########################################
## spectline_flag.g
##
## Flagging commands for NGC4038 D-array HI data
##
## JHIBBARD 1/18/02
## called by specline_doall.g
######################################### 

#########################################
##
## Flagging
##
######################################### 
## The data to be flagged were previously identified in AIPS 
## You can do the same in aips++ with the msplot tool. We
## leave it the reader to do this step and flag their data
## as appropriate.

## REQUIRES "BASENAME" TO BE DEFINED FROM WITHOUT

## Set up some flagging parameters

                        ## The following is for flagging
                        ## outliers. However, the clipping
                        ## is done on the DATA field, and
			## before calibration, so the units
			## really are not Jy.
CLIP_HIGH		:= '5Jy';  # clip data points higher than this
CLIP_LOW		:= '0.00001Jy'; # clip data points lower than this
START_TIME		:= '1996/06/03/00:56:00';
END_TIME		:= '1996/06/03/04:23:30';
NCHAN			:= 127;

include 'flagger.g'
fg:=flagger(msfile=spaste(BASENAME,'.ms'));
fg.setflagmode('flag');

#Here is an example of how you would flag a set of channels:
#fg.setchan(1:BCHAN-1);
#fg.query('ANTENNA1>=0');
#fg.setchan(ECHAN+1:NCHAN);
#fg.query('ANTENNA1>=0');

# reset flagging scope to all channels
fg.setchan(1:NCHAN);

## flag outliers 
## Note: this clipping is done on the DATA field, and
## before calibration, so the units really are not Jy.
## Range specifies the range of valid data.

fg.filter(column='DATA', 
          operation='range', 
          comparison='Amplitude', 
          range=[CLIP_LOW,CLIP_HIGH]);

## flag bad baselines
## For these data, we need to flag baseline between ant 8 & 23. 
## You would niavely think that the following would work:
##      fg.query('ANTENNA1==8 and ANTENNA2==23');
## But it doesn't; that would flag ant 9 w/24. 
## NOTE!!!! THIS MAY CHANGE IN FURTHER RELEASES OF AIPS++!!!
## To get the desired result, do it as follows

fg.query('ANTENNA1==7 and ANTENNA2==22');

## flag bad antennaes

## In these data, Antenna 18 is at the center of the array, and
## is shadowed when on source until 02:57:00. Yet some scans still
## appear in the aips++ data, so flag these (it is unblocked 
## when on the calibrators). 

fg.setantennas([18]);
fg.setids(fieldid=[3]);
fg.timerange(START_TIME,'1996/06/03/02:56:00');

## Antenna 10 had high amplitudes and anomolous phase
## for the first scan. Behaved after that.

fg.setantennas([10]);
fg.setids(fieldid=[1]);
fg.timerange(START_TIME, '1996/06/03/01:10:00');

## Antenna 4 had some high amplitudes for parts of the first 
## scan, so flag a short timerange.

fg.setantennas([4]);
fg.setids(fieldid=[1]);
fg.timerange('1996/06/03/00:57:30','1996/06/03/01:02:00');

## Antenna 14 has a low gains and phase jump, but gives us grief
## with the bandpass solution if we leave it in, so we flag it for
## the entire run. If we were self-calibrating the data, we would 
## not necessarily want to flag all these data. 

fg.setantennas([14]);
fg.setids(fieldid=[1,2,3]);
#fg.timerange('1996/06/03/00:56:00','1996/06/03/02:41:30');
fg.timerange(START_TIME, END_TIME);

fg.done();

## Uncomment out the following if you want to check that your flags 
## got applied (if you wanted to do interactive flagging, you would 
## have edit=T and include the name of a flagfile. 

#include 'msplot.g'
#mymsplot:=msplot(spaste(BASENAME,'.ms'), edit=F);