Category Archives: codes

November 2016 additions to the ASCL

Twenty-two codes were added to the ASCL in November 2016:

AIMS: Asteroseismic Inference on a Massive Scale
Carpet: Adaptive Mesh Refinement for the Cactus Framework
CMCIRSED: Far-infrared spectral energy distribution fitting for galaxies near and far
EarthShadow: Calculator for dark matter particle velocity distribution after Earth-scattering
Exo-Transmit: Radiative transfer code for calculating exoplanet transmission spectra

GalPot: Galaxy potential code
GRASP2K: Relativistic Atomic Structure Package
Icarus: Stellar binary light curve synthesis tool
Kapteyn Package: Tools for developing astronomical applications
MPDAF: MUSE Python Data Analysis Framework

OXAF: Ionizing spectra of Seyfert galaxies for photoionization modeling
phase_space_cosmo_fisher: Fisher matrix 2D contours
Pippi: Parse and plot MCMC chains
PRECESSION: Python toolbox for dynamics of spinning black-hole binaries
proEQUIB: IDL/GDL library for atomic level populations and line emissivities in statistical equilibrium

pyGMMis: Mixtures-of-Gaussians density estimation method
RHOCUBE: 3D density distributions modeling code
SlicerAstro: Astronomy (HI) extension for 3D Slicer
SNCosmo: Python library for supernova cosmology
tf_unet: Generic convolutional neural network U-Net implementation in Tensorflow

Transit Clairvoyance: Predicting multiple-planet systems for TESS
UltraNest: Pythonic Nested Sampling Development Framework and UltraNest

October 2016 additions to the ASCL

Sixteen codes were added to the ASCL in October 2016:

BurnMan: Lower mantle mineral physics toolkit
BXA: Bayesian X-ray Analysis
C3: Command-line Catalogue Crossmatch for modern astronomical surveys
CERES: Collection of Extraction Routines for Echelle Spectra

cluster-in-a-box: Statistical model of sub-millimeter emission from embedded protostellar clusters
DSDEPROJ: Direct Spectral Deprojection
Fourierdimredn: Fourier dimensionality reduction model for interferometric imaging
Freddi: Fast Rise Exponential Decay accretion Disk model Implementation

gatspy: General tools for Astronomical Time Series in Python
GSGS: In-Focus Phase Retrieval Using Non-Redundant Mask Data
MC3: Multi-core Markov-chain Monte Carlo code
MUSE-DRP: MUSE Data Reduction Pipeline

NuPyCEE: NuGrid Python Chemical Evolution Environment
Piccard: Pulsar timing data analysis package
PyMC3: Python probabilistic programming framework
velbin: radial velocity corrected for binary orbital motions

ADASS BoF: Implementing Ideas for Improving Software Citation and Credit

On Tuesday at ADASS, ASCL Advisory Committee Chair Peter Teuben led a Birds of a Feather session intended as a working session to have people put some of the ideas for improving software citation and credit into practice.

ADS now has a doc type called software

Slide from Peter’s opening presentation

He opened the session with a few remarks about last year’s BoF, similar efforts elsewhere, and examples of progress since last year. Yes, there has been progress! He then showed a list of actionable items and asked people to work on them, adding their work to a common Google doc. His slides are here.

And they did! It was the quietest BoF ever, I believe, as Keith Shortridge, Bruce Berriman, and Jessica Mink wrote about their experiences in releasing software; Renato Callado Borges and Greg Sleap provided guidance on the types of software contributions that add value to science; Alberto Accomazzi, Nuria Lorente, and Kai Polsterer listed ways one can publish and take credit for software; Peter Teuben, Steven Crawford, and possibly others pulled together a list of organization web pages about software created at the institutions, this as a way to highlight and recognize scientific software contributions; Maurizio Tomasi added a suggestion for gathering licensing information; and Thomas Robitaille, Ole Streicher, Tim Jenness, Kimberly DuPrie, and I discussed exactly what should be in the “Preferred citation field” of the ASCL and various people listed about a dozen preferred citations to be added to the ASCL and others used the Suggest a change or addition link for several software packages to provide preferred citation information.

Though Peter had asked that people work for about 30 minutes, he monitored contributions to the Google doc and saw work was still being done so did not call us back together until only 15 minutes or so were left in the session. Instead of having people report back on what they had done as originally plan, he asked for other feedback instead, as progress made was evident in the shared document, and after a bit of discussion on licensing and a few other comments, closed the session.

Though the session is over, the next phase is to put this information to use or disseminate it in some way so it can do some good and be the changes we want to see for software!

 

Montage poster at ADASS 2016

We want to share some of the posters that are appearing at ADASS this week (with permission of their authors). Montage is in the ASCL; we love this poster for several reasons, but especially because it makes clear that sustainability of the software is important!
Image of paper on the software Montagle

Abstract: The Montage toolkit is finding exceptional breadth of usage, far beyond its intended application as a mosaic engine for astronomy. New uses include:
– Visualization of complex images with data overlays: e.g. as a re-projection engine integrated into the server-side architecture of a Gbit visualization system supporting investigations of 3D printing with the X3D protocol creation of sky coverage maps for missions and projects bulk creation of sub-images of multiband photometry data creation of plots in the APLPy library.
– Creation of new data products at scale: mosaics of Gemini AO images from the Gemini Multi-Conjugate Adaptive Optics System/Gemini South Adaptive Optics Imager (GEMS/GSAOI) instrument, from the VISTA VIDEO and the UKIDSS DXS surveys welding the Herschel infrared Galactic plane (Hi-GAL) far-infrared Survey into a set of large-scale mosaics, for planetarium shows at a digital as well as for research
– As a re-projection engine to support discovery of 86 Near Earth Asteroids (a U.S. congressional mandate) in the Lincoln Near-Earth Asteroid Research Program (LINEAR).
– Integration into data processing environments: integration of the 4D image cutout tool into the VO-compliant CSIRO ASKAP Science Data Archive (CASDA) as a re-projection engine for the Dark Energy Survey (DES) pipeline.
– Discovery of imaging data at scale: use of memory mapped R-tree indices to support searches for spatially extended data, in use in Spitzer and WISE image searches and in spatial and temporal searches for WISE and KOA.
It has been cited as an exemplar application for development of next generation cyber-infrastructure in 238 papers between 2014 and 2016 to date. What has enabled this broad take-up is that Montage has been built and managed as a scalable toolkit, written in C and portable across all common *nix platforms, with minimal dependencies on third-party software, such that it can be built with a simple “make” command. All the components have proven powerful general-purpose tools in their own right, even those first developed to support mosaic creation, such as discovery of images for input to the engine and for management of mosaics. We describe how Montage is managed to assure that the benefits of the architecture are retained, and how we ensure that new development is driven by the needs of the community.

September 2016 additions to the ASCL

Twenty-five codes were added to the ASCL in September 2016:

21cmSense: Calculating the sensitivity of 21cm experiments to the EoR power spectrum
AdaptiveBin: Adaptive Binning
AIPY: Astronomical Interferometry in PYthon
Askaryan Module: Askaryan electric fields predictor
contbin: Contour binning and accumulative smoothing

CuBANz: Photometric redshift estimator
FISHPACK: Efficient FORTRAN Subprograms for the Solution of Separable Elliptic Partial Differential Equations
FISHPACK90: Efficient FORTRAN Subprograms for the Solution of Separable Elliptic Partial Differential Equations
FIT3D: Fitting optical spectra
GRASP: General-purpose Relativistic Atomic Structure Package

Kranc: Cactus modules from Mathematica equations
NSCool: Neutron star cooling code
Photutils: Photometry tools
PKDGRAV3: Parallel gravity code
PYESSENCE: Generalized Coupled Quintessence Linear Perturbation Python Code

PyPHER: Python-based PSF Homogenization kERnels
SCIMES: Spectral Clustering for Interstellar Molecular Emission Segmentation
SIP: Systematics-Insensitive Periodograms
Sky3D: Time-dependent Hartree-Fock equation solver
spectral-cube: Read and analyze astrophysical spectral data cubes

StarPy: Quenched star formation history parameters of a galaxy using MCMC
SuperBoL: Module for calculating the bolometric luminosities of supernovae
T-PHOT: PSF-matched, prior-based, multiwavelength extragalactic deconfusion photometry
TIDEV: Tidal Evolution package
Weighted EMPCA: Weighted Expectation Maximization Principal Component Analysis

August 2016 additions to the ASCL

Twenty codes were added to the ASCL in August 2016:

21CMMC: Parallelized Monte Carlo Markov Chain analysis tool for the epoch of reionization (EoR)
2DFFT: Measuring Galactic Spiral Arm Pitch Angle
appaloosa: Python-based flare finding code for Kepler light curves
AstroVis: Visualizing astronomical data cubes
BART: Bayesian Atmospheric Radiative Transfer fitting code

BASE-9: Bayesian Analysis for Stellar Evolution with nine variables
Cuba: Multidimensional numerical integration library
DOLPHOT: Stellar photometry
FilFinder: Filamentary structure in molecular clouds
Gemini IRAF: Data reduction software for the Gemini telescopes

gevolution: General Relativity Cosmological N-body code for evolution of large scale structures
LORENE: Spectral methods differential equations solver
NEBULAR: Spectrum synthesis for mixed hydrogen-helium gas in ionization equilibrium
NICIL: Non-Ideal magnetohydrodynamics Coefficients and Ionisation Library
OBERON: OBliquity and Energy balance Run on N-body systems

PROFFIT: Analysis of X-ray surface-brightness profiles
pvextractor: Position-Velocity Diagram Extractor
pyXSIM: Synthetic X-ray observations generator
SPIDERz: SuPport vector classification for IDEntifying Redshifts
Stingray: Spectral-timing software

July 2016 additions to the ASCL

Twenty codes were added to the ASCL in July 2016:

AGNfitter: SED-fitting code for AGN and galaxies from a MCMC approach
astLib: Tools for research astronomers
Atlas2bgeneral: Two-body resonance calculator
Atlas3bgeneral: Three-body resonance calculator
BLS: Box-fitting Least Squares

BoxRemap: Volume and local structure preserving mapping of periodic boxes
Cholla: 3D GPU-based hydrodynamics code for astrophysical simulation
DICE: Disk Initial Conditions Environment
HfS: Hyperfine Structure fitting tool
HIDE: HI Data Emulator

JUDE: An Utraviolet Imaging Telescope pipeline
K2PS: K2 Planet search
Kālī: Time series data modeler
LZIFU: IDL emission line fitting pipeline for integral field spectroscopy data
PICsar: Particle in cell pulsar magnetosphere simulator

Planetary3br: Three massive body resonance calculator
RT1D: 1D code for Rayleigh-Taylor instability
SEEK: Signal Extraction and Emission Kartographer
SOPIE: Sequential Off-Pulse Interval Estimation
ZASPE: Zonal Atmospheric Stellar Parameters Estimator

June 2016 additions to the ASCL

Fifteen codes were added to the ASCL in June 2016:

COMB: Compact embedded object simulations
Companion-Finder: Planets and binary companions in time series spectra
Cygrid: Cython-powered convolution-based gridding module for Python
FDIPS: Finite Difference Iterative Potential-field Solver
FLASK: Full-sky Lognormal Astro-fields Simulation Kit

HIBAYES: Global 21-cm Bayesian Monte-Carlo Model Fitting
KMDWARFPARAM: Parameters estimator for K and M dwarf stars
Lmfit: Non-Linear Least-Square Minimization and Curve-Fitting for Python
PAL: Positional Astronomy Library
Pulse Portraiture: Pulsar timing

PyMultiNest: Python interface for MultiNest
s2: Object oriented wrapper for functions on the sphere
SimpLens: Interactive gravitational lensing simulator
SWOC: Spectral Wavelength Optimization Code
uvmcmcfit: Parametric models to interferometric data fitter

April and May 2016 additions to the ASCL

Twenty-eight codes were added to the ASCL in April and May 2016:

2-DUST: Dust radiative transfer code
ASTRiDE: Automated Streak Detection for Astronomical Images
BACCHUS: Brussels Automatic Stellar Parameter
CAMELOT: Cloud Archive for MEtadata, Library and Online Toolkit
CCSNMultivar: Core-Collapse Supernova Gravitational Waves

cluster-lensing: Tools for calculating properties and weak lensing profiles of galaxy clusters
DISCO: 3-D moving-mesh magnetohydrodynamics package
DNest3: Diffusive Nested Sampling
DUO: Spectra of diatomic molecules
FDPS: Framework for Developing Particle Simulators

grtrans: Polarized general relativistic radiative transfer via ray tracing
Halotools: Galaxy-Halo connection models
K2SC: K2 Systematics Correction
LAMBDAR: Lambda Adaptive Multi-Band Deblending Algorithm in R
libpolycomp: Compression/decompression library

magicaxis: Pretty scientific plotting with minor-tick and log minor-tick support
MARZ: Redshifting Program
MUSCLE: MUltiscale Spherical-ColLapse Evolution
OpenMHD: Godunov-type code for ideal/resistive magnetohydrodynamics (MHD)
PDT: Photometric DeTrending Algorithm Using Machine Learning

SAND: Automated VLBI imaging and analyzing pipeline
Shadowfax: Moving mesh hydrodynamical integration code
Surprise Calculator: Estimating relative entropy and Surprise between samples
The Tractor: Probabilistic astronomical source detection and measurement
TMBIDL: Single dish radio astronomy data reduction package

TRIPPy: Python-based Trailed Source Photometry
TTVFaster: First order eccentricity transit timing variations (TTVs)
zeldovich-PLT: Zel’dovich approximation initial conditions generator

March 2016 additions to the ASCL

Eighteen codes were added to the ASCL in March, 2016:

Asfgrid: Asteroseismic parameters for a star
CORBITS: Efficient Geometric Probabilities of Multi-Transiting Exoplanetary Systems
Dedalus: Flexible framework for spectrally solving differential equations
DiskJockey: Protoplanetary disk modeling for dynamical mass derivation
ellc: Light curve model for eclipsing binary stars and transiting exoplanets

EQUIB: Atomic level populations and line emissivities calculator
ExoPriors: Accounting for observational bias of transiting exoplanets
FAST-PT: Convolution integrals in cosmological perturbation theory calculator
fibmeasure: Python/Cython module to find the center of back-illuminated optical fibers in metrology images
gPhoton: Time-tagged GALEX photon events analysis tools

HIIexplorer: Detect and extract integrated spectra of HII regions
PyGSM: Python interface to the Global Sky Model
PolRadTran: Polarized Radiative Transfer Model Distribution
ROBAST: ROOT-based ray-tracing library for cosmic-ray telescopes
SILSS: SPHERE/IRDIS Long-Slit Spectroscopy pipeline

SMARTIES: Spheroids Modelled Accurately with a Robust T-matrix Implementation for Electromagnetic Scattering
tpipe: Searching radio interferometry data for fast, dispersed transients
VIP: Vortex Image Processing pipeline for high-contrast direct imaging of exoplanets