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The E-MERLIN Notebook

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The E-MERLIN Notebook The e-MERLIN Notebook IRIS Collaboration F2F Meeting - 4 April 2019 Dr. Rachael Ainsworth Jodrell Bank Centre for Astrophysics University of Manchester @rachaelevelyn Overview ● Motivation ● Brief intro to e-MERLIN ● Pieces of the puzzle: ○ e-MERLIN CASA Pipeline ○ Data Archive ○ Open Notebooks ● Putting everything together: ○ e-MERLIN @ IRIS Motivation (Whitaker 2018, https://doi.org/10.6084/m9.figshare.7140050.v2 ) “Computational science has led to exciting new developments, but the nature of the work has exposed limitations in our ability to evaluate published findings. Reproducibility has the potential to serve as a minimum standard for judging scientific claims when full independent replication of a study is not possible.” (Peng 2011; https://doi.org/10.1126/science.1213847) e-MERLIN (e)MERLIN ● enhanced Multi Element Remotely Linked Interferometer Network ● An array of 7 radio telescopes spanning 217 km across the UK ● Connected by a superfast optical fibre network to its headquarters at Jodrell Bank Observatory. ● Has a unique position in the world with an angular resolution comparable to that of the Hubble Space Telescope and carrying out centimetre wavelength radio astronomy with micro-Jansky sensitivities. http://www.e-merlin.ac.uk/ (e)MERLIN ● Does not have a publicly accessible data archive. http://www.e-merlin.ac.uk/ Radio Astronomy Software: CASA ● The CASA infrastructure consists of a set of C++ tools bundled together under an iPython interface as data reduction tasks. ● This structure provides flexibility to process the data via task interface or as a python script. ● https://casa.nrao.edu/ Pieces of the puzzle e-MERLIN CASA Pipeline ● Developed openly on GitHub (Moldon, et al.) ● Python package composed of different modules that can be run together sequentially to produce calibration tables, calibrated data, assessment plots and a summary weblog. ● Can take FITS-IDI files from observatory and produce a calibrated dataset and images to check quality of observation. ● Key idea is that the pipeline provides an easy, ready to use toolkit that delivers calibrated data in a consistent, clear and repeatable way. ● http://www.e-merlin.ac.uk/tools/eMCP-2.pdf https://github.com/e-merlin/eMERLIN_CASA_pipeline (See Rohini Joshi’s slides, https://indico.ph.qmul.ac.uk/indico/conferenceDisplay.py?confId=446) Open Notebooks (e.g. Jupyter) Open Notebooks are documents that contain equations, visualisations, narrative text and live code that can be executed independently and interactively, with output visible immediately beneath the input. They bring together analysis descriptions and results, which can be executed to perform the data analysis in real time. Added value: ● Transparency in the analysis of the data ● Reproducibility ● Documentation of the entire workflow http://jupyter.org/ A CASA kernel for Jupyter ● A Jupyter kernel for CASA was developed as part of the Obelics work-package of the EU funded Asterics project. ● The kernel allows all CASA tasks to be run from inside a Jupyter notebook, albeit non-interactively. ● Tasks which normally spawn a GUI window are wrapped so that their output is saved to an image instead, which is then displayed inside the notebook. ● A custom build of CASA is required, so it’s distributed within a container. ● https://github.com/aardk/jupyter-casa CASA e-MERLIN Tutorial in a Jupyter Notebook ● Shows how to calibrate e-MERLIN data in a Jupyter Notebook using the CASA kernel for Jupyter ● Also demonstrates how to set up your very own jupyter-casa notebook on a local server that can be used as a teaching tool for Radio Astronomy. ● https://github.com/hrampadarath/e merlin-casa-jupyter Putting everything together e-MERLIN @ IRIS ● Project to develop a service to archive (e)MERLIN data & perform [interactive] data analysis in the cloud ● Inspired by CERN’s SWAN (Service for Web based ANalysis) platform ● Software involved includes CASA, Jupyter Notebooks, Python, containers, open source software, DIRAC & IRIS resources ● Move towards open & accessible data, reproducible & transparent analysis ● https://github.com/rainsworth/eMERLIN-IRIS e-MERLIN @ IRIS https://github.com/rainsworth/eMERLIN-IRIS Summary ● Project repo: https://github.com/rainsworth/eMERLIN-IRIS ● Other open source projects mentioned: ○ e-MERLIN CASA Pipeline https://github.com/e-merlin/eMERLIN_CASA_pipeline ○ e-MERLIN CASA Jupyter Notebook Tutorial/Server: https://github.com/hrampadarath/emerlin-casa-jupyter ○ Jupyter kernel for CASA: https://github.com/aardk/jupyter-casa ● Contact: ○ Email: [email protected] ○ GitHub: @rainsworth ○ Twitter: @rachaelevelyn ● License: slides are CC-BY.
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