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#     Instruction to convert ATCA files from MIRIAD to CASA
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#			MIRIAD
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!/usr/bin sh

# Load data into miriad 
ATLOD in="*.C2046" out="out.uv" options=opcorr,birdie,noauto,rfiflag

# Initial flagging (flag shadowing, bad timing, sick antennas...):
UVFLAG vis="pica.uv" select="shadow(22)" flagval=flag

# Index and split:
UVINDEX vis="out.uv" 
UVSPLIT vis="out.uv"

##############
# Further flagging if needed on single targets
# Calibration according to the needed scheme
##############

# Convert to uvfits all the files in the data_folder that need to be used for following analysis.
# Add to FITS the options=nocal,nopol,nopass in case you are converting data with no calibration applied
for file in `cat data_folder'
do
    FITS in=$file op=uvout out=$file.fits stokes=xx,yy,xy,yx options=nocal,nopol,nopass
done 


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#			CASA
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# Convert from uvfits to MS.
IMPORTUVFITS(fitsfile='$file.fits', vis='$filems', antnamescheme='old', async='False')

# Now you can deal with the  $filems as a common measurement set. Verify your conversion with
LISTOBS(vis='$filems', verbose=True)
PLOTMS(choose your parameters to see what is the status of bandpass, phase, amplitude)
CLEAN(to image your target)

# If you have more than one target (i.e. source+calibrators) and you want them in the same ms or 
# if you deal with a mosaic and you want to put all the pointings in the same ms (a.g. to image the whole mosaic area) 
# concatenate the ms to a 'unique_ms'
CONCAT(vis=['point1','point2',...], concatvis='unique_ms')

# Again check the unique_ms with
LISTOBS(vis='unique_ms', verbose=True)
CLEAN(to image your target, use imagermode='mosaic' if needed)