Search

We explore how chromatic RFI flags affect 21-cm power spectrum measurements. We particularly study flags that are coarser than the analysis resolution. We find that such RFI flags produce excess power in the EoR window in much the same way as residual RFI. We use Fast Holographic Deconvolution (FHD) simulations to explain this as a result of chromatic disruptions in the interferometric sampling function of the array. We also use these simulations in conjunction with Error Propagated Power Spectrum with InterLeaved Observed Noise ($\varepsilon$ppsilon) to show that without modifying current flagging strategies or implementing extremely accurate and complete foreground subtraction, 21-cm EoR experiments will fail to make a significant detection. As a mitigation strategy, we find that circumventing the chromatic structure altogether by flagging the entire analysis band when RFI is detected is simple to implement and highly successful. This demands a detection strategy with a low false positive rate in order to prevent excessive data loss., Including revisions from peer review

The locations of Ly-$\alpha$ emitting galaxies (LAEs) at the end of the Epoch of Reionisation (EoR) are expected to correlate with regions of ionised hydrogen, traced by the redshifted 21~cm hyperfine line. Mapping the neutral hydrogen around regions with detected and localised LAEs offers an avenue to constrain the brightness temperature of the Universe within the EoR by providing an expectation for the spatial distribution of the gas, thereby providing prior information unavailable to power spectrum measurements. We use a test set of 12 hours of observations from the Murchison Widefield Array (MWA) in extended array configuration, to constrain the neutral hydrogen signature of 58 LAEs, detected with the Subaru Hypersuprime Cam in the \textit{Silverrush} survey, centred on $z$=6.58. We assume that detectable emitters reside in the centre of ionised HII bubbles during the end of reionization, and predict the redshifted neutral hydrogen signal corresponding to the remaining neutral regions using a set of different ionised bubble radii. A prewhitening matched filter detector is introduced to assess detectability. We demonstrate the ability to detect, or place limits upon, the amplitude of brightness temperature fluctuations, and the characteristic HII bubble size. With our limited data, we constrain the brightness temperature of neutral hydrogen to $\Delta{\rm T}_B, Comment: 9 pages, 6 figures, accepted for publication in MNRAS

We present a Bayesian jackknife test for assessing the probability that a data set contains biased subsets, and, if so, which of the subsets are likely to be biased. The test can be used to assess the presence and likely source of statistical tension between different measurements of the same quantities in an automated manner. Under certain broadly applicable assumptions, the test is analytically tractable. We also provide an open-source code, chiborg, that performs both analytic and numerical computations of the test on general Gaussian-distributed data. After exploring the information theoretical aspects of the test and its performance with an array of simulations, we apply it to data from the Hydrogen Epoch of Reionization Array (HERA) to assess whether different sub-seasons of observing can justifiably be combined to produce a deeper 21 cm power spectrum upper limit. We find that, with a handful of exceptions, the HERA data in question are statistically consistent and this decision is justified. We conclude by pointing out the wide applicability of this test, including to CMB experiments and the H0 tension.

Precision calibration poses challenges to experiments probing the redshifted 21-cm signal of neutral hydrogen from the Cosmic Dawn and Epoch of Reionization (z~30-6). In both interferometric and global signal experiments, systematic calibration is the leading source of error. Though many aspects of calibration have been studied, the overlap between the two types of instruments has received less attention. We investigate the sky based calibration of total power measurements with a HERA dish and an EDGES style antenna to understand the role of auto-correlations in the calibration of an interferometer and the role of sky in calibrating a total power instrument. Using simulations we study various scenarios such as time variable gain, incomplete sky calibration model, and primary beam model. We find that temporal gain drifts, sky model incompleteness, and beam inaccuracies cause biases in the receiver gain amplitude and the receiver temperature estimates. In some cases, these biases mix spectral structure between beam and sky resulting in spectrally variable gain errors. Applying the calibration method to the HERA and EDGES data, we find good agreement with calibration via the more standard methods. Although instrumental gains are consistent with beam and sky errors similar in scale to those simulated, the receiver temperatures show significant deviations from expected values. While we show that it is possible to partially mitigate biases due to model inaccuracies by incorporating a time-dependent gain model in calibration, the resulting errors on calibration products are larger and more correlated. Completely addressing these biases will require more accurate sky and primary beam models., Comment: 16 pages, 13 figures, 1 table; accepted for publication in MNRAS main journal

The Multi-frequency Angular Power Spectrum (MAPS) is an alternative to spherically-averaged power spectra, and computes local fluctuations in the angular power spectrum without need for line-of-sight spectral transform. To test different approaches to MAPS and treatment of the foreground contamination, and compare with the spherically-averaged power spectrum, and the single-frequency angular power spectrum. We apply the MAPS to 110~hours of data in $z=6.2-7.5$ obtained for the Murchison Widefield Array Epoch of Reionisation experiment to compute the statistical power of 21~cm brightness temperature fluctuations. In the presence of bright foregrounds, a filter is applied to remove large-scale modes prior to MAPS application, significantly reducing MAPS power due to systematics. The MAPS shows a contrast of 10$^2$--10$^3$ to a simulated 21~cm cosmological signal for spectral separations of 0--4~MHz after application of the filter, reflecting results for the spherically-averaged power spectrum. The single-frequency angular power spectrum is also computed. At $z=7.5$ and $l=200$, we find an angular power of 53~mK$^2$, exceeding a simulated cosmological signal power by a factor of one thousand. Residual spectral structure, inherent to the calibrated data, and not spectral leakage from large-scale modes, is the dominant source of systematic power bias. The single-frequency angular power spectrum yields slightly poorer results compared with the spherically-averaged power spectrum, having applied a spectral filter to reduce foregrounds. Exploration of other filters may improve this result, along with consideration of wider bandwidths., 9 pages, 9 figures; accepted for publication in Astronomy & Astrophysics

We present a broadband map of polarized diffuse emission at 167-198 MHz developed from data from the Murchison Widefield Array (MWA). The map is designed to improve visibility simulation and precision calibration for 21 cm Epoch of Reionization (EoR) experiments. It covers a large swath - 11,000 sq. deg. - of the Southern Hemisphere sky in all four Stokes parameters and captures emission on angular scales of 1 to 9 degrees. The band-averaged diffuse structure is predominantly unpolarized but has significant linearly polarized structure near RA = 0 h. We evaluate the accuracy of the map by combining it with the GLEAM catalog and simulating an observation from the MWA, demonstrating that the accuracy of the short baselines (6.1-50 wavelengths) now approaches the accuracy of the longer baselines typically used for EoR calibration. We discuss how to use the map for visibility simulation for a variety of interferometric arrays. The map has potential to improve calibration accuracy for experiments such as the Hydrogen Epoch of Reionization Array (HERA) and the forthcoming Square Kilometre Array (SKA) as well as the MWA., Comment: Accepted for publication in MNRAS

Radio Frequency Interference (RFI) is one of the systematic challenges preventing 21cm interferometric instruments from detecting the Epoch of Reionization. To mitigate the effects of RFI on data analysis pipelines, numerous inpaint techniques have been developed to restore RFI corrupted data. We examine the qualitative and quantitative errors introduced into the visibilities and power spectrum due to inpainting. We perform our analysis on simulated data as well as real data from the Hydrogen Epoch of Reionization Array (HERA) Phase 1 upper limits. We also introduce a convolutional neural network that capable of inpainting RFI corrupted data in interferometric instruments. We train our network on simulated data and show that our network is capable at inpainting real data without requiring to be retrained. We find that techniques that incorporate high wavenumbers in delay space in their modeling are best suited for inpainting over narrowband RFI. We also show that with our fiducial parameters Discrete Prolate Spheroidal Sequences (DPSS) and CLEAN provide the best performance for intermittent ``narrowband'' RFI while Gaussian Progress Regression (GPR) and Least Squares Spectral Analysis (LSSA) provide the best performance for larger RFI gaps. However we caution that these qualitative conclusions are sensitive to the chosen hyperparameters of each inpainting technique. We find these results to be consistent in both simulated and real visibilities. We show that all inpainting techniques reliably reproduce foreground dominated modes in the power spectrum. Since the inpainting techniques should not be capable of reproducing noise realizations, we find that the largest errors occur in the noise dominated delay modes. We show that in the future, as the noise level of the data comes down, CLEAN and DPSS are most capable of reproducing the fine frequency structure in the visibilities of HERA data., Comment: 21 pages, 13 figures

We describe a new polarized imaging pipeline implemented in the FHD software package. The pipeline is based on the optimal mapmaking imaging approach and performs horizon-to-horizon image reconstruction in all polarization modes. We discuss the formalism behind the pipeline's polarized analysis, describing equivalent representations of the polarized beam response, or Jones matrix. We show that, for arrays where antennas have uniform polarization alignments, defining a non-orthogonal instrumental polarization basis enables accurate and efficient image reconstruction. Finally, we present a new calibration approach that leverages widefield effects to perform fully-polarized calibration. This analysis pipeline underlies the analysis of Murchison Widefield Array (MWA) data in Byrne et al. (2022, MNRAS, 510, 2011)., Published in PASA. The updated version includes an example of image reconstruction of a simulated polarized source

We quantify the effect of radio frequency interference (RFI) on measurements of the 21-cm power spectrum during the Epoch of Reionization (EoR). Specifically, we investigate how the frequency structure of RFI source emission generates contamination in higher order wave modes, which is much more problematic than smooth-spectrum foreground sources. Using a relatively optimistic EoR model, we find that even a single relatively dim RFI source can overwhelm the EoR power spectrum signal of $\sim 10\, {\rm mK}^2$ for modes $0.1 \ \lt k \lt 2 \, h\, {\rm Mpc}^{-1}$. If the total apparent RFI flux density in the final power spectrum integration is kept below 1 mJy, an EoR signal resembling this optimistic model should be detectable for modes $k \lt 0.9\, h\, {\rm Mpc}^{-1}$, given no other systematic contaminants and an error tolerance as high as 10 per cent. More pessimistic models will be more restrictive. These results emphasize the need for highly effective RFI mitigation strategies for telescopes used to search for the EoR.

The key challenge in the observation of the redshifted 21-cm signal from cosmic reionization is its separation from the much brighter foreground emission. Such separation relies on the different spectral properties of the two components, although, in real life, the foreground intrinsic spectrum is often corrupted by the instrumental response, inducing systematic effects that can further jeopardize the measurement of the 21-cm signal. In this paper, we use Gaussian Process Regression to model both foreground emission and instrumental systematics in $\sim 2$ hours of data from the Hydrogen Epoch of Reionization Array. We find that a simple co-variance model with three components matches the data well, giving a residual power spectrum with white noise properties. These consist of an "intrinsic" and instrumentally corrupted component with a coherence-scale of 20 MHz and 2.4 MHz respectively (dominating the line of sight power spectrum over scales $k_{\parallel} \le 0.2$ h cMpc$^{-1}$) and a baseline dependent periodic signal with a period of $\sim 1$ MHz (dominating over $k_{\parallel} \sim 0.4 - 0.8$h cMpc$^{-1}$) which should be distinguishable from the 21-cm EoR signal whose typical coherence-scales is $\sim 0.8$ MHz., 15 pages, 15 figures, 1 table, Accepted to MNRAS

We present a framework for identifying and flagging malfunctioning antennas in large radio interferometers. We outline two distinct categories of metrics designed to detect outliers along known failure modes of large arrays: cross-correlation metrics, based on all antenna pairs, and auto-correlation metrics, based solely on individual antennas. We define and motivate the statistical framework for all metrics used, and present tailored visualizations that aid us in clearly identifying new and existing systematics. We implement these techniques using data from 105 antennas in the Hydrogen Epoch of Reionization Array (HERA) as a case study. Finally, we provide a detailed algorithm for implementing these metrics as flagging tools on real data sets., Comment: 31 pages, 17 figures

We report on a search for low-frequency radio variability in 944 bright (> 4Jy at 154 MHz) unresolved, extragalactic radio sources monitored monthly for several years with the Murchison Widefield Array. In the majority of sources we find very low levels of variability with typical modulation indices < 5%. We detect 15 candidate low frequency variables that show significant long term variability (>2.8 years) with time-averaged modulation indices M = 3.1 - 7.1%. With 7/15 of these variable sources having peaked spectral energy distributions, and only 5.7% of the overall sample having peaked spectra, we find an increase in the prevalence of variability in this spectral class. We conclude that the variability seen in this survey is most probably a consequence of refractive interstellar scintillation and that these objects must have the majority of their flux density contained within angular diameters less than 50 milli-arcsec (which we support with multi-wavelength data). At 154 MHz we demonstrate that interstellar scintillation time-scales become long (~decades) and have low modulation indices, whilst synchrotron driven variability can only produce dynamic changes on time-scales of hundreds of years, with flux density changes less than one milli-jansky (without relativistic boosting). From this work we infer that the low frequency extra-galactic southern sky, as seen by SKA-Low, will be non-variable on time-scales shorter than one year., 19 pages, 11 figures

21 cm power spectrum observations have the potential to revolutionize our understanding of the Epoch of Reionization and Dark Energy, but require extraordinarily precise data analysis methods to separate the cosmological signal from the astrophysical and instrumental contaminants. This analysis challenge has led to a diversity of proposed analyses, including delay spectra, imaging power spectra, m-mode analysis, and numerous others. This diversity of approach is a strength, but has also led to confusion within the community about whether insights gleaned by one group are applicable to teams working in different analysis frameworks. In this paper we show that all existing analysis proposals can be classified into two distinct families based on whether they estimate the power spectrum of the measured or reconstructed sky. This subtle difference in the statistical question posed largely determines the susceptibility of the analyses to foreground emission and calibration errors, and ultimately the science different analyses can pursue. In this paper we detail the origin of the two analysis families, categorize the analyses being actively developed, and explore their relative sensitivities to foreground contamination and calibration errors., Accepted for publication in MNRAS

Observations in the lowest MWA band between $75-100$ MHz have the potential to constrain the distribution of neutral hydrogen in the intergalactic medium at redshift $\sim 13-17$. Using 15 hours of MWA data, we analyse systematics in this band such as radio-frequency interference (RFI), ionospheric and wide field effects. By updating the position of point sources, we mitigate the direction independent calibration error due to ionospheric offsets. Our calibration strategy is optimized for the lowest frequency bands by reducing the number of direction dependent calibrators and taking into account radio sources within a wider field of view. We remove data polluted by systematics based on the RFI occupancy and ionospheric conditions, finally selecting 5.5 hours of the cleanest data. Using these data, we obtain two sigma upper limits on the 21 cm power spectrum in the range of $0.1\lessapprox k \lessapprox 1 ~\rm ~h~Mpc^{-1}$ and at $z$=14.2, 15.2 and 16.5, with the lowest limit being $6.3\times 10^6 ~\rm mK^2$ at $\rm k=0.14 \rm ~h~Mpc^{-1}$ and at $z=15.2$ with a possibility of a few \% of signal loss due to direction independent calibration., Comment: 17 pages, 18 figures, accepted to MNRAS

Current attempts to measure the 21cm Power Spectrum of neutral hydrogen during the Epoch of Reionization are limited by systematics which produce measured upper limits above both the thermal noise and the expected cosmological signal. These systematics arise from a combination of observational, instrumental, and analysis effects. In order to further understand and mitigate these effects, it is instructive to explore different aspects of existing datasets. One such aspect is the choice of observing field. To date, MWA EoR observations have largely focused on the EoR0 field. In this work, we present a new detailed analysis of the EoR1 field. The EoR1 field is one of the coldest regions of the Southern radio sky, but contains the very bright radio galaxy Fornax-A. The presence of this bright extended source in the primary beam of the interferometer makes the calibration and analysis of EoR1 particularly challenging. We demonstrate the effectiveness of a recently developed shapelet model of Fornax-A in improving the results from this field. We also describe and apply a series of data quality metrics which identify and remove systematically contaminated data. With substantially improved source models, upgraded analysis algorithms and enhanced data quality metrics, we determine EoR power spectrum upper limits based on analysis of the best $\sim$14-hours data observed during 2015 and 2014 at redshifts 6.5, 6.8 and 7.1, with the lowest $2\sigma$ upper limit at z=6.5 of $\Delta^2 \leq (73.78 ~\mathrm{mK)^2}$ at $k=0.13~\mathrm{h~ Mpc^{-1}}$, improving on previous EoR1 measurement results., Comment: 18 pages, 17 figures, Accepted for publication in MNRAS

Precise measurements of the 21 cm power spectrum are crucial for understanding the physical processes of hydrogen reionization. Currently, this probe is being pursued by low-frequency radio interferometer arrays. As these experiments come closer to making a first detection of the signal, error estimation will play an increasingly important role in setting robust measurements. Using the delay power spectrum approach, we have produced a critical examination of different ways that one can estimate error bars on the power spectrum. We do this through a synthesis of analytic work, simulations of toy models, and tests on small amounts of real data. We find that, although computed independently, the different error bar methodologies are in good agreement with each other in the noise-dominated regime of the power spectrum. For our preferred methodology, the predicted probability distribution function is consistent with the empirical noise power distributions from both simulated and real data. This diagnosis is mainly in support of the forthcoming HERA upper limit, and also is expected to be more generally applicable., Comment: 35 Pages, 9 Figures, 4 Tables. Replaced with accepted ApJ version; some clarifying text added in response to referee comments with no changes to results

As current- and next-generation astronomical instruments come online, they will generate an unprecedented deluge of data. Analyzing these data in real time presents unique conceptual and computational challenges, and their long-term storage and archiving is scientifically essential for generating reliable, reproducible results. We present here the real-time processing (RTP) system for the Hydrogen Epoch of Reionization Array (HERA), a radio interferometer endeavoring to provide the first detection of the highly redshifted 21 cm signal from Cosmic Dawn and the Epoch of Reionization by an interferometer. The RTP system consists of analysis routines run on raw data shortly after they are acquired, such as calibration and detection of radio-frequency interference (RFI) events. RTP works closely with the Librarian, the HERA data storage and transfer manager which automatically ingests data and transfers copies to other clusters for post-processing analysis. Both the RTP system and the Librarian are public and open source software, which allows for them to be modified for use in other scientific collaborations. When fully constructed, HERA is projected to generate over 50 terabytes (TB) of data each night, and the RTP system enables the successful scientific analysis of these data., Comment: 15 pages, 3 figures, published in Astronomy and Computing

In 21 cm cosmology, precision calibration is key to the separation of the neutral hydrogen signal from very bright but spectrally-smooth astrophysical foregrounds. The Hydrogen Epoch of Reionization Array (HERA), an interferometer specialized for 21 cm cosmology and now under construction in South Africa, was designed to be largely calibrated using the self-consistency of repeated measurements of the same interferometric modes. This technique, known as "redundant-baseline calibration" resolves most of the internal degrees of freedom in the calibration problem. It assumes, however, on antenna elements with identical primary beams placed precisely on a redundant grid. In this work, we review the detailed implementation of the algorithms enabling redundant-baseline calibration and report results with HERA data. We quantify the effects of real-world non-redundancy and how they compare to the idealized scenario in which redundant measurements differ only in their noise realizations. Finally, we study how non-redundancy can produce spurious temporal structure in our calibration solutions--both in data and in simulations--and present strategies for mitigating that structure., Comment: 24 Pages, 19 Figures. Updated to match the accepted MNRAS version

Stomata are epidermal valves that facilitate gas exchange between plants and their environment. Stomatal patterning is regulated by the EPIDERMAL PATTERING FACTOR (EPF) family of secreted peptides: EPF1 enforces stomatal spacing, whereas EPIDERMAL PATTERNING FACTOR-LIKE9 (EPFL9), also known as Stomagen, promotes stomatal development. It remains unknown, however, how far these signaling peptides act. Utilizing Cre-lox recombination-based mosaic sectors that overexpress either EPF1 or Stomagen in Arabidopsis cotyledons, we reveal a range within the epidermis and across the cell layers in which these peptides influence patterns. To determine their effective ranges quantitatively, we developed a computational pipeline, SPACE (stomata patterning autocorrelation on epidermis), that describes probabilistic two-dimensional stomatal distributions based upon spatial autocorrelation statistics used in astrophysics. The SPACE analysis shows that, whereas both peptides act locally, the inhibitor EPF1 exerts longer range effects than the activator Stomagen. Furthermore, local perturbation of stomatal development has little influence on global two-dimensional stomatal patterning. Our findings conclusively demonstrate the nature and extent of EPF peptides as non-cell autonomous local signals and provide a means for quantitative characterization of complex spatial patterns in development. This article has an associated ‘The people behind the papers’ interview., Highlighted Article: Non-cell autonomous effects of activator and inhibitor peptides on 2D spatial patterning of stomata were quantitatively characterized using chimeric sectors and a SPACE computational pipeline.

SummaryStomata are epidermal valves that facilitate gas exchange between plants and their environment. Stomatal patterning is regulated by EPIDERMAL PATTERING FACTOR (EPF)-family of secreted peptides: EPF1 enforcing stomatal spacing, whereas EPF-LIKE9, also known as Stomagen, promoting stomatal development. It remains unknown, however, how far these signaling peptides act. Utilizing Cre-Lox recombination-based mosaic sectors that overexpress either EPF1 or Stomagen in Arabidopsis cotyledons, we reveal a range within the epidermis and across the cell layers in which these peptides influence patterns. To quantitatively determine their effective ranges, we developed a computational pipeline, SPACE (Stomata Patterning AutoCorrelation on Epidermis), that describes probabilistic two-dimensional stomatal distributions based upon spatial autocorrelation statistics used in Astrophysics. The SPACE analysis shows that, whereas both peptides act locally, the inhibitor, EPF1, exerts longer-range effects than the activator, Stomagen. Furthermore, local perturbation of stomatal development has little influence on global two-dimensional stomatal patterning. Our findings conclusively demonstrate the nature and extent of EPF peptides as non-cell autonomous local signals and provides a means to quantitatively characterize complex spatial patterns in development.Summary StatementNon-cell autonomous effects of activator and inhibitor peptides on 2-D spatial patterning of stomata were quantitatively characterized using chimeric sectors and a SPACE computational pipeline.

Characterizing the epoch of reionization (EoR) at $z\gtrsim 6$ via the redshifted 21 cm line of neutral Hydrogen (HI) is critical to modern astrophysics and cosmology, and thus a key science goal of many current and planned low-frequency radio telescopes. The primary challenge to detecting this signal is the overwhelmingly bright foreground emission at these frequencies, placing stringent requirements on the knowledge of the instruments and inaccuracies in analyses. Results from these experiments have largely been limited not by thermal sensitivity but by systematics, particularly caused by the inability to calibrate the instrument to high accuracy. The interferometric bispectrum phase is immune to antenna-based calibration and errors therein, and presents an independent alternative to detect the EoR HI fluctuations while largely avoiding calibration systematics. Here, we provide a demonstration of this technique on a subset of data from the Hydrogen Epoch of Reionization Array (HERA) to place approximate constraints on the brightness temperature of the intergalactic medium (IGM). From this limited data, at $z=7.7$ we infer "$1\sigma$" upper limits on the IGM brightness temperature to be $\le 316$ "pseudo" mK at $\kappa_\parallel=0.33$ "pseudo" $h$ Mpc$^{-1}$ (data-limited) and $\le 1000$ "pseudo" mK at $\kappa_\parallel=0.875$ "pseudo" $h$ Mpc$^{-1}$ (noise-limited). The "pseudo" units denote only an approximate and not an exact correspondence to the actual distance scales and brightness temperatures. By propagating models in parallel to the data analysis, we confirm that the dynamic range required to separate the cosmic HI signal from the foregrounds is similar to that in standard approaches, and the power spectrum of the bispectrum phase is still data-limited (at $\gtrsim 10^6$ dynamic range) indicating scope for further improvement in sensitivity as the array build-out continues., Comment: 22 pages, 12 figures (including sub-figures). Published in PhRvD. Abstract may be slightly abridged compared to the actual manuscript due to length limitations on arXiv

Precise instrumental calibration is of crucial importance to 21-cm cosmology experiments. The Murchison Widefield Array's (MWA) Phase II compact configuration offers us opportunities for both redundant calibration and sky-based calibration algorithms; using the two in tandem is a potential approach to mitigate calibration errors caused by inaccurate sky models. The MWA Epoch of Reionization (EoR) experiment targets three patches of the sky (dubbed EoR0, EoR1, and EoR2) with deep observations. Previous work in \cite{Li_2018} and \cite{Wenyang_2019} studied the effect of tandem calibration on the EoR0 field and found that it yielded no significant improvement in the power spectrum over sky-based calibration alone. In this work, we apply similar techniques to the EoR1 field and find a distinct result: the improvements in the power spectrum from tandem calibration are significant. To understand this result, we analyze both the calibration solutions themselves and the effects on the power spectrum over three nights of EoR1 observations. We conclude that the presence of the bright radio galaxy Fornax A in EoR1 degrades the performance of sky-based calibration, which in turn enables redundant calibration to have a larger impact. These results suggest that redundant calibration can indeed mitigate some level of model-incompleteness error., Comment: 20 pages, 11 figures, accepted for publication in PASA

Calibration precision is currently a limiting systematic in 21 cm cosmology experiments. While there are innumerable calibration approaches, most can be categorized as either `sky-based,' relying on an extremely accurate model of astronomical foreground emission, or `redundant,' requiring a precisely regular array with near-identical antenna response patterns. Both of these classes of calibration are inflexible to the realities of interferometric measurement. In practice, errors in the foreground model, antenna position offsets, and beam response inhomogeneities degrade calibration performance and contaminate the cosmological signal. Here we show that sky-based and redundant calibration can be unified into a highly general and physically motivated calibration framework based on a Bayesian statistical formalism. Our new framework includes sky and redundant calibration as special cases but can additionally support relaxing the rigid assumptions implicit in those approaches. Furthermore, we present novel calibration techniques such as redundant calibration for arrays with no redundant baselines, representing an alternative calibration method for imaging arrays such as the MWA Phase I. These new calibration approaches could mitigate systematics and reduce calibration error, thereby improving the precision of cosmological measurements., Comment: Accepted for publication in MNRAS. This updated version has a section exploring the effects of the unified calibration framework on simulated data and comparing unified calibration to sky-based and redundant calibration. It also has an expanded discussion of calibration biases

We analyze data from the Hydrogen Epoch of Reionization Array. This is the third in a series of papers on the closure phase delay-spectrum technique designed to detect the HI 21cm emission from cosmic reionization. We present the details of the data and models employed in the power spectral analysis, and discuss limitations to the process. We compare images and visibility spectra made with HERA data, to parallel quantities generated from sky models based on the GLEAM survey, incorporating the HERA telescope model. We find reasonable agreement between images made from HERA data, with those generated from the models, down to the confusion level. For the visibility spectra, there is broad agreement between model and data across the full band of $\sim 80$MHz. However, models with only GLEAM sources do not reproduce a roughly sinusoidal spectral structure at the tens of percent level seen in the observed visibility spectra on scales $\sim 10$ MHz on 29 m baselines. We find that this structure is likely due to diffuse Galactic emission, predominantly the Galactic plane, filling the far sidelobes of the antenna primary beam. We show that our current knowledge of the frequency dependence of the diffuse sky radio emission, and the primary beam at large zenith angles, is inadequate to provide an accurate reproduction of the diffuse structure in the models. We discuss implications due to this missing structure in the models, including calibration, and in the search for the HI 21cm signal, as well as possible mitigation techniques., Comment: 17 pages, 10 figures, accepted for the ApJ Supplement

We present a study of internal reflection and cross-coupling systematics in Phase I of the Hydrogen Epoch of Reionization Array (HERA). In a companion paper, we outlined the mathematical formalism for such systematics and presented algorithms for modeling and removing them from the data. In this work, we apply these techniques to data from HERA’s first observing season as a method demonstration. The data show evidence for systematics that, without removal, would hinder a detection of the 21 cm power spectrum for the targeted Epoch of Reionization (EoR) line-of-sight modes in the range 0.2 h -1 Mpc-1 < {k}\parallel < 0.5 h -1 Mpc-1. In particular, we find evidence for nonnegligible amounts of spectral structure in the raw autocorrelations that overlaps with the EoR window and is suggestive of complex instrumental effects. Through systematic modeling on a single night of data, we find we can recover these modes in the power spectrum down to the integrated noise floor, achieving a dynamic range in the EoR window of 106 in power (mK2 units) with respect to the bright galactic foreground signal. Future work with deeper integrations will help determine whether these systematics can continue to be mitigated down to EoR levels. For future observing seasons, HERA will have upgraded analog and digital hardware to better control these systematics in the field.

The experimental efforts to detect the redshifted 21 cm signal from the Epoch of Reionization (EoR) are limited predominantly by the chromatic instrumental systematic effect. The delay spectrum methodology for 21 cm power spectrum measurements brought new attention to the critical impact of an antenna's chromaticity on the viability of making this measurement. This methodology established a straightforward relationship between time-domain response of an instrument and the power spectrum modes accessible to a 21 cm EoR experiment. We examine the performance of a prototype of the Hydrogen Epoch of Reionization Array (HERA) array element that is currently observing in Karoo desert, South Africa. We present a mathematical framework to derive the beam integrated frequency response of a HERA prototype element in reception from the return loss measurements between 100-200 MHz and determined the extent of additional foreground contamination in the delay space. The measurement reveals excess spectral structures in comparison to the simulation studies of the HERA element. Combined with the HERA data analysis pipeline that incorporates inverse covariance weighting in optimal quadratic estimation of power spectrum, we find that in spite of its departure from the simulated response, HERA prototype element satisfies the necessary criteria posed by the foreground attenuation limits and potentially can measure the power spectrum at spatial modes as low as $k_{\parallel} > 0.1h$~Mpc$^{-1}$. The work highlights a straightforward method for directly measuring an instrument response and assessing its impact on 21 cm EoR power spectrum measurements for future experiments that will use reflector-type antenna., 13 pages, 10 figures, Submitted to APJ

Radio Frequency Interference (RFI) is an ever-present limiting factor among radio telescopes even in the most remote observing locations. When looking to retain the maximum amount of sensitivity and reduce contamination for Epoch of Reionization studies, the identification and removal of RFI is especially important. In addition to improved RFI identification, we must also take into account computational efficiency of the RFI-Identification algorithm as radio interferometer arrays such as the Hydrogen Epoch of Reionization Array grow larger in number of receivers. To address this, we present a Deep Fully Convolutional Neural Network (DFCN) that is comprehensive in its use of interferometric data, where both amplitude and phase information are used jointly for identifying RFI. We train the network using simulated HERA visibilities containing mock RFI, yielding a known "ground truth" dataset for evaluating the accuracy of various RFI algorithms. Evaluation of the DFCN model is performed on observations from the 67 dish build-out, HERA-67, and achieves a data throughput of 1.6$\times 10^{5}$ HERA time-ordered 1024 channeled visibilities per hour per GPU. We determine that relative to an amplitude only network including visibility phase adds important adjacent time-frequency context which increases discrimination between RFI and Non-RFI. The inclusion of phase when predicting achieves a Recall of 0.81, Precision of 0.58, and $F_{2}$ score of 0.75 as applied to our HERA-67 observations., Comment: 11 pages, 7 figures

One of the major challenges for pulsar timing array (PTA) experiments is the mitigation of the effects of the turbulent interstellar medium (ISM) from timing data. These can potentially lead to measurable delays and/or distortions in the pulse profiles and scale strongly with the inverse of the radio frequency. Low-frequency observations are therefore highly appealing for characterizing them. However, in order to achieve the necessary time resolution to resolve profile features of short-period millisecond pulsars, phase-coherent de-dispersion is essential, especially at frequencies below $300$ MHz. We present the lowest-frequency ($80$-$220$ MHz), coherently de-dispersed detections of one of the most promising pulsars for current and future PTAs, PSR J2241$-$5236, using our new beam-former software for the MWA's voltage capture system (VCS), which reconstructs the time series at a much higher time resolution of $\sim 1 \mu$s by re-synthesizing the recorded voltage data at $10$-kHz/$100$-$\mu$s native resolutions. Our data reveal a dual-precursor type feature in the pulse profile that is either faint or absent in high-frequency observations from Parkes. The resultant high-fidelity detections have enabled dispersion measure (DM) determinations with very high precision, of the order of $(2$-$6)\times10^{-6}$ $\rm pc\,cm^{-3}$, owing to the microsecond level timing achievable for this pulsar at the MWA's low frequencies. This underscores the usefulness of low-frequency observations for probing the ISM toward PTA pulsars and informing optimal observing strategies for PTA experiments., Comment: 09 pages, 4 figures, 2 tables

We explore methods for robust estimation of the 21 cm signal from the Epoch of Reionisation (EoR). A Kernel Density Estimator (KDE) is introduced for measuring the spatial temperature fluctuation power spectrum from the EoR. The KDE estimates the underlying probability distribution function of fluctuations as a function of spatial scale, and contains different systematic biases and errors to the typical approach to estimating the fluctuation power spectrum. Extraction of histograms of visibilities allows moments analysis to be used to discriminate foregrounds from 21 cm signal and thermal noise. We use the information available in the histograms, along with the statistical dis-similarity of foregrounds from two independent observing fields, to robustly separate foregrounds from cosmological signal, while making no assumptions about the Gaussianity of the signal. Using two independent observing fields to robustly discriminate signal from foregrounds is crucial for the analysis presented in this paper. We apply the techniques to 13 hours of Murchison Widefield Array (MWA) EoR data over two observing fields. We compare the output to that obtained with a comparative power spectrum estimation method, and demonstrate the reduced foreground contamination using this approach. Using the second moment obtained directly from the KDE distribution functions yields a factor of 2-3 improvement in power for k < 0.3hMpc^{-1} compared with a matched delay space power estimator, while weighting data by additional statistics does not offer significant improvement beyond that available for thermal noise-only weights., 19 pages, 18 figures, accepted for publication in MNRAS

We apply two methods to estimate the 21~cm bispectrum from data taken within the Epoch of Reionisation (EoR) project of the Murchison Widefield Array (MWA). Using data acquired with the Phase II compact array allows a direct bispectrum estimate to be undertaken on the multiple redundantly-spaced triangles of antenna tiles, as well as an estimate based on data gridded to the $uv$-plane. The direct and gridded bispectrum estimators are applied to 21 hours of high-band (167--197~MHz; $z$=6.2--7.5) data from the 2016 and 2017 observing seasons. Analytic predictions for the bispectrum bias and variance for point source foregrounds are derived. We compare the output of these approaches, the foreground contribution to the signal, and future prospects for measuring the bispectra with redundant and non-redundant arrays. We find that some triangle configurations yield bispectrum estimates that are consistent with the expected noise level after 10 hours, while equilateral configurations are strongly foreground-dominated. Careful choice of triangle configurations may be made to reduce foreground bias that hinders power spectrum estimators, and the 21~cm bispectrum may be accessible in less time than the 21~cm power spectrum for some wave modes, with detections in hundreds of hours., Comment: 19 pages, 10 figures, accepted for publication in PASA

We introduce a new pipeline for analyzing and mitigating radio frequency interference (RFI), which we call Sky-Subtracted Incoherent Noise Spectra (SSINS). SSINS is designed to identify and remove faint RFI below the single baseline thermal noise by employing a frequency-matched detection algorithm on baseline-averaged amplitudes of time-differenced visibilities. We demonstrate the capabilities of SSINS using the Murchison Widefield Array (MWA) in Western Australia. We successfully image aircraft flying over the array via digital television (DTV) reflection detected using SSINS and summarize an RFI occupancy survey of MWA Epoch of Reionization data. We describe how to use SSINS with new data using a documented, publicly available implementation with comprehensive usage tutorials., Comment: Publication Draft

The detection of the Epoch of Reionization (EoR) delay power spectrum using a "foreground avoidance method" highly depends on the instrument chromaticity. The systematic effects induced by the radio-telescope spread the foreground signal in the delay domain, which contaminates the EoR window theoretically observable. Applied to the Hydrogen Epoch of Reionization Array (HERA), this paper combines detailed electromagnetic and electrical simulations in order to model the chromatic effects of the instrument, and quantify its frequency and time responses. In particular, the effects of the analogue receiver, transmission cables, and mutual coupling are included. These simulations are able to accurately predict the intensity of the reflections occurring in the 150-m cable which links the antenna to the back-end. They also show that electromagnetic waves can propagate from one dish to another one through large sections of the array due to mutual coupling. The simulated system time response is attenuated by a factor $10^{4}$ after a characteristic delay which depends on the size of the array and on the antenna position. Ultimately, the system response is attenuated by a factor $10^{5}$ after 1400 ns because of the reflections in the cable, which corresponds to characterizable ${k_\parallel}$-modes above 0.7 $h\;\rm{Mpc}^{-1}$ at 150 MHz. Thus, this new study shows that the detection of the EoR signal with HERA Phase I will be more challenging than expected. On the other hand, it improves our understanding of the telescope, which is essential to mitigate the instrument chromaticity., Comment: 13 pages, 17 figures - Submitted to MNRAS - 2nd revision

Epoch of Reionisation (EoR) data analysis requires unprecedented levels of accuracy in radio interferometer pipelines. We have developed an imaging power spectrum analysis to meet these requirements and generate robust 21 cm EoR measurements. In this work, we build a signal path framework to mathematically describe each step in the analysis, from data reduction in the Fast Holographic Deconvolution (FHD) package to power spectrum generation in theεppsilon package. In particular, we focus on the distinguishing characteristics of FHD/εppsilon: highly accurate spectral calibration, extensive data verification products, and end-to-end error propagation. We present our key data analysis products in detail to facilitate understanding of the prominent systematics in image-based power spectrum analyses. As a verification to our analysis, we also highlight a full-pipeline analysis simulation to demonstrate signal preservation and lack of signal loss. This careful treatment ensures that the FHD/εppsilon power spectrum pipeline can reduce radio interferometric data to produce credible 21 cm EoR measurements.

The Murchison Widefield Array (MWA) is an open access telescope dedicated to studying the low frequency (80$-$300 MHz) southern sky. Since beginning operations in mid 2013, the MWA has opened a new observational window in the southern hemisphere enabling many science areas. The driving science objectives of the original design were to observe 21\,cm radiation from the Epoch of Reionisation (EoR), explore the radio time domain, perform Galactic and extragalactic surveys, and monitor solar, heliospheric, and ionospheric phenomena. All together 60$+$ programs recorded 20,000 hours producing 146 papers to date. In 2016 the telescope underwent a major upgrade resulting in alternating compact and extended configurations. Other upgrades, including digital back-ends and a rapid-response triggering system, have been developed since the original array was commissioned. In this paper we review the major results from the prior operation of the MWA, and then discuss the new science paths enabled by the improved capabilities. We group these science opportunities by the four original science themes, but also include ideas for directions outside these categories., Comment: 38 pages, 12 figures, accepted for publication in PASA

The Murchison Widefield Array (MWA) is an electronically steered low frequency ($, 14 pages, 5 figures, accepted for publication in PASA

The rare intermittent pulsars pose some of the most challenging questions surrounding the pulsar emission mechanism, but typically have relatively minimal low-frequency ($\lesssim$ 300 MHz) coverage. We present the first low-frequency detection of the intermittent pulsar J1107-5907 with the Murchison Widefield Array (MWA) at 154 MHz and the simultaneous detection from the recently upgraded Molonglo Observatory Synthesis Telescope (UTMOST) at 835 MHz, as part of an on-going observing campaign. During a 30-minute simultaneous observation, we detected the pulsar in its bright emission state for approximately 15 minutes, where 86 and 283 pulses were detected above a signal-to-noise threshold of 6 with the MWA and UTMOST, respectively. Of the detected pulses, 51 had counterparts at both frequencies and exhibited steep spectral indices for both the bright main pulse component and the precursor component. We find that the bright state pulse energy distribution is best parameterised by a log-normal distribution at both frequencies, contrary to previous results which suggested a power law distribution. Further low-frequency observations are required in order to explore in detail aspects such as pulse-to-pulse variability, intensity modulations and to better constrain the signal propagation effects due to the interstellar medium and intermittency characteristics at these frequencies. The spectral index, extended profile emission covering a large fraction of pulse longitude, and the broadband intermittency of PSR J1107-5907 suggests that future low-frequency pulsar searches, for instance those planned with SKA-Low, will be in an excellent position to find and investigate new pulsars of this type., 19 pages, 7 figures, 4 tables, accepted for publication in ApJ; minor updates to keep in-line with published version

Detection of the epoch of reionization H i signal requires a precise understanding of the intervening galaxies and AGN, both for instrumental calibration and foreground removal. We present a catalogue of 7394 extragalactic sources at 182 MHz detected in the RA = 0 field of the Murchison Widefield Array Epoch of Reionization observation programme. Motivated by unprecedented requirements for precision and reliability we develop new methods for source finding and selection. We apply machine learning methods to self-consistently classify the relative reliability of 9490 source candidates. A subset of 7466 are selected based on reliability class and signal-to-noise ratio criteria. These are statistically cross-matched to four other radio surveys using both position and flux density information. We find 7369 sources to have confident matches, including 90 partially resolved sources that split into a total of 192 sub-components. An additional 25 unmatched sources are included as new radio detections. The catalogue sources have a median spectral index of −0.85. Spectral flattening is seen towards lower frequencies with a median of −0.71 predicted at 182 MHz. The astrometric error is 7 arcsec compared to a 2.3 arcmin beam FWHM. The resulting catalogue covers ∼1400 deg² and is complete to approximately 80 mJy within half beam power. This provides the most reliable discrete source sky model available to date in the MWA EoR0 field for precision foreground subtraction., National Science Foundation (U.S.) (AST-0847753), National Science Foundation (U.S.) (AST-1410484), National Science Foundation (U.S.) (AST-1506024)

We present a survey for transient and variable sources, on timescales from 28 seconds to $\sim$1 year, using the Murchison Widefield Array (MWA) at 182 MHz. Down to a detection threshold of 0.285 Jy, no transient candidates were identified, making this the most constraining low-frequency survey to date and placing a limit on the surface density of transients of $, Comment: MNRAS Accepted, 17 pages, 10 figures

We analyse a 154 MHz image made from a 12 h observation with the Murchison Widefield Array (MWA) to determine the noise contribution and behaviour of the source counts down to 30 mJy. The MWA image has a bandwidth of 30.72 MHz, a field-of-view within the half-power contour of the primary beam of 570 deg^2, a resolution of 2.3 arcmin and contains 13,458 sources above 5 sigma. The rms noise in the centre of the image is 4-5 mJy/beam. The MWA counts are in excellent agreement with counts from other instruments and are the most precise ever derived in the flux density range 30-200 mJy due to the sky area covered. Using the deepest available source count data, we find that the MWA image is affected by sidelobe confusion noise at the ~3.5 mJy/beam level, due to incompletely-peeled and out-of-image sources, and classical confusion becomes apparent at ~1.7 mJy/beam. This work highlights that (i) further improvements in ionospheric calibration and deconvolution imaging techniques would be required to probe to the classical confusion limit and (ii) the shape of low-frequency source counts, including any flattening towards lower flux densities, must be determined from deeper ~150 MHz surveys as it cannot be directly inferred from higher frequency data., 13 pages, 13 figures, accepted for publication in MNRAS

The central challenge in 21~cm cosmology is isolating the cosmological signal from bright foregrounds. Many separation techniques rely on the accurate knowledge of the sky and the instrumental response, including the antenna primary beam. For drift-scan telescopes such as the Hydrogen Epoch of Reionization Array \citep[HERA, ][]{DeBoer2017} that do not move, primary beam characterization is particularly challenging because standard beam-calibration routines do not apply \citep{Cornwell2005} and current techniques require accurate source catalogs at the telescope resolution. We present an extension of the method from \citet{Pober2012} where they use beam symmetries to create a network of overlapping source tracks that break the degeneracy between source flux density and beam response and allow their simultaneous estimation. We fit the beam response of our instrument using early HERA observations and find that our results agree well with electromagnetic simulations down to a -20~dB level in power relative to peak gain for sources with high signal-to-noise ratio. In addition, we construct a source catalog with 90 sources down to a flux density of 1.4~Jy at 151~MHz., 22 pages, 22 figures, accepted for publication in ApJ