def _check_gfiles(self):
"""Checks whether all files exist
The method checks whether the files whose names
are within the class data do exist or not.
An error is reported in case that the files
do not exist.
"""
# list of the root of all
# global keys indicating a file
fkeys = ['FFNAME']
# go over all file keywords
for key in fkeys:
# identify the keyword in the list
index = self._get_gkey_index(key)
# check for existence
if index > -1:
# extract the keyvalue
kvalue = self.gkeys[index].keyvalue
# if the keyvalue is NOT None but the file does not exist
if ((kvalue.upper() is not 'NONE')
and (not os.path.isfile(config_util.getCONF(kvalue)))):
# report an error
err_msg = ("The file: {0:s} does not exist!".format(
config_util.getCONF(kvalue)))
raise aXeError(err_msg)
def _check_global_backsub(self):
"""Check for global background subtraction"""
# 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)
# open the fits image
gri_fits = fits.open(config_util.getDATA(one_input['grisim']),
'readonly')
# go to the correct header
act_header = gri_fits[ext_info['fits_ext']].header
# make sure a sky background value is set
if 'SKY_CPS' in act_header and act_header['SKY_CPS'] >= 0.0:
# close the fits
gri_fits.close()
else:
# close fits, complain and out
gri_fits.close()
err_msg = (
"{0:s}: The grism image: \n{1:s}\nhas no keyword "
"SKY_CPS>=0.0 in the extension {2:d}. This means "
"it had NO global\nsky subtraction, which is "
"required for the CRR version of aXedrizzle!".format(
self.taskname,
config_util.getDATA(one_input['grisim']),
ext_info['fits_ext']))
raise aXeError(err_msg)
def _get_grism_ext_info(self, grisim='', config='', spec_hdu=None):
"""Determine the extension information on the grism image.
Parameters
----------
grisim : str
The name of the grism images
config : str
The name of the configuration file
spec_hdu : int, None
The extention number of the spectra data
Returns
-------
ext_info : dict
A dictionary that contains the header extension
and the data extension
"""
if spec_hdu is None:
conf = configfile.ConfigFile(getCONF(config))
ext_info = get_ext_info(getDATA(grisim), conf)
else:
# make by hand the extension information
ext_info = {'axe_ext': spec_hdu, 'fits_ext': spec_hdu - 1}
# return the extension info
return ext_info
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_objPET(self):
"""Generate the object PET."""
# set the use_direct flag
# NOTE: the flag is only usefull
# for the C-version, the python
# version does not need it!
use_direct = False
if self.dirim is not None:
use_direct = True
# run SEX2GOL
axetasks.sex2gol(grism=self.grisim,
config=config_util.getCONF(self.config),
in_sex=config_util.getDATA(self.objcat),
use_direct=use_direct,
direct=config_util.getDATA(self.dirim),
dir_hdu=None,
spec_hdu=None,
out_sex=None)
# run GOL2AF
axetasks.gol2af(grism=self.grisim,
config=self.config,
mfwhm=self.params['extrfwhm'],
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=None,
in_gol=None)
# run AF2PET
axetasks.af2pet(grism=self.grisim,
config=self.config,
back=False,
out_pet=None)
# run PETCONT
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="")
# run PETFF
axetasks.petff(grism=self.grisim,
config=self.config,
back=False,
ffname=None)
def _get_dirname_information(self,
dirname=None,
config="",
grisim="",
grism_extinfo=None,
dir_hdu=None):
"""Determine the direct image information.
Parameters
----------
dirname : str
Diretory name
config : str
The name of the config file
grisim : str
The name of the grisim image
grism_extinfo : dict
Dictionary of header information
dir_hdu : fits.HDU
FITS header data unit
Returns
-------
A tuple of the direct image name and a dictionary of
extension information
"""
# check whether ANY direct image information exists
if ((dirname is None) and (dir_hdu is None)):
# set the grism image as direct image
dirname = grisim
dirname_extinfo = grism_extinfo
elif ((dirname is not None) and (dir_hdu is None)):
# load the configuration file;
# determine the extension information
conf = configfile.ConfigFile(getCONF(config))
dirname_extinfo = get_ext_info(getDATA(grisim), conf)
del conf
elif ((dirname is not None) and (dir_hdu is not None)):
# make by hand the extension information
dirname_extinfo = {'axe_ext': dir_hdu, 'fits_ext': dir_hdu - 1}
else:
# error and out
err_msg = ("Specifying NO direct image but a direct image HDU: "
"{0:d} makrs NO sense!".format(dir_hdu))
raise aXeError(err_msg)
# return the name and the extension info
return dirname, dirname_extinfo
def __init__(self,
grisim="",
objcat="",
dirim="",
config="",
dmag=None,
**params):
if grisim:
self.grisim = config_util.getDATA(grisim)
else:
raise ValueError("No grisim image specified for axeprep")
self.objcat = config_util.getDATA(objcat)
_log.info("\n**Using object catalog: {0}\n".format(self.objcat))
self.dirim = config_util.getDATA(dirim)
# make the config into a list of configs
self.config_name = config
self.config_obj = configfile.ConfigFile(config_util.getCONF(config))
self.dmag = dmag
self.params = params
# store the master background
if 'master_bck' in params:
self.master_bck = config_util.getCONF(params['master_bck'])
def _check_files(self):
"""Checks the existence of the input files"""
# check the direct image
if not os.path.isfile(config_util.getDATA(self.direct_image)):
err_msg = ("\nThe direct image is not available: {0:s}".format(
config_util.getDATA(self.direct_image)))
raise aXeSIMError(err_msg)
# check the configuration file
if not os.path.isfile(config_util.getCONF(self.configfile)):
err_msg = (
"\nThe configuration file is not available: {0:s}".format(
config_util.getCONF(self.configfile)))
raise aXeSIMError(err_msg)
# check the simulated grism image
if not os.path.isfile(config_util.getOUTSIM(self.simul_grisim)):
err_msg = ("\nThe grism image is not available: {0:s}".format(
config_util.getOUTSIM(self.simul_grisim)))
raise aXeSIMError(err_msg)
# check the IOL
if not os.path.isfile(self.iolname):
err_msg = (
"\nThe Input Object List is not available: {0:s}".format(
self.iolname))
raise aXeSIMError(err_msg)
try:
float(self.bck_flux)
except ValueError:
# check the background image
if not os.path.isfile(config_util.getCONF(self.bck_flux)):
err_msg = (
"\nThe background imagage is not available: {0:s}".format(
config_util.getCONF(self.bck_flux)))
raise aXeSIMError(err_msg)
def check_files(self):
"""Checks whether all files exist
The method checks whether the files whose names
are within the class data do exist or not.
An error is reported in case that the files
do not exist.
"""
n_sens = 0
# list of the root of all
# beamword keys indicating a file
fkeys = ['SENSITIVITY_']
# append the beam identifier to the
# keyword roots to get the full keyname
for key in fkeys:
full_keyword = key + self.ident
# go over all beam keys
for bkey in self.beamkeys:
# check whether the current keyword is right
# and whether the keyvalue is not 'None'
if ((bkey.keyword is full_keyword)
and (bkey.keyvalue.upper() is not 'NONE')):
# check for the file
if not os.path.isfile(config_util.getCONF(bkey.keyvalue)):
# report an error
err_msg = ("The file: {0:s} does not exist!".format(
config_util.getCONF(bkey.keyvalue)))
raise aXeError(err_msg)
else:
n_sens += 1
return n_sens
def __init__(self, drizzle_params, modvar=0):
"""Initializes the class"""
# get the name of the input configuration file;
# load the configuration file
config_file = drizzle_params['CONF']
config = configfile.ConfigFile(config_utils.getCONF(config_file))
# get the header
header = self._get_header()
# generate the list of keywords
keylist = self._make_keylist(config, drizzle_params, modvar)
# generate the configuration file via the super class
super(DrizzleConf, self).__init__(keylist, header)
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 _get_ext_names(self, drizzle_params):
"""Define the file names for extracting the drizzled spectra."""
ext_names = {}
# check that a root name is given;
# message and out if not
if 'ROOT' not in drizzle_params:
err_msg = 'Not root name given. Nothing to do!'
raise aXeError(err_msg)
# compose the filenames for the input list, the configuration file
# and the OAF file
ext_names['OLIS'] = drizzle_params['ROOT'] + '_2.lis'
ext_names['BLIS'] = drizzle_params['ROOT'] + '_2.BCK.lis'
ext_names['OAF'] = drizzle_params['ROOT'] + '_2.OAF'
ext_names['DRZ_OAF'] = config_utils.getDRIZZLE(ext_names['OAF'])
ext_names['BAF'] = drizzle_params['ROOT'] + '_2.BAF'
ext_names['DRZ_BAF'] = config_utils.getDRIZZLE(ext_names['BAF'])
ext_names['FITS'] = drizzle_params['ROOT'] + '.fits'
ext_names['DRZ_FITS'] = config_utils.getDRIZZLE(ext_names['FITS'])
ext_names['OPET'] = drizzle_params['ROOT'] + '_2.PET.fits'
ext_names['DRZ_OPET'] = config_utils.getDRIZZLE(ext_names['OPET'])
ext_names['BPET'] = drizzle_params['ROOT'] + '_2.BCK.PET.fits'
ext_names['DRZ_BPET'] = config_utils.getDRIZZLE(ext_names['BPET'])
ext_names['SPC'] = drizzle_params['ROOT'] + '_2.SPC.fits'
ext_names['DRZ_SPC'] = config_utils.getDRIZZLE(ext_names['SPC'])
ext_names['STP'] = drizzle_params['ROOT'] + '_2.STP.fits'
ext_names['DRZ_STP'] = config_utils.getDRIZZLE(ext_names['STP'])
ext_names['CONF'] = drizzle_params['ROOT'] + '.conf'
ext_names['CON_CONF'] = config_utils.getCONF(ext_names['CONF'])
# return the dictionary
return ext_names
def _get_opt_names(self, drizzle_params):
"""Define the file names for the optimal extraction"""
# make an empty dictionary
opt_names = {}
# check that a root name is given;
# message and out if not
if 'ROOT' not in drizzle_params:
err_msg = 'Root name not given. Nothing to do!'
raise aXeError(err_msg)
# compose the filenames for the input list, the configuration file
# and the OAF file
opt_names['OLIS'] = drizzle_params['ROOT'] + '_2.lis'
opt_names['BLIS'] = drizzle_params['ROOT'] + '_2.BCK.lis'
opt_names['OAF'] = drizzle_params['ROOT'] + '_2.OAF'
opt_names['DRZ_OAF'] = config_utils.getDRIZZLE(opt_names['OAF'])
opt_names['BAF'] = drizzle_params['ROOT'] + '_2.BAF'
opt_names['DRZ_BAF'] = config_utils.getDRIZZLE(opt_names['BAF'])
opt_names['FITS'] = drizzle_params['ROOT'] + '.fits'
opt_names['DRZ_FITS'] = config_utils.getDRIZZLE(opt_names['FITS'])
opt_names['OPET'] = drizzle_params['ROOT'] + '_2_opt.PET.fits'
opt_names['DRZ_OPET'] = config_utils.getDRIZZLE(opt_names['OPET'])
opt_names['BPET'] = drizzle_params['ROOT'] + '_2_opt.BCK.PET.fits'
opt_names['DRZ_BPET'] = config_utils.getDRIZZLE(opt_names['BPET'])
opt_names['SPC'] = drizzle_params['ROOT'] + '_2_opt.SPC.fits'
opt_names['DRZ_SPC'] = config_utils.getDRIZZLE(opt_names['SPC'])
opt_names['STP'] = drizzle_params['ROOT'] + '_2_opt.STP.fits'
opt_names['DRZ_STP'] = config_utils.getDRIZZLE(opt_names['STP'])
opt_names['CONF'] = drizzle_params['ROOT'] + '.conf'
opt_names['CON_CONF'] = config_utils.getCONF(opt_names['CONF'])
# return the dictionary
return opt_names
def run(self):
# load the configuration files;
# get the extension info
conf = configfile.ConfigFile(config_util.getCONF(self.config))
ext_info = config_util.get_ext_info(config_util.getDATA(self.grisim),
conf)
del conf
# Does this harm data that was astrodrizzled?
if (('drzfwhm' in self.params) and (self.params['drzfwhm'])
or (('cont_model' in self.params) and
(config_util.is_quant_contam(self.params['cont_model'])))):
# generate the non-linear distortions from the IDCTAB;
# and store them in the fits-file header
this_data = config_util.getDATA(self.grisim)
_log.info(
"Generating and storing nonlinear distortions in {0}".format(
this_data))
nlins = nlincoeffs.NonLinCoeffs(this_data, ext_info)
nlins.write_file()
nlins.store_coeffs()
del nlins
# make the object PET's
self._make_objPET()
# make a background PET if necessary
if 'back' in self.params and self.params['back']:
_log.info("\nMaking backpet\n")
self._make_bckPET()
# extract the spectra
if 'spectr' in self.params and self.params['spectr']:
_log.info("\nMaking spectra\n")
self._make_spectra()
# make the proper non-quantitative contamination
if ('drzfwhm' in self.params and self.params['drzfwhm']) and \
('cont_model' in self.params and not config_util.is_quant_contam(self.params['cont_model'])):
_log.info("\nmaking non quant contam\n")
self._make_drzgeocont(ext_info)
def check_simdispim_input(self, incat, config, lambda_psf, model_spectra,
model_images, nx, ny, exptime, bck_flux,
extraction, extrfwhm, orient, slitless_geom,
adj_sens):
"""Does basic checks on the parameters
The method checks whether all input values are reasonable, e.g.
the exposure time and background flux >= 0.0 and similar.
Input files are checked for existence. Also the input type is
checked for the numbers.
Parameters
----------
incat: str
name of model object table
config: str
aXe configuration file name
lambda_psf: float
wavelength the object shapes were determined at
model_spectra: str
name of model spectra
model_images: str
name of model images
nx: int
number of pixels in x
ny: int
number of pixels in y
exptime: float
exposure time
bck_flux: float
flux in background
extraction: bool
flag for default extraction
extrfwhm: float
multiplier for extraction width
orient: bool
flag for tilted extraction
slitless_geom: bool
flag for slitless optimized extraction
adj_sens: bool
flag for adjusted flux conversion
"""
# do the setup
config_util.axe_setup(axesim=True)
# check the existence of the
# model object table
if not os.path.isfile(config_util.getDATA(incat)):
msg = ("The Model Object Table does not exist: {}".format(
config_util.getDATA(incat)))
raise aXeSIMError(msg)
# check the existence of the
# axe configuration file
if not os.path.isfile(config_util.getCONF(config)):
msg = ("The aXe configuration file does not exist: {}".format(
config_util.getCONF(config)))
raise aXeSIMError(msg)
else:
# load the aXe configuration file
conf = configfile.ConfigFile(config_util.getCONF(config))
# make the internal checks
n_sens = conf.check_files(check_glob=False)
# make sure there is
# at least one sens. file
if n_sens < 1:
msg = ("There must be at least one sensitivity file in: {}".
format(config_util.getCONF(config)))
raise aXeSIMError(msg)
# check whether the configuration files
# allows the requested extraction
if extraction and (slitless_geom or adj_sens):
extr_ready = conf.confirm_extrkeys()
# error and out
if not extr_ready:
msg = ("It is not possible to perform the requested"
"extraction. The likely cause is that the configuration"
"file does NOT contain the keywords 'POBJSIZE' or "
"'SMFACTOR' or their values are NOT reasonable "
"(e.g. <0.0)!")
raise aXeSIMError(msg)
# check the lambda_psf-value
if ((lambda_psf is not None) and (lambda_psf <= 0.0)):
msg = ("Value for 'lambda_psf' must be positive: {0:s}".format(
str(lambda_psf)))
raise aXeSIMError(msg)
if (model_spectra is not None):
# check the existence of the
# model spectra file
if not os.path.isfile(config_util.getDATA(model_spectra)):
msg = ("The model spectra file does not exist: {}".format(
config_util.getDATA(model_spectra)))
raise aXeSIMError(msg)
if model_images is not None:
# check the existence of the
# model images file
if not os.path.isfile(config_util.getDATA(model_images)):
msg = ("The model images file does not exist: ".format(
config_util.getDATA(model_images)))
raise aXeSIMError(msg)
# check the nx-value
if ((nx is not None) and (nx <= 0.0)):
msg = ("Value for 'nx' or 'nx_disp' must be positive: {0:g}".
format(nx))
raise aXeSIMError(msg)
# check the ny-value
if ((ny is not None) and (ny <= 0)):
error_message = ("Value for 'ny' or 'ny_disp' must be "
"positive: {0:g}".format(ny))
raise aXeSIMError(error_message)
# check the exptime-value
if ((exptime is not None) and (exptime < 0)):
error_message = ("Value for 'exptime' or 'exptime_disp' must be "
"positive: {0:g}".format(exptime))
raise aXeSIMError(error_message)
# the extraction width must be set!
if not extrfwhm:
error_message = ("Value for 'extrfwhm' must not be 0.0 to create"
"PETs, but extrfwhm={0:0.1f}!".format(extrfwhm))
raise aXeSIMError(error_message)
# negative extraction width is significant ONLY
# if orient="NO"
if orient and extrfwhm < 0.0:
error_message = (
"Negative width extrfwhm={0:0.1f} together with "
"extraction orient=yes does NOT make sense!".format(extrfwhm))
raise aXeSIMError(error_message)
try:
# convert to float
bck = float(bck_flux)
# check for positive value
if bck < 0:
error_message = ("Value for 'bck_flux' or 'bck_flux_disp'"
" most be positive: {0:g}".format(bck_flux))
raise aXeSIMError(error_message)
# catch a string
except ValueError:
# check for existence of file
if not os.path.isfile(config_util.getCONF(bck_flux)):
error_message = (
"The background file does not exist: {0}".format(
config_util.getCONF(bck_flux)))
raise aXeSIMError(error_message)
def check_simdirim_input(self, incat, config, tpass_direct, model_spectra,
model_images, nx, ny, exptime, bck_flux):
"""Does basic checks on the parameters
The method checks whether all input values are reasonable, e.g.
the exposure time and background flux >= 0.0 and similar.
Input files are checked for existence. Also the input type is
checked for the numbers.
Parameters
----------
incat: str
name of model object table
config: str
aXe configuration file name
tpass_direct: str
total passband file
model_spectra: str
name of model spectra
model_images: str
name of model images
nx: int
number of pixels in x
ny: int
number of pixels in y
exptime: float
exposure time
bck_flux: float
flux in background
"""
# do the setup
config_util.axe_setup(axesim=True)
# check the existence of the
# model object table
if not os.path.isfile(config_util.getDATA(incat)):
error_message = (
"The Model Object Table does not exist: {0}".format(
config_util.getDATA(incat)))
raise aXeSIMError(error_message)
# check the existence of the
# axe configuration file
if not os.path.isfile(config_util.getCONF(config)):
error_message = (
"The aXe configuration file does not exist: {0}".format(
config_util.getCONF(config)))
raise aXeSIMError(error_message)
else:
# load the aXe configuration file
conf = configfile.ConfigFile(config_util.getCONF(config))
# make the internal checks
n_sens = conf.check_files(check_glob=False)
# make sure there is
# at least one sens. file
if n_sens < 1:
error_message = ("There must be at least one sensitivity "
"file in: {0}".format(
config_util.getCONF(config)))
raise aXeSIMError(error_message)
# check the existence of the
# total passband file
if not os.path.isfile(config_util.getSIMDATA(tpass_direct)):
error_message = (
"The total passband file does not exist: {0}".format(
config_util.getSIMDATA(tpass_direct)))
raise aXeSIMError(error_message)
if model_spectra is not None:
# check the existence of the
# model spectra file
if not os.path.isfile(config_util.getDATA(model_spectra)):
error_message = (
"The model spectra file does not exist: {0}".format(
config_util.getDATA(config)))
raise aXeSIMError(error_message)
if model_images is not None:
# check the existence of the
# model images file
if not os.path.isfile(config_util.getDATA(model_images)):
error_message = (
"The model images file does not exist: {0}".format(
config_util.getDATA(config)))
raise aXeSIMError(error_message)
# check the nx-value
if ((nx is not None) and (nx <= 0.0)):
error_message = ("Value for 'nx' or 'nx_dir' must be positive: "
"{0:s}".format(str(nx)))
raise aXeSIMError(error_message)
# check the ny-value
if ((ny is not None) and (ny <= 0)):
error_message = ("Value for 'ny' or 'ny_dir' must be positive: "
"{0:s}".format(str(ny)))
raise aXeSIMError(error_message)
# check the exptime-value
if ((exptime is not None) and (exptime < 0)):
error_message = ("Value for 'exptime' or 'exptime_dir' must be "
"positive: {0:s}".format(str(exptime)))
raise aXeSIMError(error_message)
if bck_flux is not None:
# check the bck_flux-value
try:
# convert to float
bck = float(bck_flux)
# check for positive value
if bck < 0:
error_message = ("Value for 'bck_flux' or 'bck_flux_dir'"
" must be positive: {0:s}".format(
str(bck_flux)))
raise aXeSIMError(error_message)
# catch a string
except ValueError:
# check for existence of file
if not os.path.isfile(config_util.getCONF(bck_flux)):
error_message = (
"The background file does not exist: {0}".format(
config_util.getCONF(bck_flux)))
raise aXeSIMError(error_message)
