Results 1001-1100 of 2452 (2411 ASCL, 41 submitted)
HIPSTER (HIgh-k Power Spectrum EstimatoR) computes small-scale power spectra and isotropic bispectra for cosmological simulations and galaxy surveys of arbitrary shape. The code computes the Legendre multipoles of the power spectrum, Pℓ(k), or bispectrum Bℓ(k1,k2), by computing weighted pair counts over the simulation box or survey, truncated at some maximum radius. The code can be run either in 'aperiodic' or 'periodic' mode for galaxy surveys or cosmological simulations respectively. HIPSTER also supports weighted spectra, for example when tracer particles are weighted by their mass in a multi-species simulation. Generalization to anisotropic bispectra is straightforward (and requires no additional computing time) and can be added on request.
HISS stacks HI (emission and absorption) spectra in a consistent and reliable manner to enable statistical analysis of average HI properties. It provides plots of the stacked spectrum and reference spectrum with any fitted function, of the stacked noise response, and of the distribution of the integrated fluxes when calculating the uncertainties. It also produces a table containing the integrated flux calculated from the fitted functions and the stacked spectrum, among other output files.
HLattice simulates scalar fields and gravity in the early universe. The code allows the user to select between symplectic integrators, descretization schemes, and metrics such as Minkowski or FRW backgrounds and adaptice schemes in an "all-in-one" configuration file.
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).
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.
HMF calculates the Halo Mass Function (HMF) given any set of cosmological parameters and fitting function and serves as the backend for the web application HMFcalc. Written in Python, it allows for dynamic accurate calculation of the transfer function with CAMB (ascl:1102.026) and efficient and self-consistent parameter updates. HMF offers exploration of the effects of cosmological parameters, redshift and fitting function on the predicted HMF.
HNBody is a new set of software utilities geared to the integration of hierarchical (nearly-Keplerian) N-body systems. Our focus is on symplectic methods, and we have included explicit support for three classes of particles (heavy, light, and massless), second and fourth order methods, post-Newtonian corrections, and the use of a symplectic corrector (among other things). For testing purposes, we also provide support for more general integration schemes (Bulirsch-Stoer & Runge-Kutta). Configuration files employing an intuitive syntax allow for easy problem setup, and many simple simulations can be done without the user compiling any code. Low-level interfaces are also available, enabling extensive customization.
HO-CHUNK calculates radiative equilibrium temperature solution, thermal and PAH/vsg emission, scattering and polarization in protostellar geometries. It is useful for computing spectral energy distributions (SEDs), polarization spectra, and images.
HOMER (Helper Of My Eternal Retrievals) is a machine-learning-accelerated Bayesian inverse modeling code. Given some data and uncertainties, the code determines the posterior distribution of a model. HOMER uses MC3 (ascl:1610.013) for its MCMC; its forward model is a neural network surrogate model trained by MARGE (ascl:2003.010). The code produces plots of the 1D marginalized posteriors, 2D pairwise posteriors, and parameter history traces, and can also overplot the 1D and 2D posteriors for comparison with another posterior. HOMER computes the Bhattacharyya coefficient to compare the similarity of two 1D marginalized posteriors.
We describe a new method (HOP) for identifying groups of particles in N-body simulations. Having assigned to every particle an estimate of its local density, we associate each particle with the densest of the Nh particles nearest to it. Repeating this process allows us to trace a path, within the particle set itself, from each particle in the direction of increasing density. The path ends when it reaches a particle that is its own densest neighbor; all particles reaching the same such particle are identified as a group. Combined with an adaptive smoothing kernel for finding the densities, this method is spatially adaptive, coordinate-free, and numerically straight-forward. One can proceed to process the output by truncating groups at a particular density contour and combining groups that share a (possibly different) density contour. While the resulting algorithm has several user-chosen parameters, we show that the results are insensitive to most of these, the exception being the outer density cutoff of the groups.
HOPE is a specialized Python just-in-time (JIT) compiler designed for numerical astrophysical applications. HOPE focuses on a subset of the language and is able to translate Python code into C++ while performing numerical optimization on mathematical expressions at runtime. To enable the JIT compilation, the user only needs to add a decorator to the function definition. By using HOPE, the user benefits from being able to write common numerical code in Python while getting the performance of compiled implementation.
HorizonGRound forward models general relativistic effects from the tracer luminosity function. It also compares relativistic corrections with the local primordial non-Gaussianity signature in ultra-large-scale clustering statistics. The package includes several recipes along with the data required to run them.
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.
The Hellenic Open University Reconstruction & Simulation (HOURS) software package contains a realistic simulation package of the detector response of very large (km3-scale) underwater neutrino telescopes, including an accurate description of all the relevant physical processes, the production of signal and background as well as several analysis strategies for triggering and pattern recognition, event reconstruction, tracking and energy estimation. HOURS also provides tools for simulating calibration techniques and other studies for estimating the detector sensitivity to several neutrino sources.
HII Region Models fits HII region models to observed radio recombination line and radio continuum data. The algorithm includes the calculations of departure coefficients to correct for non-LTE effects. HII Region Models has been used to model star formation in the nucleus of IC 342.
Hrothgar is a parallel minimizer and Markov Chain Monte Carlo generator. It has been used to solve optimization problems in astrophysics (galaxy cluster mass profiles) as well as in experimental particle physics (hadronic tau decays).
HSIM simulates observations with HARMONI on the Extremely Large Telescope. HSIM takes high spectral and spatial resolution input data cubes, encoding physical descriptions of astrophysical sources, and generates mock observed data cubes. The simulations incorporate detailed models of the sky, telescope, instrument, and detectors to produce realistic mock data. HSIM performs in-depth simulations for several key science cases as part of the design and development of the HARMONI integral field spectrograph, including the ELT AO performance, atmospheric effects and realistic detector statistics.
HSTCosmicrays finds and characterizes cosmic rays found in dark frames (exposures taken with the shutter closed) taken with instruments on the Hubble Space Telescope (HST). Dark exposures are obtained routinely by all the Hubble Space Telescope instruments for calibration. The main processing pipeline runs locally or in the cloud on AWS utilizing the HST Public Dataset.
HUAYNO implements integrators derived from second order Hamiltonian splitting for N-body dynamics. This integration scheme conserves energy and momentum with little or no systematic drift. The code uses an explicit but approximate formula for the time symmetrization that is compatible with the use of individual time steps, making an iterative scheme unnecessary. HUAYNO is available as part of the AMUSE package (ascl:1107.007).
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.
We describe the first parallel implementation of an adaptive particle-particle, particle-mesh code with smoothed particle hydrodynamics. Parallelisation of the serial code, "Hydra," is achieved by using CRAFT, a Cray proprietary language which allows rapid implementation of a serial code on a parallel machine by allowing global addressing of distributed memory.
The collisionless variant of the code has already completed several 16.8 million particle cosmological simulations on a 128 processor Cray T3D whilst the full hydrodynamic code has completed several 4.2 million particle combined gas and dark matter runs. The efficiency of the code now allows parameter-space explorations to be performed routinely using $64^3$ particles of each species. A complete run including gas cooling, from high redshift to the present epoch requires approximately 10 hours on 64 processors.
HydraLens generates gravitational lens model files for Lenstool (ascl:1102.004), PixeLens (ascl:1102.007), glafic (ascl:1010.012) and Lensmodel and can also translate lens model files among these four lens model codes. Through a GUI, the user enters a new model by specifying the type of model and is then led through screens to collect the data. Written in MS Visual Basic, the code can also translate an existing model from any of the four supported codes to any of the other three.
HydroCode1D is a 1D finite volume code that can run any problem with 1D or 2D/3D spherical symmetry including external gravity or self-gravity. The program provides, depending on the configuration, output files that contain the midpoint position, density, velocity and pressure for each cell in the grid (in SI units). The program will by default use all available threads (as given by the environment variable OMP_NUM_THREADS). This can be overwritten by giving the desired number of threads as a command line argument to the program.
The R package Hyper-Fit fits hyperplanes (hyper.fit) and creates 2D/3D visualizations (hyper.plot2d / hyper.plot3d) to produce robust 1D linear fits for 2D x vs y type data, and robust 2D plane fits to 3D x vs y vs z type data. This hyperplane fitting works generically for any N-1 hyperplane model being fit to a N dimensional dataset. All fits include intrinsic scatter in the generative model orthogonal to the hyperplane. A web interface for online fitting is also available at http://hyperfit.icrar.org.
Hyperion is a three-dimensional dust continuum Monte-Carlo radiative transfer code that is designed to be as generic as possible, allowing radiative transfer to be computed through a variety of three-dimensional grids. The main part of the code is problem-independent, and only requires an arbitrary three-dimensional density structure, dust properties, the position and properties of the illuminating sources, and parameters controlling the running and output of the code. Hyperion is parallelized, and is shown to scale well to thousands of processes. Two common benchmark models for protoplanetary disks were computed, and the results are found to be in excellent agreement with those from other codes. Finally, to demonstrate the capabilities of the code, dust temperatures, SEDs, and synthetic multi-wavelength images were computed for a dynamical simulation of a low-mass star formation region.
From a photometric catalogue, hyperz finds the redshift of each object by means of a standard SED fitting procedure, i.e. comparing the observed magnitudes with the expected ones, computed from template Spectral Energy Distributions. The set of templates used in the minimization procedure (age, metallicity, reddening, absorption in the Lyman forest, ...) is studied in detail, through both real and simulated data. The expected accuracy of photometric redshifts, as well as the fraction of catastrophic identifications and wrong detections, is given as a function of the redshift range, the set of filters considered, and the photometric accuracy. Special attention is paid to the results expected from real data.
We present a state-of-the-art primordial recombination code, HyRec, including all the physical effects that have been shown to significantly affect recombination. The computation of helium recombination includes simple analytic treatments of hydrogen continuum opacity in the He I 2 1P - 1 1S line, the He I] 2 3P - 1 1S line, and treats feedback between these lines within the on-the-spot approximation. Hydrogen recombination is computed using the effective multilevel atom method, virtually accounting for an infinite number of excited states. We account for two-photon transitions from 2s and higher levels as well as frequency diffusion in Lyman-alpha with a full radiative transfer calculation. We present a new method to evolve the radiation field simultaneously with the level populations and the free electron fraction. These computations are sped up by taking advantage of the particular sparseness pattern of the equations describing the radiative transfer. The computation time for a full recombination history is ~2 seconds. This makes our code well suited for inclusion in Monte Carlo Markov chains for cosmological parameter estimation from upcoming high-precision cosmic microwave background anisotropy measurements.
This IDL library is designed to be used on astronomical images. Its main aim is to stack data to allow a statistical detection of faint signal, using a prior. For instance, you can stack 160um data using the positions of galaxies detected at 24um or 3.6um, or use WMAP sources to stack Planck data. It can estimate error bars using bootstrap, and it can perform photometry (aperture photometry, or PSF fitting, or other that you can plug). The IAS Stacking Library works with gnomonic projections (RA---TAN), and also with HEALPIX projection.
Icarus is a stellar binary light curve synthesis tool that generates a star, given some basic binary parameters, by solving the gravitational potential equation, creating a discretized stellar grid, and populating the stellar grid with physical parameters, including temperature and surface gravity. Icarus also evaluates the outcoming flux from the star given an observer's point of view (i.e., orbital phase and orbital orientation).
ICICLE (Initial Conditions for Isolated CoLlisionless systEms) generates stable initial conditions for isolated collisionless systems that can then be used in NBody simulations. It supports the Navarro-Frenk-White, Hernquist, King and Einasto density profiles.
ICORE is a command-line driven co-addition, mosaicking, and resolution enhancement (HiRes) tool for creating science quality products from image data in FITS format and with World Coordinate System information following the FITS-WCS standard. It includes preparatory steps such as image background matching, photometric gain-matching, and pixel-outlier rejection. Co-addition and/or HiRes'ing can be performed in either the inertial WCS or in the rest frame of a moving object. Three interpolation methods are supported: overlap-area weighting, drizzle, and weighting by the detector Point Response Function (PRF). The latter enables the creation of matched-filtered products for optimal point-source detection, but most importantly allows for resolution enhancement using a spatially-dependent deconvolution method. This is a variant of the classic Richardson-Lucy algorithm with the added benefit to simultaneously register and co-add multiple images to optimize signal-to-noise and sampling of the instrumental PSF. It can assume real (or otherwise "flat") image priors, mitigate "ringing" artifacts, and assess the quality of image solutions using statistically-motivated convergence criteria. Uncertainties are also estimated and internally validated for all products. The software supports multithreading that can be configured for different architectures. Numerous example scripts are included (with test data) to co-add and/or HiRes image data from Spitzer-IRAC/MIPS, WISE, and Herschel-SPIRE.
What is the best way to pixelize a sphere? This question occurs in many practical applications, for instance when making maps (of the earth or the celestial sphere) and when doing numerical integrals over the sphere. This package consists of source code and documentation for a method which involves inscribing the sphere in a regular icosahedron and then equalizing the pixel areas.
iCosmo is a software package to perform interactive cosmological calculations for the low redshift universe. The computation of distance measures, the matter power spectrum, and the growth factor is supported for any values of the cosmological parameters. It also performs the computation of observables for several cosmological probes such as weak gravitational lensing, baryon acoustic oscillations and supernovae. The associated errors for these observables can be derived for customised surveys, or for pre-set values corresponding to current or planned instruments. The code also allows for the calculation of cosmological forecasts with Fisher matrices which can be manipulated to combine different surveys and cosmological probes. The code is written in the IDL language and thus benefits from the convenient interactive features and scientific library available in this language. iCosmo can also be used as an engine to perform cosmological calculations in batch mode, and forms a convenient evolutive platform for the development of further cosmological modules. With its extensive documentation, it may also serve as a useful resource for teaching and for newcomers in the field of cosmology.
ICSF (Intensity Conserving Spectral Fitting) "corrects" (x,y) data in which the ordinate represents the average of a quantity over a finite interval in the abscissa. A typical example is spectral data, where the average intensity over a wavelength bin (the measured quantity) is assigned to the center of the bin. If the profile is curved, the average will be different from the discrete value at the bin center location. ICSF, written in IDL and available separately and as part of SolarSoft (ascl:1208.013), corrects the intensity using an iterative procedure and cubic spline. The corrected intensity equals the "true" intensity at bin center, rather than the average over the bin. Unlike other methods that are restricted to a single fitting function, typically a spline, ICSF can be used with any function, such as a cubic spline or a Gaussian, with slight changes to the code.
iDealCam is an IDL GUI toolkit for processing multi-extension FITS file produced by CanariCam, the facility mid-IR instrument of Gran Telescopio CANARIAS (GTC). iDealCam is optimized for CanariCam data, but is also compatible with data generated by other instruments using similar detectors and data format (e.g., Michelle and T-ReCS at Gemini). iDealCam provides essential capabilities to examine, reduce, and analyze data obtained in the standard imaging or polarimetric imaging mode of CanariCam.
By combining test-particle and self-consistent techniques, we have developed a method to rapidly explore the parameter space of galactic encounters. Our method, implemented in an interactive graphics program, can be used to find the parameters required to reproduce the observed morphology and kinematics of interacting disk galaxies. We test this system on an artificial data-set of 36 equal-mass merging encounters, and show that it is usually possible to reproduce the morphology and kinematics of these encounters and that a good match strongly constrains the encounter parameters. An update to this software with additional capabilities, Identikit 2 (ascl:1102.011), is available.
Using a combination of self-consistent and test-particle techniques, Identikit 1 (ascl:1011.001) provided a way to vary the initial geometry of a galactic collision and instantly visualize the outcome. Identikit 2 uses the same techniques to define a mapping from the current morphology and kinematics of a tidal encounter back to the initial conditions. By requiring that various regions along a tidal feature all originate from a single disc with a unique orientation, this mapping can be used to derive the initial collision geometry. In addition, Identikit 2 offers a robust way to measure how well a particular model reproduces the morphology and kinematics of a pair of interacting galaxies. A set of eight self-consistent simulations is used to demonstrate the algorithm's ability to search a ten-dimensional parameter space and find near-optimal matches; all eight systems are successfully reconstructed.
IDG (Image Domain Gridding) is an imager that makes w-term corrections and a-term corrections computationally very cheap. It works with WSClean (ascl:1408.023) and supports the same cleaning and data selections options that WSClean offers in normal mode (such as cotton-schwab, multi-frequency multi-scale cleaning, and auto-masking). IDG also allows gridding with a time-variable beam including the LOFAR, AARTFAAC and MWA beam and can perform full beam or differential correction. The code requires measurement sets with four polarizations (e.g. XX/XY/YX/YY), can apply a spatially varying time-variable TEC term that can additionally be different for different antennas and output channels, and performs extremely well on GPUs.
Spectrum created by energy release in the early Universe, before recombination, creates distortions which are a superposition of μ-type, y-type and intermediate-type distortions. The final spectrum can thus be constructed from the templates, once energy injection rate as a function of redshift is known. This package contains the templates spaced at dy=0.001 for y<1 and dy=0.01 for y>1 covering a range 0.001 < y < 10. Also included is a Mathematica code which can combine these templates for user-defined rate of energy injection as a function of redshift. Silk damping, particle decay and annihilation examples are also included.
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.
iFIT determines the Sérsic law model for galaxies with imperfect Sérsic law profiles by searching for the best match between the observationally determined and theoretically expected radial variation of the mean surface brightness and light growth curve. The technique ensures quick convergence to a unique solution for both perfect and imperfect Sérsic profiles, even shallow and resolution-degraded SBPs. iFIT allows for correction of PSF convolution effects, offering the user the option of choosing between a Moffat, Gaussian, or user-supplied PSF, and is an efficient tool for the non-supervised structural characterization of large galaxy samples, such as those expected to become available with Euclid and LSST.
IFrIT (Ionization FRont Interactive Tool) is a powerful general purpose visualization tool that can be used to visualize 3-dimensional data sets. IFrIT is written in C++ and is based on the Visualization ToolKit (VTK) and, optionally, uses a GUI toolkit Qt. IFrIT can visualize scalar, vector field, tensor, and particle data. Several visualization windows can exist at the same time, each one having a full set of visualization objects. Some visualization windows can share the data between them, while other windows can be fully independent. Images from several visualization windows can be combined into one image file on the disk, tiling some windows together, and inserting reduced versions of some windows into larger other windows. A large array of features is also available, including highly advanced animation capabilities, a complex set of lights, markers to label various points in space, and a capability to "pick" a point in the scene and retrieve information about the data at this location.
IFSFIT is a general-purpose IDL library for fitting the continuum, emission lines, and absorption lines in integral field spectra. It uses PPXF (ascl:1210.002) to find the best fit stellar continuum (using a user-defined library of stellar templates and including additive polynomials), or optionally a user-defined method to find the best fit continuum. It uses MPFIT (ascl:1208.019) to simultaneously fit Gaussians to any number of emission lines and emission line velocity components. It will also fit the NaI D feature using analytic absorption and/or emission-line profiles.
IFSRED is a general-purpose library for reducing data from integral field spectrographs (IFSs). For a general IFS data cube, it contains IDL routines to: (1) find and apply a zero-point shift in a wavelength solution on a spaxel-by-spaxel basis, using sky lines; (2) find the spatial coordinates of a flux peak; (3) empirically correct for differential atmospheric refraction; (4) mosaic dithered exposures; (5) (integer) rebin; and (6) apply a telluric correction. A sky-subtraction routine for data from the Gemini Multi-Object Spectrograph and Imager (GMOS) that can be easily modified for any instrument is also included. IFSRED also contains additional software specific to reducing data from GMOS and the Gemini Near-Infrared Integral Field Spectrograph (NIFS).
We present a suite of IDL routines to interactively run GALFIT whereby the various surface brightness profiles (and their associated parameters) are represented by regions, which the User is expected to place. The regions may be saved and/or loaded from the ASCII format used by ds9 or in the Hierarchical Data Format (version 5). The software has been tested to run stably on Mac OS X and Linux with IDL 7.0.4. In addition to its primary purpose of modeling galaxy images with GALFIT, this package has several ancillary uses, including a flexible image display routines, several basic photometry functions, and qualitatively assessing Source Extractor. We distribute the package freely and without any implicit or explicit warranties, guarantees, or assurance of any kind. We kindly ask users to report any bugs, errors, or suggestions to us directly (as opposed to fixing them themselves) to ensure version control and uniformity.
This document describes the publically available numerical code "IGMtransfer", capable of performing intergalactic radiative transfer (RT) of light in the vicinity of the Lyman alpha (Lya) line. Calculating the RT in a (possibly adaptively refined) grid of cells resulting from a cosmological simulation, the code returns 1) a "transmission function", showing how the intergalactic medium (IGM) affects the Lya line at a given redshift, and 2) the "average transmission" of the IGM, making it useful for studying the results of reionization simulations.
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.
IIPImage is an advanced high-performance feature-rich image server system that enables online access to full resolution floating point (as well as other bit depth) images at terabyte scales. Paired with the VisiOmatic (ascl:1408.010) celestial image viewer, the system can comfortably handle gigapixel size images as well as advanced image features such as both 8, 16 and 32 bit depths, CIELAB colorimetric images and scientific imagery such as multispectral images. Streaming is tile-based, which enables viewing, navigating and zooming in real-time around gigapixel size images. Source images can be in either TIFF or JPEG2000 format. Whole images or regions within images can also be rapidly and dynamically resized and exported by the server from a single source image without the need to store multiple files in various sizes.
IllinoisGRMHD is an open-source, highly-extensible rewrite of the original closed-source general relativistic (ideal) magnetohydrodynamics (GRMHD) code of the Illinois Numerical Relativity (ILNR) Group. Reducing the learning curve was the primary focus of this rewrite, with the goal of facilitating community involvement in the code's use and development, as well as reducing the human effort necessary to generate new science. IllinoisGRMHD also saves computer time, generating roundoff-precision identical output to the original code on adaptive-mesh grids while being nearly twice as fast at scales of hundreds to thousands of cores.
im2shape is a Bayesian approach to the problem of accurate measurement of galaxy ellipticities for weak lensing studies, in particular cosmic shear. im2shape parameterizes galaxies as sums of Gaussians, convolved with a psf which is also a sum of Gaussians. The uncertainties in the output parameters are calculated using a Markov Chain Monte Carlo approach.
Im3shape forward-fits a galaxy model to each data image it is supplied with and reports the parameters of the best fitting model, including the ellipticity components. It uses the Discrete Fourier Transform (DFT) to render images of convolved galaxy profiles, calculates the maximum likelihood parameter values, and corrects for noise bias. IM3SHAPE is a modular C code with a significant amount of Python glue code to enable setting up new models and their options automatically.
ImageHealth (IH) is a c program that makes use of standard CFITSIO routines to examine, in an automated fashion, .FITS images with any number of extensions, find objects within those images, and determine basic parameters of those images (stellar flux, background counts, FWHM, and ellipticity, along with sky background counts) in order to provide a snapshot of the quality of those images. A variety of python wrappers have also been written to test large numbers of such images and compare the results of ImageHealth to other image analysis programs, such as SourceExtractor. Additional IH-related tools will be made available in the future.
Efforts are now focused on an implementation of IH specifically for the Dark Energy Camera; we do not envision providing support for the instrument-independent version of the code offered here though comments, questions, and feedback are welcome.
ImageJ is a public domain Java image processing program inspired by NIH Image. It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations.
IMAGINE (Interstellar MAGnetic field INference Engine) performs inference on generic parametric models of the Galaxy. The modular open source framework uses highly optimized tools and technology such as the MultiNest sampler (ascl:1109.006) and the information field theory framework NIFTy (ascl:1302.013) to create an instance of the Milky Way based on a set of parameters for physical observables, using Bayesian statistics to judge the mismatch between measured data and model prediction. The flexibility of the IMAGINE framework allows for simple refitting for newly available data sets and makes state-of-the-art Bayesian methods easily accessible particularly for random components of the Galactic magnetic field.
The IMCAT software was developed initially to do faint galaxy photometry for weak lensing studies, and provides a fairly complete set of tools for this kind of work. Unlike most packages for doing data analysis, the tools are standalone unix commands which you can invoke from the shell, via shell scripts or from perl scripts. The tools are arranges in a tree of directories. One main branch is the ’imtools’. These deal only with fits files. The most important imtool is the ’image calculator’ ’ic’ which allows one to do rather general operations on fits images. A second branch is the ’catools’ which operate only on catalogues. The key cattool is ’lc’; this effectively defines the format of IMCAT catalogues, and allows one to do very general operations on and filtering of such catalogues. A third branch is the ’imcattools’. These tend to be much more specialised than the cattools and imcattools and are focussed on faint galaxy photometry.
IMCOM allows for careful treatment of aliasing in undersampled imaging data and can be used to test the feasibility of multi-exposure observing strategies for space-based survey missions. IMCOM can also been used to explore focal plane undersampling for an optical space mission such as Euclid.
Imfit is an open-source astronomical image-fitting program specialized for galaxies but potentially useful for other sources, which is fast, flexible, and highly extensible. Its object-oriented design allows new types of image components (2D surface-brightness functions) to be easily written and added to the program. Image functions provided with Imfit include Sersic, exponential, and Gaussian galaxy decompositions along with Core-Sersic and broken-exponential profiles, elliptical rings, and three components that perform line-of-sight integration through 3D luminosity-density models of disks and rings seen at arbitrary inclinations.
Available minimization algorithms include Levenberg-Marquardt, Nelder-Mead simplex, and Differential Evolution, allowing trade-offs between speed and decreased sensitivity to local minima in the fit landscape. Minimization can be done using the standard chi^2 statistic (using either data or model values to estimate per-pixel Gaussian errors, or else user-supplied error images) or the Cash statistic; the latter is particularly appropriate for cases of Poisson data in the low-count regime.
The C++ source code for Imfit is available under the GNU Public License.
This software trains artificial neural networks to find non-linear functionals of data that maximize Fisher information: information maximizing neural networks (IMNNs). As compressing large data sets vastly simplifies both frequentist and Bayesian inference, important information may be inadvertently missed. Likelihood-free inference based on automatically derived IMNN summaries produces summaries that are good approximations to sufficient statistics. IMNNs are robustly capable of automatically finding optimal, non-linear summaries of the data even in cases where linear compression fails: inferring the variance of Gaussian signal in the presence of noise, inferring cosmological parameters from mock simulations of the Lyman-α forest in quasar spectra, and inferring frequency-domain parameters from LISA-like detections of gravitational waveforms. In this final case, the IMNN summary outperforms linear data compression by avoiding the introduction of spurious likelihood maxima.
ImpactModel, written in Cython, computes the accretion disc impact spectrum at given frequencies and can compute other model quantities as a function of time.
Aperture masking interferometric data analysis involves measuring phases and amplitudes of fringes formed by interference between holes in the pupil mask. These fringe observables can be measured by computing an analytic model of the point spread function and fitting the relevant set of spatial frequencies directly in the image plane, without recourse to numerical Fourier transforms. The ImPlaneIA pipeline converts aperture masking images to fringe observables by fitting fringes in the image plane, calibrates data from a target of interest with one or more point source calibrators, and contains some basic model-fitting routines. The pipeline can accept different mask geometries, instruments, and observing modes.
This program measures line-strength indices in fully calibrated FITS spectra. By "fully calibrated" one should understand wavelength and relative flux-calibrated data. Note that the different types of line-strength indices that can be measured with indexf (see below) do not require absolute flux calibration. If even a relative flux-calibration is absent (or deficient), the derived indices should be transformed to an appropriate spectrophotometric system. The program can also compute index errors resulting from the propagation of random errors (e.g. photon statistics, read-out noise). This option is only available if the user provides the error spectrum as an additional input FITS file to indexf. The error spectrum must contain the unbiased standard deviation (and not the variance!) for each pixel of the data spectrum. In addition, indexf also estimates the effect of errors on radial velocity. For this purpose, the program performs Monte Carlo simulations by measuring each index using randomly drawn radial velocities (following a Gaussian distribution of a given standard deviation). If no error file is employed, the program can perform numerical simulations with synthetic error spectra, the latter generated from the original data spectra and assuming randomly generated S/N ratios.
Indri models the population of single (not in binary or hierarchical systems) neutron stars. Given a starting distribution of parameters (birth place, velocity, magnetic field, and period), the code moves a set of stars through the time (by evolving spin period and magnetic field) and the space (by propagating through the Galactic potential). Upon completion of the evolution, a set of observables is computed (radio flux, position, dispersion measure) and compared with a radio survey such as the Parkes Multibeam Survey. The models' parameters are optimised by using the Markov Chain Monte Carlo technique.
The efficiency of thin disk accretion onto black holes depends on the inner boundary condition, specifically the torque applied to the disk at the last stable orbit. This is usually assumed to vanish. This code estimates the torque on a magnetized disk using a steady magnetohydrodynamic inflow model originally developed by Takahashi et al. The efficiency e can depart significantly from the classical thin disk value. In some cases e > 1, i.e., energy is extracted from the black hole.
Infall is a code for calculating the mean initial and final density profiles around a virialized dark matter halo. The initial profile is derived from the statistics of the initial Gaussian random field, accounting for the problem of peaks within peaks using the extended Press-Schechter model. Spherical collapse then yields the typical density and velocity profiles of the gas and dark matter that surrounds the final, virialized halo. In additional to the mean profile, ±1-σ profiles are calculated and can be used as an estimate of the scatter.
Inflation is a numerical code to generate power spectra and other observables through numerical solutions to flow equations. The code generates tensor and scalar power spectra as a function of wavenumber and various other parameters at specific wavenumbers of interest (such as for CMB, scalar perturbations at smaller scales, gravitational wave detection at direct detection frequencies). The output can be easily ported to publicly available Markov Chain codes to constrain cosmological parameters with data.
The inhomog library provides Raychaudhuri integration of cosmological domain-wise average scale factor evolution using an analytical formula for kinematical backreaction Q_D evolution. The inhomog main program illustrates biscale examples. The library routine lib/Omega_D_precalc.c is callable by RAMSES (ascl:1011.007) using the RAMSES extension ramses-scalav.
InitialConditions finds the initial series solutions for perturbations in our Universe. This includes all scalar (1 adiabatic, 4 isocurvature and 2 magnetic modes), vector (1 vorticity mode, 1 magnetic mode), and tensor (1 gravitational wave mode and 1 magnetic mode) perturbations including terms up to second order in the neutrino mass. It can handle the standard species (cdm, baryons, photons), and two neutrino mass eigenstates (1 light, 1 heavy).
intensitypower measures and models the auto- and cross-power spectrum multipoles of galaxy catalogs and radio intensity maps presented in spherical coordinates. It can also convert the multipoles to power spectrum wedges P(k,mu) and 2D power spectra P(k_perp,k_par). The code assumes the galaxy catalog is a set of discrete points and the radio intensity map is a pixelized continuous field which includes angular pixelization using healpix, binning in redshift channels, smoothing by a Gaussian telescope beam, and the addition of a Gaussian noise in each cell. The galaxy catalog and radio intensity map are transferred onto an FFT grid, and power spectrum multipoles are measured including curved-sky effects. Both maps include redshift-space distortions.
We describe a novel approach to accelerating Monte Carlo Markov Chains. Our focus is cosmological parameter estimation, but the algorithm is applicable to any problem for which the likelihood surface is a smooth function of the free parameters and computationally expensive to evaluate. We generate a high-order interpolating polynomial for the log-likelihood using the first points gathered by the Markov chains as a training set. This polynomial then accurately computes the majority of the likelihoods needed in the latter parts of the chains. We implement a simple version of this algorithm as a patch (InterpMC) to CosmoMC and show that it accelerates parameter estimatation by a factor of between two and four for well-converged chains. The current code is primarily intended as a "proof of concept", and we argue that there is considerable room for further performance gains. Unlike other approaches to accelerating parameter fits, we make no use of precomputed training sets or special choices of variables, and InterpMC is almost entirely transparent to the user.
The Beta Inverse code solves the inverse cumulative density function (CDF) of a Beta distribution, allowing one to sample from the Beta prior directly. The Beta distribution is well suited as a prior for the distribution of the orbital eccentricities of extrasolar planets; imposing a Beta prior on orbital eccentricity is valuable for any type of observation of an exoplanet where eccentricity can affect the model parameters (e.g. transits, radial velocities, microlensing, direct imaging). The Beta prior is an excellent description of the current, empirically determined distribution of orbital eccentricities and thus employing it naturally incorporates an observer’s prior experience of what types of orbits are probable or improbable. The default parameters in the code are currently set to the Beta distribution which best describes the entire population of exoplanets with well-constrained orbits.
InversionKit is an interactive Java program that performs rotational and structural linear inversions from frequency data.
ionFR calculates the amount of ionospheric Faraday rotation for a specific epoch, geographic location, and line-of-sight. The code uses a number of publicly available, GPS-derived total electron content maps and the most recent release of the International Geomagnetic Reference Field. ionFR can be used for the calibration of radio polarimetric observations; its accuracy had been demonstrated using LOFAR pulsar observations.
ipole is a ray-tracing code for covariant, polarized radiative transport particularly useful for modeling Event Horizon Telescope sources, though may also be used for other relativistic transport problems. The code extends the ibothros scheme for covariant, unpolarized transport using two representations of the polarized radiation field: in the coordinate frame, it parallel transports the coherency tensor, and in the frame of the plasma, it evolves the Stokes parameters under emission, absorption, and Faraday conversion. The transport step is as spacetime- and coordinate- independent as possible; the emission, absorption, and Faraday conversion step is implemented using an analytic solution to the polarized transport equation with constant coefficients. As a result, ipole is stable, efficient, and produces a physically reasonable solution even for a step with high optical depth and Faraday depth.
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.
IRACproc is a software suite that facilitates the co-addition of dithered or mapped Spitzer/IRAC data to make them ready for further analysis with application to a wide variety of IRAC observing programs. The software runs within PDL, a numeric extension for Perl available from pdl.perl.org, and as stand alone perl scripts. In acting as a wrapper for the Spitzer Science Center's MOPEX software, IRACproc improves the rejection of cosmic rays and other transients in the co-added data. In addition, IRACproc performs (optional) Point Spread Function (PSF) fitting, subtraction, and masking of saturated stars.
IRAF includes a broad selection of programs for general image processing and graphics, plus a large number of programs for the reduction and analysis of optical and IR astronomy data. Other external or layered packages are available for applications such as data acquisition or handling data from other observatories and wavelength regimes such as the Hubble Space Telescope (optical), EUVE (extreme ultra-violet), or ROSAT and AXAF (X-ray). These external packages are distributed separately from the main IRAF distribution but can be easily installed. The IRAF system also includes a complete programming environment for scientific applications, which includes a programmable Command Language scripting facility, the IMFORT Fortran/C programming interface, and the full SPP/VOS programming environment in which the portable IRAF system and all applications are written.
IRAS90 is a suite of programs for processing IRAS data. It takes advantage of Starlink's (ascl:1110.012) ADAM environment, which provides multi-platform availability of both data and the programs to process it, and the user friendly interface of the parameter entry system. The suite can determine positions in astrometric coordinates, draw grids, and offers other functions for standard astronomical measurement and standard projections.
The UKIRT IRCAM3 data reduction and analysis software package, IRCAMDR (formerly ircam_clred) analyzes and displays any 2D data image stored in the standard Starlink (ascl:1110.012) NDF data format. It reduces and analyzes IRCAM1/2 data images of 62x58 pixels and IRCAM3 images of 256x256 size. Most of the applications will work on NDF images of any physical (pixel) dimensions, for example, 1024x1024 CCD images can be processed.
IRDAP (IRDIS Data reduction for Accurate Polarimetry) accurately reduces SPHERE-IRDIS polarimetric data. It is a highly-automated end-to-end pipeline; its core feature is model-based correction of the instrumental polarization effects. IRDAP handles data taken both in field- and pupil-tracking mode and using the broadband filters Y, J, H and Ks. Data taken with the narrowband filters can be reduced as well, although with a somewhat worse accuracy. For pupil-tracking observations IRDAP can additionally apply angular differential imaging.
We describe the InfraRed Data Reduction (IRDR) software package, a small ANSI C library of fast image processing routines for automated pipeline reduction of infrared (dithered) observations. We developed the software to satisfy certain design requirements not met in existing packages (e.g., full weight map handling) and to optimize the software for large data sets (non-interactive tasks that are CPU and disk efficient). The software includes stand-alone C programs for tasks such as running sky frame subtraction with object masking, image registration and coaddition with weight maps, dither offset measurement using cross-correlation, and object mask dilation. Although we currently use the software to process data taken with CIRSI (a near-IR mosaic imager), the software is modular and concise and should be easy to adapt/reuse for other work.
Iris is a downloadable Graphical User Interface (GUI) application which allows the astronomer to build and analyze wide-band Spectral Energy Distributions (SEDs). The components of Iris have been contributed by members of the VAO. Specview, contributed by STScI, provides a GUI for reading, editing, and displaying SEDs, as well as defining models and parameter values. Sherpa, contributed by the Chandra project at SAO, provides a library of models, fit statistics, and optimization methods; the underlying I/O library, SEDLib, is a VAO product written by SAO to current IVOA (International Virtual Observatory Alliance) data model standards. NED is a service provided by IPAC for easy location of data for a given extragalactic source, including SEDs. SedImporter converts non-standard SED data files into a format supported by Iris.
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).
iSAP consists of three programs, written in IDL, which together are useful for spherical data analysis. MR/S (MultiResolution on the Sphere) contains routines for wavelet, ridgelet and curvelet transform on the sphere, and applications such denoising on the sphere using wavelets and/or curvelets, Gaussianity tests and Independent Component Analysis on the Sphere. MR/S has been designed for the PLANCK project, but can be used for many other applications. SparsePol (Polarized Spherical Wavelets and Curvelets) has routines for polarized wavelet, polarized ridgelet and polarized curvelet transform on the sphere, and applications such denoising on the sphere using wavelets and/or curvelets, Gaussianity tests and blind source separation on the Sphere. SparsePol has been designed for the PLANCK project. MS-VSTS (Multi-Scale Variance Stabilizing Transform on the Sphere), designed initially for the FERMI project, is useful for spherical mono-channel and multi-channel data analysis when the data are contaminated by a Poisson noise. It contains routines for wavelet/curvelet denoising, wavelet deconvolution, multichannel wavelet denoising and deconvolution.
ISAP, written in IDL, simplifies the process of visualizing, subsetting, shifting, rebinning, masking, combining scans with weighted means or medians, filtering, and smoothing Auto Analysis Results (AARs) from post-pipeline processing of the Infrared Space Observatory's (ISO) Short Wavelength Spectrometer (SWS) and Long Wavelength Spectrometer (LWS) data. It can also be applied to PHOT-S and CAM-CVF data, and data from practically any spectrometer. The result of a typical ISAP session is expected to be a "simple spectrum" (single-valued spectrum which may be resampled to a uniform wavelength separation if desired) that can be further analyzed and measured either with other ISAP functions, native IDL functions, or exported to other analysis package (e.g., IRAF, MIDAS) if desired. ISAP provides many tools for further analysis, line-fitting, and continuum measurements, such as routines for unit conversions, conversions from wavelength space to frequency space, line and continuum fitting, flux measurement, synthetic photometry and models such as a zodiacal light model to predict and subtract the dominant foreground at some wavelengths.
Isca provides a framework for the idealized modeling of the global circulation of planetary atmospheres at varying levels of complexity and realism. Though Isca is an outgrowth of models designed for Earth's atmosphere, it may readily be extended into other planetary regimes. Various forcing and radiation options are available. At the simple end of the spectrum a Held-Suarez case is available. An idealized grey radiation scheme, a grey scheme with moisture feedback, a two-band scheme and a multi-band scheme are also available, all with simple moist effects and astronomically-based solar forcing. At the complex end of the spectrum the framework provides a direct connection to comprehensive atmospheric general circulation models.
iSEDfit uses Bayesian inference to extract the physical properties of galaxies from their observed broadband photometric spectral energy distribution (SED). In its default mode, the inputs to iSEDfit are the measured photometry (fluxes and corresponding inverse variances) and a measurement of the galaxy redshift. Alternatively, iSEDfit can be used to estimate photometric redshifts from the input photometry alone.
After the priors have been specified, iSEDfit calculates the marginalized posterior probability distributions for the physical parameters of interest, including the stellar mass, star-formation rate, dust content, star formation history, and stellar metallicity. iSEDfit also optionally computes K-corrections and produces multiple "quality assurance" (QA) plots at each stage of the modeling procedure to aid in the interpretation of the prior parameter choices and subsequent fitting results. The software is distributed as part of the impro IDL suite.
ISIS is a complete package to process CCD images using the image Optimal subtraction method (Alard & Lupton 1998, Alard 1999). The ISIS package can find the best kernel solution even in case of kernel variations as a function of position in the image. The relevant computing time is minimal in this case and is only slightly different from finding constant kernel solutions. ISIS includes as well a number of facilities to compute the light curves of variables objects from the subtracted images. The basic routines required to build the reference frame and make the image registration are also provided in the package.
ISIS, the Interactive Spectral Interpretation System, is designed to facilitate the interpretation and analysis of high resolution X-ray spectra. It is being developed as a programmable, interactive tool for studying the physics of X-ray spectrum formation, supporting measurement and identification of spectral features, and interaction with a database of atomic structure parameters and plasma emission models.
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.
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.
iSpec is an integrated software framework written in Python for the treatment and analysis of stellar spectra and abundances. Spectra treatment functions include cosmic rays removal, continuum normalization, resolution degradation, and telluric lines identification. It can also perform radial velocity determination and correction and resampling. iSpec can also determine atmospheric parameters (i.e effective temperature, surface gravity, metallicity, micro/macroturbulence, rotation) and individual chemical abundances by using either the synthetic spectra fitting technique or equivalent widths method. The synthesis is performed with SPECTRUM (ascl:9910.002).
The ISPy3 suite of Python routines models and analyzes integrated-light spectra of stars and stellar populations. The actual spectral modeling and related tasks such as setting up model atmospheres is done via external codes. Currently, the Kurucz codes (ATLAS/SYNTHE) and MARCS/TurboSpectrum are supported, though implementing other similar codes should be relatively straight forward.
ISW and Weak Lensing Likelihood code is the likelihood code that calculates the likelihood of Integrated Sachs Wolfe and Weak Lensing of Cosmic Microwave Background using the WMAP 3year CMB maps with mass tracers such as 2MASS (2-Micron All Sky Survey), SDSS LRG (Sloan Digital Sky Survey Luminous Red Galaxies), SDSS QSOs (Sloan Digital Sky Survey Quasars) and NVSS (NRAO VLA All Sky Survey) radio sources. The details of the analysis (*thus the likelihood code) can be understood by reading the papers ISW paper and Weak lensing paper. The code does brute force theoretical matter power spectrum and calculations with CAMB. See the paper for an introduction, descriptions, and typical results from some pre-WMAP data. The code is designed to be integrated into CosmoMC. For further information concerning the integration, see Code Modification for integration into COSMOMC.
ITERA, the IDL Tool for Emission-line Ratio Analysis, is an IDL widget tool that allows you to plot ratios of any strong atomic and ionized emission lines as determined by standard photoionization and shock models. These "line ratio diagrams" can then be used to determine diagnostics for nebulae excitation mechanisms or nebulae parameters such as density, temperature, metallicity, etc. ITERA can also be used to determine line sensitivities to such parameters, compare observations with the models, or even estimate unobserved line fluxes.
IUEDR reduces IUE data. It addresses the problem of working from the IUE Guest Observer tape or disk file through to a calibrated spectrum that can be used in scientific analysis and is a complete system for IUE data reduction. IUEDR was distributed as part of the Starlink software collection (ascl:1110.012).
iWander assesses the origin of interstellar small bodies such as asteroids and comets. It includes a series of databases and tools that can be used in general for studying the dynamics of an interstellar vagabond object (small−body, interstellar spaceship and even stars).
J plots classifies and quantifies a pixelated structure, based on its principal moments of inertia, thus enabling automatic detection and objective comparisons of centrally concentrated structures (cores), elongated structures (filaments) and hollow circular structures (bubbles) from the main population of slightly irregular blobs that make up most astronomical images. Examples of how to analyze 2D or 3D datasets, enabling an unbiased analysis and comparison of simulated and observed structures are provided along with the Python code.
JAGS analyzes Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS. JAGS has three aims:
The Jeans Anisotropic MGE (JAM) modeling method uses the Multi-Gaussian Expansion parameterization for the galaxy surface brightness. The code allows for orbital anisotropy (three-integrals distribution function) and also provides the full second moment tensor, including proper motions and radial velocities.
JAVELIN (formerly known as SPEAR) is an approach to reverberation mapping that computes the lags between the AGN continuum and emission line light curves and their statistical confidence limits. It uses a damped random walk model to describe the quasar continuum variability and the ansatz that emission line variability is a scaled, smoothed and displaced version of the continuum. While currently configured only to simultaneously fit light curve means, it includes a general linear parameters formalism to fit more complex trends or calibration offsets. The noise matrix can be modified to allow for correlated errors, and the correlation matrix can be modified to use a different stochastic process. The transfer function model is presently a tophat, but this can be altered by changing the line-continuum covariance matrices. It is also able to cope with some problems in traditional reverberation mapping, such as irregular sampling, correlated errors and seasonal gaps.
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