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bootstrapinterpolate_restoredloggingtrimmed.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)
#for months april and may - flagging channels varies with time of year
foreach dest ( 2016-04*.uv.split 2016-05*.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* bootstrap/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles/${dest}/bootstrap
#make copy of the 1420 for flagging
cp -r 1934-638.1420.5.6 1934-638.1420.5.6_flaggedHI |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#flag the HI line on the new copy
uvflag vis=1934-638.1420.5.6_flaggedHI line=channel,230,3000,1,1 flagval=f |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#copy HI flagged 1420 and unflagged in HI 1419 into interpolated folder for calibration
cp -r 1934-638.1420.5.6_flaggedHI ../interpolated/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
cp -r 1934-638.1419.5.2 ../interpolated/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
cp -r 1934-638.1419.5.6 ../interpolated/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#Compute sols through interpolation method
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles/${dest}/interpolated
#flag HI line in 1419, this is only done for the interpolation method
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
uvflag vis=1934-638.1419.5.6 line=channel,200,970,1,1 flagval=f |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#calibrate interpolated method
mfcal vis=1934-638.1419.5.2 line=channel,5200,400,1,1 refant=3 interval=5 options=interpolate |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
mfcal vis=1934-638.1419.5.6 line=channel,5200,400,1,1 refant=3 interval=5 options=interpolate |& 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=interpolate |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
gpcal vis=1934-638.1419.5.2 refant=3 interval=$gpcalint options=xyvary nfbin=$gpcalnfbin |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
gpcal vis=1934-638.1419.5.6 refant=3 interval=$gpcalint options=xyvary nfbin=$gpcalnfbin |& 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
#now do the bootstrapping
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles/${dest}/bootstrap
mfcal vis=1934-638.1419.5.2 line=channel,5200,400,1,1 refant=3 interval=5 |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
mfcal vis=1934-638.1419.5.6 line=channel,5200,400,1,1 refant=3 interval=5 |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
cp -rf /priv/myrtle1/gaskap/nickill/1934project/uvfiles/${dest}/interpolated/1934-638.1420.5.6_flaggedHI ./ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
gpcopy vis=1934-638.1420.5.6_flaggedHI/ out=1934-638.1420.5.6/ options=nopass,nopol |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
cp -r 1934-638.1419.5.2/bandpass 1934-638.1420.5.6/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
echo "FINISHED ${dest}" |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
end
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles
#flagging for august
foreach dest ( 2016-08*.uv.split )
echo "STARTING ${dest}" |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles/${dest}
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
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* bootstrap/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles/${dest}/bootstrap
#make copy of the 1420 for flagging
cp -r 1934-638.1420.5.6 1934-638.1420.5.6_flaggedHI |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#flag the HI line on the new copy
uvflag vis=1934-638.1420.5.6_flaggedHI line=channel,200,3370,1,1 flagval=f |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#copy HI flagged 1420 and unflagged in HI 1419 into interpolated folder for calibration
cp -r 1934-638.1420.5.6_flaggedHI ../interpolated/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
cp -r 1934-638.1419.5.2 ../interpolated/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
cp -r 1934-638.1419.5.6 ../interpolated/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#Compute sols through interpolation method
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles/${dest}/interpolated
#flag HI line in 1419, this is only done for the interpolation method
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
uvflag vis=1934-638.1419.5.6 line=channel,220,1350,1,1 flagval=f |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#calibrate interpolated method
mfcal vis=1934-638.1419.5.2 line=channel,5200,400,1,1 refant=3 interval=5 options=interpolate |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
mfcal vis=1934-638.1419.5.6 line=channel,5200,400,1,1 refant=3 interval=5 options=interpolate |& 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=interpolate |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
gpcal vis=1934-638.1419.5.2 refant=3 interval=$gpcalint options=xyvary nfbin=$gpcalnfbin |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
gpcal vis=1934-638.1419.5.6 refant=3 interval=$gpcalint options=xyvary nfbin=$gpcalnfbin |& 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
#now do the bootstrapping
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles/${dest}/bootstrap
mfcal vis=1934-638.1419.5.2 line=channel,5200,400,1,1 refant=3 interval=5 |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
mfcal vis=1934-638.1419.5.6 line=channel,5200,400,1,1 refant=3 interval=5 |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
mfcal vis=1934-638.1420.5.6_flaggedHI line=channel,5200,400,1,1 refant=3 interval=5 |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
gpcal vis=1934-638.1419.5.2 refant=3 interval=$gpcalint options=xyvary nfbin=$gpcalnfbin |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
gpcal vis=1934-638.1419.5.6 refant=3 interval=$gpcalint options=xyvary nfbin=$gpcalnfbin |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
gpcal vis=1934-638.1420.5.6_flaggedHI/ refant=3 interval=$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
cp -r 1934-638.1419.5.2/bandpass 1934-638.1420.5.6/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
echo "FINISHED ${dest}" |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
end
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles
#flagging for november
foreach dest ( 2016-11*.uv.split )
echo "STARTING ${dest}" |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles/${dest}
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
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* bootstrap/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles/${dest}/bootstrap
#make copy of the 1420 for flagging
cp -r 1934-638.1420.5.6 1934-638.1420.5.6_flaggedHI |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#flag the HI line on the new copy
uvflag vis=1934-638.1420.5.6_flaggedHI line=channel,200,3390,1,1 flagval=f |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#copy HI flagged 1420 and unflagged in HI 1419 into interpolated folder for calibration
cp -r 1934-638.1420.5.6_flaggedHI ../interpolated/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
cp -r 1934-638.1419.5.2 ../interpolated/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
cp -r 1934-638.1419.5.6 ../interpolated/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#Compute sols through interpolation method
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles/${dest}/interpolated
#flag HI line in 1419, this is only done for the interpolation method
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
uvflag vis=1934-638.1419.5.6 line=channel,250,1300,1,1 flagval=f |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#calibrate interpolated method
mfcal vis=1934-638.1419.5.2 line=channel,5200,400,1,1 refant=3 interval=5 options=interpolate |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
mfcal vis=1934-638.1419.5.6 line=channel,5200,400,1,1 refant=3 interval=5 options=interpolate |& 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=interpolate |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
gpcal vis=1934-638.1419.5.2 refant=3 interval=$gpcalint options=xyvary nfbin=$gpcalnfbin |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
gpcal vis=1934-638.1419.5.6 refant=3 interval=$gpcalint options=xyvary nfbin=$gpcalnfbin |& 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
#now do the bootstrapping
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles/${dest}/bootstrap
mfcal vis=1934-638.1419.5.2 line=channel,5200,400,1,1 refant=3 interval=5 |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
mfcal vis=1934-638.1419.5.6 line=channel,5200,400,1,1 refant=3 interval=5 |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
mfcal vis=1934-638.1420.5.6_flaggedHI line=channel,5200,400,1,1 refant=3 interval=5 |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
gpcal vis=1934-638.1419.5.2 refant=3 interval=$gpcalint options=xyvary nfbin=$gpcalnfbin |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
gpcal vis=1934-638.1419.5.6 refant=3 interval=$gpcalint options=xyvary nfbin=$gpcalnfbin |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
gpcal vis=1934-638.1420.5.6_flaggedHI/ refant=3 interval=$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
cp -r 1934-638.1419.5.2/bandpass 1934-638.1420.5.6/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
echo "FINISHED ${dest}" |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
end
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles
#flagging for feb
foreach dest ( 2017-02*.uv.split )
echo "STARTING ${dest}" |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles/${dest}
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
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* bootstrap/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles/${dest}/bootstrap
#make copy of the 1420 for flagging
cp -r 1934-638.1420.5.6 1934-638.1420.5.6_flaggedHI |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#flag the HI line on the new copy
uvflag vis=1934-638.1420.5.6_flaggedHI line=channel,300,2990,1,1 flagval=f |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#copy HI flagged 1420 and unflagged in HI 1419 into interpolated folder for calibration
cp -r 1934-638.1420.5.6_flaggedHI ../interpolated/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
cp -r 1934-638.1419.5.2 ../interpolated/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
cp -r 1934-638.1419.5.6 ../interpolated/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#Compute sols through interpolation method
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles/${dest}/interpolated
#flag HI line in 1419, this is only done for the interpolation method
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
uvflag vis=1934-638.1419.5.6 line=channel,200,1050,1,1 flagval=f |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#calibrate interpolated method
mfcal vis=1934-638.1419.5.2 line=channel,5200,400,1,1 refant=3 interval=5 options=interpolate |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
mfcal vis=1934-638.1419.5.6 line=channel,5200,400,1,1 refant=3 interval=5 options=interpolate |& 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=interpolate |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
gpcal vis=1934-638.1419.5.2 refant=3 interval=$gpcalint options=xyvary nfbin=$gpcalnfbin |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
gpcal vis=1934-638.1419.5.6 refant=3 interval=$gpcalint options=xyvary nfbin=$gpcalnfbin |& 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
#now do the bootstrapping
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles/${dest}/bootstrap
mfcal vis=1934-638.1419.5.2 line=channel,5200,400,1,1 refant=3 interval=5 |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
mfcal vis=1934-638.1419.5.6 line=channel,5200,400,1,1 refant=3 interval=5 |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
mfcal vis=1934-638.1420.5.6_flaggedHI line=channel,5200,400,1,1 refant=3 interval=5 |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
gpcal vis=1934-638.1419.5.2 refant=3 interval=$gpcalint options=xyvary nfbin=$gpcalnfbin |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
gpcal vis=1934-638.1419.5.6 refant=3 interval=$gpcalint options=xyvary nfbin=$gpcalnfbin |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
gpcal vis=1934-638.1420.5.6_flaggedHI/ refant=3 interval=$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
cp -r 1934-638.1419.5.2/bandpass 1934-638.1420.5.6/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
echo "FINISHED ${dest}" |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
end
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles
#flagging for 2019
foreach dest ( 2019*.uv.split )
echo "STARTING ${dest}" |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles/${dest}
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
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* bootstrap/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles/${dest}/bootstrap
#make copy of the 1420 for flagging
cp -r 1934-638.1420.5.4 1934-638.1420.5.4_flaggedHI |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#flag the HI line on the new copy
uvflag vis=1934-638.1420.5.4_flaggedHI line=channel,200,3080,1,1 flagval=f |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#copy HI flagged 1420 and unflagged in HI 1419 into interpolated folder for calibration
cp -r 1934-638.1420.5.4_flaggedHI ../interpolated/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
cp -r 1934-638.1419.5.2 ../interpolated/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#Compute sols through interpolation method
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles/${dest}/interpolated
#flag HI line in 1419, this is only done for the interpolation method
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=1934-638.1419.5.2 line=channel,5200,400,1,1 refant=3 interval=5 options=interpolate |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
mfcal vis=1934-638.1420.5.4_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=1934-638.1419.5.2 refant=3 interval=$gpcalint options=xyvary nfbin=$gpcalnfbin |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
gpcal vis=1934-638.1420.5.4_flaggedHI/ refant=3 interval=$gpcalint options=xyvary nfbin=$gpcalnfbin |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
#now do the bootstrapping
cd /priv/myrtle1/gaskap/nickill/1934project/uvfiles/${dest}/bootstrap
mfcal vis=1934-638.1419.5.2 line=channel,5200,400,1,1 refant=3 interval=5 |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
mfcal vis=1934-638.1420.5.4_flaggedHI line=channel,5200,400,1,1 refant=3 interval=5 |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
gpcal vis=1934-638.1419.5.2 refant=3 interval=$gpcalint options=xyvary nfbin=$gpcalnfbin |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
gpcal vis=1934-638.1420.5.4_flaggedHI/ refant=3 interval=$gpcalint options=xyvary nfbin=$gpcalnfbin |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
gpcopy vis=1934-638.1420.5.4_flaggedHI/ out=1934-638.1420.5.4/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
cp -r 1934-638.1419.5.2/bandpass 1934-638.1420.5.4/ |& tee -a /priv/myrtle1/gaskap/nickill/1934project/uvfiles/miriadcal.log
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