def test_detrend_IO():
#the mock_flc needs ra, dec, mission, and channel only for k2sc detrending!
test_detrend(save_k2sc=True, folder='{}/tests/testfiles/'.format(PACKAGEDIR))
flc = fitsopen('{}/tests/testfiles/pony_k2sc_k2_llc_800000000-c05_kepler_v2_lc.fits'.format(PACKAGEDIR))
flc = flc[1].data
mockflc = mock_flc()
print (flc['TRTIME']-mockflc.flux)
assert (flc['TIME'] == mockflc.time).all()
assert (flc['CADENCE'] == mockflc.cadenceno).all()
def get_hdulist(fits_reference):
""" Open an HDU list from the fits reference.
Note that the reference may already be an HDUList
"""
# If the reference is a string, presume its a file path
result = fits_reference
if isinstance(fits_reference, str):
try:
result = fitsopen(fits_reference)
except Exception as exc:
raise IOError("error opening file (%s): %s: %s" %
(fits_reference, exc.__class__.__name__, exc.args[0])) from exc
return result
def test_path(self, capsys):
os.mkdir(self.temp('sub/'))
tmp_b = self.temp('sub/ascii.fits')
tmp_g = self.temp('sub/group.fits')
tmp_h = self.data('group.fits')
with hdulist.fitsopen(tmp_h) as hdu_b:
hdu_b.writeto(tmp_g)
writeto(tmp_b, np.arange(100).reshape(10, 10))
# one modified file and a directory
assert fitsdiff.main(["-q", self.data_dir, tmp_b]) == 1
assert fitsdiff.main(["-q", tmp_b, self.data_dir]) == 1
# two directories
tmp_d = self.temp('sub/')
assert fitsdiff.main(["-q", self.data_dir, tmp_d]) == 1
assert fitsdiff.main(["-q", tmp_d, self.data_dir]) == 1
with pytest.warns(UserWarning,
match=r"Field 'ORBPARM' has a repeat "
"count of 0 in its format code"):
assert fitsdiff.main(["-q", self.data_dir, self.data_dir]) == 0
# no match
tmp_c = self.data('arange.fits')
fitsdiff.main([tmp_c, tmp_d])
out, err = capsys.readouterr()
assert "'arange.fits' has no match in" in err
# globbing
with pytest.warns(UserWarning,
match=r"Field 'ORBPARM' has a repeat "
"count of 0 in its format code"):
assert fitsdiff.main(
["-q", self.data_dir + '/*.fits', self.data_dir]) == 0
assert fitsdiff.main(["-q", self.data_dir + '/g*.fits', tmp_d]) == 0
# one file and a directory
tmp_f = self.data('tb.fits')
assert fitsdiff.main(["-q", tmp_f, self.data_dir]) == 0
assert fitsdiff.main(["-q", self.data_dir, tmp_f]) == 0
def test_path(self, capsys):
os.mkdir(self.temp('sub/'))
tmp_b = self.temp('sub/ascii.fits')
tmp_g = self.temp('sub/group.fits')
tmp_h = self.data('group.fits')
with hdulist.fitsopen(tmp_h) as hdu_b:
hdu_b.writeto(tmp_g)
writeto(tmp_b, np.arange(100).reshape(10, 10))
# one modified file and a directory
assert fitsdiff.main(["-q", self.data_dir, tmp_b]) == 1
assert fitsdiff.main(["-q", tmp_b, self.data_dir]) == 1
# two directories
tmp_d = self.temp('sub/')
assert fitsdiff.main(["-q", self.data_dir, tmp_d]) == 1
assert fitsdiff.main(["-q", tmp_d, self.data_dir]) == 1
with pytest.warns(UserWarning, match="Field 'ORBPARM' has a repeat "
"count of 0 in its format code"):
assert fitsdiff.main(["-q", self.data_dir, self.data_dir]) == 0
# no match
tmp_c = self.data('arange.fits')
fitsdiff.main([tmp_c, tmp_d])
out, err = capsys.readouterr()
assert "'arange.fits' has no match in" in err
# globbing
with pytest.warns(UserWarning, match="Field 'ORBPARM' has a repeat "
"count of 0 in its format code"):
assert fitsdiff.main(["-q", self.data_dir+'/*.fits',
self.data_dir]) == 0
assert fitsdiff.main(["-q", self.data_dir+'/g*.fits', tmp_d]) == 0
# one file and a directory
tmp_f = self.data('tb.fits')
assert fitsdiff.main(["-q", tmp_f, self.data_dir]) == 0
assert fitsdiff.main(["-q", self.data_dir, tmp_f]) == 0
def from_fits_file(path):
'''
Loads a FlareLightCurve from some fits file.
If targetid is not given in the header, function
takes the last 9 digits before the first "-"
in the filename. In case of a K2 light curve
file this would be the EPIC ID.
Parameters:
-----------
path : str
path to light curve fits file
Return:
-----------
FlareLightCurve
'''
hdu = fitsopen(path)
dr = hdu[1].data
if 'TARGETID' in hdu[1].header:
targetid = hdu[1].header['TARGETID']
else:
targetid = int(path.split('-')[0][-9:])
keys = {
'time': 'TIME',
'detrended_flux': 'FLUX',
'detrended_flux_err': 'ERROR',
'cadenceno': 'CADENCE',
'flux_trends': 'TRTIME',
'campaign': 'CAMPAIGN',
'centroid_col': 'CENTROID_COL',
'centroid_row': 'CENTROID_ROW',
'time_format': 'TIME_FORMAT',
'time_scale': 'TIME_SCALE',
'ra': 'RA',
'dec': 'DEC',
'channel': 'CHANNEL',
'time_unit': 'TIME_UNIT',
'flux_unit': 'FLUX_UNIT',
'origin': 'ORIGIN',
'pos_corr1': 'X',
'pos_corr2': 'Y',
'quality': 'QUALITY',
'pixel_flux': 'PIXEL_FLUX',
'pixel_flux_err': 'PIXEL_FLUX_ERR',
'quality_bitmask': 'QUALITY_BITMASK',
'pipeline_mask': 'PIPELINE_MASK'
}
for k, v in keys.items():
if v in hdu[1].header:
keys[k] = hdu[1].header[v]
elif ((v.lower() in list(dr.names)) | (v in list(dr.names))):
keys[k] = dr[v]
else:
keys[k] = None
flc = FlareLightCurve(targetid=targetid, **keys)
hdu.close()
del dr
flc = flc[(np.isfinite(flc.detrended_flux))
& (np.isfinite(flc.detrended_flux_err))]
return flc
def from_K2SC_file(path, add_TPF=True, **kwargs):
"""
Read in a K2SC de-trended light curve and convert it to a ``FlareLightCurve``.
Parameters
------------
path : str
path to light curve
add_TPF : True or bool
Default fetches TPF for additional info. Required for
K2SC de-trending.
kwargs : dict
Keyword arguments to pass to `KeplerLightCurveFile.from_archive
<https://lightkurve.keplerscience.org/api/lightkurve.lightcurvefile.KeplerLightCurveFile.html#lightkurve.lightcurvefile.KeplerLightCurveFile.from_archive>`_
Returns
--------
FlareLightCurve
"""
if add_TPF == True:
hdu = fitsopen(path)
dr = hdu[1].data
targetid = int(path.split('-')[0][-9:])
tpf_list = search_targetpixelfile(targetid, **kwargs)
#raw flux,campaign
if len(tpf_list) > 1:
LOG.error(
'Target data identifier must be unique. Provide campaign or cadence.'
)
return
else:
ktpf = tpf_list.download()
klc = ktpf.to_lightcurve()
#Only use those cadences that are present in all TPF, KLC, and K2SC LC:
values, counts = np.unique(np.concatenate(
(klc.cadenceno, dr['CADENCE'], ktpf.cadenceno)),
return_counts=True)
cadences = values[np.where(
counts == 3
)] #you could check if counts can be 4 or more and throw an exception in that case
#note that order of cadences is irrelevant for the following to be right
dr = dr[np.isin(dr['CADENCE '], cadences)]
klc = klc[np.isin(klc.cadenceno, cadences)]
ktpf = ktpf[np.isin(ktpf.cadenceno, cadences)]
flc = FlareLightCurve(time=dr['TIME'],
flux=klc.flux,
detrended_flux=dr['FLUX'],
detrended_flux_err=dr['ERROR'],
cadenceno=dr['CADENCE'],
flux_trends=dr['TRTIME'],
targetid=targetid,
campaign=klc.campaign,
centroid_col=klc.centroid_col,
centroid_row=klc.centroid_row,
time_format=klc.time_format,
time_scale=klc.time_scale,
ra=klc.ra,
dec=klc.dec,
channel=klc.channel,
time_unit=u.day,
flux_unit=u.electron / u.s,
origin='K2SC',
pos_corr1=dr['X'],
pos_corr2=dr['Y'],
quality=klc.quality,
pixel_flux=ktpf.flux,
pixel_flux_err=ktpf.flux_err,
quality_bitmask=ktpf.quality_bitmask,
pipeline_mask=ktpf.pipeline_mask)
hdu.close()
del dr
flc = flc[(np.isfinite(flc.detrended_flux))
& (np.isfinite(flc.detrended_flux_err))]
return flc
elif add_TPF == False:
return from_fits_file(path)