def test_interpret_valid_mnemonic_bit_flags(flag, expected):
flagmap = bitmask.extend_bit_flag_map('DetectorMap', CR=1, HOT=2)
assert(
bitmask.interpret_bit_flags(bit_flags=flag, flag_name_map=flagmap)
== expected
)
def test_interpret_duplicate_flag_warning():
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
assert bitmask.interpret_bit_flags([2, 4, 4]) == 6
assert len(w)
assert issubclass(w[-1].category, UserWarning)
assert "Duplicate" in str(w[-1].message)
def _mergeUserMaskAndDQ(dq, mask, dqbits):
from astropy.nddata.bitmask import (interpret_bit_flags,
bitfield_to_boolean_mask)
dqbits = interpret_bit_flags(dqbits)
if dqbits is None:
if mask is None:
return None
else:
return mask.copy().astype(dtype=np.uint8)
if dq is None:
raise ValueError("DQ array is None while 'dqbits' is not None.")
dqmask = bitfield_to_boolean_mask(dq,
dqbits,
good_mask_value=1,
dtype=np.uint8)
if mask is None:
return dqmask
# merge user mask with DQ mask:
dqmask[mask == 0] = 0
return dqmask
def test_interpret_duplicate_flag_warning():
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
assert bitmask.interpret_bit_flags([2, 4, 4]) == 6
assert len(w)
assert issubclass(w[-1].category, UserWarning)
assert "Duplicate" in str(w[-1].message)
def build_mask(dqarr, bitvalue):
""" Builds a bit-mask from an input DQ array and a bitvalue flag
"""
bitvalue = interpret_bit_flags(bitvalue)
if bitvalue is None:
return (np.ones(dqarr.shape, dtype=np.uint8))
return np.logical_not(np.bitwise_and(dqarr, ~bitvalue)).astype(np.uint8)
def build_mask(dqarr, bitvalue):
""" Builds a bit-mask from an input DQ array and a bitvalue flag
"""
bitvalue = interpret_bit_flags(bitvalue)
if bitvalue is None:
return (np.ones(dqarr.shape, dtype=np.uint8))
return np.logical_not(np.bitwise_and(dqarr, ~bitvalue)).astype(np.uint8)
def process(self, input):
self.log.setLevel(logging.DEBUG)
img = datamodels.ModelContainer(input)
self._dqbits = interpret_bit_flags(self.dqbits, flag_name_map=pixel)
# set sky statistics:
self._skystat = SkyStats(skystat=self.skystat,
lower=self.lower,
upper=self.upper,
nclip=self.nclip,
lsig=self.lsigma,
usig=self.usigma,
binwidth=self.binwidth)
# group images by their "group id":
grp_img = img.models_grouped
# create a list of "Sky" Images and/or Groups:
images = []
grp_id = 1
for g in grp_img:
if len(g) > 1:
images.append(
SkyGroup(list(map(self._imodel2skyim, g)), id=grp_id))
grp_id += 1
elif len(g) == 1:
images.append(self._imodel2skyim(g[0]))
else:
raise AssertionError("Logical error in the pipeline code.")
# match/compute sky values:
match(images,
skymethod=self.skymethod,
match_down=self.match_down,
subtract=self.subtract)
# set sky background value in each image's meta:
for im in images:
if isinstance(im, SkyImage):
if im.is_sky_valid:
self._set_sky_background(im.meta['image_model'], im.sky)
im.meta['image_model'].meta.cal_step.skymatch = "COMPLETE"
else:
im.meta['image_model'].meta.cal_step.skymatch = "SKIPPED"
else:
for gim in im:
if gim.is_sky_valid:
self._set_sky_background(gim.meta['image_model'],
gim.sky)
gim.meta[
'image_model'].meta.cal_step.skymatch = "COMPLETE"
else:
gim.meta[
'image_model'].meta.cal_step.skymatch = "SKIPPED"
return img
def test_interpret_valid_int_bit_flags(flag, flip, expected):
assert (bitmask.interpret_bit_flags(bit_flags=flag,
flip_bits=flip) == expected)
def test_interpret_allow_single_value_str_nonflags():
assert bitmask.interpret_bit_flags(bit_flags=str(3)) == 3
def test_interpret_bad_str_syntax(flag):
with pytest.raises(ValueError):
bitmask.interpret_bit_flags(bit_flags=flag)
def process(self, input):
self.log.setLevel(logging.DEBUG)
img = datamodels.ModelContainer(input)
self._dqbits = interpret_bit_flags(self.dqbits)
# set sky stattistics:
self._skystat = SkyStats(
skystat=self.skystat,
lower=self.lower,
upper=self.upper,
nclip=self.nclip,
lsig=self.lsigma,
usig=self.usigma,
binwidth=self.binwidth
)
# group images by their "group id":
grp_img = img.models_grouped
# create a list of "Sky" Images and/or Groups:
images = []
grp_id = 1
for g in grp_img:
if len(g) > 1:
images.append(
SkyGroup(
list(map(self._imodel2skyim, g)),
id=grp_id
)
)
grp_id += 1
elif len(g) == 1:
images.append(self._imodel2skyim(g[0]))
else:
raise AssertionError("Logical error in the pipeline code.")
# match/compute sky values:
match(images, skymethod=self.skymethod, match_down=self.match_down,
subtract=self.subtract)
# set sky background value in each image's meta:
for im in images:
if isinstance(im, SkyImage):
if im.is_sky_valid:
self._set_sky_background(im.meta['image_model'], im.sky)
im.meta['image_model'].meta.cal_step.skymatch = "COMPLETE"
else:
im.meta['image_model'].meta.cal_step.skymatch = "SKIPPED"
else:
for gim in im:
if gim.is_sky_valid:
self._set_sky_background(
gim.meta['image_model'],
gim.sky
)
gim.meta['image_model'].meta.cal_step.skymatch = "COMPLETE"
else:
gim.meta['image_model'].meta.cal_step.skymatch = "SKIPPED"
return img
def test_interpret_non_flag(flag):
with pytest.raises(ValueError):
bitmask.interpret_bit_flags(bit_flags=flag)
def test_interpret_wrong_string_int_format(flag):
with pytest.raises(ValueError):
bitmask.interpret_bit_flags(bit_flags=flag)
def test_interpret_non_flag(flag):
with pytest.raises(ValueError):
bitmask.interpret_bit_flags(bit_flags=flag)
def test_interpret_none_bit_flags_as_None(flag):
assert bitmask.interpret_bit_flags(bit_flags=flag) is None
def test_interpret_None_or_str_and_flip_incompatibility(flag, flip):
with pytest.raises(TypeError):
bitmask.interpret_bit_flags(bit_flags=flag, flip_bits=flip)
def destripe_plus(inputfile,
suffix='strp',
stat='pmode1',
maxiter=15,
sigrej=2.0,
lower=None,
upper=None,
binwidth=0.3,
scimask1=None,
scimask2=None,
dqbits=None,
rpt_clean=0,
atol=0.01,
cte_correct=True,
keep_intermediate_files=False,
clobber=False,
verbose=True):
r"""Calibrate post-SM4 ACS/WFC exposure(s) and use
standalone :ref:`acsdestripe`.
This takes a RAW image and generates a FLT file containing
its calibrated and destriped counterpart.
If CTE correction is performed, FLC will also be present.
Parameters
----------
inputfile : str or list of str
Input filenames in one of these formats:
* a Python list of filenames
* a partial filename with wildcards ('\*raw.fits')
* filename of an ASN table ('j12345670_asn.fits')
* an at-file (``@input``)
suffix : str
The string to use to add to each input file name to
indicate an output product of ``acs_destripe``.
This only affects the intermediate output file that will
be automatically renamed to ``*blv_tmp.fits`` during the processing.
stat : { 'pmode1', 'pmode2', 'mean', 'mode', 'median', 'midpt' } (Default = 'pmode1')
Specifies the statistics to be used for computation of the
background in image rows:
* 'pmode1' - SEXTRACTOR-like mode estimate based on a
modified `Pearson's rule <https://en.wikipedia.org/wiki/Nonparametric_skew#Pearson.27s_rule>`_:
``2.5*median-1.5*mean``;
* 'pmode2' - mode estimate based on
`Pearson's rule <https://en.wikipedia.org/wiki/Nonparametric_skew#Pearson.27s_rule>`_:
``3*median-2*mean``;
* 'mean' - the mean of the distribution of the "good" pixels (after
clipping, masking, etc.);
* 'mode' - the mode of the distribution of the "good" pixels;
* 'median' - the median of the distribution of the "good" pixels;
* 'midpt' - estimate of the median of the distribution of the "good"
pixels based on an algorithm similar to IRAF's `imagestats` task
(``CDF(midpt)=1/2``).
.. note::
The midpoint and mode are computed in two passes through the
image. In the first pass the standard deviation of the pixels
is calculated and used with the *binwidth* parameter to compute
the resolution of the data histogram. The midpoint is estimated
by integrating the histogram and computing by interpolation
the data value at which exactly half the pixels are below that
data value and half are above it. The mode is computed by
locating the maximum of the data histogram and fitting the peak
by parabolic interpolation.
maxiter : int
This parameter controls the maximum number of iterations
to perform when computing the statistics used to compute the
row-by-row corrections.
sigrej : float
This parameters sets the sigma level for the rejection applied
during each iteration of statistics computations for the
row-by-row corrections.
lower : float, None (Default = None)
Lower limit of usable pixel values for computing the background.
This value should be specified in the units of the input image(s).
upper : float, None (Default = None)
Upper limit of usable pixel values for computing the background.
This value should be specified in the units of the input image(s).
binwidth : float (Default = 0.1)
Histogram's bin width, in sigma units, used to sample the
distribution of pixel brightness values in order to compute the
background statistics. This parameter is aplicable *only* to *stat*
parameter values of `'mode'` or `'midpt'`.
scimask1 : str or list of str
Mask images for *calibrated* ``SCI,1``, one for each input file.
Pixels with zero values will be masked out, in addition to clipping.
scimask2 : str or list of str
Mask images for *calibrated* ``SCI,2``, one for each input file.
Pixels with zero values will be masked out, in addition to clipping.
This is not used for subarrays.
dqbits : int, str, None (Default = None)
Integer sum of all the DQ bit values from the input image's DQ array
that should be considered "good" when building masks for de-striping
computations. For example, if pixels in the DQ array can be
combinations of 1, 2, 4, and 8 flags and one wants to consider
DQ "defects" having flags 2 and 4 as being acceptable for de-striping
computations, then `dqbits` should be set to 2+4=6. Then a DQ pixel
having values 2,4, or 6 will be considered a good pixel, while a DQ
pixel with a value, e.g., 1+2=3, 4+8=12, etc. will be flagged
as a "bad" pixel.
Alternatively, one can enter a comma- or '+'-separated list of
integer bit flags that should be added to obtain the final
"good" bits. For example, both ``4,8`` and ``4+8`` are equivalent to
setting `dqbits` to 12.
| Set `dqbits` to 0 to make *all* non-zero pixels in the DQ
mask to be considered "bad" pixels, and the corresponding image
pixels not to be used for de-striping computations.
| Default value (`None`) will turn off the use of image's DQ array
for de-striping computations.
| In order to reverse the meaning of the `dqbits`
parameter from indicating values of the "good" DQ flags
to indicating the "bad" DQ flags, prepend '~' to the string
value. For example, in order not to use pixels with
DQ flags 4 and 8 for sky computations and to consider
as "good" all other pixels (regardless of their DQ flag),
set `dqbits` to ``~4+8``, or ``~4,8``. To obtain the
same effect with an `int` input value (except for 0),
enter -(4+8+1)=-9. Following this convention,
a `dqbits` string value of ``'~0'`` would be equivalent to
setting ``dqbits=None``.
.. note::
DQ masks (if used), *will be* combined with user masks specified
in the `scimask1` and `scimask2` parameters (if any).
rpt_clean : int
An integer indicating how many *additional* times stripe cleaning
should be performed on the input image. Default = 0.
atol : float, None
The threshold for maximum absolute value of bias stripe correction
below which repeated cleanings can stop. When `atol` is `None`
cleaning will be repeated `rpt_clean` number of times.
Default = 0.01 [e].
cte_correct : bool
Perform CTE correction.
keep_intermediate_files : bool
Keep de-striped BLV_TMP and BLC_TMP files around for CRREJ,
if needed. Set to `True` if you want to run :func:`crrej_plus`.
clobber : bool
Specify whether or not to 'clobber' (delete then replace)
previously generated products with the same names.
verbose : bool
Print informational messages. Default = True.
Raises
------
ImportError
``stsci.tools`` not found.
IOError
Input file does not exist.
ValueError
Invalid header values or CALACS version.
"""
from astropy.nddata.bitmask import interpret_bit_flags
# Optional package dependencies
from stsci.tools import parseinput
# process input file(s) and if we have multiple input files - recursively
# call acs_destripe_plus for each input image:
flist = parseinput.parseinput(inputfile)[0]
if isinstance(scimask1, str):
mlist1 = parseinput.parseinput(scimask1)[0]
elif isinstance(scimask1, np.ndarray):
mlist1 = [scimask1.copy()]
elif scimask1 is None:
mlist1 = []
elif isinstance(scimask1, list):
mlist1 = []
for m in scimask1:
if isinstance(m, np.ndarray):
mlist1.append(m.copy())
elif isinstance(m, str):
mlist1 += parseinput.parseinput(m)[0]
else:
raise TypeError("'scimask1' must be a list of str or "
"numpy.ndarray values.")
else:
raise TypeError("'scimask1' must be either a str, or a "
"numpy.ndarray, or a list of the two type of "
"values.")
if isinstance(scimask2, str):
mlist2 = parseinput.parseinput(scimask2)[0]
elif isinstance(scimask2, np.ndarray):
mlist2 = [scimask2.copy()]
elif scimask2 is None:
mlist2 = []
elif isinstance(scimask2, list):
mlist2 = []
for m in scimask2:
if isinstance(m, np.ndarray):
mlist2.append(m.copy())
elif isinstance(m, str):
mlist2 += parseinput.parseinput(m)[0]
else:
raise TypeError("'scimask2' must be a list of str or "
"numpy.ndarray values.")
else:
raise TypeError("'scimask2' must be either a str, or a "
"numpy.ndarray, or a list of the two type of "
"values.")
n_input = len(flist)
n_mask1 = len(mlist1)
n_mask2 = len(mlist2)
if n_input == 0:
raise ValueError(
'No input file(s) provided or the file(s) do not exist')
if n_mask1 == 0:
mlist1 = [None] * n_input
elif n_mask1 != n_input:
raise ValueError('Insufficient masks for [SCI,1]')
if n_mask2 == 0:
mlist2 = [None] * n_input
elif n_mask2 != n_input:
raise ValueError('Insufficient masks for [SCI,2]')
if n_input > 1:
for img, mf1, mf2 in zip(flist, mlist1, mlist2):
destripe_plus(inputfile=img,
suffix=suffix,
stat=stat,
lower=lower,
upper=upper,
binwidth=binwidth,
maxiter=maxiter,
sigrej=sigrej,
scimask1=scimask1,
scimask2=scimask2,
dqbits=dqbits,
cte_correct=cte_correct,
keep_intermediate_files=keep_intermediate_files,
clobber=clobber,
verbose=verbose)
return
inputfile = flist[0]
scimask1 = mlist1[0]
scimask2 = mlist2[0]
# verify that the RAW image exists in cwd
cwddir = os.getcwd()
if not os.path.exists(os.path.join(cwddir, inputfile)):
raise IOError(f"{inputfile} does not exist.")
# get image's primary header:
header = fits.getheader(inputfile)
# verify masks defined (or not) simultaneously:
if (header['CCDAMP'] == 'ABCD'
and ((scimask1 is not None and scimask2 is None) or
(scimask1 is None and scimask2 is not None))):
raise ValueError("Both 'scimask1' and 'scimask2' must be specified "
"or not specified together.")
calacs_str = subprocess.check_output(['calacs.e', '--version'
]).split()[0] # nosec # noqa
calacs_ver = [int(x) for x in calacs_str.decode().split('.')]
if calacs_ver < [8, 3, 1]:
raise ValueError(f'CALACS {calacs_str} is incomptible. '
'Must be 8.3.1 or later.')
# check date for post-SM4 and if supported subarray or full frame
is_subarray = False
ctecorr = header['PCTECORR']
aperture = header['APERTURE']
detector = header['DETECTOR']
date_obs = Time(header['DATE-OBS']).mjd # Convert to MJD for comparison
# intermediate filenames
blvtmp_name = inputfile.replace('raw', 'blv_tmp')
blctmp_name = inputfile.replace('raw', 'blc_tmp')
# output filenames
tra_name = inputfile.replace('_raw.fits', '.tra')
flt_name = inputfile.replace('raw', 'flt')
flc_name = inputfile.replace('raw', 'flc')
if detector != 'WFC':
raise ValueError(f"{inputfile} is not a WFC image, please check the "
"'DETECTOR' keyword.")
if date_obs < SM4_MJD:
raise ValueError(f"{inputfile} is a pre-SM4 image.")
if header['SUBARRAY'] and cte_correct:
if aperture in SUBARRAY_LIST:
is_subarray = True
else:
LOG.warning(f'Using non-supported subarray ({aperture}), '
'turning CTE correction off')
cte_correct = False
# delete files from previous CALACS runs
if clobber:
for tmpfilename in [
blvtmp_name, blctmp_name, flt_name, flc_name, tra_name
]:
if os.path.exists(tmpfilename):
os.remove(tmpfilename)
# run ACSCCD on RAW
acsccd.acsccd(inputfile)
# modify user mask with DQ masks if requested
dqbits = interpret_bit_flags(dqbits)
if dqbits is not None:
# save 'tra' file in memory to trick the log file
# not to save first acs2d log as this is done only
# for the purpose of obtaining DQ masks.
# WISH: it would have been nice is there was an easy way of obtaining
# just the DQ masks as if data were calibrated but without
# having to recalibrate them with acs2d.
if os.path.isfile(tra_name):
with open(tra_name) as fh:
tra_lines = fh.readlines()
else:
tra_lines = None
# apply flats, etc.
acs2d.acs2d(blvtmp_name, verbose=False, quiet=True)
# extract DQ arrays from the FLT image:
dq1, dq2 = _read_DQ_arrays(flt_name)
mask1 = _get_mask(scimask1, 1)
scimask1 = acs_destripe._mergeUserMaskAndDQ(dq1, mask1, dqbits)
mask2 = _get_mask(scimask2, 2)
if dq2 is not None:
scimask2 = acs_destripe._mergeUserMaskAndDQ(dq2, mask2, dqbits)
elif mask2 is None:
scimask2 = None
# reconstruct trailer file:
if tra_lines is not None:
with open(tra_name, mode='w') as fh:
fh.writelines(tra_lines)
# delete temporary FLT image:
if os.path.isfile(flt_name):
os.remove(flt_name)
# execute destriping (post-SM4 data only)
acs_destripe.clean(blvtmp_name,
suffix,
stat=stat,
maxiter=maxiter,
sigrej=sigrej,
lower=lower,
upper=upper,
binwidth=binwidth,
mask1=scimask1,
mask2=scimask2,
dqbits=dqbits,
rpt_clean=rpt_clean,
atol=atol,
clobber=clobber,
verbose=verbose)
blvtmpsfx = f'blv_tmp_{suffix}'
os.rename(inputfile.replace('raw', blvtmpsfx), blvtmp_name)
# update subarray header
if is_subarray and cte_correct:
fits.setval(blvtmp_name, 'PCTECORR', value='PERFORM')
ctecorr = 'PERFORM'
# perform CTE correction on destriped image
if cte_correct:
if ctecorr == 'PERFORM':
acscte.acscte(blvtmp_name)
else:
LOG.warning(f"PCTECORR={ctecorr}, cannot run CTE correction")
cte_correct = False
# run ACS2D to get FLT and FLC images
acs2d.acs2d(blvtmp_name)
if cte_correct and os.path.isfile(blctmp_name):
acs2d.acs2d(blctmp_name)
# delete intermediate files
if not keep_intermediate_files:
os.remove(blvtmp_name)
if cte_correct and os.path.isfile(blctmp_name):
os.remove(blctmp_name)
info_str = f'Done.\nFLT: {flt_name}\n'
if cte_correct:
info_str += f'FLC: {flc_name}\n'
LOG.info(info_str)
def test_interpret_wrong_flag_type(flag):
with pytest.raises(TypeError):
bitmask.interpret_bit_flags(bit_flags=flag)
def test_interpret_valid_str_bit_flags(flag, expected):
assert(
bitmask.interpret_bit_flags(bit_flags=flag) == expected
)
def test_interpret_none_bit_flags_as_None(flag):
assert bitmask.interpret_bit_flags(bit_flags=flag) is None
def test_interpret_valid_int_bit_flags(flag, flip, expected):
assert(
bitmask.interpret_bit_flags(bit_flags=flag, flip_bits=flip) == expected
)
def test_interpret_bad_str_syntax(flag):
with pytest.raises(ValueError):
bitmask.interpret_bit_flags(bit_flags=flag)
def test_interpret_allow_single_value_str_nonflags():
assert bitmask.interpret_bit_flags(bit_flags=str(3)) == 3
def test_interpret_valid_str_bit_flags(flag, expected):
assert (bitmask.interpret_bit_flags(bit_flags=flag) == expected)
def test_interpret_None_or_str_and_flip_incompatibility(flag, flip):
with pytest.raises(TypeError):
bitmask.interpret_bit_flags(bit_flags=flag, flip_bits=flip)
def test_interpret_wrong_flag_type(flag):
with pytest.raises(TypeError):
bitmask.interpret_bit_flags(bit_flags=flag)
def process(self, input1, input2):
cube_models = datamodels.ModelContainer(input1)
models2d = datamodels.ModelContainer(input2)
dqbits = interpret_bit_flags(self.dqbits, flag_name_map=pixel)
# set sky statistics:
self._skystat = SkyStats(
skystat=self.skystat,
lower=self.lower,
upper=self.upper,
nclip=self.nclip,
lsig=self.lsigma,
usig=self.usigma,
binwidth=self.binwidth
)
# At this moment running 'cube_skymatch' on images whose
# background has been previously subtracted is not supported.
# Raise an exception if background was subtracted:
self._check_background(cube_models)
self._check_background(models2d)
self._reset_background(cube_models)
self._reset_background(models2d)
# create a list of SkyCubes:
skycubes = []
for cm in cube_models:
# process weights and combine with DQ:
if not hasattr(cm, 'weightmap') or cm.weightmap is None:
weights = np.ones_like(cm.data, dtype=np.float64)
else:
weights = cm.weightmap.copy()
if dqbits is not None:
dq = bitfield_to_boolean_mask(
cm.dq,
self._dqbits,
good_mask_value=0,
dtype=bool
)
weights[dq] = 0.0
wcs = cm.meta.wcs if hasattr(cm.meta, 'wcs') else None
wcsinfo = cm.meta.wcsinfo if hasattr(cm.meta, 'wcsinfo') else None
exptime = cm.meta.exposure.exposure_time
if exptime is None:
exptime = 1.0
sc = SkyCube(
data=cm.data,
wcs=wcs,
wcsinfo=wcsinfo,
weights=weights,
cube_weight=exptime,
bkg_deg=self.bkg_degree,
bkg_center=None,
id=None,
meta={'original_cube_model': cm}
)
skycubes.append(sc)
skymatch_cubes, nsubspace = match(skycubes, subtract=self.subtract)
if nsubspace > 1:
self.log.warning("Not all cubes have been sky matched as "
"some of them do not overlap.")
# save background info in 'meta' and subtract sky from 2D images
# if requested:
# model.meta.instrument.channel
for c in skymatch_cubes:
self._set_cube_bkg_meta(c.meta['original_cube_model'], c)
model2d, channel = _find_associated_2d_image(
c.meta['original_cube_model'], models2d
)
if model2d is None:
continue
self._set_model2d_bkg_meta(
c.meta['original_cube_model'],
model2d,
channel
)
if self.subtract2d:
self._apply_sky_2d(model2d, channel)
return cube_models, models2d
def process(self, input1, input2):
cube_models = datamodels.ModelContainer(input1, persist=False)
models2d = datamodels.ModelContainer(input2, persist=False)
dqbits = interpret_bit_flags(self.dqbits)
# set sky stattistics:
self._skystat = SkyStats(
skystat=self.skystat,
lower=self.lower,
upper=self.upper,
nclip=self.nclip,
lsig=self.lsigma,
usig=self.usigma,
binwidth=self.binwidth
)
# At this moment running 'cube_skymatch' on images whose
# background has been previously subtracted is not supported.
# Raise an exception if background was subtracted:
self._check_background(cube_models)
self._check_background(models2d)
self._reset_background(cube_models)
self._reset_background(models2d)
# create a list of SkyCubes:
skycubes = []
for cm in cube_models:
# process weights and combine with DQ:
if not hasattr(cm, 'weightmap') or cm.weightmap is None:
weights = np.ones_like(cm.data, dtype=np.float64)
else:
weights = cm.weightmap.copy()
if dqbits is not None:
dq = bitfield_to_boolean_mask(
cm.dq,
self._dqbits,
good_mask_value=0,
dtype=np.bool
)
weights[dq] = 0.0
wcs = cm.meta.wcs if hasattr(cm.meta, 'wcs') else None
wcsinfo = cm.meta.wcsinfo if hasattr(cm.meta, 'wcsinfo') else None
exptime = cm.meta.exposure.exposure_time
if exptime is None:
exptime = 1.0
sc = SkyCube(
data=cm.data,
wcs=wcs,
wcsinfo=wcsinfo,
weights=weights,
cube_weight=exptime,
bkg_deg=self.bkg_degree,
bkg_center=None,
id=None,
meta={'original_cube_model': cm}
)
skycubes.append(sc)
skymatch_cubes, nsubspace = match(skycubes, subtract=self.subtract)
if nsubspace > 1:
self.log.warning("Not all cubes have been sky matched as "
"some of them do not overlap.")
# save background info in 'meta' and subtract sky from 2D images
# if requested:
##### model.meta.instrument.channel
for c in skymatch_cubes:
self._set_cube_bkg_meta(c.meta['original_cube_model'], c)
model2d, channel = _find_associated_2d_image(
c.meta['original_cube_model'], models2d
)
if model2d is None:
continue
self._set_model2d_bkg_meta(
c.meta['original_cube_model'],
model2d,
channel
)
if self.subtract2d:
self._apply_sky_2d(model2d, channel)
return cube_models, models2d
def test_interpret_wrong_string_int_format(flag):
with pytest.raises(ValueError):
bitmask.interpret_bit_flags(bit_flags=flag)