Thindisk computes the line emission from a geometrically thin protoplanetary disk. It creates a datacube in FITS format that can be processed with a data reduction package (such as GILDAS, ascl:1305.010) to produce synthetic images and visibilities. These synthetic data can be compared with observations to determine the properties (e.g. central mass or inclination) of an observed disk. The disk is assumed to be in Keplerian rotation at a radius lower than the centrifugal radius (which can be set to a large value, for a purely Keplerian disk), and in infall with rotation beyond the centrifugal radius.
THERMINATOR is a Monte Carlo event generator dedicated to studies of the statistical production of particles in relativistic heavy-ion collisions. The increased functionality of the code contains the following features: The input of any shape of the freeze-out hypersurface and the expansion velocity field, including the 3+1 dimensional profiles, in particular those generated externally with various hydrodynamic codes. The hypersufraces may have variable thermal parameters, which allows for studies departing significantly from the mid-rapidity region, where the baryon chemical potential becomes large. We include a library of standard sets of hypersurfaces and velocity profiles describing the RHIC Au+Au data at sqrt(s_(NN)) = 200 GeV for various centralities, as well as those anticipated for the LHC Pb+Pb collisions at sqrt(s_(NN)) = 5.5 TeV. A separate code, FEMTO-THERMINATOR, is provided to carry out the analysis of femtoscopic correlations which are an important source of information concerning the size and expansion of the system. We also include several useful scripts that carry out auxiliary tasks, such as obtaining an estimate of the number of elastic collisions after the freeze-out, counting of particles flowing back into the fireball and violating causality (typically very few), or visualizing various results: the particle p_T-spectra, the elliptic flow coefficients, and the HBT correlation radii. We also investigate the problem of the back-flow of particles into the hydrodynamic region, as well as estimate the elastic rescattering in terms of trajectory crossings. The package is written in C++ and uses the CERN ROOT environment.
THELI is an easy-to-use, end-to-end pipeline for the reduction of any optical, near-IR and mid-IR imaging data. It combines a variety of processing algorithms and third party software into a single, homogeneous tool. Over 90 optical and infrared instruments at observatories world-wide are pre-configured; more can be added by the user. The code's online appendix contains three walk-through examples using public data (optical, near-IR and mid-IR) and additional online documentation is available for training and troubleshooting.
the-wizz clusters redshift estimates for any photometric unknown sample in a survey. The software is composed of two main parts: a pair finder and a pdf maker. The pair finder finds spatial pairs and stores the indices of all closer pairs around target reference objects in an output HDF5 data file. Users then query this data file using the indices of their unknown sample to produce an output clustering-z.
The Tractor optimizes or samples from models of astronomical objects. The approach is generative: given astronomical sources and a description of the image properties, the code produces pixel-space estimates or predictions of what will be observed in the images. This estimate can be used to produce a likelihood for the observed data given the model: assuming the model space actually includes the truth (it doesn’t, in detail), then if we had the optimal model parameters, the predicted image would differ from the actually observed image only by noise. Given a noise model of the instrument and assuming pixelwise independent noise, the log-likelihood is the negative chi-squared difference: (image - model) / noise.
The Starfish Diagram is a statistical visualization tool that simultaneously displays the properties of an individual and its parent sample through a series of histograms. The code is useful for large datasets for which one needs to understand the standing or significance of a single entry.
Given sparse or low-quality radial-velocity measurements of a star, there are often many qualitatively different stellar or exoplanet companion orbit models that are consistent with the data. The consequent multimodality of the likelihood function leads to extremely challenging search, optimization, and MCMC posterior sampling over the orbital parameters. The Joker is a custom-built Monte Carlo sampler that can produce a posterior sampling for orbital parameters given sparse or noisy radial-velocity measurements, even when the likelihood function is poorly behaved. The method produces correct samplings in orbital parameters for data that include as few as three epochs. The Joker can therefore be used to produce proper samplings of multimodal pdfs, which are still highly informative and can be used in hierarchical (population) modeling.
The Hammer can classify spectra in a variety of formats with targets spanning the MK spectral sequence. It processes a list of input spectra by automatically estimating each object's spectral type and measuring activity and metallicity tracers in late type stars. Once automatic processing is complete, an interactive interface allows the user to manually tweak the final assigned spectral type through visual comparison with a set of templates.
The Exo-Striker analyzes exoplanet orbitals, performs N-body simulations, and models the RV stellar reflex motion caused by dynamically interacting planets in multi-planetary systems. It offers a broad range of tools for detailed analysis of transit and Doppler data, including power spectrum analysis for Doppler and transit data; Keplerian and dynamical modeling of multi-planet systems; MCMC and nested sampling; Gaussian Processes modeling; and a long-term stability check of multi-planet systems. The Exo-Striker can also analyze Mean Motion Resonance (MMR) analysis, create fast fully interactive plots, and export ready-to-use LaTeX tables with best-fit parameters, errors, and statistics. It combines Fortran efficiency and Python flexibility and is cross-platform compatible (MAC OS, Linux, Windows). The tool relies on a number of open-source packages, including RVmod engine, emcee (ascl:1303.002), batman (ascl:1510.002), celerite (ascl:1709.008), and dynesty (ascl:1809.013).
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.
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.
THALASSA (Tool for High-Accuracy, Long-term Analyses for SSA) propagates orbits for bodies in the Earth-Moon-Sun system. Written in Fortran, it integrates either Newtonian equations in Cartesian coordinates or regularized equations of motion with the LSODAR (Livermore Solver for Ordinary Differential equations with Automatic Root-finding). THALASSA is a command-line tool; the repository also includes some Python3 scripts to perform batch propagations.
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.
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.
This code is no longer updated and has been superseded by T-PHOT (ascl:1609.001).
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.
TESS-Point converts astronomical target coordinates given in right ascension and declination to detector pixel coordinates for the MIT-led NASA Transiting Exoplanet Survey Satellite (TESS) spacecraft. The program can also provide detector pixel coordinates for a star by TESS input catalog identifier number and common astronomical name. Tess-point outputs the observing sector number, camera number, detector number, and pixel column and row.
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.
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.
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.
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.
Three-Body Integration performs numerical n-body simulations for mapping conditions for close approaches for the relevant parameter space of configurations and mass values of two white dwarfs and a third star. Low tertiary masses of 0.1M⊙ can be studied, and the collision probability can be estimated with good confidence for the case of nearly equal mass white dwarfs.
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.
TATTER (Two-sAmple TesT EstimatoR) performs two-sample hypothesis test. The two-sample hypothesis test is concerned with whether distributions p(x) and q(x) are different on the basis of finite samples drawn from each of them. This ubiquitous problem appears in a legion of applications, ranging from data mining to data analysis and inference. This implementation can perform the Kolmogorov-Smirnov test (for one-dimensional data only), Kullback-Leibler divergence, and Maximum Mean Discrepancy (MMD) test. The module performs a bootstrap algorithm to estimate the null distribution and compute p-value.
TATOO (Tidal-chronology Age TOOl) estimates the age of massive close-in planetary systems, even those subject to tidal spin-up, using the systems' observed properties: the mass of the planet and the star, stellar rotational, and planetary orbital periods. It can also be used as a classical gyrochronological tool and offers first order correction of the impact of tidal interaction on gyrochronology.
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.
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.
Tangra performs scientific grade data reduction of GPS time-tagged video observations, including reduction of stellar occultation light curves and astrometry of close flybys of Near Earth Objects. It offers Dark and Flat frame image correction, PSF and aperture photometry, multiple methods for deriving a background as well as extensibility via add-ins. Tangra is actively developed for Windows and the current version of the software supports UCAC2, UCAC3, UCAC4, NOMAD, PPMXL and Gaia DR2 star catalogues for astrometry. The software can perform motion-fitting for fast objects and derive a mini-normal astrometric positions. The supported video file formats are AVI, SER, ADV and AAV. Tangra can be also used with observations recorded as a sequence of FITS files. There are also versions for Linux and OS-X with more limited functionality.
Tangos builds databases (along the lines of Eagle or MultiDark) for cosmological and zoom simulations. Its
modular system generates and queries databases. It is designed to store and manage results from a user's own analysis code, provides web and python interfaces, and allows users to construct science-focused queries, including across entire merger trees, without requiring knowledge of SQL. Tangos manages the process of populating the database with science data, including auto-parallelizing the analysis. It can be customized to work with multiple python modules such as pynbody (ascl:1305.002) or yt (ascl:1011.022) to process raw simulation data; it defaults to using SQLite, but allows use of other databases as the underlying store through the use of SQLAlchemy.
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.
TALYS 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.
This Python package allows the user to setup and run an agent-based simulation of a SETI survey. The package allows the creation of a population of observing and transmitting civilisations. Each transmitter and observer conducts their activities according to an input strategy. The success of observers and transmitters can then be recorded, and multiple simulations can be run for Monte Carlo Realisation.
This package is therefore a flexible framework in which to simulate and test different SETI strategies, both as an Observer and as a Transmitter. It is primarily designed with radio SETI in mind, but is sufficiently flexible to simulate all forms of electromagnetic SETI, and potentially neutrino and gravitational wave SETI.
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.
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.
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.
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.
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.
T-RECS produces radio sources catalogs with user-defined frequencies, area and depth. It models two main populations of radio galaxies, Active Galactic Nuclei (AGNs) and Star-Forming Galaxies (SFGs), and corresponding sub-populations. T-RECS is not computationally demanding and can be run multiple times, using the same catalog inputs, to project the simulated sky onto different fields.
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).
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.
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.
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.
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.
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.
Synphot simulates photometric data and spectra, observed or otherwise. It can incorporate the user's filters, spectra, and data, and use of a pre-defined standard star (Vega), bandpass, or extinction law. synphot can also construct complicated composite spectra using different models, simulate observations, and compute photometric properties such as count rate, effective wavelength, and effective stimulus. It can manipulate a spectrum by, for example, applying redshift, or normalize it to a given flux value in a given bandpass. Synphot can also sample a spectrum at given wavelengths, plot a quick-view of a spectrum, and perform repetitive operations such as simulating the observations of multiple type of sources through multiple bandpasses. Synphot understands Astropy (ascl:1304.002) models and units and is an Astropy affiliated package.
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.
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.
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.
SYGMA (Stellar Yields for Galactic Modeling Applications) follows the ejecta of simple stellar populations as a function of time to model the enrichment and feedback from simple stellar populations. It is the basic building block of the galaxy code One-zone Model for the Evolution of GAlaxies (OMEGA, ascl:1806.018) and is part of the NuGrid Python Chemical Evolution Environment (NuPyCEE, ascl:1610.015). Stellar yields of AGB and massive stars are calculated with the same nuclear physics and are provided by the NuGrid collaboration.
The ROSAT X-Ray Background Tool (sxrbg) calculates the average X-ray background count rate and statistical uncertainty in each of the six standard bands of the ROSAT All-Sky Survey (RASS) diffuse background maps (R1, R2, R4, R5, R6, R7) for a specified astronomical position and a search region consisting of either a circle with a specified radius or an annulus with specified inner and outer radii centered on the position. The values returned by the tool are in units of 10^-6 counts/second/arcminute^2. sxrbg can also create a count-rate-based spectrum file which can be used with XSpec (ascl:9910.005) to calculate fluxes and offers support for counts statistics (cstat), an alternative method for generating a background spectrum. HEASoft (ascl:1408.004) is a prerequisite for building. The code is in the public domain.
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.
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.
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.
SWIFT runs cosmological simulations on peta-scale machines for solving gravity and SPH. It uses the Fast Multipole Method (FMM) to calculate gravitational forces between nearby particles, combining these with long-range forces provided by a mesh that captures both the periodic nature of the calculation and the expansion of the simulated universe. SWIFT currently uses a single fixed but time-variable softening length for all the particles. Many useful external potentials are also available, such as galaxy haloes or stratified boxes that are used in idealised problems. SWIFT implements a standard LCDM cosmology background expansion and solves the equations in a comoving frame; equations of state of dark-energy evolve with scale-factor. The structure of the code allows implementation for modified-gravity solvers or self-interacting dark matter schemes to be implemented. Many hydrodynamics schemes are implemented in SWIFT and the software allows users to add their own.
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.
SWarp 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.
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.
surrkick quickly and reliably extract recoils imparted to generic, precessing, black hole binaries. It uses a numerical-relativity surrogate model to obtain the gravitational waveform given a set of binary parameters, and from this waveform directly integrates the gravitational-wave linear momentum flux. This entirely bypasses the need of fitting formulae which are typically used to model black-hole recoils in astrophysical contexts.
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.
surfinBH predicts the final mass, spin and recoil velocity of the remnant of a binary black hole merger. Trained directly against numerical relativity simulations, these models are extremely accurate, reproducing the results of the simulations at the same level of accuracy as the simulations themselves. Fits such as these play a crucial role in waveform modeling and tests of general relativity with gravitational waves, performed by LIGO.
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.
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.
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.
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.
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.
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.
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 (ascl:1109.006). 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.
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.
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.
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.
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.
An extension to synphot (ascl:1811.001), stsynphot implements synthetic photometry package for HST and JWST support. The software constructs spectra from various grids of model atmosphere spectra, parameterized spectrum models, and atlases of stellar spectrophotometry. It also simulates observations specific to HST and JWST, computes photometric calibration parameters for any supported instrument mode, and plots instrument-specific sensitivity curves and calibration target spectra.
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.
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 (ascl:1106.023). The properties of the strings are described by four parameters: Gμ—dimensionless string tension; v—rms transverse velocity (as fraction of c); α—"wiggliness"; ξ—comoving correlation length of the string network. It is written as a Fortran 90 module.
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.
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).
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.
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.
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:
STIFF converts scientific FITS images to the more popular TIFF 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 implicitly 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.
STiC is a MPI-parallel non-LTE inversion code for observed full-Stokes observations. The code processes lines from multiple atoms in non-LTE, including partial redistribution effects of scattered photons in angle and frequency of scattered photons (PRD), and can be used with model atmospheres that have a complex depth stratification without introducing artifacts.
stginga customizes Ginga to aid data analysis for the data supported by STScI (e.g., HST or JWST). For instance, it provides plugins and configuration files that understand HST and JWST data products.
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.
This code has been updated and renamed to VELOCIraptor-STF (ascl:1911.020).
StePS (Stereographically Projected Cosmological Simulations) compactifies the infinite spatial extent of the Universe into a finite sphere with isotropic boundary conditions to simulate the evolution of the large-scale structure. This eliminates the need for periodic boundary conditions, which are a numerical convenience unsupported by observation and which modifies the law of force on large scales in an unrealistic fashion. StePS uses stereographic projection for space compactification and naive O(N2) force calculation; this arrives at a correlation function of the same quality more quickly than standard (tree or P3M) algorithms with similar spatial and mass resolution. The N2 force calculation is easy to adapt to modern graphics cards, hence StePS can function as a high-speed prediction tool for modern large-scale surveys.
stepped_luneburg investigates the scattered light properties of a Luneburg lens approximated as a series of concentric shells with discrete refractive indices. The optical Luneburg lens has promising applications for low-cost, continuous all-sky monitoring to obtain transit light curves of bright, nearby stars. This code implements a stack-based algorithm that tracks all reflected and refracted rays generated at each optical interface of the lens as described by Snell's law. The Luneburg lens model parameters, such as number of lens layers, the power-law that describes the refractive indices, the number of incident rays, and the initial direction of the incident wavefront can be altered to optimize lens performance. The stepped_luneburg module can be imported within the Python environment or used with scripting, and it is accompanied by two other modules, enc_int and int_map, that help the user to determine the resolving power of the lens and the strength of scattered light haloes for the purpose of quality assessment.
StePar computes the stellar atmospheric parameters Teff, log g, [Fe/H], and ξ of FGK-type stars using the Equivalent Width (EW) method. The code implements a grid of MARCS model atmospheres and uses the MOOG radiative transfer code (ascl:1202.009) and TAME (ascl:1503.003). StePar uses a Downhill Simplex minimization algorithm, running it twice for any given star, to compute the stellar atmospheric parameters.
stellarWakes uses stellar kinematic data to search for dark matter (DM) subhalos through their gravitational perturbations to the stellar phase-space distribution.
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.
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.
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.
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.
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.
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.
Smoothed Particle Hydrodynamics (SPH) is a Lagrangian particle method that approximates a continuous fluid as discrete nodes, each carrying various parameters such as mass, position, velocity, pressure, and temperature. In an SPH simulation the resolution scales with the particle density; StarSmasher is able to handle both equal-mass and equal number-density particle models. StarSmasher solves for hydro forces by calculating the pressure for each particle as a function of the particle's properties - density, internal energy, and internal properties (e.g. temperature and mean molecular weight). The code implements variational equations of motion and libraries to calculate the gravitational forces between particles using direct summation on NVIDIA graphics cards. Using a direct summation instead of a tree-based algorithm for gravity increases the accuracy of the gravity calculations at the cost of speed. The code uses a cubic spline for the smoothing kernel and an artificial viscosity prescription coupled with a Balsara Switch to prevent unphysical interparticle penetration. The code also implements an artificial relaxation force to the equations of motion to add a drag term to the calculated accelerations during relaxation integrations. Initially called StarCrash, StarSmasher was developed originally by Rasio.
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.
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.
STARRY computes light curves for various applications in astronomy: transits and secondary eclipses of exoplanets, light curves of eclipsing binaries, rotational phase curves of exoplanets, light curves of planet-planet and planet-moon occultations, and more. By modeling celestial body surface maps as sums of spherical harmonics, STARRY does all this analytically and is therefore fast, stable, and differentiable. Coded in C++ but wrapped in Python, STARRY is easy to install and use.
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.
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