Category Archives: codes

May additions to the ASCL

Seventeen codes were added to the ASCL in May 2017:

astroABC: Approximate Bayesian Computation Sequential Monte Carlo sampler
COSMOS: Carnegie Observatories System for MultiObject Spectroscopy
DMATIS: Dark Matter ATtenuation Importance Sampling
demc2: Differential evolution Markov chain Monte Carlo parameter estimator
f3: Full Frame Fotometry for Kepler Full Frame Images

fd3: Spectral disentangling of double-lined spectroscopic binary stars
FDBinary: A tool for spectral disentangling of double-lined spectroscopic binary stars
getimages: Background derivation and image flattening method
LensPop: Galaxy-galaxy strong lensing population simulation
MBProj2: Multi-Band x-ray surface brightness PROJector 2

NPTFit: Non-Poissonian Template Fitting
PCAT: Probabilistic Cataloger
PROFILER: 1D galaxy light profile decomposition
PSOAP: Precision Spectroscopic Orbits A-Parametrically
SPTCLASS: SPecTral CLASSificator code

supernovae: Photometric classification of supernovae
WeirdestGalaxies: Outlier Detection Algorithm on Galaxy Spectra

April additions to the ASCL

Fourteen codes were added to the ASCL in April 2017:

A-Track: Detecting Moving Objects in FITS images
Difference-smoothing: Measuring time delay from light curves
Multipoles: Potential gain for binary lens estimation
Photo-z-SQL: Photometric redshift estimation framework
pwkit: Astronomical utilities in Python

PySM: Python Sky Model
Quickclump: Identify clumps within a 3D FITS datacube
Shwirl: Meaningful coloring of spectral cube data with volume rendering
STATCONT: Statistical continuum level determination method for line-rich sources
Transit: Radiative-transfer code for planetary atmospheres

UDAT: A multi-purpose data analysis tool
VaST: Variability Search Toolkit
VULCAN: Chemical Kinetics For Exoplanetary Atmospheres
XID+: Next generation XID development

March additions to the ASCL

Fifteen codes were added to the ASCL in March 2017:

Atmospheric Athena: 3D Atmospheric escape model with ionizing radiative transfer
Charm: Cosmic history agnostic reconstruction method
COCOA: Simulating Observations of Star Cluster Simulations
Corrfunc: Blazing fast correlation functions on the CPU
exorings: Exoring Transit Properties

ICICLE: Initial Conditions for Isolated CoLlisionless systEms
Larch: X-ray Analysis for Synchrotron Applications using Python
MC-SPAM: Monte-Carlo Synthetic-Photometry/Atmosphere-Model
PHOTOMETRYPIPELINE: Automated photometry pipeline
PyMVPA: MultiVariate Pattern Analysis in Python

QtClassify: IFS data emission line candidates classifier
sidm-nbody: Monte Carlo N-body Simulation for Self-Interacting Dark Matter
SNRPy: Supernova remnant evolution modeling
starsense_algorithms: Performance evaluation of various star sensors
TransitSOM: Self-Organizing Map for Kepler and K2 transits

January and February additions to the ASCL

Twelve codes were added to the ASCL in January 2017:

CosmoSlik: Cosmology sampler of likelihoods
Forecaster: Mass and radii of planets predictor
GrayStar: Web-based pedagogical stellar modeling
GrayStarServer: Stellar atmospheric modeling and spectrum synthesis
GWFrames: Manipulate gravitational waveforms

KAULAKYS: Inelastic collisions between hydrogen atoms and Rydberg atoms
kcorrect: Calculate K-corrections between observed and desired bandpasses
MSWAVEF: Momentum-Space Wavefunctions
SONG: Second Order Non-Gaussianity
Spectra: Time series power spectrum calculator

The Joker: A custom Monte Carlo sampler for binary-star and exoplanet radial velocity data
Vizic: Jupyter-based interactive visualization tool for astronomical catalogs

And twelve codes were added to the ASCL in February 2017:

Chempy: A flexible chemical evolution model for abundance fitting
corner: Corner plots
GalaxyGAN: Generative Adversarial Networks for recovery of galaxy features
GRIM: General Relativistic Implicit Magnetohydrodynamics
HOURS: Simulation and analysis software for the KM3NeT

JetCurry: Modeling 3D geometry of AGN jets from 2D images
juwvid: Julia code for time-frequency analysis
KEPLER: General purpose 1D multizone hydrodynamics code
ORBE: Orbital integrator for educational purposes
stream-stream: Stellar and dark-matter streams interactions

streamgap-pepper: Effects of peppering streams with many small impacts
Validation: Codes to compare simulation data to various observations

December 2016 additions to the ASCL

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

AUTOSTRUCTURE: General program for calculation of atomic and ionic properties
BaTMAn: Bayesian Technique for Multi-image Analysis
CELib: Software library for simulations of chemical evolution
CRETE: Comet RadiativE Transfer and Excitation
dacapo_calibration: Photometric calibration code

Earthshine simulator: Idealized images of the Moon
flexCE: Flexible one-zone chemical evolution code
GAMER: GPU-accelerated Adaptive MEsh Refinement code
Grackle: Chemistry and radiative cooling library for astrophysical simulations
InversionKit: Linear inversions from frequency data

libprofit: Image creation from luminosity profiles
LSDCat: Line Source Detection and Cataloguing Tool
Meso-NH: Non-hydrostatic mesoscale atmospheric model
ProFit: Bayesian galaxy fitting tool
pylightcurve: Exoplanet lightcurve model

PyORBIT: Exoplanet orbital parameters and stellar activity
PyProfit: Wrapper for libprofit
Python-CPL: Python interface for the ESO Common Pipeline Library
QSFit: Quasar Spectral FITting
REPS: REscaled Power Spectra for initial conditions with massive neutrinos

Superplot: Graphical interface for plotting and analyzing data
Trident: Synthetic spectrum generator

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