def time_calibration(input_file):
"""
Obtain the calibration for time (hjd) by pyraf and the airmass for each image. Include in the header all information.
"""
original_path = os.getcwd()
save_path = input_file['save_path']
#change to save data reduction directory
os.chdir(save_path)
print '\n Reading the list of images ....\n'
planet = input_file['exoplanet'] #set exoplanet name
images = sorted(glob.glob('AB'+planet+'*.fits'))
print images
#include de RA,DEC and epoch of the exoplanet
RA,DEC,epoch = input_file['RA'],input_file['DEC'],input_file['epoch']
#obtain ST JD using iraf task and introduce in the header
for i in range(len(images)):
hdr = fits.getheader(images[i])
if int(split(hdr['UT'],':')[0]) < int(hdr['timezone']):
new_date = use.yesterday(hdr['date-obs'])
#print images[i], new_date
else:
new_date = hdr['date-obs']
year,month,day = split(new_date,'-')
iraf.asttimes(year=year,month=month,day=day,time=hdr['loctime'],obs=input_file['observatory'])
JD = iraf.asttimes.jd #obtain julian date
LMST = iraf.asttimes.lmst #obtain the sideral time
LMST = use.sexagesimal_format(LMST) #convert sideral time in sexagesimal format
iraf.hedit(images[i],'ST',LMST,add='yes',verify='no',show='no',update='yes') #create the ST keyword in the header
iraf.ccdhedit(images[i],'LMST',LMST,type='string') #include the mean sideral time in the header
iraf.ccdhedit(images[i],'JD',JD,type='string') #include de julian date in the header
#include RA, and DEC of the object in your header
iraf.ccdhedit(images[i],"RA",RA,type="string") #include right ascention in the header
iraf.ccdhedit(images[i],"DEC",DEC,type="string") #include declination in the header
iraf.ccdhedit(images[i],"epoch",epoch,type="string") #include epoch in the header
# use.update_progress((i+1.)/len(images))
print '\n Setting airmass ....\n'
for i in range(len(images)):
print '# ',images[i]
#iraf.hedit(images[i],'airmass',airmass,add='yes')
#iraf.hedit(images[i],'HJD',HJD,add='yes')
iraf.setairmass.observatory = input_file['observatory']
iraf.setairmass(images[i])
iraf.setjd.time = 'ut'
iraf.setjd(images[i])
print '\n.... done.\n'
#export information
hjd, jd, airmass, st = [],[],[],[]
for i in range(len(images)):
hdr = fits.getheader(images[i])
hjd.append(hdr['HJD'])
jd.append(hdr['JD'])
airmass.append(hdr['airmass'])
st.append(hdr['st'])
#saving the data
data = DataFrame([list(hjd),list(jd),list(st),list(airmass)]).T
data.columns = ['HJD','JD','ST','Airmass']
data.to_csv('results_iraf_calibrations.csv')
#change to workings directory
os.chdir(original_path)
return
def setairmass(inim, obs, ra, dec):
"""
setairmass -- update image headers with the effective airmass
obs -- SAO1-m : "sao"
ra -- target ra hh:mm:ss
dec -- target dec dd:mm:ss
location -- Put your observatory information.
*** Hourly airmass for Feige 56 ***
Epoch 2000.00: RA 12 06 47.3, dec 11 40 13
Epoch 2019.35: RA 12 07 46.6, dec 11 33 45
At midnight: UT date 2019 May 10, Moon 0.33 illum, 59 degr from obj
Local UT LMST HA secz par.angl. SunAlt MoonAlt
22 00 11 00 10 40 -1 28 1.186 -33.6 -6.3 52.1
23 00 12 00 11 40 -0 28 1.119 -12.4 -16.3 40.7
0 00 13 00 12 40 0 32 1.121 14.2 ... 29.1
1 00 14 00 13 40 1 32 1.194 34.7 ... 17.7
2 00 15 00 14 40 2 33 1.363 46.2 ... 6.6
3 00 16 00 15 40 3 33 1.701 51.8 ... ...
4 00 17 00 16 41 4 33 2.436 53.9 ... ...
5 00 18 00 17 41 5 33 4.691 53.8 ... ...
6 00 19 00 18 41 6 33 (v.low) 51.8 -15.8 ...
7 00 20 00 19 41 7 33 (down) 47.9 -5.7 ...
"""
import glob
import os, sys
from pyraf import iraf
from astropy.time import Time
from astropy.io import fits
from astropy import units as u
hdr = fits.getheader(inim)
t = Time(hdr['date-obs'],
format='isot',
scale='utc',
location=(126.95333299999999 * u.deg, 37.45704167 * u.deg,
190 * u.m))
st = t.sidereal_time('apparent') # in hourangle
set_observatory(obs)
st_hms = str(int(st.hms.h)).zfill(2) + ':' + str(int(
st.hms.m)).zfill(2) + ':' + str(int(st.hms.s)).zfill(2)
iraf.hedit(images=inim, fields='st', value=st_hms, add='yes', verify='yes')
iraf.hedit(images=inim, fields='ra', value=ra, add='yes', verify='yes')
iraf.hedit(images=inim, fields='dec', value=dec, add='yes')
print('OK.')
iraf.astutil()
iraf.setairmass(images=inim,
observatory=obs,
equinox='epoch',
date="date-obs",
exposure="exptime",
airmass="airmass",
show='yes',
ut="date-obs",
override='yes')
def cor_airmass(lstfile):
f = open(lstfile)
l = f.readlines()
f.close()
l = [tmp.split('\n')[0] for tmp in l]
fitlst = ['awftbo' + tmp for tmp in l]
for fitname in fitlst:
if os.path.isfile(fitname):
fit = pyfits.open(fitname)
objname = fit[0].header['object'].replace('_', ' ').split()[0]
print(fitname + ' ' + objname)
objname_new = find_normal_objname(objname)
if len(objname_new) == 0:
objname_new = raw_input('please input object name:')
radec = findradec(objname_new)
if len(radec) == 0:
radec = raw_input('please input ra dec of objname:')
radec = radec.split()
fitextnum = len(fit)
fit.close()
for lay in range(fitextnum):
airold = iraf.hselect(images = fitname + '[%i]' % lay, fields = 'airmass', expr = 'yes', Stdout = 1)
airold = float(airold[0])
print(fitname + ' ' + objname + ' ' + str(lay) + ' airmass old: ' + str(airold))
fitnamelay = fitname + '[%i]' % lay
iraf.hedit(images = fitnamelay, fields = 'airold',
value = airold, add = 'yes', addonly = 'yes', delete = 'no',
verify = 'no', show = 'yes', update = 'yes')
iraf.hedit(images = fitnamelay, fields = 'sname',
value = objname_new, add = 'yes', addonly = 'yes', delete = 'no',
verify = 'no', show = 'yes', update = 'yes')
iraf.hedit(images = fitnamelay, fields = 'RA',
value = radec[0], add = 'yes', addonly = 'yes', delete = 'no',
verify = 'no', show = 'yes', update = 'yes')
iraf.hedit(images = fitnamelay, fields = 'DEC',
value = radec[1], add = 'yes', addonly = 'yes', delete = 'no',
verify = 'no', show = 'yes', update = 'yes')
iraf.twodspec()
stdpath = os.path.split(os.path.realpath(__file__))[0] + os.sep + 'standarddir' + os.sep
iraf.longslit(dispaxis = 2, nsum = 1, observatory = 'Lijiang',
extinction = 'onedstds$LJextinct.dat', caldir = stdpath)
iraf.setairmass(images = fitnamelay,
observatory = 'Lijiang', intype = 'beginning',
outtype = 'effective', ra = 'ra', dec = 'dec',
equinox = 'epoch', st = 'lst', ut = 'date-obs',
date = 'date-obs', exposure = 'exptime', airmass = 'airmass',
utmiddle = 'utmiddle', scale = 750.0, show = 'yes',
override = 'yes', update = 'yes')
print('name airmass_new airmass_old')
iraf.hselect(fitnamelay, fields = '$I,airmass,airold',
expr = 'yes')
def set_airmass(fn):
fit = pyfits.open(fn)
size = len(fit)
for i, hdu in enumerate(fit):
if 'AIRMASS' in hdu.header:
airmassold = hdu.header['AIRMASS']
print('%s[%d] airmassold = %f' % (fn, i, airmassold), )
if 'AIROLD' in hdu.header:
airold = hdu.header['AIROLD']
print('%s[%d] AIROLD = %f' % (fn, i, airold))
print(
'AIROLD keyword alreay exist, the airmass old will not saved'
)
else:
iraf.hedit(images=fn + '[%d]' % i,
fields='AIROLD',
value=airmassold,
add='Yes',
addonly='Yes',
delete='No',
verify='No',
show='Yes',
update='Yes')
fit.close()
ra, dec = get_ra_dec(fn)
set_ra_dec(fn, ra, dec)
iraf.twodspec()
iraf.longslit(dispaxis=2, nsum=1, observatory='ca', caldir=stdpath)
for i in range(size):
iraf.setairmass(images=fn,
observatory='ca',
intype='beginning',
outtype='effective',
ra='ra',
dec='dec',
equinox='epoch',
st='lst',
ut='date-obs',
date='date-obs',
exposure='exptime',
airmass='airmass',
utmiddle='utmiddle',
scale=750.0,
show='yes',
override='yes',
update='yes')
def correct_airmass():
stdout = os.popen("ls Y*otbfmsw.fits").readlines()
namelst = [i.split('\n')[0] for i in stdout]
for i in xrange(len(namelst)):
fits = pyfits.open(namelst[i])
extnum = len(fits)
objname = fits[0].header['object']
fits.close()
print '#' * 50
print namelst[i], objname
name = raw_input('please input the name of object:')
ra, dec = findradec(name)
print name, ra, dec
for j in xrange(extnum):
stdout = iraf.hselect(images=namelst[i] + '[%i]' % j,
fields='airmass',
expr='yes',
Stdout=1)
airold = float(stdout[0])
print '+' * 5, namelst[i], 'ext:', j, 'airmass_old:', airold
iraf.hedit(images=namelst[i] + '[%i]' % j,
fields='airold',
value=airold,
add='yes',
addonly='yes',
delete='no',
verify='no',
show='yes',
update='yes')
iraf.hedit(images=namelst[i] + '[%i]' % j,
fields='sname',
value=name,
add='yes',
addonly='yes',
delete='no',
verify='no',
show='yes',
update='yes')
iraf.hedit(images=namelst[i] + '[%i]' % j,
fields='sname',
value=name,
add='yes',
addonly='yes',
delete='no',
verify='no',
show='yes',
update='yes')
iraf.hedit(images=namelst[i] + '[%i]' % j,
fields='ra',
value=ra,
add='yes',
addonly='yes',
delete='no',
verify='no',
show='yes',
update='yes')
iraf.hedit(images=namelst[i] + '[%i]' % j,
fields='dec',
value=dec,
add='yes',
addonly='yes',
delete='no',
verify='no',
show='yes',
update='yes')
iraf.twodspec()
iraf.longslit(dispaxis=2,
nsum=1,
observatory='Lijiang',
extinction='onedstds$LJextinct.dat',
caldir='onedstds$spec50cal/')
iraf.setairmass(images=namelst[i] + '[%i]' % j,
observatory='Lijiang',
intype='beginning',
outtype='effective',
ra='ra',
dec='dec',
equinox='epoch',
st='lst',
ut='date-obs',
date='date-obs',
exposure='exptime',
airmass='airmass',
utmiddle='utmiddle',
scale=750.0,
show='yes',
override='yes',
update='yes')
print 'name airmass_new airmass_old'
iraf.hselect(images=namelst[i] + '[%i]' % j,
fields='$I,airmass,airold',
expr='yes')
iraf.hedit(images[i],'ST',LMST,add='yes',verify='no',show='no',update='yes') #create the ST keyword in the header
iraf.ccdhedit(images[i],'LMST',LMST,type='string') #include the mean sideral time in the header
iraf.ccdhedit(images[i],'JD',JD,type='string') #include de julian date in the header
#include RA, and DEC of the object in your header
iraf.ccdhedit(images[i],"RA",RA,type="string") #include right ascention in the header
iraf.ccdhedit(images[i],"DEC",DEC,type="string") #include declination in the header
iraf.ccdhedit(images[i],"epoch",epoch,type="string") #include epoch in the header
# use.update_progress((i+1.)/len(images))
print '\n Setting airmass ....\n'
for i in range(len(images)):
print '# ',images[i]
#iraf.hedit(images[i],'airmass',airmass,add='yes')
#iraf.hedit(images[i],'HJD',HJD,add='yes')
iraf.setairmass.observatory = input_data['observatory']
iraf.setairmass(images[i])
iraf.setjd.time = 'ut'
iraf.setjd(images[i])
print '\n.... done.\n'
#export information
hjd, jd, airmass, st = [],[],[],[]
for i in range(len(images)):
hdr = fits.getheader(images[i])
hjd.append(hdr['HJD'])
jd.append(hdr['JD'])
airmass.append(hdr['airmass'])
st.append(hdr['st'])
#saving the data
data = DataFrame([list(hjd),list(jd),list(st),list(airmass)]).T
date='date-obs',
exposure='exptime',
ra='ra',
dec='dec',
epoch='equinox',
utdate=yes,
uttime=yes,
listonly=no)
iraf.setairmass('@targets_extracted',
date='date-obs',
exposure='exptime',
ra='ra',
dec='dec',
equinox='equinox',
utmiddle='utmiddle',
st='lst',
airmass='airmass',
show=yes,
update=yes,
override=yes,
intype='beginning',
outtype='middle',
ut='date-obs')
iraf.setjd('sig_//@targets_extracted',
date='date-obs',
exposure='exptime',
ra='ra',
dec='dec',
epoch='equinox',
utdate=yes,
print '\nThis is the list of local time: \n'
print '\nImage ** Local Time (isot format) ** Sideral Time (hours min seg)\n'
for i in range(len(images)):
print images[i], ' ** ', local_time[i], ' ** ', sideraltime[i]
print '\nSetting coordinates to our ' + planet + ': \n'
RA = Angle(file['RA'] + file['u.RA'])
DEC = Angle(file['DEC'] + file['u.DEC'])
coordinates = SkyCoord(RA, DEC, frame=file['frame'])
print '\nCoordinates: ', coordinates
print '\nIncluding RA,DEC,epoch in the header of the images ....\n'
#RA in hours
for i in range(len(images)):
iraf.ccdhedit(images[i], 'RA', coordinates.ra.hour, type='string')
iraf.ccdhedit(images[i], 'DEC', coordinates.dec.deg, type='string')
iraf.ccdhedit(images[i], 'epoch', file['epoch'], type='string')
iraf.ccdhedit(images[i], 'st', sideraltime[i].hour, type='string')
update_progress((i + 1.) / len(images))
print '\nCalibrating your airmass correction: \n'
print 'Setting observatory: ', file['observatory']
iraf.setairmass('AB' + planet + '*.fits')
iraf.setairmass.observatory = file['observatory']
print '\n.... done.\n'
#Setting Julian Date
print '\n Setting Julian Date\n'
iraf.setjd.time = "ut"
iraf.setjd('AB' + planet + '*.fist')
print '\n.... done.\n'
def set_airmass(fn):
"""
Set airmass of fits fn. If keyword 'AIRMASS' already exist, the old airmass
value will saved by keyword 'AIROLD'. If keyword 'AIROLD' also exist, the
old airmass value will just overwritten. If the fits fn have more than one
hdu or more than one star, this function assume they have same ra, dec and
observed in same time.
fn : fits name
type : string
"""
fit = pyfits.open(fn)
size = len(fit)
for i, hdu in enumerate(fit):
if 'AIRMASS' in hdu.header:
airmassold = hdu.header['AIRMASS']
print(
colored('%s[%d] airmassold = %f' % (fn, i, airmassold),
'blue'))
if 'AIROLD' in hdu.header:
airold = hdu.header['AIROLD']
print(colored('%s[%d] AIROLD = %f' % (fn, i, airold),
'yellow'))
print(
colored(('\'AIROLD\' keyword alreay exist, the airmass '
'old will not saved'), 'yellow'))
else:
iraf.hedit(images=fn + '[%d]' % i,
fields='AIROLD',
value=airmassold,
add='Yes',
addonly='Yes',
delete='No',
verify='No',
show='Yes',
update='Yes')
fit.close()
ra, dec = get_ra_dec(fn)
set_ra_dec(fn, ra, dec)
iraf.twodspec()
stdpath = std_path + os.sep
extfile = config_path + os.sep + 'LJextinct.dat'
iraf.longslit(dispaxis=2,
nsum=1,
observatory='Lijiang',
extinction=extfile,
caldir=stdpath)
for i in range(size):
iraf.setairmass(images=fn + '[%d]' % i,
observatory=obs.name,
intype='beginning',
outtype='effective',
ra='ra',
dec='dec',
equinox='epoch',
st='lst',
ut='date-obs',
date='date-obs',
exposure='exptime',
airmass='airmass',
utmiddle='utmiddle',
scale=750.0,
show='yes',
override='yes',
update='yes')
print '\nImage ** Local Time (isot format) ** Sideral Time (hours min seg)\n'
for i in range(len(images)):
print images[i],' ** ',local_time[i],' ** ',sideraltime[i]
print '\nSetting coordinates to our '+planet+': \n'
RA = Angle(file['RA']+file['u.RA'])
DEC = Angle(file['DEC']+file['u.DEC'])
coordinates = SkyCoord(RA,DEC,frame=file['frame'])
print '\nCoordinates: ',coordinates
print '\nIncluding RA,DEC,epoch in the header of the images ....\n'
#RA in hours
for i in range(len(images)):
iraf.ccdhedit(images[i],'RA',coordinates.ra.hour,type='string')
iraf.ccdhedit(images[i],'DEC',coordinates.dec.deg,type='string')
iraf.ccdhedit(images[i],'epoch',file['epoch'],type='string')
iraf.ccdhedit(images[i],'st',sideraltime[i].hour,type='string')
update_progress((i+1.)/len(images))
print '\nCalibrating your airmass correction: \n'
print 'Setting observatory: ',file['observatory']
iraf.setairmass('AB'+planet+'*.fits')
iraf.setairmass.observatory = file['observatory']
print '\n.... done.\n'
#Setting Julian Date
print '\n Setting Julian Date\n'
iraf.setjd.time = "ut"
iraf.setjd('AB'+planet+'*.fist')
print '\n.... done.\n'
it = 0
for j in range(len(file_list[3])):
if file_list[3][j] == '_':
it += 1
if it == 2 and file_list[3][j] != '_':
date = date + file_list[3][j]
print('Date = ' + date)
if flux_calibrate != 'n':
## begin IRAFing
print('\n' + 'Setting airmass...')
iraf.setairmass('@speclist',
observ='lapalma',
ra='cat-ra',
dec='cat-dec',
equi='cat-equi',
st='lst',
ut='utstart')
print('\n' + 'Combining spectra...')
iraf.scombine(input='@speclist',
output='allspec',
group='all',
combine='median',
gain=2.45,
reject='crreject',
lthresh=1e-30,
hthresh=hthresh2)
print('\n' + 'Applying flux calibration to sensitivity function...')
utme_old=hdr['UT-M_E']
print "[HJD] Old: %s --> New: %.6f" % (hjd_old,HJD[i])
print "[JD_E] Old: %s --> New: %.6f" % (jde_old,JD_e[i])
print "[UT-M_E] Old: %s --> New: %s" % (utme_old,mid_times[i].iso.replace(' ','T'))
elif args.action == 'updatedb':
qry="SELECT hjd_mid FROM %s WHERE image_id='%s'" % (table,t[i])
print qry
with db.cursor() as cur:
count=cur.execute(qry)
if count == 1:
qry2="UPDATE %s SET hjd_mid = %.8f WHERE image_id = '%s'" % (table, HJD[i], t[i])
print qry2
for row in cur:
print "%f --> %f" % (row[0],HJD[i])
with db.cursor() as cur2:
cur2.execute(qry2)
db.commit()
elif count == 0:
print "Image is not logged in %s" % (table)
else:
print "DUPLICATE ENTRIES IN %s FOR image_id='%s'" % (table,t[i])
raise Exception
else:
print "I'm lost..."
print "\n"
if args.action == 'update':
# ensure the airmass is ok now that utmiddle etc are fixed
iraf.setairmass(images="*.fits", ra="cat-ra", dec="cat-dec", equinox="cat-epoc", st="st", ut="utstart", date="date-obs", exposur="exptime", airmass="airmass", utmiddl="ut-mid", show="yes", update="yes", overrid="yes",mode="ql")
### Run setairmass to make sure the airmass parameter is correct
iraf.hedit(
images = file_path + file_name,\
fields = "EPOCH",\
value = 2000,\
add = 1,\
addonly = 0,\
delete = 0,\
verify = 0,\
show = 1,\
update = 1)
iraf.setairmass(
images = file_path + file_name,\
observatory = "SSO",\
intype = "beginning",\
outtype = "effective",\
ra = "RA",\
dec = "DEC",\
equinox = "EPOCH",\
st = "LST-OBS",\
ut = "UTC-OBS",\
date = "DATE-OBS",\
exposure = "EXPTIME",\
airmass = "AIRMASS",\
utmiddle = "UTCMID",\
scale = 750.0,\
show = 1,\
update = 1,\
override = 1)
