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from __future__ import division # confidence high
import pyfits
from stsci.tools import fileutil
import utils
import numpy as np
import logging, time
logger = logging.getLogger('stwcs.updatewcs.d2im')
class DET2IMCorr(object):
"""
Defines a Lookup table prior distortion correction as per WCS paper IV.
It uses a reference file defined by the D2IMFILE (suffix 'd2im') keyword
in the primary header.
Notes
-----
- Using extensions in the reference file create a WCSDVARR extensions
and add them to the science file.
- Add record-valued keywords to the science extension header to describe
the lookup tables.
- Add a keyword 'D2IMEXT' to the science extension header to store
the name of the reference file used to create the WCSDVARR extensions.
If WCSDVARR extensions exist and `D2IMFILE` is different from `D2IMEXT`,
a subsequent update will overwrite the existing extensions.
If WCSDVARR extensions were not found in the science file, they will be added.
"""
def updateWCS(cls, fobj):
"""
Parameters
----------
fobj: pyfits object
Science file, for which a distortion correction in a NPOLFILE is available
"""
logger.info("\n\tStarting DET2IM: %s" %time.asctime())
try:
assert isinstance(fobj, pyfits.HDUList)
except AssertionError:
logger.exception('\n\tInput must be a pyfits.HDUList object')
raise
cls.applyDet2ImCorr(fobj)
d2imfile = fobj[0].header['D2IMFILE']
new_kw = {'D2IMEXT': d2imfile}
return new_kw
updateWCS = classmethod(updateWCS)
def applyDet2ImCorr(cls, fobj):
"""
For each science extension in a pyfits file object:
- create a WCSDVARR extension
- update science header
- add/update D2IMEXT keyword
"""
d2imfile = fileutil.osfn(fobj[0].header['D2IMFILE'])
# Map D2IMARR EXTVER numbers to FITS extension numbers
wcsdvarr_ind = cls.getWCSIndex(fobj)
d2im_num_ext = 1
for ext in fobj:
try:
extname = ext.header['EXTNAME'].lower()
except KeyError:
continue
if extname == 'sci':
extversion = ext.header['EXTVER']
ccdchip = cls.get_ccdchip(fobj, extname='SCI', extver=extversion)
binned = utils.getBinning(fobj, extversion)
header = ext.header
# get the data arrays from the reference file
dx, dy = cls.getData(d2imfile, ccdchip)
# Determine EXTVER for the D2IMARR extension from the D2I file (EXTNAME, EXTVER) kw.
# This is used to populate DPj.EXTVER kw
for ename in zip(['DX', 'DY'], [dx, dy]):
if ename[1] is not None:
error_val = ename[1].max()
cls.addSciExtKw(header, wdvarr_ver=d2im_num_ext, d2im_extname=ename[0], error_val=error_val)
hdu = cls.createD2ImHDU(header, d2imfile=d2imfile, \
wdvarr_ver=d2im_num_ext, d2im_extname=ename[0], data=ename[1],ccdchip=ccdchip, binned=binned)
if wcsdvarr_ind and d2im_num_ext in wcsdvarr_ind:
fobj[wcsdvarr_ind[d2im_num_ext]] = hdu
else:
fobj.append(hdu)
d2im_num_ext = d2im_num_ext + 1
applyDet2ImCorr = classmethod(applyDet2ImCorr)
def getWCSIndex(cls, fobj):
"""
If fobj has WCSDVARR extensions:
returns a mapping of their EXTVER kw to file object extension numbers
if fobj does not have WCSDVARR extensions:
an empty dictionary is returned
"""
wcsd = {}
for e in range(len(fobj)):
try:
ename = fobj[e].header['EXTNAME']
except KeyError:
continue
if ename == 'D2IMARR':
wcsd[fobj[e].header['EXTVER']] = e
logger.debug("A map of D2IMARR extensions %s" % wcsd)
return wcsd
getWCSIndex = classmethod(getWCSIndex)
def addSciExtKw(cls, hdr, wdvarr_ver=None, d2im_extname=None, error_val=0.0):
"""
Adds kw to sci extension to define WCSDVARR lookup table extensions
"""
if d2im_extname =='DX':
j=1
else:
j=2
d2imerror = 'D2IMERR%s' %j
d2imdis = 'D2IMDIS%s' %j
d2imext = 'D2IM%s.' %j + 'EXTVER'
d2imnaxes = 'D2IM%s.' %j +'NAXES'
d2imaxis1 = 'D2IM%s.' %j+'AXIS.1'
d2imaxis2 = 'D2IM%s.' %j+'AXIS.2'
keys = [d2imerror, d2imdis, d2imext, d2imnaxes, d2imaxis1, d2imaxis2]
values = {d2imerror: error_val,
d2imdis: 'Lookup',
d2imext: wdvarr_ver,
d2imnaxes: 2,
d2imaxis1: 1,
d2imaxis2: 2}
comments = {d2imerror: 'Maximum error of NPOL correction for axis %s' % j,
d2imdis: 'Detector to image correction type',
d2imext: 'Version number of WCSDVARR extension containing d2im lookup table',
d2imnaxes: 'Number of independent variables in d2im function',
d2imaxis1: 'Axis number of the jth independent variable in a d2im function',
d2imaxis2: 'Axis number of the jth independent variable in a d2im function'
}
# Look for HISTORY keywords. If present, insert new keywords before them
before_key = 'HISTORY'
if before_key not in hdr:
before_key = None
for key in keys:
hdr.update(key=key, value=values[key], comment=comments[key], before=before_key)
addSciExtKw = classmethod(addSciExtKw)
def getData(cls,d2imfile, ccdchip):
"""
Get the data arrays from the reference D2I files
Make sure 'CCDCHIP' in the npolfile matches "CCDCHIP' in the science file.
"""
xdata, ydata = (None, None)
d2im = pyfits.open(d2imfile)
for ext in d2im:
d2imextname = ext.header.get('EXTNAME',"")
d2imccdchip = ext.header.get('CCDCHIP',1)
if d2imextname == 'DX' and d2imccdchip == ccdchip:
xdata = ext.data.copy()
continue
elif d2imextname == 'DY' and d2imccdchip == ccdchip:
ydata = ext.data.copy()
continue
else:
continue
d2im.close()
return xdata, ydata
getData = classmethod(getData)
def createD2ImHDU(cls, sciheader, d2imfile=None, wdvarr_ver=1, d2im_extname=None,data = None, ccdchip=1, binned=1):
"""
Creates an HDU to be added to the file object.
"""
hdr = cls.createD2ImHdr(sciheader, d2imfile=d2imfile, wdvarr_ver=wdvarr_ver, d2im_extname=d2im_extname, ccdchip=ccdchip, binned=binned)
hdu=pyfits.ImageHDU(header=hdr, data=data)
return hdu
createD2ImHDU = classmethod(createD2ImHDU)
def createD2ImHdr(cls, sciheader, d2imfile, wdvarr_ver, d2im_extname, ccdchip, binned):
"""
Creates a header for the WCSDVARR extension based on the NPOL reference file
and sci extension header. The goal is to always work in image coordinates
(also for subarrays and binned images. The WCS for the WCSDVARR extension
i ssuch that a full size npol table is created and then shifted or scaled
if the science image is a subarray or binned image.
"""
d2im = pyfits.open(d2imfile)
d2im_phdr = d2im[0].header
for ext in d2im:
try:
d2imextname = ext.header['EXTNAME']
d2imextver = ext.header['EXTVER']
except KeyError:
continue
d2imccdchip = cls.get_ccdchip(d2im, extname=d2imextname, extver=d2imextver)
if d2imextname == d2im_extname and d2imccdchip == ccdchip:
d2im_header = ext.header
break
else:
continue
d2im.close()
naxis = d2im[1].header['NAXIS']
ccdchip = d2imextname #npol_header['CCDCHIP']
kw = { 'NAXIS': 'Size of the axis',
'CDELT': 'Coordinate increment along axis',
'CRPIX': 'Coordinate system reference pixel',
'CRVAL': 'Coordinate system value at reference pixel',
}
kw_comm1 = {}
kw_val1 = {}
for key in kw.keys():
for i in range(1, naxis+1):
si = str(i)
kw_comm1[key+si] = kw[key]
for i in range(1, naxis+1):
si = str(i)
kw_val1['NAXIS'+si] = d2im_header.get('NAXIS'+si)
kw_val1['CDELT'+si] = d2im_header.get('CDELT'+si, 1.0) / binned
kw_val1['CRPIX'+si] = d2im_header.get('CRPIX'+si, 0.0)
kw_val1['CRVAL'+si] = (d2im_header.get('CRVAL'+si, 0.0) + sciheader.get('LTV'+str(i), 0)) / binned
kw_comm0 = {'XTENSION': 'Image extension',
'BITPIX': 'IEEE floating point',
'NAXIS': 'Number of axes',
'EXTNAME': 'WCS distortion array',
'EXTVER': 'Distortion array version number',
'PCOUNT': 'Special data area of size 0',
'GCOUNT': 'One data group',
}
kw_val0 = { 'XTENSION': 'IMAGE',
'BITPIX': -32,
'NAXIS': naxis,
'EXTNAME': 'D2IMARR',
'EXTVER': wdvarr_ver,
'PCOUNT': 0,
'GCOUNT': 1,
'CCDCHIP': ccdchip,
}
cdl = []
for key in kw_comm0.keys():
cdl.append((key, kw_val0[key], kw_comm0[key]))
for key in kw_comm1.keys():
cdl.append((key, kw_val1[key], kw_comm1[key]))
# Now add keywords from NPOLFILE header to document source of calibration
# include all keywords after and including 'FILENAME' from header
start_indx = -1
end_indx = 0
for i, c in enumerate(d2im_phdr):
if c == 'FILENAME':
start_indx = i
if c == '': # remove blanks from end of header
end_indx = i+1
break
if start_indx >= 0:
for card in d2im_phdr.cards[start_indx:end_indx]:
cdl.append(card)
hdr = pyfits.Header(cards=cdl)
return hdr
createD2ImHdr = classmethod(createD2ImHdr)
def get_ccdchip(cls, fobj, extname, extver):
"""
Given a science file or npol file determine CCDCHIP
"""
ccdchip = 1
if fobj[0].header['INSTRUME'] == 'ACS' and fobj[0].header['DETECTOR'] == 'WFC':
ccdchip = fobj[extname, extver].header['CCDCHIP']
elif fobj[0].header['INSTRUME'] == 'WFC3' and fobj[0].header['DETECTOR'] == 'UVIS':
ccdchip = fobj[extname, extver].header['CCDCHIP']
elif fobj[0].header['INSTRUME'] == 'WFPC2':
ccdchip = fobj[extname, extver].header['DETECTOR']
elif fobj[0].header['INSTRUME'] == 'STIS':
ccdchip = fobj[extname, extver].header['DETECTOR']
elif fobj[0].header['INSTRUME'] == 'NICMOS':
ccdchip = fobj[extname, extver].header['CAMERA']
return ccdchip
get_ccdchip = classmethod(get_ccdchip)
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