TurbuStat: Turbulence Statistics in Python

We present TurbuStat (v1.0): a Python package for computing turbulence statistics in spectral-line data cubes. TurbuStat includes implementations of fourteen methods for recovering turbulent properties from observational data. Additional features of the software include: distance metrics for comparing two data sets; a segmented linear model for fitting lines with a break-point; a two-dimensional elliptical power-law model; multi-core fast-fourier-transform support; a suite for producing simulated observations of fractional Brownian Motion fields, including two-dimensional images and optically-thin HI data cubes; and functions for creating realistic world coordinate system information for synthetic observations. This paper summarizes the TurbuStat package and provides representative examples using several different methods. TurbuStat is an open-source package and we welcome community feedback and contributions.Comment: Accepted in AJ. 21 pages, 8 figure

Hierarchical Structure of Magnetohydrodynamic Turbulence In Position-Position-Velocity Space

Magnetohydrodynamic turbulence is able to create hierarchical structures in the interstellar medium that are correlated on a wide range of scales via the energy cascade. We use hierarchical tree diagrams known as dendrograms to characterize structures in synthetic Position-Position-Velocity (PPV) emission cubes of optically thin isothermal magnetohydrodynamic turbulence. We show that the structures and degree of hierarchy observed in PPV space are related to the physics of the gas, i.e. self-gravity and the global sonic and Alfvenic Mach number. Simulations with higher Alfvenic Mach number, self-gravity and supersonic flows display enhanced hierarchical structure. We observed a strong sonic and Alfvenic dependency when we apply the the statistical moments (i.e. mean, variance, skewness, kurtosis) to the dendrogram distribution. Larger magnetic field and sonic Mach number correspond to larger values of the moments. Application of the dendrogram to 3D density cubes, also known as Position-Position-Position cubes (PPP), reveals that the dominant emission contours in PPP and PPV are related for supersonic gas but not for subsonic. We also explore the effects of smoothing, thermal broadening and velocity resolution on the dendrograms in order to make our study more applicable to observational data. These results all point to hierarchical tree diagrams as being a promising additional tool for studying ISM turbulence and star forming regions in the direction of obtaining information on the degree of self-gravity, the Mach numbers and the complicated relationship between PPV and PPP.Comment: submitted to Ap

Modelling the 3D physical structure of astrophysical sources with GASS

The era of interferometric observations leads to the need of a more and more precise description of physical structures and dynamics of star-forming regions, from pre-stellar cores to protoplanetary discs. The molecular emission can be traced in multiple physical components such as infalling envelopes, outflows and protoplanetary discs. To compare with the observations, a precise and complex radiative transfer modelling of these regions is needed. We present GASS (Generator of Astrophysical Sources Structure), a code that allows us to generate the three-dimensional (3D) physical structure model of astrophysical sources. From the GASS graphical interface, the user easily creates different components such as spherical envelopes, outflows and discs. The physical properties of these components are modelled thanks to dedicated graphical interfaces that display various figures in order to help the user and facilitate the modelling task. For each component, the code randomly generates points in a 3D grid with a sample probability weighted by the molecular density. The created models can be used as the physical structure input for 3D radiative transfer codes to predict the molecular line or continuum emission. An analysis of the output hyper-spectral cube given by such radiative transfer code can be made directly in GASS using the various post-treatment options implemented, such as calculation of moments or convolution with a beam. This makes GASS well suited to model and analyse both interferometric and single-dish data. This paper is focused on the results given by the association of GASS and LIME, a 3D radiative transfer code, and we show that the complex geometry observed in star-forming regions can be adequately handled by GASS+LIME

Finding faint HI structure in and around galaxies: scraping the barrel

Soon to be operational HI survey instruments such as APERTIF and ASKAP will produce large datasets. These surveys will provide information about the HI in and around hundreds of galaxies with a typical signal-to-noise ratio of $\sim$ 10 in the inner regions and $\sim$ 1 in the outer regions. In addition, such surveys will make it possible to probe faint HI structures, typically located in the vicinity of galaxies, such as extra-planar-gas, tails and filaments. These structures are crucial for understanding galaxy evolution, particularly when they are studied in relation to the local environment. Our aim is to find optimized kernels for the discovery of faint and morphologically complex HI structures. Therefore, using HI data from a variety of galaxies, we explore state-of-the-art filtering algorithms. We show that the intensity-driven gradient filter, due to its adaptive characteristics, is the optimal choice. In fact, this filter requires only minimal tuning of the input parameters to enhance the signal-to-noise ratio of faint components. In addition, it does not degrade the resolution of the high signal-to-noise component of a source. The filtering process must be fast and be embedded in an interactive visualization tool in order to support fast inspection of a large number of sources. To achieve such interactive exploration, we implemented a multi-core CPU (OpenMP) and a GPU (OpenGL) version of this filter in a 3D visualization environment ($\tt{SlicerAstro}$).Comment: 17 pages, 9 figures, 4 tables. Astronomy and Computing, accepte

An HI survey of the Centaurus and Sculptor Groups - Constraints on the space density of low mass galaxies

We present results of two 21-cm HI surveys performed with the Australia Telescope Compact Array in the nearby Centaurus A and Sculptor galaxy groups. These surveys are sensitive to compact HI clouds and galaxies with HI masses as low as 3E+06 Msun, and are therefore among the most sensitive extragalactic HI surveys to date. The surveys consist of sparsely spaced pointings that sample approximately 2% of the groups' area on the sky. We detected previously known group members, but we found no new HI clouds or galaxies down to the sensitivity limit of the surveys. If the HI mass function had a faint end slope of alpha = 1.5 below M_{HI} = 10^{7.5} Msun in these groups, we would have expected ~3 new objects. Cold dark matter theories of galaxy formation predict the existence of a large number low mass DM sub-halos that might appear as tiny satellites in galaxy groups. Our results support and extend similar conclusions derived from previous HI surveys that a HI rich population of these satellites does not exist.Comment: Accepted for publication in A&

Interstellar Sonic and Alfv\'enic Mach Numbers and the Tsallis Distribution

In an effort to characterize the Mach numbers of ISM magnetohydrodynamic (MHD) turbulence, we study the probability distribution functions (PDFs) of patial increments of density, velocity, and magnetic field for fourteen ideal isothermal MHD simulations at resolution 512^3. In particular, we fit the PDFs using the Tsallis function and study the dependency of fit parameters on the compressibility and magnetization of the gas. We find that the Tsallis function fits PDFs of MHD turbulence well, with fit parameters showing sensitivities to the sonic and Alfven Mach numbers. For 3D density, column density, and position-position-velocity (PPV) data we find that the amplitude and width of the PDFs shows a dependency on the sonic Mach number. We also find the width of the PDF is sensitive to global Alfvenic Mach number especially in cases where the sonic number is high. These dependencies are also found for mock observational cases, where cloud-like boundary conditions, smoothing, and noise are introduced. The ability of Tsallis statistics to characterize sonic and Alfvenic Mach numbers of simulated ISM turbulence point to it being a useful tool in the analysis of the observed ISM, especially when used simultaneously with other statistical techniques.Comment: 20 pages, 16 figures, ApJ submitte

The Topology of Large Scale Structure in the 1.2 Jy IRAS Redshift Survey

We measure the topology (genus) of isodensity contour surfaces in volume limited subsets of the 1.2 Jy IRAS redshift survey, for smoothing scales \lambda=4\hmpc, 7\hmpc, and 12\hmpc. At 12\hmpc, the observed genus curve has a symmetric form similar to that predicted for a Gaussian random field. At the shorter smoothing lengths, the observed genus curve shows a modest shift in the direction of an isolated cluster or ``meatball'' topology. We use mock catalogs drawn from cosmological N-body simulations to investigate the systematic biases that affect topology measurements in samples of this size and to determine the full covariance matrix of the expected random errors. We incorporate the error correlations into our evaluations of theoretical models, obtaining both frequentist assessments of absolute goodness-of-fit and Bayesian assessments of models' relative likelihoods. We compare the observed topology of the 1.2 Jy survey to the predictions of dynamically evolved, unbiased, gravitational instability models that have Gaussian initial conditions. The model with an $n=-1$, power-law initial power spectrum achieves the best overall agreement with the data, though models with a low-density cold dark matter power spectrum and an $n=0$ power-law spectrum are also consistent. The observed topology is inconsistent with an initially Gaussian model that has $n=-2$, and it is strongly inconsistent with a Voronoi foam model, which has a non-Gaussian, bubble topology.Comment: ApJ submitted, 39 pages, LaTeX(aasms4), 12 figures, 1 Tabl

SlicerAstro: a 3-D interactive visual analytics tool for HI data

SKA precursors are capable of detecting hundreds of galaxies in HI in a single 12 hours pointing. In deeper surveys one will probe more easily faint HI structures, typically located in the vicinity of galaxies, such as tails, filaments, and extraplanar gas. The importance of interactive visualization has proven to be fundamental for the exploration of such data as it helps users to receive immediate feedback when manipulating the data. We have developed SlicerAstro, a 3-D interactive viewer with new analysis capabilities, based on traditional 2-D input/output hardware. These capabilities enhance the data inspection, allowing faster analysis of complex sources than with traditional tools. SlicerAstro is an open-source extension of 3DSlicer, a multi-platform open source software package for visualization and medical image processing. We demonstrate the capabilities of the current stable binary release of SlicerAstro, which offers the following features: i) handling of FITS files and astronomical coordinate systems; ii) coupled 2-D/3-D visualization; iii) interactive filtering; iv) interactive 3-D masking; v) and interactive 3-D modeling. In addition, SlicerAstro has been designed with a strong, stable and modular C++ core, and its classes are also accessible via Python scripting, allowing great flexibility for user-customized visualization and analysis tasks.Comment: 18 pages, 11 figures, Accepted by Astronomy and Computing. SlicerAstro link: https://github.com/Punzo/SlicerAstro/wiki#get-slicerastr

An HI View of Galaxy Conformity: HI-rich Environment around HI-excess Galaxies

Using data taken as part of the Bluedisk project we study the connection between neutral hydrogen (HI) in the environment of spiral galaxies and that in the galaxies themselves. We measure the total HI mass present in the environment in a statistical way by studying the distribution of noise peaks in the HI data cubes obtained for 40 galaxies observed with WSRT. We find that galaxies whose HI mass fraction is high relative to standard scaling relations have an excess HI mass in the surrounding environment as well. Gas in the environment consists of gas clumps which are individually below the detection limit of our HI data. These clumps may be hosted by small satellite galaxies and\or be the high-density peaks of a more diffuse gas distribution in the inter-galactic medium. We interpret this result as an indication for a picture in which the HI-rich central galaxies accrete gas from an extended gas reservoir present in their environment.Comment: 15 pages, 13 figures. Accepted for publication in MNRA

Automated reduction of submillimetre single-dish heterodyne data from the James Clerk Maxwell Telescope using ORAC-DR

With the advent of modern multi-detector heterodyne instruments that can result in observations generating thousands of spectra per minute it is no longer feasible to reduce these data as individual spectra. We describe the automated data reduction procedure used to generate baselined data cubes from heterodyne data obtained at the James Clerk Maxwell Telescope. The system can automatically detect baseline regions in spectra and automatically determine regridding parameters, all without input from a user. Additionally it can detect and remove spectra suffering from transient interference effects or anomalous baselines. The pipeline is written as a set of recipes using the ORAC-DR pipeline environment with the algorithmic code using Starlink software packages and infrastructure. The algorithms presented here can be applied to other heterodyne array instruments and have been applied to data from historical JCMT heterodyne instrumentation.Comment: 18 pages, 13 figures, submitted to Monthly Notices of the Royal Astronomical Societ