def ssobjangdiam(srcName, epoch, ephemdata="",unit=""):
"""
srcName: solar system object name (case insensitive)
epoch: in string format (e.g. "2015/09/01:12:00:00")
ephemdata: ephemeris data (default = "", look up the standard ~/alma/JPL_Horizons in the data repo
unit: unit for the output ang. diam.
"""
defaultDataPath = os.getenv("CASAPATH").split()[0] + "/data/ephemerides/JPL-Horizons/"
me = taskinit.metool()
qa = taskinit.qatool()
if ephemdata!="":
datapath = ephemdata
else:
mjd = me.epoch("utc",epoch)['m0']['value']
datapath = findEphemTable(defaultDataPath, srcName, mjd)
me.framecomet(datapath)
me.doframe(me.epoch("utc", epoch))
me.doframe(me.observatory("ALMA"))
angdiamrad= me.cometangdiam()
if unit=="" or unit=="rad":
angdiam = angdiamrad
else:
angdiam = qa.convert(qa.quantity(angdiamrad), unit)
return angdiam
def qufromgain(caltable, badspw=[], paoffset=0.0):
mytb = taskinit.tbtool()
myme = taskinit.metool()
mytb.open(caltable + '/ANTENNA')
pos = mytb.getcol('POSITION')
meanpos = pl.mean(pos, 1)
frame = mytb.getcolkeyword('POSITION', 'MEASINFO')['Ref']
units = mytb.getcolkeyword('POSITION', 'QuantumUnits')
mpos = myme.position(frame,
str(meanpos[0]) + units[0],
str(meanpos[1]) + units[1],
str(meanpos[2]) + units[2])
myme.doframe(mpos)
# _geodetic_ latitude
latr = myme.measure(mpos, 'WGS84')['m1']['value']
print 'Latitude = ', latr * 180 / pi
mytb.open(caltable + '/FIELD')
nfld = mytb.nrows()
dirs = mytb.getcol('DELAY_DIR')[:, 0, :]
mytb.close()
print 'Found as many as ' + str(nfld) + ' fields.'
mytb.open(caltable + '/SPECTRAL_WINDOW')
nspw = mytb.nrows()
bandnames = [x.split('#')[0].split('_')[-1] for x in mytb.getcol('NAME')]
mytb.close()
print 'Found as many as ' + str(nspw) + ' spws.'
R = pl.zeros((nspw, nfld))
Q = pl.zeros((nspw, nfld))
U = pl.zeros((nspw, nfld))
mask = pl.ones((nspw, nfld), dtype=bool)
if (len(badspw) > 0):
mask[badspw, :] = False
QU = {}
mytb.open(caltable)
for ifld in range(nfld):
for ispw in range(nspw):
st = mytb.query('FIELD_ID==' + str(ifld) +
' && SPECTRAL_WINDOW_ID==' + str(ispw))
nrows = st.nrows()
if nrows > 0:
rah = dirs[0, ifld] * 12.0 / pi
decr = dirs[1, ifld]
times = st.getcol('TIME')
gains = st.getcol('CPARAM')
ants = st.getcol('ANTENNA1')
nants = ants.max() + 1
# times
time0 = 86400.0 * floor(times[0] / 86400.0)
rtimes = times - time0
# amplitude ratio
amps = pl.absolute(gains)
amps[amps == 0.0] = 1.0
ratio = amps[0, 0, :] / amps[1, 0, :]
ratio.resize(nrows / nants, nants)
# parang
parang = pl.zeros(len(times))
for itim in range(len(times)):
tm = myme.epoch('UTC', str(times[itim]) + 's')
last = myme.measure(tm, 'LAST')['m0']['value']
last -= floor(last) # days
last *= 24.0 # hours
ha = last - rah # hours
har = ha * 2.0 * pi / 24.0
parang[itim] = atan2((cos(latr) * sin(har)),
(sin(latr) * cos(decr) -
cos(latr) * sin(decr) * cos(har)))
parang.resize(nrows / nants, nants)
parang += bandpa(bandnames[ispw]) # feed pos ang offset
parang += (paoffset * pi / 180.) # manual feed pa offset
parangd = parang * (180.0 / pi)
A = pl.ones((nrows / nants, 3))
A[:, 1] = pl.cos(2 * parang[:, 0])
A[:, 2] = pl.sin(2 * parang[:, 0])
fit = pl.lstsq(A, pl.square(ratio))
ants0 = range(nants)
rsum = pl.sum(ratio[:, ants0], 1)
rsum /= len(ants0)
fit = pl.lstsq(A, pl.square(rsum))
R[ispw, ifld] = fit[0][0]
Q[ispw, ifld] = fit[0][1] / R[ispw, ifld] / 2.0
U[ispw, ifld] = fit[0][2] / R[ispw, ifld] / 2.0
P = sqrt(Q[ispw, ifld]**2 + U[ispw, ifld]**2)
X = 0.5 * atan2(U[ispw, ifld], Q[ispw, ifld]) * 180 / pi
print 'Fld=', ifld, 'Spw=', ispw, '(B=' + str(
bandnames[ispw]) + ', PA offset=' + str(
bandpa(bandnames[ispw]) * 180. /
pi) + 'deg)', 'Gx/Gy=', R[ispw, ifld], 'Q=', Q[
ispw, ifld], 'U=', U[ispw, ifld], 'P=', P, 'X=', X
else:
mask[ispw, ifld] = False
st.close()
if sum(mask[:, ifld]) > 0:
print 'For field id = ', ifld, ' there are ', sum(
mask[:, ifld]), 'good spws.'
Qm = pl.mean(Q[mask[:, ifld], ifld])
Um = pl.mean(U[mask[:, ifld], ifld])
QU[ifld] = (Qm, Um)
Qe = pl.std(Q[mask[:, ifld], ifld])
Ue = pl.std(U[mask[:, ifld], ifld])
Pm = sqrt(Qm**2 + Um**2)
Xm = 0.5 * atan2(Um, Qm) * 180 / pi
print 'Spw mean: Fld=', ifld, 'Q=', Qm, 'U=', Um, '(rms=', Qe, Ue, ')', 'P=', Pm, 'X=', Xm
mytb.close()
return QU
def qufromgain(caltable,badspw=[],paoffset=0.0):
mytb=taskinit.tbtool()
myme=taskinit.metool()
mytb.open(caltable+'/ANTENNA')
pos=mytb.getcol('POSITION')
meanpos=pl.mean(pos,1)
frame=mytb.getcolkeyword('POSITION','MEASINFO')['Ref']
units=mytb.getcolkeyword('POSITION','QuantumUnits')
mpos=myme.position(frame,
str(meanpos[0])+units[0],
str(meanpos[1])+units[1],
str(meanpos[2])+units[2])
myme.doframe(mpos)
# _geodetic_ latitude
latr=myme.measure(mpos,'WGS84')['m1']['value']
print 'Latitude = ',latr*180/pi
mytb.open(caltable+'/FIELD')
nfld=mytb.nrows()
dirs=mytb.getcol('DELAY_DIR')[:,0,:]
mytb.close()
print 'Found as many as '+str(nfld)+' fields.'
mytb.open(caltable+'/SPECTRAL_WINDOW')
nspw=mytb.nrows()
bandnames=[x.split('#')[0].split('_')[-1] for x in mytb.getcol('NAME')]
mytb.close()
print 'Found as many as '+str(nspw)+' spws.'
R=pl.zeros((nspw,nfld))
Q=pl.zeros((nspw,nfld))
U=pl.zeros((nspw,nfld))
mask=pl.ones((nspw,nfld),dtype=bool)
if (len(badspw)>0):
mask[badspw,:]=False
QU={}
mytb.open(caltable)
for ifld in range(nfld):
for ispw in range(nspw):
st=mytb.query('FIELD_ID=='+str(ifld)+' && SPECTRAL_WINDOW_ID=='+str(ispw))
nrows=st.nrows()
if nrows > 0:
rah=dirs[0,ifld]*12.0/pi
decr=dirs[1,ifld]
times=st.getcol('TIME')
gains=st.getcol('CPARAM')
ants=st.getcol('ANTENNA1')
nants=ants.max()+1
# times
time0=86400.0*floor(times[0]/86400.0)
rtimes=times-time0
# amplitude ratio
amps=pl.absolute(gains)
amps[amps==0.0]=1.0
ratio=amps[0,0,:]/amps[1,0,:]
ratio.resize(nrows/nants,nants)
# parang
parang=pl.zeros(len(times))
for itim in range(len(times)):
tm=myme.epoch('UTC',str(times[itim])+'s')
last=myme.measure(tm,'LAST')['m0']['value']
last-=floor(last) # days
last*=24.0 # hours
ha=last-rah # hours
har=ha*2.0*pi/24.0
parang[itim]=atan2( (cos(latr)*sin(har)),
(sin(latr)*cos(decr)-cos(latr)*sin(decr)*cos(har)) )
parang.resize(nrows/nants,nants)
parang+=bandpa(bandnames[ispw]) # feed pos ang offset
parang+=(paoffset*pi/180.) # manual feed pa offset
parangd=parang*(180.0/pi)
A=pl.ones((nrows/nants,3))
A[:,1]=pl.cos(2*parang[:,0])
A[:,2]=pl.sin(2*parang[:,0])
fit=pl.lstsq(A,pl.square(ratio))
ants0=range(nants)
rsum=pl.sum(ratio[:,ants0],1)
rsum/=len(ants0)
fit=pl.lstsq(A,pl.square(rsum))
R[ispw,ifld]=fit[0][0]
Q[ispw,ifld]=fit[0][1]/R[ispw,ifld]/2.0
U[ispw,ifld]=fit[0][2]/R[ispw,ifld]/2.0
P=sqrt(Q[ispw,ifld]**2+U[ispw,ifld]**2)
X=0.5*atan2(U[ispw,ifld],Q[ispw,ifld])*180/pi
print 'Fld=',ifld,'Spw=',ispw,'(B='+str(bandnames[ispw])+', PA offset='+str(bandpa(bandnames[ispw])*180./pi)+'deg)','Gx/Gy=',R[ispw,ifld],'Q=',Q[ispw,ifld],'U=',U[ispw,ifld],'P=',P,'X=',X
else:
mask[ispw,ifld]=False
st.close()
if sum(mask[:,ifld])>0:
print 'For field id = ',ifld,' there are ',sum(mask[:,ifld]),'good spws.'
Qm=pl.mean(Q[mask[:,ifld],ifld])
Um=pl.mean(U[mask[:,ifld],ifld])
QU[ifld]=(Qm,Um)
Qe=pl.std(Q[mask[:,ifld],ifld])
Ue=pl.std(U[mask[:,ifld],ifld])
Pm=sqrt(Qm**2+Um**2)
Xm=0.5*atan2(Um,Qm)*180/pi
print 'Spw mean: Fld=', ifld,'Q=',Qm,'U=',Um,'(rms=',Qe,Ue,')','P=',Pm,'X=',Xm
mytb.close()
return QU
def predictcomp(objname=None,
standard=None,
epoch=None,
minfreq=None,
maxfreq=None,
nfreqs=None,
prefix=None,
antennalist=None,
showplot=None,
savefig=None,
symb=None,
include0amp=None,
include0bl=None,
blunit=None,
bl0flux=None):
"""
Writes a component list named clist to disk and returns a dict of
{'clist': clist,
'objname': objname,
'angdiam': angular diameter in radians (if used in clist),
'standard': standard,
'epoch': epoch,
'freqs': pl.array of frequencies, in GHz,
'uvrange': pl.array of baseline lengths, in m,
'amps': pl.array of predicted visibility amplitudes, in Jy,
'savedfig': False or, if made, the filename of a plot.}
or False on error.
objname: An object supported by standard.
standard: A standard for calculating flux densities, as in setjy.
Default: 'Butler-JPL-Horizons 2010'
epoch: The epoch to use for the calculations. Irrelevant for
extrasolar standards.
minfreq: The minimum frequency to use.
Example: '342.0GHz'
maxfreq: The maximum frequency to use.
Default: minfreq
Example: '346.0GHz'
Example: '', anything <= 0, or None: use minfreq.
nfreqs: The number of frequencies to use.
Default: 1 if minfreq == maxfreq,
2 otherwise.
prefix: The component list will be saved to
prefix + '<objname>_spw0_<minfreq><epoch>.cl'
Default: ''
antennalist: An array configuration file as used by simdata.
If given, a plot of S vs. |u| will be made.
Default: '' (None, just make clist.)
showplot: Whether or not to show the plot on screen.
Subparameter of antennalist.
Default: Necessarily False if antennalist is not specified.
True otherwise.
savefig: Filename for saving a plot of S vs. |u|.
Subparameter of antennalist.
Default: False (necessarily if antennalist is not specified)
Examples: True (save to prefix + '.png')
'myplot.png' (save to myplot.png)
symb: One of matplotlib's codes for plot symbols: .:,o^v<>s+xDd234hH|_
default: '.'
include0amp: Force the lower limit of the amplitude axis to 0.
Default: False
include0bl: Force the lower limit of the baseline length axis to 0.
blunit: Unit of the baseline length
bl0flux: show zero baseline flux
"""
retval = False
try:
casalog.origin('predictcomp')
# some parameter minimally required
if objname == '':
raise Exception, "Error, objname is undefined"
if minfreq == '':
raise Exception, "Error, minfreq is undefined"
minfreqq = qa.quantity(minfreq)
minfreqHz = qa.convert(minfreqq, 'Hz')['value']
try:
maxfreqq = qa.quantity(maxfreq)
except Exception, instance:
maxfreqq = minfreqq
frequnit = maxfreqq['unit']
maxfreqHz = qa.convert(maxfreqq, 'Hz')['value']
if maxfreqHz <= 0.0:
maxfreqq = minfreqq
maxfreqHz = minfreqHz
if minfreqHz != maxfreqHz:
if nfreqs < 2:
nfreqs = 2
else:
nfreqs = 1
freqs = pl.linspace(minfreqHz, maxfreqHz, nfreqs)
myme = metool()
mepoch = myme.epoch('UTC', epoch)
#if not prefix:
## meanfreq = {'value': 0.5 * (minfreqHz + maxfreqHz),
## 'unit': frequnit}
## prefix = "%s%s_%.7g" % (objname, epoch.replace('/', '-'),
## minfreqq['value'])
## if minfreqHz != maxfreqHz:
## prefix += "to" + maxfreq
## else:
## prefix += minfreqq['unit']
## prefix += "_"
# prefix = ''
#
if not prefix:
if not os.access("./", os.W_OK):
casalog.post(
"No write access in the current directory, trying to write cl to /tmp...",
"WARN")
prefix = "/tmp/"
if not os.access(prefix, os.W_OK):
casalog.post("No write access to /tmp to write cl file",
"SEVERE")
return False
else:
prefixdir = os.path.dirname(prefix)
if prefixdir == '/' and len(prefix) > 1:
prefix = prefix + '/'
prefixdir = os.path.dirname(prefix)
if not os.path.exists(prefixdir):
prefixdirs = prefixdir.split('/')
if prefixdirs[0] == "" and len(prefixdirs) > 1:
rootdir = "/" + prefixdirs[1]
else:
rootdir = "./"
if os.access(rootdir, os.W_OK):
if prefixdir != '':
os.makedirs(prefixdir)
else:
casalog.post(
"No write access to " + rootdir + " to write cl file",
"SEVERE")
return False
# Get clist
myim = imtool()
if hasattr(myim, 'predictcomp'):
casalog.post('local im instance created', 'DEBUG1')
else:
casalog.post('Error creating a local im instance.', 'SEVERE')
return False
#print "FREQS=",freqs
# output CL file name is fixed : prefix+"spw0_"+minfreq+mepoch.cl
minfreqGHz = qa.convert(qa.quantity(minfreq), 'GHz')['value']
decimalfreq = minfreqGHz - int(minfreqGHz)
decimalepoch = mepoch['m0']['value'] - int(mepoch['m0']['value'])
if decimalfreq == 0.0:
minfreqGHzStr = str(int(minfreqGHz)) + 'GHz'
else:
minfreqGHzStr = str(minfreqGHz) + 'GHz'
if decimalepoch == 0.0:
epochStr = str(int(mepoch['m0']['value'])) + 'd'
else:
epochStr = str(mepoch['m0']['value']) + 'd'
outfilename = "spw0_" + objname + "_" + minfreqGHzStr + epochStr + '.cl'
outfilename = prefix + outfilename
if (os.path.exists(outfilename) and os.path.isdir(outfilename)):
shutil.rmtree(outfilename)
casalog.post("Removing the existing componentlist, " + outfilename)
if standard == 'Butler-JPL-Horizons 2012':
clist = predictSolarObjectCompList(objname, mepoch, freqs.tolist(),
prefix)
else:
clist = myim.predictcomp(objname, standard, mepoch, freqs.tolist(),
prefix)
#print "created componentlist =",clist
if os.path.isdir(clist):
# The spw0 is useless here, but it is added by FluxStandard for the sake of setjy.
casalog.post('The component list was saved to ' + clist)
retval = {
'clist': clist,
'objname': objname,
'standard': standard,
'epoch': mepoch,
'freqs (GHz)': 1.0e-9 * freqs,
'antennalist': antennalist
}
mycl = cltool()
mycl.open(clist)
comp = mycl.getcomponent(0)
zeroblf = comp['flux']['value']
if standard == 'Butler-JPL-Horizons 2012':
f0 = comp['spectrum']['frequency']['m0']['value']
else:
f0 = retval['freqs (GHz)'][0]
casalog.post("Zero baseline flux %s @ %sGHz " % (zeroblf, f0),
'INFO')
mycl.close(False) # False prevents the stupid warning.
for k in ('shape', 'spectrum'):
retval[k] = comp[k]
if antennalist:
retval['spectrum']['bl0flux'] = {}
retval['spectrum']['bl0flux']['value'] = zeroblf[0]
retval['spectrum']['bl0flux']['unit'] = 'Jy'
retval['savedfig'] = savefig
if not bl0flux:
zeroblf = [0.0]
retval.update(
plotcomp(retval,
showplot,
wantdict=True,
symb=symb,
include0amp=include0amp,
include0bl=include0bl,
blunit=blunit,
bl0flux=zeroblf[0]))
else:
retval['savedfig'] = None
else:
casalog.post("There was an error in making the component list.",
'SEVERE')
def plotcomp(compdict, showplot=True, wantdict=False, symb=',',
include0amp=False, include0bl=False, blunit='', bl0flux=0.0):
"""
Given a dict including
{'clist': component list,
'objname': objname,
'epoch': epoch,
'shape': component shape dict, including direction.
'freqs (GHz)': pl.array of frequencies,
'antennalist': An array configuration file as used by simdata,
'savedfig': False or, if specified, the filename to save the plot to,
'standard': setjy fluxstandard type},
and symb: One of matplotlib's codes for plot symbols: .:,o^v<>s+xDd234hH|_
default: ',': The smallest points I could find,
make a plot of visibility amplitude vs. baseline length for clist at epoch.
If antennalist is not found as is, it will look for antennalist in
os.getenv('CASAPATH').split(' ')[0] + '/data/alma/simmos/'.
showplot: Whether or not to show the plot on screen.
If wantdict is True, it returns a dictionary with the amplitudes and
baselines on success. Otherwise, it returns True or False as its estimated
success value.
include0amp: Force the lower limit of the amplitude axis to 0.
include0bl: Force the lower limit of the baseline length axis to 0.
blunit: unit of the baseline length (='' used the unit in the data or klambda)
bl0flux: Zero baseline flux
"""
def failval():
"""
Returns an appropriate failure value.
Note that mydict.update(plotcomp(wantdict=True, ...)) would give a
confusing error message if plotcomp returned False.
"""
retval = False
if wantdict:
retval = {}
return retval
retval = failval() # Default
try:
clist = compdict['clist']
objname = compdict['objname']
epoch = compdict['epoch']
epstr = mepoch_to_str(epoch)
antennalist = compdict['antennalist']
# Read the configuration info.
if not antennalist:
print "compdict['antennalist'] must be set!"
print "Try something in", os.getenv("CASAPATH").split(' ')[0] + "/data/alma/simmos/"
return failval()
# Try repodir if raw antennalist doesn't work.
if not os.path.exists(antennalist):
repodir = os.getenv("CASAPATH").split(' ')[0] + "/data/alma/simmos/"
antennalist = repodir + antennalist
su = simutil("")
stnx, stny, stnz, diam, padnames, telescopename, obsmeas = su.readantenna(antennalist)
#print "telescopename:", telescopename
# Check that the source is up.
myme = metool()
posobs = myme.observatory(telescopename)
#print "posobs:", posobs
myme.doframe(epoch)
myme.doframe(posobs)
azel = myme.measure(compdict['shape']['direction'], 'azel')
azeldegs = tuple([qa.convert(azel[m], 'deg')['value'] for m in ('m0', 'm1')])
casalog.post("(az, el): (%.2f, %.2f) degrees" % azeldegs)
# riseset blabs to the logger, so introduce it now.
casalog.post('Rise and set times of ' + objname + " from " + telescopename + ':')
approx = ''
if 'JPL' in compdict.get('standard', 'JPL'):
# The object is in the Solar System or not known to be extragalactic.
approx = "APPROXIMATE. The times do not account for the apparent motion of "\
+ objname + "."
casalog.post(" (" + approx + ")")
riset = myme.riseset(compdict['shape']['direction'])
msg = ''
if riset['rise'] == 'above':
msg = objname + " is circumpolar"
elif riset['rise'] == 'below':
msg = objname + ' is not visible from ' + telescopename
if msg:
if approx:
msg += ' around ' + mepoch_to_str(epoch)
casalog.post(msg)
else:
for t in riset:
riset[t]['str'] = mepoch_to_str(riset[t]['utc'])
casalog.post(objname + " rises at %s and sets at %s." % (riset['rise']['str'],
riset['set']['str']))
tmeridian=(riset['rise']['utc']['m0']['value']+riset['set']['utc']['m0']['value'])/2.
casalog.post(objname + ': meridian passage at ' + qa.time(str(tmeridian)+'d')[0])
if approx:
riset['NOTE'] = approx
if not azel['m1']['value'] > 0.0:
casalog.post(objname + " is not visible from " + telescopename + " at " + epstr,
'SEVERE')
if wantdict:
return riset
else:
return False
# Start a temp MS.
workingdir = os.path.abspath(os.path.dirname(clist.rstrip('/')))
tempms = tempfile.mkdtemp(prefix=objname, dir=workingdir)
mysm = smtool()
mysm.open(tempms)
su.setcfg(mysm, telescopename, stnx, stny, stnz, diam,
padnames, posobs)
#print "cfg set"
# Only 1 polarization is wanted for now.
stokes, feeds = su.polsettings(telescopename, 'RR')
casalog.post("stokes, feeds: %s, %s" % (stokes, feeds))
fband = su.bandname(compdict['freqs (GHz)'][0])
chaninc = 1.0
nchan = len(compdict['freqs (GHz)'])
if nchan > 1:
chaninc = (compdict['freqs (GHz)'][-1] - compdict['freqs (GHz)'][0]) / (nchan - 1)
mysm.setspwindow(spwname=fband,
freq=str(compdict['freqs (GHz)'][0]) + 'GHz',
deltafreq=str(chaninc) + 'GHz',
freqresolution='1Hz',
nchannels=nchan, refcode="LSRK",
stokes=stokes)
mysm.setfeed(mode=feeds, pol=[''])
mysm.setlimits(shadowlimit=0.01, elevationlimit='10deg')
mysm.setauto(0.0)
mysm.setfield(sourcename=objname,
sourcedirection=compdict['shape']['direction'],
calcode="OBJ", distance='0m')
mysm.settimes(integrationtime="1s", usehourangle=False,
referencetime=epoch)
# this only creates blank uv entries
mysm.observe(sourcename=objname, spwname=fband,
starttime="-0.5s", stoptime="0.5s", project=objname)
mysm.setdata(fieldid=[0])
mysm.setvp()
casalog.post("done setting up simulation parameters")
mysm.predict(complist=clist) # do actual calculation of visibilities:
mysm.close()
casalog.post("Simulation finished.")
mytb = tbtool()
mytb.open(tempms)
data = mytb.getcol('DATA')[0] # Again, only 1 polarization for now.
data = abs(data)
baselines = mytb.getcol('UVW')[:2,:] # Drop w.
datablunit = mytb.getcolkeywords('UVW')['QuantumUnits']
mytb.close()
#print "Got the data and baselines"
shutil.rmtree(tempms)
if datablunit[1] != datablunit[0]:
casalog.post('The baseline units are mismatched!: %s' % datablunit,
'SEVERE')
return failval()
datablunit = datablunit[0]
# uv dist unit in klambda or m
if datablunit == 'm' and blunit=='klambda':
kl = qa.constants('C')['value']/(compdict['freqs (GHz)'][0]*1e6)
blunit = 'k$\lambda$'
else:
blunit = datablunit
kl = 1.0
pl.ioff()
#baselines = pl.hypot(baselines[0]/kl, baselines[1]/kl)
baselines = pl.hypot(baselines[0], baselines[1])
#if not showplot:
# casalog.post('Sorry, not showing the plot is not yet implemented',
# 'WARN')
if showplot:
pl.ion()
pl.clf()
pl.ioff()
nfreqs = len(compdict['freqs (GHz)'])
for freqnum in xrange(nfreqs):
freq = compdict['freqs (GHz)'][freqnum]
casalog.post("Plotting " + str(freq) + " GHz.")
pl.plot(baselines/kl, data[freqnum], symb, label="%.3g GHz" % freq)
#pl.plot(baselines, data[freqnum], symb, label="%.3g GHz" % freq)
pl.xlabel("Baseline length (" + blunit + ")")
pl.ylabel("Visibility amplitude (Jy)")
if include0amp:
pl.ylim(ymin=0.0)
if include0bl:
pl.xlim(xmin=0.0)
pl.suptitle(objname + " (predicted by %s)" % compdict['standard'], fontsize=14)
#pl.suptitle(objname + " (predicted)", fontsize=14)
# Unlike compdict['antennalist'], antennalist might have had repodir
# prefixed to it.
pl.title('at ' + epstr + ' for ' + os.path.basename(compdict['antennalist']), fontsize=10)
titletxt='($%.0f^\circ$ az, $%.0f^\circ$ el)' % azeldegs
# for comparison of old and new models - omit azeldegs as all in az~0
if bl0flux > 0.0:
if len(compdict['freqs (GHz)']) == 1:
titletxt+='\n bl0 flux:%.3f Jy' % bl0flux
else:
titletxt+='\n bl0 flux:%.3f Jy @ %s GHz' % (bl0flux, compdict['freqs (GHz)'][0])
pl.legend(loc='best', title=titletxt)
#pl.legend(loc='best', title='($%.0f^\circ$ az, $%.0f^\circ$ el)' % azeldegs)
y_formatter=matplotlib.ticker.ScalarFormatter(useOffset=False)
pl.axes().yaxis.set_major_formatter(y_formatter)
if showplot:
pl.ion()
pl.draw()
if compdict.get('savedfig'):
pl.savefig(compdict.get('savedfig'))
casalog.post("Saved plot to " + str(compdict.get('savedfig')))
if wantdict:
retval = {'amps': data,
'antennalist': antennalist, # Absolute path, now.
'azel': azel,
'baselines': baselines,
'blunit': blunit,
'riseset': riset,
'savedfig': compdict.get('savedfig')}
else:
retval = True
except Exception, instance:
casalog.post(str(instance), 'SEVERE')
if os.path.isdir(tempms):
shutil.rmtree(tempms)
def plotcomp(compdict, showplot=True, wantdict=False, symb=',',
include0amp=False, include0bl=False, blunit='', bl0flux=0.0):
"""
Given a dict including
{'clist': component list,
'objname': objname,
'epoch': epoch,
'shape': component shape dict, including direction.
'freqs (GHz)': pl.array of frequencies,
'antennalist': An array configuration file as used by simdata,
'savedfig': False or, if specified, the filename to save the plot to,
'standard': setjy fluxstandard type},
and symb: One of matplotlib's codes for plot symbols: .:,o^v<>s+xDd234hH|_
default: ',': The smallest points I could find,
make a plot of visibility amplitude vs. baseline length for clist at epoch.
If antennalist is not found as is, it will look for antennalist in
os.getenv('CASAPATH').split(' ')[0] + '/data/alma/simmos/'.
showplot: Whether or not to show the plot on screen.
If wantdict is True, it returns a dictionary with the amplitudes and
baselines on success. Otherwise, it returns True or False as its estimated
success value.
include0amp: Force the lower limit of the amplitude axis to 0.
include0bl: Force the lower limit of the baseline length axis to 0.
blunit: unit of the baseline length (='' used the unit in the data or klambda)
bl0flux: Zero baseline flux
"""
def failval():
"""
Returns an appropriate failure value.
Note that mydict.update(plotcomp(wantdict=True, ...)) would give a
confusing error message if plotcomp returned False.
"""
retval = False
if wantdict:
retval = {}
return retval
retval = failval() # Default
try:
clist = compdict['clist']
objname = compdict['objname']
epoch = compdict['epoch']
epstr = mepoch_to_str(epoch)
antennalist = compdict['antennalist']
# Read the configuration info.
if not antennalist:
print "compdict['antennalist'] must be set!"
print "Try something in", os.getenv("CASAPATH").split(' ')[0] + "/data/alma/simmos/"
return failval()
# Try repodir if raw antennalist doesn't work.
if not os.path.exists(antennalist):
repodir = os.getenv("CASAPATH").split(' ')[0] + "/data/alma/simmos/"
antennalist = repodir + antennalist
su = simutil("")
stnx, stny, stnz, diam, padnames, nant, telescopename = su.readantenna(antennalist)
#print "telescopename:", telescopename
# Check that the source is up.
myme = metool()
posobs = myme.observatory(telescopename)
#print "posobs:", posobs
myme.doframe(epoch)
myme.doframe(posobs)
azel = myme.measure(compdict['shape']['direction'], 'azel')
azeldegs = tuple([qa.convert(azel[m], 'deg')['value'] for m in ('m0', 'm1')])
casalog.post("(az, el): (%.2f, %.2f) degrees" % azeldegs)
# riseset blabs to the logger, so introduce it now.
casalog.post('Rise and set times of ' + objname + " from " + telescopename + ':')
approx = ''
if 'JPL' in compdict.get('standard', 'JPL'):
# The object is in the Solar System or not known to be extragalactic.
approx = "APPROXIMATE. The times do not account for the apparent motion of "\
+ objname + "."
casalog.post(" (" + approx + ")")
riset = myme.riseset(compdict['shape']['direction'])
msg = ''
if riset['rise'] == 'above':
msg = objname + " is circumpolar"
elif riset['rise'] == 'below':
msg = objname + ' is not visible from ' + telescopename
if msg:
if approx:
msg += ' around ' + mepoch_to_str(epoch)
casalog.post(msg)
else:
for t in riset:
riset[t]['str'] = mepoch_to_str(riset[t]['utc'])
casalog.post(objname + " rises at %s and sets at %s." % (riset['rise']['str'],
riset['set']['str']))
tmeridian=(riset['rise']['utc']['m0']['value']+riset['set']['utc']['m0']['value'])/2.
casalog.post(objname + ': meridian passage at ' + qa.time(str(tmeridian)+'d')[0])
if approx:
riset['NOTE'] = approx
if not azel['m1']['value'] > 0.0:
casalog.post(objname + " is not visible from " + telescopename + " at " + epstr,
'SEVERE')
if wantdict:
return riset
else:
return False
# Start a temp MS.
workingdir = os.path.abspath(os.path.dirname(clist.rstrip('/')))
tempms = tempfile.mkdtemp(prefix=objname, dir=workingdir)
mysm = smtool()
mysm.open(tempms)
su.setcfg(mysm, telescopename, stnx, stny, stnz, diam,
padnames, posobs)
#print "cfg set"
# Only 1 polarization is wanted for now.
stokes, feeds = su.polsettings(telescopename, 'RR')
casalog.post("stokes, feeds: %s, %s" % (stokes, feeds))
fband = su.bandname(compdict['freqs (GHz)'][0])
chaninc = 1.0
nchan = len(compdict['freqs (GHz)'])
if nchan > 1:
chaninc = (compdict['freqs (GHz)'][-1] - compdict['freqs (GHz)'][0]) / (nchan - 1)
mysm.setspwindow(spwname=fband,
freq=str(compdict['freqs (GHz)'][0]) + 'GHz',
deltafreq=str(chaninc) + 'GHz',
freqresolution='1Hz',
nchannels=nchan, refcode="LSRK",
stokes=stokes)
mysm.setfeed(mode=feeds, pol=[''])
mysm.setlimits(shadowlimit=0.01, elevationlimit='10deg')
mysm.setauto(0.0)
mysm.setfield(sourcename=objname,
sourcedirection=compdict['shape']['direction'],
calcode="OBJ", distance='0m')
mysm.settimes(integrationtime="1s", usehourangle=False,
referencetime=epoch)
# this only creates blank uv entries
mysm.observe(sourcename=objname, spwname=fband,
starttime="-0.5s", stoptime="0.5s", project=objname)
mysm.setdata(fieldid=[0])
mysm.setvp()
casalog.post("done setting up simulation parameters")
mysm.predict(complist=clist) # do actual calculation of visibilities:
mysm.close()
casalog.post("Simulation finished.")
mytb = tbtool()
mytb.open(tempms)
data = mytb.getcol('DATA')[0] # Again, only 1 polarization for now.
data = abs(data)
baselines = mytb.getcol('UVW')[:2,:] # Drop w.
datablunit = mytb.getcolkeywords('UVW')['QuantumUnits']
mytb.close()
#print "Got the data and baselines"
shutil.rmtree(tempms)
if datablunit[1] != datablunit[0]:
casalog.post('The baseline units are mismatched!: %s' % datablunit,
'SEVERE')
return failval()
datablunit = datablunit[0]
# uv dist unit in klambda or m
if datablunit == 'm' and blunit=='klambda':
kl = qa.constants('C')['value']/(compdict['freqs (GHz)'][0]*1e6)
blunit = 'k$\lambda$'
else:
blunit = datablunit
kl = 1.0
pl.ioff()
#baselines = pl.hypot(baselines[0]/kl, baselines[1]/kl)
baselines = pl.hypot(baselines[0], baselines[1])
#if not showplot:
# casalog.post('Sorry, not showing the plot is not yet implemented',
# 'WARN')
if showplot:
pl.ion()
pl.clf()
pl.ioff()
nfreqs = len(compdict['freqs (GHz)'])
for freqnum in xrange(nfreqs):
freq = compdict['freqs (GHz)'][freqnum]
casalog.post("Plotting " + str(freq) + " GHz.")
pl.plot(baselines/kl, data[freqnum], symb, label="%.3g GHz" % freq)
#pl.plot(baselines, data[freqnum], symb, label="%.3g GHz" % freq)
pl.xlabel("Baseline length (" + blunit + ")")
pl.ylabel("Visibility amplitude (Jy)")
if include0amp:
pl.ylim(ymin=0.0)
if include0bl:
pl.xlim(xmin=0.0)
pl.suptitle(objname + " (predicted by %s)" % compdict['standard'], fontsize=14)
#pl.suptitle(objname + " (predicted)", fontsize=14)
# Unlike compdict['antennalist'], antennalist might have had repodir
# prefixed to it.
pl.title('at ' + epstr + ' for ' + os.path.basename(compdict['antennalist']), fontsize=10)
titletxt='($%.0f^\circ$ az, $%.0f^\circ$ el)' % azeldegs
# for comparison of old and new models - omit azeldegs as all in az~0
if bl0flux > 0.0:
if len(compdict['freqs (GHz)']) == 1:
titletxt+='\n bl0 flux:%.3f Jy' % bl0flux
else:
titletxt+='\n bl0 flux:%.3f Jy @ %s GHz' % (bl0flux, compdict['freqs (GHz)'][0])
pl.legend(loc='best', title=titletxt)
#pl.legend(loc='best', title='($%.0f^\circ$ az, $%.0f^\circ$ el)' % azeldegs)
y_formatter=matplotlib.ticker.ScalarFormatter(useOffset=False)
pl.axes().yaxis.set_major_formatter(y_formatter)
if showplot:
pl.ion()
pl.draw()
if compdict.get('savedfig'):
pl.savefig(compdict.get('savedfig'))
casalog.post("Saved plot to " + str(compdict.get('savedfig')))
if wantdict:
retval = {'amps': data,
'antennalist': antennalist, # Absolute path, now.
'azel': azel,
'baselines': baselines,
'blunit': blunit,
'riseset': riset,
'savedfig': compdict.get('savedfig')}
else:
retval = True
except Exception, instance:
casalog.post(str(instance), 'SEVERE')
if os.path.isdir(tempms):
shutil.rmtree(tempms)
def predictcomp(objname=None, standard=None, epoch=None,
minfreq=None, maxfreq=None, nfreqs=None, prefix=None,
antennalist=None, showplot=None, savefig=None, symb=None,
include0amp=None, include0bl=None, blunit=None, bl0flux=None):
"""
Writes a component list named clist to disk and returns a dict of
{'clist': clist,
'objname': objname,
'angdiam': angular diameter in radians (if used in clist),
'standard': standard,
'epoch': epoch,
'freqs': pl.array of frequencies, in GHz,
'uvrange': pl.array of baseline lengths, in m,
'amps': pl.array of predicted visibility amplitudes, in Jy,
'savedfig': False or, if made, the filename of a plot.}
or False on error.
objname: An object supported by standard.
standard: A standard for calculating flux densities, as in setjy.
Default: 'Butler-JPL-Horizons 2010'
epoch: The epoch to use for the calculations. Irrelevant for
extrasolar standards.
minfreq: The minimum frequency to use.
Example: '342.0GHz'
maxfreq: The maximum frequency to use.
Default: minfreq
Example: '346.0GHz'
Example: '', anything <= 0, or None: use minfreq.
nfreqs: The number of frequencies to use.
Default: 1 if minfreq == maxfreq,
2 otherwise.
prefix: The component list will be saved to
prefix + 'spw0_<objname>_<minfreq><epoch>.cl'
Default: ''
antennalist: An array configuration file as used by simdata.
If given, a plot of S vs. |u| will be made.
Default: '' (None, just make clist.)
showplot: Whether or not to show the plot on screen.
Subparameter of antennalist.
Default: Necessarily False if antennalist is not specified.
True otherwise.
savefig: Filename for saving a plot of S vs. |u|.
Subparameter of antennalist.
Default: False (necessarily if antennalist is not specified)
Examples: True (save to prefix + '.png')
'myplot.png' (save to myplot.png)
symb: One of matplotlib's codes for plot symbols: .:,o^v<>s+xDd234hH|_
default: '.'
include0amp: Force the lower limit of the amplitude axis to 0.
Default: False
include0bl: Force the lower limit of the baseline length axis to 0.
blunit: Unit of the baseline length
bl0flux: show zero baseline flux
"""
retval = False
try:
casalog.origin('predictcomp')
# some parameter minimally required
if objname=='':
raise Exception, "Error, objname is undefined"
if minfreq=='':
raise Exception, "Error, minfreq is undefined"
minfreqq = qa.quantity(minfreq)
minfreqHz = qa.convert(minfreqq, 'Hz')['value']
try:
maxfreqq = qa.quantity(maxfreq)
except Exception, instance:
maxfreqq = minfreqq
frequnit = maxfreqq['unit']
maxfreqHz = qa.convert(maxfreqq, 'Hz')['value']
if maxfreqHz <= 0.0:
maxfreqq = minfreqq
maxfreqHz = minfreqHz
if minfreqHz != maxfreqHz:
if nfreqs < 2:
nfreqs = 2
else:
nfreqs = 1
freqs = pl.linspace(minfreqHz, maxfreqHz, nfreqs)
myme = metool()
mepoch = myme.epoch('UTC', epoch)
#if not prefix:
## meanfreq = {'value': 0.5 * (minfreqHz + maxfreqHz),
## 'unit': frequnit}
## prefix = "%s%s_%.7g" % (objname, epoch.replace('/', '-'),
## minfreqq['value'])
## if minfreqHz != maxfreqHz:
## prefix += "to" + maxfreq
## else:
## prefix += minfreqq['unit']
## prefix += "_"
# prefix = ''
#
if not prefix:
if not os.access("./",os.W_OK):
casalog.post("No write access in the current directory, trying to write cl to /tmp...","WARN")
prefix="/tmp/"
if not os.access(prefix, os.W_OK):
casalog.post("No write access to /tmp to write cl file", "SEVERE")
return False
else:
prefixdir=os.path.dirname(prefix)
if not os.path.exists(prefixdir):
prefixdirs = prefixdir.split('/')
if prefixdirs[0]=="":
rootdir = "/" + prefixdirs[1]
else:
rootdir = "./"
if os.access(rootdir,os.W_OK):
os.makedirs(prefixdir)
else:
casalog.post("No write access to "+rootdir+" to write cl file", "SEVERE")
return False
# Get clist
myim = imtool()
if hasattr(myim, 'predictcomp'):
casalog.post('local im instance created', 'DEBUG1')
else:
casalog.post('Error creating a local im instance.', 'SEVERE')
return False
#print "FREQS=",freqs
if standard=='Butler-JPL-Horizons 2012':
clist = predictSolarObjectCompList(objname, mepoch, freqs.tolist(), prefix)
else:
clist = myim.predictcomp(objname, standard, mepoch, freqs.tolist(), prefix)
#print "created componentlist =",clist
if os.path.isdir(clist):
# The spw0 is useless here, but it is added by FluxStandard for the sake of setjy.
casalog.post('The component list was saved to ' + clist)
retval = {'clist': clist,
'objname': objname,
'standard': standard,
'epoch': mepoch,
'freqs (GHz)': 1.0e-9 * freqs,
'antennalist': antennalist}
mycl = cltool()
mycl.open(clist)
comp = mycl.getcomponent(0)
zeroblf=comp['flux']['value']
if standard=='Butler-JPL-Horizons 2012':
f0=comp['spectrum']['frequency']['m0']['value']
else:
f0=retval['freqs (GHz)'][0]
casalog.post("Zero baseline flux %s @ %sGHz " % (zeroblf, f0),'INFO')
mycl.close(False) # False prevents the stupid warning.
for k in ('shape', 'spectrum'):
retval[k] = comp[k]
if antennalist:
retval['spectrum']['bl0flux']={}
retval['spectrum']['bl0flux']['value']=zeroblf[0]
retval['spectrum']['bl0flux']['unit']='Jy'
retval['savedfig'] = savefig
if not bl0flux:
zeroblf=[0.0]
retval.update(plotcomp(retval, showplot, wantdict=True, symb=symb,
include0amp=include0amp, include0bl=include0bl, blunit=blunit, bl0flux=zeroblf[0]))
else:
retval['savedfig'] = None
else:
casalog.post("There was an error in making the component list.",
'SEVERE')
def qufromgain(caltable,badspw=[],badant=[],fieldids=[],paoffset=None):
mytb=taskinit.tbtool()
myme=taskinit.metool()
pos=myme.observatory('atca')
myme.doframe(pos)
# _geodetic_ latitude
latr=myme.measure(pos,'WGS84')['m1']['value']
#print 'latitude: ',latr*180/pi
mytb.open(caltable+'/FIELD')
nfld=mytb.nrows()
dirs=mytb.getcol('DELAY_DIR')[:,0,:]
mytb.close()
print 'Found '+str(nfld)+' fields.'
mytb.open(caltable+'/SPECTRAL_WINDOW')
freq=mytb.getcol('REF_FREQUENCY')
nspw=mytb.nrows()
mytb.close()
print 'Found '+str(nspw)+' spws.'
#sort out pa offset to apply
paoff=pl.zeros(nspw)
if paoffset==None:
# use defaults for ATCA
# (should get these from Feed subtable, but cal table doesn't have one)
for ispw in range(nspw):
if freq[ispw]<30e9 or freq[ispw]>50e9:
paoff[ispw]=45.
else:
paoff[ispw]=135.
else:
paoff=paoffset
R=pl.zeros((nspw,nfld))
Q=pl.zeros((nspw,nfld))
U=pl.zeros((nspw,nfld))
mask=pl.ones((nspw,nfld),dtype=bool)
if (len(badspw)>0):
mask[badspw,:]=False
if (len(fieldids)==0):
fieldids=range(nfld)
QU={}
mytb.open(caltable)
for ifld in fieldids:
for ispw in range(nspw):
if not mask[ispw,ifld]:
continue
st=mytb.query('FIELD_ID=='+str(ifld)+' && SPECTRAL_WINDOW_ID=='+str(ispw))
nrows=st.nrows()
if nrows > 0:
rah=dirs[0,ifld]*12.0/pi
decr=dirs[1,ifld]
times=st.getcol('TIME')
gains=st.getcol('CPARAM')
ants=st.getcol('ANTENNA1')
ntimes=len(pl.unique(times))
nants=ants.max()+1
#print nrows, ntimes, nants
# times
time0=86400.0*floor(times[0]/86400.0)
rtimes=times-time0
# amplitude ratio
amps=pl.absolute(gains)
amps[amps==0.0]=1.0
ratio=amps[0,0,:]/amps[1,0,:]
# parang
parang=pl.zeros(len(times))
for itim in range(len(times)):
tm=myme.epoch('UTC',str(times[itim])+'s')
last=myme.measure(tm,'LAST')['m0']['value']
last-=floor(last) # days
last*=24.0 # hours
ha=last-rah # hours
har=ha*2.0*pi/24.0
parang[itim]=atan2( (cos(latr)*sin(har)),
(sin(latr)*cos(decr)-cos(latr)*sin(decr)*cos(har)) )
ratio.resize(nrows/nants,nants)
parang.resize(nrows/nants,nants)
parang+=paoff[ispw]*pi/180.
parangd=parang*(180.0/pi)
A=pl.ones((nrows/nants,3))
A[:,1]=pl.cos(2*parang[:,0])
A[:,2]=pl.sin(2*parang[:,0])
fit=pl.lstsq(A,pl.square(ratio))
amask=pl.ones(nants,dtype=bool)
if len(badant)>0:
amask[badant]=False
rsum=pl.sum(ratio[:,amask],1)
rsum/=pl.sum(amask)
fit=pl.lstsq(A,pl.square(rsum))
R[ispw,ifld]=fit[0][0]
Q[ispw,ifld]=fit[0][1]/R[ispw,ifld]/2.0
U[ispw,ifld]=fit[0][2]/R[ispw,ifld]/2.0
P=sqrt(Q[ispw,ifld]**2+U[ispw,ifld]**2)
X=0.5*atan2(U[ispw,ifld],Q[ispw,ifld])*180/pi
print 'Fld=%i, Spw=%i, PA Offset=%5.1f, Gx/Gy=%5.3f, Q=%5.3f, U=%5.3f, P=%5.3f, X=%5.1f' % (ifld,ispw,paoff[ispw],R[ispw,ifld],Q[ispw,ifld],U[ispw,ifld],P,X)
else:
mask[ispw,ifld]=False
st.close()
if (sum(mask[:,ifld]))>0:
print 'For field id = ',ifld,' there are ',sum(mask[:,ifld]),'good spws.'
Qm=pl.mean(Q[mask[:,ifld],ifld])
Um=pl.mean(U[mask[:,ifld],ifld])
QU[ifld]=(Qm,Um)
Qe=pl.std(Q[mask[:,ifld],ifld])
Ue=pl.std(U[mask[:,ifld],ifld])
Pm=sqrt(Qm**2+Um**2)
Xm=0.5*atan2(Um,Qm)*180/pi
print 'Spw mean: Fld=%i Fractional: Q=%5.3f, U=%5.3f, (rms= %5.3f,%5.3f), P=%5.3f, X=%5.1f' % (ifld,Qm,Um,Qe,Ue,Pm,Xm)
mytb.close()
return QU