def searchflat(img, listflat):
from floyds.util import readhdr, readkey3
import floyds
import glob, re
from numpy import argmin, abs
hdr = readhdr(img)
JD = readkey3(hdr, 'JD')
_instrume = readkey3(hdr, 'TELID')
camera = readkey3(hdr, 'INSTRUME')
grism0 = readkey3(hdr, 'grism')
if not listflat:
directory = floyds.__path__[0] + '/archive/' + str(_instrume) + '/' + camera + '/flat/' + grism0
listflat = glob.glob(directory + '/*fits')
else:
directory = ''
if listflat:
faltfile = ''
distance = []
goodlist = []
for flat in listflat:
hdrf = readhdr(flat)
JDflat = readkey3(hdrf, 'JD')
filter1 = readkey3(hdrf, 'filter')
if filter0 == filter1:
goodlist.append(flat)
distance.append(abs(JD - JDflat))
if len(distance) >= 1:
flatfile = goodlist[argmin(distance)]
else:
flatfile = ''
else:
flatfile = ''
return flatfile, directory
def searchflat(img, listflat):
from floyds.util import readhdr, readkey3
import floyds
import glob, re
from numpy import argmin, abs
hdr = readhdr(img)
JD = readkey3(hdr, 'JD')
_instrume = readkey3(hdr, 'TELID')
grism0 = readkey3(hdr, 'grism')
if not listflat:
directory = floyds.__path__[0] + '/archive/' + str(_instrume) + '/flat/' + grism0
listflat = glob.glob(directory + '/*fits')
else:
directory = ''
if listflat:
faltfile = ''
distance = []
goodlist = []
for flat in listflat:
hdrf = readhdr(flat)
JDflat = readkey3(hdrf, 'JD')
filter1 = readkey3(hdrf, 'filter')
if filter0 == filter1:
goodlist.append(flat)
distance.append(abs(JD - JDflat))
if len(distance) >= 1:
flatfile = goodlist[argmin(distance)]
else:
flatfile = ''
else:
flatfile = ''
return flatfile, directory
def fluxcalib2d(img2d, sensfun): # flux calibrate 2d images
import pyfits
import re, string
from pyfits import open as popen
from numpy import arange, array, float32
from numpy import interp as ninterp
import floyds
from floyds.util import readhdr, readkey3, delete
_tel = floyds.util.readkey3(floyds.util.readhdr(re.sub('\n', '', img2d)),
'TELID')
if _tel == 'fts':
_extinction = 'ssoextinct.dat'
_observatory = 'sso'
elif _tel == 'ftn':
_extinction = 'maua.dat'
_observatory = 'cfht'
else:
sys.exit('ERROR: observatory not recognised')
data2d, hdr2d = pyfits.getdata(img2d, 0, header=True)
if 'GRISM' in hdr2d: _arm = hdr2d['GRISM']
else: _arm = ''
xxd = arange(len(data2d[0, :]))
crvald = popen(img2d)[0].header.get('CRVAL1')
cdd = popen(img2d)[0].header.get('CD1_1')
_exptime, _airmass = readkey3(readhdr(img2d),
'exptime'), readkey3(readhdr(img2d),
'airmass')
# read sensfunction and interpole pixel of 2D image
yys = popen(sensfun)[0].data
crvals = popen(sensfun)[0].header.get('CRVAL1')
cds = popen(sensfun)[0].header.get('CD1_1')
yys = (10**(yys / 2.5)) * cds # from sens iraf in sens flux
xxs = arange(len(yys))
aasens = crvals + (xxs) * cds
xxs2 = (aasens - crvald) / cdd
aasens2 = ninterp(xxd, xxs2, yys)
# read atmosferic function and interpole pixel of 2D image
aae, yye = floyds.util.ReadAscii2(floyds.__path__[0] +
'/standard/extinction/' + _extinction)
aae, yye = array(aae, float), array(yye, float)
xxe = (aae - crvald) / cdd
atm_xx = ninterp(xxd, xxe, yye)
aircorr = 10**(0.4 * array(atm_xx) * _airmass)
img2df = re.sub('.fits', '_2df.fits', img2d)
for i in range(len(data2d[:, 0])):
data2d[i, :] = (
(array(data2d[i, :] / _exptime) * array(aircorr)) / aasens2) * 1e20
floyds.util.delete(img2df)
pyfits.writeto(img2df, float32(data2d), hdr2d)
floyds.util.updateheader(
img2df, 0, {'SENSFUN' + _arm[0]: [string.split(sensfun, '/')[-1], '']})
floyds.util.updateheader(
img2df, 0,
{'BUNIT': ['erg/cm2/s/A 10^20', 'Physical unit of array values']})
return img2df
def phase3header(img):
import floyds
import string
from floyds.util import readhdr, readkey3
from numpy import max, min, isfinite
from astropy.io import fits
img_data = fits.open(img)[0].data
hdr = readhdr(img)
hedvec0 = {
'DATAMIN': [float(min(img_data[isfinite(img_data)])), ''],
'DATAMAX': [float(max(img_data[isfinite(img_data)])), ''],
'ORIGIN': ['ESO', 'European Southern Observatory'],
'PROCSOFT': ['floyds_' + str(floyds.__version__), 'pipeline version']
}
if readkey3(hdr, 'filter'):
hedvec0['FILTER'] = [readkey3(hdr, 'filter'), 'Filter name']
if readkey3(hdr, 'gain'):
hedvec0['GAIN'] = [
readkey3(hdr, 'gain'), 'Conversion from electrons to ADU'
]
if readkey3(hdr, 'esoid'):
hedvec0['OBID'] = [readkey3(hdr, 'esoid'), 'Observation block ID']
if readkey3(hdr, 'esoprog'):
hedvec0['PROG_ID'] = [
readkey3(hdr, 'esoprog'), 'ESO program identification'
]
if readkey3(hdr, 'tech'):
hedvec0['OBSTECH'] = [readkey3(hdr, 'tech'), 'Observation technique']
floyds.util.updateheader(img, 0, hedvec0)
def airmass(img, overwrite=True, _observatory='lasilla'):
import floyds
from floyds.util import readhdr, readkey3, delete
from pyraf import iraf
iraf.astutil(_doprint=0)
hdr = readhdr(img)
if readkey3(hdr, 'UTC'):
_UT = (readkey3(hdr, 'UTC') + (readkey3(hdr, 'exptime') / 2)) / 3600
_date = readkey3(hdr, 'date-obs')
_date = _date[0:4] + '-' + _date[4:6] + '-' + _date[6:8]
_RA = readkey3(hdr, 'RA') / 15
_DEC = readkey3(hdr, 'DEC')
f = file('airmass.txt', 'w')
f.write('mst = mst ("' + str(_date) + '",' + str(_UT) + ', obsdb ("' + str(_observatory) + '", "longitude"))\n')
f.write(
'air = airmass (' + str(_RA) + ',' + str(_DEC) + ',mst, obsdb ("' + str(_observatory) + '", "latitude"))\n')
f.write('print(air)\n')
f.close()
_air = iraf.astcalc(image=img, command="airmass.txt", Stdout=1)[0]
try:
_air = float(_air)
except:
_air = 999
delete('airmass.txt')
if overwrite and _air < 99.:
floyds.util.updateheader(img, 0, {'AIRMASS': [_air, 'mean airmass computed with astcalc']})
else:
_air = ''
return _air
def airmass(img, overwrite=True, _observatory='lasilla'):
import floyds
from floyds.util import readhdr, readkey3, delete
from pyraf import iraf
iraf.astutil(_doprint=0)
hdr = readhdr(img)
if readkey3(hdr, 'UTC'):
_UT = (readkey3(hdr, 'UTC') + (readkey3(hdr, 'exptime') / 2)) / 3600
_date = readkey3(hdr, 'date-obs')
_date = _date[0:4] + '-' + _date[4:6] + '-' + _date[6:8]
_RA = readkey3(hdr, 'RA') / 15
_DEC = readkey3(hdr, 'DEC')
f = file('airmass.txt', 'w')
f.write('mst = mst ("' + str(_date) + '",' + str(_UT) + ', obsdb ("' + str(_observatory) + '", "longitude"))\n')
f.write(
'air = airmass (' + str(_RA) + ',' + str(_DEC) + ',mst, obsdb ("' + str(_observatory) + '", "latitude"))\n')
f.write('print(air)\n')
f.close()
_air = iraf.astcalc(image=img, command="airmass.txt", Stdout=1)[0]
try:
_air = float(_air)
except:
_air = 999
delete('airmass.txt')
if overwrite and _air < 99.:
floyds.util.updateheader(img, 0, {'AIRMASS': [_air, 'mean airmass computed with astcalc']})
else:
_air = ''
return _air
def searchatmo(img, listatmo):
from floyds.util import readhdr, readkey3
import floyds
import glob, re
from numpy import argmin, abs
hdr = floyds.util.readhdr(img)
JD = readkey3(hdr, 'JD')
_instrume = readkey3(hdr, 'TELID')
grism0 = readkey3(hdr, 'grism')
if not listatmo:
directory = floyds.__path__[0] + '/archive/' + str(_instrume) + '/atmo/' + grism0
listatmo = glob.glob(directory + '/*fits')
else:
directory = ''
if listatmo:
atmofile = ''
distance = []
goodlist = []
for atmo in listatmo:
print atmo
hdra = readhdr(atmo)
JDarc = readkey3(hdra, 'JD')
grism1 = readkey3(hdra, 'grism')
# slit1=readkey3(hdra,'slit')
if grism0 == grism1:
goodlist.append(atmo)
distance.append(abs(JD - JDarc))
if len(distance) >= 1:
atmofile = goodlist[argmin(distance)]
else:
atmofile = ''
else:
atmofile = ''
return atmofile, directory
def searchatmo(img, listatmo):
from floyds.util import readhdr, readkey3
import floyds
import glob, re
from numpy import argmin, abs
hdr = floyds.util.readhdr(img)
JD = readkey3(hdr, 'JD')
_instrume = readkey3(hdr, 'TELID')
grism0 = readkey3(hdr, 'grism')
if not listatmo:
directory = floyds.__path__[0] + '/archive/' + str(_instrume) + '/atmo/' + grism0
listatmo = glob.glob(directory + '/*fits')
else:
directory = ''
if listatmo:
atmofile = ''
distance = []
goodlist = []
for atmo in listatmo:
print atmo
hdra = readhdr(atmo)
JDarc = readkey3(hdra, 'JD')
grism1 = readkey3(hdra, 'grism')
# slit1=readkey3(hdra,'slit')
if grism0 == grism1:
goodlist.append(atmo)
distance.append(abs(JD - JDarc))
if len(distance) >= 1:
atmofile = goodlist[argmin(distance)]
else:
atmofile = ''
else:
atmofile = ''
return atmofile, directory
def fluxcalib2d(img2d,sensfun): # flux calibrate 2d images
import pyfits
import re,string
from pyfits import open as popen
from numpy import arange, array, float32
from numpy import interp as ninterp
import floyds
from floyds.util import readhdr,readkey3,delete
_tel=floyds.util.readkey3(floyds.util.readhdr(re.sub('\n','',img2d)),'TELID')
if _tel=='fts':
_extinction='ssoextinct.dat'
_observatory='sso'
elif _tel=='ftn':
_extinction='maua.dat'
_observatory='cfht'
else: sys.exit('ERROR: observatory not recognised')
data2d, hdr2d = pyfits.getdata(img2d, 0, header=True)
if 'GRISM' in hdr2d: _arm=hdr2d['GRISM']
else: _arm=''
xxd=arange(len(data2d[0,:]))
crvald=popen(img2d)[0].header.get('CRVAL1')
cdd=popen(img2d)[0].header.get('CD1_1')
_exptime,_airmass=readkey3(readhdr(img2d),'exptime'),readkey3(readhdr(img2d),'airmass')
# read sensfunction and interpole pixel of 2D image
yys=popen(sensfun)[0].data
crvals=popen(sensfun)[0].header.get('CRVAL1')
cds=popen(sensfun)[0].header.get('CD1_1')
yys=(10**(yys/2.5))*cds # from sens iraf in sens flux
xxs=arange(len(yys))
aasens=crvals+(xxs)*cds
xxs2=(aasens-crvald)/cdd
aasens2=ninterp(xxd,xxs2,yys)
# read atmosferic function and interpole pixel of 2D image
aae,yye=floyds.util.ReadAscii2(floyds.__path__[0]+'/standard/extinction/'+_extinction)
aae,yye=array(aae,float),array(yye,float)
xxe=(aae-crvald)/cdd
atm_xx=ninterp(xxd,xxe,yye)
aircorr=10**(0.4*array(atm_xx)*_airmass)
img2df=re.sub('.fits','_2df.fits',img2d)
for i in range(len(data2d[:,0])): data2d[i,:]=((array(data2d[i,:]/_exptime)*array(aircorr))/aasens2)*1e20
floyds.util.delete(img2df)
pyfits.writeto(img2df, float32(data2d), hdr2d)
floyds.util.updateheader(img2df,0,{'SENSFUN'+_arm[0]:[string.split(sensfun,'/')[-1],'']})
floyds.util.updateheader(img2df,0,{'BUNIT':['erg/cm2/s/A 10^20','Physical unit of array values']})
return img2df
def searchsens(img, listsens):
from floyds.util import readhdr, readkey3
import floyds
import glob, re
from numpy import argmin, abs
hdr = readhdr(img)
if 'MJD' in hdr:
JD = readkey3(hdr, 'MJD')
elif 'MJD-OBS' in hdr:
JD = readkey3(hdr, 'MJD-OBS')
_instrume = readkey3(hdr, 'TELID')
grism0 = readkey3(hdr, 'grism')
if not listsens:
directory = floyds.__path__[0] + '/archive/' + str(
_instrume) + '/sens/' + grism0
listsens = glob.glob(directory + '/*fits')
else:
directory = ''
if listsens:
sensfile = ''
distance = []
goodlist = []
for sens in listsens:
hdrs = readhdr(sens)
if 'MJD' in hdrs:
JDsens = readkey3(hdrs, 'MJD')
elif 'MJD-OBS' in hdrs:
JDsens = readkey3(hdrs, 'MJD-OBS')
grism1 = readkey3(hdrs, 'grism') if readkey3(
hdrs, 'grism') else readkey3(hdrs, 'GRISM')
if grism0 == grism1:
goodlist.append(sens)
distance.append(abs(JD - JDsens))
if len(distance) >= 1:
sensfile = goodlist[argmin(distance)]
else:
sensfile = ''
else:
sensfile = ''
return sensfile, directory
def searchsens(img, listsens):
from floyds.util import readhdr, readkey3
import floyds
import glob, re
from numpy import argmin, abs
hdr = readhdr(img)
if 'MJD' in hdr:
JD = readkey3(hdr, 'MJD')
elif 'MJD-OBS' in hdr:
JD = readkey3(hdr, 'MJD-OBS')
_instrume = readkey3(hdr, 'TELID')
grism0 = readkey3(hdr, 'grism')
if not listsens:
directory = floyds.__path__[0] + '/archive/' + str(_instrume) + '/sens/' + grism0
listsens = glob.glob(directory + '/*fits')
else:
directory = ''
if listsens:
sensfile = ''
distance = []
goodlist = []
for sens in listsens:
hdrs = readhdr(sens)
if 'MJD' in hdrs:
JDsens = readkey3(hdrs, 'MJD')
elif 'MJD-OBS' in hdrs:
JDsens = readkey3(hdrs, 'MJD-OBS')
grism1 = readkey3(hdrs, 'grism') if readkey3(hdrs, 'grism') else readkey3(hdrs, 'GRISM')
if grism0 == grism1:
goodlist.append(sens)
distance.append(abs(JD - JDsens))
if len(distance) >= 1:
sensfile = goodlist[argmin(distance)]
else:
sensfile = ''
else:
sensfile = ''
return sensfile, directory
def name_duplicate(img, nome, ext): ###########################
import re, string, os, glob
import floyds
from floyds.util import readhdr, readkey3, delete
dimg = readkey3(readhdr(img), 'DATE-OBS')
listafile = glob.glob(nome + '_?' + ext + '.fits') + glob.glob(nome + '_??' + ext + '.fits')
if len(listafile) == 0:
nome = nome + "_1" + ext + '.fits'
else:
date = []
for l in listafile:
date.append(readkey3(readhdr(l), 'DATE-OBS'))
if dimg in date:
nome = listafile[date.index(dimg)]
else:
n = 1
while nome + '_' + str(n) + str(ext) + '.fits' in listafile:
n = n + 1
nome = nome + '_' + str(n) + str(ext) + '.fits'
return nome
def name_duplicate(img, nome, ext): ###########################
import re, string, os, glob
import floyds
from floyds.util import readhdr, readkey3, delete
dimg = readkey3(readhdr(img), 'DATE-OBS')
listafile = glob.glob(nome + '_?' + ext + '.fits') + glob.glob(nome + '_??' + ext + '.fits')
if len(listafile) == 0:
nome = nome + "_1" + ext + '.fits'
else:
date = []
for l in listafile:
date.append(readkey3(readhdr(l), 'DATE-OBS'))
if dimg in date:
nome = listafile[date.index(dimg)]
else:
n = 1
while nome + '_' + str(n) + str(ext) + '.fits' in listafile:
n = n + 1
nome = nome + '_' + str(n) + str(ext) + '.fits'
return nome
def searcharc(img, listarc):
from floyds.util import readhdr, readkey3
import floyds
import glob, re
from numpy import argmin, abs
hdr = floyds.util.readhdr(img)
JD = readkey3(hdr, 'JD')
_instrume = readkey3(hdr, 'TELID')
camera = readkey3(hdr, 'INSTRUME')
grism0 = readkey3(hdr, 'grism')
slit0 = readkey3(hdr, 'slit')
#if slit0=='6.0' and _instrume in ['fts','2m0b']: slit0='2.0'
#if slit0=='6.0' and _instrume in ['ftn','2m0a']: slit0='1.6'
if not listarc:
directory = floyds.__path__[0] + '/archive/' + str(_instrume) + '/' + camera + '/arc/' + grism0 + '/' + slit0
listarc = glob.glob(directory + '/*fits')
else:
directory = ''
if listarc:
arcfile = ''
distance = []
goodlist = []
for arc in listarc:
print arc
hdra = readhdr(arc)
JDarc = readkey3(hdra, 'JD')
grism1 = readkey3(hdra, 'grism')
slit1 = readkey3(hdra, 'slit')
if slit0 == slit1 and grism0 == grism1:
goodlist.append(arc)
distance.append(abs(JD - JDarc))
if len(distance) >= 1:
arcfile = goodlist[argmin(distance)]
else:
arcfile = ''
else:
arcfile = ''
return arcfile, directory
def spectraresolution(img):
from floyds import readkey3, readhdr
hdr = readhdr(img)
_instrume = readkey3(hdr, 'instrume')
_slit = readkey3(hdr, 'slit')
_grism = readkey3(hdr, 'grism')
risoluzioni = {}
risoluzioni['floyds'] = {}
risoluzioni['floyds']['blu', '6.0'] = 99
risoluzioni['floyds']['blu', '2.0'] = 99
risoluzioni['floyds']['blu', '1.6'] = 99
risoluzioni['floyds']['red', '6.0'] = 99
risoluzioni['floyds']['red', '2.0'] = 99
risoluzioni['floyds']['red', '1.6'] = 99
if _instrume in risoluzioni.keys():
if (_grism, _slit) in risoluzioni[_instrume].keys():
return risoluzioni[_instrume][_grism, _slit]
else:
return ''
else:
return ''
def spectraresolution(img):
from floyds import readkey3, readhdr
hdr = readhdr(img)
_instrume = readkey3(hdr, 'instrume')
_slit = readkey3(hdr, 'slit')
_grism = readkey3(hdr, 'grism')
risoluzioni = {}
risoluzioni['floyds'] = {}
risoluzioni['floyds']['blu', '6.0'] = 99
risoluzioni['floyds']['blu', '2.0'] = 99
risoluzioni['floyds']['blu', '1.6'] = 99
risoluzioni['floyds']['red', '6.0'] = 99
risoluzioni['floyds']['red', '2.0'] = 99
risoluzioni['floyds']['red', '1.6'] = 99
if _instrume in risoluzioni.keys():
if (_grism, _slit) in risoluzioni[_instrume].keys():
return risoluzioni[_instrume][_grism, _slit]
else:
return ''
else:
return ''
def correctobject(img, coordinatefile):
import os, re, sys, string
from numpy import arccos, sin, cos, pi, argmin
import floyds
from floyds.util import readstandard, readhdr, readkey3
scal = pi / 180.
std, rastd, decstd, magstd = readstandard(coordinatefile)
img = re.sub('\n', '', img)
correctcard(img)
hdr = readhdr(img)
_ra = readkey3(hdr, 'RA')
_dec = readkey3(hdr, 'DEC')
dd = arccos(
sin(_dec * scal) * sin(decstd * scal) + cos(_dec * scal) * cos(decstd * scal) * cos((_ra - rastd) * scal)) * (
(180 / pi) * 3600)
if min(dd) < 5200:
floyds.util.updateheader(img, 0, {'OBJECT': [std[argmin(dd)], 'Original target.']})
aa, bb, cc = rastd[argmin(dd)], decstd[argmin(dd)], std[argmin(dd)]
else:
aa, bb, cc = '', '', ''
return aa, bb, cc
def correctobject(img, coordinatefile):
import os, re, sys, string
from numpy import arccos, sin, cos, pi, argmin
import floyds
from floyds.util import readstandard, readhdr, readkey3
scal = pi / 180.
std, rastd, decstd, magstd = readstandard(coordinatefile)
img = re.sub('\n', '', img)
# correctcard(img)
hdr = readhdr(img)
_ra = readkey3(hdr, 'RA')
_dec = readkey3(hdr, 'DEC')
dd = arccos(
sin(_dec * scal) * sin(decstd * scal) + cos(_dec * scal) * cos(decstd * scal) * cos((_ra - rastd) * scal)) * (
(180 / pi) * 3600)
if min(dd) < 5200:
floyds.util.updateheader(img, 0, {'OBJECT': [std[argmin(dd)], 'Original target.']})
aa, bb, cc = rastd[argmin(dd)], decstd[argmin(dd)], std[argmin(dd)]
else:
aa, bb, cc = '', '', ''
return aa, bb, cc
def searcharc(img, listarc):
from floyds.util import readhdr, readkey3
import floyds
import glob, re
from numpy import argmin, abs
hdr = floyds.util.readhdr(img)
JD = readkey3(hdr, 'JD')
_instrume = readkey3(hdr, 'TELID')
grism0 = readkey3(hdr, 'grism')
slit0 = readkey3(hdr, 'slit')
#if slit0=='6.0' and _instrume in ['fts','2m0b']: slit0='2.0'
#if slit0=='6.0' and _instrume in ['ftn','2m0a']: slit0='1.6'
if not listarc:
directory = floyds.__path__[0] + '/archive/' + str(_instrume) + '/arc/' + grism0 + '/' + slit0
listarc = glob.glob(directory + '/*fits')
else:
directory = ''
if listarc:
arcfile = ''
distance = []
goodlist = []
for arc in listarc:
print arc
hdra = readhdr(arc)
JDarc = readkey3(hdra, 'JD')
grism1 = readkey3(hdra, 'grism')
slit1 = readkey3(hdra, 'slit')
if slit0 == slit1 and grism0 == grism1:
goodlist.append(arc)
distance.append(abs(JD - JDarc))
if len(distance) >= 1:
arcfile = goodlist[argmin(distance)]
else:
arcfile = ''
else:
arcfile = ''
return arcfile, directory
def phase3header(img):
import floyds
import string
from floyds.util import readhdr, readkey3
from numpy import max, min, isfinite
from pyfits import open as popen
img_data = popen(img)[0].data
hdr = readhdr(img)
hedvec0 = {'DATAMIN': [float(min(img_data[isfinite(img_data)])), ''],
'DATAMAX': [float(max(img_data[isfinite(img_data)])), ''],
'ORIGIN': ['ESO', 'European Southern Observatory'],
'PROCSOFT': ['floyds_' + str(floyds.__version__), 'pipeline version']}
if readkey3(hdr, 'filter'):
hedvec0['FILTER'] = [readkey3(hdr, 'filter'), 'Filter name']
if readkey3(hdr, 'gain'):
hedvec0['GAIN'] = [readkey3(hdr, 'gain'), 'Conversion from electrons to ADU']
if readkey3(hdr, 'esoid'):
hedvec0['OBID'] = [readkey3(hdr, 'esoid'), 'Observation block ID']
if readkey3(hdr, 'esoprog'):
hedvec0['PROG_ID'] = [readkey3(hdr, 'esoprog'), 'ESO program identification']
if readkey3(hdr, 'tech'):
hedvec0['OBSTECH'] = [readkey3(hdr, 'tech'), 'Observation technique']
floyds.util.updateheader(img, 0, hedvec0)
