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Option: do not barycenter but just apply clock correction #93

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Option: do not barycenter but just apply clock correction #93

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32 changes: 22 additions & 10 deletions nuclockutils/barycorr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -116,22 +116,28 @@ def get_barycentric_correction(orbfile, parfile, dt=5, ephem='DE421'):
kind='quadratic')


def correct_times(times, bary_fun, clock_fun=None):
cl_corr = 0
def correct_times(times, bary_fun=None, clock_fun=None):
cl_corr = bary_corr = 0
if clock_fun is not None:
cl_corr = clock_fun(times)
bary_corr = bary_fun(times)
if bary_fun is not None:
bary_corr = bary_fun(times)

return times + cl_corr + bary_corr


def apply_clock_correction(
fname, orbfile, outfile='bary.evt', clockfile=None,
fname, orbfile=None, outfile='bary.evt', clockfile=None,
parfile=None, ephem='DE421', radecsys='ICRS', overwrite=False,
nodetrend=False, shift_times=0):
nodetrend=False, shift_times=0, no_bary=False):
version = nuclockutils.__version__

bary_fun = get_barycentric_correction(orbfile, parfile, ephem=ephem)
if orbfile is None and not no_bary:
raise ValueError("Must specify orbit file")

bary_fun = None
if not no_bary:
bary_fun = get_barycentric_correction(orbfile, parfile, ephem=ephem)
with fits.open(fname, memmap=True) as hdul:
times = hdul[1].data['TIME']
unique_times = np.unique(times)
Expand Down Expand Up @@ -183,12 +189,15 @@ def apply_clock_correction(

def _default_out_file(args):
outfile = 'bary'
if not os.path.exists(args.clockfile):
if args.clockfile is None or not os.path.exists(args.clockfile):
outfile += '_noclock'
if not os.path.exists(args.parfile):
if args.parfile is None or not os.path.exists(args.parfile):
outfile += '_nopar'
if args.use_nodetrend:
outfile += '_nodetrend'
if args.no_bary:
outfile += '_nobary'

outfile += '.evt'

return outfile
Expand All @@ -201,7 +210,7 @@ def main_barycorr(args=None):
parser = argparse.ArgumentParser(description=description)

parser.add_argument("file", help="Uncorrected event file")
parser.add_argument("orbitfile", help="Orbit file")
parser.add_argument("orbitfile", help="Orbit file", default=None, type=str, nargs="?")
parser.add_argument("-p", "--parfile",
help="Parameter file in TEMPO/TEMPO2 "
"format (for precise coordinates)",
Expand All @@ -222,6 +231,9 @@ def main_barycorr(args=None):
help="Use un-detrended correction in separate FITS "
"extension",
action='store_true', default=False)
parser.add_argument("--no-bary",
help="Do not barycenter the data",
action='store_true', default=False)

args = parser.parse_args(args)

Expand All @@ -236,7 +248,7 @@ def main_barycorr(args=None):
args.file, args.orbitfile, parfile=args.parfile, outfile=outfile,
overwrite=args.overwrite, nodetrend=args.use_nodetrend,
clockfile=args.clockfile,
shift_times=args.shift_times)
shift_times=args.shift_times, no_bary=args.no_bary)

return outfile

Expand Down
13 changes: 10 additions & 3 deletions nuclockutils/tests/test_barycorr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,12 +24,19 @@ def test_read_orb_funcs(self):

@pytest.mark.remote_data
def test_barycorr(self):
outfile = main_barycorr([self.evfile, self.orbfile, self.parfile])
outfile = main_barycorr([self.evfile, self.orbfile, "-p", self.parfile])
assert os.path.exists(outfile)
with pytest.raises(RuntimeError):
main_barycorr([self.evfile, self.orbfile, self.parfile,
main_barycorr([self.evfile, self.orbfile, "-p", self.parfile,
'-o', outfile])
main_barycorr([self.evfile, self.orbfile, self.parfile,
main_barycorr([self.evfile, self.orbfile, "-p", self.parfile,
'-o', outfile, '--overwrite'])

os.unlink(outfile)

@pytest.mark.remote_data
def test_barycorr_no_bary(self):
outfile = main_barycorr([self.evfile, "--no-bary"])
assert os.path.exists(outfile)

os.unlink(outfile)