[ascl:1502.012]
SPHGR: Smoothed-Particle Hydrodynamics Galaxy Reduction

SPHGR (Smoothed-Particle Hydrodynamics Galaxy Reduction) is a python based open-source framework for analyzing smoothed-particle hydrodynamic simulations. Its basic form can run a baryonic group finder to identify galaxies and a halo finder to identify dark matter halos; it can also assign said galaxies to their respective halos, calculate halo & galaxy global properties, and iterate through previous time steps to identify the most-massive progenitors of each halo and galaxy. Data about each individual halo and galaxy is collated and easy to access.

SPHGR supports a wide range of simulations types including N-body, full cosmological volumes, and zoom-in runs. Support for multiple SPH code outputs is provided by pyGadgetReader (ascl:1411.001), mainly Gadget (ascl:0003.001) and TIPSY (ascl:1111.015).

[ascl:1502.013]
Rabacus: Analytic Cosmological Radiative Transfer Calculations

Rabacus performs analytic radiative transfer calculations in simple geometries relevant to cosmology and astrophysics; it also contains tools to calculate cosmological quantities such as the power spectrum and mass function. With core routines written in Fortran 90 and then wrapped in Python, the execution speed is thousands of times faster than equivalent routines written in pure Python.

[ascl:1502.014]
Magnetron: Fitting bursts from magnetars

Magnetron, written in Python, decomposes magnetar bursts into a superposition of small spike-like features with a simple functional form, where the number of model components is itself part of the inference problem. Markov Chain Monte Carlo (MCMC) sampling and reversible jumps between models with different numbers of parameters are used to characterize the posterior distributions of the model parameters and the number of components per burst.

[ascl:1502.015]
Camelus: Counts of Amplified Mass Elevations from Lensing with Ultrafast Simulations

Camelus provides a prediction on weak lensing peak counts from input cosmological parameters. Written in C, it samples halos from a mass function and assigns a profile, carries out ray-tracing simulations, and then counts peaks from ray-tracing maps. The creation of the ray-tracing simulations requires less computing time than N-body runs and the results is in good agreement with full N-body simulations.

[ascl:1502.016]
libnova: Celestial mechanics, astrometry and astrodynamics library

libnova is a general purpose, double precision, celestial mechanics, astrometry and astrodynamics library. Among many other calculations, it can calculate aberration, apparent position, proper motion, planetary positions, orbit velocities and lengths, angular separation of bodies, and hyperbolic motion of bodies.

[ascl:1502.017]
AMIsurvey: Calibration and imaging pipeline for radio data

AMIsurvey is a fully automated calibration and imaging pipeline for data from the AMI-LA radio observatory; it has two key dependencies. The first is drive-ami, included in this entry. Drive-ami is a Python interface to the specialized AMI-REDUCE calibration pipeline, which applies path delay corrections, automatic flags for interference, pointing errors, shadowing and hardware faults, applies phase and amplitude calibrations, Fourier transforms the data into the frequency domain, and writes out the resulting data in uvFITS format. The second is chimenea, which implements an automated imaging algorithm to convert the calibrated uvFITS into science-ready image maps. AMIsurvey links the calibration and imaging stages implemented within these packages together, configures the chimenea algorithm with parameters appropriate to data from AMI-LA, and provides a command-line interface.

[ascl:1502.018]
XFGLENSES: Gravitational lens visualizer

XFGL visualizes gravitational lenses. It has an XFORM GUI and is completely interactive with the mouse. It uses OpenGL for the simulations.

[ascl:1502.019]
XPCell: Convective plasma cells simulator

XPCell simulates convective plasma cells. The program is implemented in two versions, one using GNUPLOT and the second OpenGL. XPCell offers a GUI to introduce the parameter required by the program.

[ascl:1502.020]
ketu: Exoplanet candidate search code

ketu, written in Python, searches K2 light curves for evidence of exoplanets; the code simultaneously fits for systematic effects caused by small (few-pixel) drifts in the telescope pointing and other spacecraft issues and the transit signals of interest. Though more computationally expensive than standard search algorithms, it can be efficiently implemented and used to discover transit signals.

[ascl:1502.021]
MaLTPyNT: Quick look timing analysis for NuSTAR data

MaLTPyNT (Matteo's Libraries and Tools in Python for NuSTAR Timing) provides a quick-look timing analysis of NuSTAR data, properly treating orbital gaps and exploiting the presence of two independent detectors by using the cospectrum as a proxy for the power density spectrum. The output of the analysis is a cospectrum, or a power density spectrum, that can be fitted with XSPEC (ascl:9910.005) or ISIS (ascl:1302.002). The software also calculates time lags. Though written for NuSTAR data, MaLTPyNT can also perform standard spectral analysis on X-ray data from other satellite such as XMM-Newton and RXTE.

[ascl:1502.022]
AstroLines: Astrophysical line list generator in the H-band

AstroLines adjusts spectral line parameters (gf and damping constant) starting from an initial line list. Written in IDL and tailored to the APO Galactic Evolution Experiment (APOGEE), it runs a slightly modified version of MOOG (ascl:1202.009) to compare synthetic spectra with FTS spectra of the Sun and Arcturus.

[ascl:1502.023]
ROBOSPECT: Width fitting program

ROBOSPECT, written in C, automatically measures and deblends line equivalent widths for absorption and emission spectra. ROBOSPECT should not be used for stars with spectra in which there is no discernible continuum over large wavelength regions, nor for the most carbon-enhanced stars for which spectral synthesis would be favored. Although ROBOSPECT was designed for metal-poor stars, it is capable of fitting absorption and emission features in a variety of astronomical sources.

[ascl:1503.001]
K2flix: Kepler pixel data visualizer

K2flix makes it easy to inspect the CCD pixel data obtained by NASA's Kepler space telescope. The two-wheeled extended Kepler mission, K2, is affected by new sources of systematics, including pointing jitter and foreground asteroids, that are easier to spot by eye than by algorithm. The code takes Kepler's Target Pixel Files (TPF) as input and turns them into contrast-stretched animated gifs or MPEG-4 movies. K2flix can be used both as a command-line tool or using its Python API.

[ascl:1503.002]
Galax2d: 2D isothermal Euler equations solver

Galax2d computes the 2D stationary solution of the isothermal Euler equations of gas dynamics in a rotating galaxy with a weak bar. The gravitational potential represents a weak bar and controls the flow. A damped Newton method solves the second-order upwind discretization of the equations for a steady-state solution, using a consistent linearization and a direct solver. The code can be applied as a tool for generating flow models if used on not too fine meshes, up to 256 by 256 cells for half a disk in polar coordinates.

[ascl:1503.003]
TAME: Tool for Automatic Measurement of Equivalent-width

TAME measures the equivalent width (EWs) in high-resolution spectra. Written by IDL, TAME provides the EWs of spectral lines by profile fitting in an automatic or interactive mode and is reliable for measuring EWs in a spectrum with a spectral resolution of R ≳ 20000. It offers an interactive mode for more flexible measurement of the EW and a fully automatic mode that can simultaneously measure the EWs for a large set of lines.

[ascl:1503.004]
HELIOS-K: Opacity Calculator for Radiative Transfer

HELIOS-K is an opacity calculator for exoplanetary atmospheres. It takes a line list as an input and computes the line shapes of an arbitrary number of spectral lines (~millions to billions). HELIOS-K is capable of computing 100,000 spectral lines in 1 second; it is written in CUDA, is optimized for graphics processing units (GPUs), and can be used with the HELIOS radiative transfer code (ascl:1807.009).

[ascl:1503.005]
dust: Dust scattering and extinction in the X-ray

Written in Python, dust calculates X-ray dust scattering and extinction in the intergalactic and local interstellar media.

[ascl:1503.006]
AMADA: Analysis of Multidimensional Astronomical DAtasets

AMADA allows an iterative exploration and information retrieval of high-dimensional data sets. This is done by performing a hierarchical clustering analysis for different choices of correlation matrices and by doing a principal components analysis in the original data. Additionally, AMADA provides a set of modern visualization data-mining diagnostics. The user can switch between them using the different tabs.

[ascl:1503.007]
UniPOPS: Unified data reduction suite

Maddalena, Ronald J.; Garwood, Robert W.; Salter, Christopher J.; Stobie, Elizabeth B; Cram, Thomas R.; Morgan, Lorrie; Vance, Bob; Hudson, Jerome

UniPOPS, a suite of programs and utilities developed at the National Radio Astronomy Observatory (NRAO), reduced data from the observatory's single-dish telescopes: the Tucson 12-m, the Green Bank 140-ft, and archived data from the Green Bank 300-ft. The primary reduction programs, 'line' (for spectral-line reduction) and 'condar' (for continuum reduction), used the People-Oriented Parsing Service (POPS) as the command line interpreter. UniPOPS unified previous analysis packages and provided new capabilities; development of UniPOPS continued within the NRAO until 2004 when the 12-m was turned over to the Arizona Radio Observatory (ARO). The submitted code is version 3.5 from 2004, the last supported by the NRAO.

[ascl:1503.008]
pYSOVAR: Lightcurves analysis

The pYSOVAR code calculates properties for a stack of lightcurves, including simple descriptive statistics (mean, max, min, ...), timing (e.g. Lomb-Scargle periodograms), variability indixes (e.g. Stetson), and color properties (e.g. slope in the color-magnitude diagram). The code is written in python and is closely integrated with astropy tables. Initially, pYSOVAR was written specifically for the analysis of two clusters in the YSOVAR project, using the (not publicly released) YSOVAR database as an input. Additional functionality has been added and the code has become more general; it is now useful for other clusters in the YSOVAR dataset or for other projects that have similar data (lightcurves in one or more bands with a few hundred points for a few thousand objects), though may not work out-of-the-box for different datasets.

[ascl:1503.009]
GSD: Global Section Datafile access library

Tilanus, Remo; Meyerdierks, Horst; Jenness, Tim; Fairclough, Jon; Padman, Rachael; Redman, Russell; Cockayne, Steve

The GSD library reads data written in the James Clerk Maxwell Telescope GSD format. This format uses the General Single-Dish Data model and was used at the JCMT until 2005. The library provides an API to open GSD files and read their contents. The content of the data files is self-describing and the library can return the type and name of any component. The library is used by SPECX (ascl:1310.008), JCMTDR (ascl:1406.019) and COADD (ascl:1411.020). The SMURF (ascl:1310.007) package can convert GSD heterodyne data files to ACSIS format using this library.

[ascl:1503.010]
isochrones: Stellar model grid package

Isochrones, written in Python, simplifies common tasks often done with stellar model grids, such as simulating synthetic stellar populations, plotting evolution tracks or isochrones, or estimating the physical properties of a star given photometric and/or spectroscopic observations.

[ascl:1503.011]
VESPA: False positive probabilities calculator

Validation of Exoplanet Signals using a Probabilistic Algorithm (VESPA) calculates false positive probabilities and statistically validates transiting exoplanets. Written in Python, it uses isochrones [ascl:1503.010] and the package simpledist.

[ascl:1504.001]
UPMASK: Unsupervised Photometric Membership Assignment in Stellar Clusters

UPMASK, written in R, performs membership assignment in stellar clusters. It uses photometry and spatial positions, but can take into account other types of data. UPMASK takes into account arbitrary error models; the code is unsupervised, data-driven, physical-model-free and relies on as few assumptions as possible. The approach followed for membership assessment is based on an iterative process, principal component analysis, a clustering algorithm and a kernel density estimation.

[ascl:1504.002]
SPA: Solar Position Algorithm

The Solar Position Algorithm (SPA) calculates the solar zenith and azimuth angles in the period from the year -2000 to 6000, with uncertainties of +/- 0.0003 degrees based on the date, time, and location on Earth. SPA is implemented in C; in addition to being available for download, an online calculator using this code is available at https://www.nrel.gov/midc/solpos/spa.html.

[ascl:1504.003]
EsoRex: ESO Recipe Execution Tool

EsoRex (ESO Recipe Execution Tool) lists, configures, and executes Common Pipeline Library (CPL) (ascl:1402.010) recipes from the command line. Its features include automatically generating configuration files, recursive recipe-path searching, command line and configuration file parameters, and recipe product naming control, among many others.

[ascl:1504.004]
HOTPANTS: High Order Transform of PSF ANd Template Subtraction

HOTPANTS (High Order Transform of PSF ANd Template Subtraction) implements the Alard 1999 algorithm for image subtraction. It photometrically aligns one input image with another after they have been astrometrically aligned.

[ascl:1504.005]
chimenea: Multi-epoch radio-synthesis data imaging

Chimenea implements an heuristic algorithm for automated imaging of multi-epoch radio-synthesis data. It generates a deep image via an iterative Clean subroutine performed on the concatenated visibility set and locates steady sources in the field of view. The code then uses this information to apply constrained and then unconstrained (*i.e.*, masked/open-box) Cleans to the single-epoch observations. This obtains better results than if the single-epoch data had been processed independently without prior knowledge of the sky-model. The chimenea pipeline is built upon CASA (ascl:1107.013) subroutines, interacting with the CASA environment via the drive-casa (ascl:1504.006) interface layer.

[ascl:1504.006]
drive-casa: Python interface for CASA scripting

drive-casa provides a Python interface for scripting of CASA (ascl:1107.013) subroutines from a separate Python process, allowing for utilization alongside other Python packages which may not easily be installed into the CASA environment. This is particularly useful for embedding use of CASA subroutines within a larger pipeline. drive-casa runs plain-text casapy scripts directly; alternatively, the package includes a set of convenience routines which try to adhere to a consistent style and make it easy to chain together successive CASA reduction commands to generate a command-script programmatically.

[ascl:1504.007]
WebbPSF: James Webb Space Telescope PSF Simulation Tool

Perrin, Marshall D.; Long, Joseph; Sivaramakrishnan, Anand; Lajoie, Charles-Phillipe; Elliot, Erin; Pueyo, Laurent; Albert, Loic

WebbPSF provides a PSF simulation tool in a flexible and easy-to-use software package implemented in Python. Functionality includes support for spectroscopic modes of JWST NIRISS, MIRI, and NIRSpec, including modeling of slit losses and diffractive line spread functions.

[ascl:1504.008]
MCSpearman: Monte Carlo error analyses of Spearman's rank test

Spearman’s rank correlation test is commonly used in astronomy to discern whether a set of two variables are correlated or not. Unlike most other quantities quoted in astronomical literature, the Spearman’s rank correlation coefficient is generally quoted with no attempt to estimate the errors on its value. This code implements a number of Monte Carlo based methods to estimate the uncertainty on the Spearman’s rank correlation coefficient.

[ascl:1504.009]
Self-lensing binary code with Markov chain

The self-lensing binary code with Markov chain code was used to analyze the self-lensing binary system KOI-3278. It includes the MCMC modeling and the key figures.

[ascl:1504.010]
CosmoTransitions: Cosmological Phase Transitions

CosmoTransitions analyzes early-Universe finite-temperature phase transitions with multiple scalar fields. The code enables analysis of the phase structure of an input theory, determines the amount of supercooling at each phase transition, and finds the bubble-wall profiles of the nucleated bubbles that drive the transitions.

[ascl:1504.011]
samiDB: A Prototype Data Archive for Big Science Exploration

samiDB is an archive, database, and query engine to serve the spectra, spectral hypercubes, and high-level science products that make up the SAMI Galaxy Survey. Based on the versatile Hierarchical Data Format (HDF5), samiDB does not depend on relational database structures and hence lightens the setup and maintenance load imposed on science teams by metadata tables. The code, written in Python, covers the ingestion, querying, and exporting of data as well as the automatic setup of an HTML schema browser. samiDB serves as a maintenance-light data archive for Big Science and can be adopted and adapted by science teams that lack the means to hire professional archivists to set up the data back end for their projects.

[ascl:1504.012]
DPI: Symplectic mapping for binary star systems for the Mercury software package

DPI is a FORTRAN77 library that supplies the symplectic mapping method for binary star systems for the Mercury N-Body software package (ascl:1201.008). The binary symplectic mapping is implemented as a hybrid symplectic method that allows close encounters and collisions between massive bodies and is therefore suitable for planetary accretion simulations.

[ascl:1504.013]
kozai: Hierarchical triple systems evolution

The kozai Python package evolves hierarchical triple systems in the secular approximation. As its name implies, the kozai package is useful for studying Kozai-Lidov oscillations. The kozai package can represent and evolve hierarchical triples using either the Delaunay orbital elements or the angular momentum and eccentricity vectors. kozai contains functions to calculate the period of Kozai-Lidov oscillations and the maximum eccentricity reached; it also contains a module to study octupole order effects by averaging over individual Kozai-Lidov oscillations.

[ascl:1504.014]
abcpmc: Approximate Bayesian Computation for Population Monte-Carlo code

abcpmc is a Python Approximate Bayesian Computing (ABC) Population Monte Carlo (PMC) implementation based on Sequential Monte Carlo (SMC) with Particle Filtering techniques. It is extendable with k-nearest neighbour (KNN) or optimal local covariance matrix (OLCM) pertubation kernels and has built-in support for massively parallelized sampling on a cluster using MPI.

[ascl:1504.015]
IGMtransmission: Transmission curve computation

IGMtransmission is a Java graphical user interface that implements Monte Carlo simulations to compute the corrections to colors of high-redshift galaxies due to intergalactic attenuation based on current models of the Intergalactic Medium. The effects of absorption due to neutral hydrogen are considered, with particular attention to the stochastic effects of Lyman Limit Systems. Attenuation curves are produced, as well as colors for a wide range of filter responses and model galaxy spectra. Photometric filters are included for the Hubble Space Telescope, the Keck telescope, the Mt. Palomar 200-inch, the SUBARU telescope and UKIRT; alternative filter response curves and spectra may be readily uploaded.

[ascl:1504.016]
MRrelation: Posterior predictive mass distribution

MRrelation calculates the posterior predictive mass distribution for an individual planet. The probabilistic mass-radius relationship (M-R relation) is evaluated within a Bayesian framework, which both quantifies this intrinsic dispersion and the uncertainties on the M-R relation parameters.

[ascl:1504.017]
JWFront: Wavefronts and Light Cones for Kerr Spacetimes

JWFront visualizes wavefronts and light cones in general relativity. The interactive front-end allows users to enter the initial position values and choose the values for mass and angular momentum per unit mass. The wavefront animations are available in 2D and 3D; the light cones are visualized using the coordinate systems *(t, x, y)* or *(t, z, x)*. JWFront can be easily modified to simulate wavefronts and light cones for other spacetime by providing the Christoffel symbols in the program.

[ascl:1504.018]
D3PO: Denoising, Deconvolving, and Decomposing Photon Observations

D3PO (Denoising, Deconvolving, and Decomposing Photon Observations) addresses the inference problem of denoising, deconvolving, and decomposing photon observations. Its primary goal is the simultaneous but individual reconstruction of the diffuse and point-like photon flux given a single photon count image, where the fluxes are superimposed. A hierarchical Bayesian parameter model is used to discriminate between morphologically different signal components, yielding a diffuse and a point-like signal estimate for the photon flux components.

[ascl:1504.019]
LineProf: Line Profile Indicators

LineProf implements a series of line-profile analysis indicators and evaluates its correlation with RV data. It receives as input a list of Cross-Correlation Functions and an optional list of associated RV. It evaluates the line-profile according to the indicators and compares it with the computed RV if no associated RV is provided, or with the provided RV otherwise.

[ascl:1504.020]
BGLS: A Bayesian formalism for the generalised Lomb-Scargle periodogram

BGLS calculates the Bayesian Generalized Lomb-Scargle periodogram. It takes as input arrays with a time series, a dataset and errors on those data, and returns arrays with sampled periods and the periodogram values at those periods.

[ascl:1504.021]
SOAP 2.0: Spot Oscillation And Planet 2.0

SOAP (Spot Oscillation And Planet) 2.0 simulates the effects of dark spots and bright plages on the surface of a rotating star, computing their expected radial velocity and photometric signatures. It includes the convective blueshift and its inhibition in active regions.

[ascl:1505.001]
CALCEPH: Planetary ephemeris files access code

CALCEPH accesses binary planetary ephemeris files, including INPOPxx, JPL DExxx ,and SPICE ephemeris files. It provides a C Application Programming Interface (API) and, optionally, a Fortran 77 or 2003 interface to be called by the application. Two groups of functions enable the access to the ephemeris files, single file access functions, provided to make transition easier from the JPL functions, such as PLEPH, to this library, and many ephemeris file at the same time. Although computers have different endianess (order in which integers are stored as bytes in computer memory), CALCEPH can handles the binary ephemeris files with any endianess by automatically swaps the bytes when it performs read operations on the ephemeris file.

[ascl:1505.002]
ASteCA: Automated Stellar Cluster Analysis

ASteCA (Automated Stellar Cluster Analysis), written in Python, fully automates standard tests applied on star clusters in order to determine their characteristics, including center, radius, and stars' membership probabilities. It also determines associated intrinsic/extrinsic parameters, including metallicity, age, reddening, distance, total mass, and binarity fraction, among others.

[ascl:1505.003]
caret: Classification and Regression Training

caret (Classification And REgression Training) provides functions for training and plotting classification and regression models. It contains tools for data splitting, pre-processing, feature selection, model tuning using resampling, and variable importance estimation, as well as other functionality.

[ascl:1505.004]
KS Integration: Kelvin-Stokes integration

KS Intergration solves for mutual photometric effects produced by planets and spots allowing for analysis of planetary occultations of spots and spots regions. It proceeds by identifying integrable and non integrable arcs on the objects profiles and analytically calculates the solution exploiting the power of Kelvin-Stokes theorem. It provides the solution up to the second degree of the limb darkening law.

[ascl:1505.005]
ARoME: Analytical Rossiter-McLaughlin Effects

The ARoMe (Analytical Rossiter-McLaughlin Effects) library generates analytical Rossiter-McLaughlin (RM) effects. It models the Doppler-shift of a star during a transit measured by the fit of a cross-correlation function by a Gaussian function, fit of an observed spectrum by a modeled one, and the weighted mean.

[ascl:1505.006]
Athena3D: Flux-conservative Godunov-type algorithm for compressible magnetohydrodynamics

Written in FORTRAN, Athena3D, based on Athena (ascl:1010.014), is an implementation of a flux-conservative Godunov-type algorithm for compressible magnetohydrodynamics. Features of the Athena3D code include compressible hydrodynamics and ideal MHD in one, two or three spatial dimensions in Cartesian coordinates; adiabatic and isothermal equations of state; 1st, 2nd or 3rd order reconstruction using the characteristic variables; and numerical fluxes computed using the Roe scheme. In addition, it offers the ability to add source terms to the equations and is parallelized based on MPI.

[ascl:1505.007]
Starfish: Robust spectroscopic inference tools

Starfish is a set of tools used for spectroscopic inference. It robustly determines stellar parameters using high resolution spectral models and uses Markov Chain Monte Carlo (MCMC) to explore the full posterior probability distribution of the stellar parameters. Additional potential applications include other types of spectra, such as unresolved stellar clusters or supernovae spectra.

[ascl:1505.008]
SCEPtER: Stellar CharactEristics Pisa Estimation gRid

SCEPtER (Stellar CharactEristics Pisa Estimation gRid) estimates the stellar mass and radius given a set of observable quantities; the results are obtained by adopting a maximum likelihood technique over a grid of pre-computed stellar models. The code is quite flexible since different observables can be used, depending on their availability, as well as different grids of models.

[ascl:1505.009]
StellaR: Stellar evolution tracks and isochrones tools

stellaR accesses and manipulates publicly available stellar evolutionary tracks and isochrones from the Pisa low-mass database. It retrieves and plots the required calculations from CDS, constructs by interpolation tracks or isochrones of compositions different to the ones available in the database, constructs isochrones for age not included in the database, and extracts relevant evolutionary points from tracks or isochrones.

[ascl:1505.010]
COBS: COnstrained B-Splines

COBS (COnstrained B-Splines), written in R, creates constrained regression smoothing splines via linear programming and sparse matrices. The method has two important features: the number and location of knots for the spline fit are established using the likelihood-based Akaike Information Criterion (rather than a heuristic procedure); and fits can be made for quantiles (e.g. 25% and 75% as well as the usual 50%) in the response variable, which is valuable when the scatter is asymmetrical or non-Gaussian. This code is useful for, for example, estimating cluster ages when there is a wide spread in stellar ages at a chosen absorption, as a standard regression line does not give an effective measure of this relationship.

[ascl:1505.011]
missForest: Nonparametric missing value imputation using random forest

missForest imputes missing values particularly in the case of mixed-type data. It uses a random forest trained on the observed values of a data matrix to predict the missing values. It can be used to impute continuous and/or categorical data including complex interactions and non-linear relations. It yields an out-of-bag (OOB) imputation error estimate without the need of a test set or elaborate cross-validation and can be run in parallel to save computation time. missForest has been used to, among other things, impute variable star colors in an All-Sky Automated Survey (ASAS) dataset of variable stars with no NOMAD match.

[ascl:1505.012]
LSSGALPY: Visualization of the large-scale environment around galaxies on the 3D space

LSSGALPY provides visualization tools to compare the 3D positions of a sample (or samples) of isolated systems with respect to the locations of the large-scale structures galaxies in their local and/or large scale environments. The interactive tools use different projections in the 3D space (right ascension, declination, and redshift) to study the relation of the galaxies with the LSS. The tools permit visualization of the locations of the galaxies for different values of redshifts and redshift ranges; the relationship of isolated galaxies, isolated pairs, and isolated triplets to the galaxies in the LSS can be visualized for different values of the declinations and declination ranges.

[ascl:1505.013]
cosmoabc: Likelihood-free inference for cosmology

Ishida, Emille E. O.; Vitenti, Sandro D. P.; Penna-Lima, Mariana; Trindade, Arlindo M.; Cisewski, Jessi; de Souza, Rafael M.; Cameron, Ewan; Busti, Vinicius C.

Approximate Bayesian Computation (ABC) enables parameter inference for complex physical systems in cases where the true likelihood function is unknown, unavailable, or computationally too expensive. It relies on the forward simulation of mock data and comparison between observed and synthetic catalogs. cosmoabc is a Python Approximate Bayesian Computation (ABC) sampler featuring a Population Monte Carlo variation of the original ABC algorithm, which uses an adaptive importance sampling scheme. The code can be coupled to an external simulator to allow incorporation of arbitrary distance and prior functions. When coupled with the numcosmo library, it has been used to estimate posterior probability distributions over cosmological parameters based on measurements of galaxy clusters number counts without computing the likelihood function.

[ascl:1505.014]
FCLC: Featureless Classification of Light Curves

FCLC (Featureless Classification of Light Curves) software describes the static behavior of a light curve in a probabilistic way. Individual data points are converted to densities and consequently probability density are compared instead of features. This gives rise to an independent classification which can corroborate the usefulness of the selected features.

[ascl:1505.015]
2dfdr: Data reduction software

2dfdr is an automatic data reduction pipeline dedicated to reducing multi-fibre spectroscopy data, with current implementations for AAOmega (fed by the 2dF, KOALA-IFU, SAMI Multi-IFU or older SPIRAL front-ends), HERMES, 2dF (spectrograph), 6dF, and FMOS. A graphical user interface is provided to control data reduction and allow inspection of the reduced spectra.

[ascl:1505.016]
CUTE: Correlation Utilities and Two-point Estimation

CUTE (Correlation Utilities and Two-point Estimation) extracts any two-point statistic from enormous datasets with hundreds of millions of objects, such as large galaxy surveys. The computational time grows with the square of the number of objects to be correlated; technology provides multiple means to massively parallelize this problem and CUTE is specifically designed for these kind of calculations. Two implementations are provided: one for execution on shared-memory machines using OpenMP and one that runs on graphical processing units (GPUs) using CUDA.

[ascl:1505.017]
HALOGEN: Approximate synthetic halo catalog generator

HALOGEN generates approximate synthetic halo catalogs. Written in C, it decomposes the problem of generating cosmological tracer distributions (eg. halos) into four steps: generating an approximate density field, generating the required number of tracers from a CDF over mass, placing the tracers on field particles according to a bias scheme dependent on local density, and assigning velocities to the tracers based on velocities of local particles. It also implements a default set of four models for these steps. HALOGEN uses 2LPTic (ascl:1201.005) and CUTE (ascl:1505.016); the software is flexible and can be adapted to varying cosmologies and simulation specifications.

[ascl:1505.018]
POKER: P Of K EstimatoR

POKER (P Of K EstimatoR) estimates the angular power spectrum of a 2D map or the cross-power spectrum of two 2D maps in the flat sky limit approximation in a realistic data context: steep power spectrum, non periodic boundary conditions, arbitrary pixel resolution, non trivial masks and observation patch geometry.

[ascl:1505.019]
TFIT: Mixed-resolution data set photometry package

Laidler, Victoria G.; Papovich, Casey; Grogin, Norman A.; Idzi, Rafal; Dickinson, Mark; Ferguson, Henry C.; Hilbert, Bryan; Clubb, Kelsey; Ravindranath, Swara

TFIT measures galaxy photometry using prior knowledge of sources in a deep, high‐resolution image (HRI) to improve photometric measurements of objects in a corresponding low‐resolution image (LRI) of the same field, usually at a different wavelength. For background‐limited data, this technique produces optimally weighted photometry that maximizes signal‐to‐noise ratio (S/N). For objects not significantly detected in the low‐resolution image, it provides useful and quantitative information for setting upper limits.

This code is no longer updated and has been superseded by T-PHOT (ascl:1609.001).

[ascl:1505.020]
rvfit: Radial velocity curves fitting for binary stars or exoplanets

rvfit, developed in IDL 7.0, fits non-precessing keplerian radial velocity (RV) curves for double-line and single-line binary stars or exoplanets. It fits a simple keplerian model to the observed RV and computes the seven parameters (six for a single-line system) from the model. Some parameters can be fixed beforehand if they are known, for instance, if photometric observations are available. The fit is done using an Adaptive Simulated Annealing algorithm optimized for this specific task. Simulated Annealing methods are powerful heuristic algorithms to minimize functions in multiparametric spaces.

[ascl:1505.021]
relline: Relativistic line profiles calculation

relline calculates relativistic line profiles; it is compatible with the common X-ray data analysis software XSPEC (ascl:9910.005) and ISIS (ascl:1302.002). The two basic forms are an additive line model (RELLINE) and a convolution model to calculate relativistic smearing (RELCONV).

[ascl:1505.022]
Snoopy: General purpose spectral solver

Snoopy is a spectral 3D code that solves the MHD and Boussinesq equations, such as compressibility, particles, and Braginskii viscosity, and several other physical effects. It's useful for turbulence study involving shear and rotation. Snoopy requires the FFTW library (ascl:1201.015), and can run on parallel machine using MPI OpenMP or both at the same time.

[ascl:1505.023]
SNooPy: TypeIa supernovae analysis tools

Burns, Christopher R.; Stritzinger, Maximilian; Phillips, M. M.; Kattner, ShiAnne; Persson, S. E.; Madore, Barry F.; Freedman, Wendy L.; Boldt, Luis; Campillay, Abdo; Contreras, Carlos; Folatelli, Gaston; Gonzalez, Sergio; Krzeminski, Wojtek; Morrell, Nidia; Salgado, Francisco; Suntzeff, Nicholas B.

The SNooPy package (also known as SNpy), written in Python, contains tools for the analysis of TypeIa supernovae. It offers interactive plotting of light-curve data and models (and spectra), computation of reddening laws and K-corrections, LM non-linear least-squares fitting of light-curve data, and various types of spline fitting, including Diercx and tension. The package also includes a SNIa lightcurve template generator in the CSP passbands, estimates of Milky-Way Extinction, and a module for dealing with filters and spectra.

[ascl:1505.024]
PyTransit: Transit light curve modeling

PyTransit implements optimized versions of the Giménez and Mandel & Agol transit models for exoplanet transit light-curves. The two models are implemented natively in Fortran with OpenMP parallelization, and are accessed by an object-oriented python interface. PyTransit facilitates the analysis of photometric time series of exoplanet transits consisting of hundreds of thousands of data points, and of multipassband transit light curves from spectrophotometric observations. It offers efficient model evaluation for multicolour observations and transmission spectroscopy, built-in supersampling to account for extended exposure times, and routines to calculate the projected planet-to-star distance for circular and eccentric orbits, transit durations, and more.

[ascl:1505.025]
pyMCZ: Oxygen abundances calculations and uncertainties from strong-line flux measurements

Bianco, Federica B.; Modjaz, Maryam; Oh, Seung Man; Fierroz, David; Liu, Yuqian; Kewley, Lisa; Graur, Or

pyMCZ calculates metallicity according to a number of strong line metallicity diagnostics from spectroscopy line measurements and obtains uncertainties from the line flux errors in a Monte Carlo framework. Given line flux measurements and their uncertainties, pyMCZ produces synthetic distributions for the oxygen abundance in up to 13 metallicity scales simultaneously, as well as for E(B-V), and estimates their median values and their 68% confidence regions. The code can output the full MC distributions and their kernel density estimates.

[ascl:1505.026]
Lensed: Forward parametric modelling of strong lenses

Lensed performs forward parametric modelling of strong lenses. Using a provided model, Lensed renders the expected image of the lensing event for a large number of parameter settings, thereby exploring the space of possible realizations of the observation. It compares the expectation to the observed image by calculating the likelihood that the observation was indeed produced by the assumed model, thus reconstructing the probability distribution over the parameter space of the model. Written in C, the code uses a massively parallel ray-tracing kernel to perform the necessary calculations on a graphics processing unit (GPU), making the precise rendering of the background lensed sources fast and allowing the simultaneous optimization of tens of parameters for the selected model.

[ascl:1505.027]
BAYES-X: Bayesian inference tool for the analysis of X-ray observations of galaxy clusters

The great majority of X-ray measurements of cluster masses in the literature assume parametrized functional forms for the radial distribution of two independent cluster thermodynamic properties, such as electron density and temperature, to model the X-ray surface brightness. These radial profiles (e.g. β-model) have an amplitude normalization parameter and two or more shape parameters. BAYES-X uses a cluster model to parametrize the radial X-ray surface brightness profile and explore the constraints on both model parameters and physical parameters. Bayes-X is programmed in Fortran and uses MultiNest (ascl:1109.006) as the Bayesian inference engine.

[ascl:1505.028]
RESOLVE: Bayesian algorithm for aperture synthesis imaging in radio astronomy

RESOLVE is a Bayesian inference algorithm for image reconstruction in radio interferometry. It is optimized for extended and diffuse sources. Features include parameter-free Bayesian reconstruction of radio continuum data with a focus on extended and weak diffuse sources, reconstruction with uncertainty propagation dependent on measurement noise, and estimation of the spatial correlation structure of the radio astronomical source. RESOLVE provides full support for measurement sets and includes a simulation tool (if uv-coverage is provided).

[ascl:1505.029]
fits2hdf: FITS to HDFITS conversion

fits2hdf ports FITS files to Hierarchical Data Format (HDF5) files in the HDFITS format. HDFITS allows faster reading of data, higher compression ratios, and higher throughput. HDFITS formatted data can be presented transparently as an in-memory FITS equivalent by changing the import lines in Python-based FITS utilities. fits2hdf includes a utility to port MeasurementSets (MS) to HDF5 files.

[ascl:1505.030]
CANDID: Companion Analysis and Non-Detection in Interferometric Data

Gallenne, A.; Mérand, A.; Kervella, P.; Monnier, J. D.; Schaefer, G. H.; Baron, F.; Breitfelder, J.; Le Bouquin, J. B.; Roettenbacher, R. M.; Gieren, W.; Pietrzynski, G.; McAlister, H.; ten Brummelaar, T.; Sturmann, J.; Sturmann, L.; Turner, N.; Ridgway, S.; Kraus, S.

CANDID finds faint companion around star in interferometric data in the OIFITS format. It allows systematically searching for faint companions in OIFITS data, and if not found, estimates the detection limit. The tool is based on model fitting and Chi2 minimization, with a grid for the starting points of the companion position. It ensures all positions are explored by estimating a-posteriori if the grid is dense enough, and provides an estimate of the optimum grid density.

[ascl:1505.031]
TEA: Thermal Equilibrium Abundances

TEA (Thermal Equilibrium Abundances) calculates gaseous molecular abundances under thermochemical equilibrium conditions. Given a single T,P point or a list of T,P pairs (the thermal profile of an atmosphere) and elemental abundances, TEA calculates mole fractions of the desired molecular species. TEA uses 84 elemental species and thermodynamical data for more then 600 gaseous molecular species, and can adopt any initial elemental abundances.

[ascl:1505.032]
Planck Level-S: Planck Simulation Package

The Planck simulation package takes a cosmological model specified by the user and calculates a potential CMB sky consistent with this model, including astrophysical foregrounds, and then performs a simulated observation of this sky. This Simulation embraces many instrumental effects such as beam convolution and noise. Alternatively, the package can simulate the observation of a provided sky model, generated by another program such as the Planck Sky Model software. The Planck simulation package does not only provide Planck-like data, it can also be easily adopted to mimic the properties of other existing and upcoming CMB experiments.

[ascl:1505.033]
SNEC: SuperNova Explosion Code

SNEC (SuperNova Explosion Code) is a spherically-symmetric Lagrangian radiation-hydrodynamics code that follows supernova explosions through the envelope of their progenitor star, produces bolometric (and approximate multi-color) light curve predictions, and provides input to spectral synthesis codes for spectral modeling. SNEC's features include 1D (spherical) Lagrangian Newtonian hydrodynamics with artificial viscosity, stellar equation of state with a Saha solver ionization/recombination, equilibrium flux-limited photon diffusion with OPAL opacities and low-temperature opacities, and prediction of bolometric light curves and multi-color lightcurves (in the blackbody approximation).

[ascl:1505.034]
dStar: Neutron star thermal evolution code

dStar is a collection of modules for computing neutron star structure and evolution, and uses the numerical, utility, and equation of state libraries of MESA (ascl:1010.083).

[ascl:1506.001]
pyKLIP: PSF Subtraction for Exoplanets and Disks

Wang, Jason J.; Ruffio, Jean-Baptise; De Rosa, Robert J.; Aguilar, Jonathan; Wolff, Schuyler G.; Pueyo, Laurent

pyKLIP subtracts out the stellar PSF to search for directly-imaged exoplanets and disks using a Python implementation of the Karhunen-Loève Image Projection (KLIP) algorithm. pyKLIP supports ADI, SDI, and ADI+SDI to model the stellar PSF and offers a large array of PSF subtraction parameters to optimize the reduction. pyKLIP relies on a minimal amount of dependencies (numpy, scipy, and astropy) and parallelizes the KLIP algorithm to speed up the reduction. pyKLIP supports GPI and P1640 data and can interface with other data sources with the addition of new modules. It also can inject simulated planets and disks as well as automatically search for point sources in PSF-subtracted data.

[ascl:1506.002]
dmdd: Dark matter direct detection

The dmdd package enables simple simulation and Bayesian posterior analysis of recoil-event data from dark-matter direct-detection experiments under a wide variety of scattering theories. It enables calculation of the nuclear-recoil rates for a wide range of non-relativistic and relativistic scattering operators, including non-standard momentum-, velocity-, and spin-dependent rates. It also accounts for the correct nuclear response functions for each scattering operator and takes into account the natural abundances of isotopes for a variety of experimental target elements.

[ascl:1506.003]
PLATO Simulator: Realistic simulations of expected observations

Marcos-Arenal, P.; Zima, W.; De Ridder, J.; Aerts, C.; Huygen, R.; Samadi, R.; Green, J.; Piotto, G.; Salmon, S.; Catala, C.; Rauer, H.

PLATO Simulator is an end-to-end simulation software tool designed for the performance of realistic simulations of the expected observations of the PLATO mission but easily adaptable to similar types of missions. It models and simulates photometric time-series of CCD images by including models of the CCD and its electronics, the telescope optics, the stellar field, the jitter movements of the spacecraft, and all important natural noise sources.

[ascl:1506.004]
multiband_LS: Multiband Lomb-Scargle Periodograms

The multiband periodogram is a general extension of the well-known Lomb-Scargle approach for detecting periodic signals in time-domain data. In addition to advantages of the Lomb-Scargle method such as treatment of non-uniform sampling and heteroscedastic errors, the multiband periodogram significantly improves period finding for randomly sampled multiband light curves (e.g., Pan-STARRS, DES and LSST). The light curves in each band are modeled as arbitrary truncated Fourier series, with the period and phase shared across all bands.

[ascl:1506.005]
PyMC: Bayesian Stochastic Modelling in Python

PyMC is a python module that implements Bayesian statistical models and fitting algorithms, including Markov chain Monte Carlo. Its flexibility and extensibility make it applicable to a large suite of problems. Along with core sampling functionality, PyMC includes methods for summarizing output, plotting, goodness-of-fit and convergence diagnostics.

[ascl:1506.006]
fsclean: Faraday Synthesis CLEAN imager

Fsclean produces 3D Faraday spectra using the Faraday synthesis method, transforming directly from multi-frequency visibility data to the Faraday depth-sky plane space. Deconvolution is accomplished using the CLEAN algorithm, and the package includes Clark and Högbom style CLEAN algorithms. Fsclean reads in MeasurementSet visibility data and produces HDF5 formatted images; it handles images and data of arbitrary size, using scratch HDF5 files as buffers for data that is not being immediately processed, and is limited only by available disk space.

[ascl:1506.007]
REALMAF: Magnetic power spectra from Faraday rotation maps

REALMAF is a maximum-a-posteriori code to measure magnetic power spectra from Faraday rotation data. It uses a sophisticated model for the magnetic autocorrelation in real space, thus alleviating the need for simplifying assumptions in the processing. REALMAF treats the divergence relation of the magnetic field with a multiplicative factor in Fourier space, which allows modeling the magnetic autocorrelation as a spherically symmetric function.

[ascl:1506.008]
SPRITE: Sparsity-based super-resolution algorithm

SPRITE (Sparse Recovery of InstrumenTal rEsponse) computes a well-resolved compact source image from several undersampled and noisy observations. The algorithm is based on sparse regularization; adding a sparse penalty in the recovery leads to far better accuracy in terms of ellipticity error, especially at low S/N.

[ascl:1506.009]
HEATCVB: Coronal heating rate approximations

HEATCVB is a stand-alone Fortran 77 subroutine that estimates the local volumetric coronal heating rate with four required inputs: the radial distance r, the wind speed u, the mass density ρ, and the magnetic field strength |B0|. The primary output is the heating rate Qturb at the location defined by the input parameters. HEATCVB also computes the local turbulent dissipation rate of the waves, γ = Qturb/(2UA).

[ascl:1506.010]
VAPID: Voigt Absorption-Profile [Interstellar] Dabbler

VAPID (Voigt Absorption Profile [Interstellar] Dabbler) models interstellar absorption lines. It predicts profiles and optimizes model parameters by least-squares fitting to observed spectra. VAPID allows cloud parameters to be optimized with respect to several different data set simultaneously; those data sets may include observations of different transitions of a given species, and may have different S/N ratios and resolutions.

[ascl:1507.001]
3D-Barolo: 3D fitting tool for the kinematics of galaxies

3D-Barolo (3D-Based Analysis of Rotating Object via Line Observations) or BBarolo is a tool for fitting 3D tilted-ring models to emission-line datacubes. BBarolo works with 3D FITS files, i.e. image arrays with two spatial and one spectral dimensions. BBarolo recovers the true rotation curve and estimates the intrinsic velocity dispersion even in barely resolved galaxies (about 2 resolution elements) if the signal to noise of the data is larger than 2-3. It has source-detection and first-estimate modules, making it suitable for analyzing large 3D datasets automatically, and is a useful tool for deriving reliable kinematics for both local and high-redshift galaxies.

[ascl:1507.002]
SUPERBOX: Particle-multi-mesh code to simulate galaxies

SUPERBOX is a particle-mesh code that uses moving sub-grids to track and resolve high-density peaks in the particle distribution and a nearest grid point force-calculation scheme based on the second derivatives of the potential. The code implements a fast low-storage FFT-algorithm and allows a highly resolved treatment of interactions in clusters of galaxies, such as high-velocity encounters between elliptical galaxies and the tidal disruption of dwarf galaxies, as sub-grids follow the trajectories of individual galaxies. SUPERBOX is efficient in that the computational overhead is kept as slim as possible and is also memory efficient since it uses only one set of grids to treat galaxies in succession.

[ascl:1507.003]
Pelican: Pipeline for Extensible, Lightweight Imaging and CAlibratioN

Pelican is an efficient, lightweight C++ library for quasi-real time data processing. The library provides a framework to separate the acquisition and processing of data, allowing the scalability and flexibility to fit a number of scenarios. Though its origin was in radio astronomy, processing data as it arrives from a telescope, the framework is sufficiently generic to be useful to any application that requires the efficient processing of incoming data streams.

[ascl:1507.004]
L-PICOLA: Fast dark matter simulation code

L-PICOLA generates and evolves a set of initial conditions into a dark matter field and can include primordial non-Gaussianity in the simulation and simulate the past lightcone at run-time, with optional replication of the simulation volume. It is a fast, distributed-memory, planar-parallel code. L-PICOLA is extremely useful for both current and next generation large-scale structure surveys.

[ascl:1507.005]
slimplectic: Discrete non-conservative numerical integrator

slimplectic is a python implementation of a numerical integrator that uses a fixed time-step variational integrator formalism applied to the principle of stationary nonconservative action. It allows nonconservative effects to be included in the numerical evolution while preserving the major benefits of normally conservative symplectic integrators, particularly the accurate long-term evolution of momenta and energy. slimplectic is appropriate for exploring cosmological or celestial N-body dynamics problems where nonconservative interactions, e.g. dynamical friction or dissipative tides, can play an important role.

[ascl:1507.006]
Toyz: Large datasets and astronomical images analysis framework

Toyz is a python web framework that allows scientists to interact with large images and data sets stored on a remote server. A web application is run on the server containing the data and clients are run from web browsers on the user's computer. Toyz displays large FITS images and also renders any image format supported by Pillow (a fork of the Python Imaging Library), contains a GUI to interact with linked plots, and offers a customizable framework that allows students and researchers to create their own work spaces inside a Toyz environment. Astro-Toyz extends the features of the Toyz image viewer, allowing users to view world coordinates and align images based on their WCS.

[ascl:1507.007]
abo-cross: Hydrogen broadening cross-section calculator

Line broadening cross sections for the broadening of spectral lines by collisions with neutral hydrogen atoms have been tabulated by Anstee & O’Mara (1995), Barklem & O’Mara (1997) and Barklem, O’Mara & Ross (1998) for s–p, p–s, p–d, d–p, d–f and f–d transitions. abo-cross, written in Fortran, interpolates in these tabulations to make these data more accessible to the end user. This code can be incorporated into existing spectrum synthesis programs or used it in a stand-alone mode to compute line broadening cross sections for specific transitions.

[ascl:1507.008]
HLINOP: Hydrogen LINe OPacity in stellar atmospheres

HLINOP is a collection of codes for computing hydrogen line profiles and opacities in the conditions typical of stellar atmospheres. It includes HLINOP for approximate quick calculation of any line of neutral hydrogen (suitable for model atmosphere calculations), based on the Fortran code of Kurucz and Peterson found in ATLAS9. It also includes HLINPROF, for detailed, accurate calculation of lower Balmer line profiles (suitable for detailed analysis of Balmer lines) and HBOP, to implement the occupation probability formalism of Daeppen, Anderson and Milhalas (1987) and thus account for the merging of bound-bound and bound-free opacity (used often as a wrapper to HLINOP for model atmosphere calculations).

[ascl:1507.009]
PPInteractions: Secondary particle spectra from proton-proton interactions

PPInteractions generates the secondary particle energy spectra produced in proton-proton interactions over the entire chosen energy range for any value of the primary proton spectral index by adjusting the low energy part of the spectra (below 0.1TeV) to the high energy end of the spectra (above 0.1TeV). This code is based on the parametrization of Kelner et al (2006), in which the normalization of the low energy part of the spectra is given only for 3 values of the primary proton spectral indices (2, 2.5, 3).

[ascl:1507.010]
Astrochem: Abundances of chemical species in the interstellar medium

Astrochem computes the abundances of chemical species in the interstellar medium, as function of time. It studies the chemistry in a variety of astronomical objects, including diffuse clouds, dense clouds, photodissociation regions, prestellar cores, protostars, and protostellar disks. Astrochem reads a network of chemical reactions from a text file, builds up a system of kinetic rates equations, and solves it using a state-of-the-art stiff ordinary differential equation (ODE) solver. The Jacobian matrix of the system is computed implicitly, so the resolution of the system is extremely fast: large networks containing several thousands of reactions are usually solved in a few seconds. A variety of gas phase process are considered, as well as simple gas-grain interactions, such as the freeze-out and the desorption via several mechanisms (thermal desorption, cosmic-ray desorption and photo-desorption). The computed abundances are written in a HDF5 file, and can be plotted in different ways with the tools provided with Astrochem. Chemical reactions and their rates are written in a format which is meant to be easy to read and to edit. A tool to convert the chemical networks from the OSU and KIDA databases into this format is also provided. Astrochem is written in C, and its source code is distributed under the terms of the GNU General Public License (GPL).

[ascl:1507.011]
FAT: Fully Automated TiRiFiC

Kamphuis, P.; Józsa, G. I. G.; Oh, S-. H.; Spekkens, K.; Urbancic, N.; Serra, P.; Koribalski, B. S.; Dettmar, R.-J.

FAT (Fully Automated TiRiFiC) is an automated procedure that fits tilted-ring models to Hi data cubes of individual, well-resolved galaxies. The method builds on the 3D Tilted Ring Fitting Code (TiRiFiC, ascl:1208.008). FAT accurately models the kinematics and the morphologies of galaxies with an extent of eight beams across the major axis in the inclination range 20°-90° without the need for priors such as disc inclination. FAT's performance allows us to model the gas kinematics of many thousands of well-resolved galaxies, which is essential for future HI surveys, with the Square Kilometre Array and its pathfinders.

[ascl:1507.012]
DRAMA: Instrumentation software environment

DRAMA is a fast, distributed environment for writing instrumentation control systems. It allows low level instrumentation software to be controlled from user interfaces running on UNIX, MS Windows or VMS machines in a consistent manner. Such instrumentation tasks can run either on these machines or on real time systems such as VxWorks. DRAMA uses techniques developed by the AAO while using the Starlink-ADAM environment, but is optimized for the requirements of instrumentation control, portability, embedded systems and speed. A special program is provided which allows seamless communication between ADAM and DRAMA tasks.

[ascl:1507.013]
K-Inpainting: Inpainting for Kepler

Inpainting is a technique for dealing with gaps in time series data, as frequently occurs in asteroseismology data, that may generate spurious peaks in the power spectrum, thus limiting the analysis of the data. The inpainting method, based on a sparsity prior, judiciously fills in gaps in the data, preserving the asteroseismic signal as far as possible. This method can be applied both on ground and space-based data. The inpainting technique improves the oscillation modes detection and estimation, the impact of the observational window function is reduced, and the interpretation of the power spectrum is simplified. K-Inpainting can be used to study very long time series of many stars because its computation is very fast.

[ascl:1507.014]
getsources: Multi-scale, multi-wavelength source extraction

*getsources* is a powerful multi-scale, multi-wavelength source extraction algorithm. It analyzes fine spatial decompositions of original images across a wide range of scales and across all wavebands, cleans those single-scale images of noise and background, and constructs wavelength-independent single-scale detection images that preserve information in both spatial and wavelength dimensions. *getsources* offers several advantages over other existing methods of source extraction, including the filtering out of irrelevant spatial scales to improve detectability, especially in the crowded regions and for extended sources, the ability to combine data over all wavebands, and the full automation of the extraction process.

[ascl:1507.015]
DALI: Derivative Approximation for LIkelihoods

DALI (Derivative Approximation for LIkelihoods) is a fast approximation of non-Gaussian likelihoods. It extends the Fisher Matrix in a straightforward way and allows for a wider range of posterior shapes. The code is written in C/C++.

[ascl:1507.016]
Least Asymmetry: Centering Method

Lust, Nate B.; Britt, Daniel; Harrington, Joseph; Nymeyer, Sarah; Stevenson, Kevin B.; Ross, Emily L.; Bowman, William; Fraine, Jonathan

Least Asymmetry finds the center of a distribution of light in an image using the least asymmetry method; the code also contains center of light and fitting a Gaussian routines. All functions in Least Asymmetry are designed to take optional weights.

[ascl:1507.017]
REDSPEC: NIRSPEC data reduction

REDSPEC is an IDL based reduction package designed with NIRSPEC in mind though can be used to reduce data from other spectrographs as well. REDSPEC accomplishes spatial rectification by summing an *A+B* pair of a calibration star to produce an image with two spectra; the image is remapped on the basis of polynomial fits to the spectral traces and calculation of gaussian centroids to define their separation, producing straight spectral traces with respect to the detector rows. The raw images are remapped onto a coordinate system with uniform intervals in spatial extent along the slit and in wavelength along the dispersion axis.

[ascl:1507.018]
pyro: Python-based tutorial for computational methods for hydrodynamics

pyro is a simple python-based tutorial on computational methods for hydrodynamics. It includes 2-d solvers for advection, compressible, incompressible, and low Mach number hydrodynamics, diffusion, and multigrid. It is written with ease of understanding in mind. An extensive set of notes that is part of the Open Astrophysics Bookshelf project provides details of the algorithms.

[ascl:1507.019]
AstroStat: Statistical analysis tool

AstroStat performs statistical analysis on data and is compatible with Virtual Observatory (VO) standards. It accepts data in a variety of formats and performs various statistical tests using a menu driven interface. Analyses, performed in R, include exploratory tests, visualizations, distribution fitting, correlation and causation, hypothesis testing, multivariate analysis and clustering. AstroStat is available in two versions with an identical interface and features: as a web service that can be run using any standard browser and as an offline application.

[ascl:1507.020]
IEHI: Ionization Equilibrium for Heavy Ions

IEHI, written in Fortran, outputs a simple "coronal" ionization equilibrium (i.e., collisional ionization and auto-ionization balanced by radiative and dielectronic recombination) for a plasma at a given electron temperature.

[ascl:1508.001]
HMcode: Halo-model matter power spectrum computation

HMcode computes the halo-model matter power spectrum. It is written in Fortran90 and has been designed to quickly (~0.5s for 200 k-values across 16 redshifts on a single core) produce matter spectra for a wide range of cosmological models. In testing it was shown to match spectra produced by the 'Coyote Emulator' to an accuracy of 5 per cent for k less than 10h Mpc^-1. However, it can also produce spectra well outside of the parameter space of the emulator.

[ascl:1508.002]
NICOLE: NLTE Stokes Synthesis/Inversion Code

NICOLE, written in Fortran 90, seeks the model atmosphere that provides the best fit to the Stokes profiles (in a least-squares sense) of an arbitrary number of simultaneously-observed spectral lines from solar/stellar atmospheres. The inversion core used for the development of NICOLE is the LORIEN engine (the Lovely Reusable Inversion ENgine), which combines the SVD technique with the Levenberg-Marquardt minimization method to solve the inverse problem.

[ascl:1508.003]
REDUCEME: Long-slit spectroscopic data reduction and analysis

Cardiel, N; Gorgas, J.; Pedraz, S.; Cenarro, J.; Alonso, O; Gil de Paz, A.; García-Dabó, E.; Sánchez-Blázquez, P.; Mármol-Queraltó, E.; Toloba, E.

The astronomical data reduction package REDUCEME reduces and analyzes long-slit spectroscopic data. The package uses the unformatted FORTRAN raw data format, so requires FITS files be transformed to REDUCEME format; the reverse operation (from REDUCEME to FITS format) is also available. The package is a set of programs written in FORTRAN 77 and includes shell scripts (using the C shell syntax) to perform routine tasks; it can be extended by the inclusion of external programs. REDUCEME uses PGPLOT (ascl:1103.002) for line plots and images, and a subset of subroutines, called BUTTON, enables the user to communicate interactively with the image display employing graphic buttons. One advantage of using REDUCEME is that for each image an associated error image can also be processed throughout the reduction process, allowing for a careful control of the error propagation.

[ascl:1508.004]
FRELLED: FITS Realtime Explorer of Low Latency in Every Dimension

FRELLED (FITS Realtime Explorer of Low Latency in Every Dimension) creates 3D images in real time from 3D FITS files and is written in Python for the 3D graphics suite Blender. Users can interactively generate masks around regions of arbitrary geometry and use them to catalog sources, hide regions, and perform basic analysis (*e.g.*, image statistics within the selected region, generate contour plots, query NED and the SDSS). World coordinates are supported and multi-volume rendering is possible. FRELLED is designed for viewing HI data cubes and provides a number of tasks to commonly-used MIRIAD (ascl:1106.007) tasks (e.g. mbspect); however, many of its features are suitable for any type of data set. It also includes an n-body particle viewer with the ability to display 3D vector information as well as the ability to render time series movies of multiple FITS files and setup simple turntable rotation movies for single files.

[ascl:1508.005]
ColorPro: PSF-corrected aperture-matched photometry

ColorPro automatically obtains robust colors across images of varied PSF. To correct for the flux lost in images with poorer PSF, the "detection image" is blurred to match the PSF of these other images, allowing observation of how much flux is lost. All photometry is performed in the highest resolution frame (images being aligned given WCS information in the FITS headers), and identical apertures are used in every image. Usually isophotal apertures are used, as determined by SExtractor (ascl:1010.064). Using SExSeg (ascl:1508.006), object aperture definitions can be pre-defined and object detections from different image filters can be combined automatically into a single comprehensive "segmentation map." After producing the final photometric catalog, ColorPro can automatically run BPZ (ascl:1108.011) to obtain Bayesian Photometric Redshifts.

[ascl:1508.006]
SExSeg: SExtractor segmentation

SExSeg forces SExtractor (ascl:1010.064) to run using a pre-defined segmentation map (the definition of objects and their borders). The defined segments double as isophotal apertures. SExSeg alters the detection image based on a pre-defined segmenation map while preparing your "analysis image" by subtracting the background in a separate SExtractor run (using parameters you specify). SExtractor is then run in "double-image" mode with the altered detection image and background-subtracted analysis image.

[ascl:1508.007]
TreeCorr: Two-point correlation functions

TreeCorr efficiently computes two-point correlation functions. It can compute correlations of regular number counts, weak lensing shears, or scalar quantities such as convergence or CMB temperature fluctuations. Two-point correlations may be auto-correlations or cross-correlations, including any combination of shear, kappa, and counts. Two-point functions can be done with correct curved-sky calculation using RA, Dec coordinates, on a Euclidean tangent plane, or in 3D using RA, Dec and a distance. The front end is written in Python, which can be used as a Python module or as a standalone executable using configuration files; the actual computation of the correlation functions is done in C++ using ball trees (similar to kd trees), making the calculation extremely efficient, and when available, OpenMP is used to run in parallel on multi-core machines.

[ascl:1508.008]
NGMIX: Gaussian mixture models for 2D images

NGMIX implements Gaussian mixture models for 2D images. Both the PSF profile and the galaxy are modeled using mixtures of Gaussians. Convolutions are thus performed analytically, resulting in fast model generation as compared to methods that perform the convolution in Fourier space. For the galaxy model, NGMIX supports exponential disks and de Vaucouleurs and Sérsic profiles; these are implemented approximately as a sum of Gaussians using the fits from Hogg & Lang (2013). Additionally, any number of Gaussians can be fit, either completely free or constrained to be cocentric and co-elliptical.

[ascl:1508.009]
Trilogy: FITS image conversion software

Trilogy automatically scales and combines FITS images to produce color or grayscale images using Python scripts. The user assigns images to each color channel (RGB) or a single image to grayscale luminosity. Trilogy determines the intensity scaling automatically and independently in each channel to display faint features without saturating bright features. Each channel's scaling is determined based on a sample of the image (or summed images) and two input parameters. One parameter sets the output luminosity of "the noise," currently determined as 1-sigma above the sigma-clipped mean. The other parameter sets what fraction of the data (if any) in the sample region should be allowed to saturate. Default values for these parameters (0.15% and 0.001%, respectively) work well, but the user is able to adjust them. The scaling is accomplished using the logarithmic function y = a log(kx + 1) clipped between 0 and 1, where a and k are constants determined based on the data and desired scaling parameters as described above.

[ascl:1508.010]
SHDOM: Spherical Harmonic Discrete Ordinate Method for atmospheric radiative transfer

The Spherical Harmonic Discrete Ordinate Method (SHDOM) radiative transfer model computes polarized monochromatic or spectral band radiative transfer in a one, two, or three-dimensional medium for either collimated solar and/or thermal emission sources of radiation. The model is written in a variant of Fortran 77 and in Fortran90 and requires a Fortran 90 compiler. Also included are programs for generating the optical property files input to SHDOM from physical properties of water cloud particles and aerosols.

[ascl:1509.001]
XSHPipelineManager: Wrapper for the VLT/X-shooter Data Reduction Pipeline

XSHPipelineManager provides a framework for reducing spectroscopic observations taken by the X-shooter spectrograph at the Very Large Telescope. This Python code wraps recipes developed by the European Southern Observatory and runs the full X-shooter data reduction pipeline. The code offers full flexibility in terms of what data reduction recipes to include and which calibration files to use. During the data reduction chain restart-files are saved, making it possible to restart at any step in the chain.

[ascl:1509.002]
Tempo: Pulsar timing data analysis

Nice, D; Demorest, P.; Stairs, I.; Manchester, R.; Taylor, J.; Peters, W.; Weisberg, J.; Irwin, A.; Wex, N.; Huang, Y.

Tempo analyzes pulsar timing data. Pulse times of arrival (TOAs), pulsar model parameters, and coded instructions are read from one or more input files. The TOAs are fitted by a pulse timing model incorporating transformation to the solar-system barycenter, pulsar rotation and spin-down and, where necessary, one of several binary models. Program output includes parameter values and uncertainties, residual pulse arrival times, chi-squared statistics, and the covariance matrix of the model. In prediction mode, ephemerides of pulse phase behavior (in the form of polynomial expansions) are calculated from input timing models. Tempo is the basis for the Tempo2 (ascl:1210.015) code.

[ascl:1509.003]
AFR (ASPFitsReader): A pulsar FITS file reader and analysis package

AFR, or ASPFitsReader, reduces, processes, and manipulates pulsar data, including calibration, template profile creation, and interactive excision of radio frequency interference from pulsar profile data. It also creates times-of-arrival compatible with Tempo (ascl:1509.002) and Tempo2 (ascl:1210.015) timing software.

[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.

[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:1509.006]
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:1509.007]
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:1509.008]
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:1509.009]
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:1509.010]
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: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: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:1510.003]
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:1510.004]
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:1510.005]
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:1510.006]
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.

[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:1510.007]
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.

[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: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:1511.003]
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:1511.004]
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:1511.005]
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:1511.006]
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:1511.007]
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:1511.008]
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:1511.009]
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:1511.010]
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:1511.011]
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:1511.012]
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:1511.013]
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:1511.014]
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:1511.015]
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:1511.016]
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:1511.017]
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:1511.018]
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:1511.019]
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:1511.020]
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:1511.021]
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:1511.022]
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:1511.023]
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: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: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:1512.003]
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:1512.004]
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:1512.005]
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:1512.006]
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.

Internet Archive link provided for archival purposes; per its website, GPC is no longer distributed or available as of August 2020.

[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:1512.008]
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:1512.009]
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:1512.010]
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:1512.011]
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:1512.012]
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:1512.013]
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:1512.014]
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:1512.015]
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:1512.016]
ZeldovichRecon: Halo correlation function using the Zeldovich approximation

ZeldovichRecon computes the halo correlation function using the Zeldovich approximation. It includes 3 variants: 1.) zelrecon.cpp, which computes the various contributions to the correlation function; 2.) zelrecon_ctypes.cpp, which is designed to be called from Python using the ctypes library; and 3.) 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:1512.017]
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:1512.018]
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:1512.019]
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:1512.020]
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: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: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 https://hyperfit.icrar.org.

[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:1601.004]
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:1601.005]
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:1601.006]
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:1601.007]
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:1601.008]
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:1601.009]
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:1601.010]
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:1601.011]
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:1601.012]
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:1601.013]
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:1601.014]
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:1601.015]
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:1601.016]
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:1601.017]
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:1601.018]
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:1601.019]
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:1601.020]
ProC: Process Coordinator

Hovest, Wolfgang; Knoche, Jörg; Hell, Reinhard; Doerl, Uwe; Riller, Thomas; Matthai, Frank; Ensslin, Torsten A.; 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:1601.021]
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: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: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:1602.003]
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:1602.004]
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:1602.005]
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:1602.006]
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:1602.007]
FilTER: Filament Trait-Evaluated Reconstruction

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

[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:1602.009]
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:1602.010]
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:1602.011]
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:1602.012]
DELightcurveSimulation: Light curve simulation code

DELightcurveSimulation (also called DELCgen) 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:1602.013]
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:1602.014]
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:1602.015]
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:1602.016]
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:1602.017]
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:1602.018]
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:1602.019]
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:1602.020]
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:1602.021]
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: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: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:1603.003]
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.

[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:1603.005]
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:1603.006]
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:1603.007]
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:1603.008]
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:1603.009]
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:1603.010]
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:1603.011]
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:1603.012]
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:1603.013]
PyGDSM: Python interface to Global Diffuse Sky Models

PyGDSM (formely 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). PyGDSM uses the GSM to generate all-sky maps in Healpix format of diffuse Galactic radio emission from 10 MHz to 94 GHz. The PyGDSM module provides visualization utilities, file output in FITS format, and the ability to generate observed skies for a given location and date. PyGDSM requires Healpy (ascl:2008.022), PyEphem (ascl:1112.014), and AstroPy (ascl:1304.002).

[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:1603.015]
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:1603.016]
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:1603.017]
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. A newer version of this code, pyHIIexplorer (ascl:2206.010), is available.

[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: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-3 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: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:1604.003]
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:1604.004]
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:1604.005]
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:1604.006]
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:1604.007]
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:1604.008]
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:1604.009]
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:1604.011]
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.

Would you like to view a random code?