def save_exposure(self, frame, sci_dict, basename):
"""
Save the outputs from extraction for a given exposure
Args:
frame (:obj:`int`):
0-indexed row in the metadata table with the frame that
has been reduced.
sci_dict (:obj:`dict`):
Dictionary containing the primary outputs of extraction
basename (:obj:`str`):
The root name for the output file.
Returns:
None or SpecObjs: All of the objects saved to disk
"""
# TODO: Need some checks here that the exposure has been reduced
# Determine the headers
head1d = self.fitstbl[frame]
# Need raw file header information
rawfile = self.fitstbl.frame_paths(frame)
head2d = fits.getheader(rawfile, ext=self.spectrograph.primary_hdrext,)
refframe = 'pixel' if self.caliBrate.par['wavelengths']['reference'] == 'pixel' else \
self.caliBrate.par['wavelengths']['frame']
# Determine the paths/filenames
scipath = os.path.join(self.par['rdx']['redux_path'], self.par['rdx']['scidir'])
save.save_all(sci_dict, self.caliBrate.master_key_dict, self.caliBrate.master_dir, self.spectrograph,
head1d, head2d, scipath, basename, refframe=refframe,
update_det=self.par['rdx']['detnum'], binning=self.fitstbl['binning'][frame])
return
def main(args):
""" Executes 2d coadding
"""
# Load the file
if args.file is not None:
spectrograph, config_lines, spec2d_files = read_coadd2d_file(args.file)
# 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?
spectrograph_def_par = spectrograph.default_pypeit_par()
par = par.PypeItPar.from_cfg_lines(
cfg_lines=spectrograph_def_par.to_config(),
merge_with=config_lines)
elif args.obj is not None:
# 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['SPECTROG']
spectrograph = load_spectrograph(spectrograph_name)
par = spectrograph.default_pypeit_par()
else:
msgs.error(
'You must either input a coadd2d file with --file or an object name with --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))
par['rdx']['detnum'] = int(args.det)
# Get headers and base names
spec1d_files = [
files.replace('spec2d', 'spec1d') for files in spec2d_files
]
head1d = fits.getheader(spec1d_files[0])
head2d = fits.getheader(spec2d_files[0])
if args.basename is None:
filename = os.path.basename(spec2d_files[0])
basename = filename.split('_')[1]
else:
basename = args.basename
# Write the par to disk
par_outfile = basename + '_coadd2d.par'
print("Writing the parameters to {}".format(par_outfile))
par.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=par['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)) - set(detectors)
])))
# Loop on detectors
for det in detectors:
msgs.info("Working on detector {0}".format(det))
sci_dict[det] = {}
# Read in the images stacks and other clibration/meta data for this detector
stack_dict = coadd2d.load_coadd2d_stacks(spec2d_files, det)
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'] \
= coadd2d.extract_coadd2d(stack_dict, master_dir, det, ir_redux=ir_redux,
par=par, show=args.show, show_peaks=args.peaks,
std=args.std, samp_fact=args.samp_fact)
# 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)
# Save the results
save.save_all(sci_dict, stack_dict['master_key_dict'], master_dir,
spectrograph, head1d, head2d, scipath, basename)
def main(args):
""" Executes 2d coadding
"""
msgs.warn('PATH =' + os.getcwd())
# Load the file
if args.file is not None:
spectrograph, config_lines, spec2d_files = read_coadd2d_file(args.file)
# 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['SPECTROG']
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 psuedo images
psuedo_dict = coadd.create_psuedo_image(coadd_dict_list)
# Reduce
msgs.info('Running the extraction')
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'] = coadd.reduce(
psuedo_dict, show = args.show, show_peaks = args.peaks)
# Save psuedo image master files
coadd.save_masters(master_dir)
# 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)
# Save the results
save.save_all(sci_dict, coadd.stack_dict['master_key_dict'], master_dir, spectrograph, head1d,
head2d, scipath, basename)#, binning=coadd.binning)
def main(args):
""" Executes 2d coadding
"""
# Load the file
if args.file is not None:
spectrograph, config_lines, spec2d_files = read_coadd2d_file(args.file)
# Parameters
spectrograph_def_par = spectrograph.default_pypeit_par()
par = pypeitpar.PypeItPar.from_cfg_lines(cfg_lines=spectrograph_def_par.to_config(),
merge_with=config_lines)
elif args.obj is not None:
spec2d_files = glob.glob('./Science/spec2d_' + args.obj + '*')
head0 = fits.getheader(spec2d_files[0])
spectrograph_name = head0['SPECTROG']
spectrograph = load_spectrograph(spectrograph_name)
par = spectrograph.default_pypeit_par()
else:
msgs.error('You must either input a coadd2d file with --file or an object name with --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))
par['rdx']['detnum'] = int(args.det)
# Write the par to disk
print("Writing the parameters to {}".format(args.par_outfile))
par.to_config(args.par_outfile)
# Now run the coadds
spec1d_files = [files.replace('spec2d', 'spec1d') for files in spec2d_files]
head1d = fits.getheader(spec1d_files[0])
head2d = fits.getheader(spec2d_files[0])
filename = os.path.basename(spec2d_files[0])
basename = filename.split('_')[1]
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.newline()
msgs_string += '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)
redux_path = './'
master_dirname = os.path.basename(head2d['PYPMFDIR'])+'/'
master_dir = os.path.join(redux_path,os.path.normpath(master_dirname) + '_coadd/')
# Make the new master dir and Science dir
if os.path.exists(master_dir):
msgs.info("The following directory already exists:"+msgs.newline()+master_dir)
else:
os.mkdir(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 = select_detectors(par, spectrograph)
if len(detectors) != spectrograph.ndet:
msgs.warn('Not reducing detectors: {0}'.format(' '.join([str(d) for d in
set(np.arange(spectrograph.ndet)) - set(detectors)])))
# Loop on detectors
for det in detectors:
msgs.info("Working on detector {0}".format(det))
sci_dict[det] = {}
# Read in the images stacks and other clibration/meta data for this detector
stack_dict = coadd2d.load_coadd2d_stacks(spec2d_files, det)
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'] = coadd2d.extract_coadd2d(stack_dict, master_dir, ir_redux=ir_redux, par=par,
show=args.show, show_peaks=args.peaks, std=args.std)
# Make the science directory, and write outputs to disk
master_key_dict = stack_dict['master_key_dict']
scipath = redux_path + 'Science_coadd'
if os.path.exists(scipath):
msgs.info("The following directory already exists:" + msgs.newline() + scipath)
else:
os.mkdir(scipath)
save.save_all(sci_dict, master_key_dict, master_dir, spectrograph, head1d, head2d, scipath, basename)