Coding is one of my favourite parts of doing astrophysics and cosmology. I’ve created a fair number of scientific codes, and been involved in many more. Here’s a bit of a summary.
I do essentially all my coding on GitHub. To see everything I’m involved in, head to my profile.
My ‘Originals’
TheHaloMod
TheHaloMod is a web-application that uses my Python codes hmf and halomod to calculate halo model quantities, and serve up plots directly without ever having to install the codes, from the comfort of your web browser.
If you’re interested in the actual code behind TheHaloMod, it’s free and open-source.
The purpose of TheHaloMod is to be useful for both researchers and students trying to get into large-scale structure research. TheHaloMod was formerly known as HMFcalc, and has been well-used since its creation in 2013. TheHaloMod adds extra goodies to the original HMFcalc — namely, the ability to calculate correlation functions and power spectra of galaxies.
TheHaloMod has an associated paper describing all the calculations. Check it out!
hmf
hmf is a “python application that provides a flexible and simple way to calculate the Halo Mass Function for a range of varying parameters.”
For the non-experts, the Halo Mass Function is a critical quantity in determining properties of the large-scale structure of the Universe. It encodes the number of halos of a given mass in a given volume of the Universe, and can be predicted from some fairly neat little arguments given a cosmology that describes how the Universe is expanding. The predictions can be used to compare to observations of galaxy clusters to determine parameters of the large scale structure. The HMF is also a key ingredient in more complex predictions of the Universe, via the halo model (see below!).
The HMF (and large-scale structure) were the topic of my PhD research at UWA, in which time I wrote this code. Since then, it has been widely used, and I still maintain it (though I work in a somewhat different field now!).
hmf has an associated paper describing the Halo Mass Function, and its implementation.
halomod
halomod takes the ideas and implementations of hmf to the next level: it uses the HMF predictions as an ingredient in the halo model.
The halo model is a super-convenient analytic tool to predict the spatial distribution of “things” in the Universe. It uses dark matter halos as the basic scaffolding, and then can associate other things with the halos — eg. galaxies or diffuse gas. The predictions can be compared to observations of the spatial layout of galaxies, for example, to determine either cosmological parameters or properties of the galaxies themselves.
While I wrote the basic structure of this code during my PhD (2013-2016), I only published it much later (2020), in conjunction with a massive update of HMFcalc to TheHaloMod.
hankel
hankel is a small Python code that implements a way to do a very specific integral transform — the Hankel transform.
This transform is particularly common in astrophysics and cosmology (for instance, it is required to transform a correlation function into a power spectrum and vice versa). It is also a bit of a tricky integral to do, because it is highly oscillatory. This code implements a neat idea (not mine!) that is able to accurately perform this integral with good computational performance (in most cases).
The beginnings of hankel came together through my PhD, since I did a lot of converting correlation functions to power spectra. But when I changed fields to 21cm cosmology, I realized that the same transform is used there, and I made the package more general. It is now used in several fields of astronomy, and outside of astronomy too!
hankel has an associated article that presents the code in a little more detail.
powerbox
powerbox is a small Python code that is all about power spectra in “boxes” of arbitrary dimension. It can both create boxes with a given power spectrum, or determine the power spectrum of a given box. It does all of this with a lot of generality — we’re not just talking about 2- or 3-dimensional boxes, but boxes with an arbitrary number of dimensions (as long as your computer has enough memory!). Bring on the 5-dimensional cubes!
powerbox has an associated article — check it out!
Other Codes I Contribute To
In addition to building codes from the ground up (with the help of others in the scientific community, of course!), I also contribute to several other efforts — typically more grandiose in scale. For some of these I am a core developer or administrator, and others I just contribute something every now and then. Some of the Github Organizations I belong to are:
| 21cmFAST | 21cm Cosmology simulation and inference codes. I am a core admin in this organization. |
| RadioAstronomySoftwareGroup | Packages to aide the wider Radio Astronomy community in simulating and analysing large interferometric datasets. |
| hera-team | Repositories to simulate and analyse data from the HERA telescope. |
| edges-collab | Software to reduce and analyse data from the EDGES experiment. |
Some key software that I play a strong role in developing:
21cmFAST
21cmFAST is the premiere semi-numerical 21cm cosmological simulator. It is currently used by every 21cm cosmology experiment to derive predictions of the spatial distribution of 21cm brightness temperature, to compare to observations.
I am a core developer in this project. My role has been primarily to wrap the archaic (but fast!) C-code of the original simulator in Python, so that it can be more widely and easily used. This also has the benefit of adding a number of tests so that future development is safer and so that the code can be trusted by its many users.
The goal of wrapping the code is not trivial, and the updated package has an associated article to describe the implementation.
21cmMC
21cmMC uses 21cmFAST to compare observations with theory, and predict astrophysical and cosmological parameters. This is a beast of a process, since it must run thousands of cosmological simulations to generate the predictions. Thus, 21cmMC is highly parallelized with MPI and is geared to run on supercomputers.
21cmMC was originally written by Brad Greig, and I have worked on integrating it with the shiny new 21cmFAST.
hera_sim
hera_sim is one of the primary codes I contribute to in the HERA software suite. It is geared at simulating HERA-specific instrumental effects (thermal noise, cross-coupling, cable reflections) and injecting them into simulated (or observed!) visibilities.
The entire EDGES software suite
I am the primary developer of a new software pipeline for EDGES data. This involves data reading/writing (edges-io), calibration (edges-cal), analysis (edges-analysis) and parameter estimation (edges-estimate).
The software is developed by a small team, and I am overseeing (and contributing to) the development, in order to transform the EDGES analysis pipeline into something that is highly transparent, reproducible and accurate.