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
import time
import numpy as np

#Ant   1 = BR
#Ant   2 = EB
#Ant   3 = FD
#Ant   4 = GB
#Ant   5 = HN
#Ant   6 = KP
#Ant   7 = LA
#Ant   8 = MK
#Ant   9 = NL
#Ant  10 = PT
#Ant  11 = SC
#Ant  12 = AR

whattodo = {'load_data': False, # ->CL1
            'msort': False,
            'indxr': False,
            'preflagging': True,
            'ion_corr': True, # ->CL2
            'eops_corr': True, # ->CL3
            'par_ang_cor': True, # ->CL4
            'accor' : True, # SN1, CL5
            'mergecal': True, # HAS TO BE RUN MANUALLY
            # RUN MERGECAL
            'apcal' : True, # SN2, CL6
            'fring_ampcal' : True, #->SN3, CL7
            'bpass_ampcal': True, # BP 1
            'image_ampcal_1': True, # No EB,AR need fixing
            'selfcal_ampcal' : True, # -> SN4, CL8
            'image_ampcal_2': True, 
            'fring_phasecal' : True, #->SN5, CL9
            'image_phasecal_1': True,
            'selfcal_phasecal' :True, # -> SN6, CL10
            'clip_sensitive': True, #USE PREFLAGGING AS WELL TO CLEAN FG
            'image_phasecal_2': True, # 
            'image_ARP220': True, # No AR
            'selfcal_arp220': True, # ->SN7, CL11
            'image_ARP220_final': True,
            # Too little data for frcal to get good result, so do not save image
            'fring_frcal' : True, #->SN8, CL12
            'image_frcal_1': True, 
            'selfcal_frcal' : True, # -> SN9, CL13
            'image_frcal_2': True, 
            'export_results': True,
            }

########## Initialize observation data ##########
AIPS.userno = 1000
clint = 10.0/60 # Seconds
NAME = 'BB297C_C'
CLASS = 'UVDATA'
DISK = 1
AMPCALIM = NAME + '_AC'
PCALIM = NAME + '_PC'
TCALIM = NAME + '_TC'
FRCALIM = NAME + '_FC'
OUTPREFIX = NAME
target = 'ARP220'
ampcal = 'J1516+1932'
phasecal = 'J1532+2344'
frcal = 'J1613+3412'
sorted_class = 'MSORT'
logfile = 'log_'+OUTPREFIX+'_PTred.log'
refant = 1
uvrange = [None, 7000, 0]
#########^^^ 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/BB297C/BB297C_C.FITS1'
    fitld.outdata = outdata
    fitld.ncount = 2
    fitld.digicor = 1
    fitld.clint = clint
    fitld.wtthresh = 0.7
    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 with FITLD...'
    msort.go()
    if data.exists():
        print 'WARNING: Removing existing file ' + NAME + '.' + CLASS
        data.zap()
        print '         File removed. Proceeding with FITLD...'

if whattodo['indxr']:
    indxr = task('indxr')
    indxr.default()
    data = UV(NAME, sorted_class, DISK, 1)
    indxr.indata = data
    indxr.cparm[3] = clint
    indxr.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()
    # Flag antennas specified not having receiver in PI letter :
    # Antennas 3 FD and 9 NL: No 6cm Receiver)
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.antennas = [None, 3,9]
    uvflg.outfgver = outfgver
    uvflg.opcode = 'FLAG'
    uvflg.go()
    # Flag antenna 4, GB, unfortunately very weak fringes to ampcal, so no hope for target or pcal.
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.antennas = [None, 4]
    uvflg.outfgver = outfgver
    uvflg.opcode = 'FLAG'
    uvflg.go()
    # Flag scan for AR, EB with bad amps
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.antennas = [None, 2, 12]
    uvflg.timeran = [None, 1, 4, 0, 0, 1, 4, 10, 0]
    uvflg.outfgver = outfgver
    uvflg.opcode = 'FLAG'
    uvflg.go()
    # Flag 6-7 since waves in image
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.antennas = [None, 6]
    uvflg.baselin = [None, 7]
    uvflg.timeran = [None, 1, 0, 0, 0, 1, 4, 0, 0]
    uvflg.bif = 1
    uvflg.eif = uvflg.eif
    uvflg.outfgver = outfgver
    uvflg.opcode = 'FLAG'
    uvflg.go()
    
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.antennas = [None, 8]
    uvflg.timeran = [None, 1, 7, 40, 0, 1, 7, 45, 0]
    uvflg.bif = 4
    uvflg.eif = uvflg.eif
    uvflg.outfgver = outfgver
    uvflg.opcode = 'FLAG'
    uvflg.go()
    
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.antennas = [None, 5]
    uvflg.timeran = [None, 1, 9, 30, 0, 1, 11, 0, 0]
    uvflg.outfgver = outfgver
    uvflg.opcode = 'FLAG'
    uvflg.go()
    
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.antennas = [None, 1]
    uvflg.baselin = [None, 6]
    uvflg.timeran = [None, 1, 3, 50, 0, 1, 3, 56, 0]
    uvflg.outfgver = outfgver
    uvflg.opcode = 'FLAG'
    uvflg.go()
    
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.antennas = [None, 6]
    uvflg.timeran = [None, 1, 9, 40, 0, 1, 9, 50, 0]
    uvflg.outfgver = outfgver
    uvflg.opcode = 'FLAG'
    uvflg.go()
    
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.antennas = [None, 6]
    uvflg.timeran = [None, 0, 23, 30, 0, 0, 23, 35, 0]
    uvflg.outfgver = outfgver
    uvflg.opcode = 'FLAG'
    uvflg.go()
    
    # Flag EF
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.antennas = [None, 2]
    uvflg.outfgver = outfgver
    uvflg.opcode = 'FLAG'
    uvflg.go()


########## IONOSPHERIC CORRECTIONS ##########
# => CL2
if whattodo['ion_corr']:
    clinver = 1
    cloutver = 2
    data = UV(NAME, sorted_class, DISK, 1)
    # Remove all CL tables higher than 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)
    tecor = task('tecor')
    tecor.default()
    tecor.indata = data
    tecor.gainver = clinver
    tecor.gainuse = cloutver
    # Observation was 11-JUN-2011. According to http://mistupid.com/calendar/dayofyear.htm
    # This means day of the year DDD=162, but also 163 since long observation.
    # Fetch and uncompress file for this day
    doy = str(162)
    year = str(2011)
    tecfile = 'jplg' + doy + '0.'+year[-2:]+'i'
    if not os.path.exists(tecfile):
        os.system('wget ftp://cddis.gsfc.nasa.gov/gps/products/ionex/'+year+'/'+doy+'/' + tecfile + '.Z')
        os.system('gunzip ' + tecfile+ '.Z')
    doy = str(163)
    year = str(2011)
    tecfile = 'jplg' + doy + '0.'+year[-2:]+'i'
    if not os.path.exists(tecfile):
        os.system('wget ftp://cddis.gsfc.nasa.gov/gps/products/ionex/'+year+'/'+doy+'/' + tecfile + '.Z')
        os.system('gunzip ' + tecfile+ '.Z')
    #Reset name to first file for input to tecor 
    doy = str(162)
    year = str(2011)
    tecfile = 'jplg' + doy + '0.'+year[-2:]+'i'

    tecor.infile = 'PWD:' + tecfile
    tecor.nfiles = 2
    tecor.go()
########## EARTH ORIENTATION PARAMETERS CORRECTION ##########
# => CL3
if whattodo['eops_corr']:
    clinver = 2
    cloutver = 3
    data = UV(NAME, sorted_class, DISK, 1)
    # Remove all CL tables higher than 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)
    clcor = task('clcor')
    clcor.default()
    clcor.indata = data
    clcor.gainver = clinver
    clcor.gainuse = cloutver
    clcor.opcode = 'EOPS'
    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()
 
########## PARALLACTIC ANGLE CORRECTION ##########
# => CL4
if whattodo['par_ang_cor']:
    clinver = 3
    cloutver = 4
    data = UV(NAME, sorted_class, DISK, 1)
    # Remove all CL tables higher than 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)
    clcor = task('clcor')
    clcor.default()
    clcor.indata = data
    clcor.gainver = clinver
    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()

############# AMPLITUDE calibration ##############
# => CL5 
# => SN1(accor),
if whattodo['accor']:
    # Define initial versionnumbers, increased further down
    clinver = 4
    cloutver = 5
    snoutver = 1
## RUN ACCOR
    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)
    accor = task('accor')
    accor.indata = data
    accor.solint = 2
    accor.go()
    # Now we have a new 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.indata = data
    clcal.snver = snoutver
    clcal.invers = snoutver
    clcal.gainver = clinver
    clcal.gainuse = cloutver
    clcal.refant = refant
    clcal.interpol = '2PT'
    clcal.go()

## MERGECAL IS REQUIRED TO OBTAIN GC AND TY versions 2 from versions 1, else APCAL may fail.

if whattodo['mergecal']:
    ans = raw_input('Please run the procedure MERGECAL in AIPS before proceeding with apcal. Type Yes if you have run mergecal already.')
    if ans=='Yes':
        print 'Great!'
    else:
        print 'Mergecal needed! Exiting...'
        sys.exit()

if whattodo['apcal']:
## RUN APCAL 
    #redefine versions
    clinver = 5
    cloutver = 6
    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)
    apcal = task('apcal')
    apcal.indata = data
    apcal.tyver = 2
    apcal.gcver = 2
    apcal.snver = snoutver
    apcal.invers = 1 # WX table version
    apcal.solint = 2 # Same as accor
    apcal.go()
    # Now we have a new 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)
    # Make CL table
    clcal = task('clcal') 
    clcal.indata = data
    clcal.snver = snoutver
    clcal.invers = snoutver
    clcal.gainver = clinver
    clcal.gainuse = cloutver
    clcal.refant = refant
    clcal.interpol = '2PT'
    clcal.go()

#   FRING on AMPCAL
# => SN3
if whattodo['fring_ampcal']:
    clinver = 6
    cloutver = 7
    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)
    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.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 = 7
    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 = 7
    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, 0.1e-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.antenna = [None, -2, -12]
    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 = 7
    cloutver = 8
    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)
    # 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.aparm[9] = 1 # Pass on failed sols, for scans without these ants
    calib.dofit = [None, 2,12] # Fit 
    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, 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 = 8
    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 = 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
    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 = 8 # With ampcal corrections
    cloutver = 9
    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)
    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 = 9
    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
    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.antenna = [None, -2]
    imagr.go()


if whattodo['selfcal_phasecal']:
    clinver = 9
    cloutver = 10
    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):
        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[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.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] # Apply to all sources
    clcal.gainver = clinver
    clcal.gainuse = cloutver
    clcal.refant = refant
    clcal.go()

if whattodo['clip_sensitive']:
    outfgver = 2
    clinver = 10
    data = UV(NAME, sorted_class, DISK, 1)
    clip = task('clip')
    clip.default()
    clip.sour = [None, target, phasecal]
    clip.aparm[6] = 5e-3 # Flag very sensitive baselines
    clip.docal = 1
    clip.gainuse = clinver
    clip.stokes = 'I'
    clip.flagver = outfgver
    clip.doband = 1
    clip.bpver = 1
    clip.indata = data
    clip.outfgver = outfgver
    clip.go()

if whattodo['image_phasecal_2']:
    clinver = 10
    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
    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'
if whattodo['image_ARP220']:
    clinver = 10
    # 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, -12]
    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 = 2000
    imagr.gain = 0.1
    imagr.bcomp = [None, 100000, 100000]
    imagr.uvrange = uvrange # remove large-scale disturbances
    imagr.robust = 0.5
    imagr.antenna = [None, -12]
    imagr.go()

if whattodo['selfcal_arp220']:
    clinver = 10
    cloutver = 11
    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.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 = OUTPREFIX + '_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 = 2000
    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 = 11
    cloutver = 12
    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):
        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 = 12
    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
    imagr.clbox = [None, [None, 223,215, 297, 313]]
    imagr.nbox = 1
    imagr.antenna = [None, -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.go()

if whattodo['selfcal_frcal']:
    clinver = 12
    cloutver = 13
    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)
    # 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 = 13
    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
    imagr.clbox = [None, [None, 223,215, 297, 313]]
    imagr.nbox = 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.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:'+OUTPREFIX+'_EAST_IMAGE.FITS'
    if os.path.exists(fittp.dataout[4:]):
     os.system('rm ' + fittp.dataout[4:])
    fittp.go()
    # Export WEST
    fittp = task('fittp')
    fittp.default()
    fittp.indata = west
    fittp.dataout = 'PWD:'+OUTPREFIX+'_WEST_IMAGE.FITS'
    if os.path.exists(fittp.dataout[4:]):
     os.system('rm ' + fittp.dataout[4:])
    fittp.go()
    # Export ACAL
    im = IM(NAME+'_AC2', '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()
    # 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()

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