PYESSENCE evolves linearly perturbed coupled quintessence models with multiple (cold dark matter) CDM fluid species and multiple DE (dark energy) scalar fields, and can be used to generate quantities such as the growth factor of large scale structure for any coupled quintessence model with an arbitrary number of fields and fluids and arbitrary couplings.
The Python script/package pyExtinction computes and plots total atmospheric extinction from decomposition into physical components (Rayleigh attenuation, ozone absorption, aerosol extinction). Its default extinction parameters are adapted to mean Mauna Kea summit conditions.
PyFITS provides an interface to FITS formatted files in the Python scripting language and PyRAF, the Python-based interface to IRAF. It is useful both for interactive data analysis and for writing analysis scripts in Python using FITS files as either input or output. PyFITS is a development project of the Science Software Branch at the Space Telescope Science Institute.
Pyflation is a Python package for calculating cosmological perturbations during an inflationary expansion of the universe. The modules in the pyflation Python package can be used to run simulations of different scalar field models of the early universe. The main classes are contained in the cosmomodels module and include simulations of background fields and first order and second order perturbations. The sourceterm package contains modules required for the computation of the term required for the evolution of second order perturbations.
Alongside the Python package, the bin directory contains Python scripts which can run first and second order simulations. A helper script called pyflation-qsubstart.py sets up a full second order run (including background, first order and source calculations) to be used on queueing system which contains the qsub executable (e.g. a Rocks cluster).
pygad provides a framework for dealing with Gadget snapshots. The code reads any of the many different Gadget (ascl:0003.001) formats, allows easy masking snapshots to particles of interest, decorates the data blocks with units, allows to add automatically updating derived blocks, and provides several binning and plotting routines, among other tasks, to provide convenient, intuitive handling of the Gadget data without the need to worry about technical details. pygad provides access to single stellar population (SSP) models, has an interface to Rockstar (ascl:1210.008) output files, provides its own friends-of-friends (FoF) finder, calculates spherical overdensities, and has a sub-module to generate mock absorption lines.
PyGFit measures PSF-matched photometry from images with disparate pixel scales and PSF sizes; its primary purpose is to extract robust spectral energy distributions (SEDs) from crowded images. It fits blended sources in crowded, low resolution images with models generated from a higher resolution image, thus minimizing the impact of crowding and also yielding consistently measured fluxes in different filters which minimizes systematic uncertainty in the final SEDs.
pyGMMis is a mixtures-of-Gaussians density estimation method that accounts for arbitrary incompleteness in the process that creates the samples as long as the incompleteness is known over the entire feature space and does not depend on the sample density (missing at random). pyGMMis uses the Expectation-Maximization procedure and generates its best guess of the unobserved samples on the fly. It can also incorporate an uniform "background" distribution as well as independent multivariate normal measurement errors for each of the observed samples, and then recovers an estimate of the error-free distribution from which both observed and unobserved samples are drawn. The code automatically segments the data into localized neighborhoods, and is capable of performing density estimation with millions of samples and thousands of model components on machines with sufficient memory.
PyGSM is a Python interface for the Global Sky Model (GSM, ascl:1011.010). The GSM is a model of diffuse galactic radio emission, constructed from a variety of all-sky surveys spanning the radio band (e.g. Haslam and WMAP). PyGSM uses the GSM to generate all-sky maps in Healpix format of diffuse Galactic radio emission from 10 MHz to 94 GHz. The PyGSM module provides visualization utilities, file output in FITS format, and the ability to generate observed skies for a given location and date. PyGSM requires Healpy, PyEphem (ascl:1112.014), and AstroPy (ascl:1304.002).
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.
PyKE is a python-based PyRAF package that can also be run as a stand-alone program within a unix-based shell without compiling against PyRAF. It is a group of tasks developed for the reduction and analysis of Kepler Simple Aperture Photometry (SAP) data of individual targets with individual characteristics. The main purposes of these tasks are to i) re-extract light curves from manually-chosen pixel apertures and ii) cotrend and/or detrend the data in order to reduce or remove systematic noise structure using methods tunable to user and target-specific requirements. PyKE is an open source project and contributions of new tasks or enhanced functionality of existing tasks by the community are welcome.
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.
pyLCSIM simulates X-ray lightcurves from coherent signals and power spectrum models. Coherent signals can be specified as a sum of one or more sinusoids, each with its frequency, pulsed fraction and phase shift; or as a series of harmonics of a fundamental frequency (each with its pulsed fraction and phase shift). Power spectra can be simulated from a model of the power spectrum density (PSD) using as a template one or more of the built-in library functions. The user can also define his/her custom models. Models are additive.
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.
pylightcurve is a model for light-curves of transiting planets. It uses the four coefficients law for the stellar limb darkening and returns the relative flux, F(t), as a function of the limb darkening coefficients, an, the Rp/R* ratio and all the orbital parameters based on the nonlinear limb darkening model (Claret 2000).
pyLIMA is an open source software for microlensing modeling. Based on Python, the goal is to offer to users an efficient and user friendly package to analyze their data. The code is written and tested with professional standards, such as PEP8 or unit testing.
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.
PyMC3 performs Bayesian statistical modeling and model fitting focused on advanced Markov chain Monte Carlo and variational fitting algorithms. It offers powerful sampling algorithms, such as the No U-Turn Sampler, allowing complex models with thousands of parameters with little specialized knowledge of fitting algorithms, intuitive model specification syntax, and optimization for finding the maximum a posteriori (MAP) point. PyMC3 uses Theano to compute gradients via automatic differentiation as well as compile probabilistic programs on-the-fly to C for increased speed.
pyMCZ calculates metallicity according to a number of strong line metallicity diagnostics from spectroscopy line measurements and obtain 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.
PyMGC3 is a Python toolkit to apply the Modified Great Circle Cell Counts (mGC3) method to search for tidal streams in the Galactic Halo. The code computes pole count maps using the full mGC3/nGC3/GC3 family of methods. The original GC3 method (Johnston et al., 1996) uses positional information to search for 'great-circle-cell structures'; mGC3 makes use of full 6D data and nGC3 uses positional and proper motion data.
PyMidas is an interface between Python and MIDAS, the major ESO legacy general purpose data processing system. PyMidas allows a user to exploit both the rich legacy of MIDAS software and the power of Python scripting in a unified interactive environment. PyMidas also allows the usage of other Python-based astronomical analysis systems such as PyRAF.
PyMOC manipulates Multi-Order Coverage (MOC) maps. It supports reading and writing the three encodings mentioned in the IVOA MOC recommendation: FITS, JSON and ASCII.
PyModelFit provides a pythonic, object-oriented framework that simplifies the task of designing numerical models to fit data. This is a very broad task, and hence the current functionality of PyModelFit focuses on the simpler tasks of 1D curve-fitting, including a GUI interface to simplify interactive work (using Enthought Traits). For more complicated modeling, PyModelFit also provides a wide range of classes and a framework to support more general model/data types (2D to Scalar, 3D to Scalar, 3D to 3D, and so on).
PyMSES provides a python solution for getting data out of RAMSES (ascl:1011.007) astrophysical fluid dynamics simulations. It permits transparent manipulation of large simulations and interfaces with common Python libraries and existing code, and can serve as a post-processing toolbox for data analysis. It also does three-dimensional volume rendering with a specific algorithm optimized to work on RAMSES distributed data (Guillet et al. 2011 and Jones et a. 2011).
PyMultiNest provides programmatic access to MultiNest (ascl:1109.006) and PyCuba, integration existing Python code (numpy, scipy), and enables writing Prior & LogLikelihood functions in Python. PyMultiNest can plot and visualize MultiNest's progress and allows easy plotting, visualization and summarization of MultiNest results. The plotting can be run on existing MultiNest output, and when not using PyMultiNest for running MultiNest.
PyMVPA eases statistical learning analyses of large datasets. It offers an extensible framework with a high-level interface to a broad range of algorithms for classification, regression, feature selection, data import and export. It is designed to integrate well with related software packages, such as scikit-learn, shogun, and MDP.
Pynbody is a lightweight, portable, format-transparent analysis package for astrophysical N-body and smooth particle hydrodynamic simulations supporting PKDGRAV/Gasoline, Gadget, N-Chilada, and RAMSES AMR outputs. Written in python, the core tools are accompanied by a library of publication-level analysis routines.
PyNeb (previously PyNebular) is an update and expansion of the IRAF package NEBULAR; rewritten in Python, it is designed to be more user-friendly and powerful, increasing the speed, easiness of use, and graphic visualization of emission lines analysis. In PyNeb, the atom is represented as an n-level atom. For given density and temperature, PyNeb solves the equilibrium equations and determines the level populations. PyNeb can compute physical conditions from suitable diagnostic line ratios and level populations, critical densities and line emissivities, and can compute and display emissivity grids as a function of Te and Ne. It can also deredden line intensities, read and manage observational data, and plot and compare atomic data from different publications, and compute ionic abundances from line intensities and physical conditions and elemental abundances from ionic abundances and icfs.
PynPoint uses principal component analysis to detect and estimate the flux of exoplanets in two-dimensional imaging data. It processes many, typically several thousands, of frames to remove the light from the star so as to reveal the companion planet.
PyORBIT handles several kinds of datasets, such as radial velocity (RV), activity indexes, and photometry, to simultaneously characterize the orbital parameters of exoplanets and the noise induced by the activity of the host star. RV computation is performed using either non-interacting Kepler orbits or n-body integration. Stellar activity can be modeled either with sinusoids at the rotational period and its harmonics or Gaussian process. In addition, the code can model offsets and systematics in measurements from several instruments. The PyORBIT code is modular; new methods for stellar activity modeling or parameter estimation can easily be incorporated into the code.
PyPHER (Python-based PSF Homogenization kERnels) computes an homogenization kernel between two PSFs; the code is well-suited for PSF matching applications in both an astronomical or microscopy context. It can warp (rotation + resampling) the PSF images (if necessary), filter images in Fourier space using a regularized Wiener filter, and produce a homogenization kernel. PyPHER requires the pixel scale information to be present in the FITS files, which can if necessary be added by using the provided ADDPIXSCL method.
pyprofit is a python wrapper for libprofit (ascl:1612.003).
PyPulse handles PSRFITS files and performs subsequent analyses on pulse profiles.
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.
PyRAF is a command language for running IRAF tasks that is based on the Python scripting language. It gives users the ability to run IRAF tasks in an environment that has all the power and flexibility of Python. PyRAF can be installed along with an existing IRAF installation; users can then choose to run either PyRAF or the IRAF CL.
A python interface to the JINA reaclib nuclear reaction database
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.
The PySALT user package contains the primary reduction and analysis software tools for the SALT telescope. Currently, these tools include basic data reductions for RSS and SALTICAM in both imaging, spectroscopic, and slot modes. Basic analysis software for slot mode data is also provided. These tools are primarily written in python/PyRAF with some additional IRAF code.
PySM generates full-sky simulations of Galactic foregrounds in intensity and polarization relevant for CMB experiments. The components simulated are thermal dust, synchrotron, AME, free-free, and CMB at a given Nside, with an option to integrate over a top hat bandpass, to add white instrument noise, and to smooth with a given beam. PySM is based on the large-scale Galactic part of Planck Sky Model code and uses some of its inputs
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.
pysovo contains basic tools to work with VOEvents. Though written for specific needs, others interested in VOEvents may find it useful to examine.
PySpecKit is a Python spectroscopic analysis and reduction toolkit meant to be generally applicable to optical, infrared, and radio spectra. It is capable of reading FITS-standard and many non-standard file types including CLASS spectra. It contains procedures for line fitting including gaussian and voigt profile fitters, and baseline-subtraction routines. It is capable of more advanced line fitting using arbitrary model grids. Fitting can be done both in batch mode and interactively. PySpecKit also produces publication-quality plots with TeX axis labels and annotations. It is designed to be extensible, allowing user-written reader, writer, and fitting routines to be "plugged in." It is actively under development and currently in the 'alpha' phase, with plans for a beta release.
pysynphot is a synthetic photometry software package suitable for either library or interactive use. Intended as a modern-language successor to the IRAF/STSDAS synphot package, it provides improved algorithms that address known shortcomings in synphot, and its object-oriented design is more easily extensible than synphot's task-oriented approach. It runs under PyRAF, and a backwards compatibility mode is provided that recognizes all spectral and throughput tables, obsmodes, and spectral expressions used by synphot, to facilitate the transition for legacy code.
Python-CPL is a framework to configure and execute pipeline recipes written with the Common Pipeline Library (CPL) (ascl:1402.010) with Python2 or Python3. The input, calibration and output data can be specified as FITS files or as astropy.io.fits objects in memory. The package is used to implement the MUSE pipeline in the AstroWISE data management system.
Characterization of the frequency response of coherent radiometric receivers is a key element in estimating the flux of astrophysical emissions, since the measured signal depends on the convolution of the source spectral emission with the instrument band shape. Python-qucs automates the process of preparing input data, running simulations and exporting results of QUCS (Quasi Universal Circuit Simulator) simulations.
PythonPhot is a simple Python translation of DAOPHOT-type (ascl:1104.011) photometry procedures from the IDL AstroLib (Landsman 1993), including aperture and PSF-fitting algorithms, with a few modest additions to increase functionality and ease of use. These codes allow fast, easy, and reliable photometric measurements and are currently used in the Pan-STARRS supernova pipeline and the HST CLASH/CANDELS supernova analysis.
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.
PyTransport calculates the 2-point and 3-point function of inflationary perturbations produced during multi-field inflation. The core of PyTransport is C++ code which is automatically edited and compiled into a Python module once an inflationary potential is specified. This module can then be called to solve the background inflationary cosmology as well as the evolution of correlations of inflationary perturbations. PyTransport includes two additional modules written in Python, one to perform the editing and compilation, and one containing a suite of functions for common tasks such as looping over the core module to construct spectra and bispectra.
PyVO provides access to remote data and services of the Virtual observatory (VO) using Python. It allows archive searches for data of a particular type or related to a particular topic and query submissions to obtain data to a particular archive to download selected data products. PyVO supports querying the VAO registry; simple data access services (DAL) to access images (SIA), source catalog records (Cone Search), spectra (SSA), and spectral line emission/absorption data (SLAP); and object name resolution (for converting names of objects in the sky into positions). PyVO requires both AstroPy and NumPy.
PyWiFeS is a Python-based data reduction pipeline for the Wide Field Spectrograph (WiFeS). Its core data processing routines are built on standard scientific Python packages commonly used in astronomical applications. It includes an implementation of a global optical model of the spectrograph which provides wavelengths solutions accurate to ˜0.05 Å (RMS) across the entire detector. Through scripting, PyWiFeS can enable batch processing of large quantities of data.
pyXSIM simulates X-ray observations from astrophysical sources. X-rays probe the high-energy universe, from hot galaxy clusters to compact objects such as neutron stars and black holes and many interesting sources in between. pyXSIM generates synthetic X-ray observations of these sources from a wide variety of models, whether from grid-based simulation codes such as FLASH (ascl:1010.082), Enzo (ascl:1010.072), and Athena (ascl:1010.014), to particle-based codes such as Gadget (ascl:0003.001) and AREPO, and even from datasets that have been created “by hand”, such as from NumPy arrays. pyXSIM can also manipulate the synthetic observations it produces in various ways and export the simulated X-ray events to other software packages to simulate the end products of specific X-ray observatories. pyXSIM is an implementation of the PHOX (ascl:1112.004) algorithm and was initially the photon_simulator analysis module in yt (ascl:1011.022); it is dependent on yt.
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.
QFitsView is a FITS file viewer that can display one, two, and three-dimensional FITS files. It has three modes of operation, depending of what kind of data is being displayed. One-dimensional data are shown in an x-y plot. Two-dimensional images are shown in the main window. Three-dimensional data cubes can be displayed in a variety of ways, with the third dimension shown as a x-y plot at the bottom of the image display. QFitsView was written in C++ and uses the Qt widget library, which makes it available for all major platforms: Windows, MAC OS X, and many Unix variants.
Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. It handles roundoff errors from floating point arithmetic. It computes volumes, surface areas, and approximations to the convex hull.
QSFit performs automatic analysis of Active Galactic Nuclei (AGN) optical spectra. It provides estimates of: AGN continuum luminosities and slopes at several restframe wavelengths; luminosities, widths and velocity offsets of 20 emission lines; luminosities of iron blended lines at optical and UV wavelengths; host galaxy luminosities. The whole fitting process is customizable for specific needs, and can be extended to analyze spectra from other data sources. The ultimate purpose of QSFit is to allow astronomers to run standardized recipes to analyze the AGN data, in a simple, replicable and shareable way.
QtClassify is a GUI that helps classify emission lines found in integral field spectroscopic data. Input needed is a datacube as well as a catalog with emission lines and a signal-to-noise cube, such at that created by LSDCat (ascl:1612.002). The main idea is to take each detected line and guess what line it could be (and thus the redshift of the object). You would expect to see other lines that might not have been detected but are visible in the cube if you know where to look, which is why parts of the spectrum are shown where other lines are expected. In addition, monochromatic layers of the datacube are displayed, making it easy to spot additional emission lines.
Quickclump finds clumps in a 3D FITS datacube. It is a fast, accurate, and automated tool written in Python. Though Quickclump is primarily intended for decomposing observations of interstellar clouds into individual clumps, it can also be used for finding clumps in any 3D rectangular data.
QUICKCV is an IDL sample variance/cosmic variance calculator for some geometry.
QuickReduce quickly reduces data for ODI and is optimized for a first data inspection during acquisition at the the telescope. When installed on the ODI observer's interface, QuickReduce, coded in Python, performs all basic reduction steps as well as more advanced corrections for pupil-ghost removal, fringe correction and masking of persistent pixels and is capable enough for science-quality data reductions. It can also add an accurate astrometric WCS solution based on the 2MASS reference system as well as photometric zeropoint calibration for frames covered by the SDSS foot-print. The pipeline makes use of multiple CPU-cores wherever possible, resulting in an execution time of only a few seconds per frame, thus offering the ODI observer a convenient way to closely monitor data quality.
QYMSYM is a GPU accelerated 2nd order hybrid symplectic integrator that identifies close approaches between particles and switches from symplectic to Hermite algorithms for particles that require higher resolution integrations. This is a parallel code running with CUDA on a video card that puts the many processors on board to work while taking advantage of fast shared memory.
We present r-Java, an r-process code for open use, that performs r-process nucleosynthesis calculations. Equipped with a simple graphical user interface, r-Java is capable of carrying out nuclear statistical equilibrium (NSE) as well as static and dynamic r-process calculations for a wide range of input parameters. In this introductory paper, we present the motivation and details behind r-Java, and results from our static and dynamic simulations. Static simulations are explored for a range of neutron irradiation and temperatures. Dynamic simulations are studied with a parameterized expansion formula. Our code generates the resulting abundance pattern based on a general entropy expression that can be applied to degenerate as well as non-degenerate matter, allowing us to track the rapid density and temperature evolution of the ejecta during the initial stages of ejecta expansion. At present, our calculations are limited to the waiting-point approximation.
R3D was developed to reduce fiber-based integral field spectroscopy (IFS) data. The package comprises a set of command-line routines adapted for each of these steps, suitable for creating pipelines. The routines have been tested against simulations, and against real data from various integral field spectrographs (PMAS, PPAK, GMOS, VIMOS and INTEGRAL). Particular attention is paid to the treatment of cross-talk.
R3D unifies the reduction techniques for the different IFS instruments to a single one, in order to allow the general public to reduce different instruments data in an homogeneus, consistent and simple way. Although still in its prototyping phase, it has been proved to be useful to reduce PMAS (both in the Larr and the PPAK modes), VIMOS and INTEGRAL data. The current version has been coded in Perl, using PDL, in order to speed-up the algorithm testing phase. Most of the time critical algorithms have been translated to C[float=][/float], and it is our intention to translate all of them. However, even in this phase R3D is fast enough to produce valuable science frames in reasonable time.
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.
The large quantity and high quality of modern radio and infrared line observations require efficient modeling techniques to infer physical and chemical parameters such as temperature, density, and molecular abundances. Radex calculates the intensities of atomic and molecular lines produced in a uniform medium, based on statistical equilibrium calculations involving collisional and radiative processes and including radiation from background sources. Optical depth effects are treated with an escape probability method. The program makes use of molecular data files maintained in the Leiden Atomic and Molecular Database (LAMDA), which will continue to be improved and expanded. The performance of the program is compared with more approximate and with more sophisticated methods. An Appendix provides diagnostic plots to estimate physical parameters from line intensity ratios of commonly observed molecules. This program should form an important tool in analyzing observations from current and future radio and infrared telescopes.
RADICAL is a multi-purpose 2-D radiative transfer code for axi-symmetric circumstellar (or circum-black-hole) envelopes /disks / tori etc. It has been extensively tested and found reliable and accurate. The code has recently been supplemented with a Variable Eddington Tensor module which enables it to solve dust continuum radiative transfer problems from very low up to extremely high optical depths with only a few (about 7) iterations at most.
RADLite is a raytracer that is optimized for producing infrared line spectra and images from axisymmetric density structures, originally developed to function on top of the dust radiative transfer code RADMC. RADLite can consistently deal with a wide range of velocity gradients, such as those typical for the inner regions of protoplanetary disks. The code is intended as a back-end for chemical and excitation codes, and can rapidly produce spectra of thousands of lines for grids of models for comparison with observations. It includes functionality for simulating telescopic images for optical/IR/midIR/farIR telescopes. It takes advantage of multi-threaded CPUs and includes an escape-probability non-LTE module.
RADMC-3D is a software package for astrophysical radiative transfer calculations in arbitrary 1-D, 2-D or 3-D geometries. It is mainly written for continuum radiative transfer in dusty media, but also includes modules for gas line transfer and gas continuum transfer. RADMC-3D is a new incarnation of the older software package RADMC (ascl:1108.016).
RADMC is a 2-D Monte-Carlo code for dust continuum radiative transfer circumstellar disks and envelopes. It is based on the method of Bjorkman & Wood (ApJ 2001, 554, 615), but with several modifications to produce smoother results with fewer photon packages.
The RADPACK package, written in IDL, contains both data and software. The data are the constraints on the cosmic microwave background (CMB) angular power spectrum from all published data as of 9/99. A unique aspect of this compilation is that the non-Gaussianity of the uncertainties has been characterized. The most important program in the package, written in the IDL language, is called chisq.pro and calculates $chi^2$, for an input power spectrum, according to the offset log-normal form of Bond, Jaffe and Knox (astro-ph/9808264). chisq.pro also outputs files that are useful for examining the residuals (the difference between the predictions of the model and the data). There is an sm macro for plotting up the residuals, and a histogram of the residuals. The histogram is actually for the 'whitenend' residuals ---a linear combination of the residuals which leaves them uncorrelated and with unit variance. The expectation is that the whitened residuals will be distributed as a Gaussian with unit variance.
Raga (Relaxation in Any Geometry) is a Monte Carlo simulation method for gravitational dynamics of non-spherical stellar systems. It is based on the SMILE software (ascl:1308.001) for orbit analysis. It can simulate stellar systems with a much smaller number of particles N than the number of stars in the actual system, represent an arbitrary non-spherical potential with a basis-set or spline spherical-harmonic expansion with the coefficients of expansion computed from particle trajectories, and compute particle trajectories independently and in parallel using a high-accuracy adaptive-timestep integrator. Raga can also model two-body relaxation by local (position-dependent) velocity diffusion coefficients (as in Spitzer's Monte Carlo formulation) and adjust the magnitude of relaxation to the actual number of stars in the target system, and model the effect of a central massive black hole.
RamsesGPU is a reimplementation of RAMSES (ascl:1011.007) which drops the adaptive mesh refinement (AMR) features to optimize 3D uniform grid algorithms for modern graphics processor units (GPU) to provide an efficient software package for astrophysics applications that do not need AMR features but do require a very large number of integration time steps. RamsesGPU provides an very efficient C++/CUDA/MPI software implementation of a second order MUSCL-Handcock finite volume fluid solver for compressible hydrodynamics as a magnetohydrodynamics solver based on the constraint transport technique. Other useful modules includes static gravity, dissipative terms (viscosity, resistivity), and forcing source term for turbulence studies, and special care was taken to enhance parallel input/output performance by using state-of-the-art libraries such as HDF5 and parallel-netcdf.
A new N-body and hydrodynamical code, called RAMSES, is presented. It has been designed to study structure formation in the universe with high spatial resolution. The code is based on Adaptive Mesh Refinement (AMR) technique, with a tree based data structure allowing recursive grid refinements on a cell-by-cell basis. The N-body solver is very similar to the one developed for the ART code (Kravtsov et al. 97), with minor differences in the exact implementation. The hydrodynamical solver is based on a second-order Godunov method, a modern shock-capturing scheme known to compute accurately the thermal history of the fluid component. The accuracy of the code is carefully estimated using various test cases, from pure gas dynamical tests to cosmological ones. The specific refinement strategy used in cosmological simulations is described, and potential spurious effects associated to shock waves propagation in the resulting AMR grid are discussed and found to be negligible. Results obtained in a large N-body and hydrodynamical simulation of structure formation in a low density LCDM universe are finally reported, with 256^3 particles and 4.1 10^7 cells in the AMR grid, reaching a formal resolution of 8192^3. A convergence analysis of different quantities, such as dark matter density power spectrum, gas pressure power spectrum and individual haloes temperature profiles, shows that numerical results are converging down to the actual resolution limit of the code, and are well reproduced by recent analytical predictions in the framework of the halo model.
RATRAN is a numerical method and computer code to calculate the radiative transfer and excitation of molecular lines. The approach is based on the Monte Carlo method, and incorporates elements from Accelerated Lambda Iteration. It combines the flexibility of the former with the speed and accuracy of the latter. Convergence problems known to plague Monte Carlo methods at large optical depth (>100) are avoided by separating local contributions to the radiation field from the overall transfer problem. The random nature of the Monte Carlo method serves to verify the independence of the solution to the angular, spatial, and frequency sampling of the radiation field. This allows the method to be used in a wide variety of astrophysical problems without specific adaptations. Moreover, the code can be applied to all atoms or molecules for which collisional rate coefficients are available and any axially symmetric source model. Continuum emission and absorption by dust is explicitly taken into account but scattering is neglected. We expect this program to be an important tool in analyzing data from present and future infrared and (sub-)millimeter telescopes.
Time-distance helioseismology aims to measure and interpret the travel times of waves propagating between two points located on the solar surface. The travel times are then inverted to infer sub-surface properties that are encoded in the measurements. The trajectory of the waves generally follows that of the infinite-frequency ray path, although they are sensitive to perturbations off of this path. Finite-frequency sensitivity kernels are thus needed to give more accurate inversion results.
Ray tracing codes calculate travel time kernels for a ray. There are three main codes which calculate the group time as a function of distance, the ray paths as well as the phase and group times along the path, and the ray kernels for the sound speed squared.
The RC3 mosaicking pipeline creates color composite images and scientifically-calibrated FITS mosaics in all SDSS imaging bands for all the RC3 galaxies that lie within the survey’s footprint and on photographic plates taken by the Digitized Palomar Observatory Sky Survey (DPOSS) for the B, R, IR bands. The pipeline uses SExtractor (ascl:1010.064) for extraction and STIFF (ascl:1110.006) to generating color images. The mosaicking program uses a recursive algorithm for positional update first to correct the positional inaccuracy inherent in the RC3 catalog, then conducts the mosaicking procedure using the Astropy (ascl:1304.002) wrapper to IPAC's Montage (ascl:1010.036) software. The program is generalized into a pipeline that can be easily extended to future survey data or other source catalogs; an online interface is available at
RDGEN is a collection of routines for data handling, display, and adjusting, with a facility which helps to set up files for using with VPFIT (ascl:1408.015); it is included in the VPFIT distribution file. It is useful for setting region boundaries and initial guesses for VPFIT, for displaying the accumulated results, for examining by eye particular redshift systems and fits to them, testing that the error array is a true reflection of the rms scatter in the data, comparing spectra and generally examining and even modifying the data.
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.
In recent years, the freely available Monte Carlo code REAS for modelling radio emission from cosmic ray air showers has evolved to include the full complexity of air shower physics. However, it turned out that in REAS2 and all other time-domain models which calculate the radio emission by superposing the radiation of the single air shower electrons and positrons, the calculation of the emission contributions was not fully consistent. In this article, we present a revised implementation in REAS3, which incorporates the missing radio emission due to the variation of the number of charged particles during the air shower evolution using an "end-point formalism". With the inclusion of these emission contributions, the structure of the simulated radio pulses changes from unipolar to bipolar, and the azimuthal emission pattern becomes nearly symmetric. Remaining asymmetries can be explained by radio emission due to the variation of the net charge excess in air showers, which is automatically taken into account in the new implementation. REAS3 constitutes the first self-consistent time-domain implementation based on single particle emission taking the full complexity of air shower physics into account, and is freely available for all interested users.
REBOUND is a multi-purpose N-body code which is freely available under an open-source license. It was designed for collisional dynamics such as planetary rings but can also solve the classical N-body problem. It is highly modular and can be customized easily to work on a wide variety of different problems in astrophysics and beyond.
REBOUND comes with three symplectic integrators: leap-frog, the symplectic epicycle integrator (SEI) and a Wisdom-Holman mapping (WH). It supports open, periodic and shearing-sheet boundary conditions. REBOUND can use a Barnes-Hut tree to calculate both self-gravity and collisions. These modules are fully parallelized with MPI as well as OpenMP. The former makes use of a static domain decomposition and a distributed essential tree. Two new collision detection modules based on a plane-sweep algorithm are also implemented. The performance of the plane-sweep algorithm is superior to a tree code for simulations in which one dimension is much longer than the other two and in simulations which are quasi-two dimensional with less than one million particles.
RECFAST calculates the recombination of H, HeI, and HeII in the early Universe; this involves a line-by-line treatment of each atomic level. It differs in comparison to previous calculations in two major ways: firstly, the ionization fraction x_e is approximately 10% smaller for redshifts <~800, due to non-equilibrium processes in the excited states of H, and secondly, HeI recombination is much slower than previously thought, and is delayed until just before H recombines. RECFAST enables fast computation of the ionization history (and quantities such as the power spectrum of CMB anisotropies which depend on it) for arbitrary cosmologies.
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.
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.
Reflex provides an easy and flexible way to reduce VLT/VLTI science data using the ESO pipelines. It allows graphically specifying the sequence in which the data reduction steps are executed, including conditional stops, loops and conditional branches. It eases inspection of the intermediate and final data products and allows repetition of selected processing steps to optimize the data reduction. The data organization necessary to reduce the data is built into the system and is fully automatic; advanced users can plug their own modules and steps into the data reduction sequence. Reflex supports the development of data reduction workflows based on the ESO Common Pipeline Library. Reflex is based on the concept of a scientific workflow, whereby the data reduction cascade is rendered graphically and data seamlessly flow from one processing step to the next. It is distributed with a number of complete test datasets so users can immediately start experimenting and familiarize themselves with the system.
RegiStax is software for alignment/stacking/processing of images; it was released over 10 years ago and continues to be developed and improved. The current version is RegiStax 6, which supports the following formats: AVI, SER, RFL (RegiStax Framelist), BMP, JPG, TIF, and FIT. This version has a shorter and simpler processing sequence than its predecessor, and optimizing isn't necessary anymore as a new image alignment method optimizes directly. The interface of RegiStax 6 has been simplified to look more uniform in appearance and functionality, and RegiStax 6 now uses Multi-core processing, allowing the user to have up to have multiple cores(recommended to use maximally 4) working simultaneous during alignment/stacking.
RegPT computes the power spectrum in flat wCDM class models based on the RegPT treatment when provided with either of transfer function or matter power spectrum. It then gives the multiple-redshift outputs for power spectrum, and optionally provides correlation function data. The Fortran code has two major options for power spectrum calculations; -fast, which quickly computes the power spectrum at two-loop level (typically a few seconds) using the pre-computed data set of PT kernels for fiducial cosmological models, and -direct, in which the code first applies the fast method, and then follows the regularized expression for power spectrum to directly evaluate the multi-dimensional integrals. The output results are the power spectrum of direct calculation and difference of the results between fast and direct method. The code also gives the data set of PT diagrams necessary for power spectrum calculations from which the power spectrum can be constructed.
REPS (REscaled Power Spectra) provides accurate, one-percent level, numerical simulations of the initial conditions for massive neutrino cosmologies, rescaling the late-time linear power spectra to the simulation initial redshift.
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).
rfpipe is a fast radio interferometric transient search pipeline, and is the next generation of rtpipe (scl:1706.002).
A lightweight R-language implementation of the affine-invariant Markov Chain Monte Carlo sampling method of Goodman & Weare (2010).
RH 1.5D performs Zeeman multi-level non-local thermodynamical equilibrium calculations with partial frequency redistribution for an arbitrary amount of chemical species. Derived from the RH code and written in C, it calculates spectra from 3D, 2D or 1D atmospheric models on a column-by-column basis (or 1.5D). It includes optimization features to speed up or improve convergence, which are particularly useful in dynamic models of chromospheres. While one should be aware of its limitations, the calculation of spectra using the 1.5D or column-by-column is a good approximation in many cases, and generally allows for faster convergence and more flexible methods of improving convergence. RH 1.5D scales well to at least tens of thousands of CPU cores.
RHOCUBE models 3D density distributions on a discrete Cartesian grid and their integrated 2D maps. It can be used for a range of applications, including modeling the electron number density in LBV shells and computing the emission measure. The RHOCUBE Python package provides several 3D density distributions, including a powerlaw shell, truncated Gaussian shell, constant-density torus, dual cones, and spiralling helical tubes, and can accept additional distributions. RHOCUBE provides convenient methods for shifts and rotations in 3D, and if necessary, an arbitrary number of density distributions can be combined into the same model cube and the integration ∫ dz performed through the joint density field.
RICH (Racah Institute Computational Hydrodynamics) is a 2D hydrodynamic code based on Godunov's method. The code, largely based on AREPO, acts on an unstructured moving mesh. It differs from AREPO in the interpolation and time advancement scheme as well as a novel parallelization scheme based on Voronoi tessellation. Though not universally true, in many cases a moving mesh gives better results than a static mesh: where matter moves one way and a sound wave is traveling in the other way (such that relative to the grid the wave is not moving), a static mesh gives better results than a moving mesh. RICH is designed in an object oriented, user friendly way that facilitates incorporation of new algorithms and physical processes.
RM-CLEAN reads in dirty Q and U cubes, generates rmtf based on the frequencies given in an ASCII file, and cleans the RM spectra following the algorithm given by Brentjens (2007). The output cubes contain the clean model components and the CLEANed RM spectra. The input cubes must be reordered with mode=312, and the output cubes will have the same ordering and thus must be reordered after being written to disk. RM-CLEAN runs as a MIRIAD (ascl:1106.007) task and a Python wrapper is included with the code.
Rmfit uses a forward-folding technique to obtain the best-fit parameters for a chosen model given user-selected source and background time intervals from data files containing observed count rates and a corresponding detector response matrix. rmfit displays lightcurves and spectra using a graphical interface that enables user-defined integrated or time-resolved spectral fits and binning in either time or energy. Originally developed for the analysis of BATSE Gamma-Ray Burst (GRB) spectroscopy, rmfit is a tool for the spectroscopy of transient sources; it accommodates the Fermi GBM and LAT data and Swift BAT.
RMHB is a hierarchical Bayesian code for reverberation mapping (RM) that combines results of a sparsely sampled broad line region (BLR) light curve and a large sample of active galactic nuclei (AGN) to infer properties of the sample of the AGN. The key idea of RM is to measure the time lag τ between variations in the continuum emission from the accretion disc and subsequent response of the broad line region (BLR). The measurement of τ is typically used to estimate the physical size of the BLR and is combined with other measurements to estimate the black hole mass MBH. A major difficulty with RM campaigns is the large amount of data needed to measure τ. RMHB allows a clear interpretation of a posterior distribution for hyperparameters describing the sample of AGN.
This program determines stellar population parameters (e.g. age, metallicity, IMF slope,...), using as input a pair of line-strength indices, through the interpolation in SSP model predictions. Both linear and bivariate fits are computed to perform the interpolation.
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.
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.
Roche is a visualization and analysis tool for drawing the Roche-lobe geometry of evolving binaries. Roche can be used as a standalone program reading data from the command line or from a file generated by SeBa (ascl:1201.003). Eventually Roche will be able to read data from any other binary evolution program. Roche requires Starlab (ascl:1010.076) version 4.1.1 or later and the pgplot (ascl:1103.002) libraries. Roche creates a series of images, based on the SeBa output file SeBa.data, displaying the evolutionary state of a binary.
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