[ascl:1611.005]
Exo-Transmit: Radiative transfer code for calculating exoplanet transmission spectra

Exo-Transmit calculates the transmission spectrum of an exoplanet atmosphere given specified input information about the planetary and stellar radii, the planet's surface gravity, the atmospheric temperature-pressure (T-P) profile, the location (in terms of pressure) of any cloud layers, the composition of the atmosphere, and opacity data for the atoms and molecules that make up the atmosphere. The code solves the equation of radiative transfer for absorption of starlight passing through the planet's atmosphere as it transits, accounting for the oblique path of light through the planetary atmosphere along an Earth-bound observer's line of sight. The fraction of light absorbed (or blocked) by the planet plus its atmosphere is calculated as a function of wavelength to produce the wavelength-dependent transmission spectrum. Functionality is provided to simulate the presence of atmospheric aerosols in two ways: an optically thick (gray) cloud deck can be generated at a user-specified height in the atmosphere, and the nominal Rayleigh scattering can be increased by a specified factor.

[ascl:1611.004]
PRECESSION: Python toolbox for dynamics of spinning black-hole binaries

PRECESSION is a comprehensive toolbox for exploring the dynamics of precessing black-hole binaries in the post-Newtonian regime. It allows study of the evolution of the black-hole spins along their precession cycles, performs gravitational-wave-driven binary inspirals using both orbit-averaged and precession-averaged integrations, and predicts the properties of the merger remnant through fitting formulas obtained from numerical-relativity simulations. PRECESSION can add the black-hole spin dynamics to larger-scale numerical studies such as gravitational-wave parameter estimation codes, population synthesis models to predict gravitational-wave event rates, galaxy merger trees and cosmological simulations of structure formation, and provides fast and reliable integration methods to propagate statistical samples of black-hole binaries from/to large separations where they form to/from small separations where they become detectable, thus linking gravitational-wave observations of spinning black-hole binaries to their astrophysical formation history. The code is also useful for computing initial parameters for numerical-relativity simulations targeting specific precessing systems.

[ascl:1611.003]
MPDAF: MUSE Python Data Analysis Framework

MPDAF, the MUSE Python Data Analysis Framework, provides tools to work with MUSE-specific data (for example, raw data and pixel tables), and with more general data such as spectra, images, and data cubes. Originally written to work with MUSE data, it can also be used for other data, such as that from the Hubble Space Telescope. MPDAF also provides MUSELET, a SExtractor-based tool to detect emission lines in a data cube, and a format to gather all the information on a source in one FITS file. MPDAF was developed and is maintained by CRAL (Centre de Recherche Astrophysique de Lyon).

[ascl:1611.002]
tf_unet: Generic convolutional neural network U-Net implementation in Tensorflow

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.

[ascl:1611.001]
UltraNest: Pythonic Nested Sampling Development Framework and UltraNest

This three-component package provides a Pythonic implementation of the Nested Sampling integration algorithm for Bayesian model comparison and parameter estimation. It offers multiple implementations for constrained drawing functions and a test suite to evaluate the correctness, accuracy and efficiency of various implementations. The three components are:

- a modular framework for nested sampling algorithms (nested_sampling) and their development;
- a test framework to evaluate the performance and accuracy of algorithms (testsuite); and
- UltraNest, a fast C implementation of a mixed RadFriends/MCMC nested sampling algorithm.

[ascl:1610.016]
PyMC3: Python probabilistic programming framework

PyMC3 performs Bayesian statistical modeling and model fitting focused on advanced Markov chain Monte Carlo and variational fitting algorithms. It offers powerful sampling algorithms, such as the No U-Turn Sampler, allowing complex models with thousands of parameters with little specialized knowledge of fitting algorithms, intuitive model specification syntax, and optimization for finding the maximum a posteriori (MAP) point. PyMC3 uses Theano to compute gradients via automatic differentiation as well as compile probabilistic programs on-the-fly to C for increased speed.

[ascl:1610.015]
NuPyCEE: NuGrid Python Chemical Evolution Environment

The NuGrid Python Chemical Evolution Environment (NuPyCEE) simulates the chemical enrichment and stellar feedback of stellar populations. It contains three modules. The Stellar Yields for Galactic Modeling Applications module (SYGMA) models the enrichment and feedback of simple stellar populations which can be included in hydrodynamic simulations and semi-analytic models of galaxies. It is the basic building block of the One-zone Model for the Evolution of GAlaxies (OMEGA, ascl:1806.018) module which models the chemical evolution of galaxies such as the Milky Way and its dwarf satellites. The STELLAB (STELLar ABundances) module provides a library of observed stellar abundances useful for comparing predictions of SYGMA and OMEGA.

[ascl:1610.014]
Freddi: Fast Rise Exponential Decay accretion Disk model Implementation

Freddi (Fast Rise Exponential Decay: accretion Disk model Implementation) solves 1-D evolution equations of the Shakura-Sunyaev accretion disk. It simulates fast rise exponential decay (FRED) light curves of low mass X-ray binaries (LMXBs). The basic equation of the viscous evolution relates the surface density and viscous stresses and is of diffusion type; evolution of the accretion rate can be found on solving the equation. The distribution of viscous stresses defines the emission from the source. The standard model for the accretion disk is implied; the inner boundary of the disk is at the ISCO or can be explicitely set. The boundary conditions in the disk are the zero stress at the inner boundary and the zero accretion rate at the outer boundary. The conditions are suitable during the outbursts in X-ray binary transients with black holes. In a binary system, the accretion disk is radially confined. In Freddi, the outer radius of the disk can be set explicitely or calculated as the position of the tidal truncation radius.

[ascl:1610.013]
MC^{3}: Multi-core Markov-chain Monte Carlo code

Cubillos, Patricio; Harrington, Joseph; Lust, Nate; Foster, AJ; Stemm, Madison; Loredo, Tom; Stevenson, Kevin; Campo, Chris; Hardin, Matt; Hardy, Ryan

MC^{3} (Multi-core Markov-chain Monte Carlo) is a Bayesian statistics tool that can be executed from the shell prompt or interactively through the Python interpreter with single- or multiple-CPU parallel computing. It offers Markov-chain Monte Carlo (MCMC) posterior-distribution sampling for several algorithms, Levenberg-Marquardt least-squares optimization, and uniform non-informative, Jeffreys non-informative, or Gaussian-informative priors. MC^{3} can share the same value among multiple parameters and fix the value of parameters to constant values, and offers Gelman-Rubin convergence testing and correlated-noise estimation with time-averaging or wavelet-based likelihood estimation methods.

[ascl:1610.012]
Fourierdimredn: Fourier dimensionality reduction model for interferometric imaging

Fourierdimredn (Fourier dimensionality reduction) implements Fourier-based dimensionality reduction of interferometric data. Written in Matlab, it derives the theoretically optimal dimensionality reduction operator from a singular value decomposition perspective of the measurement operator. Fourierdimredn ensures a fast implementation of the full measurement operator and also preserves the i.i.d. Gaussian properties of the original measurement noise.

[ascl:1610.011]
BXA: Bayesian X-ray Analysis

BXA connects the nested sampling algorithm MultiNest (ascl:1109.006) to the X-ray spectral analysis environments Xspec/Sherpa for Bayesian parameter estimation and model comparison. It provides parameter estimation in arbitrary dimensions and plotting of spectral model vs. the data for best fit, posterior samples, or each component. BXA allows for model selection; it computes the evidence for the considered model, ready for use in computing Bayes factors and is not limited to nested models. It also visualizes deviations between model and data with Quantile-Quantile (QQ) plots, which do not require binning and are more comprehensive than residuals.

[ascl:1610.010]
BurnMan: Lower mantle mineral physics toolkit

BurnMan determines seismic velocities for the lower mantle. Written in Python, BurnMan calculates the isotropic thermoelastic moduli by solving the equations-of-state for a mixture of minerals defined by the user. The user may select from a list of minerals applicable to the lower mantle included or can define one. BurnMan provides choices in methodology, both for the EoS and for the multiphase averaging scheme and the results can be visually or quantitatively compared to observed seismic models.

[ascl:1610.009]
velbin: radial velocity corrected for binary orbital motions

Velbin convolves the radial velocity offsets due to binary orbital motions with a Gaussian to model an observed velocity distribution. This can be used to measure the mean velocity and velocity dispersion from an observed radial velocity distribution, corrected for binary orbital motions. Velbin fits single- or multi-epoch data with any arbitrary binary orbital parameter distribution (as long as it can be sampled properly), however it always assumes that the intrinsic velocity distribution (i.e. corrected for binary orbital motions) is a Gaussian. Velbin samples (and edits) a binary orbital parameter distribution, fits an observed radial velocity distribution, and creates a mock radial velocity distribution that can be used to provide the fitted radial velocities in the single_epoch or multi_epoch methods.

[ascl:1610.008]
cluster-in-a-box: Statistical model of sub-millimeter emission from embedded protostellar clusters

Cluster-in-a-box provides a statistical model of sub-millimeter emission from embedded protostellar clusters and consists of three modules grouped in two scripts. The first (cluster_distribution) generates the cluster based on the number of stars, input initial mass function, spatial distribution and age distribution. The second (cluster_emission) takes an input file of observations, determines the mass-intensity correlation and generates outflow emission for all low-mass Class 0 and I sources. The output is stored as a FITS image where the flux density is determined by the desired resolution, pixel scale and cluster distance.

[ascl:1610.007]
gatspy: General tools for Astronomical Time Series in Python

Gatspy contains efficient, well-documented implementations of several common routines for Astronomical time series analysis, including the Lomb-Scargle periodogram, the Supersmoother method, and others.

[ascl:1610.006]
C^{3}: Command-line Catalogue Crossmatch for modern astronomical surveys

The Command-line Catalogue Cross-matching (C^{3}) software efficiently performs the positional cross-match between massive catalogues from modern astronomical surveys, whose size have rapidly increased in the current data-driven science era. Based on a multi-core parallel processing paradigm, it is executed as a stand-alone command-line process or integrated within any generic data reduction/analysis pipeline. C^{3} provides its users with flexibility in portability, parameter configuration, catalogue formats, angular resolution, region shapes, coordinate units and cross-matching types.

[ascl:1610.005]
GSGS: In-Focus Phase Retrieval Using Non-Redundant Mask Data

GSGS does phase retrieval on images given an estimate of the pupil phase (from a non-redundant mask or other interferometric approach), the pupil geometry, and the in-focus image. The code uses a modified Gerchberg-Saxton algorithm that iterates between pupil plane and image plane to measure the pupil phase.

[ascl:1610.004]
MUSE-DRP: MUSE Data Reduction Pipeline

The MUSE pipeline turns the complex raw data of the MUSE integral field spectrograph into a ready-to-use datacube for scientific analysis.

[ascl:1610.003]
DSDEPROJ: Direct Spectral Deprojection

Deprojection of X-ray data by methods such as PROJCT, which are model dependent, can produce large and unphysical oscillating temperature profiles. Direct Spectral Deprojection (DSDEPROJ) solves some of the issues inherent to model-dependent deprojection routines. DSDEPROJ is a model-independent approach, assuming only spherical symmetry, which subtracts projected spectra from each successive annulus to produce a set of deprojected spectra.

[ascl:1610.002]
CERES: Collection of Extraction Routines for Echelle Spectra

The Collection of Extraction Routines for Echelle Spectra (CERES) constructs automated pipelines for the reduction, extraction, and analysis of echelle spectrograph data. This modular code includes tools for handling the different steps of the processing: CCD reductions, tracing of the echelle orders, optimal and simple extraction, computation of the wave-length solution, estimation of radial velocities, and rough and fast estimation of the atmospheric parameters. The standard output of pipelines constructed with CERES is a FITS cube with the optimally extracted, wavelength calibrated and instrumental drift-corrected spectrum for each of the science images. Additionally, CERES includes routines for the computation of precise radial velocities and bisector spans via the cross-correlation method, and an automated algorithm to obtain an estimate of the atmospheric parameters of the observed star.

[ascl:1610.001]
Piccard: Pulsar timing data analysis package

Piccard is a Bayesian-inference pipeline for Pulsar Timing Array (PTA) data and interacts with Tempo2 (ascl:1210.015) through libstempo. The code is used mainly for single-pulsar analysis and gravitational-wave detection purposes of full Pulsar Timing Array datasets. Modeling of the data can include correlated signals per frequency or modeled spectrum, with uniform, dipolar, quadrupolar, or anisotropic correlations; multiple error bars and EFACs per pulsar; and white and red noise. Timing models can be numerically included, either by using the design matrix (linear timing model), or by calling libstempo for the full non-linear timing model. Many types of samplers are included. For common-mode mitigation, the signals can be reconstructed mitigating arbitrary signals simultaneously.

[ascl:1609.025]
PYESSENCE: Generalized Coupled Quintessence Linear Perturbation Python Code

PYESSENCE evolves linearly perturbed coupled quintessence models with multiple (cold dark matter) CDM fluid species and multiple DE (dark energy) scalar fields, and can be used to generate quantities such as the growth factor of large scale structure for any coupled quintessence model with an arbitrary number of fields and fluids and arbitrary couplings.

[ascl:1609.024]
AdaptiveBin: Adaptive Binning

AdaptiveBin takes one or more images and adaptively bins them. If one image is supplied, then the pixels are binned by fractional error on the intensity. If two or more images are supplied, then the pixels are fractional binned by error on the combined color.

[ascl:1609.023]
contbin: Contour binning and accumulative smoothing

Contbin bins X-ray data using contours on an adaptively smoothed map. The generated bins closely follow the surface brightness, and are ideal where the surface brightness distribution is not smooth, or the spectral properties are expected to follow surface brightness. Color maps can be used instead of surface brightness maps.

[ascl:1609.022]
PyPHER: Python-based PSF Homogenization kERnels

Boucaud, Alexandre; Bocchio, Marco; Abergel, Alain; Orieux, François; Dole, Hervé; Amine Hadj-Youcef, Mohamed

PyPHER (Python-based PSF Homogenization kERnels) computes an homogenization kernel between two PSFs; the code is well-suited for PSF matching applications in both an astronomical or microscopy context. It can warp (rotation + resampling) the PSF images (if necessary), filter images in Fourier space using a regularized Wiener filter, and produce a homogenization kernel. PyPHER requires the pixel scale information to be present in the FITS files, which can if necessary be added by using the provided ADDPIXSCL method.

[ascl:1609.021]
TIDEV: Tidal Evolution package

TIDEV (Tidal Evolution package) calculates the evolution of rotation for tidally interacting bodies using Efroimsky-Makarov-Williams (EMW) formalism. The package integrates tidal evolution equations and computes the rotational and dynamical evolution of a planet under tidal and triaxial torques. TIDEV accounts for the perturbative effects due to the presence of the other planets in the system, especially the secular variations of the eccentricity. Bulk parameters include the mass and radius of the planet (and those of the other planets involved in the integration), the size and mass of the host star, the Maxwell time and Andrade's parameter. TIDEV also calculates the time scale that a planet takes to be tidally locked as well as the periods of rotation reached at the end of the spin-orbit evolution.

[ascl:1609.020]
Askaryan Module: Askaryan electric fields predictor

The Askaryan Module is a C++ class that predicts the electric fields that Askaryan-based detectors detect; it is computationally efficient and accurate, performing fully analytic calculations requiring no *a priori* MC analysis to compute the entire field, for any frequencies, times, or viewing angles chosen by the user.

[ascl:1609.019]
SuperBoL: Module for calculating the bolometric luminosities of supernovae

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.

[ascl:1609.018]
SIP: Systematics-Insensitive Periodograms

SIP (Systematics-Insensitive Periodograms) extends the generative model used to create traditional sine-fitting periodograms for finding the frequency of a sinusoid by including systematic trends based on a set of eigen light curves in the generative model in addition to using a sum of sine and cosine functions over a grid of frequencies, producing periodograms with vastly reduced systematic features. Acoustic oscillations in giant stars and measurement of stellar rotation periods can be recovered from the SIP periodograms without detrending. The code can also be applied to detection other periodic phenomena, including eclipsing binaries and short-period exoplanet candidates.

[ascl:1609.017]
spectral-cube: Read and analyze astrophysical spectral data cubes

Spectral-cube provides an easy way to read, manipulate, analyze, and write data cubes with two positional dimensions and one spectral dimension, optionally with Stokes parameters. It is a versatile data container for building custom analysis routines. It provides a uniform interface to spectral cubes, robust to the wide range of conventions of axis order, spatial projections, and spectral units that exist in the wild, and allows easy extraction of cube sub-regions using physical coordinates. It has the ability to create, combine, and apply masks to datasets and is designed to work with datasets too large to load into memory, and provide basic summary statistic methods like moments and array aggregates.

[ascl:1609.016]
PKDGRAV3: Parallel gravity code

Pkdgrav3 is an 𝒪(*N*) gravity calculation method; it uses a binary tree algorithm with fifth order fast multipole expansion of the gravitational potential, using cell-cell interactions. Periodic boundaries conditions require very little data movement and allow a high degree of parallelism; the code includes GPU acceleration for all force calculations, leading to a significant speed-up with respect to previous versions (ascl:1305.005). Pkdgrav3 also has a sophisticated time-stepping criterion based on an estimation of the local dynamical time.

[ascl:1609.015]
FIT3D: Fitting optical spectra

Sánchez, S. F.; Pérez, E.; Sánchez-Blázquez, P.; González, J. J.; Rosales-Ortega, F. F.; Cano-Díaz, M.; López-Cobá, C.; Marino, R. A.; Gil de Paz, A.; Mollá, M.; López-Sánchez, A. R.; Ascasibar, Y.; Barrera-Ballesteros, J.

FIT3D fits optical spectra to deblend the underlying stellar population and the ionized gas, and extract physical information from each component. FIT3D is focused on the analysis of Integral Field Spectroscopy data, but is not restricted to it, and is the basis of Pipe3D, a pipeline used in the analysis of datasets like CALIFA, MaNGA, and SAMI. It can run iteratively or in an automatic way to derive the parameters of a large set of spectra.

[ascl:1609.014]
Sky3D: Time-dependent Hartree-Fock equation solver

Written in Fortran 90, Sky3D solves the static or dynamic equations on a three-dimensional Cartesian mesh with isolated or periodic boundary conditions and no further symmetry assumptions. Pairing can be included in the BCS approximation for the static case. The code can be easily modified to include additional physics or special analysis of the results and requires LAPACK and FFTW3.

[ascl:1609.013]
21cmSense: Calculating the sensitivity of 21cm experiments to the EoR power spectrum

21cmSense calculates the expected sensitivities of 21cm experiments to the Epoch of Reionization power spectrum. Written in Python, it requires NumPy, SciPy, and AIPY (ascl:1609.012).

[ascl:1609.012]
AIPY: Astronomical Interferometry in PYthon

AIPY collects together tools for radio astronomical interferometry. In addition to pure-python phasing, calibration, imaging, and deconvolution code, this package includes interfaces to MIRIAD (ascl:1106.007) and HEALPix (ascl:1107.018), and math/fitting routines from SciPy.

[ascl:1609.011]
Photutils: Photometry tools

Bradley, Larry; Sipocz, Brigitta; Robitaille, Thomas; Tollerud, Erik; Deil, Christoph; Vinícius, Zè; Barbary, Kyle; Günther, Hans Moritz; Bostroem, Azalee; Droettboom, Michael; Bray, Erik; Bratholm, Lars Andersen; Pickering, T. E.; Craig, Matt; Pascual, Sergio; Greco, Johnny; Donath, Axel; Kerzendorf, Wolfgang; Littlefair, Stuart; Barentsen, Geert; D'Eugenio, Francesco; Weaver, Benjamin Alan

Photutils provides tools for detecting and performing photometry of astronomical sources. It can estimate the background and background rms in astronomical images, detect sources in astronomical images, estimate morphological parameters of those sources (e.g., centroid and shape parameters), and perform aperture and PSF photometry. Written in Python, it is an affiliated package of Astropy (ascl:1304.002).

[ascl:1609.010]
CuBANz: Photometric redshift estimator

CuBAN*z* is a photometric redshift estimator code for high redshift galaxies that uses the back propagation neural network along with clustering of the training set, making it very efficient. The training set is divided into several self learning clusters with galaxies having similar photometric properties and spectroscopic redshifts within a given span. The clustering algorithm uses the color information (i.e. u-g, g-r etc.) rather than the apparent magnitudes at various photometric bands, as the photometric redshift is more sensitive to the flux differences between different bands rather than the actual values. The clustering method enables accurate determination of the redshifts. CuBAN*z* considers uncertainty in the photometric measurements as well as uncertainty in the neural network training. The code is written in C.

[ascl:1609.009]
NSCool: Neutron star cooling code

NSCool is a 1D (i.e., spherically symmetric) neutron star cooling code written in Fortran 77. The package also contains a series of EOSs (equation of state) to build stars, a series of pre-built stars, and a TOV (Tolman- Oppenheimer-Volkoff) integrator to build stars from an EOS. It can also handle “strange stars” that have a huge density discontinuity between the quark matter and the covering thin baryonic crust. NSCool solves the heat transport and energy balance equations in whole GR, resulting in a time sequence of temperature profiles (and, in particular, a Teff - age curve). Several heating processes are included, and more can easily be incorporated. In particular it can evolve a star undergoing accretion with the resulting deep crustal heating, under a steady or time-variable accretion rate. NSCool is robust, very fast, and highly modular, making it easy to add new subroutines for new processes.

[ascl:1609.008]
GRASP: General-purpose Relativistic Atomic Structure Package

GRASP (General-purpose Relativistic Atomic Structure Package) calculates atomic structure, including energy levels, radiative rates (A-values) and lifetimes; it is a fully relativistic code based on the *jj* coupling scheme. This code has been superseded by GRASP2K (ascl:1611.007).

[ascl:1609.007]
Weighted EMPCA: Weighted Expectation Maximization Principal Component Analysis

Weighted EMPCA performs principal component analysis (PCA) on noisy datasets with missing values. Estimates of the measurement error are used to weight the input data such that the resulting eigenvectors, when compared to classic PCA, are more sensitive to the true underlying signal variations rather than being pulled by heteroskedastic measurement noise. Missing data are simply limiting cases of weight = 0. The underlying algorithm is a noise weighted expectation maximization (EM) PCA, which has additional benefits of implementation speed and flexibility for smoothing eigenvectors to reduce the noise contribution.

[ascl:1609.006]
SCIMES: Spectral Clustering for Interstellar Molecular Emission Segmentation

SCIMES identifies relevant molecular gas structures within dendrograms of emission using the spectral clustering paradigm. It is useful for decomposing objects in complex environments imaged at high resolution.

[ascl:1609.005]
FISHPACK90: Efficient FORTRAN Subprograms for the Solution of Separable Elliptic Partial Differential Equations

FISHPACK90 is a modernization of the original FISHPACK (ascl:1609.004), employing Fortran90 to slightly simplify and standardize the interface to some of the routines. This collection of Fortran programs and subroutines solves second- and fourth-order finite difference approximations to separable elliptic Partial Differential Equations (PDEs). These include Helmholtz equations in cartesian, polar, cylindrical, and spherical coordinates, as well as more general separable elliptic equations. The solvers use the cyclic reduction algorithm. When the problem is singular, a least-squares solution is computed. Singularities induced by the coordinate system are handled, including at the origin r=0 in cylindrical coordinates, and at the poles in spherical coordinates. Test programs are provided for the 19 solvers. Each serves two purposes: as a template to guide you in writing your own codes utilizing the FISHPACK90 solvers, and as a demonstration on your computer that you can correctly produce FISHPACK90 executables.

[ascl:1609.004]
FISHPACK: Efficient FORTRAN Subprograms for the Solution of Separable Elliptic Partial Differential Equations

The FISHPACK collection of Fortran77 subroutines solves second- and fourth-order finite difference approximations to separable elliptic Partial Differential Equations (PDEs). These include Helmholtz equations in cartesian, polar, cylindrical, and spherical coordinates, as well as more general separable elliptic equations. The solvers use the cyclic reduction algorithm. When the problem is singular, a least-squares solution is computed. Singularities induced by the coordinate system are handled, including at the origin r=0 in cylindrical coordinates, and at the poles in spherical coordinates.

[ascl:1609.003]
Kranc: Cactus modules from Mathematica equations

Kranc turns a tensorial description of a time dependent partial differential equation into a module for the Cactus Computational Toolkit (ascl:1102.013). This Mathematica application takes a simple continuum description of a problem and generates highly efficient and portable code, and can be used both for rapid prototyping of evolution systems and for high performance supercomputing.

[ascl:1609.002]
StarPy: Quenched star formation history parameters of a galaxy using MCMC

Smethurst, R. J.; Lintott, C. J.; Simmons, B. D.; Schawinski, K.; Marshall, P. J.; Bamford, S.; Fortson, L.; Kaviraj, S.; Masters, K. L.; Melvin, T.; Nichol, R. C.; Skibba, R. A.; Willett, K. W.

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.

[ascl:1609.001]
T-PHOT: PSF-matched, prior-based, multiwavelength extragalactic deconfusion photometry

Merlin, E.; Fontana, A.; Ferguson, H. C.; Dunlop, J. S.; Elbaz, D.; Bourne, N.; Bruce, V. A.; Buitrago, F.; Castellano, M.; Schreiber, C.; Grazian, A.; McLure, R. J.; Okumura, K.; Shu, X.; Wang, T.; Amorín, R.; Boutsia, K.; Cappelluti, N.; Comastri, A.; Derriere, S.; Faber, S. M.; Santini, P.

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).

[ascl:1608.020]
SPIDERz: SuPport vector classification for IDEntifying Redshifts

SPIDERz (SuPport vector classification for IDEntifying Redshifts) applies powerful support vector machine (SVM) optimization and statistical learning techniques to custom data sets to obtain accurate photometric redshift (photo-z) estimations. It is written for the IDL environment and can be applied to traditional data sets consisting of photometric band magnitudes, or alternatively to data sets with additional galaxy parameters (such as shape information) to investigate potential correlations between the extra galaxy parameters and redshift.

[ascl:1608.019]
NEBULAR: Spectrum synthesis for mixed hydrogen-helium gas in ionization equilibrium

NEBULAR synthesizes the spectrum of a mixed hydrogen helium gas in collisional ionization equilibrium. It is not a spectral fitting code, but it can be used to resample a model spectrum onto the wavelength grid of a real observation. It supports a wide range of temperatures and densities. NEBULAR includes free-free, free-bound, two-photon and line emission from HI, HeI and HeII. The code will either return the composite model spectrum, or, if desired, the unrescaled atomic emission coefficients. It is written in C++ and depends on the GNU Scientific Library (GSL).

[ascl:1608.018]
LORENE: Spectral methods differential equations solver

LORENE (Langage Objet pour la RElativité NumériquE) solves various problems arising in numerical relativity, and more generally in computational astrophysics. It is a set of C++ classes and provides tools to solve partial differential equations by means of multi-domain spectral methods. LORENE classes implement basic structures such as arrays and matrices, but also abstract mathematical objects, such as tensors, and astrophysical objects, such as stars and black holes.

[ascl:1608.017]
21CMMC: Parallelized Monte Carlo Markov Chain analysis tool for the epoch of reionization (EoR)

21CMMC is an efficient Python sampler of the semi-numerical reionization simulation code 21cmFAST (ascl:1102.023). It can recover constraints on astrophysical parameters from current or future 21 cm EoR experiments, accommodating a variety of EoR models, as well as priors on individual model parameters and the reionization history. By studying the resulting impact on the EoR astrophysical constraints, 21CMMC can be used to optimize foreground cleaning algorithms; interferometer designs; observing strategies; alternate statistics characterizing the 21cm signal; and synergies with other observational programs.

[ascl:1608.016]
NICIL: Non-Ideal magnetohydrodynamics Coefficients and Ionisation Library

NICIL (Non-Ideal magnetohydrodynamics Coefficients and Ionisation Library) calculates the ionization values and the coefficients of the non-ideal magnetohydrodynamics terms of Ohmic resistivity, the Hall effect, and ambipolar diffusion. Written as a standalone Fortran90 module that can be implemented in existing codes, NICIL is fully parameterizable, allowing the user to choose which processes to include and decide the values of the free parameters. The module includes both cosmic ray and thermal ionization; the former includes two ion species and three species of dust grains (positively charged, negatively charged and neutral), and the latter includes five elements which can be doubly ionized.

[ascl:1608.015]
2DFFT: Measuring Galactic Spiral Arm Pitch Angle

Davis, Benjamin L.; Berrier, Joel C.; Shields, Douglas W.; Kennefick, Julia; Kennefick, Daniel; Seigar, Marc S.; Lacy, Claud H. S.; Puerari, Ivânio

2DFFT utilizes two-dimensional fast Fourier transformations of images of spiral galaxies to isolate and measure the pitch angles of their spiral arms; this provides a quantitative way to measure this morphological feature and allows comparison of spiral galaxy pitch angle to other galactic parameters and test spiral arm genesis theories. 2DFFT requires fourn.c from *Numerical Recipes in C* (Press et al. 1989).

P2DFFT (ascl:1806.011) is a parallelized version of 2DFFT.

[ascl:1608.014]
gevolution: General Relativity Cosmological N-body code for evolution of large scale structures

The N-body code *gevolution* complies with general relativity principles at every step; it calculates all six metric degrees of freedom in Poisson gauge. N-body particles are evolved by solving the geodesic equation written in terms of a canonical momentum to remain valid for relativistic particles. *gevolution* can be extended to include different kinds of dark energy or modified gravity models, going beyond the usually adopted quasi-static approximation. A weak field expansion is the central element of *gevolution*; this permits the code to treat settings in which no strong gravitational fields appear, including arbitrary scenarios with relativistic sources as long as gravitational fields are not very strong. The framework is well suited for cosmology, but may also be useful for astrophysical applications with moderate gravitational fields where a Newtonian treatment is insufficient.

[ascl:1608.013]
DOLPHOT: Stellar photometry

DOLPHOT is a stellar photometry package that was adapted from HSTphot for general use. It supports two modes; the first is a generic PSF-fitting package, which uses analytic PSF models and can be used for any camera. The second mode uses ACS PSFs and calibrations, and is effectively an ACS adaptation of HSTphot. A number of utility programs are also included with the DOLPHOT distribution, including basic image reduction routines.

[submitted]
ExoPlanet

ExoPlanet provides a graphical interface for the construction, evaluation and application of a machine learning model in predictive analysis. With the back-end built using the numpy and scikit-learn libraries, ExoPlanet couples fast and well tested algorithms, a UI designed over the PyQt framework, and graphs rendered using Matplotlib. This serves to provide the user with a rich interface, rapid analytics and interactive visuals.

ExoPlanet is designed to have a minimal learning curve to allow researchers to focus more on the applicative aspect of machine learning algorithms rather than their implementation details and supports both methods of learning, providing algorithms for unsupervised and supervised training, which may be done with continuous or discrete labels. The parameters of each algorithms can be adjusted to ensure the best fit for the data. Training data is read from a CSV file, and after training is complete, ExoPlanet automates the building of the visual representations for the trained model. Once training and evaluation yield satisfactory results, the model may be used to make data based predictions on a new data set.

[ascl:1608.012]
OBERON: OBliquity and Energy balance Run on N-body systems

OBERON (OBliquity and Energy balance Run on N-body systems) models the climate of Earthlike planets under the effects of an arbitrary number and arrangement of other bodies, such as stars, planets and moons. The code, written in C++, simultaneously computes N body motions using a 4th order Hermite integrator, simulates climates using a 1D latitudinal energy balance model, and evolves the orbital spin of bodies using the equations of Laskar (1986a,b).

[ascl:1608.011]
PROFFIT: Analysis of X-ray surface-brightness profiles

PROFFIT analyzes X-ray surface-brightness profiles for data from any X-ray instrument. It can extract surface-brightness profiles in circular or elliptical annuli, using constant or logarithmic bin size, from the image centroid, the surface-brightness peak, or any user-given center, and provides surface-brightness profiles in any circular or elliptical sectors. It offers background map support to extract background profiles, can excise areas using SAO DS9-compatible (ascl:0003.002) region files to exclude point sources, provides fitting with a number of built-in models, including the popular beta model, double beta, cusp beta, power law, and projected broken power law, uses chi-squared or C statistic, and can fit on the surface-brightness or counts data. It has a command-line interface similar to HEASOFT’s XSPEC (ascl:9910.005) package, provides interactive help with a description of all the commands, and results can be saved in FITS, ROOT or TXT format.

[ascl:1608.010]
pvextractor: Position-Velocity Diagram Extractor

Given a path defined in sky coordinates and a spectral cube, pvextractor extracts a slice of the cube along that path and along the spectral axis to produce a position-velocity or position-frequency slice. The path can be defined programmatically in pixel or world coordinates, and can also be drawn interactively using a simple GUI. Pvextractor is the main function, but also includes a few utilities related to header trimming and parsing.

[ascl:1608.009]
FilFinder: Filamentary structure in molecular clouds

FilFinder extracts and analyzes filamentary structure in molecular clouds. In particular, it is capable of uniformly extracting structure over a large dynamical range in intensity. It returns the main filament properties: local amplitude and background, width, length, orientation and curvature. FilFinder offers additional tools to, for example, create a filament-only image based on the properties of the radial fits. The resulting mask and skeletons may be saved in FITS format, and property tables may be saved as a CSV, FITS or LaTeX table.

[ascl:1608.008]
Cuba: Multidimensional numerical integration library

The Cuba library offers four independent routines for multidimensional numerical integration: Vegas, Suave, Divonne, and Cuhre. The four algorithms work by very different methods, and can integrate vector integrands and have very similar Fortran, C/C++, and Mathematica interfaces. Their invocation is very similar, making it easy to cross-check by substituting one method by another. For further safeguarding, the output is supplemented by a chi-square probability which quantifies the reliability of the error estimate.

[ascl:1608.007]
BASE-9: Bayesian Analysis for Stellar Evolution with nine variables

Robinson, Elliot; von Hippel, Ted; Stein, Nathan; Stenning, David; Wagner-Kaiser, Rachel; Si, Shijing; van Dyk, David

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).

[ascl:1608.006]
Gemini IRAF: Data reduction software for the Gemini telescopes

The Gemini IRAF package processes observational data obtained with the Gemini telescopes. It is an external package layered upon IRAF and supports data from numerous instruments, including FLAMINGOS-2, GMOS-N, GMOS-S, GNIRS, GSAOI, NIFS, and NIRI. The Gemini IRAF package is organized into sub-packages; it contains a generic tools package, "gemtools", along with instrument-specific packages. The raw data from the Gemini facility instruments are stored as Multi-Extension FITS (MEF) files. Therefore, all the tasks in the Gemini IRAF package, intended for processing data from the Gemini facility instruments, are capable of handling MEF files.

[ascl:1608.005]
AstroVis: Visualizing astronomical data cubes

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.

[ascl:1608.004]
BART: Bayesian Atmospheric Radiative Transfer fitting code

Cubillos, Patricio; Blecic, Jasmina; Harrington, Joseph; Rojo, Patricio; Lust, Nate; Bowman, Oliver; Stemm, Madison; Foster, Andrew; Loredo, Thomas J.; Fortney, Jonathan; Madhusudhan, Nikku

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.

[ascl:1608.003]
appaloosa: Python-based flare finding code for Kepler light curves

The appaloosa suite automates flare-finding in every Kepler light curves. It builds quiescent light curve models that include long- and short-cadence data through iterative de-trending and includes completeness estimates via artificial flare injection and recovery tests.

[ascl:1608.002]
pyXSIM: Synthetic X-ray observations generator

pyXSIM simulates X-ray observations from astrophysical sources. X-rays probe the high-energy universe, from hot galaxy clusters to compact objects such as neutron stars and black holes and many interesting sources in between. pyXSIM generates synthetic X-ray observations of these sources from a wide variety of models, whether from grid-based simulation codes such as FLASH (ascl:1010.082), Enzo (ascl:1010.072), and Athena (ascl:1010.014), to particle-based codes such as Gadget (ascl:0003.001) and AREPO, and even from datasets that have been created “by hand”, such as from NumPy arrays. pyXSIM can also manipulate the synthetic observations it produces in various ways and export the simulated X-ray events to other software packages to simulate the end products of specific X-ray observatories. pyXSIM is an implementation of the PHOX (ascl:1112.004) algorithm and was initially the photon_simulator analysis module in yt (ascl:1011.022); it is dependent on yt.

[ascl:1608.001]
Stingray: Spectral-timing software

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.

[ascl:1607.020]
SEEK: Signal Extraction and Emission Kartographer

Akeret, Joel; Seehars, Sebastian; Chang, Chihway; Monstein, Christian; Amara, Adam; Refregier, Alexandre

SEEK (Signal Extraction and Emission Kartographer) processes time-ordered-data from single dish radio telescopes or from the simulation pipline HIDE (ascl:1607.019), removes artifacts from Radio Frequency Interference (RFI), automatically applies flux calibration, and recovers the astronomical radio signal. With its companion code HIDE (ascl:1607.019), it provides end-to-end simulation and processing of radio survey data.

[ascl:1607.019]
HIDE: HI Data Emulator

Akeret, Joel; Seehars, Sebastian; Chang, Chihway; Monstein, Christian; Amara, Adam; Refregier, Alexandre

HIDE (HI Data Emulator) forward-models the process of collecting astronomical radio signals in a single dish radio telescope instrument and outputs pixel-level time-ordered-data. Written in Python, HIDE models the noise and RFI modeling of the data and with its companion code SEEK (ascl:1607.020) provides end-to-end simulation and processing of radio survey data.

[ascl:1607.018]
LZIFU: IDL emission line fitting pipeline for integral field spectroscopy data

LZIFU (LaZy-IFU) is an emission line fitting pipeline for integral field spectroscopy (IFS) data. Written in IDL, the pipeline turns IFS data to 2D emission line flux and kinematic maps for further analysis. LZIFU has been applied and tested extensively to various IFS data, including the SAMI Galaxy Survey, the Wide-Field Spectrograph (WiFeS), the CALIFA survey, the S7 survey and the MUSE instrument on the VLT.

[ascl:1607.017]
BoxRemap: Volume and local structure preserving mapping of periodic boxes

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.

[ascl:1607.016]
astLib: Tools for research astronomers

astLib is a set of Python modules for performing astronomical plots, some statistics, common calculations, coordinate conversions, and manipulating FITS images with World Coordinate System (WCS) information through PyWCSTools, a simple wrapping of WCSTools (ascl:1109.015).

[ascl:1607.015]
RT1D: 1D code for Rayleigh-Taylor instability

The parallel one-dimensional moving-mesh hydrodynamics code RT1D reproduces the multidimensional dynamics from Rayleigh-Taylor instability in supernova remnants.

[ascl:1607.014]
SOPIE: Sequential Off-Pulse Interval Estimation

SOPIE (Sequential Off-Pulse Interval Estimation) provides functions to non-parametrically estimate the off-pulse interval of a source function originating from a pulsar. The technique is based on a sequential application of P-values obtained from goodness-of-fit tests for the uniform distribution, such as the Kolmogorov-Smirnov, Cramér-von Mises, Anderson-Darling and Rayleigh goodness-of-fit tests.

[ascl:1607.013]
Kālī: Time series data modeler

The fully parallelized and vectorized software package Kālī models time series data using various stochastic processes such as continuous-time ARMA (C-ARMA) processes and uses Bayesian Markov Chain Monte-Carlo (MCMC) for inferencing a stochastic light curve. Kālī is written in c++ with Python language bindings for ease of use. Kālī is named jointly after the Hindu goddess of time, change, and power and also as an acronym for KArma LIbrary.

[ascl:1607.012]
ZASPE: Zonal Atmospheric Stellar Parameters Estimator

ZASPE (Zonal Atmospheric Stellar Parameters Estimator) computes the atmospheric stellar parameters (Teff, log(g), [Fe/H] and vsin(i)) from echelle spectra via least squares minimization with a pre-computed library of synthetic spectra. The minimization is performed only in the most sensitive spectral zones to changes in the atmospheric parameters. The uncertainities and covariances computed by ZASPE assume that the principal source of error is the systematic missmatch between the observed spectrum and the sythetic one that produces the best fit. ZASPE requires a grid of synthetic spectra and can use any pre-computed library minor modifications.

[ascl:1607.011]
HfS: Hyperfine Structure fitting tool

HfS fits the hyperfine structure of spectral lines, with multiple velocity components. The HfS_nh3 procedures included in HfS fit simultaneously the hyperfine structure of the NH_{3} (J,K)= (1,1) and (2,2) inversion transitions, and perform a standard analysis to derive the NH_{3} column density, rotational temperature T_{rot}, and kinetic temperature Tk. HfS uses a Monte Carlo approach for fitting the line parameters, with special attention to the derivation of the parameter uncertainties. HfS includes procedures that make use of parallel computing for fitting spectra from a data cube.

[ascl:1607.009]
PICsar: Particle in cell pulsar magnetosphere simulator

PICsar simulates the magnetosphere of an aligned axisymmetric pulsar and can be used to simulate other arbitrary electromagnetics problems in axisymmetry. Written in Fortran, this special relativistic, electromagnetic, charge conservative particle in cell code features stretchable body-fitted coordinates that follow the surface of a sphere, simplifying the application of boundary conditions in the case of the aligned pulsar; a radiation absorbing outer boundary, which allows a steady state to be set up dynamically and maintained indefinitely from transient initial conditions; and algorithms for injection of charged particles into the simulation domain. PICsar is parallelized using MPI and has been used on research problems with ~1000 CPUs.

[ascl:1607.010]
K2PS: K2 Planet search

K2PS is an Oxford K2 planet search pipeline. Written in Python, it searches for transit-like signals from the k2sc-detrended light curves.

[ascl:1607.008]
BLS: Box-fitting Least Squares

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.

[ascl:1607.007]
JUDE: An Utraviolet Imaging Telescope pipeline

JUDE (Jayant's UVIT Data Explorer) converts the Level 1 data (FITS binary table) from the Ultraviolet Imaging Telescope (UVIT) on ASTROSAT into three output files: a photon event list as a function of frame number (FITS binary table); a FITS image file with two extensions; and a PNG file created from the FITS image file with an automated scaling.

[ascl:1607.006]
Cholla: 3D GPU-based hydrodynamics code for astrophysical simulation

Cholla (Computational Hydrodynamics On ParaLLel Architectures) models the Euler equations on a static mesh and evolves the fluid properties of thousands of cells simultaneously using GPUs. It can update over ten million cells per GPU-second while using an exact Riemann solver and PPM reconstruction, allowing computation of astrophysical simulations with physically interesting grid resolutions (>256^3) on a single device; calculations can be extended onto multiple devices with nearly ideal scaling beyond 64 GPUs.

[ascl:1607.005]
Planetary3br: Three massive body resonance calculator

Given two planets P1 and P2 with arbitrary orbits, planetary3br calculates all possible semimajor axes that a third planet P0 can have in order for the system to be in a three body resonance; these are identified by the combination k0*P0 + k1*P1 + k2*P2. P1 and P2 are assumed to be not in an exact two-body resonance. The program also calculates three "strengths" of the resonance, one for each planet, which are only indicators of the dynamical relevance of the resonance on each planet. Sample input data are available along with the Fortran77 source code.

[ascl:1607.004]
Atlas3bgeneral: Three-body resonance calculator

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.

[ascl:1607.003]
Atlas2bgeneral: Two-body resonance calculator

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.

[ascl:1607.002]
DICE: Disk Initial Conditions Environment

DICE models initial conditions of idealized galaxies to study their secular evolution or their more complex interactions such as mergers or compact groups using N-Body/hydro codes. The code can set up a large number of components modeling distinct parts of the galaxy, and creates 3D distributions of particles using a N-try MCMC algorithm which does not require a prior knowledge of the distribution function. The gravitational potential is then computed on a multi-level Cartesian mesh by solving the Poisson equation in the Fourier space. Finally, the dynamical equilibrium of each component is computed by integrating the Jeans equations for each particles. Several galaxies can be generated in a row and be placed on Keplerian orbits to model interactions. DICE writes the initial conditions in the Gadget1 or Gadget2 (ascl:0003.001) format and is fully compatible with Ramses (ascl:1011.007).

[ascl:1607.001]
AGNfitter: SED-fitting code for AGN and galaxies from a MCMC approach

AGNfitter is a fully Bayesian MCMC method to fit the spectral energy distributions (SEDs) of active galactic nuclei (AGN) and galaxies from the sub-mm to the UV; it enables robust disentanglement of the physical processes responsible for the emission of sources. Written in Python, AGNfitter makes use of a large library of theoretical, empirical, and semi-empirical models to characterize both the nuclear and host galaxy emission simultaneously. The model consists of four physical emission components: an accretion disk, a torus of AGN heated dust, stellar populations, and cold dust in star forming regions. AGNfitter determines the posterior distributions of numerous parameters that govern the physics of AGN with a fully Bayesian treatment of errors and parameter degeneracies, allowing one to infer integrated luminosities, dust attenuation parameters, stellar masses, and star formation rates.

[ascl:1606.015]
FLASK: Full-sky Lognormal Astro-fields Simulation Kit

FLASK (Full-sky Lognormal Astro-fields Simulation Kit) makes tomographic realizations on the sphere of an arbitrary number of correlated lognormal or Gaussian random fields; it can create joint simulations of clustering and lensing with sub-per-cent accuracy over relevant angular scales and redshift ranges. It is C++ code parallelized with OpenMP; FLASK generates fast full-sky simulations of cosmological large-scale structure observables such as multiple matter density tracers (galaxies, quasars, dark matter haloes), CMB temperature anisotropies and weak lensing convergence and shear fields. The mutiple fields can be generated tomographically in an arbitrary number of redshift slices and all their statistical properties (including cross-correlations) are determined by the angular power spectra supplied as input and the multivariate lognormal (or Gaussian) distribution assumed for the fields. Effects like redshift space distortions, doppler distortions, magnification biases, evolution and intrinsic aligments can be introduced in the simulations via the input power spectra which must be supplied by the user.

[ascl:1606.014]
Lmfit: Non-Linear Least-Square Minimization and Curve-Fitting for Python

Newville, Matthew; Stensitzki, Till; Allen, Daniel B; Rawlik, Michal; Ingargiola, Antonino; Nelson, Andrew

Lmfit provides a high-level interface to non-linear optimization and curve fitting problems for Python. Lmfit builds on and extends many of the optimization algorithm of scipy.optimize, especially the Levenberg-Marquardt method from optimize.leastsq. Its enhancements to optimization and data fitting problems include using Parameter objects instead of plain floats as variables, the ability to easily change fitting algorithms, and improved estimation of confidence intervals and curve-fitting with the Model class. Lmfit includes many pre-built models for common lineshapes.

[ascl:1606.013]
Pulse Portraiture: Pulsar timing

Pulse Portraiture is a wideband pulsar timing code written in python. It uses an extension of the FFTFIT algorithm (Taylor 1992) to simultaneously measure a phase (TOA) and dispersion measure (DM). The code includes a Gaussian-component-based portrait modeling routine. The code uses the python interface to the pulsar data analysis package PSRCHIVE (ascl:1105.014) and also requires the non-linear least-squares minimization package lmfit (ascl:1606.014).

[ascl:1606.012]
KMDWARFPARAM: Parameters estimator for K and M dwarf stars

KMDWARFPARAM estimates the physical parameters of a star with mass M < 0.8 M_sun given one or more observational constraints. The code runs a Markov-Chain Monte Carlo procedure to estimate the parameter values and their uncertainties.

[ascl:1606.011]
FDIPS: Finite Difference Iterative Potential-field Solver

FDIPS is a finite difference iterative potential-field solver that can generate the 3D potential magnetic field solution based on a magnetogram. It is offered as an alternative to the spherical harmonics approach, as when the number of spherical harmonics is increased, using the raw magnetogram data given on a grid that is uniform in the sine of the latitude coordinate can result in inaccurate and unreliable results, especially in the polar regions close to the Sun. FDIPS is written in Fortran 90 and uses the MPI library for parallel execution.

[ascl:1606.010]
SimpLens: Interactive gravitational lensing simulator

SimpLens illustrates some of the theoretical ideas important in gravitational lensing in an interactive way. After setting parameters for elliptical mass distribution and external mass, SimpLens displays the mass profile and source position, the lens potential and image locations, and indicate the image magnifications and contours of virtual light-travel time. A lens profile can be made shallower or steeper with little change in the image positions and with only total magnification affected.

[ascl:1606.009]
Companion-Finder: Planets and binary companions in time series spectra

Companion-Finder looks for planets and binary companions in time series spectra by searching for the spectral lines of stellar companions to other stars observed with high-precision radial-velocity surveys.

[ascl:1606.008]
s2: Object oriented wrapper for functions on the sphere

The s2 package can represent any arbitrary function defined on the sphere. Both real space map and harmonic space spherical harmonic representations are supported. Basic sky representations have been extended to simulate full sky noise distributions and Gaussian cosmic microwave background realisations. Support for the representation and convolution of beams is also provided. The code requires HEALPix (ascl:1107.018) and CFITSIO (ascl:1010.001).

[ascl:1606.007]
COMB: Compact embedded object simulations

COMB supports the simulation on the sphere of compact objects embedded in a stochastic background process of specified power spectrum. Support is provided to add additional white noise and convolve with beam functions. Functionality to support functions defined on the sphere is provided by the S2 code (ascl:1606.008); HEALPix (ascl:1107.018) and CFITSIO (ascl:1010.001) are also required.

[ascl:1606.006]
uvmcmcfit: Parametric models to interferometric data fitter

Uvmcmcfit fits parametric models to interferometric data. It is ideally suited to extract the maximum amount of information from marginally resolved observations with interferometers like the Atacama Large Millimeter Array (ALMA), Submillimeter Array (SMA), and Plateau de Bure Interferometer (PdBI). uvmcmcfit uses emcee (ascl:1303.002) to do Markov Chain Monte Carlo (MCMC) and can measure the goodness of fit from visibilities rather than deconvolved images, an advantage when there is strong gravitational lensing and in other situations. uvmcmcfit includes a pure-Python adaptation of Miriad’s (ascl:1106.007) uvmodel task to generate simulated visibilities given observed visibilities and a model image and a simple ray-tracing routine that allows it to account for both strongly lensed systems (where multiple images of the lensed galaxy are detected) and weakly lensed systems (where only a single image of the lensed galaxy is detected).

[ascl:1606.005]
PyMultiNest: Python interface for MultiNest

PyMultiNest provides programmatic access to MultiNest (ascl:1109.006) and PyCuba, integration existing Python code (numpy, scipy), and enables writing Prior & LogLikelihood functions in Python. PyMultiNest can plot and visualize MultiNest's progress and allows easy plotting, visualization and summarization of MultiNest results. The plotting can be run on existing MultiNest output, and when not using PyMultiNest for running MultiNest.

[ascl:1606.004]
HIBAYES: Global 21-cm Bayesian Monte-Carlo Model Fitting

HIBAYES implements fully-Bayesian extraction of the sky-averaged (global) 21-cm signal from the Cosmic Dawn and Epoch of Reionization in the presence of foreground emission. User-defined likelihood and prior functions are called by the sampler PyMultiNest (ascl:1606.005) in order to jointly explore the full (signal plus foreground) posterior probability distribution and evaluate the Bayesian evidence for a given model. Implemented models, for simulation and fitting, include gaussians (HI signal) and polynomials (foregrounds). Some simple plotting and analysis tools are supplied. The code can be extended to other models (physical or empirical), to incorporate data from other experiments, or to use alternative Monte-Carlo sampling engines as required.

[ascl:1606.003]
Cygrid: Cython-powered convolution-based gridding module for Python

The Python module Cygrid grids (resamples) data to any collection of spherical target coordinates, although its typical application involves FITS maps or data cubes. The module supports the FITS world coordinate system (WCS) standard; its underlying algorithm is based on the convolution of the original samples with a 2D Gaussian kernel. A lookup table scheme allows parallelization of the code and is combined with the HEALPix tessellation of the sphere for fast neighbor searches. Cygrid's runtime scales between O(n) and O(nlog n), with n being the number of input samples.

[ascl:1606.002]
PAL: Positional Astronomy Library

The PAL library is a partial re-implementation of Pat Wallace's popular SLALIB library written in C using a Gnu GPL license and layered on top of the IAU's SOFA library (or the BSD-licensed ERFA) where appropriate. PAL attempts to stick to the SLA C API where possible.

[ascl:1606.001]
SWOC: Spectral Wavelength Optimization Code

SWOC (Spectral Wavelength Optimization Code) determines the wavelength ranges that provide the optimal amount of information to achieve the required science goals for a spectroscopic study. It computes a figure-of-merit for different spectral configurations using a user-defined list of spectral features, and, utilizing a set of flux-calibrated spectra, determines the spectral regions showing the largest differences among the spectra.

[ascl:1605.017]
Surprise Calculator: Estimating relative entropy and Surprise between samples

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.

[ascl:1605.016]
zeldovich-PLT: Zel'dovich approximation initial conditions generator

zeldovich-PLT generates Zel'dovich approximation (ZA) initial conditions (i.e. first-order Lagrangian perturbation theory) for cosmological N-body simulations, optionally applying particle linear theory (PLT) corrections.

[ascl:1605.015]
SAND: Automated VLBI imaging and analyzing pipeline

The Search And Non-Destroy (SAND) is a VLBI data reduction pipeline composed of a set of Python programs based on the AIPS interface provided by ObitTalk. It is designed for the massive data reduction of multi-epoch VLBI monitoring research. It can automatically investigate calibrated visibility data, search all the radio emissions above a given noise floor and do the model fitting either on the CLEANed image or directly on the uv data. It then digests the model-fitting results, intelligently identifies the multi-epoch jet component correspondence, and recognizes the linear or non-linear proper motion patterns. The outputs including CLEANed image catalogue with polarization maps, animation cube, proper motion fitting and core light curves. For uncalibrated data, a user can easily add inline modules to do the calibration and self-calibration in a batch for a specific array.

[ascl:1605.014]
DUO: Spectra of diatomic molecules

Duo computes rotational, rovibrational and rovibronic spectra of diatomic molecules. The software, written in Fortran 2003, solves the Schrödinger equation for the motion of the nuclei for the simple case of uncoupled, isolated electronic states and also for the general case of an arbitrary number and type of couplings between electronic states. Possible couplings include spin–orbit, angular momenta, spin-rotational and spin–spin. Introducing the relevant couplings using so-called Born–Oppenheimer breakdown curves can correct non-adiabatic effects.

[ascl:1605.013]
grtrans: Polarized general relativistic radiative transfer via ray tracing

grtrans calculates ray tracing radiative transfer in the Kerr metric, including the full treatment of polarised radiative transfer and parallel transport along geodesics, for comparing theoretical models of black hole accretion flows and jets with observations. The code is written in Fortran 90 and parallelizes with OpenMP; the full code and several components have Python interfaces. grtrans includes Geokerr (ascl:1011.015) and requires cfitsio (ascl:1010.001) and pyfits (ascl:1207.009).

[ascl:1605.012]
K2SC: K2 Systematics Correction

K2SC (K2 Systematics Correction) models instrumental systematics and astrophysical variability in light curves from the K2 mission. It enables the user to remove both position-dependent systematics and time-dependent variability (e.g., for transit searches) or to remove systematics while preserving variability (for variability studies). K2SC automatically computes estimates of the period, amplitude and evolution timescale of the variability for periodic variables and can be run on ASCII and FITS light curve files. Written in Python, this pipeline requires NumPy, SciPy, MPI4Py, Astropy (ascl:1304.002), and George (ascl:1511.015).

[ascl:1605.011]
DISCO: 3-D moving-mesh magnetohydrodynamics package

DISCO evolves orbital fluid motion in two and three dimensions, especially at high Mach number, for studying astrophysical disks. The software uses a moving-mesh approach with a dynamic cylindrical mesh that can shear azimuthally to follow the orbital motion of the gas, thus removing diffusive advection errors and permitting longer timesteps than a static grid. DISCO uses an HLLD Riemann solver and a constrained transport scheme compatible with the mesh motion to implement magnetohydrodynamics.

[ascl:1605.010]
TRIPPy: Python-based Trailed Source Photometry

Fraser, Wesley C.; Alexandersen, Mike; Schwamb, Megan E.; Marsset, Michael E.; Pike, Rosemary E.; Kavelaars, JJ; Bannister, Michele T.; Benecchi, Susan; Delsanti, Audrey

TRIPPy (TRailed Image Photometry in Python) uses a pill-shaped aperture, a rectangle described by three parameters (trail length, angle, and radius) to improve photometry of moving sources over that done with circular apertures. It can generate accurate model and trailed point-spread functions from stationary background sources in sidereally tracked images. Appropriate aperture correction provides accurate, unbiased flux measurement. TRIPPy requires numpy, scipy, matplotlib, Astropy (ascl:1304.002), and stsci.numdisplay; emcee (ascl:1303.002) and SExtractor (ascl:1010.064) are optional.

[ascl:1605.009]
ASTRiDE: Automated Streak Detection for Astronomical Images

ASTRiDE detects streaks in astronomical images using a "border" of each object (i.e. "boundary-tracing" or "contour-tracing") and their morphological parameters. Fast moving objects such as meteors, satellites, near-Earth objects (NEOs), or even cosmic rays can leave streak-like traces in the images; ASTRiDE can detect not only long streaks but also relatively short or curved streaks.

[ascl:1605.008]
PDT: Photometric DeTrending Algorithm Using Machine Learning

PDT removes systematic trends in light curves. It finds clusters of light curves that are highly correlated using machine learning, constructs one master trend per cluster and detrends an individual light curve using the constructed master trends by minimizing residuals while constraining coefficients to be positive.

[ascl:1605.007]
MUSCLE: MUltiscale Spherical-ColLapse Evolution

MUSCLE (MUltiscale Spherical ColLapse Evolution) produces low-redshift approximate N-body realizations accurate to few-Megaparsec scales. It applies a spherical-collapse prescription on multiple Gaussian-smoothed scales. It achieves higher accuracy than perturbative schemes (Zel'dovich and second-order Lagrangian perturbation theory - 2LPT), and by including the void-in-cloud process (voids in large-scale collapsing regions), solves problems with a single-scale spherical-collapse scheme.

[ascl:1605.006]
CAMELOT: Cloud Archive for MEtadata, Library and Online Toolkit

Ginsburg, Adam; Kruijssen, J. M. Diederik; Longmore, Steven N.; Koch, Eric; Glover, Simon C. O.; Dale, James E.; Commerçon, Benoît; Giannetti, Andrea; McLeod, Anna F.; Testi, Leonardo; Zahorecz, Sarolta; Rathborne, Jill M.; Zhang, Qizhou; Fontani, Francesco; Beltrán, Maite T.; Rivilla, Victor M.

CAMELOT facilitates the comparison of observational data and simulations of molecular clouds and/or star-forming regions. The central component of CAMELOT is a database summarizing the properties of observational data and simulations in the literature through pertinent metadata. The core functionality allows users to upload metadata, search and visualize the contents of the database to find and match observations/simulations over any range of parameter space.

To bridge the fundamental disconnect between inherently 2D observational data and 3D simulations, the code uses key physical properties that, in principle, are straightforward for both observers and simulators to measure — the surface density (Sigma), velocity dispersion (sigma) and radius (R). By determining these in a self-consistent way for all entries in the database, it should be possible to make robust comparisons.

[ascl:1605.005]
TMBIDL: Single dish radio astronomy data reduction package

The IDL package reduces and analyzes radio astronomy data. It translates SDFITS files into TMBIDL format, and can average and display spectra, remove baselines, and fit Gaussian models.

[ascl:1605.004]
BACCHUS: Brussels Automatic Code for Characterizing High accUracy Spectra

BACCHUS (Brussels Automatic Code for Characterizing High accUracy Spectra) derives stellar parameters (T_{eff}, 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).

[ascl:1605.003]
Shadowfax: Moving mesh hydrodynamical integration code

Shadowfax simulates galaxy evolution. Written in object-oriented modular C++, it evolves a mixture of gas, subject to the laws of hydrodynamics and gravity, and any collisionless fluid only subject to gravity, such as cold dark matter or stars. For the hydrodynamical integration, it makes use of a (co-) moving Lagrangian mesh. The code has a 2D and 3D version, contains utility programs to generate initial conditions and visualize simulation snapshots, and its input/output is compatible with a number of other simulation codes, e.g. Gadget2 (ascl:0003.001) and GIZMO (ascl:1410.003).

[ascl:1605.002]
cluster-lensing: Tools for calculating properties and weak lensing profiles of galaxy clusters

The cluster-lensing package calculates properties and weak lensing profiles of galaxy clusters. Implemented in Python, it includes cluster mass-richness and mass-concentration scaling relations, and NFW halo profiles for weak lensing shear, the differential surface mass density ΔΣ(r), and for magnification, Σ(r). Optionally the calculation will include the effects of cluster miscentering offsets.

[ascl:1605.001]
MARZ: Redshifting Program

MARZ analyzes objects and produces high quality spectroscopic redshift measurements. Spectra not matched correctly by the automatic algorithm can be redshifted manually by cycling automatic results, manual template comparison, or marking spectral features. The software has an intuitive interface and powerful automatic matching capabilities on spectra, and can be run interactively or from the command line, and runs as a Web application. MARZ can be run on a local server; it is also available for use on a public server.

[ascl:1604.012]
TTVFaster: First order eccentricity transit timing variations (TTVs)

TTVFaster implements analytic formulae for transit time variations (TTVs) that are accurate to first order in the planet–star mass ratios and in the orbital eccentricities; the implementations are available in several languages, including IDL, Julia, Python and C. These formulae compare well with more computationally expensive N-body integrations in the low-eccentricity, low mass-ratio regime when applied to simulated and to actual multi-transiting Kepler planet systems.

[ascl:1604.011]
FDPS: Framework for Developing Particle Simulators

Iwasawa, Masaki; Tanikawa, Ataru; Hosono, Natsuki; Nitadori, Keigo; Muranushi, Takayuki; Makino, Junichiro

FDPS provides the necessary functions for efficient parallel execution of particle-based simulations as templates independent of the data structure of particles and the functional form of the interaction. It is used to develop particle-based simulation programs for large-scale distributed-memory parallel supercomputers. FDPS includes templates for domain decomposition, redistribution of particles, and gathering of particle information for interaction calculation. It uses algorithms such as Barnes-Hut tree method for long-range interactions; methods to limit the calculation to neighbor particles are used for short-range interactions. FDPS reduces the time and effort necessary to write a simple, sequential and unoptimized program of O(N^2) calculation cost, and produces compiled programs that will run efficiently on large-scale parallel supercomputers.

[ascl:1604.009]
CCSNMultivar: Core-Collapse Supernova Gravitational Waves

CCSNMultivar aids the analysis of core-collapse supernova gravitational waves. It includes multivariate regression of Fourier transformed or time domain waveforms, hypothesis testing for measuring the influence of physical parameters, and the Abdikamalov et. al. catalog for example use. CCSNMultivar can optionally incorporate additional uncertainty due to detector noise and approximate waveforms from anywhere within the parameter space.

[ascl:1604.008]
The Tractor: Probabilistic astronomical source detection and measurement

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.

[ascl:1604.007]
DNest3: Diffusive Nested Sampling

DNest3 is a C++ implementation of Diffusive Nested Sampling (ascl:1010.029), a Markov Chain Monte Carlo (MCMC) algorithm for Bayesian Inference and Statistical Mechanics. Relative to older DNest versions, DNest3 has improved performance (in terms of the sampling overhead, likelihood evaluations still dominate in general) and is cleaner code: implementing new models should be easier than it was before. In addition, DNest3 is multi-threaded, so one can run multiple MCMC walkers at the same time, and the results will be combined together.

[ascl:1604.006]
2-DUST: Dust radiative transfer code

2-DUST is a general-purpose dust radiative transfer code for an axisymmetric system that reveals the global energetics of dust grains in the shell and the 2-D projected morphologies of the shell that are strongly dependent on the mixed effects of the axisymmetric dust distribution and inclination angle. It can be used to model a variety of axisymmetric astronomical dust systems.

[ascl:1604.005]
Halotools: Galaxy-Halo connection models

Hearin, Andrew; Tollerud, Erik; Robitaille,Thomas; Droettboom, Michael; Zentner, Andrew; Bray, Erik; Craig, Matt; Bradley, Larry; Barbary, Kyle; Deil, Christoph; Tan, Kevin; Becker, Matthew R.; More, Surhud; Günther, Hans Moritz; Sipocz, Brigitta

Halotools builds and tests models of the galaxy-halo connection and analyzes catalogs of dark matter halos. The core functions of the package include fast generation of synthetic galaxy populations using HODs, abundance matching, and related methods; efficient algorithms for calculating galaxy clustering, lensing, z-space distortions, and other astronomical statistics; a modular, object-oriented framework for designing galaxy evolution models; and end-to-end support for reducing halo catalogs and caching them as hdf5 files.

[ascl:1604.004]
magicaxis: Pretty scientific plotting with minor-tick and log minor-tick support

The R suite magicaxis makes useful and pretty plots for scientific plotting and includes functions for base plotting, with particular emphasis on pretty axis labelling in a number of circumstances that are often used in scientific plotting. It also includes functions for generating images and contours that reflect the 2D quantile levels of the data designed particularly for output of MCMC posteriors where visualizing the location of the 68% and 95% 2D quantiles for covariant parameters is a necessary part of the post MCMC analysis, can generate low and high error bars, and allows clipping of values, rejection of bad values, and log stretching.

[ascl:1604.003]
LAMBDAR: Lambda Adaptive Multi-Band Deblending Algorithm in R

LAMBDAR measures galaxy fluxes from an arbitrary FITS image, covering an arbitrary photometric wave-band, when provided all parameters needed to construct galactic apertures at the required locations for multi-band matched aperture galactic photometry. Through sophisticated matched aperture photometry, the package develops robust Spectral Energy Distributions (SEDs) and accurately establishes the physical properties of galactic objects. LAMBDAR was based on a package detailed in Bourne et al. (2012) that determined galactic fluxes in low resolution Herschel images.

[ascl:1604.002]
libpolycomp: Compression/decompression library

Libpolycomp compresses and decompresses one-dimensional streams of numbers by means of several algorithms. It is well-suited for time-ordered data acquired by astronomical instruments or simulations. One of the algorithms, called "polynomial compression", combines two widely-used ideas (namely, polynomial approximation and filtering of Fourier series) to achieve substantial compression ratios for datasets characterized by smoothness and lack of noise. Notable examples are the ephemerides of astronomical objects and the pointing information of astronomical telescopes. Other algorithms implemented in this C library are well known and already widely used, e.g., RLE, quantization, deflate (via libz) and Burrows-Wheeler transform (via libbzip2). Libpolycomp can compress the timelines acquired by the Planck/LFI instrument with an overall compression ratio of ~9, while other widely known programs (gzip, bzip2) reach compression ratios less than 1.5.

[ascl:1604.001]
OpenMHD: Godunov-type code for ideal/resistive magnetohydrodynamics (MHD)

OpenMHD is a Godunov-type finite-volume code for ideal/resistive magnetohydrodynamics (MHD). It is written in Fortran 90 and is parallelized by using MPI-2 and OpenMP. The code was originally developed for studying magnetic reconnection problems and has been made publicly available in the hope that others may find it useful.

[ascl:1603.018]
PolRadTran: Polarized Radiative Transfer Model Distribution

PolRadTran is a plane-parallel polarized radiative transfer model. It is used to compute the radiance exiting a vertically inhomogeneous atmosphere containing randomly-oriented particles. Both solar and thermal sources of radiation are considered. A direct method of incorporating the polarized scattering information is combined with the doubling and adding method to produce a relatively simple formulation.

[ascl:1603.017]
HIIexplorer: Detect and extract integrated spectra of HII regions

HIIexplorer detects and extracts the integrated spectra of HII regions from IFS datacubes. The procedure assumes H ii regions are peaky/isolated structures with a strong ionized gas emission, clearly above the continuum emission and the average ionized gas emission across the galaxy and that H ii regions have a typical physical size of about a hundred or a few hundreds of parsecs, which corresponds to a typical projected size at the distance of the galaxies of a few arcsec for galaxies at z~0.016. All input parameters can be derived from either a visual inspection and/or a statistical analysis of the Hα emission line map. The algorithm produces a segmentation FITS file describing the pixels associated to each H ii region.

[ascl:1603.016]
ellc: Light curve model for eclipsing binary stars and transiting exoplanets

ellc analyzes the light curves of detached eclipsing binary stars and transiting exoplanet systems. The model represents stars as triaxial ellipsoids, and the apparent flux from the binary is calculated using Gauss-Legendre integration over the ellipses that are the projection of these ellipsoids on the sky. The code can also calculate the fluxweighted radial velocity of the stars during an eclipse (Rossiter-McLaghlin effect). ellc can model a wide range of eclipsing binary stars and extrasolar planetary systems, and can enable the use of modern Monte Carlo methods for data analysis and model testing.

[ascl:1603.015]
Dedalus: Flexible framework for spectrally solving differential equations

Dedalus solves differential equations using spectral methods. It implements flexible algorithms to solve initial-value, boundary-value, and eigenvalue problems with broad ranges of custom equations and spectral domains. Its primary features include symbolic equation entry, multidimensional parallelization, implicit-explicit timestepping, and flexible analysis with HDF5. The code is written primarily in Python and features an easy-to-use interface. The numerical algorithm produces highly sparse systems for many equations which are efficiently solved using compiled libraries and MPI.

[ascl:1603.014]
fibmeasure: Python/Cython module to find the center of back-illuminated optical fibers in metrology images

fibmeasure finds the precise locations of the centers of back-illuminated optical fibers in images. It was developed for astronomical fiber positioning feedback via machine vision cameras and is optimized for high-magnification images where fibers appear as resolvable circles. It was originally written during the design of the WEAVE pick-and-place fiber positioner for the William Herschel Telescope.

[ascl:1603.013]
PyGSM: Python interface to the Global Sky Model

PyGSM is a Python interface for the Global Sky Model (GSM, ascl:1011.010). The GSM is a model of diffuse galactic radio emission, constructed from a variety of all-sky surveys spanning the radio band (e.g. Haslam and WMAP). PyGSM uses the GSM to generate all-sky maps in Healpix format of diffuse Galactic radio emission from 10 MHz to 94 GHz. The PyGSM module provides visualization utilities, file output in FITS format, and the ability to generate observed skies for a given location and date. PyGSM requires Healpy, PyEphem (ascl:1112.014), and AstroPy (ascl:1304.002).

[ascl:1603.012]
tpipe: Searching radio interferometry data for fast, dispersed transients

Visibilities from radio interferometers have not traditionally been used to study the fast transient sky. Millisecond transients (e.g., fast radio bursts) and periodic sources (e.g., pulsars) have been studied with single-dish radio telescopes and a software stack developed over the past few decades. tpipe is an initial attempt to develop the fast transient algorithms for visibility data. Functions exist for analysis of visibilties, such as reading data, flagging data, applying interferometric gain calibration, and imaging. These functions are given equal footing as time-domain techniques like filters and dedispersion.

tpipe has been largely superseded by rtpipe (ascl:1706.002).

[ascl:1603.011]
DiskJockey: Protoplanetary disk modeling for dynamical mass derivation

DiskJockey derives dynamical masses for T Tauri stars using the Keplerian motion of their circumstellar disks, applied to radio interferometric data from the Atacama Large Millimeter Array (ALMA) and the Submillimeter Array (SMA). The package relies on RADMC-3D (ascl:1202.015) to perform the radiative transfer of the disk model. DiskJockey is designed to work in a parallel environment where the calculations for each frequency channel can be distributed to independent processors. Due to the computationally expensive nature of the radiative synthesis, fitting sizable datasets (e.g., SMA and ALMA) will require a substantial amount of CPU cores to explore a posterior distribution in a reasonable timeframe.

[ascl:1603.010]
ExoPriors: Accounting for observational bias of transiting exoplanets

ExoPriors calculates a log-likelihood penalty for an input set of transit parameters to account for observational bias (geometric and signal-to-noise ratio detection bias) of transiting exoplanets. Written in Python, the code calculates this log-likelihood penalty in one of seven user-specified cases specified with Boolean input parameters for geometric and/or SNR bias, grazing or non-grazing events, and occultation events.

[ascl:1603.009]
Asfgrid: Asteroseismic parameters for a star

asfgrid computes asteroseismic parameters for a star with given stellar parameters and vice versa. Written in Python, it determines delta_nu, nu_max or masses via interpolation over a grid.

[ascl:1603.008]
ROBAST: ROOT-based ray-tracing library for cosmic-ray telescopes

ROBAST (ROOT-based simulator for ray tracing) is a non-sequential ray-tracing simulation library developed for wide use in optical simulations of gamma-ray and cosmic-ray telescopes. The library is written in C++ and fully utilizes the geometry library of the ROOT analysis framework, and can build the complex optics geometries typically used in cosmic ray experiments and ground-based gamma-ray telescopes.

[ascl:1603.007]
SMARTIES: Spheroids Modelled Accurately with a Robust T-matrix Implementation for Electromagnetic Scattering

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

[ascl:1603.006]
FAST-PT: Convolution integrals in cosmological perturbation theory calculator

FAST-PT calculates 1-loop corrections to the matter power spectrum in cosmology. The code utilizes Fourier methods combined with analytic expressions to reduce the computation time down to scale as N log N, where N is the number of grid point in the input linear power spectrum. FAST-PT is extremely fast, enabling mode-coupling integral computations fast enough to embed in Monte Carlo Markov Chain parameter estimation.

[ascl:1603.005]
EQUIB: Atomic level populations and line emissivities calculator

Howarth, I. D.; Adams, S.; Clegg, R. E. S.; Ruffle, D. P.; Liu, X.-W.; Pritchet, C. J.; Ercolano, B.

The Fortran program EQUIB solves the statistical equilibrium equation for each ion and yields atomic level populations and line emissivities for given physical conditions, namely electron temperature and electron density, appropriate to the zones in an ionized nebula where the ions are expected to exist.

[ascl:1603.004]
gPhoton: Time-tagged GALEX photon events analysis tools

Written in Python, gPhoton calibrates and sky-projects the ~1.1 trillion ultraviolet photon events detected by the microchannel plates on the Galaxy Evolution Explorer Spacecraft (GALEX), archives these events in a publicly accessible database at the Mikulski Archive for Space Telescopes (MAST), and provides tools for working with the database to extract scientific results, particularly over short time domains. The software includes a re-implementation of core functionality of the GALEX mission calibration pipeline to produce photon list files from raw spacecraft data as well as a suite of command line tools to generate calibrated light curves, images, and movies from the MAST database.

[ascl:1603.003]
VIP: Vortex Image Processing pipeline for high-contrast direct imaging of exoplanets

Gomez Gonzalez, Carlos Alberto; Wertz, Olivier; Christiaens, Valentin; Absil, Olivier; Mawet, Dimitri

VIP (Vortex Image Processing pipeline) provides pre- and post-processing algorithms for high-contrast direct imaging of exoplanets. Written in Python, VIP provides a very flexible framework for data exploration and image processing and supports high-contrast imaging observational techniques, including angular, reference-star and multi-spectral differential imaging. Several post-processing algorithms for PSF subtraction based on principal component analysis are available as well as the LLSG (Local Low-rank plus Sparse plus Gaussian-noise decomposition) algorithm for angular differential imaging. VIP also implements the negative fake companion technique coupled with MCMC sampling for rigorous estimation of the flux and position of potential companions.

[submitted]
millennium-tap-query: A Python Tool to Query the Millennium Simulation UWS/TAP client

millennium-tap-query is a simple wrapper for the Python package requests to deal with connections to the Millennium TAP Web Client. With this tool you can perform basic or advanced queries to the Millennium Simulation database and download the data products. millennium-tap-query is similar to the TAP query tool in the German Astrophysical Virtual Observatory (GAVO) VOtables package.

[ascl:1603.002]
CORBITS: Efficient Geometric Probabilities of Multi-Transiting Exoplanetary Systems

CORBITS (Computed Occurrence of Revolving Bodies for the Investigation of Transiting Systems) computes the probability that any particular group of exoplanets can be observed to transit from a collection of conjectured exoplanets orbiting a star. The efficient, semi-analytical code computes the areas bounded by circular curves on the surface of a sphere by applying elementary differential geometry. CORBITS is faster than previous algorithms, based on comparisons with Monte Carlo simulations, and tests show that it is extremely accurate even for highly eccentric planets.

[ascl:1603.001]
SILSS: SPHERE/IRDIS Long-Slit Spectroscopy pipeline

The ESO's VLT/SPHERE instrument includes a unique long-slit spectroscopy (LSS) mode coupled with Lyot coronagraphy in its infrared dual-band imager and spectrograph (IRDIS) for spectral characterization of young, giant exoplanets detected by direct imaging. The SILSS pipeline is a combination of the official SPHERE pipeline and additional custom IDL routines developed within the SPHERE consortium for the speckle subtraction and spectral extraction of a companion's spectrum; it offers a complete end-to-end pipeline, from raw data (science+calibrations) to a final spectrum of the companion. SILSS works on both the low-resolution (LRS) and medium-resolution (MRS) data, and allows correction for some of the known biases of the instrument. Documentation is included in the header of the main routine of the pipeline.

[ascl:1602.021]
COLAcode: COmoving Lagrangian Acceleration code

COLAcode is a serial particle mesh-based N-body code illustrating the COLA (COmoving Lagrangian Acceleration) method; it solves for Large Scale Structure (LSS) in a frame that is comoving with observers following trajectories calculated in Lagrangian Perturbation Theory (LPT). It differs from standard N-body code by trading accuracy at small-scales to gain computational speed without sacrificing accuracy at large scales. This is useful for generating large ensembles of accurate mock halo catalogs required to study galaxy clustering and weak lensing; such catalogs are needed to perform detailed error analysis for ongoing and future surveys of LSS.

[ascl:1602.020]
mbb_emcee: Modified Blackbody MCMC

Mbb_emcee fits modified blackbodies to photometry data using an affine invariant MCMC. It has large number of options which, for example, allow computation of the IR luminosity or dustmass as part of the fit. Carrying out a fit produces a HDF5 output file containing the results, which can either be read directly, or read back into a mbb_results object for analysis. Upper and lower limits can be imposed as well as Gaussian priors on the model parameters. These additions are useful for analyzing poorly constrained data. In addition to standard Python packages scipy, numpy, and cython, mbb_emcee requires emcee (ascl:1303.002), Astropy (ascl:1304.002), h5py, and for unit tests, nose.

[ascl:1602.019]
CLOC: Cluster Luminosity Order-Statistic Code

CLOC computes cluster order statistics, *i.e.* the luminosity distribution of the Nth most luminous cluster in a population. It is flexible and requires few assumptions, allowing for parametrized variations in the initial cluster mass function and its upper and lower cutoffs, variations in the cluster age distribution, stellar evolution and dust extinction, as well as observational uncertainties in both the properties of star clusters and their underlying host galaxies. It uses Markov chain Monte Carlo methods to search parameter space to find best-fitting values for the parameters describing cluster formation and disruption, and to obtain rigorous confidence intervals on the inferred values.

[ascl:1602.018]
POPPY: Physical Optics Propagation in PYthon

Perrin, Marshall; Long, Joseph; Douglas, Ewan; Sivaramakrishnan, Anand; Slocum, Christine; and others

POPPY (Physical Optics Propagation in PYthon) simulates physical optical propagation including diffraction. It implements a flexible framework for modeling Fraunhofer and Fresnel diffraction and point spread function formation, particularly in the context of astronomical telescopes. POPPY provides the optical modeling framework for WebbPSF (ascl:1504.007) and was developed as part of a simulation package for JWST, but is available separately and is broadly applicable to many kinds of imaging simulations.

[ascl:1602.017]
CHIP: Caltech High-res IRS Pipeline

CHIP (Caltech High-res IRS Pipeline) reduces high signal-to-noise short-high and long-high Spitzer-IRS spectra, especially that taken with dedicated background exposures. Written in IDL, it is independent of other Spitzer reduction tools except IRSFRINGE (ascl:1602.016).

[ascl:1602.016]
IRSFRINGE: Interactive tool for fringe removal from Spitzer IRS spectra

IRSFRINGE is an IDL-based GUI package that allows observers to interactively remove fringes from IRS spectra. Fringes that originate from the detector subtrates are observed in the IRS Short-High (SH) and Long-High (LH) modules. In the Long-Low (LL) module, another fringe component is seen as a result of the pre-launch change in one of the LL filters. The fringes in the Short-Low (SL) module are not spectrally resolved. the fringes are already largely removed in the pipeline processing when the flat field is applied. However, this correction is not perfect and remaining fringes can be removed with IRSFRINGE from data in each module. IRSFRINGE is available as a stand-alone package and is also part of the Spectroscopic Modeling, Analysis and Reduction Tool (SMART, ascl:1210.021).

[ascl:1602.015]
GANDALF: Graphical Astrophysics code for N-body Dynamics And Lagrangian Fluids

GANDALF, a successor to SEREN (ascl:1102.010), is a hybrid self-gravitating fluid dynamics and collisional N-body code primarily designed for investigating star formation and planet formation problems. GANDALF uses various implementations of Smoothed Particle Hydrodynamics (SPH) to perform hydrodynamical simulations of gas clouds undergoing gravitational collapse to form new stars (or other objects), and can perform simulations of pure N-body dynamics using high accuracy N-body integrators, model the intermediate phase of cluster evolution, and provide visualizations via its python interface as well as interactive simulations. Although based on many of the SEREN routines, GANDALF has been largely re-written from scratch in C++ using more optimal algorithms and data structures.

[ascl:1602.014]
k2photometry: Read, reduce and detrend K2 photometry

Van Eylen, Vincent; Nowak, Grzegorz; Albrecht, Simon; Palle, Enric; Ribas, Ignasi; Bruntt, Hans; Perger, Manuel; Gandolfi, Davide; Hirano, Teriyuki; Sanchis-Ojeda, Roberto; Kiilerich, Amanda; Arranz, Jorge P.; Badenas, Mariona; Dai, Fei; Deeg, Hans J.; Guenther, Eike W.; Montanes-Rodriguez, Pilar; Narita, Norio; Rogers, Leslie A.; Bejar, Victor J. S.; Shrotriya, Tushar S.; Winn, Joshua N.; Sebastian, Daniel

k2photometry reads, reduces and detrends K2 photometry and searches for transiting planets. MAST database pixel files are used as input; the output includes raw lightcurves, detrended lightcurves and a transit search can be performed as well. Stellar variability is not typically well-preserved but parameters can be tweaked to change that. The BLS algorithm used to detect periodic events is a Python implementation by Ruth Angus and Dan Foreman-Mackey (https://github.com/dfm/python-bls).

[ascl:1602.013]
TailZ: Redshift distributions estimator of photometric samples of galaxies

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.

[ascl:1602.012]
DELightcurveSimulation: Light curve simulation code

DELightcurveSimulation simulates light curves with any given power spectral density and any probability density function, following the algorithm described in Emmanoulopoulos *et al.* (2013). The simulated products have exactly the same variability and statistical properties as the observed light curves. The code is a Python implementation of the Mathematica code provided by Emmanoulopoulos *et al.*

[ascl:1602.011]
Celestial: Common astronomical conversion routines and functions

The R package Celestial contains common astronomy conversion routines, particularly the HMS and degrees schemes, and a large range of functions for calculating properties of different cosmologies (as used by the cosmocalc website). This includes distances, ages, growth rate/factor and densities (e.g., Omega evolution and critical energy density). It also includes functions for calculating thermal properties of the CMB and Planck's equations and virial properties of halos in different cosmologies, and standard NFW and weak-lensing formulas and low level orbital routines for calculating Roche properties, Vis-Viva and free-fall times.

[ascl:1602.010]
The Cannon: Data-driven method for determining stellar parameters and abundances from stellar spectra

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.

[ascl:1602.009]
LensTools: Weak Lensing computing tools

LensTools implements a wide range of routines frequently used in Weak Gravitational Lensing, including tools for image analysis, statistical processing and numerical theory predictions. The package offers many useful features, including complete flexibility and easy customization of input/output formats; efficient measurements of power spectrum, PDF, Minkowski functionals and peak counts of convergence maps; survey masks; artificial noise generation engines; easy to compute parameter statistical inferences; ray tracing simulations; and many others. It requires standard numpy and scipy, and depending on tools used, may require Astropy (ascl:1304.002), emcee (ascl:1303.002), matplotlib, and mpi4py.

[ascl:1602.008]
NuCraft: Oscillation probabilities for atmospheric neutrinos calculator

NuCraft calculates oscillation probabilities for atmospheric neutrinos, taking into account matter effects and the Earth's atmosphere, and supports an arbitrary number of sterile neutrino flavors with easily configurable continuous Earth models. Continuous modeling of the Earth instead of the often-used approximation of four layers with constant density and consideration of the smearing of baseline lengths due to the variable neutrino production heights in Earth's atmosphere each lead to deviations of 10% or more for conventional neutrinos between 1 and 10 GeV.

[ascl:1602.007]
FilTER: Filament Trait-Evaluated Reconstruction

FilTER (Filament Trait-Evaluated Reconstruction) post-processes output from DisPerSE (ascl:1302.015

[ascl:1602.006]
LIRA: LInear Regression in Astronomy

LIRA (LInear Regression in Astronomy) performs Bayesian linear regression that accounts for heteroscedastic errors in both the independent and the dependent variables, intrinsic scatters (in both variables), time evolution of slopes, normalization and scatters, Malmquist and Eddington bias, and break of linearity. The posterior distribution of the regression parameters is sampled with a Gibbs method exploiting the JAGS (ascl:1209.002) library.

[ascl:1602.005]
LRGS: Linear Regression by Gibbs Sampling

LRGS (Linear Regression by Gibbs Sampling) implements a Gibbs sampler to solve the problem of multivariate linear regression with uncertainties in all measured quantities and intrinsic scatter. LRGS extends an algorithm by Kelly (2007) that used Gibbs sampling for performing linear regression in fairly general cases in two ways: generalizing the procedure for multiple response variables, and modeling the prior distribution of covariates using a Dirichlet process.

[ascl:1602.004]
DUSTYWAVE: Linear waves in gas and dust

Written in Fortran, DUSTYWAVE computes the exact solution for linear waves in a two-fluid mixture of gas and dust. The solutions are general with respect to both the dust-to-gas ratio and the amplitude of the drag coefficient.

[ascl:1602.003]
ZAP: Zurich Atmosphere Purge

ZAP (Zurich Atmosphere Purge) provides sky subtraction for integral field spectroscopy; its approach is based on principal component analysis (PCA) developed for the Multi Unit Spectrographic Explorer (MUSE) integral field spectrograph. ZAP employs filtering and data segmentation to enhance the inherent capabilities of PCA for sky subtraction. ZAP reduces sky emission residuals while robustly preserving the flux and line shapes of astronomical sources; this method works in a variety of observational situations from sparse fields with a low density of sources to filled fields in which the target source fills the field of view. With the inclusion of both of these situations the method is generally applicable to many different science cases and should also be useful for other instrumentation.

[ascl:1602.002]
pyraf-dbsp: Reduction pipeline for the Palomar Double Beam Spectrograph

pyraf-dbsp is a PyRAF-based (ascl:1207.011) reduction pipeline for optical spectra taken with the Palomar 200-inch Double Beam Spectrograph. The pipeline provides a simplified interface for basic reduction of single-object spectra with minimal overhead. It is suitable for quicklook classification of transients as well as moderate-precision (few km/s) radial velocity work.

[ascl:1602.001]
Automark: Automatic marking of marked Poisson process in astronomical high-dimensional datasets

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.

[ascl:1601.021]
ISO: Isochrone construction

ISO transforms MESA history files into a uniform basis for interpolation and then constructs new stellar evolution tracks and isochrones from that basis. It is written in Fortran and requires MESA (ascl:1010.083), primarily for interpolation. Though designed to ingest MESA star history files, tracks from other stellar evolution codes can be incorporated by loading the tracks into the data structures used in the codes.

[ascl:1601.020]
ProC: Process Coordinator

Hovest, Wolfgang; Knoche, Jörg; Hell, Reinhard; Doerl, Uwe; Riller, Thomas; Matthai, Frank; Ensslin, Torsten; Rachen, Jörg; Robbers, Georg; Adorf, Hans-Martin; Reinecke, Martin; Bartelmann, Matthias

ProC (short for Process Coordinator) is a versatile workflow engine that allows the user to build, run and manage workflows with just a few clicks. It automatically documents every processing step, making every modification to data reproducible. ProC provides a graphical user interface for constructing complex data processing workflows out of a given set of computer programs. The user can, for example, specify that only data products which are affected by a change in the input data are updated selectively, avoiding unnecessary computations. The ProC suite is flexible and satisfies basic needs of data processing centers that have to be able to restructure their data processing along with the development of a project.

[ascl:1601.019]
WzBinned: Binned and uncorrelated estimates of dark energy EOS extractor

WzBinned extracts binned and uncorrelated estimates of dark energy equation of state w(z) using Type Ia supernovae Hubble diagram and other cosmological probes and priors. It can handle an arbitrary number of input distance modulus data (entered as an input file SNdata.dat) and various existing cosmological information.

[ascl:1601.018]
MATPHOT: Stellar photometry and astrometry with discrete point spread functions

A discrete Point Spread Function (PSF) is a sampled version of a continuous two-dimensional PSF. The shape information about the photon scattering pattern of a discrete PSF is typically encoded using a numerical table (matrix) or a FITS image file. MATPHOT shifts discrete PSFs within an observational model using a 21-pixel- wide damped sinc function and position partial derivatives are computed using a five-point numerical differentiation formula. MATPHOT achieves accurate and precise stellar photometry and astrometry of undersampled CCD observations by using supersampled discrete PSFs that are sampled two, three, or more times more finely than the observational data.

[ascl:1601.017]
BASCS: Bayesian Separation of Close Sources

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.

[ascl:1601.016]
Fit Kinematic PA: Fit the global kinematic position-angle of galaxies

Fit kinematic PA measures the global kinematic position-angle (PA) from integral field observations of a galaxy stellar or gas kinematics; the code is available in IDL and Python.

[ascl:1601.015]
QDPHOT: Quick & Dirty PHOTometry

QDPHOT is a fast CCD stellar photometry task which quickly produces CCD stellar photometry from two CCD images of a star field. It was designed to be a data mining tool for finding high-quality stellar observations in the data archives of the National Virtual Observatory. QDPHOT typically takes just a few seconds to analyze two Hubble Space Telescope WFPC2 observations of Local Group star clusters. It is also suitable for real-time data-quality analysis of CCD observations; on-the-fly instrumental color-magnitude diagrams can be produced at the telescope console during the few seconds between CCD readouts.

[ascl:1601.014]
Nulike: Neutrino telescope likelihood tools

Nulike is software for including full event-level information in likelihood calculations for neutrino telescope searches for dark matter annihilation. It includes both angular and spectral information about neutrino events as well as their total number, and can be used for single models without reference to the rest of a parameter space.

[ascl:1601.013]
ImpactModel: Black Hole Accretion Disk Impact Model

ImpactModel, written in Cython, computes the accretion disc impact spectrum at given frequencies and can compute other model quantities as a function of time.

[ascl:1601.012]
SavGolFilterCov: Savitzky Golay filter for data with error covariance

A Savitzky–Golay filter is often applied to data to smooth the data without greatly distorting the signal; however, almost all data inherently comes with noise, and the noise properties can differ from point to point. This python script improves upon the traditional Savitzky-Golay filter by accounting for error covariance in the data. The inputs and arguments are modeled after scipy.signal.savgol_filter.

[ascl:1601.011]
LACEwING: LocAting Constituent mEmbers In Nearby Groups

LACEwING (LocAting Constituent mEmbers In Nearby Groups) uses the kinematics (positions and motions) of stars to determine if they are members of one of 10 nearby young moving groups or 4 nearby open clusters within 100 parsecs. It is written for Python 2.7 and depends upon Numpy, Scipy, and Astropy (ascl:1304.002) modules. LACEwING can be used as a stand-alone code or as a module in other code. Additional python programs are present in the repository for the purpose of recalibrating the code and producing other analyses, including a traceback analysis.

[ascl:1601.010]
PARAVT: Parallel Voronoi Tessellation

PARAVT offers massive parallel computation of Voronoi tessellations (VT hereafter) in large data sets. The code is focused for astrophysical purposes where VT densities and neighbors are widely used. There are several serial Voronoi tessellation codes, however no open source and parallel implementations are available to handle the large number of particles/galaxies in current N-body simulations and sky surveys. Parallelization is implemented under MPI and VT using Qhull library. Domain decomposition take into account consistent boundary computation between tasks, and support periodic conditions. In addition, the code compute neighbors lists, Voronoi density and Voronoi cell volumes for each particle, and can compute density on a regular grid.

[ascl:1601.009]
K2fov: Field of view software for NASA's K2 mission

K2fov allows users to transform celestial coordinates into K2's pixel coordinate system for the purpose of preparing target proposals and field of view visualizations. In particular, the package, written in Python, adds the "K2onSilicon" and "K2findCampaigns" tools to the command line, allowing the visibility of targets to be checked in a user-friendly way.

[ascl:1601.008]
CosmicPy: Interactive cosmology computations

CosmicPy performs simple and interactive cosmology computations for forecasting cosmological parameters constraints; it computes tomographic and 3D Spherical Fourier-Bessel power spectra as well as Fisher matrices for galaxy clustering. Written in Python, it relies on a fast C++ implementation of Fourier-Bessel related computations, and requires NumPy, SciPy, and Matplotlib.

[ascl:1601.007]
LIRA: Low-counts Image Reconstruction and Analysis

LIRA (Low-counts Image Reconstruction and Analysis) deconvolves any unknown sky components, provides a fully Poisson 'goodness-of-fit' for any best-fit model, and quantifies uncertainties on the existence and shape of unknown sky. It does this without resorting to χ2 or rebinning, which can lose high-resolution information. It is written in R and requires the FITSio package.

[ascl:1601.006]
SAGE: Semi-Analytic Galaxy Evolution

Croton, Darren J.; Stevens, Adam R. H.; Tonini, Chiara; Garel, Thibault; Bernyk, Maksym; Bibiano, Antonio; Hodkinson, Luke; Mutch, Simon J.; Poole, Gregory B.; Shattow, Genevieve M.

SAGE (Semi-Analytic Galaxy Evolution) models galaxy formation in a cosmological context. SAGE has been rebuilt to be modular and customizable. The model runs on any dark matter cosmological N-body simulation whose trees are organized in a supported format and contain a minimum set of basic halo properties.

[ascl:1601.005]
ctools: Cherenkov Telescope Science Analysis Software

Knödlseder, Jürgen; Mayer, Michael; Deil, Christoph; Buehler, Rolf; Bregeon, Johan; Martin, Pierrick

ctools provides tools for the scientific analysis of Cherenkov Telescope Array (CTA) data. Analysis of data from existing Imaging Air Cherenkov Telescopes (such as H.E.S.S., MAGIC or VERITAS) is also supported, provided that the data and response functions are available in the format defined for CTA. ctools comprises a set of ftools-like binary executables with a command-line interface allowing for interactive step-wise data analysis. A Python module allows control of all executables, and the creation of shell or Python scripts and pipelines is supported. ctools provides cscripts, which are Python scripts complementing the binary executables. Extensions of the ctools package by user defined binary executables or Python scripts is supported. ctools are based on GammaLib (ascl:1110.007).

[ascl:1601.004]
Odyssey: Ray tracing and radiative transfer in Kerr spacetime

Odyssey is a GPU-based General Relativistic Radiative Transfer (GRRT) code for computing images and/or spectra in Kerr metric describing the spacetime around a rotating black hole. Odyssey is implemented in CUDA C/C++. For flexibility, the namespace structure in C++ is used for different tasks; the two default tasks presented in the source code are the redshift of a Keplerian disk and the image of a Keplerian rotating shell at 340GHz. Odyssey_Edu, an educational software package for visualizing the ray trajectories in the Kerr spacetime that uses Odyssey, is also available.

[ascl:1601.003]
SCOUSE: Semi-automated multi-COmponent Universal Spectral-line fitting Engine

Henshaw, J. D.; Longmore, S. N.; Kruijssen, J. M. D.; Davies, B.; Bally, J.; Barnes, A.; Battersby, C.; Burton, M.; Cunningham, M. R.; Dale, J. E.; Ginsburg, A.; Immer, K.; Jones, P. A.; Kendrew, S.; Mills, E. A. C.; Molinari, S.; Moore, T. J. T.; Ott, J.; Pillai, T.; Rathborne, J.; Schilke, P.; Schmiedeke, A.; Testi, L.; Walker, D.; Walsh, A.; Zhang, Q.

The Semi-automated multi-COmponent Universal Spectral-line fitting Engine (SCOUSE) is a spectral line fitting algorithm that fits Gaussian files to spectral line emission. It identifies the spatial area over which to fit the data and generates a grid of spectral averaging areas (SAAs). The spatially averaged spectra are fitted according to user-provided tolerance levels, and the best fit is selected using the Akaike Information Criterion, which weights the chisq of a best-fitting solution according to the number of free-parameters. A more detailed inspection of the spectra can be performed to improve the fit through an iterative process, after which SCOUSE integrates the new solutions into the solution file.

[ascl:1601.002]
Hyper-Fit: Fitting routines for multidimensional data with multivariate Gaussian uncertainties

The R package Hyper-Fit fits hyperplanes (hyper.fit) and creates 2D/3D visualizations (hyper.plot2d / hyper.plot3d) to produce robust 1D linear fits for 2D x vs y type data, and robust 2D plane fits to 3D x vs y vs z type data. This hyperplane fitting works generically for any N-1 hyperplane model being fit to a N dimensional dataset. All fits include intrinsic scatter in the generative model orthogonal to the hyperplane. A web interface for online fitting is also available at http://hyperfit.icrar.org.

[ascl:1601.001]
TRADES: TRAnsits and Dynamics of Exoplanetary Systems

TRADES (TRAnsits and Dynamics of Exoplanetary Systems) simultaneously fits observed radial velocities and transit times data to determine the orbital parameters of exoplanetary systems from observational data. It uses a dynamical simulator for N-body systems that also fits the available data during the orbital integration and determines the best combination of the orbital parameters using grid search, χ2 minimization, genetic algorithms, particle swarm optimization, and bootstrap analysis.

[ascl:1512.020]
TACT: The Action Computation Tool

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.

[ascl:1512.019]
UPSILoN: AUtomated Classification of Periodic Variable Stars using MachIne LearNing

UPSILoN (AUtomated Classification of Periodic Variable Stars using MachIne LearNing) classifies periodic variable stars such as Delta Scuti stars, RR Lyraes, Cepheids, Type II Cepheids, eclipsing binaries, and long-period variables (i.e. superclasses), and their subclasses (e.g. RR Lyrae ab, c, d, and e types) using well-sampled light curves from any astronomical time-series surveys in optical bands regardless of their survey-specific characteristics such as color, magnitude, and sampling rate. UPSILoN consists of two parts, one which extracts variability features from a light curve, and another which classifies a light curve, and returns extracted features, a predicted class, and a class probability. In principle, UPSILoN can classify any light curves having arbitrary number of data points, but using light curves with more than ~80 data points provides the best classification quality.

[ascl:1512.018]
growl: Growth factor and growth rate of expanding universes

Growl calculates the linear growth factor Da and its logarithmic derivative dln D/dln a in expanding Friedmann-Robertson-Walker universes with arbitrary matter and vacuum densities. It permits rapid and stable numerical evaluation.

[ascl:1512.017]
FFTLog: Fast Fourier or Hankel transform

FFTLog is a set of Fortran subroutines that compute the fast Fourier or Hankel (= Fourier-Bessel) transform of a periodic sequence of logarithmically spaced points. FFTLog can be regarded as a natural analogue to the standard Fast Fourier Transform (FFT), in the sense that, just as the normal FFT gives the exact (to machine precision) Fourier transform of a linearly spaced periodic sequence, so also FFTLog gives the exact Fourier or Hankel transform, of arbitrary order m, of a logarithmically spaced periodic sequence.

[ascl:1512.016]
ZeldovichRecon: Halo correlation function using the Zeldovich approximation

ZeldovichRecon computes the halo correlation function using the Zeldovich approximation. It includes 3 variants:

- zelrecon.cpp, which computes the various contributions to the correlation function;

- zelrecon_ctypes.cpp, which is designed to be called from Python using the ctypes library; and

- a version which implements the "ZEFT" formalism of "A Lagrangian effective field theory" [arxiv:1506.05264] including the alpha term described in that paper.

[ascl:1512.015]
Spirality: Spiral arm pitch angle measurement

Shields, Douglas W.; Boe, Benjamin; Pfountz, Casey; Davis, Benjamin L.; Hartley, Matthew; Pour Imani, Hamed; Slade, Zac; Kennefick, Daniel; Kennefick, Julia

Spirality measures spiral arm pitch angles by fitting galaxy images to spiral templates of known pitch. Written in MATLAB, the code package also includes GenSpiral, which produces FITS images of synthetic spirals, and SpiralArmCount, which uses a one-dimensional Fast Fourier Transform to count the spiral arms of a galaxy after its pitch is determined.

[ascl:1512.014]
TM: Torus Mapper

TM (Torus Mapper) produces models for orbits in action-angle coordinates in axisymmetric potentials using torus mapping, a non-perturbative technique for creating orbital tori for specified values of the action integrals. It can compute a star's position at any time given an orbital torus and a star’s position at a reference time, and also provides a way to choose initial conditions for N-body simulations of realistic disc galaxies that start in perfect equilibrium. TM provides some advantages over use of a standard time-stepper to create orbits.

[ascl:1512.013]
CounterPoint: Zeeman-split absorption lines

CounterPoint works in concert with MoogStokes (ascl:1308.018). It applies the Zeeman effect to the atomic lines in the region of study, splitting them into the correct number of Zeeman components and adjusting their relative intensities according to the predictions of Quantum Mechanics, and finally creates a Moog-readable line list for use with MoogStokes. CounterPoint has the ability to use VALD and HITRAN line databases for both atomic and molecular lines.

[ascl:1512.012]
DiffuseModel: Modeling the diffuse ultraviolet background

DiffuseModel calculates the scattered radiation from dust scattering in the Milky Way based on stars from the Hipparcos catalog. It uses Monte Carlo to implement multiple scattering and assumes a user-supplied grid for the dust distribution. The output is a FITS file with the diffuse light over the Galaxy. It is intended for use in the UV (900 - 3000 A) but may be modified for use in other wavelengths and galaxies.

[ascl:1512.011]
ExoData: Open Exoplanet Catalogue exploration and analysis tool

ExoData is a python interface for accessing and exploring the Open Exoplanet Catalogue. It allows searching of planets (including alternate names) and easy navigation of hierarchy, parses spectral types and fills in missing parameters based on programmable specifications, and provides easy reference of planet parameters such as GJ1214b.ra, GJ1214b.T, and GJ1214b.R. It calculates values such as transit duration, can easily rescale units, and can be used as an input catalog for large scale simulation and analysis of planets.

[ascl:1512.010]
CubeIndexer: Indexer for regions of interest in data cubes

Chilean Virtual Observatory; Araya, Mauricio; Candia, Gabriel; Gregorio, Rodrigo; Mendoza, Marcelo; Solar, Mauricio

CubeIndexer indexes regions of interest (ROIs) in data cubes reducing the necessary storage space. The software can process data cubes containing megabytes of data in fractions of a second without human supervision, thus allowing it to be incorporated into a production line for displaying objects in a virtual observatory. The software forms part of the Chilean Virtual Observatory (ChiVO) and provides the capability of content-based searches on data cubes to the astronomical community.

[ascl:1512.009]
DRACULA: Dimensionality Reduction And Clustering for Unsupervised Learning in Astronomy

Aguena, Michel; Busti, Vinicius C.; Camacho, Hugo; Sasdelli, Michele; Ishida, Emille E. O.; Vilalta, Ricardo; Trindade, Arlindo M. M.; Gieseke, Fabien; de Souza, Rafael S.; Fantaye, Yabebal T.; Mazzali, Paolo A.

DRACULA classifies objects using dimensionality reduction and clustering. The code has an easy interface and can be applied to separate several types of objects. It is based on tools developed in scikit-learn, with some usage requiring also the H2O package.

[ascl:1512.008]
Bisous model: Detecting filamentary pattern in point processes

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.

[ascl:1512.007]
AstroBlend: Visualization package for use with Blender

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.

[ascl:1512.006]
GPC: General Polygon Clipper library

The University of Manchester GPC library is a flexible and highly robust polygon set operations library for use with C, C#, Delphi, Java, Perl, Python, Haskell, Lua, VB.Net and other applications. It supports difference, intersection, exclusive-or and union clip operations, and polygons may be comprised of multiple disjoint contours. Contour vertices may be given in any order - clockwise or anticlockwise, and contours may be convex, concave or self-intersecting, and may be nested (i.e. polygons may have holes). Output may take the form of either polygon contours or tristrips, and hole and external contours are differentiated in the result. GPC is free for non-profit and educational use; a Commercial Use License is required for commercial use.

[ascl:1512.005]
ALFA: Automated Line Fitting Algorithm

ALFA fits emission line spectra of arbitrary wavelength coverage and resolution, fully automatically. It uses a catalog of lines which may be present to construct synthetic spectra, the parameters of which are then optimized by means of a genetic algorithm. Uncertainties are estimated using the noise structure of the residuals. An emission line spectrum containing several hundred lines can be fitted in a few seconds using a single processor of a typical contemporary desktop or laptop PC. Data cubes in FITS format can be analysed using multiple processors, and an analysis of tens of thousands of deep spectra obtained with instruments such as MUSE will take a few hours.

[ascl:1512.004]
EDRSX: Extensions to the EDRS package

EDRSX extends the Electronography Data Reduction System (EDRS, ascl:1512.0030). It makes more versatile analysis of IRAS images than was otherwise available possible. EDRSX provides facilities for converting images into and out of EDRS format, accesses RA and DEC information stored with IRAS images, and performs several standard image processing operations such as displaying image histograms and statistics, and Fourier transforms. This enables such operations to be performed as estimation and subtraction of non-linear backgrounds, de-striping of IRAS images, modelling of image features, and easy aligning of separate images, among others.

[ascl:1512.003]
EDRS: Electronography Data Reduction System

The Electronography Data Reduction System (EDRS) reduces and analyzes large format astronomical images and was written to be used from within ASPIC (ascl:1510.006). In its original form it specialized in the reduction of electronographic data but was built around a set of utility programs which were widely applicable to astronomical images from other sources. The programs align and calibrate images, handle lists of (X,Y) positions, apply linear geometrical transformations and do some stellar photometry. This package is now obsolete.

[ascl:1512.002]
GetData: A filesystem-based, column-oriented database format for time-ordered binary data

The GetData Project is the reference implementation of the Dirfile Standards, a filesystem-based, column-oriented database format for time-ordered binary data. Dirfiles provide a fast, simple format for storing and reading data, suitable for both quicklook and analysis pipelines. GetData provides a C API and bindings exist for various other languages. GetData is distributed under the terms of the GNU Lesser General Public License.

[ascl:1512.001]
IRACpm: Distortion correction for IRAC astrometric data

The IRACpm R package applies a 7-8 order distortion correction to IRAC astrometric data from the Spitzer Space Telescope and includes a function for measuring apparent proper motions between different Epochs. These corrections are applicable only to positions measured by APEX; cryogenic images benefit from a correction for varying intra-pixel sensitivity prior to the application of the distortion.

[ascl:1511.023]
PromptNuFlux: Prompt atmospheric neutrino flux calculator

PromptNuFlux computes the prompt atmospheric neutrino flux E3Φ(GeV2/(cm2ssr)), including the total associated theory uncertainty, for a range of energies between E=103 GeV and E=107.5 GeV. Results are available for five different parametrizations of the input cosmic ray flux: BPL, H3P, H3A, H14a, H14b.

[ascl:1511.022]
ZInCo: Zoomed Initial Conditions

ZInCo manipulates existing initial conditions (ICs) compatible with GADGET-2/3 (ascl:0003.001) ICs, allowing different flavors of zoom-in simulations rather then producing new ICs from scratch. The code can manipulate initial conditions with multiple types of particles, unlike the vast majority of zoom-in ICs codes available, preserving their properties and random field. This allows ZInCo to take advantage of other codes that produce ICs featuring a broad range of different cosmologies; it can be used also on existing ICs even in the unlikely case nothing is known about their properties. The code is written in C++ and parallelized using MPI.

[ascl:1511.021]
EPIC: E-field Parallel Imaging Correlator

E-field Parallel Imaging Correlator (EPIC), a highly parallelized Object Oriented Python package, implements the Modular Optimal Frequency Fourier (MOFF) imaging technique. It also includes visibility-based imaging using the software holography technique and a simulator for generating electric fields from a sky model. EPIC can accept dual-polarization inputs and produce images of all four instrumental cross-polarizations.

[ascl:1511.020]
Mercury-T: Tidally evolving multi-planet systems code

Mercury-T calculates the evolution of semi-major axis, eccentricity, inclination, rotation period and obliquity of the planets as well as the rotation period evolution of the host body; it is based on the N-body code Mercury (Chambers 1999, ascl:1201.008). It is flexible, allowing computation of the tidal evolution of systems orbiting any non-evolving object (if its mass, radius, dissipation factor and rotation period are known), but also evolving brown dwarfs (BDs) of mass between 0.01 and 0.08 M⊙, an evolving M-dwarf of 0.1 M⊙, an evolving Sun-like star, and an evolving Jupiter.

[ascl:1511.019]
CosmoBolognaLib: Open source C++ libraries for cosmological calculations

CosmoBolognaLib contains numerical libraries for cosmological calculations; written in C++, it is intended to define a common numerical environment for cosmological investigations of the large-scale structure of the Universe. The software aids in handling real and simulated astronomical catalogs by measuring one-point, two-point and three-point statistics in configuration space and performing cosmological analyses. These open source libraries can be included in either C++ or Python codes.

[ascl:1511.018]
LDC3: Three-parameter limb darkening coefficient sampling

LDC3 samples physically permissible limb darkening coefficients for the Sing et al. (2009) three-parameter law. It defines the physically permissible intensity profile as being everywhere-positive, monotonically decreasing from center to limb and having a curl at the limb. The approximate sampling method is analytic and thus very fast, reproducing physically permissible samples in 97.3% of random draws (high validity) and encompassing 94.4% of the physically permissible parameter volume (high completeness).

[ascl:1511.017]
DES exposure checker: Dark Energy Survey image quality control crowdsourcer

DES exposure checker renders science-grade images directly to a web browser and allows users to mark problematic features from a set of predefined classes, thus allowing image quality control for the Dark Energy Survey to be crowdsourced through its web application. Users can also generate custom labels to help identify previously unknown problem classes; generated reports are fed back to hardware and software experts to help mitigate and eliminate recognized issues. These problem reports allow rapid correction of artifacts that otherwise may be too subtle or infrequent to be recognized.

[ascl:1511.016]
JKTLD: Limb darkening coefficients

JKTLD outputs theoretically-calculated limb darkening (LD) strengths for equations (LD laws) which predict the amount of LD as a function of the part of the star being observed. The coefficients of these laws are obtained by bilinear interpolation (in effective temperature and surface gravity) in published tables of coefficients calculated from stellar model atmospheres by several researchers. Many observations of stars require the strength of limb darkening (LD) to be estimated, which can be done using theoretical models of stellar atmospheres; JKTLD can help in these circumstances.

[ascl:1511.015]
George: Gaussian Process regression

George is a fast and flexible library, implemented in C++ with Python bindings, for Gaussian Process regression useful for accounting for correlated noise in astronomical datasets, including those for transiting exoplanet discovery and characterization and stellar population modeling.

[ascl:1511.014]
HumVI: Human Viewable Image creation

HumVI creates a composite color image from sets of input FITS files, following the Lupton et al (2004, ascl:1511.013) composition algorithm. Written in Python, it takes three FITS files as input and returns a color composite, color-saturated png image with an arcsinh stretch. HumVI reads the zero points out of the FITS headers and uses them to put all the images on the same flux scale; photometrically calibrated images produce the best results.

[ascl:1511.013]
CCDtoRGB: RGB image production from three-band astronomical images

Lupton, Robert; Blanton, Michael R.; Fekete, George; Hogg, David W.; O'Mullane, Wil; Szalay, Alex; Wherry, Nicholas

CCDtoRGB produces red‐green‐blue (RGB) composites from three‐band astronomical images, ensuring an object with a specified astronomical color has a unique color in the RGB image rather than burnt‐out white stars. Use of an arcsinh stretch shows faint objects while simultaneously preserving the structure of brighter objects in the field, such as the spiral arms of large galaxies.

[ascl:1511.012]
milkywayproject_triggering: Correlation functions for two catalog datasets

This triggering code calculates the correlation function between two astrophysical data catalogs using the Landy-Szalay approximator generalized for heterogeneous datasets (Landy & Szalay, 1993; Bradshaw et al, 2011) or the auto-correlation function of one dataset. It assumes that one catalog has positional information as well as an object size (effective radius), and the other only positional information.

[ascl:1511.011]
SparsePZ: Sparse Representation of Photometric Redshift PDFs

SparsePZ uses sparse basis representation to fully represent individual photometric redshift probability density functions (PDFs). This approach requires approximately half the parameters for the same multi-Gaussian fitting accuracy, and has the additional advantage that an entire PDF can be stored by using a 4-byte integer per basis function. Only 10-20 points per galaxy are needed to reconstruct both the individual PDFs and the ensemble redshift distribution, N(z), to an accuracy of 99.9 per cent when compared to the one built using the original PDFs computed with a resolution of δz = 0.01, reducing the required storage of 200 original values by a factor of 10-20. This basis representation can be directly extended to a cosmological analysis, thereby increasing computational performance without losing resolution or accuracy.

[ascl:1511.010]
Galileon-Solver: N-body code

Galileon-Solver adds an extra force to PMCode (ascl:9909.001) using a modified Poisson equation to provide a non-linearly transformed density field, with the operations all performed in real space. The code's implicit spherical top-hat assumption only works over fairly long distance averaging scales, where the coarse-grained picture it relies on is a good approximation of reality; it uses discrete Fourier transforms and cyclic reduction in the usual way.

[ascl:1511.009]
Pangloss: Reconstructing lensing mass

Pangloss reconstructs all the mass within a light cone through the Universe. Understanding complex mass distributions like this is important for accurate time delay lens cosmography, and also for accurate lens magnification estimation. It aspires to use all available data in an attempt to make the best of all mass maps.

[ascl:1511.008]
MCAL: M dwarf metallicity and temperature calculator

MCAL calculates high precision metallicities and effective temperatures for M dwarfs; the method behaves properly down to R = 40 000 and S/N = 25, and results were validated against a sample of stars in common with SOPHIE high resolution spectra.

[ascl:1511.007]
MHF: MLAPM Halo Finder

MHF is a Dark Matter halo finder that is based on the refinement grids of MLAPM. The grid structure of MLAPM adaptively refines around high-density regions with an automated refinement algorithm, thus naturally "surrounding" the Dark Matter halos, as they are simply manifestations of over-densities within (and exterior) to the underlying host halo. Using this grid structure, MHF restructures the hierarchy of nested isolated MLAPM grids into a "grid tree". The densest cell in the end of a tree branch marks center of a prospective Dark Matter halo. All gravitationally bound particles about this center are collected to obtain the final halo catalog. MHF automatically finds halos within halos within halos.

[ascl:1511.006]
T-Matrix: Codes for Computing Electromagnetic Scattering by Nonspherical and Aggregated Particles

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.

[ascl:1511.005]
pyhrs: Spectroscopic data reduction package for SALT

The pyhrs package reduces data from the High Resolution Spectrograph (HRS) on the Southern African Large Telescope (SALT). HRS is a dual-beam, fiber fed echelle spectrectrograph with four modes of operation: low (R~16000), medium (R~34000), high (R~65000), and high stability (R~65000). pyhrs, written in Python, includes all of the steps necessary to reduce HRS low, medium, and high resolution data; this includes basic CCD reductions, order identification, wavelength calibration, and extraction of the spectra.

[ascl:1511.004]
Xgremlin: Interferograms and spectra from Fourier transform spectrometers analysis

Xgremlin is a hardware and operating system independent version of the data analysis program Gremlin used for Fourier transform spectrometry. Xgremlin runs on PCs and workstations that use the X11 window system, including cygwin in Windows. It is used to Fourier transform interferograms, plot spectra, perform phase corrections, perform intensity and wavenumber calibration, and find and fit spectral lines. It can also be used to construct synthetic spectra, subtract continua, compare several different spectra, and eliminate ringing around lines.

[ascl:1511.003]
SkyView Virtual Telescope

The SkyView Virtual telescope provides access to survey datasets ranging from radio through the gamma-ray regimes. Over 100 survey datasets are currently available. The SkyView library referenced here is used as the basis for the SkyView web site (at http://skvyiew.gsfc.nasa.gov) but is designed for individual use by researchers as well.

SkyView's approach to access surveys is distinct from most other toolkits. Rather than providing links to the original data, SkyView attempts to immediately re-render the source data in the user-requested reference frame, projection, scaling, orientation, etc. The library includes a set of geometry transformation and mosaicking tools that may be integrated into other applications independent of SkyView.

[ascl:1511.002]
JSPAM: Interacting galaxies modeller

JSPAM models galaxy collisions using a restricted n-body approach to speed up computation. Instead of using a softened point-mass potential, the software supports a modified version of the three component potential created by Hernquist (1994, ApJS 86, 389). Although spherically symmetric gravitationally potentials and a Gaussian model for the bulge are used to increase computational efficiency, the potential mimics that of a fully consistent n-body model of a galaxy. Dynamical friction has been implemented in the code to improve the accuracy of close approaches between galaxies. Simulations using this code using thousands of particles over the typical interaction times of a galaxy interaction take a few seconds on modern desktop workstations, making it ideal for rapidly prototyping the dynamics of colliding galaxies. Extensive testing of the code has shown that it produces nearly identical tidal features to those from hierarchical tree codes such as Gadget but using a fraction of the computational resources. This code was used in the Galaxy Zoo: Mergers project and is very well suited for automated fitting of galaxy mergers with automated pattern fitting approaches such as genetic algorithms. Java and Fortran versions of the code are available.

[ascl:1511.001]
SuperFreq: Numerical determination of fundamental frequencies of an orbit

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.

[ascl:1510.007]
ccdproc: CCD data reduction software

Craig, M. W.; Crawford, S. M.; Deil, Christoph; Gomez, Carlos; Günther, Hans Moritz; Heidt, Nathan; Horton, Anthony; Karr, Jennifer; Nelson, Stefan; Ninan, Joe Phillip; Pattnaik, Punyaslok; Rol, Evert; Schoenell, William; Seifert, Michael; Singh, Sourav; Sipocz, Brigitta; Stotts, Connor; Streicher, Ole; Tollerud, Erik; Walker, Nathan; ccdproc contributors

Ccdproc is an affiliated package for the AstroPy package for basic data reductions of CCD images. The ccdproc package provides many of the necessary tools for processing of ccd images built on a framework to provide error propagation and bad pixel tracking throughout the reduction process.

[submitted]
Xsmurf - Measuring multifractal properties with the continuous wavelet transform modulus maxima (WTMM) method

Xsmurf is a software package written in C/Tcl/Tk that implements the continuous wavelet transform modulus maxima method, an image processing tool for measuring fractal and multifractal properties in experimental and simulation data.

Multifractal analysis is described in the following page: http://www.scholarpedia.org/article/Wavelet-based_multifractal_analysis

Xsmurf has been used in multiple applications in astrophysics, e.g. :

- analysis of solar magnetograms for characterizing complexity of evolving regions

- fractal/multifractal nature and anisotropic structure of Galactic atomic hydrogen (H I)

- analysis of simulation data (velocity field, ...) of turbulent flow

[ascl:1510.006]
ASPIC: STARLINK image processing package

Davenhall, A. C.; Hartley, Ken F.; Penny, Alan J.; Kelly, B. D.; King, Dave J.; Lupton, W. F.; Tudhope, D.; Pike, C. D.; Cooke, J. A.; Pence, W. D.; Wallace, Patrick T.; Brownrigg, D. R. K.; Baines, Dave W. T.; Warren-Smith, Rodney F.; McNally, B. V.; Bell, L. L.; Jones, T. A.; Terrett, Dave L.; Pearce, D. J.; Carey, J. V.; Currie, Malcolm J.; Benn, Chris; Beard, S. M.; Giddings, Jack R.; Balona, Luis A.; Harrison, B.; Wood, Roger; Sparkes, Bill; Allan, Peter M.; Berry, David S.; Shirt, J. V.

ASPIC handled basic astronomical image processing. Early releases concentrated on image arithmetic, standard filters, expansion/contraction/selection/combination of images, and displaying and manipulating images on the ARGS and other devices. Later releases added new astronomy-specific applications to this sound framework. The ASPIC collection of about 400 image-processing programs was written using the Starlink "interim" environment in the 1980; the software is now obsolete.

[ascl:1510.005]
GALFORM: Galactic modeling

GALFORM is a semi-analytic model for calculating the formation and evolution of galaxies in hierarchical clustering cosmologies. Using a Monte Carlo algorithm to follow the merging evolution of dark matter haloes with arbitrary mass resolution, it incorporates realistic descriptions of the density profiles of dark matter haloes and the gas they contain. It follows the chemical evolution of gas and stars, and the associated production of dust and includes a detailed calculation of the sizes of discs and spheroids.

[ascl:1510.004]
DEBiL: Detached Eclipsing Binary Light curve fitter

DEBiL rapidly fits a large number of light curves to a simple model. It is the central component of a pipeline for systematically identifying and analyzing eclipsing binaries within a large dataset of light curves; the results of DEBiL can be used to flag light curves of interest for follow-up analysis.

[ascl:1510.003]
PyLDTk: Python toolkit for calculating stellar limb darkening profiles and model-specific coefficients for arbitrary filters

PyLDTk automates the calculation of custom stellar limb darkening (LD) profiles and model-specific limb darkening coefficients (LDC) using the library of PHOENIX-generated specific intensity spectra by Husser et al. (2013). It facilitates exoplanet transit light curve modeling, especially transmission spectroscopy where the modeling is carried out for custom narrow passbands. PyLDTk construct model-specific priors on the limb darkening coefficients prior to the transit light curve modeling. It can also be directly integrated into the log posterior computation of any pre-existing transit modeling code with minimal modifications to constrain the LD model parameter space directly by the LD profile, allowing for the marginalization over the whole parameter space that can explain the profile without the need to approximate this constraint by a prior distribution. This is useful when using a high-order limb darkening model where the coefficients are often correlated, and the priors estimated from the tabulated values usually fail to include these correlations.

[ascl:1510.002]
batman: BAsic Transit Model cAlculatioN in Python

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.

[ascl:1510.001]
GGADT: Generalized Geometry Anomalous Diffraction Theory

GGADT uses anomalous diffraction theory (ADT) to compute the differential scattering cross section (or the total cross sections as a function of energy) for a specified grain of arbitrary geometry (natively supports spheres, ellipsoids, and clusters of spherical monomers). It is written in Fortran 95. ADT is valid when the grain is large compared to the wavelength of incident light. GGADT can calculate either the integrated cross sections (absorption, scattering, extinction) as a function of energy, or it can calculate the differential scattering cross section as a function of scattering angle.

[ascl:1509.010]
PyCS : Python Curve Shifting

PyCS is a software toolbox to estimate time delays between multiple images of strongly lensed quasars, from resolved light curves such as obtained by the COSMOGRAIL monitoring program. The pycs package defines a collection of classes and high level functions, that you can script in a flexible way. PyCS makes it easy to compare different point estimators (including your own) without much code integration. The package heavily depends on numpy, scipy, and matplotlib.

[ascl:1509.009]
OPERA: Objective Prism Enhanced Reduction Algorithms

OPERA (Objective Prism Enhanced Reduction Algorithms) automatically analyzes astronomical images using the objective-prism (OP) technique to register thousands of low resolution spectra in large areas. It detects objects in an image, extracts one-dimensional spectra, and identifies the emission line feature. The main advantages of this method are: 1) to avoid subjectivity inherent to visual inspection used in past studies; and 2) the ability to obtain physical parameters without follow-up spectroscopy.

[ascl:1509.008]
GFARGO: FARGO for GPU

GFARGO is a GPU version of FARGO (ascl:1102.017). It is written in C and C for CUDA and runs only on NVIDIA’s graphics cards. Though it corresponds to the standard, isothermal version of FARGO, not all functionalities of the CPU version have been translated to CUDA. The code is available in single and double precision versions, the latter compatible with FERMI architectures. GFARGO can run on a graphics card connected to the display, allowing the user to see in real time how the fields evolve.

[ascl:1509.007]
pycola: N-body COLA method code

pycola is a multithreaded Python/Cython N-body code, implementing the Comoving Lagrangian Acceleration (COLA) method in the temporal and spatial domains, which trades accuracy at small-scales to gain computational speed without sacrificing accuracy at large scales. This is especially useful for cheaply generating large ensembles of accurate mock halo catalogs required to study galaxy clustering and weak lensing. The COLA method achieves its speed by calculating the large-scale dynamics exactly using LPT while letting the N-body code solve for the small scales, without requiring it to capture exactly the internal dynamics of halos.

[ascl:1509.006]
FARGO3D: Hydrodynamics/magnetohydrodynamics code

A successor of FARGO (ascl:1102.017), FARGO3D is a versatile HD/MHD code that runs on clusters of CPUs or GPUs, with special emphasis on protoplanetary disks. FARGO3D offers Cartesian, cylindrical or spherical geometry; 1-, 2- or 3-dimensional calculations; and orbital advection (aka FARGO) for HD and MHD calculations. As in FARGO, a simple Runge-Kutta N-body solver may be used to describe the orbital evolution of embedded point-like objects. There is no need to know CUDA; users can develop new functions in C and have them translated to CUDA automatically to run on GPUs.

[ascl:1509.005]
TRUVOT: True Background Technique for the Swift UVOT Grisms

TRUVOT decontaminates Swift UVOT grism spectra for transient objects. The technique makes use of template images in a process similar to image subtraction.

[ascl:1509.004]
FalconIC: Initial conditions generator for cosmological N-body simulations in Newtonian, Relativistic and Modified theories

FalconIC generates discrete particle positions, velocities, masses and pressures based on linear Boltzmann solutions that are computed by libraries such as CLASS and CAMB. FalconIC generates these initial conditions for any species included in the selection, including Baryons, Cold Dark Matter and Dark Energy fluids. Any species can be set in Eulerian (on a fixed grid) or Lagrangian (particle motion) representation, depending on the gauge and reality chosen. That is, for relativistic initial conditions in the synchronous comoving gauge, Dark Matter can only be described in an Eulerian representation. For all other choices (Relativistic in Longitudinal gauge, Newtonian with relativistic expansion rates, Newtonian without any notion of radiation), all species can be treated in all representations. The code also computes spectra. FalconIC is useful for comparative studies on initial conditions.

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