# Simulations for SKA gain errors investigation
# Modhurita Mitra, modhurita@gmail.com
# 29 July 2019

Working directory on Dawn cluster at University of Groningen: /home/users/modhurita/SKA_gain_errors

# Python scripts:

Function definitions: definitions.py
Driver script: run_simulation.py

General parameters for the simulation are set at the top of the driver script. Other specific simulation parameters can be set in the OSKAR setup file, setup_SKA_core.ini.

# Software used:

For creating visibilities: OSKAR, v. 2.6.1
For concatenating visibilities: CASA, v. 5.1.1-5
For imaging: wsclean, v. 2.4
For power spectrum generation: F. Mertens' power spectrum generation code, v. 0.3.0: /home/users/modhurita/ps_eor-0.3.0/simple_ps.py

Source this file for the software above to run properly:
   $ source /software/users/lofarsoft/dawn/lofarsoft.sh_forOSKAR.sh

The simulations were run on node 131 of the Dawn cluster.

# Input files for simulating visibilities in OSKAR:

Setup file: setup_SKA_core.ini
Telescope configuration directory: SKA_core.tm
Skymodels directory: skymodels_mf

# Source image files used:

21-cm EoR signal: fg_image_1.17arcmin.fits
Foreground signal: eor_image_1.17arcmin.fits

The intensity is in units of K, and the image size is 512x512 pixels over a FoV of 10 degrees, making the pixel spacing 1.17 arcmin.

These image files are derived by adding appropriate fits headers to the EoR image, eor_standard.fits, and the foreground diffuse emission image, GalFG_standard.fits, from V. Jelic.

# SEFD calculation:

Calculated assuming station SEFD of 2500 Jy at 115 MHz.

# Skymodels creation:

The EoR and FG OSKAR skymodel files in the directory skymodels_mf are created by using the script create_skymodels_mf.py. The intensity units in the skymodel are in Jy/pixel.

# Creating the simulated datasets:

1. Set simulation parameters (observational and telescope parameters) in the OSKAR setup file.
2. Set general parameters (time and frequency steps, directory locations, etc.) at the top of the driver file.
3. Run the driver file:
   $ python run_simulated.py
   
   This will create the results directory, containing the following 3 subdirectories:
   - images_mf: Contains images and PSFs at each frequency
   - data_mf: Contains power spectra in text file format
   - plots_mf: Contains plots of power spectra
   
# Analysis of results:

  Text files from subdirectories of data_mf are put in a single directory, datafiles, to be used for analysis in the Jupyter notebook gain_errors_analysis.ipynb. Plots from the notebook are saved in the plots directory.

# Results: Presentation.pdf 

  Contains the results presented at the SKA EoR/CD Science Team Meeting in Zagreb, Croatia, in September 2017.

# Paper draft: SKAGainErrors.zip

  Contains LaTeX draft of paper describing results, and associated files and images.