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Synthetic datacube creation from simulations.

Project description

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Overview

MARTINI is a modular package for the creation of synthetic resolved HI line observations (data cubes) of smoothed-particle hydrodynamics simulations of galaxies. The various aspects of the mock-observing process are divided logically into sub-modules handling the data cube, source, beam, noise, spectral model and SPH kernel. MARTINI is object-oriented: each sub-module provides a class (or classes) which can be configured as desired. For most sub-modules, base classes are provided to allow for straightforward customization. Instances of each sub-module class are given as parameters to the Martini class; a mock observation is then constructed by calling a handful of functions to execute the desired steps in the mock-observing process.

Citing MARTINI

If your use of MARTINI leads to a publication, please acknowledge this and link to the github page, ideally specifying the version used (git commit ID or version number). Please cite the MARTINI entry in the ASCL (indexed on ADS), and the original paper:

  @MISC{2019ascl.soft11005O,
       author = {{Oman}, Kyle A.},
        title = "{MARTINI: Mock spatially resolved spectral line observations of simulated galaxies}",
     keywords = {Software},
 howpublished = {Astrophysics Source Code Library, record ascl:1911.005},
         year = 2019,
        month = nov,
          eid = {ascl:1911.005},
        pages = {ascl:1911.005},
archivePrefix = {ascl},
       eprint = {1911.005},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2019ascl.soft11005O},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
   }

  @ARTICLE{2019MNRAS.482..821O,
       author = {{Oman}, Kyle A. and {Marasco}, Antonino and {Navarro}, Julio F. and {Frenk}, Carlos S. and {Schaye}, Joop and {Ben{\'\i}tez-Llambay}, Alejandro},
        title = "{Non-circular motions and the diversity of dwarf galaxy rotation curves}",
      journal = {\mnras},
     keywords = {ISM: kinematics and dynamics, galaxies: haloes, galaxies: structure, dark matter, Astrophysics - Astrophysics of Galaxies, Astrophysics - Cosmology and Nongalactic Astrophysics},
         year = 2019,
        month = jan,
       volume = {482},
       number = {1},
        pages = {821-847},
          doi = {10.1093/mnras/sty2687},
archivePrefix = {arXiv},
       eprint = {1706.07478},
 primaryClass = {astro-ph.GA},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2019MNRAS.482..821O},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
   }

Installation Notes

MARTINI works with python3 (version 3.7 or higher), and does not support python2.

Stable releases are available via PyPI (pip install astromartini) and the numbered releases (starting from 2.0.0) on github. The github main branch is actively developed: things will change, bugs will happen. Any feedback is greatly appreciated via github or kyle.a.oman@durham.ac.uk.

The easiest way to install martini is from PyPI by doing python3 -m pip install astromartini. Output to .fits files is supported by default; if output to .hdf5 format is desired use python3 -m pip install astromartini[hdf5_output] instead. This will also handle the installation of the required dependencies. Other optional features require additional dependencies hosted on PyPI. In particular, EAGLE, Illustris/TNG and Simba users who wish to use the custom source modules for those simulations in MARTINI can automatically install the optional dependencies with python3 -m pip install astromartini[eaglesource], or [simbasource] or [tngsource].

Installing from github

Choose a branch. Unless you want to install the latest (possibly buggy) main branch, installing with PyPI should usually be preferred. From the branch page (e.g. https://github.com/kyleaoman/martini/tree/2.0.X), click the green ‘Code’ button and follow instructions to obtain the files. Unpack the zip file if necessary. You should then be able to do python3 -m pip install martini/[optional], where optional should be replaced by a comma separated list of optional dependencies. If this fails check that martini/ is a path pointing to the directory containing the pyproject.toml file for MARTINI. The currently available options are:

  • hdf5_output: Supports output to hdf5 files via the h5py package. Since h5py is hosted on PyPI, this option may be used when installing via PyPI.

  • eaglesource: Dependencies for the martini.sources.EAGLESource module, which greatly simplifies reading input from EAGLE simulation snapshots. Installs my Hdecompose package, providing implementations of the Rahmati et al. (2013) method for computing netural hydrogen fractions and the Blitz & Rosolowsky (2006) method for atomic/molecular fractions. Also installs my python-only version of John Helly’s read_eagle package for quick extraction of particles in a simulation sub-volume. h5py is also required.

  • tngsource: Dependencies for the martini.sources.TNGSource module, which greatly simplifies reading input from IllustrisTNG (and original Illustris) snapshots. Installs my Hdecompose package, providing implementations of the Rahmati et al. (2013) method for computing netural hydrogen fractions and the Blitz & Rosolowsky (2006) method for atomic/molecular fractions.

  • magneticumsource: Dependencies for the martini.sources.MagneticumSource module, which supports the Magneticum simulations via my fork of the g3t package by Antonio Ragagnin.

  • sosource: Dependencies for the martini.sources.SOSource module, which provides unofficial support for several simulation datasets hosted on specific systems. This is intended mostly for my own use, but APOSTLE, C-EAGLE/Hydrangea and Auriga users may contact me for further information.

Getting started

See the help for martini.Martini for an example script to configure MARTINI and create a datacube. This example can be run by doing:

python -c "from martini import demo; demo()"

MARTINI has (so far) been successfully run on the output of these simulations:

  • EAGLE

  • APOSTLE

  • C-EAGLE/Hydrangea

  • Illustris

  • IllustrisTNG

  • Auriga

  • MaGICC (and therefore in principle NIHAO)

  • Magneticum

  • Simba

I attempt to support publicly available simulations with a customized source module. If your simulation is public and not supported, please contact me. Currently custom source modules exist for:

Example notebooks are available for supported simulations.

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