def pimagr (aipsname,aipsclass,docalib,source='',imsize=256,cellsize=0.1,\
nchav=-1,disk=1,gainuse=0,robust=0,niter=100,outname='',\
antennas = [], stokes='I'):
imagr = AIPSTask('imagr')
imagr.inname = aipsname
imagr.inclass = aipsclass
imagr.docalib = docalib
imagr.indisk = disk
imagr.stokes = stokes
imagr.imsize[1:] = [imsize, imsize]
imagr.cellsize[1:] = [cellsize, cellsize]
if len(antennas):
imagr.antennas[1:] = antennas
# imagr.baseline[1:] = antennas
if source == '':
try:
su = AIPSUVData(aipsname, aipsclass, disk, 1).table('SU', 1)
imagr.source[1] = su[0]['source']
except:
print 'Unable to extract source from source table'
if nchav == -1:
try:
h = AIPSUVData(aipsname, aipsclass, disk, 1).header
imagr.nchav = h['naxis'][h['ctype'].index('FREQ')]
except:
imagr.nchav = 0
imagr.gainuse = gainuse
imagr.robust = robust
imagr.niter = niter
imagr.outname = outname
# imagr.inp()
imagr.go()
def peel_source(uvdata, pols, source_no, RA_shift, Dec_shift):
for i in range(len(pols)):
pol_data = AIPSUVData(uvdata.name,pols[i],uvdata.indisk,uvdata.seq)
tasav = AIPSTask('TASAV')
tasav.indata = uvdata
tasav.outname = 'SC_SN'
tasav.outdisk = indisk
tasav.go()
sntables = AIPSUVData('SC_SN','TASAV',indisk,1)
sncor = AIPSTask('SNCOR')
sncor.indata = sntables
sncor.opcode = 'PNEG'
for i in range(5):
sncor.snver = i+1
sncor.go()
split = AIPSTask('SPLIT')
split.indata = uvdata
split.sources[1] = sourceID
split.docalib = 2
split.outdisk = indisk
split.go()
uvdata.zap()
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 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 zapexisting(inna, incl, indisk=1):
for i in AIPSCat()[indisk]:
if i['name'] == inna and i['klass'] == incl:
if i['type'] == 'MA':
AIPSImage(inna, incl, indisk, i['seq']).clrstat()
AIPSImage(inna, incl, indisk, i['seq']).zap()
else:
AIPSUVData(inna, incl, indisk, i['seq']).clrstat()
AIPSUVData(inna, incl, indisk, i['seq']).zap()
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 psplit (aipsname,source,indisk,logdir='./'):
uvdata = AIPSUVData (aipsname,'FITS',indisk,1)
split = AIPSTask ('split')
split.indata = uvdata
split.outclass = 'SPLIT'
split.docalib = 1
stdout = sys.stdout; sys.stdout = open(logdir+aipsname+'.log','a')
split.go()
sys.stdout.close(); sys.stdout = stdout
uvdata = AIPSUVData(source,'SPLIT',indisk,1)
uvdata.rename(aipsname,'SPLIT',1)
def __split_and_fittp(self, startTime, endTime, partNumber, scanNumber):
# temporary UVData to store the split, destroyed in the end
tempDiskNo = 1
tempSeqNo = 3
tempUVData = AIPSUVData('PSRALL', 'SPLIT ', tempDiskNo, tempSeqNo)
self.__clear(tempUVData)
splitTask = AIPSTask('SPLIT')
splitTask.indata = self.allUVData
splitTask.timerang = AIPSList([
0, startTime.hour, startTime.minute, startTime.second, 0,
endTime.hour, endTime.minute, endTime.second
])
splitTask.outdisk = tempDiskNo
splitTask.outseq = tempSeqNo
try:
splitTask.go()
except RuntimeError:
print("!!!!Warning: SPLIT failed at " + startTime.isoformat() +
" - " + endTime.isoformat() + " possibly no data")
# if SPLIT is successful, start FITTP
if tempUVData.exists():
fittpTask = AIPSTask('FITTP')
fittpTask.dataout = (
'/jop87_2/scratch/huang/rp024c/grid_trial/pulses/' +
self.prefix + '.PART' + str(partNumber) + '.UVFITS')
fittpTask.indata = tempUVData
fittpTask.go()
def self_calibration(uvdata, source_no, RA_shift, Dec_shift, solints, sc_type, pols, imsize, niter,refant):
nchan = uvdata.header.naxis[2]
sutable = uvdata.table('SU',1)
sourceID = str(sutable[0].source)
for i in range(len(solints)):
print('Self calibration iteration %d' % i)
for j in range(len(pols)):
print('Iteration %d: Imaging source number %d' % (i,source_no))
imagr = AIPSTask('IMAGR')
pol_data = AIPSUVData(uvdata.name,pols[j],indisk,uvdata.seq)
print pol_data.klass
print pols[j]
imagr.indata = pol_data
imagr.sources[1] = sourceID
#imagr.cellsize = AIPSList([findmaxb(uvdata)[0],findmaxb(uvdata)[1]])
imagr.cellsize = AIPSList([0.2,0.2])
imagr.imsize = AIPSList(imsize)
imagr.docalib = 2
imagr.gainuse = i+1
imagr.stokes = pols[j]
imagr.rashift[1] = RA_shift
imagr.decshift[1] = Dec_shift
imagr.niter = niter
imagr.nchav = nchan
imagr.outname = 'S%s_SC%s' % (source_no,str(i+1))
imagr.outdisk = indisk
imagr.go()
image = AIPSImage('S%s_SC%s' % (source_no,str(i+1)),'%sCL001'%pols[j][0],indisk,1)
print('Iteration %d: Making calibrations soln w/ solint=%.1f min and %s type' % (i,solints[i],sc_type[i]))
calib = AIPSTask('CALIB')
calib.indata = pol_data
calib.calsour[1] = sourceID
calib.docalib = 2
calib.in2data = image
calib.refant = refant
calib.solint = solints[i]
calib.aparm[1:] = 3, 0, 0, 0, 0, 0, 3, 0
calib.ncomp[1] = -1000000
calib.soltype = 'L1'
calib.solmode = sc_type[i]
calib.snver = i+1
calib.go()
print('Iteration %d: Applying SN table %d' % (i,i))
clcal = AIPSTask('CLCAL')
clcal.indata = pol_data
clcal.calsour[1] = sourceID
clcal.sources[1] = sourceID
clcal.opcode = 'CALP'
clcal.interpol = 'AMBG'
clcal.snver = i+1
clcal.invers = i+1
clcal.gainver = i+1
clcal.gainuse = i+2
clcal.cutoff = 60
clcal.dobtween = 0
clcal.refant = refant
clcal.go()
def zaptabs(inna, incl, indisk, inseq, tabtype, top, bottom):
uv = AIPSUVData(inna, incl, indisk, inseq)
for i in range(top, bottom - 1, -1):
try:
uv.table(tabtype, i).zap()
except:
pass
def imgseq (inna,incl,indisk,inseq):
uvdata = AIPSUVData (inna,incl,indisk,inseq)
for i in AIPSCat()[1]:
if i['name']==inna and i['klass']=='IMGSEQ':
AIPSImage(inna,'IMGSEQ',indisk,i['seq']).zap()
if i['name']==inna and i['klass']=='ICL001':
AIPSImage(inna,'ICL001',indisk,i['seq']).zap()
imagr=AIPSTask('imagr')
imagr.indata = uvdata
imagr.cellsize[1:] = [0.2,0.2]
imagr.imsize[1:] = [1024,1024]
imagr.uvwtfn = 'NA'
imagr.uvrange[1:] = [5.0,100000.0]
imagr.source[1] = 'BEAM_1'
imagr.outname = inna
imagr.niter = 200
imagr.nchav = 54
uvtap = [400.0,200.0,100.0,50.0]
beam = [0.5,0.9,1.8,5.0]
for i in range(4):
imagr.uvtaper[1:] = [uvtap[i],uvtap[i]]
imagr.bmaj,imagr.bmin = beam[i],beam[i]
imagr.go()
AIPSImage(inna,'IBM001',indisk,1).zap()
AIPSImage(inna,'ICL001',indisk,1).rename(inna,'IMGSEQ',indisk,0)
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 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 aipszap(aipsname, aipsclass, indisk=1):
pca = AIPSCat()
for j in pca[indisk]:
if j['name'] == aipsname and j['klass'] == aipsclass:
if j['type'] == 'UV':
data = AIPSUVData(aipsname, aipsclass, indisk, j['seq'])
else:
data = AIPSImage(aipsname, aipsclass, indisk, j['seq'])
data.zap()
def fullcal(fringe_inna, fcl, indisk, refant):
zaptabs(fringe_inna, fcl, indisk, 1, 'SN', 10, 1)
zaptabs(fringe_inna, fcl, indisk, 1, 'CL', 10, 2)
zapim(fringe_inna, 'ICL001', indisk, 10, 1)
zapim(fringe_inna, 'IBM001', indisk, 10, 1)
# source = AIPSUVData(fringe_inna,fcl,indisk,1).sources[0]
source = 'BEAM_1'
pfring (fringe_inna,refant,[0],source,solint=5,\
weightit=1,zero=5,aipsclass=fcl,\
suppress_rate=1) # delay cal -> SN1
psnsmo(fringe_inna, fcl, indisk, 'VLBI') # edited delay -> SN2
pclcal(fringe_inna, indisk, 2, aipsclass=fcl) # SN2 -> CL2
pcalib (fringe_inna,fcl,indisk,0.5,refant,\
docalib=1) # phase cal w/CL2 -> SN3
pclcal(fringe_inna, indisk, 3, aipsclass=fcl) # SN3+CL2 ->CL3
pimagr(fringe_inna, fcl, 1) # image with CL3 -> ICL001.1
pcalib (fringe_inna,fcl,indisk,0.5,refant,\
solmode='A&P',docalib=1,in2name=fringe_inna,\
in2class='ICL001',in2seq=1,calsour=source) # CL3/ICL001.1 -> SN4
pclcal(fringe_inna, indisk, 4, aipsclass=fcl) # SN4 + CL3 -> CL4
pimagr(fringe_inna, fcl, 1) # image with CL4 -> ICL001.2
for i in [4, 3, 2, 1]:
AIPSUVData(fringe_inna, fcl, indisk, 1).table('SN', i).zap()
for i in [4, 3, 2]:
AIPSUVData(fringe_inna, fcl, indisk, 1).table('CL', i).zap()
pfring (fringe_inna,refant,[0],source,solint=5,\
weightit=1,zero=5,aipsclass=fcl,\
suppress_rate=1,in2name=fringe_inna,\
in2class='ICL001',in2seq=2,docalib=-1) # delay cal w/ICL001.2 -> SN1
psnsmo(fringe_inna, fcl, indisk, 'VLBI') # edited delay ->SN2
pclcal(fringe_inna, indisk, 2, aipsclass=fcl) # SN2 -> CL2
pcalib (fringe_inna,fcl,indisk,0.5,refant,\
docalib=1,in2name=fringe_inna,\
in2class='ICL001',in2seq=2) # phase cal w/CL2,ICL001.2 -> SN3
pclcal(fringe_inna, indisk, 3, aipsclass=fcl) # SN3+CL2 -> CL3
pimagr(fringe_inna, fcl, 1) # image w/CL3 -> ICL001.3
source = AIPSUVData(fringe_inna, fcl, indisk, 1).sources[0]
pcalib (fringe_inna,fcl,indisk,0.5,refant,\
solmode='A&P',docalib=1,\
in2name=fringe_inna, in2class='ICL001',
in2seq=3,calsour=source) # CL3/ICL001.3 -> SN4
pclcal(fringe_inna, indisk, 4, aipsclass=fcl) # SN4 + CL3 -> CL4
pimagr(fringe_inna, fcl, 1) # image with CL4 -> ICL001.4
def tasaver(uvdata, name):
tasav = AIPSTask('TASAV')
tasav.indata = uvdata
tasav.outname = name[:8]
tasav.go()
os.system('rm -r eg078e_%s.TASAV' % name[:8])
fittp = AIPSTask('FITTP')
fittp.indata = AIPSUVData(name[:8], 'TASAV', 1, 1)
fittp.dataout = 'PWD:eg078e_%s.TASAV' % name[:8]
fittp.go()
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 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 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 runfitld(datain, indisk, thisdir):
fitld = AIPSTask('FITLD')
fitld.datain = datain # "datain" is correct here (use "indata" in most other places)
fitld.outdisk = indisk
fitld.digicor = -1
fitld.douvcomp = -1
fitld.clint = 8 / 60
fitld.bif = 1
fitld.eif = 0
fitld.outdata = AIPSUVData('TMP', 'UVDATA', indisk, thisdir)
fitld.go()
def get_uv(self, e):
"""Get a AIPSUVData object form the AIPS entry.
Args:
e: A catalog entry, like what's returned from get_entry()
Returns:
AIPS UVData object.
"""
return AIPSUVData(e.name, e.klass, self.DISK_ID, e.seq)
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 pfring (aipsname,refant,antennas,source,indisk=1,delaywin=600,ratewin=20,\
solint=1,snr=2,logdir='./',weightit=3,zero=0,aipsclass='FITS',\
aipsseq=1,suppress_rate=0,in2name='',in2class='',in2seq=1,\
docalib=-1):
uvdata = AIPSUVData (aipsname,aipsclass,indisk,aipsseq)
fring = AIPSTask ('FRING')
fring.refant = refant
fring.indata = uvdata
fring.calsour[1:] = [source]
fring.antennas[1:] = antennas
if in2name!='' and in2class=='':
uv2data = AIPSUVData (in2name, in2class, indisk, in2seq)
fring.in2data = uv2data
fring.solint = solint
fring.aparm[1:] = [0,0,0,0,0,2,snr,0,0]
fring.dparm[1:] = [0,delaywin,ratewin,0,0,0,0,zero,suppress_rate]
fring.weightit = weightit
fring.docalib = docalib
stdout = sys.stdout; sys.stdout = open(logdir+aipsname+'.log','a')
# fring.inp()
fring.go()
sys.stdout.close(); sys.stdout = stdout
def uvcop(uvdata,timer=[0,0,0,0],sources=[],antennas=[],uvcopprm=[1,0,0,1,0,0,0]):
uvcop = AIPSTask('uvcop')
uvcop.indata = uvdata
uvcop.outname = uvdata.name
uvcop.outclass = 'UVCOP'
uvcop.outseq = uvdata.seq
uvcop.outdisk = uvdata.disk
uvcop.timer[1:] = timer
uvcop.antennas[1:] = antennas
uvcop.sources[1:] = sources
uvcop.uvcopprm[1:] = uvcopprm
uvcop()
return AIPSUVData(uvdata.name,'UVCOP',uvdata.disk,uvdata.seq)
def pload (filename,aipsname,indisk,outcl,logdir='./',doindxr=True):
fitld = AIPSTask ('FITLD')
fitld.datain = str(filename)
fitld.outna = aipsname
fitld.outcl = outcl
fitld.dokeep = 1
fitld.outdisk = indisk
stdout = sys.stdout; sys.stdout = open(logdir+aipsname+'.log','a')
fitld.go ()
if doindxr:
uvdata = AIPSUVData (aipsname,'FITS',1,1)
indxr = AIPSTask ('INDXR')
indxr.cparm[1:] = [0,0,0.1,0,0,0,0,0,0,0]
indxr.indata = uvdata
indxr.go()
sys.stdout.close(); sys.stdout = stdout
def pfring (aipsname,refant,antennas,source,indisk,delaywin=600,ratewin=20,\
solint=1,snr=2,logfiledir='./'):
uvdata = AIPSUVData(aipsname, 'FITS', indisk, 1)
fring = AIPSTask('FRING')
fring.refant = refant
fring.indata = uvdata
fring.calsour[1:] = [source]
fring.antennas[1:] = antennas
fring.solint = solint
fring.aparm[1:] = [0, 0, 0, 0, 0, 2, snr, 0, 0]
fring.dparm[1:] = [0, delaywin, ratewin, 0, 0, 0, 0, 0, 0]
fring.weightit = 1
stdout = sys.stdout
sys.stdout = open(logfiledir + aipsname + '.log', 'a')
fring.go()
sys.stdout.close()
sys.stdout = stdout
def find_difmap_chan(inna, incl, indisk=1, inseq=1):
INCR = 1
if incl == '':
output = inna.split('/')[-1] if '/' in inna else inna
try:
AIPSUVData('DIFMAP', 'UVDATA', indisk, inseq).zap()
print 'Removed DIFMAP.UVDATA.%d disk %d' % (inseq, indisk)
except:
pass
fitld = AIPSTask('fitld')
fitld.datain = inna if '/' in inna else './' + inna
fitld.outname = 'DIFMAP'
fitld.outclass = 'UVDATA'
fitld.outdisk = indisk
fitld.outseq = inseq
fitld.go()
inna, incl = 'DIFMAP', 'UVDATA'
else:
output = '%s_%s' % (inna, incl)
data = WizAIPSUVData(inna, incl, indisk, inseq)
for i in data:
v = i.visibility
na = np.asarray(np.ravel(v[:, :, 0, 0]), dtype='bool')
try:
a = na | a
except:
a = np.copy(na)
bstart, bend = [], []
for i in range(len(a)):
if (i == 0 and a[i]) or (i != 0 and a[i] and not a[i - 1]):
bstart.append(i + 1)
if (i != 0 and not a[i] and a[i - 1]):
bend.append(i)
if (a[i] and i == len(a) - 1):
bend.append(len(a))
fo = open('dchan_%s' % (output), 'w')
fo.write('select I,')
for i in range(len(bstart)):
fo.write('%d,%d' % (bstart[i], bend[i]))
if i != len(bstart) - 1:
fo.write(',')
fo.write('\n')
fo.close()
def fittp(imdata,outfile=''):
uvdata=AIPSUVData(*imdata)
if outfile=='':
outfile=uvdata.header['object']
while os.path.isfile(aips_out+outfile):
outname=outfile.split('.')[0]
filetype=outfile.split('.')[-1]
outname=outname.split('_')
try:
outname[-1]= str(int(outname[-1])+1)
except ValueError:
outname.append('2')
outfile='_'.join(outname)+'.'+filetype
fittp = AIPSTask('fittp')
fittp.indata = uvdata
fittp.dataout = aips_out+outfile
HF.print_inp_to_log(fittp,'FITTP')
fittp()
def getuvdata(cno, disk=1):
'''
get AIPSUVData object at a specified AIPS Catalogue number and AIPS Disk.
Args:
cno (int):
AIPS Catalogue Number
disk (int, default=1):
Number of AIPS Disk
Returns:
AIPSUVData object
'''
cat = pcat(output=True, doprint=False, disk=disk)
isdata = False
for catdata in cat:
if catdata["cno"] == cno:
isdata = True
break
if not isdata:
raise ValueError("No data at cno=%d and disk=%d" % (cno, disk))
return AIPSUVData(catdata["name"], catdata["klass"], disk, catdata["seq"])
def pfring (aipsname,refant,antennas,source,indisk=1,delaywin=600,ratewin=20,\
solint=1,snr=2,dparm4=0,logdir='./',weightit=1,zero=0,aipsclass='FITS',\
aipsseq=1,suppress_rate=0):
uvdata = AIPSUVData(aipsname, aipsclass, indisk, aipsseq)
fring = AIPSTask('FRING')
fring.refant = refant
fring.indata = uvdata
fring.calsour[1:] = [source]
fring.antennas[1:] = antennas
fring.solint = solint
fring.aparm[1:] = [0, 0, 0, 0, 0, 2, snr, 0, 0]
fring.dparm[1:] = [
0, delaywin, ratewin, dparm4, 0, 0, 0, zero, suppress_rate
]
fring.weightit = weightit
stdout = sys.stdout
sys.stdout = open(logdir + aipsname + '.log', 'a')
# fring.inp()
fring.go()
sys.stdout.close()
sys.stdout = stdout
