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Merge pull request #165 from xpsi-group/annaw_clpaperupdates
Paper, changelog, code of conduct corrections
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CHANGELOG.rst

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.. ^^^^^^^^^^^
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[v1.0] - 2022-09-23
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[v1.0] - 2022-09-26
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~~~~~~~~~~~~~~~~~~~
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Summary

docs/source/Modeling_without_statistics.ipynb

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"* the [Photosphere](photosphere.rst#xpsi.Photosphere.Photosphere) class;\n",
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"* the [HotRegion](hotregion.rst#xpsi.HotRegion.HotRegion) class;\n",
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"* the [Elsewhere](elsewhere.rst#xpsi.Elsewhere.Elsewhere) class (optionally used in conjuction with HotRegion instances);\n",
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"* the [Everywhere](elsewhere.rst#xpsi.Elsewhere.Elsewhere) class (cannot be used with HotRegion instances);\n",
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"* the [Everywhere](everywhere.rst#xpsi.Everywhere.Everywhere) class (cannot be used with HotRegion instances);\n",
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"* and four low-level user-modifiable routines for evaluation of a parametrised specific intensity model.\n",
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"\n",
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"For this demonstration we will assume that the surface radiation field *elsewhere* (other than the hot regions) can be ignored in the soft X-ray regime our model instrument is sensitive to. We will not be utilizing the [Elsewhere](elsewhere.rst#xpsi.Elsewhere.Elsewhere) class, for which their exists a distinct tutorial (**Global surface emission**). For more advanced modelling, we can simply write custom *derived* classes, and instantiate those derived classes to construct objects for our model. In particular, a common pattern will be to subclass the [HotRegion](hotregion.rst#xpsi.HotRegion.HotRegion) class. Let's start with the [Spacetime](spacetime.rst#xpsi.Spacetime.Spacetime) class."

docs/source/code_of_conduct.rst

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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported to the community leaders in the X-PSI :ref:`team` responsible for
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enforcement. All complaints will be reviewed and investigated promptly and
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fairly. If contacting the X-PSI :ref:`team` is not an option, please directly
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contact Thomas E. Riley (t.e.riley[at]uva.nl) and/or
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Anna L. Watts (A.L.Watts[at]uva.nl).
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All community leaders are obligated to respect the privacy and security of the
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fairly. All community leaders are obligated to respect the privacy and security of the
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reporter of any incident.
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Enforcement Guidelines

joss/paper.md

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index: 2
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- name: Institut de Recherche en Astrophysique et Planétologie, UPS-OMP, CNRS, CNES, 9 avenue du Colonel Roche, BP 44346, F-31028 Toulouse Cedex 4, France
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index: 3
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date: 23 September 2022
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date: 26 September 2022
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bibliography: xpsijoss.bib
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---
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# Summary
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Stars play host to exotic environments that cannot be simulated in terrestrial
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laboratories. The focus of this work is neutron stars, thought to be the most
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compact extended objects in the Universe. Observable radiation from a neutron
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star encodes information about fundamental physics (gravity, electromagnetism,
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and nuclear forces) and astrophysical processes (such as the state and evolution
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of a stellar magnetosphere). Neutron stars are often detected by astronomers
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because their radiative signal - in radio, X-ray and gamma-rays - is pulsed due to bulk stellar rotation. By modeling the physical process that generates data registered by telescopes, astronomers and astrostatisticians can make inferential statements
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about the nature of the extreme Universe.
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# Summary
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X-PSI is a software package designed to simulate rotationally-modified (pulsed)
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surface X-ray emission from neutron stars and to perform Bayesian
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statistical inference on real or simulated pulse profile data sets. Model parameters
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of interest include neutron star mass and radius and the system geometry and
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properties of the hot emitting surface regions.
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# Statement of need
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There exist open-source libraries and packages to support a subset of the
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modeling treated in astrophysical literature. They provide frameworks,
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toolsets, model implementations, and so on. One sub-field for which there does
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not exist such an open-source project, is for the *statistical modeling* of
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X-ray signals that pulse due to rotational modulation of asymmetric emission
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from the surface of a neutron star. Pulsing X-ray signals from neutron stars
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are modeled to statistically estimate parameters such as stellar mass and
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Rotationally modulated (pulsed) X-ray signals from neutron stars
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can be modeled to statistically estimate parameters such as stellar mass and
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radius, and properties of the surface radiation field such as a map of
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temperature. The mass and radius of a neutron star are a function of the
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equation of state of internal matter (especially the dense matter in the core)
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distant telescope. Pulse-profile modelling to infer neutron star parameters
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is a major science goal for both current X-ray telescopes such as the Neutron
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Star Interior Composition ExploreR (NICER, @Gendreau2016) and future telescopes
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@Watts2019.
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[@Watts2019].
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There are a small number of open-source libraries for simulating the X-ray
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While there are some open-source libraries for simulating the X-ray
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signals from rapidly spinning neutron stars and more generally from the
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vicinity of general relativistic compact objects (including black holes).
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An example is the Arcmancer
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library of @Pihajoki:2018, a general purpose toolbox that is wrapped by an
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updated version of the bender library of @Nattila:2016 for the purpose of
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simulating X-ray signals from hot regions on the surfaces of rapidly rotating
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neutron stars. However the scope of these projects does not include statistical modeling, which
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vicinity of general relativistic compact objects including black holes [@Nattila:2016;@Pihajoki:2018] the scope
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of these projects does not include statistical modeling, which
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necessitates tractable parametrised models and a modular framework for
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constructing those models. X-PSI provides this functionality.
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constructing those models. X-PSI addresses this need, coupling code for likelihood
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functionality (simulation) with existing open-source software for posterior sampling (inference).
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# The X-PSI package and science use
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panel).\label{fig:animation_snapshot}](fig1.png){width=100%}
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X-PSI is being used by the NICER collaboration for pulse-profile modeling of X-ray emission from rotation-powered
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millisecond pulsars. Publications that have directly applied the X-PSI package thus far are
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@Riley:2019 and @Riley:2021. Many more papers have used the accompanying
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open-source analysis pipeline and products published on Zenodo; these products
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may be accessed using the linked DOIs of @Riley:2019:Zenodo and
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@Riley:2021:Zenodo. The first were @Raaijmakers:2019 and
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millisecond pulsars [@Riley:2019;@Riley:2021]. Many more papers have used the accompanying
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open-source analysis pipeline and products published on Zenodo [@Riley:2019:Zenodo;
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@Riley:2021:Zenodo]. The first were @Raaijmakers:2019 and
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@Bilous:2019, respectively on the topics of dense matter inference and
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multipolar magnetic fields.
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compatible, and release versions are freely available on GitHub under the MIT
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license. Extensive documentation, step-by-step tutorials, and reproduction
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code for existing data analyses, are available
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via the project github, along with a growing suite of unit tests. Future plans
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via the GitHub repository, along with a growing suite of unit tests. Future plans
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include migration to Python 3, further improvements to post-processing software,
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and the implementation of an expanded suite of atmosphere models.
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[@IPython2007], Jupyter [@Kluyver:2016aa], MultiNest [@MultiNest_2009],
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PyMultiNest [@PyMultiNest], GetDist [@Lewis19], nestcheck
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[@higson2018nestcheck;@higson2018sampling;@higson2019diagnostic], fgivenx
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[@fgivenx].
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[@fgivenx], emcee [@emcee].
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# Acknowledgements
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All University of Amsterdam co-authors acknowledge
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support from ERC Consolidator grant No. 865768 AEONS (PI: ALW). DH is supported by the
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Women In Science Excel (WISE) programme of the Netherlands Organisation for
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Scientific Research (NWO). SG acknowledges the support of the CNES. More detailed acknowledgements are written in the project
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documentation [hosted](https://xpsi-group.github.io/xpsi/acknowledgements.html)
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on GitHub.
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documentation [hosted on GitHub](https://xpsi-group.github.io/xpsi/acknowledgements.html).
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# References

joss/xpsijoss.bib

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Informed by Radio Timing and XMM-Newton
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Spectroscopy: Nested Samples for Millisecond
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Pulsar Parameter Estimation}},
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month = sep,
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year = 2022,
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month = apr,
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year = 2021,
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publisher = {Zenodo},
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version = {v1.0.2},
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doi = {10.5281/zenodo.7096886},
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url = {https://doi.org/10.5281/zenodo.7096886}
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version = {v1.0.0},
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doi = {10.5281/zenodo.4697625},
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url = {https://doi.org/10.5281/zenodo.4697625}
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}
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@dataset{Riley:2019:Zenodo,
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Strohmayer, Tod E.},
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title = {{A NICER View of PSR J0030+0451: Nested Samples for
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Millisecond Pulsar Parameter Estimation}},
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month = sep,
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year = 2022,
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month = dec,
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year = 2019,
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publisher = {Zenodo},
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version = {v1.3.0},
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doi = {10.5281/zenodo.7096789},
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url = {https://doi.org/10.5281/zenodo.7096789}
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version = {v1.0.0},
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doi = {10.5281/zenodo.3386449},
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url = {https://doi.org/10.5281/zenodo.3386449}
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}
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@ARTICLE{Raaijmakers:2019,
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adsnote = {Provided by the SAO/NASA Astrophysics Data System}
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}
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@ARTICLE{emcee,
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author = {{Foreman-Mackey}, Daniel and {Hogg}, David W. and {Lang}, Dustin and {Goodman}, Jonathan},
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title = "{emcee: The MCMC Hammer}",
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journal = {\pasp},
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keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Physics - Computational Physics, Statistics - Computation},
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year = 2013,
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month = mar,
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volume = {125},
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number = {925},
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pages = {306},
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doi = {10.1086/670067},
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archivePrefix = {arXiv},
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eprint = {1202.3665},
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primaryClass = {astro-ph.IM},
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adsurl = {https://ui.adsabs.harvard.edu/abs/2013PASP..125..306F},
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adsnote = {Provided by the SAO/NASA Astrophysics Data System}
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}
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