluxcor[splblueindex:splredindex + 1] = splineresult.copy()
plt.plot(splwave, splineresult, drawstyle='steps-mid')
print('Is this acceptable')
answer = yesno('y')
if (answer == 'y'):
flux = fluxcor.copy()
spldone = True
logging.info(
'File {} blotched with spline from {} to {}'.format(
hop[0].obname, wave[splblueindex],
wave[splredindex]))
else:
done = True
print('Do another region?')
another = yesno('n')
if (another == 'n'):
done = True
hop[0].flux = flux.copy()
return hop
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 fitspl(wave, flux, airlimit, fig, cal=None):
"""fit spline to spectrum"""
import numpy as np
import matplotlib.pyplot as plt
from scipy.interpolate import splrep, splev
import tmath.wombat.womconfig as womconfig
from tmath.wombat.womget_element import womget_element
from tmath.pydux.wave_telluric import wave_telluric
from tmath.wombat.yesno import yesno
from tmath.wombat.onclick import onclick
from tmath.wombat.onkeypress import onkeypress
import glob
# global nsplinepoints, tmpsplptsx, tmpsplptsy, pflag
# starting points for spline
bandpts = np.array([3000, 3050, 3090, 3200, 3430, 3450, 3500, 3550, 3600, \
3650, 3700, 3767, 3863, 3945, 4025, 4144, 4200, 4250, \
4280, 4390, 4450, 4500, 4600, 4655, 4717, 4750, 4908, \
4950, 5000, 5050, 5100, 5150, 5200, 5250, 5280, 5350, \
5387, 5439, 5500, 5550, 6100, 6150, 6400, 6430, 6650, \
6700, 6750, 6800, 7450, 7500, 7550, 8420, 8460, 8520, \
8570, 8600, 8725, 8770, 9910, 10000, 10200, 10300, \
10400, 10500, 10600, 10700])
locsinrange = np.logical_and((bandpts > wave[10]), (bandpts < wave[-10]))
useband = bandpts[locsinrange]
for i, _ in enumerate(useband):
index = womget_element(wave, useband[i])
useband[i] = index
# useband now has indices of wavelength positions
if (min(flux) < 0):
flux[np.where(flux < 0)] = 0.0
plt.cla()
plt.plot(wave, flux, drawstyle='steps-mid', color='k')
xmin, xmax = plt.xlim()
ymin, ymax = plt.ylim()
plt.xlim([xmin, xmax])
plt.ylim([ymin, ymax])
if (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)
wavetell = wave.copy()
fluxtell = flux.copy()
wavetell[loc] = np.nan
fluxtell[loc] = np.nan
plt.plot(wavetell, fluxtell, drawstyle='steps-mid', color='violet')
if '../../master_files/' + cal + '_splpts_master.txt' not in glob.glob(
'../../master_files/*'):
womconfig.nsplinepoints = len(useband)
womconfig.tmpsplptsx = wave[useband].copy().tolist()
womconfig.tmpsplptsy = []
for i, _ in enumerate(useband):
womconfig.tmpsplptsy.append(
np.median(flux[useband[i] - 2:useband[i] + 3]))
spline = splrep(womconfig.tmpsplptsx, womconfig.tmpsplptsy, k=3)
else:
masterx, mastery = np.genfromtxt('../../master_files/' + cal +
'_splpts_master.txt')
womconfig.nsplinepoints = len(masterx)
womconfig.tmpsplptsx = masterx
womconfig.tmpsplptsy = mastery
spline = splrep(womconfig.tmpsplptsx, womconfig.tmpsplptsy, k=3)
splineresult = splev(wave, spline)
plt.cla()
plt.plot(wave, flux, drawstyle='steps-mid', color='k')
plt.plot(wavetell, fluxtell, drawstyle='steps-mid', color='violet')
if (len(womconfig.tmpsplptsx) > 0):
plt.plot(womconfig.tmpsplptsx, womconfig.tmpsplptsy, 'ro')
plt.plot(wave, splineresult, color='g')
plt.xlabel('Wavelength')
plt.ylabel('Flux')
plt.xlim([xmin, xmax])
plt.ylim([ymin, ymax])
plt.pause(0.01)
done = False
print('Is this OK? ')
answer = yesno('n')
if (answer == 'y'):
done = True
splptsy = [
z for _, z in sorted(zip(womconfig.tmpsplptsx, womconfig.tmpsplptsy))
]
splptsx = sorted(womconfig.tmpsplptsx)
while (not done):
plotdone = False
while (not plotdone):
plt.cla()
plt.plot(wave, flux, drawstyle='steps-mid', color='k')
plt.plot(wavetell, fluxtell, drawstyle='steps-mid', color='violet')
if (len(womconfig.tmpsplptsx) > 0):
plt.plot(womconfig.tmpsplptsx, womconfig.tmpsplptsy, 'ro')
plt.plot(wave, splineresult, color='g')
plt.xlabel('Wavelength')
plt.ylabel('Flux')
plt.xlim([xmin, xmax])
plt.ylim([ymin, ymax])
plt.pause(0.01)
print('Change scale? ')
answer = yesno('n')
if (answer == 'y'):
plt.cla()
plt.plot(wave, flux, drawstyle='steps-mid', color='k')
plt.plot(wavetell,
fluxtell,
drawstyle='steps-mid',
color='violet')
if (len(womconfig.tmpsplptsx) > 0):
plt.plot(womconfig.tmpsplptsx, womconfig.tmpsplptsy, 'ro')
plt.plot(wave, splineresult, color='g')
plt.xlabel('Wavelength')
plt.ylabel('Flux')
print('Click corners of box to change plot scale')
newlims = plt.ginput(2, timeout=-1)
xmin = newlims[0][0]
ymin = newlims[0][1]
xmax = newlims[1][0]
ymax = newlims[1][1]
plt.cla()
plt.plot(wave, flux, drawstyle='steps-mid', color='k')
plt.plot(wavetell,
fluxtell,
drawstyle='steps-mid',
color='violet')
if (len(womconfig.tmpsplptsx) > 0):
plt.plot(womconfig.tmpsplptsx, womconfig.tmpsplptsy, 'ro')
plt.plot(wave, splineresult, color='g')
plt.xlabel('Wavelength')
plt.ylabel('Flux')
plt.xlim([xmin, xmax])
plt.ylim([ymin, ymax])
plotdone = True
else:
plotdone = True
cid = fig.canvas.mpl_connect('button_press_event', onclick)
cid2 = fig.canvas.mpl_connect('key_press_event', onkeypress)
print('\nClick on continuum points for spline fit.')
print('Left button or (a) = add point')
print('Middle button or (s) = delete point')
print('Right button or (d) = done\n')
womconfig.pflag = ''
while (womconfig.pflag != 'done'):
plt.pause(0.01)
fig.canvas.mpl_disconnect(cid)
fig.canvas.mpl_disconnect(cid2)
splptsy = [
z
for _, z in sorted(zip(womconfig.tmpsplptsx, womconfig.tmpsplptsy))
]
splptsx = sorted(womconfig.tmpsplptsx)
spline = splrep(splptsx, splptsy, k=3)
splineresult = splev(wave, spline)
plt.plot(wave, splineresult, drawstyle='steps-mid', color='g')
plt.pause(0.01)
print('Is this fit OK? ')
answer = yesno('y')
if (answer == 'y'):
done = True
if cal != None:
np.savetxt('../../master_files/' + cal + '_splpts_master.txt',
[splptsx, splptsy])
return splineresult
def secondcat(wave, obj1, obj2, sig1, sig2, secondtimeflag, wavebeg, waveend,
brscale):
import numpy as np
import matplotlib.pyplot as plt
from tmath.wombat.womget_element import womget_element
from tmath.wombat.inputter_single import inputter_single
from tmath.wombat.yesno import yesno
print('\nCombining two calibrated spectra for second-order correction')
waveblue = wave
wavered = wave
fluxblue = obj1
fluxred = obj2
fluxtemp = fluxred
if (not secondtimeflag):
print('Plotting blue side as blue, red side as red')
indexblue = womget_element(waveblue, wavered[0])
indexred = womget_element(wavered, waveblue[-1])
meanblue = np.mean(fluxblue[indexblue:])
meanred = np.mean(fluxred[0:indexred])
if ((meanblue / meanred) > 1.2) or (meanblue / meanred < 0.8):
print('Averages very different, scaling red to blue for plot')
scale = meanblue / meanred
print('Red multiplied by {}'.format(scale))
fluxtemp = fluxred * scale
plt.clf()
plt.plot(waveblue[indexblue:],
fluxblue[indexblue:],
drawstyle='steps-mid',
color='b')
plt.plot(wavered[0:indexred],
fluxred[:indexred],
drawstyle='steps-mid',
color='r')
plt.xlabel('Wavelength')
plt.ylabel('Flux')
donescale = False
while (not donescale):
print('Change y-scale?')
answer = yesno('n')
if (answer == 'y'):
ymin, ymax = scaleparse()
plt.ylim([ymin, ymax])
plt.pause(0.01)
print('Do again?')
answer = yesno('n')
if (answer == 'n'):
donescale = True
regiondone = False
while (not regiondone):
print(
'\nOK, mark the two end points of the region to compute average'
)
endpoints = plt.ginput(2, timeout=-1)
element1 = endpoints[0][0]
element2 = endpoints[1][0]
plt.plot(endpoints, 'ro')
if (element1 > element2):
element1, element2 = element2, element1
binend = womget_element(waveblue, element2)
binbeg = womget_element(waveblue, element1)
if (binend > len(waveblue) - 1):
binend = len(waveblue) - 1
if (binbeg < indexblue):
binbeg = indexblue
print('\nAre these points OK?')
answer = yesno('y')
if (answer == 'y'):
regiondone = False
else:
plt.plot(endpoints, 'wo')
wavebeg = waveblue[binbeg]
waveend = waveblue[binend]
binbegred = womget_element(wavered, wavebeg)
binendred = womget_element(wavered, waveend)
meanblue = np.mean(fluxblue[binbeg:binend + 1])
meanred = np.mean(fluxred[binbegred:binendred + 1])
print('Average for {}:{}'.format(wavebeg, waveend))
print('Blue side: {}'.format(meanblue))
print('Red side: {}'.format(meanred))
brscale = inputter_single('Scale to blue or red? (b/r) ', 'br')
if (brscale == 'b'):
print('Scaling to blue by {}'.format(meanblue / meanred))
fluxred = fluxred * meanblue / meanred
else:
print('Scaling to red by {}'.format(meanred / meanblue))
fluxblue = fluxblue * meanred / meanblue
print('\nPlotting blue side as blue, red side as red')
plt.clf()
plt.plot(waveblue[binbeg:binend + 1],
fluxblue[binbeg:binend + 1],
drawstyle='steps-mid',
color='b')
plt.plot(wavered[binbegred:binendred + 1],
fluxred[binbegred:binendred + 1],
drawstyle='steps-mid',
color='r')
plt.xlabel('Wavelength')
plt.ylabel('Flux')
donescale = False
while (not donescale):
print('Change y-scale?')
answer = yesno('n')
if (answer == 'y'):
ymin, ymax = scaleparse()
plt.ylim([ymin, ymax])
plt.pause(0.01)
print('Do again?')
answer = yesno('n')
if (answer == 'n'):
donescale = True
regiondone = False
while (not regiondone):
print('\nOK, mark the two end points of the region to combine')
endpoints = plt.ginput(2, timeout=-1)
element1 = endpoints[0][0]
element2 = endpoints[1][0]
plt.plot(endpoints, 'ro')
if (element1 > element2):
element1, element2 = element2, element1
binend = womget_element(waveblue, element2)
binbeg = womget_element(waveblue, element1)
if (binend > len(waveblue) - 1):
binend = len(waveblue) - 1
if (binbeg < indexblue):
binbeg = indexblue
print('\nAre these points OK?')
answer = yesno('y')
if (answer == 'y'):
regiondone = False
else:
plt.plot(endpoints, 'wo')
wavebeg = waveblue[binbeg]
waveend = waveblue[binend]
binbegred = womget_element(wavered, wavebeg)
binendred = womget_element(wavered, waveend)
else:
binbeg = womget_element(waveblue, wavebeg)
binend = womget_element(waveblue, waveend)
binbegred = womget_element(wavered, wavebeg)
binendred = womget_element(wavered, waveend)
meanblue = np.mean(fluxblue[binbeg:binend + 1])
meanred = np.mean(fluxred[binbegred:binendred + 1])
if (brscale == 'b'):
scale = meanblue / meanred
fluxred = fluxred * scale
sig2 = sig2 * scale
else:
scale = meanred / meanblue
fluxblue = fluxblue * scale
sig1 = sig1 * scale
overflux = (fluxblue[binbeg:binend + 1] +
fluxred[binbegred:binendred + 1]) / 2.0
oversig = np.sqrt(sig1[binbeg:binend + 1]**2 +
sig2[binbegred:binendred + 1]**2)
newwave = waveblue.copy()
newflux = fluxblue.copy()
newsig = sig1.copy()
newsig[binbeg:binend + 1] = oversig
newsig[binend + 1:] = sig2[binendred + 1:]
newflux[binbeg:binend + 1] = overflux
newflux[binend + 1:] = fluxred[binendred + 1:]
plt.clf()
plt.pause(0.01)
axarr = fig.subplots(2, sharex=True)
fig.subplots_adjust(hspace=0)
axarr[0].plot(waveblue[binbeg:binend + 1],
fluxblue[binbeg:binend + 1],
drawstyle='steps-mid',
color='b')
axarr[0].plot(wavered[binbegred:binendred + 1],
fluxred[binbegred:binendred + 1],
drawstyle='steps-mid',
color='r')
axarr[0].plot(waveblue[binbeg:binend + 1],
overflux,
drawstyle='steps-mid',
color='k')
axarr[0].set_title('Overlap region--with average')
axarr[0].set_ylabel('Flux')
plt.pause(0.01)
axarr[1].plot(newwave, newflux, drawstyle='steps-mid', color='k')
axarr[1].plot(newwave[binbeg:binend + 1],
newflux[binbeg:binend + 1],
drawstyle='steps-mid',
color='r')
axarr[1].set_xlabel('Wavelength')
axarr[1].set_ylabel('Flux')
plt.pause(0.01)
return newflux, newsig, wavebeg, waveend, brscale
def womcat(hop):
"""concatenate data with overlapping wavelength regions"""
import numpy as np
import logging
import matplotlib.pyplot as plt
from tmath.wombat.inputter import inputter
from tmath.wombat.inputter_single import inputter_single
from tmath.wombat.womget_element import womget_element
from tmath.wombat.yesno import yesno
from tmath.wombat.get_screen_size import get_screen_size
from tmath.wombat.womwaverange2 import womwaverange2
from tmath.wombat import HOPSIZE
from matplotlib.widgets import Cursor
plt.ion()
screen_width, screen_height = get_screen_size()
screenpos = '+{}+{}'.format(int(screen_width * 0.2),
int(screen_height * 0.05))
fig = plt.figure()
ax = fig.add_subplot(111)
cursor = Cursor(ax, useblit=True, color='k', linewidth=1)
fig.canvas.manager.window.wm_geometry(screenpos)
fig.canvas.set_window_title('Cat')
fig.set_size_inches(9, 6)
# turns off key stroke interaction
fig.canvas.mpl_disconnect(fig.canvas.manager.key_press_handler_id)
print("\nThis will combine blue and red pieces from two hoppers\n")
hopnum1 = 0
hopnum2 = 0
while (hopnum1 < 1) or (hopnum1 > HOPSIZE):
hopnum1 = inputter('Enter first hopper: ', 'int', False)
while (hopnum2 < 1) or (hopnum2 > HOPSIZE):
hopnum2 = inputter('Enter second hopper: ', 'int', False)
if (hop[hopnum1].wave[0] > hop[hopnum2].wave[0]):
hopnum1, hopnum2 = hopnum2, hopnum1
wdelt1 = hop[hopnum1].wave[1] - hop[hopnum1].wave[0]
wdelt2 = hop[hopnum2].wave[1] - hop[hopnum2].wave[0]
# check if wavelength dispersion same
if (abs(wdelt1 - wdelt2) > 0.00001):
print('Spectra do not have same Angstrom/pixel')
print('Blue side: {}'.format(wdelt1))
print('Red side: {}'.format(wdelt2))
return hop
if hop[hopnum1].wave[-1] < hop[hopnum2].wave[0]:
print('Spectra do not overlap\n')
return hop
print("\nOverlap range is {} to {}".format(hop[hopnum2].wave[0],
hop[hopnum1].wave[-1]))
print("\nPlotting blue side as blue, red side as red\n")
waveblue = hop[hopnum1].wave.copy()
fluxblue = hop[hopnum1].flux.copy()
varblue = hop[hopnum1].var.copy()
wavered = hop[hopnum2].wave.copy()
fluxred = hop[hopnum2].flux.copy()
varred = hop[hopnum2].var.copy()
indexblue = womget_element(waveblue, wavered[0])
indexred = womget_element(wavered, waveblue[-1])
fluxcor = 1.0
blue_mean = np.mean(fluxblue[indexblue:])
red_mean = np.mean(fluxred[0:indexred + 1])
if (blue_mean / red_mean < 0.8) or (blue_mean / red_mean > 1.2):
fluxcor = blue_mean / red_mean
print("Averages very different, scaling red to blue for plot")
print("Red multiplied by {}".format(fluxcor))
plt.cla()
plt.plot(waveblue[indexblue:],
fluxblue[indexblue:],
drawstyle='steps-mid',
color='b')
plt.plot(wavered[0:indexred],
fluxred[0:indexred] * fluxcor,
drawstyle='steps-mid',
color='r')
plt.xlabel('Wavelength')
plt.ylabel('Flux')
plt.pause(0.01)
print('Change scale?')
answer = yesno('n')
if (answer == 'y'):
xmin_old, xmax_old = plt.xlim()
ymin_old, ymax_old = plt.ylim()
done = False
while (not done):
plt.xlim([xmin_old, xmax_old])
plt.ylim([ymin_old, ymax_old])
print('Click corners of box to change plot scale')
newlims = plt.ginput(2, timeout=-1)
xmin = newlims[0][0]
ymin = newlims[0][1]
xmax = newlims[1][0]
ymax = newlims[1][1]
plt.xlim([xmin, xmax])
plt.ylim([ymin, ymax])
print('Is this OK?')
loopanswer = yesno('y')
if (loopanswer == 'y'):
done = True
print('\nEnter method to select wavelength ranges\n')
mode = inputter_single(
'Enter (w)avelengths or mark with the (m)ouse? (w/m) ', 'wm')
print('\nChoose end points of region to compute average\n')
waveb, waver, mode = womwaverange2(waveblue[indexblue:],
fluxblue[indexblue:],
wavered[0:indexred],
fluxred[0:indexred] * fluxcor, mode)
indexblueb = womget_element(waveblue, waveb)
indexbluer = womget_element(waveblue, waver)
indexredb = womget_element(wavered, waveb)
indexredr = womget_element(wavered, waver)
mean_blue = np.mean(fluxblue[indexblueb:indexbluer + 1])
mean_red = np.mean(fluxred[indexredb:indexredr + 1])
print("\nAverage for {}:{}".format(waveb, waver))
print("Blue side: {}".format(mean_blue))
print("Red side: {}\n".format(mean_red))
brscale = inputter_single('Scale to blue or red (b/r)? ', 'br')
if (brscale == 'b'):
brscalefac = mean_blue / mean_red
logging.info('Cat scaling to blue by {}'.format(brscalefac))
fluxred = fluxred * brscalefac
varred = varred * brscalefac**2
else:
brscalefac = mean_red / mean_blue
logging.info('Cat scaling to red by {}'.format(brscalefac))
fluxblue = fluxblue * brscalefac
varblue = varblue * brscalefac**2
# print("\nPlotting blue side as blue, red side as red\n")
# plt.cla()
# plt.plot(waveblue[indexblueb:indexbluer+1],fluxblue[indexblueb:indexbluer+1],drawstyle='steps-mid',color='b')
# plt.plot(wavered[indexredb:indexredr+1],fluxred[indexredb:indexredr+1],drawstyle='steps-mid',color='r')
# plt.xlabel('Wavelength')
# plt.ylabel('Flux')
# plt.pause(0.01)
# print('Change scale?')
# answer=yesno('n')
# if (answer == 'y'):
# xmin_old,xmax_old=plt.xlim()
# ymin_old,ymax_old=plt.ylim()
# done=False
# while (not done):
# plt.xlim([xmin_old,xmax_old])
# plt.ylim([ymin_old,ymax_old])
# print('Click corners of box to change plot scale')
# newlims=plt.ginput(2,timeout=-1)
# xmin=newlims[0][0]
# ymin=newlims[0][1]
# xmax=newlims[1][0]
# ymax=newlims[1][1]
# plt.xlim([xmin,xmax])
# plt.ylim([ymin,ymax])
# print('Is this OK?')
# loopanswer=yesno('y')
# if (loopanswer == 'y'):
# done=True
# print('\nChoose end points of region to compute average\n')
# waveb,waver,mode=womwaverange2(waveblue[indexblueb:indexbluer+1],
# fluxblue[indexblueb:indexbluer+1],
# wavered[indexredb:indexredr+1],
# fluxred[indexredb:indexredr+1],mode)
# indexblueb=womget_element(waveblue,waveb)
# indexbluer=womget_element(waveblue,waver)
# indexredb=womget_element(wavered,waveb)
# indexredr=womget_element(wavered,waver)
# ewadd=inputter_single('Add overlap region (e)qually or with (w)eights (e/w)?','ew')
# if (ewadd == 'e'):
# overflux=(fluxblue[indexblueb:indexbluer+1]+fluxred[indexredb:indexredr+1])/2.
# overvar=(varblue[indexblueb:indexbluer+1]+varred[indexredb:indexredr+1])
#replacing with inverse variance weighted average
overflux = np.average([
fluxblue[indexblueb:indexbluer + 1], fluxred[indexredb:indexredr + 1]
],
weights=[
1. / varblue[indexblueb:indexbluer + 1],
1. / varred[indexredb:indexredr + 1]
],
axis=0)
overvar = np.sum(
[varblue[indexblueb:indexbluer + 1], varred[indexredb:indexredr + 1]],
axis=0)
logging.info('Cat combined sides with inverse variance weighted average')
# else:
# wei_done = False
# while (not wei_done):
# weiblue=inputter('Enter fractional weight for blue side: ','float',False)
# weired=inputter('Enter fractional weight for red side: ','float',False)
# if (np.abs((weiblue+weired)-1.0) > 0.000001):
# print('Weights do not add to 1.0')
# else:
# wei_done = True
# overflux=(fluxblue[indexblueb:indexbluer+1]*weiblue+
# fluxred[indexredb:indexredr+1]*weired)
# overvar=(varblue[indexblueb:indexbluer+1]*weiblue**2+
# varred[indexredb:indexredr+1]*weired**2)
# logging.info('Cat adds blue side with weight {} and red side with weight {}'.format(weiblue, weired))
newbluewave = waveblue[:indexblueb]
newblueflux = fluxblue[:indexblueb]
newbluevar = varblue[:indexblueb]
overwave = waveblue[indexblueb:indexbluer + 1]
newredwave = wavered[indexredr + 1:]
newredflux = fluxred[indexredr + 1:]
newredvar = varred[indexredr + 1:]
newwave = np.concatenate([newbluewave, overwave, newredwave])
newflux = np.concatenate([newblueflux, overflux, newredflux])
newvar = np.concatenate([newbluevar, overvar, newredvar])
logging.info('File {} and'.format(hop[hopnum1].obname))
logging.info('File {} concatenated'.format(hop[hopnum2].obname))
logging.info('over wavelength range {} to {}'.format(
waveblue[indexblueb], waveblue[indexbluer]))
plt.clf()
axarr = fig.subplots(2)
axarr[0].plot(overwave, overflux, drawstyle='steps-mid', color='k')
axarr[0].plot(waveblue[indexblueb:indexbluer + 1],
fluxblue[indexblueb:indexbluer + 1],
drawstyle='steps-mid',
color='b')
axarr[0].plot(wavered[indexredb:indexredr + 1],
fluxred[indexredb:indexredr + 1],
drawstyle='steps-mid',
color='r')
axarr[0].set_title('Overlap region, with inputs and combination')
axarr[1].set_ylabel('Flux')
axarr[1].plot(newwave, newflux, drawstyle='steps-mid', color='k')
axarr[1].plot(newwave[indexblueb:indexbluer + 1],
newflux[indexblueb:indexbluer + 1],
drawstyle='steps-mid',
color='r')
plt.pause(0.01)
hopout = 0
while (hopout < 1) or (hopout > HOPSIZE):
hopout = inputter('Enter hopper to store combined spectrum: ', 'int',
False)
hop[hopout].wave = newwave
hop[hopout].flux = newflux
hop[hopout].var = newvar
hop[hopout].obname = hop[hopnum1].obname
hop[hopout].header = hop[hopnum1].header
plt.close()
#fig.clf()
#plt.cla()
return hop
def main():
secondord = False
gratcode2 = ''
# logging straight from docs.python.org cookbook page
# INFO level to screen and cal.log
# DEBUG level only to cal.log
logging.getLogger('matplotlib').setLevel(logging.WARNING)
logging.basicConfig(level=logging.DEBUG,
format='%(asctime)s %(message)s',
datefmt='%Y-%m-%d %H:%M:%S',
filename='cal.log',
filemode='a')
# define a Handler which writes INFO messages or higher to the sys.stderr
console = logging.StreamHandler()
console.setLevel(logging.INFO)
# set a format which is simpler for console use
formatter = logging.Formatter('%(message)s')
# tell the handler to use this format
console.setFormatter(formatter)
# add the handler to the root logger
logging.getLogger('').addHandler(console)
user = getpass.getuser()
print('Hello, {} \n'.format(user))
logging.debug('CAL starts')
logging.debug('{} running things'.format(user))
print(' ')
print('This program is a driver for the calibration routines.')
print('It expects files that have been dispersion calibrated,')
print('usually through IRAF (you know, with a -d- in front).')
print('(In other words, include the d in your file names.)')
print(' ')
print('Do you want to use second-order correction?\n')
answer = yesno('n')
if (answer == 'y'):
secondord = True
#axarr=fig.subplots(2,sharex=True)
#fig.subplots_adjust(hspace=0)
print('\nWe now need a grating code, such as opt or ir2.')
print('This will be used to keep track of the fluxstar and')
print('bstar as in fluxstaropt.fits or bstarir2.fits\n')
gratcode = inputter('Enter the grating code: ', 'string', False)
print(' ')
if (secondord):
gratcode2 = inputter('Enter the second-order grating code: ', 'string', False)
print(' ')
print('Enter the file containing the list of objects')
print('(should be dispersion-corrected)\n')
done = False
while (not done):
# objectlist = inputter('Object list file: ', 'string', False)
dfiles=glob.glob('d*.fits')
for d in dfiles:
if gratcode in d:
listfile= open(d.split('_ex.fits')[0],"w+")
listfile.write(d)
listfile.close()
objectlist = listfile.name
if (os.path.isfile(objectlist)):
done = True
else:
print('No such file')
print('\nDo you want to fit a flux star?\n')
answer = yesno('y')
if (answer == 'y'):
plt.close()
fluxfile = getfitsfile('flux star', '.fits')
pydux.mkfluxstar(fluxfile, gratcode)
if (secondord):
print(' ')
fluxfile2 = getfitsfile('second flux star', '.fits')
pydux.mkfluxstar(fluxfile2, gratcode2)
else:
try:
fluxfits = fits.open('fluxstar'+gratcode+'.fits')
fluxfile = fluxfits[0].header['FLUXFILE']
fluxfits.close()
# except FileNotFoundError:
except KeyError:
fluxfile = 'Unknown'
if (secondord):
try:
fluxfits2 = fits.open('fluxstar'+gratcode2+'.fits')
fluxfile2 = fluxfits2[0].header['FLUXFILE']
fluxfits2.close()
# except FileNotFoundError:
except KeyError:
fluxfile2 = 'Unknown'
print('\nDo you want to apply the flux star(s) to the data?\n')
answer = yesno('y')
if (answer == 'y'):
pydux.calibrate(objectlist, gratcode, secondord, gratcode2)
print('\nDo you want to fit a b-star?\n')
answer = yesno('y')
if (answer == 'y'):
plt.close()
print('\nDo you want to use the flux star {}'.format(fluxfile))
print('as the b-star?\n')
same = yesno('y')
print(' ')
if (same == 'n'):
bfile = getfitsfile('b-star', '.fits')
else:
bfile = fluxfile
bfile = 'c'+gratcode+bfile
pydux.mkbstar(bfile, gratcode)
if (secondord):
print('\nDo you want to use the flux star {}'.format(fluxfile2))
print('as the b-star?\n')
same = yesno('y')
if (same == 'n'):
bfile2 = getfitsfile('b-star', '.fits')
else:
bfile2 = fluxfile2
bfile2 = 'c'+gratcode+bfile2
pydux.mkbstar(bfile2, gratcode2)
print('\nFinal calibration (atmos. removal, sky line wave. adjust, etc.)?')
answer = yesno('y')
if (answer == 'y'):
plt.close()
pydux.final(objectlist, gratcode, secondord, gratcode2, user)
print('\nThere, was that so hard?')
def womirfilters(hop):
"""calculate photometric values from spectra"""
import numpy as np
import logging
from tmath.wombat.filtermag import filtermag
from tmath.wombat.yesno import yesno
from tmath.wombat.inputter import inputter
from tmath.wombat.inputter_single import inputter_single
print('NOTE: The routine expects an f_lambda spectrum')
print(' I will try to guess if the spectrum')
print(' has been scaled by 1E15')
print(' ')
print(' Check this before believing fluxes')
print(' ')
print('NOTE Also: These are the 2MASS filter curves')
print(' ')
flux = hop[0].flux.copy()
if (np.mean(flux) > 0.00001):
flux = flux * 1.e-15
filtwave = np.zeros((109, 3))
filttran = np.zeros((109, 3))
filtwave[:,0]=[1.050, 1.051, 1.062, 1.066, 1.070, 1.075, 1.078, 1.082, \
1.084, 1.087, 1.089, 1.093, 1.096, 1.102, 1.105, 1.107, 1.109, 1.112, \
1.116, 1.117, 1.120, 1.123, 1.128, 1.129, 1.132, 1.134, 1.138, 1.140, \
1.143, 1.147, 1.154, 1.159, 1.164, 1.167, 1.170, 1.173, 1.175, 1.179, \
1.182, 1.186, 1.188, 1.192, 1.195, 1.199, 1.202, 1.209, 1.216, 1.221, \
1.227, 1.231, 1.236, 1.240, 1.244, 1.247, 1.253, 1.255, 1.258, 1.260, \
1.265, 1.270, 1.275, 1.279, 1.286, 1.292, 1.297, 1.302, 1.305, 1.307, \
1.310, 1.313, 1.316, 1.319, 1.323, 1.326, 1.330, 1.333, 1.334, 1.336, \
1.339, 1.343, 1.346, 1.349, 1.353, 1.355, 1.360, 1.363, 1.370, 1.373, \
1.377, 1.383, 1.388, 1.392, 1.395, 1.396, 1.397, 1.398, 1.400, 1.401, \
1.402, 1.404, 1.406, 1.407, 1.410, 1.412, 1.416, 1.421, 1.426, 1.442, \
1.450]
filttran[:,0]=[0.0000, 0.0000, 0.0000, 0.0023, 0.0087, 0.0150, 0.0309, 0.0690, \
0.1136, 0.1709, 0.2282, 0.2886, 0.3491, 0.4255, 0.4668, 0.5209, \
0.5687, 0.6228, 0.6546, 0.6864, 0.7150, 0.7437, 0.7595, 0.7595, \
0.7435, 0.7276, 0.6861, 0.6575, 0.6224, 0.5873, 0.5649, 0.5840, \
0.6157, 0.6571, 0.6857, 0.7271, 0.7685, 0.8162, 0.8416, 0.8511, \
0.8447, 0.8256, 0.7937, 0.7554, 0.7172, 0.6757, 0.6629, 0.6883, \
0.7391, 0.7869, 0.8505, 0.8823, 0.8950, 0.8854, 0.8471, 0.8184, \
0.7802, 0.7324, 0.6845, 0.6239, 0.5889, 0.5729, 0.5728, 0.5918, \
0.6172, 0.6681, 0.6968, 0.7286, 0.7667, 0.7954, 0.8431, 0.8813, \
0.9194, 0.9353, 0.9257, 0.9225, 0.9129, 0.8906, 0.8524, 0.8141, \
0.7854, 0.7599, 0.7439, 0.7375, 0.7247, 0.7183, 0.7087, 0.7023, \
0.7022, 0.7181, 0.7339, 0.7147, 0.6829, 0.6446, 0.6160, 0.5873, \
0.5172, 0.4662, 0.3770, 0.2305, 0.1350, 0.1126, 0.0712, 0.0362, \
0.0170, 0.0042, 0.0009, 0.0007, 0.0000]
filtwave[0:57,1]=[1.315, 1.341, 1.368, 1.397, 1.418, 1.440, 1.462, 1.478, \
1.486, 1.493, 1.504, 1.515, 1.528, 1.539, 1.546, 1.551, 1.556, 1.565, \
1.572, 1.577, 1.583, 1.592, 1.597, 1.602, 1.613, 1.619, 1.628, 1.633, \
1.642, 1.648, 1.657, 1.659, 1.671, 1.684, 1.701, 1.715, 1.727, 1.739, \
1.746, 1.751, 1.753, 1.756, 1.764, 1.775, 1.785, 1.790, 1.796, 1.803, \
1.810, 1.813, 1.818, 1.828, 1.835, 1.850, 1.871, 1.893, 1.914]
filttran[0:57,1]=[0.0014, 0.0014, 0.0000, 0.0000, 0.0014, 0.0028, 0.0070, \
0.0252, 0.0700, 0.1807, 0.3529, 0.4972, 0.6527, 0.7591, 0.8109, \
0.8319, 0.8403, 0.8389, 0.8305, 0.8235, 0.8193, 0.8277, 0.8347, \
0.8375, 0.8319, 0.8193, 0.8081, 0.8053, 0.8095, 0.8165, 0.8263, \
0.8305, 0.8375, 0.8431, 0.8501, 0.8529, 0.8543, 0.8529, 0.8445, \
0.8305, 0.8151, 0.7927, 0.7255, 0.6275, 0.5084, 0.4258, 0.3291, \
0.2101, 0.1275, 0.0882, 0.0560, 0.0294, 0.0154, 0.0070, 0.0028, \
0.0014, 0.0000]
filtwave[0:76,2]=[1.900, 1.915, 1.927, 1.934, 1.939, 1.948, 1.957, 1.962, \
1.969, 1.976, 1.981, 1.989, 1.990, 1.998, 2.008, 2.014, 2.019, 2.028, \
2.037, 2.045, 2.061, 2.072, 2.075, 2.082, 2.089, 2.099, 2.106, 2.113, \
2.120, 2.124, 2.138, 2.145, 2.155, 2.169, 2.176, 2.185, 2.197, 2.208, \
2.213, 2.218, 2.232, 2.237, 2.248, 2.256, 2.260, 2.263, 2.265, 2.270, \
2.272, 2.276, 2.277, 2.281, 2.284, 2.286, 2.291, 2.293, 2.295, 2.297, \
2.299, 2.306, 2.311, 2.316, 2.320, 2.325, 2.328, 2.335, 2.339, 2.344, \
2.346, 2.352, 2.361, 2.363, 2.370, 2.375, 2.384, 2.399]
filttran[0:76,2]=[0.0000, 0.0013, 0.0027, 0.0040, 0.0082, 0.0153, 0.0293, \
0.0462, 0.0743, 0.1222, 0.1714, 0.2672, 0.3517, 0.4263, 0.6262, \
0.6797, 0.7487, 0.7853, 0.8120, 0.8303, 0.8485, 0.8513, 0.8583, \
0.8597, 0.8667, 0.8751, 0.8765, 0.8835, 0.8891, 0.8863, 0.8848, \
0.8819, 0.8805, 0.8748, 0.8804, 0.8818, 0.8902, 0.8986, 0.9014, \
0.8999, 0.8999, 0.8956, 0.8913, 0.8969, 0.8997, 0.8997, 0.9053, \
0.9109, 0.9166, 0.9109, 0.9025, 0.8870, 0.8686, 0.8433, 0.7714, \
0.7292, 0.6650, 0.5950, 0.5333, 0.4094, 0.3108, 0.2234, 0.1544, \
0.1234, 0.0896, 0.0599, 0.0416, 0.0320, 0.0300, 0.0162, 0.0063, \
0.0007, 0.0034, 0.0020, 0.0006, 0.0000]
filtwave = filtwave * 10000.0
filtsize = [109, 57, 76]
# Holds the filter zero-points as determined from
# Vega model by Dreiling & Bell (ApJ, 241,736, 1980)
#
# B 6.268e-9 erg cm-2 s-1 A-1
# V 3.604e-9
# R 2.161e-9
# I 1.126e-9
#
# The following zero-points are from Lamla
# (Landolt-Boernstein Vol. 2b, eds. K. Schaifer &
# H.H. Voigt, Berlin: Springer, p. 73, 1982 QC61.L332)
#
# U 4.22e-9 erg cm-2 s-1 A-1
#
# J 3.1e-10
# H 1.2e-10
# K 3.9e-11
#
# U B V R I
zeropoint = [3.1e-10, 1.2e-10, 3.9e-11]
mag = np.zeros(3)
filtflux = mag.copy()
coverage = mag.copy()
efflambda = mag.copy()
totflux = mag.copy()
filtername = ['J', 'H', 'K']
for i, _ in enumerate(filtername):
filtw = filtwave[0:filtsize[i], i]
filtt = filttran[0:filtsize[i], i]
mag[i], filtflux[i], coverage[i], efflambda[i], totflux[i]= \
filtermag(hop[0].wave,flux, filtw, filtt, \
zeropoint[i])
logging.info('For object {}'.format(hop[0].obname))
logging.info(
'Filter magnitude Flux(erg/s/cm^2/A) Flux(erg/s/cm^2) Coverage(%) Eff. Lambda'
)
for i in range(0, 3):
if (mag[i] > 99):
logging.info(
' {:1s} FILTER AND SPECTRUM DO NOT OVERLAP'.format(
filtername[i]))
else:
logging.info(
' {:1s} {:6.3f} {:10.4e} {:10.4e} {:5.1f} {:7.1f}'
.format(filtername[i], mag[i], filtflux[i], totflux[i],
coverage[i] * 100., efflambda[i]))
print(' ')
logging.info('Colors')
colortab = [[0, 1], [1, 2]]
for i in range(0, 2):
if (mag[colortab[i][0]] > 99) or (mag[colortab[i][1]] > 99):
logging.info(
'{}-{} ONE OR BOTH FILTERS DO NOT OVERLAP SPECTRUM'.format(
filtername[colortab[i][0]], filtername[colortab[i][1]]))
else:
logging.info('{:1s}-{:1s} {:12.4f}'.format(
filtername[colortab[i][0]], filtername[colortab[i][1]],
mag[colortab[i][0]] - mag[colortab[i][1]]))
print('\nWould you like to scale the spectrum to match photometry?\n')
answer = yesno('n')
if (answer == 'y'):
print('\nWhich filter do you have?')
scalefilt = inputter_single_mix('J/H/K: ', 'JHK')
filtindex = filtername.index(scalefilt)
scalemag = inputter(
'Enter your value for filter {}: '.format(filtername[filtindex]),
'float', False)
print(' ')
logging.info('Scaling {} from {}={:6.3f} to {}={}'.format(
hop[0].obname, filtername[filtindex], mag[filtindex],
filtername[filtindex], scalemag))
logging.info('Multiplying by {:.3f}'.format(
10**(0.4 * (mag[filtindex] - scalemag))))
hop[0].flux = hop[0].flux * 10**(0.4 * (mag[filtindex] - scalemag))
return hop
def womfilters(hop):
"""calculate photometric values from spectra"""
import numpy as np
import logging
from tmath.wombat.filtermag import filtermag
from tmath.wombat.yesno import yesno
from tmath.wombat.inputter import inputter
from tmath.wombat.inputter_single import inputter_single
print('NOTE: The routine expects an f_lambda spectrum')
print(' I will try to guess if the spectrum')
print(' has been scaled by 1E15')
print(' ')
print(' Check this before believing fluxes')
print(' ')
flux=hop[0].flux.copy()
if (np.mean(flux) > 0.00001):
flux = flux *1.e-15
filtwave=np.zeros((141,10))
filttran=np.zeros((141,10))
filtwave[0:21, 1] = [3600.00, 3700.00, 3800.00, 3900.00, \
4000.00, 4100.00, 4200.00, 4300.00, \
4400.00, 4500.00, 4600.00, 4700.00, \
4800.00, 4900.00, 5000.00, 5100.00, \
5200.00, 5300.00, 5400.00, 5500.00, \
5600.00]
filttran[0:21, 1] = [0.00000, 0.03000, 0.13400, 0.56700, \
0.92000, 0.97800, 1.00000, 0.97800, \
0.93500, 0.85300, 0.74000, 0.64000, \
0.53600, 0.42400, 0.32500, 0.23500, \
0.15000, 0.09500, 0.04300, 0.00900, \
0.00000]
filtwave[0:24, 2] = [4700.00, 4800.00, 4900.00, 5000.00, \
5100.00, 5200.00, 5300.00, 5400.00, \
5500.00, 5600.00, 5700.00, 5800.00, \
5900.00, 6000.00, 6100.00, 6200.00, \
6300.00, 6400.00, 6500.00, 6600.00, \
6700.00, 6800.00, 6900.00, 7000.00]
filttran[0:24:, 2] = [0.00000, 0.03000, 0.16300, 0.45800, \
0.78000, 0.96700, 1.00000, 0.97300, \
0.89800, 0.79200, 0.68400, 0.57400, \
0.46100, 0.35900, 0.27000, 0.19700, \
0.13500, 0.08100, 0.04500, 0.02500, \
0.01700, 0.01300, 0.00900, 0.00000]
filtwave[0:24, 3] = [5500.00, 5600.00, 5700.00, 5800.00, \
5900.00, 6000.00, 6100.00, 6200.00, \
6300.00, 6400.00, 6500.00, 6600.00, \
6700.00, 6800.00, 6900.00, 7000.00, \
7100.00, 7200.00, 7300.00, 7400.00, \
7500.00, 8000.00, 8500.00, 9000.00]
filttran[0:24:, 3] = [0.00000, 0.23000, 0.74000, 0.91000, \
0.98000, 1.00000, 0.98000, 0.96000, \
0.93000, 0.90000, 0.86000, 0.81000, \
0.78000, 0.72000, 0.67000, 0.61000, \
0.56000, 0.51000, 0.46000, 0.40000, \
0.35000, 0.14000, 0.03000, 0.00000]
filtwave[0:23, 4] = [7000.00, 7100.00, 7200.00, 7300.00, \
7400.00, 7500.00, 7600.00, 7700.00, \
7800.00, 7900.00, 8000.00, 8100.00, \
8200.00, 8300.00, 8400.00, 8500.00, \
8600.00, 8700.00, 8800.00, 8900.00, \
9000.00, 9100.00, 9200.00]
filttran[0:23, 4] = [0.00000, 0.02400, 0.23200, 0.55500, \
0.78500, 0.91000, 0.96500, 0.98500, \
0.99000, 0.99500, 1.00000, 1.00000, \
0.99000, 0.98000, 0.95000, 0.91000, \
0.86000, 0.75000, 0.56000, 0.33000, \
0.15000, 0.03000, 0.00000]
filtwave[0:24, 0] = [3050.00, 3100.00, 3150.00, 3200.00, \
3250.00, 3300.00, 3350.00, 3400.00, \
3450.00, 3500.00, 3550.00, 3600.00, \
3650.00, 3700.00, 3750.00, 3800.00, \
3850.00, 3900.00, 3950.00, 4000.00, \
4050.00, 4100.00, 4150.00, 4200.00]
filttran[0:24, 0] = [0.00000, 0.02000, 0.07700, 0.13500, \
0.20400, 0.28200, 0.38500, 0.49300, \
0.60000, 0.70500, 0.82000, 0.90000, \
0.95900, 0.99300, 1.00000, 0.97500, \
0.85000, 0.64500, 0.40000, 0.22300, \
0.12500, 0.05700, 0.00500, 0.00000]
filtwave[0:47,5]=[2980., 3005., 3030., 3055., 3080., 3105., 3130., \
3155., 3180.,3205., 3230., 3255., 3280., 3305., \
3330., 3355., 3380., 3405., 3430., 3455., 3480., \
3505., 3530., 3555., 3580., 3605., 3630., 3655., \
3680., 3705., 3730., 3755., 3780., 3805., 3830., \
3855., 3880., 3905., 3930., 3955., 3980., 4005., \
4030., 4055., 4080., 4105., 4130.]
filttran[0:47,5]=[0. , 0.0014, 0.0071, 0.0127, 0.0198, 0.0314, \
0.0464, 0.0629, 0.0794, 0.0949, 0.1093, 0.1229, \
0.1352, 0.1458, 0.1545, 0.1617, 0.1679, 0.1737, \
0.1786, 0.1819, 0.1842, 0.186 , 0.187 , 0.1868, \
0.1862, 0.1858, 0.1853, 0.1841, 0.1812, 0.1754, \
0.1669, 0.1558, 0.1419, 0.1247, 0.1054, 0.0851, \
0.0634, 0.0405, 0.0216, 0.011 , 0.0062, 0.0032, \
0.0015, 0.0008, 0.0006, 0.0003, 0. ]
filtwave[0:89,6]=[3630., 3655., 3680., 3705., 3730., 3755., 3780., \
3805., 3830., 3855., 3880., 3905., 3930., 3955., \
3980., 4005., 4030., 4055., 4080., 4105., 4130., \
4155., 4180., 4205., 4230., 4255., 4280., 4305., \
4330., 4355., 4380., 4405., 4430., 4455., 4480., \
4505., 4530., 4555., 4580., 4605., 4630., 4655., \
4680., 4705., 4730., 4755., 4780., 4805., 4830., \
4855., 4880., 4905., 4930., 4955., 4980., 5005., \
5030., 5055., 5080., 5105., 5130., 5155., 5180., \
5205., 5230., 5255., 5280., 5305., 5330., 5355., \
5380., 5405., 5430., 5455., 5480., 5505., 5530., \
5555., 5580., 5605., 5630., 5655., 5680., 5705., \
5730., 5755., 5780., 5805., 5830.]
filttran[0:89,6]=[0.000e+00, 5.000e-04, 1.300e-03, 2.200e-03, \
3.000e-03, 3.900e-03, 5.500e-03, 8.700e-03, \
1.620e-02, 3.010e-02, 5.000e-02, 7.450e-02, \
1.024e-01, 1.324e-01, 1.629e-01, 1.924e-01, \
2.191e-01, 2.419e-01,2.609e-01, 2.767e-01, \
2.899e-01, 3.010e-01, 3.105e-01, 3.186e-01, \
3.258e-01, 3.324e-01, 3.385e-01, 3.442e-01, \
3.496e-01, 3.548e-01, 3.596e-01, 3.640e-01, \
3.678e-01, 3.709e-01, 3.736e-01, 3.763e-01, \
3.792e-01, 3.827e-01, 3.863e-01, 3.899e-01, \
3.931e-01, 3.955e-01, 3.973e-01, 3.986e-01, \
3.997e-01, 4.008e-01, 4.019e-01, 4.030e-01, \
4.043e-01, 4.057e-01, 4.073e-01, 4.091e-01, \
4.110e-01, 4.129e-01, 4.147e-01, 4.165e-01, \
4.181e-01, 4.194e-01, 4.201e-01, 4.201e-01, \
4.191e-01, 4.169e-01, 4.147e-01, 4.115e-01, \
3.988e-01, 3.684e-01, 3.233e-01, 2.690e-01, \
2.112e-01, 1.550e-01, 1.043e-01, 6.270e-02, \
3.370e-02, 1.900e-02, 1.280e-02, 8.700e-03, \
5.700e-03, 3.700e-03, 2.400e-03, 1.700e-03, \
1.400e-03, 1.200e-03, 1.000e-03, 9.000e-04, \
7.000e-04, 5.000e-04, 3.000e-04, 1.000e-04, 0.000e+00]
filtwave[0:75,7]=[5380., 5405., 5430., 5455., 5480., 5505., 5530., \
5555., 5580., 5605., 5630., 5655., 5680., 5705., \
5730., 5755., 5780., 5805., 5830., 5855., 5880., \
5905., 5930., 5955., 5980., 6005., 6030., 6055., \
6080., 6105., 6130., 6155., 6180., 6205., 6230., \
6255., 6280., 6305., 6330., 6355., 6380., 6405., \
6430., 6455., 6480., 6505., 6530., 6555., 6580., \
6605., 6630., 6655., 6680., 6705., 6730., 6755., \
6780., 6805., 6830., 6855., 6880., 6905., 6930., \
6955., 6980., 7005., 7030., 7055., 7080., 7105., \
7130., 7155., 7180., 7205., 7230.]
filttran[0:75,7]=[0.000e+00, 1.600e-03, 1.130e-02, 2.970e-02, \
5.680e-02, 9.230e-02, 1.356e-01, 1.856e-01, \
2.390e-01, 2.917e-01, 3.395e-01, 3.794e-01, \
4.116e-01, 4.371e-01, 4.570e-01, 4.723e-01, \
4.839e-01, 4.925e-01, 4.990e-01, 5.040e-01, \
5.080e-01, 5.112e-01, 5.141e-01, 5.169e-01, \
5.194e-01, 5.213e-01, 5.222e-01, 5.220e-01, \
5.212e-01, 5.202e-01, 5.197e-01, 5.202e-01, \
5.215e-01, 5.233e-01, 5.254e-01, 5.275e-01, \
5.294e-01, 5.310e-01, 5.319e-01, 5.320e-01, \
5.316e-01, 5.310e-01, 5.305e-01, 5.302e-01, \
5.299e-01, 5.290e-01, 5.271e-01, 5.241e-01, \
5.211e-01, 5.176e-01, 5.057e-01, 4.775e-01, \
4.341e-01, 3.792e-01, 3.162e-01, 2.488e-01, \
1.824e-01, 1.225e-01, 7.470e-02, 4.300e-02, \
2.470e-02, 1.550e-02, 1.120e-02, 8.300e-03, \
5.900e-03, 4.100e-03, 2.900e-03, 2.100e-03, \
1.600e-03, 1.300e-03, 1.000e-03, 8.000e-04, \
5.000e-04, 2.000e-04, 0.000e+00]
filtwave[0:89,8]=[6430., 6455., 6480., 6505., 6530., 6555., 6580., \
6605., 6630., 6655., 6680., 6705., 6730., 6755., \
6780., 6805., 6830., 6855., 6880., 6905., 6930., \
6955., 6980., 7005., 7030., 7055., 7080., 7105., \
7130., 7155., 7180., 7205., 7230., 7255., 7280., \
7305., 7330., 7355., 7380., 7405., 7430., 7455., \
7480., 7505., 7530., 7555., 7580., 7605., 7630., \
7655., 7680., 7705., 7730., 7755., 7780., 7805., \
7830., 7855., 7880., 7905., 7930., 7955., 7980., \
8005., 8030., 8055., 8080., 8105., 8130., 8155., \
8180., 8205., 8230., 8255., 8280., 8305., 8330., \
8355., 8380., 8405., 8430., 8455., 8480., 8505., \
8530., 8555., 8580., 8605., 8630.]
filttran[0:89,8]=[0.000e+00, 1.000e-04, 3.000e-04, 4.000e-04, 5.000e-04, \
4.000e-04, 3.000e-04, 5.000e-04, 1.000e-03, 2.100e-03, \
3.600e-03, 6.000e-03, 1.110e-02, 2.080e-02, 3.660e-02, \
5.970e-02, 9.130e-02, 1.317e-01, 1.779e-01, 2.260e-01, \
2.719e-01, 3.125e-01, 3.470e-01, 3.755e-01, 3.978e-01, \
4.142e-01, 4.256e-01, 4.331e-01, 4.377e-01, 4.405e-01, \
4.416e-01, 4.411e-01, 4.392e-01, 4.358e-01, 4.315e-01, \
4.265e-01, 4.214e-01, 4.165e-01, 4.119e-01, 4.077e-01, \
4.039e-01, 4.006e-01, 3.975e-01, 3.943e-01, 3.906e-01, \
3.862e-01, 3.812e-01, 3.757e-01, 3.700e-01, 3.641e-01, \
3.583e-01, 3.526e-01, 3.473e-01, 3.424e-01, 3.379e-01, \
3.337e-01, 3.297e-01, 3.259e-01, 3.224e-01, 3.194e-01, \
3.169e-01, 3.150e-01, 3.132e-01, 3.111e-01, 3.081e-01, \
3.039e-01, 2.996e-01, 2.945e-01, 2.803e-01, 2.493e-01, \
2.060e-01, 1.578e-01, 1.118e-01, 7.430e-02, 4.580e-02, \
2.570e-02, 1.340e-02, 7.700e-03, 5.500e-03, 3.700e-03, \
2.300e-03, 1.500e-03, 1.100e-03, 1.100e-03, 1.100e-03, \
9.000e-04, 6.000e-04, 3.000e-04, 0.000e+00]
filtwave[0:141,9]=[ 7730., 7755., 7780., 7805., 7830., 7855., 7880., \
7905., 7930., 7955., 7980., 8005., 8030., 8055., \
8080., 8105., 8130., 8155., 8180., 8205., 8230., \
8255., 8280., 8305., 8330., 8355., 8380., 8405., \
8430., 8455., 8480., 8505., 8530., 8555., 8580., \
8605., 8630., 8655., 8680., 8705., 8730., 8755., \
8780., 8805., 8830., 8855., 8880., 8905., 8930., \
8955., 8980., 9005., 9030., 9055., 9080., 9105.,\
9130., 9155., 9180., 9205., 9230., 9255., 9280.,\
9305., 9330., 9355., 9380., 9405., 9430., 9455., \
9480., 9505., 9530., 9555., 9580., 9605., 9630., \
9655., 9680., 9705., 9730., 9755., 9780., 9805., \
9830., 9855., 9880., 9905., 9930., 9955., 9980., \
10005., 10030., 10055., 10080., 10105., 10130., 10155.,\
10180., 10205., 10230., 10255., 10280., 10305., 10330.,\
10355., 10380., 10405., 10430., 10455., 10480., 10505.,\
10530., 10555., 10580., 10605., 10630., 10655., 10680.,\
10705., 10730., 10755., 10780., 10805., 10830., 10855.,\
10880., 10905., 10930., 10955., 10980., 11005., 11030.,\
11055., 11080., 11105., 11130., 11155., 11180., 11205.,\
11230.]
filttran[0:141,9]=[0.00e+00, 0.00e+00, 1.00e-04, 1.00e-04, 1.00e-04, \
2.00e-04, 2.00e-04, 3.00e-04, 5.00e-04, 7.00e-04, \
1.10e-03, 1.70e-03, 2.70e-03, 4.00e-03, 5.80e-03, \
8.20e-03, 1.14e-02, 1.55e-02, 2.02e-02, 2.55e-02, \
3.11e-02, 3.69e-02, 4.28e-02, 4.84e-02, 5.36e-02, \
5.83e-02, 6.25e-02, 6.61e-02, 6.93e-02, 7.20e-02, \
7.44e-02, 7.63e-02, 7.79e-02, 7.92e-02, 8.01e-02, \
8.08e-02, 8.12e-02, 8.13e-02, 8.12e-02, 8.07e-02, \
8.01e-02, 7.91e-02, 7.79e-02, 7.66e-02, 7.50e-02, \
7.34e-02, 7.16e-02, 6.98e-02, 6.79e-02, 6.61e-02, \
6.42e-02, 6.24e-02, 6.07e-02, 5.90e-02, 5.74e-02, \
5.59e-02, 5.46e-02, 5.35e-02, 5.24e-02, 5.15e-02, \
5.05e-02, 4.96e-02, 4.85e-02, 4.74e-02, 4.62e-02, \
4.50e-02, 4.38e-02, 4.26e-02, 4.15e-02, 4.04e-02, \
3.93e-02, 3.83e-02, 3.73e-02, 3.63e-02, 3.53e-02, \
3.42e-02, 3.31e-02, 3.19e-02, 3.07e-02, 2.94e-02, \
2.80e-02, 2.67e-02, 2.53e-02, 2.40e-02, 2.27e-02, \
2.13e-02, 2.01e-02, 1.88e-02, 1.76e-02, 1.65e-02, \
1.53e-02, 1.43e-02, 1.32e-02, 1.22e-02, 1.12e-02, \
1.03e-02, 9.40e-03, 8.60e-03, 7.80e-03, 7.10e-03, \
6.40e-03, 5.80e-03, 5.20e-03, 4.70e-03, 4.20e-03, \
3.80e-03, 3.50e-03, 3.10e-03, 2.80e-03, 2.60e-03, \
2.40e-03, 2.20e-03, 2.00e-03, 1.90e-03, 1.80e-03, \
1.60e-03, 1.50e-03, 1.40e-03, 1.30e-03, 1.20e-03, \
1.10e-03, 1.00e-03, 9.00e-04, 8.00e-04, 8.00e-04, \
7.00e-04, 7.00e-04, 6.00e-04, 6.00e-04, 5.00e-04, \
5.00e-04, 4.00e-04, 4.00e-04, 3.00e-04, 3.00e-04, \
2.00e-04, 2.00e-04, 1.00e-04, 1.00e-04, 0.00e+00, \
0.00e+00]
filtsize = [24, 21, 24, 24, 23, 47, 89, 75, 89, 141]
# Holds the filter zero-points as determined from
# Vega model by Dreiling & Bell (ApJ, 241,736, 1980)
#
# B 6.268e-9 erg cm-2 s-1 A-1
# V 3.604e-9
# R 2.161e-9
# I 1.126e-9
#
# The following zero-points are from Lamla
# (Landolt-Boernstein Vol. 2b, eds. K. Schaifer &
# H.H. Voigt, Berlin: Springer, p. 73, 1982 QC61.L332)
#
# U 4.22e-9 erg cm-2 s-1 A-1
#
# J 3.1e-10
# H 1.2e-10
# K 3.9e-11
#
# U B V R I
zp_johnson = np.array([4.22e-9, 6.268e-9, 3.604e-9, 2.161e-9, 1.126e-9])
leff_sloan=np.array([3560., 4830., 6260., 7670., 9100])
zp_sloan=3.631e-20*2.99792458e18/(leff_sloan*leff_sloan)
zeropoint=np.concatenate([zp_johnson,zp_sloan])
mag=np.zeros(10)
filtflux=mag.copy()
coverage=mag.copy()
efflambda=mag.copy()
totflux=mag.copy()
filtername = ['U', 'B', 'V', 'R', 'I','u','g','r','i','z']
for i,_ in enumerate(filtername):
filtw=filtwave[0:filtsize[i],i]
filtt=filttran[0:filtsize[i],i]
mag[i], filtflux[i], coverage[i], efflambda[i], totflux[i]= \
filtermag(hop[0].wave,flux, filtw, filtt, \
zeropoint[i])
logging.info('For object {}'.format(hop[0].obname))
logging.info('Filter magnitude Flux(erg/s/cm^2/A) Flux(erg/s/cm^2) Coverage(%) Eff. Lambda')
for i in range(0,5):
if (mag[i] > 99):
logging.info(' {:1s} FILTER AND SPECTRUM DO NOT OVERLAP'.format(filtername[i]))
else:
logging.info(' {:1s} {:6.3f} {:10.4e} {:10.4e} {:5.1f} {:6.1f}'.format(filtername[i],mag[i],filtflux[i],totflux[i],coverage[i]*100.,efflambda[i]))
for i in range(5,10):
if (mag[i] > 99):
logging.info(' {:1s} FILTER AND SPECTRUM DO NOT OVERLAP'.format(filtername[i]))
else:
logging.info(' {:1s} {:6.3f} {:10.4e} {:10.4e} {:5.1f} {:6.1f}'.format(filtername[i],mag[i],filtflux[i],totflux[i],coverage[i]*100.,efflambda[i]))
print(' ')
logging.info('Colors')
colortab=[[0,1],[1,2],[2,3],[2,4],[5,6],[6,7],[7,8],[8,9]]
for i in range(0,4):
if (mag[colortab[i][0]] > 99) or (mag[colortab[i][1]] > 99):
logging.info('{}-{} ONE OR BOTH FILTERS DO NOT OVERLAP SPECTRUM'.format(filtername[colortab[i][0]],filtername[colortab[i][1]]))
else:
logging.info('{:1s}-{:1s} {:12.4f}'.format(filtername[colortab[i][0]],filtername[colortab[i][1]],mag[colortab[i][0]]-mag[colortab[i][1]]))
for i in range(4,8):
if (mag[colortab[i][0]] > 99) or (mag[colortab[i][1]] > 99):
logging.info('{}-{} ONE OR BOTH FILTERS DO NOT OVERLAP SPECTRUM'.format(filtername[colortab[i][0]],filtername[colortab[i][1]]))
else:
logging.info('{:1s}-{:1s} {:12.4f}'.format(filtername[colortab[i][0]],filtername[colortab[i][1]],mag[colortab[i][0]]-mag[colortab[i][1]]))
print('\nWould you like to scale the spectrum to match photometry?\n')
answer=yesno('n')
if (answer == 'y'):
print('\nWhich filter do you have?')
scalefilt=inputter_single_mix('U/B/V/R/I/u/g/r/i/z: ','UBVRIugriz')
filtindex=filtername.index(scalefilt)
scalemag=inputter('Enter your value for filter {}: '.format(filtername[filtindex]),'float',False)
print(' ')
logging.info('Scaling {} from {}={:6.3f} to {}={}'.format(hop[0].obname,filtername[filtindex],mag[filtindex],filtername[filtindex],scalemag))
logging.info('Multiplying by {:.3f}'.format(10**(0.4*(mag[filtindex]-scalemag))))
hop[0].flux=hop[0].flux*10**(0.4*(mag[filtindex]-scalemag))
return hop
def fitspl_dev(wave, flux, airlimit, fig, cal=None):
import numpy as np
import matplotlib.pyplot as plt
from scipy.interpolate import splrep, splev
import tmath.wombat.womconfig as womconfig
from tmath.wombat.womget_element import womget_element
from tmath.pydux.wave_telluric import wave_telluric
from tmath.wombat.yesno import yesno
from tmath.wombat.onclick import onclick
from tmath.wombat.onkeypress import onkeypress
import glob
"""fit spline to spectrum"""
# starting points for spline
# bandpts = np.array([3000, 3050, 3090, 3200, 3430, 3450, 3500, 3550, 3600, \
# 3650, 3700, 3767, 3863, 3945, 4025, 4144, 4200, 4250, \
# 4280, 4390, 4450, 4500, 4600, 4655, 4717, 4750, 4908, \
# 4950, 5000, 5050, 5100, 5150, 5200, 5250, 5280, 5350, \
# 5387, 5439, 5500, 5550, 6100, 6150, 6400, 6430, 6650, \
# 6700, 6750, 6800, 7450, 7500, 7550, 8420, 8460, 8520, \
# 8570, 8600, 8725, 8770, 9910, 10000, 10200, 10300, \
# 10400, 10500, 10600, 10700])
binWidth = 60
bandpts = np.arange(3000, 11000, binWidth)
locsinrange = np.logical_and((bandpts > wave[10]), (bandpts < wave[-10]))
#useband=bandpts[locsinrange]
# now mask based on spectral features
# you can add mask features here, and the feature name can
# be anything, they aren't used explicitly
featureMask = {}
# empirical masks from Dimitriadis
featureMask['feature1'] = [3722.56 - 10.0 / 2., 3722.56 + 10.0 / 2.]
featureMask['feature2'] = [3736.90 - 15.0 / 2., 3736.90 + 15.0 / 2.]
featureMask['feature3'] = [3752.00 - 15.0 / 2., 3752.00 + 15.0 / 2.]
featureMask['feature4'] = [3772.00 - 17.0 / 2., 3772.00 + 17.0 / 2.]
featureMask['feature5'] = [3800.00 - 18.0 / 2., 3800.00 + 18.0 / 2.]
featureMask['feature6'] = [3835.38 - 20.0 / 2., 3835.38 + 20.0 / 2.]
featureMask['feature7'] = [3889.05 - 24.0 / 2., 3889.05 + 24.0 / 2.]
featureMask['feature8'] = [3933.66 - 16.0 / 2., 3933.66 + 16.0 / 2.]
featureMask['feature9'] = [3970.07 - 18.0 / 2., 3970.07 + 18.0 / 2.]
featureMask['feature10'] = [4101.74 - 28.0 / 2., 4101.74 + 28.0 / 2.]
featureMask['feature11'] = [4340.46 - 30.0 / 2., 4340.46 + 30.0 / 2.]
featureMask['feature12'] = [4471.48 - 20.0 / 2., 4471.48 + 20.0 / 2.]
featureMask['feature13'] = [4685.70 - 30.0 / 2., 4685.70 + 30.0 / 2.]
featureMask['feature14'] = [4861.36 - 35.0 / 2., 4861.36 + 35.0 / 2.]
featureMask['feature15'] = [5411.52 - 35.0 / 2., 5411.52 + 35.0 / 2.]
featureMask['feature16'] = [5889.95 - 32.0 / 2., 5889.95 + 32.0 / 2.]
featureMask['feature17'] = [6562.85 - 40.0 / 2., 6562.85 + 40.0 / 2.]
featureMask['feature18'] = [8498.02 - 25.0 / 2., 8498.02 + 25.0 / 2.]
featureMask['feature19'] = [8542.09 - 25.0 / 2., 8542.09 + 25.0 / 2.]
featureMask['feature20'] = [8662.14 - 25.0 / 2., 8662.14 + 25.0 / 2.]
featureMask['feature21'] = [8763.96 - 20.0 / 2., 8763.96 + 20.0 / 2.]
featureMask['feature22'] = [8865.75 - 25.0 / 2., 8865.75 + 25.0 / 2.]
featureMask['feature23'] = [9010.00 - 28.0 / 2., 9010.00 + 28.0 / 2.]
featureMask['feature24'] = [9213.90 - 30.0 / 2., 9213.90 + 30.0 / 2.]
featureMask['feature25'] = [9545.97 - 34.0 / 2., 9545.97 + 34.0 / 2.]
featureMask['telluric1'] = [3216.0 - binWidth / 2., 3420.0 + binWidth / 2.]
#featureMask['telluric2'] = [5600.0-binWidth/2., 6050.0+binWidth/2.]
featureMask['telluric3'] = [6250.0 - binWidth / 2., 6360.0 + binWidth / 2.]
featureMask['telluric4'] = [6450.0 - binWidth / 2., 6530.0 + binWidth / 2.]
featureMask['telluric5'] = [6840.0 - binWidth / 2., 7410.0 + binWidth / 2.]
featureMask['telluric6'] = [7560.0 - binWidth / 2., 8410.0 + binWidth / 2.]
featureMask['telluric7'] = [8925.0 - binWidth / 2., 9900.0 + binWidth / 2.]
# inital testing masks from XIDL
# featureMask['balmer1'] = [3714.0-binWidth/2., 3723.0+binWidth/2.]
# featureMask['balmer2'] = [3650.0-binWidth/2., 3820.0+binWidth/2.]
# featureMask['balmer3'] = [3725.0-binWidth/2., 3735.0+binWidth/2.]
# featureMask['balmer4'] = [3740.0-binWidth/2., 3755.0+binWidth/2.]
# featureMask['balmer5'] = [3760.0-binWidth/2., 3775.0+binWidth/2.]
# featureMask['balmer6'] = [3785.0-binWidth/2., 3806.0+binWidth/2.]
# featureMask['balmer7'] = [3810.0-binWidth/2., 3820.0+binWidth/2.]
# featureMask['balmer8'] = [3824.0-binWidth/2., 3841.0+binWidth/2.]
# featureMask['balmer9'] = [3880.0-binWidth/2., 3895.0+binWidth/2.]
# featureMask['balmer10'] = [3957.0-binWidth/2., 3979.0+binWidth/2.]
# featureMask['balmer11'] = [4000.0-binWidth/2., 4030.0+binWidth/2.]
# featureMask['balmer12'] = [4087.0-binWidth/2., 4120.0+binWidth/2.]
# featureMask['balmer13'] = [4135.0-binWidth/2., 4145.0+binWidth/2.]
# featureMask['balmer14'] = [4328.0-binWidth/2., 4355.0+binWidth/2.]
# featureMask['balmer15'] = [4677.0-binWidth/2., 4692.0+binWidth/2.]
# featureMask['balmer16'] = [4830.0-binWidth/2., 4931.0+binWidth/2.]
# featureMask['balmer17'] = [5402.0-binWidth/2., 5417.0+binWidth/2.]
# featureMask['balmer18'] = [6535.0-binWidth/2., 6590.0+binWidth/2.]
# featureMask['telluric1'] = [3216.0-binWidth/2., 3420.0+binWidth/2.]
# #featureMask['telluric2'] = [5600.0-binWidth/2., 6050.0+binWidth/2.]
# featureMask['telluric3'] = [6250.0-binWidth/2., 6360.0+binWidth/2.]
# featureMask['telluric4'] = [6450.0-binWidth/2., 6530.0+binWidth/2.]
# featureMask['telluric5'] = [6840.0-binWidth/2., 7410.0+binWidth/2.]
# featureMask['telluric6'] = [7560.0-binWidth/2., 8410.0+binWidth/2.]
# featureMask['telluric7'] = [8925.0-binWidth/2., 9900.0+binWidth/2.]
# generate a mask via a boolean array that excludes regions in stellar features
maskInds = np.full(len(bandpts), True, dtype=bool)
for i, key in enumerate(featureMask.keys()):
featureMaskInds = np.logical_or((bandpts < featureMask[key][0]),
(bandpts > featureMask[key][1]))
maskInds *= featureMaskInds
fullMask = locsinrange * maskInds
# apply the mask
useband = bandpts[fullMask]
for i, _ in enumerate(useband):
index = womget_element(wave, useband[i])
useband[i] = index
# useband now has indices of wavelength positions
if (min(flux) < 0):
flux[np.where(flux < 0)] = 0.0
plt.cla()
plt.plot(wave, flux, drawstyle='steps-mid', color='k')
xmin, xmax = plt.xlim()
ymin, ymax = plt.ylim()
plt.xlim([xmin, xmax])
plt.ylim([ymin, ymax])
if (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)
wavetell = wave.copy()
fluxtell = flux.copy()
wavetell[loc] = np.nan
fluxtell[loc] = np.nan
plt.plot(wavetell, fluxtell, drawstyle='steps-mid', color='violet')
if '../../master_files/' + cal + '_splpts_master.txt' not in glob.glob(
'../../master_files/*'):
womconfig.nsplinepoints = len(useband)
womconfig.tmpsplptsx = wave[useband].copy().tolist()
womconfig.tmpsplptsy = []
for i, _ in enumerate(useband):
womconfig.tmpsplptsy.append(
np.median(flux[useband[i] - 2:useband[i] + 3]))
spline = splrep(womconfig.tmpsplptsx, womconfig.tmpsplptsy, k=3)
else:
masterx, mastery = np.genfromtxt('../../master_files/' + cal +
'_splpts_master.txt')
womconfig.nsplinepoints = len(masterx)
womconfig.tmpsplptsx = list(masterx)
womconfig.tmpsplptsy = list(mastery)
# print (type(womconfig.tmpsplptsx))
spline = splrep(womconfig.tmpsplptsx, womconfig.tmpsplptsy, k=3)
splineresult = splev(wave, spline)
plt.cla()
plt.plot(wave, flux, drawstyle='steps-mid', color='k')
plt.plot(wavetell, fluxtell, drawstyle='steps-mid', color='violet')
if (len(womconfig.tmpsplptsx) > 0):
plt.plot(womconfig.tmpsplptsx, womconfig.tmpsplptsy, 'ro')
plt.plot(wave, splineresult, color='g')
plt.xlabel('Wavelength')
plt.ylabel('Flux')
plt.xlim([xmin, xmax])
plt.ylim([ymin, ymax])
plt.pause(0.01)
done = False
print('Is this OK? ')
answer = yesno('n')
if (answer == 'y'):
done = True
splptsy = [
z for _, z in sorted(zip(womconfig.tmpsplptsx, womconfig.tmpsplptsy))
]
splptsx = sorted(womconfig.tmpsplptsx)
while (not done):
plotdone = False
while (not plotdone):
plt.cla()
plt.plot(wave, flux, drawstyle='steps-mid', color='k')
plt.plot(wavetell, fluxtell, drawstyle='steps-mid', color='violet')
if (len(womconfig.tmpsplptsx) > 0):
plt.plot(womconfig.tmpsplptsx, womconfig.tmpsplptsy, 'ro')
plt.plot(wave, splineresult, color='g')
plt.xlabel('Wavelength')
plt.ylabel('Flux')
plt.xlim([xmin, xmax])
plt.ylim([ymin, ymax])
plt.pause(0.01)
print('Change scale? ')
answer = yesno('n')
if (answer == 'y'):
plt.cla()
plt.plot(wave, flux, drawstyle='steps-mid', color='k')
plt.plot(wavetell,
fluxtell,
drawstyle='steps-mid',
color='violet')
if (len(womconfig.tmpsplptsx) > 0):
plt.plot(womconfig.tmpsplptsx, womconfig.tmpsplptsy, 'ro')
plt.plot(wave, splineresult, color='g')
plt.xlabel('Wavelength')
plt.ylabel('Flux')
print('Click corners of box to change plot scale')
newlims = plt.ginput(2, timeout=-1)
xmin = newlims[0][0]
ymin = newlims[0][1]
xmax = newlims[1][0]
ymax = newlims[1][1]
plt.cla()
plt.plot(wave, flux, drawstyle='steps-mid', color='k')
plt.plot(wavetell,
fluxtell,
drawstyle='steps-mid',
color='violet')
if (len(womconfig.tmpsplptsx) > 0):
plt.plot(womconfig.tmpsplptsx, womconfig.tmpsplptsy, 'ro')
plt.plot(wave, splineresult, color='g')
plt.xlabel('Wavelength')
plt.ylabel('Flux')
plt.xlim([xmin, xmax])
plt.ylim([ymin, ymax])
plotdone = True
else:
plotdone = True
cid = fig.canvas.mpl_connect('button_press_event', onclick)
cid2 = fig.canvas.mpl_connect('key_press_event', onkeypress)
print('\nClick on continuum points for spline fit.')
print('Left button or (a) = add point')
print('Middle button or (s) = delete point')
print('Right button or (d) = done\n')
womconfig.pflag = ''
while (womconfig.pflag != 'done'):
plt.pause(0.01)
fig.canvas.mpl_disconnect(cid)
fig.canvas.mpl_disconnect(cid2)
splptsy = [
z
for _, z in sorted(zip(womconfig.tmpsplptsx, womconfig.tmpsplptsy))
]
splptsx = sorted(womconfig.tmpsplptsx)
spline = splrep(splptsx, splptsy, k=3)
splineresult = splev(wave, spline)
plt.plot(wave, splineresult, drawstyle='steps-mid', color='g')
plt.pause(0.01)
print('Is this fit OK? ')
answer = yesno('y')
if (answer == 'y'):
done = True
if cal != None:
np.savetxt('../../master_files/' + cal + '_splpts_master.txt',
[splptsx, splptsy])
return splineresult
def womgau(hop):
"""fit gaussian to line"""
import numpy as np
import logging
import matplotlib.pyplot as plt
from scipy.optimize import curve_fit
from tmath.wombat.womwaverange import womwaverange
from tmath.wombat.womget_element import womget_element
from tmath.wombat.inputter import inputter
from tmath.wombat.inputter_single import inputter_single
from tmath.wombat.gauss import gauss
from tmath.wombat.gauss_cont import gauss_cont
from tmath.wombat.yesno import yesno
print(' ')
logging.info('Object is {}'.format(hop[0].obname))
print(' ')
print('Spectrum runs from {} to {}'.format(hop[0].wave[0],
hop[0].wave[-1]))
print(' ')
print('This routine expects the spectrum to be in flambda units.')
print('It also expects a linear wavelength scale.')
print(' ')
print('Choose general region of spectrum\n')
nwave, nflux, mode = womwaverange(hop[0].wave, hop[0].flux, 'none')
print('\nNow pick the exact range for the fit')
waveint, fluxint, mode = womwaverange(nwave, nflux, mode)
indexblue = womget_element(nwave, waveint[0])
indexred = womget_element(nwave, waveint[-1])
if (mode == 'w'):
done = False
while (not done):
print(' ')
wavecenter = inputter('Enter approximate center of Gaussian : ',
'float', False)
indexcenter = womget_element(waveint, wavecenter)
if (indexcenter <= 0) or (wavecenter > waveint[-1]):
print('Bad central wavelength, try again')
else:
done = True
else:
done = False
while (not done):
print('Mark the approximate center of the Gaussian')
pickcent = plt.ginput(1, timeout=-1)
indexcenter = womget_element(waveint, pickcent[0][0])
print('\nApproximate center at {}'.format(waveint[indexcenter]))
print('\nIs this OK?')
answer = yesno('y')
if (answer == 'y'):
done = True
weights = np.sqrt(hop[0].var[indexblue:indexred + 1])
print(' ')
continuum = inputter_single(
'Do you want to fit gaussian with (c)ontinuum, or (n)o continuum? ',
'cn')
if (continuum == 'c'):
p = [fluxint[indexcenter], waveint[indexcenter], 3.0, 1.0, waveint[0]]
result = curve_fit(gauss_cont,
waveint,
fluxint,
sigma=weights,
p0=p,
absolute_sigma=True,
full_output=True)
else:
p = [fluxint[indexcenter], waveint[indexcenter], 3.0]
result = curve_fit(gauss,
waveint,
fluxint,
sigma=weights,
p0=p,
absolute_sigma=True,
full_output=True)
coefferr = np.sqrt(np.diag(result[1]))
coeff = result[0]
# make 'finer-grained' version of fit, 0.2A/pix for calculations
wavecalc = np.arange(2 * 5 * 50 * abs(
coeff[2])) * 0.2 + coeff[1] - 0.2 * 5 * 50 * abs(coeff[2])
calccenter = womget_element(wavecalc, coeff[1])
if (continuum == 'c'):
fluxcalc = gauss_cont(wavecalc, *coeff)
fluxcont = wavecalc * coeff[3] + coeff[4]
fluxgaussian = fluxcalc - fluxcont
linecont = fluxcont[calccenter]
else:
fluxcalc = gauss(wavecalc, *coeff)
deltafit = wavecalc[1] - wavecalc[0]
calcindexblue = womget_element(wavecalc, waveint[0])
calcindexred = womget_element(wavecalc, waveint[-1])
sumfluxcalc = np.sum(fluxcalc[calcindexblue:calcindexred + 1] * deltafit)
sumallfluxcalc = np.sum(fluxcalc * deltafit)
chi = (result[2]['fvec']**2).sum()
redchi = chi / (len(waveint) - len(coeff))
if (continuum == 'c'):
sumfluxgaussian = np.sum(fluxgaussian[calcindexblue:calcindexred + 1] *
deltafit)
sumallfluxgaussian = np.sum(fluxgaussian * deltafit)
sumfluxcont = np.sum(fluxcont[calcindexblue:calcindexred + 1] *
deltafit)
sumallfluxcont = np.sum(fluxcont * deltafit)
# propagate uncertainty (from old version) not sure this is correct
height_pct = coefferr[0] / coeff[0]
sigma_pct = coefferr[2] / coeff[2]
flux_pct = np.sqrt(height_pct**2 + sigma_pct**2)
sumfluxgaussiansig = sumfluxgaussian * flux_pct
sumallfluxgaussiansig = sumallfluxgaussian * flux_pct
plt.cla()
plt.plot(nwave, nflux, drawstyle='steps-mid', color='k')
plt.ylabel('Flux')
plt.xlabel('Wavelength')
xmin, xmax = plt.xlim()
ymin, ymax = plt.ylim()
plt.plot(wavecalc, fluxcalc, drawstyle='steps-mid', color='b')
if (continuum == 'c'):
plt.plot(wavecalc, fluxgaussian, drawstyle='steps-mid', color='r')
plt.plot(wavecalc, fluxcont, drawstyle='steps-mid', color='g')
plt.plot([waveint[0], waveint[0]], [ymin, ymax], color='k', linestyle='--')
plt.plot([waveint[-1], waveint[-1]], [ymin, ymax],
color='k',
linestyle='--')
plt.xlim([xmin, xmax])
plt.ylim([ymin, ymax])
logging.info('For object {} Gaussian fit'.format(hop[0].obname))
if (continuum == 'c'):
print(
'\nData = Black, Fit = Blue, Continuum = Green, Fit-Continuum = Red\n'
)
else:
print('\nData = Black, Fit = Blue\n')
logging.info('Height {:16.8f}+/-{:16.8f}'.format(
coeff[0], coefferr[0]))
logging.info('Center {:16.8f}+/-{:16.8f}'.format(
coeff[1], coefferr[1]))
logging.info('Sigma {:16.8f}+/-{:16.8f}'.format(
coeff[2], coefferr[2]))
if (continuum == 'c'):
logging.info('Slope {:16.8f}+/-{:16.8f}'.format(
coeff[3], coefferr[3]))
logging.info('Y-intercept {:16.8f}+/-{:16.8f}'.format(
coeff[4], coefferr[4]))
logging.info('FWHM {:16.8f}+/-{:16.8f}'.format(
2.35482 * np.abs(coeff[2]), 2.35482 * coefferr[2]))
logging.info(
'Flux between dotted lines (Gaussian): {:16.8f}+/-{:16.8f}'.format(
sumfluxgaussian, sumfluxgaussiansig))
logging.info('EW between dotted lines (Gaussian): {:16.8f}'.format(
sumfluxgaussian / linecont))
logging.info('Flux for full (Gaussian): {:16.8f}+/-{:16.8f}'.format(
sumallfluxgaussian, sumallfluxgaussiansig))
logging.info('EW for full (Gaussian): {:16.8f}'.format(
sumallfluxgaussian / linecont))
logging.info(
'Continuum flux at line center: {:16.8f}'.format(linecont))
logging.info('Chi^2: {}'.format(chi))
logging.info('Reduced chi^2: {}'.format(redchi))
logging.info('All fluxes might need to be scaled by 1e-15')
print(' ')
return hop
def womspl(hop, fig):
"""fit spline to spectrum"""
import matplotlib.pyplot as plt
import numpy as np
import copy
from tmath.wombat.womplot import womplot
from tmath.wombat.onclick import onclick
from scipy.interpolate import splrep, splev
from tmath.wombat.inputter import inputter
from tmath.wombat.yesno import yesno
from tmath.wombat import HOPSIZE
import tmath.wombat.womconfig as womconfig
# global nsplinepoints, tmpsplptsx, tmpsplptsy, pflag
print('\nObject is {}\n'.format(hop[0].obname))
womplot(hop)
xmin, xmax = plt.xlim()
ymin, ymax = plt.ylim()
plt.xlim([xmin, xmax])
plt.ylim([ymin, ymax])
womconfig.nsplinepoints = 0
womconfig.tmpsplptsx = []
womconfig.tmpsplptsy = []
done = False
while (not done):
plt.cla()
plt.plot(hop[0].wave, hop[0].flux, drawstyle='steps-mid')
if (len(womconfig.tmpsplptsx) > 0):
plt.plot(womconfig.tmpsplptsx, womconfig.tmpsplptsy, 'ro')
plt.xlabel('Wavelength')
plt.ylabel('Flux')
plt.title(hop[0].obname)
plt.xlim([xmin, xmax])
plt.ylim([ymin, ymax])
cid = fig.canvas.mpl_connect('button_press_event', onclick)
print('\nClick on continuum points for spline fit.')
print('Left button = add point')
print('Middle button = delete point')
print('Right button = done\n')
womconfig.pflag = ''
while (womconfig.pflag != 'done'):
plt.pause(0.01)
fig.canvas.mpl_disconnect(cid)
splptsy = [
z
for _, z in sorted(zip(womconfig.tmpsplptsx, womconfig.tmpsplptsy))
]
splptsx = sorted(womconfig.tmpsplptsx)
spline = splrep(splptsx, splptsy, k=3)
splineresult = splev(hop[0].wave, spline)
plt.plot(hop[0].wave, splineresult, drawstyle='steps-mid')
plt.pause(0.01)
print('Is this fit OK? ')
answer = yesno('y')
if (answer == 'y'):
done = True
print('\nSubtract spline fit from flux?\n')
sub = yesno('n')
if (sub == 'y'):
hop[0].flux = hop[0].flux - splineresult
print('\nStore spline in hopper?\n')
store = yesno('y')
if (store == 'y'):
hopnum = 0
while (hopnum < 1) or (hopnum > HOPSIZE):
hopnum = inputter('Store in which hopper: ', 'int', False)
hop[hopnum] = copy.deepcopy(hop[0])
hop[hopnum].flux = splineresult.copy()
hop[hopnum].obname = hop[hopnum].obname + 'spline'
hop[hopnum].var = np.zeros(len(hop[0].wave))
return hop
def womzap(hop):
"""routine to zap outliers (CRs)"""
import numpy as np
import matplotlib.pyplot as plt
import logging
from tmath.wombat.inputter import inputter
from tmath.wombat.inputter_single import inputter_single
from tmath.wombat.yesno import yesno
from tmath.wombat.wshow import wshow
plt.cla()
plt.plot(hop[0].wave,hop[0].flux,drawstyle='steps-mid')
plt.xlabel('Wavelength')
plt.ylabel('Flux')
plt.title(hop[0].obname)
wshow()
print('\nRoutine to zap outliers\n')
done = False
while (not done):
nsig=inputter('Enter zapping threshold in sigmas (0=replace all with median): ','float',False)
print(' ')
boxsize=inputter('Enter box size for computing statistics: (odd integer < 45) ','int',False)
if (boxsize < 3) or (boxsize > 45) or (nsig < 0):
print('Invalid boxsize or sigma')
else:
done = True
if (boxsize % 2 == 0):
boxsize=boxsize+1
half=int(boxsize/2.)
newflux=hop[0].flux.copy()
if (nsig > 0):
mode=inputter_single('Use inter(q)uartile or (m)edian variance (q/m)? ','qm')
if (mode == 'm'):
for i in range(half,len(newflux)-half):
sample=newflux[i-half:i+half+1]
medval=np.median(sample)
varpix=(sample[half]-medval)**2
sum=-1.0*varpix
for k in range(0,boxsize):
diff=sample[k]-medval
sum=sum+diff*diff
sum=sum/(boxsize-1)
if (varpix > nsig*nsig*sum):
newflux[i]=medval
if (mode == 'q'):
for i in range(half,len(newflux)-half):
sample=newflux[i-half:i+half+1]
medval=np.median(sample)
q25=np.percentile(sample,25.)
q75=np.percentile(sample,75.)
qsig=0.7414272*(q75-q25)
diff=abs(sample[half]-medval)
if (diff > nsig*qsig):
newflux[i]=medval
if (nsig == 0):
from scipy.ndimage.filters import median_filter
newflux=median_filter(newflux,boxsize)
plt.plot(hop[0].wave,newflux,drawstyle='steps-mid')
print('Does this zapping look good?')
good=yesno('y')
if (good == 'y'):
hop[0].flux=newflux.copy()
logging.debug('File {} zapped with sigma {} and boxsize {}'.format\
(hop[0].obname,nsig,boxsize))
else:
print('OK, active spectrum unchanged')
#FIX var
return hop
def telluric_remove(bstarwave,
bstar,
bairmass,
wave,
object,
airmass,
variance,
spectrum,
shift=None):
import numpy as np
import pdb
import matplotlib.pyplot as plt
from tmath.wombat.inputter import inputter
from tmath.wombat.yesno import yesno
from tmath.wombat.womscipyrebin import womscipyrebin
from tmath.wombat.womget_element import womget_element
from tmath.pydux.xcor import xcor
from tmath.pydux.finalscaler import finalscaler
bstartmp = womscipyrebin(bstarwave, bstar, wave)
# plt.cla()
# plt.plot(bstarwave,bstartmp)
# plt.pause(0.01)
# answer=yesno('y')
print('\nThe ratio of airmasses (object/B-star) is {}'.format(airmass /
bairmass))
if (airmass / bairmass > 3.0) or (airmass / bairmass < 0.33):
print('\nWARNING: OBJECT AND B-STAR HAVE WILDLY DIFFERENT')
print('AIRMASSES: ATMOSPHERIC BAND DIVISION MAY BE LOUSY\n')
wmin = wave[0]
wmax = wave[-1]
npix = len(object)
wdelt = wave[1] - wave[0]
print('wdelt', wdelt)
lag = np.zeros(3)
lagflag = [False] * 3
xfactor = 10
maxlag = 200
if not shift:
print('\nCross-correlating object with B-star spectrum\n')
fig = plt.figure()
axarr = fig.subplots(2, 1)
if (wmin < 6200) and (wmax > 6400) and (wmax < 6900):
indblue = womget_element(wave, 6200)
indred = womget_element(wave, 6400)
lag[0] = xcor(object[indblue:indred + 1],
bstartmp[indblue:indred + 1], xfactor, maxlag)
lagflag[0] = True
print('The shift at the 6250A band is {} angstroms'.format(lag[0] *
wdelt))
if (wmin < 6800) and (wmax > 6500):
indblue = womget_element(wave, 6800)
indred = womget_element(wave, 6950)
scale = 1. / np.max(object[indblue:indred + 1])
obb = scale * object[indblue:indred + 1]
bb = bstartmp[indblue:indred + 1]
lag[1] = xcor(obb, bb, xfactor, maxlag)
lagflag[1] = True
print('The shift at the B band is {} angstroms'.format(lag[1] *
wdelt))
plt.cla()
# ymin,ymax=finalscaler(object)
# plt.plot(wave,object,drawstyle='steps-mid',color='r')
# plt.plot(wave,newobject,drawstyle='steps-mid',color='k')
ymin, ymax = finalscaler(bstartmp[indblue:indred + 1])
axarr[0].plot(wave[indblue:indred + 1],
scale * object[indblue:indred + 1],
drawstyle='steps-mid',
color='r')
axarr[0].plot(wave[indblue:indred + 1],
bstartmp[indblue:indred + 1],
drawstyle='steps-mid',
color='k')
axarr[0].plot(wave[indblue:indred + 1] + lag[1] * wdelt,
bstartmp[indblue:indred + 1],
drawstyle='steps-mid',
color='g')
plt.pause(0.01)
if (wmin < 7500) and (wmax > 8000):
indblue = womget_element(wave, 7500)
indred = womget_element(wave, 8000)
scale = 1. / np.max(object[indblue:indred + 1])
lag[2] = xcor(scale * object[indblue:indred + 1],
bstartmp[indblue:indred + 1], xfactor, maxlag)
print('The shift at the A band is {} angstroms'.format(lag[2] *
wdelt))
lagflag[2] = True
# ymin,ymax=finalscaler(object)
# plt.plot(wave,object,drawstyle='steps-mid',color='r')
# plt.plot(wave,newobject,drawstyle='steps-mid',color='k')
ymin, ymax = finalscaler(bstartmp[indblue:indred + 1])
axarr[1].plot(wave[indblue:indred + 1],
scale * object[indblue:indred + 1],
drawstyle='steps-mid',
color='r')
axarr[1].plot(wave[indblue:indred + 1],
bstartmp[indblue:indred + 1],
drawstyle='steps-mid',
color='k')
axarr[1].plot(wave[indblue:indred + 1] + lag[2] * wdelt,
bstartmp[indblue:indred + 1],
drawstyle='steps-mid',
color='g')
plt.pause(0.01)
check = inputter('Check plot [enter when done]: ', 'string', False)
if (sum(lagflag) > 0):
avglag = np.sum(lag) / sum(lagflag)
angshift = avglag * wdelt
print('The mean shift is {} Angstroms'.format(angshift))
else:
angshift = 0.0
plt.close()
else:
angshift = shift
fig = plt.figure(figsize=[9, 5])
telluric_done = False
bstartmpcopy = bstartmp.copy()
while (not telluric_done):
print('Applying a shift of {} Angstroms'.format(angshift))
bstartmp = bstartmpcopy.copy()
tmp = womscipyrebin(wave + angshift, bstartmp, wave)
bstartmp = tmp.copy()
bstartmp = bstartmp**((airmass / bairmass)**0.55)
# newobject=object/bstartmp
newobject = spectrum / bstartmp
bvar = variance / bstartmp
print('\nPlotting before and after atmospheric band correction\n')
plt.cla()
# ymin,ymax=finalscaler(object)
# plt.plot(wave,object,drawstyle='steps-mid',color='r')
# plt.plot(wave,newobject,drawstyle='steps-mid',color='k')
ymin, ymax = finalscaler(spectrum)
plt.plot(wave, spectrum, drawstyle='steps-mid', color='r')
plt.plot(wave, newobject, drawstyle='steps-mid', color='k')
plt.ylim([ymin, ymax])
plt.pause(0.01)
if not shift:
print('Is this OK?')
answer = yesno('y')
if (answer == 'n'):
angshift = inputter('Enter B-star shift in Angstroms: ',
'float', False)
else:
telluric_done = True
else:
check = inputter('Check plot [enter when done]: ', 'string', False)
telluric_done = True
plt.close()
return newobject, bvar, angshift
