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VLA_reduction_script.py
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VLA_reduction_script.py
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#################################################
#VLA CASA Continuum Reduction Script
#################################################
'''CASA script to be used for the flagging, calibration and imaging of VLA Continuum Data
INPUT: Parameter file detailing all data and imaging parameters (param_dir_file set below)
OUTPUT: (1) Calibrated Split MS for each band (and base-band) -- [target]_[obsDate]_[band]_[baseband].ms
(2) Continuum images in each band (and base-band) -- [target]_[obsDate]_[band]_[baseband]_clean1.image(.tt0).pbcor
(3) (optional) Stokes Cube in each full band -- [target]_[obsDate]_[band]_polcube_IQUV.image(.tt0).pbcor
(4) (optional) Individual Stokes images in each full band -- [target]_[obsDate]_[band]_polcube.[I,Q,U, or V]
(5) (optional) Polarization PA and Fractional Polarization images -- [target]_[obsDate]_[band]_polcube.[PA or FP]
(6) File of flux densities from image(stokes)/UV plane fitting -- imfit_results.txt/uvfit_results.txt
NOTES: - All output images & intermediate data products are put in my_dir directory set below.
- All output images are also converted to fits format (just append .fits to end of images above)
- This script is intended to be used with raw data.
- All input logged in user_input.log.
- If autoflag is used summary presented in autoflag_log.txt
Written by: Alex J. Tetarenko
Last Updated: Aug 2019
Tested in CASA versions up to 5.4
USAGE: Set path to parameter file (line 49) and output directory (line 60), then,
run execfile('VLA_reduction_script.py') within CASA'''
print '##################################################'
print 'Welcome to Alexs VLA Continuum Reduction Script'
print '##################################################\n'
#packages you may need
from astropy.io import fits
import numpy as np
import re
import sys
import imp
import os
import linecache
#import find
import warnings
import webbrowser
import datetime
warnings.filterwarnings('ignore')
from utils_CASA import imfit_point, phselfcal, writeDict,source_dict_create,setjy_parse,last_field_parse
from ekoch_casa_tools import set_imagermode,has_field,set_cellsize,set_imagesize,find_expected_beams,getBaselinePercentile,get_mosaic_info
import uvmultifit as uvm
from astropy.io import ascii
import analysisUtils as au
#define output directory
my_dir='/export/data2/atetarenko/Cygx3/VLA/results/ep1/subC_K/'
if not os.path.isdir(my_dir):
os.system('mkdir '+my_dir)
os.system('chown ubuntu '+my_dir)
os.system('chmod -R u+r '+my_dir)
os.system('chmod -R u+w '+my_dir)
os.system('chmod -R u+x '+my_dir)
print 'You have set your output directory to ', my_dir,'\n'
print 'All output images & intermediate data products are put in this directory.\n'
#param file location
param_dir_file='/export/data2/atetarenko/Cygx3/VLA/params_vla_subA_K.txt'
print 'You have set your param file to ', param_dir_file,'\n'
print 'Please make sure all parameters are correct, they will change for each data set!\n'
#make dictionary to write all user input variables to for log
dict_log=[]
#################################################
#Defining Parameters Section
#################################################
print 'Reading in parameters...\n'
#read in param file
f=open(param_dir_file)
data_params=imp.load_source('data_params','',f)
f.close()
#data set params
ms_name=data_params.ms_name
ms_name_prefix=ms_name.strip('.ms')
obsDate=data_params.obsDate
target=data_params.target
bands=data_params.bands
spw_bands=data_params.spw_bands
scans=data_params.scans
bitdata=data_params.bitdata
remakems=data_params.remakems
doImage=data_params.doImage
bandsIM=data_params.bandsIM
pol_calib=data_params.pol_calib
#general image params
use_auto=data_params.use_auto
mythreshold=data_params.mythreshold
myimsize=data_params.myimsize
mycell=data_params.mycell
myniter=data_params.myniter
decon=data_params.decon
mynterms=data_params.mynterms
mystokes=data_params.mystokes
multiscale=data_params.multiscale
robust=data_params.robust
weighting=data_params.weighting
outlierfile=data_params.outlierfile
#mask options
mymask=data_params.mymask
#uv fitting
uv_fit=data_params.uv_fit
uv_initp=data_params.uv_initp
#write all variables to log dictionary
dict_log.extend([('ms_name_input',ms_name),('ms_name_prefix_input',ms_name_prefix),('obsDate', obsDate),('target',target),\
('bands_input',bands),('spw_bands_input',spw_bands),('scans_input',scans),('bitdata',bitdata),('remakeMS',remakems),\
('mythreshold',mythreshold),('myimsize',myimsize),('mycell',mycell),('myniter',myniter),('mynterms',mynterms),('pol_calib',pol_calib),\
('mystokes',mystokes),('mymask',mymask),('uv_fit',uv_fit),('doImage',doImage),('bandsIM',bandsIM),('use_auto',use_auto),('uv init param file',uv_initp)])
#################################################
#################################################
#Examining and Splitting Data Section
#################################################
#listobs first
if not os.path.isfile(my_dir+obsDate+'_listfile.txt'):
print 'Making listobs file...'
listobs(ms_name,listfile=my_dir+obsDate+'_listfile.txt')
else:
print 'Listobs file already exists'
seelo=raw_input('Do you want to see the listobs? y or n-->')
if seelo=='y':
os.system('gedit '+my_dir+obsDate+'_listfile.txt &')
else:
print 'Okay. Moving on.'
seeurl=raw_input('Do you want to open the log file in your web browser?y or n-->')
if seeurl =='y':
webbrowser.open('http://www.vla.nrao.edu/cgi-bin/oplogs.cgi', new=0, autoraise=True)
print 'Moving on to making split data sets.\n'
else:
print 'Okay. Moving on to making split data sets.\n'
print '****************************************************************'
print 'You have selected the ',bands,' bands to reduce.'
print '****************************************************************\n'
print 'We need to split the data into these individual bands to reduce seperately.\n'
ms_name_list=[]
for i in range(0,len(bands)):
#make split data sets of different bands if they dont exist
if not os.path.isdir(my_dir+'data_'+obsDate+'_'+bands[i]+'.ms'):
print 'Making split MS for ', bands[i],' band...'
split(vis=ms_name,outputvis=my_dir+'data_'+obsDate+'_'+bands[i]+'.ms',\
spw=spw_bands[i],datacolumn='data',scan=scans[i])
flagmanager(vis=my_dir+'data_'+obsDate+'_'+bands[i]+'.ms',mode='save',\
versionname=target+'_'+obsDate+'_'+bands[i]+'_initial',\
comment='after initial split')
ms_name_list.append(my_dir+'data_'+obsDate+'_'+bands[i]+'.ms')
elif remakems=='T':
print 'Remaking MS for ',bands[i],' band...'
os.system('rm -rf '+my_dir+'data_'+obsDate+'_'+bands[i]+'.ms')
os.system('mv '+my_dir+'data_'+obsDate+'_'+bands[i]+'.ms.flagversions '+my_dir+'data_'+obsDate+'_'+bands[i]+'.ms.flagversions_old')
split(vis=ms_name,outputvis=my_dir+'data_'+obsDate+'_'+bands[i]+'.ms',\
spw=spw_bands[i],datacolumn='data',scan=scans[i])
os.system('mv '+my_dir+'data_'+obsDate+'_'+bands[i]+'.ms.flagversions_old '+my_dir+'data_'+obsDate+'_'+bands[i]+'.ms.flagversions')
ms_name_list.append(my_dir+'data_'+obsDate+'_'+bands[i]+'.ms')
app_f=raw_input('Do you want to apply a previous flag version? y or n--> ')
if app_f=='y':
print 'Listing versions in flag manager...'
flagmanager(vis=my_dir+'data_'+obsDate+'_'+bands[i]+'.ms',mode='list')
version_fm=raw_input('Please enter version name to restore--> ')
flagmanager(vis=my_dir+'data_'+obsDate+'_'+bands[i]+'.ms',mode='restore',\
versionname=version_fm,merge='replace')
os.system('rm -rf '+my_dir+'data_'+obsDate+'_'+bands[i]+'.ms.flagversions')
flagmanager(vis=my_dir+'data_'+obsDate+'_'+bands[i]+'.ms',mode='save',\
versionname=target+'_'+obsDate+'_'+bands[i]+'_reapply',\
comment='after reapply previous flags')
else:
os.system('rm -rf '+my_dir+'data_'+obsDate+'_'+bands[i]+'.ms.flagversions')
flagmanager(vis=my_dir+'data_'+obsDate+'_'+bands[i]+'.ms',mode='save',\
versionname=target+'_'+obsDate+'_'+bands[i]+'_initial',\
comment='after initial split')
else:
print 'Split MS for ',bands[i],' already exists.'
ms_name_list.append(my_dir+'data_'+obsDate+'_'+bands[i]+'.ms')
dict_log.append(('ms_name_list',ms_name_list))
#################################################
print 'Beginning reduction process...'
#will loop through reduction procedure for all split data sets
#first define sub-bands
bandL_dict=dict([("L", 'l1'),("S", 's2'),("C", 'c5'),("X", 'x9'),("Ku", 'ku14'),\
("K", 'k21'),("Ka", 'ka31'),("Q", 'q40')])
bandU_dict=dict([("L", 'l2'),("S", 's3'),("C", 'c7'),("X", 'x11'),("Ku", 'ku17'),\
("K", 'k26'),("Ka", 'ka36'),("Q", 'q45')])
#will loop through all split data sets now
for kk in range(0,len(ms_name_list)):
if kk==0:
firstf='y'
else:
firstf='n'
print 'Starting with ',ms_name_list[kk],' data set.'
print 'Running listobs. Please examine file for fields ids & spw ranges.'
os.system('rm -rf '+my_dir+obsDate+'_'+bands[kk]+'_listfile.txt')
listobs(ms_name_list[kk],listfile=my_dir+obsDate+'_'+bands[kk]+'_listfile.txt')
os.system('gedit '+my_dir+obsDate+'_'+bands[kk]+'_listfile.txt &')
raw_input('Please press enter when ready to continue.')
#define variables specific to each band
src_dict,quakint=source_dict_create(my_dir+obsDate+'_'+bands[kk]+'_listfile.txt')
intentbp='CALIBRATE_BANDPASS#UNSPECIFIED'
intentsec='CALIBRATE_PHASE#UNSPECIFIED'
intenttar='OBSERVE_TARGET#UNSPECIFIED'
intentpolang='CALIBRATE_POL_ANGLE#UNSPECIFIED'
intentpoleak='CALIBRATE_POL_LEAKAGE#UNSPECIFIED'
bpf_lst=[]
second_lst=[]
target_lst=[]
polleak_lst=[]
spw_low=raw_input('Please enter spw range for lowest freq. base-band, e.g., 0~7-->')
spw_high=raw_input('Please enter spw range for highest freq. base-band, e.g., 8~15-->')
for ik in range(0,len(src_dict['Fields'])):
if intentbp in src_dict['Fields'][str(ik)]['Intent'] and intentpoleak not in src_dict['Fields'][str(ik)]['Intent']:
bpf_lst.append(str(ik))
timerbp_lst=src_dict['Fields'][str(ik)]['scantimes'].split(',')
timerbp=timerbp_lst[0].split('~')[0]+'~'+timerbp_lst[-1].split('~')[1]
elif intentsec in src_dict['Fields'][str(ik)]['Intent']:
second_lst.append(str(ik))
elif intenttar in src_dict['Fields'][str(ik)]['Intent']:
target_lst.append(str(ik))
elif intentpoleak in src_dict['Fields'][str(ik)]['Intent']:
polleak_lst.append(str(ik))
else:
raise ValueError ('Unknown source intent parameter, please check listobs')
if pol_calib=='y':
pol_values=ascii.read("pol_vla_prop.txt",names=['B','Freq','3C48Pol','3C48Ang','3C138Pol','3C138Ang','3C147Pol','3C147Ang','3C286Pol','3C286Ang'])
bands_dict={}
bands_dict['Band']={}
bands_dict['Band']['C']=['C5','C7']
bands_dict['Band']['L']=['L1','L2']
bands_dict['Band']['S']=['S2','S3']
bands_dict['Band']['X']=['X9','X11']
bands_dict['Band']['K']=['K21','K25']
bands_dict['Band']['Ku']=['Ku13','Ku17']
bands_dict['Band']['Ka']=['Ka36','Ka43']
if intentpolang in src_dict['Fields'][str(ik)]['Intent']:
id_polPA=str(ik)
str_nme=src_dict['Fields'][str(ik)]['Name'].split('=')[1]
indL=np.where(pol_values['B']==bands_dict['Band'][bands[kk]][0])[0][0]
indU=np.where(pol_values['B']==bands_dict['Band'][bands[kk]][1])[0][0]
pol_angL=pol_values[str_nme+'Ang'][indL]
frac_polL=float(pol_values[str_nme+'Pol'][indL])/100.
pol_angU=pol_values[str_nme+'Ang'][indU]
frac_polU=float(pol_values[str_nme+'Pol'][indU])/100.
testarr=np.array([pol_angL.find('LL'),pol_angU.find('LL'),pol_values[str_nme+'Pol'][indL].find('LL'),pol_values[str_nme+'Pol'][indU].find('LL')])
testarr2=np.array([pol_angL.find('NA'),pol_angU.find('NA'),pol_values[str_nme+'Pol'][indL].find('NA'),pol_values[str_nme+'Pol'][indU].find('NA')])
if np.count_nonzero(testarr)<4 or np.count_nonzero(testarr2)<4:
raise ValueError('Unable to find polarization properties of polang cal')
elif intentpoleak in src_dict['Fields'][str(ik)]['Intent']:
id_leak=str(ik)
#print 'Please enter the following data set specifics:'
bpf_cal=",".join(map(str, bpf_lst))#raw_input('Please enter field id for bandpass cal (if >1 seperate by comma)-->')
#bpf_lst=bpf_cal.split(',')
second_cal=",".join(map(str, second_lst))#raw_input('Please enter field id for secondary cal (if >1 seperate by comma)-->')
#second_lst=second_cal.split(',')
polleak_cal=",".join(map(str, polleak_lst))#raw_input('Please enter field id for pol cal (if >1 seperate by comma, if none press enter)-->')
#if polleak_cal=='':
#polleak_lst=[]
#else:
#polleak_lst=polleak_cal.split(',')
target_id=",".join(map(str, target_lst))#raw_input('Please enter field id for target (if >1 seperate by comma)-->')
#target_lst=target_id.split(',')
#timerbp=raw_input('Please enter the time range of the bandpass cal scan(s). e.g., 11:43:30.0~11:47:27.0-->')
if pol_calib=='y':
#id_polPA,id_leak=raw_input('Please enter field ids for pol PA cal, and leakage cal (e.g., polPA,leak)-->').split(',')
#pol_angL,frac_polL=raw_input('For lower baseband, please enter known pol angle in degrees and frac. polarization in decimal form (e.g., ang,frac)-->').split(',')
#pol_angU,frac_polU=raw_input('For upper baseband, please enter known pol angle in degrees and frac. polarization in decimal form (e.g., ang,frac)-->').split(',')
dict_log.append(('id_polPA',id_polPA))
dict_log.append(('id_polleak',id_leak))
dict_log.append(('pola_angL',pol_angL))
dict_log.append(('frac_pol_decimalL',frac_polL))
dict_log.append(('pola_angU',pol_angU))
dict_log.append(('frac_pol_decimalU',frac_polU))
field_lst=[]
[field_lst.append(i) for i in bpf_lst]
[field_lst.append(i) for i in second_lst]
[field_lst.append(i) for i in polleak_lst]
#spw_low=raw_input('Please enter lower base-band spw range. e.g., 0~15-->')
#spw_high=raw_input('Please enter upper base-band spw range. e.g., 0~15-->')
if int(spw_low.split('~')[0]) < int(spw_high.split('~')[0]):
spw_full=spw_low.split('~')[0]+'~'+spw_high.split('~')[1]
else:
spw_full=spw_high.split('~')[0]+'~'+spw_low.split('~')[1]
band=bands[kk]
ms_name=ms_name_list[kk]
ms_name_prefix=ms_name.strip('.ms')
band_low=bandL_dict[band]
band_high=bandU_dict[band]
date=obsDate+'_'+band
ant_plot=my_dir+'antennas_'+date+'.png'
ant_cal=my_dir+date+'.antpos'
opac_cal=my_dir+date+'.opac'
gc_cal=my_dir+date+'.gaincurve'
req_cal=my_dir+date+'.req'
cal_table_prefix=my_dir+target+'_'+date
split_low=cal_table_prefix+'_'+band_low+'.ms'
split_high=cal_table_prefix+'_'+band_high+'.ms'
split_full=cal_table_prefix+'_comb.ms'
#add to log dictionary
dict_log.append((ms_name_prefix+'_bpf_cal',bpf_lst))
dict_log.append((ms_name_prefix+'_second_cal',second_lst))
dict_log.append((ms_name_prefix+'_polleak_cal',polleak_lst))
dict_log.append((ms_name_prefix+'_target_id',target_lst))
dict_log.append((ms_name_prefix+'_time_range_bp',timerbp))
dict_log.append((ms_name_prefix+'_spw_low',spw_low))
dict_log.append((ms_name_prefix+'_spw_high',spw_high))
dict_log.append((ms_name_prefix+'_spw_full',spw_full))
dict_log.append((ms_name_prefix+'_band',band))
dict_log.append((ms_name_prefix+'_band_low',band_low))
dict_log.append((ms_name_prefix+'_band_high',band_high))
#########################################
#Reference antenna and initial flagging
#########################################
#plot antenna positions to determne reference antenna near centre of array that
#is present throughout whole observation and has no problems
print 'Plotting antenna positions. Please choose a reference antenna near centre of array.'
os.system('rm -rf '+ant_plot)
plotants(vis=ms_name,figfile=ant_plot)
ref_ant=raw_input('Please enter reference antenna. e.g., ea02-->')
check_inref=re.compile('ea\d{2}')
while not check_inref.match(ref_ant):
print 'Invalid antenna expression.'
ref_ant=raw_input('Please enter reference antenna. e.g., ea02-->')
dict_log.append((ms_name_prefix+'_ref_ant',ref_ant))
flag_done=raw_input('Is the data set already flagged?y or n-->')
dict_log.append((ms_name_prefix+'_flag_done',flag_done))
if flag_done=='n':
#initial flagging
print 'Starting Initial Flagging...'
flag_dummy=raw_input('Do you want to flag the dummy scans?y or n-->')
dict_log.append((ms_name_prefix+'_flag_dummy',flag_dummy))
if flag_dummy=='y':
dum_scan=raw_input('Please enter dummy scan ids. e.g., 1,2-->')
print 'Flagging Dummy scan(s) ', dum_scan,' ...'
dict_log.append((ms_name_prefix+'_dum_scan',dum_scan))
flagdata(vis=ms_name, flagbackup=True, mode='manual', scan=dum_scan)
else:
print 'Dummy scans not flagged.'
flag_shad=raw_input('Do you want to flag the shadow data?y or n-->')
dict_log.append((ms_name_prefix+'_flag_shad',flag_shad))
if flag_shad=='y':
print 'Flagging Shadow data...'
flagdata(vis=ms_name, mode='shadow')
else:
print 'Shadow data not flagged.'
flag_zero=raw_input('Do you want to flag the zero amp data?y or n-->')
dict_log.append((ms_name_prefix+'_flag_zero',flag_zero))
if flag_zero=='y':
print 'Flagging zero amp data...'
flagdata(vis=ms_name, autocorr=True)
flagdata(vis=ms_name,mode='clip',clipzeros=True)
else:
print 'Zero amp data not flagged.'
flag_end=raw_input('Do you want to flag the end channels?y or n-->')
dict_log.append((ms_name_prefix+'_flag_end_chan',flag_end))
if flag_end=='y':
beg=raw_input('Please enter beginning channels to flag. e.g., 0~3-->')
endd=raw_input('Please enter end channels to flag. e.g., 60~63-->')
print 'Flagging beginning channels ',beg,' and end channels ',endd,' ...'
dict_log.append((ms_name_prefix+'_flag_beg_chan',beg))
dict_log.append((ms_name_prefix+'_flag_end_chan',endd))
flagdata(vis=ms_name,spw=spw_full+':'+beg,field='',antenna='')
flagdata(vis=ms_name,spw=spw_full+':'+endd,field='',antenna='')
else:
print 'End channels not flagged.'
flag_badant=raw_input('Do you want to flag the bad antennas from log file?y or n-->')
dict_log.append((ms_name_prefix+'_flag_bad_ant',flag_badant))
if flag_badant=='y':
bada=raw_input('Please enter bad ants to flag. e.g. ea01,ea02-->')
print 'Flagging bad ants ', bada,' ...'
dict_log.append((ms_name_prefix+'_badant',bada))
flagdata(vis=ms_name, flagbackup=True, mode='manual', antenna=bada)
else:
print 'No bad ants flagged.'
print 'Flagging samples at start of each scan...'
#quakint=raw_input('Please enter integration time in seconds. e.g., 3-->')
dict_log.append((ms_name_prefix+'_flag_quack_int_time',quakint))
flagdata(vis=ms_name, mode='quack', quackinterval=float(quakint), quackmode='beg',quackincrement=True)
########################################
########################################
#detailed flagging
########################################
print 'Examining Data for detailed flagging...'
print 'Look for obvious bad data.'
print 'Keep track of ants/spws/channels to flag. You will be prompted for their values after plotting.'
print '(1) Amp vs time...'
avgtime_plotms=raw_input('Please enter avg time interval in seconds, e.g., 60-->')
plotms(vis=ms_name,xaxis="time",yaxis="amp",coloraxis="field",iteraxis="antenna",\
avgtime=avgtime_plotms)
raw_input('Please press enter when ready to continue.')
autoflag=raw_input('Is the RFI bad enough that you need to do autoflag?y or n-->')
dict_log.append((ms_name_prefix+'_flag_autoflag',autoflag))
########################################
#Auto-flagging (if needed)
#########################################
if autoflag=='y':
print 'Preparing data for autoflag procedure...'
print 'Solving for baseline solutions...'
#baseline solutions
os.system('rm -rf '+ ant_cal)
os.system('rm -rf '+ gc_cal)
os.system('rm -rf '+ opac_cal)
os.system('rm -rf '+ req_cal)
gencal(vis=ms_name, caltable=ant_cal,caltype='antpos')
if band in ['Ku','K','Ka','Q']:
print 'Solving for gain-elevation curves...'
#gain-elev curves
gencal(ms_name,caltable=gc_cal,caltype='gc')
print 'Solving for opacity corrections...'
#opacity corrections
clearstat()
myTau = plotweather(vis=ms_name, doPlot=True)
gencal(vis=ms_name,caltable=opac_cal, caltype='opac',spw=spw_full,parameter=myTau)
if bitdata==3:
print 'Solving for requantizer gains...'
#requantizer gains
gencal(ms_name,caltable=req_cal,caltype='rq')
print 'Hanning smooth of data...'
#hanning smooth data
os.system('rm -rf '+ ms_name_prefix+'_hs.ms')
hanningsmooth(vis=ms_name,datacolumn='all', outputvis=ms_name_prefix+'_hs.ms')
ms_name=ms_name_prefix+'_hs.ms'
ms_name_prefix=ms_name.strip('.ms')
#plot hanning smoothed data
print 'Plotting Hanning smoothed data of target...'
plotms(vis=ms_name, field=target_id, antenna=ref_ant, spw=spw_full,\
xaxis='freq', yaxis='amp', coloraxis='spw', symbolshape = 'circle',\
correlation='RR,LL')
raw_input('Please press enter when ready to continue.')
print 'Using secondary cal to do preliminary bandpass...'
print 'Plotting Amp vs channel...'
print 'Choose 3 channel range for each spw free of RFI.'
plotms(vis=ms_name, field=second_cal,antenna=ref_ant, \
xaxis='channel', yaxis='amp', iteraxis='spw',yselfscale=True, \
correlation='RR,LL', symbolshape='circle')
raw_input('Please press enter when ready to continue.')
spw_string_rfifree=raw_input('Enter spw string for RFI free channels. e.g., 0:30~33,1:30~33-->')
dict_log.append((ms_name_prefix+'_autoflag_rfi_free_chan',spw_string_rfifree))
print 'Performing gaincal for initial phase solutions...'
os.system('rm -rf '+cal_table_prefix+'.initPhautoF')
gaincal(vis=ms_name, caltable=cal_table_prefix+'.initPhautoF',\
field=second_cal, solint='int', spw=spw_string_rfifree, refant=ref_ant, \
minblperant=3, minsnr=3.0, calmode='p')
print 'Doing bandpass...'
os.system('rm -rf '+cal_table_prefix+'.initBPautoF')
bandpass(vis=ms_name, caltable=cal_table_prefix+'.initBPautoF', \
field=second_cal, solint='inf', combine='scan', refant=ref_ant,\
minblperant=3, minsnr=10.0, gaintable=[cal_table_prefix+'.initPhautoF'],\
interp=['', 'nearest'], solnorm=False)
print 'Inspecting solutions...'
print 'Look for spws which have so much RFI they are a lost cause.'
print 'Amp vs freq...'
plotcal(caltable=cal_table_prefix+'.initBPautoF', xaxis='freq', yaxis='amp',\
iteration='antenna', subplot=331)
raw_input('Please press enter when ready to continue.')
print 'Phase vs frequency...'
plotcal(caltable=cal_table_prefix+'.initBPautoF', xaxis='freq', yaxis='phase',\
iteration='antenna', subplot=331)
raw_input('Please press enter when ready to continue.')
spw_string_rfiflag=raw_input('Enter spw/channels string to flag (enter if none). e.g., 8,9:20~23,10:32-->')
dict_log.append((ms_name_prefix+'_autoflag_rfi_flag',spw_string_rfiflag))
if spw_string_rfiflag=='':
print 'No flagging done.'
else:
flagdata(vis=ms_name, spw=spw_string_rfiflag)
print 'Applying calibration...'
applycal(vis=ms_name, gaintable=[cal_table_prefix+'.initBPautoF'], calwt=False)
print 'Beginning autoflag...'
print 'Will test first then apply after.'
cont_af='y'
while cont_af=='y':
fdev,tdev=raw_input('Please enter deviations of amp (sigma) in freq and time to flag. e.g., 4 4-->').split(' ')
flagdata(vis=ms_name, mode='rflag', field=second_cal,spw='', \
datacolumn='corrected', freqdevscale=int(fdev), timedevscale=int(tdev), \
action='calculate', display='both', flagbackup=False)
raw_input('Please press enter when ready to continue.')
print 'Extending flags in freq and time...'
print 'Growtime means a channel is flagged if > X% of times already flagged.'
print 'Growfreq means entire spectrum for an integration is flagged if >Y% of channels already flagged'
growf,growt=raw_input('Please enter growfreq and growtime params. e.g., 90.0 50.0-->').split(' ')
flagdata(vis=ms_name, mode='extend', spw='', growtime=float(growt), \
growfreq=float(growf), action='calculate', display='data', flagbackup=False)
raw_input('Please press enter when ready to continue.')
cont_af=raw_input('Do you want to try different autoflag param values?y or n-->')
print 'Now applying autoflag selections...'
fdev,tdev,growf,growt=raw_input('Please enter final fdev,tdev,growf,growt. e.g., 4 4 90.0 50.0-->').split(' ')
dict_log.append((ms_name_prefix+'_autoflag_fdev',fdev))
dict_log.append((ms_name_prefix+'_autoflag_tdev',tdev))
dict_log.append((ms_name_prefix+'_autoflag_growf',growf))
dict_log.append((ms_name_prefix+'_autoflag_growt',growt))
flagdata(vis=ms_name, mode='rflag', field='',spw='', datacolumn='corrected',\
freqdevscale=int(fdev), timedevscale=int(tdev), action='apply')
flagdata(vis=ms_name, mode='extend', spw='', growtime=float(growt), growfreq=float(growf), action='apply')
print 'Writing autoflag log...'
flagInfo = flagdata(vis=ms_name, mode='summary')
openf=open(my_dir+'autoflag_log.txt','w')
openf.write('Autoflag stats for '+str(band)+' band:')
for i in flagInfo['field'].keys():
print("\n %2.1f%% of %s are flagged.\n" % (100.0*flagInfo['field'][i]['flagged']/flagInfo['field'][i]['total'],i))
openf.write(("\n %2.1f%% of %s are flagged.\n" % (100.0*flagInfo['field'][i]['flagged']/flagInfo['field'][i]['total'],i)))
print("Spectral windows are flagged as follows:")
for spw in range(0,int(spw_full.split('~')[1])+1):
print("SPW %s: %2.1f%%" % (spw, 100.0 * flagInfo['spw'][str(spw)]['flagged'] / flagInfo['spw']\
[str(spw)]['total']))
openf.write(("\nSPW %s: %2.1f%%" % (spw, 100.0 * flagInfo['spw'][str(spw)]['flagged'] / flagInfo['spw']\
[str(spw)]['total'])))
openf.close()
print 'Autoflag finished. Back to normal flagging procedure...'
#########################################
else:
print 'Autoflag not selected.'
print '(2) Baselines versus antenna to look for bad antennas,bad channels/spws...'
#lastf,fant=raw_input('Please enter last field id and first antenna. e.g., 2 ea01-->').split(' ')
lastf,fant=last_field_parse(my_dir+obsDate+'_'+bands[kk]+'_listfile.txt')
dict_log.append((ms_name_prefix+'_flag_lastfield',lastf))
dict_log.append((ms_name_prefix+'_flag_firstant',fant))
plotms(vis=ms_name,field=lastf,spw='', antenna=fant,correlation='RR,LL',xaxis='antenna2',yaxis='amp')
raw_input('Please press enter when ready to continue.')
print '(3) Bandpass for reference antenna (second_cal)...'
print 'Look for bad spws and RFI spikes'
print 'Toggle through baselines!!'
print 'Amp first...'
plotms(vis=ms_name,field=second_cal, spw='',antenna=ref_ant+'&*',correlation='RR,LL',\
xaxis='frequency',yaxis='amp',iteraxis='baseline')
raw_input('Please press enter when ready to continue.')
print 'Phase next...'
print 'RR correlation...'
plotms(vis=ms_name,field=second_cal, spw='',antenna=ref_ant+'&*',correlation='RR',\
xaxis='frequency',yaxis='phase',iteraxis='baseline')
raw_input('Please press enter when ready to continue.')
print 'LL correlation...'
plotms(vis=ms_name,field=second_cal, spw='',antenna=ref_ant+'&*',correlation='LL',\
xaxis='frequency',yaxis='phase',iteraxis='baseline')
raw_input('Please press enter when ready to continue.')
print '(4A) Baselines (all not just to ref antenna) vs amp for target...'
plotms(vis=ms_name,field=target_id, xaxis='baseline', yaxis='amp', spw='', iteraxis='spw',\
correlation='RR,LL', coloraxis='antenna1', symbolshape = 'circle')
raw_input('Please press enter when ready to continue.')
print '(4B) Amp vs uvdist for target...'
plotms(vis=ms_name, field=target_id, xaxis='uvdist', yaxis='amp', spw='', iteraxis='spw',\
correlation='RR,LL', coloraxis='antenna1', symbolshape = 'circle')
raw_input('Please press enter when ready to continue.')
print '(5) Data stream plot...'
plotms(vis=ms_name,field='',correlation='RR,LL',timerange='',\
antenna=fant,spw='',xaxis='time',yaxis='antenna2',\
plotrange=[-1,-1,0,28],coloraxis='field')
raw_input('Please press enter when ready to continue.')
print 'Flagging...'
badasf=raw_input('Please enter bad ant,spw, field, and scan/timerange to flag (enter if none). e.g., ea10,ea12;5:4~9;3;9:52:10.0~9:53:10.0 ;5;3;4,5-->').split(' ')
dict_log.append((ms_name_prefix+'_flag_antspwfield',badasf))
if '' in badasf:
print 'Nothing to flag.'
else:
print 'Flagging selected data.'
for i in range(0,len(badasf)):
strg=badasf[i].split(';')
while len(strg)!=4:
print 'Flagging parameters incorrect for',i+1,' entry'
strg=raw_input('Please enter flaggin parameters again, e.g., ;4:50;1;--<').split(';')
if ':' in strg[3]:
flagdata(vis=ms_name,flagbackup=True, mode='manual', antenna=strg[0],spw=strg[1],field=strg[2],timerange=strg[3])
else:
flagdata(vis=ms_name,flagbackup=True, mode='manual', antenna=strg[0],spw=strg[1],field=strg[2],scan=strg[3])
print 'Final check of flagged data...'
plotms(vis=ms_name,field=second_cal,spw='', antenna=ref_ant,correlation='RR,LL',xaxis='frequency',yaxis='amp')
raw_input('Please press enter when ready to continue.')
flag_again=raw_input('Do you need to do more flagging? y or n-->')
count_f=1
while flag_again=='y':
badasf2=raw_input('Please enter bad ant,spw,field,scan/timerange to flag (enter if none). e.g., ea10,ea12;5:4~9;3;9:52:10.0~9:53:10.0 ;5;3;4,5-->').split(' ')
dict_log.append((ms_name_prefix+'_flag_antspwfield_'+str(count_f),badasf2))
if '' in badasf2:
print 'Nothing to flag.'
else:
print 'Flagging selected data.'
for i in range(0,len(badasf2)):
strg2=badasf2[i].split(';')
while len(strg2)!=4:
print 'Flagging parameters incorrect for',i+1,' entry'
strg2=raw_input('Please enter flaggin parameters again, e.g., ;4:50;1;--<').split(';')
if ':' in strg2[3]:
flagdata(vis=ms_name,flagbackup=True, mode='manual', antenna=strg2[0],spw=strg2[1],field=strg2[2],timerange=strg2[3])
else:
flagdata(vis=ms_name,flagbackup=True, mode='manual', antenna=strg2[0],spw=strg2[1],field=strg2[2],scan=strg2[3])
print 'Plotting...'
plotms(vis=ms_name,field=second_cal,spw='', antenna=ref_ant,correlation='RR,LL',xaxis='frequency',yaxis='amp')
raw_input('Please press enter when ready to continue.')
count_f=count_f+1
flag_again=raw_input('Do you need to do more flagging? y or n-->')
else:
autoflag=raw_input('Did you autoflag?y or n-->')
dict_log.append((ms_name_prefix+'_flag_autoflag',autoflag))
lastf,fant=last_field_parse(my_dir+obsDate+'_'+bands[kk]+'_listfile.txt')
dict_log.append((ms_name_prefix+'_flag_lastfield',lastf))
dict_log.append((ms_name_prefix+'_flag_firstant',fant))
if autoflag=='y':
ms_name=ms_name_prefix+'_hs.ms'
ms_name_prefix=ms_name.strip('.ms')
listobs(ms_name,listfile=my_dir+obsDate+'_'+bands[kk]+'_listfile_hs.txt')
os.system('gedit '+my_dir+obsDate+'_'+bands[kk]+'_listfile_hs.txt &')
newref=raw_input('Do you need to change ref_ant?y or n-->')
if newref=='y':
plotants(vis=ms_name,figfile=ant_plot)
ref_ant=raw_input('Please enter new reference antenna. e.g., ea02-->')
dict_log.append((ms_name_prefix+'_ref_ant2',ref_ant))
intera=raw_input('Flagging is finished. Do you want to do interactive calibration?y or n-->')
dict_log.append((ms_name_prefix+'_interactive',intera))
writeDict(dict_log, my_dir+'user_input_'+date+'flag.logg',str(datetime.datetime.now()))
flagmanager(vis=ms_name,mode='save',\
versionname=target+'_'+obsDate+'_flagging',\
comment='after flagging')
if intera=='n':
print 'You have chosen to not do interactive calibration.'
print 'No plots will be made and no additional flagging is required.'
print 'Please go do something else for a while.'
print 'You will not be prompted until imaging.'
print '*********************************************************************'
else:
print 'The rest of the script is interactive. Please stay by the computer.'
print '*********************************************************************'
########################################
########################################
##baseline,gain curve, opacity solutions
#(if no autoflag)
########################################
if autoflag=='n':
print 'Solving for baseline solutions...'
#baseline solutions
os.system('rm -rf '+ant_cal)
os.system('rm -rf '+gc_cal)
os.system('rm -rf '+opac_cal)
os.system('rm -rf '+req_cal)
gencal(vis=ms_name, caltable=ant_cal,caltype='antpos')
if band in ['Ku','K','Ka','Q']:
print 'Solving for gain-elevation curves...'
#gain-elev curves
gencal(ms_name,caltable=gc_cal,caltype='gc')
print 'Solving for opacity corrections...'
#opacity corrections
clearstat()
myTau = plotweather(vis=ms_name, doPlot=True)
gencal(vis=ms_name,caltable=opac_cal, caltype='opac',spw=spw_full,parameter=myTau)
if bitdata==3:
print 'Solving for requantizer gains...'
#requantizer gains
gencal(ms_name,caltable=req_cal,caltype='rq')
#####################################
#make list of pre gain tables to be applied in tandem below
gt_lst_low=[]
gf_lst_low=[]
gi_lst_low=[]
gt_lst_high=[]
gf_lst_high=[]
gi_lst_high=[]
if os.path.isdir(ant_cal):
gt_lst_low.append(ant_cal)
gf_lst_low.append('')
gi_lst_low.append('')
gt_lst_high.append(ant_cal)
gf_lst_high.append('')
gi_lst_high.append('')
if os.path.isdir(gc_cal):
gt_lst_low.append(gc_cal)
gf_lst_low.append('')
gi_lst_low.append('')
gt_lst_high.append(gc_cal)
gf_lst_high.append('')
gi_lst_high.append('')
if os.path.isdir(opac_cal):
gt_lst_low.append(opac_cal)
gf_lst_low.append('')
gi_lst_low.append('')
gt_lst_high.append(opac_cal)
gf_lst_high.append('')
gi_lst_high.append('')
if os.path.isdir(req_cal):
gt_lst_low.append(req_cal)
gf_lst_low.append('')
gi_lst_low.append('')
gt_lst_high.append(req_cal)
gf_lst_high.append('')
gi_lst_high.append('')
#####################################
#fluxscale
#####################################
#list models available
print 'Setting flux scale...'
print 'Listing flux models available.'
setjy(vis=ms_name, listmodels=True)
print 'Set fluxscale for lower base-band...'
#flux_mod_low=raw_input('Please enter flux model for lower base-band. e.g., 3C48_C.im-->')
flux_mod_low=src_dict['Fields'][bpf_cal]['Name'].split('=')[1]+'_'+bands[kk]+'.im'
print 'Using '+flux_mod_low+' for flux model in lower baseband'
dict_log.append((ms_name_prefix+'_fluxmodlsb',flux_mod_low))
setjy(vis=ms_name,field=bpf_cal,standard='Perley-Butler 2013',
model=flux_mod_low,usescratch=False,scalebychan=True,spw=spw_low)
if pol_calib=='y':
flux_low_polL,flux_up_polL,nu_low_polL,nu_up_polL=setjy_parse(spw_low)
spw_pol_low=spw_low#raw_input('Please enter reference spw for lsb pol cal (e.g., 0)-->')
#nu_low_polL,nu_up_polL=raw_input('Please enter the low/up frequency (MHz) in reference channel; [enter] if not doing pol cal (e.g., low,up)-->').split(',')
#flux_low_polL,flux_up_polL=raw_input('Please enter the low/up fluxes (Jy) in reference channel; [enter] if not doing pol cal (e.g., low,up)-->').split(',')
dict_log.append((ms_name_prefix+'_pol_nu_lsb_low',nu_low_polL))
dict_log.append((ms_name_prefix+'_pol_nu_lsb_up',nu_up_polL))
dict_log.append((ms_name_prefix+'_pol_flux_lsb_low',flux_low_polL))
dict_log.append((ms_name_prefix+'_pol_flux_lsb_up',flux_up_polL))
print 'Set fluxscale for upper base-band...'
#flux_mod_high=raw_input('Please enter flux model for upper base-band. e.g., 3C48_C.im-->')
if bands[kk]=='C':
flux_mod_high=src_dict['Fields'][bpf_cal]['Name'].split('=')[1]+'_'+'X'+'.im'
else:
flux_mod_high=src_dict['Fields'][bpf_cal]['Name'].split('=')[1]+'_'+bands[kk]+'.im'
print 'Using '+flux_mod_high+' for flux model in upper baseband'
dict_log.append((ms_name_prefix+'_fluxmodusb',flux_mod_high))
setjy(vis=ms_name,field=bpf_cal,standard='Perley-Butler 2013',
model=flux_mod_high,usescratch=False,scalebychan=True,spw=spw_high)
if pol_calib=='y':
spw_pol_high=spw_high#raw_input('Please enter reference spw for usb pol cal (e.g., 8)-->')
flux_low_polU,flux_up_polU,nu_low_polU,nu_up_polU=setjy_parse(spw_high)
#nu_low_polU,nu_up_polU=raw_input('Please enter the low/up frequency (MHz) in reference channel; [enter] if not doing pol cal (e.g., low,up)-->').split(',')
#flux_low_polU,flux_up_polU=raw_input('Please enter the low/up fluxes (Jy) in reference channel; [enter] if not doing pol cal (e.g., low,up)-->').split(',')
dict_log.append((ms_name_prefix+'_pol_nu_usb_low',nu_low_polU))
dict_log.append((ms_name_prefix+'_pol_nu_usb_up',nu_up_polU))
dict_log.append((ms_name_prefix+'_pol_flux_usb_low',flux_low_polU))
dict_log.append((ms_name_prefix+'_pol_flux_usb_up',flux_up_polU))
########################################
########################################
##initial phase cal before bandpass
########################################
os.system('rm -rf '+cal_table_prefix+'_phase_int_all.cal')
os.system('rm -rf '+cal_table_prefix+'_phase_int_all2.cal')
os.system('rm -rf '+cal_table_prefix+'_phase_int_bp.cal')
os.system('rm -rf '+cal_table_prefix+'_phase_int_bp2.cal')
print 'Initial phase cal before bandpass...'
if intera=='y':
print 'First look for RFI free channels in lower base-band...'
plotms(vis=ms_name, spw=spw_low, antenna=ref_ant, xaxis='freq', yaxis='amp',iteraxis='field',\
correlation='RR,LL', coloraxis='spw', symbolshape = 'circle')
raw_input('Please press enter when ready to continue.')
rfifree_low=raw_input('Please enter rfi free channels for lower base-band. e.g. 0~7:27~36-->')
dict_log.append((ms_name_prefix+'_initphase_rfifreelsb',rfifree_low))
gaincal(vis=ms_name, caltable=cal_table_prefix+'_phase_int_all.cal',field=",".join(field_lst),\
refant=ref_ant, spw=rfifree_low,gaintype='G',calmode='p', solint='int', minsnr=2.0,gaintable=gt_lst_low)
print 'Plotting solutions...'
plotcal(caltable=cal_table_prefix+'_phase_int_all.cal',xaxis='time',yaxis='phase',\
poln='R',iteration='antenna',plotrange=[-1,-1,-180,180],field='',antenna='')
raw_input('Please press enter when ready to continue.')
plotcal(caltable=cal_table_prefix+'_phase_int_all.cal',xaxis='time',yaxis='phase',\
poln='L',iteration='antenna',plotrange=[-1,-1,-180,180],field='')
raw_input('Please press enter when ready to continue.')
badantsf3a=raw_input('Please enter bad ants to flag (enter if none). e.g., ea10,ea16-->')
dict_log.append((ms_name_prefix+'_initphase_flag_badantlsb',badantsf3a))
if badantsf3a=='':
print 'No antennas to flag.'
else:
print 'Flagging selected ants.'
flagdata(vis=ms_name,flagbackup=True, mode='manual', antenna=badantsf3a,spw=spw_low)
print 'Look for RFI free channels in upper base-band...'
plotms(vis=ms_name, spw=spw_high, antenna=ref_ant, xaxis='freq', yaxis='amp',iteraxis='field',\
correlation='RR,LL', coloraxis='spw', symbolshape = 'circle')
raw_input('Please press enter when ready to continue.')
rfifree_high=raw_input('Please enter rfi free channels for upper base-band. e.g. 8~15:27~36-->')
dict_log.append((ms_name_prefix+'_initphase_rfifreeusb',rfifree_high))
gaincal(vis=ms_name, caltable=cal_table_prefix+'_phase_int_all2.cal', field=",".join(field_lst),\
refant=ref_ant, spw=rfifree_high,gaintype='G',calmode='p', solint='int', minsnr=2.0,gaintable=gt_lst_high)
print 'Plotting solutions...'
plotcal(caltable=cal_table_prefix+'_phase_int_all2.cal',xaxis='time',yaxis='phase',\
poln='R',iteration='antenna',plotrange=[-1,-1,-180,180],field='',antenna='')
raw_input('Please press enter when ready to continue.')
plotcal(caltable=cal_table_prefix+'_phase_int_all2.cal',xaxis='time',yaxis='phase',\
poln='L',iteration='antenna',plotrange=[-1,-1,-180,180],field='')
raw_input('Please press enter when ready to continue.')
badantsf3b=raw_input('Please enter bad ants to flag (enter if none). e.g., ea10,ea16-->')
dict_log.append((ms_name_prefix+'_initphase_flag_badantusb',badantsf3b))
if badantsf3b=='':
print 'No antennas to flag.'
else:
print 'Flagging selected ants.'
flagdata(vis=ms_name,flagbackup=True, mode='manual', antenna=badantsf3b,spw=spw_high)
print 'Doing only Bandpass cal solution...'
print 'Lower base-band...'
gaincal(vis=ms_name, caltable=cal_table_prefix+'_phase_int_bp.cal',field=bpf_cal, refant=ref_ant,\
spw=rfifree_low,gaintype='G',calmode='p', solint='int', minsnr=2.0,gaintable=gt_lst_low)
print 'Plotting solutions...'
plotcal(caltable=cal_table_prefix+'_phase_int_bp.cal',xaxis='time',yaxis='phase',\
poln='R',iteration='antenna',plotrange=[-1,-1,-180,180],field=bpf_cal,antenna='',\
timerange=timerbp)
raw_input('Please press enter when ready to continue.')
plotcal(caltable=cal_table_prefix+'_phase_int_bp.cal',xaxis='time',yaxis='phase',\
poln='L',iteration='antenna',plotrange=[-1,-1,-180,180],field=bpf_cal,antenna='',\
timerange=timerbp)
raw_input('Please press enter when ready to continue.')
print 'Upper base-band...'
gaincal(vis=ms_name, caltable=cal_table_prefix+'_phase_int_bp2.cal', field=bpf_cal, refant=ref_ant,\
spw=rfifree_high,gaintype='G',calmode='p', solint='int', minsnr=2.0,gaintable=gt_lst_high)
print 'Plotting solutions...'
plotcal(caltable=cal_table_prefix+'_phase_int_bp2.cal',xaxis='time',yaxis='phase',\
poln='R',iteration='antenna',plotrange=[-1,-1,-180,180],field=bpf_cal,antenna='',\
timerange=timerbp)
raw_input('Please press enter when ready to continue.')
plotcal(caltable=cal_table_prefix+'_phase_int_bp2.cal',xaxis='time',yaxis='phase',\
poln='L',iteration='antenna',plotrange=[-1,-1,-180,180],field=bpf_cal,antenna='',\
timerange=timerbp)
raw_input('Please press enter when ready to continue.')
else:
gaincal(vis=ms_name, caltable=cal_table_prefix+'_phase_int_all.cal',field=",".join(field_lst),\
refant=ref_ant, spw=spw_low+':27~36',gaintype='G',calmode='p', solint='int', minsnr=2.0,gaintable=gt_lst_low)
gaincal(vis=ms_name, caltable=cal_table_prefix+'_phase_int_all2.cal', field=",".join(field_lst),\
refant=ref_ant, spw=spw_high+':27~36',gaintype='G',calmode='p', solint='int', minsnr=2.0,gaintable=gt_lst_high)
gaincal(vis=ms_name, caltable=cal_table_prefix+'_phase_int_bp.cal',field=bpf_cal, refant=ref_ant,\
spw=spw_low+':27~36',gaintype='G',calmode='p', solint='int', minsnr=2.0,gaintable=gt_lst_low)
gaincal(vis=ms_name, caltable=cal_table_prefix+'_phase_int_bp2.cal', field=bpf_cal, refant=ref_ant,\
spw=spw_high+':27~36',gaintype='G',calmode='p', solint='int', minsnr=2.0,gaintable=gt_lst_high)
gt_lst_high.append(cal_table_prefix+'_phase_int_bp2.cal')
gt_lst_low.append(cal_table_prefix+'_phase_int_bp.cal')
########################################
########################################
#Delay calibration
########################################
os.system('rm -rf '+cal_table_prefix+'.K0')
os.system('rm -rf '+cal_table_prefix+'_2.K0')
print 'Delay calibration...'
if intera=='y':
print 'Lower base-band...'
gaincal(vis=ms_name,caltable=cal_table_prefix+'.K0', field=bpf_cal,\
refant=ref_ant,spw=spw_low,gaintype='K', solint='inf',combine='scan',\
minsnr=2, gaintable=gt_lst_low)
print 'Plotting solutions...'
plotcal(caltable=cal_table_prefix+'.K0',xaxis='antenna',yaxis='delay',figfile='plotcal_K0-delay.png')
raw_input('Please press enter when ready to continue.')
badantsf4a=raw_input('Please enter bad ants to flag (enter if none). e.g., ea10,ea16-->')
badspf4a=raw_input('Please enter bad spws for thes bad ants (enter if none). e.g., 5~7-->')
dict_log.append((ms_name_prefix+'_delay_flag_badantlsb',badantsf4a))
dict_log.append((ms_name_prefix+'_delay_flag_badswksb',badspf4a))
if badantsf4a=='':
print 'No antennas to flag.'
else:
print 'Flagging selected ants.'
flagdata(vis=ms_name,flagbackup=True, mode='manual', antenna=badantsf4a,spw=badspf4a)
print 'Upper base-band...'
gaincal(vis=ms_name,caltable=cal_table_prefix+'_2.K0', field=bpf_cal,\
refant=ref_ant,spw=spw_high,gaintype='K', solint='inf',combine='scan',\
minsnr=2, gaintable=gt_lst_high)
print 'Plotting solutions...'
plotcal(caltable=cal_table_prefix+'_2.K0',xaxis='antenna',yaxis='delay',figfile='plotcal_K02-delay.png')
raw_input('Please press enter when ready to continue.')
badantsf4b=raw_input('Please enter bad ants to flag (enter if none). e.g., ea10,ea16-->')
badspf4b=raw_input('Please enter bad spws for thes bad ants (enter if none). e.g., 5~7-->')
dict_log.append((ms_name_prefix+'_delay_flag_badantusb',badantsf4b))
dict_log.append((ms_name_prefix+'_delay_flag_badswusb',badspf4b))
if badantsf4b=='':
print 'No antennas to flag.'
else:
print 'Flagging selected ants.'
flagdata(vis=ms_name,flagbackup=True, mode='manual', antenna=badantsf4b,spw=badspf4b)
else:
gaincal(vis=ms_name,caltable=cal_table_prefix+'.K0', field=bpf_cal,\
refant=ref_ant,spw=spw_low,gaintype='K', solint='inf',combine='scan',\
minsnr=2, gaintable=gt_lst_low)
gaincal(vis=ms_name,caltable=cal_table_prefix+'_2.K0', field=bpf_cal,\
refant=ref_ant,spw=spw_high,gaintype='K', solint='inf',combine='scan',\
minsnr=2, gaintable=gt_lst_high)
gt_lst_low.append(cal_table_prefix+'.K0')
gt_lst_high.append(cal_table_prefix+'_2.K0')
gf_lst_low.append('')
gi_lst_low.append('')
gf_lst_high.append('')
gi_lst_high.append('')
########################################
########################################
#Bandpass calibration
########################################
os.system('rm -rf '+cal_table_prefix+'.B0')
os.system('rm -rf '+cal_table_prefix+'_2.B0')
print 'Bandpass calibration...'
if intera=='y':
print 'Lower base-band...'
bandpass(vis=ms_name,caltable=cal_table_prefix+'.B0',field=bpf_cal,spw=spw_low,\
refant=ref_ant,solnorm=True,combine='scan', solint='inf',bandtype='B',\
gaintable=gt_lst_low)
print 'Plotting solutions...'
plotcal(caltable= cal_table_prefix+'.B0',poln='R', xaxis='chan',yaxis='amp',field= bpf_cal,\
subplot=221, iteration='antenna',figfile='plotcal_BP-B0-R-amp.png')
raw_input('Please press enter when ready to continue.')
plotcal(caltable= cal_table_prefix+'.B0',poln='L', xaxis='chan',yaxis='amp',field= bpf_cal,\
subplot=221, iteration='antenna',figfile='plotcal_BP-B0-L-amp.png')
raw_input('Please press enter when ready to continue.')
plotcal(caltable= cal_table_prefix+'.B0',poln='R', xaxis='chan',yaxis='phase',field= bpf_cal,\
subplot=221, iteration='antenna',plotrange=[-1,-1,-180,180],figfile='plotcal_BP-B0-R-phase.png')
raw_input('Please press enter when ready to continue.')
plotcal(caltable= cal_table_prefix+'.B0',poln='L', xaxis='chan',yaxis='phase',field= bpf_cal,\
subplot=221, iteration='antenna',plotrange=[-1,-1,-180,180],figfile='plotcal_BP-B0-L-phase.png')
raw_input('Please press enter when ready to continue.')
print 'Upper base-band...'
bandpass(vis=ms_name,caltable=cal_table_prefix+'_2.B0',field=bpf_cal,spw=spw_high,\
refant=ref_ant,solnorm=True,combine='scan', solint='inf',bandtype='B',\
gaintable=gt_lst_high)
print 'Plotting solutions...'
plotcal(caltable= cal_table_prefix+'_2.B0',poln='R', xaxis='chan',yaxis='amp',field= bpf_cal,\
subplot=221, iteration='antenna',figfile='plotcal_BP-B02-R-amp.png')
raw_input('Please press enter when ready to continue.')
plotcal(caltable= cal_table_prefix+'_2.B0',poln='L', xaxis='chan',yaxis='amp',field= bpf_cal,\
subplot=221, iteration='antenna',figfile='plotcal_BP-B02-L-amp.png')
raw_input('Please press enter when ready to continue.')
plotcal(caltable= cal_table_prefix+'_2.B0',poln='R', xaxis='chan',yaxis='phase',field= bpf_cal,\
subplot=221, iteration='antenna',plotrange=[-1,-1,-180,180],figfile='plotcal_BP-B02-R-phase.png')
raw_input('Please press enter when ready to continue.')
plotcal(caltable= cal_table_prefix+'_2.B0',poln='L', xaxis='chan',yaxis='phase',field= bpf_cal,\
subplot=221, iteration='antenna',plotrange=[-1,-1,-180,180],figfile='plotcal_BP-B02-L-phase.png')
raw_input('Please press enter when ready to continue.')
else:
bandpass(vis=ms_name,caltable=cal_table_prefix+'.B0',field=bpf_cal,spw=spw_low,\
refant=ref_ant,solnorm=True,combine='scan', solint='inf',bandtype='B',\
gaintable=gt_lst_low)
bandpass(vis=ms_name,caltable=cal_table_prefix+'_2.B0',field=bpf_cal,spw=spw_high,\
refant=ref_ant,solnorm=True,combine='scan', solint='inf',bandtype='B',\
gaintable=gt_lst_high)
gt_lst_low.append(cal_table_prefix+'.B0')
gt_lst_high.append(cal_table_prefix+'_2.B0')
gf_lst_low.append('')
gi_lst_low.append('')
gf_lst_high.append('')
gi_lst_high.append('')
########################################
########################################
#gain cal
########################################
os.system('rm -rf '+cal_table_prefix+'.G1')
os.system('rm -rf '+cal_table_prefix+'_2.G1')
gt_lst_low.remove(cal_table_prefix+'_phase_int_bp.cal')
gt_lst_high.remove(cal_table_prefix+'_phase_int_bp2.cal')
print 'Gain cal...'
print 'First BP/flux cal for both base-bands...'
for i in range(0,len(bpf_lst)):
gaincal(vis=ms_name,caltable=cal_table_prefix+'.G1',field=bpf_lst[i],spw=spw_low,\
solint='inf',refant=ref_ant,gaintype='G',calmode='ap',solnorm=False, gaintable=gt_lst_low)
gaincal(vis=ms_name,caltable=cal_table_prefix+'_2.G1',field=bpf_lst[i],spw=spw_high,\
solint='inf',refant=ref_ant,gaintype='G',calmode='ap',solnorm=False, gaintable=gt_lst_high)
print 'Append second cals to same table...'
for i in range(0,len(second_lst)):
gaincal(vis=ms_name,caltable=cal_table_prefix+'.G1',field=second_lst[i],spw=spw_low,\
solint='inf',refant=ref_ant,gaintype='G',calmode='ap', gaintable=gt_lst_low,append=True)
gaincal(vis=ms_name,caltable=cal_table_prefix+'_2.G1',field=second_lst[i],spw=spw_high,\
solint='inf',refant=ref_ant,gaintype='G',calmode='ap', gaintable=gt_lst_high,append=True)
if len(polleak_lst)>0:
print 'Append polleak cals to same table...'
for i in range(0,len(polleak_lst)):
gaincal(vis=ms_name,caltable=cal_table_prefix+'.G1',field=polleak_lst[i],spw=spw_low,\
solint='inf',refant=ref_ant,gaintype='G',calmode='ap', gaintable=gt_lst_low,append=True)
gaincal(vis=ms_name,caltable=cal_table_prefix+'_2.G1',field=polleak_lst[i],spw=spw_high,\
solint='inf',refant=ref_ant,gaintype='G',calmode='ap', gaintable=gt_lst_high,append=True)
if intera=='y':
print 'Plotting solutions...'
print 'Lower base-band phases...'
plotcal(caltable=cal_table_prefix+'.G1',xaxis='time',yaxis='phase',poln='R',\
plotrange=[-1,-1,-180,180],iteration='antenna')
raw_input('Please press enter when ready to continue.')
plotcal(caltable=cal_table_prefix+'.G1',xaxis='time',yaxis='phase',poln='L',\
plotrange=[-1,-1,-180,180],iteration='antenna')
raw_input('Please press enter when ready to continue.')
print 'Lower base-band amps...'
plotcal(caltable=cal_table_prefix+'.G1',xaxis='time',yaxis='amp',poln='R',iteration='antenna')
raw_input('Please press enter when ready to continue.')
plotcal(caltable=cal_table_prefix+'.G1',xaxis='time',yaxis='amp',poln='L',iteration='antenna')
raw_input('Please press enter when ready to continue.')
print 'Upper base-band phases...'
plotcal(caltable=cal_table_prefix+'_2.G1',xaxis='time',yaxis='phase',poln='R',\
plotrange=[-1,-1,-180,180],iteration='antenna')
raw_input('Please press enter when ready to continue.')
plotcal(caltable=cal_table_prefix+'_2.G1',xaxis='time',yaxis='phase',poln='L',\
plotrange=[-1,-1,-180,180],iteration='antenna')
raw_input('Please press enter when ready to continue.')
print 'Upper base-band amps...'
plotcal(caltable=cal_table_prefix+'_2.G1',xaxis='time',yaxis='amp',poln='R',iteration='antenna')
raw_input('Please press enter when ready to continue.')
plotcal(caltable=cal_table_prefix+'_2.G1',xaxis='time',yaxis='amp',poln='L',iteration='antenna')
raw_input('Please press enter when ready to continue.')
print 'Check phase stability of reference antenna (diff between R and L stable over time)...'
print 'Lower base-band...'
plotcal(caltable=cal_table_prefix+'.G1', xaxis='time', yaxis='phase',poln='/',\
plotrange=[-1,-1,-180,180],iteration='spw')
raw_input('Please press enter when ready to continue.')
print 'Upper base-band...'
plotcal(caltable=cal_table_prefix+'_2.G1', xaxis='time', yaxis='phase',poln='/',\
plotrange=[-1,-1,-180,180],iteration='spw')
raw_input('Please press enter when ready to continue.')