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

# No ar here, just:
#Ant   1 = BR       BX=  -226572.9769 BY= -1345828.7533 BZ=  1099750.4987
#Ant   2 = EB       BX= -5540964.0057 BY=  3860560.9017 BZ=  1273367.8511
#Ant   3 = FD       BX=  1214503.5183 BY=  -254548.9312 BZ=  -395100.7808
#Ant   4 = HN       BX=  -194967.8015 BY=  2289130.2027 BZ=   695243.0259
#Ant   5 = KP       BX=  1056832.3678 BY=  -970945.9432 BZ=  -269735.1510
#Ant   6 = LA       BX=   889141.2169 BY=  -447723.6887 BZ=    82060.6707
#Ant   7 = MK       BX=  -757068.7854 BY= -4869875.8096 BZ= -1478765.7511
#Ant   8 = NL       BX=   422093.0754 BY=   803943.9257 BZ=   599787.8318
#Ant   9 = OV       BX=   589841.0956 BY= -1485798.7401 BZ=   211554.1685
#Ant  10 = PT       BX=   965324.1573 BY=  -627489.5002 BZ=   -51651.3857
#Ant  11 = SC       BX=   597663.5742 BY=  3631749.6583 BZ= -1694323.4119
#Ant  12 = Y        BX=   984174.5641 BY=  -583173.3221 BZ=   -72187.5661

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
            'fring_ampcal' : True, #->SN2, CL6
            'bpass_ampcal': True, # BP 1
            'acscl': True, # SN3, CL7
            'mergecal': True, # HAS TO BE RUN MANUALLY
            #RUN MERGECAL
            'apcal' : True, # SN4,5 CL8
            'image_ampcal_1': True,
            'selfcal_ampcal' : True, # -> SN6, CL9
            'clip_ampcal': True, #USE PREFLAGGING AS WELL TO CLEAN FG. ALSO CLEAR OTHER SOURCES
            'image_ampcal_2': True, 
            'fring_phasecal' : True, #->SN7, CL10
            'image_phasecal_1': True,
            'selfcal_phasecal' : True, # -> SN8, CL11
            'clip_sensitive': True, #USE PREFLAGGING AS WELL TO CLEAN FG. ALSO CLEAR OTHER SOURCES
            'image_phasecal_2': True, # 
            'image_ARP220': True,
            'selfcal_arp220': True, # ->SN9, CL12
            'image_ARP220_final': True,
            'export_results': True,
            'save_calsols': True,
            }
 
########## Initialize observation data ##########
AIPS.userno = 1000
clint = 10.0/60 # Seconds
NAME = 'BB335A_X'
CLASS = 'UVDATA'
DISK = 1
AMPCALIM = NAME + '_AC'
PCALIM = NAME + '_PC'
TCALIM = NAME + '_TC'
OUTPREFIX = NAME
WTMODCLASS = NAME + 'W'
target = 'ARP220'
ampcal = 'J1516+1932'
phasecal = 'J1532+2344'
sorted_class = 'MSORT'
logfile = 'log_'+OUTPREFIX+'_PTred.log'
refant = 1
#########^^^ 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/BB335A/X/BB335A_X.FITS'
    fitld.outdata = outdata
    fitld.ncount = 1
    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 ampspikes, also flagged by smoothing the SN4 to SN5
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.antenna = [None, 8]
    uvflg.timeran = [None, 0, 20, 50, 0, 0, 20, 54, 0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.antenna = [None, 8]
    uvflg.timeran = [None, 1, 0, 40, 0, 1, 0, 50, 0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.antenna = [None, 8]
    uvflg.timeran = [None, 1, 4, 50, 0, 1, 5, 0, 0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
    # Qack for EB since fail in start of scans
    quack = task('quack')
    quack.default()
    quack.indata = data
    quack.antenna = [None,2]
    quack.opcode = 'BEG'
    #quack.sour = [None, ampcal]
    quack.aparm[2] = 30.0/60
    quack.go()
    # Flag amp spike
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.antenna = [None, 12]
    uvflg.timeran = [None, 0, 21, 40, 0, 0, 22, 10, 0]
    uvflg.bif = 1
    uvflg.eif = 1
    uvflg.opcode = 'FLAG'
    uvflg.go()
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.antenna = [None, 12]
    uvflg.timeran = [None, 0, 21, 20, 0, 0, 21, 30, 0]
    uvflg.bif = 3
    uvflg.eif = 3
    uvflg.opcode = 'FLAG'
    uvflg.go()
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.antenna = [None, 12]
    uvflg.timeran = [None, 0, 21, 5, 0, 0, 21, 10, 0]
    uvflg.bif = 7
    uvflg.eif = 7
    uvflg.opcode = 'FLAG'
    uvflg.go()
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.antenna = [None, 11]
    uvflg.timeran = [None, 1, 5, 28, 40, 1, 29, 45]
    uvflg.opcode = 'FLAG'
    uvflg.go()
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.antenna = [None, 3,8]
    uvflg.timeran = [None, 1, 5, 8, 0, 1, 5, 10, 0]
    uvflg.opcode = 'FLAG'
    uvflg.go()
    
    # Flag too sensitive baseline
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.antenna = [None, 2]
    uvflg.baselin = [None, 12]
    uvflg.opcode = 'FLAG'
    #uvflg.go()

    # Flag edge channels
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.bchan = 1
    uvflg.echan = 4
    uvflg.opcode = 'FLAG'
    uvflg.go()
    uvflg = task('uvflg')
    uvflg.default()
    uvflg.indata = data
    uvflg.bchan = 61
    uvflg.echan = 64
    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 01-AUGY-2014 and streched into the night over to 2 of august. 
    # According to http://mistupid.com/calendar/dayofyear.htm
    # This means day of the year DDD=213 and 214
    # Fetch and uncompress file for this day
    doy = str(213)
    year = str(2014)
    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(214)
    year = str(2014)
    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(213)
    year = str(2014)
    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 = 0 # use defaults
    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 = 'SELF'
    clcal.go()

#   FRING on AMPCAL
if whattodo['fring_ampcal']:
    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)
    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 = 6
    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]=6 # Normalize amps using power and all channels
    # according to VLBAS_37
    bpass.go()

if whattodo['acscl']:
    # Define initial versionnumbers
    clinver = 6
    cloutver = 7
    snoutver = 3
    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)
    data = UV(NAME, sorted_class, DISK, 1)
    acscl = task('acscl')
    acscl.indata = data
    acscl.solint = 0 # Use default
    acscl.doband = 1
    acscl.bpver = bpinver
    acscl.gainuse = clinver
    acscl.docal = 1
    acscl.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 = 'SELF'
    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 = 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)
    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()
    snsmo = task('snsmo')
    snsmo.indata = data
    snsmo.inver = snoutver
    snsmo.outver = snoutver+1
    snsmo.smotype = 'AMPL'
    snsmo.bparm[1] = 1.0/3600 # Smoothing in time in seconds to ensure no smoothing
    # DO NOT SMOOTH; INSTEAD CLIP WITH MWF
    snsmo.cparm[1] = 30.0/60 #in hours
    snsmo.cparm[6] = 3 # Max amp deviation
    snsmo.doblank = -1 # Since cannot be used with AMPL
    snsmo.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+1
    clcal.invers = snoutver+1
    clcal.gainver = clinver
    clcal.gainuse = cloutver
    clcal.refant = refant
    clcal.interpol = 'SELF'
    clcal.go()
    
    ## Flag gainspikes for antenna 8
    #data = UV(NAME, sorted_class, DISK, 1)
    #clcor = task('clcor')
    #clcor.default()
    #clcor.clcorprm = [None, 0.0,0] # multiply by 0
    #clcor.antenna = [None, 8, 0]
    #clcor.gainver = cloutver
    #clcor.gainuse = cloutver
    #clcor.indata = data
    #clcor.opcode = 'GAIN'
    #clcor.timeran = [None, 0, 20, 50, 0, 0, 20, 54, 0]
    #clcor.go()
    ## Flag gainspikes for antenna 8
    #data = UV(NAME, sorted_class, DISK, 1)
    #clcor = task('clcor')
    #clcor.default()
    #clcor.clcorprm = [None, 0.0,0] # multiply by 0
    #clcor.antenna = [None, 8, 0]
    #clcor.gainver = cloutver
    #clcor.gainuse = cloutver
    #clcor.indata = data
    #clcor.opcode = 'GAIN'
    #clcor.timeran = [None, 1, 0, 40, 0, 1, 0, 50, 0]
    #clcor.go()
    ## Flag gainspikes for antenna 8
    #data = UV(NAME, sorted_class, DISK, 1)
    #clcor = task('clcor')
    #clcor.default()
    #clcor.clcorprm = [None, 0.0,0] # multiply by 0
    #clcor.antenna = [None, 8, 0]
    #clcor.gainver = cloutver
    #clcor.gainuse = cloutver
    #clcor.indata = data
    #clcor.opcode = 'GAIN'
    #clcor.timeran = [None, 1, 4, 50, 0, 1, 5, 0, 0]
    #clcor.go()



if whattodo['image_ampcal_1']:
    clinver = 8
    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 = [None, 7000,0]
    imagr.antenna = [None, -2, -12]
    imagr.nbox = 1
    imagr.clbox = [None, [None, 230, 222, 278, 290]]
    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 = 8
    cloutver = 9
    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)
    # 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, 2,5,12] # 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['clip_ampcal']:
    outfgver = 2
    clinver = 9
    data = UV(NAME, sorted_class, DISK, 1)
    clip = task('clip')
    clip.default()
    clip.aparm[6] = 1e-3 # Flag very sensitive baselines
    clip.sources = [None, ampcal]
    clip.docal = 1
    clip.gainuse = clinver
    clip.flagver = outfgver
    clip.doband = 1
    clip.bpver = 1
    clip.indata = data
    clip.outfgver = outfgver
    clip.go()

if whattodo['image_ampcal_2']:
    clinver = 9
    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 = [None, 7000, 0]
    #imagr.uvtaper = [None, 160000,160000]

    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 = 9 # With ampcal corrections
    cloutver = 10
    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)
    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] = 100#ns, delay win, already fitted bulk on ampcal
    fring.dparm[3] = 50#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 = 10
    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 = [None, 7000, 0]
    imagr.nbox = 1
    imagr.clbox = [None, [None, 232, 227, 283, 287]]
    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 = 10
    cloutver = 11
    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
    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 = 11
    data = UV(NAME, sorted_class, DISK, 1)
    clip = task('clip')
    clip.default()
    clip.aparm[6] = 1e-3 # Flag very sensitive baselines
    clip.sources = [None, phasecal, target]
    clip.docal = 1
    clip.gainuse = clinver
    clip.flagver = outfgver
    clip.doband = 1
    clip.bpver = 1
    clip.indata = data
    clip.outfgver = outfgver
    clip.go()
    # Also clip amps
    clip = task('clip')
    clip.default()
    clip.aparm[1] = 3 # Flag amp spikes
    clip.sources = [None, phasecal, target]
    clip.docal = 1
    clip.gainuse = clinver
    clip.flagver = outfgver
    clip.doband = 1
    clip.bpver = 1
    clip.indata = data
    clip.outfgver = outfgver
    clip.go()


if whattodo['image_phasecal_2']:
    clinver = 11
    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 = [None, 7000,0]
    #imagr.uvtaper = [None, 160000,160000]
    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 = 11
    # 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, 8192,4096]
    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 = [None, 7000,0] # 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 = clinver
    imagr.flagver = 0
    imagr.nchav = 512
    imagr.doband = 1
    imagr.bpver = 1
    imagr.imsize = [None, 8192,4096]
    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 = [None, 7000,0] # remove large-scale disturbances
    imagr.robust = 0.5
    imagr.go()

if whattodo['selfcal_arp220']:
    clinver = 11
    cloutver = 12
    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):
        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 = [None, 7000,0]
    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']:
    clinver = 12
    # 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, 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 = [None, 7000,0] # 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 = 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, 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 = [None, 7000,0] # 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:'+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()
    
    fittp = task('fittp')
    fittp.default()
    fittp.indata = IM(NAME+'_FIN','IBM001', 1, 1)
    fittp.dataout = 'PWD:'+NAME+'_EAST_BEAM.FITS'
    if os.path.exists(fittp.dataout[4:]):
     os.system('rm ' + fittp.dataout[4:])
    fittp.go()
    fittp = task('fittp')
    fittp.default()
    fittp.indata = IM(NAME+'_FIN','IBM002', 1, 1)
    fittp.dataout = 'PWD:'+NAME+'_WEST_BEAM.FITS'
    if os.path.exists(fittp.dataout[4:]):
     os.system('rm ' + fittp.dataout[4:])
    fittp.go()

if whattodo['save_calsols']:
    snver = 9
    # Remove all PL tables
    data = UV(NAME, sorted_class, DISK, 1)

    data.zap_table('PL', -1)
    snplt = task('snplt')
    snplt.indata = data
    snplt.bif = 1
    snplt.eif = 1
    snplt.stokes = 'RR'
    snplt.optype = 'PHAS'
    snplt.sour = [None, target]
    snplt.inext = 'SN'
    snplt.inver = snver
    snplt.nplots = 6
    #snplt.pixrange = [None -180,180]
    snplt.dotv = -1
    snplt.go()
    outname = NAME+'_ARP220_SELFCAL_SOLS.EPS'
    if os.path.exists(outname):
        os.system('rm ' + outname)
    lwpla = task('lwpla')
    lwpla.indata = data
    lwpla.plver = 1
    lwpla.inver = 99
    lwpla.outfile = 'PWD:'+outname
    #lwpla.docolor = 1
    lwpla.go()

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