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JVLA_Lband.py
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JVLA_Lband.py
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import os, glob
import numpy as np
import subprocess
pi = np.pi
# fix for rficonsole LD_LIBRARY_PATH (cannot handle libgfortran provided by casapy)
#for the AOFlagger in the Reinout environment
#my_env = os.environ.copy()
#my_env["LD_LIBRARY_PATH"]="/lib:/usr/lib:/home/rvweeren/software/lofar/opt/LofIm/lib64:/home/rvweeren/software/root/lib:/home/rvweeren/software/heasoft-6.16/x86_64-unknown-linux-gnu-libc2.19-0/lib"
#GDG: no my_env in the subprocess for AOFlagger
# parang
# setjy modimage
# interp nearest
# timeragne
# check that modimage is right band (twice in scripts)
# no tfcrop flaggin, problem for calibrator scans with more than 50% flagged due to slews for example
# Nov 2015
# fixed tfcrop problem by unflag and flag action with tb.open
# linearflag in applycal last step!!
# changed to Taylor Butler 2013
# fixed aoflagger call with LD_LIBRARY_PATH and new rfis
basevis = 'A2.MS' # something.MS
spwlist = ['0','1','2','3','4','5','6','7','8','9','10','11','12','13','14','15']
uvlimit = "<100000klambda"
uvlimitp= "<100000klambda"
targetname = "XDCPJ0044-20"
phasecalname = "J2357-1125"
bandpasscalname = "0542+498=3C147"
polangcalname = "0521+166=3C138"
basevisnoMS = basevis.replace('.MS','')
path_plot = basevisnoMS+'_plots/'
path_data = basevisnoMS+'_data/'
num_ant = 27
num_plots = (num_ant/4)
ref_ant = 'ea20'
def flag_stat(ms):
default('flagdata')
t = flagdata(vis=ms, mode='summary', field='', scan='', spwchan=False, spwcorr=False, basecnt=False, action='calculate', flagbackup=False, savepars=False)
log = 'Flag statistics:'
log += '\nAntenna, '
for k in sorted(t['antenna']):
log += k +': %d.2%% - ' % (100.*t['antenna'][k]['flagged']/t['antenna'][k]['total'])
log += '\nCorrelation, '
for k, v in list(t['correlation'].items()):
log += k +': %d.2%% - ' % (100.*v['flagged']/v['total'])
log += '\nSpw, '
for k, v in list(t['spw'].items()):
log += k +': %d.2%% - ' % (100.*v['flagged']/v['total'])
log += '\nTotal: %d.2%%' % (100.*t['flagged']/t['total'])
print(log.replace(' - \n','\n'))
# delete and re-create MS-specific paths
if os.path.exists(path_plot): os.system('rm -r '+path_plot)
os.makedirs(path_plot)
if os.path.exists(path_data): os.system('rm -r '+path_data)
os.makedirs(path_data)
allspw_dataset = path_data+'allspw.MS'
allspw_target = path_data+'target.MS'
# listobs
if os.path.exists(basevis.replace('MS', 'listobs')): os.system('rm '+basevis.replace('MS', 'listobs'))
listobs( vis=basevis, listfile=basevis.replace('MS', 'listobs') )
for spw_id in spwlist:
print("Working on SPW", spw_id)
path_plot_spw = path_plot+'/spw%02i/' % int(spw_id)
os.makedirs(path_plot_spw)
path_data_spw = path_data+'/spw%02i/' % int(spw_id)
os.makedirs(path_data_spw)
hsmooth_file = path_data_spw+'hsmooth.MS'
outname_phasecal = path_data_spw+'phasecal.MS'
outname_bandpass = path_data_spw+'bandpass.MS'
outname_polang = path_data_spw+'polang.MS'
outname_target = path_data_spw+'target.MS'
calgceff = path_data_spw+'cal.gceff'
calantpos = path_data_spw+'cal.antpos'
calgcal1 = path_data_spw+'cal.gcal1' # P
calbp1 = path_data_spw+'cal.bcal1'
calgcal2 = path_data_spw+'cal.gcal2' # P
calk1 = path_data_spw+'cal.kcal1'
calbp2 = path_data_spw+'cal.bcal2'
calgcal3 = path_data_spw+'cal.gcal3' # AP
calkross1 = path_data_spw+'cal.kross1'
caldf1 = path_data_spw+'cal.dcal1'
calxf1 = path_data_spw+'cal.xcal1'
calgcal_loc = path_data_spw+'cal.gcalloc'
#apply the hanning smooth because of the RFI
default("hanningsmooth")
hanningsmooth(vis=basevis, datacolumn="data", outputvis=hsmooth_file, spw=spw_id)
# remove setup scan
default("flagdata")
flagdata(vis=hsmooth_file, flagbackup=False, mode='manual', scan='1')
# FLAG SHADOW
default("flagdata")
flagdata(vis=hsmooth_file,mode="shadow",flagbackup=False)
# first half of spw3 is shit
#if spw_id == '04':
# flagdata(vis=hsmooth_file, mode="manual", spw="0:0~32", flagbackup=False)
# TFCROP FLAG
#flagdata(vis=hsmooth_file,mode="tfcrop",autocorr=False,inpfile="",reason="any",spw="",field="",antenna="",
# uvrange="",timerange="",correlation="",scan="",intent="",array="",observation="",feed="",
# clipminmax=[],datacolumn="DATA",clipoutside=True,channelavg=False,clipzeros=False,quackinterval=1.0,
# quackmode="beg",quackincrement=False,tolerance=0.0,addantenna="",lowerlimit=0.0,upperlimit=90.0,
# ntime="scan",combinescans=False,timecutoff=4.0,freqcutoff=3.0,timefit="line",freqfit="poly",
# maxnpieces=7,flagdimension="freqtime",usewindowstats="none",halfwin=1,winsize=3,timedev="",
# freqdev="",timedevscale=5.0,freqdevscale=5.0,spectralmax=1000000.0,spectralmin=0.0,extendpols=True,
# growtime=50.0,growfreq=50.0,growaround=False,flagneartime=False,flagnearfreq=False,minrel=0.0,
# maxrel=1.0,minabs=0,maxabs=-1,spwchan=False,spwcorr=False,basecnt=False,action="apply",display="",
# flagbackup=False,savepars=False,cmdreason="",outfile="")
# GENCAL GAIN CURVE
gencal(vis=hsmooth_file,caltable=calgceff,caltype="gceff",spw="",antenna="",pol="",parameter=[])
# ANTPOS
gencal(vis=hsmooth_file,caltable=calantpos,caltype='antpos',spw="",antenna="",pol="",parameter=[])
if os.path.isdir(calantpos):
print('Antenna position corrections found')
applycal(vis=hsmooth_file, gaintable=[calgceff,calantpos], calwt=False, flagbackup=False)
else:
print('Antenna position corrections NOT found')
applycal(vis=hsmooth_file, gaintable=calgceff, calwt=False, flagbackup=False)
# BANDPASS
default("split")
split(vis=hsmooth_file,outputvis=outname_bandpass,datacolumn="corrected",field=bandpasscalname)
# POLANG
default("split")
split(vis=hsmooth_file,outputvis=outname_polang,datacolumn="corrected",field=polangcalname)
#Phasecal, + bandpass for fluxscale
default("split")
split(vis=hsmooth_file,outputvis=outname_phasecal,datacolumn="corrected",field=bandpasscalname+','+phasecalname)
# TARGET
default("split")
split(vis=hsmooth_file,outputvis=outname_target,datacolumn="corrected",field=targetname)
os.system('rm -rf ' + hsmooth_file)
setjy(vis=outname_bandpass, field=bandpasscalname, spw="", usescratch=True)
setjy(vis=outname_phasecal, field=bandpasscalname, spw="", usescratch=True)
setjy(vis=outname_polang, field=polangcalname, spw="", usescratch=True)
# Fix polarisation
tb.open(outname_polang, nomodify=False)
data = tb.getcol('MODEL_DATA')
if '3C286' in polangcalname:
RLphase = 33.0*2.0
polfrac = 0.095 # at 1.45GHz
elif '3C138' in polangcalname:
RLphase = -11.*2.0
polfrac = 0.075
StokesI = (0.5*(np.copy(data[0,:,:]) + np.copy(data[3,:,:])))
Q = StokesI*polfrac*np.cos(RLphase*pi/180.0)
U = StokesI*polfrac*np.sin(RLphase*pi/180.0)
RL = (Q + (complex(0,1)*U))
LR = (Q - (complex(0,1)*U))
data[1,:,:] = RL
data[2,:,:] = LR
tb.putcol('MODEL_DATA', data)
tb.flush()
tb.close()
##################
# INITPH 1
gaincal(vis=outname_bandpass, caltable=calgcal1, spw="0:25~35", calmode='p', solint="int", refant=ref_ant, parang=True)
figure_name='initph'
for i in range(num_plots+1):
ant_plot=str(i*4)+'~'+str(i*4+3)
plotcal(caltable=calgcal1, xaxis='time', yaxis='phase', subplot=221, antenna=ant_plot, iteration='antenna',
plotrange=[-1,-1,-180,180], figfile=path_plot_spw+figure_name+str(i+1)+'.png')
# BANDPASS 1
bandpass(vis=outname_bandpass, caltable=calbp1, solint="inf", combine="scan,field", refant=ref_ant, gaintable=[calgcal1], parang=True)
figure_name='initbpassA'
for i in range(num_plots+1):
ant_plot=str(i*4)+'~'+str(i*4+3)
plotcal(caltable=calbp1, xaxis='freq', yaxis='amp', subplot=221, antenna=ant_plot, iteration='antenna', \
plotrange=[], figfile=path_plot_spw+figure_name+str(i+1)+'.png')
figure_name='initbpassP'
for i in range(num_plots+1):
ant_plot=str(i*4)+'~'+str(i*4+3)
plotcal(caltable=calbp1, xaxis='freq', yaxis='phase', subplot=221, antenna=ant_plot, iteration='antenna', \
plotrange=[-1,-1,-180,180], figfile=path_plot_spw+figure_name+str(i+1)+'.png')
# apply above solution to the individual sources for flagging purposes (rficonsole)
applycal(vis=outname_bandpass, gaintable=[calgcal1,calbp1], interp=['linear','linear,linear'], calwt=False, flagbackup=False)
applycal(vis=outname_polang, gaintable=[calgcal1,calbp1], interp=['linear','linear,linear'], calwt=False, flagbackup=False)
#################
# INITPH 2
gaincal(vis=outname_bandpass, caltable=calgcal2, spw="0:25~35", calmode='p', solint="int", refant=ref_ant, parang=True)
figure_name='initph2'
for i in range(num_plots+1):
ant_plot=str(i*4)+'~'+str(i*4+3)
plotcal(caltable=calgcal2, xaxis='time', yaxis='phase', subplot=221, antenna=ant_plot, iteration='antenna', \
plotrange=[-1,-1,-180,180], figfile=path_plot_spw+figure_name+str(i+1)+'.png')
# DELAY
gaincal(vis=outname_bandpass, caltable=calk1, spw="0:2~61", selectdata=True, uvrange=uvlimit,\
solint="inf", combine="scan,field", refant=ref_ant, gaintype="K", gaintable=[calgcal2], parang=True)
figure_name='delay'
plotcal(caltable=calk1, xaxis='antenna', yaxis='delay', figfile=path_plot_spw+figure_name+'.png')
# BANDPASS 2
gt = [calgcal2,calk1]
bandpass(vis=outname_bandpass, caltable=calbp2, selectdata=True, uvrange=uvlimit, solint="inf", combine="scan,field", \
refant=ref_ant, gaintable=gt, parang=True)
figure_name='bpassA'
for i in range(num_plots+1):
ant_plot=str(i*4)+'~'+str(i*4+3)
plotcal(caltable=calbp2, xaxis='freq', yaxis='amp', subplot=221, antenna=ant_plot, iteration='antenna',
plotrange=[], figfile=path_plot_spw+figure_name+str(i+1)+'.png')
figure_name='bpassP'
for i in range(num_plots+1):
ant_plot=str(i*4)+'~'+str(i*4+3)
plotcal(caltable=calbp2, xaxis='freq', yaxis='phase', subplot=221, antenna=ant_plot, iteration='antenna',
plotrange=[-1,-1,-180,180], figfile=path_plot_spw+figure_name+str(i+1)+'.png')
# GAIN CAL
gt = [calk1,calbp2]
gaincal(vis=outname_bandpass, caltable=calgcal3, spw="0:2~61", calmode='ap', solint="inf", refant=ref_ant, gaintable=gt, interp=['linear','nearest'], parang=True)
figure_name='finalamp'
plotcal(caltable=calgcal3, xaxis='antenna', yaxis='amp', figfile=path_plot_spw+figure_name+'.png')
figure_name='finalph'
plotcal(caltable=calgcal3, xaxis='antenna', yaxis='phase', plotrange=[-1,-1,-180,180], figfile=path_plot_spw+figure_name+'.png')
##################
# KCROSS: residual differences on the reference antenna
gt = [calgcal3,calbp2,calk1]
gaincal(vis=outname_polang, caltable=calkross1, spw="0:2~61", selectdata=True, uvrange=uvlimitp, \
solint="inf", combine="scan", refant=ref_ant, gaintype="KCROSS",append=False, gaintable=gt, interp=['linear','linear','linear,linear'], parang=True)
figure_name='KCROSS'
plotcal(caltable=calkross1, xaxis='antenna', yaxis='delay',figfile=path_plot_spw+figure_name+'.png')
# Df on unpol cal (if using phasecal solve with Df+QU)
gt = [calgcal3, calbp2, calk1, calkross1]
polcal(vis=outname_bandpass, caltable=caldf1, selectdata=True, uvrange=uvlimit, solint="inf", combine="scan", \
refant=ref_ant, poltype="Df", gaintable=gt, interp=['linear','linear','linear','linear'], spwmap=[])
figure_name='Df_real'
for i in range(num_plots+1):
ant_plot=str(i*4)+'~'+str(i*4+3)
plotcal(caltable=caldf1, xaxis='freq', yaxis='real', subplot=221, \
antenna=ant_plot, iteration='antenna', figfile=path_plot_spw+figure_name+str(i+1)+'.png')
figure_name='Df_imag'
for i in range(num_plots+1):
ant_plot=str(i*4)+'~'+str(i*4+3)
plotcal(caltable=caldf1, xaxis='freq', yaxis='imag', subplot=221, \
antenna=ant_plot, iteration='antenna', figfile=path_plot_spw+figure_name+str(i+1)+'.png')
# Xf
gt = [calgcal3, calbp2, calk1, calkross1, caldf1]
polcal(vis=outname_polang, caltable=calxf1, selectdata=True, uvrange=uvlimit, solint="inf", combine="scan", \
refant=ref_ant, poltype="Xf", gaintable=gt, interp=['linear','linear','linear','linear','nearest'])
figure_name='Xf.png'
plotcal(caltable=calxf1, xaxis='chan', yaxis='phase', plotrange=[-1,-1,-180,180], figfile=path_plot_spw+figure_name)
###################
# Local cal (amp for elevation dependent problems)
gt = [calbp2,calk1,calkross1,caldf1,calxf1]
gaincal(vis=outname_phasecal, caltable=calgcal_loc, spw="0:2~61", \
selectdata=True, uvrange=uvlimit, solint="10min", refant=ref_ant, \
gaintype="G", calmode="ap", gaintable=gt, interp=['linear,linear','nearest','nearest','nearest,linear'], parang=True)
# FLUXSCALE (fitorder not "used" as we have only 1 spw)
fluxscale(vis=outname_phasecal, caltable=calgcal_loc, fluxtable=calgcal_loc, reference=[bandpasscalname], transfer=phasecalname)
plotcal(caltable=calgcal_loc, xaxis='time', yaxis='amp', figfile=path_plot_spw+'loc_amp.png')
plotcal(caltable=calgcal_loc, xaxis='time', yaxis='phase', plotrange=[-1,-1,-180,180], figfile=path_plot_spw+'loc_ph.png')
# # APPLY
# gt = [calgcal_loc,calbp2,calk1,calkross1,caldf1,calxf1]
# applycal(vis=outname_target, gaintable=gt, interp=['linear','nearest','nearest','nearest','nearest','nearest'], parang=True, calwt=False, flagbackup=False)
#
# # TFCROP FLAG
# flagdata(vis=outname_target,mode="tfcrop",autocorr=False,inpfile="",reason="any",spw="",field="",antenna="", \
# uvrange="",timerange="",correlation="",scan="",intent="",array="",observation="",feed="", \
# clipminmax=[],datacolumn="corrected",clipoutside=True,channelavg=False,clipzeros=False,quackinterval=1.0,\
# quackmode="beg",quackincrement=False,tolerance=0.0,addantenna="",lowerlimit=0.0,upperlimit=90.0, \
# ntime="scan",combinescans=False,timecutoff=4.0,freqcutoff=3.0,timefit="line",freqfit="poly", \
# maxnpieces=7,flagdimension="freqtime",usewindowstats="none",halfwin=1,winsize=3,timedev="", \
# freqdev="",timedevscale=5.0,freqdevscale=5.0,spectralmax=1000000.0,spectralmin=0.0,extendpols=True, \
# growtime=50.0,growfreq=50.0,growaround=False,flagneartime=False,flagnearfreq=False,minrel=0.0, \
# maxrel=1.0,minabs=0,maxabs=-1,spwchan=False,spwcorr=False,basecnt=False,action="apply",display="",\
# flagbackup=False,savepars=False,cmdreason="",outfile="")
#
# #RFLAG FLAG
# flagdata(vis=outname_target,mode="rflag",autocorr=False,inpfile="",reason="any",spw="",field="",antenna="", \
# uvrange="",timerange="",correlation="",scan="",intent="",array="",observation="",feed="", \
# clipminmax=[],datacolumn="corrected",clipoutside=True,channelavg=False,clipzeros=False,quackinterval=1.0,\
# quackmode="beg",quackincrement=False,tolerance=0.0,addantenna="",lowerlimit=0.0,upperlimit=90.0, \
# ntime="scan",combinescans=False,timecutoff=4.0,freqcutoff=3.0,timefit="line",freqfit="poly", \
# maxnpieces=7,flagdimension="freqtime",usewindowstats="none",halfwin=1,winsize=3,timedev="", \
# freqdev="",timedevscale=5.0,freqdevscale=5.0,spectralmax=1000000.0,spectralmin=0.0,extendpols=True, \
# growtime=50.0,growfreq=50.0,growaround=False,flagneartime=False,flagnearfreq=False,minrel=0.0, \
# maxrel=1.0,minabs=0,maxabs=-1,spwchan=False,spwcorr=False,basecnt=False,action="apply",display="",\
# flagbackup=False,savepars=False,cmdreason="",outfile="")
# Apply again, but now with the calibration flagging on
gt = [calgcal_loc,calbp2,calk1,calkross1,caldf1,calxf1]
applycal(vis=outname_target, gaintable=gt, interp=['linear','linear,linearflag','nearest','nearest','nearest,linearflag','nearest,linearflag'], parang=True, calwt=False, flagbackup=False)
#put together all the spw in one dataset (that is still divided into 16 spw)
all_spwlist = sorted(glob.glob(basevisnoMS+'_data/spw??/target.MS'))
concat(vis=all_spwlist, concatvis=allspw_dataset)
flag_stat(allspw_dataset)
sys.exit()
# flag bad spw/antennas looking at plots
#badspw='2,3,4,8,9'
#flagdata(vis=allspw_dataset, mode="manual", spw=badspw, flagbackup=False)
#run AOFlagger to better remove the RFI
subprocess.call('aoflagger -strategy ~/scripts/JVLA_Lband-flag.rfis -column CORRECTED_DATA '+allspw_dataset, shell=True)
flag_stat(allspw_dataset)
#split and avareging; we ignore the initial and final channel because they are bad (total of 16 channels)
split(vis=allspw_dataset, outputvis=allspw_target, datacolumn='corrected', field=targetname, width=4, timebin='10s')
# the allspw_target can now be used for the selfcal part