import os
from astropy.io import fits
from astropy.table import Table
from glue.config import data_translator
from jdaviz.core.registries import data_parser_registry
import lightkurve
import numpy as np
from lcviz.viewers import PhaseScatterView, TimeScatterView
from lcviz.plugins.plot_options import PlotOptions
__all__ = ["light_curve_parser"]
mission_sub_intervals = {
'kepler': {'prefix': 'Q', 'card': 'QUARTER'},
'k2': {'prefix': 'C', 'card': 'CAMPAIGN'},
'tess': {'prefix': 'S', 'card': 'SECTOR'},
'tess dvt': {'prefix': '', 'card': 'EXTNAME'}
}
@data_parser_registry("tess_dvt_parser")
def tess_dvt_parser(app, file_obj, data_label=None, show_in_viewer=True, **kwargs):
'''
Read a TESS DVT file and create a lightkurve object
'''
hdulist = fits.open(file_obj)
ephem_plugin = app._jdaviz_helper.plugins.get('Ephemeris', None)
extname = kwargs.pop('extname')
# Loop through the TCEs in the file. If we only want one (specified by
# `extname` keyword) then only load that one into the viewers and ephemeris.
for hdu in hdulist[1:]:
data = Table(hdu.data)
# don't load some columns with names that may
# conflict with components generated later by lcviz
data.remove_column('PHASE')
data.remove_column('CADENCENO')
# Remove rows that have NaN data
data = data[~np.isnan(data['LC_INIT'])]
header = hdu.header
time_offset = int(header['TUNIT1'] .split('- ')[1].split(',')[0])
data['TIME'] += time_offset
lc = lightkurve.LightCurve(data=data,
time=data['TIME'],
flux=data['LC_INIT'],
flux_err=data['LC_INIT_ERR'])
lc.meta = hdulist[0].header
lc.meta['MISSION'] = 'TESS DVT'
lc.meta['FLUX_ORIGIN'] = "LC_INIT"
lc.meta['EXTNAME'] = header['EXTNAME']
if extname is not None and header['EXTNAME'] != extname:
show_ext_in_viewer = False
else:
show_ext_in_viewer = show_in_viewer
light_curve_parser(app, lc, data_label=data_label,
show_in_viewer=show_ext_in_viewer, **kwargs)
# add ephemeris information from the DVT extension
if ephem_plugin is not None and show_ext_in_viewer:
ephem_plugin.period = header['TPERIOD']
ephem_plugin.t0 = header['TEPOCH'] + time_offset - app.data_collection[0].coords.reference_time.jd # noqa
[docs]
@data_parser_registry("light_curve_parser")
def light_curve_parser(app, file_obj, data_label=None, show_in_viewer=True, **kwargs):
# load a LightCurve or TargetPixelFile object:
cls_with_translator = (
lightkurve.LightCurve,
lightkurve.targetpixelfile.KeplerTargetPixelFile,
lightkurve.targetpixelfile.TessTargetPixelFile
)
# load local FITS file from disk by its path:
if isinstance(file_obj, str) and os.path.exists(file_obj):
if data_label is None:
data_label = os.path.splitext(os.path.basename(file_obj))[0]
light_curve = lightkurve.read(file_obj)
elif isinstance(file_obj, cls_with_translator):
light_curve = file_obj
else:
raise NotImplementedError(f"could not parse light_curve with type {type(file_obj)}")
# handle flux_origin default
mission = light_curve.meta.get('MISSION', '').lower()
flux_origin = light_curve.meta.get('FLUX_ORIGIN', None) # i.e. PDCSAP or SAP
# make a data label:
if data_label is None:
data_label = light_curve.meta.get('OBJECT', 'Light curve')
if isinstance(light_curve, lightkurve.targetpixelfile.TargetPixelFile):
data_label += '[TPF]'
elif mission in mission_sub_intervals:
# the sub-interval label is something like "Q9" for Kepler or
# "S9" for TESS. If it's already in the proposed data label, skip;
# otherwise, append it.
sub_interval_label = (
f' [{mission_sub_intervals[mission]["prefix"]}'
f'{light_curve.meta.get(mission_sub_intervals[mission]["card"])}]'
)
data_label += sub_interval_label
if flux_origin == 'flux' or (flux_origin is None and 'flux' in getattr(light_curve, 'columns', [])): # noqa
# then make a copy of this column so it won't be lost when changing with the flux_column
# plugin
light_curve['flux:orig'] = light_curve['flux']
if 'flux_err' in light_curve.columns:
light_curve['flux:orig_err'] = light_curve['flux_err']
light_curve.meta['FLUX_ORIGIN'] = 'flux:orig'
if 'FILENAME' in light_curve.meta:
light_curve.meta['FILENAME'] = os.path.basename(light_curve.meta['FILENAME'])
data = _data_with_reftime(app, light_curve)
app.add_data(data, data_label)
if isinstance(light_curve, lightkurve.targetpixelfile.TargetPixelFile):
# ensure an image/cube/TPF viewer exists
# TODO: move this to an event listener on add_data so that we can also remove when empty?
from jdaviz.core.events import NewViewerMessage
from lcviz.viewers import CubeView
if show_in_viewer:
found_viewer = False
for viewer_id, viewer in app._viewer_store.items():
if isinstance(viewer, CubeView):
app.add_data_to_viewer(viewer_id, data_label)
found_viewer = True
if not found_viewer:
app._on_new_viewer(NewViewerMessage(CubeView, data=None, sender=app),
vid='image', name='image')
app.add_data_to_viewer('image', data_label)
# set TPF viewer's stretch to custom defaults:
plot_options_plugin = PlotOptions(app=app)
if plot_options_plugin is not None:
plot_options_plugin._default_tpf_stretch()
else:
if show_in_viewer:
for viewer_id, viewer in app._viewer_store.items():
if isinstance(viewer, (TimeScatterView, PhaseScatterView)):
app.add_data_to_viewer(viewer_id, data_label)
# add to any known phase viewers
ephem_plugin = app._jdaviz_helper.plugins.get('Ephemeris', None)
if ephem_plugin is not None:
for viewer in ephem_plugin._obj._get_phase_viewers():
app.add_data_to_viewer(viewer.reference, data_label)
def _data_with_reftime(app, light_curve):
# grab the first-found reference time in the data collection:
ff_reference_time = None
for existing_data in app.data_collection:
if hasattr(existing_data, 'meta') and 'reference_time' in existing_data.meta:
ff_reference_time = existing_data.meta.get('reference_time', None)
if ff_reference_time is not None:
break
# convert to glue Data manually, so we may edit the `dt` component if necessary:
handler, _ = data_translator.get_handler_for(light_curve)
return handler.to_data(light_curve, reference_time=ff_reference_time)
