import os, sys
from astropy.io import fits
from AIPS import AIPS
from AIPSTask import AIPSTask as task
from AIPSData import AIPSUVData as UV
from Wizardry.AIPSData import AIPSUVData as WUV
from Wizardry.AIPSData import AIPSImage as WIM
from AIPSData import AIPSImage as IM
import time
import numpy as np

# Used for amp selfcal etc. We trust the VLBA.
vlba_antennas = [None, 8, 9, 10, 11, 12, 13, 14, 15, 16]

whattodo = {'load_data': True, # ->CL1
            'load_tables': True,
            'add_AR_to_table': True,
            'preflagging': True,
            'copy_JIVE_CL': True, #-> CL2. 
            # Contains A priori AMP + ones (1s) (in add_AR-step)
            # for AR since ampcal for AR was missing 
            # (no TY, GC etc.), Parr. angle is included also for AR.
            'fring_ampcal' : True, #->SN1
            'bpass_ampcal': True, # BP 1
            'image_ampcal_1': True, 
            'selfcal_ampcal' : True, # -> SN2, CL4
            'image_ampcal_2': True,
            'selfcal_ampcal_2' : True, # -> SN3, CL5 CORRECT AR
            'image_ampcal_3': True,
            'fring_phasecal' : True, #->SN4, CL6
            'image_phasecal_1':True,
            'selfcal_phasecal' : True, # -> SN5,6, CL7
            'clip_phasecal': True, #USE PREFLAGGING AS WELL TO CLEAN FG
            'image_phasecal_2': True, # 
            'image_ARP220': True, # NO AR
            'selfcal_arp220': True, # ->SN7, CL8, NO AR
            'image_ARP220_2': True, # NO AR
            'selfcal_arp220_2': True, # ->SN8, CL9 ONLY AR
            'image_ARP220_final': True,
            'fring_frcal' : True, #->SN9, CL10
            'image_frcal_1': True, 
            'selfcal_frcal' : True, # -> SN10, CL11
            'image_frcal_2': True, 
            'export_results': True,
            }
 
########## Initialize observation data ##########
AIPS.userno = 1000
clint = 15.0/60 # Seconds, same as JIVE table
NAME = 'GC031B_C'
TABNAME = NAME
CLASS = 'UVDATA'
TABCLASS = 'TAB'
DISK = 1
AMPCALIM = NAME + 'AC'
PCALIM = NAME + 'PC'
TCALIM = NAME + 'TC'
TCALIM2 = TCALIM + '2'
FRCALIM = NAME + '_FC'
target = 'ARP220'
ampcal = 'J1516+1932'
phasecal = 'J1532+2344'
frcal = 'J1613+3412'
uvrange = [None, 7000, 0]
sorted_class = CLASS
logfile = 'log_'+NAME+'_PTred.log'
refant = 2
#########^^^ END OF CONFIG VARIABLES ^^^################
tic = time.time()
########## Initialize Log file ##########
try:
 os.system('cp ' + logfile + ' ' + logfile + '.old')
 #os.system('rm -f ' + logfile) # Will append, is good so don't remove.
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/GC031B/gc031b_1_1.IDI1'
    fitld.outdata = outdata
    fitld.ncount = 2
    fitld.digicor = -1
    fitld.clint = clint
    fitld.doconcat = 1
    fitld.wtthresh = 0.3
    if outdata.exists():
        print 'WARNING: Removing existing file ' + NAME + '.' + CLASS
        outdata.zap()
        print '         File removed. Proceeding with FITLD...'
    fitld.go()
######### LOAD CAL TABLES ########
if whattodo['load_tables']:
    fitld = task('fitld')
    fitld.default()
    outdata = UV(TABNAME, TABCLASS, DISK, 1)
    fitld.datain = '/data1/eskil/RAWDATA/GC031B/gc031b.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()

######### AR is missing from pipeline ampcal, no ampcal available. So set it to ones and correct with selfcal. ####
if whattodo['add_AR_to_table']:
    cloutver = 4 # 2 is the one we correct, 3 contains pipeline FRING.
    data = UV(TABNAME, TABCLASS, 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)
    indata = UV(TABNAME, TABCLASS, DISK, 1)
    outdata = UV(TABNAME, TABCLASS, DISK, 1)
    tacop = task('tacop')
    tacop.default()
    tacop.indata = indata
    tacop.outdata = outdata
    tacop.inext = 'CL'
    tacop.inver = 2
    tacop.outver = 4
    tacop.ncount = 1
    tacop.go()
    # Now add ones for antenna AR (17) by copy-paste
    # from CL1 which is naive CL from pipeline with no 
    # corrections.
    wizard_data = WUV(TABNAME, TABCLASS, DISK, 1)
    oldcl = wizard_data.table('CL', 1)
    newcl = wizard_data.table('CL', 4)
    
    #Copy entries of ones for AR to the corrected table.
    for row in oldcl:
        if row.antenna_no == 17: # AR is antenna 17 in this dataset.
            newcl.append(row)
    oldcl.close()
    newcl.close()
   
    # Add parrallactic corrections for AR
    data = UV(TABNAME, TABCLASS, DISK, 1)
    clcor = task('clcor')
    clcor.default()
    clcor.indata = data
    clcor.antenna = [None, 17]
    clcor.gainver = cloutver
    clcor.gainuse = cloutver
    clcor.opcode = 'PANG'
    clcor.clcorprm = [None, 1, 0] 
    if not os.path.exists('./usno_finals.erp'):
     os.system('wget http://gemini.gsfc.nasa.gov/solve_save/usno_finals.erp')
    clcor.infile = 'PWD:usno_finals.erp'
    clcor.go()


########## PREFLAGGING ##########
#Flag data known to be bad (whole antennas etc.)
if whattodo['preflagging']:
    # Copy flag table provided from JIVE
    # This will flag when antennas off source etc.
    indata = UV(TABNAME, TABCLASS, DISK, 1)
    outdata = UV(NAME, sorted_class, DISK, 1)
    # Remove all FG tables
    outdata.zap_table('FG', -1)
    tacop = task('tacop')
    tacop.default()
    tacop.indata = indata
    tacop.outdata = outdata
    tacop.inext = 'FG'
    tacop.inver = 1
    tacop.outver = 1
    tacop.ncount = 1
    tacop.go()
    # Manual additional flagging below:
    infgver = 1
    outfgver = 2
    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()
   #Flag all data for elevations less than 10 deg
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.aparm = [None, -90, 10]
    uvflg.reason = 'el.lt.10deg'
    uvflg.opcode = 'FLAG'
    uvflg.go()
   #Flag antennas known to be bad = Onsala (3)
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antennas = [None, 3]
    uvflg.reason = 'no data'
    uvflg.opcode = 'FLAG'
    uvflg.go()
   #Flag antenna 16 IF since spike in CL2amp
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antennas = [None, 16]
    uvflg.reason = 'AmpSpikeInCL2'
    uvflg.timeran = [None, 0,17,40,0,0,18,0,0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
   #Flag antenna 16 IF since spike in CL2amp
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antennas = [None, 16]
    uvflg.reason = 'AmpSpikeInCL2'
    uvflg.timeran = [None, 0,0,0,0,0,13,50,0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
   #Flag antenna 15 IF since spikes in CL2 amp
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antennas = [None, 15]
    uvflg.reason = 'AmpSpikeInCL2'
    uvflg.timeran = [None, 0,0,0,0,0,15,8,0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
   #Flag antenna 11 IF since spikes in CL2 amp
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antennas = [None, 11]
    uvflg.reason = 'AmpSpikeInCL2'
    uvflg.timeran = [None, 0,0,0,0,0,14,0,0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
   #Flag antenna 14 IF since spikes in CL2 amp
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antennas = [None, 14]
    uvflg.reason = 'AmpSpikeInCL2'
    uvflg.timeran = [None, 0,0,0,0,0,14,20,0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
   #Flag amp spike
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.reason = 'AmpSpike'
    uvflg.timeran = [None, 0, 17, 30, 0, 0, 17, 40, 0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
   #Flag bad delay
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.bif = 4
    uvflg.eif = 4
    uvflg.stokes = 'RR'
    uvflg.antenna = [None, 5]
    uvflg.timeran = [None, 0, 16, 0, 0, 0, 18, 0, 0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
   #Flag
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antenna = [None, 17]
    uvflg.timeran = [None, 0, 16, 54, 0, 0, 16, 56, 0]
    uvflg.opcode = 'FLAG'
    #uvflg.go()
   #Flag
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antenna = [None, 1]
    uvflg.timeran = [None, 0, 18, 50, 0, 0, 18, 55, 0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
   #Flag
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antenna = [None, 1]
    uvflg.timeran = [None, 0, 18, 30, 0, 0, 18, 40, 0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
   #Flag
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antenna = [None, 1,7]
    uvflg.timeran = [None, 0, 13, 22, 0, 0, 13, 30, 0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
   #Flag
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antenna = [None, 1,7]
    uvflg.timeran = [None, 0, 12, 16, 0, 0, 12, 20, 0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
   #Flag
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antenna = [None, 1]
    uvflg.timeran = [None, 0, 15, 15, 0, 0, 15, 20, 0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
   #Flag
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antenna = [None, 1,7]
    uvflg.timeran = [None, 0, 9, 26, 0, 0, 9, 27, 0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
   #Flag
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antenna = [None, 7]
    uvflg.timeran = [None, 0, 8, 10, 0, 0, 8, 15, 0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
   #Flag
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antenna = [None, 17]
    uvflg.timeran = [None, 0, 16, 58, 0, 0, 17, 0, 0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
   #Flag
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antenna = [None, 2]
    uvflg.baselin = [None, 17]
    uvflg.timeran = [None, 0, 18, 50, 0, 0, 18, 55, 0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
   #Flag
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antenna = [None, 1]
    uvflg.timeran = [None, 0, 8, 10, 0, 0, 8, 15, 0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
   #Flag
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antenna = [None, 1,7]
    uvflg.timeran = [None, 0, 10, 8, 0, 0, 10, 10, 0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
   #Flag
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antenna = [None, 7]
    uvflg.timeran = [None, 0, 16, 10, 0, 0, 16, 15, 0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
   #Flag
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antenna = [None, 17]
    uvflg.timeran = [None, 0, 16, 30, 0, 0, 16, 35, 0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
   #Flag
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antenna = [None, 8]
    uvflg.timeran = [None, 0, 15, 30, 0, 0, 16, 0, 0]
    uvflg.opcode = 'FLAG'
    uvflg.sour = [None, ampcal]
    uvflg.go()
    quack = task('quack')
    quack.default()
    quack.antenna = [None, 1,2,7]
    quack.indata = data
    quack.opcode = 'BEG'
    quack.aparm[2] = 4.0/60
    quack.go()
    quack = task('quack')
    quack.default()
    quack.antenna = [None, 1,2,7]
    quack.indata = data
    quack.opcode = 'ENDB'
    quack.aparm[2] = 4.0/60
    quack.go()
   #Flag
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antenna = [None, 17]
    uvflg.timeran = [None, 0, 16, 20, 0, 0, 16, 35, 0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
   #Flag
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antenna = [None, 9]
    uvflg.bif = 3
    uvflg.eif = 3
    uvflg.timeran = [None, 0, 18, 26, 0, 0, 18, 29, 0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
   #Flag
    data = UV(NAME, sorted_class, DISK, 1)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.outfgver = outfgver
    uvflg.antenna = [None, 9]
    uvflg.timeran = [None, 0, 18, 29, 0, 0, 18, 30, 0]
    uvflg.opcode = 'FLAG'
    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 = 4 # Use modified table with AR added as ones. No parang for AR, but short time and can fix in FRING.
    tacop.ncount = 1
    tacop.outver = cloutver
    tacop.go()

#   FRING on AMPCAL
# => SN1
if whattodo['fring_ampcal']:
    clinver = 2
    snoutver = 1
    cloutver = 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)
    fring=task('fring')
    fring.default()
    fring.indata = data
    fring.docalib = 1
    fring.gainuse = clinver
    fring.calsour = [None, ampcal]
    fring.refant = refant
    fring.solint = 5 # Longer than scan
    fring.snver = snoutver
    fring.dparm[2] = 50#ns, delay win
    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, ampcal]
    clcal.sour = [None, ''] # All sources
    clcal.gainver = clinver
    clcal.gainuse = cloutver
    clcal.refant = refant
    clcal.go()

if whattodo['bpass_ampcal']:
    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)
    data = UV(NAME, sorted_class, DISK, 1)
    bpass = task('bpass')
    bpass.default()
    bpass.indata = data
    bpass.calsour = [None,ampcal]
    bpass.timeran = [None, 0] # Use all scans to get all ants
    bpass.gainuse = clinver
    bpass.docal = 1
    bpass.refant = 1
    bpass.solint = -1 # Whole timerange
    bpass.flagver = 0
    bpass.outvers = bpoutver
    bpass.doband = -1
    bpass.bpassprm[10]=1 # Normalize amps using all channels
    bpass.go()
    
if whattodo['image_ampcal_1']:
    clinver = 3
    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 = 32
    imagr.stokes = 'I'
    imagr.cellsize = [None, 0.1e-3, 0.1e-3]
    imagr.imsize = [None, 512,512]
    imagr.docalib = 1
    imagr.dotv = -1
    imagr.outname = imagename
    imagr.outdisk = imagedisk
    imagr.outseq = imageseq
    imagr.niter = 300
    imagr.uvrange = uvrange
    imagr.antennas = vlba_antennas
    imagr.baselin = imagr.antenna
    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.go()

if whattodo['selfcal_ampcal']:
    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)
    # FIT ANTENNA 3, with proper timeran not to flag things
    data = UV(NAME, sorted_class, DISK, 1)
    calib = task('calib')
    calib.default()
    calib.indata = data
    calib.in2data = IM(AMPCALIM + '1', 'ICL001', 1, 1)
    calib.calsour = [None, ampcal]
    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[6] = 1 # Print level
    calib.weightit = 1
    calib.soltype = 'L1R'
    calib.doband = 1
    calib.bpver = 1
    calib.aparm[1] = 4 # Min no antennas
    calib.antenna = [None, -17]
    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, ''] # Apply to all sources
    clcal.gainver = clinver
    clcal.gainuse = cloutver
    clcal.refant = refant
    clcal.go()

if whattodo['image_ampcal_2']:
    clinver = 4
    imagename = AMPCALIM+'2'
    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 = 32
    imagr.stokes = 'I'
    imagr.cellsize = [None, 0.1e-3, 0.1e-3]
    imagr.imsize = [None, 512,512]
    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.uvrange = uvrange
    imagr.antenna = [None, -17]
    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.go()

if whattodo['selfcal_ampcal_2']:
    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.in2data = IM(AMPCALIM+'2', 'ICL001', 1, 1)
    calib.calsour = [None, ampcal]
    calib.refant = refant
    calib.dofit = [None, 17] # Fit ONLY Ar (17)
    calib.docalib = 1
    calib.gainuse = clinver
    calib.flagver = 0
    calib.snver = snoutver
    calib.solmode = 'A&P'
    calib.solint = 5 # Longer than scan
    calib.aparm[7] = 5 # SNR
    #calib.aparm[3] = 1 # AVG RR,LL, 
    calib.aparm[6] = 1 # Print level
    #calib.aparm[5] = 1 # AVG ifs
    calib.aparm[9] = 1 # Needed when fitting AR
    calib.doband = 1
    calib.bpver = 1
    calib.weightit = 1
    calib.uvran = 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, ''] # Apply to all sources
    clcal.gainver = clinver
    clcal.gainuse = cloutver
    clcal.refant = refant
    clcal.go()

if whattodo['image_ampcal_3']:
    clinver = 5
    imagename = AMPCALIM+'3'
    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 = 32
    imagr.stokes = 'I'
    imagr.cellsize = [None, 0.1e-3, 0.1e-3]
    imagr.imsize = [None, 512,512]
    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.uvrange = uvrange
    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.go()

#   FRING on PHASECAL
if whattodo['fring_phasecal']:
    clinver = 5 # With ampcal corrections
    cloutver = 6
    snoutver = 4
    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, phasecal]
    fring.refant = refant
    fring.solint = 3 # Longer than scan
    fring.dparm[2] = 50#ns, delay win, already fitted bulk on ampcal
    fring.dparm[3] = 15#mHz, rate win
    #fring.aparm[3] = 1 # AVG RR,LL
    #fring.aparm[4] = 1 # AVG freqs in IFs
    #fring.aparm[5] = 1 # AVG IFs
    fring.snver = snoutver
    fring.doband = 1
    fring.bpver = 1
    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):
        print "WARNING: Deleting CL" + str(i)
        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, phasecal]
    clcal.sour = [None, phasecal, target]
    clcal.gainver = clinver
    clcal.gainuse = cloutver
    clcal.refant = refant
    clcal.go()

if whattodo['image_phasecal_1']:
    clinver = 6
    imagename = PCALIM + '1'
    imagedisk = 1
    imageseq = 1
    data = UV(NAME, sorted_class, DISK, 1)
    imagr = task('imagr')
    imagr.default()
    imagr.indata = data
    imagr.sources = [None, phasecal]
    imagr.gainuse = clinver
    imagr.flagver = 0
    imagr.nchav = 512
    imagr.stokes = 'I'
    imagr.cellsize = [None, 0.1e-3, 0.1e-3]
    imagr.imsize = [None, 512,512]
    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.uvrang = uvrange
    imagr.antenna = [None, -1, -17]
    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_phasecal']:
    clinver = 6
    cloutver = 7
    snoutver = 5 # and 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):
        print "WARNING: Deleting SN" + str(i)
        data.zap_table('SN', i)
    data = UV(NAME, sorted_class, DISK, 1)
    calib = task('calib')
    calib.default()
    calib.indata = data
    calib.in2data = IM(PCALIM + '1', 'ICL001', 1, 1)
    calib.calsour = [None, phasecal]
    calib.refant = refant
    calib.docalib = 1
    calib.gainuse = clinver
    calib.flagver = 0
    calib.snver = snoutver
    calib.solmode = 'A&P'
    calib.solint = 3 # Longer than scan
    calib.aparm[1] = 4 # Minant
    calib.aparm[7] = 5 # SNR
    #calib.aparm[3] = 1 # AVG RR,LL, 
    calib.aparm[6] = 1 # Print level
    #calib.aparm[5] = 1 # AVG ifs
    calib.weightit = 1
    calib.soltype = 'L1R'
    calib.doband = 1
    calib.bpver = 1
    calib.uvran = uvrange
    calib.go()

    # CLIP solutions
    data = UV(NAME, sorted_class, DISK, 1)
    snsmo = task('snsmo')
    snsmo.default()
    snsmo.indata = data
    snsmo.samptype = 'MWF'
    snsmo.cparm[1] = 2 # hours, clipping time ampl
    snsmo.cparm[6] = 0.2 # Max deviation, ampl
    snsmo.inver = snoutver
    snsmo.outver = snoutver + 1
    snsmo.smotype = 'AMPL' # 
    snsmo.refant = refant
    snsmo.doblank = -1
    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):
        print "WARNING: Deleting CL" + str(i)
        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 + 1
    clcal.invers = snoutver + 1
    clcal.calsour = [None, phasecal]
    clcal.sour = [None, phasecal, target] # Apply to all sources
    clcal.gainver = clinver
    clcal.gainuse = cloutver
    clcal.refant = refant
    clcal.go()

if whattodo['clip_phasecal']:
    outfgver = 2
    data = UV(NAME, sorted_class, DISK, 1)
    clip = task('clip')
    clip.default()
    clip.sour = [None, phasecal, target]
    clip.aparm[1] = 2.0 # Max Jy
    clip.stokes = 'I'
    clip.docal = 1
    clip.flagver = outfgver
    clip.doband = 1
    clip.bpver = 1
    clip.indata = data
    clip.outfgver = outfgver
    clip.go()

if whattodo['image_phasecal_2']:
    clinver = 7
    imagename = PCALIM + '2'
    imagedisk = 1
    imageseq = 1
    data = UV(NAME, sorted_class, DISK, 1)
    imagr = task('imagr')
    imagr.default()
    imagr.indata = data
    imagr.sources = [None, phasecal]
    imagr.gainuse = clinver
    imagr.flagver = 0
    imagr.nchav = 512
    imagr.stokes = 'I'
    imagr.cellsize = [None, 0.1e-3, 0.1e-3]
    imagr.imsize = [None, 512,512]
    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
    #imagr.antenna = [None, -17]
    #imagr.baselin = imagr.antenna
    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()

############### IMAGE ARP220 ######################
# Load these outside if to be available also for export later
arpfilename = TCALIM
arpfiledisk = 1
arpfileseq = 1
arpfileclass = 'ICL001'
arpfileclass2 = 'ICL002'
clinver = 7
if whattodo['image_ARP220']:
    # 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(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. 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, 4096,2048]
    imagr.cellsize = [None, 0.2e-3, 0.2e-3]
    imagr.stokes = 'I'
    imagr.nfield = 2
    imagr.overlap = 1
    imagr.do3dimag = 1
    imagr.rashift = [None, 0.6, -0.35]
    imagr.decshift = [None, 0.02, 0.18]
    imagr.docalib = 1
    imagr.dotv = -1
    imagr.outname = arpfilename
    imagr.outdisk = arpfiledisk
    imagr.outseq = arpfileseq
    imagr.niter = 500
    imagr.gain = 0.1
    imagr.uvrange = uvrange # remove large-scale disturbances
    imagr.robust = 0.5
    imagr.antenna = [None, -17]
    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.nchav = 512
    imagr.doband = 1
    imagr.bpver = 1
    imagr.imsize = [None, 4096,2048]
    imagr.cellsize = [None, 0.2e-3, 0.2e-3]
    imagr.stokes = 'I'
    imagr.nfield = 2
    imagr.overlap = 1
    imagr.do3dimag = 1
    imagr.rashift = [None, 0.6, -0.35]
    imagr.decshift = [None, 0.02, 0.18]
    imagr.docalib = 1
    imagr.dotv = -1
    imagr.outname = arpfilename
    imagr.outdisk = arpfiledisk
    imagr.outseq = arpfileseq
    imagr.outver = 1
    imagr.niter = 1000
    imagr.gain = 0.1
    imagr.bcomp = [None, 100000, 100000]
    imagr.uvrange = uvrange # remove large-scale disturbances
    imagr.robust = 0.5
    imagr.antenna = [None, -17]
    imagr.go()

if whattodo['selfcal_arp220']:
    clinver = 7
    cloutver = 8
    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):
        print "WARNING: Deleting SN" + str(i)
        data.zap_table('SN', i)
    data = UV(NAME, sorted_class, 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 = 10 # Longer than scan
    calib.aparm[1] = 3 # min No. of antennas to include first 45 min.
    calib.aparm[7] = 2 # 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 = 'L1R'
    calib.doband = 1
    calib.bpver = 1
    calib.uvrange = uvrange
    calib.antenna = [None, -17]
    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):
        print "WARNING: Deleting CL" + str(i)
        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] # 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 = TCALIM2
arpfiledisk = 1
arpfileseq = 1
arpfileclass = 'ICL001'
arpfileclass2 = 'ICL002'
clinver = 8
if whattodo['image_ARP220_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(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. 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, 4096,2048]
    imagr.cellsize = [None, 0.2e-3, 0.2e-3]
    imagr.stokes = 'I'
    imagr.nfield = 2
    imagr.overlap = 1
    imagr.do3dimag = 1
    imagr.rashift = [None, 0.6, -0.35]
    imagr.decshift = [None, 0.02, 0.18]
    imagr.docalib = 1
    imagr.dotv = -1
    imagr.outname = arpfilename
    imagr.outdisk = arpfiledisk
    imagr.outseq = arpfileseq
    imagr.niter = 500
    imagr.gain = 0.1
    imagr.uvrange = uvrange # remove large-scale disturbances
    imagr.robust = 0.5
    imagr.antenna = [None, -17]
    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.nchav = 512
    imagr.doband = 1
    imagr.bpver = 1
    imagr.imsize = [None, 4096,2048]
    imagr.cellsize = [None, 0.2e-3, 0.2e-3]
    imagr.stokes = 'I'
    imagr.nfield = 2
    imagr.overlap = 1
    imagr.do3dimag = 1
    imagr.rashift = [None, 0.6, -0.35]
    imagr.decshift = [None, 0.02, 0.18]
    imagr.docalib = 1
    imagr.dotv = -1
    imagr.outname = arpfilename
    imagr.outdisk = arpfiledisk
    imagr.outseq = arpfileseq
    imagr.outver = 1
    imagr.niter = 1000
    imagr.gain = 0.1
    imagr.bcomp = [None, 100000, 100000]
    imagr.uvrange = uvrange # remove large-scale disturbances
    imagr.robust = 0.5
    imagr.antenna = [None, -17]
    imagr.go()

if whattodo['selfcal_arp220_2']:
    clinver = 8
    cloutver = 9
    snoutver = 8
    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):
        print "WARNING: Deleting SN" + str(i)
        data.zap_table('SN', i)
    data = UV(NAME, sorted_class, 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(TCALIM2, '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 = 10 # Longer than scan
    calib.aparm[1] = 3 # min No. of antennas to include first 45 min.
    calib.aparm[7] = 2 # SNR
    calib.aparm[3] = 1 # AVG RR,LL, 
    calib.aparm[6] = 1 # Print level
    calib.aparm[5] = 1 # AVG ifs
    calib.aparm[9] = 1 # Needed when fitting only AR
    calib.cmethod = 'DFT'
    calib.weightit = 1
    calib.soltype = 'L1R'
    calib.doband = 1
    calib.bpver = 1
    calib.uvrange = uvrange
    calib.dofit = [None, 17]
    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):
        print "WARNING: Deleting CL" + str(i)
        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] # 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 = NAME + '_FIN'
arpfiledisk = 1
arpfileseq = 1
arpfileclass = 'ICL001'
arpfileclass2 = 'ICL002'
if whattodo['image_ARP220_final']:
    # 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(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. To clean (for later removal) of the strongest sources
    imagr.gainuse = 0
    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, 0.6, -0.35]
    imagr.decshift = [None, 0.02, 0.18]
    imagr.docalib = 1
    imagr.dotv = -1
    imagr.outname = arpfilename
    imagr.outdisk = arpfiledisk
    imagr.outseq = arpfileseq
    imagr.niter = 500
    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(NAME, sorted_class, DISK, 1)
    imagr = task('imagr')
    imagr.default()
    imagr.indata = data
    imagr.sources = [None, target]
    imagr.gainuse = 0
    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, 0.6, -0.35]
    imagr.decshift = [None, 0.02, 0.18]
    imagr.docalib = 1
    imagr.dotv = -1
    imagr.outname = arpfilename
    imagr.outdisk = arpfiledisk
    imagr.outseq = arpfileseq
    imagr.outver = 1
    imagr.niter = 3000
    imagr.gain = 0.1
    imagr.bcomp = [None, 100000, 100000]
    imagr.uvrange = uvrange # remove large-scale disturbances
    imagr.robust = 0.5
    imagr.go()

#   FRING on FRCAL
if whattodo['fring_frcal']:
    clinver = 9
    cloutver = 10
    snoutver = 9
    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, frcal]
    fring.refant = refant
    fring.solint = 10 # Longer than scan
    fring.snver = snoutver
    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, frcal]
    clcal.sour = [None, frcal]
    clcal.gainver = clinver
    clcal.gainuse = cloutver
    clcal.refant = refant
    clcal.go()

if whattodo['image_frcal_1']:
    clinver = 10
    imagename = FRCALIM + '1'
    imagedisk = 1
    imageseq = 1
    data = UV(NAME, sorted_class, DISK, 1)
    imagr = task('imagr')
    imagr.default()
    imagr.indata = data
    imagr.sources = [None, frcal]
    imagr.gainuse = clinver
    imagr.flagver = 0
    imagr.nchav = 512
    imagr.stokes = 'I'
    imagr.cellsize = [None, 0.1e-3, 0.1e-3]
    imagr.imsize = [None, 512,512]
    imagr.docalib = 1
    imagr.dotv = -1
    imagr.outname = imagename
    imagr.outdisk = imagedisk
    imagr.outseq = imageseq
    imagr.niter = 300
    imagr.doband = 1
    imagr.bpver = 1
    imagr.uvrange = uvrange
    imagr.robust = 0.5
    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.go()

if whattodo['selfcal_frcal']:
    clinver = 10
    cloutver = 11
    snoutver = 10
    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)
    # FIT ANTENNA 3, with proper timeran not to flag things
    data = UV(NAME, sorted_class, DISK, 1)
    calib = task('calib')
    calib.default()
    calib.indata = data
    calib.in2data = IM(FRCALIM + '1', 'ICL001', 1, 1)
    calib.calsour = [None, frcal]
    calib.refant = refant
    calib.docalib = 1
    calib.gainuse = clinver
    calib.flagver = 0
    calib.snver = snoutver
    calib.solmode = 'A&P'
    calib.solint = 1 # 
    calib.aparm[7] = 5 # SNR
    calib.cmethod = 'DFT'
    calib.aparm[6] = 1 # Print level
    calib.aparm[9] = 1 # Pass on failed sols, for scans without these ants
    calib.doband = 1
    calib.bpver = 1
    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, frcal]
    clcal.sour = [None, frcal]
    clcal.gainver = clinver
    clcal.gainuse = cloutver
    clcal.refant = refant
    clcal.go()

if whattodo['image_frcal_2']:
    clinver = 11
    imagename = FRCALIM+'2'
    imagedisk = 1
    imageseq = 1
    data = UV(NAME, sorted_class, DISK, 1)
    imagr = task('imagr')
    imagr.default()
    imagr.indata = data
    imagr.sources = [None, frcal]
    imagr.gainuse = clinver
    imagr.flagver = 0
    imagr.nchav = 512
    imagr.stokes = 'I'
    imagr.cellsize = [None, 0.1e-3, 0.1e-3]
    imagr.imsize = [None, 512,512]
    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.uvrange = uvrange
    imagr.robust = 0.5
    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.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()
    f = fits.open(NAME+'_EAST_IMAGE.FITS', mode='update')
    f[0].data *=0.7
    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()
    f = fits.open(NAME+'_WEST_IMAGE.FITS', mode='update')
    f[0].data *=0.7
    f.flush()
    f.close()
    
    # Export FRCAL
    im = IM(NAME+'_FC2', 'ICL001', 1, 1)
    fittp = task('fittp')
    fittp.default()
    fittp.indata = im
    fittp.dataout = 'PWD:'+NAME+'_J1613+3412_IMAGE.FITS'
    if os.path.exists(fittp.dataout[4:]):
     os.system('rm ' + fittp.dataout[4:])
    fittp.go()
    f = fits.open(NAME+'_J1613+3412_IMAGE.FITS', mode='update')
    f[0].data *=0.7
    f.flush()
    f.close()
    # Export ACAL
    im = IM(NAME+'AC3', 'ICL001', 1, 1)
    fittp = task('fittp')
    fittp.default()
    fittp.indata = im
    fittp.dataout = 'PWD:'+NAME+'_J1516+1932_IMAGE.FITS'
    if os.path.exists(fittp.dataout[4:]):
     os.system('rm ' + fittp.dataout[4:])
    fittp.go()
    f = fits.open(NAME+'_J1516+1932_IMAGE.FITS', mode='update')
    f[0].data *=0.7
    f.flush()
    f.close()
    # Export PCAL
    im = IM(NAME+'PC2', 'ICL001', 1, 1)
    fittp = task('fittp')
    fittp.default()
    fittp.indata = im
    fittp.dataout = 'PWD:'+NAME+'_J1532+2344_IMAGE.FITS'
    if os.path.exists(fittp.dataout[4:]):
     os.system('rm ' + fittp.dataout[4:])
    fittp.go()
    f = fits.open(NAME+'_J1532+2344_IMAGE.FITS', mode='update')
    f[0].data *=0.7
    f.flush()
    f.close()


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