def main(args):
if args.file is not None:
spectrograph_name, config_lines, spec2d_files = io.read_spec2d_file(
args.file, filetype="coadd3d")
else:
msgs.error('You must input a coadd3d file')
# Coadd the files
coadd_cube(spec2d_files, det=args.det, overwrite=args.overwrite)
def main(args):
if args.file is None:
msgs.error('You must input a coadd3d file')
else:
spectrograph_name, config_lines, spec2d_files = io.read_spec2d_file(args.file, filetype="coadd3d")
spectrograph = load_spectrograph(spectrograph_name)
# Parameters
spectrograph_def_par = spectrograph.default_pypeit_par()
parset = par.PypeItPar.from_cfg_lines(cfg_lines=spectrograph_def_par.to_config(),
merge_with=config_lines)
# If detector was passed as an argument override whatever was in the coadd3d file
if args.det is not None:
msgs.info("Restricting to detector={}".format(args.det))
parset['rdx']['detnum'] = int(args.det)
# Coadd the files
coadd_cube(spec2d_files, parset, overwrite=args.overwrite)
def main(args):
""" Executes 2d coadding
"""
msgs.info('PATH =' + os.getcwd())
# Load the file
if args.file is not None:
spectrograph_name, config_lines, spec2d_files \
= io.read_spec2d_file(args.file, filetype="coadd2d")
spectrograph = load_spectrograph(spectrograph_name)
# Parameters
# TODO: Shouldn't this reinstantiate the same parameters used in
# the PypeIt run that extracted the objects? Why are we not
# just passing the pypeit file?
# JFH: The reason is that the coadd2dfile may want different reduction parameters
# DP: I think config_specific_par() is more appropriate here. default_pypeit_par()
# is included in config_specific_par()
# NOTE `config_specific_par` works with the spec2d files because we construct the header
# of those files to include all the relevant keywords from the raw file.
spectrograph_cfg_lines = spectrograph.config_specific_par(
spec2d_files[0]).to_config()
parset = par.PypeItPar.from_cfg_lines(
cfg_lines=spectrograph_cfg_lines, merge_with=config_lines)
elif args.obj is not None:
# TODO: We should probably be reading the pypeit file and using
# those parameters here rather than using the default parset.
# TODO: This needs to define the science path
spec2d_files = glob.glob('./Science/spec2d_*' + args.obj + '*')
head0 = fits.getheader(spec2d_files[0])
spectrograph_name = head0['PYP_SPEC']
spectrograph = load_spectrograph(spectrograph_name)
# NOTE `config_specific_par` works with the spec2d files because we construct the header
# of those files to include all the relevant keywords from the raw file.
spectrograph_cfg_lines = spectrograph.config_specific_par(
spec2d_files[0]).to_config()
parset = par.PypeItPar.from_cfg_lines(
cfg_lines=spectrograph_cfg_lines)
else:
return msgs.error(
'You must provide either a coadd2d file (--file) or an object name (--obj)'
)
# If detector was passed as an argument override whatever was in the coadd2d_file
if args.det is not None:
msgs.info("Restricting reductions to detector={}".format(args.det))
# parset['rdx']['detnum'] = par.util.eval_tuple(args.det.split(','))
# TODO this needs to be adjusted if we want to pass (as inline command) mosaic detectors
parset['rdx']['detnum'] = [int(d) for d in args.det.split(',')]
# Get headers (if possible) and base names
spec1d_files = [
files.replace('spec2d', 'spec1d') for files in spec2d_files
]
head1d = None
for spec1d_file in spec1d_files:
if os.path.isfile(spec1d_file):
head1d = fits.getheader(spec1d_file)
break
if head1d is None:
msgs.warn(
"No 1D spectra so am generating a dummy header for output")
head1d = io.initialize_header()
head2d = fits.getheader(spec2d_files[0])
if args.basename is None:
#TODO Fix this, currently does not work if target names have - or _
filename_first = os.path.basename(spec2d_files[0])
filename_last = os.path.basename(spec2d_files[-1])
prefix_first = (filename_first.split('_')[1]).split('-')[0]
prefix_last = (filename_last.split('_')[1]).split('-')[0]
objname = (filename_first.split('-')[1]).split('_')[0]
basename = '{:s}-{:s}-{:s}'.format(prefix_first, prefix_last,
objname)
else:
basename = args.basename
# TODO Heliocentric for coadd2d needs to be thought through. Currently turning it off.
parset['calibrations']['wavelengths']['refframe'] = 'observed'
# TODO Flexure correction for coadd2d needs to be thought through. Currently turning it off.
parset['flexure']['spec_method'] = 'skip'
# Write the par to disk
par_outfile = basename + '_coadd2d.par'
print("Writing the parameters to {}".format(par_outfile))
parset.to_config(par_outfile,
exclude_defaults=True,
include_descr=False)
# Now run the coadds
skysub_mode = head2d['SKYSUB']
findobj_mode = head2d['FINDOBJ']
bkg_redux = True if 'DIFF' in skysub_mode else False
find_negative = True if 'NEG' in findobj_mode else False
# Print status message
msgs_string = 'Reducing target {:s}'.format(basename) + msgs.newline()
msgs_string += 'Coadding frame sky-subtraced with {:s}'.format(
skysub_mode)
msgs_string += 'Searching for objects that are {:s}'.format(
findobj_mode)
msgs_string += msgs.newline(
) + 'Combining frames in 2d coadd:' + msgs.newline()
for f, file in enumerate(spec2d_files):
msgs_string += 'Exp {0}: {1:s}'.format(
f, os.path.basename(file)) + msgs.newline()
msgs.info(msgs_string)
# TODO: This needs to be added to the parameter list for rdx
redux_path = os.getcwd()
master_dirname = os.path.basename(head2d['PYPMFDIR']) + '_coadd'
master_dir = os.path.join(redux_path, master_dirname)
# Make the new Master dir
if not os.path.isdir(master_dir):
msgs.info(
'Creating directory for Master output: {0}'.format(master_dir))
os.makedirs(master_dir)
# Instantiate the sci_dict
sci_dict = OrderedDict() # This needs to be ordered
sci_dict['meta'] = {}
sci_dict['meta']['vel_corr'] = 0.
sci_dict['meta']['bkg_redux'] = bkg_redux
sci_dict['meta']['find_negative'] = find_negative
# Make QA coadd directory
parset['rdx']['qadir'] += '_coadd'
qa_path = os.path.join(parset['rdx']['redux_path'],
parset['rdx']['qadir'], 'PNGs')
if not os.path.isdir(qa_path):
os.makedirs(qa_path)
# Find the detectors to reduce
# detectors = PypeIt.select_detectors(detnum=parset['rdx']['detnum'], ndet=spectrograph.ndet)
detectors = spectrograph.select_detectors(
subset=parset['rdx']['detnum'])
# if len(detectors) != spectrograph.ndet:
# msgs.warn('Not reducing detectors: {0}'.format(' '.join([str(d) for d in
# set(np.arange(spectrograph.ndet) + 1) - set(detectors)])))
msgs.info(f'Detectors to work on: {detectors}')
# Only_slits?
if args.only_slits:
parset['coadd2d']['only_slits'] = [
int(item) for item in args.only_slits.split(',')
]
# container for specobjs
all_specobjs = specobjs.SpecObjs()
# container for spec2dobj
all_spec2d = spec2dobj.AllSpec2DObj()
# set some meta
all_spec2d['meta']['bkg_redux'] = bkg_redux
all_spec2d['meta']['find_negative'] = find_negative
# Loop on detectors
for det in detectors:
msgs.info("Working on detector {0}".format(det))
# Instantiate Coadd2d
coadd = coadd2d.CoAdd2D.get_instance(
spec2d_files,
spectrograph,
parset,
det=det,
offsets=parset['coadd2d']['offsets'],
weights=parset['coadd2d']['weights'],
spec_samp_fact=args.spec_samp_fact,
spat_samp_fact=args.spat_samp_fact,
bkg_redux=bkg_redux,
find_negative=find_negative,
debug_offsets=args.debug_offsets,
debug=args.debug)
# TODO Add this stuff to a run method in coadd2d
# Coadd the slits
coadd_dict_list = coadd.coadd(
only_slits=parset['coadd2d']['only_slits'])
# Create the pseudo images
pseudo_dict = coadd.create_pseudo_image(coadd_dict_list)
# Reduce
msgs.info('Running the extraction')
# TODO -- This should mirror what is in pypeit.extract_one
# TODO -- JFH :: This ought to return a Spec2DObj and SpecObjs which
# would be slurped into AllSpec2DObj and all_specobsj, as below.
# TODO -- JFH -- Check that the slits we are using are correct
sci_dict[coadd.detname] = {}
sci_dict[coadd.detname]['sciimg'], sci_dict[coadd.detname]['sciivar'], \
sci_dict[coadd.detname]['skymodel'], sci_dict[coadd.detname]['objmodel'], \
sci_dict[coadd.detname]['ivarmodel'], sci_dict[coadd.detname]['outmask'], \
sci_dict[coadd.detname]['specobjs'], sci_dict[coadd.detname]['detector'], \
sci_dict[coadd.detname]['slits'], sci_dict[coadd.detname]['tilts'], \
sci_dict[coadd.detname]['waveimg'] \
= coadd.reduce(pseudo_dict, show=args.show, show_peaks=args.peaks, basename=basename)
# Tack on detector (similarly to pypeit.extract_one)
for sobj in sci_dict[coadd.detname]['specobjs']:
sobj.DETECTOR = sci_dict[coadd.detname]['detector']
# fill the specobjs container
all_specobjs.add_sobj(sci_dict[coadd.detname]['specobjs'])
# fill the spec2dobj container but first ...
# pull out maskdef_designtab from sci_dict[det]['slits']
maskdef_designtab = sci_dict[
coadd.detname]['slits'].maskdef_designtab
slits = copy.deepcopy(sci_dict[coadd.detname]['slits'])
slits.maskdef_designtab = None
# fill up
all_spec2d[coadd.detname] = spec2dobj.Spec2DObj(
sciimg=sci_dict[coadd.detname]['sciimg'],
ivarraw=sci_dict[coadd.detname]['sciivar'],
skymodel=sci_dict[coadd.detname]['skymodel'],
objmodel=sci_dict[coadd.detname]['objmodel'],
ivarmodel=sci_dict[coadd.detname]['ivarmodel'],
scaleimg=np.array([1.0], dtype=np.float),
bpmmask=sci_dict[coadd.detname]['outmask'],
detector=sci_dict[coadd.detname]['detector'],
slits=slits,
waveimg=sci_dict[coadd.detname]['waveimg'],
tilts=sci_dict[coadd.detname]['tilts'],
sci_spat_flexure=None,
sci_spec_flexure=None,
vel_corr=None,
vel_type=None,
maskdef_designtab=maskdef_designtab)
# Save pseudo image master files
#coadd.save_masters()
# SAVE TO DISK
# Make the new Science dir
# TODO: This needs to be defined by the user
scipath = os.path.join(redux_path, 'Science_coadd')
if not os.path.isdir(scipath):
msgs.info(
'Creating directory for Science output: {0}'.format(scipath))
os.makedirs(scipath)
# THE FOLLOWING MIMICS THE CODE IN pypeit.save_exposure()
subheader = spectrograph.subheader_for_spec(head2d, head2d)
# Write spec1D
if all_specobjs.nobj > 0:
outfile1d = os.path.join(scipath,
'spec1d_{:s}.fits'.format(basename))
all_specobjs.write_to_fits(subheader, outfile1d)
# Info
outfiletxt = os.path.join(scipath,
'spec1d_{:s}.txt'.format(basename))
sobjs = specobjs.SpecObjs.from_fitsfile(outfile1d,
chk_version=False)
sobjs.write_info(outfiletxt, spectrograph.pypeline)
# Build header for spec2d
outfile2d = os.path.join(scipath, 'spec2d_{:s}.fits'.format(basename))
pri_hdr = all_spec2d.build_primary_hdr(
head2d,
spectrograph,
subheader=subheader,
# TODO -- JFH :: Decide if we need any of these
redux_path=None,
master_key_dict=None,
master_dir=None)
# Write spec2d
all_spec2d.write_to_fits(outfile2d, pri_hdr=pri_hdr)
def main(args):
""" Executes 2d coadding
"""
msgs.warn('PATH =' + os.getcwd())
# Load the file
if args.file is not None:
spectrograph_name, config_lines, spec2d_files = io.read_spec2d_file(
args.file, filetype="coadd2d")
spectrograph = load_spectrograph(spectrograph_name)
# Parameters
# TODO: Shouldn't this reinstantiate the same parameters used in
# the PypeIt run that extracted the objects? Why are we not
# just passing the pypeit file?
# JFH: The reason is that the coadd2dfile may want different reduction parameters
spectrograph_def_par = spectrograph.default_pypeit_par()
parset = par.PypeItPar.from_cfg_lines(
cfg_lines=spectrograph_def_par.to_config(),
merge_with=config_lines)
elif args.obj is not None:
# TODO: We should probably be reading the pypeit file and using those parameters here rather than using the
# default parset.
# TODO: This needs to define the science path
spec2d_files = glob.glob('./Science/spec2d_*' + args.obj + '*')
head0 = fits.getheader(spec2d_files[0])
spectrograph_name = head0['PYP_SPEC']
spectrograph = load_spectrograph(spectrograph_name)
parset = spectrograph.default_pypeit_par()
else:
msgs.error(
'You must either input a coadd2d file with --file or an object name with --obj'
)
# Update with configuration specific parameters (which requires science file) and initialize spectrograph
spectrograph_cfg_lines = spectrograph.config_specific_par(
spec2d_files[0]).to_config()
parset = par.PypeItPar.from_cfg_lines(cfg_lines=spectrograph_cfg_lines,
merge_with=parset.to_config())
# If detector was passed as an argument override whatever was in the coadd2d_file
if args.det is not None:
msgs.info("Restricting reductions to detector={}".format(args.det))
parset['rdx']['detnum'] = int(args.det)
# Get headers (if possible) and base names
spec1d_files = [
files.replace('spec2d', 'spec1d') for files in spec2d_files
]
head1d = None
for spec1d_file in spec1d_files:
if os.path.isfile(spec1d_file):
head1d = fits.getheader(spec1d_file)
break
if head1d is None:
msgs.warn("No 1D spectra so am generating a dummy header for output")
head1d = io.initialize_header()
head2d = fits.getheader(spec2d_files[0])
if args.basename is None:
filename = os.path.basename(spec2d_files[0])
basename = filename.split('_')[2]
else:
basename = args.basename
# Write the par to disk
par_outfile = basename + '_coadd2d.par'
print("Writing the parameters to {}".format(par_outfile))
parset.to_config(par_outfile)
# Now run the coadds
skysub_mode = head2d['SKYSUB']
ir_redux = True if 'DIFF' in skysub_mode else False
# Print status message
msgs_string = 'Reducing target {:s}'.format(basename) + msgs.newline()
msgs_string += 'Performing coadd of frames reduce with {:s} imaging'.format(
skysub_mode)
msgs_string += msgs.newline(
) + 'Combining frames in 2d coadd:' + msgs.newline()
for file in spec2d_files:
msgs_string += '{0:s}'.format(os.path.basename(file)) + msgs.newline()
msgs.info(msgs_string)
# TODO: This needs to be added to the parameter list for rdx
redux_path = os.getcwd()
master_dirname = os.path.basename(head2d['PYPMFDIR']) + '_coadd'
master_dir = os.path.join(redux_path, master_dirname)
# Make the new Master dir
if not os.path.isdir(master_dir):
msgs.info(
'Creating directory for Master output: {0}'.format(master_dir))
os.makedirs(master_dir)
# Instantiate the sci_dict
sci_dict = OrderedDict() # This needs to be ordered
sci_dict['meta'] = {}
sci_dict['meta']['vel_corr'] = 0.
sci_dict['meta']['ir_redux'] = ir_redux
# Find the detectors to reduce
detectors = PypeIt.select_detectors(detnum=parset['rdx']['detnum'],
ndet=spectrograph.ndet)
if len(detectors) != spectrograph.ndet:
msgs.warn('Not reducing detectors: {0}'.format(' '.join([
str(d)
for d in set(np.arange(spectrograph.ndet) + 1) - set(detectors)
])))
# Loop on detectors
for det in detectors:
msgs.info("Working on detector {0}".format(det))
sci_dict[det] = {}
# Instantiate Coadd2d
coadd = coadd2d.CoAdd2D.get_instance(
spec2d_files,
spectrograph,
parset,
det=det,
offsets=parset['coadd2d']['offsets'],
weights=parset['coadd2d']['weights'],
ir_redux=ir_redux,
debug_offsets=args.debug_offsets,
debug=args.debug,
samp_fact=args.samp_fact)
# Coadd the slits
coadd_dict_list = coadd.coadd(
only_slits=None) # TODO implement only_slits later
# Create the pseudo images
pseudo_dict = coadd.create_pseudo_image(coadd_dict_list)
# Reduce
msgs.info('Running the extraction')
# TODO -- This should mirror what is in pypeit.extract_one
# TODO -- JFH :: This ought to return a Spec2DObj and SpecObjs which would be slurped into
# AllSpec2DObj and all_specobsj, as below.
# TODO -- JFH -- Check that the slits we are using are correct
sci_dict[det]['sciimg'], sci_dict[det]['sciivar'], sci_dict[det]['skymodel'], sci_dict[det]['objmodel'], \
sci_dict[det]['ivarmodel'], sci_dict[det]['outmask'], sci_dict[det]['specobjs'], sci_dict[det]['detector'], \
sci_dict[det]['slits'], sci_dict[det]['tilts'], sci_dict[det]['waveimg'] = coadd.reduce(
pseudo_dict, show = args.show, show_peaks = args.peaks)
# Save pseudo image master files
#coadd.save_masters()
# Make the new Science dir
# TODO: This needs to be defined by the user
scipath = os.path.join(redux_path, 'Science_coadd')
if not os.path.isdir(scipath):
msgs.info('Creating directory for Science output: {0}'.format(scipath))
os.makedirs(scipath)
# THE FOLLOWING MIMICS THE CODE IN pypeit.save_exposure()
# TODO -- These lines should be above once reduce() passes back something sensible
all_specobjs = specobjs.SpecObjs()
for det in detectors:
all_specobjs.add_sobj(sci_dict[det]['specobjs'])
# Write
outfile1d = os.path.join(scipath, 'spec1d_{:s}.fits'.format(basename))
subheader = spectrograph.subheader_for_spec(head2d, head2d)
all_specobjs.write_to_fits(subheader, outfile1d)
# 2D spectra
# TODO -- These lines should be above once reduce() passes back something sensible
all_spec2d = spec2dobj.AllSpec2DObj()
all_spec2d['meta']['ir_redux'] = ir_redux
for det in detectors:
all_spec2d[det] = spec2dobj.Spec2DObj(
det=det,
sciimg=sci_dict[det]['sciimg'],
ivarraw=sci_dict[det]['sciivar'],
skymodel=sci_dict[det]['skymodel'],
objmodel=sci_dict[det]['objmodel'],
ivarmodel=sci_dict[det]['ivarmodel'],
scaleimg=np.array([1.0], dtype=np.float),
bpmmask=sci_dict[det]['outmask'],
detector=sci_dict[det]['detector'],
slits=sci_dict[det]['slits'],
waveimg=sci_dict[det]['waveimg'],
tilts=sci_dict[det]['tilts'],
sci_spat_flexure=None,
sci_spec_flexure=None,
vel_corr=None,
vel_type=None)
# Build header
outfile2d = os.path.join(scipath, 'spec2d_{:s}.fits'.format(basename))
pri_hdr = all_spec2d.build_primary_hdr(
head2d,
spectrograph,
subheader=subheader,
# TODO -- JFH :: Decide if we need any of these
redux_path=None,
master_key_dict=None,
master_dir=None)
# Write
all_spec2d.write_to_fits(outfile2d, pri_hdr=pri_hdr)