def bls_serial_pfind(
times,
mags,
errs,
magsarefluxes=False,
startp=0.1, # search from 0.1 d to...
endp=100.0, # ... 100.0 d -- don't search full timebase
stepsize=5.0e-4,
mintransitduration=0.01, # minimum transit length in phase
maxtransitduration=0.4, # maximum transit length in phase
ndurations=100,
autofreq=True, # figure out f0, nf, and df automatically
blsobjective='likelihood',
blsmethod='fast',
blsoversample=10,
blsmintransits=3,
blsfreqfactor=10.0,
periodepsilon=0.1,
nbestpeaks=5,
sigclip=10.0,
endp_timebase_check=True,
verbose=True,
raiseonfail=False):
'''Runs the Box Least Squares Fitting Search for transit-shaped signals.
Based on the version of BLS in Astropy 3.1:
`astropy.stats.BoxLeastSquares`. If you don't have Astropy 3.1, this module
will fail to import. Note that by default, this implementation of
`bls_serial_pfind` doesn't use the `.autoperiod()` function from
`BoxLeastSquares` but uses the same auto frequency-grid generation as the
functions in `periodbase.kbls`. If you want to use Astropy's implementation,
set the value of `autofreq` kwarg to 'astropy'.
The dict returned from this function contains a `blsmodel` key, which is the
generated model from Astropy's BLS. Use the `.compute_stats()` method to
calculate the required stats like SNR, depth, duration, etc.
Parameters
----------
times,mags,errs : np.array
The magnitude/flux time-series to search for transits.
magsarefluxes : bool
If the input measurement values in `mags` and `errs` are in fluxes, set
this to True.
startp,endp : float
The minimum and maximum periods to consider for the transit search.
stepsize : float
The step-size in frequency to use when constructing a frequency grid for
the period search.
mintransitduration,maxtransitduration : float
The minimum and maximum transitdurations (in units of phase) to consider
for the transit search.
ndurations : int
The number of transit durations to use in the period-search.
autofreq : bool or str
If this is True, the values of `stepsize` and `nphasebins` will be
ignored, and these, along with a frequency-grid, will be determined
based on the following relations::
nphasebins = int(ceil(2.0/mintransitduration))
if nphasebins > 3000:
nphasebins = 3000
stepsize = 0.25*mintransitduration/(times.max()-times.min())
minfreq = 1.0/endp
maxfreq = 1.0/startp
nfreq = int(ceil((maxfreq - minfreq)/stepsize))
If this is False, you must set `startp`, `endp`, and `stepsize` as
appropriate.
If this is str == 'astropy', will use the
`astropy.stats.BoxLeastSquares.autoperiod()` function to calculate the
frequency grid instead of the kbls method.
blsobjective : {'likelihood','snr'}
Sets the type of objective to optimize in the `BoxLeastSquares.power()`
function.
blsmethod : {'fast','slow'}
Sets the type of method to use in the `BoxLeastSquares.power()`
function.
blsoversample : {'likelihood','snr'}
Sets the `oversample` kwarg for the `BoxLeastSquares.power()` function.
blsmintransits : int
Sets the `min_n_transits` kwarg for the `BoxLeastSquares.autoperiod()`
function.
blsfreqfactor : float
Sets the `frequency_factor` kwarg for the `BoxLeastSquares.autperiod()`
function.
periodepsilon : float
The fractional difference between successive values of 'best' periods
when sorting by periodogram power to consider them as separate periods
(as opposed to part of the same periodogram peak). This is used to avoid
broad peaks in the periodogram and make sure the 'best' periods returned
are all actually independent.
nbestpeaks : int
The number of 'best' peaks to return from the periodogram results,
starting from the global maximum of the periodogram peak values.
sigclip : float or int or sequence of two floats/ints or None
If a single float or int, a symmetric sigma-clip will be performed using
the number provided as the sigma-multiplier to cut out from the input
time-series.
If a list of two ints/floats is provided, the function will perform an
'asymmetric' sigma-clip. The first element in this list is the sigma
value to use for fainter flux/mag values; the second element in this
list is the sigma value to use for brighter flux/mag values. For
example, `sigclip=[10., 3.]`, will sigclip out greater than 10-sigma
dimmings and greater than 3-sigma brightenings. Here the meaning of
"dimming" and "brightening" is set by *physics* (not the magnitude
system), which is why the `magsarefluxes` kwarg must be correctly set.
If `sigclip` is None, no sigma-clipping will be performed, and the
time-series (with non-finite elems removed) will be passed through to
the output.
endp_timebase_check : bool
If True, will check if the ``endp`` value is larger than the time-base
of the observations. If it is, will change the ``endp`` value such that
it is half of the time-base. If False, will allow an ``endp`` larger
than the time-base of the observations.
verbose : bool
If this is True, will indicate progress and details about the frequency
grid used for the period search.
raiseonfail : bool
If True, raises an exception if something goes wrong. Otherwise, returns
None.
Returns
-------
dict
This function returns a dict, referred to as an `lspinfo` dict in other
astrobase functions that operate on periodogram results. This is a
standardized format across all astrobase period-finders, and is of the
form below::
{'bestperiod': the best period value in the periodogram,
'bestlspval': the periodogram peak associated with the best period,
'nbestpeaks': the input value of nbestpeaks,
'nbestlspvals': nbestpeaks-size list of best period peak values,
'nbestperiods': nbestpeaks-size list of best periods,
'lspvals': the full array of periodogram powers,
'frequencies': the full array of frequencies considered,
'periods': the full array of periods considered,
'durations': the array of durations used to run BLS,
'blsresult': Astropy BLS result object (BoxLeastSquaresResult),
'blsmodel': Astropy BLS BoxLeastSquares object used for work,
'stepsize': the actual stepsize used,
'nfreq': the actual nfreq used,
'durations': the durations array used,
'mintransitduration': the input mintransitduration,
'maxtransitduration': the input maxtransitdurations,
'method':'bls' -> the name of the period-finder method,
'kwargs':{ dict of all of the input kwargs for record-keeping}}
'''
# get rid of nans first and sigclip
stimes, smags, serrs = sigclip_magseries(times,
mags,
errs,
magsarefluxes=magsarefluxes,
sigclip=sigclip)
# make sure there are enough points to calculate a spectrum
if len(stimes) > 9 and len(smags) > 9 and len(serrs) > 9:
# if we're setting up everything automatically
if isinstance(autofreq, bool) and autofreq:
# use heuristic to figure out best timestep
stepsize = 0.25 * mintransitduration / (stimes.max() -
stimes.min())
# now figure out the frequencies to use
minfreq = 1.0 / endp
maxfreq = 1.0 / startp
nfreq = int(npceil((maxfreq - minfreq) / stepsize))
# say what we're using
if verbose:
LOGINFO('min P: %s, max P: %s, nfreq: %s, '
'minfreq: %s, maxfreq: %s' %
(startp, endp, nfreq, minfreq, maxfreq))
LOGINFO('autofreq = True: using AUTOMATIC values for '
'freq stepsize: %s, ndurations: %s, '
'min transit duration: %s, max transit duration: %s' %
(stepsize, ndurations, mintransitduration,
maxtransitduration))
use_autoperiod = False
elif isinstance(autofreq, bool) and not autofreq:
minfreq = 1.0 / endp
maxfreq = 1.0 / startp
nfreq = int(npceil((maxfreq - minfreq) / stepsize))
# say what we're using
if verbose:
LOGINFO('min P: %s, max P: %s, nfreq: %s, '
'minfreq: %s, maxfreq: %s' %
(startp, endp, nfreq, minfreq, maxfreq))
LOGINFO('autofreq = False: using PROVIDED values for '
'freq stepsize: %s, ndurations: %s, '
'min transit duration: %s, max transit duration: %s' %
(stepsize, ndurations, mintransitduration,
maxtransitduration))
use_autoperiod = False
elif isinstance(autofreq, str) and autofreq == 'astropy':
use_autoperiod = True
minfreq = 1.0 / endp
maxfreq = 1.0 / startp
else:
LOGERROR("unknown autofreq kwarg encountered. can't continue...")
return None
# check the minimum frequency
if ((minfreq < (1.0 / (stimes.max() - stimes.min())))
and endp_timebase_check):
LOGWARNING('the requested max P = %.3f is larger than '
'the time base of the observations = %.3f, '
' will make minfreq = 2 x 1/timebase' %
(endp, stimes.max() - stimes.min()))
minfreq = 2.0 / (stimes.max() - stimes.min())
LOGWARNING('new minfreq: %s, maxfreq: %s' % (minfreq, maxfreq))
# run BLS
try:
# astropy's BLS requires durations in units of time
durations = nplinspace(mintransitduration * startp,
maxtransitduration * startp, ndurations)
# set up the correct units for the BLS model
if magsarefluxes:
blsmodel = BoxLeastSquares(stimes * u.day,
smags * u.dimensionless_unscaled,
dy=serrs * u.dimensionless_unscaled)
else:
blsmodel = BoxLeastSquares(stimes * u.day,
smags * u.mag,
dy=serrs * u.mag)
# use autoperiod if requested
if use_autoperiod:
periods = nparray(
blsmodel.autoperiod(durations,
minimum_period=startp,
maximum_period=endp,
minimum_n_transit=blsmintransits,
frequency_factor=blsfreqfactor))
nfreq = periods.size
if verbose:
LOGINFO("autofreq = 'astropy', used .autoperiod() with "
"minimum_n_transit = %s, freq_factor = %s "
"to generate the frequency grid" %
(blsmintransits, blsfreqfactor))
LOGINFO(
'stepsize = %.5f, nfreq = %s, minfreq = %.5f, '
'maxfreq = %.5f, ndurations = %s' %
(abs(1.0 / periods[1] - 1.0 / periods[0]), nfreq, 1.0 /
periods.max(), 1.0 / periods.min(), durations.size))
# otherwise, use kbls method
else:
frequencies = minfreq + nparange(nfreq) * stepsize
periods = 1.0 / frequencies
if nfreq > 5.0e5:
if verbose:
LOGWARNING('more than 5.0e5 frequencies to go through; '
'this will take a while. '
'you might want to use the '
'abls.bls_parallel_pfind function instead')
# run the periodogram
blsresult = blsmodel.power(periods * u.day,
durations * u.day,
objective=blsobjective,
method=blsmethod,
oversample=blsoversample)
# get the peak values
lsp = nparray(blsresult.power)
# find the nbestpeaks for the periodogram: 1. sort the lsp array
# by highest value first 2. go down the values until we find
# five values that are separated by at least periodepsilon in
# period
# make sure to get only the finite peaks in the periodogram
# this is needed because BLS may produce infs for some peaks
finitepeakind = npisfinite(lsp)
finlsp = lsp[finitepeakind]
finperiods = periods[finitepeakind]
# make sure that finlsp has finite values before we work on it
try:
bestperiodind = npargmax(finlsp)
except ValueError:
LOGERROR('no finite periodogram values '
'for this mag series, skipping...')
return {
'bestperiod': npnan,
'bestlspval': npnan,
'nbestpeaks': nbestpeaks,
'nbestinds': None,
'nbestlspvals': None,
'nbestperiods': None,
'lspvals': None,
'periods': None,
'durations': None,
'method': 'bls',
'blsresult': None,
'blsmodel': None,
'kwargs': {
'startp': startp,
'endp': endp,
'stepsize': stepsize,
'mintransitduration': mintransitduration,
'maxtransitduration': maxtransitduration,
'ndurations': ndurations,
'blsobjective': blsobjective,
'blsmethod': blsmethod,
'blsoversample': blsoversample,
'blsntransits': blsmintransits,
'blsfreqfactor': blsfreqfactor,
'autofreq': autofreq,
'periodepsilon': periodepsilon,
'nbestpeaks': nbestpeaks,
'sigclip': sigclip,
'magsarefluxes': magsarefluxes
}
}
sortedlspind = npargsort(finlsp)[::-1]
sortedlspperiods = finperiods[sortedlspind]
sortedlspvals = finlsp[sortedlspind]
# now get the nbestpeaks
nbestperiods, nbestlspvals, nbestinds, peakcount = ([
finperiods[bestperiodind]
], [finlsp[bestperiodind]], [bestperiodind], 1)
prevperiod = sortedlspperiods[0]
# find the best nbestpeaks in the lsp and their periods
for period, lspval, ind in zip(sortedlspperiods, sortedlspvals,
sortedlspind):
if peakcount == nbestpeaks:
break
perioddiff = abs(period - prevperiod)
bestperiodsdiff = [abs(period - x) for x in nbestperiods]
# print('prevperiod = %s, thisperiod = %s, '
# 'perioddiff = %s, peakcount = %s' %
# (prevperiod, period, perioddiff, peakcount))
# this ensures that this period is different from the last
# period and from all the other existing best periods by
# periodepsilon to make sure we jump to an entire different
# peak in the periodogram
if (perioddiff > (periodepsilon * prevperiod)
and all(x > (periodepsilon * period)
for x in bestperiodsdiff)):
nbestperiods.append(period)
nbestlspvals.append(lspval)
nbestinds.append(ind)
peakcount = peakcount + 1
prevperiod = period
# generate the return dict
resultdict = {
'bestperiod': finperiods[bestperiodind],
'bestlspval': finlsp[bestperiodind],
'nbestpeaks': nbestpeaks,
'nbestinds': nbestinds,
'nbestlspvals': nbestlspvals,
'nbestperiods': nbestperiods,
'lspvals': lsp,
'frequencies': frequencies,
'periods': periods,
'durations': durations,
'blsresult': blsresult,
'blsmodel': blsmodel,
'stepsize': stepsize,
'nfreq': nfreq,
'mintransitduration': mintransitduration,
'maxtransitduration': maxtransitduration,
'method': 'bls',
'kwargs': {
'startp': startp,
'endp': endp,
'stepsize': stepsize,
'mintransitduration': mintransitduration,
'maxtransitduration': maxtransitduration,
'ndurations': ndurations,
'blsobjective': blsobjective,
'blsmethod': blsmethod,
'blsoversample': blsoversample,
'blsntransits': blsmintransits,
'blsfreqfactor': blsfreqfactor,
'autofreq': autofreq,
'periodepsilon': periodepsilon,
'nbestpeaks': nbestpeaks,
'sigclip': sigclip,
'magsarefluxes': magsarefluxes
}
}
return resultdict
except Exception as e:
LOGEXCEPTION('BLS failed!')
if raiseonfail:
raise
return {
'bestperiod': npnan,
'bestlspval': npnan,
'nbestinds': None,
'nbestpeaks': nbestpeaks,
'nbestlspvals': None,
'nbestperiods': None,
'lspvals': None,
'periods': None,
'durations': None,
'blsresult': None,
'blsmodel': None,
'stepsize': stepsize,
'nfreq': nfreq,
'mintransitduration': mintransitduration,
'maxtransitduration': maxtransitduration,
'method': 'bls',
'kwargs': {
'startp': startp,
'endp': endp,
'stepsize': stepsize,
'mintransitduration': mintransitduration,
'maxtransitduration': maxtransitduration,
'ndurations': ndurations,
'blsobjective': blsobjective,
'blsmethod': blsmethod,
'blsoversample': blsoversample,
'blsntransits': blsmintransits,
'blsfreqfactor': blsfreqfactor,
'autofreq': autofreq,
'periodepsilon': periodepsilon,
'nbestpeaks': nbestpeaks,
'sigclip': sigclip,
'magsarefluxes': magsarefluxes
}
}
else:
LOGERROR('no good detections for these times and mags, skipping...')
return {
'bestperiod': npnan,
'bestlspval': npnan,
'nbestinds': None,
'nbestpeaks': nbestpeaks,
'nbestlspvals': None,
'nbestperiods': None,
'lspvals': None,
'periods': None,
'durations': None,
'blsresult': None,
'blsmodel': None,
'stepsize': stepsize,
'nfreq': None,
'nphasebins': None,
'mintransitduration': mintransitduration,
'maxtransitduration': maxtransitduration,
'method': 'bls',
'kwargs': {
'startp': startp,
'endp': endp,
'stepsize': stepsize,
'mintransitduration': mintransitduration,
'maxtransitduration': maxtransitduration,
'ndurations': ndurations,
'blsobjective': blsobjective,
'blsmethod': blsmethod,
'blsoversample': blsoversample,
'blsntransits': blsmintransits,
'blsfreqfactor': blsfreqfactor,
'autofreq': autofreq,
'periodepsilon': periodepsilon,
'nbestpeaks': nbestpeaks,
'sigclip': sigclip,
'magsarefluxes': magsarefluxes
}
}
def from_lightcurve(lc, **kwargs):
"""Creates a Periodogram from a LightCurve using the Box Least Squares (BLS) method."""
time_unit = (kwargs.pop("time_unit", "day"))
if time_unit not in dir(u):
raise ValueError('{} is not a valid unit for time.'.format(time_unit))
try:
from astropy.stats import BoxLeastSquares
except ImportError:
raise Exception("BLS requires AstroPy v3.1 or later")
# BoxLeastSquares will not work if flux or flux_err contain NaNs
lc = lc.remove_nans()
if np.isfinite(lc.flux_err).all():
dy = lc.flux_err
else:
dy = None
bls = BoxLeastSquares(lc.time, lc.flux, dy)
duration = kwargs.pop("duration", 0.25)
minimum_period = kwargs.pop("minimum_period", None)
maximum_period = kwargs.pop("maximum_period", None)
period = kwargs.pop("period", None)
if minimum_period is None:
if 'period' in kwargs:
minimum_period = period.min()
else:
minimum_period = np.max([np.median(np.diff(lc.time)) * 4,
np.max(duration) + np.median(np.diff(lc.time))])
if maximum_period is None:
if 'period' in kwargs:
maximum_period = period.max()
else:
maximum_period = (np.max(lc.time) - np.min(lc.time)) / 3.
frequency_factor = kwargs.pop("frequency_factor", 10)
df = frequency_factor * np.min(duration) / (np.max(lc.time) - np.min(lc.time))**2
npoints = int(((1/minimum_period) - (1/maximum_period))/df)
# Too many points
if npoints > 1e5:
log.warning('`period` contains {} points.'
'Periodogram is likely to be large, and slow to evaluate. '
'Consider setting `frequency_factor` to a higher value.'
''.format(np.round(npoints, 4)))
# Way too many points
if npoints > 1e7:
raise ValueError('`period` contains {} points.'
'Periodogram is too large to evaluate. '
'Consider setting `frequency_factor` to a higher value.'
''.format(np.round(npoints, 4)))
period = kwargs.pop("period",
bls.autoperiod(duration,
minimum_period=minimum_period,
maximum_period=maximum_period,
frequency_factor=frequency_factor))
result = bls.power(period, duration, **kwargs)
if not isinstance(result.period, u.quantity.Quantity):
result.period = u.Quantity(result.period, time_unit)
if not isinstance(result.power, u.quantity.Quantity):
result.power = result.power * u.dimensionless_unscaled
return BoxLeastSquaresPeriodogram(frequency=1. / result.period,
power=result.power,
default_view='period',
label=lc.label,
targetid=lc.targetid,
transit_time=result.transit_time,
duration=result.duration,
depth=result.depth,
bls_result=result,
snr=result.depth_snr,
bls_obj=bls,
time=lc.time,
flux=lc.flux,
time_unit=time_unit)
def bls_parallel_pfind(
times,
mags,
errs,
magsarefluxes=False,
startp=0.1, # by default, search from 0.1 d to...
endp=100.0, # ... 100.0 d -- don't search full timebase
stepsize=1.0e-4,
mintransitduration=0.01, # minimum transit length in phase
maxtransitduration=0.4, # maximum transit length in phase
ndurations=100,
autofreq=True, # figure out f0, nf, and df automatically
blsobjective='likelihood',
blsmethod='fast',
blsoversample=5,
blsmintransits=3,
blsfreqfactor=10.0,
nbestpeaks=5,
periodepsilon=0.1, # 0.1
sigclip=10.0,
endp_timebase_check=True,
verbose=True,
nworkers=None,
):
'''Runs the Box Least Squares Fitting Search for transit-shaped signals.
Breaks up the full frequency space into chunks and passes them to parallel
BLS workers.
Based on the version of BLS in Astropy 3.1:
`astropy.stats.BoxLeastSquares`. If you don't have Astropy 3.1, this module
will fail to import. Note that by default, this implementation of
`bls_parallel_pfind` doesn't use the `.autoperiod()` function from
`BoxLeastSquares` but uses the same auto frequency-grid generation as the
functions in `periodbase.kbls`. If you want to use Astropy's implementation,
set the value of `autofreq` kwarg to 'astropy'. The generated period array
will then be broken up into chunks and sent to the individual workers.
NOTE: the combined BLS spectrum produced by this function is not identical
to that produced by running BLS in one shot for the entire frequency
space. There are differences on the order of 1.0e-3 or so in the respective
peak values, but peaks appear at the same frequencies for both methods. This
is likely due to different aliasing caused by smaller chunks of the
frequency space used by the parallel workers in this function. When in
doubt, confirm results for this parallel implementation by comparing to
those from the serial implementation above.
In particular, when you want to get reliable estimates of the SNR, transit
depth, duration, etc. that Astropy's BLS gives you, rerun `bls_serial_pfind`
with `startp`, and `endp` close to the best period you want to characterize
the transit at. The dict returned from that function contains a `blsmodel`
key, which is the generated model from Astropy's BLS. Use the
`.compute_stats()` method to calculate the required stats.
Parameters
----------
times,mags,errs : np.array
The magnitude/flux time-series to search for transits.
magsarefluxes : bool
If the input measurement values in `mags` and `errs` are in fluxes, set
this to True.
startp,endp : float
The minimum and maximum periods to consider for the transit search.
stepsize : float
The step-size in frequency to use when constructing a frequency grid for
the period search.
mintransitduration,maxtransitduration : float
The minimum and maximum transitdurations (in units of phase) to consider
for the transit search.
ndurations : int
The number of transit durations to use in the period-search.
autofreq : bool or str
If this is True, the values of `stepsize` and `nphasebins` will be
ignored, and these, along with a frequency-grid, will be determined
based on the following relations::
nphasebins = int(ceil(2.0/mintransitduration))
if nphasebins > 3000:
nphasebins = 3000
stepsize = 0.25*mintransitduration/(times.max()-times.min())
minfreq = 1.0/endp
maxfreq = 1.0/startp
nfreq = int(ceil((maxfreq - minfreq)/stepsize))
If this is False, you must set `startp`, `endp`, and `stepsize` as
appropriate.
If this is str == 'astropy', will use the
`astropy.stats.BoxLeastSquares.autoperiod()` function to calculate the
frequency grid instead of the kbls method.
blsobjective : {'likelihood','snr'}
Sets the type of objective to optimize in the `BoxLeastSquares.power()`
function.
blsmethod : {'fast','slow'}
Sets the type of method to use in the `BoxLeastSquares.power()`
function.
blsoversample : {'likelihood','snr'}
Sets the `oversample` kwarg for the `BoxLeastSquares.power()` function.
blsmintransits : int
Sets the `min_n_transits` kwarg for the `BoxLeastSquares.autoperiod()`
function.
blsfreqfactor : float
Sets the `frequency_factor` kwarg for the `BoxLeastSquares.autoperiod()`
function.
periodepsilon : float
The fractional difference between successive values of 'best' periods
when sorting by periodogram power to consider them as separate periods
(as opposed to part of the same periodogram peak). This is used to avoid
broad peaks in the periodogram and make sure the 'best' periods returned
are all actually independent.
nbestpeaks : int
The number of 'best' peaks to return from the periodogram results,
starting from the global maximum of the periodogram peak values.
sigclip : float or int or sequence of two floats/ints or None
If a single float or int, a symmetric sigma-clip will be performed using
the number provided as the sigma-multiplier to cut out from the input
time-series.
If a list of two ints/floats is provided, the function will perform an
'asymmetric' sigma-clip. The first element in this list is the sigma
value to use for fainter flux/mag values; the second element in this
list is the sigma value to use for brighter flux/mag values. For
example, `sigclip=[10., 3.]`, will sigclip out greater than 10-sigma
dimmings and greater than 3-sigma brightenings. Here the meaning of
"dimming" and "brightening" is set by *physics* (not the magnitude
system), which is why the `magsarefluxes` kwarg must be correctly set.
If `sigclip` is None, no sigma-clipping will be performed, and the
time-series (with non-finite elems removed) will be passed through to
the output.
endp_timebase_check : bool
If True, will check if the ``endp`` value is larger than the time-base
of the observations. If it is, will change the ``endp`` value such that
it is half of the time-base. If False, will allow an ``endp`` larger
than the time-base of the observations.
verbose : bool
If this is True, will indicate progress and details about the frequency
grid used for the period search.
nworkers : int or None
The number of parallel workers to launch for period-search. If None,
nworkers = NCPUS.
Returns
-------
dict
This function returns a dict, referred to as an `lspinfo` dict in other
astrobase functions that operate on periodogram results. This is a
standardized format across all astrobase period-finders, and is of the
form below::
{'bestperiod': the best period value in the periodogram,
'bestlspval': the periodogram peak associated with the best period,
'nbestpeaks': the input value of nbestpeaks,
'nbestlspvals': nbestpeaks-size list of best period peak values,
'nbestperiods': nbestpeaks-size list of best periods,
'lspvals': the full array of periodogram powers,
'frequencies': the full array of frequencies considered,
'periods': the full array of periods considered,
'durations': the array of durations used to run BLS,
'blsresult': Astropy BLS result object (BoxLeastSquaresResult),
'blsmodel': Astropy BLS BoxLeastSquares object used for work,
'stepsize': the actual stepsize used,
'nfreq': the actual nfreq used,
'durations': the durations array used,
'mintransitduration': the input mintransitduration,
'maxtransitduration': the input maxtransitdurations,
'method':'bls' -> the name of the period-finder method,
'kwargs':{ dict of all of the input kwargs for record-keeping}}
'''
# get rid of nans first and sigclip
stimes, smags, serrs = sigclip_magseries(times,
mags,
errs,
magsarefluxes=magsarefluxes,
sigclip=sigclip)
# make sure there are enough points to calculate a spectrum
if len(stimes) > 9 and len(smags) > 9 and len(serrs) > 9:
# if we're setting up everything automatically
if isinstance(autofreq, bool) and autofreq:
# use heuristic to figure out best timestep
stepsize = 0.25 * mintransitduration / (stimes.max() -
stimes.min())
# now figure out the frequencies to use
minfreq = 1.0 / endp
maxfreq = 1.0 / startp
nfreq = int(npceil((maxfreq - minfreq) / stepsize))
# say what we're using
if verbose:
LOGINFO('min P: %s, max P: %s, nfreq: %s, '
'minfreq: %s, maxfreq: %s' %
(startp, endp, nfreq, minfreq, maxfreq))
LOGINFO('autofreq = True: using AUTOMATIC values for '
'freq stepsize: %s, ndurations: %s, '
'min transit duration: %s, max transit duration: %s' %
(stepsize, ndurations, mintransitduration,
maxtransitduration))
use_autoperiod = False
elif isinstance(autofreq, bool) and not autofreq:
minfreq = 1.0 / endp
maxfreq = 1.0 / startp
nfreq = int(npceil((maxfreq - minfreq) / stepsize))
# say what we're using
if verbose:
LOGINFO('min P: %s, max P: %s, nfreq: %s, '
'minfreq: %s, maxfreq: %s' %
(startp, endp, nfreq, minfreq, maxfreq))
LOGINFO('autofreq = False: using PROVIDED values for '
'freq stepsize: %s, ndurations: %s, '
'min transit duration: %s, max transit duration: %s' %
(stepsize, ndurations, mintransitduration,
maxtransitduration))
use_autoperiod = False
elif isinstance(autofreq, str) and autofreq == 'astropy':
use_autoperiod = True
minfreq = 1.0 / endp
maxfreq = 1.0 / startp
else:
LOGERROR("unknown autofreq kwarg encountered. can't continue...")
return None
# check the minimum frequency
if ((minfreq < (1.0 / (stimes.max() - stimes.min())))
and endp_timebase_check):
LOGWARNING('the requested max P = %.3f is larger than '
'the time base of the observations = %.3f, '
' will make minfreq = 2 x 1/timebase' %
(endp, stimes.max() - stimes.min()))
minfreq = 2.0 / (stimes.max() - stimes.min())
LOGWARNING('new minfreq: %s, maxfreq: %s' % (minfreq, maxfreq))
#############################
## NOW RUN BLS IN PARALLEL ##
#############################
# fix number of CPUs if needed
if not nworkers or nworkers > NCPUS:
nworkers = NCPUS
if verbose:
LOGINFO('using %s workers...' % nworkers)
# check if autoperiod is True and get the correct period-grid
if use_autoperiod:
# astropy's BLS requires durations in units of time
durations = nplinspace(mintransitduration * startp,
maxtransitduration * startp, ndurations)
# set up the correct units for the BLS model
if magsarefluxes:
blsmodel = BoxLeastSquares(stimes * u.day,
smags * u.dimensionless_unscaled,
dy=serrs * u.dimensionless_unscaled)
else:
blsmodel = BoxLeastSquares(stimes * u.day,
smags * u.mag,
dy=serrs * u.mag)
periods = nparray(
blsmodel.autoperiod(durations * u.day,
minimum_period=startp,
maximum_period=endp,
minimum_n_transit=blsmintransits,
frequency_factor=blsfreqfactor))
frequencies = 1.0 / periods
nfreq = frequencies.size
if verbose:
LOGINFO("autofreq = 'astropy', used .autoperiod() with "
"minimum_n_transit = %s, freq_factor = %s "
"to generate the frequency grid" %
(blsmintransits, blsfreqfactor))
LOGINFO('stepsize = %s, nfreq = %s, minfreq = %.5f, '
'maxfreq = %.5f, ndurations = %s' %
(abs(frequencies[1] - frequencies[0]), nfreq, 1.0 /
periods.max(), 1.0 / periods.min(), durations.size))
del blsmodel
del durations
# otherwise, use kbls method
else:
frequencies = minfreq + nparange(nfreq) * stepsize
# break up the tasks into chunks
csrem = int(fmod(nfreq, nworkers))
csint = int(float(nfreq / nworkers))
chunk_minfreqs, chunk_nfreqs = [], []
for x in range(nworkers):
this_minfreqs = frequencies[x * csint]
# handle usual nfreqs
if x < (nworkers - 1):
this_nfreqs = frequencies[x * csint:x * csint + csint].size
else:
this_nfreqs = frequencies[x * csint:x * csint + csint +
csrem].size
chunk_minfreqs.append(this_minfreqs)
chunk_nfreqs.append(this_nfreqs)
# populate the tasks list
#
# task[0] = times
# task[1] = mags
# task[2] = errs
# task[3] = magsarefluxes
# task[4] = minfreq
# task[5] = nfreq
# task[6] = stepsize
# task[7] = nphasebins
# task[8] = mintransitduration
# task[9] = maxtransitduration
# task[10] = blsobjective
# task[11] = blsmethod
# task[12] = blsoversample
# populate the tasks list
tasks = [(stimes, smags, serrs, magsarefluxes, chunk_minf, chunk_nf,
stepsize, ndurations, mintransitduration, maxtransitduration,
blsobjective, blsmethod, blsoversample)
for (chunk_minf,
chunk_nf) in zip(chunk_minfreqs, chunk_nfreqs)]
if verbose:
for ind, task in enumerate(tasks):
LOGINFO('worker %s: minfreq = %.6f, nfreqs = %s' %
(ind + 1, task[4], task[5]))
LOGINFO('running...')
# return tasks
# start the pool
pool = Pool(nworkers)
results = pool.map(_parallel_bls_worker, tasks)
pool.close()
pool.join()
del pool
# now concatenate the output lsp arrays
lsp = npconcatenate([x['power'] for x in results])
periods = 1.0 / frequencies
# find the nbestpeaks for the periodogram: 1. sort the lsp array
# by highest value first 2. go down the values until we find
# five values that are separated by at least periodepsilon in
# period
# make sure to get only the finite peaks in the periodogram
# this is needed because BLS may produce infs for some peaks
finitepeakind = npisfinite(lsp)
finlsp = lsp[finitepeakind]
finperiods = periods[finitepeakind]
# make sure that finlsp has finite values before we work on it
try:
bestperiodind = npargmax(finlsp)
except ValueError:
LOGERROR('no finite periodogram values '
'for this mag series, skipping...')
return {
'bestperiod': npnan,
'bestlspval': npnan,
'nbestpeaks': nbestpeaks,
'nbestinds': None,
'nbestlspvals': None,
'nbestperiods': None,
'lspvals': None,
'periods': None,
'durations': None,
'method': 'bls',
'blsresult': None,
'blsmodel': None,
'kwargs': {
'startp': startp,
'endp': endp,
'stepsize': stepsize,
'mintransitduration': mintransitduration,
'maxtransitduration': maxtransitduration,
'ndurations': ndurations,
'blsobjective': blsobjective,
'blsmethod': blsmethod,
'blsoversample': blsoversample,
'autofreq': autofreq,
'periodepsilon': periodepsilon,
'nbestpeaks': nbestpeaks,
'sigclip': sigclip,
'magsarefluxes': magsarefluxes
}
}
sortedlspind = npargsort(finlsp)[::-1]
sortedlspperiods = finperiods[sortedlspind]
sortedlspvals = finlsp[sortedlspind]
# now get the nbestpeaks
nbestperiods, nbestlspvals, nbestinds, peakcount = ([
finperiods[bestperiodind]
], [finlsp[bestperiodind]], [bestperiodind], 1)
prevperiod = sortedlspperiods[0]
# find the best nbestpeaks in the lsp and their periods
for period, lspval, ind in zip(sortedlspperiods, sortedlspvals,
sortedlspind):
if peakcount == nbestpeaks:
break
perioddiff = abs(period - prevperiod)
bestperiodsdiff = [abs(period - x) for x in nbestperiods]
# this ensures that this period is different from the last
# period and from all the other existing best periods by
# periodepsilon to make sure we jump to an entire different
# peak in the periodogram
if (perioddiff > (periodepsilon * prevperiod)
and all(x > (periodepsilon * period)
for x in bestperiodsdiff)):
nbestperiods.append(period)
nbestlspvals.append(lspval)
nbestinds.append(ind)
peakcount = peakcount + 1
prevperiod = period
# generate the return dict
resultdict = {
'bestperiod': finperiods[bestperiodind],
'bestlspval': finlsp[bestperiodind],
'nbestpeaks': nbestpeaks,
'nbestinds': nbestinds,
'nbestlspvals': nbestlspvals,
'nbestperiods': nbestperiods,
'lspvals': lsp,
'frequencies': frequencies,
'periods': periods,
'durations': [x['durations'] for x in results],
'blsresult': [x['blsresult'] for x in results],
'blsmodel': [x['blsmodel'] for x in results],
'stepsize': stepsize,
'nfreq': nfreq,
'mintransitduration': mintransitduration,
'maxtransitduration': maxtransitduration,
'method': 'bls',
'kwargs': {
'startp': startp,
'endp': endp,
'stepsize': stepsize,
'mintransitduration': mintransitduration,
'maxtransitduration': maxtransitduration,
'ndurations': ndurations,
'blsobjective': blsobjective,
'blsmethod': blsmethod,
'blsoversample': blsoversample,
'autofreq': autofreq,
'periodepsilon': periodepsilon,
'nbestpeaks': nbestpeaks,
'sigclip': sigclip,
'magsarefluxes': magsarefluxes
}
}
return resultdict
else:
LOGERROR('no good detections for these times and mags, skipping...')
return {
'bestperiod': npnan,
'bestlspval': npnan,
'nbestinds': None,
'nbestpeaks': nbestpeaks,
'nbestlspvals': None,
'nbestperiods': None,
'lspvals': None,
'periods': None,
'durations': None,
'blsresult': None,
'blsmodel': None,
'stepsize': stepsize,
'nfreq': None,
'nphasebins': None,
'mintransitduration': mintransitduration,
'maxtransitduration': maxtransitduration,
'method': 'bls',
'kwargs': {
'startp': startp,
'endp': endp,
'stepsize': stepsize,
'mintransitduration': mintransitduration,
'maxtransitduration': maxtransitduration,
'ndurations': ndurations,
'blsobjective': blsobjective,
'blsmethod': blsmethod,
'blsoversample': blsoversample,
'autofreq': autofreq,
'periodepsilon': periodepsilon,
'nbestpeaks': nbestpeaks,
'sigclip': sigclip,
'magsarefluxes': magsarefluxes
}
}
def find_and_mask_transits(time,
flux,
flux_err,
periods,
durations,
nplanets=1):
"""
Iteratively find and mask transits in the flattened light curve.
Args:
time (array): The time array.
flux (array): The flux array. You'll get the best results
if this is flattened.
flux_err (array): The array of flux uncertainties.
periods (array): The array of periods to search over for BLS.
For example, periods = np.linspace(0.5, 20, 10)
durations (array): The array of durations to search over for BLS.
For example, durations = np.linspace(0.05, 0.2, 10)
nplanets (Optional[int]): The number of planets you'd like to search for.
This function will interatively find and remove nplanets. Default is 1.
Returns:
transit_masks (list): a list of masks that correspond to the in
transit points of each light curve. To mask out transits do
time[~transit_masks[index]], etc.
"""
cum_transit = np.ones(len(time), dtype=bool)
_time, _flux, _flux_err = time * 1, flux * 1, flux_err * 1
t0s, durs, porbs = [np.zeros(nplanets) for i in range(3)]
transit_masks = []
for i in range(nplanets):
bls = BoxLeastSquares(t=_time, y=_flux, dy=_flux_err)
bls.power(periods, durations)
print("periods")
periods = bls.autoperiod(durations,
minimum_n_transit=3,
frequency_factor=5.0)
print("results")
results = bls.autopower(durations, frequency_factor=5.0)
# Find the period of the peak
print("find_period")
period = results.period[np.argmax(results.power)]
print("extract")
# Extract the parameters of the best-fit model
index = np.argmax(results.power)
porbs[i] = results.period[index]
t0s[i] = results.transit_time[index]
durs[i] = results.duration[index]
# # Plot the periodogram
# fig, ax = plt.subplots(1, 1, figsize=(10, 5))
# ax.plot(results.period, results.power, "k", lw=0.5)
# ax.set_xlim(results.period.min(), results.period.max())
# ax.set_xlabel("period [days]")
# ax.set_ylabel("log likelihood")
# # Highlight the harmonics of the peak period
# ax.axvline(period, alpha=0.4, lw=4)
# for n in range(2, 10):
# ax.axvline(n*period, alpha=0.4, lw=1, linestyle="dashed")
# ax.axvline(period / n, alpha=0.4, lw=1, linestyle="dashed")
# plt.show()
# plt.plot(_time, _flux, ".")
# plt.xlim(1355, 1360)
print("mask")
in_transit = bls.transit_mask(_time, porbs[i], 2 * durs[i], t0s[i])
transit_masks.append(in_transit)
_time, _flux, _flux_err = _time[~in_transit], _flux[~in_transit], \
_flux_err[~in_transit]
return transit_masks, t0s, durs, porbs