kloodia/bigpython · Datasets at Hugging Face

partition stringclasses 3 values	func_name stringlengths 1 134	docstring stringlengths 1 46.9k	path stringlengths 4 223	original_string stringlengths 75 104k	code stringlengths 75 104k	docstring_tokens listlengths 1 1.97k	repo stringlengths 7 55	language stringclasses 1 value	url stringlengths 87 315	code_tokens listlengths 19 28.4k	sha stringlengths 40 40
valid	jhk_to_sdssg	Converts given J, H, Ks mags to an SDSS g magnitude value. Parameters ---------- jmag,hmag,kmag : float 2MASS J, H, Ks mags of the object. Returns ------- float The converted SDSS g band magnitude.	astrobase/magnitudes.py	def jhk_to_sdssg(jmag,hmag,kmag): '''Converts given J, H, Ks mags to an SDSS g magnitude value. Parameters ---------- jmag,hmag,kmag : float 2MASS J, H, Ks mags of the object. Returns ------- float The converted SDSS g band magnitude. ''' return convert_constant...	def jhk_to_sdssg(jmag,hmag,kmag): '''Converts given J, H, Ks mags to an SDSS g magnitude value. Parameters ---------- jmag,hmag,kmag : float 2MASS J, H, Ks mags of the object. Returns ------- float The converted SDSS g band magnitude. ''' return convert_constant...	[ "Converts", "given", "J", "H", "Ks", "mags", "to", "an", "SDSS", "g", "magnitude", "value", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/magnitudes.py#L296-L316	[ "def", "jhk_to_sdssg", "(", "jmag", ",", "hmag", ",", "kmag", ")", ":", "return", "convert_constants", "(", "jmag", ",", "hmag", ",", "kmag", ",", "SDSSG_JHK", ",", "SDSSG_JH", ",", "SDSSG_JK", ",", "SDSSG_HK", ",", "SDSSG_J", ",", "SDSSG_H", ",", "SDSSG...	2922a14619d183fb28005fa7d02027ac436f2265
valid	jhk_to_sdssr	Converts given J, H, Ks mags to an SDSS r magnitude value. Parameters ---------- jmag,hmag,kmag : float 2MASS J, H, Ks mags of the object. Returns ------- float The converted SDSS r band magnitude.	astrobase/magnitudes.py	def jhk_to_sdssr(jmag,hmag,kmag): '''Converts given J, H, Ks mags to an SDSS r magnitude value. Parameters ---------- jmag,hmag,kmag : float 2MASS J, H, Ks mags of the object. Returns ------- float The converted SDSS r band magnitude. ''' return convert_constant...	def jhk_to_sdssr(jmag,hmag,kmag): '''Converts given J, H, Ks mags to an SDSS r magnitude value. Parameters ---------- jmag,hmag,kmag : float 2MASS J, H, Ks mags of the object. Returns ------- float The converted SDSS r band magnitude. ''' return convert_constant...	[ "Converts", "given", "J", "H", "Ks", "mags", "to", "an", "SDSS", "r", "magnitude", "value", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/magnitudes.py#L320-L340	[ "def", "jhk_to_sdssr", "(", "jmag", ",", "hmag", ",", "kmag", ")", ":", "return", "convert_constants", "(", "jmag", ",", "hmag", ",", "kmag", ",", "SDSSR_JHK", ",", "SDSSR_JH", ",", "SDSSR_JK", ",", "SDSSR_HK", ",", "SDSSR_J", ",", "SDSSR_H", ",", "SDSSR...	2922a14619d183fb28005fa7d02027ac436f2265
valid	jhk_to_sdssi	Converts given J, H, Ks mags to an SDSS i magnitude value. Parameters ---------- jmag,hmag,kmag : float 2MASS J, H, Ks mags of the object. Returns ------- float The converted SDSS i band magnitude.	astrobase/magnitudes.py	def jhk_to_sdssi(jmag,hmag,kmag): '''Converts given J, H, Ks mags to an SDSS i magnitude value. Parameters ---------- jmag,hmag,kmag : float 2MASS J, H, Ks mags of the object. Returns ------- float The converted SDSS i band magnitude. ''' return convert_constant...	def jhk_to_sdssi(jmag,hmag,kmag): '''Converts given J, H, Ks mags to an SDSS i magnitude value. Parameters ---------- jmag,hmag,kmag : float 2MASS J, H, Ks mags of the object. Returns ------- float The converted SDSS i band magnitude. ''' return convert_constant...	[ "Converts", "given", "J", "H", "Ks", "mags", "to", "an", "SDSS", "i", "magnitude", "value", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/magnitudes.py#L344-L364	[ "def", "jhk_to_sdssi", "(", "jmag", ",", "hmag", ",", "kmag", ")", ":", "return", "convert_constants", "(", "jmag", ",", "hmag", ",", "kmag", ",", "SDSSI_JHK", ",", "SDSSI_JH", ",", "SDSSI_JK", ",", "SDSSI_HK", ",", "SDSSI_J", ",", "SDSSI_H", ",", "SDSSI...	2922a14619d183fb28005fa7d02027ac436f2265
valid	jhk_to_sdssz	Converts given J, H, Ks mags to an SDSS z magnitude value. Parameters ---------- jmag,hmag,kmag : float 2MASS J, H, Ks mags of the object. Returns ------- float The converted SDSS z band magnitude.	astrobase/magnitudes.py	def jhk_to_sdssz(jmag,hmag,kmag): '''Converts given J, H, Ks mags to an SDSS z magnitude value. Parameters ---------- jmag,hmag,kmag : float 2MASS J, H, Ks mags of the object. Returns ------- float The converted SDSS z band magnitude. ''' return convert_constant...	def jhk_to_sdssz(jmag,hmag,kmag): '''Converts given J, H, Ks mags to an SDSS z magnitude value. Parameters ---------- jmag,hmag,kmag : float 2MASS J, H, Ks mags of the object. Returns ------- float The converted SDSS z band magnitude. ''' return convert_constant...	[ "Converts", "given", "J", "H", "Ks", "mags", "to", "an", "SDSS", "z", "magnitude", "value", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/magnitudes.py#L368-L388	[ "def", "jhk_to_sdssz", "(", "jmag", ",", "hmag", ",", "kmag", ")", ":", "return", "convert_constants", "(", "jmag", ",", "hmag", ",", "kmag", ",", "SDSSZ_JHK", ",", "SDSSZ_JH", ",", "SDSSZ_JK", ",", "SDSSZ_HK", ",", "SDSSZ_J", ",", "SDSSZ_H", ",", "SDSSZ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	absolute_gaia_magnitude	Calculates the GAIA absolute magnitude for object (or array of objects). Given a G mag and the parallax measured by GAIA, gets the absolute mag using the usual equation:: G - M_G = 5 x log10(d_pc) - 5 M_G = 5 - 5log10(d_pc) + G Parameters ---------- gaia_mag : float or array-like...	astrobase/magnitudes.py	def absolute_gaia_magnitude(gaia_mag, gaia_parallax_mas, gaia_mag_err=None, gaia_parallax_err_mas=None): '''Calculates the GAIA absolute magnitude for object (or array of objects). Given a G mag and the parallax measured by GAI...	def absolute_gaia_magnitude(gaia_mag, gaia_parallax_mas, gaia_mag_err=None, gaia_parallax_err_mas=None): '''Calculates the GAIA absolute magnitude for object (or array of objects). Given a G mag and the parallax measured by GAI...	[ "Calculates", "the", "GAIA", "absolute", "magnitude", "for", "object", "(", "or", "array", "of", "objects", ")", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/magnitudes.py#L437-L511	[ "def", "absolute_gaia_magnitude", "(", "gaia_mag", ",", "gaia_parallax_mas", ",", "gaia_mag_err", "=", "None", ",", "gaia_parallax_err_mas", "=", "None", ")", ":", "# get the distance", "# we're using the naive calculation of d. this is inaccurate as stated in", "# Bailer-Jones 2...	2922a14619d183fb28005fa7d02027ac436f2265
valid	aov_theta	Calculates the Schwarzenberg-Czerny AoV statistic at a test frequency. Parameters ---------- times,mags,errs : np.array The input time-series and associated errors. frequency : float The test frequency to calculate the theta statistic at. binsize : float The phase bin siz...	astrobase/periodbase/saov.py	def aov_theta(times, mags, errs, frequency, binsize=0.05, minbin=9): '''Calculates the Schwarzenberg-Czerny AoV statistic at a test frequency. Parameters ---------- times,mags,errs : np.array The input time-series and associated errors. frequency : float The test fre...	def aov_theta(times, mags, errs, frequency, binsize=0.05, minbin=9): '''Calculates the Schwarzenberg-Czerny AoV statistic at a test frequency. Parameters ---------- times,mags,errs : np.array The input time-series and associated errors. frequency : float The test fre...	[ "Calculates", "the", "Schwarzenberg", "-", "Czerny", "AoV", "statistic", "at", "a", "test", "frequency", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/periodbase/saov.py#L70-L162	[ "def", "aov_theta", "(", "times", ",", "mags", ",", "errs", ",", "frequency", ",", "binsize", "=", "0.05", ",", "minbin", "=", "9", ")", ":", "period", "=", "1.0", "/", "frequency", "fold_time", "=", "times", "[", "0", "]", "phased", "=", "phase_mags...	2922a14619d183fb28005fa7d02027ac436f2265
valid	_aov_worker	This is a parallel worker for the function below. Parameters ---------- task : tuple This is of the form below:: task[0] = times task[1] = mags task[2] = errs task[3] = frequency task[4] = binsize task[5] = minbin Return...	astrobase/periodbase/saov.py	def _aov_worker(task): '''This is a parallel worker for the function below. Parameters ---------- task : tuple This is of the form below:: task[0] = times task[1] = mags task[2] = errs task[3] = frequency task[4] = binsize ...	def _aov_worker(task): '''This is a parallel worker for the function below. Parameters ---------- task : tuple This is of the form below:: task[0] = times task[1] = mags task[2] = errs task[3] = frequency task[4] = binsize ...	[ "This", "is", "a", "parallel", "worker", "for", "the", "function", "below", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/periodbase/saov.py#L166-L202	[ "def", "_aov_worker", "(", "task", ")", ":", "times", ",", "mags", ",", "errs", ",", "frequency", ",", "binsize", ",", "minbin", "=", "task", "try", ":", "theta", "=", "aov_theta", "(", "times", ",", "mags", ",", "errs", ",", "frequency", ",", "binsi...	2922a14619d183fb28005fa7d02027ac436f2265
valid	get_frequency_grid	This calculates a frequency grid for the period finding functions in this module. Based on the autofrequency function in astropy.stats.lombscargle. http://docs.astropy.org/en/stable/_modules/astropy/stats/lombscargle/core.html#LombScargle.autofrequency Parameters ---------- times : np.array ...	astrobase/periodbase/__init__.py	def get_frequency_grid(times, samplesperpeak=5, nyquistfactor=5, minfreq=None, maxfreq=None, returnf0dfnf=False): '''This calculates a frequency grid for the period finding functions in this module...	def get_frequency_grid(times, samplesperpeak=5, nyquistfactor=5, minfreq=None, maxfreq=None, returnf0dfnf=False): '''This calculates a frequency grid for the period finding functions in this module...	[ "This", "calculates", "a", "frequency", "grid", "for", "the", "period", "finding", "functions", "in", "this", "module", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/periodbase/__init__.py#L78-L137	[ "def", "get_frequency_grid", "(", "times", ",", "samplesperpeak", "=", "5", ",", "nyquistfactor", "=", "5", ",", "minfreq", "=", "None", ",", "maxfreq", "=", "None", ",", "returnf0dfnf", "=", "False", ")", ":", "baseline", "=", "times", ".", "max", "(", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	independent_freq_count	This estimates M: the number of independent frequencies in the periodogram. This follows the terminology on page 3 of Zechmeister & Kurster (2009):: M = DELTA_f / delta_f where:: DELTA_f = freq.max() - freq.min() delta_f = 1.0/(times.max() - times.min()) Parameters ---------...	astrobase/periodbase/__init__.py	def independent_freq_count(frequencies, times, conservative=True): '''This estimates M: the number of independent frequencies in the periodogram. This follows the terminology on page 3 of Zechmeister & Kurster (2009):: M = DELTA_f / delta_f where:: DELTA_f = freq.max() - freq.min() ...	def independent_freq_count(frequencies, times, conservative=True): '''This estimates M: the number of independent frequencies in the periodogram. This follows the terminology on page 3 of Zechmeister & Kurster (2009):: M = DELTA_f / delta_f where:: DELTA_f = freq.max() - freq.min() ...	[ "This", "estimates", "M", ":", "the", "number", "of", "independent", "frequencies", "in", "the", "periodogram", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/periodbase/__init__.py#L141-L188	[ "def", "independent_freq_count", "(", "frequencies", ",", "times", ",", "conservative", "=", "True", ")", ":", "M", "=", "frequencies", ".", "ptp", "(", ")", "*", "times", ".", "ptp", "(", ")", "if", "conservative", ":", "M_eff", "=", "min", "(", "[", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	bootstrap_falsealarmprob	Calculates the false alarm probabilities of periodogram peaks using bootstrap resampling of the magnitude time series. The false alarm probability here is defined as:: (1.0 + sum(trialbestpeaks[i] > peak[j]))/(ntrialbestpeaks + 1) for each best periodogram peak j. The index i is for each bootstra...	astrobase/periodbase/__init__.py	def bootstrap_falsealarmprob(lspinfo, times, mags, errs, nbootstrap=250, magsarefluxes=False, sigclip=10.0, npeaks=No...	def bootstrap_falsealarmprob(lspinfo, times, mags, errs, nbootstrap=250, magsarefluxes=False, sigclip=10.0, npeaks=No...	[ "Calculates", "the", "false", "alarm", "probabilities", "of", "periodogram", "peaks", "using", "bootstrap", "resampling", "of", "the", "magnitude", "time", "series", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/periodbase/__init__.py#L268-L500	[ "def", "bootstrap_falsealarmprob", "(", "lspinfo", ",", "times", ",", "mags", ",", "errs", ",", "nbootstrap", "=", "250", ",", "magsarefluxes", "=", "False", ",", "sigclip", "=", "10.0", ",", "npeaks", "=", "None", ")", ":", "# figure out how many periods to w...	2922a14619d183fb28005fa7d02027ac436f2265
valid	make_combined_periodogram	This just puts all of the period-finders on a single periodogram. This will renormalize all of the periodograms so their values lie between 0 and 1, with values lying closer to 1 being more significant. Periodograms that give the same best periods will have their peaks line up together. Parameters ...	astrobase/periodbase/__init__.py	def make_combined_periodogram(pflist, outfile, addmethods=False): '''This just puts all of the period-finders on a single periodogram. This will renormalize all of the periodograms so their values lie between 0 and 1, with values lying closer to 1 being more significant. Periodograms that give the same...	def make_combined_periodogram(pflist, outfile, addmethods=False): '''This just puts all of the period-finders on a single periodogram. This will renormalize all of the periodograms so their values lie between 0 and 1, with values lying closer to 1 being more significant. Periodograms that give the same...	[ "This", "just", "puts", "all", "of", "the", "period", "-", "finders", "on", "a", "single", "periodogram", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/periodbase/__init__.py#L509-L589	[ "def", "make_combined_periodogram", "(", "pflist", ",", "outfile", ",", "addmethods", "=", "False", ")", ":", "import", "matplotlib", ".", "pyplot", "as", "plt", "for", "pf", "in", "pflist", ":", "if", "pf", "[", "'method'", "]", "==", "'pdm'", ":", "plt...	2922a14619d183fb28005fa7d02027ac436f2265
valid	read_original_textlc	Read .epdlc, and .tfalc light curves and return a corresponding labelled dict (if LC from <2012) or astropy table (if >=2012). Each has different keys that can be accessed via .keys() Input: lcpath: path (string) to light curve data, which is a textfile with HAT LC data. Example: dat = rea...	astrobase/hatsurveys/texthatlc.py	def read_original_textlc(lcpath): ''' Read .epdlc, and .tfalc light curves and return a corresponding labelled dict (if LC from <2012) or astropy table (if >=2012). Each has different keys that can be accessed via .keys() Input: lcpath: path (string) to light curve data, which is a textfile wit...	def read_original_textlc(lcpath): ''' Read .epdlc, and .tfalc light curves and return a corresponding labelled dict (if LC from <2012) or astropy table (if >=2012). Each has different keys that can be accessed via .keys() Input: lcpath: path (string) to light curve data, which is a textfile wit...	[ "Read", ".", "epdlc", "and", ".", "tfalc", "light", "curves", "and", "return", "a", "corresponding", "labelled", "dict", "(", "if", "LC", "from", "<2012", ")", "or", "astropy", "table", "(", "if", ">", "=", "2012", ")", ".", "Each", "has", "different",...	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/hatsurveys/texthatlc.py#L54-L167	[ "def", "read_original_textlc", "(", "lcpath", ")", ":", "LOGINFO", "(", "'reading original HAT text LC: {:s}'", ".", "format", "(", "lcpath", ")", ")", "N_lines_to_parse_comments", "=", "50", "with", "open", "(", "lcpath", ",", "'rb'", ")", "as", "file", ":", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	traptransit_fit_magseries	This fits a trapezoid transit model to a magnitude time series. Parameters ---------- times,mags,errs : np.array The input mag/flux time-series to fit a trapezoid planet-transit model to. period : float The period to use for the model fit. transitparams : list of floats ...	astrobase/lcfit/transits.py	def traptransit_fit_magseries(times, mags, errs, transitparams, sigclip=10.0, plotfit=False, magsarefluxes=False, verbose=True): '''This fits a trapezoid transit mode...	def traptransit_fit_magseries(times, mags, errs, transitparams, sigclip=10.0, plotfit=False, magsarefluxes=False, verbose=True): '''This fits a trapezoid transit mode...	[ "This", "fits", "a", "trapezoid", "transit", "model", "to", "a", "magnitude", "time", "series", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/transits.py#L85-L401	[ "def", "traptransit_fit_magseries", "(", "times", ",", "mags", ",", "errs", ",", "transitparams", ",", "sigclip", "=", "10.0", ",", "plotfit", "=", "False", ",", "magsarefluxes", "=", "False", ",", "verbose", "=", "True", ")", ":", "stimes", ",", "smags", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	_get_value	This decides if a value is to be fit for or is fixed in a model fit. When you want to get the value of some parameter, but you're not sure if it's being fit or if it is fixed. then, e.g. for `period`:: period_value = _get_value('period', fitparams, fixedparams)	astrobase/lcfit/transits.py	def _get_value(quantitystr, fitparams, fixedparams): """This decides if a value is to be fit for or is fixed in a model fit. When you want to get the value of some parameter, but you're not sure if it's being fit or if it is fixed. then, e.g. for `period`:: period_value = _get_value('period', fitp...	def _get_value(quantitystr, fitparams, fixedparams): """This decides if a value is to be fit for or is fixed in a model fit. When you want to get the value of some parameter, but you're not sure if it's being fit or if it is fixed. then, e.g. for `period`:: period_value = _get_value('period', fitp...	[ "This", "decides", "if", "a", "value", "is", "to", "be", "fit", "for", "or", "is", "fixed", "in", "a", "model", "fit", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/transits.py#L409-L426	[ "def", "_get_value", "(", "quantitystr", ",", "fitparams", ",", "fixedparams", ")", ":", "# for Mandel-Agol fitting, sometimes we want to fix some parameters,", "# and fit others. this function allows that flexibility.", "fitparamskeys", ",", "fixedparamskeys", "=", "fitparams", "....	2922a14619d183fb28005fa7d02027ac436f2265
valid	_transit_model	This returns a BATMAN planetary transit model. Parameters ---------- times : np.array The times at which the model will be evaluated. t0 : float The time of periastron for the transit. per : float The orbital period of the planet. rp : float The stellar radiu...	astrobase/lcfit/transits.py	def _transit_model(times, t0, per, rp, a, inc, ecc, w, u, limb_dark, exp_time_minutes=2, supersample_factor=7): '''This returns a BATMAN planetary transit model. Parameters ---------- times : np.array The times at which the model will be evaluated. t0 : float Th...	def _transit_model(times, t0, per, rp, a, inc, ecc, w, u, limb_dark, exp_time_minutes=2, supersample_factor=7): '''This returns a BATMAN planetary transit model. Parameters ---------- times : np.array The times at which the model will be evaluated. t0 : float Th...	[ "This", "returns", "a", "BATMAN", "planetary", "transit", "model", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/transits.py#L429-L500	[ "def", "_transit_model", "(", "times", ",", "t0", ",", "per", ",", "rp", ",", "a", ",", "inc", ",", "ecc", ",", "w", ",", "u", ",", "limb_dark", ",", "exp_time_minutes", "=", "2", ",", "supersample_factor", "=", "7", ")", ":", "params", "=", "batma...	2922a14619d183fb28005fa7d02027ac436f2265
valid	_log_prior_transit	Assume priors on all parameters have uniform probability.	astrobase/lcfit/transits.py	def _log_prior_transit(theta, priorbounds): ''' Assume priors on all parameters have uniform probability. ''' # priorbounds contains the input priors, and because of how we previously # sorted theta, its sorted keys tell us which parts of theta correspond to # which physical quantities. all...	def _log_prior_transit(theta, priorbounds): ''' Assume priors on all parameters have uniform probability. ''' # priorbounds contains the input priors, and because of how we previously # sorted theta, its sorted keys tell us which parts of theta correspond to # which physical quantities. all...	[ "Assume", "priors", "on", "all", "parameters", "have", "uniform", "probability", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/transits.py#L503-L521	[ "def", "_log_prior_transit", "(", "theta", ",", "priorbounds", ")", ":", "# priorbounds contains the input priors, and because of how we previously", "# sorted theta, its sorted keys tell us which parts of theta correspond to", "# which physical quantities.", "allowed", "=", "True", "for...	2922a14619d183fb28005fa7d02027ac436f2265
valid	_log_likelihood_transit	Given a batman TransitModel and its proposed parameters (theta), update the batman params object with the proposed parameters and evaluate the gaussian likelihood. Note: the priorbounds are only needed to parse theta.	astrobase/lcfit/transits.py	def _log_likelihood_transit(theta, params, model, t, flux, err_flux, priorbounds): ''' Given a batman TransitModel and its proposed parameters (theta), update the batman params object with the proposed parameters and evaluate the gaussian likelihood. Note: the priorbound...	def _log_likelihood_transit(theta, params, model, t, flux, err_flux, priorbounds): ''' Given a batman TransitModel and its proposed parameters (theta), update the batman params object with the proposed parameters and evaluate the gaussian likelihood. Note: the priorbound...	[ "Given", "a", "batman", "TransitModel", "and", "its", "proposed", "parameters", "(", "theta", ")", "update", "the", "batman", "params", "object", "with", "the", "proposed", "parameters", "and", "evaluate", "the", "gaussian", "likelihood", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/transits.py#L528-L568	[ "def", "_log_likelihood_transit", "(", "theta", ",", "params", ",", "model", ",", "t", ",", "flux", ",", "err_flux", ",", "priorbounds", ")", ":", "u", "=", "[", "]", "for", "ix", ",", "key", "in", "enumerate", "(", "sorted", "(", "priorbounds", ".", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	_log_likelihood_transit_plus_line	Given a batman TransitModel and its proposed parameters (theta), update the batman params object with the proposed parameters and evaluate the gaussian likelihood. Note: the priorbounds are only needed to parse theta.	astrobase/lcfit/transits.py	def _log_likelihood_transit_plus_line(theta, params, model, t, data_flux, err_flux, priorbounds): ''' Given a batman TransitModel and its proposed parameters (theta), update the batman params object with the proposed parameters and evaluate the gaussian likelihood. ...	def _log_likelihood_transit_plus_line(theta, params, model, t, data_flux, err_flux, priorbounds): ''' Given a batman TransitModel and its proposed parameters (theta), update the batman params object with the proposed parameters and evaluate the gaussian likelihood. ...	[ "Given", "a", "batman", "TransitModel", "and", "its", "proposed", "parameters", "(", "theta", ")", "update", "the", "batman", "params", "object", "with", "the", "proposed", "parameters", "and", "evaluate", "the", "gaussian", "likelihood", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/transits.py#L571-L625	[ "def", "_log_likelihood_transit_plus_line", "(", "theta", ",", "params", ",", "model", ",", "t", ",", "data_flux", ",", "err_flux", ",", "priorbounds", ")", ":", "u", "=", "[", "]", "for", "ix", ",", "key", "in", "enumerate", "(", "sorted", "(", "priorbo...	2922a14619d183fb28005fa7d02027ac436f2265
valid	log_posterior_transit	Evaluate posterior probability given proposed model parameters and the observed flux timeseries.	astrobase/lcfit/transits.py	def log_posterior_transit(theta, params, model, t, flux, err_flux, priorbounds): ''' Evaluate posterior probability given proposed model parameters and the observed flux timeseries. ''' lp = _log_prior_transit(theta, priorbounds) if not np.isfinite(lp): return -np.inf else: r...	def log_posterior_transit(theta, params, model, t, flux, err_flux, priorbounds): ''' Evaluate posterior probability given proposed model parameters and the observed flux timeseries. ''' lp = _log_prior_transit(theta, priorbounds) if not np.isfinite(lp): return -np.inf else: r...	[ "Evaluate", "posterior", "probability", "given", "proposed", "model", "parameters", "and", "the", "observed", "flux", "timeseries", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/transits.py#L628-L638	[ "def", "log_posterior_transit", "(", "theta", ",", "params", ",", "model", ",", "t", ",", "flux", ",", "err_flux", ",", "priorbounds", ")", ":", "lp", "=", "_log_prior_transit", "(", "theta", ",", "priorbounds", ")", "if", "not", "np", ".", "isfinite", "...	2922a14619d183fb28005fa7d02027ac436f2265
valid	log_posterior_transit_plus_line	Evaluate posterior probability given proposed model parameters and the observed flux timeseries.	astrobase/lcfit/transits.py	def log_posterior_transit_plus_line(theta, params, model, t, flux, err_flux, priorbounds): ''' Evaluate posterior probability given proposed model parameters and the observed flux timeseries. ''' lp = _log_prior_transit_plus_line(theta, priorbounds) if not np....	def log_posterior_transit_plus_line(theta, params, model, t, flux, err_flux, priorbounds): ''' Evaluate posterior probability given proposed model parameters and the observed flux timeseries. ''' lp = _log_prior_transit_plus_line(theta, priorbounds) if not np....	[ "Evaluate", "posterior", "probability", "given", "proposed", "model", "parameters", "and", "the", "observed", "flux", "timeseries", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/transits.py#L641-L654	[ "def", "log_posterior_transit_plus_line", "(", "theta", ",", "params", ",", "model", ",", "t", ",", "flux", ",", "err_flux", ",", "priorbounds", ")", ":", "lp", "=", "_log_prior_transit_plus_line", "(", "theta", ",", "priorbounds", ")", "if", "not", "np", "....	2922a14619d183fb28005fa7d02027ac436f2265
valid	mandelagol_fit_magseries	This fits a Mandel & Agol (2002) planetary transit model to a flux time series. You can fit and fix whatever parameters you want. It relies on Kreidberg (2015)'s BATMAN implementation for the transit model, emcee to sample the posterior (Foreman-Mackey et al 2013), `corner` to plot it, and `h5py` to sa...	astrobase/lcfit/transits.py	def mandelagol_fit_magseries( times, mags, errs, fitparams, priorbounds, fixedparams, trueparams=None, burninpercent=0.3, plotcorner=False, samplesavpath=False, n_walkers=50, n_mcmc_steps=400, eps=1e-4, skipsampling=False, ...	def mandelagol_fit_magseries( times, mags, errs, fitparams, priorbounds, fixedparams, trueparams=None, burninpercent=0.3, plotcorner=False, samplesavpath=False, n_walkers=50, n_mcmc_steps=400, eps=1e-4, skipsampling=False, ...	[ "This", "fits", "a", "Mandel", "&", "Agol", "(", "2002", ")", "planetary", "transit", "model", "to", "a", "flux", "time", "series", ".", "You", "can", "fit", "and", "fix", "whatever", "parameters", "you", "want", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/transits.py#L661-L1060	[ "def", "mandelagol_fit_magseries", "(", "times", ",", "mags", ",", "errs", ",", "fitparams", ",", "priorbounds", ",", "fixedparams", ",", "trueparams", "=", "None", ",", "burninpercent", "=", "0.3", ",", "plotcorner", "=", "False", ",", "samplesavpath", "=", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	mandelagol_and_line_fit_magseries	The model fit by this function is: a Mandel & Agol (2002) transit, PLUS a line. You can fit and fix whatever parameters you want. A typical use case: you want to measure transit times of individual SNR >~ 50 transits. You fix all the transit parameters except for the mid-time, and also fit for a line l...	astrobase/lcfit/transits.py	def mandelagol_and_line_fit_magseries( times, mags, errs, fitparams, priorbounds, fixedparams, trueparams=None, burninpercent=0.3, plotcorner=False, timeoffset=0, samplesavpath=False, n_walkers=50, n_mcmc_steps=400, eps=1e-4...	def mandelagol_and_line_fit_magseries( times, mags, errs, fitparams, priorbounds, fixedparams, trueparams=None, burninpercent=0.3, plotcorner=False, timeoffset=0, samplesavpath=False, n_walkers=50, n_mcmc_steps=400, eps=1e-4...	[ "The", "model", "fit", "by", "this", "function", "is", ":", "a", "Mandel", "&", "Agol", "(", "2002", ")", "transit", "PLUS", "a", "line", ".", "You", "can", "fit", "and", "fix", "whatever", "parameters", "you", "want", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/transits.py#L1063-L1530	[ "def", "mandelagol_and_line_fit_magseries", "(", "times", ",", "mags", ",", "errs", ",", "fitparams", ",", "priorbounds", ",", "fixedparams", ",", "trueparams", "=", "None", ",", "burninpercent", "=", "0.3", ",", "plotcorner", "=", "False", ",", "timeoffset", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	list_trilegal_filtersystems	This just lists all the filter systems available for TRILEGAL.	astrobase/services/trilegal.py	def list_trilegal_filtersystems(): ''' This just lists all the filter systems available for TRILEGAL. ''' print('%-40s %s' % ('FILTER SYSTEM NAME','DESCRIPTION')) print('%-40s %s' % ('------------------','-----------')) for key in sorted(TRILEGAL_FILTER_SYSTEMS.keys()): print('%-40s %s...	def list_trilegal_filtersystems(): ''' This just lists all the filter systems available for TRILEGAL. ''' print('%-40s %s' % ('FILTER SYSTEM NAME','DESCRIPTION')) print('%-40s %s' % ('------------------','-----------')) for key in sorted(TRILEGAL_FILTER_SYSTEMS.keys()): print('%-40s %s...	[ "This", "just", "lists", "all", "the", "filter", "systems", "available", "for", "TRILEGAL", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/services/trilegal.py#L478-L487	[ "def", "list_trilegal_filtersystems", "(", ")", ":", "print", "(", "'%-40s %s'", "%", "(", "'FILTER SYSTEM NAME'", ",", "'DESCRIPTION'", ")", ")", "print", "(", "'%-40s %s'", "%", "(", "'------------------'", ",", "'-----------'", ")", ")", "for", "key", "in", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	query_galcoords	This queries the TRILEGAL model form, downloads results, and parses them. Parameters ---------- gal_lon,gal_lat : float These are the center galactic longitude and latitude in degrees. filtersystem : str This is a key in the TRILEGAL_FILTER_SYSTEMS dict. Use the function :py:f...	astrobase/services/trilegal.py	def query_galcoords(gal_lon, gal_lat, filtersystem='sloan_2mass', field_deg2=1.0, usebinaries=True, extinction_sigma=0.1, magnitude_limit=26.0, maglim_filtercol=4, ...	def query_galcoords(gal_lon, gal_lat, filtersystem='sloan_2mass', field_deg2=1.0, usebinaries=True, extinction_sigma=0.1, magnitude_limit=26.0, maglim_filtercol=4, ...	[ "This", "queries", "the", "TRILEGAL", "model", "form", "downloads", "results", "and", "parses", "them", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/services/trilegal.py#L491-L804	[ "def", "query_galcoords", "(", "gal_lon", ",", "gal_lat", ",", "filtersystem", "=", "'sloan_2mass'", ",", "field_deg2", "=", "1.0", ",", "usebinaries", "=", "True", ",", "extinction_sigma", "=", "0.1", ",", "magnitude_limit", "=", "26.0", ",", "maglim_filtercol"...	2922a14619d183fb28005fa7d02027ac436f2265
valid	query_radecl	This runs the TRILEGAL query for decimal equatorial coordinates. Parameters ---------- ra,decl : float These are the center equatorial coordinates in decimal degrees filtersystem : str This is a key in the TRILEGAL_FILTER_SYSTEMS dict. Use the function :py:func:`astrobase.serv...	astrobase/services/trilegal.py	def query_radecl(ra, decl, filtersystem='sloan_2mass', field_deg2=1.0, usebinaries=True, extinction_sigma=0.1, magnitude_limit=26.0, maglim_filtercol=4, trilegal_version=1.6, ...	def query_radecl(ra, decl, filtersystem='sloan_2mass', field_deg2=1.0, usebinaries=True, extinction_sigma=0.1, magnitude_limit=26.0, maglim_filtercol=4, trilegal_version=1.6, ...	[ "This", "runs", "the", "TRILEGAL", "query", "for", "decimal", "equatorial", "coordinates", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/services/trilegal.py#L808-L928	[ "def", "query_radecl", "(", "ra", ",", "decl", ",", "filtersystem", "=", "'sloan_2mass'", ",", "field_deg2", "=", "1.0", ",", "usebinaries", "=", "True", ",", "extinction_sigma", "=", "0.1", ",", "magnitude_limit", "=", "26.0", ",", "maglim_filtercol", "=", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	read_model_table	This reads a downloaded TRILEGAL model file. Parameters ---------- modelfile : str Path to the downloaded model file to read. Returns ------- np.recarray Returns the model table as a Numpy record array.	astrobase/services/trilegal.py	def read_model_table(modelfile): ''' This reads a downloaded TRILEGAL model file. Parameters ---------- modelfile : str Path to the downloaded model file to read. Returns ------- np.recarray Returns the model table as a Numpy record array. ''' infd = gzip.op...	def read_model_table(modelfile): ''' This reads a downloaded TRILEGAL model file. Parameters ---------- modelfile : str Path to the downloaded model file to read. Returns ------- np.recarray Returns the model table as a Numpy record array. ''' infd = gzip.op...	[ "This", "reads", "a", "downloaded", "TRILEGAL", "model", "file", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/services/trilegal.py#L932-L954	[ "def", "read_model_table", "(", "modelfile", ")", ":", "infd", "=", "gzip", ".", "open", "(", "modelfile", ")", "model", "=", "np", ".", "genfromtxt", "(", "infd", ",", "names", "=", "True", ")", "infd", ".", "close", "(", ")", "return", "model" ]	2922a14619d183fb28005fa7d02027ac436f2265
valid	_time_independent_equals	This compares two values in constant time. Taken from tornado: https://github.com/tornadoweb/tornado/blob/ d4eb8eb4eb5cc9a6677e9116ef84ded8efba8859/tornado/web.py#L3060	astrobase/cpserver/checkplotserver_handlers.py	def _time_independent_equals(a, b): ''' This compares two values in constant time. Taken from tornado: https://github.com/tornadoweb/tornado/blob/ d4eb8eb4eb5cc9a6677e9116ef84ded8efba8859/tornado/web.py#L3060 ''' if len(a) != len(b): return False result = 0 if isinstance(a...	def _time_independent_equals(a, b): ''' This compares two values in constant time. Taken from tornado: https://github.com/tornadoweb/tornado/blob/ d4eb8eb4eb5cc9a6677e9116ef84ded8efba8859/tornado/web.py#L3060 ''' if len(a) != len(b): return False result = 0 if isinstance(a...	[ "This", "compares", "two", "values", "in", "constant", "time", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/cpserver/checkplotserver_handlers.py#L3032-L3051	[ "def", "_time_independent_equals", "(", "a", ",", "b", ")", ":", "if", "len", "(", "a", ")", "!=", "len", "(", "b", ")", ":", "return", "False", "result", "=", "0", "if", "isinstance", "(", "a", "[", "0", "]", ",", "int", ")", ":", "# python3 byt...	2922a14619d183fb28005fa7d02027ac436f2265
valid	FrontendEncoder.default	Overrides the default serializer for `JSONEncoder`. This can serialize the following objects in addition to what `JSONEncoder` can already do. - `np.array` - `bytes` - `complex` - `np.float64` and other `np.dtype` objects Parameters ---------- ...	astrobase/cpserver/checkplotserver_handlers.py	def default(self, obj): '''Overrides the default serializer for `JSONEncoder`. This can serialize the following objects in addition to what `JSONEncoder` can already do. - `np.array` - `bytes` - `complex` - `np.float64` and other `np.dtype` objects Para...	def default(self, obj): '''Overrides the default serializer for `JSONEncoder`. This can serialize the following objects in addition to what `JSONEncoder` can already do. - `np.array` - `bytes` - `complex` - `np.float64` and other `np.dtype` objects Para...	[ "Overrides", "the", "default", "serializer", "for", "JSONEncoder", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/cpserver/checkplotserver_handlers.py#L48-L85	[ "def", "default", "(", "self", ",", "obj", ")", ":", "if", "isinstance", "(", "obj", ",", "np", ".", "ndarray", ")", ":", "return", "obj", ".", "tolist", "(", ")", "elif", "isinstance", "(", "obj", ",", "bytes", ")", ":", "return", "obj", ".", "d...	2922a14619d183fb28005fa7d02027ac436f2265
valid	IndexHandler.initialize	handles initial setup.	astrobase/cpserver/checkplotserver_handlers.py	def initialize(self, currentdir, assetpath, cplist, cplistfile, executor, readonly, baseurl): ''' handles initial setup. ''' self.currentdir = currentdir self.assetpath = assetpath self.currentproject = cplist self.cplistfile = cplistfile ...	def initialize(self, currentdir, assetpath, cplist, cplistfile, executor, readonly, baseurl): ''' handles initial setup. ''' self.currentdir = currentdir self.assetpath = assetpath self.currentproject = cplist self.cplistfile = cplistfile ...	[ "handles", "initial", "setup", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/cpserver/checkplotserver_handlers.py#L408-L421	[ "def", "initialize", "(", "self", ",", "currentdir", ",", "assetpath", ",", "cplist", ",", "cplistfile", ",", "executor", ",", "readonly", ",", "baseurl", ")", ":", "self", ".", "currentdir", "=", "currentdir", "self", ".", "assetpath", "=", "assetpath", "...	2922a14619d183fb28005fa7d02027ac436f2265
valid	IndexHandler.get	This handles GET requests to the index page. TODO: provide the correct baseurl from the checkplotserver options dict, so the frontend JS can just read that off immediately.	astrobase/cpserver/checkplotserver_handlers.py	def get(self): '''This handles GET requests to the index page. TODO: provide the correct baseurl from the checkplotserver options dict, so the frontend JS can just read that off immediately. ''' # generate the project's list of checkplots project_checkplots = self.curr...	def get(self): '''This handles GET requests to the index page. TODO: provide the correct baseurl from the checkplotserver options dict, so the frontend JS can just read that off immediately. ''' # generate the project's list of checkplots project_checkplots = self.curr...	[ "This", "handles", "GET", "requests", "to", "the", "index", "page", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/cpserver/checkplotserver_handlers.py#L424-L457	[ "def", "get", "(", "self", ")", ":", "# generate the project's list of checkplots", "project_checkplots", "=", "self", ".", "currentproject", "[", "'checkplots'", "]", "project_checkplotbasenames", "=", "[", "os", ".", "path", ".", "basename", "(", "x", ")", "for"...	2922a14619d183fb28005fa7d02027ac436f2265
valid	CheckplotHandler.get	This handles GET requests to serve a specific checkplot pickle. This is an AJAX endpoint; returns JSON that gets converted by the frontend into things to render.	astrobase/cpserver/checkplotserver_handlers.py	def get(self, checkplotfname): '''This handles GET requests to serve a specific checkplot pickle. This is an AJAX endpoint; returns JSON that gets converted by the frontend into things to render. ''' if checkplotfname: # do the usual safing self.checkp...	def get(self, checkplotfname): '''This handles GET requests to serve a specific checkplot pickle. This is an AJAX endpoint; returns JSON that gets converted by the frontend into things to render. ''' if checkplotfname: # do the usual safing self.checkp...	[ "This", "handles", "GET", "requests", "to", "serve", "a", "specific", "checkplot", "pickle", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/cpserver/checkplotserver_handlers.py#L485-L980	[ "def", "get", "(", "self", ",", "checkplotfname", ")", ":", "if", "checkplotfname", ":", "# do the usual safing", "self", ".", "checkplotfname", "=", "xhtml_escape", "(", "base64", ".", "b64decode", "(", "url_unescape", "(", "checkplotfname", ")", ")", ")", "#...	2922a14619d183fb28005fa7d02027ac436f2265
valid	CheckplotHandler.post	This handles POST requests. Also an AJAX endpoint. Updates the persistent checkplot dict using the changes from the UI, and then saves it back to disk. This could definitely be faster by just loading the checkplot into a server-wide shared dict or something.	astrobase/cpserver/checkplotserver_handlers.py	def post(self, cpfile): '''This handles POST requests. Also an AJAX endpoint. Updates the persistent checkplot dict using the changes from the UI, and then saves it back to disk. This could definitely be faster by just loading the checkplot into a server-wide shared dict or some...	def post(self, cpfile): '''This handles POST requests. Also an AJAX endpoint. Updates the persistent checkplot dict using the changes from the UI, and then saves it back to disk. This could definitely be faster by just loading the checkplot into a server-wide shared dict or some...	[ "This", "handles", "POST", "requests", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/cpserver/checkplotserver_handlers.py#L984-L1121	[ "def", "post", "(", "self", ",", "cpfile", ")", ":", "# if self.readonly is set, then don't accept any changes", "# return immediately with a 400", "if", "self", ".", "readonly", ":", "msg", "=", "\"checkplotserver is in readonly mode. no updates allowed.\"", "resultdict", "=",...	2922a14619d183fb28005fa7d02027ac436f2265
valid	CheckplotListHandler.get	This handles GET requests for the current checkplot-list.json file. Used with AJAX from frontend.	astrobase/cpserver/checkplotserver_handlers.py	def get(self): ''' This handles GET requests for the current checkplot-list.json file. Used with AJAX from frontend. ''' # add the reviewed key to the current dict if it doesn't exist # this will hold all the reviewed objects for the frontend if 'reviewed' not ...	def get(self): ''' This handles GET requests for the current checkplot-list.json file. Used with AJAX from frontend. ''' # add the reviewed key to the current dict if it doesn't exist # this will hold all the reviewed objects for the frontend if 'reviewed' not ...	[ "This", "handles", "GET", "requests", "for", "the", "current", "checkplot", "-", "list", ".", "json", "file", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/cpserver/checkplotserver_handlers.py#L1150-L1164	[ "def", "get", "(", "self", ")", ":", "# add the reviewed key to the current dict if it doesn't exist", "# this will hold all the reviewed objects for the frontend", "if", "'reviewed'", "not", "in", "self", ".", "currentproject", ":", "self", ".", "currentproject", "[", "'revi...	2922a14619d183fb28005fa7d02027ac436f2265
valid	CheckplotListHandler.post	This handles POST requests. Saves the changes made by the user on the frontend back to the current checkplot-list.json file.	astrobase/cpserver/checkplotserver_handlers.py	def post(self): '''This handles POST requests. Saves the changes made by the user on the frontend back to the current checkplot-list.json file. ''' # if self.readonly is set, then don't accept any changes # return immediately with a 400 if self.readonly: ...	def post(self): '''This handles POST requests. Saves the changes made by the user on the frontend back to the current checkplot-list.json file. ''' # if self.readonly is set, then don't accept any changes # return immediately with a 400 if self.readonly: ...	[ "This", "handles", "POST", "requests", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/cpserver/checkplotserver_handlers.py#L1168-L1233	[ "def", "post", "(", "self", ")", ":", "# if self.readonly is set, then don't accept any changes", "# return immediately with a 400", "if", "self", ".", "readonly", ":", "msg", "=", "\"checkplotserver is in readonly mode. no updates allowed.\"", "resultdict", "=", "{", "'status'...	2922a14619d183fb28005fa7d02027ac436f2265
valid	LCToolHandler.get	This handles a GET request to run a specified LC tool. Parameters ---------- cpfile : str This is the checkplot file to run the tool on. Returns ------- str Returns a JSON response. Notes ----- The URI structure is:: ...	astrobase/cpserver/checkplotserver_handlers.py	def get(self, cpfile): '''This handles a GET request to run a specified LC tool. Parameters ---------- cpfile : str This is the checkplot file to run the tool on. Returns ------- str Returns a JSON response. Notes -----...	def get(self, cpfile): '''This handles a GET request to run a specified LC tool. Parameters ---------- cpfile : str This is the checkplot file to run the tool on. Returns ------- str Returns a JSON response. Notes -----...	[ "This", "handles", "a", "GET", "request", "to", "run", "a", "specified", "LC", "tool", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/cpserver/checkplotserver_handlers.py#L1264-L3005	[ "def", "get", "(", "self", ",", "cpfile", ")", ":", "if", "cpfile", ":", "self", ".", "cpfile", "=", "(", "xhtml_escape", "(", "base64", ".", "b64decode", "(", "url_unescape", "(", "cpfile", ")", ")", ")", ")", "# see if this plot is in the current project",...	2922a14619d183fb28005fa7d02027ac436f2265
valid	StandaloneHandler.initialize	This handles initial setup of the `RequestHandler`.	astrobase/cpserver/checkplotserver_handlers.py	def initialize(self, executor, secret): ''' This handles initial setup of the `RequestHandler`. ''' self.executor = executor self.secret = secret	def initialize(self, executor, secret): ''' This handles initial setup of the `RequestHandler`. ''' self.executor = executor self.secret = secret	[ "This", "handles", "initial", "setup", "of", "the", "RequestHandler", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/cpserver/checkplotserver_handlers.py#L3064-L3071	[ "def", "initialize", "(", "self", ",", "executor", ",", "secret", ")", ":", "self", ".", "executor", "=", "executor", "self", ".", "secret", "=", "secret" ]	2922a14619d183fb28005fa7d02027ac436f2265
valid	StandaloneHandler.get	This handles GET requests. Returns the requested checkplot pickle's information as JSON. Requires a pre-shared secret `key` argument for the operation to complete successfully. This is obtained from a command-line argument.	astrobase/cpserver/checkplotserver_handlers.py	def get(self): '''This handles GET requests. Returns the requested checkplot pickle's information as JSON. Requires a pre-shared secret `key` argument for the operation to complete successfully. This is obtained from a command-line argument. ''' provided_key = self.ge...	def get(self): '''This handles GET requests. Returns the requested checkplot pickle's information as JSON. Requires a pre-shared secret `key` argument for the operation to complete successfully. This is obtained from a command-line argument. ''' provided_key = self.ge...	[ "This", "handles", "GET", "requests", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/cpserver/checkplotserver_handlers.py#L3076-L3500	[ "def", "get", "(", "self", ")", ":", "provided_key", "=", "self", ".", "get_argument", "(", "'key'", ",", "default", "=", "None", ")", "if", "not", "provided_key", ":", "LOGGER", ".", "error", "(", "'standalone URL hit but no secret key provided'", ")", "retdi...	2922a14619d183fb28005fa7d02027ac436f2265
valid	extinction_query	This queries the 2MASS DUST service to find the extinction parameters for the given `lon`, `lat`. Parameters ---------- lon,lat: float These are decimal right ascension and declination if `coordtype = 'equatorial'`. These are are decimal Galactic longitude and latitude if `coor...	astrobase/services/dust.py	def extinction_query(lon, lat, coordtype='equatorial', sizedeg=5.0, forcefetch=False, cachedir='~/.astrobase/dust-cache', verbose=True, timeout=10.0, jitter=5.0): '''Thi...	def extinction_query(lon, lat, coordtype='equatorial', sizedeg=5.0, forcefetch=False, cachedir='~/.astrobase/dust-cache', verbose=True, timeout=10.0, jitter=5.0): '''Thi...	[ "This", "queries", "the", "2MASS", "DUST", "service", "to", "find", "the", "extinction", "parameters", "for", "the", "given", "lon", "lat", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/services/dust.py#L88-L257	[ "def", "extinction_query", "(", "lon", ",", "lat", ",", "coordtype", "=", "'equatorial'", ",", "sizedeg", "=", "5.0", ",", "forcefetch", "=", "False", ",", "cachedir", "=", "'~/.astrobase/dust-cache'", ",", "verbose", "=", "True", ",", "timeout", "=", "10.0"...	2922a14619d183fb28005fa7d02027ac436f2265
valid	smooth_magseries_gaussfilt	This smooths the magseries with a Gaussian kernel. Parameters ---------- mags : np.array The input mags/flux time-series to smooth. windowsize : int This is a odd integer containing the smoothing window size. windowfwhm : int This is an odd integer containing the FWHM of ...	astrobase/varbase/trends.py	def smooth_magseries_gaussfilt(mags, windowsize, windowfwhm=7): '''This smooths the magseries with a Gaussian kernel. Parameters ---------- mags : np.array The input mags/flux time-series to smooth. windowsize : int This is a odd integer containing the smoothing window size. ...	def smooth_magseries_gaussfilt(mags, windowsize, windowfwhm=7): '''This smooths the magseries with a Gaussian kernel. Parameters ---------- mags : np.array The input mags/flux time-series to smooth. windowsize : int This is a odd integer containing the smoothing window size. ...	[ "This", "smooths", "the", "magseries", "with", "a", "Gaussian", "kernel", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varbase/trends.py#L121-L147	[ "def", "smooth_magseries_gaussfilt", "(", "mags", ",", "windowsize", ",", "windowfwhm", "=", "7", ")", ":", "convkernel", "=", "Gaussian1DKernel", "(", "windowfwhm", ",", "x_size", "=", "windowsize", ")", "smoothed", "=", "convolve", "(", "mags", ",", "convker...	2922a14619d183fb28005fa7d02027ac436f2265
valid	smooth_magseries_savgol	This smooths the magseries with a Savitsky-Golay filter. Parameters ---------- mags : np.array The input mags/flux time-series to smooth. windowsize : int This is a odd integer containing the smoothing window size. polyorder : int This is an integer containing the polynom...	astrobase/varbase/trends.py	def smooth_magseries_savgol(mags, windowsize, polyorder=2): '''This smooths the magseries with a Savitsky-Golay filter. Parameters ---------- mags : np.array The input mags/flux time-series to smooth. windowsize : int This is a odd integer containing the smoothing window size. ...	def smooth_magseries_savgol(mags, windowsize, polyorder=2): '''This smooths the magseries with a Savitsky-Golay filter. Parameters ---------- mags : np.array The input mags/flux time-series to smooth. windowsize : int This is a odd integer containing the smoothing window size. ...	[ "This", "smooths", "the", "magseries", "with", "a", "Savitsky", "-", "Golay", "filter", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varbase/trends.py#L150-L175	[ "def", "smooth_magseries_savgol", "(", "mags", ",", "windowsize", ",", "polyorder", "=", "2", ")", ":", "smoothed", "=", "savgol_filter", "(", "mags", ",", "windowsize", ",", "polyorder", ")", "return", "smoothed" ]	2922a14619d183fb28005fa7d02027ac436f2265
valid	_old_epd_diffmags	This calculates the difference in mags after EPD coefficients are calculated. final EPD mags = median(magseries) + epd_diffmags()	astrobase/varbase/trends.py	def _old_epd_diffmags(coeff, fsv, fdv, fkv, xcc, ycc, bgv, bge, mag): ''' This calculates the difference in mags after EPD coefficients are calculated. final EPD mags = median(magseries) + epd_diffmags() ''' return -(coeff[0]fsv2. + coeff[1]fsv + coeff[2]fdv*2....	def _old_epd_diffmags(coeff, fsv, fdv, fkv, xcc, ycc, bgv, bge, mag): ''' This calculates the difference in mags after EPD coefficients are calculated. final EPD mags = median(magseries) + epd_diffmags() ''' return -(coeff[0]fsv2. + coeff[1]fsv + coeff[2]fdv*2....	[ "This", "calculates", "the", "difference", "in", "mags", "after", "EPD", "coefficients", "are", "calculated", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varbase/trends.py#L182-L211	[ "def", "_old_epd_diffmags", "(", "coeff", ",", "fsv", ",", "fdv", ",", "fkv", ",", "xcc", ",", "ycc", ",", "bgv", ",", "bge", ",", "mag", ")", ":", "return", "-", "(", "coeff", "[", "0", "]", "", "fsv", "*", "2.", "+", "coeff", "[", "1", "]...	2922a14619d183fb28005fa7d02027ac436f2265
valid	_old_epd_magseries	Detrends a magnitude series given in mag using accompanying values of S in fsv, D in fdv, K in fkv, x coords in xcc, y coords in ycc, background in bgv, and background error in bge. smooth is used to set a smoothing parameter for the fit function. Does EPD voodoo.	astrobase/varbase/trends.py	def _old_epd_magseries(times, mags, errs, fsv, fdv, fkv, xcc, ycc, bgv, bge, epdsmooth_windowsize=21, epdsmooth_sigclip=3.0, epdsmooth_func=smooth_magseries_signal_medfilt, epdsmooth_extraparams=None): ...	def _old_epd_magseries(times, mags, errs, fsv, fdv, fkv, xcc, ycc, bgv, bge, epdsmooth_windowsize=21, epdsmooth_sigclip=3.0, epdsmooth_func=smooth_magseries_signal_medfilt, epdsmooth_extraparams=None): ...	[ "Detrends", "a", "magnitude", "series", "given", "in", "mag", "using", "accompanying", "values", "of", "S", "in", "fsv", "D", "in", "fdv", "K", "in", "fkv", "x", "coords", "in", "xcc", "y", "coords", "in", "ycc", "background", "in", "bgv", "and", "back...	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varbase/trends.py#L215-L308	[ "def", "_old_epd_magseries", "(", "times", ",", "mags", ",", "errs", ",", "fsv", ",", "fdv", ",", "fkv", ",", "xcc", ",", "ycc", ",", "bgv", ",", "bge", ",", "epdsmooth_windowsize", "=", "21", ",", "epdsmooth_sigclip", "=", "3.0", ",", "epdsmooth_func", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	_epd_function	This is the EPD function to fit using a smoothed mag-series.	astrobase/varbase/trends.py	def _epd_function(coeffs, fsv, fdv, fkv, xcc, ycc, bgv, bge, iha, izd): ''' This is the EPD function to fit using a smoothed mag-series. ''' return (coeffs[0]fsvfsv + coeffs[1]fsv + coeffs[2]fdvfdv + coeffs[3]fdv + coeffs[4]fkvfkv + c...	def _epd_function(coeffs, fsv, fdv, fkv, xcc, ycc, bgv, bge, iha, izd): ''' This is the EPD function to fit using a smoothed mag-series. ''' return (coeffs[0]fsvfsv + coeffs[1]fsv + coeffs[2]fdvfdv + coeffs[3]fdv + coeffs[4]fkvfkv + c...	[ "This", "is", "the", "EPD", "function", "to", "fit", "using", "a", "smoothed", "mag", "-", "series", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varbase/trends.py#L316-L343	[ "def", "_epd_function", "(", "coeffs", ",", "fsv", ",", "fdv", ",", "fkv", ",", "xcc", ",", "ycc", ",", "bgv", ",", "bge", ",", "iha", ",", "izd", ")", ":", "return", "(", "coeffs", "[", "0", "]", "", "fsv", "", "fsv", "+", "coeffs", "[", "...	2922a14619d183fb28005fa7d02027ac436f2265
valid	_epd_residual	This is the residual function to minimize using scipy.optimize.leastsq.	astrobase/varbase/trends.py	def _epd_residual(coeffs, mags, fsv, fdv, fkv, xcc, ycc, bgv, bge, iha, izd): ''' This is the residual function to minimize using scipy.optimize.leastsq. ''' f = _epd_function(coeffs, fsv, fdv, fkv, xcc, ycc, bgv, bge, iha, izd) residual = mags - f return residual	def _epd_residual(coeffs, mags, fsv, fdv, fkv, xcc, ycc, bgv, bge, iha, izd): ''' This is the residual function to minimize using scipy.optimize.leastsq. ''' f = _epd_function(coeffs, fsv, fdv, fkv, xcc, ycc, bgv, bge, iha, izd) residual = mags - f return residual	[ "This", "is", "the", "residual", "function", "to", "minimize", "using", "scipy", ".", "optimize", ".", "leastsq", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varbase/trends.py#L347-L355	[ "def", "_epd_residual", "(", "coeffs", ",", "mags", ",", "fsv", ",", "fdv", ",", "fkv", ",", "xcc", ",", "ycc", ",", "bgv", ",", "bge", ",", "iha", ",", "izd", ")", ":", "f", "=", "_epd_function", "(", "coeffs", ",", "fsv", ",", "fdv", ",", "fk...	2922a14619d183fb28005fa7d02027ac436f2265
valid	_epd_residual2	This is the residual function to minimize using scipy.optimize.least_squares. This variant is for :py:func:`.epd_magseries_extparams`.	astrobase/varbase/trends.py	def _epd_residual2(coeffs, times, mags, errs, fsv, fdv, fkv, xcc, ycc, bgv, bge, iha, izd): '''This is the residual function to minimize using scipy.optimize.least_squares. This variant is for :py:func:`.epd_magseries_extparams`. ''' f = _epd_function(coeffs,...	def _epd_residual2(coeffs, times, mags, errs, fsv, fdv, fkv, xcc, ycc, bgv, bge, iha, izd): '''This is the residual function to minimize using scipy.optimize.least_squares. This variant is for :py:func:`.epd_magseries_extparams`. ''' f = _epd_function(coeffs,...	[ "This", "is", "the", "residual", "function", "to", "minimize", "using", "scipy", ".", "optimize", ".", "least_squares", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varbase/trends.py#L359-L371	[ "def", "_epd_residual2", "(", "coeffs", ",", "times", ",", "mags", ",", "errs", ",", "fsv", ",", "fdv", ",", "fkv", ",", "xcc", ",", "ycc", ",", "bgv", ",", "bge", ",", "iha", ",", "izd", ")", ":", "f", "=", "_epd_function", "(", "coeffs", ",", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	epd_magseries	Detrends a magnitude series using External Parameter Decorrelation. Requires a set of external parameters similar to those present in HAT light curves. At the moment, the HAT light-curve-specific external parameters are: - S: the 'fsv' column in light curves, - D: the 'fdv' column in light curves, ...	astrobase/varbase/trends.py	def epd_magseries(times, mags, errs, fsv, fdv, fkv, xcc, ycc, bgv, bge, iha, izd, magsarefluxes=False, epdsmooth_sigclip=3.0, epdsmooth_windowsize=21, epdsmooth_func=smooth_magseries_savgol, epdsmooth_extraparams...	def epd_magseries(times, mags, errs, fsv, fdv, fkv, xcc, ycc, bgv, bge, iha, izd, magsarefluxes=False, epdsmooth_sigclip=3.0, epdsmooth_windowsize=21, epdsmooth_func=smooth_magseries_savgol, epdsmooth_extraparams...	[ "Detrends", "a", "magnitude", "series", "using", "External", "Parameter", "Decorrelation", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varbase/trends.py#L375-L575	[ "def", "epd_magseries", "(", "times", ",", "mags", ",", "errs", ",", "fsv", ",", "fdv", ",", "fkv", ",", "xcc", ",", "ycc", ",", "bgv", ",", "bge", ",", "iha", ",", "izd", ",", "magsarefluxes", "=", "False", ",", "epdsmooth_sigclip", "=", "3.0", ",...	2922a14619d183fb28005fa7d02027ac436f2265
valid	epd_magseries_extparams	This does EPD on a mag-series with arbitrary external parameters. Parameters ---------- times,mags,errs : np.array The input mag/flux time-series to run EPD on. externalparam_arrs : list of np.arrays This is a list of ndarrays of external parameters to decorrelate against. The...	astrobase/varbase/trends.py	def epd_magseries_extparams( times, mags, errs, externalparam_arrs, initial_coeff_guess, magsarefluxes=False, epdsmooth_sigclip=3.0, epdsmooth_windowsize=21, epdsmooth_func=smooth_magseries_savgol, epdsmooth_extraparams=None, object...	def epd_magseries_extparams( times, mags, errs, externalparam_arrs, initial_coeff_guess, magsarefluxes=False, epdsmooth_sigclip=3.0, epdsmooth_windowsize=21, epdsmooth_func=smooth_magseries_savgol, epdsmooth_extraparams=None, object...	[ "This", "does", "EPD", "on", "a", "mag", "-", "series", "with", "arbitrary", "external", "parameters", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varbase/trends.py#L582-L781	[ "def", "epd_magseries_extparams", "(", "times", ",", "mags", ",", "errs", ",", "externalparam_arrs", ",", "initial_coeff_guess", ",", "magsarefluxes", "=", "False", ",", "epdsmooth_sigclip", "=", "3.0", ",", "epdsmooth_windowsize", "=", "21", ",", "epdsmooth_func", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	rfepd_magseries	This uses a `RandomForestRegressor` to de-correlate the given magseries. Parameters ---------- times,mags,errs : np.array The input mag/flux time-series to run EPD on. externalparam_arrs : list of np.arrays This is a list of ndarrays of external parameters to decorrelate again...	astrobase/varbase/trends.py	def rfepd_magseries(times, mags, errs, externalparam_arrs, magsarefluxes=False, epdsmooth=True, epdsmooth_sigclip=3.0, epdsmooth_windowsize=21, epdsmooth_func=smooth_magseries_savgol, ...	def rfepd_magseries(times, mags, errs, externalparam_arrs, magsarefluxes=False, epdsmooth=True, epdsmooth_sigclip=3.0, epdsmooth_windowsize=21, epdsmooth_func=smooth_magseries_savgol, ...	[ "This", "uses", "a", "RandomForestRegressor", "to", "de", "-", "correlate", "the", "given", "magseries", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varbase/trends.py#L789-L952	[ "def", "rfepd_magseries", "(", "times", ",", "mags", ",", "errs", ",", "externalparam_arrs", ",", "magsarefluxes", "=", "False", ",", "epdsmooth", "=", "True", ",", "epdsmooth_sigclip", "=", "3.0", ",", "epdsmooth_windowsize", "=", "21", ",", "epdsmooth_func", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	lcfit_features	This calculates various features related to fitting models to light curves. This function: - calculates `R_ij` and `phi_ij` ratios for Fourier fit amplitudes and phases. - calculates the reduced chi-sq for fourier, EB, and planet transit fits. - calculates the reduced chi-sq for fourier, E...	astrobase/varclass/periodicfeatures.py	def lcfit_features(times, mags, errs, period, fourierorder=5, # these are depth, duration, ingress duration transitparams=(-0.01,0.1,0.1), # these are depth, duration, depth ratio, secphase ebparams=(-0.2,0.3,0.7,0.5), ...	def lcfit_features(times, mags, errs, period, fourierorder=5, # these are depth, duration, ingress duration transitparams=(-0.01,0.1,0.1), # these are depth, duration, depth ratio, secphase ebparams=(-0.2,0.3,0.7,0.5), ...	[ "This", "calculates", "various", "features", "related", "to", "fitting", "models", "to", "light", "curves", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varclass/periodicfeatures.py#L63-L484	[ "def", "lcfit_features", "(", "times", ",", "mags", ",", "errs", ",", "period", ",", "fourierorder", "=", "5", ",", "# these are depth, duration, ingress duration", "transitparams", "=", "(", "-", "0.01", ",", "0.1", ",", "0.1", ")", ",", "# these are depth, dur...	2922a14619d183fb28005fa7d02027ac436f2265
valid	periodogram_features	This calculates various periodogram features (for each periodogram). The following features are obtained: - For all best periods from all periodogram methods in `pgramlist`, calculates the number of these with peaks that are at least `sampling_peak_multiplier` x time-sampling periodogram peak at t...	astrobase/varclass/periodicfeatures.py	def periodogram_features(pgramlist, times, mags, errs, sigclip=10.0, pdiff_threshold=1.0e-4, sidereal_threshold=1.0e-4, sampling_peak_multiplier=5.0, sampling_startp=None, ...	def periodogram_features(pgramlist, times, mags, errs, sigclip=10.0, pdiff_threshold=1.0e-4, sidereal_threshold=1.0e-4, sampling_peak_multiplier=5.0, sampling_startp=None, ...	[ "This", "calculates", "various", "periodogram", "features", "(", "for", "each", "periodogram", ")", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varclass/periodicfeatures.py#L488-L816	[ "def", "periodogram_features", "(", "pgramlist", ",", "times", ",", "mags", ",", "errs", ",", "sigclip", "=", "10.0", ",", "pdiff_threshold", "=", "1.0e-4", ",", "sidereal_threshold", "=", "1.0e-4", ",", "sampling_peak_multiplier", "=", "5.0", ",", "sampling_sta...	2922a14619d183fb28005fa7d02027ac436f2265
valid	phasedlc_features	This calculates various phased LC features for the object. Some of the features calculated here come from: Kim, D.-W., Protopapas, P., Bailer-Jones, C. A. L., et al. 2014, Astronomy and Astrophysics, 566, A43, and references therein (especially Richards, et al. 2011). Parameters ---------- ...	astrobase/varclass/periodicfeatures.py	def phasedlc_features(times, mags, errs, period, nbrtimes=None, nbrmags=None, nbrerrs=None): '''This calculates various phased LC features for the object. Some of the features cal...	def phasedlc_features(times, mags, errs, period, nbrtimes=None, nbrmags=None, nbrerrs=None): '''This calculates various phased LC features for the object. Some of the features cal...	[ "This", "calculates", "various", "phased", "LC", "features", "for", "the", "object", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varclass/periodicfeatures.py#L820-L1085	[ "def", "phasedlc_features", "(", "times", ",", "mags", ",", "errs", ",", "period", ",", "nbrtimes", "=", "None", ",", "nbrmags", "=", "None", ",", "nbrerrs", "=", "None", ")", ":", "# get the finite values", "finind", "=", "np", ".", "isfinite", "(", "ti...	2922a14619d183fb28005fa7d02027ac436f2265
valid	stellingwerf_pdm_theta	This calculates the Stellingwerf PDM theta value at a test frequency. Parameters ---------- times,mags,errs : np.array The input time-series and associated errors. frequency : float The test frequency to calculate the theta statistic at. binsize : float The phase bin size...	astrobase/periodbase/spdm.py	def stellingwerf_pdm_theta(times, mags, errs, frequency, binsize=0.05, minbin=9): ''' This calculates the Stellingwerf PDM theta value at a test frequency. Parameters ---------- times,mags,errs : np.array The input time-series and associated errors. frequenc...	def stellingwerf_pdm_theta(times, mags, errs, frequency, binsize=0.05, minbin=9): ''' This calculates the Stellingwerf PDM theta value at a test frequency. Parameters ---------- times,mags,errs : np.array The input time-series and associated errors. frequenc...	[ "This", "calculates", "the", "Stellingwerf", "PDM", "theta", "value", "at", "a", "test", "frequency", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/periodbase/spdm.py#L71-L141	[ "def", "stellingwerf_pdm_theta", "(", "times", ",", "mags", ",", "errs", ",", "frequency", ",", "binsize", "=", "0.05", ",", "minbin", "=", "9", ")", ":", "period", "=", "1.0", "/", "frequency", "fold_time", "=", "times", "[", "0", "]", "phased", "=", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	_stellingwerf_pdm_worker	This is a parallel worker for the function below. Parameters ---------- task : tuple This is of the form below:: task[0] = times task[1] = mags task[2] = errs task[3] = frequency task[4] = binsize task[5] = minbin Return...	astrobase/periodbase/spdm.py	def _stellingwerf_pdm_worker(task): ''' This is a parallel worker for the function below. Parameters ---------- task : tuple This is of the form below:: task[0] = times task[1] = mags task[2] = errs task[3] = frequency task[4] = ...	def _stellingwerf_pdm_worker(task): ''' This is a parallel worker for the function below. Parameters ---------- task : tuple This is of the form below:: task[0] = times task[1] = mags task[2] = errs task[3] = frequency task[4] = ...	[ "This", "is", "a", "parallel", "worker", "for", "the", "function", "below", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/periodbase/spdm.py#L145-L182	[ "def", "_stellingwerf_pdm_worker", "(", "task", ")", ":", "times", ",", "mags", ",", "errs", ",", "frequency", ",", "binsize", ",", "minbin", "=", "task", "try", ":", "theta", "=", "stellingwerf_pdm_theta", "(", "times", ",", "mags", ",", "errs", ",", "f...	2922a14619d183fb28005fa7d02027ac436f2265
valid	stellingwerf_pdm	This runs a parallelized Stellingwerf phase-dispersion minimization (PDM) period search. 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...	astrobase/periodbase/spdm.py	def stellingwerf_pdm(times, mags, errs, magsarefluxes=False, startp=None, endp=None, stepsize=1.0e-4, autofreq=True, normalize=False, ...	def stellingwerf_pdm(times, mags, errs, magsarefluxes=False, startp=None, endp=None, stepsize=1.0e-4, autofreq=True, normalize=False, ...	[ "This", "runs", "a", "parallelized", "Stellingwerf", "phase", "-", "dispersion", "minimization", "(", "PDM", ")", "period", "search", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/periodbase/spdm.py#L186-L487	[ "def", "stellingwerf_pdm", "(", "times", ",", "mags", ",", "errs", ",", "magsarefluxes", "=", "False", ",", "startp", "=", "None", ",", "endp", "=", "None", ",", "stepsize", "=", "1.0e-4", ",", "autofreq", "=", "True", ",", "normalize", "=", "False", "...	2922a14619d183fb28005fa7d02027ac436f2265
valid	analytic_false_alarm_probability	This returns the analytic false alarm probabilities for periodogram peak values. FIXME: this doesn't actually work. Fix later. The calculation follows that on page 3 of Zechmeister & Kurster (2009):: FAP = 1 − [1 − Prob(z > z0)]**M where:: M is the number of independent frequencies ...	astrobase/periodbase/spdm.py	def analytic_false_alarm_probability(lspinfo, times, conservative_nfreq_eff=True, peakvals=None, inplace=True): '''This returns the analytic false alarm probabilities f...	def analytic_false_alarm_probability(lspinfo, times, conservative_nfreq_eff=True, peakvals=None, inplace=True): '''This returns the analytic false alarm probabilities f...	[ "This", "returns", "the", "analytic", "false", "alarm", "probabilities", "for", "periodogram", "peak", "values", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/periodbase/spdm.py#L491-L605	[ "def", "analytic_false_alarm_probability", "(", "lspinfo", ",", "times", ",", "conservative_nfreq_eff", "=", "True", ",", "peakvals", "=", "None", ",", "inplace", "=", "True", ")", ":", "from", "scipy", ".", "stats", "import", "beta", "frequencies", "=", "1.0"...	2922a14619d183fb28005fa7d02027ac436f2265
valid	keplermag_to_sdssr	Converts magnitude measurements in Kepler band to SDSS r band. Parameters ---------- keplermag : float or array-like The Kepler magnitude value(s) to convert to fluxes. kic_sdssg,kic_sdssr : float or array-like The SDSS g and r magnitudes of the object(s) from the Kepler Input ...	astrobase/astrokep.py	def keplermag_to_sdssr(keplermag, kic_sdssg, kic_sdssr): '''Converts magnitude measurements in Kepler band to SDSS r band. Parameters ---------- keplermag : float or array-like The Kepler magnitude value(s) to convert to fluxes. kic_sdssg,kic_sdssr : float or array-like The SDSS g...	def keplermag_to_sdssr(keplermag, kic_sdssg, kic_sdssr): '''Converts magnitude measurements in Kepler band to SDSS r band. Parameters ---------- keplermag : float or array-like The Kepler magnitude value(s) to convert to fluxes. kic_sdssg,kic_sdssr : float or array-like The SDSS g...	[ "Converts", "magnitude", "measurements", "in", "Kepler", "band", "to", "SDSS", "r", "band", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L138-L165	[ "def", "keplermag_to_sdssr", "(", "keplermag", ",", "kic_sdssg", ",", "kic_sdssr", ")", ":", "kic_sdssgr", "=", "kic_sdssg", "-", "kic_sdssr", "if", "kic_sdssgr", "<", "0.8", ":", "kepsdssr", "=", "(", "keplermag", "-", "0.2", "*", "kic_sdssg", ")", "/", "...	2922a14619d183fb28005fa7d02027ac436f2265
valid	read_kepler_fitslc	This extracts the light curve from a single Kepler or K2 LC FITS file. This works on the light curves available at MAST: - `kplr{kepid}-{somedatething}_llc.fits` files from the Kepler mission - `ktwo{epicid}-c{campaign}_llc.fits` files from the K2 mission Parameters ---------- lcfits : str ...	astrobase/astrokep.py	def read_kepler_fitslc( lcfits, headerkeys=LCHEADERKEYS, datakeys=LCDATAKEYS, sapkeys=LCSAPKEYS, pdckeys=LCPDCKEYS, topkeys=LCTOPKEYS, apkeys=LCAPERTUREKEYS, appendto=None, normalize=False, ): '''This extracts the light curve from a single Kepl...	def read_kepler_fitslc( lcfits, headerkeys=LCHEADERKEYS, datakeys=LCDATAKEYS, sapkeys=LCSAPKEYS, pdckeys=LCPDCKEYS, topkeys=LCTOPKEYS, apkeys=LCAPERTUREKEYS, appendto=None, normalize=False, ): '''This extracts the light curve from a single Kepl...	[ "This", "extracts", "the", "light", "curve", "from", "a", "single", "Kepler", "or", "K2", "LC", "FITS", "file", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L244-L611	[ "def", "read_kepler_fitslc", "(", "lcfits", ",", "headerkeys", "=", "LCHEADERKEYS", ",", "datakeys", "=", "LCDATAKEYS", ",", "sapkeys", "=", "LCSAPKEYS", ",", "pdckeys", "=", "LCPDCKEYS", ",", "topkeys", "=", "LCTOPKEYS", ",", "apkeys", "=", "LCAPERTUREKEYS", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	consolidate_kepler_fitslc	This gets all Kepler/K2 light curves for the given `keplerid` in `lcfitsdir`. Searches recursively in `lcfitsdir` for all of the files belonging to the specified `keplerid`. Sorts the light curves by time. Returns an `lcdict`. This is meant to be used to consolidate light curves for a single object...	astrobase/astrokep.py	def consolidate_kepler_fitslc(keplerid, lcfitsdir, normalize=True, headerkeys=LCHEADERKEYS, datakeys=LCDATAKEYS, sapkeys=LCSAPKEYS, pdckeys=...	def consolidate_kepler_fitslc(keplerid, lcfitsdir, normalize=True, headerkeys=LCHEADERKEYS, datakeys=LCDATAKEYS, sapkeys=LCSAPKEYS, pdckeys=...	[ "This", "gets", "all", "Kepler", "/", "K2", "light", "curves", "for", "the", "given", "keplerid", "in", "lcfitsdir", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L615-L802	[ "def", "consolidate_kepler_fitslc", "(", "keplerid", ",", "lcfitsdir", ",", "normalize", "=", "True", ",", "headerkeys", "=", "LCHEADERKEYS", ",", "datakeys", "=", "LCDATAKEYS", ",", "sapkeys", "=", "LCSAPKEYS", ",", "pdckeys", "=", "LCPDCKEYS", ",", "topkeys", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	read_k2sff_lightcurve	This reads a K2 SFF (Vandenberg+ 2014) light curve into an `lcdict`. Use this with the light curves from the K2 SFF project at MAST. Parameters ---------- lcfits : str The filename of the FITS light curve file downloaded from MAST. Returns ------- lcdict Returns an `lcdi...	astrobase/astrokep.py	def read_k2sff_lightcurve(lcfits): '''This reads a K2 SFF (Vandenberg+ 2014) light curve into an `lcdict`. Use this with the light curves from the K2 SFF project at MAST. Parameters ---------- lcfits : str The filename of the FITS light curve file downloaded from MAST. Returns --...	def read_k2sff_lightcurve(lcfits): '''This reads a K2 SFF (Vandenberg+ 2014) light curve into an `lcdict`. Use this with the light curves from the K2 SFF project at MAST. Parameters ---------- lcfits : str The filename of the FITS light curve file downloaded from MAST. Returns --...	[ "This", "reads", "a", "K2", "SFF", "(", "Vandenberg", "+", "2014", ")", "light", "curve", "into", "an", "lcdict", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L816-L945	[ "def", "read_k2sff_lightcurve", "(", "lcfits", ")", ":", "# read the fits file", "hdulist", "=", "pyfits", ".", "open", "(", "lcfits", ")", "lchdr", ",", "lcdata", "=", "hdulist", "[", "1", "]", ".", "header", ",", "hdulist", "[", "1", "]", ".", "data", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	kepler_lcdict_to_pkl	This writes the `lcdict` to a Python pickle. Parameters ---------- lcdict : lcdict This is the input `lcdict` to write to a pickle. outfile : str or None If this is None, the object's Kepler ID/EPIC ID will determined from the `lcdict` and used to form the filename of the outp...	astrobase/astrokep.py	def kepler_lcdict_to_pkl(lcdict, outfile=None): '''This writes the `lcdict` to a Python pickle. Parameters ---------- lcdict : lcdict This is the input `lcdict` to write to a pickle. outfile : str or None If this is None, the object's Kepler ID/EPIC ID will determined from the ...	def kepler_lcdict_to_pkl(lcdict, outfile=None): '''This writes the `lcdict` to a Python pickle. Parameters ---------- lcdict : lcdict This is the input `lcdict` to write to a pickle. outfile : str or None If this is None, the object's Kepler ID/EPIC ID will determined from the ...	[ "This", "writes", "the", "lcdict", "to", "a", "Python", "pickle", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L953-L983	[ "def", "kepler_lcdict_to_pkl", "(", "lcdict", ",", "outfile", "=", "None", ")", ":", "if", "not", "outfile", ":", "outfile", "=", "'%s-keplc.pkl'", "%", "lcdict", "[", "'objectid'", "]", ".", "replace", "(", "' '", ",", "'-'", ")", "# we're using pickle.HIGH...	2922a14619d183fb28005fa7d02027ac436f2265
valid	read_kepler_pklc	This turns the pickled lightcurve file back into an `lcdict`. Parameters ---------- picklefile : str The path to a previously written Kepler LC picklefile generated by `kepler_lcdict_to_pkl` above. Returns ------- lcdict Returns an `lcdict` (this is useable by most as...	astrobase/astrokep.py	def read_kepler_pklc(picklefile): '''This turns the pickled lightcurve file back into an `lcdict`. Parameters ---------- picklefile : str The path to a previously written Kepler LC picklefile generated by `kepler_lcdict_to_pkl` above. Returns ------- lcdict Return...	def read_kepler_pklc(picklefile): '''This turns the pickled lightcurve file back into an `lcdict`. Parameters ---------- picklefile : str The path to a previously written Kepler LC picklefile generated by `kepler_lcdict_to_pkl` above. Returns ------- lcdict Return...	[ "This", "turns", "the", "pickled", "lightcurve", "file", "back", "into", "an", "lcdict", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L987-L1025	[ "def", "read_kepler_pklc", "(", "picklefile", ")", ":", "if", "picklefile", ".", "endswith", "(", "'.gz'", ")", ":", "infd", "=", "gzip", ".", "open", "(", "picklefile", ",", "'rb'", ")", "else", ":", "infd", "=", "open", "(", "picklefile", ",", "'rb'"...	2922a14619d183fb28005fa7d02027ac436f2265
valid	filter_kepler_lcdict	This filters the Kepler `lcdict`, removing nans and bad observations. By default, this function removes points in the Kepler LC that have ANY quality flags set. Parameters ---------- lcdict : lcdict An `lcdict` produced by `consolidate_kepler_fitslc` or `read_kepler_fitslc`. ...	astrobase/astrokep.py	def filter_kepler_lcdict(lcdict, filterflags=True, nanfilter='sap,pdc', timestoignore=None): '''This filters the Kepler `lcdict`, removing nans and bad observations. By default, this function removes points in the Kepler LC that hav...	def filter_kepler_lcdict(lcdict, filterflags=True, nanfilter='sap,pdc', timestoignore=None): '''This filters the Kepler `lcdict`, removing nans and bad observations. By default, this function removes points in the Kepler LC that hav...	[ "This", "filters", "the", "Kepler", "lcdict", "removing", "nans", "and", "bad", "observations", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L1058-L1182	[ "def", "filter_kepler_lcdict", "(", "lcdict", ",", "filterflags", "=", "True", ",", "nanfilter", "=", "'sap,pdc'", ",", "timestoignore", "=", "None", ")", ":", "cols", "=", "lcdict", "[", "'columns'", "]", "# filter all bad LC points as noted by quality flags", "if"...	2922a14619d183fb28005fa7d02027ac436f2265
valid	_epd_function	This is the EPD function to fit. Parameters ---------- coeffs : array-like of floats Contains the EPD coefficients that will be used to generate the EPD fit function. fluxes : array-like The flux measurement array being used. xcc,ycc : array-like Arrays of the x a...	astrobase/astrokep.py	def _epd_function(coeffs, fluxes, xcc, ycc, bgv, bge): '''This is the EPD function to fit. Parameters ---------- coeffs : array-like of floats Contains the EPD coefficients that will be used to generate the EPD fit function. fluxes : array-like The flux measurement array b...	def _epd_function(coeffs, fluxes, xcc, ycc, bgv, bge): '''This is the EPD function to fit. Parameters ---------- coeffs : array-like of floats Contains the EPD coefficients that will be used to generate the EPD fit function. fluxes : array-like The flux measurement array b...	[ "This", "is", "the", "EPD", "function", "to", "fit", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L1190-L1229	[ "def", "_epd_function", "(", "coeffs", ",", "fluxes", ",", "xcc", ",", "ycc", ",", "bgv", ",", "bge", ")", ":", "epdf", "=", "(", "coeffs", "[", "0", "]", "+", "coeffs", "[", "1", "]", "", "npsin", "(", "2", "", "MPI", "*", "xcc", ")", "+",...	2922a14619d183fb28005fa7d02027ac436f2265
valid	_epd_residual	This is the residual function to minimize using scipy.optimize.leastsq. Parameters ---------- coeffs : array-like of floats Contains the EPD coefficients that will be used to generate the EPD fit function. fluxes : array-like The flux measurement array being used. xcc,ycc...	astrobase/astrokep.py	def _epd_residual(coeffs, fluxes, xcc, ycc, bgv, bge): '''This is the residual function to minimize using scipy.optimize.leastsq. Parameters ---------- coeffs : array-like of floats Contains the EPD coefficients that will be used to generate the EPD fit function. fluxes : array-li...	def _epd_residual(coeffs, fluxes, xcc, ycc, bgv, bge): '''This is the residual function to minimize using scipy.optimize.leastsq. Parameters ---------- coeffs : array-like of floats Contains the EPD coefficients that will be used to generate the EPD fit function. fluxes : array-li...	[ "This", "is", "the", "residual", "function", "to", "minimize", "using", "scipy", ".", "optimize", ".", "leastsq", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L1233-L1265	[ "def", "_epd_residual", "(", "coeffs", ",", "fluxes", ",", "xcc", ",", "ycc", ",", "bgv", ",", "bge", ")", ":", "f", "=", "_epd_function", "(", "coeffs", ",", "fluxes", ",", "xcc", ",", "ycc", ",", "bgv", ",", "bge", ")", "residual", "=", "fluxes",...	2922a14619d183fb28005fa7d02027ac436f2265
valid	epd_kepler_lightcurve	This runs EPD on the Kepler light curve. Following Huang et al. 2015, we fit the following EPD function to a smoothed light curve, and then subtract it to obtain EPD corrected magnitudes:: f = c0 + c1sin(2pix) + c2cos(2pix) + c3sin(2piy) + c4cos(2piy) + c5sin(4pi*...	astrobase/astrokep.py	def epd_kepler_lightcurve(lcdict, xccol='mom_centr1', yccol='mom_centr2', timestoignore=None, filterflags=True, writetodict=True, epdsmooth=5): '''This runs EPD...	def epd_kepler_lightcurve(lcdict, xccol='mom_centr1', yccol='mom_centr2', timestoignore=None, filterflags=True, writetodict=True, epdsmooth=5): '''This runs EPD...	[ "This", "runs", "EPD", "on", "the", "Kepler", "light", "curve", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L1269-L1472	[ "def", "epd_kepler_lightcurve", "(", "lcdict", ",", "xccol", "=", "'mom_centr1'", ",", "yccol", "=", "'mom_centr2'", ",", "timestoignore", "=", "None", ",", "filterflags", "=", "True", ",", "writetodict", "=", "True", ",", "epdsmooth", "=", "5", ")", ":", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	rfepd_kepler_lightcurve	This uses a `RandomForestRegressor` to fit and decorrelate Kepler light curves. Fits the X and Y positions, the background, and background error. By default, this function removes points in the Kepler LC that have ANY quality flags set. Parameters ---------- lcdict : lcdict An `l...	astrobase/astrokep.py	def rfepd_kepler_lightcurve( lcdict, xccol='mom_centr1', yccol='mom_centr2', timestoignore=None, filterflags=True, writetodict=True, epdsmooth=23, decorr='xcc,ycc', nrftrees=200 ): '''This uses a `RandomForestRegressor` to fit and decorrelate K...	def rfepd_kepler_lightcurve( lcdict, xccol='mom_centr1', yccol='mom_centr2', timestoignore=None, filterflags=True, writetodict=True, epdsmooth=23, decorr='xcc,ycc', nrftrees=200 ): '''This uses a `RandomForestRegressor` to fit and decorrelate K...	[ "This", "uses", "a", "RandomForestRegressor", "to", "fit", "and", "decorrelate", "Kepler", "light", "curves", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L1476-L1691	[ "def", "rfepd_kepler_lightcurve", "(", "lcdict", ",", "xccol", "=", "'mom_centr1'", ",", "yccol", "=", "'mom_centr2'", ",", "timestoignore", "=", "None", ",", "filterflags", "=", "True", ",", "writetodict", "=", "True", ",", "epdsmooth", "=", "23", ",", "dec...	2922a14619d183fb28005fa7d02027ac436f2265
valid	detrend_centroid	Detrends the x and y coordinate centroids for a Kepler light curve. Given an `lcdict` for a single quarter of Kepler data, returned by `read_kepler_fitslc`, this function returns this same dictionary, appending detrended centroid_x and centroid_y values. Here "detrended" means "finite, SAP quality fla...	astrobase/astrokep.py	def detrend_centroid(lcd, detrend='legendre', sigclip=None, mingap=0.5): '''Detrends the x and y coordinate centroids for a Kepler light curve. Given an `lcdict` for a single quarter of Kepler data, returned by `read_kepler_fitslc`, this function returns this same dictionary, appending detrended centro...	def detrend_centroid(lcd, detrend='legendre', sigclip=None, mingap=0.5): '''Detrends the x and y coordinate centroids for a Kepler light curve. Given an `lcdict` for a single quarter of Kepler data, returned by `read_kepler_fitslc`, this function returns this same dictionary, appending detrended centro...	[ "Detrends", "the", "x", "and", "y", "coordinate", "centroids", "for", "a", "Kepler", "light", "curve", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L1699-L1935	[ "def", "detrend_centroid", "(", "lcd", ",", "detrend", "=", "'legendre'", ",", "sigclip", "=", "None", ",", "mingap", "=", "0.5", ")", ":", "qnum", "=", "npunique", "(", "lcd", "[", "'quarter'", "]", ")", "try", ":", "assert", "qnum", ".", "size", "=...	2922a14619d183fb28005fa7d02027ac436f2265
valid	get_centroid_offsets	After running `detrend_centroid`, this gets positions of centroids during transits, and outside of transits. These positions can then be used in a false positive analysis. This routine requires knowing the ingress and egress times for every transit of interest within the quarter this routine is being ...	astrobase/astrokep.py	def get_centroid_offsets(lcd, t_ing_egr, oot_buffer_time=0.1, sample_factor=3): '''After running `detrend_centroid`, this gets positions of centroids during transits, and outside of transits. These positions can then be used in a false positive analysis. This routine requires knowing the ingress and e...	def get_centroid_offsets(lcd, t_ing_egr, oot_buffer_time=0.1, sample_factor=3): '''After running `detrend_centroid`, this gets positions of centroids during transits, and outside of transits. These positions can then be used in a false positive analysis. This routine requires knowing the ingress and e...	[ "After", "running", "detrend_centroid", "this", "gets", "positions", "of", "centroids", "during", "transits", "and", "outside", "of", "transits", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L1939-L2055	[ "def", "get_centroid_offsets", "(", "lcd", ",", "t_ing_egr", ",", "oot_buffer_time", "=", "0.1", ",", "sample_factor", "=", "3", ")", ":", "# NOTE:", "# Bryson+ (2013) gives a more complicated and more correct approach to this", "# problem, computing offsets relative to positions...	2922a14619d183fb28005fa7d02027ac436f2265
valid	_get_legendre_deg_ctd	This is a helper function for centroid detrending.	astrobase/astrokep.py	def _get_legendre_deg_ctd(npts): '''This is a helper function for centroid detrending. ''' from scipy.interpolate import interp1d degs = nparray([4,5,6,10,15]) pts = nparray([1e2,3e2,5e2,1e3,3e3]) fn = interp1d(pts, degs, kind='linear', bounds_error=False, ...	def _get_legendre_deg_ctd(npts): '''This is a helper function for centroid detrending. ''' from scipy.interpolate import interp1d degs = nparray([4,5,6,10,15]) pts = nparray([1e2,3e2,5e2,1e3,3e3]) fn = interp1d(pts, degs, kind='linear', bounds_error=False, ...	[ "This", "is", "a", "helper", "function", "for", "centroid", "detrending", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L2063-L2077	[ "def", "_get_legendre_deg_ctd", "(", "npts", ")", ":", "from", "scipy", ".", "interpolate", "import", "interp1d", "degs", "=", "nparray", "(", "[", "4", ",", "5", ",", "6", ",", "10", ",", "15", "]", ")", "pts", "=", "nparray", "(", "[", "1e2", ","...	2922a14619d183fb28005fa7d02027ac436f2265
valid	_legendre_dtr	This calculates the residual and chi-sq values for a Legendre function fit. Parameters ---------- x : np.array Array of the independent variable. y : np.array Array of the dependent variable. y_err : np.array Array of errors associated with each `y` value. Used to cal...	astrobase/astrokep.py	def _legendre_dtr(x, y, y_err, legendredeg=10): '''This calculates the residual and chi-sq values for a Legendre function fit. Parameters ---------- x : np.array Array of the independent variable. y : np.array Array of the dependent variable. y_err : np.array Arra...	def _legendre_dtr(x, y, y_err, legendredeg=10): '''This calculates the residual and chi-sq values for a Legendre function fit. Parameters ---------- x : np.array Array of the independent variable. y : np.array Array of the dependent variable. y_err : np.array Arra...	[ "This", "calculates", "the", "residual", "and", "chi", "-", "sq", "values", "for", "a", "Legendre", "function", "fit", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L2085-L2130	[ "def", "_legendre_dtr", "(", "x", ",", "y", ",", "y_err", ",", "legendredeg", "=", "10", ")", ":", "try", ":", "p", "=", "Legendre", ".", "fit", "(", "x", ",", "y", ",", "legendredeg", ")", "fit_y", "=", "p", "(", "x", ")", "except", "Exception",...	2922a14619d183fb28005fa7d02027ac436f2265
valid	timebinlc	This bins the given light curve file in time using the specified bin size. Parameters ---------- lcfile : str The file name to process. binsizesec : float The time bin-size in seconds. outdir : str or None If this is a str, the output LC will be written to `outdir`. If th...	astrobase/lcproc/lcbin.py	def timebinlc(lcfile, binsizesec, outdir=None, lcformat='hat-sql', lcformatdir=None, timecols=None, magcols=None, errcols=None, minbinelems=7): '''This bins the given light curve file in time using the s...	def timebinlc(lcfile, binsizesec, outdir=None, lcformat='hat-sql', lcformatdir=None, timecols=None, magcols=None, errcols=None, minbinelems=7): '''This bins the given light curve file in time using the s...	[ "This", "bins", "the", "given", "light", "curve", "file", "in", "time", "using", "the", "specified", "bin", "size", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/lcbin.py#L87-L249	[ "def", "timebinlc", "(", "lcfile", ",", "binsizesec", ",", "outdir", "=", "None", ",", "lcformat", "=", "'hat-sql'", ",", "lcformatdir", "=", "None", ",", "timecols", "=", "None", ",", "magcols", "=", "None", ",", "errcols", "=", "None", ",", "minbinelem...	2922a14619d183fb28005fa7d02027ac436f2265
valid	timebinlc_worker	This is a parallel worker for the function below. Parameters ---------- task : tuple This is of the form:: task[0] = lcfile task[1] = binsizesec task[3] = {'outdir','lcformat','lcformatdir', 'timecols','magcols','errcols','minbinelems'} ...	astrobase/lcproc/lcbin.py	def timebinlc_worker(task): ''' This is a parallel worker for the function below. Parameters ---------- task : tuple This is of the form:: task[0] = lcfile task[1] = binsizesec task[3] = {'outdir','lcformat','lcformatdir', 'timeco...	def timebinlc_worker(task): ''' This is a parallel worker for the function below. Parameters ---------- task : tuple This is of the form:: task[0] = lcfile task[1] = binsizesec task[3] = {'outdir','lcformat','lcformatdir', 'timeco...	[ "This", "is", "a", "parallel", "worker", "for", "the", "function", "below", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/lcbin.py#L253-L286	[ "def", "timebinlc_worker", "(", "task", ")", ":", "lcfile", ",", "binsizesec", ",", "kwargs", "=", "task", "try", ":", "binnedlc", "=", "timebinlc", "(", "lcfile", ",", "binsizesec", ",", "", "", "kwargs", ")", "LOGINFO", "(", "'%s binned using %s sec -> %...	2922a14619d183fb28005fa7d02027ac436f2265
valid	parallel_timebin	This time-bins all the LCs in the list using the specified bin size. Parameters ---------- lclist : list of str The input LCs to process. binsizesec : float The time bin size to use in seconds. maxobjects : int or None If provided, LC processing will stop at `lclist[maxob...	astrobase/lcproc/lcbin.py	def parallel_timebin(lclist, binsizesec, maxobjects=None, outdir=None, lcformat='hat-sql', lcformatdir=None, timecols=None, magcols=None, errcols=None, ...	def parallel_timebin(lclist, binsizesec, maxobjects=None, outdir=None, lcformat='hat-sql', lcformatdir=None, timecols=None, magcols=None, errcols=None, ...	[ "This", "time", "-", "bins", "all", "the", "LCs", "in", "the", "list", "using", "the", "specified", "bin", "size", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/lcbin.py#L290-L379	[ "def", "parallel_timebin", "(", "lclist", ",", "binsizesec", ",", "maxobjects", "=", "None", ",", "outdir", "=", "None", ",", "lcformat", "=", "'hat-sql'", ",", "lcformatdir", "=", "None", ",", "timecols", "=", "None", ",", "magcols", "=", "None", ",", "...	2922a14619d183fb28005fa7d02027ac436f2265
valid	parallel_timebin_lcdir	This time bins all the light curves in the specified directory. Parameters ---------- lcdir : list of str Directory containing the input LCs to process. binsizesec : float The time bin size to use in seconds. maxobjects : int or None If provided, LC processing will stop a...	astrobase/lcproc/lcbin.py	def parallel_timebin_lcdir(lcdir, binsizesec, maxobjects=None, outdir=None, lcformat='hat-sql', lcformatdir=None, timecols=None, ma...	def parallel_timebin_lcdir(lcdir, binsizesec, maxobjects=None, outdir=None, lcformat='hat-sql', lcformatdir=None, timecols=None, ma...	[ "This", "time", "bins", "all", "the", "light", "curves", "in", "the", "specified", "directory", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/lcbin.py#L383-L477	[ "def", "parallel_timebin_lcdir", "(", "lcdir", ",", "binsizesec", ",", "maxobjects", "=", "None", ",", "outdir", "=", "None", ",", "lcformat", "=", "'hat-sql'", ",", "lcformatdir", "=", "None", ",", "timecols", "=", "None", ",", "magcols", "=", "None", ","...	2922a14619d183fb28005fa7d02027ac436f2265
valid	get_varfeatures	This runs :py:func:`astrobase.varclass.varfeatures.all_nonperiodic_features` on a single LC file. Parameters ---------- lcfile : str The input light curve to process. outfile : str The filename of the output variable features pickle that will be generated. timecols : ...	astrobase/lcproc/lcvfeatures.py	def get_varfeatures(lcfile, outdir, timecols=None, magcols=None, errcols=None, mindet=1000, lcformat='hat-sql', lcformatdir=None): '''This runs :py:func:`astrobase.varclass.var...	def get_varfeatures(lcfile, outdir, timecols=None, magcols=None, errcols=None, mindet=1000, lcformat='hat-sql', lcformatdir=None): '''This runs :py:func:`astrobase.varclass.var...	[ "This", "runs", ":", "py", ":", "func", ":", "astrobase", ".", "varclass", ".", "varfeatures", ".", "all_nonperiodic_features", "on", "a", "single", "LC", "file", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/lcvfeatures.py#L96-L279	[ "def", "get_varfeatures", "(", "lcfile", ",", "outdir", ",", "timecols", "=", "None", ",", "magcols", "=", "None", ",", "errcols", "=", "None", ",", "mindet", "=", "1000", ",", "lcformat", "=", "'hat-sql'", ",", "lcformatdir", "=", "None", ")", ":", "t...	2922a14619d183fb28005fa7d02027ac436f2265
valid	_varfeatures_worker	This wraps varfeatures.	astrobase/lcproc/lcvfeatures.py	def _varfeatures_worker(task): ''' This wraps varfeatures. ''' try: (lcfile, outdir, timecols, magcols, errcols, mindet, lcformat, lcformatdir) = task return get_varfeatures(lcfile, outdir, timecols=timecols, magcol...	def _varfeatures_worker(task): ''' This wraps varfeatures. ''' try: (lcfile, outdir, timecols, magcols, errcols, mindet, lcformat, lcformatdir) = task return get_varfeatures(lcfile, outdir, timecols=timecols, magcol...	[ "This", "wraps", "varfeatures", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/lcvfeatures.py#L283-L301	[ "def", "_varfeatures_worker", "(", "task", ")", ":", "try", ":", "(", "lcfile", ",", "outdir", ",", "timecols", ",", "magcols", ",", "errcols", ",", "mindet", ",", "lcformat", ",", "lcformatdir", ")", "=", "task", "return", "get_varfeatures", "(", "lcfile"...	2922a14619d183fb28005fa7d02027ac436f2265
valid	serial_varfeatures	This runs variability feature extraction for a list of LCs. Parameters ---------- lclist : list of str The list of light curve file names to process. outdir : str The directory where the output varfeatures pickle files will be written. maxobjects : int The number of LCs t...	astrobase/lcproc/lcvfeatures.py	def serial_varfeatures(lclist, outdir, maxobjects=None, timecols=None, magcols=None, errcols=None, mindet=1000, lcformat='hat-sql', lcfo...	def serial_varfeatures(lclist, outdir, maxobjects=None, timecols=None, magcols=None, errcols=None, mindet=1000, lcformat='hat-sql', lcfo...	[ "This", "runs", "variability", "feature", "extraction", "for", "a", "list", "of", "LCs", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/lcvfeatures.py#L304-L372	[ "def", "serial_varfeatures", "(", "lclist", ",", "outdir", ",", "maxobjects", "=", "None", ",", "timecols", "=", "None", ",", "magcols", "=", "None", ",", "errcols", "=", "None", ",", "mindet", "=", "1000", ",", "lcformat", "=", "'hat-sql'", ",", "lcform...	2922a14619d183fb28005fa7d02027ac436f2265
valid	parallel_varfeatures	This runs variable feature extraction in parallel for all LCs in `lclist`. Parameters ---------- lclist : list of str The list of light curve file names to process. outdir : str The directory where the output varfeatures pickle files will be written. maxobjects : int The ...	astrobase/lcproc/lcvfeatures.py	def parallel_varfeatures(lclist, outdir, maxobjects=None, timecols=None, magcols=None, errcols=None, mindet=1000, lcformat='hat-sql', ...	def parallel_varfeatures(lclist, outdir, maxobjects=None, timecols=None, magcols=None, errcols=None, mindet=1000, lcformat='hat-sql', ...	[ "This", "runs", "variable", "feature", "extraction", "in", "parallel", "for", "all", "LCs", "in", "lclist", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/lcvfeatures.py#L376-L454	[ "def", "parallel_varfeatures", "(", "lclist", ",", "outdir", ",", "maxobjects", "=", "None", ",", "timecols", "=", "None", ",", "magcols", "=", "None", ",", "errcols", "=", "None", ",", "mindet", "=", "1000", ",", "lcformat", "=", "'hat-sql'", ",", "lcfo...	2922a14619d183fb28005fa7d02027ac436f2265
valid	parallel_varfeatures_lcdir	This runs parallel variable feature extraction for a directory of LCs. Parameters ---------- lcdir : str The directory of light curve files to process. outdir : str The directory where the output varfeatures pickle files will be written. fileglob : str or None The file gl...	astrobase/lcproc/lcvfeatures.py	def parallel_varfeatures_lcdir(lcdir, outdir, fileglob=None, maxobjects=None, timecols=None, magcols=None, errcols=None, ...	def parallel_varfeatures_lcdir(lcdir, outdir, fileglob=None, maxobjects=None, timecols=None, magcols=None, errcols=None, ...	[ "This", "runs", "parallel", "variable", "feature", "extraction", "for", "a", "directory", "of", "LCs", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/lcvfeatures.py#L458-L598	[ "def", "parallel_varfeatures_lcdir", "(", "lcdir", ",", "outdir", ",", "fileglob", "=", "None", ",", "maxobjects", "=", "None", ",", "timecols", "=", "None", ",", "magcols", "=", "None", ",", "errcols", "=", "None", ",", "recursive", "=", "True", ",", "m...	2922a14619d183fb28005fa7d02027ac436f2265
valid	checkplot_pickle_to_png	This reads the checkplot pickle or dict provided, and writes out a PNG. The output PNG contains most of the information in the input checkplot pickle/dict, and can be used to quickly glance through the highlights instead of having to review the checkplot with the `checkplotserver` webapp. This is usefu...	astrobase/checkplot/pkl_png.py	def checkplot_pickle_to_png( checkplotin, outfile, extrarows=None ): '''This reads the checkplot pickle or dict provided, and writes out a PNG. The output PNG contains most of the information in the input checkplot pickle/dict, and can be used to quickly glance through the highlight...	def checkplot_pickle_to_png( checkplotin, outfile, extrarows=None ): '''This reads the checkplot pickle or dict provided, and writes out a PNG. The output PNG contains most of the information in the input checkplot pickle/dict, and can be used to quickly glance through the highlight...	[ "This", "reads", "the", "checkplot", "pickle", "or", "dict", "provided", "and", "writes", "out", "a", "PNG", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/checkplot/pkl_png.py#L75-L1129	[ "def", "checkplot_pickle_to_png", "(", "checkplotin", ",", "outfile", ",", "extrarows", "=", "None", ")", ":", "# figure out if the checkplotpickle is a filename", "# python 3", "if", "sys", ".", "version_info", "[", ":", "2", "]", ">", "(", "3", ",", "2", ")", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	cp2png	This is just a shortened form of the function above for convenience. This only handles pickle files as input. Parameters ---------- checkplotin : str File name of a checkplot pickle file to convert to a PNG. extrarows : list of tuples This is a list of 4-element tuples containing...	astrobase/checkplot/pkl_png.py	def cp2png(checkplotin, extrarows=None): '''This is just a shortened form of the function above for convenience. This only handles pickle files as input. Parameters ---------- checkplotin : str File name of a checkplot pickle file to convert to a PNG. extrarows : list of tuples ...	def cp2png(checkplotin, extrarows=None): '''This is just a shortened form of the function above for convenience. This only handles pickle files as input. Parameters ---------- checkplotin : str File name of a checkplot pickle file to convert to a PNG. extrarows : list of tuples ...	[ "This", "is", "just", "a", "shortened", "form", "of", "the", "function", "above", "for", "convenience", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/checkplot/pkl_png.py#L1133-L1199	[ "def", "cp2png", "(", "checkplotin", ",", "extrarows", "=", "None", ")", ":", "if", "checkplotin", ".", "endswith", "(", "'.gz'", ")", ":", "outfile", "=", "checkplotin", ".", "replace", "(", "'.pkl.gz'", ",", "'.png'", ")", "else", ":", "outfile", "=", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	flare_model	This is a flare model function, similar to Kowalski+ 2011. From the paper by Pitkin+ 2014: http://adsabs.harvard.edu/abs/2014MNRAS.445.2268P Parameters ---------- flareparams : list of float This defines the flare model:: [amplitude, flare_peak_time, ...	astrobase/lcmodels/flares.py	def flare_model(flareparams, times, mags, errs): '''This is a flare model function, similar to Kowalski+ 2011. From the paper by Pitkin+ 2014: http://adsabs.harvard.edu/abs/2014MNRAS.445.2268P Parameters ---------- flareparams : list of float This defines the flare model:: ...	def flare_model(flareparams, times, mags, errs): '''This is a flare model function, similar to Kowalski+ 2011. From the paper by Pitkin+ 2014: http://adsabs.harvard.edu/abs/2014MNRAS.445.2268P Parameters ---------- flareparams : list of float This defines the flare model:: ...	[ "This", "is", "a", "flare", "model", "function", "similar", "to", "Kowalski", "+", "2011", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcmodels/flares.py#L18-L90	[ "def", "flare_model", "(", "flareparams", ",", "times", ",", "mags", ",", "errs", ")", ":", "(", "amplitude", ",", "flare_peak_time", ",", "rise_gaussian_stdev", ",", "decay_time_constant", ")", "=", "flareparams", "zerolevel", "=", "np", ".", "median", "(", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	flare_model_residual	This returns the residual between model mags and the actual mags. Parameters ---------- flareparams : list of float This defines the flare model:: [amplitude, flare_peak_time, rise_gaussian_stdev, decay_time_constant] where: `am...	astrobase/lcmodels/flares.py	def flare_model_residual(flareparams, times, mags, errs): ''' This returns the residual between model mags and the actual mags. Parameters ---------- flareparams : list of float This defines the flare model:: [amplitude, flare_peak_time, rise_gaussian...	def flare_model_residual(flareparams, times, mags, errs): ''' This returns the residual between model mags and the actual mags. Parameters ---------- flareparams : list of float This defines the flare model:: [amplitude, flare_peak_time, rise_gaussian...	[ "This", "returns", "the", "residual", "between", "model", "mags", "and", "the", "actual", "mags", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcmodels/flares.py#L94-L138	[ "def", "flare_model_residual", "(", "flareparams", ",", "times", ",", "mags", ",", "errs", ")", ":", "modelmags", ",", "_", ",", "_", ",", "_", "=", "flare_model", "(", "flareparams", ",", "times", ",", "mags", ",", "errs", ")", "return", "(", "mags", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	cache_clean_handler	This periodically cleans up the ~/.astrobase cache to save us from disk-space doom. Parameters ---------- min_age_hours : int Files older than this number of hours from the current time will be deleted. Returns ------- Nothing.	astrobase/lcproc/awsrun.py	def cache_clean_handler(min_age_hours=1): """This periodically cleans up the ~/.astrobase cache to save us from disk-space doom. Parameters ---------- min_age_hours : int Files older than this number of hours from the current time will be deleted. Returns ------- Noth...	def cache_clean_handler(min_age_hours=1): """This periodically cleans up the ~/.astrobase cache to save us from disk-space doom. Parameters ---------- min_age_hours : int Files older than this number of hours from the current time will be deleted. Returns ------- Noth...	[ "This", "periodically", "cleans", "up", "the", "~", "/", ".", "astrobase", "cache", "to", "save", "us", "from", "disk", "-", "space", "doom", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/awsrun.py#L194-L225	[ "def", "cache_clean_handler", "(", "min_age_hours", "=", "1", ")", ":", "# find the files to delete", "cmd", "=", "(", "\"find ~ec2-user/.astrobase -type f -mmin +{mmin} -exec rm -v '{{}}' \\;\"", ")", "mmin", "=", "'%.1f'", "%", "(", "min_age_hours", "*", "60.0", ")", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	shutdown_check_handler	This checks the AWS instance data URL to see if there's a pending shutdown for the instance. This is useful for AWS spot instances. If there is a pending shutdown posted to the instance data URL, we'll use the result of this function break out of the processing loop and shut everything down ASAP before...	astrobase/lcproc/awsrun.py	def shutdown_check_handler(): """This checks the AWS instance data URL to see if there's a pending shutdown for the instance. This is useful for AWS spot instances. If there is a pending shutdown posted to the instance data URL, we'll use the result of this function break out of the processing loop...	def shutdown_check_handler(): """This checks the AWS instance data URL to see if there's a pending shutdown for the instance. This is useful for AWS spot instances. If there is a pending shutdown posted to the instance data URL, we'll use the result of this function break out of the processing loop...	[ "This", "checks", "the", "AWS", "instance", "data", "URL", "to", "see", "if", "there", "s", "a", "pending", "shutdown", "for", "the", "instance", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/awsrun.py#L229-L272	[ "def", "shutdown_check_handler", "(", ")", ":", "url", "=", "'http://169.254.169.254/latest/meta-data/spot/instance-action'", "try", ":", "resp", "=", "requests", ".", "get", "(", "url", ",", "timeout", "=", "1.0", ")", "resp", ".", "raise_for_status", "(", ")", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	runcp_producer_loop	This sends checkplot making tasks to the input queue and monitors the result queue for task completion. Parameters ---------- lightcurve_list : str or list of str This is either a string pointing to a file containing a list of light curves filenames to process or the list itself. The n...	astrobase/lcproc/awsrun.py	def runcp_producer_loop( lightcurve_list, input_queue, input_bucket, result_queue, result_bucket, pfresult_list=None, runcp_kwargs=None, process_list_slice=None, purge_queues_when_done=False, delete_queues_when_done=False, download_...	def runcp_producer_loop( lightcurve_list, input_queue, input_bucket, result_queue, result_bucket, pfresult_list=None, runcp_kwargs=None, process_list_slice=None, purge_queues_when_done=False, delete_queues_when_done=False, download_...	[ "This", "sends", "checkplot", "making", "tasks", "to", "the", "input", "queue", "and", "monitors", "the", "result", "queue", "for", "task", "completion", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/awsrun.py#L280-L564	[ "def", "runcp_producer_loop", "(", "lightcurve_list", ",", "input_queue", ",", "input_bucket", ",", "result_queue", ",", "result_bucket", ",", "pfresult_list", "=", "None", ",", "runcp_kwargs", "=", "None", ",", "process_list_slice", "=", "None", ",", "purge_queues_...	2922a14619d183fb28005fa7d02027ac436f2265
valid	runcp_producer_loop_savedstate	This wraps the function above to allow for loading previous state from a file. Parameters ---------- use_saved_state : str or None This is the path to the saved state pickle file produced by a previous run of `runcp_producer_loop`. Will get all of the arguments to run another i...	astrobase/lcproc/awsrun.py	def runcp_producer_loop_savedstate( use_saved_state=None, lightcurve_list=None, input_queue=None, input_bucket=None, result_queue=None, result_bucket=None, pfresult_list=None, runcp_kwargs=None, process_list_slice=None, download_when_done=T...	def runcp_producer_loop_savedstate( use_saved_state=None, lightcurve_list=None, input_queue=None, input_bucket=None, result_queue=None, result_bucket=None, pfresult_list=None, runcp_kwargs=None, process_list_slice=None, download_when_done=T...	[ "This", "wraps", "the", "function", "above", "to", "allow", "for", "loading", "previous", "state", "from", "a", "file", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/awsrun.py#L568-L722	[ "def", "runcp_producer_loop_savedstate", "(", "use_saved_state", "=", "None", ",", "lightcurve_list", "=", "None", ",", "input_queue", "=", "None", ",", "input_bucket", "=", "None", ",", "result_queue", "=", "None", ",", "result_bucket", "=", "None", ",", "pfres...	2922a14619d183fb28005fa7d02027ac436f2265
valid	runcp_consumer_loop	This runs checkplot pickle making in a loop until interrupted. Consumes work task items from an input queue set up by `runcp_producer_loop` above. For the moment, we don't generate neighbor light curves since this would require a lot more S3 calls. Parameters ---------- in_queue_url : str ...	astrobase/lcproc/awsrun.py	def runcp_consumer_loop( in_queue_url, workdir, lclist_pkl_s3url, lc_altexts=('',), wait_time_seconds=5, cache_clean_timer_seconds=3600.0, shutdown_check_timer_seconds=60.0, sqs_client=None, s3_client=None ): """This runs checkplot pickle maki...	def runcp_consumer_loop( in_queue_url, workdir, lclist_pkl_s3url, lc_altexts=('',), wait_time_seconds=5, cache_clean_timer_seconds=3600.0, shutdown_check_timer_seconds=60.0, sqs_client=None, s3_client=None ): """This runs checkplot pickle maki...	[ "This", "runs", "checkplot", "pickle", "making", "in", "a", "loop", "until", "interrupted", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/awsrun.py#L726-L1153	[ "def", "runcp_consumer_loop", "(", "in_queue_url", ",", "workdir", ",", "lclist_pkl_s3url", ",", "lc_altexts", "=", "(", "''", ",", ")", ",", "wait_time_seconds", "=", "5", ",", "cache_clean_timer_seconds", "=", "3600.0", ",", "shutdown_check_timer_seconds", "=", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	runpf_consumer_loop	This runs period-finding in a loop until interrupted. Consumes work task items from an input queue set up by `runpf_producer_loop` above. Parameters ---------- in_queue_url : str The SQS URL of the input queue to listen to for work assignment messages. The task orders will include...	astrobase/lcproc/awsrun.py	def runpf_consumer_loop( in_queue_url, workdir, lc_altexts=('',), wait_time_seconds=5, shutdown_check_timer_seconds=60.0, sqs_client=None, s3_client=None ): """This runs period-finding in a loop until interrupted. Consumes work task items from an input qu...	def runpf_consumer_loop( in_queue_url, workdir, lc_altexts=('',), wait_time_seconds=5, shutdown_check_timer_seconds=60.0, sqs_client=None, s3_client=None ): """This runs period-finding in a loop until interrupted. Consumes work task items from an input qu...	[ "This", "runs", "period", "-", "finding", "in", "a", "loop", "until", "interrupted", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/awsrun.py#L1454-L1821	[ "def", "runpf_consumer_loop", "(", "in_queue_url", ",", "workdir", ",", "lc_altexts", "=", "(", "''", ",", ")", ",", "wait_time_seconds", "=", "5", ",", "shutdown_check_timer_seconds", "=", "60.0", ",", "sqs_client", "=", "None", ",", "s3_client", "=", "None",...	2922a14619d183fb28005fa7d02027ac436f2265
valid	gaussianeb_fit_magseries	This fits a double inverted gaussian EB model to a magnitude time series. Parameters ---------- times,mags,errs : np.array The input mag/flux time-series to fit the EB model to. period : float The period to use for EB fit. ebparams : list of float This is a list containin...	astrobase/lcfit/eclipses.py	def gaussianeb_fit_magseries(times, mags, errs, ebparams, sigclip=10.0, plotfit=False, magsarefluxes=False, verbose=True): '''This fits a double inverted gaussian EB model...	def gaussianeb_fit_magseries(times, mags, errs, ebparams, sigclip=10.0, plotfit=False, magsarefluxes=False, verbose=True): '''This fits a double inverted gaussian EB model...	[ "This", "fits", "a", "double", "inverted", "gaussian", "EB", "model", "to", "a", "magnitude", "time", "series", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/eclipses.py#L63-L382	[ "def", "gaussianeb_fit_magseries", "(", "times", ",", "mags", ",", "errs", ",", "ebparams", ",", "sigclip", "=", "10.0", ",", "plotfit", "=", "False", ",", "magsarefluxes", "=", "False", ",", "verbose", "=", "True", ")", ":", "stimes", ",", "smags", ",",...	2922a14619d183fb28005fa7d02027ac436f2265
valid	spline_fit_magseries	This fits a univariate cubic spline to the phased light curve. This fit may be better than the Fourier fit for sharply variable objects, like EBs, so can be used to distinguish them from other types of variables. Parameters ---------- times,mags,errs : np.array The input mag/flux time-ser...	astrobase/lcfit/nonphysical.py	def spline_fit_magseries(times, mags, errs, period, knotfraction=0.01, maxknots=30, sigclip=30.0, plotfit=False, ignoreinitfail=False, magsarefluxes=False, ...	def spline_fit_magseries(times, mags, errs, period, knotfraction=0.01, maxknots=30, sigclip=30.0, plotfit=False, ignoreinitfail=False, magsarefluxes=False, ...	[ "This", "fits", "a", "univariate", "cubic", "spline", "to", "the", "phased", "light", "curve", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/nonphysical.py#L72-L263	[ "def", "spline_fit_magseries", "(", "times", ",", "mags", ",", "errs", ",", "period", ",", "knotfraction", "=", "0.01", ",", "maxknots", "=", "30", ",", "sigclip", "=", "30.0", ",", "plotfit", "=", "False", ",", "ignoreinitfail", "=", "False", ",", "mags...	2922a14619d183fb28005fa7d02027ac436f2265
valid	savgol_fit_magseries	Fit a Savitzky-Golay filter to the magnitude/flux time series. SG fits successive sub-sets (windows) of adjacent data points with a low-order polynomial via least squares. At each point (magnitude), it returns the value of the polynomial at that magnitude's time. This is made significantly cheaper tha...	astrobase/lcfit/nonphysical.py	def savgol_fit_magseries(times, mags, errs, period, windowlength=None, polydeg=2, sigclip=30.0, plotfit=False, magsarefluxes=False, verbose=True): '''Fit a Savitzky-...	def savgol_fit_magseries(times, mags, errs, period, windowlength=None, polydeg=2, sigclip=30.0, plotfit=False, magsarefluxes=False, verbose=True): '''Fit a Savitzky-...	[ "Fit", "a", "Savitzky", "-", "Golay", "filter", "to", "the", "magnitude", "/", "flux", "time", "series", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/nonphysical.py#L271-L484	[ "def", "savgol_fit_magseries", "(", "times", ",", "mags", ",", "errs", ",", "period", ",", "windowlength", "=", "None", ",", "polydeg", "=", "2", ",", "sigclip", "=", "30.0", ",", "plotfit", "=", "False", ",", "magsarefluxes", "=", "False", ",", "verbose...	2922a14619d183fb28005fa7d02027ac436f2265
valid	legendre_fit_magseries	Fit an arbitrary-order Legendre series, via least squares, to the magnitude/flux time series. This is a series of the form:: p(x) = c_0L_0(x) + c_1L_1(x) + c_2L_2(x) + ... + c_nL_n(x) where L_i's are Legendre polynomials (also called "Legendre functions of the first kind") and c_i's are t...	astrobase/lcfit/nonphysical.py	def legendre_fit_magseries(times, mags, errs, period, legendredeg=10, sigclip=30.0, plotfit=False, magsarefluxes=False, verbose=True): '''Fit an arbitrary-order Legendre series, vi...	def legendre_fit_magseries(times, mags, errs, period, legendredeg=10, sigclip=30.0, plotfit=False, magsarefluxes=False, verbose=True): '''Fit an arbitrary-order Legendre series, vi...	[ "Fit", "an", "arbitrary", "-", "order", "Legendre", "series", "via", "least", "squares", "to", "the", "magnitude", "/", "flux", "time", "series", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/nonphysical.py#L491-L676	[ "def", "legendre_fit_magseries", "(", "times", ",", "mags", ",", "errs", ",", "period", ",", "legendredeg", "=", "10", ",", "sigclip", "=", "30.0", ",", "plotfit", "=", "False", ",", "magsarefluxes", "=", "False", ",", "verbose", "=", "True", ")", ":", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	update_checkplotdict_nbrlcs	For all neighbors in a checkplotdict, make LCs and phased LCs. Parameters ---------- checkplotdict : dict This is the checkplot to process. The light curves for the neighbors to the object here will be extracted from the stored file paths, and this function will make plots of these...	astrobase/lcproc/checkplotgen.py	def update_checkplotdict_nbrlcs( checkplotdict, timecol, magcol, errcol, lcformat='hat-sql', lcformatdir=None, verbose=True, ): '''For all neighbors in a checkplotdict, make LCs and phased LCs. Parameters ---------- checkplotdict : dict This is the chec...	def update_checkplotdict_nbrlcs( checkplotdict, timecol, magcol, errcol, lcformat='hat-sql', lcformatdir=None, verbose=True, ): '''For all neighbors in a checkplotdict, make LCs and phased LCs. Parameters ---------- checkplotdict : dict This is the chec...	[ "For", "all", "neighbors", "in", "a", "checkplotdict", "make", "LCs", "and", "phased", "LCs", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/checkplotgen.py#L102-L394	[ "def", "update_checkplotdict_nbrlcs", "(", "checkplotdict", ",", "timecol", ",", "magcol", ",", "errcol", ",", "lcformat", "=", "'hat-sql'", ",", "lcformatdir", "=", "None", ",", "verbose", "=", "True", ",", ")", ":", "try", ":", "formatinfo", "=", "get_lcfo...	2922a14619d183fb28005fa7d02027ac436f2265
valid	runcp	This makes a checkplot pickle for the given period-finding result pickle produced by `lcproc.periodfinding.runpf`. Parameters ---------- pfpickle : str or None This is the filename of the period-finding result pickle file created by `lcproc.periodfinding.runpf`. If this is None, the ch...	astrobase/lcproc/checkplotgen.py	def runcp( pfpickle, outdir, lcbasedir, lcfname=None, cprenorm=False, lclistpkl=None, nbrradiusarcsec=60.0, maxnumneighbors=5, makeneighborlcs=True, fast_mode=False, gaia_max_timeout=60.0, gaia_mirror=None, xmatchinf...	def runcp( pfpickle, outdir, lcbasedir, lcfname=None, cprenorm=False, lclistpkl=None, nbrradiusarcsec=60.0, maxnumneighbors=5, makeneighborlcs=True, fast_mode=False, gaia_max_timeout=60.0, gaia_mirror=None, xmatchinf...	[ "This", "makes", "a", "checkplot", "pickle", "for", "the", "given", "period", "-", "finding", "result", "pickle", "produced", "by", "lcproc", ".", "periodfinding", ".", "runpf", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/checkplotgen.py#L402-L906	[ "def", "runcp", "(", "pfpickle", ",", "outdir", ",", "lcbasedir", ",", "lcfname", "=", "None", ",", "cprenorm", "=", "False", ",", "lclistpkl", "=", "None", ",", "nbrradiusarcsec", "=", "60.0", ",", "maxnumneighbors", "=", "5", ",", "makeneighborlcs", "=",...	2922a14619d183fb28005fa7d02027ac436f2265
valid	runcp_worker	This is the worker for running checkplots. Parameters ---------- task : tuple This is of the form: (pfpickle, outdir, lcbasedir, kwargs). Returns ------- list of str The list of checkplot pickles returned by the `runcp` function.	astrobase/lcproc/checkplotgen.py	def runcp_worker(task): ''' This is the worker for running checkplots. Parameters ---------- task : tuple This is of the form: (pfpickle, outdir, lcbasedir, kwargs). Returns ------- list of str The list of checkplot pickles returned by the `runcp` function. ''' ...	def runcp_worker(task): ''' This is the worker for running checkplots. Parameters ---------- task : tuple This is of the form: (pfpickle, outdir, lcbasedir, kwargs). Returns ------- list of str The list of checkplot pickles returned by the `runcp` function. ''' ...	[ "This", "is", "the", "worker", "for", "running", "checkplots", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/checkplotgen.py#L910-L937	[ "def", "runcp_worker", "(", "task", ")", ":", "pfpickle", ",", "outdir", ",", "lcbasedir", ",", "kwargs", "=", "task", "try", ":", "return", "runcp", "(", "pfpickle", ",", "outdir", ",", "lcbasedir", ",", "", "", "kwargs", ")", "except", "Exception", ...	2922a14619d183fb28005fa7d02027ac436f2265
valid	parallel_cp	This drives the parallel execution of `runcp` for a list of periodfinding result pickles. Parameters ---------- pfpicklelist : list of str or list of Nones This is the list of the filenames of the period-finding result pickles to process. To make checkplots using the light curves direc...	astrobase/lcproc/checkplotgen.py	def parallel_cp( pfpicklelist, outdir, lcbasedir, fast_mode=False, lcfnamelist=None, cprenorm=False, lclistpkl=None, gaia_max_timeout=60.0, gaia_mirror=None, nbrradiusarcsec=60.0, maxnumneighbors=5, makeneighborlcs=True, ...	def parallel_cp( pfpicklelist, outdir, lcbasedir, fast_mode=False, lcfnamelist=None, cprenorm=False, lclistpkl=None, gaia_max_timeout=60.0, gaia_mirror=None, nbrradiusarcsec=60.0, maxnumneighbors=5, makeneighborlcs=True, ...	[ "This", "drives", "the", "parallel", "execution", "of", "runcp", "for", "a", "list", "of", "periodfinding", "result", "pickles", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/checkplotgen.py#L941-L1235	[ "def", "parallel_cp", "(", "pfpicklelist", ",", "outdir", ",", "lcbasedir", ",", "fast_mode", "=", "False", ",", "lcfnamelist", "=", "None", ",", "cprenorm", "=", "False", ",", "lclistpkl", "=", "None", ",", "gaia_max_timeout", "=", "60.0", ",", "gaia_mirror...	2922a14619d183fb28005fa7d02027ac436f2265
valid	parallel_cp_pfdir	This drives the parallel execution of `runcp` for a directory of periodfinding pickles. Parameters ---------- pfpickledir : str This is the directory containing all of the period-finding pickles to process. outdir : str The directory the checkplot pickles will be written t...	astrobase/lcproc/checkplotgen.py	def parallel_cp_pfdir(pfpickledir, outdir, lcbasedir, pfpickleglob='periodfinding-.pkl', lclistpkl=None, cprenorm=False, nbrradiusarcsec=60.0, maxnumneighbors=5, ...	def parallel_cp_pfdir(pfpickledir, outdir, lcbasedir, pfpickleglob='periodfinding-.pkl', lclistpkl=None, cprenorm=False, nbrradiusarcsec=60.0, maxnumneighbors=5, ...	[ "This", "drives", "the", "parallel", "execution", "of", "runcp", "for", "a", "directory", "of", "periodfinding", "pickles", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/checkplotgen.py#L1239-L1483	[ "def", "parallel_cp_pfdir", "(", "pfpickledir", ",", "outdir", ",", "lcbasedir", ",", "pfpickleglob", "=", "'periodfinding-.pkl'", ",", "lclistpkl", "=", "None", ",", "cprenorm", "=", "False", ",", "nbrradiusarcsec", "=", "60.0", ",", "maxnumneighbors", "=", "...	2922a14619d183fb28005fa7d02027ac436f2265
valid	runpf	This runs the period-finding for a single LC. Parameters ---------- lcfile : str The light curve file to run period-finding on. outdir : str The output directory where the result pickle will go. timecols : list of str or None The timecol keys to use from the lcdict in cal...	astrobase/lcproc/periodsearch.py	def runpf(lcfile, outdir, timecols=None, magcols=None, errcols=None, lcformat='hat-sql', lcformatdir=None, pfmethods=('gls','pdm','mav','win'), pfkwargs=({},{},{},{}), sigclip=10.0, getblssnr=False, nworkers=NC...	def runpf(lcfile, outdir, timecols=None, magcols=None, errcols=None, lcformat='hat-sql', lcformatdir=None, pfmethods=('gls','pdm','mav','win'), pfkwargs=({},{},{},{}), sigclip=10.0, getblssnr=False, nworkers=NC...	[ "This", "runs", "the", "period", "-", "finding", "for", "a", "single", "LC", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/periodsearch.py#L108-L457	[ "def", "runpf", "(", "lcfile", ",", "outdir", ",", "timecols", "=", "None", ",", "magcols", "=", "None", ",", "errcols", "=", "None", ",", "lcformat", "=", "'hat-sql'", ",", "lcformatdir", "=", "None", ",", "pfmethods", "=", "(", "'gls'", ",", "'pdm'",...	2922a14619d183fb28005fa7d02027ac436f2265
valid	_runpf_worker	This runs the runpf function.	astrobase/lcproc/periodsearch.py	def _runpf_worker(task): ''' This runs the runpf function. ''' (lcfile, outdir, timecols, magcols, errcols, lcformat, lcformatdir, pfmethods, pfkwargs, getblssnr, sigclip, nworkers, minobservations, excludeprocessed) = task if os.path.exists(lcfile): pfresult = runpf(lcfile, ...	def _runpf_worker(task): ''' This runs the runpf function. ''' (lcfile, outdir, timecols, magcols, errcols, lcformat, lcformatdir, pfmethods, pfkwargs, getblssnr, sigclip, nworkers, minobservations, excludeprocessed) = task if os.path.exists(lcfile): pfresult = runpf(lcfile, ...	[ "This", "runs", "the", "runpf", "function", "." ]	waqasbhatti/astrobase	python	https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/periodsearch.py#L461-L489	[ "def", "_runpf_worker", "(", "task", ")", ":", "(", "lcfile", ",", "outdir", ",", "timecols", ",", "magcols", ",", "errcols", ",", "lcformat", ",", "lcformatdir", ",", "pfmethods", ",", "pfkwargs", ",", "getblssnr", ",", "sigclip", ",", "nworkers", ",", ...	2922a14619d183fb28005fa7d02027ac436f2265

valid

jhk_to_sdssg

Converts given J, H, Ks mags to an SDSS g magnitude value. Parameters ---------- jmag,hmag,kmag : float 2MASS J, H, Ks mags of the object. Returns ------- float The converted SDSS g band magnitude.

astrobase/magnitudes.py

def jhk_to_sdssg(jmag,hmag,kmag): '''Converts given J, H, Ks mags to an SDSS g magnitude value. Parameters ---------- jmag,hmag,kmag : float 2MASS J, H, Ks mags of the object. Returns ------- float The converted SDSS g band magnitude. ''' return convert_constant...

[ "Converts", "given", "J", "H", "Ks", "mags", "to", "an", "SDSS", "g", "magnitude", "value", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/magnitudes.py#L296-L316

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2922a14619d183fb28005fa7d02027ac436f2265

valid

jhk_to_sdssr

Converts given J, H, Ks mags to an SDSS r magnitude value. Parameters ---------- jmag,hmag,kmag : float 2MASS J, H, Ks mags of the object. Returns ------- float The converted SDSS r band magnitude.

astrobase/magnitudes.py

def jhk_to_sdssr(jmag,hmag,kmag): '''Converts given J, H, Ks mags to an SDSS r magnitude value. Parameters ---------- jmag,hmag,kmag : float 2MASS J, H, Ks mags of the object. Returns ------- float The converted SDSS r band magnitude. ''' return convert_constant...

[ "Converts", "given", "J", "H", "Ks", "mags", "to", "an", "SDSS", "r", "magnitude", "value", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/magnitudes.py#L320-L340

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2922a14619d183fb28005fa7d02027ac436f2265

valid

jhk_to_sdssi

Converts given J, H, Ks mags to an SDSS i magnitude value. Parameters ---------- jmag,hmag,kmag : float 2MASS J, H, Ks mags of the object. Returns ------- float The converted SDSS i band magnitude.

astrobase/magnitudes.py

def jhk_to_sdssi(jmag,hmag,kmag): '''Converts given J, H, Ks mags to an SDSS i magnitude value. Parameters ---------- jmag,hmag,kmag : float 2MASS J, H, Ks mags of the object. Returns ------- float The converted SDSS i band magnitude. ''' return convert_constant...

[ "Converts", "given", "J", "H", "Ks", "mags", "to", "an", "SDSS", "i", "magnitude", "value", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/magnitudes.py#L344-L364

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2922a14619d183fb28005fa7d02027ac436f2265

valid

jhk_to_sdssz

Converts given J, H, Ks mags to an SDSS z magnitude value. Parameters ---------- jmag,hmag,kmag : float 2MASS J, H, Ks mags of the object. Returns ------- float The converted SDSS z band magnitude.

astrobase/magnitudes.py

def jhk_to_sdssz(jmag,hmag,kmag): '''Converts given J, H, Ks mags to an SDSS z magnitude value. Parameters ---------- jmag,hmag,kmag : float 2MASS J, H, Ks mags of the object. Returns ------- float The converted SDSS z band magnitude. ''' return convert_constant...

[ "Converts", "given", "J", "H", "Ks", "mags", "to", "an", "SDSS", "z", "magnitude", "value", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/magnitudes.py#L368-L388

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2922a14619d183fb28005fa7d02027ac436f2265

valid

absolute_gaia_magnitude

Calculates the GAIA absolute magnitude for object (or array of objects). Given a G mag and the parallax measured by GAIA, gets the absolute mag using the usual equation:: G - M_G = 5 x log10(d_pc) - 5 M_G = 5 - 5log10(d_pc) + G Parameters ---------- gaia_mag : float or array-like...

astrobase/magnitudes.py

def absolute_gaia_magnitude(gaia_mag, gaia_parallax_mas, gaia_mag_err=None, gaia_parallax_err_mas=None): '''Calculates the GAIA absolute magnitude for object (or array of objects). Given a G mag and the parallax measured by GAI...

[ "Calculates", "the", "GAIA", "absolute", "magnitude", "for", "object", "(", "or", "array", "of", "objects", ")", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/magnitudes.py#L437-L511

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2922a14619d183fb28005fa7d02027ac436f2265

valid

aov_theta

Calculates the Schwarzenberg-Czerny AoV statistic at a test frequency. Parameters ---------- times,mags,errs : np.array The input time-series and associated errors. frequency : float The test frequency to calculate the theta statistic at. binsize : float The phase bin siz...

astrobase/periodbase/saov.py

def aov_theta(times, mags, errs, frequency, binsize=0.05, minbin=9): '''Calculates the Schwarzenberg-Czerny AoV statistic at a test frequency. Parameters ---------- times,mags,errs : np.array The input time-series and associated errors. frequency : float The test fre...

[ "Calculates", "the", "Schwarzenberg", "-", "Czerny", "AoV", "statistic", "at", "a", "test", "frequency", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/periodbase/saov.py#L70-L162

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2922a14619d183fb28005fa7d02027ac436f2265

valid

_aov_worker

This is a parallel worker for the function below. Parameters ---------- task : tuple This is of the form below:: task[0] = times task[1] = mags task[2] = errs task[3] = frequency task[4] = binsize task[5] = minbin Return...

astrobase/periodbase/saov.py

def _aov_worker(task): '''This is a parallel worker for the function below. Parameters ---------- task : tuple This is of the form below:: task[0] = times task[1] = mags task[2] = errs task[3] = frequency task[4] = binsize ...

[ "This", "is", "a", "parallel", "worker", "for", "the", "function", "below", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/periodbase/saov.py#L166-L202

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2922a14619d183fb28005fa7d02027ac436f2265

valid

get_frequency_grid

This calculates a frequency grid for the period finding functions in this module. Based on the autofrequency function in astropy.stats.lombscargle. http://docs.astropy.org/en/stable/_modules/astropy/stats/lombscargle/core.html#LombScargle.autofrequency Parameters ---------- times : np.array ...

astrobase/periodbase/__init__.py

def get_frequency_grid(times, samplesperpeak=5, nyquistfactor=5, minfreq=None, maxfreq=None, returnf0dfnf=False): '''This calculates a frequency grid for the period finding functions in this module...

[ "This", "calculates", "a", "frequency", "grid", "for", "the", "period", "finding", "functions", "in", "this", "module", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/periodbase/__init__.py#L78-L137

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2922a14619d183fb28005fa7d02027ac436f2265

valid

independent_freq_count

This estimates M: the number of independent frequencies in the periodogram. This follows the terminology on page 3 of Zechmeister & Kurster (2009):: M = DELTA_f / delta_f where:: DELTA_f = freq.max() - freq.min() delta_f = 1.0/(times.max() - times.min()) Parameters ---------...

astrobase/periodbase/__init__.py

def independent_freq_count(frequencies, times, conservative=True): '''This estimates M: the number of independent frequencies in the periodogram. This follows the terminology on page 3 of Zechmeister & Kurster (2009):: M = DELTA_f / delta_f where:: DELTA_f = freq.max() - freq.min() ...

[ "This", "estimates", "M", ":", "the", "number", "of", "independent", "frequencies", "in", "the", "periodogram", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/periodbase/__init__.py#L141-L188

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2922a14619d183fb28005fa7d02027ac436f2265

valid

bootstrap_falsealarmprob

Calculates the false alarm probabilities of periodogram peaks using bootstrap resampling of the magnitude time series. The false alarm probability here is defined as:: (1.0 + sum(trialbestpeaks[i] > peak[j]))/(ntrialbestpeaks + 1) for each best periodogram peak j. The index i is for each bootstra...

astrobase/periodbase/__init__.py

def bootstrap_falsealarmprob(lspinfo, times, mags, errs, nbootstrap=250, magsarefluxes=False, sigclip=10.0, npeaks=No...

[ "Calculates", "the", "false", "alarm", "probabilities", "of", "periodogram", "peaks", "using", "bootstrap", "resampling", "of", "the", "magnitude", "time", "series", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/periodbase/__init__.py#L268-L500

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2922a14619d183fb28005fa7d02027ac436f2265

valid

make_combined_periodogram

This just puts all of the period-finders on a single periodogram. This will renormalize all of the periodograms so their values lie between 0 and 1, with values lying closer to 1 being more significant. Periodograms that give the same best periods will have their peaks line up together. Parameters ...

astrobase/periodbase/__init__.py

def make_combined_periodogram(pflist, outfile, addmethods=False): '''This just puts all of the period-finders on a single periodogram. This will renormalize all of the periodograms so their values lie between 0 and 1, with values lying closer to 1 being more significant. Periodograms that give the same...

[ "This", "just", "puts", "all", "of", "the", "period", "-", "finders", "on", "a", "single", "periodogram", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/periodbase/__init__.py#L509-L589

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2922a14619d183fb28005fa7d02027ac436f2265

valid

read_original_textlc

Read .epdlc, and .tfalc light curves and return a corresponding labelled dict (if LC from <2012) or astropy table (if >=2012). Each has different keys that can be accessed via .keys() Input: lcpath: path (string) to light curve data, which is a textfile with HAT LC data. Example: dat = rea...

astrobase/hatsurveys/texthatlc.py

def read_original_textlc(lcpath): ''' Read .epdlc, and .tfalc light curves and return a corresponding labelled dict (if LC from <2012) or astropy table (if >=2012). Each has different keys that can be accessed via .keys() Input: lcpath: path (string) to light curve data, which is a textfile wit...

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waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/hatsurveys/texthatlc.py#L54-L167

[ "def", "read_original_textlc", "(", "lcpath", ")", ":", "LOGINFO", "(", "'reading original HAT text LC: {:s}'", ".", "format", "(", "lcpath", ")", ")", "N_lines_to_parse_comments", "=", "50", "with", "open", "(", "lcpath", ",", "'rb'", ")", "as", "file", ":", ...

2922a14619d183fb28005fa7d02027ac436f2265

valid

traptransit_fit_magseries

This fits a trapezoid transit model to a magnitude time series. Parameters ---------- times,mags,errs : np.array The input mag/flux time-series to fit a trapezoid planet-transit model to. period : float The period to use for the model fit. transitparams : list of floats ...

astrobase/lcfit/transits.py

def traptransit_fit_magseries(times, mags, errs, transitparams, sigclip=10.0, plotfit=False, magsarefluxes=False, verbose=True): '''This fits a trapezoid transit mode...

[ "This", "fits", "a", "trapezoid", "transit", "model", "to", "a", "magnitude", "time", "series", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/transits.py#L85-L401

[ "def", "traptransit_fit_magseries", "(", "times", ",", "mags", ",", "errs", ",", "transitparams", ",", "sigclip", "=", "10.0", ",", "plotfit", "=", "False", ",", "magsarefluxes", "=", "False", ",", "verbose", "=", "True", ")", ":", "stimes", ",", "smags", ...

2922a14619d183fb28005fa7d02027ac436f2265

valid

_get_value

This decides if a value is to be fit for or is fixed in a model fit. When you want to get the value of some parameter, but you're not sure if it's being fit or if it is fixed. then, e.g. for `period`:: period_value = _get_value('period', fitparams, fixedparams)

astrobase/lcfit/transits.py

def _get_value(quantitystr, fitparams, fixedparams): """This decides if a value is to be fit for or is fixed in a model fit. When you want to get the value of some parameter, but you're not sure if it's being fit or if it is fixed. then, e.g. for `period`:: period_value = _get_value('period', fitp...

[ "This", "decides", "if", "a", "value", "is", "to", "be", "fit", "for", "or", "is", "fixed", "in", "a", "model", "fit", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/transits.py#L409-L426

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2922a14619d183fb28005fa7d02027ac436f2265

valid

_transit_model

This returns a BATMAN planetary transit model. Parameters ---------- times : np.array The times at which the model will be evaluated. t0 : float The time of periastron for the transit. per : float The orbital period of the planet. rp : float The stellar radiu...

astrobase/lcfit/transits.py

def _transit_model(times, t0, per, rp, a, inc, ecc, w, u, limb_dark, exp_time_minutes=2, supersample_factor=7): '''This returns a BATMAN planetary transit model. Parameters ---------- times : np.array The times at which the model will be evaluated. t0 : float Th...

[ "This", "returns", "a", "BATMAN", "planetary", "transit", "model", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/transits.py#L429-L500

[ "def", "_transit_model", "(", "times", ",", "t0", ",", "per", ",", "rp", ",", "a", ",", "inc", ",", "ecc", ",", "w", ",", "u", ",", "limb_dark", ",", "exp_time_minutes", "=", "2", ",", "supersample_factor", "=", "7", ")", ":", "params", "=", "batma...

2922a14619d183fb28005fa7d02027ac436f2265

valid

_log_prior_transit

Assume priors on all parameters have uniform probability.

astrobase/lcfit/transits.py

def _log_prior_transit(theta, priorbounds): ''' Assume priors on all parameters have uniform probability. ''' # priorbounds contains the input priors, and because of how we previously # sorted theta, its sorted keys tell us which parts of theta correspond to # which physical quantities. all...

[ "Assume", "priors", "on", "all", "parameters", "have", "uniform", "probability", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/transits.py#L503-L521

[ "def", "_log_prior_transit", "(", "theta", ",", "priorbounds", ")", ":", "# priorbounds contains the input priors, and because of how we previously", "# sorted theta, its sorted keys tell us which parts of theta correspond to", "# which physical quantities.", "allowed", "=", "True", "for...

2922a14619d183fb28005fa7d02027ac436f2265

valid

_log_likelihood_transit

Given a batman TransitModel and its proposed parameters (theta), update the batman params object with the proposed parameters and evaluate the gaussian likelihood. Note: the priorbounds are only needed to parse theta.

astrobase/lcfit/transits.py

def _log_likelihood_transit(theta, params, model, t, flux, err_flux, priorbounds): ''' Given a batman TransitModel and its proposed parameters (theta), update the batman params object with the proposed parameters and evaluate the gaussian likelihood. Note: the priorbound...

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waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/transits.py#L528-L568

[ "def", "_log_likelihood_transit", "(", "theta", ",", "params", ",", "model", ",", "t", ",", "flux", ",", "err_flux", ",", "priorbounds", ")", ":", "u", "=", "[", "]", "for", "ix", ",", "key", "in", "enumerate", "(", "sorted", "(", "priorbounds", ".", ...

2922a14619d183fb28005fa7d02027ac436f2265

valid

_log_likelihood_transit_plus_line

Given a batman TransitModel and its proposed parameters (theta), update the batman params object with the proposed parameters and evaluate the gaussian likelihood. Note: the priorbounds are only needed to parse theta.

astrobase/lcfit/transits.py

def _log_likelihood_transit_plus_line(theta, params, model, t, data_flux, err_flux, priorbounds): ''' Given a batman TransitModel and its proposed parameters (theta), update the batman params object with the proposed parameters and evaluate the gaussian likelihood. ...

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waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/transits.py#L571-L625

[ "def", "_log_likelihood_transit_plus_line", "(", "theta", ",", "params", ",", "model", ",", "t", ",", "data_flux", ",", "err_flux", ",", "priorbounds", ")", ":", "u", "=", "[", "]", "for", "ix", ",", "key", "in", "enumerate", "(", "sorted", "(", "priorbo...

2922a14619d183fb28005fa7d02027ac436f2265

valid

log_posterior_transit

Evaluate posterior probability given proposed model parameters and the observed flux timeseries.

astrobase/lcfit/transits.py

def log_posterior_transit(theta, params, model, t, flux, err_flux, priorbounds): ''' Evaluate posterior probability given proposed model parameters and the observed flux timeseries. ''' lp = _log_prior_transit(theta, priorbounds) if not np.isfinite(lp): return -np.inf else: r...

[ "Evaluate", "posterior", "probability", "given", "proposed", "model", "parameters", "and", "the", "observed", "flux", "timeseries", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/transits.py#L628-L638

[ "def", "log_posterior_transit", "(", "theta", ",", "params", ",", "model", ",", "t", ",", "flux", ",", "err_flux", ",", "priorbounds", ")", ":", "lp", "=", "_log_prior_transit", "(", "theta", ",", "priorbounds", ")", "if", "not", "np", ".", "isfinite", "...

2922a14619d183fb28005fa7d02027ac436f2265

valid

log_posterior_transit_plus_line

Evaluate posterior probability given proposed model parameters and the observed flux timeseries.

astrobase/lcfit/transits.py

def log_posterior_transit_plus_line(theta, params, model, t, flux, err_flux, priorbounds): ''' Evaluate posterior probability given proposed model parameters and the observed flux timeseries. ''' lp = _log_prior_transit_plus_line(theta, priorbounds) if not np....

[ "Evaluate", "posterior", "probability", "given", "proposed", "model", "parameters", "and", "the", "observed", "flux", "timeseries", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/transits.py#L641-L654

[ "def", "log_posterior_transit_plus_line", "(", "theta", ",", "params", ",", "model", ",", "t", ",", "flux", ",", "err_flux", ",", "priorbounds", ")", ":", "lp", "=", "_log_prior_transit_plus_line", "(", "theta", ",", "priorbounds", ")", "if", "not", "np", "....

2922a14619d183fb28005fa7d02027ac436f2265

valid

mandelagol_fit_magseries

This fits a Mandel & Agol (2002) planetary transit model to a flux time series. You can fit and fix whatever parameters you want. It relies on Kreidberg (2015)'s BATMAN implementation for the transit model, emcee to sample the posterior (Foreman-Mackey et al 2013), `corner` to plot it, and `h5py` to sa...

astrobase/lcfit/transits.py

def mandelagol_fit_magseries( times, mags, errs, fitparams, priorbounds, fixedparams, trueparams=None, burninpercent=0.3, plotcorner=False, samplesavpath=False, n_walkers=50, n_mcmc_steps=400, eps=1e-4, skipsampling=False, ...

[ "This", "fits", "a", "Mandel", "&", "Agol", "(", "2002", ")", "planetary", "transit", "model", "to", "a", "flux", "time", "series", ".", "You", "can", "fit", "and", "fix", "whatever", "parameters", "you", "want", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/transits.py#L661-L1060

[ "def", "mandelagol_fit_magseries", "(", "times", ",", "mags", ",", "errs", ",", "fitparams", ",", "priorbounds", ",", "fixedparams", ",", "trueparams", "=", "None", ",", "burninpercent", "=", "0.3", ",", "plotcorner", "=", "False", ",", "samplesavpath", "=", ...

2922a14619d183fb28005fa7d02027ac436f2265

valid

mandelagol_and_line_fit_magseries

The model fit by this function is: a Mandel & Agol (2002) transit, PLUS a line. You can fit and fix whatever parameters you want. A typical use case: you want to measure transit times of individual SNR >~ 50 transits. You fix all the transit parameters except for the mid-time, and also fit for a line l...

astrobase/lcfit/transits.py

def mandelagol_and_line_fit_magseries( times, mags, errs, fitparams, priorbounds, fixedparams, trueparams=None, burninpercent=0.3, plotcorner=False, timeoffset=0, samplesavpath=False, n_walkers=50, n_mcmc_steps=400, eps=1e-4...

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waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/transits.py#L1063-L1530

[ "def", "mandelagol_and_line_fit_magseries", "(", "times", ",", "mags", ",", "errs", ",", "fitparams", ",", "priorbounds", ",", "fixedparams", ",", "trueparams", "=", "None", ",", "burninpercent", "=", "0.3", ",", "plotcorner", "=", "False", ",", "timeoffset", ...

2922a14619d183fb28005fa7d02027ac436f2265

valid

list_trilegal_filtersystems

This just lists all the filter systems available for TRILEGAL.

astrobase/services/trilegal.py

def list_trilegal_filtersystems(): ''' This just lists all the filter systems available for TRILEGAL. ''' print('%-40s %s' % ('FILTER SYSTEM NAME','DESCRIPTION')) print('%-40s %s' % ('------------------','-----------')) for key in sorted(TRILEGAL_FILTER_SYSTEMS.keys()): print('%-40s %s...

[ "This", "just", "lists", "all", "the", "filter", "systems", "available", "for", "TRILEGAL", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/services/trilegal.py#L478-L487

[ "def", "list_trilegal_filtersystems", "(", ")", ":", "print", "(", "'%-40s %s'", "%", "(", "'FILTER SYSTEM NAME'", ",", "'DESCRIPTION'", ")", ")", "print", "(", "'%-40s %s'", "%", "(", "'------------------'", ",", "'-----------'", ")", ")", "for", "key", "in", ...

2922a14619d183fb28005fa7d02027ac436f2265

valid

query_galcoords

This queries the TRILEGAL model form, downloads results, and parses them. Parameters ---------- gal_lon,gal_lat : float These are the center galactic longitude and latitude in degrees. filtersystem : str This is a key in the TRILEGAL_FILTER_SYSTEMS dict. Use the function :py:f...

astrobase/services/trilegal.py

def query_galcoords(gal_lon, gal_lat, filtersystem='sloan_2mass', field_deg2=1.0, usebinaries=True, extinction_sigma=0.1, magnitude_limit=26.0, maglim_filtercol=4, ...

[ "This", "queries", "the", "TRILEGAL", "model", "form", "downloads", "results", "and", "parses", "them", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/services/trilegal.py#L491-L804

[ "def", "query_galcoords", "(", "gal_lon", ",", "gal_lat", ",", "filtersystem", "=", "'sloan_2mass'", ",", "field_deg2", "=", "1.0", ",", "usebinaries", "=", "True", ",", "extinction_sigma", "=", "0.1", ",", "magnitude_limit", "=", "26.0", ",", "maglim_filtercol"...

2922a14619d183fb28005fa7d02027ac436f2265

valid

query_radecl

This runs the TRILEGAL query for decimal equatorial coordinates. Parameters ---------- ra,decl : float These are the center equatorial coordinates in decimal degrees filtersystem : str This is a key in the TRILEGAL_FILTER_SYSTEMS dict. Use the function :py:func:`astrobase.serv...

astrobase/services/trilegal.py

def query_radecl(ra, decl, filtersystem='sloan_2mass', field_deg2=1.0, usebinaries=True, extinction_sigma=0.1, magnitude_limit=26.0, maglim_filtercol=4, trilegal_version=1.6, ...

[ "This", "runs", "the", "TRILEGAL", "query", "for", "decimal", "equatorial", "coordinates", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/services/trilegal.py#L808-L928

[ "def", "query_radecl", "(", "ra", ",", "decl", ",", "filtersystem", "=", "'sloan_2mass'", ",", "field_deg2", "=", "1.0", ",", "usebinaries", "=", "True", ",", "extinction_sigma", "=", "0.1", ",", "magnitude_limit", "=", "26.0", ",", "maglim_filtercol", "=", ...

2922a14619d183fb28005fa7d02027ac436f2265

valid

read_model_table

This reads a downloaded TRILEGAL model file. Parameters ---------- modelfile : str Path to the downloaded model file to read. Returns ------- np.recarray Returns the model table as a Numpy record array.

astrobase/services/trilegal.py

def read_model_table(modelfile): ''' This reads a downloaded TRILEGAL model file. Parameters ---------- modelfile : str Path to the downloaded model file to read. Returns ------- np.recarray Returns the model table as a Numpy record array. ''' infd = gzip.op...

[ "This", "reads", "a", "downloaded", "TRILEGAL", "model", "file", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/services/trilegal.py#L932-L954

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2922a14619d183fb28005fa7d02027ac436f2265

valid

_time_independent_equals

This compares two values in constant time. Taken from tornado: https://github.com/tornadoweb/tornado/blob/ d4eb8eb4eb5cc9a6677e9116ef84ded8efba8859/tornado/web.py#L3060

astrobase/cpserver/checkplotserver_handlers.py

def _time_independent_equals(a, b): ''' This compares two values in constant time. Taken from tornado: https://github.com/tornadoweb/tornado/blob/ d4eb8eb4eb5cc9a6677e9116ef84ded8efba8859/tornado/web.py#L3060 ''' if len(a) != len(b): return False result = 0 if isinstance(a...

[ "This", "compares", "two", "values", "in", "constant", "time", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/cpserver/checkplotserver_handlers.py#L3032-L3051

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2922a14619d183fb28005fa7d02027ac436f2265

valid

FrontendEncoder.default

Overrides the default serializer for `JSONEncoder`. This can serialize the following objects in addition to what `JSONEncoder` can already do. - `np.array` - `bytes` - `complex` - `np.float64` and other `np.dtype` objects Parameters ---------- ...

astrobase/cpserver/checkplotserver_handlers.py

def default(self, obj): '''Overrides the default serializer for `JSONEncoder`. This can serialize the following objects in addition to what `JSONEncoder` can already do. - `np.array` - `bytes` - `complex` - `np.float64` and other `np.dtype` objects Para...

[ "Overrides", "the", "default", "serializer", "for", "JSONEncoder", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/cpserver/checkplotserver_handlers.py#L48-L85

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2922a14619d183fb28005fa7d02027ac436f2265

valid

IndexHandler.initialize

handles initial setup.

astrobase/cpserver/checkplotserver_handlers.py

def initialize(self, currentdir, assetpath, cplist, cplistfile, executor, readonly, baseurl): ''' handles initial setup. ''' self.currentdir = currentdir self.assetpath = assetpath self.currentproject = cplist self.cplistfile = cplistfile ...

[ "handles", "initial", "setup", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/cpserver/checkplotserver_handlers.py#L408-L421

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2922a14619d183fb28005fa7d02027ac436f2265

valid

IndexHandler.get

This handles GET requests to the index page. TODO: provide the correct baseurl from the checkplotserver options dict, so the frontend JS can just read that off immediately.

astrobase/cpserver/checkplotserver_handlers.py

def get(self): '''This handles GET requests to the index page. TODO: provide the correct baseurl from the checkplotserver options dict, so the frontend JS can just read that off immediately. ''' # generate the project's list of checkplots project_checkplots = self.curr...

[ "This", "handles", "GET", "requests", "to", "the", "index", "page", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/cpserver/checkplotserver_handlers.py#L424-L457

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2922a14619d183fb28005fa7d02027ac436f2265

valid

CheckplotHandler.get

This handles GET requests to serve a specific checkplot pickle. This is an AJAX endpoint; returns JSON that gets converted by the frontend into things to render.

astrobase/cpserver/checkplotserver_handlers.py

def get(self, checkplotfname): '''This handles GET requests to serve a specific checkplot pickle. This is an AJAX endpoint; returns JSON that gets converted by the frontend into things to render. ''' if checkplotfname: # do the usual safing self.checkp...

[ "This", "handles", "GET", "requests", "to", "serve", "a", "specific", "checkplot", "pickle", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/cpserver/checkplotserver_handlers.py#L485-L980

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2922a14619d183fb28005fa7d02027ac436f2265

valid

CheckplotHandler.post

This handles POST requests. Also an AJAX endpoint. Updates the persistent checkplot dict using the changes from the UI, and then saves it back to disk. This could definitely be faster by just loading the checkplot into a server-wide shared dict or something.

astrobase/cpserver/checkplotserver_handlers.py

def post(self, cpfile): '''This handles POST requests. Also an AJAX endpoint. Updates the persistent checkplot dict using the changes from the UI, and then saves it back to disk. This could definitely be faster by just loading the checkplot into a server-wide shared dict or some...

[ "This", "handles", "POST", "requests", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/cpserver/checkplotserver_handlers.py#L984-L1121

[ "def", "post", "(", "self", ",", "cpfile", ")", ":", "# if self.readonly is set, then don't accept any changes", "# return immediately with a 400", "if", "self", ".", "readonly", ":", "msg", "=", "\"checkplotserver is in readonly mode. no updates allowed.\"", "resultdict", "=",...

2922a14619d183fb28005fa7d02027ac436f2265

valid

CheckplotListHandler.get

This handles GET requests for the current checkplot-list.json file. Used with AJAX from frontend.

astrobase/cpserver/checkplotserver_handlers.py

def get(self): ''' This handles GET requests for the current checkplot-list.json file. Used with AJAX from frontend. ''' # add the reviewed key to the current dict if it doesn't exist # this will hold all the reviewed objects for the frontend if 'reviewed' not ...

[ "This", "handles", "GET", "requests", "for", "the", "current", "checkplot", "-", "list", ".", "json", "file", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/cpserver/checkplotserver_handlers.py#L1150-L1164

[ "def", "get", "(", "self", ")", ":", "# add the reviewed key to the current dict if it doesn't exist", "# this will hold all the reviewed objects for the frontend", "if", "'reviewed'", "not", "in", "self", ".", "currentproject", ":", "self", ".", "currentproject", "[", "'revi...

2922a14619d183fb28005fa7d02027ac436f2265

valid

CheckplotListHandler.post

This handles POST requests. Saves the changes made by the user on the frontend back to the current checkplot-list.json file.

astrobase/cpserver/checkplotserver_handlers.py

def post(self): '''This handles POST requests. Saves the changes made by the user on the frontend back to the current checkplot-list.json file. ''' # if self.readonly is set, then don't accept any changes # return immediately with a 400 if self.readonly: ...

[ "This", "handles", "POST", "requests", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/cpserver/checkplotserver_handlers.py#L1168-L1233

[ "def", "post", "(", "self", ")", ":", "# if self.readonly is set, then don't accept any changes", "# return immediately with a 400", "if", "self", ".", "readonly", ":", "msg", "=", "\"checkplotserver is in readonly mode. no updates allowed.\"", "resultdict", "=", "{", "'status'...

2922a14619d183fb28005fa7d02027ac436f2265

valid

LCToolHandler.get

This handles a GET request to run a specified LC tool. Parameters ---------- cpfile : str This is the checkplot file to run the tool on. Returns ------- str Returns a JSON response. Notes ----- The URI structure is:: ...

astrobase/cpserver/checkplotserver_handlers.py

def get(self, cpfile): '''This handles a GET request to run a specified LC tool. Parameters ---------- cpfile : str This is the checkplot file to run the tool on. Returns ------- str Returns a JSON response. Notes -----...

[ "This", "handles", "a", "GET", "request", "to", "run", "a", "specified", "LC", "tool", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/cpserver/checkplotserver_handlers.py#L1264-L3005

[ "def", "get", "(", "self", ",", "cpfile", ")", ":", "if", "cpfile", ":", "self", ".", "cpfile", "=", "(", "xhtml_escape", "(", "base64", ".", "b64decode", "(", "url_unescape", "(", "cpfile", ")", ")", ")", ")", "# see if this plot is in the current project",...

2922a14619d183fb28005fa7d02027ac436f2265

valid

StandaloneHandler.initialize

This handles initial setup of the `RequestHandler`.

astrobase/cpserver/checkplotserver_handlers.py

def initialize(self, executor, secret): ''' This handles initial setup of the `RequestHandler`. ''' self.executor = executor self.secret = secret

[ "This", "handles", "initial", "setup", "of", "the", "RequestHandler", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/cpserver/checkplotserver_handlers.py#L3064-L3071

[ "def", "initialize", "(", "self", ",", "executor", ",", "secret", ")", ":", "self", ".", "executor", "=", "executor", "self", ".", "secret", "=", "secret" ]

2922a14619d183fb28005fa7d02027ac436f2265

valid

StandaloneHandler.get

This handles GET requests. Returns the requested checkplot pickle's information as JSON. Requires a pre-shared secret `key` argument for the operation to complete successfully. This is obtained from a command-line argument.

astrobase/cpserver/checkplotserver_handlers.py

def get(self): '''This handles GET requests. Returns the requested checkplot pickle's information as JSON. Requires a pre-shared secret `key` argument for the operation to complete successfully. This is obtained from a command-line argument. ''' provided_key = self.ge...

[ "This", "handles", "GET", "requests", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/cpserver/checkplotserver_handlers.py#L3076-L3500

[ "def", "get", "(", "self", ")", ":", "provided_key", "=", "self", ".", "get_argument", "(", "'key'", ",", "default", "=", "None", ")", "if", "not", "provided_key", ":", "LOGGER", ".", "error", "(", "'standalone URL hit but no secret key provided'", ")", "retdi...

2922a14619d183fb28005fa7d02027ac436f2265

valid

extinction_query

This queries the 2MASS DUST service to find the extinction parameters for the given `lon`, `lat`. Parameters ---------- lon,lat: float These are decimal right ascension and declination if `coordtype = 'equatorial'`. These are are decimal Galactic longitude and latitude if `coor...

astrobase/services/dust.py

def extinction_query(lon, lat, coordtype='equatorial', sizedeg=5.0, forcefetch=False, cachedir='~/.astrobase/dust-cache', verbose=True, timeout=10.0, jitter=5.0): '''Thi...

[ "This", "queries", "the", "2MASS", "DUST", "service", "to", "find", "the", "extinction", "parameters", "for", "the", "given", "lon", "lat", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/services/dust.py#L88-L257

[ "def", "extinction_query", "(", "lon", ",", "lat", ",", "coordtype", "=", "'equatorial'", ",", "sizedeg", "=", "5.0", ",", "forcefetch", "=", "False", ",", "cachedir", "=", "'~/.astrobase/dust-cache'", ",", "verbose", "=", "True", ",", "timeout", "=", "10.0"...

2922a14619d183fb28005fa7d02027ac436f2265

valid

smooth_magseries_gaussfilt

This smooths the magseries with a Gaussian kernel. Parameters ---------- mags : np.array The input mags/flux time-series to smooth. windowsize : int This is a odd integer containing the smoothing window size. windowfwhm : int This is an odd integer containing the FWHM of ...

astrobase/varbase/trends.py

def smooth_magseries_gaussfilt(mags, windowsize, windowfwhm=7): '''This smooths the magseries with a Gaussian kernel. Parameters ---------- mags : np.array The input mags/flux time-series to smooth. windowsize : int This is a odd integer containing the smoothing window size. ...

[ "This", "smooths", "the", "magseries", "with", "a", "Gaussian", "kernel", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varbase/trends.py#L121-L147

[ "def", "smooth_magseries_gaussfilt", "(", "mags", ",", "windowsize", ",", "windowfwhm", "=", "7", ")", ":", "convkernel", "=", "Gaussian1DKernel", "(", "windowfwhm", ",", "x_size", "=", "windowsize", ")", "smoothed", "=", "convolve", "(", "mags", ",", "convker...

2922a14619d183fb28005fa7d02027ac436f2265

valid

smooth_magseries_savgol

This smooths the magseries with a Savitsky-Golay filter. Parameters ---------- mags : np.array The input mags/flux time-series to smooth. windowsize : int This is a odd integer containing the smoothing window size. polyorder : int This is an integer containing the polynom...

astrobase/varbase/trends.py

def smooth_magseries_savgol(mags, windowsize, polyorder=2): '''This smooths the magseries with a Savitsky-Golay filter. Parameters ---------- mags : np.array The input mags/flux time-series to smooth. windowsize : int This is a odd integer containing the smoothing window size. ...

[ "This", "smooths", "the", "magseries", "with", "a", "Savitsky", "-", "Golay", "filter", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varbase/trends.py#L150-L175

[ "def", "smooth_magseries_savgol", "(", "mags", ",", "windowsize", ",", "polyorder", "=", "2", ")", ":", "smoothed", "=", "savgol_filter", "(", "mags", ",", "windowsize", ",", "polyorder", ")", "return", "smoothed" ]

2922a14619d183fb28005fa7d02027ac436f2265

valid

_old_epd_diffmags

This calculates the difference in mags after EPD coefficients are calculated. final EPD mags = median(magseries) + epd_diffmags()

astrobase/varbase/trends.py

def _old_epd_diffmags(coeff, fsv, fdv, fkv, xcc, ycc, bgv, bge, mag): ''' This calculates the difference in mags after EPD coefficients are calculated. final EPD mags = median(magseries) + epd_diffmags() ''' return -(coeff[0]*fsv**2. + coeff[1]*fsv + coeff[2]*fdv**2....

[ "This", "calculates", "the", "difference", "in", "mags", "after", "EPD", "coefficients", "are", "calculated", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varbase/trends.py#L182-L211

[ "def", "_old_epd_diffmags", "(", "coeff", ",", "fsv", ",", "fdv", ",", "fkv", ",", "xcc", ",", "ycc", ",", "bgv", ",", "bge", ",", "mag", ")", ":", "return", "-", "(", "coeff", "[", "0", "]", "*", "fsv", "**", "2.", "+", "coeff", "[", "1", "]...

2922a14619d183fb28005fa7d02027ac436f2265

valid

_old_epd_magseries

Detrends a magnitude series given in mag using accompanying values of S in fsv, D in fdv, K in fkv, x coords in xcc, y coords in ycc, background in bgv, and background error in bge. smooth is used to set a smoothing parameter for the fit function. Does EPD voodoo.

astrobase/varbase/trends.py

def _old_epd_magseries(times, mags, errs, fsv, fdv, fkv, xcc, ycc, bgv, bge, epdsmooth_windowsize=21, epdsmooth_sigclip=3.0, epdsmooth_func=smooth_magseries_signal_medfilt, epdsmooth_extraparams=None): ...

[ "Detrends", "a", "magnitude", "series", "given", "in", "mag", "using", "accompanying", "values", "of", "S", "in", "fsv", "D", "in", "fdv", "K", "in", "fkv", "x", "coords", "in", "xcc", "y", "coords", "in", "ycc", "background", "in", "bgv", "and", "back...

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varbase/trends.py#L215-L308

[ "def", "_old_epd_magseries", "(", "times", ",", "mags", ",", "errs", ",", "fsv", ",", "fdv", ",", "fkv", ",", "xcc", ",", "ycc", ",", "bgv", ",", "bge", ",", "epdsmooth_windowsize", "=", "21", ",", "epdsmooth_sigclip", "=", "3.0", ",", "epdsmooth_func", ...

2922a14619d183fb28005fa7d02027ac436f2265

valid

_epd_function

This is the EPD function to fit using a smoothed mag-series.

astrobase/varbase/trends.py

def _epd_function(coeffs, fsv, fdv, fkv, xcc, ycc, bgv, bge, iha, izd): ''' This is the EPD function to fit using a smoothed mag-series. ''' return (coeffs[0]*fsv*fsv + coeffs[1]*fsv + coeffs[2]*fdv*fdv + coeffs[3]*fdv + coeffs[4]*fkv*fkv + c...

[ "This", "is", "the", "EPD", "function", "to", "fit", "using", "a", "smoothed", "mag", "-", "series", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varbase/trends.py#L316-L343

[ "def", "_epd_function", "(", "coeffs", ",", "fsv", ",", "fdv", ",", "fkv", ",", "xcc", ",", "ycc", ",", "bgv", ",", "bge", ",", "iha", ",", "izd", ")", ":", "return", "(", "coeffs", "[", "0", "]", "*", "fsv", "*", "fsv", "+", "coeffs", "[", "...

2922a14619d183fb28005fa7d02027ac436f2265

valid

_epd_residual

This is the residual function to minimize using scipy.optimize.leastsq.

astrobase/varbase/trends.py

def _epd_residual(coeffs, mags, fsv, fdv, fkv, xcc, ycc, bgv, bge, iha, izd): ''' This is the residual function to minimize using scipy.optimize.leastsq. ''' f = _epd_function(coeffs, fsv, fdv, fkv, xcc, ycc, bgv, bge, iha, izd) residual = mags - f return residual

[ "This", "is", "the", "residual", "function", "to", "minimize", "using", "scipy", ".", "optimize", ".", "leastsq", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varbase/trends.py#L347-L355

[ "def", "_epd_residual", "(", "coeffs", ",", "mags", ",", "fsv", ",", "fdv", ",", "fkv", ",", "xcc", ",", "ycc", ",", "bgv", ",", "bge", ",", "iha", ",", "izd", ")", ":", "f", "=", "_epd_function", "(", "coeffs", ",", "fsv", ",", "fdv", ",", "fk...

2922a14619d183fb28005fa7d02027ac436f2265

valid

_epd_residual2

This is the residual function to minimize using scipy.optimize.least_squares. This variant is for :py:func:`.epd_magseries_extparams`.

astrobase/varbase/trends.py

def _epd_residual2(coeffs, times, mags, errs, fsv, fdv, fkv, xcc, ycc, bgv, bge, iha, izd): '''This is the residual function to minimize using scipy.optimize.least_squares. This variant is for :py:func:`.epd_magseries_extparams`. ''' f = _epd_function(coeffs,...

[ "This", "is", "the", "residual", "function", "to", "minimize", "using", "scipy", ".", "optimize", ".", "least_squares", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varbase/trends.py#L359-L371

[ "def", "_epd_residual2", "(", "coeffs", ",", "times", ",", "mags", ",", "errs", ",", "fsv", ",", "fdv", ",", "fkv", ",", "xcc", ",", "ycc", ",", "bgv", ",", "bge", ",", "iha", ",", "izd", ")", ":", "f", "=", "_epd_function", "(", "coeffs", ",", ...

2922a14619d183fb28005fa7d02027ac436f2265

valid

epd_magseries

Detrends a magnitude series using External Parameter Decorrelation. Requires a set of external parameters similar to those present in HAT light curves. At the moment, the HAT light-curve-specific external parameters are: - S: the 'fsv' column in light curves, - D: the 'fdv' column in light curves, ...

astrobase/varbase/trends.py

def epd_magseries(times, mags, errs, fsv, fdv, fkv, xcc, ycc, bgv, bge, iha, izd, magsarefluxes=False, epdsmooth_sigclip=3.0, epdsmooth_windowsize=21, epdsmooth_func=smooth_magseries_savgol, epdsmooth_extraparams...

[ "Detrends", "a", "magnitude", "series", "using", "External", "Parameter", "Decorrelation", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varbase/trends.py#L375-L575

[ "def", "epd_magseries", "(", "times", ",", "mags", ",", "errs", ",", "fsv", ",", "fdv", ",", "fkv", ",", "xcc", ",", "ycc", ",", "bgv", ",", "bge", ",", "iha", ",", "izd", ",", "magsarefluxes", "=", "False", ",", "epdsmooth_sigclip", "=", "3.0", ",...

2922a14619d183fb28005fa7d02027ac436f2265

valid

epd_magseries_extparams

This does EPD on a mag-series with arbitrary external parameters. Parameters ---------- times,mags,errs : np.array The input mag/flux time-series to run EPD on. externalparam_arrs : list of np.arrays This is a list of ndarrays of external parameters to decorrelate against. The...

astrobase/varbase/trends.py

def epd_magseries_extparams( times, mags, errs, externalparam_arrs, initial_coeff_guess, magsarefluxes=False, epdsmooth_sigclip=3.0, epdsmooth_windowsize=21, epdsmooth_func=smooth_magseries_savgol, epdsmooth_extraparams=None, object...

[ "This", "does", "EPD", "on", "a", "mag", "-", "series", "with", "arbitrary", "external", "parameters", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varbase/trends.py#L582-L781

[ "def", "epd_magseries_extparams", "(", "times", ",", "mags", ",", "errs", ",", "externalparam_arrs", ",", "initial_coeff_guess", ",", "magsarefluxes", "=", "False", ",", "epdsmooth_sigclip", "=", "3.0", ",", "epdsmooth_windowsize", "=", "21", ",", "epdsmooth_func", ...

2922a14619d183fb28005fa7d02027ac436f2265

valid

rfepd_magseries

This uses a `RandomForestRegressor` to de-correlate the given magseries. Parameters ---------- times,mags,errs : np.array The input mag/flux time-series to run EPD on. externalparam_arrs : list of np.arrays This is a list of ndarrays of external parameters to decorrelate again...

astrobase/varbase/trends.py

def rfepd_magseries(times, mags, errs, externalparam_arrs, magsarefluxes=False, epdsmooth=True, epdsmooth_sigclip=3.0, epdsmooth_windowsize=21, epdsmooth_func=smooth_magseries_savgol, ...

[ "This", "uses", "a", "RandomForestRegressor", "to", "de", "-", "correlate", "the", "given", "magseries", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varbase/trends.py#L789-L952

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2922a14619d183fb28005fa7d02027ac436f2265

valid

lcfit_features

This calculates various features related to fitting models to light curves. This function: - calculates `R_ij` and `phi_ij` ratios for Fourier fit amplitudes and phases. - calculates the reduced chi-sq for fourier, EB, and planet transit fits. - calculates the reduced chi-sq for fourier, E...

astrobase/varclass/periodicfeatures.py

def lcfit_features(times, mags, errs, period, fourierorder=5, # these are depth, duration, ingress duration transitparams=(-0.01,0.1,0.1), # these are depth, duration, depth ratio, secphase ebparams=(-0.2,0.3,0.7,0.5), ...

[ "This", "calculates", "various", "features", "related", "to", "fitting", "models", "to", "light", "curves", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varclass/periodicfeatures.py#L63-L484

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2922a14619d183fb28005fa7d02027ac436f2265

valid

periodogram_features

This calculates various periodogram features (for each periodogram). The following features are obtained: - For all best periods from all periodogram methods in `pgramlist`, calculates the number of these with peaks that are at least `sampling_peak_multiplier` x time-sampling periodogram peak at t...

astrobase/varclass/periodicfeatures.py

def periodogram_features(pgramlist, times, mags, errs, sigclip=10.0, pdiff_threshold=1.0e-4, sidereal_threshold=1.0e-4, sampling_peak_multiplier=5.0, sampling_startp=None, ...

[ "This", "calculates", "various", "periodogram", "features", "(", "for", "each", "periodogram", ")", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varclass/periodicfeatures.py#L488-L816

[ "def", "periodogram_features", "(", "pgramlist", ",", "times", ",", "mags", ",", "errs", ",", "sigclip", "=", "10.0", ",", "pdiff_threshold", "=", "1.0e-4", ",", "sidereal_threshold", "=", "1.0e-4", ",", "sampling_peak_multiplier", "=", "5.0", ",", "sampling_sta...

2922a14619d183fb28005fa7d02027ac436f2265

valid

phasedlc_features

This calculates various phased LC features for the object. Some of the features calculated here come from: Kim, D.-W., Protopapas, P., Bailer-Jones, C. A. L., et al. 2014, Astronomy and Astrophysics, 566, A43, and references therein (especially Richards, et al. 2011). Parameters ---------- ...

astrobase/varclass/periodicfeatures.py

def phasedlc_features(times, mags, errs, period, nbrtimes=None, nbrmags=None, nbrerrs=None): '''This calculates various phased LC features for the object. Some of the features cal...

[ "This", "calculates", "various", "phased", "LC", "features", "for", "the", "object", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/varclass/periodicfeatures.py#L820-L1085

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2922a14619d183fb28005fa7d02027ac436f2265

valid

stellingwerf_pdm_theta

This calculates the Stellingwerf PDM theta value at a test frequency. Parameters ---------- times,mags,errs : np.array The input time-series and associated errors. frequency : float The test frequency to calculate the theta statistic at. binsize : float The phase bin size...

astrobase/periodbase/spdm.py

def stellingwerf_pdm_theta(times, mags, errs, frequency, binsize=0.05, minbin=9): ''' This calculates the Stellingwerf PDM theta value at a test frequency. Parameters ---------- times,mags,errs : np.array The input time-series and associated errors. frequenc...

[ "This", "calculates", "the", "Stellingwerf", "PDM", "theta", "value", "at", "a", "test", "frequency", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/periodbase/spdm.py#L71-L141

[ "def", "stellingwerf_pdm_theta", "(", "times", ",", "mags", ",", "errs", ",", "frequency", ",", "binsize", "=", "0.05", ",", "minbin", "=", "9", ")", ":", "period", "=", "1.0", "/", "frequency", "fold_time", "=", "times", "[", "0", "]", "phased", "=", ...

2922a14619d183fb28005fa7d02027ac436f2265

valid

_stellingwerf_pdm_worker

This is a parallel worker for the function below. Parameters ---------- task : tuple This is of the form below:: task[0] = times task[1] = mags task[2] = errs task[3] = frequency task[4] = binsize task[5] = minbin Return...

astrobase/periodbase/spdm.py

def _stellingwerf_pdm_worker(task): ''' This is a parallel worker for the function below. Parameters ---------- task : tuple This is of the form below:: task[0] = times task[1] = mags task[2] = errs task[3] = frequency task[4] = ...

[ "This", "is", "a", "parallel", "worker", "for", "the", "function", "below", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/periodbase/spdm.py#L145-L182

[ "def", "_stellingwerf_pdm_worker", "(", "task", ")", ":", "times", ",", "mags", ",", "errs", ",", "frequency", ",", "binsize", ",", "minbin", "=", "task", "try", ":", "theta", "=", "stellingwerf_pdm_theta", "(", "times", ",", "mags", ",", "errs", ",", "f...

2922a14619d183fb28005fa7d02027ac436f2265

valid

stellingwerf_pdm

This runs a parallelized Stellingwerf phase-dispersion minimization (PDM) period search. 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...

astrobase/periodbase/spdm.py

def stellingwerf_pdm(times, mags, errs, magsarefluxes=False, startp=None, endp=None, stepsize=1.0e-4, autofreq=True, normalize=False, ...

[ "This", "runs", "a", "parallelized", "Stellingwerf", "phase", "-", "dispersion", "minimization", "(", "PDM", ")", "period", "search", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/periodbase/spdm.py#L186-L487

[ "def", "stellingwerf_pdm", "(", "times", ",", "mags", ",", "errs", ",", "magsarefluxes", "=", "False", ",", "startp", "=", "None", ",", "endp", "=", "None", ",", "stepsize", "=", "1.0e-4", ",", "autofreq", "=", "True", ",", "normalize", "=", "False", "...

2922a14619d183fb28005fa7d02027ac436f2265

valid

analytic_false_alarm_probability

This returns the analytic false alarm probabilities for periodogram peak values. FIXME: this doesn't actually work. Fix later. The calculation follows that on page 3 of Zechmeister & Kurster (2009):: FAP = 1 − [1 − Prob(z > z0)]**M where:: M is the number of independent frequencies ...

astrobase/periodbase/spdm.py

def analytic_false_alarm_probability(lspinfo, times, conservative_nfreq_eff=True, peakvals=None, inplace=True): '''This returns the analytic false alarm probabilities f...

[ "This", "returns", "the", "analytic", "false", "alarm", "probabilities", "for", "periodogram", "peak", "values", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/periodbase/spdm.py#L491-L605

[ "def", "analytic_false_alarm_probability", "(", "lspinfo", ",", "times", ",", "conservative_nfreq_eff", "=", "True", ",", "peakvals", "=", "None", ",", "inplace", "=", "True", ")", ":", "from", "scipy", ".", "stats", "import", "beta", "frequencies", "=", "1.0"...

2922a14619d183fb28005fa7d02027ac436f2265

valid

keplermag_to_sdssr

Converts magnitude measurements in Kepler band to SDSS r band. Parameters ---------- keplermag : float or array-like The Kepler magnitude value(s) to convert to fluxes. kic_sdssg,kic_sdssr : float or array-like The SDSS g and r magnitudes of the object(s) from the Kepler Input ...

astrobase/astrokep.py

def keplermag_to_sdssr(keplermag, kic_sdssg, kic_sdssr): '''Converts magnitude measurements in Kepler band to SDSS r band. Parameters ---------- keplermag : float or array-like The Kepler magnitude value(s) to convert to fluxes. kic_sdssg,kic_sdssr : float or array-like The SDSS g...

[ "Converts", "magnitude", "measurements", "in", "Kepler", "band", "to", "SDSS", "r", "band", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L138-L165

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2922a14619d183fb28005fa7d02027ac436f2265

valid

read_kepler_fitslc

This extracts the light curve from a single Kepler or K2 LC FITS file. This works on the light curves available at MAST: - `kplr{kepid}-{somedatething}_llc.fits` files from the Kepler mission - `ktwo{epicid}-c{campaign}_llc.fits` files from the K2 mission Parameters ---------- lcfits : str ...

astrobase/astrokep.py

def read_kepler_fitslc( lcfits, headerkeys=LCHEADERKEYS, datakeys=LCDATAKEYS, sapkeys=LCSAPKEYS, pdckeys=LCPDCKEYS, topkeys=LCTOPKEYS, apkeys=LCAPERTUREKEYS, appendto=None, normalize=False, ): '''This extracts the light curve from a single Kepl...

[ "This", "extracts", "the", "light", "curve", "from", "a", "single", "Kepler", "or", "K2", "LC", "FITS", "file", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L244-L611

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2922a14619d183fb28005fa7d02027ac436f2265

valid

consolidate_kepler_fitslc

This gets all Kepler/K2 light curves for the given `keplerid` in `lcfitsdir`. Searches recursively in `lcfitsdir` for all of the files belonging to the specified `keplerid`. Sorts the light curves by time. Returns an `lcdict`. This is meant to be used to consolidate light curves for a single object...

astrobase/astrokep.py

def consolidate_kepler_fitslc(keplerid, lcfitsdir, normalize=True, headerkeys=LCHEADERKEYS, datakeys=LCDATAKEYS, sapkeys=LCSAPKEYS, pdckeys=...

[ "This", "gets", "all", "Kepler", "/", "K2", "light", "curves", "for", "the", "given", "keplerid", "in", "lcfitsdir", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L615-L802

[ "def", "consolidate_kepler_fitslc", "(", "keplerid", ",", "lcfitsdir", ",", "normalize", "=", "True", ",", "headerkeys", "=", "LCHEADERKEYS", ",", "datakeys", "=", "LCDATAKEYS", ",", "sapkeys", "=", "LCSAPKEYS", ",", "pdckeys", "=", "LCPDCKEYS", ",", "topkeys", ...

2922a14619d183fb28005fa7d02027ac436f2265

valid

read_k2sff_lightcurve

This reads a K2 SFF (Vandenberg+ 2014) light curve into an `lcdict`. Use this with the light curves from the K2 SFF project at MAST. Parameters ---------- lcfits : str The filename of the FITS light curve file downloaded from MAST. Returns ------- lcdict Returns an `lcdi...

astrobase/astrokep.py

def read_k2sff_lightcurve(lcfits): '''This reads a K2 SFF (Vandenberg+ 2014) light curve into an `lcdict`. Use this with the light curves from the K2 SFF project at MAST. Parameters ---------- lcfits : str The filename of the FITS light curve file downloaded from MAST. Returns --...

[ "This", "reads", "a", "K2", "SFF", "(", "Vandenberg", "+", "2014", ")", "light", "curve", "into", "an", "lcdict", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L816-L945

[ "def", "read_k2sff_lightcurve", "(", "lcfits", ")", ":", "# read the fits file", "hdulist", "=", "pyfits", ".", "open", "(", "lcfits", ")", "lchdr", ",", "lcdata", "=", "hdulist", "[", "1", "]", ".", "header", ",", "hdulist", "[", "1", "]", ".", "data", ...

2922a14619d183fb28005fa7d02027ac436f2265

valid

kepler_lcdict_to_pkl

This writes the `lcdict` to a Python pickle. Parameters ---------- lcdict : lcdict This is the input `lcdict` to write to a pickle. outfile : str or None If this is None, the object's Kepler ID/EPIC ID will determined from the `lcdict` and used to form the filename of the outp...

astrobase/astrokep.py

def kepler_lcdict_to_pkl(lcdict, outfile=None): '''This writes the `lcdict` to a Python pickle. Parameters ---------- lcdict : lcdict This is the input `lcdict` to write to a pickle. outfile : str or None If this is None, the object's Kepler ID/EPIC ID will determined from the ...

[ "This", "writes", "the", "lcdict", "to", "a", "Python", "pickle", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L953-L983

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2922a14619d183fb28005fa7d02027ac436f2265

valid

read_kepler_pklc

This turns the pickled lightcurve file back into an `lcdict`. Parameters ---------- picklefile : str The path to a previously written Kepler LC picklefile generated by `kepler_lcdict_to_pkl` above. Returns ------- lcdict Returns an `lcdict` (this is useable by most as...

astrobase/astrokep.py

def read_kepler_pklc(picklefile): '''This turns the pickled lightcurve file back into an `lcdict`. Parameters ---------- picklefile : str The path to a previously written Kepler LC picklefile generated by `kepler_lcdict_to_pkl` above. Returns ------- lcdict Return...

[ "This", "turns", "the", "pickled", "lightcurve", "file", "back", "into", "an", "lcdict", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L987-L1025

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2922a14619d183fb28005fa7d02027ac436f2265

valid

filter_kepler_lcdict

This filters the Kepler `lcdict`, removing nans and bad observations. By default, this function removes points in the Kepler LC that have ANY quality flags set. Parameters ---------- lcdict : lcdict An `lcdict` produced by `consolidate_kepler_fitslc` or `read_kepler_fitslc`. ...

astrobase/astrokep.py

def filter_kepler_lcdict(lcdict, filterflags=True, nanfilter='sap,pdc', timestoignore=None): '''This filters the Kepler `lcdict`, removing nans and bad observations. By default, this function removes points in the Kepler LC that hav...

[ "This", "filters", "the", "Kepler", "lcdict", "removing", "nans", "and", "bad", "observations", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L1058-L1182

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2922a14619d183fb28005fa7d02027ac436f2265

valid

_epd_function

This is the EPD function to fit. Parameters ---------- coeffs : array-like of floats Contains the EPD coefficients that will be used to generate the EPD fit function. fluxes : array-like The flux measurement array being used. xcc,ycc : array-like Arrays of the x a...

astrobase/astrokep.py

def _epd_function(coeffs, fluxes, xcc, ycc, bgv, bge): '''This is the EPD function to fit. Parameters ---------- coeffs : array-like of floats Contains the EPD coefficients that will be used to generate the EPD fit function. fluxes : array-like The flux measurement array b...

[ "This", "is", "the", "EPD", "function", "to", "fit", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L1190-L1229

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2922a14619d183fb28005fa7d02027ac436f2265

valid

_epd_residual

This is the residual function to minimize using scipy.optimize.leastsq. Parameters ---------- coeffs : array-like of floats Contains the EPD coefficients that will be used to generate the EPD fit function. fluxes : array-like The flux measurement array being used. xcc,ycc...

astrobase/astrokep.py

def _epd_residual(coeffs, fluxes, xcc, ycc, bgv, bge): '''This is the residual function to minimize using scipy.optimize.leastsq. Parameters ---------- coeffs : array-like of floats Contains the EPD coefficients that will be used to generate the EPD fit function. fluxes : array-li...

[ "This", "is", "the", "residual", "function", "to", "minimize", "using", "scipy", ".", "optimize", ".", "leastsq", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L1233-L1265

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2922a14619d183fb28005fa7d02027ac436f2265

valid

epd_kepler_lightcurve

This runs EPD on the Kepler light curve. Following Huang et al. 2015, we fit the following EPD function to a smoothed light curve, and then subtract it to obtain EPD corrected magnitudes:: f = c0 + c1*sin(2*pi*x) + c2*cos(2*pi*x) + c3*sin(2*pi*y) + c4*cos(2*pi*y) + c5*sin(4*pi*...

astrobase/astrokep.py

def epd_kepler_lightcurve(lcdict, xccol='mom_centr1', yccol='mom_centr2', timestoignore=None, filterflags=True, writetodict=True, epdsmooth=5): '''This runs EPD...

[ "This", "runs", "EPD", "on", "the", "Kepler", "light", "curve", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L1269-L1472

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2922a14619d183fb28005fa7d02027ac436f2265

valid

rfepd_kepler_lightcurve

This uses a `RandomForestRegressor` to fit and decorrelate Kepler light curves. Fits the X and Y positions, the background, and background error. By default, this function removes points in the Kepler LC that have ANY quality flags set. Parameters ---------- lcdict : lcdict An `l...

astrobase/astrokep.py

def rfepd_kepler_lightcurve( lcdict, xccol='mom_centr1', yccol='mom_centr2', timestoignore=None, filterflags=True, writetodict=True, epdsmooth=23, decorr='xcc,ycc', nrftrees=200 ): '''This uses a `RandomForestRegressor` to fit and decorrelate K...

[ "This", "uses", "a", "RandomForestRegressor", "to", "fit", "and", "decorrelate", "Kepler", "light", "curves", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L1476-L1691

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2922a14619d183fb28005fa7d02027ac436f2265

valid

detrend_centroid

Detrends the x and y coordinate centroids for a Kepler light curve. Given an `lcdict` for a single quarter of Kepler data, returned by `read_kepler_fitslc`, this function returns this same dictionary, appending detrended centroid_x and centroid_y values. Here "detrended" means "finite, SAP quality fla...

astrobase/astrokep.py

def detrend_centroid(lcd, detrend='legendre', sigclip=None, mingap=0.5): '''Detrends the x and y coordinate centroids for a Kepler light curve. Given an `lcdict` for a single quarter of Kepler data, returned by `read_kepler_fitslc`, this function returns this same dictionary, appending detrended centro...

[ "Detrends", "the", "x", "and", "y", "coordinate", "centroids", "for", "a", "Kepler", "light", "curve", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L1699-L1935

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2922a14619d183fb28005fa7d02027ac436f2265

valid

get_centroid_offsets

After running `detrend_centroid`, this gets positions of centroids during transits, and outside of transits. These positions can then be used in a false positive analysis. This routine requires knowing the ingress and egress times for every transit of interest within the quarter this routine is being ...

astrobase/astrokep.py

def get_centroid_offsets(lcd, t_ing_egr, oot_buffer_time=0.1, sample_factor=3): '''After running `detrend_centroid`, this gets positions of centroids during transits, and outside of transits. These positions can then be used in a false positive analysis. This routine requires knowing the ingress and e...

[ "After", "running", "detrend_centroid", "this", "gets", "positions", "of", "centroids", "during", "transits", "and", "outside", "of", "transits", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L1939-L2055

[ "def", "get_centroid_offsets", "(", "lcd", ",", "t_ing_egr", ",", "oot_buffer_time", "=", "0.1", ",", "sample_factor", "=", "3", ")", ":", "# NOTE:", "# Bryson+ (2013) gives a more complicated and more correct approach to this", "# problem, computing offsets relative to positions...

2922a14619d183fb28005fa7d02027ac436f2265

valid

_get_legendre_deg_ctd

This is a helper function for centroid detrending.

astrobase/astrokep.py

def _get_legendre_deg_ctd(npts): '''This is a helper function for centroid detrending. ''' from scipy.interpolate import interp1d degs = nparray([4,5,6,10,15]) pts = nparray([1e2,3e2,5e2,1e3,3e3]) fn = interp1d(pts, degs, kind='linear', bounds_error=False, ...

[ "This", "is", "a", "helper", "function", "for", "centroid", "detrending", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L2063-L2077

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2922a14619d183fb28005fa7d02027ac436f2265

valid

_legendre_dtr

This calculates the residual and chi-sq values for a Legendre function fit. Parameters ---------- x : np.array Array of the independent variable. y : np.array Array of the dependent variable. y_err : np.array Array of errors associated with each `y` value. Used to cal...

astrobase/astrokep.py

def _legendre_dtr(x, y, y_err, legendredeg=10): '''This calculates the residual and chi-sq values for a Legendre function fit. Parameters ---------- x : np.array Array of the independent variable. y : np.array Array of the dependent variable. y_err : np.array Arra...

[ "This", "calculates", "the", "residual", "and", "chi", "-", "sq", "values", "for", "a", "Legendre", "function", "fit", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/astrokep.py#L2085-L2130

[ "def", "_legendre_dtr", "(", "x", ",", "y", ",", "y_err", ",", "legendredeg", "=", "10", ")", ":", "try", ":", "p", "=", "Legendre", ".", "fit", "(", "x", ",", "y", ",", "legendredeg", ")", "fit_y", "=", "p", "(", "x", ")", "except", "Exception",...

2922a14619d183fb28005fa7d02027ac436f2265

valid

timebinlc

This bins the given light curve file in time using the specified bin size. Parameters ---------- lcfile : str The file name to process. binsizesec : float The time bin-size in seconds. outdir : str or None If this is a str, the output LC will be written to `outdir`. If th...

astrobase/lcproc/lcbin.py

def timebinlc(lcfile, binsizesec, outdir=None, lcformat='hat-sql', lcformatdir=None, timecols=None, magcols=None, errcols=None, minbinelems=7): '''This bins the given light curve file in time using the s...

[ "This", "bins", "the", "given", "light", "curve", "file", "in", "time", "using", "the", "specified", "bin", "size", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/lcbin.py#L87-L249

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2922a14619d183fb28005fa7d02027ac436f2265

valid

timebinlc_worker

This is a parallel worker for the function below. Parameters ---------- task : tuple This is of the form:: task[0] = lcfile task[1] = binsizesec task[3] = {'outdir','lcformat','lcformatdir', 'timecols','magcols','errcols','minbinelems'} ...

astrobase/lcproc/lcbin.py

def timebinlc_worker(task): ''' This is a parallel worker for the function below. Parameters ---------- task : tuple This is of the form:: task[0] = lcfile task[1] = binsizesec task[3] = {'outdir','lcformat','lcformatdir', 'timeco...

[ "This", "is", "a", "parallel", "worker", "for", "the", "function", "below", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/lcbin.py#L253-L286

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2922a14619d183fb28005fa7d02027ac436f2265

valid

parallel_timebin

This time-bins all the LCs in the list using the specified bin size. Parameters ---------- lclist : list of str The input LCs to process. binsizesec : float The time bin size to use in seconds. maxobjects : int or None If provided, LC processing will stop at `lclist[maxob...

astrobase/lcproc/lcbin.py

def parallel_timebin(lclist, binsizesec, maxobjects=None, outdir=None, lcformat='hat-sql', lcformatdir=None, timecols=None, magcols=None, errcols=None, ...

[ "This", "time", "-", "bins", "all", "the", "LCs", "in", "the", "list", "using", "the", "specified", "bin", "size", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/lcbin.py#L290-L379

[ "def", "parallel_timebin", "(", "lclist", ",", "binsizesec", ",", "maxobjects", "=", "None", ",", "outdir", "=", "None", ",", "lcformat", "=", "'hat-sql'", ",", "lcformatdir", "=", "None", ",", "timecols", "=", "None", ",", "magcols", "=", "None", ",", "...

2922a14619d183fb28005fa7d02027ac436f2265

valid

parallel_timebin_lcdir

This time bins all the light curves in the specified directory. Parameters ---------- lcdir : list of str Directory containing the input LCs to process. binsizesec : float The time bin size to use in seconds. maxobjects : int or None If provided, LC processing will stop a...

astrobase/lcproc/lcbin.py

def parallel_timebin_lcdir(lcdir, binsizesec, maxobjects=None, outdir=None, lcformat='hat-sql', lcformatdir=None, timecols=None, ma...

[ "This", "time", "bins", "all", "the", "light", "curves", "in", "the", "specified", "directory", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/lcbin.py#L383-L477

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2922a14619d183fb28005fa7d02027ac436f2265

valid

get_varfeatures

This runs :py:func:`astrobase.varclass.varfeatures.all_nonperiodic_features` on a single LC file. Parameters ---------- lcfile : str The input light curve to process. outfile : str The filename of the output variable features pickle that will be generated. timecols : ...

astrobase/lcproc/lcvfeatures.py

def get_varfeatures(lcfile, outdir, timecols=None, magcols=None, errcols=None, mindet=1000, lcformat='hat-sql', lcformatdir=None): '''This runs :py:func:`astrobase.varclass.var...

[ "This", "runs", ":", "py", ":", "func", ":", "astrobase", ".", "varclass", ".", "varfeatures", ".", "all_nonperiodic_features", "on", "a", "single", "LC", "file", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/lcvfeatures.py#L96-L279

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2922a14619d183fb28005fa7d02027ac436f2265

valid

_varfeatures_worker

This wraps varfeatures.

astrobase/lcproc/lcvfeatures.py

def _varfeatures_worker(task): ''' This wraps varfeatures. ''' try: (lcfile, outdir, timecols, magcols, errcols, mindet, lcformat, lcformatdir) = task return get_varfeatures(lcfile, outdir, timecols=timecols, magcol...

[ "This", "wraps", "varfeatures", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/lcvfeatures.py#L283-L301

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2922a14619d183fb28005fa7d02027ac436f2265

valid

serial_varfeatures

This runs variability feature extraction for a list of LCs. Parameters ---------- lclist : list of str The list of light curve file names to process. outdir : str The directory where the output varfeatures pickle files will be written. maxobjects : int The number of LCs t...

astrobase/lcproc/lcvfeatures.py

def serial_varfeatures(lclist, outdir, maxobjects=None, timecols=None, magcols=None, errcols=None, mindet=1000, lcformat='hat-sql', lcfo...

[ "This", "runs", "variability", "feature", "extraction", "for", "a", "list", "of", "LCs", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/lcvfeatures.py#L304-L372

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2922a14619d183fb28005fa7d02027ac436f2265

valid

parallel_varfeatures

This runs variable feature extraction in parallel for all LCs in `lclist`. Parameters ---------- lclist : list of str The list of light curve file names to process. outdir : str The directory where the output varfeatures pickle files will be written. maxobjects : int The ...

astrobase/lcproc/lcvfeatures.py

def parallel_varfeatures(lclist, outdir, maxobjects=None, timecols=None, magcols=None, errcols=None, mindet=1000, lcformat='hat-sql', ...

[ "This", "runs", "variable", "feature", "extraction", "in", "parallel", "for", "all", "LCs", "in", "lclist", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/lcvfeatures.py#L376-L454

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2922a14619d183fb28005fa7d02027ac436f2265

valid

parallel_varfeatures_lcdir

This runs parallel variable feature extraction for a directory of LCs. Parameters ---------- lcdir : str The directory of light curve files to process. outdir : str The directory where the output varfeatures pickle files will be written. fileglob : str or None The file gl...

astrobase/lcproc/lcvfeatures.py

def parallel_varfeatures_lcdir(lcdir, outdir, fileglob=None, maxobjects=None, timecols=None, magcols=None, errcols=None, ...

[ "This", "runs", "parallel", "variable", "feature", "extraction", "for", "a", "directory", "of", "LCs", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/lcvfeatures.py#L458-L598

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2922a14619d183fb28005fa7d02027ac436f2265

valid

checkplot_pickle_to_png

This reads the checkplot pickle or dict provided, and writes out a PNG. The output PNG contains most of the information in the input checkplot pickle/dict, and can be used to quickly glance through the highlights instead of having to review the checkplot with the `checkplotserver` webapp. This is usefu...

astrobase/checkplot/pkl_png.py

def checkplot_pickle_to_png( checkplotin, outfile, extrarows=None ): '''This reads the checkplot pickle or dict provided, and writes out a PNG. The output PNG contains most of the information in the input checkplot pickle/dict, and can be used to quickly glance through the highlight...

[ "This", "reads", "the", "checkplot", "pickle", "or", "dict", "provided", "and", "writes", "out", "a", "PNG", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/checkplot/pkl_png.py#L75-L1129

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2922a14619d183fb28005fa7d02027ac436f2265

valid

cp2png

This is just a shortened form of the function above for convenience. This only handles pickle files as input. Parameters ---------- checkplotin : str File name of a checkplot pickle file to convert to a PNG. extrarows : list of tuples This is a list of 4-element tuples containing...

astrobase/checkplot/pkl_png.py

def cp2png(checkplotin, extrarows=None): '''This is just a shortened form of the function above for convenience. This only handles pickle files as input. Parameters ---------- checkplotin : str File name of a checkplot pickle file to convert to a PNG. extrarows : list of tuples ...

[ "This", "is", "just", "a", "shortened", "form", "of", "the", "function", "above", "for", "convenience", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/checkplot/pkl_png.py#L1133-L1199

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2922a14619d183fb28005fa7d02027ac436f2265

valid

flare_model

This is a flare model function, similar to Kowalski+ 2011. From the paper by Pitkin+ 2014: http://adsabs.harvard.edu/abs/2014MNRAS.445.2268P Parameters ---------- flareparams : list of float This defines the flare model:: [amplitude, flare_peak_time, ...

astrobase/lcmodels/flares.py

def flare_model(flareparams, times, mags, errs): '''This is a flare model function, similar to Kowalski+ 2011. From the paper by Pitkin+ 2014: http://adsabs.harvard.edu/abs/2014MNRAS.445.2268P Parameters ---------- flareparams : list of float This defines the flare model:: ...

[ "This", "is", "a", "flare", "model", "function", "similar", "to", "Kowalski", "+", "2011", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcmodels/flares.py#L18-L90

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2922a14619d183fb28005fa7d02027ac436f2265

valid

flare_model_residual

This returns the residual between model mags and the actual mags. Parameters ---------- flareparams : list of float This defines the flare model:: [amplitude, flare_peak_time, rise_gaussian_stdev, decay_time_constant] where: `am...

astrobase/lcmodels/flares.py

def flare_model_residual(flareparams, times, mags, errs): ''' This returns the residual between model mags and the actual mags. Parameters ---------- flareparams : list of float This defines the flare model:: [amplitude, flare_peak_time, rise_gaussian...

[ "This", "returns", "the", "residual", "between", "model", "mags", "and", "the", "actual", "mags", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcmodels/flares.py#L94-L138

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2922a14619d183fb28005fa7d02027ac436f2265

valid

cache_clean_handler

This periodically cleans up the ~/.astrobase cache to save us from disk-space doom. Parameters ---------- min_age_hours : int Files older than this number of hours from the current time will be deleted. Returns ------- Nothing.

astrobase/lcproc/awsrun.py

def cache_clean_handler(min_age_hours=1): """This periodically cleans up the ~/.astrobase cache to save us from disk-space doom. Parameters ---------- min_age_hours : int Files older than this number of hours from the current time will be deleted. Returns ------- Noth...

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waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/awsrun.py#L194-L225

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2922a14619d183fb28005fa7d02027ac436f2265

valid

shutdown_check_handler

This checks the AWS instance data URL to see if there's a pending shutdown for the instance. This is useful for AWS spot instances. If there is a pending shutdown posted to the instance data URL, we'll use the result of this function break out of the processing loop and shut everything down ASAP before...

astrobase/lcproc/awsrun.py

def shutdown_check_handler(): """This checks the AWS instance data URL to see if there's a pending shutdown for the instance. This is useful for AWS spot instances. If there is a pending shutdown posted to the instance data URL, we'll use the result of this function break out of the processing loop...

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waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/awsrun.py#L229-L272

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2922a14619d183fb28005fa7d02027ac436f2265

valid

runcp_producer_loop

This sends checkplot making tasks to the input queue and monitors the result queue for task completion. Parameters ---------- lightcurve_list : str or list of str This is either a string pointing to a file containing a list of light curves filenames to process or the list itself. The n...

astrobase/lcproc/awsrun.py

def runcp_producer_loop( lightcurve_list, input_queue, input_bucket, result_queue, result_bucket, pfresult_list=None, runcp_kwargs=None, process_list_slice=None, purge_queues_when_done=False, delete_queues_when_done=False, download_...

[ "This", "sends", "checkplot", "making", "tasks", "to", "the", "input", "queue", "and", "monitors", "the", "result", "queue", "for", "task", "completion", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/awsrun.py#L280-L564

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2922a14619d183fb28005fa7d02027ac436f2265

valid

runcp_producer_loop_savedstate

This wraps the function above to allow for loading previous state from a file. Parameters ---------- use_saved_state : str or None This is the path to the saved state pickle file produced by a previous run of `runcp_producer_loop`. Will get all of the arguments to run another i...

astrobase/lcproc/awsrun.py

def runcp_producer_loop_savedstate( use_saved_state=None, lightcurve_list=None, input_queue=None, input_bucket=None, result_queue=None, result_bucket=None, pfresult_list=None, runcp_kwargs=None, process_list_slice=None, download_when_done=T...

[ "This", "wraps", "the", "function", "above", "to", "allow", "for", "loading", "previous", "state", "from", "a", "file", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/awsrun.py#L568-L722

[ "def", "runcp_producer_loop_savedstate", "(", "use_saved_state", "=", "None", ",", "lightcurve_list", "=", "None", ",", "input_queue", "=", "None", ",", "input_bucket", "=", "None", ",", "result_queue", "=", "None", ",", "result_bucket", "=", "None", ",", "pfres...

2922a14619d183fb28005fa7d02027ac436f2265

valid

runcp_consumer_loop

This runs checkplot pickle making in a loop until interrupted. Consumes work task items from an input queue set up by `runcp_producer_loop` above. For the moment, we don't generate neighbor light curves since this would require a lot more S3 calls. Parameters ---------- in_queue_url : str ...

astrobase/lcproc/awsrun.py

def runcp_consumer_loop( in_queue_url, workdir, lclist_pkl_s3url, lc_altexts=('',), wait_time_seconds=5, cache_clean_timer_seconds=3600.0, shutdown_check_timer_seconds=60.0, sqs_client=None, s3_client=None ): """This runs checkplot pickle maki...

[ "This", "runs", "checkplot", "pickle", "making", "in", "a", "loop", "until", "interrupted", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/awsrun.py#L726-L1153

[ "def", "runcp_consumer_loop", "(", "in_queue_url", ",", "workdir", ",", "lclist_pkl_s3url", ",", "lc_altexts", "=", "(", "''", ",", ")", ",", "wait_time_seconds", "=", "5", ",", "cache_clean_timer_seconds", "=", "3600.0", ",", "shutdown_check_timer_seconds", "=", ...

2922a14619d183fb28005fa7d02027ac436f2265

valid

runpf_consumer_loop

This runs period-finding in a loop until interrupted. Consumes work task items from an input queue set up by `runpf_producer_loop` above. Parameters ---------- in_queue_url : str The SQS URL of the input queue to listen to for work assignment messages. The task orders will include...

astrobase/lcproc/awsrun.py

def runpf_consumer_loop( in_queue_url, workdir, lc_altexts=('',), wait_time_seconds=5, shutdown_check_timer_seconds=60.0, sqs_client=None, s3_client=None ): """This runs period-finding in a loop until interrupted. Consumes work task items from an input qu...

[ "This", "runs", "period", "-", "finding", "in", "a", "loop", "until", "interrupted", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/awsrun.py#L1454-L1821

[ "def", "runpf_consumer_loop", "(", "in_queue_url", ",", "workdir", ",", "lc_altexts", "=", "(", "''", ",", ")", ",", "wait_time_seconds", "=", "5", ",", "shutdown_check_timer_seconds", "=", "60.0", ",", "sqs_client", "=", "None", ",", "s3_client", "=", "None",...

2922a14619d183fb28005fa7d02027ac436f2265

valid

gaussianeb_fit_magseries

This fits a double inverted gaussian EB model to a magnitude time series. Parameters ---------- times,mags,errs : np.array The input mag/flux time-series to fit the EB model to. period : float The period to use for EB fit. ebparams : list of float This is a list containin...

astrobase/lcfit/eclipses.py

def gaussianeb_fit_magseries(times, mags, errs, ebparams, sigclip=10.0, plotfit=False, magsarefluxes=False, verbose=True): '''This fits a double inverted gaussian EB model...

[ "This", "fits", "a", "double", "inverted", "gaussian", "EB", "model", "to", "a", "magnitude", "time", "series", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/eclipses.py#L63-L382

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2922a14619d183fb28005fa7d02027ac436f2265

valid

spline_fit_magseries

This fits a univariate cubic spline to the phased light curve. This fit may be better than the Fourier fit for sharply variable objects, like EBs, so can be used to distinguish them from other types of variables. Parameters ---------- times,mags,errs : np.array The input mag/flux time-ser...

astrobase/lcfit/nonphysical.py

def spline_fit_magseries(times, mags, errs, period, knotfraction=0.01, maxknots=30, sigclip=30.0, plotfit=False, ignoreinitfail=False, magsarefluxes=False, ...

[ "This", "fits", "a", "univariate", "cubic", "spline", "to", "the", "phased", "light", "curve", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/nonphysical.py#L72-L263

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2922a14619d183fb28005fa7d02027ac436f2265

valid

savgol_fit_magseries

Fit a Savitzky-Golay filter to the magnitude/flux time series. SG fits successive sub-sets (windows) of adjacent data points with a low-order polynomial via least squares. At each point (magnitude), it returns the value of the polynomial at that magnitude's time. This is made significantly cheaper tha...

astrobase/lcfit/nonphysical.py

def savgol_fit_magseries(times, mags, errs, period, windowlength=None, polydeg=2, sigclip=30.0, plotfit=False, magsarefluxes=False, verbose=True): '''Fit a Savitzky-...

[ "Fit", "a", "Savitzky", "-", "Golay", "filter", "to", "the", "magnitude", "/", "flux", "time", "series", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/nonphysical.py#L271-L484

[ "def", "savgol_fit_magseries", "(", "times", ",", "mags", ",", "errs", ",", "period", ",", "windowlength", "=", "None", ",", "polydeg", "=", "2", ",", "sigclip", "=", "30.0", ",", "plotfit", "=", "False", ",", "magsarefluxes", "=", "False", ",", "verbose...

2922a14619d183fb28005fa7d02027ac436f2265

valid

legendre_fit_magseries

Fit an arbitrary-order Legendre series, via least squares, to the magnitude/flux time series. This is a series of the form:: p(x) = c_0*L_0(x) + c_1*L_1(x) + c_2*L_2(x) + ... + c_n*L_n(x) where L_i's are Legendre polynomials (also called "Legendre functions of the first kind") and c_i's are t...

astrobase/lcfit/nonphysical.py

def legendre_fit_magseries(times, mags, errs, period, legendredeg=10, sigclip=30.0, plotfit=False, magsarefluxes=False, verbose=True): '''Fit an arbitrary-order Legendre series, vi...

[ "Fit", "an", "arbitrary", "-", "order", "Legendre", "series", "via", "least", "squares", "to", "the", "magnitude", "/", "flux", "time", "series", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcfit/nonphysical.py#L491-L676

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2922a14619d183fb28005fa7d02027ac436f2265

valid

update_checkplotdict_nbrlcs

For all neighbors in a checkplotdict, make LCs and phased LCs. Parameters ---------- checkplotdict : dict This is the checkplot to process. The light curves for the neighbors to the object here will be extracted from the stored file paths, and this function will make plots of these...

astrobase/lcproc/checkplotgen.py

def update_checkplotdict_nbrlcs( checkplotdict, timecol, magcol, errcol, lcformat='hat-sql', lcformatdir=None, verbose=True, ): '''For all neighbors in a checkplotdict, make LCs and phased LCs. Parameters ---------- checkplotdict : dict This is the chec...

[ "For", "all", "neighbors", "in", "a", "checkplotdict", "make", "LCs", "and", "phased", "LCs", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/checkplotgen.py#L102-L394

[ "def", "update_checkplotdict_nbrlcs", "(", "checkplotdict", ",", "timecol", ",", "magcol", ",", "errcol", ",", "lcformat", "=", "'hat-sql'", ",", "lcformatdir", "=", "None", ",", "verbose", "=", "True", ",", ")", ":", "try", ":", "formatinfo", "=", "get_lcfo...

2922a14619d183fb28005fa7d02027ac436f2265

valid

runcp

This makes a checkplot pickle for the given period-finding result pickle produced by `lcproc.periodfinding.runpf`. Parameters ---------- pfpickle : str or None This is the filename of the period-finding result pickle file created by `lcproc.periodfinding.runpf`. If this is None, the ch...

astrobase/lcproc/checkplotgen.py

def runcp( pfpickle, outdir, lcbasedir, lcfname=None, cprenorm=False, lclistpkl=None, nbrradiusarcsec=60.0, maxnumneighbors=5, makeneighborlcs=True, fast_mode=False, gaia_max_timeout=60.0, gaia_mirror=None, xmatchinf...

[ "This", "makes", "a", "checkplot", "pickle", "for", "the", "given", "period", "-", "finding", "result", "pickle", "produced", "by", "lcproc", ".", "periodfinding", ".", "runpf", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/checkplotgen.py#L402-L906

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2922a14619d183fb28005fa7d02027ac436f2265

valid

runcp_worker

This is the worker for running checkplots. Parameters ---------- task : tuple This is of the form: (pfpickle, outdir, lcbasedir, kwargs). Returns ------- list of str The list of checkplot pickles returned by the `runcp` function.

astrobase/lcproc/checkplotgen.py

def runcp_worker(task): ''' This is the worker for running checkplots. Parameters ---------- task : tuple This is of the form: (pfpickle, outdir, lcbasedir, kwargs). Returns ------- list of str The list of checkplot pickles returned by the `runcp` function. ''' ...

[ "This", "is", "the", "worker", "for", "running", "checkplots", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/checkplotgen.py#L910-L937

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2922a14619d183fb28005fa7d02027ac436f2265

valid

parallel_cp

This drives the parallel execution of `runcp` for a list of periodfinding result pickles. Parameters ---------- pfpicklelist : list of str or list of Nones This is the list of the filenames of the period-finding result pickles to process. To make checkplots using the light curves direc...

astrobase/lcproc/checkplotgen.py

def parallel_cp( pfpicklelist, outdir, lcbasedir, fast_mode=False, lcfnamelist=None, cprenorm=False, lclistpkl=None, gaia_max_timeout=60.0, gaia_mirror=None, nbrradiusarcsec=60.0, maxnumneighbors=5, makeneighborlcs=True, ...

[ "This", "drives", "the", "parallel", "execution", "of", "runcp", "for", "a", "list", "of", "periodfinding", "result", "pickles", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/checkplotgen.py#L941-L1235

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2922a14619d183fb28005fa7d02027ac436f2265

valid

parallel_cp_pfdir

This drives the parallel execution of `runcp` for a directory of periodfinding pickles. Parameters ---------- pfpickledir : str This is the directory containing all of the period-finding pickles to process. outdir : str The directory the checkplot pickles will be written t...

astrobase/lcproc/checkplotgen.py

def parallel_cp_pfdir(pfpickledir, outdir, lcbasedir, pfpickleglob='periodfinding-*.pkl*', lclistpkl=None, cprenorm=False, nbrradiusarcsec=60.0, maxnumneighbors=5, ...

[ "This", "drives", "the", "parallel", "execution", "of", "runcp", "for", "a", "directory", "of", "periodfinding", "pickles", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/checkplotgen.py#L1239-L1483

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2922a14619d183fb28005fa7d02027ac436f2265

valid

runpf

This runs the period-finding for a single LC. Parameters ---------- lcfile : str The light curve file to run period-finding on. outdir : str The output directory where the result pickle will go. timecols : list of str or None The timecol keys to use from the lcdict in cal...

astrobase/lcproc/periodsearch.py

def runpf(lcfile, outdir, timecols=None, magcols=None, errcols=None, lcformat='hat-sql', lcformatdir=None, pfmethods=('gls','pdm','mav','win'), pfkwargs=({},{},{},{}), sigclip=10.0, getblssnr=False, nworkers=NC...

[ "This", "runs", "the", "period", "-", "finding", "for", "a", "single", "LC", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/periodsearch.py#L108-L457

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2922a14619d183fb28005fa7d02027ac436f2265

valid

_runpf_worker

This runs the runpf function.

astrobase/lcproc/periodsearch.py

def _runpf_worker(task): ''' This runs the runpf function. ''' (lcfile, outdir, timecols, magcols, errcols, lcformat, lcformatdir, pfmethods, pfkwargs, getblssnr, sigclip, nworkers, minobservations, excludeprocessed) = task if os.path.exists(lcfile): pfresult = runpf(lcfile, ...

[ "This", "runs", "the", "runpf", "function", "." ]

waqasbhatti/astrobase

python

https://github.com/waqasbhatti/astrobase/blob/2922a14619d183fb28005fa7d02027ac436f2265/astrobase/lcproc/periodsearch.py#L461-L489

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2922a14619d183fb28005fa7d02027ac436f2265