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from __future__ import division # confidence high
import os
import pyfits
from stwcs.wcsutil import HSTWCS
from stwcs import utils
import corrections, makewcs
import dgeo, det2im
from pytools import parseinput, fileutil
import apply_corrections
#Note: The order of corrections is important
__docformat__ = 'restructuredtext'
__version__ = '0.5'
def updatewcs(input, vacorr=True, tddcorr=True, dgeocorr=True, d2imcorr=True, checkfiles=True):
"""
Purpose
=======
Updates HST science files with the best available calibration information.
This allows users to retrieve from the archive self contained science files
which do not require additional reference files.
Basic WCS keywords are updated in the process and new keywords (following WCS
Paper IV and the SIP convention) as well as new extensions are added to the science files.
Example
=======
>>>from stwcs import updatewcs
>>>updatewcs.updatewcs(filename)
Dependencies
============
`pytools`
`pyfits`
`pywcs`
:Parameters:
`input`: a python list of file names or a string (wild card characters allowed)
input files may be in fits, geis or waiver fits format
`vacorr`: boolean
If True, vecocity aberration correction will be applied
`tddcorr`: boolean
If True, time dependent distortion correction will be applied
`dgeocorr`: boolean
If True, a Lookup table distortion will be applied
`d2imcorr`: boolean
If True, detector to image correction will be applied
`checkfiles`: boolean
If True, the format of the input files will be checked,
geis and waiver fits files will be converted to MEF format.
Default value is True for standalone mode.
"""
files = parseinput.parseinput(input)[0]
if checkfiles:
files = checkFiles(files)
if not files:
print 'No valid input, quitting ...\n'
return
for f in files:
acorr = apply_corrections.setCorrections(f, vacorr=vacorr, \
tddcorr=tddcorr,dgeocorr=dgeocorr, d2imcorr=d2imcorr)
#restore the original WCS keywords
utils.restoreWCS(f, wcskey='O', clobber=True)
makecorr(f, acorr)
return files
def makecorr(fname, allowed_corr):
"""
Purpose
=======
Applies corrections to the WCS of a single file
:Parameters:
`fname`: string
file name
`acorr`: list
list of corrections to be applied
"""
f = pyfits.open(fname, mode='update')
#Determine the reference chip and create the reference HSTWCS object
nrefchip, nrefext = getNrefchip(f)
ref_wcs = HSTWCS(fobj=f, ext=nrefext)
ref_wcs.readModel(update=True,header=f[nrefext].header)
ref_wcs.copyWCS(header=f[nrefext].header, wcskey='O', wcsname='OPUS', clobber=True)
if 'DET2IMCorr' in allowed_corr:
det2im.DET2IMCorr.updateWCS(f)
for i in range(len(f))[1:]:
# Perhaps all ext headers should be corrected (to be consistent)
extn = f[i]
if extn.header.has_key('extname'):
extname = extn.header['extname'].lower()
if extname == 'sci':
sciextver = extn.header['extver']
ref_wcs.restore(f[nrefext].header, wcskey="O")
hdr = extn.header
ext_wcs = HSTWCS(fobj=f, ext=i)
ext_wcs.copyWCS(header=hdr, wcskey='O', wcsname='OPUS', clobber=True)
ext_wcs.readModel(update=True,header=hdr)
for c in allowed_corr:
if c != 'DGEOCorr' and c != 'DET2IMCorr':
corr_klass = corrections.__getattribute__(c)
kw2update = corr_klass.updateWCS(ext_wcs, ref_wcs)
for kw in kw2update:
hdr.update(kw, kw2update[kw])
idcname = os.path.split(fileutil.osfn(ext_wcs.idctab))[1]
wname = ''.join(['IDC_',idcname.split('_idc.fits')[0]])
wkey = getKey(hdr, wname)
ext_wcs.copyWCS(header=hdr, wcskey=wkey, wcsname=wname, clobber=True)
elif extname in ['err', 'dq', 'sdq']:
cextver = extn.header['extver']
if cextver == sciextver:
ext_wcs.copyWCS(header=extn.header, wcskey=" ", wcsname=" ")
else:
cextver = extn.header['extver']
continue
if 'DGEOCorr' in allowed_corr:
kw2update = dgeo.DGEOCorr.updateWCS(f)
for kw in kw2update:
f[1].header.update(kw, kw2update[kw])
f.close()
def getKey(header, wcsname):
"""
If WCSNAME is found in header, return its key, else return
the next available key. This is used to update a specific WCS
repeatedly and not generate new keys every time.
"""
wkey = utils.next_wcskey(header)
names = utils.wcsnames(header)
for item in names.items():
if item[1] == wcsname:
wkey = item[0]
return wkey
def getNrefchip(fobj):
"""
This handles the fact that WFPC2 subarray observations
may not include chip 3 which is the default reference chip for
full observations. Also for subarrays chip 3 may not be the third
extension in a MEF file.
"""
Nrefext = 1
instrument = fobj[0].header['INSTRUME']
if instrument == 'WFPC2':
detectors = [img.header['DETECTOR'] for img in fobj[1:]]
if 3 not in detectors:
Nrefchip=detectors[0]
Nrefext = 1
else:
Nrefchip = 3
Nrefext = detectors.index(3) + 1
elif instrument == 'ACS':
detector = fobj[0].header['DETECTOR']
if detector == 'WFC':
Nrefchip =2
else:
Nrefchip = 1
elif instrument == 'NICMOS':
Nrefchip = fobj[0].header['CAMERA']
elif instrument == 'WFC3':
detector = fobj[0].header['DETECTOR']
if detector == 'UVIS':
Nrefchip =2
else:
Nrefchip = 1
else:
Nrefchip = 1
return Nrefchip, Nrefext
def checkFiles(input):
"""
Purpose
=======
Checks that input files are in the correct format.
Converts geis and waiver fits files to multiextension fits.
"""
from pytools.check_files import geis2mef, waiver2mef, checkFiles
removed_files = []
newfiles = []
for file in input:
try:
imgfits,imgtype = fileutil.isFits(file)
except IOError:
print "Warning: File %s could not be found\n" %file
print "Removing file %s from input list" %file
removed_files.append(file)
continue
# Check for existence of waiver FITS input, and quit if found.
# Or should we print a warning and continue but not use that file
if imgfits:
if imgtype == 'waiver':
newfilename = waiver2mef(file, convert_dq=True)
if newfilename == None:
print "Removing file %s from input list - could not convert waiver to mef" %file
removed_files.append(file)
else:
newfiles.append(newfilename)
else:
newfiles.append(file)
# If a GEIS image is provided as input, create a new MEF file with
# a name generated using 'buildFITSName()'
# Convert the corresponding data quality file if present
if not imgfits:
newfilename = geis2mef(file, convert_dq=True)
if newfilename == None:
print "Removing file %s from input list - could not convert geis to mef" %file
removed_files.append(file)
else:
newfiles.append(newfilename)
if removed_files:
print 'The following files will be removed from the list of files to be processed :\n'
for f in removed_files:
print f
newfiles = checkFiles(newfiles)[0]
return newfiles
def getCorrections(instrument):
"""
Print corrections available for an instrument
:Parameters:
`instrument`: string, one of 'WFPC2', 'NICMOS', 'STIS', 'ACS', 'WFC3'
"""
acorr = apply_corrections.allowed_corrections[instrument]
print "The following corrections will be performed for instrument %s\n" % instrument
for c in acorr: print c,': ' , apply_corrections.cnames[c]
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