def create_calibration(cal_type, calibrant_medians, calibrant_concentrations, calibrant_weightings, calibrant_error, calibrant_flags): """ Completes a iterative calibration that checks if the calibrants fall within the specified limits, otherwise the calibrants are flagged and not used and a recalibration takes place. This goes until all calibrants are within specification, or there is only 30% left. :param cal_type: :param calibrant_medians: :param calibrant_concentrations: :param calibrant_weightings: :param calibrant_error: :param calibrant_flags: :return: """ repeat_calibration = True calibration_iteration = 0 # TODO: Massive todo I've f'd this up royally, it works and works well, but it is not clean at all. # Subset on if the flag isn't bad medians_to_fit = [x for i, x in enumerate(calibrant_medians) if calibrant_flags[i] in [1, 2, 4, 5, 6]] concs_to_fit = [x for i, x in enumerate(calibrant_concentrations) if calibrant_flags[i] in [1, 2, 4, 5, 6]] weightings_to_fit = [x for i, x in enumerate(calibrant_weightings) if calibrant_flags[i] in [1, 2, 4, 5, 6]] original_indexes = [x for i, x in enumerate(range(len(calibrant_medians))) if calibrant_flags[i] in [1, 2, 4, 5, 6]] flags_to_fit = [x for x in calibrant_flags] while repeat_calibration: try: calibration_iteration += 1 if cal_type == 'Linear': cal_coefficients = polyfit(medians_to_fit, concs_to_fit, 1, w=weightings_to_fit) fp = nppoly1d(cal_coefficients) y_fitted = [fp(x) for x in calibrant_medians] cal_coefficients = list(cal_coefficients) elif cal_type == 'Quadratic': cal_coefficients = polyfit(medians_to_fit, concs_to_fit, 2, w=weightings_to_fit) fp = nppoly1d(cal_coefficients) y_fitted = [fp(x) for x in calibrant_medians] cal_coefficients = list(cal_coefficients) else: logging.error('ERROR: No calibration type specified for nutrient') raise NameError('No calibration type could be applied') repeat_calibration = False calibrant_residuals = [] for i, x in enumerate(concs_to_fit): cal_residual = x - fp(medians_to_fit[i]) calibrant_residuals.append(cal_residual) max_residual_index = int(npargmax(npabs(nparray(calibrant_residuals)))) if abs(calibrant_residuals[max_residual_index]) > (2 * calibrant_error) and flags_to_fit[ max_residual_index] != 92: repeat_calibration = True weightings_to_fit[max_residual_index] = 0 flags_to_fit[max_residual_index] = 91 medians_to_fit.pop(max_residual_index) concs_to_fit.pop(max_residual_index) weightings_to_fit.pop(max_residual_index) original_indexes.pop(max_residual_index) flags_to_fit.pop(max_residual_index) calibrant_flags[original_indexes[max_residual_index]] = 91 calibrant_weightings[original_indexes[max_residual_index]] = 0 if calibrant_error < abs(calibrant_residuals[max_residual_index]) < (2 * calibrant_error) and flags_to_fit[ max_residual_index] != 6: repeat_calibration = True weightings_to_fit[max_residual_index] = 0.5 flags_to_fit[max_residual_index] = 92 calibrant_flags[original_indexes[max_residual_index]] = 92 calibrant_weightings[original_indexes[max_residual_index]] = 0.5 if calibration_iteration > 7: repeat_calibration = False except IndexError: pass final_residuals = [(x - fp(calibrant_medians[i])) for i, x in enumerate(calibrant_concentrations)] r_squared_score = r_squared(calibrant_concentrations, y_fitted) return cal_coefficients, calibrant_flags, calibrant_weightings, final_residuals, r_squared_score
def scipylsp_parallel( times, mags, errs, # ignored but for consistent API startp, endp, nbestpeaks=5, periodepsilon=0.1, # 0.1 stepsize=1.0e-4, nworkers=4, sigclip=None, timebin=None): ''' This uses the LSP function from the scipy library, which is fast as hell. We try to make it faster by running LSP for sections of the omegas array in parallel. ''' # make sure there are no nans anywhere finiteind = np.isfinite(mags) & np.isfinite(errs) ftimes, fmags, ferrs = times[finiteind], mags[finiteind], errs[finiteind] if len(ftimes) > 0 and len(fmags) > 0: # sigclip the lightcurve if asked to do so if sigclip: worktimes, workmags, _ = sigclip_magseries(ftimes, fmags, ferrs, sigclip=sigclip) LOGINFO('ndet after sigclipping = %s' % len(worktimes)) else: worktimes = ftimes workmags = fmags # bin the lightcurve if asked to do so if timebin: binned = time_bin_magseries(worktimes, workmags, binsize=timebin) worktimes = binned['binnedtimes'] workmags = binned['binnedmags'] # renormalize the working mags to zero and scale them so that the # variance = 1 for use with our LSP functions normmags = (workmags - np.median(workmags)) / np.std(workmags) startf = 1.0 / endp endf = 1.0 / startp omegas = 2 * np.pi * np.arange(startf, endf, stepsize) # partition the omegas array by nworkers tasks = [] chunksize = int(float(len(omegas)) / nworkers) + 1 tasks = [ omegas[x * chunksize:x * chunksize + chunksize] for x in range(nworkers) ] # map to parallel workers if (not nworkers) or (nworkers > NCPUS): nworkers = NCPUS LOGINFO('using %s workers...' % nworkers) pool = Pool(nworkers) tasks = [(worktimes, normmags, x) for x in tasks] lsp = pool.map(parallel_scipylsp_worker, tasks) pool.close() pool.join() lsp = np.concatenate(lsp) periods = 2.0 * np.pi / omegas # 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 we only get finite lsp values finitepeakind = npisfinite(lsp) finlsp = lsp[finitepeakind] finperiods = periods[finitepeakind] bestperiodind = npargmax(finlsp) sortedlspind = np.argsort(finlsp)[::-1] sortedlspperiods = finperiods[sortedlspind] sortedlspvals = finlsp[sortedlspind] prevbestlspval = sortedlspvals[0] # now get the nbestpeaks nbestperiods, nbestlspvals, peakcount = ([finperiods[bestperiodind]], [finlsp[bestperiodind]], 1) prevperiod = sortedlspperiods[0] # find the best nbestpeaks in the lsp and their periods for period, lspval in zip(sortedlspperiods, sortedlspvals): 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 and all(x > periodepsilon for x in bestperiodsdiff)): nbestperiods.append(period) nbestlspvals.append(lspval) peakcount = peakcount + 1 prevperiod = period return { 'bestperiod': finperiods[bestperiodind], 'bestlspval': finlsp[bestperiodind], 'nbestpeaks': nbestpeaks, 'nbestlspvals': nbestlspvals, 'nbestperiods': nbestperiods, 'lspvals': lsp, 'omegas': omegas, 'periods': periods, 'method': 'sls' } else: LOGERROR('no good detections for these times and mags, skipping...') return { 'bestperiod': npnan, 'bestlspval': npnan, 'nbestpeaks': nbestpeaks, 'nbestlspvals': None, 'nbestperiods': None, 'lspvals': None, 'periods': None, 'method': 'sls' }
def maxidx(x): return 100 * (int(npargmax(x)) + 1) / length
def aov_periodfind(times, mags, errs, magsarefluxes=False, startp=None, endp=None, stepsize=1.0e-4, autofreq=True, normalize=True, phasebinsize=0.05, mindetperbin=9, nbestpeaks=5, periodepsilon=0.1, sigclip=10.0, nworkers=None, verbose=True): '''This runs a parallelized Analysis-of-Variance (AoV) period search. NOTE: `normalize = True` here as recommended by Schwarzenberg-Czerny 1996, i.e. mags will be normalized to zero and rescaled so their variance = 1.0. Parameters ---------- times,mags,errs : np.array The mag/flux time-series with associated measurement errors to run the period-finding on. magsarefluxes : bool If the input measurement values in `mags` and `errs` are in fluxes, set this to True. startp,endp : float or None 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. autofreq : bool If this is True, the value of `stepsize` will be ignored and the :py:func:`astrobase.periodbase.get_frequency_grid` function will be used to generate a frequency grid based on `startp`, and `endp`. If these are None as well, `startp` will be set to 0.1 and `endp` will be set to `times.max() - times.min()`. normalize : bool This sets if the input time-series is normalized to 0.0 and rescaled such that its variance = 1.0. This is the recommended procedure by Schwarzenberg-Czerny 1996. phasebinsize : float The bin size in phase to use when calculating the AoV theta statistic at a test frequency. mindetperbin : int The minimum number of elements in a phase bin to consider it valid when calculating the AoV theta statistic at a test frequency. nbestpeaks : int The number of 'best' peaks to return from the periodogram results, starting from the global maximum of the periodogram peak values. 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. 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. nworkers : int The number of parallel workers to use when calculating the periodogram. verbose : bool If this is True, will indicate progress and details about the frequency grid used for the period search. 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, 'periods': the full array of periods considered, 'method':'aov' -> 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: # get the frequencies to use if startp: endf = 1.0/startp else: # default start period is 0.1 day endf = 1.0/0.1 if endp: startf = 1.0/endp else: # default end period is length of time series startf = 1.0/(stimes.max() - stimes.min()) # if we're not using autofreq, then use the provided frequencies if not autofreq: frequencies = nparange(startf, endf, stepsize) if verbose: LOGINFO( 'using %s frequency points, start P = %.3f, end P = %.3f' % (frequencies.size, 1.0/endf, 1.0/startf) ) else: # this gets an automatic grid of frequencies to use frequencies = get_frequency_grid(stimes, minfreq=startf, maxfreq=endf) if verbose: LOGINFO( 'using autofreq with %s frequency points, ' 'start P = %.3f, end P = %.3f' % (frequencies.size, 1.0/frequencies.max(), 1.0/frequencies.min()) ) # map to parallel workers if (not nworkers) or (nworkers > NCPUS): nworkers = NCPUS if verbose: LOGINFO('using %s workers...' % nworkers) pool = Pool(nworkers) # renormalize the working mags to zero and scale them so that the # variance = 1 for use with our LSP functions if normalize: nmags = (smags - npmedian(smags))/npstd(smags) else: nmags = smags tasks = [(stimes, nmags, serrs, x, phasebinsize, mindetperbin) for x in frequencies] lsp = pool.map(_aov_worker, tasks) pool.close() pool.join() del pool lsp = nparray(lsp) 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 filter out non-finite values 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, 'nbestlspvals':None, 'nbestperiods':None, 'lspvals':None, 'periods':None, 'method':'aov', 'kwargs':{'startp':startp, 'endp':endp, 'stepsize':stepsize, 'normalize':normalize, 'phasebinsize':phasebinsize, 'mindetperbin':mindetperbin, 'autofreq':autofreq, 'periodepsilon':periodepsilon, 'nbestpeaks':nbestpeaks, 'sigclip':sigclip}} sortedlspind = npargsort(finlsp)[::-1] sortedlspperiods = finperiods[sortedlspind] sortedlspvals = finlsp[sortedlspind] # now get the nbestpeaks nbestperiods, nbestlspvals, peakcount = ( [finperiods[bestperiodind]], [finlsp[bestperiodind]], 1 ) prevperiod = sortedlspperiods[0] # find the best nbestpeaks in the lsp and their periods for period, lspval in zip(sortedlspperiods, sortedlspvals): 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) peakcount = peakcount + 1 prevperiod = period return {'bestperiod':finperiods[bestperiodind], 'bestlspval':finlsp[bestperiodind], 'nbestpeaks':nbestpeaks, 'nbestlspvals':nbestlspvals, 'nbestperiods':nbestperiods, 'lspvals':lsp, 'periods':periods, 'method':'aov', 'kwargs':{'startp':startp, 'endp':endp, 'stepsize':stepsize, 'normalize':normalize, 'phasebinsize':phasebinsize, 'mindetperbin':mindetperbin, 'autofreq':autofreq, 'periodepsilon':periodepsilon, 'nbestpeaks':nbestpeaks, 'sigclip':sigclip}} else: LOGERROR('no good detections for these times and mags, skipping...') return {'bestperiod':npnan, 'bestlspval':npnan, 'nbestpeaks':nbestpeaks, 'nbestlspvals':None, 'nbestperiods':None, 'lspvals':None, 'periods':None, 'method':'aov', 'kwargs':{'startp':startp, 'endp':endp, 'stepsize':stepsize, 'normalize':normalize, 'phasebinsize':phasebinsize, 'mindetperbin':mindetperbin, 'autofreq':autofreq, 'periodepsilon':periodepsilon, 'nbestpeaks':nbestpeaks, 'sigclip':sigclip}}
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=0.8, # maximum transit length in phase nphasebins=200, autofreq=True, # figure out f0, nf, and df automatically periodepsilon=0.1, nbestpeaks=5, sigclip=10.0, verbose=True): '''Runs the Box Least Squares Fitting Search for transit-shaped signals. Based on eebls.f from Kovacs et al. 2002 and python-bls from Foreman-Mackey et al. 2015. This is the serial version (which is good enough in most cases because BLS in Fortran is fairly fast). If nfreq > 5e5, this will take a while. ''' # 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 autofreq: # figure out the best number of phasebins to use nphasebins = int(np.ceil(2.0 / mintransitduration)) # 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(np.ceil((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, nphasebins: %s, ' 'min transit duration: %s, max transit duration: %s' % (stepsize, nphasebins, mintransitduration, maxtransitduration)) else: minfreq = 1.0 / endp maxfreq = 1.0 / startp nfreq = int(np.ceil((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, nphasebins: %s, ' 'min transit duration: %s, max transit duration: %s' % (stepsize, nphasebins, mintransitduration, maxtransitduration)) 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 ' 'periodbase.bls_parallel_pfind function instead') if minfreq < (1.0 / (stimes.max() - stimes.min())): if verbose: 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()) if verbose: LOGINFO('new minfreq: %s, maxfreq: %s' % (minfreq, maxfreq)) # run BLS try: blsresult = _bls_runner(stimes, smags, nfreq, minfreq, stepsize, nphasebins, mintransitduration, maxtransitduration) # find the peaks in the BLS. this uses wavelet transforms to # smooth the spectrum and find peaks. a similar thing would be # to do a convolution with a gaussian kernel or a tophat # function, calculate d/dx(result), then get indices where this # is zero # blspeakinds = find_peaks_cwt(blsresults['power'], # nparray([2.0,3.0,4.0,5.0])) frequencies = minfreq + nparange(nfreq) * stepsize periods = 1.0 / frequencies lsp = 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, 'nbestlspvals': None, 'nbestperiods': None, 'lspvals': None, 'periods': None, 'method': 'bls', 'kwargs': { 'startp': startp, 'endp': endp, 'stepsize': stepsize, 'mintransitduration': mintransitduration, 'maxtransitduration': maxtransitduration, 'nphasebins': nphasebins, 'autofreq': autofreq, 'periodepsilon': periodepsilon, 'nbestpeaks': nbestpeaks, 'sigclip': sigclip } } sortedlspind = np.argsort(finlsp)[::-1] sortedlspperiods = finperiods[sortedlspind] sortedlspvals = finlsp[sortedlspind] prevbestlspval = sortedlspvals[0] # now get the nbestpeaks nbestperiods, nbestlspvals, peakcount = ([ finperiods[bestperiodind] ], [finlsp[bestperiodind]], 1) prevperiod = sortedlspperiods[0] # find the best nbestpeaks in the lsp and their periods for period, lspval in zip(sortedlspperiods, sortedlspvals): 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 * prevperiod) for x in bestperiodsdiff)): nbestperiods.append(period) nbestlspvals.append(lspval) peakcount = peakcount + 1 prevperiod = period # generate the return dict resultdict = { 'bestperiod': finperiods[bestperiodind], 'bestlspval': finlsp[bestperiodind], 'nbestpeaks': nbestpeaks, 'nbestlspvals': nbestlspvals, 'nbestperiods': nbestperiods, 'lspvals': lsp, 'frequencies': frequencies, 'periods': periods, 'blsresult': blsresult, 'stepsize': stepsize, 'nfreq': nfreq, 'nphasebins': nphasebins, 'mintransitduration': mintransitduration, 'maxtransitduration': maxtransitduration, 'method': 'bls', 'kwargs': { 'startp': startp, 'endp': endp, 'stepsize': stepsize, 'mintransitduration': mintransitduration, 'maxtransitduration': maxtransitduration, 'nphasebins': nphasebins, 'autofreq': autofreq, 'periodepsilon': periodepsilon, 'nbestpeaks': nbestpeaks, 'sigclip': sigclip } } return resultdict except Exception as e: LOGEXCEPTION('BLS failed!') return { 'bestperiod': npnan, 'bestlspval': npnan, 'nbestpeaks': nbestpeaks, 'nbestlspvals': None, 'nbestperiods': None, 'lspvals': None, 'periods': None, 'stepsize': stepsize, 'nfreq': nfreq, 'nphasebins': nphasebins, 'mintransitduration': mintransitduration, 'maxtransitduration': maxtransitduration, 'method': 'bls', 'kwargs': { 'startp': startp, 'endp': endp, 'stepsize': stepsize, 'mintransitduration': mintransitduration, 'maxtransitduration': maxtransitduration, 'nphasebins': nphasebins, 'autofreq': autofreq, 'periodepsilon': periodepsilon, 'nbestpeaks': nbestpeaks, 'sigclip': sigclip } } else: LOGERROR('no good detections for these times and mags, skipping...') return { 'bestperiod': npnan, 'bestlspval': npnan, 'nbestpeaks': nbestpeaks, 'nbestlspvals': None, 'nbestperiods': None, 'lspvals': None, 'periods': None, 'stepsize': stepsize, 'nfreq': None, 'nphasebins': None, 'mintransitduration': mintransitduration, 'maxtransitduration': maxtransitduration, 'method': 'bls', 'kwargs': { 'startp': startp, 'endp': endp, 'stepsize': stepsize, 'mintransitduration': mintransitduration, 'maxtransitduration': maxtransitduration, 'nphasebins': nphasebins, 'autofreq': autofreq, 'periodepsilon': periodepsilon, 'nbestpeaks': nbestpeaks, 'sigclip': sigclip } }
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=0.8, # maximum transit length in phase nphasebins=200, autofreq=True, # figure out f0, nf, and df automatically nbestpeaks=5, periodepsilon=0.1, # 0.1 nworkers=None, sigclip=10.0, verbose=True): '''Runs the Box Least Squares Fitting Search for transit-shaped signals. Based on eebls.f from Kovacs et al. 2002 and python-bls from Foreman-Mackey et al. 2015. Breaks up the full frequency space into chunks and passes them to parallel BLS 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. ''' # 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 autofreq: # figure out the best number of phasebins to use nphasebins = int(np.ceil(2.0 / mintransitduration)) # 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(np.ceil((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, nphasebins: %s, ' 'min transit duration: %s, max transit duration: %s' % (stepsize, nphasebins, mintransitduration, maxtransitduration)) else: minfreq = 1.0 / endp maxfreq = 1.0 / startp nfreq = int(np.ceil((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, nphasebins: %s, ' 'min transit duration: %s, max transit duration: %s' % (stepsize, nphasebins, mintransitduration, maxtransitduration)) # check the minimum frequency if minfreq < (1.0 / (stimes.max() - stimes.min())): minfreq = 2.0 / (stimes.max() - stimes.min()) if verbose: 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())) LOGINFO('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) # break up the tasks into chunks frequencies = minfreq + nparange(nfreq) * stepsize 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) # chunk_minfreqs = [frequencies[x*chunksize] for x in range(nworkers)] # chunk_nfreqs = [frequencies[x*chunksize:x*chunksize+chunksize].size # for x in range(nworkers)] # populate the tasks list tasks = [(stimes, smags, chunk_minf, chunk_nf, stepsize, nphasebins, mintransitduration, maxtransitduration) for (chunk_nf, chunk_minf) in zip(chunk_minfreqs, chunk_nfreqs)] if verbose: for ind, task in enumerate(tasks): LOGINFO('worker %s: minfreq = %.6f, nfreqs = %s' % (ind + 1, task[3], task[2])) 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 = np.concatenate([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, 'nbestlspvals': None, 'nbestperiods': None, 'lspvals': None, 'periods': None, 'method': 'bls', 'kwargs': { 'startp': startp, 'endp': endp, 'stepsize': stepsize, 'mintransitduration': mintransitduration, 'maxtransitduration': maxtransitduration, 'nphasebins': nphasebins, 'autofreq': autofreq, 'periodepsilon': periodepsilon, 'nbestpeaks': nbestpeaks, 'sigclip': sigclip } } sortedlspind = np.argsort(finlsp)[::-1] sortedlspperiods = finperiods[sortedlspind] sortedlspvals = finlsp[sortedlspind] prevbestlspval = sortedlspvals[0] # now get the nbestpeaks nbestperiods, nbestlspvals, peakcount = ([finperiods[bestperiodind]], [finlsp[bestperiodind]], 1) prevperiod = sortedlspperiods[0] # find the best nbestpeaks in the lsp and their periods for period, lspval in zip(sortedlspperiods, sortedlspvals): 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 * prevperiod) for x in bestperiodsdiff)): nbestperiods.append(period) nbestlspvals.append(lspval) peakcount = peakcount + 1 prevperiod = period # generate the return dict resultdict = { 'bestperiod': finperiods[bestperiodind], 'bestlspval': finlsp[bestperiodind], 'nbestpeaks': nbestpeaks, 'nbestlspvals': nbestlspvals, 'nbestperiods': nbestperiods, 'lspvals': lsp, 'frequencies': frequencies, 'periods': periods, 'blsresult': results, 'stepsize': stepsize, 'nfreq': nfreq, 'nphasebins': nphasebins, 'mintransitduration': mintransitduration, 'maxtransitduration': maxtransitduration, 'method': 'bls', 'kwargs': { 'startp': startp, 'endp': endp, 'stepsize': stepsize, 'mintransitduration': mintransitduration, 'maxtransitduration': maxtransitduration, 'nphasebins': nphasebins, 'autofreq': autofreq, 'periodepsilon': periodepsilon, 'nbestpeaks': nbestpeaks, 'sigclip': sigclip } } return resultdict else: LOGERROR('no good detections for these times and mags, skipping...') return { 'bestperiod': npnan, 'bestlspval': npnan, 'nbestpeaks': nbestpeaks, 'nbestlspvals': None, 'nbestperiods': None, 'lspvals': None, 'periods': None, 'blsresult': None, 'stepsize': stepsize, 'nfreq': None, 'nphasebins': None, 'mintransitduration': mintransitduration, 'maxtransitduration': maxtransitduration, 'method': 'bls', 'kwargs': { 'startp': startp, 'endp': endp, 'stepsize': stepsize, 'mintransitduration': mintransitduration, 'maxtransitduration': maxtransitduration, 'nphasebins': nphasebins, 'autofreq': autofreq, 'periodepsilon': periodepsilon, 'nbestpeaks': nbestpeaks, 'sigclip': sigclip } }
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 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 pgen_lsp( times, mags, errs, magsarefluxes=False, startp=None, endp=None, autofreq=True, nbestpeaks=5, periodepsilon=0.1, # 0.1 stepsize=1.0e-4, nworkers=None, workchunksize=None, sigclip=10.0, glspfunc=glsp_worker, verbose=True): '''This calculates the generalized LSP given times, mags, errors. Uses the algorithm from Zechmeister and Kurster (2009). By default, this calculates a frequency grid to use automatically, based on the autofrequency function from astropy.stats.lombscargle. If startp and endp are provided, will generate a frequency grid based on these instead. ''' # get rid of nans first and sigclip stimes, smags, serrs = sigclip_magseries(times, mags, errs, magsarefluxes=magsarefluxes, sigclip=sigclip) # get rid of zero errs nzind = np.nonzero(serrs) stimes, smags, serrs = stimes[nzind], smags[nzind], serrs[nzind] # make sure there are enough points to calculate a spectrum if len(stimes) > 9 and len(smags) > 9 and len(serrs) > 9: # get the frequencies to use if startp: endf = 1.0 / startp else: # default start period is 0.1 day endf = 1.0 / 0.1 if endp: startf = 1.0 / endp else: # default end period is length of time series startf = 1.0 / (stimes.max() - stimes.min()) # if we're not using autofreq, then use the provided frequencies if not autofreq: omegas = 2 * np.pi * np.arange(startf, endf, stepsize) if verbose: LOGINFO( 'using %s frequency points, start P = %.3f, end P = %.3f' % (omegas.size, 1.0 / endf, 1.0 / startf)) else: # this gets an automatic grid of frequencies to use freqs = get_frequency_grid(stimes, minfreq=startf, maxfreq=endf) omegas = 2 * np.pi * freqs if verbose: LOGINFO('using autofreq with %s frequency points, ' 'start P = %.3f, end P = %.3f' % (omegas.size, 1.0 / freqs.max(), 1.0 / freqs.min())) # map to parallel workers if (not nworkers) or (nworkers > NCPUS): nworkers = NCPUS if verbose: LOGINFO('using %s workers...' % nworkers) pool = Pool(nworkers) tasks = [(stimes, smags, serrs, x) for x in omegas] if workchunksize: lsp = pool.map(glspfunc, tasks, chunksize=workchunksize) else: lsp = pool.map(glspfunc, tasks) pool.close() pool.join() del pool lsp = np.array(lsp) periods = 2.0 * np.pi / omegas # 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 filter out non-finite values of lsp 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, 'nbestlspvals': None, 'nbestperiods': None, 'lspvals': None, 'omegas': omegas, 'periods': None, 'method': 'gls', 'kwargs': { 'startp': startp, 'endp': endp, 'stepsize': stepsize, 'autofreq': autofreq, 'periodepsilon': periodepsilon, 'nbestpeaks': nbestpeaks, 'sigclip': sigclip } } sortedlspind = np.argsort(finlsp)[::-1] sortedlspperiods = finperiods[sortedlspind] sortedlspvals = finlsp[sortedlspind] prevbestlspval = sortedlspvals[0] # now get the nbestpeaks nbestperiods, nbestlspvals, peakcount = ([finperiods[bestperiodind]], [finlsp[bestperiodind]], 1) prevperiod = sortedlspperiods[0] # find the best nbestpeaks in the lsp and their periods for period, lspval in zip(sortedlspperiods, sortedlspvals): 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 * prevperiod) for x in bestperiodsdiff)): nbestperiods.append(period) nbestlspvals.append(lspval) peakcount = peakcount + 1 prevperiod = period return { 'bestperiod': finperiods[bestperiodind], 'bestlspval': finlsp[bestperiodind], 'nbestpeaks': nbestpeaks, 'nbestlspvals': nbestlspvals, 'nbestperiods': nbestperiods, 'lspvals': lsp, 'omegas': omegas, 'periods': periods, 'method': 'gls', 'kwargs': { 'startp': startp, 'endp': endp, 'stepsize': stepsize, 'autofreq': autofreq, 'periodepsilon': periodepsilon, 'nbestpeaks': nbestpeaks, 'sigclip': sigclip } } else: LOGERROR('no good detections for these times and mags, skipping...') return { 'bestperiod': npnan, 'bestlspval': npnan, 'nbestpeaks': nbestpeaks, 'nbestlspvals': None, 'nbestperiods': None, 'lspvals': None, 'omegas': None, 'periods': None, 'method': 'gls', 'kwargs': { 'startp': startp, 'endp': endp, 'stepsize': stepsize, 'autofreq': autofreq, 'periodepsilon': periodepsilon, 'nbestpeaks': nbestpeaks, 'sigclip': sigclip } }
def aov_periodfind( times, mags, errs, magsarefluxes=False, autofreq=True, startp=None, endp=None, normalize=True, stepsize=1.0e-4, phasebinsize=0.05, mindetperbin=9, nbestpeaks=5, periodepsilon=0.1, # 0.1 sigclip=10.0, nworkers=None, verbose=True): '''This runs a parallel AoV period search. NOTE: normalize = True here as recommended by Schwarzenberg-Czerny 1996, i.e. mags will be normalized to zero and rescaled so their variance = 1.0 ''' # 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: # get the frequencies to use if startp: endf = 1.0 / startp else: # default start period is 0.1 day endf = 1.0 / 0.1 if endp: startf = 1.0 / endp else: # default end period is length of time series startf = 1.0 / (stimes.max() - stimes.min()) # if we're not using autofreq, then use the provided frequencies if not autofreq: frequencies = np.arange(startf, endf, stepsize) if verbose: LOGINFO( 'using %s frequency points, start P = %.3f, end P = %.3f' % (frequencies.size, 1.0 / endf, 1.0 / startf)) else: # this gets an automatic grid of frequencies to use frequencies = get_frequency_grid(stimes, minfreq=startf, maxfreq=endf) if verbose: LOGINFO('using autofreq with %s frequency points, ' 'start P = %.3f, end P = %.3f' % (frequencies.size, 1.0 / frequencies.max(), 1.0 / frequencies.min())) # map to parallel workers if (not nworkers) or (nworkers > NCPUS): nworkers = NCPUS if verbose: LOGINFO('using %s workers...' % nworkers) pool = Pool(nworkers) # renormalize the working mags to zero and scale them so that the # variance = 1 for use with our LSP functions if normalize: nmags = (smags - npmedian(smags)) / npstd(smags) else: nmags = smags tasks = [(stimes, nmags, serrs, x, phasebinsize, mindetperbin) for x in frequencies] lsp = pool.map(aov_worker, tasks) pool.close() pool.join() del pool lsp = nparray(lsp) 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 filter out non-finite values 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, 'nbestlspvals': None, 'nbestperiods': None, 'lspvals': None, 'periods': None, 'method': 'aov', 'kwargs': { 'startp': startp, 'endp': endp, 'stepsize': stepsize, 'normalize': normalize, 'phasebinsize': phasebinsize, 'mindetperbin': mindetperbin, 'autofreq': autofreq, 'periodepsilon': periodepsilon, 'nbestpeaks': nbestpeaks, 'sigclip': sigclip } } sortedlspind = np.argsort(finlsp)[::-1] sortedlspperiods = finperiods[sortedlspind] sortedlspvals = finlsp[sortedlspind] prevbestlspval = sortedlspvals[0] # now get the nbestpeaks nbestperiods, nbestlspvals, peakcount = ([finperiods[bestperiodind]], [finlsp[bestperiodind]], 1) prevperiod = sortedlspperiods[0] # find the best nbestpeaks in the lsp and their periods for period, lspval in zip(sortedlspperiods, sortedlspvals): 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 * prevperiod) for x in bestperiodsdiff)): nbestperiods.append(period) nbestlspvals.append(lspval) peakcount = peakcount + 1 prevperiod = period return { 'bestperiod': finperiods[bestperiodind], 'bestlspval': finlsp[bestperiodind], 'nbestpeaks': nbestpeaks, 'nbestlspvals': nbestlspvals, 'nbestperiods': nbestperiods, 'lspvals': lsp, 'periods': periods, 'method': 'aov', 'kwargs': { 'startp': startp, 'endp': endp, 'stepsize': stepsize, 'normalize': normalize, 'phasebinsize': phasebinsize, 'mindetperbin': mindetperbin, 'autofreq': autofreq, 'periodepsilon': periodepsilon, 'nbestpeaks': nbestpeaks, 'sigclip': sigclip } } else: LOGERROR('no good detections for these times and mags, skipping...') return { 'bestperiod': npnan, 'bestlspval': npnan, 'nbestpeaks': nbestpeaks, 'nbestlspvals': None, 'nbestperiods': None, 'lspvals': None, 'periods': None, 'method': 'aov', 'kwargs': { 'startp': startp, 'endp': endp, 'stepsize': stepsize, 'normalize': normalize, 'phasebinsize': phasebinsize, 'mindetperbin': mindetperbin, 'autofreq': autofreq, 'periodepsilon': periodepsilon, 'nbestpeaks': nbestpeaks, 'sigclip': sigclip } }
def tls_parallel_pfind( times, mags, errs, magsarefluxes=None, startp=0.1, # search from 0.1 d to... endp=None, # determine automatically from times tls_oversample=5, tls_mintransits=3, tls_transit_template='default', tls_rstar_min=0.13, tls_rstar_max=3.5, tls_mstar_min=0.1, tls_mstar_max=2.0, periodepsilon=0.1, nbestpeaks=5, sigclip=10.0, verbose=True, nworkers=None): """Wrapper to Hippke & Heller (2019)'s "transit least squares", which is BLS, but with a slightly better template (and niceties in the implementation). A few comments: * The time series must be in units of days. * The frequency sampling Hippke & Heller (2019) advocate for is cubic in frequencies, instead of linear. Ofir (2014) found that the linear-in-frequency sampling (which is correct for sinusoidal signal detection) isn't optimal for a Keplerian box signal. He gave an equation for "optimal" sampling. `tlsoversample` is the factor by which to oversample over that. The grid can be imported independently via:: from transitleastsquares import period_grid The spacing equations are given here: https://transitleastsquares.readthedocs.io/en/latest/Python%20interface.html#period-grid * The boundaries of the period search are by default 0.1 day to 99% the baseline of times. Parameters ---------- times,mags,errs : np.array The magnitude/flux time-series to search for transits. magsarefluxes : bool `transitleastsquares` requires fluxes. Therefore if magsarefluxes is set to false, the passed mags are converted to fluxes. All output dictionary vectors include fluxes, not mags. startp,endp : float The minimum and maximum periods to consider for the transit search. tls_oversample : int Factor by which to oversample the frequency grid. tls_mintransits : int Sets the `min_n_transits` kwarg for the `BoxLeastSquares.autoperiod()` function. tls_transit_template: str `default`, `grazing`, or `box`. tls_rstar_min,tls_rstar_max : float The range of stellar radii to consider when generating a frequency grid. In uniits of Rsun. tls_mstar_min,tls_mstar_max : float The range of stellar masses to consider when generating a frequency grid. In units of Msun. 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. verbose : bool Kept for consistency with `periodbase` functions. 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. The format is similar to the other astrobase period-finders -- it contains the nbestpeaks, which is the most important thing. (But isn't entirely standardized.) Crucially, it also contains "tlsresult", which is a dictionary with transitleastsquares spectra (used to get the SDE as defined in the TLS paper), statistics, transit period, mid-time, duration, depth, SNR, and the "odd_even_mismatch" statistic. The full key list is:: dict_keys(['SDE', 'SDE_raw', 'chi2_min', 'chi2red_min', 'period', 'period_uncertainty', 'T0', 'duration', 'depth', 'depth_mean', 'depth_mean_even', 'depth_mean_odd', 'transit_depths', 'transit_depths_uncertainties', 'rp_rs', 'snr', 'snr_per_transit', 'snr_pink_per_transit', 'odd_even_mismatch', 'transit_times', 'per_transit_count', 'transit_count', 'distinct_transit_count', 'empty_transit_count', 'FAP', 'in_transit_count', 'after_transit_count', 'before_transit_count', 'periods', 'power', 'power_raw', 'SR', 'chi2', 'chi2red', 'model_lightcurve_time', 'model_lightcurve_model', 'model_folded_phase', 'folded_y', 'folded_dy', 'folded_phase', 'model_folded_model']) The descriptions are here: https://transitleastsquares.readthedocs.io/en/latest/Python%20interface.html#return-values The remaining resultdict is:: resultdict = { 'tlsresult':tlsresult, 'bestperiod': the best period value in the periodogram, 'bestlspval': the 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, 'periods': the full array of periods considered, 'tlsresult': Astropy tls result object (BoxLeastSquaresResult), 'tlsmodel': Astropy tls BoxLeastSquares object used for work, 'method':'tls' -> the name of the period-finder method, 'kwargs':{ dict of all of the input kwargs for record-keeping} } """ # set NCPUS for HTLS if nworkers is None: nworkers = NCPUS # convert mags to fluxes because this method requires them if not magsarefluxes: LOGWARNING('transitleastsquares requires relative flux...') LOGWARNING('converting input mags to relative flux...') LOGWARNING('and forcing magsarefluxes=True...') mag_0, f_0 = 12.0, 1.0e4 flux = f_0 * 10.0**(-0.4 * (mags - mag_0)) flux /= np.nanmedian(flux) # if the errors are provided as mag errors, convert them to flux if errs is not None: flux_errs = flux * (errs / mags) else: flux_errs = None mags = flux errs = flux_errs magsarefluxes = True # uniform weights for errors if none given if errs is None: errs = np.ones_like(mags) * 1.0e-4 # get rid of nans first and sigclip stimes, smags, serrs = sigclip_magseries(times, mags, errs, magsarefluxes=magsarefluxes, sigclip=sigclip) stimes, smags, serrs = resort_by_time(stimes, smags, serrs) # make sure there are enough points to calculate a spectrum if not (len(stimes) > 9 and len(smags) > 9 and len(serrs) > 9): LOGERROR('no good detections for these times and mags, skipping...') resultdict = { 'tlsresult': npnan, 'bestperiod': npnan, 'bestlspval': npnan, 'nbestpeaks': nbestpeaks, 'nbestinds': None, 'nbestlspvals': None, 'nbestperiods': None, 'lspvals': None, 'periods': None, 'method': 'tls', 'kwargs': { 'startp': startp, 'endp': endp, 'tls_oversample': tls_oversample, 'tls_ntransits': tls_mintransits, 'tls_transit_template': tls_transit_template, 'tls_rstar_min': tls_rstar_min, 'tls_rstar_max': tls_rstar_max, 'tls_mstar_min': tls_mstar_min, 'tls_mstar_max': tls_mstar_max, 'periodepsilon': periodepsilon, 'nbestpeaks': nbestpeaks, 'sigclip': sigclip, 'magsarefluxes': magsarefluxes } } return resultdict # if the end period is not provided, set it to # 99% of the time baseline. (for two transits). if endp is None: endp = 0.99 * (np.nanmax(stimes) - np.nanmin(stimes)) # run periodogram model = transitleastsquares(stimes, smags, serrs) tlsresult = model.power(use_threads=nworkers, show_progress_bar=False, R_star_min=tls_rstar_min, R_star_max=tls_rstar_max, M_star_min=tls_mstar_min, M_star_max=tls_mstar_max, period_min=startp, period_max=endp, n_transits_min=tls_mintransits, transit_template=tls_transit_template, oversampling_factor=tls_oversample) # get the peak values lsp = nparray(tlsresult.power) periods = nparray(tlsresult.periods) # 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 tls 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...') resultdict = { 'tlsresult': npnan, 'bestperiod': npnan, 'bestlspval': npnan, 'nbestpeaks': nbestpeaks, 'nbestinds': None, 'nbestlspvals': None, 'nbestperiods': None, 'lspvals': None, 'periods': None, 'method': 'tls', 'kwargs': { 'startp': startp, 'endp': endp, 'tls_oversample': tls_oversample, 'tls_ntransits': tls_mintransits, 'tls_transit_template': tls_transit_template, 'tls_rstar_min': tls_rstar_min, 'tls_rstar_max': tls_rstar_max, 'tls_mstar_min': tls_mstar_min, 'tls_mstar_max': tls_mstar_max, 'periodepsilon': periodepsilon, 'nbestpeaks': nbestpeaks, 'sigclip': sigclip, 'magsarefluxes': magsarefluxes } } return resultdict 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 = { 'tlsresult': tlsresult, 'bestperiod': finperiods[bestperiodind], 'bestlspval': finlsp[bestperiodind], 'nbestpeaks': nbestpeaks, 'nbestinds': nbestinds, 'nbestlspvals': nbestlspvals, 'nbestperiods': nbestperiods, 'lspvals': lsp, 'periods': periods, 'method': 'tls', 'kwargs': { 'startp': startp, 'endp': endp, 'tls_oversample': tls_oversample, 'tls_ntransits': tls_mintransits, 'tls_transit_template': tls_transit_template, 'tls_rstar_min': tls_rstar_min, 'tls_rstar_max': tls_rstar_max, 'tls_mstar_min': tls_mstar_min, 'tls_mstar_max': tls_mstar_max, 'periodepsilon': periodepsilon, 'nbestpeaks': nbestpeaks, 'sigclip': sigclip, 'magsarefluxes': magsarefluxes } } return resultdict