def select_detectors(detnum=None, ndet=1, slitspatnum=None):
"""
Return the 1-indexed list of detectors to reduce.
Args:
detnum (:obj:`int`, :obj:`list`, optional):
One or more detectors to reduce. If None, return the
full list for the provided number of detectors (`ndet`).
ndet (:obj:`int`, optional):
The number of detectors for this instrument. Only used
if `detnum is None`.
Returns:
list: List of detectors to be reduced
"""
if detnum is not None and slitspatnum is not None:
msgs.error(
"You cannot specify both detnum and slitspatnum. Too painful for over-writing SpecObjs"
)
if detnum is None and slitspatnum is None:
return np.arange(1, ndet + 1).tolist()
elif detnum is not None:
return np.atleast_1d(detnum).tolist()
else:
return slittrace.parse_slitspatnum(slitspatnum)[0].tolist()
def write_to_fits(self,
subheader,
outfile,
overwrite=True,
update_det=None,
slitspatnum=None,
debug=False):
"""
Write the set of SpecObj objects to one multi-extension FITS file
Args:
outfile (str):
subheader (:obj:`dict`):
overwrite (bool, optional):
slitspatnum (:obj:`str` or :obj:`list`, optional):
Restricted set of slits for reduction
update_det (int or list, optional):
If provided, do not clobber the existing file but only update
the indicated detectors. Useful for re-running on a subset of detectors
"""
if os.path.isfile(outfile) and (not overwrite):
msgs.warn("Outfile exists. Set overwrite=True to clobber it")
return
# If the file exists and update_det (and slit_spat_num) is provided, use the existing header
# and load up all the other hdus so that we only over-write the ones
# we are updating
if os.path.isfile(outfile) and (update_det is not None
or slitspatnum is not None):
_specobjs = SpecObjs.from_fitsfile(outfile)
mask = np.ones(_specobjs.nobj, dtype=bool)
# Update_det
if update_det is not None:
# Pop out those with this detector (and slit if slit_spat_num is provided)
for det in np.atleast_1d(update_det):
mask[_specobjs.DET == det] = False
elif slitspatnum is not None: # slitspatnum
dets, spat_ids = slittrace.parse_slitspatnum(slitspatnum)
for det, spat_id in zip(dets, spat_ids):
mask[(_specobjs.DET == det)
& (_specobjs.SLITID == spat_id)] = False
_specobjs = _specobjs[mask]
# Add in the new
for sobj in self.specobjs:
_specobjs.add_sobj(sobj)
else:
_specobjs = self.specobjs
# Build up the Header
header = initialize_header(primary=True)
for key in subheader.keys():
header[key.upper()] = subheader[key]
# Init
prihdu = fits.PrimaryHDU()
hdus = [prihdu]
prihdu.header = header
# Add class info
prihdu.header['DMODCLS'] = (self.__class__.__name__, 'Datamodel class')
prihdu.header['DMODVER'] = (self.version, 'Datamodel version')
detector_hdus = {}
nspec, ext = 0, 0
# Loop on the SpecObj objects
for sobj in _specobjs:
if sobj is None:
continue
# HDUs
if debug:
import pdb
pdb.set_trace()
shdul = sobj.to_hdu()
if len(shdul) == 2: # Detector?
detector_hdus[sobj['DET']] = shdul[1]
shdu = [shdul[0]]
elif len(shdul) == 1: # Detector?
shdu = shdul
else:
msgs.error("Should not get here...")
# Check -- If sobj had only 1 array, the BinTableHDU test will fail
assert len(shdu) == 1, 'Bad data model!!'
assert isinstance(shdu[0],
fits.hdu.table.BinTableHDU), 'Bad data model2'
#shdu[0].header['DMODCLS'] = (self.__class__.__name__, 'Datamodel class')
#shdu[0].header['DMODVER'] = (self.version, 'Datamodel version')
# Name
shdu[0].name = sobj.NAME
# Extension
keywd = 'EXT{:04d}'.format(ext)
prihdu.header[keywd] = sobj.NAME
ext += 1
nspec += 1
# Append
hdus += shdu
# Deal with Detectors
for key, item in detector_hdus.items():
# TODO - Add EXT to the primary header for these??
prefix = specobj.det_hdu_prefix(key)
# Name
if prefix not in item.name: # In case we are re-loading
item.name = specobj.det_hdu_prefix(key) + item.name
# Append
hdus += [item]
# A few more for the header
prihdu.header['NSPEC'] = nspec
# Code versions
initialize_header(hdr=prihdu.header)
# Finish
hdulist = fits.HDUList(hdus)
if debug:
import pdb
pdb.set_trace()
hdulist.writeto(outfile, overwrite=overwrite)
msgs.info("Wrote 1D spectra to {:s}".format(outfile))
return