def time_sort_data():
"""Time-sort data in AIPS with the UVSRT task."""
print_header("Time-sorting data")
uvsrt = AIPSTask('uvsrt')
uvsrt.userno = AIPS.userno
# -------------------------------------------------------------------------
# UVSRT the data
# -------------------------------------------------------------------------
# sort data to prevent down stream problems
uvsrt.indisk = uvsrt.outdisk = DISK_ID
uvsrt.baddisk[1] = BADDISK
uvsrt.outcl = 'UVSRT'
uvsrt.sort = 'TB'
last = cat.last_entry()
uvsrt.inname = last.name
uvsrt.inclass = last.klass
uvsrt.inseq = last.seq
# will write to entry 1 because input sdf/uv files were removed
uvsrt.go()
nfiles = len(cat)
for dbcon_entry in range(nfiles-1):
cat.zap_entry(-1) # remove the DBCON entries
def runuvconfrompoint(antenna_file,
outname,
start_freq,
start_wavelength,
dec,
min_ha,
max_ha,
t_int,
channel_inc,
n_chan,
blockage,
w_term=0):
uvcon = AIPSTask('UVCON')
uvcon.infile = antenna_file
#uvcon.in2name = fitsfil.name
#uvcon.in2class = fitsfil.klass
#uvcon.in2seq = fitsfil.seq
#uvcon.in2disk = 1
uvcon.outname = outname
#uvcon.nmaps = 1
#uvcon.cmethod = 'DFT'
#uvcon.cmodel = 'COMP'
uvcon.smodel[1:] = 1, 0, 0, 0, 0, 0, 0
uvcon.aparm[1:] = start_freq, start_wavelength, \
dec, min_ha, max_ha, 0,\
t_int, channel_inc, n_chan, \
blockage
uvcon.bparm[1:] = 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
uvcon.do3dimag = w_term
#uvcon.inp()
uvcon.go()
def prtan(uvdata):
outprint = aips_out+uvdata.name+'_prtan.txt'
HF.delete_file(outprint)
prtan = AIPSTask('prtan')
prtan.indata = uvdata
prtan.docrt = -1
prtan.outprint = outprint
prtan()
def runuvfix(datafile, inname, indisk, thisdir):
uvfix = AIPSTask('UVFIX')
klass = datafile.klass
uvfix.indata = datafile
uvfix.outdata = AIPSUVData(datafile.name,'UVFIX',indisk,thisdir)
uvfix.go()
datafile.zap()
datafile = AIPSUVData(inname,'UVFIX',indisk,thisdir)
datafile.rename(inname, klass, thisdir)
def rungetjy(indata, sources, calsour, bif, eif, snver):
getjy = AIPSTask('GETJY')
getjy.indata = indata
getjy.sources[1:] = sources
getjy.calsour[1:] = calsour
getjy.bif = bif
getjy.eif = eif
getjy.snver = snver
getjy.go()
def runtabedCopy(indata, inext, invers, outdata, outvers):
tabed = AIPSTask('TABED')
tabed.indata = indata
tabed.inext = inext
tabed.invers = invers
tabed.outdata = outdata
tabed.outvers = outvers
tabed.optype = 'COPY'
tabed.go()
def msort(uvdata):
sys.stdout.write('Sorting data by runing MSORT.')
msort = AIPSTask('msort')
msort.outdata = uvdata
msort.outclass = 'MSORT'
msort.indata = uvdata
HF.print_inp_to_log(msort,'MSORT')
msort()
return AIPSUVData(uvdata.name,'MSORT',uvdata.disk,uvdata.seq)
def runsnplt(indata, inext, invers, sources, nplots, optype, dotv):
snplt = AIPSTask('SNPLT')
snplt.indata = indata
snplt.inext= inext
snplt.invers = invers
snplt.sources[1:] = sources
snplt.nplots = nplots
snplt.optype = optype
snplt.dotv = dotv
snplt.go()
def runquickpossm(indata, source):
possm = AIPSTask('POSSM')
possm.indata = indata
possm.source[1:] = source
possm.aparm[9] = 1
possm.nplots = 6
possm.solint = 30 # plot every 30min
possm.stokes = 'HALF'
possm.flagver = 0
possm.go()
def _prtuv(split_data, channel):
prtuv = AIPSTask('prtuv')
prtuv.default
prtuv.channel = channel
prtuv.indata = split_data
prtuv.dparm[7] = 1
prtuv.cparm[10] = 0.01
prtuv.docrt = -1
removefile('/tmp/prtuv.tmp')
prtuv.outprint = '/tmp/prtuv.tmp'
prtuv.go()
def ptacop(name1, class1, name2, class2, ttype, innum, outnum, disk):
tacop = AIPSTask('TACOP')
tacop.indata = AIPSUVData(name1, class1, disk, 1)
tacop.outdata = AIPSUVData(name2, class2, disk, 1)
tacop.inext = ttype
tacop.invers = innum
tacop.outvers = outnum
tacop.go()
def runlistr(indata, sources, optype, docrt, outprint):
listr = AIPSTask('LISTR')
listr.indata = indata
listr.sources[1:] = sources
listr.optype = optype
listr.docrt = docrt
listr.outprint = outprint
listr.go()
def tget(taskname):
'''
get AIPSTask() object
Args:
taskname (str): the name of AIPS Task to be called
Returns:
AIPSTask object
'''
task = AIPSTask(taskname)
task.defaults()
return task
def tabed(uvdata,ine='an',optype='repl',keyvalue=[5,0],aparm=[5,0,0,4,4,14,0],inv=1,outv=1):
tabed = AIPSTask('tabed')
tabed.indata = uvdata
tabed.outdata = uvdata
tabed.inext = ine
tabed.invers = inv
tabed.outvers = outv
tabed.aparm[1:]=aparm
tabed.keyvalue[1:]=keyvalue
tabed.optype = optype
HF.print_inp_to_log(tabed,'TABED')
tabed()
def slcol(imdata,outfile,inv=1,nfiles=0,pixxy=[0,0],opc='MODL', aparm=[1,1,0]):
slcol = AIPSTask('slcol')
slcol.indata = imdata
slcol.outtext = outfile
slcol.nfiles = nfiles
slcol.invers = inv
slcol.zinc = 0
slcol.pixxy[1:] = pixxy
slcol.opcode = opc
slcol.aparm[1:] = aparm
HF.print_inp_to_log(slcol,'SLCOL')
slcol()
def pwtmod (aipsname, refant, antennas, supweight=50.0, indisk=1):
uvdata = AIPSUVData (aipsname, 'FITS', indisk, 1)
wtmod = AIPSTask ('WTMOD')
wtmod.indata = uvdata
wtmod.outdata = uvdata
wtmod.antwt[1:] = [1]*len(antennas)
wtmod.antwt[antennas.index(refant)+1] = supweight
wtmod.inp()
wtmod.go()
def rungetjy(indata, sources, calsour, bif, eif, snver):
getjy = AIPSTask('GETJY')
getjy.indata = indata
getjy.sources[1:] = sources
getjy.calsour[1:] = calsour
getjy.bif = bif
getjy.eif = eif
getjy.snver = snver
getjy.go()
def initial_flag(uvdata, tasav, disk, refant):
tacop = AIPSTask('TACOP')
tacop.indata = tasav
tacop.inext = 'FG'
tacop.invers = 1
tacop.ncount = 1
tacop.outdata = uvdata
tacop.go()
print 'copied EVN flag file to data, now go manually flag please'
def runsetjy(indata, sources, bif, eif, zerosp, optype):
setjy = AIPSTask('SETJY')
setjy.indata = indata
setjy.sources[1:] = sources
setjy.bif = bif
setjy.eif = eif
setjy.zerosp[1:] = zerosp, 0, 0, 0
setjy.optype = optype
setjy.go()
def runfittp(uvdata, fittpdir, fittpfile):
fittp = AIPSTask('FITTP')
fittp.indata = uvdata
fittp.doall = -1
fittp.intype = ''
fittp.outtape = 1
srcname = re.sub(r"\s+", '-', fittpfile)
fittp.dataout = os.path.join(fittpdir, srcname)
print "Saving to disk: ", uvdata.name, uvdata.klass, uvdata.seq
fittp.go()
def douvcon_casa():
AIPS.userno = AIPSUSER
cc = np.array([[0., 0., 1.]])
np.save('cc', cc)
os.system('python douvcon_casa.py')
#load data into AIPS
fitld = AIPSTask('fitld')
fitld.datain = './temp.fits'
fitld.outname = 'UVSIM'
fitld.outclass = 'FITS'
fitld.outdisk = indisk
fitld.inp()
fitld.go()
def runsousp(indata, sources):
sousp = AIPSTask('SOUSP')
sousp.indata = indata
sousp.sources[1:] = sources
sousp.order = 1
sousp.dotv = -1
sousp.go()
return sousp.specindx
def greys (aipsname, incl, indisk, pmin, pmax, stfac, stvers, logfiledir='./'):
greys = AIPSTask('greys')
greys.inname = aipsname
greys.inclass = incl
greys.indisk = indisk
greys.pixrange[1:] = [float(pmin),float(pmax)]
greys.dotv = -1
greys.stfac = stfac
try:
greys.stvers = stvers # does not exist in some aips versions
except:
pass
stdout = sys.stdout; sys.stdout = open(logfiledir+aipsname+'.log','a')
greys.go()
sys.stdout.close(); sys.stdout = stdout
def index(inname, inclass, inseq, indisk):
indxr = AIPSTask('indxr')
indxr.default
indxr.inname = inname
indxr.inclass = inclass
indxr.inseq = inseq
indxr.indisk = indisk
indxr.go()
def pclcal (aipsname,indisk,inver,aipsclass='FITS',logdir='./',\
snver=-1,gainver=0,gainuse=0):
uvdata = AIPSUVData (aipsname,aipsclass,indisk,1)
clcal = AIPSTask ('clcal')
clcal.indata = uvdata
clcal.inver = inver
clcal.snver = inver if snver==-1 else snver
clcal.gainver = gainver
clcal.gainuse = gainuse
stdout = sys.stdout; sys.stdout = open(logdir+aipsname+'.log','a')
clcal.go()
sys.stdout.close(); sys.stdout = stdout
def psnsmo(aipsname,aipsclass,indisk,smotype,boxcar=2,delaycut=50,smooth=1):
snsmo = AIPSTask('snsmo')
snsmo.inname = aipsname
snsmo.inclass = aipsclass
snsmo.indisk = indisk
snsmo.smotype = smotype
if smotype=='DELA' or smotype=='VLBI':
snsmo.bparm[4] = snsmo.bparm[5] = snsmo.bparm[9] = snsmo.bparm[10] = smooth
snsmo.cparm[4] = snsmo.cparm[5] = boxcar
snsmo.cparm[9] = snsmo.cparm[10] = delaycut
snsmo.doblank = -1
snsmo.go()
def make_average_map(restfreq, uniqueid):
print_header("Making average map")
sqash = AIPSTask('sqash')
# squash the frequency axis to make a continuum image
sqash.indisk = DISK_ID
sqash.outdisk = DISK_ID
last = cat.last_entry()
sqash.inname = last.name
sqash.inclass = last.klass
sqash.inseq = last.seq
sqash.bdrop = 3 # squash frequency axis
sqash.go()
outcont = write_average_map(restfreq, uniqueid)
return outcont
def __init__(self, name):
""" Create Obit task object
Creates task object and calls server function to parse TDF
file to obtain task specific parametrs and documentation.
Following is a list of class members:
_default_dict = Dictionary with default values of parameters
_input_list = List of input parameters in order
_output_list = List of output parameters in order
_min_dict = Parameter minimum values as a List
_max_dict = Parameter maximum values as a List
_hlp_dict = Parameter descriptions (list of strings)
as a dictionary
_strlen_dict = String parameter lengths as dictionary
_help_string = Task Help documentation as list of strings
_explain_string = Task Explain documentation as list of strings
_short_help = One line description of task
_message_list = list of execution messages
retCode = Task return code, 0=Finished OK
debug = If true save task parameter file
logFile = if given, the name of the file in which to
write messages
doWait = True if synchronous operation wished
Current parameter values are given as class members.
"""
self._task_type = 'OBIT'
AIPSTask.__init__(self, name)
self._remainder = "" # Partial message buffer
if self.userno == 0:
self.userno = 1
# Set disk directory names
#print "DEBUG ObitTask._init__ before ",FITS.disks
dirs = []
for x in FITS.disks:
if x != None:
#print "DEBUG ObitTask._init__ ",x.dirname
dirs.append(x.dirname)
#print "DEBUG ObitTask._init__ before ",FITS.disks
self.__dict__["FITSdirs"] = dirs
#print "DEBUG ObitTask._init__ after ",self.__dict__["FITSdirs"]
dirs = []
for x in AIPS.disks:
if x != None:
#print "DEBUG ObitTask._init__ ",x.dirname
dirs.append(x.dirname)
self.__dict__["AIPSdirs"] = dirs
def runprtmsg(prtask, outprint):
prtmsg = AIPSTask('PRTMSG')
clrmsg = AIPSTask('CLRMSG')
prtmsg.prtask = prtask
prtmsg.docrt = -1
prtmsg.outprint = outprint
# RUN VERB
prtmsg.go()
clrmsg()
def sl2pl(imdata,inv=0,domod=0,dores=0):
sl2pl = AIPSTask('sl2pl')
sl2pl.indata = imdata
sl2pl.invers = inv
sl2pl.domodel = domod
sl2pl.doslice = 1
sl2pl.doresid = dores
sl2pl.dotv = -1
#HF.print_inp_to_log(sl2pl,'SL2PL')
sl2pl()
def runfittp(uvdata, fittpdir, fittpfile):
fittp = AIPSTask('FITTP')
fittp.indata = uvdata
fittp.doall = -1
fittp.intype = ''
fittp.outtape = 1
srcname = re.sub(r"\s+", '-', fittpfile)
fittp.dataout = os.path.join(fittpdir, srcname)
print "Saving to disk: ", uvdata.name, uvdata.klass, uvdata.seq
fittp.go()
def pang(uvdata,suba=0):
clcor = AIPSTask('clcor')
clcor.indata = uvdata
clcor.opcode = 'PANG'
clcor.subarray = suba
clcor.gainv = uvdata.table_highver('CL')
clcor.gainu = uvdata.table_highver('CL')+1
clcor.clcorprm[1] = 1
HF.print_inp_to_log(clcor,'CLCOR PANG')
clcor()
def runmsort(indata):
print 'Running MSORT.'
msort = AIPSTask('MSORT')
msort.indata = indata
msort.outdata = indata
msort.sort = 'TB'
msort.go()
def write_fits(outname):
fittp = AIPSTask('fittp')
# Write the last Entry in the catalog to disk
fittp.indisk = DISK_ID
last = cat.last_entry()
fittp.inname = last.name
fittp.inclass = last.klass
fittp.inseq = last.seq
if os.path.exists(outname):
os.remove(outname)
print 'Removed existing file to make room for new one :', outname
fittp.dataout = 'PWD:' + outname
fittp.go()
def help(obj):
if isinstance(obj, AIPSTask):
obj.help()
elif type(obj) == type(""):
AIPSTask(obj).help()
else:
_help(obj)
pass
return
def swpol(uvdata,antennas):
swpol = AIPSTask('swpol')
swpol.indata = uvdata
swpol.antennas[1:] = antennas
swpol.outname = uvdata.name
swpol.outclass = 'SWPOL'
swpol.outseq = uvdata.seq
swpol.outdisk = uvdata.disk
HF.print_inp_to_log(swpol,'SWPOL')
swpol()
return AIPSUVData(uvdata.name,'SWPOL',uvdata.disk,uvdata.seq)
def acscl(uvdata,gainu=0,bpv=1,doband=1):
acscl = AIPSTask('acscl')
acscl.indata = uvdata
#acscl.timer[1:] = [0]
acscl.solint = 0
acscl.docalib = 1
acscl.gainuse =gainu
acscl.bpver=bpv
acscl.doband=doband
HF.print_inp_to_log(acscl,'ACSCL')
acscl()
def lwpla(aipsname, incl, indisk, outfile, logfiledir='./'):
lwpla = AIPSTask('lwpla')
lwpla.inname = aipsname
lwpla.inclass = incl
lwpla.indisk = indisk
lwpla.outfile = outfile
stdout = sys.stdout
sys.stdout = open(logfiledir + aipsname + '.log', 'a')
lwpla.go()
sys.stdout.close()
sys.stdout = stdout
def runsousp(indata, sources):
sousp = AIPSTask('SOUSP')
sousp.indata = indata
sousp.sources[1:] = sources
sousp.order = 1
sousp.dotv = -1
sousp.go()
return sousp.specindx
def make_average_map(restfreq, uniqueid):
print_header("Making average map")
sqash = AIPSTask("sqash")
# squash the frequency axis to make a continuum image
sqash.indisk = DISK_ID
sqash.outdisk = DISK_ID
last = cat.last_entry()
sqash.inname = last.name
sqash.inclass = last.klass
sqash.inseq = last.seq
sqash.bdrop = 3 # squash frequency axis
sqash.go()
outcont = write_average_map(restfreq, uniqueid)
return outcont
def lwpla (aipsname,incl,indisk,outfile,logfiledir='./'):
lwpla = AIPSTask('lwpla')
lwpla.inname = aipsname
lwpla.inclass = incl
lwpla.indisk = indisk
lwpla.outfile = outfile
stdout = sys.stdout; sys.stdout = open(logfiledir+aipsname+'.log','a')
lwpla.go()
sys.stdout.close(); sys.stdout = stdout
def stars (aipsname, incl, indisk, intext='./starsfile',logfiledir='./'):
stars = AIPSTask('stars')
stars.inname = aipsname
stars.inclass = incl
stars.indisk = indisk
try:
stars.stvers = 0 # does not exist in some AIPS versions
except:
pass
stars.intext = './starsfile'
stdout = sys.stdout; sys.stdout = open(logfiledir+aipsname+'.log','a')
stars.go()
sys.stdout.close(); sys.stdout = stdout
def runmsort(indata):
print 'Running MSORT.'
msort = AIPSTask('MSORT')
msort.indata = indata
msort.outdata = indata
msort.sort = 'TB'
msort.go()
def write_fits(outname):
fittp = AIPSTask("fittp")
# Write the last Entry in the catalog to disk
fittp.indisk = DISK_ID
last = cat.last_entry()
fittp.inname = last.name
fittp.inclass = last.klass
fittp.inseq = last.seq
if os.path.exists(outname):
os.remove(outname)
print "Removed existing file to make room for new one :", outname
fittp.dataout = "PWD:" + outname
fittp.go()
def load_into_aips(myfiles):
"""Load files into AIPS with UVLOD task."""
uvlod = AIPSTask('uvlod')
uvlod.outdisk = DISK_ID # write all input data to a select disk
uvlod.userno = AIPS.userno
first_file = True # to help determine center freq to use
for this_file in myfiles: # input all AIPS single dish FITS files
print 'Adding {0} to AIPS.'.format(this_file)
uvlod.datain = 'PWD:' + this_file
uvlod.go()
# get the center frequency of the sdf file that was just loaded
last = cat.last_entry()
spectra = cat.get_uv(last)
center_freq = spectra.header.crval[2]
# if this is the first file loaded, look for
# the same frequency in the next ones
if first_file:
expected_freq = center_freq
first_file = False
# if frequency of sdf file just loaded and 1st file differ by
# more than 100 kHz, do not use the current file
if abs(expected_freq - center_freq) > 1e5:
print 'Frequencies differ: {0} != {1}'.format(center_freq, expected_freq)
print ' Rejecting {0}'.format(this_file)
spectra.zap()
def runprtmsg(prtask, outprint):
prtmsg = AIPSTask('PRTMSG')
clrmsg = AIPSTask('CLRMSG')
prtmsg.prtask = prtask
prtmsg.docrt = -1
prtmsg.outprint = outprint
# RUN VERB
prtmsg.go()
clrmsg()
def pclcal (aipsname,indisk,inver,logfiledir='./'):
uvdata = AIPSUVData (aipsname,'FITS',indisk,1)
clcal = AIPSTask ('clcal')
clcal.indata = uvdata
clcal.inver = inver
clcal.snver = inver
stdout = sys.stdout; sys.stdout = open(logfiledir+aipsname+'.log','a')
clcal.go()
sys.stdout.close(); sys.stdout = stdout
def runlwpla(indata, outfile):
plver=0
outfile = re.sub(r"\s+", '-', outfile)
for tab in indata.tables :
if 'PL' in tab[1] :
plver = plver + 1
if os.path.exists(outfile) :
os.remove(outfile)
lwpla = AIPSTask('LWPLA')
lwpla.indata = indata
lwpla.plver = 1
lwpla.inver = plver
lwpla.outfile = outfile
lwpla.msgkill = -10
lwpla.go()
# Remove PL tables
indata.zap_table('PL', -1)
def runuvsrt(datafile, inname, indisk, thisdir):
uvsrt = AIPSTask('UVSRT')
klass = datafile.klass
uvsrt.indata = datafile
uvsrt.outdata = AIPSUVData(datafile.name,'UVSRT',indisk,datafile.seq)
uvsrt.sort = 'TB'
uvsrt.go()
datafile.zap()
datafile = AIPSUVData(inname,'UVSRT',indisk,thisdir)
datafile.rename(inname,klass,thisdir)
def runtasav(uvdata, fittpdir, fittpfile, indisk):
# Backup the FG tables after flagging
tasav = AIPSTask('TASAV')
tasavfil = AIPSUVData(uvdata.name, 'TASAV', indisk, uvdata.seq)
tasav.indata = uvdata
tasav.outdata = tasavfil
tasav.outseq = uvdata.seq
print "Saving tables for ", uvdata.name, uvdata.klass, uvdata.seq
tasav.go()
runfittp(tasavfil, fittpdir, fittpfile)
tasavfil.zap()
def psplit (aipsname,source,indisk,logfiledir='./'):
uvdata = AIPSUVData (aipsname,'FITS',indisk,1)
split = AIPSTask ('split')
split.indata = uvdata
split.outclass = 'SPLIT'
split.docalib = 1
stdout = sys.stdout; sys.stdout = open(logfiledir+aipsname+'.log','a')
split.go()
sys.stdout.close(); sys.stdout = stdout
uvdata = AIPSUVData(source,'SPLIT',indisk,1)
uvdata.rename(aipsname,'SPLIT',1)
def load_into_aips(myfiles):
"""Load files into AIPS with UVLOD task."""
# mandl = AIPSTask('mandl')
# mandl.outdisk = DISK_ID
# mandl.go()
print_header("Loading data into AIPS")
uvlod = AIPSTask('uvlod')
uvlod.outdisk = DISK_ID # write all input data to a select disk
uvlod.userno = AIPS.userno
first_file = True # to help determine center freq to use
for this_file in myfiles: # input all AIPS single dish FITS files
if not os.path.exists(this_file):
print 'WARNING: can not find file: {0}'.format(this_file)
continue
print 'Adding {0} to AIPS.'.format(this_file)
# AIPS has problems with long filenames so we create a symlink to a short filename
if os.path.exists(tmpfn):
os.unlink(tmpfn)
os.symlink(this_file, tmpfn)
uvlod.datain = 'PWD:' + tmpfn
uvlod.go()
os.unlink(tmpfn) # remove the temporary symlink
# get the center frequency of the sdf file that was just loaded
last = cat.last_entry()
spectra = cat.get_uv(last)
center_freq = spectra.header.crval[2]
# if this is the first file loaded, look for
# the same frequency in the next ones
if first_file:
expected_freq = center_freq
first_file = False
# if frequency of sdf file just loaded and 1st file differ by
# more than 100 kHz, do not use the current file
if abs(expected_freq - center_freq) > 1e5:
print 'Frequencies differ: {0} != {1}'.format(center_freq, expected_freq)
print ' Rejecting {0}'.format(this_file)
spectra.zap()
def run_dbcon(entryA, entryB):
"""Combine the data in AIPS with the DBCON task"""
dbcon = AIPSTask('dbcon')
# always do firs
dbcon.indisk = dbcon.outdisk = dbcon.in2disk = DISK_ID
dbcon.userno = AIPS.userno
file1 = cat.get_entry(entryA)
dbcon.inname = file1.name
dbcon.inclass = file1.klass
dbcon.inseq = file1.seq
file2 = cat.get_entry(entryB)
dbcon.in2name = file2.name
dbcon.in2class = file2.klass
dbcon.in2seq = file2.seq
dbcon.reweight[1] = 0
dbcon.reweight[2] = 0
print 'combining 1: ', dbcon.inname, dbcon.inclass, dbcon.inseq
print 'combining 2: ', dbcon.in2name, dbcon.in2class, dbcon.in2seq
dbcon.go()
# 'Flags_1021+6803.fits',
# 'Flags_1022+6806.fits',
# 'Flags_1331+305.fits',
# 'Flags_1020+6806.fits',
# 'Flags_1021+6809.fits',
# 'Flags_1022+6812.fits',
# 'Flags_1407+284.fits']
filelist = ['Flags_1022+6749.fits']
# 'Flags_1331+305.fits',
# 'Flags_1407+284.fits']
flag_dir = '/scratch/nas_mberc2/SuperCLASS/Data/eMERLIN/2C_20150720/flags/'
fitld = AIPSTask('FITLD')
fitld.outdisk = dsk
tacop = AIPSTask('TACOP')
uvcop = AIPSTask('UVCOP')
clip = AIPSTask('CLIP')
#move = AIPSTask('MOVE')
for f in filelist:
src = f.split('_')[-1].split('.')[0]
# fitld.datain = flag_dir+f
# outdata = AIPSUVData(src,'FG_TAB',dsk,1)
from AIPSTask import AIPSTask, AIPSList
from AIPSData import *
from AIPSData import AIPSUVData, AIPSImage
from Wizardry.AIPSData import AIPSUVData as WizAIPSUVData
from Wizardry.AIPSData import AIPSImage as WizAIPSImage
import sys
import os
import math
AIPS.userno=int(sys.argv[1]) # retrieve AIPS pipeline user number
myfiles = sys.argv[2:] # make a list of input files
mydisk=2 # choose a good default work disk
AIPSCat().zap() # empty the catalog
uvlod=AIPSTask('uvlod') # Create structures for AIPS tasks
sdgrd=AIPSTask('sdgrd')
fittp=AIPSTask('fittp')
dbcon=AIPSTask('dbcon')
trans=AIPSTask('trans')
imlin=AIPSTask('imlin')
avspc=AIPSTask('avspc')
subim=AIPSTask('subim')
sqash=AIPSTask('sqash')
for thisFile in myfiles: # input all AIPS single dish FITS files
print thisFile
uvlod.datain='PWD:'+thisFile
print uvlod.datain
uvlod.outdisk=mydisk
uvlod.go()
restFreqMHz = float(sys.argv[3]) # rest Frequency (MHz)
velocityKmS = float(sys.argv[4]) # velocity (km/s)
velWidthKmS = float(sys.argv[5]) # velocity Full Width (km/s)
mydisk=2
defaultName = 'Pipeline'
#Enforce name > 5 characters
if len(outName) < 6:
outName = defaultName[0:(6-len(outName))] + outName
print 'Outname : ',outName
print 'RestFreq: ',restFreqMHz, ' (MHz)'
print 'Velocity: ',velocityKmS,' (km/s)'
print 'VelWidth: ',velWidthKmS,' (km/s)'
fittp=AIPSTask('fittp')
momnt=AIPSTask('momnt')
subim=AIPSTask('subim')
image = AIPSImage(AIPSCat()[mydisk][-1].name, 'IMLIN', mydisk, 1)
# now read parameters passed inside the data header
nChan = round(image.header.naxis[0])
refChan = image.header.crpix[0]
nuRef = image.header.crval[0]
dNu = image.header.cdelt[0]
print nChan, refChan, nuRef, dNu
#set rest frequency to select out the line
restFreq = restFreqMHz * 1.e6
import os
import urllib
AIPS.userno = 1999
# Download a smallish FITS file from the EVN archive.
url = 'http://archive.jive.nl/exp/N03L1_030225/fits/n03l1_1_1.IDI1'
file = '/tmp/' + os.path.basename(url)
if not os.path.isfile(file):
urllib.urlretrieve(url, file)
assert(os.path.isfile(file))
name = os.path.basename(url).split('_')[0].upper()
uvdata = AIPSUVData(name, 'UVDATA', 1, 1)
if uvdata.exists():
uvdata.zap()
fitld = AIPSTask('fitld')
fitld.datain = file
fitld.outdata = uvdata
fitld.douvcomp = 0
fitld.msgkill = 2
fitld.go()
uvdata = WizAIPSUVData(name, 'UVDATA', 1, 1, AIPS.userno)
for vis in uvdata:
vis.visibility[0][0][0][2] = 1.234
vis.update()
continue
from AIPS import AIPS
from AIPSTask import AIPSTask
from AIPSData import AIPSImage
AIPS.userno = 1999
image = AIPSImage('MANDELBROT', 'MANDL', 1, 1)
if image.exists():
image.zap()
mandl = AIPSTask('mandl')
mandl.outdata = image
mandl.imsize[1:] = [ 512, 512 ]
mandl.go()
try:
header = image.header
print 'Dimension: %dx%d' % (header.naxis[0], header.naxis[1])
print image.tables
finally:
image.zap()
# Download a smallish FITS file from the EVN archive.
url = 'http://archive.jive.nl/exp/N03L1_030225/fits/n03l1_1_1.IDI1'
file = '/tmp/' + os.path.basename(url)
if not os.path.isfile(file):
urllib.urlretrieve(url, file)
assert(os.path.isfile(file))
name = os.path.basename(url).split('_')[0].upper()
uvdata = AIPSUVData(name, 'UVDATA', 1, 1)
if uvdata.exists():
uvdata.zap()
pass
assert(not uvdata.exists())
fitld = AIPSTask('fitld')
fitld.datain = file
fitld.outdata = uvdata
fitld.msgkill = 2
fitld()
assert(uvdata.exists())
tv = AIPSTV()
# Wait a bit to make sure the address used by the AIPS TV can be
# reused again.
time.sleep(30)
try:
tv.start()
def __init__(self, iterNum, **args):
self.iterNum = iterNum
self.args = args
AIPS.userno=self.args["user"]#username
snInit = 0
clInit = 1
AIPSTask.msgkill = -5 #makes the output less verbose
uvdata = AIPSUVData(self.args["name"], 'UVDATA', 1, self.args["inseq"])
cleaninseq = iterNum
imageClean = AIPSImage(self.args["name"], 'ICL001', 1, cleaninseq)
imageDirty = AIPSImage(self.args["name"], 'IBM001', 1, cleaninseq)
imageCleanSC = AIPSImage(self.args["source"], 'ICL001', 1, 1)
imageDirtySC = AIPSImage(self.args["source"], 'IBM001', 1, 1)
flag = AIPSUVData(self.args["name"], 'TASAV', 1, 100)
if uvdata.exists() and iterNum == 1:
print("Data is already present")
ans1 = raw_input('\033[33mDo you want to zap the data (yes/no)? \033[0m').upper()
if ans1 == 'YES':
print("Zapping data and reloading.")
uvdata.clrstat()
uvdata.zap()
fitld = AIPSTask('fitld')
fitld.datain = self.args["dataPath"]
fitld.outname = self.args["name"]
fitld.outseq = self.args["inseq"]
fitld.ncount = self.args["fileCount"]
fitld.doconcat = 1
#fitldFL = AIPSTask("FITLD")
#fitldFL.datain = args["flagPath"]
#fitldFL.outname = self.args["name"]
#fitldFL.outseq = 100
#fitldFL.ncount = 1
#fitldFL.go()
snVers = 0
clVers = 1
fitld.go()
else:
ans2 = raw_input('\033[33mDo you want to zap the tables and images(yes/no)? \033[0m').upper()
if ans2 == 'YES':
print("Zapping tables/images.")
uvdata.clrstat()
uvdata.zap_table('SN', -1)
uvdata.zap_table('FL', -1)
tablesToDelete = 0
for i in uvdata.tables:
if i[1] == 'AIPS CL' and i[0]>tablesToDelete:
tablesToDelete = i[0]
for k in range(tablesToDelete,1,-1):
uvdata.zap_table('CL', k)
snVers = 0
clVers = 1
else:
print("Going direclty to imaging.")
"""
snVers = 0
clVers = 0
for i in uvdata.tables:
if i[1] == 'AIPS SN' and i[0] > snVers:
snVers = i[0]
if i[1] == 'AIPS CL' and i[0] > clVers:
clVers = i[0]
"""
clVers = int(raw_input("What cl table would you like to use? "))
loc = location_finder.Location_finder(clVers, **self.args)
sys.exit()
elif not uvdata.exists():
print("Loading data")
fitld = AIPSTask('fitld')
fitld.datain = self.args["dataPath"]
fitld.outname = self.args["name"]
fitld.outseq = self.args["inseq"]
fitld.ncount = self.args["fileCount"]
fitld.doconcat = 1
fitld.go()
#fitldFL = AIPSTask("FITLD")
#fitldFL.datain = args["flagPath"]
#fitldFL.outname = self.args["name"]
#fitldFL.outseq = 100
#fitldFL.ncount = 1
#fitldFL.go()
snVers = 0
clVers = 1
else:
snVers = 0
clVers = 0
for i in uvdata.tables:
if i[1] == 'AIPS SN' and i[0] > snVers:
snVers = i[0]
if i[1] == 'AIPS CL' and i[0] > clVers:
clVers = i[0]
print("Deleting tables.")
uvdata.zap_table('SN', -1)
for k in range(clVers,1,-1):
uvdata.zap_table('CL', k)
snVers = 0
clVers = 1
if imageClean.exists():
imageClean.clrstat()
imageClean.zap()
if imageDirty.exists():
imageDirty.clrstat()
imageDirty.zap()
if flag.exists():
flag.clrstat()
flag.zap()
fitldFL = AIPSTask("FITLD")
fitldFL.datain = args["flagPath"]
fitldFL.outname = self.args["name"]
fitldFL.outseq = 100
fitldFL.ncount = 1
fitldFL.go()
print("Copying flagging")
tacop = AIPSTask("TACOP")
tacop.indata = flag
tacop.invers = 3
tacop.ncount = 1
tacop.outname = self.args["name"]
tacop.outseq = self.args["inseq"]
tacop.outclass = 'UVDATA'
tacop.outdisk = 1
tacop.outver = 0
tacop.inext = 'FG'
tacop.go()
if self.args["doBP"]:
uvdata.zap_table('BP', -1) #create a new bp table for each reftelly
print("Running bandpass")
bpass = AIPSTask('BPASS')
bpass.indata = uvdata
bpass.calsour[1] = self.args["bandPassCal"]
bpass.timer = self.args["time"]
bpass.refant = self.args["refTelly"]
if self.args["excludeTelly"]:
bpass.antennas[1:] = self.args["excludedTellys"]
bpass.go()
"""
uvdata.zap_table('TY', -1)
uvdata.zap_table('GC', -1)
print("Running antab")
antab = AIPSTask('ANTAB')
antab.indata = uvdata
antab.calin = self.args["antPath"]
antab.go()
print("Running apcal")
apcal = AIPSTask('APCAL')
apcal.indata = uvdata
apcal.timer = self.args["time"]
apcal.tyver = 1
apcal.gcver = 1
apcal.go()
snVers = snVers + 1
print("apcal made snVers {0}".format(snVers))
#applies new SN table to CL
print("Running clcal.")
clcal = AIPSTask('clcal')
clcal.indata = uvdata
clcal.calsour[1] = self.args["cal"]
clcal.timerang = self.args["time"]
clcal.snver = snVers
clcal.inver = snVers
clcal.gainver = clInit #apply to original cl
clcal.timer = self.args["time"]
clcal.interpol = "ambg"
clcal.opcode = "calp"
clcal.refant = self.args["refTelly"]
clcal.go()
clVers = clVers + 1
print("clcal made cl table {0}".format(clVers))
"""
print("Running Fring.")
fring = AIPSTask('fring') #finds fringes
fring.indata = uvdata
fring.docalib = 1
fring.gainuse = clVers
if self.args["excludeTelly"]:
fring.antennas[1:] = self.args["excludedTellys"]
fring.calsour[1] = self.args["cal"]
fring.bchan = self.args["bchan"]
fring.echan = self.args["echan"]
fring.timer = self.args["time"]
fring.refant = self.args["refTelly"]
if self.args["doBP"]:
fring.doband = 1
fring.bpver = 1
fring.go()
snVers = snVers + 1
SN = 0
for i in uvdata.tables:
if i[1] == 'AIPS SN' and i[0]>SN:
SN = i[0]
if not SN == snVers:
sys.exit("SN table number missmatch")
print("Fring created SN table {0}".\
format(snVers))
#applies new SN table to CL
print("Running clcal.")
clcal = AIPSTask('clcal')
clcal.indata = uvdata
clcal.calsour[1] = self.args["cal"]
clcal.timerang = self.args["time"]
if self.args["excludeTelly"]:
clcal.antennas[1:] = self.args["excludedTellys"]
clcal.snver = snVers
clcal.inver = snVers
clcal.gainver = clInit #apply to original cl
clcal.timer = self.args["time"]
clcal.interpol = "ambg"
clcal.opcode = "calp"
clcal.refant = self.args["refTelly"]
clcal.go()
"""
clcal.snver = snVers
clcal.inver = snVers
clcal.gainver = clVers
clcal.go()
"""
CL = 0
clVers = clVers + 1
clFring = clVers
for i in uvdata.tables:
if i[1] == 'AIPS CL' and i[0]>CL:
CL = i[0]
if not CL == clVers:
sys.exit("CL table number missmatch")
print("Clcal created CL table {0}".\
format(clVers))
#determines calibration, creates new SN
print("Running calib")
calib = AIPSTask('calib')
calib.indata = uvdata
calib.calsour[1] = self.args["cal"]
calib.docalib = 1
calib.gainuse = clVers
if self.args["excludeTelly"]:
calib.antennas[1:] = self.args["excludedTellys"]
calib.smodel[1] = 1
calib.solint = 0.2
calib.soltype = 'L1'
calib.solmode = 'P'
if self.args["doBP"]:
calib.doband = 1
calib.bpver = 1
calib.timer = self.args["time"]
calib.refant = self.args["refTelly"]
calib.go()
snVers = snVers + 1
SN = 0
for i in uvdata.tables:
if i[1] == 'AIPS SN' and i[0]>SN:
SN = i[0]
if not SN == snVers:
sys.exit("SN table number missmatch")
print("Calib created SN table {0}".\
format(snVers))
#takes SN table created by calib and applies to CL
print("Running clcal")
clcal.sources[1] = self.args["cal"]
clcal.snver = snVers
clcal.inver = snVers
clcal.gainver = clVers
clcal.go() #Apply only to cal
clVers = clVers + 1
CL = 0
for i in uvdata.tables:
if i[1] == 'AIPS CL' and i[0]>CL:
CL = i[0]
if not CL == clVers:
sys.exit("CL table number missmatch")
print("Clcal created CL table {0}".format(clVers))
#cleans the image
print("Running imagr")
imagr = AIPSTask('IMAGR')
imagr.indata = uvdata
imagr.sources[1] = self.args["cal"]
imagr.timerang = self.args["time"]
imagr.docalib = 1
imagr.outseq = iterNum #test to force it to make file
imagr.gainuse = clVers
imagr.bchan = self.args["bchan"]
imagr.echan = self.args["echan"]
imagr.nchav = (self.args["echan"]-self.args["bchan"] + 1)
if self.args["doBP"]:
imagr.doband = 1
imagr.bpver = 1
if self.args["excludeTelly"]:
imagr.antennas[1:] = self.args["excludedTellys"]
imagr.cellsize = AIPSList([0.0001,0.0001])
imagr.imsize = AIPSList([256,256])
imagr.nboxes = len(self.args["CalCleanBox"])
imagr.clbox[1:] = self.args["CalCleanBox"]
imagr.niter = 1000
imagr.go()
print("Done with imagr")
#to get last positive row
latestImgTable = 0
for j in imageClean.tables:
if j[1] == 'AIPS CC' and j[0]>latestImgTable:
latestImgTable = j[0]
ccTable = imageClean.table('CC', latestImgTable)
for row, i in enumerate(ccTable, start=2): #start @ 2 to get last positive
if i['flux']<0:
lastPositive = row
break
print("The last positive component number is: {0}".\
format(lastPositive))
print("Running Calib")
calibSelf = AIPSTask('calib')
calibSelf.in2data = imageClean
calibSelf.indata = uvdata
calibSelf.calsour[1] = self.args["cal"]
calibSelf.docalib = 1
calibSelf.gainuse = clFring
calibSelf.solint = 0.2
calibSelf.soltype = 'L1'
calibSelf.solmode = 'A&P'
if self.args["excludeTelly"]:
calibSelf.antennas[1:] = self.args["excludedTellys"]
calibSelf.ncomp[1] = lastPositive
calibSelf.timer = self.args["time"]
if self.args["doBP"]:
calibSelf.doband = 1
calibSelf.bpver = 1
calibSelf.go()
snVers = snVers + 1
SN = 0
for i in uvdata.tables:
if i[1] == 'AIPS SN' and i[0]>SN:
SN = i[0]
if not SN == snVers:
print("SN = {0} , snVers = {1}".format(SN, snVers))
sys.exit("SN table number missmatch")
print("calibSelf created SN table {0}".format(snVers))
#makes contour plot
kntr = AIPSTask('KNTR')
kntr.indata = imageClean
kntr.levs = AIPSList([-1,1,2,3,4,5,7,10])
kntr.dogrey = -1
kntr.dotv = -1
kntr.dovect = - 1
#kntr.blc[1] = .80*self.args["fitBox"][1]
#kntr.blc[2] = .80*self.args["fitBox"][2]
#kntr.trc[1] = 1.20*self.args["fitBox"][3]
#kntr.trc[2] = 1.20*self.args["fitBox"][4]
kntr.go()
lwmp = AIPSTask('LWPLA')
lwmp.indata = imageClean
lwmp.plver = 1
lwmp.invers = 1
lwmp.outfile = os.getcwd() + '/images_{0}/{1}_time{2}'.format(self.args["date"],self.args["cal"],self.iterNum) + '.ps'
lwmp.go()
print("Running clcal")
clcal.snver = snVers
clcal.inver = snVers
clcal.sources[1] = self.args["cal"]
clcal.calsour[1] = self.args["cal"]
clcal.gainver = clVers
print("clVers = {0}".format(clVers))
clcal.go() #Apply only to cal
clVers = clVers + 1
CL = 0
for i in uvdata.tables:
if i[1] == 'AIPS CL' and i[0]>CL:
CL = i[0]
if not CL == clVers:
sys.exit("CL table number missmatch")
print("clcal created CL table {0}".format(clVers))
print("Running clcal.")
clcalFinal = AIPSTask('clcal')
clcalFinal.indata = uvdata
clcalFinal.sources[1] = self.args["source"]
clcalFinal.calsour[1] = self.args["cal"]
clcalFinal.timerang = self.args["time"]
clcalFinal.snver = snVers
clcalFinal.inver = snVers
clcalFinal.gainver = clFring
if self.args["excludeTelly"]:
clcalFinal.antennas[1:] = self.args["excludedTellys"]
clcalFinal.timer = self.args["time"]
clcalFinal.refant = self.args["refTelly"]
print("clFring = {0}".format(clFring))
clcalFinal.go()
clVers = clVers +1
CL = 0
for i in uvdata.tables:
if i[1] == 'AIPS CL' and i[0]>CL:
CL = i[0]
if not CL == clVers:
sys.exit("CL table number missmatch")
print("clcalFinal created CL table {0}".format(clVers))
print("Running imagr")
imagrSC = AIPSTask('IMAGR')
imagrSC.indata = uvdata
imagrSC.sources[1] = self.args["source"]
imagrSC.timerang = self.args["time"]
imagrSC.docalib = 1
imagrSC.outseq = 1
imagrSC.outname = self.args["source"]
imagrSC.gainuse = clVers
imagrSC.bchan = self.args["SCbchan"]
imagrSC.echan = self.args["SCechan"]
imagrSC.nchav = (self.args["SCechan"]-self.args["SCbchan"] + 1)
if self.args["doBP"]:
imagrSC.doband = 1
imagrSC.bpver = 1
if self.args["excludeTelly"]:
imagrSC.antennas[1:] = self.args["excludedTellys"]
imagrSC.cellsize = AIPSList([0.0001,0.0001])
imagrSC.imsize = AIPSList([256,256])
imagrSC.nboxes = 1
imagrSC.clbox[1] = self.args["fitBox"]
imagrSC.niter = 1000
imagrSC.go()
print("Done with imagr")
#makes contour plot
kntrSC = AIPSTask('KNTR')
kntrSC.indata = imageCleanSC
kntrSC.levs = AIPSList([2,3,4,5,7,10,13,17])
kntrSC.dogrey = -1
kntrSC.dotv = -1
kntrSC.dovect = - 1
#kntr.blc[1] = .80*self.args["fitBox"][1]
#kntr.blc[2] = .80*self.args["fitBox"][2]
#kntr.trc[1] = 1.20*self.args["fitBox"][3]
#kntr.trc[2] = 1.20*self.args["fitBox"][4]
kntrSC.go()
lwmpSC = AIPSTask('LWPLA')
lwmpSC.indata = imageCleanSC
lwmpSC.plver = 1
lwmpSC.invers = 1
lwmpSC.outfile = os.getcwd() + '/images_{0}/{1}_time{2}'.format(self.args["date"],self.args["source"],self.iterNum) + '.ps'
lwmpSC.go()
loc = location_finder.Location_finder(clVers, **self.args)
imageClean.zap()
imageDirty.zap()
imageCleanSC.zap()
imageDirtySC.zap()
flag.zap()
with open(os.getcwd() + '/images_{0}/params{1}.txt'.format(self.args["date"],self.iterNum),'w') as f:
for l in self.args:
f.write("\n{0}".format(l))
