.sh

#! /bin/bash
#SBATCH -M zeus
#SBATCH --cpus-per-task 24
#SBATCH --mem 120G
#SBATCH -t 24:00:00
#SBATCH --nodes 1
#SBATCH --partition workq
#SBATCH --account pawsey0286
#SBATCh --export=ABSMEM

set -e
set -x

shopt -s expand_aliases
source ~/.bash_aliases
source ~/.profile

vis=$1

wsclean \
  -name original-full \
  -scale 2asec \
  -size 9000 9000 \
  -mgain 0.8 \
  -niter 999999 \
  -nmiter 20 \
  -pol i \
  -auto-mask 8 \
  -auto-threshold 1.5 \
  -channels-out 6 \
  -fit-spectral-pol 2 \
  -join-channels \
  -weight briggs 0.5 \
  -nwlayers-factor 3 \
  -data-column DATA \
  -deconvolution-channels 2 \
  -padding 1.6 \
  -abs-mem $ABSMEM \
  -minuvw-m 60 \
  $vis 2>&1 | grep -v GFLOPS --line-buffered | tee original-full.log

wsclean \
  -name original \
  -scale 1.5asec \
  -size 8000 8000 \
  -mgain 0.8 \
  -niter 999999 \
  -nmiter 12 \
  -pol i \
  -auto-threshold 3 \
  -channels-out 6 \
  -fit-spectral-pol 2 \
  -join-channels \
  -weight briggs 0 \
  -nwlayers-factor 3 \
  -stop-negative \
  -data-column DATA \
  -deconvolution-channels 2 \
  -padding 1.6 \
  -abs-mem $ABSMEM \
  -minuvw-m 60 \
  $vis 2>&1 | grep -v GFLOPS --line-buffered | tee original.log

casa -nologger --agg --nogui -c "gaincal(vis='${vis}', caltable='selfcal1.gcal', solint='60s', uvrange='> 70', calmode='p')"
casa -nologger --agg --nogui -c "applycal(vis='${vis}', gaintable=['selfcal1.gcal'])"

wsclean \
  -name afterselfcal1 \
  -scale 1.5asec \
  -size 8000 8000 \
  -mgain 0.8 \
  -niter 999999 \
  -nmiter 12 \
  -pol i \
  -auto-threshold 3 \
  -channels-out 6 \
  -fit-spectral-pol 2 \
  -join-channels \
  -weight briggs 0 \
  -nwlayers-factor 3 \
  -stop-negative \
  -deconvolution-channels 2 \
  -padding 1.6 \
  -abs-mem $ABSMEM \
  -minuvw-m 60 \
  $vis 2>&1 | grep -v GFLOPS --line-buffered | tee afterselfcal1.log

casa -nologger --agg --nogui -c "gaincal(vis='${vis}', caltable='selfcal2.gcal', solint='60s', uvrange='> 70', calmode='p', gaintable=['selfcal1.gcal'])"
casa -nologger --agg --nogui -c "applycal(vis='${vis}', gaintable=['selfcal1.gcal', 'selfcal2.gcal'])"

wsclean \
  -name afterselfcal2 \
  -scale 1.5asec \
  -size 8000 8000 \
  -mgain 0.8 \
  -niter 999999 \
  -nmiter 12 \
  -pol i \
  -auto-threshold 3 \
  -channels-out 6 \
  -fit-spectral-pol 2 \
  -join-channels \
  -weight briggs 0 \
  -nwlayers-factor 3 \
  -stop-negative \
  -deconvolution-channels 2 \
  -padding 1.6 \
  -abs-mem $ABSMEM \
  -minuvw-m 60 \
  $vis 2>&1 | grep -v GFLOPS --line-buffered | tee afterselfcal2.log

casa -nologger --agg --nogui -c "gaincal(vis='${vis}', caltable='selfcal3.gcal', solint='60s', uvrange='> 70', calmode='ap', gaintable=['selfcal1.gcal', 'selfcal2.gcal'])"
casa -nologger --agg --nogui -c "applycal(vis='${vis}', gaintable=['selfcal1.gcal', 'selfcal2.gcal', 'selfcal3.gcal'])"

#wsclean \
#  -name afterselfcal3 \
#  -scale 2.5asec \
#  -size 5000 5000 \
#  -mgain 0.8 \
#  -niter 999999 \
#  -nmiter 12 \
#  -pol i \
#  -auto-threshold 3 \
#  -channels-out 6 \
#  -fit-spectral-pol 2 \
#  -join-channels \
#  -weight briggs 0 \
#  -use-idg \
#  -idg-mode hybrid \
#  -stop-negative \
#  $vis | tee afterselfcal3.log

#casa -nologger --agg --nogui -c "gaincal(vis='${vis}', caltable='selfcal4.gcal', solint='60s', uvrange='> 70', calmode='ap', gaintable=['selfcal1.gcal', 'selfcal2.gcal', 'selfcal3.gcal'])"
#casa -nologger --agg --nogui -c "applycal(vis='${vis}', gaintable=['selfcal1.gcal', 'selfcal2.gcal', 'selfcal3.gcal', 'selfcal4.gcal'])"

#wsclean \
#  -name afterselfcal4 \
#  -scale 2.5asec \
#  -size 5000 5000 \
#  -mgain 0.8 \
#  -niter 999999 \
#  -nmiter 12 \
#  -pol i \
#  -auto-threshold 3 \
#  -channels-out 6 \
#  -fit-spectral-pol 2 \
#  -join-channels \
#  -weight briggs 0 \
#  -use-idg \
#  -idg-mode hybrid \
#  -stop-negative \
#  $vis | tee afterselfcal4.log

#casa -nologger --agg --nogui -c "bandpass(vis='${vis}', caltable='selfcal5.bpass', solint='30min', uvrange='> 70', gaintable=['selfcal1.gcal', 'selfcal2.gcal', 'selfcal3.gcal', 'selfcal4.gcal'])"
#casa -nologger --agg --nogui -c "applycal(vis='${vis}', gaintable=['selfcal1.gcal', 'selfcal2.gcal', 'selfcal3.gcal', 'selfcal4.gcal', 'selfcal5.bpass'])"

wsclean \
  -name final-full \
  -scale 2asec \
  -size 9000 9000 \
  -mgain 0.8 \
  -niter 9999999 \
  -nmiter 20 \
  -pol i \
  -auto-mask 8 \
  -auto-threshold 1 \
  -channels-out 6 \
  -fit-spectral-pol 2 \
  -join-channels \
  -weight briggs 0.5 \
  -nwlayers-factor 3 \
  -deconvolution-channels 2 \
  -padding 1.6 \
  -abs-mem $ABSMEM \
  -minuvw-m 60 \
  $vis 2>&1 | grep -v GFLOPS --line-buffered | tee final-full.log