SL1M deconvolves radio synthesis images based on direct inversion of the measured visibilities that can deal with the non-coplanar base line effect and can be applied to telescopes with direction dependent gains. The code is more computationally demanding than some existing methods, but is highly parallelizable and scale well to clusters of CPUs and GPUs. The algorithm is also extremely flexible, allowing the solution of the deconvolution problem on arbitrarily placed pixels.

SLALIB is a library of routines that make accurate and reliable positional-astronomy applications easier to write. Most SLALIB routines are concerned with astronomical position and time, but a number have wider trigonometrical, numerical or general applications. A Fortran implementation of SLALIB under GPL licensing is available as part of Starlink (ascl:1110.012).

Many fields in science and engineering measure data that inherently live on non-Euclidean geometries, such as the sphere. Techniques developed in the Euclidean setting must be extended to other geometries. Due to recent interest in geometric deep learning, analogues of Euclidean techniques must also handle general manifolds or graphs. Often, data are only observed over partial regions of manifolds, and thus standard whole-manifold techniques may not yield accurate predictions. In this thesis, a new wavelet basis is designed for datasets like these.

Although many definitions of spherical convolutions exist, none fully emulate the Euclidean definition. A novel spherical convolution is developed, designed to tackle the shortcomings of existing methods. The so-called sifting convolution exploits the sifting property of the Dirac delta and follows by the inner product of a function with the translated version of another. This translation operator is analogous to the Euclidean translation in harmonic space and exhibits some useful properties. In particular, the sifting convolution supports directional kernels; has an output that remains on the sphere; and is efficient to compute. The convolution is entirely generic and thus may be used with any set of basis functions. An application of the sifting convolution with a topographic map of the Earth demonstrates that it supports directional kernels to perform anisotropic filtering.

Slepian wavelets are built upon the eigenfunctions of the Slepian concentration problem of the manifold - a set of bandlimited functions which are maximally concentrated within a given region. Wavelets are constructed through a tiling of the Slepian harmonic line by leveraging the existing scale-discretised framework. A straightforward denoising formalism demonstrates a boost in signal-to-noise for both a spherical and general manifold example. Whilst these wavelets were inspired by spherical datasets, like in cosmology, the wavelet construction may be utilised for manifold or graph data.

SlicerAstro extends 3D Slicer, a multi-platform package for visualization and medical image processing, to provide a 3-D interactive viewer with 3-D human-machine interaction features, based on traditional 2-D input/output hardware, and analysis capabilities.

The semi-spectral linear MHD (SLiM) code follows the interaction of linear waves through an inhomogeneous three-dimensional solar atmosphere. The background model allows almost arbitrary perturbations of density, temperature, sound speed as well as magnetic and velocity fields. The code is useful in understanding the helioseismic signatures of various solar features, including sunspots.

Slim performs lossless compression on binary data files. Written in C++, it operates very rapidly and achieves better compression on noisy physics data than general-purpose tools designed primarily for text.

slimplectic is a python implementation of a numerical integrator that uses a fixed time-step variational integrator formalism applied to the principle of stationary nonconservative action. It allows nonconservative effects to be included in the numerical evolution while preserving the major benefits of normally conservative symplectic integrators, particularly the accurate long-term evolution of momenta and energy. slimplectic is appropriate for exploring cosmological or celestial N-body dynamics problems where nonconservative interactions, e.g. dynamical friction or dissipative tides, can play an important role.

SLIT (Sparse Lens Inversion Technique) provides a method for inversion of lensed images in the frame of strong gravitational lensing. The code requires the input image along with lens mass profile and a PSF. The user then has to chose a maximum number of iterations after which the algorithm will stop if not converged and a image size ratio to the input image to set the resolution of the reconstructed source. Results are displayed in pyplot windows.

SLOPES computes six least-squares linear regression lines for bivariate datasets of the form (x_i,y_i) with unknown population distributions. Measurement errors, censoring (nondetections) or other complications are not treated. The lines are: the ordinary least-squares regression of y on x, OLS(Y|X); the inverse regression of x on y, OLS(X_Y); the angular bisector of the OLS lines; the orthogonal regression line; the reduced major axis, and the mean-OLS line. The latter four regressions treat the variables symmetrically, while the first two regressions are asymmetrical. Uncertainties for the regression coefficients of each method are estimated via asymptotic formulae, bootstrap resampling, and bivariate normal simulation. These methods, derivation of the regression coefficient uncertainties, and discussions of their use are provided in three papers listed below. The user is encouraged to read and reference these studies.

Stellar Locus Regression (SLR) is a simple way to calibrate colors at the 1-2% level, and magnitudes at the sub-5% level as limited by 2MASS, without the traditional use of standard stars. With SLR, stars in any field are "standards." This is an entirely new way to calibrate photometry. SLR exploits the simple fact that most stars lie along a well defined line in color-color space called the stellar locus. Cross-match point-sources in flattened images taken through different passbands and plot up all color vs color combinations, and you will see the stellar locus with little effort. SLR calibrates colors by fitting these colors to a standard line. Cross-match with 2MASS on top of that, and SLR will deliver calibrated magnitudes as well.

The effects of stochasticity on the luminosities of stellar populations are an often neglected but crucial element for understanding populations in the low mass or low star formation rate regime. To address this issue, we present SLUG, a new code to "Stochastically Light Up Galaxies". SLUG synthesizes stellar populations using a Monte Carlo technique that treats stochastic sampling properly including the effects of clustering, the stellar initial mass function, star formation history, stellar evolution, and cluster disruption. This code produces many useful outputs, including i) catalogs of star clusters and their properties, such as their stellar initial mass distributions and their photometric properties in a variety of filters, ii) two dimensional histograms of color-magnitude diagrams of every star in the simulation, iii) and the photometric properties of field stars and the integrated photometry of the entire simulated galaxy. After presenting the SLUG algorithm in detail, we validate the code through comparisons with starburst99 in the well-sampled regime, and with observed photometry of Milky Way clusters. Finally, we demonstrate the SLUG's capabilities by presenting outputs in the stochastic regime.

Smart provides pre-processing for LP-VIcode (ascl:1501.007). It computes the accelerations and variational equations given a generic user-defined potential function, eliminating the need to calculate manually the accelerations and variational equations.

SMART is an IDL-based software tool, developed by the IRS Instrument Team at Cornell University, that allows users to reduce and analyze Spitzer data from all four modules of the Infrared Spectrograph, including the peak-up arrays. The software is designed to make full use of the ancillary files generated in the Spitzer Science Center pipeline so that it can either remove or flag artifacts and corrupted data and maximize the signal-to-noise ratio in the extraction routines. It can be run in both interactive and batch modes. SMART includes visualization tools for assessing data quality, basic arithmetic operations for either two-dimensional images or one-dimensional spectra, extraction of both point and extended sources, and a suite of spectral analysis tools.

SMARTIES calculates the optical properties of oblate and prolate spheroidal particles, with comparable capabilities and ease-of-use as Mie theory for spheres. This suite of MATLAB codes provides a fully documented implementation of an improved T-matrix algorithm for the theoretical modelling of electromagnetic scattering by particles of spheroidal shape. Included are scripts that cover a range of scattering problems relevant to nanophotonics and plasmonics, including calculation of far-field scattering and absorption cross-sections for fixed incidence orientation, orientation-averaged cross-sections and scattering matrix, surface-field calculations as well as near-fields, wavelength-dependent near-field and far-field properties, and access to lower-level functions implementing the T-matrix calculations, including the T-matrix elements which may be calculated more accurately than with competing codes.

Spectroscopy Made Easy (SME) is IDL software and a compiled external library that fits an observed high-resolution stellar spectrum with a synthetic spectrum to determine stellar parameters. The SME external library is available for Mac, Linux, and Windows systems. Atomic and molecular line data formatted for SME may be obtained from VALD. SME can solve for empirical log(gf) and damping parameters, using an observed spectrum of a star (usually the Sun) as a constraint.

SMERFS (Stochastic Markov Evaluation of Random Fields on the Sphere) creates large realizations of random fields on the sphere. It uses a fast algorithm based on Markov properties and fast Fourier Transforms in 1d that generates samples on an n X n grid in O(n² log n) and efficiently derives the necessary conditional covariance matrices.

SMILE is interactive software for studying a variety of 2D and 3D models, including arbitrary potentials represented by a basis-set expansion, a spherical-harmonic expansion with coefficients being smooth functions of radius (splines), or a set of fixed point masses. Its main features include:

• orbit integration in various 2d and 3d potentials (including N-body and basis-set representations of an arbitrary potential);
• methods for analysis of orbital class, fundamental frequencies, regular or chaotic nature of an orbit, computation of Lyapunov exponents;
• Poincaré sections (in 2d) and frequency maps (in 3d) for analyzing orbital structure of potential;
• construction of self-consistent Schwarzschild models; and
• convenient visualization and integrated GUI environment, and a console scriptable version.

SMILI uses sparse sampling techniques and other regularization methods for interferometric imaging. The python-interfaced library is mainly designed for very long baseline interferometry, and has been under the active development primarily for the Event Horizon Telescope (EHT).

SMMOL (Spherical Multi-level MOLecular line radiative transfer) is a molecular line radiative transfer code that uses Accelerated Lambda Iteration to solve the coupled level population and line transfer problem in spherical geometry. The code uses a discretized grid and a ray tracing methodology. SMMOL is designed for high optical depth regimes and can cope with maser emission as long as the spatial-velocity sampling is fine enough.

Smooth calculates several mean quantities for all particles in an N-Body simulation output file. The program produces a file for each type of output specified on the command line. This output file is in ASCII format with one smoothed quantity for each particle. The program uses a symmetric SPH (Smoothed Particle Hydrodynamics) smoothing kernel to find the mean quantities.

smops interpolates input sub-band model FITS images, such as those produced by WSClean (ascl:1408.023), into more finely channelized sub-band model FITS images, thus generating model images at a higher frequency resolution. It is a Python-based command line tool. For example, given input model FITS images initially created from sub-dividing a given bandwidth into four, smops can subdivide that bandwidth further, resulting in more finely channelized model images, to a specified frequency resolution. This smooths out the stepwise behavior of models across frequency, which can improve the results of self-calibration with such models.

SMURF reduces submillimeter single-dish continuum and heterodyne data. It is mainly targeted at data produced by the James Clerk Maxwell Telescope but data from other telescopes have been reduced using the package. SMURF is released as part of the bundle that comprises Starlink (ascl:1110.012) and most of the packages that use it. The two key commands are MAKEMAP for the creation of maps from sub millimeter continuum data and MAKECUBE for the creation of data cubes from heterodyne array instruments. The software can also convert data from legacy JCMT file formats to the modern form to allow it to be processed by MAKECUBE. SMURF is a core component of the ORAC-DR (ascl:1310.001) data reduction pipeline for JCMT.

SNANA is a general analysis package for supernova (SN) light curves that contains a simulation, light curve fitter, and cosmology fitter. The software is designed with the primary goal of using SNe Ia as distance indicators for the determination of cosmological parameters, but it can also be used to study efficiencies for analyses of SN rates, estimate contamination from non-Ia SNe, and optimize future surveys. Several SN models are available within the same software architecture, allowing technical features such as K-corrections to be consistently used among multiple models, and thus making it easier to make detailed comparisons between models. New and improved light-curve models can be easily added. The software works with arbitrary surveys and telescopes and has already been used by several collaborations, leading to more robust and easy-to-use code. This software is not intended as a final product release, but rather it is designed to undergo continual improvements from the community as more is learned about SNe.

SNAPDRAGONS (Stellar Numbers And Parameters Determined Routinely And Generated Observing N-body Systems) is a simplified version of the population synthesis code Galaxia (ascl:1101.007), using a different process to generate the stellar catalog. It splits each N-body particle from the galaxy simulation into an appropriate number of stellar particles to create a mock catalog of observable stars from the N-body model. SNAPDRAGON uses the same isochrones and extinction map as Galaxia.

SNCosmo synthesizes supernova spectra and photometry from SN models, and has functions for fitting and sampling SN model parameters given photometric light curve data. It offers fast implementations of several commonly used extinction laws and can be used to construct SN models that include dust. The SNCosmo library includes supernova models such as SALT2, MLCS2k2, Hsiao, Nugent, PSNID, SNANA and Whalen models, as well as a variety of built-in bandpasses and magnitude systems, and provides convenience functions for reading and writing peculiar data formats used in other packages. The library is extensible, allowing new models, bandpasses, and magnitude systems to be defined using an object-oriented interface.

SNEC (SuperNova Explosion Code) is a spherically-symmetric Lagrangian radiation-hydrodynamics code that follows supernova explosions through the envelope of their progenitor star, produces bolometric (and approximate multi-color) light curve predictions, and provides input to spectral synthesis codes for spectral modeling. SNEC's features include 1D (spherical) Lagrangian Newtonian hydrodynamics with artificial viscosity, stellar equation of state with a Saha solver ionization/recombination, equilibrium flux-limited photon diffusion with OPAL opacities and low-temperature opacities, and prediction of bolometric light curves and multi-color lightcurves (in the blackbody approximation).

SNEWPY uses simulated supernovae data to generate a time series of neutrino spectral fluences at Earth or the total time-integrated spectral fluence. The code can also process generated data through SNOwGLoBES (ascl:2109.019) and collate its output into the observable channels of each detector. Data from core-collapse, thermonuclear, and pair-instability supernovae simulations are included in the package.

We present an algorithm to identify the type of an SN spectrum and to determine its redshift and age. This algorithm, based on the correlation techniques of Tonry & Davis, is implemented in the Supernova Identification (SNID) code. It is used by members of ongoing high-redshift SN searches to distinguish between type Ia and type Ib/c SNe, and to identify "peculiar" SNe Ia. We develop a diagnostic to quantify the quality of a correlation between the input and template spectra, which enables a formal evaluation of the associated redshift error. Furthermore, by comparing the correlation redshifts obtained using SNID with those determined from narrow lines in the SN host galaxy spectrum, we show that accurate redshifts (with a typical error less than 0.01) can be determined for SNe Ia without a spectrum of the host galaxy. Last, the age of an input spectrum is determined with a typical 3-day accuracy, shown here by using high-redshift SNe Ia with well-sampled light curves. The success of the correlation technique confirms the similarity of some SNe Ia at low and high redshifts. The SNID code, which is available to the community, can also be used for comparative studies of SN spectra, as well as comparisons between data and models.

snmachine reads in photometric supernova light curves, extracts useful features from them, and subsequently performs supervised machine learning to classify supernovae based on their light curves. This python library is also flexible enough to easily extend to general transient classification.

Snoopy is a spectral 3D code that solves the MHD and Boussinesq equations, such as compressibility, particles, and Braginskii viscosity, and several other physical effects. It's useful for turbulence study involving shear and rotation. Snoopy requires the FFTW library (ascl:1201.015), and can run on parallel machine using MPI OpenMP or both at the same time.

The SNooPy package (also known as SNpy), written in Python, contains tools for the analysis of TypeIa supernovae. It offers interactive plotting of light-curve data and models (and spectra), computation of reddening laws and K-corrections, LM non-linear least-squares fitting of light-curve data, and various types of spline fitting, including Diercx and tension. The package also includes a SNIa lightcurve template generator in the CSP passbands, estimates of Milky-Way Extinction, and a module for dealing with filters and spectra.

Snowball models atmospheric loss in order to constrain an atmosphere's cumulative impact of historic X-ray and extreme ultraviolet radiation-driven mass loss. The escape model interpolates the BaSTI luminosity evolution grid to the observed mass and luminosity of the host star.

SNOwGLoBES (SuperNova Observatories with GLoBES) computes interaction rates and distributions of observed quantities for supernova burst neutrinos in common detector materials. The code provides a very simple and fast code and data package for tests of observability of physics signatures in current and future detectors, and for evaluation of relative sensitivities of different detector configurations. The event estimates are made using available cross-sections and parameterized detector responses. Water, argon, scintillator and lead-based configurations are included. The package makes use of GLoBES (ascl:2109.018). SNOwGLoBES is not intended to replace full detector simulations; however output should be useful for many types of studies, and simulation results can be incorporated.

SNRPy (Super Nova Remnant Python) models supernova remnant (SNR) evolution and is useful for understanding SNR evolution and to model observations of SNR for obtaining good estimates of SNR properties. It includes all phases for the standard path of evolution for spherically symmetric SNRs and includes alternate evolutionary models, including evolution in a cloudy ISM, the fractional energy loss model, and evolution in a hot low-density ISM. The graphical interface takes in various parameters and produces outputs such as shock radius and velocity vs. time, SNR surface brightness profile and spectrum.

SNSEDextend extrapolates core-collapse and Type Ia Spectral Energy Distributions (SEDs) into the UV and IR for use in simulations and photometric classifications. The user provides a library of existing SED templates (such as those in the authors' SN SED Repository) along with new photometric constraints in the UV and/or NIR wavelength ranges. The software then extends the existing template SEDs so their colors match the input data at all phases. SNSEDextend can also extend the SALT2 spectral time-series model for Type Ia SN for a "first-order" extrapolation of the SALT2 model components, suitable for use in survey simulations and photometric classification tools; as the code does not do a rigorous re-training of the SALT2 model, the results should not be relied on for precision applications such as light curve fitting for cosmology.

Supernova Time Delays (SNTD) simulates and measures time delay of multiply-imaged supernovae, and offers an improved characterization of the uncertainty caused by microlensing. Lensing time delays can be determined by fitting the multiple light curves of these objects; measuring these delays provide precise tests of lens models or constraints on the Hubble constant and other cosmological parameters that are independent of the local distance ladder. Fitting the effects of microlensing without an accurate prior often leads to biases in the time delay measurement and over-fitting to the data; this can be mitigated by using a Gaussian Process Regression (GPR) technique to determine the uncertainty due to microlensing. SNTD can produce accurate simulations for wide-field time domain surveys such as LSST and WFIRST.

so_noise_models is the N(ell) noise curve projection code for the Simons Observatory. The code, written in pure Python, consists of several independent sub-modules, representing each version of the noise code. The usage of the models can vary substantially from version to version. The package also includes demo code that that demonstrates usage of the noise models, such as by producing noise curve plots, effective noise power spectra for SO LAT component-separated CMB T, E, B, and Compton-y maps, and lensing noise curves from SO LAT component-separated CMB T, E, B maps.

SOAP (Spot Oscillation And Planet) 2.0 simulates the effects of dark spots and bright plages on the surface of a rotating star, computing their expected radial velocity and photometric signatures. It includes the convective blueshift and its inhibition in active regions.

SOAP-GPU is a revision of SOAP 2 (ascl:1504.021), which simulates spectral time series with the effect of active regions (spot, faculae or both). In addition to the traditional outputs of SOAP 2.0 (the cross-correlation function and extracted parameters: radial velocity, bisector span, full width at half maximum), SOAP-GPU generates the integrated spectra at each phase for given input spectra and spectral resolution. Additional capabilities include fast spectral simulation of stellar activity due to GPU acceleration, simulation of more complicated active region structures with superposition between active regions, and more realistic line bisectors, based on solar observations, that varies as function of mu angle for both quiet and active regions. In addition, SOAP-GPU accepts any input high resolution observed spectra. The PHOENIX synthetic spectral library are already implemented at the code level which allows users to simulate stellar activity for stars other than the Sun. Furthermore, SOAP-GPU simulates realistic spectral time series with either spot number/SDO image as additional inputs. The code is written in C and provides python scripts for input pre-processing and output post-processing.

SOFA (Standards Of Fundamental Astronomy) is a collection of subprograms, in source-code form, that implement official IAU algorithms for fundamental astronomy computations. SOFA offers more than 160 routines for fundamental astronomy, including time scales (including dealing with leap seconds), Earth rotation, sidereal time, precession, nutation, polar motion, astrometry and transforms between various reference systems (e.g. BCRS, ICRS, GCRS, CIRS, TIRS, ITRS). The subprograms are supported by 55 vector/matrix routines, and are available in both Fortran77 and C implementations.

SoFiA 2 is a fully automated spectral-line source finding pipeline originally intended for the detection of galaxies in large HI data cubes. It is a reimplementation of parts of the original SoFiA pipeline (ascl:1412.001) in the C programming language and uses OpenMP for multithreading, making it substantially faster and more memory-efficient than its predecessor. At its core, SoFiA 2 uses the Smooth + Clip algorithm for source finding which operates by spatially and spectrally smoothing the data on multiple scales and applying a user-defined flux threshold relative to the noise level in each iteration. A wide range of useful preconditioning and post-processing filters is available, including noise normalization, flagging of artifacts and reliability filtering. In addition to global data products and source catalogs in different formats, SoFiA 2 can also generate cutout images and spectra for each individual detection.

SoFiA is a flexible source finding pipeline designed to detect and parameterize sources in 3D spectral-line data cubes. SoFiA combines several powerful source finding and parameterization algorithms, including wavelet denoising, spatial and spectral smoothing, source mask optimization, spectral profile fitting, and calculation of the reliability of detections. In addition to source catalogues in different formats, SoFiA can also generate a range of output data cubes and images, including source masks, moment maps, sub-cubes, position-velocity diagrams, and integrated spectra. The pipeline is controlled by simple parameter files and can either be invoked on the command line or interactively through a modern graphical user interface.

A reimplementation of this pipeline using OpenMPI, SoFiA 2 (ascl:2109.005), is available.

SoFiAX is a web-based platform to merge and interact with the results of parallel execution of SoFiA HI source finding software [ascl:1412.001] and other steps of processing ASKAP Wallaby HI survey data.

Solar-MACH (Solar MAgnetic Connection HAUS) derives and visualizes the spatial configuration and solar magnetic connection of different observers (i.e., spacecraft or planets) in the heliosphere at different times. It provides publication-ready figures for analyzing Solar Energetic Particle events (SEPs) or solar transients such as Coronal Mass Ejections (CMEs). Solar-MACH is available as a Python package; a Streamlit-enabled tool that runs in a browser is also available (solar-mach.github.io)

SolarAxionFlux quantifies systematic differences and statistical uncertainties in the calculation of the solar axion flux from axion-photon and axion-electron interactions. Determining the limitations of these calculations can be used to identify potential improvements and help determine axion model parameters more accurately.

SolarKAT mitigates solar interference in MeerKAT data and recovers the visibilities rather than discarding them; this solar imaging pipeline takes 1GC calibrated data in Measurement Set format as input. Written in Python, the pipeline employs solar tracking, subtraction, and peeling techniques to enhance data quality by significantly reducing solar radio interference. This is achieved while preserving the flux measurements in the main field. SolarKAT is versatile and can be applied to general radio astronomy observations and solar radio astronomy; additionally, generated solar images can be used for weather forecasting. SolarKAT is deployed in Stimela (ascl:2305.007). It is based on existing radio astronomy software, including CASA (ascl:1107.013), breizorro (ascl:2305.009), WSclean (ascl:1408.023), Quartical (ascl:2305.006), and Astropy (ascl:1304.002).

SolarSoft is a set of integrated software libraries, data bases, and system utilities which provide a common programming and data analysis environment for Solar Physics. The SolarSoftWare (SSW) system is built from Yohkoh, SOHO, SDAC and Astronomy libraries and draws upon contributions from many members of those projects. It is primarily an IDL based system, although some instrument teams integrate executables written in other languages. The SSW environment provides a consistent look and feel at widely distributed co-investigator institutions to facilitate data exchange and to stimulate coordinated analysis. Commonalities and overlap in solar data and analysis goals are exploited to permit application of fundamental utilities to the data from many different solar instruments. The use of common libraries, utilities, techniques and interfaces minimizes the learning curve for investigators who are analyzing new solar data sets, correlating results from multiple experiments or performing research away from their home institution.

SolAster provides querying, analysis, and calculation methods to independently derive 'sun-as-a-star' RV variations using SDO/HMI data for any time span since SDO has begun observing. Scaling factors are provided in order to calculate RVs comparable to magnitudes measured by ground-based spectrographs (HARPS-N and NEID). In addition, there are routines to calculate magnetic observables to compare with RV variations and determine what is driving Solar activity.

SolTrack computes the position of the Sun, the rise and set times and azimuths, and transit times and altitudes. It includes corrections for aberration and parallax, and has a simple routine to correct for atmospheric refraction, taking into account local atmospheric conditions. SolTrack is derived from the Fortran library libTheSky (ascl:2209.018). The package can be used to track the Sun on a low-specs machine, such as a microcontroller or PLC, and can be used for (highly) concentrated (photovoltaic) solar power or accurate solar-energy modeling.

SONG computes the non-linear evolution of the Universe in order to predict cosmological observables such as the bispectrum of the Cosmic Microwave Background (CMB). More precisely, it is a second-order Boltzmann code, as it solves the Einstein and Boltzmann equations up to second order in the cosmological perturbations.