def correctcard(img):
from pyfits import open as popen
from numpy import asarray
import re
hdulist = popen(img)
a = hdulist[0]._verify('fix')
_header = hdulist[0].header
for i in range(len(a)):
if not a[i]:
a[i] = ['']
ww = asarray([i for i in range(len(a)) if (re.sub(' ', '', a[i][0]) != '')])
if len(ww) > 0:
newheader = []
headername = []
for j in _header.items():
headername.append(j[0])
newheader.append(j[1])
hdulist.close()
imm = popen(img, mode='update')
_header = imm[0].header
for i in ww:
if headername[i]:
try:
_header.update(headername[i], newheader[i])
except:
_header.update(headername[i], 'xxxx')
imm.flush()
imm.close()
def correctcard(img):
from pyfits import open as popen
from numpy import asarray
import re
hdulist = popen(img)
a = hdulist[0]._verify('fix')
_header = hdulist[0].header
for i in range(len(a)):
if not a[i]:
a[i] = ['']
ww = asarray([i for i in range(len(a)) if (re.sub(' ', '', a[i][0]) != '')])
if len(ww) > 0:
newheader = []
headername = []
for j in _header.items():
headername.append(j[0])
newheader.append(j[1])
hdulist.close()
imm = popen(img, mode='update')
_header = imm[0].header
for i in ww:
if headername[i]:
try:
_header.update(headername[i], newheader[i])
except:
_header.update(headername[i], 'xxxx')
imm.flush()
imm.close()
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 _correct_extended_fits_keywords(log, pathToFits):
"""
*Values within the fits header should be no longer than 80 characters*
**Key Arguments:**
- ``log`` -- logger
- ``pathToFits`` -- path the the FITS file
**Return:**
- None
"""
################ > IMPORTS ################
## STANDARD LIB ##
import re
## THIRD PARTY ##
from pyfits import open as popen
from numpy import asarray
## LOCAL APPLICATION ##
################ > VARIABLE SETTINGS ######
################ >ACTION(S) ################
hdulist = popen(pathToFits)
a = hdulist[0]._verify('fix')
_header = hdulist[0].header
for i in range(len(a)):
if not a[i]:
a[i] = ['']
ww = asarray([i for i in range(len(a)) if (
re.sub(' ', '', a[i][0]) != '')])
if len(ww) > 0:
newheader = []
headername = []
for j in _header.items():
headername.append(j[0])
newheader.append(j[1])
hdulist.close()
imm = popen(pathToFits, mode='update')
_header = imm[0].header
for i in ww:
if headername[i]:
try:
_header.update(headername[i], newheader[i])
except:
_header.update(headername[i], 'xxxx')
imm.flush()
imm.close()
return
def readhdr(img):
from pyfits import open as popen
try:
hdr = popen(img)[0].header
except:
from floyds.util import correctcard
try:
correctcard(img)
except:
import sys
sys.exit('image ' + str(img) + ' is corrupted, delete it and start again')
hdr = popen(img)[0].header
return hdr
def sortbyJD(lista):
from pyfits import open as popen
from numpy import array
JDlist = []
for img in lista:
hdr = popen(img)[0].header
if 'MJD' in hdr:
JDlist.append(popen(img)[0].header.get('MJD'))
else:
JDlist.append(popen(img)[0].header.get('MJD-OBS'))
lista = array(lista)
JDlist = array(JDlist)
inds = JDlist.argsort()
sortedlista = lista[inds]
return list(sortedlista)
def readhdr(img):
from pyfits import open as popen
try:
hdr = popen(img)[0].header
except:
from floyds.util import correctcard
try:
correctcard(img)
except:
import sys
sys.exit('image ' + str(img) + ' is corrupted, delete it and start again')
hdr = popen(img)[0].header
return hdr
def sortbyJD(lista):
from pyfits import open as popen
from numpy import array
JDlist = []
for img in lista:
hdr = popen(img)[0].header
if 'MJD' in hdr:
JDlist.append(popen(img)[0].header.get('MJD'))
else:
JDlist.append(popen(img)[0].header.get('MJD-OBS'))
lista = array(lista)
JDlist = array(JDlist)
inds = JDlist.argsort()
sortedlista = lista[inds]
return list(sortedlista)
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 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)
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)