def _skymatch(imageList, paramDict, in_memory, clean, logfile):
# '_skymatch' converts input imageList and other parameters to
# data structures accepted by the "skymatch" package.
# It also creates a temporary mask by combining 'static' mask,
# DQ image, and user-supplied mask. The combined mask is then
# passed to 'skymatch' to be used for excluding "bad" pixels.
#header keyword that contains the sky that's been subtracted
skyKW = "MDRIZSKY"
nimg = len(imageList)
if nimg == 0:
ml.logentry("Skymatch needs at least one images to perform{0}" \
"sky matching. Nothing to be done.",os.linesep)
return
# create a list of input file names as provided by the user:
user_fnames = []
loaded_fnames = []
filemaskinfos = nimg * [None]
for img in imageList:
user_fnames.append(img._original_file_name)
loaded_fnames.append(img._filename)
# parse sky mask catalog file (if any):
catfile = paramDict['skymask_cat']
if catfile:
#extname = imageList[0].scienceExt
#assert(extname is not None and extname != '')
catfile = catfile.strip()
mfindx = parse_at_file(fname=catfile,
default_ext=('SCI', '*'),
default_mask_ext=0,
clobber=False,
fnamesOnly=True,
doNotOpenDQ=True,
match2Images=user_fnames,
im_fmode='update',
dq_fmode='readonly',
msk_fmode='readonly',
logfile=MultiFileLog(console=True),
verbose=True)
for p in mfindx:
filemaskinfos[p[1]] = p[0]
# step through the list of input images and create
# combined (static + DQ + user supplied, if any) mask, and
# create a list of FileExtMaskInfo objects to be passed
# to 'skymatch' function.
#
# This needs to be done in several steps, mostly due to the fact that
# the mask catalogs use "original" (e.g., GEIS, WAIVER FITS) file names
# while ultimately we want to open the version converted to MEF. Second
# reason is that we want to combine user supplied masks with DQ+static
# masks provided by astrodrizzle.
new_fi = []
sky_bits = interpret_bit_flags(paramDict['sky_bits'])
for i in range(nimg):
# extract extension information:
extname = imageList[i].scienceExt
extver = imageList[i].group
if extver is None:
extver = imageList[i].getExtensions()
assert (extname is not None and extname != '')
assert (extver)
# create a new FileExtMaskInfo object
fi = FileExtMaskInfo(default_ext=(extname, '*'),
default_mask_ext=0,
clobber=False,
doNotOpenDQ=True,
fnamesOnly=False,
im_fmode='update',
dq_fmode='readonly',
msk_fmode='readonly')
# set image file and extensions:
fi.image = loaded_fnames[i]
extlist = [(extname, ev) for ev in extver]
fi.append_ext(extlist)
# set user masks if any (this will open the files for a later use):
fi0 = filemaskinfos[i]
if fi0 is not None:
nmask = len(fi0.mask_images)
for m in range(nmask):
mask = fi0.mask_images[m]
ext = fi0.maskext[m]
fi.append_mask(mask, ext)
fi.finalize()
# combine user masks with static masks:
assert (len(extlist) == fi.count
) #TODO: <-- remove after thorough testing
masklist = []
mextlist = []
for k in range(fi.count):
if fi.mask_images[k].closed:
umask = None
else:
umask = fi.mask_images[k].hdu[fi.maskext[k]].data
(mask, mext) = _buildStaticDQUserMask(imageList[i], extlist[k],
sky_bits,
paramDict['use_static'],
fi.mask_images[k],
fi.maskext[k], in_memory)
masklist.append(mask)
mextlist.append(mext)
# replace the original user-supplied masks with the
# newly computed combined static+DQ+user masks:
fi.clear_masks()
for k in range(fi.count):
if in_memory and mask is not None:
# os.stat() on the "original_fname" of the mask will fail
# since this is a "virtual" mask. Therefore we need to compute
# mask_stat ourselves. We will simply use id(data) for this:
mstat = os.stat_result((0, id(mask.hdu)) + 8 * (0, ))
fi.append_mask(masklist[k], mextlist[k], mask_stat=mstat)
else:
fi.append_mask(masklist[k], mextlist[k])
if masklist[k]:
masklist[k].release()
fi.finalize()
new_fi.append(fi)
# Run skymatch algorithm:
skymatch(new_fi,
skymethod=paramDict['skymethod'],
skystat=paramDict['skystat'],
lower=paramDict['skylower'],
upper=paramDict['skyupper'],
nclip=paramDict['skyclip'],
lsigma=paramDict['skylsigma'],
usigma=paramDict['skyusigma'],
binwidth=paramDict['skywidth'],
skyuser_kwd=skyKW,
units_kwd='BUNIT',
readonly=not paramDict['skysub'],
dq_bits=None,
optimize='inmemory' if in_memory else 'balanced',
clobber=True,
clean=clean,
verbose=True,
flog=MultiFileLog(console=True, enableBold=False),
_taskname4history='AstroDrizzle')
# Populate 'subtractedSky' and 'computedSky' of input image objects:
for i in range(nimg):
assert (not new_fi[i].fnamesOnly and not new_fi[i].image.closed)
image = imageList[i]
skysubimage = new_fi[i].image.hdu
numchips = image._numchips
extname = image.scienceExt
assert (os.path.samefile(image._filename, skysubimage.filename()))
for extver in range(1, numchips + 1, 1):
chip = image[extname, extver]
if not chip.group_member:
continue
subtracted_sky = skysubimage[extname, extver].header.get(skyKW, 0.)
chip.subtractedSky = subtracted_sky
chip.computedSky = subtracted_sky
# clean-up:
for fi in new_fi:
fi.release_all_images()
def _skymatch(imageList, paramDict, in_memory, clean, logfile):
# '_skymatch' converts input imageList and other parameters to
# data structures accepted by the "skymatch" package.
# It also creates a temporary mask by combining 'static' mask,
# DQ image, and user-supplied mask. The combined mask is then
# passed to 'skymatch' to be used for excluding "bad" pixels.
skyKW="MDRIZSKY" #header keyword that contains the sky that's been subtracted
nimg = len(imageList)
if nimg == 0:
ml.logentry("Skymatch needs at least one images to perform{0}" \
"sky matching. Nothing to be done.",os.linesep)
return
# create a list of input file names as provided by the user:
user_fnames = []
loaded_fnames = []
filemaskinfos = nimg * [ None ]
for img in imageList:
user_fnames.append(img._original_file_name)
loaded_fnames.append(img._filename)
# parse sky mask catalog file (if any):
catfile = paramDict['skymask_cat']
if catfile:
#extname = imageList[0].scienceExt
#assert(extname is not None and extname != '')
catfile = catfile.strip()
mfindx = parse_at_file(fname = catfile,
default_ext = ('SCI','*'),
default_mask_ext = 0,
clobber = False,
fnamesOnly = True,
doNotOpenDQ = True,
match2Images = user_fnames,
im_fmode = 'update',
dq_fmode = 'readonly',
msk_fmode = 'readonly',
logfile = MultiFileLog(console=True),
verbose = True)
for p in mfindx:
filemaskinfos[p[1]] = p[0]
# step through the list of input images and create
# combined (static + DQ + user supplied, if any) mask, and
# create a list of FileExtMaskInfo objects to be passed
# to 'skymatch' function.
#
# This needs to be done in several steps, mostly due to the fact that
# the mask catalogs use "original" (e.g., GEIS, WAIVER FITS) file names
# while ultimately we want to open the version converted to MEF. Second
# reason is that we want to combine user supplied masks with DQ+static
# masks provided by astrodrizzle.
new_fi = []
sky_bits = bitmask.interpret_bits_value(paramDict['sky_bits'])
for i in range(nimg):
# extract extension information:
extname = imageList[i].scienceExt
extver = imageList[i].group
if extver is None:
extver = imageList[i].getExtensions()
assert(extname is not None and extname != '')
assert(extver)
# create a new FileExtMaskInfo object
fi = FileExtMaskInfo(default_ext=(extname,'*'),
default_mask_ext=0,
clobber=False,
doNotOpenDQ=True,
fnamesOnly=False,
im_fmode='update',
dq_fmode='readonly',
msk_fmode='readonly')
# set image file and extensions:
fi.image = loaded_fnames[i]
extlist = [ (extname,ev) for ev in extver ]
fi.append_ext(extlist)
# set user masks if any (this will open the files for a later use):
fi0 = filemaskinfos[i]
if fi0 is not None:
nmask = len(fi0.mask_images)
for m in range(nmask):
mask = fi0.mask_images[m]
ext = fi0.maskext[m]
fi.append_mask(mask, ext)
fi.finalize()
# combine user masks with static masks:
assert(len(extlist) == fi.count) #TODO: <-- remove after thorough testing
masklist = []
mextlist = []
for k in range(fi.count):
if fi.mask_images[k].closed:
umask = None
else:
umask = fi.mask_images[k].hdu[fi.maskext[k]].data
(mask, mext) = _buildStaticDQUserMask(imageList[i], extlist[k],
sky_bits, paramDict['use_static'],
fi.mask_images[k], fi.maskext[k], in_memory)
masklist.append(mask)
mextlist.append(mext)
# replace the original user-supplied masks with the
# newly computed combined static+DQ+user masks:
fi.clear_masks()
for k in range(fi.count):
if in_memory and mask is not None:
# os.stat() on the "original_fname" of the mask will fail
# since this is a "virtual" mask. Therefore we need to compute
# mask_stat ourselves. We will simply use id(data) for this:
mstat = os.stat_result((0,id(mask.hdu)) + 8*(0,))
fi.append_mask(masklist[k], mextlist[k], mask_stat=mstat)
else:
fi.append_mask(masklist[k], mextlist[k])
if masklist[k]:
masklist[k].release()
fi.finalize()
new_fi.append(fi)
# Run skymatch algorithm:
skymatch(new_fi,
skymethod = paramDict['skymethod'],
skystat = paramDict['skystat'],
lower = paramDict['skylower'],
upper = paramDict['skyupper'],
nclip = paramDict['skyclip'],
lsigma = paramDict['skylsigma'],
usigma = paramDict['skyusigma'],
binwidth = paramDict['skywidth'],
skyuser_kwd = skyKW,
units_kwd = 'BUNIT',
readonly = not paramDict['skysub'],
dq_bits = None,
optimize = 'inmemory' if in_memory else 'balanced',
clobber = True,
clean = clean,
verbose = True,
flog = MultiFileLog(console = True, enableBold = False),
_taskname4history = 'AstroDrizzle')
# Populate 'subtractedSky' and 'computedSky' of input image objects:
for i in range(nimg):
assert(not new_fi[i].fnamesOnly and not new_fi[i].image.closed)
image = imageList[i]
skysubimage = new_fi[i].image.hdu
numchips = image._numchips
extname = image.scienceExt
assert(os.path.samefile(image._filename, skysubimage.filename()))
for extver in range(1,numchips+1,1):
chip = image[extname,extver]
if not chip.group_member:
continue
subtracted_sky = skysubimage[extname,extver].header[skyKW]
chip.subtractedSky = subtracted_sky
chip.computedSky = subtracted_sky
# clean-up:
for fi in new_fi:
fi.release_all_images()