def _get_dpp_list(self, inima, confterm, back):
"""Determine the name of all DPP files"""
DPP_list = []
# generate the input list for aXe
axe_inputs = axeinputs.aXeInput(inima, confterm)
# go over the list of all inputs
for an_input in axe_inputs:
# load the configuration file
conf = configfile.ConfigFile(
config_util.getCONF(an_input['config']))
# get the image extensions
ext_info = config_util.get_ext_info(
config_util.getDATA(an_input['grisim']), conf)
# get the name of all axe files
axe_names = config_util.get_axe_names(an_input['grisim'], ext_info)
# if requested,
# append the background DPP file
if back:
DPP_list.append(axe_names['BCK_DPP'])
else:
# append the 'normal' DPP name to the list
DPP_list.append(axe_names['DPP'])
# return the DPP list
return DPP_list
def _check_dpps(self, back=False):
# go over all inputs
for one_input in self.axe_inputs:
# load the config file and get the extension information
conf = configfile.ConfigFile(
config_util.getCONF(one_input['config']))
ext_info = config_util.get_ext_info(
config_util.getDATA(one_input['grisim']), conf)
# derive the aXe names
axe_names = config_util.get_axe_names(one_input['grisim'],
ext_info)
# check the DPP file
if not os.path.isfile(config_util.getOUTPUT(axe_names['DPP'])):
# error and out
err_msg = (
f"{self.taskname}: The DPP file: {config_util.getOUTPUT(axe_names['DPP'])}"
f" does not exist!")
raise aXeError(err_msg)
# check for the background DPP file
if back and not os.path.isfile(
config_util.getOUTPUT(axe_names['BCK_DPP'])):
# error and out
err_msg = (
f"{self.taskname}: The DPP file: {config_util.getOUTPUT(axe_names['BCK_DPP'])}"
f" does not exist!")
raise aXeError(err_msg)
def _make_drzgeocont(self, ext_info):
# get the aXe names
axe_names = config_util.get_axe_names(self.grisim, ext_info)
# for the name of a special contamination OAF
cont_oaf = config_util.getOUTPUT(axe_names['OAF'].replace(
'.OAF', '_{0:s}.OAF'.format(int(self.params['drzfwhm'] * 10.0))))
# run GOL2AF,
# getting the special OAF as output
axetasks.gol2af(grism=self.grisim,
config=self.config,
mfwhm=self.params['drzfwhm'],
back=False,
orient=self.params['orient'],
slitless_geom=self.params['slitless_geom'],
exclude=self.params['exclude'],
lambda_mark=self.params['lambda_mark'],
dmag=self.dmag,
out_af=cont_oaf,
in_gol=None)
# run PETCONT,
# using the special OAF as input
axetasks.petcont(grism=self.grisim,
config=self.config,
cont_model=self.params['cont_model'],
model_scale=self.params['model_scale'],
spec_models=None,
object_models=None,
inter_type=self.params['inter_type'],
lambda_psf=self.params['lambda_psf'],
cont_map=True,
in_af=cont_oaf)
def _check_fluxcubes(self):
# go over all inputs
for one_input in self.axe_inputs:
# load the config file and get the extension information
conf = configfile.ConfigFile(config_util.getCONF(one_input['config']))
ext_info = config_util.get_ext_info(config_util.getDATA(one_input['grisim']), conf)
# derive the aXe names
axe_names = config_util.get_axe_names(one_input['grisim'], ext_info)
# check the fluxcube
if not os.path.isfile(config_util.getDATA(axe_names['FLX'])):
# error and out
err_msg = ("{0:s}: The fluxcube file: {1:s} does not exist!"
.format(self.taskname,
config_util.getDATA(axe_names['FLX'])))
raise aXeError(err_msg)
def _subtract_wfc3irsky(self, ext_info):
"""Special sky subtraction for WFC3 IR images"""
# get the axe names
axe_names = config_util.get_axe_names(self.grisim, ext_info)
# check for a previous background subtraction
try:
fits.getval(self.grisim, 'AXEPRBCK', exten=ext_info['fits_ext'])
_log.info(
f"WARNING: Image {self.grisim} seems to be already background "
"subtracted! Continuing anyways...")
except KeyError:
_log.info(
"Previous subtraction not recorded, proceeding with background subtraction."
)
scalebck = axelowlev.aXe_SCALEBCK(
os.path.split(self.grisim)[-1],
os.path.split(axe_names['MSK'])[-1],
os.path.split(self.config_name)[-1],
os.path.split(self.master_bck)[-1])
try:
scalebck.runall()
except aXeError:
_log.info("There was a problem with the background subtraction, "
"continuing without it")
return False
# check whether the background image exists
bckfilename = config_util.getOUTPUT(axe_names['SGRI'])
if not os.path.isfile(bckfilename):
err_msg = ("The background image: {0:s} does NOT exist!".format(
bckfilename))
raise aXeError(err_msg)
fits_image = fits.open(bckfilename, ext=0, mode='readonly')
sky_frac = fits_image[0].header["FRACFIN"]
scal_val = fits_image[0].header["SCALVAL"]
bck_data = fits_image[1].data
fits_image.close()
if sky_frac < 0.1:
_log.info(
"Low fraction of sky pixels found (<10%) continuing WITHOUT"
" sky subtraction")
return False
# Subtract the scaled background image from the grism image
grism_file = fits.open(self.grisim, mode='update')
grism_file[ext_info['ext_version']].data -= bck_data
grism_header = grism_file[ext_info['fits_ext']].header
# write some information into the
# grism image header
grism_header['AXEPRBCK'] = (
'Done', 'flag that background subtraction was done')
grism_header['SKY_IMG'] = (self.master_bck,
'name of the 1st master background image')
# write some scaling information into the header
grism_header['F_SKYPIX'] = (float(sky_frac),
'fraction of pixels used for scaling')
grism_header['SKY_CPS'] = (
float(scal_val), 'scale used for master sky == sky value [cps]')
# close the grism image and sacve and the scaled image
grism_file.close()
return True
def _subtract_nicsky(self, ext_info):
"""Special sky subtraction for NICMOS images"""
# get the axe names
axe_names = config_util.get_axe_names(self.grisim, ext_info)
# check for a previous background subtraction
fits_img = fits.open(self.grisim, 'readonly')
fits_head = fits_img[ext_info['fits_ext']].header
# npix = int(fits_head['NAXIS1']) * int(fits_head['NAXIS1'])
if 'AXEPRBCK' in fits_head:
# warn that this is the second time
_log.info(
f"WARNING: Image {self.grisim} seems to be already background "
"subtracted!")
# close the fits
fits_img.close()
# do the special background fitting for NICMOS
if self.params['backped'] is not None:
nicback = axelowlev.aXe_NICBACK(self.grisim, self.config_name,
self.master_bck,
self.params['backped'])
else:
nicback = axelowlev.aXe_NICBACK(self.grisim, self.config_name,
self.master_bck)
nicback.runall()
del nicback
# check whether the background image exists
if not os.path.isfile(config_util.getOUTPUT(axe_names['NBCK'])):
err_msg = ("The background image: {0:s} does NOT exist!".format(
config_util.getOUTPUT(axe_names['NBCK'])))
raise aXeError(err_msg)
# Subtract the scaled background image from the grism image
# copy the image to the output directory first
sci_file = fits.open(self.grisim, mode='update')
bck_file = fits.open(config_util.getOUTPUT(axe_names['NBCK']),
'readonly')
sci_file['SCI', ext_info['ext_version']].data -= bck_file[1].data
sci_file.close()
bck_file.close()
# open the background image
fits_img = fits.open(config_util.getOUTPUT(axe_names['NBCK']),
'readonly')
fits_head = fits_img['BCK'].header
# open the grism image and isolate the correct extension header
grism_img = fits.open(self.grisim, mode='update')
grism_header = grism_img[ext_info['fits_ext']].header
if 'SKY_SCAL' in fits_head and 'F_SKYPIX' in fits_head:
# transfer important keywords
# to the grism image
grism_header['SKY_SCAL'] = (float(fits_head['SKY_SCAL']),
'scaling value of background')
grism_header['F_SKYPIX'] = (float(fits_head['F_SKYPIX']),
'fraction of pixels used for scaling')
# close the fits again
fits_img.close()
# write some keywords
grism_header['AXEPRBCK'] = (
'Done', 'flag that background subtraction was done')
grism_header['SKY_IMG'] = (self.master_bck,
'name of the 1st master background image')
if self.params['backped'] is not None:
grism_header['SKY_IMG2'] = (
self.params['backped'],
'name of the 2nd master background image')
# close the image again
grism_img.close()
return True
def _subtract_sky(self, ext_info, flag=-1.0e10):
"""Perform a classical background subtraction."""
# Derive the name of all aXe products for a given image
axe_names = config_util.get_axe_names(self.grisim, ext_info)
msk_image_sc = axe_names['MSK'] + '[SCI]'
# check for a previous background subtraction
with fits.open(self.grisim, mode='update') as grism_file:
if 'AXEPRBCK' in grism_file[ext_info['fits_ext']].header:
# warn that this is the second time
_log.info("WARNING: Image %25s seems to be already background "
"subtracted!".format(self.grisim))
# Compute the ratio of the grism SCI image to the background image
sci_data = grism_file['SCI', ext_info['ext_version']].data
sci_header = grism_file['SCI', ext_info['ext_version']].header
npix = int(sci_header["NAXIS1"]) * int(sci_header["NAXIS2"])
bck_data = fits.getdata(self.master_bck)
ratio_data = sci_data / bck_data
# Flag pixels in the ratio image based on the grism image DQ array
grism_dq_data = grism_file['DQ', ext_info['ext_version']].data
ratio_data[grism_dq_data > 0.5] = flag
# Flag pixels in the ratio image based on the grism image MSK file
msk_file = fits.open(
config_util.getOUTPUT(msk_image_sc.split("[")[0]), 'readonly')
msk_data = msk_file['SCI'].data
msk_file.close()
ratio_data[msk_data < -900000] = flag
# Flag pixels in the background image based on the grism image DQ
# and MSK file
bck_data[grism_dq_data > 0.5] = flag
bck_data[msk_data < -900000] = flag
# Compute stats for the ratio image
stats = imagestats.ImageStats(ratio_data[ratio_data > flag],
fields='midpt,stddev,npix',
lower=None,
upper=None,
nclip=3,
lsig=3.0,
usig=3.0,
binwidth=0.01)
# Compute stats for the background image
bstats = imagestats.ImageStats(bck_data[bck_data > flag],
fields='midpt,stddev,npix',
lower=None,
upper=None,
nclip=3,
lsig=3.0,
usig=3.0,
binwidth=0.01)
# Subtract the scaled background from the grism image
# Reload a clean version of background
bck_data = fits.getdata(self.master_bck)
grism_file['SCI',
ext_info['ext_version']].data -= bck_data * stats.midpt
grism_header = grism_file['SCI', ext_info['ext_version']].header
# write some header iformation
grism_header['SKY_SCAL'] = (float(
stats.midpt), 'scaling value for the master background')
grism_header['SKY_MAST'] = (float(
bstats.midpt), 'average value of the master background')
grism_header['SKY_IMG'] = (self.master_bck,
'name of the master background image')
grism_header['F_SKYPIX'] = (float(stats.npix) / float(npix),
'fraction of pixels used for scaling')
grism_header['AXEPRBCK'] = (
'Done', 'flag that background subtraction was done')
return 0