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Synthetic data generation package for the Event Horizon Telescope

Installation

Two options:

  1. Use docker if you'd like to be system independent.

  2. Build on Ubuntu 16.04 using the following steps:

  • Visit Kern-3 and follow the few-step instructions
  • sudo apt-get install meqtrees casalite simms pyxis wsclean
  • build aatm
  • see additional, more standard modules below
  • add required paths below

Requirements

simms: python wrapper for creating empty Measurement Sets using the CASA simulate tool

WSClean: predicts visibilities using the Radio Interferometry Measurement Equation

MeqTrees: predicts visibilities using the Radio Interferometry Measurement Equation (for ASCII sky models)

Pyxis: python-esque scripting language for MeqTrees

CASA: v4.3 and above

AATM v0.5: mean atmospheric simulator (average opacities, sky brightness temp). (Download mirrored here)

Non-standard python modules required

  • numpy
  • matplotlib
  • pyfits
  • pyrap
  • termcolor
  • mpltools
  • seaborn

PATHS to set

Add the following to the PATH enviroment variable (if they are not installed in standard locations):

  • export PATH=/path/to/simms/simms/bin:/path/to/CASA/bin:$PATH

And the following to the PYTHONPATH environment variable:

  • export PYTHONPATH=/path/to/MeqSilhouette/framework:$PYTHONPATH

Add the following environment variable to point to your MeqSilhouette directory:

  • export MEQS_DIR=/path/to/MeqSilhouette

Finally, add a symbolic link to the MeqTrees simulator script to the framework directory within MeqSilhouette:

  • ln -s /path/to/meqtrees-cattery/Siamese/turbo-sim.py /path/to/MeqSilhouette/framework/turbo-sim.py

Running MeqSilhouette

To run this synthetic data generator, you need:

  1. a driver script (e.g. driver/run_meqsilouette.py)
  2. a configuration file (e.g. input/eht230.json). The file 'jsonformat.txt' explains each parameter used in the json file.

The software can be run in three primary modes:

###a) Through the terminal

$python driver/run_meqsilhouette.py input/eht230.json

###b) In a Juypter (ipython) Notebook

Start up notebook

from run_meqsilhouette import *

config = '/path/to/config.json' sim = run_meqsilhouette(config)

###c) In a Docker container

While setting up the required enviroment to run MeqSilhouette is just a few step process (for Ubuntu 14.04, 16.04), one can avoid system dependencies entirely with Docker.

###d) In a virtual environment

A number of python packages must be installed before MeqSilhouette could be run in a virtual environment. The following can be installed using pip install:

  • numpy
  • python-casacore==2.1.2 (to get pyrap to run)
  • pyfits
  • scipy==0.17 (to avoid "Incorrect qhull library called" error)
  • astLib
  • termcolor
  • matplotlib
  • seaborn
  • pandas
  • mpltools

If an ImportError is thrown by pyfits for the modules gdbm and/or winreg, a quick and dirty fix is to open the file

/path-to-virtualenv/lib/python2.7/site-packages/pyfits/extern/six.py

and comment out the lines:

MovedModule("dbm_gnu", "gdbm", "dbm.gnu")

MovedModule("winreg", "_winreg")

Configuration file

All paths are relative to $MEQS_DIR defined above

The configuration file is a simple .json file and contains the basic observational setup which are loosely grouped into the following parameter groups:

  • general parameters (paths, output options, etc.)
  • measurement set parameters (pre-pended with "ms_")
  • imaging parameters (pre-pended with "im_")
  • tropospheric parameters (pre-pended with a "trop_")
  • antenna pointing error parameters (pre-pended "pointing_")

The following two important paths are specified in the configuration file:

  • "ms_antenna_table": input ANTENNA table for chosen array (CASA format)
  • "station_info" input station-specific information (SEFDs, station names)

Commonly encountered problems

  1. If MeqSilhouette cannot find aatm, add the following paths to the following environment variables:

export LD_LIBRARY_PATH=/path/to/aatm-0.5/lib:$LD_LIBRARY_PATH

export PATH=/path/to/aatm-0.5/bin:$PATH

  1. aatm will not compile without boost program options. In ubuntu 16.04, the relevant packages are libboost-program-options-dev, libboost-program-options1.58-dev, and libboost-program-options1.58.0

Additional links

  • Measurement Set structure and definition link