SExSeg forces SExtractor (ascl:1010.064) to run using a pre-defined segmentation map (the definition of objects and their borders). The defined segments double as isophotal apertures. SExSeg alters the detection image based on a pre-defined segmenation map while preparing your "analysis image" by subtracting the background in a separate SExtractor run (using parameters you specify). SExtractor is then run in "double-image" mode with the altered detection image and background-subtracted analysis image.
This new software optimally detects, de-blends, measures and classifies sources from astronomical images: SExtractor (Source Extractor). A very reliable star/galaxy separation can be achieved on most images using a neural network trained with simulated images. Salient features of SExtractor include its ability to work on very large images, with minimal human intervention, and to deal with a wide variety of object shapes and magnitudes. It is therefore particularly suited to the analysis of large extragalactic surveys.
SFH is an efficient IDL tool that quickly computes accurate predictions for the baryon budget history in a galactic halo.
SFoF is a friends-of-friends galaxy cluster detection algorithm that operates in either spectroscopic or photometric redshift space. The linking parameters, both transverse and along the line-of-sight, change as a function of redshift to account for selection effects.
SGNAPS allows the user to plot a one-dimensional spectrum, together with the corresponding two-dimensional and a reference spectrum (for example the sky spectrum). This makes it possible to check on the reality of spectral features that are present in the one-dimensional spectrum, which could be due to bad sky subtraction or fringing residuals. It is also possible to zoom in and out all three spectra, edit the one-dimensional spectrum, smooth it with a simple square window function, measure the signal to noise over a selected wavelength interval, and fit the position of a selected spectral line. SGNAPS also allows the astronomer to obtain quick redshift estimates by providing a tool to fit or mark the position of a spectral line, and a function that will compute a list of possible redshifts based on a list of known lines in galaxy spectra. SGNAPS is derived from the plotting tools of VIPGI and contains almost all of their capabilities.
SgrbWorldModel, written in Fortran 90, presents an attempt at modeling the population distribution of the Short-duration class of Gamma-Ray Bursts (SGRBs) as detected by the NASA's now-defunct Burst And Transient Source Experiment (BATSE) onboard the Compton Gamma Ray Observatory (CGRO). It is assumed that the population distribution of SGRBs is well fit by a multivariate log-normal distribution, whose differential cosmological rate of occurrence follows the Star-Formation-Rate (SFR) convolved with a log-normal binary-merger delay-time distribution. The best-fit parameters of the model are then found by maximizing the likelihood of the observed data by the BATSE detectors via a native built-in Adaptive Metropolis-Hastings Markov-Chain Monte Carlo (AMH-MCMC)Sampler that is part of the code. A model for the detection algorithm of the BATSE detectors is also provided.
Shadowfax simulates galaxy evolution. Written in object-oriented modular C++, it evolves a mixture of gas, subject to the laws of hydrodynamics and gravity, and any collisionless fluid only subject to gravity, such as cold dark matter or stars. For the hydrodynamical integration, it makes use of a (co-) moving Lagrangian mesh. The code has a 2D and 3D version, contains utility programs to generate initial conditions and visualize simulation snapshots, and its input/output is compatible with a number of other simulation codes, e.g. Gadget2 (ascl:0003.001) and GIZMO (ascl:1410.003).
Complicated cosmic string loops will fragment until they reach simple, non-intersecting ("stable") configurations. Through extensive numerical study we characterize these attractor loop shapes including their length, velocity, kink, and cusp distributions. We find that an initial loop containing $M$ harmonic modes will, on average, split into 3M stable loops. These stable loops are approximately described by the degenerate kinky loop, which is planar and rectangular, independently of the number of modes on the initial loop. This is confirmed by an analytic construction of a stable family of perturbed degenerate kinky loops. The average stable loop is also found to have a 40% chance of containing a cusp. We examine the properties of stable loops of different lengths and find only slight variation. Finally we develop a new analytic scheme to explicitly solve the string constraint equations.
Shape is a flexible interactive 3D morpho-kinematical modeling application for astrophysics. It reduces the restrictions on the physical assumptions, data type and amount required for a reconstruction of an object's morphology. It applies interactive graphics and allows astrophysicists to provide a-priori knowledge about the object by interactively defining 3D structural elements. By direct comparison of model prediction with observational data, model parameters can then be automatically optimized to fit the observation.
Shapelets are a complete, orthonormal set of 2D basis functions constructed from Laguerre or Hermite polynomials weighted by a Gaussian. A linear combination of these functions can be used to model any image, in a similar way to Fourier or wavelet synthesis. The shapelet decomposition is particularly efficient for images localized in space, and provide a high level of compression for individual galaxies in astronomical data. The basis has many elegant mathematical properties that make it convenient for image analysis and processing.
Shark is a flexible semi-analytic galaxy formation model for easy exploration of different physical processes. Shark has been implemented with several models for gas cooling, active galactic nuclei, stellar and photo-ionization feedback, and star formation (SF). The software can determine the stellar mass function and stellar–halo mass relation at z=0–4; cosmic evolution of the star formation rate density, stellar mass, atomic and molecular hydrogen; local gas scaling relations; and structural galaxy properties. It performs particularly well for the mass–size relation for discs/bulges, the gas–stellar mass and stellar mass–metallicity relations. Shark is written in C++11 and has been parallelized with OpenMP.
The Spherical Harmonic Discrete Ordinate Method (SHDOM) radiative transfer model computes polarized monochromatic or spectral band radiative transfer in a one, two, or three-dimensional medium for either collimated solar and/or thermal emission sources of radiation. The model is written in a variant of Fortran 77 and in Fortran90 and requires a Fortran 90 compiler. Also included are programs for generating the optical property files input to SHDOM from physical properties of water cloud particles and aerosols.
SHELLSPEC is designed to calculate lightcurves, spectra and images of interacting binaries and extrasolar planets immersed in a moving circumstellar environment which is optically thin. It solves simple radiative transfer along the line of sight in moving media. The assumptions include LTE and optional known state quantities and velocity fields in 3D. Optional (non)transparent objects such as a spot, disc, stream, jet, shell or stars as well as an empty space may be defined (embedded) in 3D and their composite synthetic spectrum calculated. Roche model can be used as a boundary condition for the radiative tranfer. The program does not solve the inverse problem of finding the stellar and orbital parameters.
Current and upcoming wide-field, ground-based, broad-band imaging surveys promise to address a wide range of outstanding problems in galaxy formation and cosmology. Several such uses of ground-based data, especially weak gravitational lensing, require highly precise measurements of galaxy image statistics with careful correction for the effects of the point-spread function (PSF). The SHERA (SHEar Reconvolution Analysis) software simulates ground-based imaging data with realistic galaxy morphologies and observing conditions, starting from space-based data (from COSMOS, the Cosmological Evolution Survey) and accounting for the effects of the space-based PSF. This code simulates ground-based data, optionally with a weak lensing shear applied, in a model-independent way using a general Fourier space formalism. The utility of this pipeline is that it allows for a precise, realistic assessment of systematic errors due to the method of data processing, for example in extracting weak lensing galaxy shape measurements or galaxy radial profiles, given user-supplied observational conditions and real galaxy morphologies. Moreover, the simulations allow for the empirical test of error estimates and determination of parameter degeneracies, via generation of many noise maps. The public release of this software, along with a large sample of cleaned COSMOS galaxy images (corrected for charge transfer inefficiency), should enable upcoming ground-based imaging surveys to achieve their potential in the areas of precision weak lensing analysis, galaxy profile measurement, and other applications involving detailed image analysis.
This code is no longer maintained and has been superseded by GalSim (ascl:1402.009).
Sherpa is the CIAO (ascl:1311.006) modeling and fitting application made available by the Chandra X-ray Center (CXC). It can be used for analysis of images, spectra and time series from many telescopes, including optical telescopes such as Hubble. Sherpa is flexible, modular and extensible. It has an IPython user interface and it is also an importable Python module. Sherpa models, optimization and statistic functions are available via both C++ and Python for software developers wishing to link such functions directly to their own compiled code.
The CIAO 4.3 Sherpa release supports fitting of 1-D X-ray spectra from Chandra and other X-ray missions, as well as 1-D non-X-ray data, including ASCII data arrays, radial profiles, and lightcurves. The options for grating data analysis include fitting the spectrum with multiple response files required for overlapping orders in LETG observations. Modeling of 2-D spatial data is fully supported, including the PSF and exposure maps. User specified models can be added to Sherpa with advanced "user model" functionality.
SHTOOLS is an archive of fortran 95 based software that can be used to perform (among others) spherical harmonic transforms and reconstructions, rotations of spherical harmonic coefficients, and multitaper spectral analyses on the sphere. The package accommodates any standard normalization of the spherical harmonic functions ("geodesy" 4π normalized, Schmidt semi-normalized, orthonormalized, and unnormalized), and either real or complex spherical harmonics can be employed. Spherical harmonic transforms are calculated by exact quadrature rules using either (1) the sampling theorem of Driscoll and Healy (1994) where data are equally sampled (or spaced) in latitude and longitude, or (2) Gauss-Legendre quadrature. A least squares inversion routine for irregularly sampled data is included as well. The Condon-Shortley phase factor of (-1)m can be used or excluded with the associated Legendre functions. The spherical harmonic transforms are accurate to approximately degree 2800, corresponding to a spatial resolution of better than 4 arc minutes. Routines are included for performing localized multitaper spectral analyses and standard gravity calculations, such as computation of the geoid, and the determination of the potential associated with finite-amplitude topography. The routines are fast. Spherical harmonic transforms and reconstructions take on the order of 1 second for bandwidths less than 600 and about 3 minutes for bandwidths close to 2800.
Shwirl visualizes spectral data cubes with meaningful coloring methods. The program has been developed to investigate transfer functions, which combines volumetric elements (or voxels) to set the color, and graphics shaders, functions used to compute several properties of the final image such as color, depth, and/or transparency, as enablers for scientific visualization of astronomical data. The program uses Astropy (ascl:1304.002) to handle FITS files and World Coordinate System, Qt (and PyQt) for the user interface, and VisPy, an object-oriented Python visualization library binding onto OpenGL.
sic (Sparse Inpainting Code) generates Gaussian, isotropic CMB realizations, masks them, and recovers the large-scale masked data using sparse inpainting; it is written in Fortran90.
sick infers astrophysical parameters from noisy observed spectra. Phenomena that can alter the data (e.g., redshift, continuum, instrumental broadening, outlier pixels) are modeled and simultaneously inferred with the astrophysical parameters of interest. This package relies on emcee (ascl:1303.002); it is best suited for situations where a grid of model spectra already exists, and one would like to infer model parameters given some data.
SICON (Stokes Inversion based on COnvolutional Neural networks) provides a three-dimensional cube of thermodynamical and magnetic properties from the interpretation of two-dimensional maps of Stokes profiles by use of a convolutional neural network. In addition to being much faster than parallelized inversion codes, SICON, when trained on synthetic Stokes profiles from two numerical simulations of different structures of the solar atmosphere, also provided a three-dimensional view of the physical properties of the region of interest in geometrical height, and pressure and Wilson depression properties that are decontaminated from the blurring effect of instrumental point spread functions.
Self-Interacting Dark Matter (SIDM) is a hypothetical model for cold dark matter in the Universe. A strong interaction between dark matter particles introduce a different physics inside dark-matter haloes, making the density profile cored, reduce the number of subhaloes, and trigger gravothermal collapse. sidm-nbody is an N-body simulation code with Direct Simulation Monte Carlo scattering for self interaction, and some codes to analyse gravothermal collapse of isolated haloes. The N-body simulation is based on GADGET 1.1.
SiFTO is an empirical method for modeling Type Ia supernova (SN Ia) light curves by manipulating a spectral template. We make use of high-redshift SN data when training the model, allowing us to extend it bluer than rest-frame U. This increases the utility of our high-redshift SN observations by allowing us to use more of the available data. We find that when the shape of the light curve is described using a stretch prescription, applying the same stretch at all wavelengths is not an adequate description. SiFTO therefore uses a generalization of stretch which applies different stretch factors as a function of both the wavelength of the observed filter and the stretch in the rest-frame B band. SiFTO has been compared to other published light-curve models by applying them to the same set of SN photometry, and it's been demonstrated that SiFTO and SALT2 perform better than the alternatives when judged by the scatter around the best-fit luminosity distance relationship. When SiFTO and SALT2 are trained on the same data set the cosmological results agree.
SIGPROC is a package designed to standardize the initial analysis of the many types of fast-sampled pulsar data. Currently recognized machines are the Wide Band Arecibo Pulsar Processor (WAPP), the Penn State Pulsar Machine (PSPM), the Arecibo Observatory Fourier Transform Machine (AOFTM), the Berkeley Pulsar Processors (BPP), the Parkes/Jodrell 1-bit filterbanks (SCAMP) and the filterbank at the Ooty radio telescope (OOTY). The SIGPROC tools should help users look at their data quickly, without the need to write (yet) another routine to read data or worry about big/little endian compatibility (byte swapping is handled automatically).
The ESO's VLT/SPHERE instrument includes a unique long-slit spectroscopy (LSS) mode coupled with Lyot coronagraphy in its infrared dual-band imager and spectrograph (IRDIS) for spectral characterization of young, giant exoplanets detected by direct imaging. The SILSS pipeline is a combination of the official SPHERE pipeline and additional custom IDL routines developed within the SPHERE consortium for the speckle subtraction and spectral extraction of a companion's spectrum; it offers a complete end-to-end pipeline, from raw data (science+calibrations) to a final spectrum of the companion. SILSS works on both the low-resolution (LRS) and medium-resolution (MRS) data, and allows correction for some of the known biases of the instrument. Documentation is included in the header of the main routine of the pipeline.
The SIM5 library contains routines for relativistic raytracing and radiation transfer in GR. Written C with a Python interface, it has a special focus on raytracing from accretion disks, tori, hot spots or any other 3D configuration of matter in Kerr geometry, but it can be used with any other metric as well. It handles both optically thick and thin sources as well as transport of polarization of the radiation and calculates the propagation of light rays from the source to an observer through a curved spacetime. It supports parallelization and runs on GPUs.
SimCADO is a python package which allows the user to simulate observations with any NIR/Vis imaging system. The package was originally designed to simulate images for the European extremely large telescope (ELT) and MICADO, however with the proper input it is capable of simulating observations from many different Telescope + Instrument configurations.
The documentation can be found here: https://simcado.readthedocs.io/en/latest/
SimFast 21 generates a simulation of the cosmological 21cm signal. While limited to low spatial resolution, the next generation low-frequency radio interferometers that target 21 cm observations during the era of reionization and prior will have instantaneous fields-of-view that are many tens of square degrees on the sky. Predictions related to various statistical measurements of the 21 cm brightness temperature must then be pursued with numerical simulations of reionization with correspondingly large volume box sizes, of order 1000 Mpc on one side. The authors pursued a semi-numerical scheme to simulate the 21 cm signal during and prior to Reionization by extending a hybrid approach where simulations are performed by first laying down the linear dark matter density field, accounting for the non-linear evolution of the density field based on second-order linear perturbation theory as specified by the Zel'dovich approximation, and then specifying the location and mass of collapsed dark matter halos using the excursion-set formalism. The location of ionizing sources and the time evolving distribution of ionization field is also specified using an excursion-set algorithm. They account for the brightness temperature evolution through the coupling between spin and gas temperature due to collisions, radiative coupling in the presence of Lyman-alpha photons and heating of the intergalactic medium, such as due to a background of X-ray photons. The method is capable of producing the required large volume simulations with adequate resolution in a reasonable time so a large number of realizations can be obtained with variations in assumptions related to astrophysics and background cosmology that govern the 21 cm signal.
This is an implementation of a fairly simple-minded luminosity distance fitter, intended for use with supernova data. The calculational technique is based on evaluating the $chi^2$ of the model fit on a grid and marginalization over various nuisance parameters. Of course, the nature of these things is that this code has gotten steadily more complex, so perhaps the simple moniker is no longer justified.
SimpLens illustrates some of the theoretical ideas important in gravitational lensing in an interactive way. After setting parameters for elliptical mass distribution and external mass, SimpLens displays the mass profile and source position, the lens potential and image locations, and indicate the image magnifications and contours of virtual light-travel time. A lens profile can be made shallower or steeper with little change in the image positions and with only total magnification affected.
The R-package SimSpin measures the kinematics of a galaxy simulation as if it had been observed using an IFU. The functions included in the package can produce a kinematic data cube and measure the "observables" from this data cube, specifically the observable spin parameter λr. This package, once installed, is fully documented and tested.
simuTrans models transit light curves affected by gravity-darkened stars. The code defines a star on a grid by modeling the brightness of each point as blackbody emission, then sets a series of parameters and uses emcee (ascl:1303.002) to explore the posterior probability distribution for the remaining fitted parameters and determine their best-fit values.
SIMX simulates a photon-counting detector's response to an input source, including a simplified model of any telescope. The code is not a full ray-trace, but a convolution tool that uses standard descriptions of telescope PSF (via either a simple Gaussian parameter, an energy-dependent encircled-energy function, or an image of the PSF) and the detector response (using the OGIP response function) to model how sources will appear. simx uses a predefined set of PSFs, vignetting information, and instrumental responses and outputs to make the simulation. It is designed to be a 'approximation' tool to estimate issues such as source confusion, background effects, pileup, and other similar issues.
The SINFONI pipeline reduces data from the Very Large Telescope's SINFONI (Spectrograph for INtegral Field Observations in the Near Infrared) instrument. It can evaluate the detector linearity and generate a corresponding non linear pixel map, create a master dark and a hot-pixel map, a master flat and a map of pixels which have intensities greater than a given threshold. It can also compute the optical distortions and slitlets distances, and perform wavelength calibration, PSF, telluric standard and other science data reduction, and can coadd bad pixel maps, collapse a cube to an image over a given wavelength range, perform cube arithmetics, among other useful tasks.
SofteningLength: Because Newton's law of Gravitation diverges as the relative separations |r'-r| tends to zero, it is common to add a positive constant λ also known as the "softening length", i.e. :
SingLe determines the appropriate value of this Softening Length λ for a given disc local structure (thickness 2h and vertical stratification ρ), in the axially symmetric, flat disc limit, preserving at best the Newtonian character of the gravitational potential and associated forces. Mass density ρ(z) is assumed to be locally expandable in the z-direction according to:
SIP (Systematics-Insensitive Periodograms) extends the generative model used to create traditional sine-fitting periodograms for finding the frequency of a sinusoid by including systematic trends based on a set of eigen light curves in the generative model in addition to using a sum of sine and cosine functions over a grid of frequencies, producing periodograms with vastly reduced systematic features. Acoustic oscillations in giant stars and measurement of stellar rotation periods can be recovered from the SIP periodograms without detrending. The code can also be applied to detection other periodic phenomena, including eclipsing binaries and short-period exoplanet candidates.
SIR is a general-purpose code capable of dealing with gradients of the physical quantities with height. It admits one and two-component model atmospheres. It allows the recovery of the stratification of the temperature, the magnetic field vector, and the line of sight velocity through the atmosphere, and the micro- and macroturbulence velocities - which are assumed to be constant with depth. It is based on the response functions, which enter a Marquardt nonlinear least-squares algorithm in a natural way. Response functions are calculated at the same time as the full radiative transfer equation for polarized light is integrated, which determines values of many free parameters in a reasonable computation time. SIR demonstrates high stability, accuracy, and uniqueness of results, even when simulated observations present signal-to-noise ratios of the order of the lowest acceptable values in real observations.
SITools2 is a CNES generic tool performed by a joint effort between CNES and scientific laboratories. SITools provides a self-manageable data access layer deployed on already existing scientific laboratory databases. This new version of SITools is a JAVA-based framework, under open source license, that provides a portable archive system, highly configurable, easy to use by laboratories, with a plugin mechanism so developers can add their own applications.
SIXTE simulates X-Ray telescope observation; the software performs instrument performance analyses and produces simulated event files for mission and analysis studies. SIXTE strives to find a compromise between exactness of the simulation and speed. Using calibration files such as the PSF, RMF and ARF makes efficient simulations possible at comparably high speed, even though they include nonlinear effects such as pileup. Setups for some current and future missions, such as XMM-Newton and Athena, are included in the package; others can be added by the user with relatively little effort through specifying the main instrument characteristics in a flexible, human-readable XML-based format. Properties of X-ray sources to be simulated are described in a detector-independent format, i.e., the same input can be used for simulating observations with all available instruments, and the same input can also be used for simulations with the SIMX simulator. The input files are easily generated from standard data such as XSPEC (ascl:9910.005) spectral models or FITS images with tools provided with the SIXTE distribution. The input data scale well from single point sources up to very complicated setups.
SKID finds gravitationally bound groups in N-body simulations. The SKID program will group different types of particles depending on the type of input binary file. This could be either dark matter particles, gas particles, star particles or gas and star particles depending on what is in the input tipsy binary file. Once groups with at least a certain minimum number of members have been determined, SKID will remove particles which are not bound to the group. SKID must use the original positions of all the particles to determine whether or not particles are bound. This procedure which we call unbinding, is again dependent on the type of grouping we are dealing with. There are two cases, one for dark matter only or star particles only (case 1 unbinding), the other for inputs including gas (also stars in a dark matter environment this is case 2 unbinding).
Skid version 1.3 is a much improved version of the old denmax-1.1 version. The new name was given to avoid confusion with the DENMAX program of Gelb & Bertschinger, and although it is based on the same idea it represents a substantial evolution in the method.
SKIRT is a radiative transfer code based on the Monte Carlo technique. The name SKIRT, acronym for Stellar Kinematics Including Radiative Transfer, reflects the original motivation for its creation: it has been developed to study the effects of dust absorption and scattering on the observed kinematics of dusty galaxies. In a second stage, the SKIRT code was extended with a module to self-consistently calculate the dust emission spectrum under the assumption of local thermal equilibrium. This LTE version of SKIRT has been used to model the dust extinction and emission of various types of galaxies, as well as circumstellar discs and clumpy tori around active galactic nuclei. A new, extended version of SKIRT code can perform efficient 3D radiative transfer calculations including a self-consistent calculation of the dust temperature distribution and the associated FIR/submm emission with a full incorporation of the emission of transiently heated grains and PAH molecules.
Written in Fortran 90, Sky3D solves the static or dynamic equations on a three-dimensional Cartesian mesh with isolated or periodic boundary conditions and no further symmetry assumptions. Pairing can be included in the BCS approximation for the static case. The code can be easily modified to include additional physics or special analysis of the results and requires LAPACK and FFTW3.
SkyCat is a tool that combines visualization of images and access to catalogs and archive data for astronomy. The tool, developed in Tcl/Tk, was originally conceived as a demo of the capabilities of the class library that was developed for the VLT. The Skycat sources currently consist of five packages:
Skycorr is an instrument-independent sky subtraction code that uses physically motivated line group scaling in the reference sky spectrum by a fitting approach for an improved sky line removal in the object spectrum. Possible wavelength shifts between both spectra are corrected by fitting Chebyshev polynomials and advanced rebinning without resolution decrease. For the correction, the optimized sky line spectrum and the automatically separated sky continuum (without scaling) is subtracted from the input object spectrum. Tests show that Skycorr performs well (per cent level residuals) for data in different wavelength regimes and of different resolution, even in the cases of relatively long time lags between the object and the reference sky spectrum. Lower quality results are mainly restricted to wavelengths not dominated by airglow lines or pseudo continua by unresolved strong emission bands.
Skyfield computes positions for the stars, planets, and satellites in orbit around the Earth. Its results should agree with the positions generated by the United States Naval Observatory and their Astronomical Almanac to within 0.0005 arcseconds (which equals half a “mas” or milliarcsecond). It computes geocentric coordinates or topocentric coordinates specific to your location on the Earth’s surface. Skyfield accepts AstroPy (ascl:1304.002) time objects as input and can return results in native AstroPy units but is not dependend on AstroPy nor its compiled libraries.
SkyMaker is a program that simulates astronomical images. It accepts object lists in ASCII generated by the Stuff program to produce realistic astronomical fields. SkyMaker is part of the EFIGI development project.
The general-purpose nuclear reaction network SkyNet evolves the abundances of nuclear species under the influence of nuclear reactions. SkyNet can be used to compute the nucleosynthesis evolution in all astrophysical scenarios where nucleosynthesis occurs. Any list of isotopes can be evolved and SkyNet supports various different types of nuclear reactions. SkyNet is modular, permitting new or existing physics, such as nuclear reactions or equations of state, to be easily added or modified.
SkyNet is an efficient and robust neural network training code for machine learning. It is able to train large and deep feed-forward neural networks, including autoencoders, for use in a wide range of supervised and unsupervised learning applications, such as regression, classification, density estimation, clustering and dimensionality reduction. SkyNet is implemented in C/C++ and fully parallelized using MPI.
The SkyView Virtual telescope provides access to survey datasets ranging from radio through the gamma-ray regimes. Over 100 survey datasets are currently available. The SkyView library referenced here is used as the basis for the SkyView web site (at http://skvyiew.gsfc.nasa.gov) but is designed for individual use by researchers as well.
SkyView's approach to access surveys is distinct from most other toolkits. Rather than providing links to the original data, SkyView attempts to immediately re-render the source data in the user-requested reference frame, projection, scaling, orientation, etc. The library includes a set of geometry transformation and mosaicking tools that may be integrated into other applications independent of SkyView.
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).
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.
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 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:
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.
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).
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.
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.
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.
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.
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 is a flexible source finding pipeline designed to detect and parameterise sources in 3D spectral-line data cubes. SoFiA combines several powerful source finding and parameterisation algorithms, including wavelet denoising, spatial and spectral smoothing, source mask optimisation, 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.
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.
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.
SOPHIA (Simulations Of Photo Hadronic Interactions in Astrophysics) solves problems connected to photohadronic processes in astrophysical environments and can also be used for radiation and background studies at high energy colliders such as LEP2 and HERA, as well as for simulations of photon induced air showers. SOPHIA implements well established phenomenological models, symmetries of hadronic interactions in a way that describes correctly the available exclusive and inclusive photohadronic cross section data obtained at fixed target and collider experiments.
SOPHISM models astronomical instrumentation from the entrance of the telescope to data acquisition at the detector, along with software blocks dealing with, for example, demodulation, inversion, and compression. The code performs most analyses done with light in astronomy, such as differential photometry, spectroscopy, and polarimetry. The simulator offers flexibility and implementation of new effects and subsystems, making it user-adaptable for a wide variety of instruments. SOPHISM can be used for all stages of instrument definition, design, operation, and lifetime tracking evaluation.
SOPIE (Sequential Off-Pulse Interval Estimation) provides functions to non-parametrically estimate the off-pulse interval of a source function originating from a pulsar. The technique is based on a sequential application of P-values obtained from goodness-of-fit tests for the uniform distribution, such as the Kolmogorov-Smirnov, Cramér-von Mises, Anderson-Darling and Rayleigh goodness-of-fit tests.
SOPT (Sparse OPTimisation) is a C implementation of the Sparsity Averaging Reweighted Analysis (SARA) algorithm. The approach relies on the observation that natural images exhibit strong average sparsity; average sparsity outperforms state-of-the-art priors that promote sparsity in a single orthonormal basis or redundant frame, or that promote gradient sparsity.
SP_Ace (Stellar Parameters And Chemical abundances Estimator) estimates the stellar parameters Teff, log g, [M/H], and elemental abundances. It employs 1D stellar atmosphere models in Local Thermodynamic Equilibrium (LTE). The code is highly automated and suitable for analyzing the spectra of large spectroscopic surveys with low or medium spectral resolution (R = 2000-20 000). A web service for calculating these values with the software is also available.
The Solar Position Algorithm (SPA) calculates the solar zenith and azimuth angles in the period from the year -2000 to 6000, with uncertainties of +/- 0.0003 degrees based on the date, time, and location on Earth. SPA is implemented in C; in addition to being available for download, an online calculator using this code is available at http://www.nrel.gov/midc/solpos/spa.html.
SpacePy provides data analysis and visualization tools for the space science community. Written in Python, it builds on the capabilities of the NumPy and MatPlotLib packages to make basic data analysis, modeling and visualization easier. It contains modules for handling many complex time formats, obtaining data from the OMNI database, and accessing the powerful Onera library. It contains a library of commonly used empirical relationships, performs association analysis, coordinate transformations, radiation belt modeling, and CDF reading, and creates publication quality plots.
SpaghettiLens allows citizen scientists to model gravitational lenses collaboratively; the software should also be easily adaptable to any other, reasonably similar problem. It lets volunteers execute a computer intensive task that cannot be easily executed client side and relies on citizen scientists collaborating. SpaghettiLens makes survey data available to citizen scientists, manages the model configurations generated by the volunteers, stores the resulting model configuration, and delivers the actual model. A model can be shared and discussed with other volunteers and revised, and new child models can be created, resulting in a branching version tree of models that explore different possibilities. Scientists can choose a collection of models; discussion among volunteers and scientists prune the tree to determine which models will receive further analysis.
SPAM searches for imprints of Hu-Sawicki f(R) gravity on the rotation curves of the SPARC (Spitzer Photometry and Accurate Rotation Curves) sample using the MCMC sampler emcee (ascl:1303.002). The code provides attributes for inspecting the MCMC chains and translating names of parameters to indices. The SPAM package also contains plotting scripts.
SPAM is a extension to AIPS for reducing high-resolution, low-frequency radio interferometric observations. Direction-dependent ionospheric calibration and image-plane ripple suppression are among the features that help to make high-quality sub-GHz images. Data reductions are captured in well-tested Python scripts that execute AIPS tasks directly (mostly during initial data reduction steps), call high-level functions that make multiple AIPS or ParselTongue calls, and require few manual operations.
SPAMCART generates synthetic spectral energy distributions and intensity maps from smoothed particle hydrodynamics simulation snapshots. It follows discrete luminosity packets as they propagate through a density field, and computes the radiative equilibrium temperature of the ambient dust from their trajectories. The sources can be extended and/or embedded, and discrete and/or diffuse. The density is not mapped on to a grid, and therefore the calculation is performed at exactly the same resolution as the hydrodynamics. The code strictly adheres to Kirchhoff's law of radiation. The algorithm is based on the Lucy Monte Carlo radiative transfer method and is fairly simple to implement, as it uses data structures that are already constructed for other purposes in modern particle codes
The Seismic Propagation through Active Regions and Convection (SPARC) code was developed by S. Hanasoge. The acoustic wavefield in SPARC is simulated by numerically solving the linearised 3-D Euler equations in Cartesian geometry (e.g., see Hanasoge, Duvall and Couvidat (2007)). Spatial derivatives are calculated using sixth-order compact finite differences (Lele,1992) and time evolution is achieved through the repeated application of an optimized second-order five-stage Runge-Kutta scheme (Hu, 1996). Periodic horizontal boundaries are used.
SPARK (Software Package for Astronomical Reduction with KMOS) reduces data from the K-band Multi Object Spectrograph (KMOS) for the VLT. In many cases, science data can be processed using a single recipe; alternately, all functions this recipe provides can be performed using other recipes provided as tools. Among the functions the recipes provide are sky subtraction, cube reconstruction with the application of flexure corrections, dividing out the telluric spectrum, applying an illumination correction, aligning the cubes, and then combinging them. The result is a set of files which contain the combined datacube and associated noise cube for each of the 24 integral field unit (IFUs). The pipeline includes simple error propagation.
SparsePZ uses sparse basis representation to fully represent individual photometric redshift probability density functions (PDFs). This approach requires approximately half the parameters for the same multi-Gaussian fitting accuracy, and has the additional advantage that an entire PDF can be stored by using a 4-byte integer per basis function. Only 10-20 points per galaxy are needed to reconstruct both the individual PDFs and the ensemble redshift distribution, N(z), to an accuracy of 99.9 per cent when compared to the one built using the original PDFs computed with a resolution of δz = 0.01, reducing the required storage of 200 original values by a factor of 10-20. This basis representation can be directly extended to a cosmological analysis, thereby increasing computational performance without losing resolution or accuracy.
SpcAudace processes long slit spectra with automated pipelines and performs astrophysical analysis of the latter data. These powerful pipelines do all the required steps in one pass: standard preprocessing, masking of bad pixels, geometric corrections, registration, optimized spectrum extraction, wavelength calibration and instrumental response computation and correction. Both high and low resolution long slit spectra are managed for stellar and non-stellar targets. Many types of publication-quality figures can be easily produced: pdf and png plots or annotated time series plots. Astrophysical quantities can be derived from individual or large amount of spectra with advanced functions: from line profile characteristics to equivalent width and periodogram. More than 300 documented functions are available and can be used into TCL scripts for automation. SpcAudace is based on Audela open source software.
SpDust is an IDL program that evaluates the spinning dust emissivity for user-provided environmental conditions. A new version of the code became available in March, 2010.
The DEEP2 DEIMOS Data Reduction Pipeline ("spec2d") is an IDL-based, automated software package designed to reduce Keck/DEIMOS multi-slit spectroscopic observations, collected as part of the DEEP2 Galaxy Redshift Survey. The pipeline is best suited for handling data taken with the 1200 line/mm grating tilted towards the red (lambda_c ~ 7800Å). The spec2d reduction package takes the raw DEIMOS data as its input and produces a variety of outputs including 2-d slit spectra and 1-d object spectra.
Specdre performs spectroscopy data reduction and analysis. General features of the package include data cube manipulation, arc line calibration, resampling and spectral fitting. Particular care is taken with error propagation, including tracking covariance. SPECDRE is distributed as part of the Starlink software collection (ascl:1110.012).
SpecPro is an interactive program for viewing and analyzing spectra, particularly in the context of modern imaging surveys. In addition to displaying the 1D and 2D spectrum, SpecPro can simultaneously display available stamp images as well as the spectral energy distribution of a source. This extra information can help significantly in assessing a spectrum.
Specstack creates stacked spectra using a simple algorithm with sigma-clipping to combine the spectra of galaxies in the rest-frame into a single averaged spectrum. Though written originally for galaxy spectra, it also works for other types of objects. It is written in Python and is started from the command-line.
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