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selfcalv19_withmodel-amp.py
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selfcalv19_withmodel-amp.py
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import matplotlib
#matplotlib.use('GTK')
import numpy
import os
import sys
from scipy import interpolate
import time
from subprocess import Popen, PIPE, STDOUT
import pyrap.tables as pt
import uuid
pi = numpy.pi
import pwd
import logging
from facet_utilities import run,bg
from makecleanmask import do_makecleanmask
# location of this script - all scripts/parsets it uses are contained in subdirectory 'use'
# to run casa when not logged in
# Step 0. Run in screen
# Step 1. Xvfb :5 &
# Step 2. setenv DISPLAY :5
# run the program in screen and to exit screen: screen -d
# v19
# - change ndppp job submit for better control over jobs running
# - add hardcoded groups (get_group)
def create_merged_parmdb_spline(parmdb_a,parmdb_p, parmdb_t, parmdb_out,cellsizetime_a, cellsizetime_b):
import lofar.parmdb
pdb_a = lofar.parmdb.parmdb(parmdb_a)
pdb_p = lofar.parmdb.parmdb(parmdb_p)
pdb_t = lofar.parmdb.parmdb(parmdb_t)
parms_a = pdb_a.getValuesGrid("*")
parms_p = pdb_p.getValuesGrid("*")
parms_t = pdb_t.getValuesGrid("*")
os.system('rm -rf ' + parmdb_out)
keynames_p = parms_p.keys()
keynames_a = parms_a.keys()
for key in keynames_p:
# copy over the scalar phases
scalarp = numpy.copy(parms_p[key]['values'][:,0])
parms_t[key]['values'][:,0] = scalarp
for key in keynames_a:
logging.debug(key)
tmp1 = numpy.copy(parms_t[key]['values'][:,0])
tmp2 = numpy.copy(parms_a[key]['values'][:,0])
time_t = 1.0*numpy.arange(len(tmp1))
time_a = (numpy.float(cellsizetime_a/cellsizetime_p)*numpy.arange(len(tmp2))) + (0.5*cellsizetime_a/cellsizetime_p)
el = ((numpy.max(time_t) - numpy.max(time_a[:-1]))/2 )+ numpy.max(time_a[:-1])
time_a[len(time_a)-1] = el
# to avoid edge effects in spline add values edges to be the last values from BBS
time_a = numpy.copy(numpy.append(0,time_a))
time_a = numpy.append(time_a, numpy.max(time_t))
val_start = tmp2[0]
val_end = tmp2[len(tmp2)-1]
tmp2 = numpy.copy(numpy.append(val_start,tmp2))
tmp2 = numpy.append(tmp2,val_end)
x = numpy.copy(time_a)
y = numpy.copy(tmp2)
# SPLINE INTERPOL of AMPS
tck = interpolate.splrep(x,y,s=0)
xnew = time_t
ynew = interpolate.splev(xnew,tck,der=0)
parms_t[key]['values'][:,0] = ynew
pdbnew = lofar.parmdb.parmdb(parmdb_out, create=True)
pdbnew.addValues(parms_t)
pdbnew.flush()
#lofar.expion.parmdbmain.store_parms(parmdb_out, parms_t, create_new = True)
return
def create_merged_parmdb(ms, parmdb_a,parmdb_p, parmdb_t, parmdb_out,cellsizetime_a, cellsizetime_b):
import lofar.parmdb
#pdb_pre = lofar.parmdb.parmdb(pre_apply_parmdb)
pdb_a = lofar.parmdb.parmdb(parmdb_a)
pdb_p = lofar.parmdb.parmdb(parmdb_p)
pdb_t = lofar.parmdb.parmdb(parmdb_t)
#parms_pre = pdb_pre.getValuesGrid("*")
parms_a = pdb_a.getValuesGrid("*")
parms_p = pdb_p.getValuesGrid("*")
parms_t = pdb_t.getValuesGrid("*")
os.system('rm -rf ' + parmdb_out)
keynames_p = parms_p.keys()
keynames_a = parms_a.keys()
length = numpy.int(cellsizetime_b)
for key in keynames_p:
# copy over the CommonScalar phases, TEC, clock
# just to get axis length
tmp1 = numpy.copy(parms_t[key]['values'][:, 0])
for idx in range(len(tmp1)):
el = numpy.float(idx)/numpy.float(length)
el = numpy.int(numpy.floor(el))
parms_t[key]['values'][idx,0] = numpy.copy(parms_p[key]['values'][el,0])
pol_list = ['0:0','1:1']
gain = 'Gain'
anttab = pt.table(ms + '/ANTENNA')
antenna_list = anttab.getcol('NAME')
anttab.close()
#length = numpy.int(cellsizetime_a/cellsizetime_b)
length = numpy.int(cellsizetime_a)
for pol in pol_list:
for antenna in antenna_list:
#real1 = numpy.copy(parms_pre[gain + ':' + pol + ':Real:'+ antenna]['values'][:, 0])
real2 = numpy.copy(parms_a[gain + ':' + pol + ':Real:'+ antenna]['values'][:, 0])
#imag1 = numpy.copy(parms_pre[gain + ':' + pol + ':Imag:'+ antenna]['values'][:, 0])
imag2 = numpy.copy(parms_a[gain + ':' + pol + ':Imag:'+ antenna]['values'][:, 0])
# just to get axis length
tmp1 = numpy.copy(parms_t[gain + ':' + pol + ':Imag:'+ antenna]['values'][:, 0])
#G1 = real1 + 1j*imag1
G2 = real2 + 1j*imag2
Gnew = G2
for idx in range(len(tmp1)):
el = numpy.float(idx)/numpy.float(length)
el = numpy.int(numpy.floor(el))
parms_t[gain + ':' + pol + ':Imag:'+ antenna]['values'][idx,0] = numpy.copy(numpy.imag(Gnew[el]))
parms_t[gain + ':' + pol + ':Real:'+ antenna]['values'][idx,0] = numpy.copy(numpy.real(Gnew[el]))
#for key in keynames_a:
# print key
# tmp1 = numpy.copy(parms_t[key]['values'][:,0])
# tmp2 = numpy.copy(parms_a[key]['values'][:,0])
# length = numpy.int(cellsizetime_a/cellsizetime_b)
# for idx in range(len(tmp1)):
#
# el = numpy.float(idx)/numpy.float(length)
# el = numpy.int(numpy.floor(el))
# #print idx, el
# parms_t[key]['values'][idx,0] = tmp2[el]
#lofar.expion.parmdbmain.store_parms(parmdb_out, parms_t, create_new = True)
pdbnew = lofar.parmdb.parmdb(parmdb_out, create=True)
pdbnew.addValues(parms_t)
pdbnew.flush()
return
def make_image(mslist, cluster, callnumber, threshpix, threshisl, nterms, atrous_do, imsize, region, ncores, SCRIPTPATH):
do_mask = True
niter = 1000 # 7500 causes nasty clean artifacts
mscale = 'False'
if atrous_do:
mscale = 'True'
average = True # average the data a lot to speed up the imaging,
# ONLY average for small FOV, otherwise timesmearing is a problem
#average data
if average:
b=bg(maxp=2)
for ms in (mslist):
ndppp_parset = ms + '_NDPPP.parset'
ndppplog = ndppp_parset.replace('.parset','.log')
os.system('rm -f ' + ndppp_parset)
output = ms + '.tmpavg'
os.system('rm -rf ' + output)
f=open(ndppp_parset, 'w')
f.write('msin = %s\n' % ms)
f.write('msin.datacolumn = CORRECTED_DATA\n')
f.write('msout = %s\n' % output)
f.write('msout.writefullresflag=False\n')
f.write('steps=[avg]\n')
f.write('rficonsole.type=aoflagger\n')
f.write('avg.type = squash\n')
f.write('avg.freqstep = 1\n')
f.write('avg.timestep = 12\n') # is the default
f.close()
ndpppcmd = 'NDPPP ' + ndppp_parset+ ' >'+ndppplog+' 2>&1'
b.run(ndpppcmd)
#os.system (ndpppcmd)
b.wait()
#output=numpy.int(Popen(cmd, shell=True, stdout=PIPE).communicate()[0])
#while output > 0 :
#time.sleep(10)
#output=numpy.int(Popen(cmd, shell=True, stdout=PIPE).communicate()[0])
#pid = (Popen('pgrep NDPPP', shell=True, stdout=PIPE).communicate()[0])
##print pid
#pid_list = pid.split()
#for pidnr in pid_list:
##print 'PID', numpy.int(pidnr)
#os.system('kill -s CONT ' + str(pidnr))
ms = ''
for m in mslist:
if average:
ms = ms + ' ' + m + '.tmpavg'
else:
ms = ms + ' ' + m
imout = 'im'+ callnumber +'_cluster'+cluster+'nm'
logging.debug(ms + ' ' + imout + ' ' + 'None' + ' ' + '1mJy' + ' ' + str(niter) + ' ' + str(nterms))
if do_mask:
if cluster == 'a2256': ## special case for a2256
niter = niter*15 # clean very deep here
run('casapy --nogui --logfile casapy-'+imout+'.log -c '+SCRIPTPATH+'/casapy_cleanv4.py ' + ms + ' ' + imout + ' ' + 'None' +\
' ' + '1mJy' + ' ' + str(niter) + ' ' + str(nterms) + ' ' + str(imsize) + ' ' + mscale)
# make mask
if nterms > 1:
do_makecleanmask(imout +'.image.tt0',threshpix,threshisl,atrous_do,ncores=ncores)
# run('python '+SCRIPTPATH+'/makecleanmask.py --threshpix '+str(threshpix)+\
# ' --threshisl '+str(threshisl) +' --atrous_do '+ str(atrous_do) +' ' +imout +'.image.tt0')
else:
do_makecleanmask(imout +'.image',threshpix,threshisl,atrous_do,ncores=ncores)
# run('python '+SCRIPTPATH+'/makecleanmask.py --threshpix '+str(threshpix)+\
# ' --threshisl '+str(threshisl) +' --atrous_do '+ str(atrous_do) + ' ' + imout +'.image')
# clean image with manual mask
mask = imout+'.cleanmask'
niter = 1000
imout = 'im'+ callnumber +'_cluster'+cluster
if region != 'empty' : ## special cases
niter = niter*3
run('casapy --nogui --logfile casapy-'+imout+'.log -c '+SCRIPTPATH+'/casapy_cleanv4.py '+ ms + ' ' + imout + ' ' + mask+','+region + \
' ' + '1mJy' + ' ' + str(niter) + ' ' + str(nterms) + ' ' + str(imsize) + ' ' + mscale)
else:
run('casapy --nogui --logfile casapy-'+imout+'.log -c '+SCRIPTPATH+'/casapy_cleanv4.py '+ ms + ' ' + imout + ' ' + mask + \
' ' + '1mJy' + ' ' + str(niter) + ' ' + str(nterms) + ' ' + str(imsize) + ' ' + mscale)
# convert to FITS
if nterms > 1:
run('image2fits in=' + imout +'.image.tt0' + ' ' + 'out='+ imout + '.fits')
else:
run('image2fits in=' + imout +'.image' + ' ' + 'out='+ imout + '.fits')
if not os.path.exists(imout+'.fits'):
raise Exception('Imaging Error: '+imout+'.fits does not exist' )
if average:
logging.debug('rm -rf {}'.format(ms))
os.system('rm -rf ' + ms)
return imout,imout+'.mask'
def runbbs(mslist, skymodel, parset, parmdb, applycal, TEC, clusterdesc, db, dbuser, dbname):
#NOTE WORK FROM MODEL_DATA (contains correct phase data from 10SB calibration)
#NOTE WORK FROM DATA if TEC
if TEC:
key = str(uuid.uuid4())
key = key[0:12]
if clusterdesc=='default':
# allow 'default' which gives the old behaviour, for now
username = pwd.getpwuid(os.getuid())[0]
cdparset='/home/'+username+'/pgsql-setup.txt'
if os.path.isfile(cdparset):
logging.debug('Getting pgsql setup from {}'.format(cdparset))
lines=[line.strip() for line in open(cdparset)]
clusterdesc=lines[0]
db=lines[1]
dbuser=lines[2]
dbname=lines[3]
elif 'para' in os.uname()[1]:
clusterdesc = '/home/wwilliams/para/paranew.clusterdesc'
db = 'kolkje'
dbuser = 'shimwell'
dbname = 'shimwell'
else:
clusterdesc = '/home/williams/clusterdesc/cep3.clusterdesc'
db = 'ldb002.offline.lofar'
dbuser = 'postgres'
dbname = username
if len(mslist) == 10000: # 34 does not work now!!!!!!
# this is a very special case for a full run, manually here to run with 3 solver controls
vdslist = ''
run('makevds '+clusterdesc+' ' + ms)
vdslist = vdslist + ms + '.vds '
else:
vdslist = ''
for ms in mslist:
run('makevds '+clusterdesc+' ' + ms)
vdslist = vdslist + ms + '.vds '
gds = 'tec.gds'
logging.debug(vdslist)
run('combinevds ' + gds + ' '+ vdslist)
cmd1= 'calibrate -f --key ' + key + ' --cluster-desc '+clusterdesc +' --instrument-name ' + parmdb + ' '
cmd2= '--db '+db + ' --db-user '+ dbuser + ' '+ ' --db-name '+ dbname + ' ' + gds + ' ' + parset + ' ' + skymodel + ' ' + '. > ' + gds + '.bbslog'
bbscmd = cmd1 + cmd2
ntries = 0
done = 0
while (ntries < 10) and (done < 1):
logging.debug('calibrate try {}'.format(ntries))
# let run 'proceed on failure' as the test for failure is done here to allow retries
run(bbscmd, proceed=True)
#done = 0
#while(done < 1):
cmd = "grep '\[OK\] done!' " + gds + ".bbslog"
output=Popen(cmd, shell=True, stdout=PIPE).communicate()[0]
if 'OK' in output:
done += 1
logging.debug('{} is done'.format(gds))
else:
#cmd = "grep 'FAIL' " + gds + ".bbslog"
#output=Popen(cmd, shell=True, stdout=PIPE).communicate()[0]
#if 'FAIL' in output:
logging.warning('calibrate failed, trying again...')
ntries += 1
time.sleep(5)
# after ntries exceeded is it still at FAIL
cmd = "grep 'FAIL' " + gds + ".bbslog"
output=Popen(cmd, shell=True, stdout=PIPE).communicate()[0]
if 'FAIL' in output:
raise Exception('calibrate has failed too many times' )
else:
# Normal calibrate for amplitude
b=bg()
for ms in mslist:
log = ms + '.bbslog'
if applycal:
cmd = 'calibrate-stand-alone --parmdb-name ' + parmdb + ' ' + ms + ' ' + parset + ' ' + skymodel + '>' + log + ' 2>&1'
#cmd = 'calibrate-stand-alone -t 4 --parmdb-name ' + parmdb + ' ' + ms + ' ' + parset + ' ' + skymodel + '>' + log
else:
cmd = 'calibrate-stand-alone -f --parmdb-name ' + parmdb + ' ' + ms + ' ' + parset + ' ' + skymodel + '>' + log + ' 2>&1'
#cmd = 'calibrate-stand-alone -t 4 -f --parmdb-name ' + parmdb + ' ' + ms + ' ' + parset + ' ' + skymodel + '>' + log
b.run(cmd)
time.sleep(10)
b.wait()
return
def create_scalarphase_parset(timestep, TEC, clock, groups, FFT, uvrange):
bbs_parset = 'scalarphase.parset'
os.system('rm -f ' + bbs_parset)
f=open(bbs_parset, 'w')
if TEC:
f.write('Strategy.InputColumn = DATA\n')
f.write('Strategy.UseSolver = T\n')
else:
f.write('Strategy.InputColumn = MODEL_DATA\n')
f.write('Strategy.UseSolver = F\n')
f.write('Strategy.ChunkSize = 960\n')
f.write('Strategy.Steps = [solve,correct]\n')
if FFT:
f.write('Step.solve.Model.Sources = [@MODEL_DATA]\n')
else:
f.write('Step.solve.Model.Sources = []\n')
f.write('Step.solve.Model.Cache.Enable = T\n')
f.write('Step.solve.Model.Phasors.Enable = F\n')
f.write('Step.solve.Model.DirectionalGain.Enable = F\n')
f.write('Step.solve.Model.Gain.Enable = F\n')
if TEC:
f.write('Step.solve.Model.TEC.Enable = T\n')
f.write('Step.solve.Solve.CalibrationGroups = [%s]\n' % groups)
if clock:
f.write('Step.solve.Model.Clock.Enable = T\n')
f.write('Step.solve.Model.Rotation.Enable = F\n')
f.write('Step.solve.Model.CommonScalarPhase.Enable = T \n')
f.write('Step.solve.Operation = SOLVE\n')
if TEC:
if clock:
f.write('Step.solve.Solve.Parms = ["CommonScalarPhase:*","TEC:*","Clock:*"]\n')
else:
f.write('Step.solve.Solve.Parms = ["CommonScalarPhase:*","TEC:*"]\n')
else:
f.write('Step.solve.Solve.Parms = ["CommonScalarPhase:*"]\n')
f.write('Step.solve.Solve.CellSize.Freq = 0\n')
f.write('Step.solve.Solve.CellSize.Time = %s\n' % str(timestep))
f.write('Step.solve.Solve.CellChunkSize = 120\n')
f.write('Step.solve.Solve.PropagateSolutions = T\n')
f.write('Step.solve.Solve.Options.MaxIter = 100\n')
f.write('Step.solve.Solve.Options.LMFactor = 1.0\n')
f.write('Step.solve.Solve.Options.BalancedEqs = F\n')
f.write('Step.solve.Solve.Options.UseSVD = T\n')
f.write('Step.solve.Model.Beam.Enable = F\n')
f.write('Step.solve.Solve.UVRange = [%s]\n' % uvrange)
f.write('Step.solve.Solve.Mode = COMPLEX \n')
f.write('Step.correct.Model.Sources = []\n')
f.write('Step.correct.Model.CommonScalarPhase.Enable= T\n')
f.write('Step.correct.Model.Cache.Enable = T\n')
if TEC:
f.write('Step.correct.Model.TEC.Enable = T\n')
if clock:
f.write('Step.correct.Model.Clock.Enable = T\n')
f.write('Step.correct.Model.DirectionalGain.Enable = F\n')
f.write('Step.correct.Model.Gain.Enable = F\n')
f.write('Step.correct.Model.Phasors.Enable = F\n')
f.write('Step.correct.Operation = CORRECT\n')
f.write('Step.correct.Output.Column = CORRECTED_DATA\n')
f.write('Step.correct.Model.Beam.Enable = F\n')
f.write('Step.correct.Output.WriteCovariance = F\n')
f.close()
return bbs_parset
def create_scalarphase_parset_p(timestep, TEC, clock, groups, FFT, uvrange):
bbs_parset = 'scalarphase_p.parset'
os.system('rm -f ' + bbs_parset)
f=open(bbs_parset, 'w')
if TEC:
f.write('Strategy.InputColumn = DATA\n')
f.write('Strategy.UseSolver = T\n')
else:
f.write('Strategy.InputColumn = MODEL_DATA\n')
f.write('Strategy.UseSolver = F\n')
f.write('Strategy.ChunkSize = 960\n')
f.write('Strategy.Steps = [solve,correct]\n')
if FFT:
f.write('Step.solve.Model.Sources = [@MODEL_DATA]\n')
else:
f.write('Step.solve.Model.Sources = []\n')
f.write('Step.solve.Model.Cache.Enable = T\n')
f.write('Step.solve.Model.Phasors.Enable = F\n')
f.write('Step.solve.Model.DirectionalGain.Enable = F\n')
f.write('Step.solve.Model.Gain.Enable = F\n')
if TEC:
f.write('Step.solve.Model.TEC.Enable = T\n')
f.write('Step.solve.Solve.CalibrationGroups = [%s]\n' % groups)
if clock:
f.write('Step.solve.Model.Clock.Enable = T\n')
f.write('Step.solve.Model.Rotation.Enable = F\n')
f.write('Step.solve.Model.CommonScalarPhase.Enable = T \n')
f.write('Step.solve.Operation = SOLVE\n')
if TEC:
if clock:
f.write('Step.solve.Solve.Parms = ["CommonScalarPhase:*","TEC:*","Clock:*"]\n')
else:
f.write('Step.solve.Solve.Parms = ["CommonScalarPhase:*","TEC:*"]\n')
else:
f.write('Step.solve.Solve.Parms = ["CommonScalarPhase:*"]\n')
f.write('Step.solve.Solve.CellSize.Freq = 0\n')
f.write('Step.solve.Solve.CellSize.Time = %s\n' % str(timestep))
f.write('Step.solve.Solve.CellChunkSize = 120\n')
f.write('Step.solve.Solve.PropagateSolutions = T\n')
f.write('Step.solve.Solve.Options.MaxIter = 100\n')
f.write('Step.solve.Solve.Options.LMFactor = 1.0\n')
f.write('Step.solve.Solve.Options.BalancedEqs = F\n')
f.write('Step.solve.Solve.Options.UseSVD = T\n')
f.write('Step.solve.Model.Beam.Enable = F\n')
f.write('Step.solve.Solve.UVRange = [%s]\n' % uvrange)
f.write('Step.solve.Solve.Mode = COMPLEX \n')
f.write('Step.correct.Model.Sources = []\n')
f.write('Step.correct.Model.CommonScalarPhase.Enable= T\n')
f.write('Step.correct.Model.Cache.Enable = T\n')
f.write('Step.correct.Model.DirectionalGain.Enable = F\n')
if TEC:
f.write('Step.correct.Model.TEC.Enable = T\n')
if clock:
f.write('Step.correct.Model.Clock.Enable = T\n')
f.write('Step.correct.Model.Gain.Enable = F\n')
f.write('Step.correct.Model.Phasors.Enable = F\n')
f.write('Step.correct.Operation = CORRECT\n')
f.write('Step.correct.Output.Column = CORRECTED_DATA_PHASE\n')
f.write('Step.correct.Model.Beam.Enable = F\n')
f.write('Step.correct.Output.WriteCovariance = F\n')
f.close()
return bbs_parset
def create_amponly_parset(timestep, FFT, uvrange):
bbs_parset = 'amplitudeonly.parset'
os.system('rm -f ' + bbs_parset)
f=open(bbs_parset, 'w')
f.write('Strategy.InputColumn = CORRECTED_DATA_PHASE\n')
f.write('Strategy.ChunkSize = 1440\n')
f.write('Strategy.UseSolver = F\n')
f.write('Strategy.Steps = [solve]\n')
if FFT:
f.write('Step.solve.Model.Sources = [@MODEL_DATA]\n')
else:
f.write('Step.solve.Model.Sources = []\n')
f.write('Step.solve.Model.Cache.Enable = T\n')
f.write('Step.solve.Model.Phasors.Enable = F\n') ## T
f.write('Step.solve.Model.DirectionalGain.Enable = F\n')
f.write('Step.solve.Model.Gain.Enable = T\n')
f.write('Step.solve.Model.Rotation.Enable = F\n')
f.write('Step.solve.Model.CommonScalarPhase.Enable = F\n')
f.write('Step.solve.Operation = SOLVE\n')
f.write('Step.solve.Solve.Parms = ["Gain:0:0:*","Gain:1:1:*"]\n') ## ["Gain:0:0:Ampl:*","Gain:1:1:Ampl:*"]
# to test
f.write('Step.solve.Solve.CellSize.Freq = 0\n')
f.write('Step.solve.Solve.CellSize.Time = %s\n' %str(timestep))
f.write('Step.solve.Solve.CellChunkSize = 12\n')
f.write('Step.solve.Solve.PropagateSolutions = T\n')
f.write('Step.solve.Solve.Options.MaxIter = 100\n')
f.write('Step.solve.Solve.Options.LMFactor = 1.0\n')
f.write('Step.solve.Solve.Options.BalancedEqs = F\n')
f.write('Step.solve.Solve.Options.UseSVD = T\n')
f.write('Step.solve.Model.Beam.Enable = F\n')
f.write('Step.solve.Solve.UVRange = [%s]\n' % uvrange) ## [600]
f.write('Step.solve.Solve.Mode = COMPLEX\n')
f.close()
return bbs_parset
def create_scalarphase_parset_p2(timestep, TEC, clock, groups, FFT, uvrange):
bbs_parset = 'scalarphase_p2.parset'
os.system('rm -f ' + bbs_parset)
f=open(bbs_parset, 'w')
f.write('Strategy.InputColumn = CORRECTED_DATA_AMP\n')
f.write('Strategy.ChunkSize = 960\n')
if TEC:
f.write('Strategy.UseSolver = T\n')
else:
f.write('Strategy.UseSolver = F\n')
f.write('Strategy.Steps = [solve,correct]\n')
if FFT:
f.write('Step.solve.Model.Sources = [@MODEL_DATA]\n')
else:
f.write('Step.solve.Model.Sources = []\n')
f.write('Step.solve.Model.Cache.Enable = T\n')
f.write('Step.solve.Model.Phasors.Enable = F\n')
f.write('Step.solve.Model.DirectionalGain.Enable = F\n')
f.write('Step.solve.Model.Gain.Enable = F\n')
if TEC:
f.write('Step.solve.Model.TEC.Enable = T\n')
f.write('Step.solve.Solve.CalibrationGroups = [%s]\n' % groups)
if clock:
f.write('Step.solve.Model.Clock.Enable = T\n')
f.write('Step.solve.Model.Rotation.Enable = F\n')
f.write('Step.solve.Model.CommonScalarPhase.Enable = T \n')
f.write('Step.solve.Operation = SOLVE\n')
if TEC:
if clock:
f.write('Step.solve.Solve.Parms = ["CommonScalarPhase:*","TEC:*","Clock:*"]\n')
else:
f.write('Step.solve.Solve.Parms = ["CommonScalarPhase:*","TEC:*"]\n')
else:
f.write('Step.solve.Solve.Parms = ["CommonScalarPhase:*"]\n')
f.write('Step.solve.Solve.CellSize.Freq = 0\n')
f.write('Step.solve.Solve.CellSize.Time = %s\n' % str(timestep))
f.write('Step.solve.Solve.CellChunkSize = 120\n')
f.write('Step.solve.Solve.PropagateSolutions = T\n')
f.write('Step.solve.Solve.Options.MaxIter = 100\n')
f.write('Step.solve.Solve.Options.LMFactor = 1.0\n')
f.write('Step.solve.Solve.Options.BalancedEqs = F\n')
f.write('Step.solve.Solve.Options.UseSVD = T\n')
f.write('Step.solve.Model.Beam.Enable = F\n')
f.write('Step.solve.Solve.UVRange = [%s]\n' % uvrange)
f.write('Step.solve.Solve.Mode = COMPLEX \n')
f.write('Step.correct.Model.Sources = []\n')
f.write('Step.correct.Model.CommonScalarPhase.Enable= T\n')
f.write('Step.correct.Model.Cache.Enable = T\n')
f.write('Step.correct.Model.DirectionalGain.Enable = F\n')
f.write('Step.correct.Model.Gain.Enable = F\n')
if TEC:
f.write('Step.correct.Model.TEC.Enable = T\n')
if clock:
f.write('Step.correct.Model.Clock.Enable = T\n')
f.write('Step.correct.Model.Phasors.Enable = F\n')
f.write('Step.correct.Operation = CORRECT\n')
f.write('Step.correct.Output.Column = CORRECTED_DATA_PHASE\n')
f.write('Step.correct.Model.Beam.Enable = F\n')
f.write('Step.correct.Output.WriteCovariance = F\n')
f.close()
return bbs_parset
def get_group(thismslist):
nms = len(thismslist)
if nms > 37:
raise Exception('too many blocks....')
if nms == 37: group = "5,5,5,5,5,6,6"
elif nms == 36: group = "6,6,6,6,6,6"
elif nms == 35: group = "5,6,6,6,6,6"
elif nms == 34: group = "5,5,6,6,6,6"
elif nms == 33: group = "5,5,5,6,6,6"
elif nms == 32: group = "5,5,5,5,6,6"
elif nms == 31: group = "5,5,5,5,5,6"
elif nms == 30: group = "6,6,6,6,6"
elif nms == 29: group = "5,6,6,6,6"
elif nms == 28: group = "5,5,6,6,6"
elif nms == 27: group = "5,5,5,6,6"
elif nms == 26: group = "5,5,5,5,6"
elif nms == 25: group = "5,5,5,5,5"
elif nms == 24: group = "6,6,6,6"
elif nms == 23: group = "5,6,6,6"
elif nms == 22: group = "5,5,6,6,"
elif nms == 21: group = "5,5,5,6"
elif nms == 20: group = "5,5,5,5"
elif nms == 19: group = "4,5,5,5"
elif nms == 18: group = "6,6,6"
elif nms == 17: group = "5,6,6"
elif nms == 16: group = "5,5,6"
elif nms == 15: group = "5,5,5"
elif nms == 14: group = "4,5,5"
elif nms == 13: group = "4,4,5"
elif nms == 12: group = "6,6"
elif nms == 11: group = "5,6"
elif nms == 10: group = "5,5"
elif nms == 9: group = "4,5"
elif nms == 8: group = "4,4"
elif nms == 7: group = "3,4"
else: group = str(nms)
return group
def do_selfcal(mslist, cluster, atrous_do, imsize, nterms,
cellsizetime_a, cellsizetime_p, TECi, clocki, HRi,
region, clusterdesc, dbserver, dbuser, dbname,
SCRIPTPATH, ncores=8, config=None, model=None):
TEC = False
FFT = False
clock= False
HR = False # high dynamic range
if TECi == "True":
TEC = True
if clocki == "True":
clock = True
if HRi == "HD":
HR = True
if imsize <=2048:
wplanes = 1
FFT = True # FFT image into MODEL_DATA
if imsize >= 512:
wplanes = 64
if imsize > 799:
wplanes = 96
if imsize > 1023:
wplanes = 128
if imsize > 1599:
wplanes = 180
if imsize > 1800:
wplanes = 196
if imsize > 2049:
wplanes = 256
#if imsize > 3000:
# wplanes = 448
#if imsize > 4095:
# wplanes = 512
logging.info('mslist {}'.format(mslist))
logging.info('source {}'.format(cluster))
logging.info('atrous_do {}'.format(atrous_do))
logging.info('imsize {} '.format(imsize))
logging.info('TEC is {} and clock is {}'.format(TEC, clock))
msinputlist = ''
for m in mslist:
msinputlist = msinputlist + ' ' + m
#if len(mslist) == 29:
#group = "9,10,10"
#elif len(mslist) == 28:
#group = "7,7,7,7"
#elif len(mslist) == 20:
##group = "10,10"
#group = "7,7,6"
#elif len(mslist) == 16:
#group = "8,8"
#else:
#group = str(len(mslist))
group = get_group(mslist)
logging.info('GROUP {}'.format(group))
uvrange = '80'
#uvrange = '400'
merge_parmdb = True
phasors = False # if true only solve for amps on long timescales
smooth = False # seems that smooth does not help the selfcal (various reasons for that)
# 1. boundaries of flagged vs non-flagged data are sharp (should not be smoothed)
# 2. there sre some strong ampl various at low elevations
smooth = True # sometimes almost 0.0 amplitude, causes ripples
phasezero = True # reset phases from ap calibration
if model is None:
#### MAKE IMAGE 0 ###
logging.info('Make image 0')
imout,mask = make_image(mslist, cluster, '0', 10, 6, nterms, atrous_do, imsize, region, ncores, SCRIPTPATH)
#####################
### CALIBRATE WITH BBS PHASE ONLY 1 ###
# create skymodel for BBS
run(SCRIPTPATH+'/casapy2bbs.py -m '+ mask + ' ' +'-t ' + str(nterms)+ ' ' + imout+'.model ' + imout+'.skymodel')
if FFT:
os.system('casapy --nogui -c '+SCRIPTPATH+'/ft_v2.py ' + msinputlist + ' ' + imout+'.model' \
+ ' ' + str(nterms) + ' '+ str(wplanes))
# phase only calibrate
skymodel = imout+'.skymodel'
parset = create_scalarphase_parset(cellsizetime_p, TEC, clock, group, FFT, uvrange)
runbbs(mslist, skymodel, parset, 'instrument', False, TEC, clusterdesc, dbserver, dbuser, dbname)
#NOTE WORK FROM MODEL_DATA (contains correct phase data from 10SB calibration)
######################################
### MAKE IMAGE 1 ###
logging.info('Make image 1')
imout,mask = make_image(mslist, cluster, '1', 15, 15, nterms, atrous_do, imsize, region, ncores, SCRIPTPATH)
####################
### CALIBRATE WITH BBS PHASE ONLY 2 ###
# create skymodel for BBS
run(SCRIPTPATH+'/casapy2bbs.py -m '+ mask + ' ' +'-t ' + str(nterms)+ ' ' + imout+'.model ' + imout+'.skymodel')
if FFT:
run('casapy --nogui -c '+SCRIPTPATH+'/ft_v2.py ' + msinputlist + ' ' + imout+'.model' \
+ ' ' + str(nterms) + ' '+ str(wplanes))
# phase only calibrate
skymodel = imout+'.skymodel'
parset = create_scalarphase_parset(cellsizetime_p, TEC, clock, group, FFT, uvrange)
runbbs(mslist, skymodel, parset, 'instrument', False, TEC,clusterdesc, dbserver, dbuser, dbname) #NOTE WORK FROM MODEL_DATA (contains correct phase data from 10SB calibration)
######################################
### MAKE IMAGE 2 ###
logging.info('Make image 2')
imout,mask = make_image(mslist, cluster, '2', 15, 15, nterms, atrous_do, imsize, region, ncores, SCRIPTPATH)
####################
### CALIBRATE WITH BBS PHASE+AMP 1 ###
run(SCRIPTPATH+'/casapy2bbs.py -m '+ mask + ' ' +'-t ' + str(nterms)+ ' ' + imout+'.model ' + imout+'.skymodel')
if FFT:
run('casapy --nogui -c '+SCRIPTPATH+'/ft_v2.py ' + msinputlist + ' ' + imout+'.model' \
+ ' ' + str(nterms) + ' '+ str(wplanes))
skymodel = imout+'.skymodel'
parset = create_scalarphase_parset_p(cellsizetime_p, TEC, clock, group, FFT, uvrange)
# solve +apply phases
runbbs(mslist, skymodel, parset, 'instrument_phase0', False, TEC, clusterdesc, dbserver, dbuser, dbname)
# solve amps
parmdb = 'instrument_amps0'
parset = create_amponly_parset(cellsizetime_a, FFT, uvrange)
runbbs(mslist, skymodel, parset, parmdb, False, False, clusterdesc, dbserver, dbuser, dbname)
for ms in mslist:
# remove outliers from the solutions
if phasors:
run('python '+SCRIPTPATH+'/smoothcal_rx42.py ' + ms + ' ' + ms+'/'+parmdb + ' ' + ms+'/'+parmdb+'_smoothed'+' > '+ms+'_'+parmdb+'_smoothed.log')
else:
run('python '+SCRIPTPATH+'/smoothcal_a2256_nophasors.py ' + ms + ' ' + ms+'/'+parmdb + ' ' + ms+'/'+parmdb+'_smoothed'+' > '+ms+'_'+parmdb+'_smoothed.log')
# apply amps
if smooth:
runbbs(mslist, skymodel,SCRIPTPATH+'/apply_amplitudeonly.parset', parmdb+'_smoothed', True, False, clusterdesc, dbserver, dbuser, dbname)
else:
runbbs(mslist, skymodel,SCRIPTPATH+'/apply_amplitudeonly.parset', parmdb, True, False, clusterdesc, dbserver, dbuser, dbname)
### MAKE IMAGE 3 ###
logging.info('Make image 3')
imout,mask = make_image(mslist, cluster, '3', 10, 10, nterms, atrous_do, imsize, region, ncores, SCRIPTPATH)
#### CALIBRATE BBS PHASE+AMP 2 ###
# make model
run(SCRIPTPATH+'/casapy2bbs.py -m '+ mask + ' ' +'-t ' + str(nterms)+ ' ' + imout+'.model ' + imout+'.skymodel')
if FFT:
run('casapy --nogui -c '+SCRIPTPATH+'/ft_v2.py ' + msinputlist + ' ' + imout+'.model' \
+ ' ' + str(nterms) + ' '+ str(wplanes))
#parmdb keep from previous step
skymodel = imout+'.skymodel'
# reset the phases from instrument_amps0 to zero to prevent large phase corrections from incorrect AP solve
if phasezero:
inputparmdb = parmdb +'_smoothed'
outputparmdb = parmdb +'_smoothed_phasezero'
for ms in mslist:
run('python '+SCRIPTPATH+'/setphasezero.py ' + ms + ' ' + ms+'/'+inputparmdb +' ' + ms+'/'+outputparmdb)
else:
outputparmdb = parmdb +'_smoothed'
# phase only cal
skymodel = imout+'.skymodel'
parset = create_scalarphase_parset_p(cellsizetime_p, TEC, clock, group, FFT, uvrange)
runbbs(mslist, skymodel, parset, 'instrument_phase1', False, TEC, clusterdesc, dbserver, dbuser, dbname)
# solve amps
parmdb = 'instrument_amps1'
parset = create_amponly_parset(cellsizetime_a, FFT, uvrange)
runbbs(mslist, skymodel, parset,parmdb, False, False, clusterdesc, dbserver, dbuser, dbname)
for ms in mslist:
# remove outliers from the solutions
if phasors:
run('python '+SCRIPTPATH+'/smoothcal_rx42.py ' + ms + ' ' + ms+'/'+parmdb + ' ' + ms+'/'+parmdb+'_smoothed'+' > '+ms+'_'+parmdb+'_smoothed.log')
else:
run('python '+SCRIPTPATH+'/smoothcal_a2256_nophasors.py ' + ms + ' ' + ms+'/'+parmdb + ' ' + ms+'/'+parmdb+'_smoothed'+' > '+ms+'_'+parmdb+'_smoothed.log')
# apply amps
if smooth:
runbbs(mslist, skymodel,SCRIPTPATH+'/apply_amplitudeonly.parset',parmdb+'_smoothed', True, False, clusterdesc, dbserver, dbuser, dbname)
else:
runbbs(mslist, skymodel,SCRIPTPATH+'/apply_amplitudeonly.parset',parmdb, True, False, clusterdesc, dbserver, dbuser, dbname)
### MAKE IMAGE 4 ###
logging.info('Make image 4')
imout,mask = make_image(mslist, cluster, '4', 10, 10, nterms, atrous_do, imsize, region, ncores, SCRIPTPATH)
else:
### As for image 4 ###
### the model variable contains a full path to a CASA sky model for the field
logging.info('Calibrating using pre-existing model '+model)
imout='model_image_'+cluster
mask=imout+'.mask'
origmask=model.replace('model','mask')
# delete any old versions, and copy over the model
for suffix in ['model','mask']:
os.system('rm -rf '+imout+'.'+suffix)
run('cp -r '+model+' '+imout+'.model')
run('cp -r '+origmask+' '+imout+'.mask')
# now proceed as though this was the previous image!
run(SCRIPTPATH+'/casapy2bbs.py -m '+ mask + ' ' +'-t ' + str(nterms)+ ' ' + imout+'.model' + ' ' + imout+'.skymodel')
if FFT:
run('casapy --nogui -c '+SCRIPTPATH+'/ft_v2.py ' + msinputlist + ' ' + imout+'.model' \
+ ' ' + str(nterms) + ' '+ str(wplanes))
skymodel = imout+'.skymodel'
parset = create_scalarphase_parset_p(cellsizetime_p, TEC, clock, group, FFT, uvrange)
# solve +apply phases
runbbs(mslist, skymodel, parset, 'instrument_phase1', False, TEC, clusterdesc, dbserver, dbuser, dbname)
# solve amps
parmdb = 'instrument_amps1'
parset = create_amponly_parset(cellsizetime_a, FFT, uvrange)
runbbs(mslist, skymodel, parset, parmdb, False, False, clusterdesc, dbserver, dbuser, dbname)
for ms in mslist:
# remove outliers from the solutions
if phasors:
run('python '+SCRIPTPATH+'/smoothcal_rx42.py ' + ms + ' ' + ms+'/'+parmdb + ' ' + ms+'/'+parmdb+'_smoothed'+' > '+ms+'_'+parmdb+'_smoothed.log')
else:
run('python '+SCRIPTPATH+'/smoothcal_a2256_nophasors.py ' + ms + ' ' + ms+'/'+parmdb + ' ' + ms+'/'+parmdb+'_smoothed'+' > '+ms+'_'+parmdb+'_smoothed.log')
# apply amps
if smooth:
runbbs(mslist, skymodel,SCRIPTPATH+'/apply_amplitudeonly.parset', parmdb+'_smoothed', True, False, clusterdesc, dbserver, dbuser, dbname)
else:
runbbs(mslist, skymodel,SCRIPTPATH+'/apply_amplitudeonly.parset', parmdb, True, False, clusterdesc, dbserver, dbuser, dbname)
### MAKE IMAGE 4 ###
logging.info('Make image 4')
imout,mask = make_image(mslist, cluster, '4', 10, 10, nterms, atrous_do, imsize, region, ncores, SCRIPTPATH)
### CREATE FINAL MODEL ###
logging.info('Create final model')
skymodelf= 'im_cluster'+cluster+ '.final.skymodel'
run(SCRIPTPATH+'/casapy2bbs.py -m '+ mask + ' ' +'-t ' + str(nterms)+ ' ' + imout+'.model ' + skymodelf)
if FFT:
run('casapy --nogui -c '+SCRIPTPATH+'/ft_v2.py ' + msinputlist + ' ' + imout+'.model' \
+ ' ' + str(nterms) + ' '+ str(wplanes))
### CREATED MERGED PARMDB SCALARPHASE+AMPS ###
### INCLUDES SPLINE INTERPOLARION OF AMPS ###
if merge_parmdb:
logging.info('Merge parmdb')
if phasors:
dummyparset = SCRIPTPATH+'/scalarphase+amp.parset'
else:
if TEC:
dummyparset = SCRIPTPATH+'/scalarphase+ap+TEC.parset'
else:
dummyparset = SCRIPTPATH+'/scalarphase+ap.parset'
if TEC:
if clock:
dummyparmdb = 'instrument_template_TECclock'
else:
dummyparmdb = 'instrument_template_Gain_TEC_CSphase'
#if not os.path.isdir(dummyparmdb):
#runbbs([mslist[0]], skymodel,dummyparset, dummyparmdb, True, False)
# TO SPEED THINGS UP, hard coded for BOOTES - i.e. the above has already been run
for ms in mslist:
os.system('rm -rf ' + ms +'/' + dummyparmdb)
os.system('cp -r ' + dummyparmdb + ' ' + ms + '/instrument_template')
if smooth:
parmdb_a = 'instrument_amps1_smoothed' # last/best ampplitude(+phase) parmdb
else:
parmdb_a = 'instrument_amps1' # last/best ampplitude(+phase) parmdb
parmdb_p = 'instrument_phase1' # last/best CommonScalarPhase parmdb
parmdbout = 'instrument_merged'