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ALMA_cont_red_script.py
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ALMA_cont_red_script.py
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#################################################
#ALMA CASA Continuum Reduction Script
#################################################
'''CASA script to be used for the flagging, calibration and imaging of ALMA Continuum Data (Cycle 4 and above)
INPUT: Parameter file detailing all data and imaging parameters (param_dir_file set below)
OUTPUT: (1) Calibrated Split MS for full band (and each spw) -- data_[target]_[obsDate]_[band]_[TID]_([spw]_)calibrated.ms
(2) Continuum images for full band (and each epw) -- [target]_[obsDate]_[band]_[TID]_([spw]_)im.image.pbcor
(3) File of flux densities from image(stokes)/UV plane fitting -- imfit_results_[band].txt/uvfit_results_[band].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; can be asdm or ms format.
- All input logged in user_input.logg.
Written by: Alex J. Tetarenko
Last Updated: Aug 2019
Tested in CASA versions up to 5.4
USAGE: Set path to parameter file (line 46) and output directory (line 57), then,
run execfile('ALMA_cont_red_script.py') within CASA
'''
#au.getObservationDateRangeFromASDM(asdm)
print '##################################################'
print 'Welcome to Alexs ALMA 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/ALMA_maxi1820/reduced/ep3_jul06_B/'
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
print 'All output images & intermediate data products are put in this directory.\n'
#param file location
param_dir_file='/export/data2/atetarenko/ALMA_maxi1820/reduced/params_alma3B.txt'
print 'You have set your param file to ', param_dir_file
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...'
#read in param file
f=open(param_dir_file)
data_params=imp.load_source('data_params','',f)
f.close()
#data set params
raw_type=data_params.raw_type
d_name=data_params.d_name
obsDate=data_params.obsDate
target=data_params.target
band=data_params.band
doImage=data_params.doImage
bandsIM=data_params.bandsIM
#general image params
mythreshold=data_params.mythreshold
myimsize=data_params.myimsize
mycell=data_params.mycell
myniter=data_params.myniter
mynterms=data_params.mynterms
decon=data_params.decon
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([('raw_data_type',raw_type),('d_name_input',d_name),('obsDate', obsDate),('target',target),\
('bands_input',band),('do imaging',doImage),('bands to image',bandsIM),('weighting',weighting),('outfile',outlierfile),\
('mythreshold',mythreshold),('myimsize',myimsize),('mycell',mycell),('myniter',myniter),('mynterms',mynterms),\
('mystokes',mystokes),('mymask',mymask),('uv_fit',uv_fit),('multiscale',multiscale),('robust',robust),('uv init param file',uv_initp)])
#################################################
#################################################
#Convert & Split Data Section
#################################################
#convert raw data to MS if needed
if raw_type=='asdm':
print 'Converting raw data from asdm to MS format...'
os.system('rm -rf '+my_dir+'data_MS.ms')
os.system('rm -rf '+my_dir+'data_MS.ms.flagversions')
os.system('rm -rf '+my_dir+'data_'+target+'_'+obsDate+'_'+band+'pretw.ms')
os.system('rm -rf '+my_dir+'data_'+target+'_'+obsDate+'_'+band+'pretw.ms.flagversions')
importasdm(asdm = d_name, vis=my_dir+'data_MS', asis='*')
print 'Making split MS for ', band,' band...'
split(vis=my_dir+'data_MS',outputvis=my_dir+'data_'+target+'_'+obsDate+'_'+band+'_'+'pretw.ms',datacolumn='data')
os.system('rm -rf '+my_dir+'data_MS.ms')
os.system('rm -rf '+my_dir+'data_MS.ms.flagversions')
else:
print 'Raw data is already in MS format'
print 'Splitting out raw data into new MS...'
os.system('rm -rf '+my_dir+'data_'+target+'_'+obsDate+'_'+band+'pretw.ms')
os.system('rm -rf '+my_dir+'data_'+target+'_'+obsDate+'_'+band+'pretw.ms.flagversions')
split(vis=d_name,outputvis=my_dir+'data_'+target+'_'+obsDate+'_'+band+'_'+'pretw.ms',datacolumn='data')
ms_name=my_dir+'data_'+target+'_'+obsDate+'_'+band+'_'+'pretw.ms'
flagmanager(vis=ms_name,mode='save',versionname=target+'_'+obsDate+'_'+band+'_initial',comment='after initial split')
#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'
print 'Opening listobs file...'
os.system('gedit '+my_dir+obsDate+'_listfile.txt &')
raw_input('Please press enter when ready to continue.')
#enter some data specifics
num_spw=raw_input('Please enter the total number of spws in the data set. e.g. 25--> ')
science_spw=au.getScienceSpws(ms_name,intent='OBSERVE_TARGET#ON_SOURCE',returnString=True).split(',')
bpf_cal=raw_input('Please enter bandpass cals (if >1 seperate by comma)--> ')
bpf_lst=bpf_cal.split(',')
bp_scan=raw_input('Please enter bandpass cal scan(s), e.g., 2,3--> ')
flux_cal=raw_input('Please enter flux cals (if >1 seperate by comma)--> ')
flux_lst=flux_cal.split(',')
second_cal=raw_input('Please enter second cals (if >1 seperate by comma)--> ')
second_lst=second_cal.split(',')
prim_cal,check_src=raw_input('Of these second cals, which is primary and which is check src, e.g., prim,check--> ').split(',')
target_id=raw_input('Please enter target id (if >1 seperate by comma)--> ')
target_lst=target_id.split(',')
cal_lst=list(set(bpf_lst+second_lst+flux_lst))
full_lst=list(set(bpf_lst+second_lst+flux_lst+target_lst))
cal_lst.sort()
full_lst.sort()
dict_log.append(('number of spws',num_spw))
dict_log.append(('bandpass cals',bpf_cal))
dict_log.append(('flux cals',flux_cal))
dict_log.append(('second cals',second_cal))
dict_log.append(('targets',target_id))
dict_log.append(('prim cal',prim_cal))
dict_log.append(('check cal',check_src))
#ant postions
print 'Plotting antenna positions. Please choose a reference antenna near centre of array.'
os.system('rm -rf '+my_dir+'antennas_'+obsDate+'.png')
plotants(vis=ms_name,figfile=my_dir+'antennas_'+obsDate+'.png')
ref_ant=raw_input('Please enter reference antenna. e.g., DV23-->')
dict_log.append(('ref_ant',ref_ant))
#################################################
#################################################
#Tsys and WVR Section
#################################################
#Each ms include tables that contain the Tsys and WVR measurements associated with
#the visibility data. We must create calibration tables from these measurements.
cal_table_prefix=my_dir+obsDate+'_'+band
wvr_cal=my_dir+obsDate+'_'+band+'.wvr'
tsys_cal=my_dir+obsDate+'_'+band+'.tsys'
#wvr
print 'Computing WVR corrections...'
os.system('rm -rf '+wvr_cal)
wvrgcal(vis=ms_name, caltable=wvr_cal, segsource=True, toffset=-1)
#tsys
print 'Computing Tsys corrections...'
os.system('rm -rf '+tsys_cal)
gencal(vis=ms_name, caltable=tsys_cal, caltype='tsys')
#figure out which sources have tsys measurments and which dont
print 'Showing listobs for Tsys measurments...'
os.system('rm -rf '+my_dir+obsDate+'_listfile_tsys.txt')
listobs(vis=ms_name, verbose=False, selectdata=True, intent='CALIBRATE_ATMOS*',\
listfile=my_dir+obsDate+'_listfile_tsys.txt')
os.system('gedit '+my_dir+obsDate+'_listfile_tsys.txt &')
raw_input('Please press enter when ready to continue.')
tsys_fields=raw_input('Please enter fields with Tsys measurments, e.g., 1,2,3--> ').split(',')
tsys_fields_wo=raw_input('Please enter fields without Tsys measurments, e.g., 1,2,3--> ').split(',')
tsys_spws=raw_input('Please enter multi-channel spws with Tsys measurments, e.g., 17,18,19--> ').split(',')
dict_log.append(('tsys fields',tsys_fields))
dict_log.append(('no tsys fields',tsys_fields_wo))
dict_log.append(('tsys spws',tsys_spws))
#tsys vs time
print 'Plotting Tsys vs time...cycle through ants'
plotcal(caltable=tsys_cal, xaxis='time',yaxis='tsys',plotrange=[0,0,100,500],\
iteration='antenna',subplot=421,poln='',spw=tsys_spws[0],showgui=True)
raw_input('Please press enter when ready to continue.')
#tsys vs freq
print 'Plotting Tsys vs freq...cycle through ants'
plotcal(caltable=tsys_cal, xaxis='freq', yaxis='tsys', spw='',subplot=111, iteration='antenna')
raw_input('Please press enter when ready to continue.')
tsys_detail=raw_input('Do you want a detailed look at Tsys?y or n?--> ')
if tsys_detail=='y':
#tsys vs freq
print 'Check Tsys solutions. Look out for bad ants/times for flagging.'
print 'Plotting Tsys vs freq...'
for field_TS in tsys_fields:
for spw_TS in tsys_spws:
print ' Field:', field_TS, ' SPW: ',spw_TS,
plotbandpass(caltable=tsys_cal, xaxis='freq',yaxis='amp',showtsky=True,\
subplot=22,field=field_TS,spw=spw_TS, interactive=True,plotrange=[0,0,0,0])
raw_input('Please press enter when ready to continue.')
print 'Plotting Tsys vs freq...all scans'
for field_TS in tsys_fields:
for spw_TS in tsys_spws:
print ' Field:', field_TS, ' SPW: ',spw_TS,
plotbandpass(caltable=tsys_cal, xaxis='freq',yaxis='amp',showtsky=True,\
subplot=22,field=field_TS,spw=spw_TS, interactive=True,plotrange=[0,0,0,0],overlay='time')
raw_input('Please press enter when ready to continue.')
print 'Plotting Tsys vs freq...all ants'
for field_TS in tsys_fields:
for spw_TS in tsys_spws:
print ' Field:', field_TS, ' SPW: ',spw_TS,
plotbandpass(caltable=tsys_cal, xaxis='freq',yaxis='amp',showtsky=True,\
subplot=22,field=field_TS,spw=spw_TS, interactive=True,plotrange=[0,0,0,0],overlay='antenna')
raw_input('Please press enter when ready to continue.')
#apply tsys and wvr corrections
print 'Applying corrections for sources with Tsys...'
#creat spw map if needed for those spws without tsys measurments
tsysmap = range(int(num_spw))
print 'The science spws are: ', ",".join(science_spw)
map_spw=raw_input('Please enter the tsys spws to map these to if needed. e.g., 1,2,5,7 (enter if none)--> ').split(',')
dict_log.append(('map spws',map_spw))
if len(map_spw)==len(science_spw):
for s in range(0,len(map_spw)):
if map_spw[s] != '':
tsysmap[int(science_spw[s])] = int(map_spw[s])
#apply
for field_TS in tsys_fields:
applycal(vis=ms_name, spw=",".join(science_spw), field=field_TS, gainfield=field_TS,\
gaintable=[tsys_cal, wvr_cal], spwmap=[tsysmap,[]],interp=['linear,spline','nearest'],\
flagbackup=False, calwt=True)
print 'Applying corrections for sources without Tsys...'
#enter replacments fields for those sources without tsys measurments
print 'The fields without tsys are: ', ",".join(tsys_fields_wo)
nocal_replace=raw_input('Please enter the replacement fields closest in time/space, e.g., 1,2,3--> ').split(',')
dict_log.append(('tsys replacment fields',nocal_replace))
#apply
for ts in range(0,len(tsys_fields_wo)):
applycal(vis=ms_name, spw=",".join(science_spw), field=tsys_fields_wo[ts],\
gaintable=[tsys_cal, wvr_cal], spwmap=[tsysmap,[]],gainfield=[nocal_replace[ts],tsys_fields_wo[ts]],\
interp=['linear,spline','nearest'],flagbackup=False,calwt=True)
print 'Check Tsys/WVR corrected data...'
print 'Cycle through spws, looks for bad channels.'
strongF=raw_input('Please enter the fields to check (usually the brightest cals), e.g., 1,2,3--> ')
dict_log.append(('brightest cals for tys check',strongF))
print 'Before...'
plotms(vis=ms_name,spw=",".join(science_spw),xaxis='frequency',yaxis='amp',field=strongF,\
antenna='*&*',avgtime='1e8',avgscan=True,coloraxis='field',iteraxis='spw',\
xselfscale=True,ydatacolumn='data',showgui=True)
raw_input('Please press enter when ready to continue.')
print 'After...'
plotms(vis=ms_name,spw=",".join(science_spw),xaxis='frequency',yaxis='amp',field=strongF,\
antenna='*&*',avgtime='1e8',avgscan=True,coloraxis='field',iteraxis='spw',\
xselfscale=True,ydatacolumn='corrected',showgui=True)
raw_input('Please press enter when ready to continue.')
#split out science data
print 'Splitting out science data...'
os.system('rm -rf ' + my_dir+'data_'+target+'_'+obsDate+'_'+band+'_'+'posttw.ms')
os.system('rm -rf ' + my_dir+'data_'+target+'_'+obsDate+'_'+band+'_'+'posttw.ms.flagversions')
split(vis=ms_name,outputvis=my_dir+'data_'+target+'_'+obsDate+'_'+band+'_'+'posttw.ms',\
datacolumn='corrected',spw=",".join(science_spw))
ms_name=my_dir+'data_'+target+'_'+obsDate+'_'+band+'_'+'posttw.ms'
#listobs
print 'Opening listobs for split data set...'
os.system('rm -rf '+my_dir+obsDate+'_listfile_aftertw.txt')
listobs(ms_name,listfile=my_dir+obsDate+'_listfile_aftertw.txt')
os.system('gedit '+my_dir+obsDate+'_listfile_aftertw.txt &')
raw_input('Please press enter when ready to continue.')
flagmanager(vis=ms_name,mode='save',versionname=target+'_'+obsDate+'_'+band+'_tsyswvr',comment='after tsys/wvr')
#################################################
#################################################
#Flagging and Inspection Section
#################################################
print 'Starting apriori flagging...'
#autocorrelation data
print 'Flagging autocorrelation data...'
flagdata(vis=ms_name, mode='manual', autocorr=True, action = 'apply', flagbackup=True)
#shadowed data
print 'Flagging shadowed data...'
flagdata(vis=ms_name, mode='shadow',tolerance=12.0, action='apply', flagbackup=False)
#pointing/atmosphere/dummy scan data
print 'Flagging pointing and atmosphere data...'
flagdata(vis=ms_name,mode='manual',intent='*POINTING*', flagbackup=False)
flagdata(vis=ms_name,mode='manual',intent='*ATMOSPHERE*', flagbackup=False)
dum_scan=raw_input('Please enter any dummy scans to flag, e.g., 1,2,3 (enter if none)--> ')
dict_log.append(('flagged dummy scans',dum_scan))
flagdata(vis=ms_name, flagbackup=True, mode='manual', scan=dum_scan)
#bad ants from log or wvr/tsys
badants=raw_input('Please enter bad ants from log or wvr/tsys correction, e.g., DA43,DA52 (enter if none)--> ')
dict_log.append(('flagged bad ants',badants))
if badants=='':
print 'No bad ants to flag.'
else:
print 'Flagging bad ants: ',badants
flagdata(vis=ms_name, mode='manual', antenna=badants, action='apply', flagbackup=False)
#end channels
flag_end=raw_input('Do you want to flag end channels? y or n--> ')
dict_log.append(('flag end channels',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., 124~127-->')
dict_log.append(('beg channels flagged',beg))
dict_log.append(('end channels flagged',endd))
print 'Flagging beginning channels ',beg,' and end channels ',endd,' ...'
flagdata(vis=ms_name,spw='0~'+str(len(science_spw)-1)+':'+beg,field='',antenna='')
flagdata(vis=ms_name,spw='0~'+str(len(science_spw)-1)+':'+endd,field='',antenna='')
else:
print 'End channels not flagged.'
print 'Starting 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...iterating over spw'
print 'Look for bad or low amp data.'
plotms(vis=ms_name,spw='',xaxis='time',yaxis='amp',field='',avgchannel='128',\
coloraxis='field',iteraxis='spw',showgui=True)
raw_input('Please press enter when ready to continue.')
print '(2) Phase vs freq (ref_ant only,bpf cal only)...iterating over spw'
print 'Significant delay errors or baseline errors will show up as phase slopes here.'
plotms(vis=ms_name,spw='',xaxis='frequency',yaxis='phase',field=bpf_cal,antenna=ref_ant,\
avgtime='1e8',avgscan=True,coloraxis='baseline',iteraxis='spw',xselfscale=True,showgui=True)
raw_input('Please press enter when ready to continue.')
print '(2) Amp vs freq (second cals and target only)...iterating over spw'
print 'Look for birdies.'
plotms(vis=ms_name,spw='',xaxis='frequency',yaxis='amp',field=second_cal+','+target_id,\
avgtime='1e8',avgscan=True,coloraxis='field',iteraxis='spw',xselfscale=True,yselfscale=True,showgui=True)
raw_input('Please press enter when ready to continue.')
print '(3) BP and flux cal spectral features...'
print 'Look for absorbtion and emission features.'
plotms(vis=ms_name,spw='',xaxis='channel',yaxis='amp',field=bpf_cal,\
avgtime='1e8',coloraxis='field',iteraxis='spw',showgui=True)
raw_input('Please press enter when ready to continue.')
if flux_cal != bpf_cal:
plotms(vis=ms_name,spw='',xaxis='channel',yaxis='amp',field=flux_cal,\
avgtime='1e8',coloraxis='field',iteraxis='spw',showgui=True)
raw_input('Please press enter when ready to continue.')
print 'Flagging...'
badasf=raw_input('Please enter bad ant,spw,field,corr,and timerange to flag (enter if none). e.g., DV10,DA12;5:4~9;3;YY;9:52:10.0~9:53:10.0 ;5;3;;-->').split(' ')
dict_log.append(('flags',badasf))
if '' in badasf:
print 'Nothing to flag.'
else:
print 'Flagging selected data.'
for i in range(0,len(badasf)):
strg=badasf[i].split(';')
flagdata(vis=ms_name,flagbackup=True, mode='manual', antenna=strg[0],spw=strg[1],field=strg[2],correlation=strg[3],timerange=strg[4])
print 'Final check of flagged data...'
plotms(vis=ms_name,spw='',xaxis='frequency',yaxis='amp',field=second_cal+','+target_id,\
avgtime='1e8',avgscan=True,coloraxis='field',iteraxis='spw',xselfscale=True,yselfscale=True,showgui=True)
raw_input('Please press enter when ready to continue.')
flag_again=raw_input('Do you need to do more flagging? y or n-->')
dict_log.append(('flag again',flag_again))
countf=1
while flag_again=='y':
badasf2=raw_input('Please enter bad ant,spw,field,corr,and timerange to flag (enter if none). e.g., DV10,DA12;5:4~9;3;YY;9:52:10.0~9:53:10.0 ;5;3;;-->').split(' ')
raw_input('Press enter to flag selected data.')
dict_log.append(('flags2'+str(countf),badasf2))
if '' in badasf2:
print 'Nothing to flag.'
else:
print 'Flagging selected data.'
for i in range(0,len(badasf2)):
strg2=badasf2[i].split(';')
flagdata(vis=ms_name,flagbackup=True, mode='manual', antenna=strg2[0],spw=strg2[1],field=strg2[2],correlation=strg2[3],timerange=strg2[4])
print 'Plotting...'
plotms(vis=ms_name,spw='',xaxis='frequency',yaxis='amp',field=second_cal+','+target_id,\
avgtime='1e8',avgscan=True,coloraxis='field',iteraxis='spw',xselfscale=True,yselfscale=True,showgui=True)
raw_input('Please press enter when ready to continue.')
raw_input('Press enter to continue.')
flag_again=raw_input('Do you need to do more flagging? y or n-->')
countf=countf+1
#save flags
flagmanager(vis=ms_name,mode='save',versionname=target+'_'+obsDate+'_'+band+'_flagging',comment='after flagging')
writeDict(dict_log, my_dir+'user_input_'+obsDate+'_flag.logg',str(datetime.datetime.now()))
#################################################
#################################################
#Antenna positions correction
#################################################
#make list of pre gain tables to be applied in tandem below
gt_lst=[]
do_ant=raw_input('Do you wish to do antenna positions corrections? y or n?--> ')
dict_log.append(('ant corrections',do_ant))
if do_ant=='y':
#antpos
cor_ants=raw_input('Please enter ants to be corrected, e.g., DA48,DA65--> ')
raw_input('Please press enter when ready to continue.')
cor_pos=raw_input('Please enter set of three number corrections for each antenna in tandem, e.g., -1,-2,3,4,5,6--> ').split(',')
cor_lst=[float(i) for i in cor_pos]
gencal(caltable=cal_table_prefix+'.antpos',
vis=ms_name, caltype='antpos',
parameter=cor_lst, antenna=cor_ants)
gt_lst.append(cal_table_prefix+'.antpos')
#################################################
#################################################
#Set up flux model
#################################################
print 'Setting the flux model...'
flux_man=raw_input('Do you need to manually set the flux cal values? y or n-->')
dict_log.append(('manually set flux model',flux_man))
if flux_man=='n':
setjy(vis=ms_name,field=flux_cal,usescratch=False,standard='Butler-JPL-Horizons 2012',scalebychan=False)
print 'Plotting flux model...'
plotms(vis=ms_name,field=flux_cal,xaxis='uvdist',yaxis='amp',coloraxis='spw',ydatacolumn='model',showgui=True,avgtime='1e8')
raw_input('Please press enter when ready to continue.')
else:
f_man=raw_input('Please enter cal name--> ')
#nu_man=raw_input('Please enter central freq in GHz for each science spw, e.g., 90.496,92.434--> ').split(',')
nu_man=au.getScienceFrequencies(ms_name)
#ds=raw_input('Please enter date of obs, e.g. 20170911--> ')
ds=au.getObservationStartDate(ms_name).split(' ')[0]
dict_log.append(('manual field',f_man))
dict_log.append(('manual nus',nu_man))
#dict_log.append(('manual date',ds))
for i in range(0,len(science_spw)):
sj_val=au.getALMAFlux(f_man,str(nu_man[i]/1e9)+' GHz',date=ds.replace('-',''))
dict_log.append(('manual si',sj_val['spectralIndex']))
setjy(fluxdensity=[float(sj_val['fluxDensity']), 0.0, 0.0, 0.0], scalebychan=True,\
vis=ms_name, spw=str(i),spix=float(sj_val['spectralIndex']),\
field=flux_cal, reffreq=str(nu_man[i]/1e9)+' GHz',\
selectdata=True, standard='manual', usescratch=True)
#################################################
#################################################
#Bandpass cal
#################################################
#first look at bandpass cal in time
print 'Examining bandpass cal...'
print 'First look for middle channels for initial phase cal before bandpass...'
plotms(vis=ms_name, spw='0~'+str(len(science_spw)-1), antenna=ref_ant, xaxis='freq', yaxis='amp',iteraxis='spw',\
coloraxis='spw', symbolshape = 'circle',avgtime='1e8',avgscan=True,field=bpf_cal,scan=bp_scan)
raw_input('Please press enter when ready to continue.')
bp_chan=raw_input('Please enter middle channels, e.g., 0~3:60~80--> ')
dict_log.append(('BP channels',bp_chan))
print 'Initial phase solution before bandpass...'
gaincal(vis=ms_name,caltable=cal_table_prefix+'.bpphase.gcal',field=bpf_cal,\
spw=bp_chan,refant=ref_ant,\
calmode='p',solint='int',minsnr=2.0,minblperant=4,intent='CALIBRATE_BANDPASS#ON_SOURCE')
gt_lst.append(cal_table_prefix+'.bpphase.gcal')
print 'Plotting solutions...'
print 'XX'
plotcal(caltable=cal_table_prefix+'.bpphase.gcal',xaxis='time',yaxis='phase',spw='',antenna='',\
iteration='antenna',subplot=421,plotrange=[0,0,-180,180],poln='X',showgui=True)
raw_input('Please press enter when ready to continue.')
print 'YY'
plotcal(caltable=cal_table_prefix+'.bpphase.gcal',xaxis='time',yaxis='phase',spw='',antenna='',\
iteration='antenna',subplot=421,plotrange=[0,0,-180,180],poln='X',showgui=True)
raw_input('Please press enter when ready to continue.')
print 'BP solution...'
bandpass(vis=ms_name,caltable=cal_table_prefix+'.bandpass.bcal',field=bpf_cal,spw='',combine='',\
refant=ref_ant,solint='inf',solnorm=True,minblperant=4, bandtype='B',\
fillgaps=3,gaintable=gt_lst,intent='CALIBRATE_BANDPASS#ON_SOURCE')
print 'Plotting solutions...'
for ii in range(0,len(science_spw)):
print 'Amp for Spw ', ii
plotbandpass(cal_table_prefix+'.bandpass.bcal',xaxis='freq',yaxis='amp', spw=str(i),antenna='',\
subplot=42, showatm=True,interactive=True)
raw_input('Please press enter when ready to continue.')
print 'Phase for Spw ', ii
plotbandpass(cal_table_prefix+'.bandpass.bcal',xaxis='freq',yaxis='phase', spw=str(i),antenna='',\
subplot=42, showatm=True,interactive=True)
raw_input('Please press enter when ready to continue.')
gt_lst.remove(cal_table_prefix+'.bpphase.gcal')
gt_lst.append(cal_table_prefix+'.bandpass.bcal')
#################################################
#################################################
#antenna-based phase and amplitude gain cal
#################################################
#(1) we will do amp and phase separetly as the phase changes on a much shorter timescale than the amplitude
#(2) also do seperate olution for application to target later. We do this as phase-scatter within a scan can
#dominate the interpolation between calibrator scans, so solve for the phase on the scan time rather then int.
print 'Gain calibration...'
#phase for cals
print 'Short phase solution for cals...'
gaincal(vis=ms_name,caltable=cal_table_prefix+'.intphase.gcal',field=",".join(cal_lst),\
spw='',refant=ref_ant,calmode='p',solint='int',minsnr=2.0,minblperant=4,gaintable=gt_lst)
#phase for target
print 'Longer phase solution for target...'
gaincal(vis=ms_name,caltable=cal_table_prefix+'.scanphase.gcal',field=",".join(cal_lst),\
spw='',refant=ref_ant,calmode='p',solint='inf',minsnr=2.0,minblperant=4,gaintable=gt_lst)
gt_lst.append(cal_table_prefix+'.intphase.gcal')
#amp
print 'Amp solution...'
gaincal(vis=ms_name,caltable=cal_table_prefix+'.amp.gcal',field=",".join(cal_lst),\
spw='',refant=ref_ant,calmode='ap',solint='inf',minsnr=2.0,minblperant=4,gaintable=gt_lst)
print 'Plotting phase solutions...'
print 'First short solution...'
plotcal(caltable=cal_table_prefix+'.intphase.gcal',xaxis='time',yaxis='phase',\
antenna='',spw='',field=",".join(cal_lst),iteration='antenna',subplot=421,\
plotrange=[0,0,-180,180],poln='X',showgui=True)
raw_input('Please press enter when ready to continue.')
plotcal(caltable=cal_table_prefix+'.intphase.gcal',xaxis='time',yaxis='phase',\
antenna='',spw='',field=",".join(cal_lst),iteration='antenna',subplot=421,\
plotrange=[0,0,-180,180],poln='Y',showgui=True)
raw_input('Please press enter when ready to continue.')
print 'Second long solution...'
plotcal(caltable=cal_table_prefix+'.scanphase.gcal',xaxis='time',yaxis='phase',\
antenna='',spw='',field=",".join(cal_lst),iteration='antenna',subplot=421,\
plotrange=[0,0,-180,180],poln='X',showgui=True)
raw_input('Please press enter when ready to continue.')
plotcal(caltable=cal_table_prefix+'.scanphase.gcal',xaxis='time',yaxis='phase',\
antenna='',spw='',field=",".join(cal_lst),iteration='antenna',subplot=421,\
plotrange=[0,0,-180,180],poln='Y',showgui=True)
raw_input('Please press enter when ready to continue.')
print 'Look for residual phase error...'
print 'Should not be scatter of more than a few degrees'
plotcal(caltable=cal_table_prefix+'.amp.gcal',xaxis='time',\
yaxis='phase',antenna='',spw='',field=",".join(cal_lst),\
plotrange=[0,0,-1,1],iteration='antenna',subplot=421,showgui=True)
raw_input('Please press enter when ready to continue.')
print 'Plotting amp solutions...'
plotcal(caltable=cal_table_prefix+'.amp.gcal',xaxis='time',yaxis='amp',\
antenna='',iteration='antenna',subplot=421,spw='',poln='X',\
plotrange=[0,0,0.0,0],showgui=True)
raw_input('Please press enter when ready to continue.')
plotcal(caltable=cal_table_prefix+'.amp.gcal',xaxis='time',yaxis='amp',\
antenna='',iteration='antenna',subplot=421,spw='',poln='Y',\
plotrange=[0,0,0.0,0],showgui=True)
raw_input('Please press enter when ready to continue.')
gt_lst.append(cal_table_prefix+'.amp.gcal')
#################################################
#################################################
#flux cal
#################################################
print 'Flux calibration...'
maps=raw_input('Was the reference field observed in all spws that transfer fields were? y or n?--> ')
dict_log.append(('fluxscale maps',maps))
if maps=='y':
fluxscale(vis=ms_name,caltable=cal_table_prefix+'.amp.gcal',\
fluxtable=cal_table_prefix+'.flux.cal',reference=flux_cal,\
listfile=cal_table_prefix+'.fluxscale.txt')
else:
maps_val=raw_input('Please enter map, e.g., 0,0,3,3--> ').split(',')
fluxscale(vis=ms_name,caltable=cal_table_prefix+'.amp.gcal',\
fluxtable=cal_table_prefix+'.flux.cal',reference=flux_cal,\
refspwmap=[int(maps_val[0]),int(maps_val[1]),int(maps_val[2]),int(maps_val[3])],\
listfile=cal_table_prefix+'.fluxscale.txt')
print 'Plotting solutions...'
plotcal(caltable=cal_table_prefix+'.flux.cal',xaxis='time',yaxis='amp',\
antenna='',iteration='antenna',subplot=421,spw='',poln='X',\
plotrange=[0,0,0.0,0],showgui=True)
raw_input('Please press enter when ready to continue.')
plotcal(caltable=cal_table_prefix+'.flux.cal',xaxis='time',yaxis='amp',\
antenna='',iteration='antenna',subplot=421,spw='',poln='X',\
plotrange=[0,0,0.0,0],showgui=True)
raw_input('Please press enter when ready to continue.')
gt_lst.remove(cal_table_prefix+'.amp.gcal')
gt_lst.append(cal_table_prefix+'.flux.cal')
#################################################
#################################################
#apply cal solutions
#################################################
print 'Apply calibration solutions...'
if do_ant=='n':
#bandpass cal
print 'Bandpass cals.'
for i in range(0,len(bpf_lst)):
applycal(vis=ms_name,field=bpf_lst[i],gaintable=gt_lst,\
interp=['nearest','nearest','nearest'],\
gainfield=[bpf_lst[i],bpf_lst[i],bpf_lst[i]], flagbackup=True, calwt=False)
#flux cal if different from bandpass cal
print 'Flux cals.'
for i in range(0,len(flux_lst)):
if flux_lst[i] not in bpf_lst:
applycal(vis=ms_name,field=flux_lst[i],gaintable=gt_lst,\
interp=['nearest','nearest','nearest'],\
gainfield=[bpf_cal,flux_lst[i],flux_lst[i]], flagbackup=True, calwt=False)
#primary phase cal if different from bandpass and flux cals
print 'Primary phase cal.'
for i in range(0,len(second_lst)):
if second_lst[i] not in bpf_lst and second_lst[i] not in flux_lst and second_lst[i] != check_src:
applycal(vis=ms_name,field=second_lst[i],gaintable=gt_lst,\
interp=['nearest','nearest','nearest'],\
gainfield=[bpf_cal,second_lst[i],second_lst[i]], flagbackup=True, calwt=False)
#check source
print 'Secondary phase cal/check source.'
if check_src != '':
applycal(vis=ms_name,field=check_src,gaintable=[cal_table_prefix+'.bandpass.bcal',\
cal_table_prefix+'.scanphase.gcal',cal_table_prefix+'.flux.cal'],\
interp=['nearest','linear','linear'],gainfield=[bpf_cal,prim_cal,prim_cal],\
flagbackup=True, calwt=False)
#target
print 'Target.'
for i in range(0,len(target_lst)):
applycal(vis=ms_name,field=target_lst[i],gaintable=[cal_table_prefix+'.bandpass.bcal',\
cal_table_prefix+'.scanphase.gcal',cal_table_prefix+'.flux.cal'],\
interp=['nearest','linear','linear'],\
gainfield=[bpf_cal,second_cal,second_cal], flagbackup=True, calwt=False)
elif do_ant=='y':
#bandpass cal
print 'Bandpass cals.'
for i in range(0,len(bpf_lst)):
applycal(vis=ms_name,field=bpf_lst[i],gaintable=gt_lst,\
interp=['','nearest','nearest','nearest'],\
gainfield=['',bpf_lst[i],bpf_lst[i],bpf_lst[i]], flagbackup=True, calwt=False)
#flux cal if different from bandpass cal
print 'Flux cals.'
for i in range(0,len(flux_lst)):
if flux_lst[i] not in bpf_lst:
applycal(vis=ms_name,field=flux_lst[i],gaintable=gt_lst,\
interp=['','nearest','nearest','nearest'],\
gainfield=['',bpf_cal,flux_lst[i],flux_lst[i]], flagbackup=True, calwt=False)
#primary phase cal if different from bandpass and flux cals
print 'Primary phase cal.'
for i in range(0,len(second_lst)):
if second_lst[i] not in bpf_lst and second_lst[i] not in flux_lst and second_lst[i] != check_src:
applycal(vis=ms_name,field=second_lst[i],gaintable=gt_lst,\
interp=['','nearest','nearest','nearest'],\
gainfield=['',bpf_cal,second_lst[i],second_lst[i]], flagbackup=True, calwt=False)
#check source
print 'Secondary phase cal/check source.'
if check_src != '':
applycal(vis=ms_name,field=check_src,gaintable=[cal_table_prefix+'.antpos',cal_table_prefix+'.bandpass.bcal',\
cal_table_prefix+'.scanphase.gcal',cal_table_prefix+'.flux.cal'],\
interp=['','nearest','linear','linear'],gainfield=['',bpf_cal,prim_cal,prim_cal],\
flagbackup=True, calwt=False)
#target
print 'Target.'
for i in range(0,len(target_lst)):
applycal(vis=ms_name,field=target_lst[i],gaintable=[cal_table_prefix+'.antpos',cal_table_prefix+'.bandpass.bcal',\
cal_table_prefix+'.scanphase.gcal',cal_table_prefix+'.flux.cal'],\
interp=['','nearest','linear','linear'],\
gainfield=['',bpf_cal,second_cal,second_cal], flagbackup=True, calwt=False)
flagmanager(vis=ms_name,mode='save',versionname=target+'_'+obsDate+'_'+band+'_applycal',comment='after applycal')
#################################################
#################################################
#check corrected data
#################################################
print 'Checking corrected data...'
print '(1) Amp vs time for all sources'
plotms(vis=ms_name,spw='',xaxis='time',yaxis='amp',field='',avgchannel='128',\
coloraxis='field',iteraxis='spw',ydatacolumn='corrected',showgui=True)
raw_input('Please press enter when ready to continue.')
print '(2) Phase vs time for cals'
plotms(vis=ms_name,spw='',xaxis='time',yaxis='phase',field=",".join(cal_lst),avgchannel='128',
coloraxis='field',iteraxis='spw',ydatacolumn='corrected',showgui=True)
raw_input('Please press enter when ready to continue.')
if check_src != '':
print 'Checking phase transfer...'
print 'Applying check src solutions to itself and compare to transfer solutions.'
if do_ant=='n':
applycal(vis=ms_name,field=check_src,gaintable=gt_lst,\
interp=['nearest','nearest','nearest'],gainfield=[bpf_cal,check_src,check_src],\
flagbackup=True, calwt=False)
elif do_ant=='y':
applycal(vis=ms_name,field=check_src,gaintable=gt_lst,\
interp=['','nearest','nearest','nearest'],gainfield=['',bpf_cal,check_src,check_src],\
flagbackup=True, calwt=False)
print 'Plotting again...'
print '(1) Amp vs time for all sources'
plotms(vis=ms_name,spw='',xaxis='time',yaxis='amp',field='',avgchannel='128',\
coloraxis='field',iteraxis='spw',ydatacolumn='corrected',showgui=True)
raw_input('Please press enter when ready to continue.')
print '(2) Phase vs time for cals'
plotms(vis=ms_name,spw='',xaxis='time',yaxis='phase',field=",".join(cal_lst),\
avgchannel='128',coloraxis='field',iteraxis='spw',ydatacolumn='corrected',showgui=True)
raw_input('Please press enter when ready to continue.')
print 'Reapply first solutions from primary cal to check src...'
if do_ant=='n':
applycal(vis=ms_name,field=check_src,gaintable=[cal_table_prefix+'.bandpass.bcal',\
cal_table_prefix+'.scanphase.gcal',cal_table_prefix+'.flux.cal'],\
interp=['nearest','linear','linear'],gainfield=[bpf_cal,prim_cal,prim_cal],\
flagbackup=True, calwt=False)
elif do_ant=='y':
applycal(vis=ms_name,field=check_src,gaintable=[cal_table_prefix+'.antpos',cal_table_prefix+'.bandpass.bcal',\
cal_table_prefix+'.scanphase.gcal',cal_table_prefix+'.flux.cal'],\
interp=['','nearest','linear','linear'],gainfield=['',bpf_cal,prim_cal,prim_cal],\
flagbackup=True, calwt=False)
print 'Checking spectral calibration...'
print 'Interate over spws.'
print 'First bandpass and flux cals...'
cals_add=[]
for cal in flux_lst:
if cal not in bpf_lst:
cals_add.append(cal)
if cals_add==[]:
plotms(vis=ms_name,spw='',xaxis='frequency',yaxis='amp',field=bpf_cal,\
avgtime='1e8',avgscan=True,coloraxis='field',ydatacolumn='corrected',\
iteraxis='spw',xselfscale=True,showgui=True)
raw_input('Please press enter when ready to continue.')
else:
plotms(vis=ms_name,spw='',xaxis='frequency',yaxis='amp',field=bpf_cal+','+",".join(cals_add),\
avgtime='1e8',avgscan=True,coloraxis='field',ydatacolumn='corrected',\
iteraxis='spw',xselfscale=True,showgui=True)
raw_input('Please press enter when ready to continue.')
print 'Next phase cals...'
plotms(vis=ms_name,spw='',xaxis='frequency',yaxis='amp',field=second_cal,\
avgtime='1e8',avgscan=True,coloraxis='field',ydatacolumn='corrected',\
iteraxis='spw',xselfscale=True,showgui=True)
raw_input('Please press enter when ready to continue.')
print 'Now the target...'
plotms(vis=ms_name,spw='',xaxis='frequency',yaxis='amp',field=target_id,\
avgtime='1e8',avgscan=True,coloraxis='field',ydatacolumn='corrected',\
iteraxis='spw',xselfscale=True,showgui=True)
raw_input('Please press enter when ready to continue.')
extraf=raw_input('Do you need to do additional flagging? y or n-->')
countf=1
if extraf=='y':
while extraf=='y':
badasfextra=raw_input('Please enter bad ant,spw,field, correlation, and timerange to flag (enter if none). e.g., DV10,DA12;5:4~9;3;YY;10:52:11.0~10:53:11.0 ;5;3;-->').split(' ')
dict_log.append(('flags2'+str(countf),badasfextra))
if '' in badasfextra:
print 'Nothing to flag.'
extraf=raw_input('Do you need to do additional flagging? y or n-->')
else:
print 'Flagging selected data.'
for i in range(0,len(badasfextra)):
strge=badasfextra[i].split(';')
flagdata(vis=ms_name,flagbackup=True, mode='manual', antenna=strge[0],spw=strge[1],field=strge[2],correlation=strge[3],timerange=strge[4])
raw_input('press enter to continue.')
extraf=raw_input('Do you need to do additional flagging? y or n-->')
countf=countf+1
else:
print 'No extra flagging requested.'
flagmanager(vis=ms_name,mode='save',versionname=target+'_'+obsDate+'_'+band+'_addflag',comment='after additional flagging')
#################################################
#################################################
#split out target data
#################################################
print 'Splitting out target data...'
#full MS
for iii in range(0,len(target_lst)):
print 'Full band for TID: ',target_lst[iii]
ms_name_final=my_dir+'data_'+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'_calibrated.ms'
os.system('rm -rf '+ms_name_final)
split(vis=ms_name,outputvis=ms_name_final,datacolumn='corrected',\
field=target_lst[iii],antenna='',spw='')
#individual spws
for k in range(0,len(science_spw)):
print 'SPW: ', k, ' for TID: ',target_lst[iii]
ms_name_finalspw=my_dir+'data_'+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'_spw'+str(k)+'_calibrated.ms'
os.system('rm -rf '+ms_name_finalspw)
split(vis=ms_name,outputvis=ms_name_finalspw,datacolumn='corrected',\
field=target_lst[iii],antenna='',spw=str(k))
#################################################
#################################################
#Imaging
#################################################
if doImage=='T':
print 'Starting Imaging...'
dopscbb='n'
dopscs='n'
for iii in range(0,len(target_lst)):
print 'Beginnning Imaging of target id: ', target_lst[iii]
if 'A' in bandsIM:
vis=my_dir+'data_'+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'_calibrated.ms'
print 'Imaging all base-bands together...'
if mymask=='':
print 'Using interactive mode so you can make a mask...'
print 'Cleaning...'
os.system('rm -rf '+my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'fullbandim*')
tclean(vis=vis,imagename=my_dir+target+'_'+obsDate+'_'+band+'_TID_cal'+'fullbandim',\
specmode='mfs',gridder='standard',imsize=myimsize,cell=mycell,spw='',deconvolver=decon,\
gain=0.1,weighting=weighting,robust=robust,nterms=mynterms, mask='',\
interactive=True,threshold=mythreshold,niter=myniter,pbcor=False,scales=multiscale)
raw_input('Please press enter to continue when you are done.')
else:
print 'Cleaning...'
print 'This make take awhile, please go do something else for a while.'
os.system('rm -rf '+my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'fullbandim*')
tclean(vis=vis,imagename=my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'fullbandim',\
mode='mfs',gridder='standard',imsize=myimsize,cell=mycell,spw='',deconvolver=decon,\
gain=0.1,weighting=weighting,robust=robust,nterms=mynterms, mask=mymask,\
interactive=False,threshold=mythreshold,niter=myniter,pbcor=False,scales=multiscale)
raw_input('Please press enter to continue when you are done.')
os.system('rm -rf '+my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'fullbandim.image.pbcor')
os.system('rm -rf '+my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'fullbandim.image.pbcor.fits')
if int(mynterms) > 1 and decon=='mtmfs':
os.system('rm -rf '+my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'fullbandim.image')
os.system('rm -rf '+my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'fullbandim.pb')
os.system('mv '+my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'fullbandim.image.tt0 '+my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'fullbandim.image')
os.system('mv '+my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'fullbandim.pb.tt0 '+my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'fullbandim.pb')
immath(imagename=[my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+\
'fullbandim.image',my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'fullbandim.pb'],\
expr='IM0/IM1',outfile=my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'fullbandim.image.pbcor')
exportfits(imagename=my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'fullbandim.image.pbcor',\
fitsimage=my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'fullbandim.image.pbcor.fits')
imagenbb=my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'fullbandim.image.pbcor'
fluxbb,errbb,unitbb,freqbb,errbb_real=imfit_point(imagenbb,my_dir,'I')
print 'Combined base-band flux density of ',fluxbb,' +/- ',errbb, unitbb
print 'Local RMS in Combined base-band image is: ',errbb_real,' Jy'
dopscbb=raw_input('Do you want to do phase selfcal?y or n-->')
dict_log.append(('selfcal full bb',dopscbb))
if dopscbb=='y':
selfcal_both,scim_both=phselfcal(vis,mycell,mynterms,myimsize,mythreshold,ref_ant,my_dir,target,\
obsDate,band,'n',outlierfile,multiscale,robust,weighting)
fluxbb_sc,errbb_sc,unitbb_sc,freqbb_sc,errbb_real_sc=imfit_point(scim_both,my_dir)
print 'Combined base-band flux density post selfcal of ',fluxbb_sc,' +/- ',errbb_sc, unitbb_sc
print 'Local RMS in Combined base-band image post selfcal is: ',errbb_real_sc,' Jy'
if 'S' in bandsIM:
spw_presc=[]
spw_postsc=[]
print 'Imaging base-band spws separetly...'
for j in range(0,len(science_spw)):
print 'Imaging spw: ',j
vis=my_dir+'data_'+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'_spw'+str(j)+'_calibrated.ms'
if mymask=='':
print 'Using interactive mode so you can make a mask...'
print 'Cleaning...'
os.system('rm -rf '+my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'_spw'+str(j)+'im*')
tclean(vis=vis,imagename=my_dir+target+'_'+obsDate+'_'+band+'_TID'+target+'_spw'+str(j)+'im',\
specmode='mfs',gridder='standard',imsize=myimsize,cell=mycell,spw='',deconvolver=decon,\
gain=0.1,weighting=weighting,robust=robust,nterms=mynterms, mask='',\
interactive=True,threshold=mythreshold,niter=myniter,pbcor=False,scales=multiscale)
raw_input('Please press enter to continue when you are done.')
else:
print 'Cleaning...'
print 'This make take awhile, please go do something else for a while.'
os.system('rm -rf '+my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'_spw'+str(j)+'im*')
tclean(vis=vis,imagename=my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'_spw'+str(j)+'im',\
mode='mfs',gridder='standard',imsize=myimsize,cell=mycell,spw='',deconvolver=decon,\
gain=0.1,weighting=weighting,robust=robust,nterms=mynterms, mask=mymask,\
interactive=False,threshold=mythreshold,niter=myniter,pbcor=False,scales=multiscale)
raw_input('Please press enter to continue when you are done.')
os.system('rm -rf '+my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'_spw'+str(j)+'im.image.pbcor')
os.system('rm -rf '+my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'_spw'+str(j)+'im.image.pbcor.fits')
if int(mynterms) > 1 and decon=='mtmfs':
os.system('rm -rf '+my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'_spw'+str(j)+'im.image')
os.system('rm -rf '+my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'_spw'+str(j)+'im.pb')
os.system('mv '+my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'_spw'+str(j)+'im.image.tt0 '+my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'_spw'+str(j)+'im.image')
os.system('mv '+my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'_spw'+str(j)+'im.pb.tt0 '+my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'_spw'+str(j)+'im.pb')
immath(imagename=[my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+\
'_spw'+str(j)+'im.image',my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'_spw'+str(j)+'im.pb'],\
expr='IM0/IM1',outfile=my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'_spw'+str(j)+'im.image.pbcor')
exportfits(imagename=my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'_spw'+str(j)+'im.image.pbcor',\
fitsimage=my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'_spw'+str(j)+'im.image.pbcor.fits')
imagens=my_dir+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'_spw'+str(j)+'im.image.pbcor'
fluxs,errs,units,freqs,errs_real=imfit_point(imagens,my_dir,'I')
print 'Spw ', j,' flux density of ',fluxs,' +/- ',errs, units
print 'Local RMS in image is: ',errs_real,' Jy'
spw_presc.append([freqs,fluxs,errs,units,errs_real])
dopscs=raw_input('Do you want to do phase selfcal?y or n-->')
dict_log.append(('selfcal spws',dopscs))
if dopscs=='y':
selfcal_s,scim_s=phselfcal(vis,mycell,mynterms,myimsize,mythreshold,ref_ant,my_dir,target,\
obsDate,band,'n',outlierfile,multiscale,robust,weighting)
fluxs_sc,errs_sc,units_sc,freqs_sc,errs_real_sc=imfit_point(scim_s,my_dir)
print 'Combined base-band flux density post selfcal of ',fluxs_sc,' +/- ',errs_sc, units_sc
print 'Local RMS in Combined base-band image post selfcal is: ',errs_real_sc,' Jy'
spw_postsc.append([freqs_sc,fluxs_sc,errs_sc,units_sc,errs_real_sc])
#writing imfit result to file
print 'Writing imfit results to file...'
if iii==0:
resul_file=open(my_dir+'imfit_results'+'_'+band+'.txt','w')
resul_file.write('#freq flux err unit err_real\n')
else:
resul_file=open(my_dir+'imfit_results.txt','a')
if 'A' in bandsIM:
if dopscbb=='n':
resul_file.write('Target'+str(target_id[iii])+':\n')
resul_file.write('{0} {1} {2} {3} {4}\n'.format(freqbb,fluxbb,errbb,unitbb,errbb_real))
else:
resul_file.write('Target'+str(target_id[iii])+':\n')
resul_file.write('Pre-selfcal:\n')
resul_file.write('{0} {1} {2} {3} {4}\n'.format(freqbb,fluxbb,errbb,unitbb,errbb_real))
resul_file.write('Post selfcal:\n')
resul_file.write('{0} {1} {2} {3} {4}\n'.format(freqbb_sc,fluxbb_sc,errbb_sc,unitbb_sc,errbb_real_sc))
if 'S' in bandsIM:
for kk in range(0,len(science_spw)):
if dopscs=='n':
vals=spw_presc[kk]
resul_file.write('Target'+str(target_id[iii])+' SPW'+str(kk)+':\n')
resul_file.write('{0} {1} {2} {3} {4}\n'.format(vals[0],vals[1],vals[2],vals[3],vals[4]))
else:
resul_file.write('Target'+str(target_id[iii])+' SPW'+str(kk)+':\n')
resul_file.write('Pre-selfcal:\n')
vals=spw_presc[kk]
resul_file.write('{0} {1} {2} {3} {4}\n'.format(vals[0],vals[1],vals[2],vals[3],vals[4]))
resul_file.write('Post selfcal:\n')
vals2=spw_postsc[kk]
resul_file.write('{0} {1} {2} {3} {4}\n'.format(vals2[0],vals2[1],vals2[2],vals2[3],vals2[4]))
resul_file.close()
###########################################
###########################################
#UVfitting
###########################################
if uv_fit=='T':
print 'UV fitting...'
for iii in range(0,len(target_lst)):
print 'Beginnning UV fitting of target id: ', target_lst[iii]
stokes_param=mystokes
vis=my_dir+'data_'+target+'_'+obsDate+'_'+band+'_TID'+target_lst[iii]+'_calibrated.ms'
phcen_rad=vishead(vis=vis,mode='get',hdkey='ptcs')
phcen=au.rad2radec(phcen_rad[0]['r1'][0][0][0],phcen_rad[0]['r1'][1][0][0],hmsdms=True).replace(',','')
if uv_initp != '':
file_uv0=open(uv_initp)
uv_num=sum(1 for line in file_uv0)-1
file_uv0.close()
initp_array=np.loadtxt(uv_initp)
init_uv=[]
if uv_num==1:
init_uv.extend([initp_array[0],initp_array[1],initp_array[2]])
else:
for jj in range(0,uv_num):
init_uv.extend([initp_array[jj,0],initp_array[jj,1],initp_array[jj,2]])
else:
init_uv=[]
uv_num=1
comp_uv=[]
var_uv=[]
for jj in range(0,uv_num):
comp_uv.append('delta')
var_uv.extend(['p['+str(3*jj)+'],p['+str(3*jj+1)+'],p['+str(3*jj+2)+']'])
#
print 'Combined base-band...'
combboth=vis.strip('.ms')
mstransform(vis=vis, outputvis=combboth+'_mstrans.ms', combinespws=True, spw='',datacolumn='data')
if uv_initp=='':
fitfulluv=uvm.uvmultifit(vis=combboth+'_mstrans.ms', spw='', column = "data",\
uniform=False, model=comp_uv,stokes = stokes_param, var=var_uv, phase_center =phcen,\
outfile = my_dir+'combmodelfit.dat', OneFitPerChannel=False ,\
cov_return=False,finetune=False, method="levenberg")
else:
fitfulluv=uvm.uvmultifit(vis=combboth+'_mstrans.ms', spw='', column = "data",\
uniform=False, model=comp_uv,stokes = stokes_param, var=var_uv, phase_center =phcen,\
outfile = my_dir+'combmodelfit.dat', OneFitPerChannel=False ,p_ini=init_uv,\
cov_return=False,finetune=False, method="levenberg")
src_uv_init=fitfulluv.result['Parameters'][2]
src_uv_err=fitfulluv.result['Uncertainties'][2]
print 'Writing uvfit results to file...'
if iii==0:
resuluv_file=open(my_dir+'uvfit_results'+'_'+band+'.txt','w')
else:
resuluv_file=open(my_dir+'uvfit_results'+'_'+band+'.txt','a')
resuluv_file.write('{0} {1} {2} {3}\n'.format('combined',src_uv_init,src_uv_err))
resuluv_file.close()
###########################################
###########################################
#Obs info
###########################################
print 'Observation INFO:'
#obs dates in MJD
start_d=au.getObservationStartDate(ms_name_final)
endd_d=au.getObservationStopDate(ms_name_final)
start_m=au.dateStringToMJD(start_d)
end_m=au.dateStringToMJD(endd_d)
mjd_err=((end_m-start_m)/2.)
mjd_mid=mjd_err+start_m
dict_log.append(('mjd_mid',mjd_mid))
dict_log.append(('mjd_err',mjd_err))
print 'OBS MJD= ',mjd_mid, '+/- ',mjd_err
raw_input('Please press enter when ready to continue.\n')
#time on src
min_onsrc=au.timeOnSource(ms_name_final)
print 'Time on Target Source: ',min_onsrc['minutes_on_science'],'minutes'
dict_log.append(('min_on_src',min_onsrc['minutes_on_science']))
raw_input('Please press enter when ready to continue.\n')