astroABC is a Python implementation of an Approximate Bayesian Computation Sequential Monte Carlo (ABC SMC) sampler for parameter estimation. astroABC allows for massive parallelization using MPI, a framework that handles spawning of processes across multiple nodes. It has the ability to create MPI groups with different communicators, one for the sampler and several others for the forward model simulation, which speeds up sampling time considerably. For smaller jobs the Python multiprocessing option is also available.
ASCII tables continue to be one of the most popular and widely used data exchange formats in astronomy. AstroAsciiData, written in Python, imports all reasonably well-formed ASCII tables. It retains formatting of data values, allows column-first access, supports SExtractor style headings, performs column sorting, and exports data to other formats, including FITS, Numpy/Numarray, and LaTeX table format. It also offers interchangeable comment character, column delimiter and null value.
AstroBEAR is a modular hydrodynamic & magnetohydrodynamic code environment designed for a variety of astrophysical applications. It uses the BEARCLAW package, a multidimensional, Eulerian computational code used to solve hyperbolic systems of equations. AstroBEAR allows adaptive-mesh-refinment (AMR) simulations in 2, 2.5 (i.e., cylindrical), and 3 dimensions, in either cartesian or curvilinear coordinates. Parallel applications are supported through the MPI architecture. AstroBEAR is written in Fortran 90/95 using standard libraries.
AstroBEAR supports hydrodynamic (HD) and magnetohydrodynamic (MHD) applications using a variety of spatial and temporal methods. MHD simulations are kept divergence-free via the constrained transport (CT) methods of Balsara & Spicer. Three different equation of state environments are available: ideal gas, gas with differing isentropic γ, and the analytic Thomas-Fermi formulation of A.R. Bell.
AstroBlend is a visualization package for use in the three dimensional animation and modeling software, Blender. It reads data in via a text file or can use pre-fab isosurface files stored as OBJ or Wavefront files. AstroBlend supports a variety of codes such as FLASH (ascl:1010.082), Enzo (ascl:1010.072), and Athena (ascl:1010.014), and combines artistic 3D models with computational astrophysics datasets to create models and animations.
Astrochem computes the abundances of chemical species in the interstellar medium, as function of time. It studies the chemistry in a variety of astronomical objects, including diffuse clouds, dense clouds, photodissociation regions, prestellar cores, protostars, and protostellar disks. Astrochem reads a network of chemical reactions from a text file, builds up a system of kinetic rates equations, and solves it using a state-of-the-art stiff ordinary differential equation (ODE) solver. The Jacobian matrix of the system is computed implicitly, so the resolution of the system is extremely fast: large networks containing several thousands of reactions are usually solved in a few seconds. A variety of gas phase process are considered, as well as simple gas-grain interactions, such as the freeze-out and the desorption via several mechanisms (thermal desorption, cosmic-ray desorption and photo-desorption). The computed abundances are written in a HDF5 file, and can be plotted in different ways with the tools provided with Astrochem. Chemical reactions and their rates are written in a format which is meant to be easy to read and to edit. A tool to convert the chemical networks from the OSU and KIDA databases into this format is also provided. Astrochem is written in C, and its source code is distributed under the terms of the GNU General Public License (GPL).
AstroCV processes and analyzes big astronomical datasets, and is intended to provide a community repository of high performance Python and C++ algorithms used for image processing and computer vision. The library offers methods for object recognition, segmentation and classification, with emphasis in the automatic detection and classification of galaxies.
The gyrokinetic simulation code AstroGK is developed to study fundamental aspects of kinetic plasmas and for applications mainly to astrophysical problems. AstroGK is an Eulerian slab code that solves the electromagnetic Gyrokinetic-Maxwell equations in five-dimensional phase space, and is derived from the existing gyrokinetics code GS2 by removing magnetic geometry effects. Algorithms used in the code are described. The code is benchmarked using linear and nonlinear problems. Serial and parallel performance scalings are also presented.
AstroImageJ is generic ImageJ (ascl:1206.013) with customizations to the base code and a packaged set of astronomy specific plugins. It reads and writes FITS images with standard headers, displays astronomical coordinates for images with WCS, supports photometry for developing color-magnitude data, offers flat field, scaled dark, and non-linearity processing, and includes tools for precision photometry that can be used during real-time data acquisition.
AstroLines adjusts spectral line parameters (gf and damping constant) starting from an initial line list. Written in IDL and tailored to the APO Galactic Evolution Experiment (APOGEE), it runs a slightly modified version of MOOG (ascl:1202.009) to compare synthetic spectra with FTS spectra of the Sun and Arcturus.
ASTROM performs "plate reductions" by taking user-provided star positions and the (x,y) coordinates of the corresponding star images and establishes the relationship between (x,y) and (ra,dec), thus enabling the coordinates of unknown stars to be determined. ASTROM is distributed with the Starlink software (ascl:1110.012) and uses SLALIB (ascl:1403.025).
Over the past few years, the role of visualization for scientific purpose has grown up enormously. Astronomy makes an extended use of visualization techniques to analyze data, and scientific visualization has became a fundamental part of modern researches in Astronomy. With the evolution of high performance computers, numerical simulations have assumed a great role in the scientific investigation, allowing the user to run simulation with higher and higher resolution. Data produced in these simulations are often multi-dimensional arrays with several physical quantities. These data are very hard to manage and to analyze efficiently. Consequently the data analysis and visualization tools must follow the new requirements of the research. AstroMD is a tool for data analysis and visualization of astrophysical data and can manage different physical quantities and multi-dimensional data sets. The tool uses virtual reality techniques by which the user has the impression of travelling through a computer-based multi-dimensional model.
Astrometrica is an interactive software tool for scientific grade astrometric data reduction of CCD images. The current version of the software is for the Windows 32bit operating system family. Astrometrica reads FITS (8, 16 and 32 bit integer files) and SBIG image files. The size of the images is limited only by available memory. It also offers automatic image calibration (Dark Frame and Flat Field correction), automatic reference star identification, automatic moving object detection and identification, and access to new-generation star catalogs (PPMXL, UCAC 3 and CMC-14), in addition to online help and other features. Astrometrica is shareware, available for use for a limited period of time (100 days) for free; special arrangements can be made for educational projects.
Astrometry.net is a reliable and robust system that takes as input an astronomical image and returns as output the pointing, scale, and orientation of that image (the astrometric calibration or World Coordinate System information). The system requires no first guess, and works with the information in the image pixels alone; that is, the problem is a generalization of the "lost in space" problem in which nothing—not even the image scale—is known. After robust source detection is performed in the input image, asterisms (sets of four or five stars) are geometrically hashed and compared to pre-indexed hashes to generate hypotheses about the astrometric calibration. A hypothesis is only accepted as true if it passes a Bayesian decision theory test against a null hypothesis. With indices built from the USNO-B catalog and designed for uniformity of coverage and redundancy, the success rate is >99.9% for contemporary near-ultraviolet and visual imaging survey data, with no false positives. The failure rate is consistent with the incompleteness of the USNO-B catalog; augmentation with indices built from the Two Micron All Sky Survey catalog brings the completeness to 100% with no false positives. We are using this system to generate consistent and standards-compliant meta-data for digital and digitized imaging from plate repositories, automated observatories, individual scientific investigators, and hobbyists.
Written in Python, AstroML is a library of statistical and machine learning routines for analyzing astronomical data in python, loaders for several open astronomical datasets, and a large suite of examples of analyzing and visualizing astronomical datasets. An optional companion library, astroML_addons, is available; it requires a C compiler and contains faster and more efficient implementations of certain algorithms in compiled code.
astroplan is a flexible toolbox for observation planning and scheduling. It is powered by Astropy (ascl:1304.002); it works for Python beginners and new observers, and is powerful enough for observatories preparing nightly and long-term schedules as well. It calculates rise/set/meridian transit times, alt/az positions for targets at observatories anywhere on Earth, and offers built-in plotting convenience functions for standard observation planning plots (airmass, parallactic angle, sky maps). It can also determine the observability of sets of targets given an arbitrary set of constraints (i.e., altitude, airmass, moon separation/illumination, etc.).
Astropoltlib is a multi-language astronomical library of plots, a collection of templates useful for creating paper-quality figures. Most of the codes for producing the plots are written in IDL and/or Python; a very few are written in Mathematica. Any plot can be downloaded and customized to one's own needs.
AstroPoP reduces almost any CCD photometry and image polarimetry data. For photometry reduction, the code performs source finding, aperture and PSF photometry, astrometry calibration using different automated and non-automated methods and automated source identification and magnitude calibration based on online and local catalogs. For polarimetry, the code resolves linear and circular Stokes parameters produced by image beam splitter or polarizer polarimeters. In addition to the modular functions, ready-to-use pipelines based in configuration files and header keys are also provided with the code. AstroPOP was initially developed to reduce the IAGPOL polarimeter data installed at Observatório Pico dos Dias (Brazil).
Astropy provides a common framework, core package of code, and affiliated packages for astronomy in Python. Development is actively ongoing, with major packages such as PyFITS, PyWCS, vo, and asciitable already merged in. Astropy is intended to contain much of the core functionality and some common tools needed for performing astronomy and astrophysics with Python.
Astropysics is a library containing a variety of utilities and algorithms for reducing, analyzing, and visualizing astronomical data. Best of all, it encourages the user to leverage the existing capabilities of Python to make this quick, easy, and as painless as cutting-edge science can even actually be. There do exist other Python packages with some of the capabilities of this project, but the goal of this project is to integrate all these tools together and make them interact in the most straightforward ways possible.
Astroquery allows users to access online astronomical data from a wide range of sources; it is an Astropy-affiliated package. Each web service has its own sub-package for interfacing with a particular data source.
ASTRORAY employs a method of ray tracing and performs polarized radiative transfer of (cyclo-)synchrotron radiation. The radiative transfer is conducted in curved space-time near rotating black holes described by Kerr-Schild metric. Three-dimensional general relativistic magneto hydrodynamic (3D GRMHD) simulations, in particular performed with variations of the HARM code, serve as an input to ASTRORAY. The code has been applied to reproduce the sub-mm synchrotron bump in the spectrum of Sgr A*, and to test the detectability of quasi-periodic oscillations in its light curve. ASTRORAY can be readily applied to model radio/sub-mm polarized spectra of jets and cores of other low-luminosity active galactic nuclei. For example, ASTRORAY is uniquely suitable to self-consistently model Faraday rotation measure and circular polarization fraction in jets.
AstroSim is a Second Life based prototype application for synchronous collaborative visualization targeted at astronomers.
AstroStat performs statistical analysis on data and is compatible with Virtual Observatory (VO) standards. It accepts data in a variety of formats and performs various statistical tests using a menu driven interface. Analyses, performed in R, include exploratory tests, visualizations, distribution fitting, correlation and causation, hypothesis testing, multivariate analysis and clustering. AstroStat is available in two versions with an identical interface and features: as a web service that can be run using any standard browser and as an offline application.
AstroTaverna is a plugin for Taverna Workbench that provides the means to build astronomy workflows using Virtual Observatory services discovery and efficient manipulation of VOTables (based on STIL tool set). It integrates SAMP-enabled software, allowing data exchange and communication among local VO tools, as well as the ability to execute Aladin scripts and macros.
AstroVis enables rapid visualization of large data files on platforms supporting the OpenGL rendering library. Radio astronomical observations are typically three dimensional and stored as data cubes. AstroVis implements a scalable approach to accessing these files using three components: a File Access Component (FAC) that reduces the impact of reading time, which speeds up access to the data; the Image Processing Component (IPC), which breaks up the data cube into smaller pieces that can be processed locally and gives a representation of the whole file; and Data Visualization, which implements an approach of Overview + Detail to reduces the dimensions of the data being worked with and the amount of memory required to store it. The result is a 3D display paired with a 2D detail display that contains a small subsection of the original file in full resolution without reducing the data in any way.
ASURV (Astronomical SURVival Statistics) provides astronomy survival analysis for right- and left-censored data including the maximum-likelihood Kaplan-Meier estimator and several univariate two-sample tests, bivariate correlation measures, and linear regressions. ASURV is written in FORTRAN 77, and is stand-alone and does not call any specialized libraries.
Athena is a grid-based code for astrophysical magnetohydrodynamics (MHD). It was developed primarily for studies of the interstellar medium, star formation, and accretion flows. The code has been designed to be easily extensible for use with static and adaptive mesh refinement. It combines higher-order Godunov methods with the constrained transport (CT) technique to enforce the divergence-free constraint on the magnetic field. Discretization is based on cell-centered volume-averages for mass, momentum, and energy, and face-centered area-averages for the magnetic field. Novel features of the algorithm include (1) a consistent framework for computing the time- and edge-averaged electric fields used by CT to evolve the magnetic field from the time- and area-averaged Godunov fluxes, (2) the extension to MHD of spatial reconstruction schemes that involve a dimensionally-split time advance, and (3) the extension to MHD of two different dimensionally-unsplit integration methods. Implementation of the algorithm in both C and Fortran95 is detailed, including strategies for parallelization using domain decomposition. Results from a test suite which includes problems in one-, two-, and three-dimensions for both hydrodynamics and MHD are given, not only to demonstrate the fidelity of the algorithms, but also to enable comparisons to other methods. The source code is freely available for download on the web.
athena is a 2d-tree code that estimates second-order correlation functions from input galaxy catalogues. These include shear-shear correlations (cosmic shear), position-shear (galaxy-galaxy lensing) and position-position (spatial angular correlation). Written in C, it includes a power-spectrum estimator implemented in Python; this script also calculates the aperture-mass dispersion. A test data set is available.
Written in FORTRAN, Athena3D, based on Athena (ascl:1010.014), is an implementation of a flux-conservative Godunov-type algorithm for compressible magnetohydrodynamics. Features of the Athena3D code include compressible hydrodynamics and ideal MHD in one, two or three spatial dimensions in Cartesian coordinates; adiabatic and isothermal equations of state; 1st, 2nd or 3rd order reconstruction using the characteristic variables; and numerical fluxes computed using the Roe scheme. In addition, it offers the ability to add source terms to the equations and is parallelized based on MPI.
atlant is a public numerical code for fast calculations of cosmological recombination of primordial hydrogen-helium plasma is presented. This code is based on the three-level approximation (TLA) model of recombination and allows us to take into account some "fine'' physical effects of cosmological recombination simultaneously with using fudge factors.
ATLAS12 is an opacity sampling model atmosphere program to allow computation of models with individual abundances using line data. ATLAS12 is able to compute the same models as ATLAS9 which uses pretabulated opacities, plus models with arbitrary abundances. ATLAS12 sampled fluxes are quite accurate for predicting the total flux except in the intermediate or narrow bandpass intervals because the sample size is too small.
For a massless test particle and given a planetary system, Atlas2bgeneral calculates all resonances in a given range of semimajor axes with all the planets taken one by one. Planets are assumed in fixed circular and coplanar orbits and the test particle with arbitrary orbit. A sample input data file to calculate the two-body resonances is available for use with the Fortran77 source code.
For a massless test particle and given a planetary system, atlas3bgeneral calculates all three body resonances in a given range of semimajor axes with all the planets taken by pairs. Planets are assumed in fixed circular and coplanar orbits and the test particle with arbitrary orbit. A sample input data file to calculate the three-body resonances is available for use with the Fortran77 source code.
ATLAS9 computes model atmospheres using a fixed set of pretabulated opacities, allowing one to work on huge numbers of stars and interpolate in large grids of models to determine parameters quickly. The code works with two different sets of opacity distribution functions (ODFs), one with “big” wavelength intervals covering the whole spectrum and the other with 1221 “little” wavelength intervals covering the whole spectrum. The ODFs use a 12-step representation; the radiation field is computed starting with the highest step and working down. If a lower step does not matter because the line opacity is small relative to the continuum at all depths, all the lower steps are lumped together and not computed to save time.
Atmospheric Athena simulates hydrodynamic escape from close-in giant planets in 3D. It uses the Athena hydrodynamics code (ascl:1010.014) with a new ionizing radiative transfer implementation to self-consistently model photoionization driven winds from the planet. The code is fully compatible with static mesh refinement and MPI parallelization and can handle arbitrary planet potentials and stellar initial conditions.
The ATOOLS package of applications provides an interface to the AST library (ascl:1404.016), allowing quick experiments to be performed from the shell. It manipulates descriptions of coordinate frames and mappings in the form of AST objects and performs other functions, with each application within the package corresponding closely to one of the functions in the AST library.
ATV displays and analyses astronomical images using the IDL image-processing language. It allows interactive control of the image scaling, color table, color stretch, and zoom, with support for world coordinate systems. It also does point-and-click aperture photometry, simple spectral extractions, and can produce publication-quality postscript output images.
Autoastrom performs automated astrometric corrections on an astronomical image by automatically detecting objects in the frame, retrieving a reference catalogue, cross correlating the catalog with CCDPACK (ascl:1403.021) or MATCH, and using the ASTROM (ascl:1406.008) application to calculate a correction. It is distributed as part of the Starlink software collection (ascl:1110.012).
Automark models photon counts collected form observation of variable-intensity astronomical sources. It aims to mark the abrupt changes in the corresponding wavelength distribution of the emission automatically. In the underlying methodology, change points are embedded into a marked Poisson process, where photon wavelengths are regarded as marks and both the Poisson intensity parameter and the distribution of the marks are allowed to change.
AUTOSTRUCTURE calculates atomic and ionic energy levels, radiative rates, autoionization rates, photoionization cross sections, plane-wave Born and distorted-wave excitation cross sections in LS- and intermediate-coupling using non- or (kappa-averaged) relativistic wavefunctions. These can then be further processed to form Auger yields, fluorescence yields, partial and total dielectronic and radiative recombination cross sections and rate coefficients, photoabsorption cross sections, and monochromatic opacities, among other properties.
aXe is a spectroscopic data extraction software package that was designed to handle large format spectroscopic slitless images such as those from the Wide Field Camera 3 (WFC3) and the Advanced Camera for Surveys (ACS) on HST. aXe is a PyRAF/IRAF package that consists of several tasks and is distributed as part of the Space Telescope Data Analysis System (STSDAS). The various aXe tasks perform specific parts of the extraction and calibration process and are successively used to produce extracted spectra.
BACCHUS (Brussels Automatic Code for Characterizing High accUracy Spectra) derives stellar parameters (Teff, log g, metallicity, microturbulence velocity and rotational velocity), equivalent widths, and abundances. The code includes on the fly spectrum synthesis, local continuum normalization, estimation of local S/N, automatic line masking, four methods for abundance determinations, and a flagging system aiding line selection. BACCHUS relies on the grid of MARCS model atmospheres, Masseron's model atmosphere thermodynamic structure interpolator, and the radiative transfer code Turbospectrum (ascl:1205.004).
BAGEMASS calculates the posterior probability distribution for the mass and age of a star from its observed mean density and other observable quantities using a grid of stellar models that densely samples the relevant parameter space. It is written in Fortran and requires FITSIO (ascl:1010.001).
BAMBI (Blind Accelerated Multimodal Bayesian Inference) is a Bayesian inference engine that combines the benefits of SkyNet (ascl:1312.007) with MultiNest (ascl:1109.006). It operated by simultaneously performing Bayesian inference using MultiNest and learning the likelihood function using SkyNet. Once SkyNet has learnt the likelihood to sufficient accuracy, inference finishes almost instantaneously.
bamr is an MPI implementation of a Bayesian analysis of neutron star mass and radius data that determines the mass versus radius curve and the equation of state of dense matter. Written in C++, bamr provides some EOS models. This code requires O2scl (ascl:1408.019) be installed before compilation.
BANYAN_Sigma calculates the membership probability that a given astrophysical object belongs to one of the currently known 27 young associations within 150 pc of the Sun, using Bayesian inference. This tool uses the sky position and proper motion measurements of an object, with optional radial velocity (RV) and distance (D) measurements, to derive a Bayesian membership probability. By default, the priors are adjusted such that a probability threshold of 90% will recover 50%, 68%, 82% or 90% of true association members depending on what observables are input (only sky position and proper motion, with RV, with D, with both RV and D, respectively). The algorithm is implemented in a Python package, in IDL, and is also implemented as an interactive web page.
Using the 2-point correlation function, BAOlab aids the study of Baryon Acoustic Oscillations (BAO). The code generates a model-dependent covariance matrix which can change the results both for BAO detection and for parameter constraints.
BAOlab is an image processing package written in C that should run on nearly any UNIX system with just the standard C libraries. It reads and writes images in standard FITS format; 16- and 32-bit integer as well as 32-bit floating-point formats are supported. Multi-extension FITS files are currently not supported. Among its tools are ishape for size measurements of compact sources, mksynth for generating synthetic images consisting of a background signal including Poisson noise and a number of pointlike sources, imconvol for convolving two images (a “source” and a “kernel”) with each other using fast fourier transforms (FFTs) and storing the output as a new image, and kfit2d for fitting a two-dimensional King model to an image.
Barcode (BAyesian Reconstruction of COsmic DEnsity fields) samples the primordial density fields compatible with a set of dark matter density tracers after cosmic evolution observed in redshift space. It uses a redshift space model based on the analytic solution of coherent flows within a Hamiltonian Monte Carlo posterior sampling of the primordial density field; this method is applicable to analytically derivable structure formation models, such as the Zel'dovich approximation, but also higher order schemes such as augmented Lagrangian perturbation theory or even particle mesh models. The algorithm is well-suited for analysis of the dark matter cosmic web implied by the observed spatial distribution of galaxy clusters, such as obtained from X-ray, SZ or weak lensing surveys, as well as that of the intergalactic medium sampled by the Lyman alpha forest. In these cases, virialized motions are negligible and the tracers cannot be modeled as point-like objects. Barcode can be used in all of these contexts as a baryon acoustic oscillation reconstruction algorithm.
BART implements a Bayesian, Monte Carlo-driven, radiative-transfer scheme for extracting parameters from spectra of planetary atmospheres. BART combines a thermochemical-equilibrium code, a one-dimensional line-by-line radiative-transfer code, and the Multi-core Markov-chain Monte Carlo statistical module to constrain the atmospheric temperature and chemical-abundance profiles of exoplanets.
BARYCORR is a Python interface for ZBARYCORR (ascl:1807.017); it requires the measured redshift and returns the corrected barycentric velocity and time correction.
barycorrpy (BCPy) is a Python implementation of Wright and Eastman's 2014 code (ascl:1807.017) that calculates precise barycentric corrections well below the 1 cm/s level. This level of precision is required in the search for 1 Earth mass planets in the Habitable Zones of Sun-like stars by the Radial Velocity (RV) method, where the maximum semi-amplitude is about 9 cm/s. BCPy was developed for the pipeline for the next generation Doppler Spectrometers - Habitable-zone Planet Finder (HPF) and NEID. An automated leap second management routine improves upon the one available in Astropy. It checks for and downloads a new leap second file before converting from the UT time scale to TDB. The code also includes a converter for JDUTC to BJDTDB.
BASCS models spatial and spectral information from overlapping sources and the background, and jointly estimates all individual source parameters. The use of spectral information improves the detection of both faint and closely overlapping sources and increases the accuracy with which source parameters are inferred.
The BASE-9 (Bayesian Analysis for Stellar Evolution with nine variables) software suite recovers star cluster and stellar parameters from photometry and is useful for analyzing single-age, single-metallicity star clusters, binaries, or single stars, and for simulating such systems. BASE-9 uses a Markov chain Monte Carlo (MCMC) technique along with brute force numerical integration to estimate the posterior probability distribution for the age, metallicity, helium abundance, distance modulus, line-of-sight absorption, and parameters of the initial-final mass relation (IFMR) for a cluster, and for the primary mass, secondary mass (if a binary), and cluster probability for every potential cluster member. The MCMC technique is used for the cluster quantities (the first six items listed above) and numerical integration is used for the stellar quantities (the last three items in the above list).
BASE is a novel program for the combined or separate Bayesian analysis of astrometric and radial-velocity measurements of potential exoplanet hosts and binary stars. The tool fulfills two major tasks of exoplanet science, namely the detection of exoplanets and the characterization of their orbits. BASE was developed to provide the possibility of an integrated Bayesian analysis of stellar astrometric and Doppler-spectroscopic measurements with respect to their binary or planetary companions’ signals, correctly treating the astrometric measurement uncertainties and allowing to explore the whole parameter space without the need for informative prior constraints. The tool automatically diagnoses convergence of its Markov chain Monte Carlo (MCMC) sampler to the posterior and regularly outputs status information. For orbit characterization, BASE delivers important results such as the probability densities and correlations of model parameters and derived quantities. BASE is a highly configurable command-line tool developed in Fortran 2008 and compiled with GFortran. Options can be used to control the program’s behaviour and supply information such as the stellar mass or prior information. Any option can be supplied in a configuration file and/or on the command line.
BASIN (Beowulf Analysis Symbolic INterface) is a flexible, integrated suite of tools for multiuser parallel data analysis and visualization that allows researchers to harness the power of Beowulf PC clusters and multi-processor machines without necessarily being experts in parallel programming. It also includes general tools for data distribution and parallel operations on distributed data for developing libraries for specific tasks.
batman provides fast calculation of exoplanet transit light curves and supports calculation of light curves for any radially symmetric stellar limb darkening law. It uses an integration algorithm for models that cannot be quickly calculated analytically, and in typical use, the batman Python package can calculate a million model light curves in well under ten minutes for any limb darkening profile.
Bayesian Technique for Multi-image Analysis (BaTMAn) characterizes any astronomical dataset containing spatial information and performs a tessellation based on the measurements and errors provided as input. The algorithm iteratively merges spatial elements as long as they are statistically consistent with carrying the same information (i.e. identical signal within the errors). The output segmentations successfully adapt to the underlying spatial structure, regardless of its morphology and/or the statistical properties of the noise. BaTMAn identifies (and keeps) all the statistically-significant information contained in the input multi-image (e.g. an IFS datacube). The main aim of the algorithm is to characterize spatially-resolved data prior to their analysis.
The great majority of X-ray measurements of cluster masses in the literature assume parametrized functional forms for the radial distribution of two independent cluster thermodynamic properties, such as electron density and temperature, to model the X-ray surface brightness. These radial profiles (e.g. β-model) have an amplitude normalization parameter and two or more shape parameters. BAYES-X uses a cluster model to parametrize the radial X-ray surface brightness profile and explore the constraints on both model parameters and physical parameters. Bayes-X is programmed in Fortran and uses MultiNest (ascl:1109.006) as the Bayesian inference engine.
BayesFlare identifies flaring events in light curves released by the Kepler mission; it identifies even weak events by making use of the flare signal shape. The package contains functions to perform Bayesian hypothesis testing comparing the probability of light curves containing flares to that of them containing noise (or non-flare-like) artifacts. BayesFlare includes functions in its amplitude-marginalizer suite to account for underlying sinusoidal variations in light curve data; it includes such variations in the signal model, and then analytically marginalizes over them.
Bayesian Blocks is a time-domain algorithm for detecting localized structures (bursts), revealing pulse shapes within bursts, and generally characterizing intensity variations. The input is raw time series data, in almost any form. Three data modes are elaborated: (1) time-tagged events, (2) binned counts, and (3) measurements at arbitrary times with normal errors. The output is the most probable segmentation of the observation interval into sub-intervals during which the signal is perceptibly constant, i.e. has no statistically significant variations. The idea is not that the source is deemed to actually have this discontinuous, piecewise constant form, rather that such an approximate and generic model is often useful. Treatment of data gaps, variable exposure, extension to piecewise linear and piecewise exponential representations, multi-variate time series data, analysis of variance, data on the circle, other data modes, and dispersed data are included.
This implementation is exact and replaces the greedy, approximate, and outdated algorithm implemented in BLOCK.
BayesVP offers a Bayesian approach for modeling Voigt profiles in absorption spectroscopy. The code fits the absorption line profiles within specified wavelength ranges and generates posterior distributions for the column density, Doppler parameter, and redshifts of the corresponding absorbers. The code uses publicly available efficient parallel sampling packages to sample posterior and thus can be run on parallel platforms. BayesVP supports simultaneous fitting for multiple absorption components in high-dimensional parameter space. The package includes additional utilities such as explicit specification of priors of model parameters, continuum model, Bayesian model comparison criteria, and posterior sampling convergence check.
BCcodes computes bolometric corrections and synthetic colors in up to 5 filters for input values of the stellar parameters Teff, log(g), [Fe/H], E(B-V) and [alpha/Fe].
The BEARCLAW package is a multidimensional, Eulerian AMR-capable computational code written in Fortran to solve hyperbolic systems for astrophysical applications. It is part of AstroBEAR, a hydrodynamic & magnetohydrodynamic code environment designed for a variety of astrophysical applications which allows simulations in 2, 2.5 (i.e., cylindrical), and 3 dimensions, in either cartesian or curvilinear coordinates.
BEHR is a standalone command-line C program designed to quickly estimate the hardness ratios and their uncertainties for astrophysical sources. It is especially useful in the Poisson regime of low counts, and computes the proper uncertainty regardless of whether the source is detected in both passbands or not.
Bessel, written in the C programming language, uses an accurate scheme for evaluating Bessel functions of high order. It has been extensively tested against a number of other routines, demonstrating its accuracy and efficiency.
The "busy function" accurately describes the characteristic double-horn HI profile of many galaxies. Implemented in a C/C++ library and Python module called BF_dist, it is a continuous, differentiable function that consists of only two basic functions, the error function, erf(x), and a polynomial, |x|^n, of degree n >= 2. BF_dist offers great flexibility in fitting a wide range of HI profiles from the Gaussian profiles of dwarf galaxies to the broad, asymmetric double-horn profiles of spiral galaxies, and can be used to parametrize observed HI spectra of galaxies and the construction of spectral templates for simulations and matched filtering algorithms accurately and efficiently.
BGLS calculates the Bayesian Generalized Lomb-Scargle periodogram. It takes as input arrays with a time series, a dataset and errors on those data, and returns arrays with sampled periods and the periodogram values at those periods.
BHDD (BlackHolesDarkDress) simulates primordial black hole (PBH) binaries that are clothed in dark matter (DM) halos. The software uses N-body simulations and analytical estimates to follow the evolution of PBH binaries formed in the early Universe.
bhint is a post-Newtonian, high-precision integrator for stellar systems surrounding a super-massive black hole. The algorithm makes use of the fact that the Keplerian orbits in such a potential can be calculated directly and are only weakly perturbed. For a given average number of steps per orbit, bhint is almost a factor of 100 more accurate than the standard Hermite method.
BHMcalc provides renditions of the instantaneous circumbinary habital zone (CHZ) and also calculates BHM properties of the system including those related to the rotational evolution of the stellar components and the combined XUV and SW fluxes as measured at different distances from the binary. Moreover, it provides numerical results that can be further manipulated and used to calculate other properties.
BHSKY (copyright 1999 by Robert J. Nemiroff) computes the visual distortion effects visible to an observer traveling around and descending near a non-rotating black hole. The codes are general relativistically accurate and incorporate concepts such as large-angle deflections, image magnifications, multiple imaging, blue-shifting, and the location of the photon sphere. Once star.dat is edited to define the position and orientation of the observer relative to the black hole, bhsky_table should be run to create a table of photon deflection angles. Next bhsky_image reads this table and recomputes the perceived positions of stars in star.num, the Yale Bright Star Catalog. Lastly, bhsky_camera plots these results. The code currently tracks only the two brightest images of each star, and hence becomes noticeably incomplete within 1.1 times the Schwarzschild radius.
BIANCHI provides functionality to support the simulation of Bianchi Type VIIh induced temperature fluctuations in CMB maps of a universe with shear and rotation. The implementation is based on the solutions to the Bianchi models derived by Barrow et al. (1985), which do not incorporate any dark energy component. Functionality is provided to compute the induced fluctuations on the sphere directly in either real or harmonic space.
The Bayesian Inference Engine (BIE) is an object-oriented library of tools written in C++ designed explicitly to enable Bayesian update and model comparison for astronomical problems. To facilitate "what if" exploration, BIE provides a command line interface (written with Bison and Flex) to run input scripts. The output of the code is a simulation of the Bayesian posterior distribution from which summary statistics e.g. by taking moments, or determine confidence intervals and so forth, can be determined. All of these quantities are fundamentally integrals and the Markov Chain approach produces variates $ heta$ distributed according to $P( heta|D)$ so moments are trivially obtained by summing of the ensemble of variates.
Bifrost is a stream processing framework that eases the development of high-throughput processing CPU/GPU pipelines. It is designed for digital signal processing (DSP) applications within radio astronomy. Bifrost uses a flexible ring buffer implementation that allows different signal processing blocks to be connected to form a pipeline. Each block may be assigned to a CPU core, and the ring buffers are used to transport data to and from blocks. Processing blocks may be run on either the CPU or GPU, and the ring buffer will take care of memory copies between the CPU and GPU spaces.
Big MACS is a Python program that estimates an accurate photometric calibration from only an input catalog of stellar magnitudes and filter transmission functions. The user does not have to measure color terms which can be difficult to characterize. Supplied with filter transmission functions, Big MACS synthesizes an expected stellar locus for your data and then simultaneously solves for all unknown zeropoints when fitting to the instrumental locus. The code uses a spectroscopic model for the SDSS stellar locus in color-color space and filter functions to compute expected locus. The stellar locus model is corrected for Milky Way reddening. If SDSS or 2MASS photometry is available for stars in field, Big MACS can yield a highly accurate absolute calibration.
Binary computes the evolution of an accretion disc interacting with a binary system. It has been developed and used to study the coupled evolution of supermassive BH binaries and gaseous accretion discs.
binaryBHexp (binary black hole explorer) uses surrogate models of numerical simulations to generate on-the-fly interactive visualizations of precessing binary black holes. These visualizations can be generated in a few seconds and at any point in the 7-dimensional parameter space of the underlying surrogate models. These visualizations provide a valuable means to understand and gain insights about binary black hole systems and gravitational physics such as those detected by the LIGO gravitational wave detector.
The BI-spectra and Non-Gaussianity Operator (BINGO) code, written in Fortran, computes the scalar bi-spectrum and the non-Gaussianity parameter fNL in single field inflationary models involving the canonical scalar field. BINGO can calculate all the different contributions to the bi-spectrum and the parameter fNL for an arbitrary triangular configuration of the wavevectors.
BinMag examines theoretical stellar spectra computed with Synth/SynthMag/Synmast/Synth3/SME spectrum synthesis codes and compare them to observations. An IDL widget program, BinMag applies radial velocity shift and broadening to the theoretical spectra to account for the effects of stellar rotation, radial-tangential macroturbulence, instrumental smearing. The code can also simulate spectra of spectroscopic binary stars by appropriate coaddition of two synthetic spectra. Additionally, BinMag can be used to measure equivalent width, fit line profile shapes with analytical functions, and to automatically determine radial velocity and broadening parameters. BinMag interfaces with the Synth3 (ascl:1212.010) and SME (ascl:1202.013) codes, allowing the user to determine chemical abundances and stellar atmospheric parameters from the observed spectra.
Binsim produces images of interacting binaries for any system parameters. Though not suitable for modeling light curves or spectra, the resulting images are helpful in visualizing the geometry of a given system and are also helpful in talks and educational work. The code uses the OpenGL API to do the 3D rendering. The software can produce images of cataclysmic variables and X-ray binaries, and can render the mass donor star, an axisymmetric disc (without superhumps, warps or spirals), the accretion stream and hotspot, and a "corona."
The BINSYN program suite is a collection of programs for analysis of binary star systems with or without an optically thick accretion disk. BINSYN produces synthetic spectra of individual binary star components plus a synthetic spectrum of the system. If the system includes an accretion disk, BINSYN also produces a separate synthetic spectrum of the disk face and rim. A system routine convolves the synthetic spectra with filter profiles of several photometric standards to produce absolute synthetic photometry output. The package generates synthetic light curves and determines an optimized solution for system parameters.
The Bisous model is a marked point process that models multi-dimensional patterns. The Bisous filament finder works directly with galaxy distribution data and the model intrinsically takes into account the connectivity of the filamentary network. The Bisous model generates the visit map (the probability to find a filament at a given point) together with the filament orientation field; these two fields are used to extract filament spines from the data.
Bitshuffle rearranges typed, binary data for improving compression; the algorithm is implemented in a python/C package within the Numpy framework. The library can be used alongside HDF5 to compress and decompress datasets and is integrated through the dynamically loaded filters framework. Algorithmically, Bitshuffle is closely related to HDF5's Shuffle filter except it operates at the bit level instead of the byte level. Arranging a typed data array in to a matrix with the elements as the rows and the bits within the elements as the columns, Bitshuffle "transposes" the matrix, such that all the least-significant-bits are in a row, etc. This transposition is performed within blocks of data roughly 8kB long; this does not in itself compress data, but rearranges it for more efficient compression. A compression library is necessary to perform the actual compression. This scheme has been used for compression of radio data in high performance computing.
The Fermi-LAT Background Estimator (BKGE) is a publicly available open-source tool that can estimate the expected background of the Fermi-LAT for any observational conguration and duration. It produces results in the form of text files, ROOT files, gtlike source-model files (for LAT maximum likelihood analyses), and PHA I/II FITS files (for RMFit/XSpec spectral fitting analyses). Its core is written in C++ and its user interface in Python.
BLOBCAT is a source extraction software that utilizes the flood fill algorithm to detect and catalog blobs, or islands of pixels representing sources, in 2D astronomical images. The software is designed to process radio-wavelength images of both Stokes I intensity and linear polarization, the latter formed through the quadrature sum of Stokes Q and U intensities or as a by-product of rotation measure synthesis. BLOBCAT corrects for two systematic biases to enable the flood fill algorithm to accurately measure flux densities for Gaussian sources. BLOBCAT exhibits accurate measurement performance in total intensity and, in particular, linear polarization, and is particularly suited to the analysis of large survey data.
Bayesian Blocks is a time-domain algorithm for detecting localized structures (bursts), revealing pulse shapes, and generally characterizing intensity variations. The input is raw counting data, in any of three forms: time-tagged photon events, binned counts, or time-to-spill data. The output is the most probable segmentation of the observation into time intervals during which the photon arrival rate is perceptibly constant, i.e. has no statistically significant variations. The idea is not that the source is deemed to have this discontinuous, piecewise constant form, rather that such an approximate and generic model is often useful. The analysis is based on Bayesian statistics.
This code is obsolete and yields approximate results; see Bayesian Blocks instead for an algorithm guaranteeing exact global optimization.
BLS (Box-fitting Least Squares) is a box-fitting algorithm that analyzes stellar photometric time series to search for periodic transits of extrasolar planets. It searches for signals characterized by a periodic alternation between two discrete levels, with much less time spent at the lower level.
bmcmc is a general purpose Markov Chain Monte Carlo package for Bayesian data analysis. It uses an adaptive scheme for automatic tuning of proposal distributions. It can also handle Bayesian hierarchical models by making use of the Metropolis-Within-Gibbs scheme.
BOND determines oxygen and nitrogen abundances in giant H II regions by comparison with a large grid of photoionization models. The grid spans a wide range in O/H, N/O and ionization parameter U, and covers different starburst ages and nebular geometries. Unlike other statistical methods, BOND relies on the [Ar III]/[Ne III] emission line ratio to break the oxygen abundance bimodality. By doing so, it can measure oxygen and nitrogen abundances without assuming any a priori relation between N/O and O/H. BOND takes into account changes in the hardness of the ionizing radiation field, which can come about due to the ageing of H II regions or the stochastically sampling of the IMF. The emission line ratio He I/Hβ, in addition to commonly used strong lines, constrains the hardness of the ionizing radiation field. BOND relies on the emission line ratios [O III]/Hβ, [O II]/Hβ and [N II]/Hβ, [Ar III]/Hβ, [Ne III]/Hβ, He I/Hβ as its input parameters, while its output values are the measurements and uncertainties for O/H and N/O.
Bonsai is a gravitational N-body tree-code that runs completely on the GPU. This reduces the amount of time spent on communication with the CPU. The code runs on NVIDIA GPUs and on a GTX480 it is able to integrate ~2.8M particles per second. The tree construction and traverse algorithms are portable to many-core devices which have support for CUDA or OpenCL programming languages.
BOOTTRAN calculates error bars for Keplerian orbital parameters for both single- and multiple-planet systems. It takes the best-fit parameters and radial velocity data (BJD, velocity, errors) and calculates the error bars from sampling distribution estimated via bootstrapping. It is recommended to be used together with the RVLIN package, which find best-fit Keplerian orbital parameters. Both RVLIN and BOOTTRAN are compatible with multiple-telescope data. BOOTTRAN also calculates the transit time and secondary eclipse time and their associated error bars. The algorithm is described in the appendix of the associated article.
The basic mechanisms responsible for producing winds from cool, late-type stars are still largely unknown. We take inspiration from recent progress in understanding solar wind acceleration to develop a physically motivated model of the time-steady mass loss rates of cool main-sequence stars and evolved giants. This model follows the energy flux of magnetohydrodynamic turbulence from a subsurface convection zone to its eventual dissipation and escape through open magnetic flux tubes. We show how Alfven waves and turbulence can produce winds in either a hot corona or a cool extended chromosphere, and we specify the conditions that determine whether or not coronal heating occurs. These models do not utilize arbitrary normalization factors, but instead predict the mass loss rate directly from a star's fundamental properties. We take account of stellar magnetic activity by extending standard age-activity-rotation indicators to include the evolution of the filling factor of strong photospheric magnetic fields. We compared the predicted mass loss rates with observed values for 47 stars and found significantly better agreement than was obtained from the popular scaling laws of Reimers, Schroeder, and Cuntz. The algorithm used to compute cool-star mass loss rates is provided as a self-contained and efficient IDL computer code. We anticipate that the results from this kind of model can be incorporated straightforwardly into stellar evolution calculations and population synthesis techniques.
BoxRemap remaps the cubical domain of a cosmological simulation into simple non-cubical shapes. It can be used for on-the-fly remappings of the simulation geometry and is volume-preserving; remapped geometry has the same volume V = L3 as the original simulation box. The remappings are structure-preserving (local neighboring structures are mapped to neighboring places) and one-to-one, with every particle/halo/galaxy/etc. appearing once and only once in the remapped volume.
Photometric redshift estimation is becoming an increasingly important technique, although the currently existing methods present several shortcomings which hinder their application. Most of those drawbacks are efficiently eliminated when Bayesian probability is consistently applied to this problem. The use of prior probabilities and Bayesian marginalization allows the inclusion of valuable information, e.g. the redshift distributions or the galaxy type mix, which is often ignored by other methods. In those cases when the a priori information is insufficient, it is shown how to `calibrate' the prior distributions, using even the data under consideration. There is an excellent agreement between the 108 HDF spectroscopic redshifts and the predictions of the method, with a rms error Delta z/(1+z_spec) = 0.08 up to z<6 and no systematic biases nor outliers. The results obtained are more reliable than those of standard techniques even when the latter include near-IR colors. The Bayesian formalism developed here can be generalized to deal with a wide range of problems which make use of photometric redshifts, e.g. the estimation of individual galaxy characteristics as the metallicity, dust content, etc., or the study of galaxy evolution and the cosmological parameters from large multicolor surveys. Finally, using Bayesian probability it is possible to develop an integrated statistical method for cluster mass reconstruction which simultaneously considers the information provided by gravitational lensing and photometric redshifts.
BRATS (Broadband Radio Astronomy ToolS) provides tools for the spectral analysis of broad-bandwidth radio data and legacy support for narrowband telescopes. It can fit models of spectral ageing on small spatial scales, offers automatic selection of regions based on user parameters (e.g. signal to noise), and automatic determination of the best-fitting injection index. It includes statistical testing, including Chi-squared, error maps, confidence levels and binning of model fits, and can map spectral index as a function of position. It also provides the ability to reconstruct sources at any frequency for a given model and parameter set, subtract any two FITS images and output residual maps, easily combine and scale FITS images in the image plane, and resize radio maps.
BRUCE and KYLIE, written in Fortran 77, synthesize the spectra of pulsating stars. BRUCE constructs a point-sampled model for the surface of a rotating, gravity-darkened star, and then subjects this model to perturbations arising from one or more non-radial pulsation modes. Departures from adiabaticity can be taken into account, as can the Coriolis force through adoption of the so-called traditional approximation. BRUCE writes out a time-sequence of perturbed surface models. This sequence is read in by KYLIE, which synthesizes disk-integrated spectra for the models by co-adding the specific intensity emanating from each visible point toward the observer. The specific intensity is calculated by interpolation in a large temperature-gravity-wavelength-angle grid of pre-calculated intensity spectra.
Brut, written in Python, identifies bubbles in infrared images of the Galactic midplane; it uses a database of known bubbles from the Milky Way Project and Spitzer images to build an automatic bubble classifier. The classifier is based on the Random Forest algorithm, and uses the WiseRF implementation of this algorithm.
BSE is a rapid binary star evolution code. It can model circularization of eccentric orbits and synchronization of stellar rotation with the orbital motion owing to tidal interaction in detail. Angular momentum loss mechanisms, such as gravitational radiation and magnetic braking, are also modelled. Wind accretion, where the secondary may accrete some of the material lost from the primary in a wind, is allowed with the necessary adjustments made to the orbital parameters in the event of any mass variations. Mass transfer occurs if either star fills its Roche lobe and may proceed on a nuclear, thermal or dynamical time-scale. In the latter regime, the radius of the primary increases in response to mass-loss at a faster rate than the Roche-lobe of the star. Prescriptions to determine the type and rate of mass transfer, the response of the secondary to accretion and the outcome of any merger events are in place in BSE.
BSGMODEL is used to construct the disk and spheroid components of the Galaxy from which the distribution of visible stars and mass in the Galaxy is calculated. The computer files accessible here are available for export use. The modifications are described in comment lines in the software. The Galaxy model software has been installed and used by different people for a large variety of purposes (see, e. g., the the review "Star Counts and Galactic Structure'', Ann. Rev. Astron. Ap. 24, 577, 1986 ).
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