# This epoch is maser phase-referenced. However, it was found that the four IFs were not aligned properly
# by FRING. This was seen as elongation of all sources in the final ARP 220 image. The elongation was
# tracked down to phase offsets between the IFs. To solve this, an additional round of self/cal on 
# Arp 220 itself is needed at the end to align the IFs.
import os, sys
from AIPS import AIPS
from AIPSTask import AIPSTask as task
from AIPSData import AIPSUVData as UV
from AIPSData import AIPSImage as IM
from Wizardry.AIPSData import AIPSUVData as WUV
import time
import numpy as np
from astropy.io import fits


vlba_antennas = [None, 7, 8, 10, 11, 12, 13, 14,15,16]
#Ant   1 = EF       BX= -2035730.5908 BY=  3903997.9986 BZ=   944870.7061
#Ant   2 = JB       BX= -1527991.6694 BY=  3459180.9208 BZ=  1130925.9470
#Ant   3 = MC       BX= -2267162.8344 BY=  4466383.3831 BZ=   493999.1049
#Ant   4 = NT       BX= -2452185.5784 BY=  5058805.9113 BZ=  -149075.5630
#Ant   5 = TR       BX= -2866742.7368 BY=  3826889.8528 BZ=  1121476.6501
#Ant   6 = WB       BX= -2077498.3049 BY=  3698496.3511 BZ=  1109361.4695
#Ant   7 = SC       BX=  2908567.8905 BY=   258587.7432 BZ= -2022820.5578
#Ant   8 = HN       BX=  1497562.5200 BY=  -404703.4321 BZ=   366745.9437
#Ant   9 = GB       BX=  1716572.8066 BY= -1109936.2377 BZ=   -11830.8348
#Ant  10 = NL       BX=  1171294.0304 BY= -1979534.0004 BZ=   271290.8158
#Ant  11 = FD       BX=  1230186.1187 BY= -3300462.9311 BZ=  -723597.7747
#Ant  12 = LA       BX=   852532.0368 BY= -3276914.6695 BZ=  -246436.3331
#Ant  13 = PT       BX=   814275.7325 BY= -3468372.3518 BZ=  -380148.3819
#Ant  14 = KP       BX=   696519.6907 BY= -3803737.2232 BZ=  -598232.1448
#Ant  15 = OV       BX=    20700.9144 BY= -3966289.1940 BZ=  -116942.8652
#Ant  16 = BR       BX=  -575196.8162 BY= -3390937.5591 BZ=   771253.5045
#Ant  17 = AR       BX=  2894296.7903 BY=    28545.4381 BZ= -1960839.6861

# Note regarding maser calibration:
# Earth rotation is 0.3km/s. 
# At Lband this means maximum relative difference of the
# antennas of (0.3km/s / speed of light) * 1650MHz=1.65Khz.
# this is nothing compared to the continuum channel width of 250kHz. 
# For finding rates, phases and amps, we do not need CVEL.
# Maser lines are found by inspection in POSSM to be in channel range 13-20.
# This is consistent with theory:
# Rest frame freqs of maser lines are 1665 and 1667 MHz, 
# Redshift translates to -30MHz, so measured is 1635 and 1637 MHz.
# IF1 has LowerEdge at 1634 MHz with 32 channels covering 8MHz. This means that 
# masers are in middle 16 channels 9 to 24. These 16 channels cover
# 4MHz in bandwidth, i.e. from 1634 to 1638 MHz. 
# From possm we see that peak is mostly in channel 17.
masercal_bchan = 17
masercal_echan = 17
masercal_bif = 1
masercal_eif = 1
masercal_nchav = 512



whattodo = {'load_data': False, # ->CL1
            'msort': False,
            'indxr': False,
            'load_tables': False,
            'preflagging': False,
            'copy_JIVE_CL': False, #-> CL2.  ALL ants seem OK.
            'fring_ampcal+ff' : False, #->SN1, CL3
            'bpass_ff': False, # BP 1, ants 1-13. Using FF
            'bpass_ampcal': False, # BP 1, ants 14-17. Using ampcal.
            'image_ff_1': False, 
            'selfcal_ff' : False, # -> SN2, CL4
            'image_ff_2': False, 
            # Make image of J1516+1932 for reference to other epochs. 
            # First need phasecal.
            'selfcal_ampcal' : False, # -> SN3, CL5 # pcal only
            'image_ampcal_1': False, 

            'selfcal_target_maser' : False, # -> SN4, CL6. USING POINT MODEL
            'image_ARP220_maser_1': False,
            'selfcal_target_maser_2' : False, # -> SN5, CL7 Using image model, PHASE ONLY, 1min
            'image_ARP220_maser_2': False,
            'selfcal_target_maser_3' : False, # -> SN6, CL8. AMP + PHASE. Using model 2, 5min.
            'apply_maser_ampcal': False,
            'image_ARP220_maser_3': False,
            'split': False,
            'fixwt': False,
            'multi': False,

            'calculate_shifts': True, # Calculate shifts for Arp220 imaging. MUST be enabled to set variables used by imaging.
            'flag_maser': True,
            'image_ARP220': True, # For phase selfcal, to bring IFs in sync
            'selfcal_arp220': True, # ->SN1, CL2
            'image_ARP220_V': True,
            ######
            'image_ARP220_final': True,
            'export_results': True,
            }

########## Initialize observation data ##########
AIPS.userno = 1000
clint = 1.0/60 # Seconds
NAME = '021A_L'
TABNAME = NAME
CLASS = 'UVDATA'
WTCLASS = 'WTMAX'
MCLASS = NAME
sorted_class = 'MSORT'
TABCLASS = 'TAB'
DISK = 1
AMPCALIM = NAME + '_AC'
FFCALIM = NAME + '_FC'
PCALIM = NAME + '_PC'
TCALIM = NAME + '_TC'
TCALIM2 = TCALIM + '2'
OUTPREFIX = NAME
target = 'ARP220'
ampcal = '1516+193'
ff = '1613+341'
uvrange = [None, 5000, 0]
logfile = 'log_'+OUTPREFIX+'_PTred.log'
refant = 10
#########^^^ END OF CONFIG VARIABLES ^^^################
tic = time.time()
########## Initialize Log file ##########
try:
 os.system('cp ' + logfile + ' ' + logfile + '.old')
 os.system('rm -f ' + logfile)
except:
 pass
AIPS.log = open(logfile, 'a')
AIPS.log.write('whattodo = '+repr(whattodo)+'\n')

########## LOAD DATA ##########
if whattodo['load_data']:
    fitld = task('fitld')
    fitld.default()
    outdata = UV(NAME, CLASS, DISK, 1)
    fitld.datain = '/data1/eskil/RAWDATA/GD021A/gd021a_2_1.IDI1'
    fitld.outdata = outdata
    fitld.ncount = 3
    fitld.digicor = -1 # Not for JIVE
    fitld.clint = clint
    fitld.wtthresh = 0.3
    fitld.doconcat = 1
    fitld.douvcomp = -1
    if outdata.exists():
        print 'WARNING: Removing existing file ' + NAME + '.' + CLASS
        outdata.zap()
        print '         File removed. Proceeding with FITLD...'
    fitld.go()

if whattodo['msort']:
    msort = task('msort')
    data = UV(NAME, CLASS, DISK, 1)
    outdata = UV(NAME, sorted_class, DISK, 1)
    msort.default()
    msort.indata = data
    msort.outdata = outdata
    msort.sort = 'TB'
    if outdata.exists():
        print 'WARNING: Removing existing file ' + NAME + '.' + sorted_class
        outdata.zap()
        print '         File removed. Proceeding...'
    msort.go()
    if data.exists():
        print 'WARNING: Removing existing file ' + NAME + '.' + CLASS
        data.zap()
        print '         File removed. Proceeding...'

if whattodo['indxr']:
    indxr = task('indxr')
    indxr.default()
    data = UV(NAME, sorted_class, DISK, 1)
    indxr.indata = data
    indxr.cparm[3] = clint
    indxr.go()

######### LOAD CAL TABLES ########
if whattodo['load_tables']:
    fitld = task('fitld')
    fitld.default()
    outdata = UV(TABNAME, TABCLASS, DISK, 1)
    fitld.datain = '/data1/eskil/RAWDATA/GD021A/pipeline/gd021a_2.tasav.FITS'
    fitld.outdata = outdata
    fitld.ncount = 1
    if outdata.exists():
        print 'WARNING: Removing existing file ' + TABNAME + '.' + TABCLASS
        outdata.zap()
        print '         File removed. Proceeding with FITLD...'
    fitld.go()

########## PREFLAGGING ##########
#Flag data known to be bad (whole antennas etc.)
if whattodo['preflagging']:
    data = UV(NAME, sorted_class, DISK, 1)
    infgver = 1
    outfgver = 2
    # Remove all FG tables higher than infgver.
    for i in range(data.table_highver('FG'), infgver, -1):
     data.zap_table('FG', i)
    data = UV(NAME, sorted_class, DISK, 1)
    # Copy flag table 1 to flagtable 2
    tacop = task('tacop')
    tacop.default()
    tacop.indata = data
    tacop.inext = 'FG'
    tacop.inver = infgver
    tacop.ncount = 1
    tacop.outdata = data
    tacop.outvers = outfgver
    tacop.go()
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.timeran = [None, 1, 4, 25, 0, 1, 4, 28, 0]
    uvflg.sour = [None, ff]
    uvflg.opcode = 'FLAG'
    uvflg.go()
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antenna = [None, 1, 2,5]
    uvflg.timeran = [None, 1, 4, 0, 0, 1, 5, 0, 0]
    uvflg.sour = [None, ff]
    uvflg.opcode = 'FLAG'
    uvflg.go()
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antenna = [None, 12]
    uvflg.timeran = [None, 1, 8, 0, 0, 1, 8, 20, 30]
    uvflg.sour = [None, ff]
    uvflg.opcode = 'FLAG'
    uvflg.go()
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antenna = [None, 1]
    uvflg.timeran = [None, 0, 19, 43, 0, 0, 19, 50, 0]
    uvflg.bif = 3
    uvflg.eif = 3
    uvflg.sour = [None, ff]
    uvflg.opcode = 'FLAG'
    uvflg.go()
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antenna = [None, 6]
    uvflg.timeran = [None, 0, 0, 0, 0, 0, 21, 0, 0]
    uvflg.bif = 2
    uvflg.eif = 4
    uvflg.sour = [None, ff]
    uvflg.opcode = 'FLAG'
    uvflg.go()
    
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.timeran = [None, 1, 12, 0, 0, 1, 12, 7, 0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
    
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.antenna = [None, 1]
    uvflg.outfgver = outfgver
    uvflg.timeran = [None, 0, 17, 0, 0, 0, 17, 24, 0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
    
    # Quack
    quack = task('quack')
    quack.default()
    quack.indata = data
    quack.antenna = [None, 11, 16]
    quack.opcode = 'BEG'
    quack.aparm[2] = 20.0/60
    quack.timeran = [None, 1, 10, 0, 0, 2, 0, 0, 0]
    quack.go()
    
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.reason = 'ampspike'
    uvflg.opcode = 'FLAG'
    uvflg.timeran = [None, 1, 3, 25, 0, 1, 3, 30, 0]
    uvflg.go()
    
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.reason = 'ampspike'
    uvflg.opcode = 'FLAG'
    uvflg.timeran = [None, 1, 4, 30, 0, 1, 4, 32, 0]
    uvflg.go()
    
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.bchan = 1
    uvflg.echan = 3
    uvflg.reason = 'EDGE'
    uvflg.opcode = 'FLAG'
    uvflg.go()
    
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.bchan = 30
    uvflg.echan = 32
    uvflg.reason = 'EDGE'
    uvflg.opcode = 'FLAG'
    uvflg.go()
    
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.reason = 'ampspike'
    uvflg.opcode = 'FLAG'
    uvflg.sour = [None, ff]
    uvflg.antenna = [None, 1]
    uvflg.timeran = [None, 0, 0, 0, 0, 0, 16, 0, 0]
    uvflg.go()
    
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.opcode = 'FLAG'
    uvflg.sour = [None, target]
    uvflg.antenna = [None, 1]
    uvflg.timeran = [None, 1, 4, 0, 0, 1, 4, 30, 0]
    uvflg.go()
    
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.opcode = 'FLAG'
    uvflg.sour = [None, target]
    uvflg.antenna = [None, 2]
    uvflg.timeran = [None, 1, 3, 50, 0, 1, 4, 10, 0]
    uvflg.go()
    
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.opcode = 'FLAG'
    uvflg.sour = [None, target]
    uvflg.antenna = [None, 5,2]
    uvflg.timeran = [None, 1, 4, 0, 0, 1, 6, 0, 0]
    uvflg.go()
    
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.opcode = 'FLAG'
    uvflg.sour = [None, target]
    uvflg.antenna = [None, 9]
    uvflg.timeran = [None, 0, 0, 0, 0, 1, 1, 0, 0]
    uvflg.go()
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.opcode = 'FLAG'
    uvflg.sour = [None, target]
    uvflg.timeran = [None, 1, 3, 48, 0, 1, 3, 49, 0]
    uvflg.go()

########## Use a priori Amp Cal an Parallactic angle correction from Jive ##########
# => CL2
if whattodo['copy_JIVE_CL']:
    indata = UV(TABNAME, TABCLASS, DISK, 1)
    outdata = UV(NAME, sorted_class, DISK, 1)
    cloutver = 2
    # Remove all CL tables higher than version cloutver-1.
    for i in range(outdata.table_highver('CL'), cloutver-1, -1):
        outdata.zap_table('CL', i)
    tacop = task('tacop')
    tacop.default()
    tacop.indata = indata
    tacop.outdata = outdata
    tacop.inext = 'CL'
    tacop.inver = 2
    tacop.ncount = 1
    tacop.outver = cloutver
    tacop.go()

if whattodo['fring_ampcal+ff']:
    clinver = 2
    cloutver = 3
    snoutver = 1
    data = UV(NAME, sorted_class, DISK, 1)
    # Remove all SN tables higher than version snoutver-1.
    for i in range(data.table_highver('SN'), snoutver-1, -1):
        data.zap_table('SN', i)
    data = UV(NAME, sorted_class, DISK, 1)
    fring=task('fring')
    fring.default()
    fring.indata = data
    fring.docalib = 1
    fring.gainuse = clinver
    fring.calsour = [None, ff, ampcal]
    fring.refant = refant
    fring.solint = 0.5
    fring.snver = snoutver
    fring.uvrange = uvrange
    fring.dparm[9] = 1 # Do not fit rate
    fring.go()

    # Apply SN-table
    data = UV(NAME, sorted_class, DISK, 1)
    # Remove all CL tables higher than version cloutver-1.
    for i in range(data.table_highver('CL'), cloutver-1, -1):
        data.zap_table('CL', i)
    data = UV(NAME, sorted_class, DISK, 1)
    # Make CL table
    clcal = task('clcal') 
    clcal.default()
    clcal.indata = data
    clcal.snver = snoutver
    clcal.invers = snoutver
    clcal.calsour = [None, ff, ampcal]
    clcal.sour = [None, ''] # All sources
    clcal.gainver = clinver
    clcal.gainuse = cloutver
    clcal.refant = refant
    clcal.go()

if whattodo['bpass_ff']:
    clinver = 3
    bpoutver = 1
    data = UV(NAME, sorted_class, DISK, 1)
    # Remove all BP tables higher than version bpoutver-1.
    for i in range(data.table_highver('BP'), bpoutver-1, -1):
        data.zap_table('BP', i)
    data = UV(NAME, sorted_class, DISK, 1)
    bpass = task('bpass')
    bpass.default()
    bpass.indata = data
    bpass.calsour = [None,ff]
    bpass.gainuse = clinver
    bpass.docal = 1
    bpass.refant = 1
    bpass.solint = -1 # Whole timerange
    bpass.timeran = [None, 0, 23, 50, 0, 1, 10, 0, 0]
    bpass.flagver = 0
    bpass.outvers = bpoutver
    bpass.doband = -1
    bpass.bpassprm[10]=1 # Normalize amps using all channels
    #bpass.antennas = [None, 1,2,3,4,5,6,7,8,9,10,11,12,13]
    bpass.antennas = [None, -14,-15,-16,-17]
    bpass.go()

if whattodo['bpass_ampcal']:
    clinver = 3
    bpoutver = 1
    data = UV(NAME, sorted_class, DISK, 1)
    bpass = task('bpass')
    bpass.default()
    bpass.indata = data
    bpass.calsour = [None,ampcal]
    bpass.gainuse = clinver
    bpass.docal = 1
    bpass.refant = 1
    bpass.solint = 10 # Whole timerange
    bpass.timeran = [None, 1, 3, 0, 0, 1, 3, 30, 0]
    bpass.flagver = 0
    bpass.outvers = bpoutver
    bpass.doband = -1
    bpass.bpassprm[10]=1 # Normalize amps using all channels
    bpass.bpassprm[1]=1 # Use autocorrdata. Fails with cross corr for some reason for these antennas.
    bpass.antennas = [None, 14,15,16,17]
    bpass.go()

if whattodo['image_ff_1']:
    clinver = 3
    imagename = FFCALIM + '1'
    imagedisk = 1
    imageseq = 1
    data = UV(NAME, sorted_class, DISK, 1)
    imagr = task('imagr')
    imagr.default()
    imagr.indata = data
    imagr.sources = [None, ff]
    imagr.gainuse = clinver
    imagr.flagver = 0
    imagr.nchav = 512
    imagr.stokes = 'I'
    imagr.cellsize = [None, 0.4e-3, 0.4e-3]
    imagr.imsize = [None, 1024, 1024]
    imagr.docalib = 1
    imagr.dotv = -1
    imagr.outname = imagename
    imagr.outdisk = imagedisk
    imagr.outseq = imageseq
    imagr.niter = 100
    imagr.doband = 1
    imagr.bpver = 1
    if imagr.niter == 0:
        imageclass = 'IIM001'
    else:
        imageclass = 'ICL001'
    # Remove previous old image
    image = IM(imagename, imageclass, imagedisk, imageseq)
    if image.exists():
     image.zap()
    # Also remove old beam image
    image = IM(imagename, 'IBM001', imagedisk, imageseq)
    if image.exists():
     image.zap()
    imagr.robust = 0.5
    imagr.uvrange = uvrange
    imagr.go()


if whattodo['selfcal_ff']:
    clinver = 3
    cloutver = 4
    snoutver = 2
    data = UV(NAME, sorted_class, DISK, 1)
    # Remove all SN tables higher than version snoutver-1.
    for i in range(data.table_highver('SN'), snoutver-1, -1):
        data.zap_table('SN', i)
    data = UV(NAME, sorted_class, DISK, 1)
    calib = task('calib')
    calib.default()
    calib.indata = data
    calib.in2data = IM(FFCALIM + '1', 'ICL001', 1, 1)
    calib.calsour = [None, ff]
    calib.refant = refant
    calib.docalib = 1
    calib.gainuse = clinver
    calib.flagver = 0
    calib.snver = snoutver
    calib.solmode = 'A&P'
    calib.solint = 5 # 
    calib.aparm[7] = 5 # SNR
    calib.cmethod = 'DFT'
    calib.aparm[1] = 4 # Min no antenna
    calib.aparm[6] = 1 # Print level
    calib.weightit = 1
    calib.doband = 1
    calib.bpver = 1
    calib.uvrange = uvrange
    calib.timeran = [None, 0, 22, 0, 0, 2, 0, 0, 0] # Skip initial EVN timerange with many failed sols
    calib.go()
    # Apply SN-table
    data = UV(NAME, sorted_class, DISK, 1)
    # Remove all CL tables higher than version cloutver-1.
    for i in range(data.table_highver('CL'), cloutver-1, -1):
        data.zap_table('CL', i)
    data = UV(NAME, sorted_class, DISK, 1)
    # Make CL table
    clcal = task('clcal') 
    clcal.default()
    clcal.indata = data
    clcal.snver = snoutver
    clcal.invers = snoutver
    clcal.calsour = [None, ff] # Use sols from Ampcal 
    clcal.sour = [None, ''] # Apply to all sources
    clcal.gainver = clinver
    clcal.gainuse = cloutver
    clcal.refant = refant
    clcal.go()

if whattodo['image_ff_2']:
    clinver = 4
    imagename = FFCALIM+'2'
    imagedisk = 1
    imageseq = 1
    data = UV(NAME, sorted_class, DISK, 1)
    imagr = task('imagr')
    imagr.default()
    imagr.indata = data
    imagr.sources = [None, ff]
    imagr.gainuse = clinver
    imagr.flagver = 0
    imagr.nchav = 512
    imagr.stokes = 'I'
    imagr.cellsize = [None, 0.4e-3, 0.4e-3]
    imagr.imsize = [None, 1024, 1024]
    imagr.docalib = 1
    imagr.dotv = -1
    imagr.doband = 1
    imagr.bpver = 1
    imagr.outname = imagename
    imagr.outdisk = imagedisk
    imagr.outseq = imageseq
    imagr.niter = 100
    if imagr.niter == 0:
        imageclass = 'IIM001'
    else:
        imageclass = 'ICL001'
    # Remove previous old image
    image = IM(imagename, imageclass, imagedisk, imageseq)
    if image.exists():
     image.zap()
    # Also remove old beam image
    image = IM(imagename, 'IBM001', imagedisk, imageseq)
    if image.exists():
     image.zap()
    imagr.robust = 0.5
    imagr.uvrange = uvrange
    imagr.go()


if whattodo['selfcal_ampcal']:
    clinver = 4
    cloutver = 5
    snoutver = 3
    data = UV(NAME, sorted_class, DISK, 1)
    # Remove all SN tables higher than version snoutver-1.
    for i in range(data.table_highver('SN'), snoutver-1, -1):
        data.zap_table('SN', i)
    data = UV(NAME, sorted_class, DISK, 1)
    calib = task('calib')
    calib.default()
    calib.indata = data
    calib.calsour = [None, ampcal]
    calib.refant = refant
    calib.docalib = 1
    calib.gainuse = clinver
    calib.flagver = 0
    calib.snver = snoutver
    calib.solmode = 'P'
    calib.solint = 5 # 
    calib.aparm[1] = 3 # Min no antennas
    calib.aparm[7] = 5 # SNR
    calib.cmethod = 'DFT'
    calib.aparm[6] = 1 # Print level
    calib.weightit = 1
    calib.doband = 1
    calib.bpver = 1
    calib.uvrange = uvrange
    calib.go()
    # Apply SN-table
    data = UV(NAME, sorted_class, DISK, 1)
    # Remove all CL tables higher than version cloutver-1.
    for i in range(data.table_highver('CL'), cloutver-1, -1):
        data.zap_table('CL', i)
    data = UV(NAME, sorted_class, DISK, 1)
    # Make CL table
    clcal = task('clcal') 
    clcal.default()
    clcal.indata = data
    clcal.snver = snoutver
    clcal.invers = snoutver
    clcal.calsour = [None, ampcal] # Use sols from Ampcal 
    clcal.sour = [None, ampcal] # Apply to all sources
    clcal.gainver = clinver
    clcal.gainuse = cloutver
    clcal.refant = refant
    clcal.go()

if whattodo['image_ampcal_1']:
    clinver = 5
    imagename = AMPCALIM+'1'
    imagedisk = 1
    imageseq = 1
    data = UV(NAME, sorted_class, DISK, 1)
    imagr = task('imagr')
    imagr.default()
    imagr.indata = data
    imagr.sources = [None, ampcal]
    imagr.gainuse = clinver
    imagr.flagver = 0
    imagr.nchav = 512
    imagr.stokes = 'I'
    imagr.cellsize = [None, 0.4e-3, 0.4e-3]
    imagr.imsize = [None, 1024, 1024]
    imagr.docalib = 1
    imagr.dotv = -1
    imagr.doband = 1
    imagr.bpver = 1
    imagr.outname = imagename
    imagr.outdisk = imagedisk
    imagr.outseq = imageseq
    imagr.niter = 300
    imagr.uvran = uvrange
    if imagr.niter == 0:
        imageclass = 'IIM001'
    else:
        imageclass = 'ICL001'
    # Remove previous old image
    image = IM(imagename, imageclass, imagedisk, imageseq)
    if image.exists():
     image.zap()
    # Also remove old beam image
    image = IM(imagename, 'IBM001', imagedisk, imageseq)
    if image.exists():
     image.zap()
    imagr.robust = 0.5
    imagr.go()

if whattodo['selfcal_target_maser']:
    clinver = 5
    cloutver = 6
    snoutver = 4
    bpinver = 1

    data = UV(NAME, sorted_class, DISK, 1)
    # Remove all SN tables higher than version snoutver-1.
    for i in range(data.table_highver('SN'), snoutver-1, -1):
        data.zap_table('SN', i)
        print "Deleting SN "+str(i)
    data = UV(NAME, sorted_class, DISK, 1)
    calib = task('calib')
    calib.default()
    calib.indata = data
    calib.calsour = [None, target]
    calib.refant = refant
    calib.docalib = 1
    calib.gainuse = clinver
    calib.doband = 1
    calib.bpver = bpinver
    calib.snver = snoutver
    calib.ichansel[1] = [None, masercal_bchan, masercal_echan, 1, masercal_bif]
    calib.solmode = 'P'
    calib.soltype = 'L1R'
    calib.weightit = 1
    calib.solint = 1
    calib.aparm[1] = 3 # Min no of antennas
    calib.aparm[7] = 1 # SNR
    calib.aparm[3] = 1 # AVG RR,LL, 
    calib.aparm[6] = 3 # Print level
    calib.uvrange = uvrange
    calib.go()

    # replace if 2-4 sols with if1
    sncor = task('sncor')
    sncor.indata = data
    sncor.opcode = 'CPSN'
    sncor.sncorprm[1] = 1 # maser IF
    sncor.bif = 2
    sncor.eif = 4
    sncor.snver = snoutver
    sncor.go()
    
    # Apply SN-table
    data = UV(NAME, sorted_class, DISK, 1)
    # Remove all CL tables higher than version cloutver-1.
    for i in range(data.table_highver('CL'), cloutver-1, -1):
        data.zap_table('CL', i)
    data = UV(NAME, sorted_class, DISK, 1)
    # Make CL table
    clcal = task('clcal') 
    clcal.default()
    clcal.indata = data
    clcal.snver = snoutver
    clcal.invers = snoutver
    clcal.calsour = [None, target]
    clcal.sour = [None, target]
    clcal.gainver = clinver
    clcal.gainuse = cloutver
    clcal.refant = refant
    clcal.opcode = 'CALP'
    clcal.go()

if whattodo['image_ARP220_maser_1']:
    arpfilename = NAME + 'MAS1'
    arpfiledisk = 1
    arpfileseq = 1
    arpfileclass = 'ICL001'
    bpinver = 1
    clinver = 6
    # FIRST CLEAN WITH SMALL BOXES
    # Remove previous old images
    image = IM(arpfilename, arpfileclass, arpfiledisk, arpfileseq)
    if image.exists():
        image.zap()
    # Also remove old beam images
    image = IM(arpfilename, 'IBM001', arpfiledisk, arpfileseq)
    if image.exists():
        image.zap()
    data = UV(NAME, sorted_class, DISK, 1)
    imagr = task('imagr')
    imagr.default()
    imagr.indata = data
    imagr.sources = [None, target]
    imagr.im2parm = [None, 1, 5.0, 10.0, 0] # Require island to have 
                                           # SNR 5 and peak SNR10.
    imagr.gainuse = clinver
    imagr.flagver = 0
    imagr.doband = 1
    imagr.bpver = bpinver
    imagr.nchav = masercal_nchav
    imagr.stokes = 'I'
    imagr.nfield = 1
    imagr.docalib = 1
    imagr.dotv = -1
    imagr.uvrange = uvrange
    imagr.outname = arpfilename
    imagr.outdisk = arpfiledisk
    imagr.outseq = arpfileseq
    imagr.niter = 100
    imagr.cellsize = [None, 0.40e-3, 0.40e-3]
    imagr.imsize =[None, 1024,1024]  
    imagr.gain = 0.1
    imagr.bchan = masercal_bchan
    imagr.echan = masercal_echan
    imagr.bif = masercal_bif
    imagr.eif = masercal_eif
    imagr.go()
    # CLEAN WITH LARGE (NO) BOXES
    arpboxfile = ''
    data = UV(NAME, sorted_class, DISK, 1)
    imagr = task('imagr')
    imagr.default()
    imagr.indata = data
    imagr.sources = [None, target]
    imagr.gainuse = clinver
    imagr.flagver = 0
    imagr.doband = 1
    imagr.bpver = bpinver
    imagr.nchav = masercal_nchav
    imagr.stokes = 'I'
    imagr.nfield = 1
    imagr.docalib = 1
    imagr.dotv = -1
    imagr.uvrange = uvrange
    imagr.outname = arpfilename
    imagr.outdisk = arpfiledisk
    imagr.outseq = arpfileseq
    imagr.outver = 1
    imagr.niter = 300
    imagr.cellsize = [None, 0.40e-3, 0.40e-3]
    imagr.imsize =[None, 1024,1024]  
    imagr.gain = 0.1
    imagr.bcomp = [None, 100000, 100000]
    imagr.bchan = masercal_bchan
    imagr.echan = masercal_echan
    imagr.bif = masercal_bif
    imagr.eif = masercal_eif
    imagr.go()

if whattodo['selfcal_target_maser_2']:
    clinver = 6
    cloutver = 7
    bpinver = 1
    snoutver = 5

    data = UV(NAME, sorted_class, DISK, 1)
    # Remove all SN tables higher than version snoutver-1.
    for i in range(data.table_highver('SN'), snoutver-1, -1):
        data.zap_table('SN', i)
        print "Deleting SN "+str(i)
    data = UV(NAME, sorted_class, DISK, 1)
    calib = task('calib')
    calib.default()
    calib.indata = data
    calib.calsour = [None, target]
    calib.refant = refant
    calib.docalib = 1
    calib.gainuse = clinver
    calib.doband = 1
    calib.bpver = bpinver
    calib.snver = snoutver
    calib.ichansel[1] = [None, masercal_bchan, masercal_echan, 1, masercal_bif]
    calib.solmode = 'P'
    calib.soltype = 'L1R'
    calib.weightit = 1
    calib.in2data = IM(NAME + 'MAS1', 'ICL001', 1, 1)
    calib.nmaps = 1
    calib.solint = 1
    calib.aparm[1] = 3 # Min no of antennas
    calib.aparm[7] = 1# SNR
    calib.aparm[3] = 1 # AVG RR,LL, 
    calib.aparm[6] = 1 # Print level
    calib.uvrange = uvrange
    calib.go()
    
    # replace if 2-4 sols with if1
    sncor = task('sncor')
    sncor.indata = data
    sncor.opcode = 'CPSN'
    sncor.sncorprm[1] = 1 # maser IF
    sncor.bif = 2
    sncor.eif = 4
    sncor.snver = snoutver
    sncor.go()
    
    # Apply SN-table
    data = UV(NAME, sorted_class, DISK, 1)
    # Remove all CL tables higher than version cloutver-1.
    for i in range(data.table_highver('CL'), cloutver-1, -1):
        data.zap_table('CL', i)
    data = UV(NAME, sorted_class, DISK, 1)
    # Make CL table
    clcal = task('clcal') 
    clcal.default()
    clcal.indata = data
    clcal.snver = snoutver
    clcal.invers = snoutver
    clcal.calsour = [None, target]
    clcal.sour = [None, target]
    clcal.gainver = clinver
    clcal.gainuse = cloutver
    clcal.refant = refant
    clcal.opcode = 'CALP'
    clcal.go()

if whattodo['image_ARP220_maser_2']:
    arpfilename = NAME + 'MAS2'
    arpfiledisk = 1
    arpfileseq = 1
    arpfileclass = 'ICL001'
    bpinver = 1
    clinver = 7
    # FIRST CLEAN WITH SMALL BOXES
    # Remove previous old images
    image = IM(arpfilename, arpfileclass, arpfiledisk, arpfileseq)
    if image.exists():
        image.zap()
    # Also remove old beam images
    image = IM(arpfilename, 'IBM001', arpfiledisk, arpfileseq)
    if image.exists():
        image.zap()
    data = UV(NAME, sorted_class, DISK, 1)
    imagr = task('imagr')
    imagr.default()
    imagr.indata = data
    imagr.sources = [None, target]
    imagr.im2parm = [None, 1, 5.0, 10.0, 0] # Require island to have 
                                           # SNR 5 and peak SNR10.
    imagr.gainuse = clinver
    imagr.flagver = 0
    imagr.doband = 1
    imagr.bpver = bpinver
    imagr.nchav = masercal_nchav
    imagr.stokes = 'I'
    imagr.nfield = 1
    imagr.docalib = 1
    imagr.dotv = -1
    imagr.uvrange = uvrange
    imagr.outname = arpfilename
    imagr.outdisk = arpfiledisk
    imagr.outseq = arpfileseq
    imagr.niter = 100
    imagr.cellsize = [None, 0.40e-3, 0.40e-3]
    imagr.imsize =[None, 1024,1024]  
    imagr.gain = 0.1
    imagr.bchan = masercal_bchan
    imagr.echan = masercal_echan
    imagr.bif = masercal_bif
    imagr.eif = masercal_eif
    imagr.go()
    # CLEAN WITH LARGE (NO) BOXES
    arpboxfile = ''
    data = UV(NAME, sorted_class, DISK, 1)
    imagr = task('imagr')
    imagr.default()
    imagr.indata = data
    imagr.sources = [None, target]
    imagr.gainuse = clinver
    imagr.flagver = 0
    imagr.doband = 1
    imagr.bpver = bpinver
    imagr.nchav = masercal_nchav
    imagr.stokes = 'I'
    imagr.nfield = 1
    imagr.docalib = 1
    imagr.dotv = -1
    imagr.uvrange = uvrange
    imagr.outname = arpfilename
    imagr.outdisk = arpfiledisk
    imagr.outseq = arpfileseq
    imagr.outver = 1
    imagr.niter = 300
    imagr.cellsize = [None, 0.40e-3, 0.40e-3]
    imagr.imsize =[None, 1024,1024]  
    imagr.gain = 0.1
    imagr.bcomp = [None, 100000, 100000]
    imagr.bchan = masercal_bchan
    imagr.echan = masercal_echan
    imagr.bif = masercal_bif
    imagr.eif = masercal_eif
    imagr.go()

if whattodo['selfcal_target_maser_3']:
    clinver = 7
    bpinver = 1
    snoutver = 6

    data = UV(NAME, sorted_class, DISK, 1)
    # Remove all SN tables higher than version snoutver-1.
    for i in range(data.table_highver('SN'), snoutver-1, -1):
        data.zap_table('SN', i)
        print "Deleting SN "+str(i)
    data = UV(NAME, sorted_class, DISK, 1)
    calib = task('calib')
    calib.default()
    calib.indata = data
    calib.calsour = [None, target]
    calib.refant = refant
    calib.docalib = 1
    calib.gainuse = clinver
    calib.doband = 1
    calib.bpver = bpinver
    calib.snver = snoutver
    calib.ichansel[1] = [None, masercal_bchan, masercal_echan, 1, masercal_bif]
    calib.solmode = 'A&P'
    calib.soltype = 'L1R'
    calib.weightit = 1
    calib.in2data = IM(NAME + 'MAS2', 'ICL001', 1, 1)
    calib.nmaps = 1
    calib.solint = 10
    calib.aparm[1] = 3 # Min no of antennas
    calib.aparm[7] = 2# SNR
    calib.aparm[3] = 1 # AVG RR,LL, 
    calib.aparm[6] = 1 # Print level
    calib.uvrange = uvrange
    calib.go()
    
    # replace if 2-4 sols with if1
    sncor = task('sncor')
    sncor.indata = data
    sncor.opcode = 'CPSN'
    sncor.sncorprm[1] = 1 # maser IF
    sncor.bif = 2
    sncor.eif = 4
    sncor.snver = snoutver
    sncor.go()
    
if whattodo['apply_maser_ampcal']:
    cloutver = 8
    clinver = 7
    sninver = 6
    snoutver = 7
    data = UV(NAME, sorted_class, DISK, 1)
    # Remove all SN tables higher than version snoutver-1.
    for i in range(data.table_highver('SN'), snoutver-1, -1):
        data.zap_table('SN', i)
        print "Deleting SN "+str(i)
    data = UV(NAME, sorted_class, DISK, 1)
    snsmo = task('snsmo')
    snsmo.indata = data
    snsmo.inver = sninver
    snsmo.outver = snoutver
    snsmo.smotype = 'BOTH'
    snsmo.bparm[1] = 2.0 # Smoothing time in hours
    snsmo.bparm[2] = 2.0 # Smoothing time in hours
    snsmo.cparm[1] = 2.0 # MWF filter width in hours
    snsmo.cparm[6] = 1 # Max amp deviation, MWF 
    snsmo.antenna = [None, -17]
    snsmo.go()

    # Apply SN-table
    data = UV(NAME, sorted_class, DISK, 1)
    # Remove all CL tables higher than version cloutver-1.
    for i in range(data.table_highver('CL'), cloutver-1, -1):
        data.zap_table('CL', i)
    data = UV(NAME, sorted_class, DISK, 1)
    # Make CL table
    clcal = task('clcal') 
    clcal.default()
    clcal.indata = data
    clcal.snver = snoutver
    clcal.invers = snoutver
    clcal.calsour = [None, target]
    clcal.sour = [None, target]
    clcal.gainver = clinver
    clcal.gainuse = cloutver
    clcal.refant = refant
    clcal.opcode = 'CALP'
    clcal.go()

if whattodo['image_ARP220_maser_3']:
    arpfilename = NAME + 'MAS3'
    arpfiledisk = 1
    arpfileseq = 1
    arpfileclass = 'ICL001'
    bpinver = 1
    clinver = 8
    # FIRST CLEAN WITH SMALL BOXES
    # Remove previous old images
    image = IM(arpfilename, arpfileclass, arpfiledisk, arpfileseq)
    if image.exists():
        image.zap()
    # Also remove old beam images
    image = IM(arpfilename, 'IBM001', arpfiledisk, arpfileseq)
    if image.exists():
        image.zap()
    data = UV(NAME, sorted_class, DISK, 1)
    imagr = task('imagr')
    imagr.default()
    imagr.indata = data
    imagr.sources = [None, target]
    imagr.im2parm = [None, 1, 5.0, 10.0, 0] # Require island to have 
                                           # SNR 5 and peak SNR10.
    imagr.gainuse = clinver
    imagr.flagver = 0
    imagr.doband = 1
    imagr.bpver = bpinver
    imagr.nchav = masercal_nchav
    imagr.stokes = 'I'
    imagr.nfield = 1
    imagr.docalib = 1
    imagr.dotv = -1
    imagr.uvrange = uvrange
    imagr.outname = arpfilename
    imagr.outdisk = arpfiledisk
    imagr.outseq = arpfileseq
    imagr.niter = 100
    imagr.cellsize = [None, 0.40e-3, 0.40e-3]
    imagr.imsize =[None, 1024,1024]  
    imagr.gain = 0.1
    imagr.bchan = masercal_bchan
    imagr.echan = masercal_echan
    imagr.bif = masercal_bif
    imagr.eif = masercal_eif
    imagr.go()
    # CLEAN WITH LARGE (NO) BOXES
    arpboxfile = ''
    data = UV(NAME, sorted_class, DISK, 1)
    imagr = task('imagr')
    imagr.default()
    imagr.indata = data
    imagr.sources = [None, target]
    imagr.gainuse = clinver
    imagr.flagver = 0
    imagr.doband = 1
    imagr.bpver = bpinver
    imagr.nchav = masercal_nchav
    imagr.stokes = 'I'
    imagr.nfield = 1
    imagr.docalib = 1
    imagr.dotv = -1
    imagr.uvrange = uvrange
    imagr.outname = arpfilename
    imagr.outdisk = arpfiledisk
    imagr.outseq = arpfileseq
    imagr.outver = 1
    imagr.niter = 300
    imagr.cellsize = [None, 0.40e-3, 0.40e-3]
    imagr.imsize =[None, 1024,1024]  
    imagr.gain = 0.1
    imagr.bcomp = [None, 100000, 100000]
    imagr.bchan = masercal_bchan
    imagr.echan = masercal_echan
    imagr.bif = masercal_bif
    imagr.eif = masercal_eif
    imagr.go()

if whattodo['split']:
    clinver = 8
    fginver = 0
    data = UV(NAME, sorted_class, DISK, 1)
    split = task('split')
    split.default()
    split.indata = data
    split.docal = 1
    split.doband = 1
    split.bpver = 1
    split.sour = [None, target]
    split.gainuse =clinver
    split.flagver = fginver
    split.outclass = 'SP'
    tdata = UV(target, split.outclass, 1, 1)
    if tdata.exists():
        tdata.zap()
    split.go()

if whattodo['fixwt']:
    idata = UV(target, 'SP', 1, 1)
    odata = UV(target, 'FIXWT', 1, 1)
    fixwt = task('fixwt')
    fixwt.default()
    fixwt.indata = idata
    fixwt.outdata = odata
    fixwt.solint = 5
    if odata.exists():
        odata.zap()
    fixwt.go()

if whattodo['multi']:
    idata = UV(target, 'FIXWT', 1, 1)
    odata = UV(target, MCLASS, 1, 1)
    multi = task('multi')
    multi.default()
    multi.indata = idata
    multi.outdata = odata
    if odata.exists():
        odata.zap()
    multi.go()
    indxr = task('indxr')
    indxr.default()
    data = UV(target, MCLASS, DISK, 1)
    indxr.indata = data
    indxr.cparm[3] = clint
    indxr.go()

if whattodo['calculate_shifts']:
    # The maser self-calibration align the position to the wrong place, since
    # the maser was supposed to be in the wrong place. We fix this by changing
    # the coordinates of the output FITS images when saving to disk.  But, we
    # need to calculate the shifts from the "wrong" maser position here, to get
    # the images aligned pixelwise.
    # From the phase-referenced epoch BB297A we get the maser peak position as
    # R.A. 15h34m57s.22435
    # Dec. 23d30'11''.6644
    # which in decimal degrees, for AIPS, means
    maser_ra_bb297 = (15.0+34.0/60.0+57.22435/3600.0)*360.0/24 # degrees
    maser_dec_bb297 = 23+30.0/60.0+11.6644/3600.0 # degrees
    # Self-cal on maser will set the maser position to the source position in
    # the UVFITS header.
    # From AIPS memo 117, the UVFITS coordinates are defined as
    # RAAPP Source apparent equatorial position RA coordinate
    # DECAPP Source apparent equatorial position DEC coordinate
    # RAEPO Source J2000 equatorial position RA coordinate
    # DECPO Source J2000 equatorial position DEC coordinate
    # RAOBS Pointing right ascension of equinox
    # RADEC Pointing declination of equinox

    # We want to compare the RAEPO, DECEPO pair with the maser coordinates.
    # For the phased-referenced epochs, Arp 220 pointing is set between the
    # two nuclei at 15:34:57.2500  23:30:11.330, or in decimal deg
    # from BP129_C header:
    arp220_ra_bb297 = 233.73854166666666287711
    arp220_dec_bb297 = 23.50314722222221419656
    # Relative to these coordinates, we use the shifts 
    arp220_rashifts_bb297 = np.array([0.6, -0.35]) # in arcsec
    arp220_decshifts_bb297 = np.array([0.02, 0.18]) # in arcsec
    # to image the two Arp220 nuclei.
    # What are the corresponding shift for this epoch, i.e.
    # what would be the relative shifts with respect to the maser?

    # First, get the current maser coordinates
    wdata = WUV(NAME, sorted_class, 1, 1)
    sutab = wdata.table('SU',1)
    for row in sutab:
        if 'ARP220' in row.source:
            this_ra = row.raepo
            this_dec = row.decepo
    sutab.close()
    # this_ra, and this_dec are now the coordinates of the maser in this 
    # epoch. 
    # Then, calculate the difference between the actual maser position,
    # not the one in this epoch, and the point between the two nuclei
    #dmas_ra = maser_ra_bb297-this_ra
    #dmas_dec = maser_dec_bb297-this_dec
    dra = arp220_ra_bb297-maser_ra_bb297
    ddec = arp220_dec_bb297-maser_dec_bb297
    # now convert this to arcseconds, to have same unit as IMAGR wants
    # i.e. units of shifts given above
    dra_arcsec = dra*np.cos((np.pi/180.0)*arp220_dec_bb297)*3600 # scale with cos(DEC)
    ddec_arcsec = ddec*3600

    masercal_rashift = arp220_rashifts_bb297 + dra_arcsec
    masercal_decshift = arp220_decshifts_bb297 + ddec_arcsec
    # Convert to right type for imagr
    masercal_rashift = [float(i) for i in masercal_rashift]
    masercal_decshift = [float(i) for i in masercal_decshift]

if whattodo['flag_maser']:
    # FLAG maser for final imaging
    data = UV(target, MCLASS, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = 1
    uvflg.bif = masercal_bif
    uvflg.eif = masercal_eif
    uvflg.reason = 'Away with maser'
    uvflg.opcode = 'FLAG'
    uvflg.bchan = 10
    uvflg.echan = 20
    uvflg.go()

############### IMAGE ARP220 ######################
# Load these outside if to be available also for export later
arpfilename = TCALIM
arpfiledisk = 1
arpfileseq = 1
arpfileclass = 'ICL001'
arpfileclass2 = 'ICL002'
if whattodo['image_ARP220']:
    clinver = 8
    # FIRST CLEAN WITH SMALL BOXES
    # Remove previous old images
    image = IM(arpfilename, arpfileclass, arpfiledisk, arpfileseq)
    if image.exists():
        image.zap()
    image = IM(arpfilename, arpfileclass2, arpfiledisk, arpfileseq)
    if image.exists():
        image.zap()
    # Also remove old beam images
    image = IM(arpfilename, 'IBM001', arpfiledisk, arpfileseq)
    if image.exists():
        image.zap()
    image = IM(arpfilename, 'IBM002', arpfiledisk, arpfileseq)
    if image.exists():
        image.zap()
    data = UV(target, MCLASS, DISK, 1)
    imagr = task('imagr')
    imagr.default()
    imagr.indata = data
    imagr.sources = [None, target]
    imagr.im2parm = [None, 1, 5.0, 10.0, 0] # Require island to have SNR 5 and peak SNR10. To clean (for later removal) of the strongest sources
    imagr.gainuse = clinver
    imagr.flagver = 1 # without maser
    imagr.nchav = 512
    imagr.doband = -1
    imagr.bpver = 1
    imagr.imsize = [None, 1024,512]
    imagr.cellsize = [None, 0.5e-3, 0.5e-3]
    imagr.stokes = 'I'
    imagr.nfield = 2
    imagr.overlap = 1
    imagr.do3dimag = 1
    imagr.rashift = [None,] + masercal_rashift
    imagr.decshift = [None,] + masercal_decshift
    imagr.docalib = -1
    imagr.dotv = -1
    imagr.outname = arpfilename
    imagr.outdisk = arpfiledisk
    imagr.outseq = arpfileseq
    imagr.niter = 50
    imagr.gain = 0.1
    imagr.uvrange = uvrange # remove large-scale disturbances
    imagr.robust = 0.5
    imagr.bif = 1
    imagr.eif = 1
    imagr.go()
    # CLEAN WITH LARGE (NO) BOXES
    arpboxfile = ''
    data = UV(target, MCLASS, DISK, 1)
    imagr = task('imagr')
    imagr.default()
    imagr.indata = data
    imagr.sources = [None, target]
    imagr.gainuse = clinver
    imagr.flagver = 1 # without maser
    imagr.nchav = 512
    imagr.doband = -1
    imagr.bpver = 1
    imagr.imsize = [None, 1024,512]
    imagr.cellsize = [None, 0.5e-3, 0.5e-3]
    imagr.stokes = 'I'
    imagr.nfield = 2
    imagr.overlap = 1
    imagr.do3dimag = 1
    imagr.rashift = [None,] + masercal_rashift
    imagr.decshift = [None,] + masercal_decshift
    imagr.docalib = -1
    imagr.dotv = -1
    imagr.outname = arpfilename
    imagr.outdisk = arpfiledisk
    imagr.outseq = arpfileseq
    imagr.outver = 1
    imagr.niter = 500
    imagr.gain = 0.1
    imagr.bcomp = [None, 100000, 100000]
    imagr.uvrange = uvrange # remove large-scale disturbances
    imagr.robust = 0.5
    imagr.bif = 1
    imagr.eif = 1
    imagr.go()

if whattodo['selfcal_arp220']:
    clinver = 1
    cloutver = 2
    snoutver = 1
    data = UV(target, MCLASS, DISK, 1)
    # Remove all SN tables higher than version snoutver-1.
    for i in range(data.table_highver('SN'), snoutver-1, -1):
        print "WARNING: Deleting SN" + str(i)
        data.zap_table('SN', i)
    data = UV(target, MCLASS, DISK, 1)
    calib = task('calib')
    calib.default()
    calib.indata = data
    # Do not use any model, just a point works fine for phasecal
    calib.in2data = IM(TCALIM, 'ICL001', 1, 1)
    calib.calsour = [None, target]
    calib.nmaps = 2
    calib.refant = refant
    calib.docalib = 1
    calib.gainuse = clinver
    calib.flagver = 0
    calib.snver = snoutver
    calib.solmode = 'P'
    calib.solint = 5 # Longer than scan
    #calib.aparm[1] = 3 # min No. of antennas to include first 45 min.
    calib.aparm[7] = 1 # SNR
    calib.aparm[3] = 1 # AVG RR,LL, 
    calib.aparm[6] = 1 # Print level
    #calib.aparm[5] = 1 # AVG ifs
    calib.cmethod = 'DFT'
    calib.weightit = 1
    calib.soltype = 'L1'
    calib.uvrange = uvrange
    calib.go()
    
    # Apply SN-table
    data = UV(target, MCLASS, DISK, 1)
    # Remove all CL tables higher than version cloutver-1.
    for i in range(data.table_highver('CL'), cloutver-1, -1):
        print "WARNING: Deleting CL" + str(i)
        data.zap_table('CL', i)
    data = UV(target, MCLASS, DISK, 1)
    # Make CL table
    clcal = task('clcal') 
    clcal.default()
    clcal.indata = data
    clcal.snver = snoutver
    clcal.invers = snoutver
    clcal.calsour = [None, target]
    clcal.sour = [None, target] # Apply to target
    clcal.gainver = clinver
    clcal.gainuse = cloutver
    clcal.refant = refant
    clcal.go()

############### IMAGE ARP220 ######################
# Load these outside if to be available also for export later
arpfilename = TCALIM+'V'
arpfiledisk = 1
arpfileseq = 1
arpfileclass = 'VCL001'
arpfileclass2 = 'VCL002'
if whattodo['image_ARP220_V']:
    clinver = 2
    # FIRST CLEAN WITH SMALL BOXES
    # Remove previous old images
    image = IM(arpfilename, arpfileclass, arpfiledisk, arpfileseq)
    if image.exists():
        image.zap()
    image = IM(arpfilename, arpfileclass2, arpfiledisk, arpfileseq)
    if image.exists():
        image.zap()
    # Also remove old beam images
    image = IM(arpfilename, 'VBM001', arpfiledisk, arpfileseq)
    if image.exists():
        image.zap()
    image = IM(arpfilename, 'VBM002', arpfiledisk, arpfileseq)
    if image.exists():
        image.zap()
    # CLEAN WITH LARGE (NO) BOXES
    arpboxfile = ''
    data = UV(target, MCLASS, DISK, 1)
    imagr = task('imagr')
    imagr.default()
    imagr.indata = data
    imagr.sources = [None, target]
    imagr.gainuse = clinver
    imagr.flagver = 0
    imagr.nchav = 512
    imagr.doband = -1
    imagr.bpver = 1
    imagr.imsize = [None, 2048,1024]
    imagr.cellsize = [None, 0.4e-3, 0.4e-3]
    imagr.stokes = 'V'
    imagr.nfield = 2
    imagr.overlap = 1
    imagr.do3dimag = 1
    imagr.rashift = [None,] + masercal_rashift
    imagr.decshift = [None,] + masercal_decshift
    imagr.docalib = 1
    imagr.dotv = -1
    imagr.outname = arpfilename
    imagr.outdisk = arpfiledisk
    imagr.outseq = arpfileseq
    imagr.outver = 1
    imagr.niter = 1
    imagr.gain = 0.1
    imagr.uvrange = uvrange # remove large-scale disturbances
    imagr.robust = 0.5
    imagr.go()


############### IMAGE ARP220 ######################
# Load these outside if to be available also for export later
arpfilename = NAME + '_FIN'
arpfiledisk = 1
arpfileseq = 1
arpfileclass = 'ICL001'
arpfileclass2 = 'ICL002'
if whattodo['image_ARP220_final']:
    clinver = 2
    # FIRST CLEAN WITH SMALL BOXES
    # Remove previous old images
    image = IM(arpfilename, arpfileclass, arpfiledisk, arpfileseq)
    if image.exists():
        image.zap()
    image = IM(arpfilename, arpfileclass2, arpfiledisk, arpfileseq)
    if image.exists():
        image.zap()
    # Also remove old beam images
    image = IM(arpfilename, 'IBM001', arpfiledisk, arpfileseq)
    if image.exists():
        image.zap()
    image = IM(arpfilename, 'IBM002', arpfiledisk, arpfileseq)
    if image.exists():
        image.zap()
    # Clean with latest gainuse
    data = UV(target, MCLASS, DISK, 1)
    imagr = task('imagr')
    imagr.default()
    imagr.indata = data
    imagr.sources = [None, target]
    imagr.im2parm = [None, 1, 5.0, 10.0, 0] # Require island to have SNR 5 and peak SNR10. To clean (for later removal) of the strongest sources
    imagr.gainuse = clinver
    imagr.flagver = 0
    imagr.nchav = 512
    imagr.doband = -1
    imagr.bpver = 1
    imagr.imsize = [None, 8192, 8192]
    imagr.cellsize = [None, 0.1e-3, 0.1e-3]
    imagr.stokes = 'I'
    imagr.nfield = 2
    imagr.overlap = 1
    imagr.do3dimag = 1
    imagr.rashift = [None,] + masercal_rashift
    imagr.decshift = [None,] + masercal_decshift
    imagr.docalib = 1
    imagr.dotv = -1
    imagr.outname = arpfilename
    imagr.outdisk = arpfiledisk
    imagr.outseq = arpfileseq
    imagr.niter = 50
    imagr.gain = 0.1
    imagr.uvrange = uvrange # remove large-scale disturbances
    imagr.robust = 0.5
    imagr.go()
    # CLEAN WITH LARGE (NO) BOXES
    arpboxfile = ''
    data = UV(target, MCLASS, DISK, 1)
    imagr = task('imagr')
    imagr.default()
    imagr.indata = data
    imagr.sources = [None, target]
    imagr.gainuse = clinver
    imagr.flagver = 0
    imagr.nchav = 512
    imagr.doband = -1
    imagr.bpver = 1
    imagr.imsize = [None, 8192, 8192]
    imagr.cellsize = [None, 0.1e-3, 0.1e-3]
    imagr.stokes = 'I'
    imagr.nfield = 2
    imagr.overlap = 1
    imagr.do3dimag = 1
    imagr.rashift = [None,] + masercal_rashift
    imagr.decshift = [None,] + masercal_decshift
    imagr.docalib = 1
    imagr.dotv = -1
    imagr.outname = arpfilename
    imagr.outdisk = arpfiledisk
    imagr.outseq = arpfileseq
    imagr.outver = 1
    imagr.niter = 500
    imagr.gain = 0.1
    imagr.bcomp = [None, 100000, 100000]
    imagr.uvrange = uvrange # remove large-scale disturbances
    imagr.robust = 0.5
    imagr.go()

############### EXPORT RESULTS ######################
if whattodo['export_results']:
    east = IM(arpfilename, arpfileclass, arpfiledisk, arpfileseq)
    west = IM(arpfilename, arpfileclass2, arpfiledisk, arpfileseq)
   
    # Export EAST
    fittp = task('fittp')
    fittp.default()
    fittp.indata = east
    fittp.dataout = 'PWD:'+NAME+'_EAST_IMAGE.FITS'
    if os.path.exists(fittp.dataout[4:]):
     os.system('rm ' + fittp.dataout[4:])
    fittp.go()
    # Change coordinates of file based on BB297A maser reference position
    f = fits.open(NAME+'_EAST_IMAGE.FITS', mode='update')
    hdr = f[0].header
    hdr['CRVAL1'] = arp220_ra_bb297+arp220_rashifts_bb297[0]/(3600.0*np.cos(arp220_dec_bb297*np.pi/180))
    hdr['CRVAL2'] = arp220_dec_bb297+arp220_decshifts_bb297[0]/(3600.0)
    f.flush()
    f.close()

    # Export WEST
    fittp = task('fittp')
    fittp.default()
    fittp.indata = west
    fittp.dataout = 'PWD:'+NAME+'_WEST_IMAGE.FITS'
    if os.path.exists(fittp.dataout[4:]):
     os.system('rm ' + fittp.dataout[4:])
    fittp.go()
    # Change coordinates of file based on BB297A maser reference position
    f = fits.open(NAME+'_WEST_IMAGE.FITS', mode='update')
    hdr = f[0].header
    hdr['CRVAL1'] = arp220_ra_bb297+arp220_rashifts_bb297[1]/(3600.0*np.cos(arp220_dec_bb297*np.pi/180))
    hdr['CRVAL2'] = arp220_dec_bb297+arp220_decshifts_bb297[1]/(3600.0)
    f.flush()
    f.close()
    
    # Export J1516
    fittp = task('fittp')
    fittp.default()
    fittp.indata = IM(AMPCALIM+'1', 'ICL001', 1, 1)
    fittp.dataout = 'PWD:'+NAME+'_J1516_IMAGE.FITS'
    if os.path.exists(fittp.dataout[4:]):
     os.system('rm ' + fittp.dataout[4:])
    fittp.go()
    
    # Export MASER
    masim = IM(NAME+'MAS3', 'ICL001', 1, 1)
    fittp = task('fittp')
    fittp.default()
    fittp.indata = masim
    fittp.dataout = 'PWD:'+NAME+'_MASER_IMAGE.FITS'
    if os.path.exists(fittp.dataout[4:]):
     os.system('rm ' + fittp.dataout[4:])
    fittp.go()
    # Change coordinates of file based on BB297A maser reference position
    f = fits.open(NAME+'_MASER_IMAGE.FITS', mode='update')
    hdr = f[0].header
    hdr['CRVAL1'] = maser_ra_bb297
    hdr['CRVAL2'] = maser_dec_bb297
    f.flush()
    f.close()

tac = time.time()
processtime = tac-tic
print 'OVERALL PROCESS TIME: ',processtime,' SECONDS. or ', processtime/60.0, 'minutes'