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5_bootstrapinterpolate_newprocess.sh
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#!/bin/csh
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles
date |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
set gpcalint = (1)
set gpcalintgap = (0.5)
set gpcalnfbin = (1)
#only april and may 2017 and 2018 have 1419.5.6 data and they are unusable as a result so 1419.5.6 need not be considered
#should it be required later just add a line identical to instances of 1419.5.2 with the names changed below it
#flagging channels varies with time of year
foreach dest ( 2016-04*.uv.split 2016-05*.uv.split 2016-08*.uv.split 2016-11*.uv.split 2017-02*.uv.split 2019*.uv.split )
echo "STARTING ${dest}" |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles/${dest}
pwd |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#remove preivous calibrations
rm -rf interpolated |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
rm -rf bootstrap |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#start cal
mkdir interpolated |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
mkdir bootstrap |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#move data into the bootstrap directory
cp -r 1934-638.14* bootstrap/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles/${dest}/bootstrap
#make copy of the 1420 for flagging
cp -r 1934-638.1420.5.* 1934-638.1420.5.6_flaggedHI |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#flag the HI line on the new copy
if ( ${dest} =~ 2016-04*.uv.split ) uvflag vis=1934-638.1420.5.6_flaggedHI line=channel,230,3000,1,1 flagval=f |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
if ( ${dest} =~ 2016-05*.uv.split ) uvflag vis=1934-638.1420.5.6_flaggedHI line=channel,230,3000,1,1 flagval=f |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
if ( ${dest} =~ 2016-08*.uv.split ) uvflag vis=1934-638.1420.5.6_flaggedHI line=channel,200,3370,1,1 flagval=f |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
if ( ${dest} =~ 2016-11*.uv.split ) uvflag vis=1934-638.1420.5.6_flaggedHI line=channel,200,3390,1,1 flagval=f |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
if ( ${dest} =~ 2017-02*.uv.split ) uvflag vis=1934-638.1420.5.6_flaggedHI line=channel,300,2990,1,1 flagval=f |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
if ( ${dest} =~ 2019*.uv.split ) uvflag vis=1934-638.1420.5.6_flaggedHI line=channel,200,3080,1,1 flagval=f |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#copy HI flagged 1420 and unflagged in HI 1419 into interpolated folder for calibration
cp -r 1934-638.1420.5.6_flaggedHI ../interpolated/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
cp -r 1934-638.1419.5.2 ../interpolated/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#Compute sols through interpolation method
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles/${dest}/interpolated
#flag HI line in 1419, this is only done for the interpolation method
if ( ${dest} =~ 2016-04*.uv.split ) uvflag vis=1934-638.1419.5.2 line=channel,200,970,1,1 flagval=f |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
if ( ${dest} =~ 2016-05*.uv.split ) uvflag vis=1934-638.1419.5.2 line=channel,200,970,1,1 flagval=f |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
if ( ${dest} =~ 2016-08*.uv.split ) uvflag vis=1934-638.1419.5.2 line=channel,220,1350,1,1 flagval=f |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
if ( ${dest} =~ 2016-11*.uv.split ) uvflag vis=1934-638.1419.5.2 line=channel,250,1300,1,1 flagval=f |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
if ( ${dest} =~ 2017-02*.uv.split ) uvflag vis=1934-638.1419.5.2 line=channel,200,1050,1,1 flagval=f |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
if ( ${dest} =~ 2019*.uv.split ) uvflag vis=1934-638.1419.5.2 line=channel,260,970,1,1 flagval=f |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#calibrate interpolated method
mfcal vis=1934-638.1420.5.6_flaggedHI/ line=channel,5200,400,1,1 refant=3 interval=5 options=interpolate |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
gpcal vis=1934-638.1420.5.6_flaggedHI/ refant=3 interval=$gpcalint options=xyvary nfbin=$gpcalnfbin |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
gpcopy vis=1934-638.1420.5.6_flaggedHI/ out=1934-638.1420.5.6/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log #repeated because wildcards not supported in out parameter
#now do the bootstrapping
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles/${dest}/bootstrap
mfcal vis=1934-638.1419.5.2 line=channel,5200,400,1,1 refant=3 interval=5 |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
mfcal vis=1934-638.1420.5.6_flaggedHI/ line=channel,5200,400,1,1 refant=3 interval=5 |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
cp -rf 1934-638.1419.5.2/bandpass 1934-638.1420.5.6_flaggedHI/bandpass |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
delhd in=1934-638.1420.5.6_flaggedHI/gains |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
mfcal vis=1934-638.1420.5.6_flaggedHI/ line=channel,5200,400,1,1 refant=3 interval=5 options=nopassol |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
gpcal vis=1934-638.1420.5.6_flaggedHI/ line=channel,5200,400,1,1 refant=3 interval=$gpcalint options=xyvary nfbin=$gpcalnfbin |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
if ( ${dest} =~ 2019*.uv.split ) gpcopy vis=1934-638.1420.5.6_flaggedHI/ out=1934-638.1420.5.4/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log # 2019 has different ID tag for 1420
gpcopy vis=1934-638.1420.5.6_flaggedHI/ out=1934-638.1420.5.6/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log #repeated because wildcards not supported in out parameter
echo "FINISHED ${dest}" |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
end
echo "EVERYTHING IS DONE" |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log