SPEX is optimized for the analysis and interpretation of high-resolution cosmic X-ray spectra. The software is especially suited for fitting spectra obtained by current X-ray observatories like XMM-Newton, Chandra, and Suzaku. SPEX can fit multiple spectra with different model components simultaneously and handles highly complex models with many free parameters.
Spextool (Spectral EXtraction tool) is an IDL-based data reduction package for SpeX, a medium resolution near-infrared spectrograph on the NASA IRTF. It performs all of the steps necessary to produce spectra ready for analysis and publication including non-linearity corrections, flat fielding, wavelength calibration, telluric correction, flux calibration, and order merging.
We describe a fast tree algorithm for gravitational N-body simulation on SIMD parallel computers. The tree construction uses fast, parallel sorts. The sorted lists are recursively divided along their x, y and z coordinates. This data structure is a completely balanced tree (i.e., each particle is paired with exactly one other particle) and maintains good spatial locality. An implementation of this tree-building algorithm on a 16k processor Maspar MP-1 performs well and constitutes only a small fraction (approximately 15%) of the entire cycle of finding the accelerations. Each node in the tree is treated as a monopole. The tree search and the summation of accelerations also perform well. During the tree search, node data that is needed from another processor is simply fetched. Roughly 55% of the tree search time is spent in communications between processors. We apply the code to two problems of astrophysical interest. The first is a simulation of the close passage of two gravitationally, interacting, disk galaxies using 65,636 particles. We also simulate the formation of structure in an expanding, model universe using 1,048,576 particles. Our code attains speeds comparable to one head of a Cray Y-MP, so single instruction, multiple data (SIMD) type computers can be used for these simulations. The cost/performance ratio for SIMD machines like the Maspar MP-1 make them an extremely attractive alternative to either vector processors or large multiple instruction, multiple data (MIMD) type parallel computers. With further optimizations (e.g., more careful load balancing), speeds in excess of today's vector processing computers should be possible.
The Spherical Library provides an efficient and accurate mathematical representation of shapes on the celestial sphere, such as sky coverage and footprints. Shapes of arbitrary complexity and size can be dynamically created from simple building blocks, whose exact area is also analytically computed. This methodology is also perfectly suited for censoring problematic parts of datasets, e.g., bad seeing, satelite trails or diffraction spikes of bright stars.
Spheroid determines the size distribution of polarizing interstellar dust grains based on electromagnetic scattering by spheroidal particles. It contains subroutines to treat the case of complex refractive indices, and also includes checks for some limiting cases.
SPHGR (Smoothed-Particle Hydrodynamics Galaxy Reduction) is a python based open-source framework for analyzing smoothed-particle hydrodynamic simulations. Its basic form can run a baryonic group finder to identify galaxies and a halo finder to identify dark matter halos; it can also assign said galaxies to their respective halos, calculate halo & galaxy global properties, and iterate through previous time steps to identify the most-massive progenitors of each halo and galaxy. Data about each individual halo and galaxy is collated and easy to access.
SPHGR supports a wide range of simulations types including N-body, full cosmological volumes, and zoom-in runs. Support for multiple SPH code outputs is provided by pyGadgetReader (ascl:1411.001), mainly Gadget (ascl:0003.001) and TIPSY (ascl:1111.015).
SPHRAY, a Smoothed Particle Hydrodynamics (SPH) ray tracer, is designed to solve the 3D, time dependent, radiative transfer (RT) equations for arbitrary density fields. The SPH nature of SPHRAY makes the incorporation of separate hydrodynamics and gravity solvers very natural. SPHRAY relies on a Monte Carlo (MC) ray tracing scheme that does not interpolate the SPH particles onto a grid but instead integrates directly through the SPH kernels. Given initial conditions and a description of the sources of ionizing radiation, the code will calculate the non-equilibrium ionization state (HI, HII, HeI, HeII, HeIII, e) and temperature (internal energy/entropy) of each SPH particle. The sources of radiation can include point like objects, diffuse recombination radiation, and a background field from outside the computational volume. The MC ray tracing implementation allows for the quick introduction of new physics and is parallelization friendly. A quick Axis Aligned Bounding Box (AABB) test taken from computer graphics applications allows for the acceleration of the raytracing component. We present the algorithms used in SPHRAY and verify the code by performing all the test problems detailed in the recent Radiative Transfer Comparison Project of Iliev et. al. The Fortran 90 source code for SPHRAY and example SPH density fields are made available online.
SPHYNX addresses subsonic hydrodynamical instabilities and strong shocks; it is Newtonian, grounded on the Euler-Lagrange formulation of the smoothed-particle hydrodynamics technique, and density based. SPHYNX uses an integral approach for estimating gradients, a flexible family of interpolators to suppress pairing instability, and incorporates volume elements to provides better partition of the unity.
SPIDERz (SuPport vector classification for IDEntifying Redshifts) applies powerful support vector machine (SVM) optimization and statistical learning techniques to custom data sets to obtain accurate photometric redshift (photo-z) estimations. It is written for the IDL environment and can be applied to traditional data sets consisting of photometric band magnitudes, or alternatively to data sets with additional galaxy parameters (such as shape information) to investigate potential correlations between the extra galaxy parameters and redshift.
This is a python2.7 implementation of a parallax of pulsation method for Cepheids stars, described in Mérand et al. (Astronomy & Astrophysics 584-80, 2015)
Spirality measures spiral arm pitch angles by fitting galaxy images to spiral templates of known pitch. Written in MATLAB, the code package also includes GenSpiral, which produces FITS images of synthetic spirals, and SpiralArmCount, which uses a one-dimensional Fast Fourier Transform to count the spiral arms of a galaxy after its pitch is determined.
SPLASH (formerly SUPERSPHPLOT) is a visualization tool for output from (astrophysical) simulations using the Smoothed Particle Hydrodynamics (SPH) method in one, two and three dimensions. It is written in Fortran 90 and utilises the PGPLOT graphics subroutine library to do the actual plotting. It is based around a command-line menu structure but utilises the interactive capabilities of PGPLOT to manipulate data interactively in the plotting window.
SPLASH is a fully interactive program; visualizations can be changed rapidly at the touch of a button (e.g. zooming, rotating, shifting cross section positions etc). Data is read directly from the code dump format giving rapid access to results and the visualization is advanced forwards and backwards through timesteps by single keystrokes. SPLASH uses the SPH kernel to render plots of not only density but other physical quantities, giving a smooth representation of the data.
SPLAT-VO is an extension of the SPLAT (Spectral Analysis Tool, ascl:1402.007) graphical tool for displaying, comparing, modifying and analyzing astronomical spectra; it includes facilities that allow it to work as part of the Virtual Observatory (VO). SPLAT-VO comes in two different forms, one for querying and downloading spectra from SSAP servers and one for interoperating with VO tools, such as TOPCAT (ascl:1101.010).
SPLAT is a graphical tool for displaying, comparing, modifying and analyzing astronomical spectra stored in NDF, FITS and TEXT files as well as in NDX format. It can read in many spectra at the same time and then display these as line plots. Display windows can show one or several spectra at the same time and can be interactively zoomed and scrolled, centered on specific wavelengths, provide continuous coordinate readout, produce printable hardcopy and be configured in many ways. Analysis facilities include the fitting of a polynomial to selected parts of a spectrum, the fitting of Gaussian, Lorentzian and Voigt profiles to emission and absorption lines and the filtering of spectra using average, median and line-shape window functions as well as wavelet denoising. SPLAT also supports a full range of coordinate systems for spectra, which allows coordinates to be displayed and aligned in many different coordinate systems (wavelength, frequency, energy, velocity) and transformed between these and different standards of rest (topocentric, heliocentric, dynamic and kinematic local standards of rest, etc). SPLAT is distributed as part of the Starlink (ascl:1110.012) software collection.
Splotch is a light and fast, publicly available, ray-tracer software tool which supports the effective visualization of cosmological simulations data. The algorithm it relies on is designed to deal with point-like data, optimizing the ray-tracing calculation by ordering the particles as a function of their 'depth', defined as a function of one of the coordinates or other associated parameters. Realistic three-dimensional impressions are reached through a composition of the final colour in each pixel properly calculating emission and absorption of individual volume elements.
SPOTROD is a model for planetary transits of stars with an arbitrary limb darkening law and a number of homogeneous, circular spots on their surface. It facilitates analysis of anomalies due to starspot eclipses, and is a free, open source implementation written in C with a Python API.
SPRITE (Sparse Recovery of InstrumenTal rEsponse) computes a well-resolved compact source image from several undersampled and noisy observations. The algorithm is based on sparse regularization; adding a sparse penalty in the recovery leads to far better accuracy in terms of ellipticity error, especially at low S/N.
The SPS software simulates the operation of the Spectral and Photometric Imaging Receiver on-board the ESA’s Herschel Space Observatory. It is coded using the Interactive Data Language (IDL), and produces simulated data at the level-0 stage (non-calibrated data in digitised units). The primary uses for the simulator are to:
The SPT lensing likelihood code, written in Fortran90, performs a Gaussian likelihood based upon the lensing potential power spectrum using a file from CAMB (ascl:1102.026) which contains the normalization required to get the power spectrum that the likelihood call is expecting.
SPTCLASS assigns semi-automatic spectral types to a sample of stars. The main code includes three spectral classification schemes: the first one is optimized to classify stars in the mass range of TTS (K5 or later, hereafter LATE-type scheme); the second one is optimized to classify stars in the mass range of IMTTS (F late to K early, hereafter Gtype scheme), and the third one is optimized to classify stars in the mass range of HAeBe (F5 or earlier, hereafter HAeBe scheme). SPTCLASS has an interactive module that allows the user to select the best result from the three schemes and analyze the input spectra.
SSE is a rapid single-star evolution (SSE) code; these analytical formulae cover all phases of evolution from the zero-age main-sequence up to and including remnant phases. It is valid for masses in the range 0.1-100 Msun and metallicity can be varied. The SSE package contains a prescription for mass loss by stellar winds. It also follows the evolution of rotational angular momentum for the star.
Stagger is an astrophysical MHD code actively used to model star formation. It is equipped with a multi-frequency radiative transfer module and a comprehensive equation of state module that includes a large number of atomic and molecular species, to be able to compute realistic 3-D models of the near-surface layers of stars. The current version of the code allows a discretization that explicitly conserves mass, momentum, energy, and magnetic flux. The tensor formulation of the viscosity ensures that the viscous force is insensitive to the coordinate system orientation, thereby avoiding artificial grid-alignment.
Database management is an increasingly important part of astronomical data analysis. Astronomers need easy and convenient ways of storing, editing, filtering, and retrieving data about data. Commercial databases do not provide good solutions for many of the everyday and informal types of database access astronomers need. The Starbase database system with simple data file formatting rules and command line data operators has been created to answer this need. The system includes a complete set of relational and set operators, fast search/index and sorting operators, and many formatting and I/O operators. Special features are included to enhance the usefulness of the database when manipulating astronomical data. The software runs under UNIX, MSDOS and IRAF.
Starburst99 is a comprehensive set of model predictions for spectrophotometric and related properties of galaxies with active star formation. The models are presented in a homogeneous way for five metallicities between Z = 0.040 and 0.001 and three choices of the initial mass function. The age coverage is 10^6 to 10^9 yr. Spectral energy distributions are used to compute colors and other quantities.
StarCrash is a parallel fortran code based on Smoothed Particle Hydrodynamics (SPH) techniques to calculate the 3-d evolution of self-gravitating fluid systems. The code in particularly suited to the study of stellar interactions, such as mergers of binary star systems and stellar collisions. The StarCrash code comes with several important features, including:
StarFinder is an IDL code for the deep analysis of stellar fields, designed for Adaptive Optics well-sampled images with high and low Strehl ratio. The Point Spread Function is extracted directly from the frame, to take into account the actual structure of the instrumental response and the atmospheric effects. The code is written in IDL language and organized in the form of a self-contained widget-based application, provided with a series of tools for data visualization and analysis. A description of the method and some applications to Adaptive Optics data are presented.
StarFISH is a suite of programs designed to determine the star formation history (SFH) of a stellar population, given multicolor stellar photometry and a library of theoretical isochrones. It constructs a library of synthetic color-magnitude diagrams from the isochrones, which includes the effects of extinction, photometric errors and completeness, and binarity. A minimization routine is then used to determine the linear combination of synthetic CMDs that best matches the observed photometry. The set of amplitudes modulating each synthetic CMD describes the star formation history of the observed stellar population.
Starfish is a set of tools used for spectroscopic inference. It robustly determines stellar parameters using high resolution spectral models and uses Markov Chain Monte Carlo (MCMC) to explore the full posterior probability distribution of the stellar parameters. Additional potential applications include other types of spectra, such as unresolved stellar clusters or supernovae spectra.
Traditionally, a simulation of a dense stellar system required choosing an initial model, running an integrator, and analyzing the output. Almost all of the effort went into writing a clever integrator that could handle binaries, triples and encounters between various multiple systems efficiently. Recently, the scope and complexity of these simulations has increased dramatically, for three reasons: 1) the sheer size of the data sets, measured in Terabytes, make traditional 'awking and grepping' of a single output file impractical; 2) the addition of stellar evolution data brings qualitatively new challenges to the data reduction; 3) increased realism of the simulations invites realistic forms of 'SOS': Simulations of Observations of Simulations, to be compared directly with observations. We are now witnessing a shift toward the construction of archives as well as tailored forms of visualization including the use of virtual reality simulators and planetarium domes, and a coupling of both with budding efforts in constructing virtual observatories. This review describes these new trends, presenting Starlab as the first example of a full software environment for realistic large-scale simulations of dense stellar systems.
The study of stellar populations in galaxies is entering a new era with the availability of large and high quality databases of both observed galactic spectra and state-of-the-art evolutionary synthesis models. The power of spectral synthesis can be investigated as a mean to estimate physical properties of galaxies. Spectral synthesis is nothing more than the decomposition of an observed spectrum in terms of a superposition of a base of simple stellar populations of various ages and metallicities, producing astrophysically interesting output such as the star-formation and chemical enrichment histories of a galaxy, its extinction and velocity dispersion. This is what the STARLIGHT spectral synthesis code does.
Starlink Figaro is an independently-maintained fork of Figaro (ascl:1203.013) that runs in the Starlink software environment (ascl:1110.012). It is a general-purpose data reduction package targeted mainly at optical/IR spectroscopy. It uses the NDF data format and the ADAM libraries for parameters and messaging.
Starlink has many applications within it to meet a variety of needs; it includes:
STARMAN is a stellar photometry package designed for the reduction of data from imaging systems. Its main components are crowded-field photometry programs, aperture photometry programs, a star finding program, and a CCD reduction program.
Image and table handling are served by a large number of programs which have a general use in photometry and other types of work. The package is a coherent whole, for use in the entire process of stellar photometry from raw images to the final standard-system magnitudes and their plotting as color-magnitude and color-color diagrams. It was distributed as part of the Starlink software collection (ascl:1110.012).
StarPy derives the quenching star formation history (SFH) of a single galaxy through the Bayesian Markov Chain Monte Carlo method code emcee (ascl:1303.002). The sample function implements the emcee EnsembleSampler function for the galaxy colors input. Burn-in is run and calculated for the length specified before the sampler is reset and then run for the length of steps specified. StarPy provides the ability to use the look-up tables provided or creating your own.
We have developed a detailed stellar evolution code capable of following the simultaneous evolution of both stars in a binary system, together with their orbital properties. To demonstrate the capabilities of the code we investigate potential progenitors for the Type IIb supernova 1993J, which is believed to have been an interacting binary system prior to its primary exploding. We use our detailed binary stellar evolution code to model this system to determine the possible range of primary and secondary masses that could have produced the observed characteristics of this system, with particular reference to the secondary. Using the luminosities and temperatures for both stars (as determined by Maund et al. 2004) and the remaining mass of the hydrogen envelope of the primary at the time of explosion, we find that if mass transfer is 100 per cent efficient the observations can be reproduced by a system consisting of a 15 solar mass primary and a 14 solar mass secondary in an orbit with an initial period of 2100 days. With a mass transfer efficiency of 50 per cent, a more massive system consisting of a 17 solar mass primary and a 16 solar mass secondary in an initial orbit of 2360 days is needed. We also investigate some of the uncertainties in the evolution, including the effects of tidal interaction, convective overshooting and thermohaline mixing.
The Matlab starsense_algorithms package evaluates the performance of various star sensors through the implementation of centroiding, geometric voting and QUEST algorithms. The physical parameters of a star sensor are parametrized and by changing these parameters, performance estimators such as sky coverage, memory requirement, and timing requirements can be estimated for the selected star sensor.
STATCONT determines the continuum emission level in line-rich spectral data by inspecting the intensity distribution of a given spectrum by using different statistical approaches. The sigma-clipping algorithm provides the most accurate continuum level determination, together with information on the uncertainty in its determination; this uncertainty is used to correct the final continuum emission level. In general, STATCONT obtains accuracies of < 10 % in the continuum determination, and < 5 % in most cases. The main products of the software are the continuum emission level, together with its uncertainty, and data cubes containing only spectral line emission, i.e. continuum-subtracted data cubes. STATCONT also includes the option to estimate the spectral index or variation of the continuum emission with frequency.
statpl estimates the parameter of power-law distributed data and calculates goodness-of-fit tests for them. Many objects studied in astronomy follow a power-law distribution function (DF), for example the masses of stars or star clusters. Such data is often analyzed by generating a histogram and fitting a straight line to it. The parameters obtained in this way can be severely biased, and the properties of the underlying DF, such as its shape or a possible upper limit, are difficult to extract. statpl is an (effectively) bias-free estimator for the exponent and the upper limit.
STECKMAP stands for STEllar Content and Kinematics via Maximum A Posteriori likelihood. It is a tool for interpreting galaxy spectra in terms of their stellar populations through the derivation of their star formation history, age-metallicity relation, kinematics and extinction. The observed spectrum is projected onto a temporal sequence of models of single stellar populations, so as to determine a linear combination of these models that best fits the observed spectrum. The weights of the various components of this linear combination indicate the stellar content of the population. This procedure is regularized using various penalizing functions. The principles of the method are detailed in Ocvirk et al. 2006.
STELLA is a one-dimensional multi-group radiation hydrodynamics code. STELLA incorporates implicit hydrodynamics coupled to a multi-group non-equilibrium radiative transfer for modeling SN II-L light curves. The non-equilibrium description of radiation is crucial for this problem since the presupernova envelope may be of low mass and very dilute. STELLA implicitly treats time dependent equations of the angular moments of intensity averaged over a frequency bin. Local thermodynamic equilibrium is assumed to determine the ionization levels of materials.
stellaR accesses and manipulates publicly available stellar evolutionary tracks and isochrones from the Pisa low-mass database. It retrieves and plots the required calculations from CDS, constructs by interpolation tracks or isochrones of compositions different to the ones available in the database, constructs isochrones for age not included in the database, and extracts relevant evolutionary points from tracks or isochrones.
Cosmic ray electrons scatter on the photon fields around stars, including the sun, to create gamma rays by the inverse Compton effect. Stellarics computes the spectrum and angular distribution of this emission. The software also includes general-purpose routines for inverse Compton scattering on a given electron spectrum, for example for interstellar or astrophysical source modelling.
STF is a general structure finder designed to find halos, subhaloes, and tidal debris in N-body simulations. The current version is designed to read in "particle data" (that is SPH N-body data), but a simple modification of the I/O can have it read grid data from Grid based codes.
STIFF is a program that converts scientific FITS1 images to the more popular TIFF2 format for illustration purposes. Most FITS readers and converters do not do a proper job at converting FITS image data to 8 bits. 8-bit images stored in JPEG, PNG or TIFF files have the intensities implicitely stored in a non-linear way. Most current FITS image viewers and converters provide the user an incorrect translation of the FITS image content by simply rescaling linearly input pixel values. A first consequence is that the people working on astronomical images usually have to apply narrow intensity cuts or square-root or logarithmic intensity transformations to actually see something on their deep-sky images. A less obvious consequence is that colors obtained by combining images processed this way are not consistent across such a large range of surface brightnesses. Though with other software the user is generally afforded a choice of nonlinear transformations to apply in order to make the faint stuff stand out more clearly in the images, with the limited selection of choices provides, colors will not be accurately rendered, and some manual tweaking will be necessary. The purpose of STIFF is to produce beautiful pictures in an automatic and consistent way.
The STIL Tool Set is a set of command-line tools based on STIL, the Starlink Tables Infrastructure Library. It deals with the processing of tabular data; the package has been designed for, but is not restricted to, astronomical tables such as object catalogues. Some of the tools are generic and can work with multiple formats (including FITS, VOTable, CSV, SQL and ASCII), and others are specific to the VOTable format. In some ways, STILTS forms the command-line counterpart of the GUI table analysis tool TOPCAT. The package is robust, fully documented, and designed for efficiency, especially with very large datasets.
Facilities offered include:
Stingray is a spectral-timing software package for astrophysical X-ray (and more) data. The package merges existing efforts for a (spectral-)timing package in Python and is composed of a library of time series methods (including power spectra, cross spectra, covariance spectra, and lags); scripts to load FITS data files from different missions; a simulator of light curves and event lists that includes different kinds of variability and more complicated phenomena based on the impulse response of given physical events (e.g. reverberation); and a GUI to ease the learning curve for new users.
STOKES was designed to perform three-dimensional radiative transfer simulations for astronomical applications. The code also considers the polarization properties of the radiation. The program is based on the Monte-Carlo method and treats optical and ultraviolet polarization induced by scattering off free electrons or dust grains. Emission and scattering regions can be arranged in various geometries within the model space, the computed continuum and line spectra can be evaluated at different inclinations and azimuthal viewing angles.
STools contains a variety of simple tools for spectroscopy, such as reading an IRAF-formatted (multispec) echelle spectrum in FITS, measuring the wavelength of the center of a line, Gaussian convolution, deriving synthetic photometry from an input spectrum, and extracting and interpolating a MARCS model atmosphere (standard composition).
streamgap-pepper computes the effect of subhalo fly-bys on cold tidal streams based on the action-angle representation of streams. A line-of-parallel-angle approach is used to calculate the perturbed distribution function of a given stream segment by undoing the effect of all impacts. This approach allows one to compute the perturbed stream density and track in any coordinate system in minutes for realizations of the subhalo distribution down to 10^5 Msun, accounting for the stream's internal dispersion and overlapping impacts. This code uses galpy (ascl:1411.008) and the streampepperdf.py galpy extension, which implements the fast calculation of the perturbed stream structure.
StringFast implements a method for efficient computation of the C_l spectra induced by a network of strings, which is fast enough to be used in Markov Chain Monte Carlo analyses of future data. This code allows the user to calculate TT, EE, and BB power spectra (scalar [for TT and EE], vector, and tensor modes) for "wiggly" cosmic strings. StringFast uses the output of the public code CMBACT. The properties of the strings are described by four parameters:
The Space Telescope Science Data Analysis System (STSDAS) is a software package for reducing and analyzing astronomical data. It is layered on top of IRAF and provides general-purpose tools for astronomical data analysis as well as routines specifically designed for HST data. In particular, STSDAS contains all the programs used for the calibration and reduction of HST data in the STScI post-observation processing pipelines.
Stuff is a program that simulates “perfect” astronomical catalogues. It generate object lists in ASCII which can read by the SkyMaker program to produce realistic astronomical fields. Stuff is part of the EFIGI development project.
SunPy is a community-developed free and open-source software package for solar physics and is an alternative to the SolarSoft data analysis environment. SunPy provides data structures for representing the most common solar data types (images, lightcurves, and spectra) and integration with the Virtual Solar Observatory (VSO) and the Heliophysics Event Knowledgebase (HEK) for data acquisition.
Sunrise is a Monte Carlo radiation transfer code for calculating absorption and scattering of light to study the effects of dust in hydrodynamic simulations of interacting galaxies. It uses an adaptive mesh refinement grid to describe arbitrary geometries of emitting and absorbing/scattering media, with spatial dynamical range exceeding 104; it can efficiently generate images of the emerging radiation at arbitrary points in space and spectral energy distributions of simulated galaxies run with the Gadget, Gasoline, Arepo, Enzo or ART codes. In addition to the monochromatic radiative transfer typically used by Monte Carlo codes, Sunrise can propagate a range of wavelengths simultaneously. This "polychromatic" algorithm gives significant improvements in efficiency and accuracy when spectral features are calculated.
This IDL code creates a thick magneto-static structure with parameters of a typical sunspot in a solar like photosphere - chromosphere. The variable parameters are field strength on the axis, radius, and Wilson depression (displacement of the atmosphere on the axis with respect to the field-free atmosphere). Output are magnetic field vector, pressure and density distributions with radius and height. The structure has azimuthal symmetry. The codes are relatively self explanatory and the download packages contain README files.
SuperBayeS is a package for fast and efficient sampling of supersymmetric theories. It uses Bayesian techniques to explore multidimensional SUSY parameter spaces and to compare SUSY predictions with observable quantities, including sparticle masses, collider observables, dark matter abundance, direct detection cross sections, indirect detection quantities etc. Scanning can be performed using Markov Chain Monte Carlo (MCMC) technology or even more efficiently by employing a new scanning technique called, MultiNest. which implements the nested sampling algorithm. Using MultiNest, a full 8-dimensional scan of the CMSSM takes about 12 hours on 10 2.4GHz CPUs. There is also an option for old-style fixed-grid scanning. A discussion forum for SuperBayeS is available.
The package combines SoftSusy, DarkSusy, FeynHiggs, Bdecay, MultiNest and MicrOMEGAs. Some of the routines and the plotting tools are based on CosmoMC.
SuperBayeS comes with SuperEGO, a MATLAB graphical user interface tool for interactive plotting of the results. SuperEGO has been developed by Rachid Lemrani and is based on CosmoloGUI by Sarah Bridle.
SuperBoL calculates the bolometric lightcurves of Type II supernovae using observed photometry; it includes three different methods for calculating the bolometric luminosity: quasi-bolometric, direct, and bolometric correction. SuperBoL propagates uncertainties in the input data through the calculations made by the code, allowing for error bars to be included in plots of the lightcurve.
SUPERBOX is a particle-mesh code that uses moving sub-grids to track and resolve high-density peaks in the particle distribution and a nearest grid point force-calculation scheme based on the second derivatives of the potential. The code implements a fast low-storage FFT-algorithm and allows a highly resolved treatment of interactions in clusters of galaxies, such as high-velocity encounters between elliptical galaxies and the tidal disruption of dwarf galaxies, as sub-grids follow the trajectories of individual galaxies. SUPERBOX is efficient in that the computational overhead is kept as slim as possible and is also memory efficient since it uses only one set of grids to treat galaxies in succession.
SuperFreq numerically estimates the fundamental frequencies and orbital actions of pre-computed orbital time series. It is an implementation of a version of the Numerical Analysis of Fundamental Frequencies close to that by Monica Valluri, which itself is an implementation of an algorithm first used by Jacques Laskar.
Flux-averaging justifies the use of the distance-redshift relation for a smooth universe in the analysis of type Ia supernova (SN Ia) data. Flux-averaging of SN Ia data is required to yield cosmological parameter constraints that are free of the bias induced by weak gravitational lensing. SN Ia data are converted into flux. For a given cosmological model, the distance dependence of the data is removed, then the data are binned in redshift, and placed at the average redshift in each redshift bin. The likelihood of the given cosmological model is then computed using "flux statistics''. These Fortran codes compute the likelihood of an arbitrary cosmological model [with given H(z)/H_0] using flux-averaged Type Ia supernova data.
Supernovae classifies supernovae using their light curves directly as inputs to a deep recurrent neural network, which learns information from the sequence of observations. Observational time and filter fluxes are used as inputs; since the inputs are agnostic, additional data such as host galaxy information can also be included.
Superplot calculates and plots statistical quantities relevant to parameter inference from a "chain" of samples drawn from a parameter space produced by codes such as MultiNest (ascl:1109.006), BAYES-X (ascl:1505.027), and PolyChord (ascl:1502.011). It offers a graphical interface for browsing a chain of many variables quickly and can produce numerous kinds of publication quality plots, including one- and two-dimensional profile likelihood, three-dimensional scatter plots, and confidence intervals and credible regions. Superplot can also save plots in PDF format, create a summary text file, and export a plot as a pickled object for importing and manipulating in a Python interpreter.
The Surprise is a measure for consistency between posterior distributions and operates in parameter space. It can be used to analyze either the compatibility of separately analyzed posteriors from two datasets, or the posteriors from a Bayesian update. The Surprise Calculator estimates relative entropy and Surprise between two samples, assuming they are Gaussian. The software requires the R package CompQuadForm to estimate the significance of the Surprise, and rpy2 to interface R with Python.
Swarm-NG is a C++ library for the efficient direct integration of many n-body systems using highly-parallel Graphics Processing Units (GPU). Swarm-NG focuses on many few-body systems, e.g., thousands of systems with 3...15 bodies each, as is typical for the study of planetary systems; the code parallelizes the simulation, including both the numerical integration of the equations of motion and the evaluation of forces using NVIDIA's "Compute Unified Device Architecture" (CUDA) on the GPU. Swarm-NG includes optimized implementations of 4th order time-symmetrized Hermite integration and mixed variable symplectic integration as well as several sample codes for other algorithms to illustrate how non-CUDA-savvy users may themselves introduce customized integrators into the Swarm-NG framework. Applications of Swarm-NG include studying the late stages of planet formation, testing the stability of planetary systems and evaluating the goodness-of-fit between many planetary system models and observations of extrasolar planet host stars (e.g., radial velocity, astrometry, transit timing). While Swarm-NG focuses on the parallel integration of many planetary systems,the underlying integrators could be applied to a wide variety of problems that require repeatedly integrating a set of ordinary differential equations many times using different initial conditions and/or parameter values.
SWarp is a program that resamples and co-adds together FITS images using any arbitrary astrometric projection defined in the WCS standard. It operates on pre-reduced images and their weight-maps. Based on the astrometric and photometric calibrations derived at an earlier phase of the pipeline, SWarp re-maps ("warps") the pixels to a perfect projection system, and co-adds them in an optimum way, according to their relative weights. SWarp's astrometric engine is based on a customized version of Calabretta's WCSLib 2.6 and supports all of the projections defined in the 2000 version of the WCS proposal.
SWIFT follows the long-term dynamical evolution of a swarm of test particles in the solar system. The code efficiently and accurately handles close approaches between test particles and planets while retaining the powerful features of recently developed mixed variable symplectic integrators. Four integration techniques are included: Wisdom-Holman Mapping; Regularized Mixed Variable Symplectic (RMVS) method; fourth order T+U Symplectic (TU4) method; and Bulirsch-Stoer method. The package is designed so that the calls to each of these look identical so that it is trivial to replace one with another. Complex data manipulations and results can be analyzed with the graphics packace SwiftVis.
SwiftVis is a tool originally developed as part of a rewrite of Swift to be used for analysis and plotting of simulations performed with Swift and Swifter. The extensibility built into the design has allowed us to make SwiftVis a general purpose analysis and plotting package customized to be usable by the planetary science community at large. SwiftVis is written in Java and has been tested on Windows, Linux, and Mac platforms. Its graphical interface allows users to do complex analysis and plotting without having to write custom code.
SWOC (Spectral Wavelength Optimization Code) determines the wavelength ranges that provide the optimal amount of information to achieve the required science goals for a spectroscopic study. It computes a figure-of-merit for different spectral configurations using a user-defined list of spectral features, and, utilizing a set of flux-calibrated spectra, determines the spectral regions showing the largest differences among the spectra.
SWOT (Super W Of Theta) computes two-point statistics for very large data sets, based on “divide and conquer” algorithms, mainly, but not limited to data storage in binary trees, approximation at large scale, parellelization (open MPI), and bootstrap and jackknife resampling methods “on the fly”. It currently supports projected and 3D galaxy auto and cross correlations, galaxy-galaxy lensing, and weighted histograms.
SYNAPPS is a spectrum fitter embedding a highly parameterized synthetic SN spectrum calculation within a parallel asynchronous optimizer. This open-source code is aimed primarily at the problem of systematically interpreting large sets of SN spectroscopy data.
SYNMAG is a tool for producing synthetic aperture magnitudes to enable fast matched photometry at the catalog level without reprocessing imaging data. Aperture magnitudes are the most widely tabulated flux measurements in survey catalogs; obtaining reliable, matched photometry for galaxies imaged by different observatories represents a key challenge in the era of wide-field surveys spanning more than several hundred square degrees. Methods such as flux fitting, profile fitting, and PSF homogenization followed by matched-aperture photometry are all computationally expensive. An alternative solution called "synthetic aperture photometry" exploits galaxy profile fits in one band to efficiently model the observed, point-spread-function-convolved light profile in other bands and predict the flux in arbitrarily sized apertures.
SYNOW is a highly parameterized spectrum synthesis code used primarily for direct (empirical) analysis of SN spectra. The code is based on simple assumptions : spherical symmetry; homologous expansion; a sharp photosphere that emits a blackbody continuous spectrum; and line formation by resonance scattering, treated in the Sobolev approximation. Synow does not do continuum transport, it does not solve rate equations, and it does not calculate ionization ratios. Its main function is to take line multiple scattering into account so that it can be used in an empirical spirit to make line identifications and estimate the velocity at the photosphere (or pseudo-photosphere) and the velocity interval within which each ion is detected. these quantities provide constraints on the composition structure of the ejected matter.
Synspec is a user-oriented package written in FORTRAN for modeling stellar atmospheres and for stellar spectroscopic diagnostics. It assumes an existing model atmosphere, calculated previously with Tlusty or taken from the literature (for instance, from the Kurucz grid of models). The opacity sources (continua, atomic and molecular lines) are fully specified by the user. An arbitrary stellar rotation and instrumental profile can be applied to the synthetic spectrum.
Synth3 is a non-magnetic spectrum synthesis code. It works with model atmospheres in Kurucz format and VALD Sf line lists and features element stratification, molecular equilibrium and individual microturbulence for each line. Disk integration can be done with s3di which is included in the archive. Synth3 computes spectra emergent from the stellar atmospheres with a depth-dependent chemical composition if depth-dependent abundance is provided in the input model atmosphere file.
Systemic Console is a tool for advanced analysis of exoplanetary data. It comprises a graphical tool for fitting radial velocity and transits datasets and a library of routines for non-interactive calculations. Among its features are interactive plotting of RV curves and transits, combined fitting of RV and transit timing (primary and secondary), interactive periodograms and FAP estimation, and bootstrap and MCMC error estimation. The console package includes public radial velocity and transit data.
SZpack is a numerical library which allows fast and precise computation of the Sunyaev-Zeldovich (SZ) signal for hot, moving clusters of galaxies. Both explicit numerical integration as well as approximate representation of the SZ signals can be obtained. Variations of the electron temperature and bulk velocity along the line-of-sight can be included. SZpack allows very fast and precise (<~0.001% at frequencies h nu <~ 30kT_g and electron temperature kTe ~ 75 keV) computation and its accuracy practically eliminates uncertainties related to more expensive numerical evaluation of the Boltzmann collision term. It furthermore cleanly separates kinematic corrections from scattering physics, effects that previously have not been clarified.
The T-Matrix package includes codes to compute electromagnetic scattering by homogeneous, rotationally symmetric nonspherical particles in fixed and random orientations, randomly oriented two-sphere clusters with touching or separated components, and multi-sphere clusters in fixed and random orientations. All codes are written in Fortran-77. LAPACK-based, extended-precision, Gauss-elimination- and NAG-based, and superposition codes are available, as are double-precision superposition, parallelized double-precision, double-precision Lorenz-Mie codes, and codes for the computation of the coefficients for the generalized Chebyshev shape.
T-PHOT extracts accurate photometry from low-resolution images of extragalactic fields, where the blending of sources can be a serious problem for accurate and unbiased measurement of fluxes and colors. It gathers data from a high-resolution image of a region of the sky and uses the source positions and morphologies to obtain priors for the photometric analysis of the lower resolution image of the same field. T-PHOT handles different types of datasets as input priors, including a list of objects that will be used to obtain cutouts from the real high-resolution image, a set of analytical models (as .fits stamps), and a list of unresolved, point-like sources, useful for example for far-infrared wavelength domains. T-PHOT yields accurate estimations of fluxes within the intrinsic uncertainties of the method when systematic errors are taken into account (which can be done using a flagging code given in the output), and handles multiwavelength optical to far-infrared image photometry. T-PHOT was developed as part of the ASTRODEEP project (www.astrodeep.eu).
This IDL code returns the dust temperature of a galaxy from its redshift, SFR and stellar mass; it can also predict the observed monochromatic fluxes of the galaxy. These monochromatic fluxes correspond to those of a DH SED template with the appropriate dust temperature and the appropriate normalization. Dust temperatures and fluxes predictions are only valid and provided in the redshift, stellar mass, SSFR and wavelength ranges 0 < z < 2.5, Mstar> 10^10 Msun, 10^-11 < SSFR[yr-1]< 10^-7 and 30um < lambda_rest < 2mm.
TA-DA is a pre-compiled IDL widget-based application which greatly simplifies and improves the analysis of stellar photometric data in comparison with theoretical models and allows the derivation of stellar parameters from multi-band photometry. It is flexible and can address a number of problems, from the interpolation of stellar models or sets of stellar physical parameters in general to the computation of synthetic photometry in arbitrary filters or units. It also analyzes observed color-magnitude diagrams and allows a Bayesian derivation of stellar parameters (and extinction) based on multi-band data.
TAC-maker allows for rapid and interactive calculation of synthetic planet transits by numerical computations of the integrals, allowing the use of an arbitrary limb-darkening law of the host star. This advantage together with the practically arbitrary precision of the calculations makes the code a valuable tool for the continuously increasing photometric precision of ground-based and space observations.
The Action Computation Tool (TACT) tests methods for estimating actions, angles and frequencies of orbits in both axisymmetric and triaxial potentials, including general spherical potentials, analytic potentials (Isochrone and Harmonic oscillator), axisymmetric Stackel fudge, average generating function from orbit (AvGF), and others. It is written in C++; code is provided to compile the routines into a Python library. TM (ascl:1512.014) and LAPACK are required to access some features.
TailZ estimates redshift distributions of photometric samples of galaxies selected photometrically given a subsample with measured spectroscopic redshifts. The approach uses a non-parametric Voronoi tessellation density estimator to interpolate the galaxy distribution in the redshift and photometric color space. The Voronoi tessellation estimator performs well at reconstructing the tails of the redshift distribution of individual galaxies and gives unbiased estimates of the first and second moments.
TALYS is software that simulates nuclear reactions which involve neutrons, gamma-rays, protons, deuterons, tritons, helions and alpha-particles, in the 1 keV-200MeV energy range. A suite of nuclear reaction models has been implemented into a single code system, enabling one to evaluate basically all nuclear reactions beyond the resonance range. In particular, TALYS estimates the Maxwellian-averaged reaction rates that are of astrophysical relevance. This enables reaction rates to be calculated with increased accuracy and reliability and the approximations of previous codes to be investigated. The TALYS predictions for the thermonuclear rates of relevance to astrophysics are detailed and compared with those derived by widely-used codes for the same nuclear ingredients. TALYS predictions may differ significantly from those of previous codes, in particular for nuclei for which no or little nuclear data is available. The pre-equilibrium process is shown to influence the astrophysics rates of exotic neutron-rich nuclei significantly. The TALYS code provides a tool to estimate all nuclear reaction rates of relevance to astrophysics with improved accuracy and reliability.
TAME measures the equivalent width (EWs) in high-resolution spectra. Written by IDL, TAME provides the EWs of spectral lines by profile fitting in an automatic or interactive mode and is reliable for measuring EWs in a spectrum with a spectral resolution of R ≳ 20000. It offers an interactive mode for more flexible measurement of the EW and a fully automatic mode that can simultaneously measure the EWs for a large set of lines.
Tapir is a set of tools, written in Perl, that provides a web interface for showing the observability of periodic astronomical events, such as exoplanet transits or eclipsing binaries. The package provides tools for creating finding charts for each target and airmass plots for each event. The code can access target lists that are stored on-line in a Google spreadsheet or in a local text file.
TARDIS creates synthetic spectra for supernova ejecta and is sufficiently fast to allow exploration of the complex parameter spaces of models for SN ejecta. TARDIS uses Monte Carlo methods to obtain a self-consistent description of the plasma state and to compute a synthetic spectrum. It is written in Python with a modular design that facilitates the implementation of a range of physical approximations that can be compared to assess both accuracy and computational expediency; this allows users to choose a level of sophistication appropriate for their application.
TAU is a 1D line-by-line radiative transfer code for modeling transmission spectra of close-in extrasolar planets. The code calculates the optical path through the planetary atmosphere of the radiation from the host star and quantifies the absorption due to the modeled composition in a transmission spectrum of transit depth as a function of wavelength. The code is written in C++ and is parallelized using OpenMP.
TEA (Thermal Equilibrium Abundances) calculates gaseous molecular abundances under thermochemical equilibrium conditions. Given a single T,P point or a list of T,P pairs (the thermal profile of an atmosphere) and elemental abundances, TEA calculates mole fractions of the desired molecular species. TEA uses 84 elemental species and thermodynamical data for more then 600 gaseous molecular species, and can adopt any initial elemental abundances.
TelFit calculates the best-fit telluric absorption spectrum in high-resolution optical and near-IR spectra. The best-fit model can then be divided out to remove the telluric contamination. Written in Python, TelFit is essentially a wrapper to LBLRTM, the Line-By-Line Radiative Transfer Model, and simplifies the process of generating a telluric model.
Tempo analyzes pulsar timing data. Pulse times of arrival (TOAs), pulsar model parameters, and coded instructions are read from one or more input files. The TOAs are fitted by a pulse timing model incorporating transformation to the solar-system barycenter, pulsar rotation and spin-down and, where necessary, one of several binary models. Program output includes parameter values and uncertainties, residual pulse arrival times, chi-squared statistics, and the covariance matrix of the model. In prediction mode, ephemerides of pulse phase behavior (in the form of polynomial expansions) are calculated from input timing models. Tempo is the basis for the Tempo2 (ascl:1210.015) code.
Tempo2 is a pulsar timing package developed to be used both for general pulsar timing applications and also for pulsar timing array research in which data-sets from multiple pulsars need to be processed simultaneously. It was initially developed by George Hobbs and Russell Edwards as part of the Parkes Pulsar Timing Array project. Tempo2 is based on the original Tempo (ascl:1509.002) code and can be used (from the command-line) in a similar fashion. It is very versatile and can be extended by plugins.
tf_unet mitigates radio frequency interference (RFI) signals in radio data using a special type of Convolutional Neural Network, the U-Net, that enables the classification of clean signal and RFI signatures in 2D time-ordered data acquired from a radio telescope. The code is not tied to a specific segmentation and can be used, for example, to detect radio frequency interference (RFI) in radio astronomy or galaxies and stars in widefield imaging data. This U-Net implementation can outperform classical RFI mitigation algorithms.
TFIT measures galaxy photometry using prior knowledge of sources in a deep, high‐resolution image (HRI) to improve photometric measurements of objects in a corresponding low‐resolution image (LRI) of the same field, usually at a different wavelength. For background‐limited data, this technique produces optimally weighted photometry that maximizes signal‐to‐noise ratio (S/N). For objects not significantly detected in the low‐resolution image, it provides useful and quantitative information for setting upper limits.
TGCat is an archive of Chandra transmission grating spectra and a suite of software for processing such data. Users can browse and categorize Chandra gratings observations quickly and easily, generate custom plots of resulting response corrected spectra on-line without the need for special software and download analysis ready products from multiple observations in one convenient operation. Data processing for the catalog is done with a suite of ISIS/S-Lang scripts; the software is available for download. These ISIS scripts wrap and call CIAO tools for reprocessing from "Level 1" (acis_process_events or hrc_process_events) through "Level 2" (binned spectra, via tg_resolve_events and tgextract), compute responses (grating "RMFs" and "ARFs", via mkgrmf and mkgarf), and make summary plots.
The Cannon is a data-driven method for determining stellar labels (physical parameters and chemical abundances) from stellar spectra in the context of vast spectroscopic surveys. It fits for the spectral model given training spectra and labels, with the polynomial order for the spectral model decided by the user, infers labels for the test spectra, and provides diagnostic output for monitoring and evaluating the process. It offers SNR-independent continuum normalization, performs well at lower signal-to-noise, and is very accurate.
We present the DTFE public software, a code for reconstructing fields from a discrete set of samples/measurements using the maximum of information contained in the point distribution. The code is written in C++ using the CGAL library and is parallelized using OpenMP. The software was designed for the analysis of cosmological data but can be used in other fields where one must interpolate quantities given at a discrete point set. The software comes with a wide suite of options to facilitate the analysis of 2- and 3-dimensional data and of both numerical simulations and galaxy redshift surveys. For comparison purposes, the code also implements the TSC and SPH grid interpolation methods. The code comes with an extensive user guide detailing the program options, examples and the inner workings of the code.
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