pySYD option glossary

Below is a complete list of pySYD parameters in alphabetical order.

-a, --ask

the option to select which trial (or estimate) of numax to use from the first module

• dest = args.ask

• type = bool

• default = False

• action = store_true

• see also: –trials, –ntrials

--all, --showall

creates an additional figure that shows all the iterated background models, which will highlight the selected model

• dest = args.showall

• type = bool

• default = False

• action = store_true

-b, --bg, --background

controls the background-fitting procedure – BUT this should never be touched since a majority of the work done in the software happens here and it should not need to be turned off

• dest = args.background

• type = bool

• default = True

• action = store_false

--basis

which basis to use for the background fitting (i.e. 'a_b', 'pgran_tau', 'tau_sigma'), NOT OPERATIONAL YET

• dest = args.basis

• type = str

• default = 'tau_sigma'

--bf, --box, --boxfilter

box filter width for plotting the power spectrum TODO: make sure this does not affect any actual measurements and this is just an aesthetic

• dest = args.box_filter

• type = float

• default = 1.0

• unit = \(\mu \mathrm{Hz}\)

--bin, --binning

interval for the binning of spectrum in \(\mathrm{log(}\mu\mathrm{Hz)}\) this bins equally in logspace

• dest = args.binning

• type = float

• default = 0.005

• unit = log(\(\mu \mathrm{Hz}\))

--bm, --mode, --bmode

which mode to choose when binning. Choices are ~["mean", "median", "gaussian"]

• dest = args.mode

• type = str

• default = "mean"

--ce, --cm, --color

change the colormap used in the echelle diagram, which is 'binary' by default

• dest = args.cmap

• type = str

• default = 'binary'

--cv, --value

the clip value to use for the output echelle diagram if and only if args.clip_ech is True. If none is provided, it will use a value that is 3x the median value of the folded power spectrum

• dest = args.clip_value

• type = float

• default = 3.0

• unit = fractional psd

--cli

this should never be touched - for internal workings on how to retrieve and save parameters

• dest = args.cli

• type = bool

• default = True

• action = store_true

-d, --show, --display

show output figures, which is not recommended if running many stars

• dest = args.show

• type = bool

• default = False

• action = store_true

--dnu

option to provide the spacing to fold the power spectrum and “whiten” effects due to mixed modes (pysyd.target.Target.whiten_mixed), which also requires a lower and upper folded frequency (i.e. <= dnu) via –le and –ue

• dest = args.dnu

• type = float

• nargs = '*'

• default = None

• **REQUIRES:** –le/–lowere and –ue/–uppere

-e, --est, --estimate

turn off the first module that searches and idenities power excess due to solar-like oscillations, which will automatically happen if numax is provided

• dest = args.estimate

• type = bool

• default = True

• action = store_false

--ew, --exwidth

the fractional value of the width to use surrounding the power excess, which is computed using a solar scaling relation (and then centered on the estimated \(\nu_{\mathrm{max}}\))

• dest = args.width

• type = float

• default = 1.0

• unit = fractional \(\mu \mathrm{Hz}\)

• see also: –lp, –lowerp, –up, –upperp

-f, --fft

use the numpy.correlate module instead of FFTs to compute the ACF

• dest = args.fft

• type = bool

• default = True

• action = store_false

--file, --list, --todo

the path to the text file that contains the list of stars to process, which is convenient for running many stars

• dest = args.file

• type = str

• default = TODODIR

• see also: –star, –stars

-g, --globe, --global

do not estimate the global asteroseismic parameter numax and dnu. This is helpful for the application to cool dwarfs, where detecting solar-like oscillations is quite difficult but you’d still like to characterize the granulation components.

• dest = args.globe

• type = bool

• default = True

• action = store_false

--gap, --gaps

what constitutes a time series gap (i.e. how many cadences)

• dest = args.gap

• type = int

• default = 20

• see also: -x, –stitch, –stitching

-i, --ie, --interpech

turn on the bilinear interpolation of the plotted echelle diagram

• dest = args.interp_ech

• type = bool

• default = False

• action = store_true

• see also: –se, –smoothech

--in, --input, --inpdir

path to the input data

• dest = args.inpdir

• type = str

• default = INPDIR

--infdir

path to relevant pySYD information (defined in init file)

• dest = args.infdir

• type = str

• default = INFDIR

• see also: –file, –info, –information, –list, –todo

--info, --information

path to the csv containing all the stellar information (although not required)

• dest = args.info

• type = str

• default = star_info.csv

--iw, --indwidth

width of binning for the power spectrum used in the first module TODO: CHECK THIS

• dest = args.ind_width

• type = float

• default = 20.0

• unit = \(\mu \mathrm{Hz}\)

-k, --kc, --kepcorr

turn on the Kepler short-cadence artefact correction module. if you don’t know what a Kepler short-cadence artefact is, chances are you shouldn’t mess around with this option yet

• dest = args.kepcorr

• type = bool

• default = False

• action = store_true

--laws, --nlaws

force the number of red-noise component(s). fun fact: the older IDL version of SYD fixed this number to 2 for the Kepler legacy sample – now we have made it customizable all the way down to an individual star!

• dest = args.n_laws

• type = int

• default = None

• see also: -w, -wn, –fixwn

--lb, --lowerb

the lower frequency limit of the power spectrum to use in the background-fitting routine. Please note: unless \(\nu_{\mathrm{max}}\) is known, it is highly recommended that you do not fix this beforehand

• dest = args.lower_bg

• type = float

• nargs = '*'

• default = 1.0

• unit = \(\mu \mathrm{Hz}\)

• see also: –ub, –upperb

--le, --lowere

the lower frequency limit of the folded power spectrum to “whiten” mixed modes before estimating the final value for dnu

• dest = args.lower_ech

• type = float

• nargs = '*'

• default = None

• unit = \(\mu \mathrm{Hz}\)

• REQUIRES: –ue/–uppere and –dnu

--lp, --lowerp

to change the lower frequency limit of the zoomed in power spectrum (i.e. the region with the supposed power excess due to oscillations). Similar to –ew but instead of a fractional value w.r.t. the scaled solar value, you can provide hard boundaries in this case TODO check if it requires and upper bound – pretty sure it doesn’t but should check

• dest = args.lower_ps

• type = float

• nargs = '*'

• default = None

• unit = \(\mu \mathrm{Hz}\)

• see also: –up, –upperp

--lx, --lowerx

the lower limit of the power spectrum to use in the first module (to estimate numax)

• dest = args.lower_ex

• type = float

• default = 1.0

• unit = \(\mu \mathrm{Hz}\)

• see also: –ux, –upperx

-m, --samples

option to save the samples from the Monte-Carlo sampling (i.e. parameter posteriors) in case you’d like to reproduce your own plots, etc.

• dest = args.samples

• type = bool

• default = False

• action = store_true

--mc, --iter, --mciter

number of Monte-Carlo-like iterations. This is 1 by default, since you should always check the data and output figures before running the sampling algorithm. But for purposes of generating uncertainties, n=200 is typically sufficient.

• dest = args.mc_iter

• type = int

• default = 1

--metric

which model metric to use for the best-fit background model, current choices are ~['bic', 'aic'] but still being developed and tested

• dest = args.metric

• type = str

• default = 'bic'

-n, --notch

use notching technique to reduce effects from mixes modes (pretty sure this is not full functional yet, creates weird effects for higher SNR cases)

• dest = args.notching

• type = bool

• default = False

• action = store_true

--notebook

similar to –cli, this should not need to be touched and is primarily for internal workings and how to retrieve parameters

• dest = args.notebook

• type = bool

• default = False

• action = store_true

--nox, --nacross

specifies the number of bins (i.e. the resolution) to use for the x-axis of the echelle diagram – fixing this number if complicated because it depends on both the resolution of the power spectrum as well as the characteristic frequency separation. This is another example where, if you don’t know what this means, you probably should not change it.

• dest = args.nox

• type = int

• default = None

• see also: –noy, –ndown, –norders, –npb

--noy, --ndown, --norders

specifies the number of bins (or radial orders) to use on the y-axis of the echelle diagram NEW: option to shift the entire figure by n orders - the first part of the string is the number of orders to plot and the +/- n is the number orders to shift the ED by

• dest = args.noy

• type = str

• default = 0+0

• see also: –nox, –nacross, –npb

--npb

option for echelle diagram to use information from the spacing and frequency resolution to calculate a better grid resolution (npb == number per bin)

• dest = args.npb

• type = int

• default = 10

• see also: –nox, –nacross, –noy, –ndown, –norders

--nt, --nthread, --nthreads

the number of processes to run in parallel. If nothing is provided when you run in pysyd.parallel mode, the software will use the multiprocessing package to determine the number of CPUs on the operating system and then adjust accordingly. In short: this probably does not need to be changed

• dest = args.n_threads

• type = int

• default = 0

--numax

brute force method to bypass the first module and provide an initial starting value for \(\rm \nu_{max}\) Asserts len(args.numax) == len(args.targets) * dest = args.numax * type = float * nargs = '*' * default = None * unit = \(\mu \mathrm{Hz}\)

-o, --overwrite

newer option to overwrite existing files with the same name/path since it will now add extensions with numbers to avoid overwriting these files

• dest = args.overwrite

• type = bool

• default = False

• action = store_true

--of, --over, --oversample

the oversampling factor of the provided power spectrum. Default is 0, which means it is calculated from the time series data. Note: this needs to be provided if there is no time series data!

• dest = args.oversampling_factor

• type = int

• default = None

--out, --output, --outdir

path to save results to

• dest = args.outdir

• type = str

• default = 'OUTDIR'

--peak, --peaks, --npeaks

the number of peaks to identify in the autocorrelation function

• dest = args.n_peaks

• type = int

• default = 5

--rms, --nrms

the number of points used to estimate the amplitudes of individual background (red-noise) components Note: this should only rarely need to be touched

• dest = args.n_rms

• type = int

• default = 20

-s, --save

turn off the automatic saving of output figures and files

• dest = args.save

• type = bool

• default = True

• action = store_false

--se, --smoothech

option to smooth the echelle diagram output using a box filter of this width

• dest = args.smooth_ech

• type = float

• default = None

• unit = \(\mu \mathrm{Hz}\)

• see also: -e, –ie, –interpech

--sm, --smpar

the value of the smoothing parameter to estimate the smoothed numax (that is really confusing) note: typical values range from 1-4 but this is fixed based on years of trial & error

• dest = args.sm_par

• type = float

• default = None

• unit = fractional \(\mu \mathrm{Hz}\)

--sp, --smoothps

the box filter width used for smoothing of the power spectrum. The default is 2.5 but will switch to 0.5 for more evolved stars (if \(\rm \nu_{max}\) < 500 \(\mu \mathrm{Hz}\))

• dest = args.smooth_ps

• type = float

• default = 2.5

• unit = \(\mu \mathrm{Hz}\)

--star, --stars

list of stars to process. Default is None, which will read in the star list from args.file instead

• dest = args.star

• type = str

• nargs = '*'

• default = None

• see also: –file, –list, –todo

--step, --steps

the step width for the collapsed autocorrelation function w.r.t. the fraction of the boxsize. Please note: this should not be adjusted

• dest = args.step

• type = float

• default = 0.25

• unit = fractional \(\mu \mathrm{Hz}\)

--sw, --smoothwidth

the width of the box filter that is used to smooth the power spectrum

• dest = args.smooth_width

• type = float

• default = 20.0

• unit = \(\mu \mathrm{Hz}\)

• see also: –sp, –smoothps

Warning

All parameters are optimized for most star types but some may need adjusting. An example is the smoothing width (--sw), which is 20 muHz by default, but may need to be adjusted based on the nyquist frequency and frequency resolution of the input power spectrum.

--thresh, --threshold

the fractional value of the autocorrelation function’s full width at half maximum (which is important in this scenario because it is used to determine \(\Delta\nu\))

• dest = args.threshold

• type = float

• default = 1.0

• unit = fractional \(\mu \mathrm{Hz}\)

--trials, --ntrials

the number of trials used to estimate numax in the first module – can be bypassed if –numax is provided.

• dest = args.n_trials

• type = int

• default = 3

--ub, --upperb

the upper limit of the power spectrum used in the background-fitting module Please note: unless \(\nu_{\mathrm{max}}\) is known, it is highly recommended that you do not fix this beforehand

• dest = args.upper_bg

• type = float

• nargs = '*'

• default = 6000.0

• unit = \(\mu \mathrm{Hz}\)

• see also: –lb, –lowerb

--ue, --uppere

the upper frequency limit of the folded power spectrum used to “whiten” mixed modes before determining the correct \(\Delta\nu\)

• dest = args.upper_ech

• type = float

• nargs = '*'

• default = None

• unit = \(\mu \mathrm{Hz}\)

• REQUIRES: –le/–lowere and –dnu

--up, --upperp

the upper frequency limit used for the zoomed in power spectrum. In other words, this is an option to use a different upper bound than the one determined automatically

• dest = args.upper_ps

• type = float

• nargs = '*'

• default = None

• unit = \(\mu \mathrm{Hz}\)

• see also: –lp, –lowerp

--ux, --upperx

the upper frequency limit of the power spectrum to use in the first module

• dest = args.upper_ex

• type = float

• default = 6000.0

• unit = \(\mu \mathrm{Hz}\)

• see also: –lx, –lowerx

-v, --verbose

turn on the verbose output (also not recommended when running many stars, and definitely not when in parallel mode) Check this but I think it will be disabled automatically if the parallel mode is True

• dest = args.verbose

• type = bool

• default = False

• action = store_true

-w, --wn, --fixwn

fix the white noise level in the background fitting TODO: this still needs to be tested

• dest = args.fix

• type = bool

• default = False

• action = store_true

• see also: –laws, –nlaws

-x, --stitch, --stitching

correct for large gaps in time series data by ‘stitching’ the light curve

• dest = args.stitch

• type = bool

• default = False

• action = store_true

• see also: –gap, –gaps

-y, --hey

plugin for Daniel Hey’s interactive echelle package but is not currently implemented TODO

• dest = args.hey

• type = bool

• default = False

• action = store_true