def main(args, unit_test=False):
""" Runs fluxing steps
"""
import os
import numpy as np
from pypeit import fluxspec
from pypeit.core import flux
from pypeit.par import pypeitpar
# Load the file
spectrograph, config_lines, flux_dict = read_fluxfile(args.flux_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)
if unit_test:
path = os.path.join(os.getenv('PYPEIT_DEV'), 'Cooked', 'Science')
par['fluxcalib']['std_file'] = os.path.join(
path, par['fluxcalib']['std_file'])
for kk, spec1d_file, flux_file in zip(
np.arange(len(flux_dict['spec1d_files'])),
flux_dict['spec1d_files'], flux_dict['flux_files']):
flux_dict['spec1d_files'][kk] = os.path.join(path, spec1d_file)
flux_dict['flux_files'][kk] = os.path.join(path, flux_file)
# Write the par to disk
print("Writing the parameters to {}".format(args.par_outfile))
par.to_config(args.par_outfile)
# Instantiate
FxSpec = fluxspec.instantiate_me(spectrograph,
par['fluxcalib'],
debug=args.debug)
# Generate sensfunc??
if par['fluxcalib']['std_file'] is not None:
# Load standard
_, _ = FxSpec.load_objs(par['fluxcalib']['std_file'], std=True)
## For echelle, the code will deal with the standard star in the ech_fluxspec.py
#if not spectrograph.pypeline == 'Echelle':
# Find the star
_ = FxSpec.find_standard()
# Sensitivity
_ = FxSpec.generate_sensfunc()
# Output
_ = FxSpec.save_sens_dict(FxSpec.sens_dict,
par['fluxcalib']['sensfunc'])
# Show
if args.plot:
FxSpec.show_sensfunc()
# Flux?
if len(flux_dict) > 0:
for spec1d_file, flux_file in zip(flux_dict['spec1d_files'],
flux_dict['flux_files']):
FxSpec.flux_science(spec1d_file)
FxSpec.write_science(flux_file)
def main(args):
""" Runs the 1d coadding steps
"""
# Load the file
config_lines, spec1dfiles, objids = read_coaddfile(args.coadd1d_file)
# Append path for testing
if args.test_spec_path is not None:
spec1dfiles = [
os.path.join(args.test_spec_path, ifile) for ifile in spec1dfiles
]
# Read in spectrograph from spec1dfile header
header = fits.getheader(spec1dfiles[0])
# NOTE: This was some test code for Travis. Keep it around for now
# in case we need to do this again. (KBW)
# try:
# header = fits.getheader(spec1dfiles[0])
# except Exception as e:
# raise Exception('{0}\n {1}\n {2}\n'.format(spec1dfiles[0], os.getcwd(),
# os.getenv('TRAVIS_BUILD_DIR', default='None'))) from e
spectrograph = load_spectrograph(header['PYP_SPEC'])
# 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)
# Write the par to disk
print("Writing the parameters to {}".format(args.par_outfile))
par.to_config(args.par_outfile)
sensfile = par['coadd1d']['sensfuncfile']
coaddfile = par['coadd1d']['coaddfile']
# Testing?
if args.test_spec_path is not None:
if sensfile is not None:
sensfile = os.path.join(args.test_spec_path, sensfile)
coaddfile = os.path.join(args.test_spec_path, coaddfile)
if spectrograph.pypeline is 'Echelle' and sensfile is None:
msgs.error(
'You must specify set the sensfuncfile in the .coadd1d file for Echelle coadds'
)
# Instantiate
coAdd1d = coadd1d.CoAdd1D.get_instance(spec1dfiles,
objids,
spectrograph=spectrograph,
par=par['coadd1d'],
sensfile=sensfile,
debug=args.debug,
show=args.show)
# Run
coAdd1d.run()
# Save to file
coAdd1d.save(coaddfile)
msgs.info('Coadding complete')
def main(args):
""" Runs the 1d coadding steps
"""
# Load the file
config_lines, spec1dfiles, objids = read_coaddfile(args.coadd1d_file)
# Append path for testing
if args.test_spec_path is not None:
spec1dfiles = [os.path.join(args.test_spec_path, ifile) for ifile in spec1dfiles]
# Read in spectrograph from spec1dfile header
header = fits.getheader(spec1dfiles[0])
# NOTE: This was some test code for Travis. Keep it around for now
# in case we need to do this again. (KBW)
# try:
# header = fits.getheader(spec1dfiles[0])
# except Exception as e:
# raise Exception('{0}\n {1}\n {2}\n'.format(spec1dfiles[0], os.getcwd(),
# os.getenv('TRAVIS_BUILD_DIR', default='None'))) from e
spectrograph = load_spectrograph(header['PYP_SPEC'])
# 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)
# Write the par to disk
print("Writing the parameters to {}".format(args.par_outfile))
par.to_config(args.par_outfile)
sensfile = par['coadd1d']['sensfuncfile']
coaddfile = par['coadd1d']['coaddfile']
# Testing?
if args.test_spec_path is not None:
if sensfile is not None:
sensfile = os.path.join(args.test_spec_path, sensfile)
coaddfile = os.path.join(args.test_spec_path, coaddfile)
if spectrograph.pypeline is 'Echelle' and sensfile is None:
msgs.error('You must specify set the sensfuncfile in the .coadd1d file for Echelle coadds')
# TODO JFH I really dislike that the parsets are used to hold actually run time specific information and not
# i.e. parameter defaults, or values of parameters. The problem is there is no other easy way to pass this information
# in via a .coadd1d file, since the parsets parse in a simply way. Otherwise I have to waste time trying to parse
# text files, whereas there are things like yaml and json that do this well already.
# Instantiate
coadd = coadd1d.CoAdd1D.get_instance(spec1dfiles, objids, sensfile=sensfile, par=par['coadd1d'],
debug=args.debug, show=args.show)
# Run
coadd.run()
# Save to file
coadd.save(coaddfile)
msgs.info('Coadding complete')
def main(args):
""" Runs fluxing steps
"""
# Load the file
config_lines, spec1dfiles, sensfiles_in = read_fluxfile(args.flux_file)
# Read in spectrograph from spec1dfile header
header = fits.getheader(spec1dfiles[0])
spectrograph = load_spectrograph(header['PYP_SPEC'])
# 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)
# Write the par to disk
print("Writing the parameters to {}".format(args.par_outfile))
par.to_config(args.par_outfile)
# Chck the sizes of the inputs
nspec = len(spec1dfiles)
if len(sensfiles_in) == 1:
# Use one sens file for each spec1d
sensfiles = nspec * sensfiles_in
elif len(sensfiles_in) == nspec:
# One sensfile specified / spec1d
sensfiles = sensfiles_in
elif len(sensfiles_in
) == 0 and par['fluxcalib']['use_archived_sens'] == True:
# No sensfile specified, but an archived sensfunc can be used.
sf_archive = SensFileArchive.get_instance(spectrograph.name)
sensfiles = nspec * [
sf_archive.get_archived_sensfile(spec1dfiles[0])
]
else:
msgs.error(
'Invalid format for .flux file.' + msgs.newline() +
'You must specify a single sensfile on the first line of the flux block,'
+ msgs.newline() +
'or specify a sensfile for every spec1dfile in the flux block,'
+ msgs.newline() +
'or specify "use_archived_sens = True" to use an archived sensfile.'
+ msgs.newline() +
'Run pypeit_flux_calib --help for information on the format')
# Instantiate
FxCalib = fluxcalibrate.FluxCalibrate.get_instance(
spec1dfiles, sensfiles, par=par['fluxcalib'], debug=args.debug)
msgs.info('Flux calibration complete')
return 0
def main(args):
""" Runs fluxing steps
"""
# Load the file
config_lines, spec1dfiles, sensfiles = read_fluxfile(args.flux_file)
# Read in spectrograph from spec1dfile header
header = fits.getheader(spec1dfiles[0])
spectrograph = load_spectrograph(header['PYP_SPEC'])
# 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)
# Write the par to disk
print("Writing the parameters to {}".format(args.par_outfile))
par.to_config(args.par_outfile)
# Instantiate
FxCalib = fluxcalibrate.FluxCalibrate.get_instance(spec1dfiles,
sensfiles,
par=par['fluxcalib'],
debug=args.debug)
msgs.info('Flux calibration complete')
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
"""
# 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)