def test_setup_not_alfosc():
droot = os.path.join(os.environ['PYPEIT_DEV'], 'RAW_DATA/not_alfosc/grism4')
droot += '/ALD'
pargs = setup.parse_args(['-r', droot, '-s', 'not_alfosc'])
setup.main(pargs)
cwd = os.getcwd()
setup_dir = os.path.join(cwd, 'setup_files')
assert os.path.isdir(setup_dir), 'No setup_files directory created'
files = glob.glob(os.path.join(setup_dir, 'not_alfosc*'))
ext = [f.split('.')[-1] for f in files]
expected = expected_file_extensions()
assert np.all([e in ext for e in expected]), \
'Did not find all setup file extensions: {0}'.format(expected)
# Build a PypeIt file
pargs = setup.parse_args(['-r', droot, '-s', 'not_alfosc', '-c', 'A', '-d', data_path('')])
setup.main(pargs)
pypeit_file = data_path('not_alfosc_A/not_alfosc_A.pypeit')
# TODO: Why is this using pypeit.PypeIt and not pypeitsetup.PypeItSetup?
pypeIt = pypeit.PypeIt(pypeit_file, calib_only=True)
# Clean-up
shutil.rmtree(setup_dir)
shutil.rmtree(data_path('not_alfosc_A'))
def main(args):
import os
import sys
import traceback
from pypeit import check_requirements
from pypeit import pypeit
from pypeit import pypeitsetup
from pypeit import debugger
# Initiate logging for bugs and command line help
# These messages will not be saved to a log file
# Set the default variables
qck = False
cpu = 1
#vrb = 2
# Load options from command line
splitnm = os.path.splitext(args.pypeit_file)
if splitnm[1] != '.pypeit':
msgs.error("Bad extension for PypeIt reduction file." +
msgs.newline() + ".pypeit is required")
logname = splitnm[0] + ".log"
# Load PypeIt file to get the spectrograph (might happen twice but that is ok)
pypeitSetup = pypeitsetup.PypeItSetup.from_pypeit_file(args.pypeit_file)
pypeIt = pypeit.PypeIt(args.pypeit_file,
verbosity=args.verbosity,
reuse_masters=args.use_masters,
overwrite=args.overwrite,
logname=logname,
show=args.show)
# JFH I don't see why this is an optional argument here. We could allow the user to modify an infinite number of parameters
# from the command line? Why do we have the PypeIt file then? This detector can be set in the pypeit file.
# Detector?
if args.detector is not None:
msgs.info("Restricting reductions to detector={}".format(
args.detector))
pypeIt.par['rdx']['detnum'] = int(args.detector)
pypeIt.reduce_all()
msgs.info('Data reduction complete')
# QA HTML
msgs.info('Generating QA HTML')
pypeIt.build_qa()
return 0
def main(args):
import os
from pypeit import pypeit
# Initiate logging for bugs and command line help
# These messages will not be saved to a log file
# Set the default variables
qck = False
cpu = 1
#vrb = 2
# Load options from command line
splitnm = os.path.splitext(args.pypeit_file)
if splitnm[1] != '.pypeit':
msgs.error("Bad extension for PypeIt reduction file." +
msgs.newline() + ".pypeit is required")
logname = splitnm[0] + ".log"
# Instantiate the main pipeline reduction object
pypeIt = pypeit.PypeIt(args.pypeit_file,
verbosity=args.verbosity,
reuse_masters=~args.do_not_reuse_masters,
overwrite=args.overwrite,
redux_path=args.redux_path,
calib_only=args.calib_only,
logname=logname,
show=args.show)
# JFH I don't see why this is an optional argument here. We could allow the user to modify an infinite number of parameters
# from the command line? Why do we have the PypeIt file then? This detector can be set in the pypeit file.
# Detector?
if args.detector is not None:
msgs.info("Restricting reductions to detector={}".format(
args.detector))
pypeIt.par['rdx']['detnum'] = int(args.detector)
if args.calib_only:
pypeIt.calib_all()
else:
pypeIt.reduce_all()
msgs.info('Data reduction complete')
# QA HTML
msgs.info('Generating QA HTML')
pypeIt.build_qa()
return 0
def main(args):
import os
from pypeit import pypeit
from pypeit import msgs
# Load options from command line
splitnm = os.path.splitext(args.pypeit_file)
if splitnm[1] != '.pypeit':
msgs.error('Input file must have a .pypeit extension!')
# Instantiate the main pipeline reduction object
pypeIt = pypeit.PypeIt(args.pypeit_file,
verbosity=1,
calib_only=True,
show=False)
# Grab the info without running
calib_dict = pypeIt.calib_all(run=False)
msgs.info('Data reduction complete')
msgs.close()
return calib_dict
def main(args):
import os
import sys
import numpy as np
from IPython import embed
from pypeit import pypeit
from pypeit import pypeitsetup
from pypeit.core import framematch
from pypeit import msgs
# Setup
data_files = [os.path.join(args.full_rawpath, args.fileA),
os.path.join(args.full_rawpath,args.fileB)]
ps = pypeitsetup.PypeItSetup(data_files, path='./', spectrograph_name='keck_nires')
ps.build_fitstbl()
# TODO -- Get the type_bits from 'science'
bm = framematch.FrameTypeBitMask()
file_bits = np.zeros(2, dtype=bm.minimum_dtype())
file_bits[0] = bm.turn_on(file_bits[0], ['arc', 'science', 'tilt'])
file_bits[1] = bm.turn_on(file_bits[0], ['arc', 'science', 'tilt'])
ps.fitstbl.set_frame_types(file_bits)
ps.fitstbl.set_combination_groups()
# Extras
ps.fitstbl['setup'] = 'A'
# A-B
ps.fitstbl['bkg_id'] = [2,1]
# Calibrations
master_dir = os.getenv('NIRES_MASTERS')
if master_dir is None:
msgs.error('You need to set an Environmental variable NIRES_MASTERS that points at the '
'Master Calibs')
# Config the run
cfg_lines = ['[rdx]']
cfg_lines += [' spectrograph = {0}'.format('keck_nires')]
cfg_lines += [' redux_path = {0}'.format(os.path.join(os.getcwd(),'keck_nires_A'))]
# Calibrations
cfg_lines += ['[baseprocess]']
cfg_lines += [' use_biasimage = False']
cfg_lines += [' use_overscan = False']
cfg_lines += [' use_pixelflat = False']
cfg_lines += ['[calibrations]']
cfg_lines += [' master_dir = {0}'.format(master_dir)]
cfg_lines += [' raise_chk_error = False']
cfg_lines += ['[scienceframe]']
cfg_lines += [' [[process]]']
cfg_lines += [' mask_cr = False']
cfg_lines += ['[reduce]']
cfg_lines += [' [[extraction]]']
cfg_lines += [' skip_optimal = True']
if args.box_radius is not None: # Boxcar radius
cfg_lines += [' boxcar_radius = {0}'.format(args.box_radius)]
cfg_lines += [' [[findobj]]']
cfg_lines += [' skip_second_find = True']
# Write
ofiles = ps.fitstbl.write_pypeit(configs='A', write_bkg_pairs=True, cfg_lines=cfg_lines)
if len(ofiles) > 1:
msgs.error("Bad things happened..")
# Instantiate the main pipeline reduction object
pypeIt = pypeit.PypeIt(ofiles[0], verbosity=2,
reuse_masters=True, overwrite=True,
logname='nires_proc_AB.log', show=False)
# Run
pypeIt.reduce_all()
msgs.info('Data reduction complete')
# QA HTML
msgs.info('Generating QA HTML')
pypeIt.build_qa()
return 0
def main(pargs):
import os
import numpy as np
from IPython import embed
from pypeit import pypeit
from pypeit import pypeitsetup
from pypeit.core import framematch
spec = pargs.spectrograph
# Config the run
cfg_lines = ['[rdx]']
cfg_lines += [' spectrograph = {0}'.format(spec)]
cfg_lines += [
' redux_path = {0}_A'.format(os.path.join(os.getcwd(), spec))
]
cfg_lines += [' detnum = {0}'.format(pargs.det)]
if pargs.ignore_headers:
cfg_lines += [' ignore_bad_headers = True']
cfg_lines += ['[scienceframe]']
cfg_lines += [' [[process]]']
cfg_lines += [' cr_reject = False']
if pargs.user_pixflat is not None:
cfg_lines += ['[calibrations]']
cfg_lines += [' [[flatfield]]']
cfg_lines += [' frame = {0}'.format(pargs.user_pixflat)]
cfg_lines += ['[reduce]']
cfg_lines += [' [[extraction]]']
cfg_lines += [' skip_optimal = True']
if pargs.box_radius is not None: # Boxcar radius
cfg_lines += [' boxcar_radius = {0}'.format(pargs.box_radius)]
cfg_lines += [' [[findobj]]']
cfg_lines += [' skip_second_find = True']
# Data files
data_files = [
os.path.join(pargs.full_rawpath, pargs.arc),
os.path.join(pargs.full_rawpath, pargs.flat),
os.path.join(pargs.full_rawpath, pargs.science)
]
# Setup
ps = pypeitsetup.PypeItSetup(data_files,
path='./',
spectrograph_name=spec,
cfg_lines=cfg_lines)
ps.build_fitstbl()
# TODO -- Get the type_bits from 'science'
bm = framematch.FrameTypeBitMask()
file_bits = np.zeros(3, dtype=bm.minimum_dtype())
file_bits[0] = bm.turn_on(file_bits[0], ['arc', 'tilt'])
file_bits[1] = bm.turn_on(
file_bits[1],
['pixelflat', 'trace'] if pargs.user_pixflat is None else 'trace')
file_bits[2] = bm.turn_on(file_bits[2], 'science')
# PypeItSetup sorts according to MJD
# Deal with this
asrt = []
for ifile in data_files:
bfile = os.path.basename(ifile)
idx = ps.fitstbl['filename'].data.tolist().index(bfile)
asrt.append(idx)
asrt = np.array(asrt)
# Set bits
ps.fitstbl.set_frame_types(file_bits[asrt])
ps.fitstbl.set_combination_groups()
# Extras
ps.fitstbl['setup'] = 'A'
# Write
ofiles = ps.fitstbl.write_pypeit('',
configs=['A'],
write_bkg_pairs=True,
cfg_lines=cfg_lines)
if len(ofiles) > 1:
msgs.error("Bad things happened..")
# Instantiate the main pipeline reduction object
pypeIt = pypeit.PypeIt(ofiles[0],
verbosity=2,
reuse_masters=True,
overwrite=True,
logname='mos.log',
show=False)
# Run
pypeIt.reduce_all()
msgs.info('Data reduction complete')
# QA HTML
msgs.info('Generating QA HTML')
pypeIt.build_qa()
return 0
def main(args: argparse.Namespace):
t = time.perf_counter()
# need an arc frame and a flat frame
root = args.fname.rstrip('0123456789.fits')
paths = glob.glob(f'{root}*.fits')
spectrograph = 'p200_dbsp_red' if 'red' in os.path.basename(
args.fname) else 'p200_dbsp_blue'
arm = spectrograph.split('_')[-1]
CFG_LINES = get_cfg_lines(spectrograph)
flatimg = ""
arcimg = ""
sciimg = args.fname
calib_only = not os.path.isfile(sciimg)
if calib_only:
for path in paths:
with fits.open(path) as hdul:
if not flatimg:
if hdul[0].header['OBJECT'] == 'flat' or hdul[0].header[
'IMGTYPE'] == 'flat':
flatimg = path
if not arcimg:
if hdul[0].header['OBJECT'] == 'arcs' or hdul[0].header[
'IMGTYPE'] == 'cal':
arcimg = path
if flatimg and arcimg:
break
if not (flatimg and arcimg):
raise Exception(
f"Could not find a flat and an arc frame in the same directory as {root}!"
)
files = [arcimg, flatimg]
else:
files = [sciimg]
ps = PypeItSetup(files,
path="./",
spectrograph_name=spectrograph,
cfg_lines=CFG_LINES)
ps.build_fitstbl()
bm = framematch.FrameTypeBitMask()
file_bits = np.zeros(len(files), dtype=bm.minimum_dtype())
if calib_only:
file_bits[0] = bm.turn_on(file_bits[0], ['arc', 'tilt'])
file_bits[1] = bm.turn_on(file_bits[1],
['pixelflat', 'trace', 'illumflat'])
else:
file_bits[0] = bm.turn_on(file_bits[0], 'science')
asrt = np.array([
ps.fitstbl['filename'].data.tolist().index(os.path.basename(fname))
for fname in files
])
ps.fitstbl.set_frame_types(file_bits[asrt])
ps.fitstbl.set_combination_groups()
ps.fitstbl['setup'] = 'A'
ofiles = ps.fitstbl.write_pypeit(configs='A', cfg_lines=CFG_LINES)
pypeIt = pypeit.PypeIt(ofiles[0],
verbosity=0,
reuse_masters=True,
overwrite=True,
logname='dbsp_ql.log',
show=False,
calib_only=calib_only)
if calib_only:
pypeIt.calib_all()
else:
pypeIt.reduce_all()
pypeIt.build_qa()
output_spec2ds = list(filter(lambda f: os.path.isfile(os.path.join('Science', f)), [
pypeIt.spec_output_file(i, True) \
for i in range(len(pypeIt.fitstbl.table)) \
if pypeIt.fitstbl.table[i]['frametype'] in ['science']
]))
output_spec1ds = list(filter(lambda f: os.path.isfile(os.path.join('Science', f)), [
pypeIt.spec_output_file(i) \
for i in range(len(pypeIt.fitstbl.table)) \
if pypeIt.fitstbl.table[i]['frametype'] in ['science']
]))
if output_spec1ds and not calib_only:
sensfiles = [
resource_filename("dbsp_drp", f"data/sens_{arm}_archived.fits")
]
FxCalib = fluxcalibrate.FluxCalibrate.get_instance(
output_spec1ds, sensfiles, par=ps.par['fluxcalib'])
print(f"Time elapsed: {time.perf_counter() - t}s.")
if not calib_only and not args.no_show:
p1 = Process(target=show_spec2d_helper, args=(output_spec2ds[0], ))
p1.start()
if output_spec1ds:
with fits.open(output_spec1ds[0]) as hdul:
specs = len(hdul) - 2
parr = [None] * specs
for i in range(specs):
parr[i] = Process(target=show_spec1d_helper,
args=(str(i), output_spec1ds[0]))
parr[i].start()
def main(pargs):
import os
import numpy as np
from IPython import embed
from pypeit import pypeit
from pypeit import pypeitsetup
from pypeit.core import framematch
spec = 'keck_deimos'
# Setup
data_files = [
os.path.join(pargs.full_rawpath, pargs.arc),
os.path.join(pargs.full_rawpath, pargs.flat),
os.path.join(pargs.full_rawpath, pargs.science)
]
ps = pypeitsetup.PypeItSetup(data_files, path='./', spectrograph_name=spec)
ps.build_fitstbl()
# TODO -- Get the type_bits from 'science'
bm = framematch.FrameTypeBitMask()
bits = [
bm.bits[iftype]
for iftype in ['arc', 'pixelflat', 'trace', 'science', 'tilt']
]
ps.fitstbl.set_frame_types(
np.array(
[2**bits[0] + 2**bits[4], 2**bits[1] + 2**bits[2],
2**bits[3]])) # 1=arc, 16=pixelflat, 32=science, trace=128
ps.fitstbl.set_combination_groups()
# Extras
ps.fitstbl['setup'] = 'A'
# Config the run
rdx_path = '{0}_A'.format(os.path.join(os.getcwd(), spec))
cfg_lines = ['[rdx]']
cfg_lines += [' spectrograph = {0}'.format(spec)]
cfg_lines += [' redux_path = {0}'.format(rdx_path)]
cfg_lines += [' detnum = {0}'.format(pargs.det)]
cfg_lines += ['[calibrations]']
cfg_lines += [' [[scienceframe]]']
cfg_lines += [' [[process]]']
cfg_lines += [' cr_reject = False']
cfg_lines += ['[scienceimage]']
cfg_lines += [' boxcar_only = True']
cfg_lines += [' skip_second_find = True']
# Boxcar radius
if pargs.box_radius is not None:
cfg_lines += [' boxcar_radius = {0}'.format(pargs.box_radius)]
# Write
ofiles = ps.fitstbl.write_pypeit('',
configs=['A'],
write_bkg_pairs=True,
cfg_lines=cfg_lines)
if len(ofiles) > 1:
msgs.error("Bad things happened..")
# Instantiate the main pipeline reduction object
pypeIt = pypeit.PypeIt(ofiles[0],
verbosity=2,
reuse_masters=True,
overwrite=True,
logname='deimos.log',
show=False)
# Run
pypeIt.reduce_all()
msgs.info('Data reduction complete')
# QA HTML
msgs.info('Generating QA HTML')
pypeIt.build_qa()
return 0