def cl2skycat(componentlist='', skycat=''):
"""
Converts a componentlist dictionary or componnent list file on disk
to a skycatalog to overlay on image in the viewer
"""
qa = casac.quanta()
cl = casac.componentlist()
tb = casac.table()
if (type(componentlist) == str):
cl.open(componentlist)
elif (type(componentlist) == dict):
cl.purge()
cl.fromrecord(componentlist)
if (cl.length() == 0):
print "no components found"
return
des = {}
des['Type'] = {'valueType': 'string'}
des['Long'] = {'valueType': 'double'}
des['Lat'] = {'valueType': 'double'}
des['COMP_ID'] = {'valueType': 'string'}
des['RA'] = {'valueType': 'string'}
des['DEC'] = {'valueType': 'string'}
des['FluxValue'] = {'valueType': 'double'}
tb.create(tablename=skycat, tabledesc=des, nrow=cl.length())
eltype = []
nam = []
RA = []
DEC = []
lati = np.zeros((cl.length(), ))
longi = np.zeros((cl.length(), ))
fluxval = np.zeros((cl.length(), ))
for k in range(cl.length()):
longi[k] = qa.convert(cl.getrefdir(k)['m0'], 'deg')['value']
lati[k] = qa.convert(cl.getrefdir(k)['m1'], 'deg')['value']
fluxval[k] = cl.getfluxvalue(k)[0]
RA.append(qa.time(cl.getrefdir(k)['m0'], prec=10))
DEC.append(qa.angle(cl.getrefdir(k)['m1'], prec=10))
eltype.append(cl.getrefdir(k)['refer'])
nam.append(str(k))
tb.putcol('Type', eltype)
tb.putcol('RA', RA)
tb.putcol('DEC', DEC)
tb.putcol('COMP_ID', nam)
tb.putcol('Long', longi)
tb.putcol('Lat', lati)
tb.putcol('FluxValue', fluxval)
tb.putcolkeyword(columnname='Long', keyword='UNIT', value='deg')
tb.putcolkeyword(columnname='Lat', keyword='UNIT', value='deg')
tb.putinfo({'type': 'Skycatalog'})
tb.done()
def _muellerModelDataReader(self):
"""
read flux density from the asteroid models by
Mueller
"""
from casac import casac
qa = casac.quanta()
date=qa.time(str(self.mjd)+'d',form='ymd')[0]
yr=date.split('/')[0]
#if int(yr) < 2015: yr = '2015'
if self.src in self.knownsrcdict.keys():
filename = self.datapath+self.src+"_ALMA_TPMprediction_"+yr+"_"+self.knownsrcdict[self.src]['interval']+".txt"
#print "filename=",filename
import glob
flist = glob.glob(filename)
if len(flist)==1:
#print "Reading model data: ",flist[0]
with open(flist[0],"r") as f:
data = f.readlines()
freqs = self._checkheader(data)
if len(freqs)==0:
raise IOError("Problem in reading model data file!")
i = np.abs(freqs-self.freq).argmin()
reffreq = freqs[i]
maindata = []
mjds = []
fluxes = []
for line in data[8:]:
if line.find('----')<0:
maindata.append(line)
mjds.append(float(line.split()[5]))
fluxes.append(float(line.split()[i+5]))
mjdarr = np.array(mjds)
flxarr = np.array(fluxes)
# find flux density of nearest in time
t = np.abs(mjdarr-self.mjd).argmin()
refflux = flxarr[t]
#print "flxarr=",flxarr
#print "freq, mjd=",self.freq,self.mjd
print "refflux@reffreq=%s@%s at %s" % (refflux,reffreq,mjdarr[t])
elif len(flist)==0:
raise IOError("Cannot find the model file for "+self.src+" for date="+date+".")
return (reffreq, refflux)
def setSolarObjectJy(self,field,spw,scalebychan, timerange,observation, scan, intent, useephemdir, usescratch=False):
"""
Set flux density of a solar system object using Bryan Butler's new
python model calculation code.
A single time stamp (first time stamp of MS after selections are applied) is
currently used per execution. For flux observation done in a long time span
may need to run multiple setjy with selections by time range (or scans).
"""
#retval = True
output = {}
cleanupcomps = True # leave generated cl files
#from taskinit import *
from taskinit import gentools
qa = casac.quanta()
(myms, mytb, mycl, myme, mycb, mymsmd) = gentools(['ms','tb','cl','me', 'cb','msmd'])
# prepare parameters need to pass to the Bryan's code
# make ms selections
# get source name
# get time ranges
# get spwused and get frequency ranges
sel={}
sel['field']=field
sel['spw']=spw
sel['timerange']=timerange
sel['observation']=str(observation)
sel['scan']=scan
sel['scanintent']=intent
measframes=['REST','LSRK','LSRD','BARY','GEO','TOPO','GALACTO','LGROUP','CMB']
myms.open(self.vis)
myms.msselect(sel,False)
scansummary=myms.getscansummary()
nscan=len(scansummary.keys())
selectedids=myms.msselectedindices()
fieldids=selectedids['field']
obsids=selectedids['observationid']
myms.close()
mytb.open(self.vis+'/OBSERVATION')
if len(obsids)==0:
getrow=0
else:
getrow=obsids[0]
observatory=mytb.getcell('TELESCOPE_NAME',getrow)
mytb.close()
mytb.open(self.vis+'/FIELD')
colnames = mytb.colnames()
if len(fieldids)==0:
fieldids = range(mytb.nrows())
# frame reference for field position
phdir_info=mytb.getcolkeyword("PHASE_DIR","MEASINFO")
if phdir_info.has_key('Ref'):
fieldref=phdir_info['Ref']
elif phdir_info.has_key('TabRefTypes'):
colnames=mytb.colnames()
for col in colnames:
if col=='PhaseDir_Ref':
fieldrefind=mytb.getcell(col,fieldids[0])
fieldref=phdir_info['TabRefTypes'][fieldrefind]
else:
fieldref=''
srcnames={}
fielddirs={}
ftimes={}
ephemid={}
for fid in fieldids:
#srcnames.append(mytb.getcell('NAME',int(fid)))
srcnames[fid]=(mytb.getcell('NAME',int(fid)))
#fielddirs[fid]=(mytb.getcell('PHASE_DIR',int(fid)))
ftimes[fid]=(mytb.getcell('TIME',int(fid)))
if colnames.count('EPHEMERIS_ID'):
ephemid[fid]=(mytb.getcell('EPHEMERIS_ID',int(fid)))
else:
ephemid[fid]=-1
mytb.close() # close FIELD table
# need to get a list of time
# but for now for test just get a time centroid of the all scans
# get time range
# Also, this needs to be done per source
# gather freq info from Spw table
mytb.open(self.vis+'/SPECTRAL_WINDOW')
nspw = mytb.nrows()
freqcol=mytb.getvarcol('CHAN_FREQ')
freqwcol=mytb.getvarcol('CHAN_WIDTH')
fmeasrefcol=mytb.getcol('MEAS_FREQ_REF')
reffreqs=mytb.getcol('REF_FREQUENCY')
mytb.close()
# store all parameters need to call solar_system_fd for all sources
inparams={}
validfids = [] # keep track of valid fid that has data (after selection)
# if same source name ....need handle this...
for fid in fieldids:
sel['field']=str(fid)
myms.open(self.vis)
#reset the selection
try:
status=myms.msselect(sel)
except:
#skip this field
continue
if not status:
continue
validfids.append(fid)
trange=myms.range('time')
#if not inparams.has_key(srcnames[fid]):
# inparams[srcnames[fid]]={}
if not inparams.has_key(fid):
inparams[fid]={}
inparams[fid]['fieldname']=srcnames[fid]
#tc = (trange['time'][0]+trange['time'][1])/2. #in sec.
# use first timestamp to be consistent with the ALMA Control
# old setjy (Butler-JPL-Horizons 2010) seems to be using
# time in FIELD... but here is first selected time in main table
if ephemid[fid]==-1: # keep old behavior
tc = trange['time'][0] #in sec.
tmsg = "Time used for the model calculation (=first time stamp of the selected data) for field "
else: # must have ephem table attached...
tc = ftimes[fid]#in sec.
tmsg = "Time used for the model calculation for field "
#if inparams[srcnames[fid]].has_key('mjd'):
# inparams[srcnames[fid]]['mjds'][0].append([myme.epoch('utc',qa.quantity(tc,'s'))['m0']['value']])
#else:
# inparams[srcnames[fid]]['mjds']=[myme.epoch('utc',qa.quantity(tc,'s'))['m0']['value']]
if inparams[fid].has_key('mjd'):
inparams[fid]['mjds'][0].append([myme.epoch('utc',qa.quantity(tc,'s'))['m0']['value']])
else:
inparams[fid]['mjds']=[myme.epoch('utc',qa.quantity(tc,'s'))['m0']['value']]
usedtime = qa.time(qa.quantity(tc,'s'),form='ymd')[0]
self._casalog.post(tmsg+str(fid)+":"+usedtime)
# get a correct direction measure
mymsmd.open(self.vis)
dirdic = mymsmd.phasecenter(int(fid))
mymsmd.close()
# check if frame is J2000 and if not do the transform
if dirdic['refer'] != 'J2000':
myme.doframe(myme.observatory(observatory))
myme.doframe(myme.epoch('utc', qa.quantity(tc,'s')))
azeldir = myme.measure(dirdic,'AZELGEO')
dirdic=myme.measure(azeldir,'J2000')
fielddirs[fid]=(numpy.array([[dirdic['m0']['value']],[dirdic['m1']['value']]]))
# somehow it gives you duplicated ids .... so need to uniquify
selspws= list(set(myms.msselectedindices()['spw']))
# make sure it is int rather than numpy.int32, etc.
selspws = [int(ispw) for ispw in selspws]
#inparams[srcnames[fid]]['spwids']= selspws if len(selspws)!=0 else range(nspw)
inparams[fid]['spwids']= selspws if len(selspws)!=0 else range(nspw)
#create a list of freq ranges with selected spws
# should worry about freq order???
freqlist=[]
freqlistraw=[]
framelist=[]
#for idx in inparams[srcnames[fid]]['spwids']:
for idx in inparams[fid]['spwids']:
freqs=freqcol['r'+str(idx+1)]
freqws=freqwcol['r'+str(idx+1)]
fmeasref=fmeasrefcol[idx]
#if scalebychan=T, this has to be min, max determined from
# chan_freq(channel center)+/- chan width.
if scalebychan:
# pack into list of list of list (freqlist[nf][nspw])
perspwfreqlist=[]
for nf in range(len(freqs)):
fl = freqs[nf][0]-freqws[nf][0]/2.
fh = freqs[nf][0]+freqws[nf][0]/2.
perspwfreqlist.append([fl,fh])
freqlist.append(perspwfreqlist)
else:
if (len(freqs)==1):
fl = freqs[0][0]-freqws[0][0]/2.
fh = freqs[0][0]+freqws[0][0]/2.
freqlist.append([float(fl),float(fh)])
else:
freqlist.append([float(min(freqs)),float(max(freqs))])
framelist.append(measframes[fmeasref])
freqlistraw.append(freqs.transpose()[0].tolist()) # data chanfreq list
#inparams[srcnames[fid]]['freqlist']=freqlist
#inparams[srcnames[fid]]['freqlistraw']=freqlistraw
#inparams[srcnames[fid]]['framelist']=framelist
#inparams[srcnames[fid]]['reffreqs']=reffreqs
inparams[fid]['freqlist']=freqlist
inparams[fid]['freqlistraw']=freqlistraw
inparams[fid]['framelist']=framelist
inparams[fid]['reffreqs']=reffreqs
myms.close()
# call Bryan's code
# errcode: list of list - inner list - each values for range of freqs
# flluxes: list of list
# fluxerrs:
# size: [majoraxis, minoraxis, pa]
# direction: direction for each time stamp
#
#import solar_system_setjy as ss_setjy
import solar_system_setjy as SSsetjy
retdict={} # for returning flux densities?
ss_setjy=SSsetjy.solar_system_setjy()
#for src in srcnames:
self.clnamelist=[]
for vfid in validfids:
src=srcnames[vfid]
#mjds=inparams[src]['mjds']
mjds=inparams[vfid]['mjds']
fluxes=[]
# call solar_system_fd() per spw (for scalebychan freqlist has an extra dimention)
#nspwused=len(inparams[src]['freqlist'])
nspwused=len(inparams[vfid]['freqlist'])
# warning for many channels but it is really depends on the source
if scalebychan:
maxnf=0
for ispw in range(nspwused):
#nf = len(inparams[src]['freqlist'][ispw])
nf = len(inparams[vfid]['freqlist'][ispw])
maxnf = max(nf,maxnf)
if maxnf >= 3840 and src.upper()!="MARS": # mars shoulde be ok
self._casalog.post("Processing %s spw(s) and at least some of them are a few 1000 channels or more. This may take \
many minutes (>3min per spw for 3840 channels) in some cases. Please be patient." % nspwused,"WARN")
for i in range(nspwused): # corresponds to n spw
if type(freqlist[0][0])==list:
#infreqs=inparams[src]['freqlist'][i]
infreqs=inparams[vfid]['freqlist'][i]
else:
#infreqs=[inparams[src]['freqlist'][i]]
infreqs=[inparams[vfid]['freqlist'][i]]
self._casalog.post("Calling solar_system_fd: %s(%s) for spw%s freqs=%s" % (src, vfid,i,freqlist[i]),'DEBUG1')
(errcodes, subfluxes, fluxerrs, sizes, dirs)=\
ss_setjy.solar_system_fd(source_name=src, MJDs=mjds, frequencies=infreqs, observatory=observatory, casalog=self._casalog)
# for old code
#(errcodes, subfluxes, fluxerrs, sizes, dirs)=\
# ss_setjy.solar_system_fd(source_name=src, MJDs=mjds, frequencies=infreqs, casalog=self._casalog)
# for nf freq ranges, nt mjds
# errcodes[nf][nt], subfluxes[nf][nt], fluxerrs[nf][nt], sizes[nt], dirs[nt]
self._casalog.post("+++++ solar_system_fd() returned values +++++", 'DEBUG1')
self._casalog.post(" fluxes(fds)=%s" % subfluxes, 'DEBUG1')
self._casalog.post(" sizes=%s" % sizes, 'DEBUG1')
self._casalog.post(" directions=%s\n" % dirs, 'DEBUG1')
# packed fluxes for all spws
fluxes.append(subfluxes)
# fluxes has fluxesi[nspw][nf][nt]
# ------------------------------------------------------------------------
# For testing with hardcoded values without calling solar_system_fd()...
#errcodes=[[0,0,0,0,0]]
#fluxes=[[26.40653147,65.23839313,65.23382757,65.80638802,69.33396562]]
#fluxerrs=[[0.0,0.0,0.0,0.0,0.0]]
#sizes=[[3.6228991032674371,3.6228991032674371,0.0]]
#dirs=[{'m0': {'unit': 'rad', 'value': 0.0}, 'm1': {'unit': 'rad', 'value': 0.0}, 'refer': 'J2000', 'type': 'direction'}]
# ------------------------------------------------------------------------
# local params for selected src
#framelist=inparams[src]['framelist']
#freqlist=inparams[src]['freqlist']
#freqlistraw=inparams[src]['freqlistraw']
#reffreqs=inparams[src]['reffreqs']
#spwids=inparams[src]['spwids']
framelist=inparams[vfid]['framelist']
freqlist=inparams[vfid]['freqlist']
freqlistraw=inparams[vfid]['freqlistraw']
reffreqs=inparams[vfid]['reffreqs']
spwids=inparams[vfid]['spwids']
clrecs=odict.odict()
labels = []
# loop for over for multiple directions (=multiple MJDs) for a given src
for i in range(len(dirs)): # this is currently only length of 1 since no multiple timestamps were used
# check errcode - error code would be there per flux per time (dir)
reterr=testerrs(errcodes[i],src)
if reterr == 2:
continue
#dirstring = [dirs[i]['refer'],qa.tos(dirs[i]['m0']),qa.tos(dirs[i]['m1'])]
if useephemdir:
dirstring = [dirs[i]['refer'],qa.tos(dirs[i]['m0']),qa.tos(dirs[i]['m1'])]
dirmsg = "Using the source position from the ephemeris table in the casa data directory: "
else:
#dirstring = [fieldref, str(fielddirs[fieldids[0]][0][0])+'rad', str(fielddirs[fieldids[0]][1][0])+'rad']
# extract field direction of first id of the selected field ids
#dirstring = [fieldref, "%.18frad" % (fielddirs[fieldids[0]][0][0]), "%.18frad" % (fielddirs[fieldids[0]][1][0])]
#dirstring = [fieldref, "%.18frad" % (fielddirs[vfid][0][0]), "%.18frad" % (fielddirs[vfid][1][0])]
# by now the direction should be in J2000
dirstring = ['J2000', "%.18frad" % (fielddirs[vfid][0][0]), "%.18frad" % (fielddirs[vfid][1][0])]
dirmsg = "Using the source position in the MS (or in the attached ephemeris table, if any): "
self._casalog.post(dirmsg+str(dirstring))
# setup componentlists
# need to set per dir
# if scalebychan=F, len(freqs) corresponds to nspw selected
# Need to put in for-loop to create cl for each time stamp? or scan?
#clpath='/tmp/'
clpath='./'
# construct cl name (multiple spws in one componentlist table)
selreffreqs = [reffreqs[indx] for indx in spwids]
minfreq = min(selreffreqs)
maxfreq = max(selreffreqs)
freqlabel = '%.3f-%.3fGHz' % (minfreq/1.e9, maxfreq/1.e9)
#tmlabel = '%.1fd' % (tc/86400.)
mjd=inparams[vfid]['mjds'][0]
tmlabel = '%.1fd' % (mjd)
#clabel = src+'_spw'+str(spwids[j])+'_'+freqlabel+'_'+tmlabel
#clabel0 = src+'_'+freqlabel+'_'+tmlabel
#pid=str(os.getpid())
#clname = clpath+clabel0+"_"+pid+'.cl'
clabel0 = src+'_'+freqlabel+'_'+tmlabel+"_"+os.path.basename(self.vis)
clname = clpath+clabel0+'.cl'
#debug
self._casalog.post("Create componentlist: %s for vfid=%s" % (clname,vfid),'DEBUG1')
if (os.path.exists(clname)):
shutil.rmtree(clname)
iiflux=[]
iinfreq=[]
# for logging/output dict - pack each freq list for each spw
freqsforlog=[]
for j in range(len(freqlist)): # loop over nspw
freqlabel = '%.3fGHz' % (reffreqs[int(spwids[j])]/1.e9)
clabel=src+'_spw'+str(spwids[j])+'_'+freqlabel+'_'+tmlabel
#print "addcomponent...for spw=",spwids[j]," i=",i," flux=",fluxes[j][i]
if scalebychan:
index= 2.0
sptype = 'spectral index'
else:
index= 0.0
sptype = 'constant'
# adjust to change in returned flux shape. An extra [] now seems to be gone. 2012-09-27
iflux=fluxes[j][i][0]
#print "addcomponent with flux=%s at frequency=%s" %\
# (iflux,str(reffreqs[int(spwids[j])]/1.e9)+'GHz')
# i - time stamps = 0 for now, j = a freq range
infreq=freqlist[j][0][0] if type(freqlist[j][0])==list else freqlist[j][0]
# for a single CL with multple spws
if j ==0: infreq0=infreq
# --- version for 'multi-spws in a single comp single CL'
# accumulate all frequencies from all spws to a list
#if not scalebychan:
#freqlist[j] for j spw should contain a list with two freqs (min and max of
# of the spw and the same fluxes should be set for the freqs so that cl.setspectrum
# with tabular would not interpolate inside each spw
##iinfreq.extend(freqlist[j])
# nch = len(freqlistraw[j])
# iinfreq.extend(freqlistraw[j])
# assigning the same flux to the two freqs
##iiflux.extend([iflux,iflux])
# for ich in range(nch):
# iiflux.extend([iflux])
#else:
# iiflux.extend(fluxes[j][i])
# if type(freqlist[j][0])==list and len(freqlist[j][0])>1:
# for fr in freqlist[j]:
# iinfreq.append((fr[1]+fr[0])/2)
# else:
# if type(freqlist[j])==list:
# iinfreq.append((freqlist[j][1]+freqlist[j][0])/2)
# else:
# iinfreq.append(freqlist[j])
# freqsforlog.append(iinfreq)
# -----------------------------------------------------------------------------------
self._casalog.post("addcomponent with flux=%s at frequency=%s" %\
# (fluxes[j][i][0],str(reffreqs[int(spwids[j])]/1.e9)+'GHz'), 'INFO1')
(iflux,str(reffreqs[int(spwids[j])]/1.e9)+'GHz'), 'INFO1')
#
mycl.addcomponent(iflux,fluxunit='Jy', polarization="Stokes", dir=dirstring,
shape='disk', majoraxis=str(sizes[i][0])+'arcsec', minoraxis=str(sizes[i][1])+'arcsec',
positionangle=str(sizes[i][2])+'deg', freq=[framelist[0],str(infreq)+'Hz'],
spectrumtype=sptype, index=index, label=clabel)
if scalebychan:
# use tabular form to set flux for each channel
# This may be redundant
if type(fluxes[j][i]) ==list and len(fluxes[j][i])> 1:
if type(freqlist[j][0])==list and len(freqlist[j][0])>1:
freqs=[]
for fr in freqlist[j]:
freqs.append((fr[1]+fr[0])/2)
clind = mycl.length() - 1
mycl.setspectrum(which=clind, type='tabular', tabularfreqs=freqs, tabularflux=fluxes[j][0],
tabularframe=framelist[j])
### === per spw process end here
# - version that put all spws into a component -
# set a single component freq set at the the lower edge of first spw
#mycl.addcomponent(iiflux[0],fluxunit='Jy', polarization="Stokes", dir=dirstring,
# shape='disk', majoraxis=str(sizes[i][0])+'arcsec', minoraxis=str(sizes[i][1])+'arcsec',
# positionangle=str(sizes[i][2])+'deg', freq=[framelist[0],str(infreq0)+'Hz'],
# spectrumtype=sptype, index=index, label=clabel)
# if it's list of fluxes try to put in tabular form
#if type(fluxes[j][i]) ==list and len(fluxes[j][i])> 1:
# if len(iiflux)> 1:
#print "framelist[j]=",framelist[j]
#if type(freqlist[j][0])==list and len(freqlist[j][0])>1:
# freqs=[]
# for fr in freqlist[j]:
# freqs.append((fr[1]+fr[0])/2)
#else:
# freqs=freqlist[j]
#clind = mycl.length() - 1
# mycl.setspectrum(which=clind, type='tabular', tabularfreqs=freqs, tabularflux=fluxes[j][0],
#tabularframe=framelist[j])
# mycl.setspectrum(which=clind, type='tabular', tabularfreqs=iinfreq, tabularflux=iiflux,
# tabularframe=framelist[0])
#mycl.rename(clname)
#put in a record for log output
#clrecs[clabel] = mycl.torecord()
clrecs[clabel0] = mycl.torecord()
clrecs[clabel0]['allfluxinfo']=fluxes
clrecs[clabel0]['allfreqinfo']=freqsforlog
clrecs[clabel0]['spwids']=spwids
mycl.rename(clname) # - A CL per field
mycl.close(False) # False for not to send a warning message
mycl.done()
# if scratch=F check if the virtual model already exist
# for the field if it is clear it.
# if j==0 and (not usescratch):
# mytb.open(self.vis, nomodify=False)
# kwds = mytb.getkeywords()
# modelkwd='definedmodel_field_'+str(vfid)
# if kwds.has_key(modelkwd):
# clmodname=kwds[modelkwd]
# mytb.removekeyword(clmodname)
# mytb.removekeyword(modelkwd)
# mytb.close()
mycb.open(self.vis,addcorr=False,addmodel=False)
mycb.delmod(otf=True,field=str(vfid),spw=spwids, scr=False)
mycb.close()
# finally, put the componentlist as model
#tqlstr=''
#if intent!='':
# tqlstr='any(STATE_ID=='+str(stateids.tolist())+')'
# Currently still need to do per spw (see the comment below...)
# assuming CL contains nrow = nspw components
mycl.open(clname)
clinrec = mycl.torecord()
mycl.close(False)
mycl.done()
ncomp = clinrec['nelements']
if ncomp != len(spwids):
raise Exception, "Inconsistency in generated componentlist...Please submit a bug report."
for icomp in range(ncomp):
#self.im.selectvis(spw=spwids[icomp],field=field,observation=observation,time=timerange,intent=intent)
ok = self.im.selectvis(spw=spwids[icomp],field=vfid,observation=observation,time=timerange,intent=intent)
# for MMS, particular subms may not contain the particular spw, so skip for such a case
if ok:
newclinrec = {}
newclinrec['nelements']=1
newclinrec['component0']=clinrec['component'+str(icomp)]
mycl.fromrecord(newclinrec)
cdir = os.getcwd()
if os.access(cdir,os.W_OK):
tmpclpath = cdir+"/"
elif os.access("/tmp",os.W_OK):
tmpclpath = "/tmp/"
#tmpclpath=tmpclpath+"_tmp_setjyCLfile_"+pid
tmpclpath=tmpclpath+os.path.basename(self.vis)+"_tmp_setjyCLfile"
if os.path.exists(tmpclpath):
shutil.rmtree(tmpclpath)
mycl.rename(tmpclpath)
mycl.close(False)
self.im.ft(complist=tmpclpath)
# --------------------------------------------------------------------------------------------
# Currently this does not work properly for some case. Need ft can handle multi-component CL
# with the way to map which component apply to which spw
# Unable when such functionality is implemented in im.ft()
#self.im.selectvis(spw=spwids,field=field,observation=observation,time=timerange,intent=intent)
#self.im.ft(complist=clname) <= e.g. im.ft(comprec) where comrec = {'spw-mapping':[...],comprecs}..
# --------------------------------------------------------------------------------------------
#debug: set locally saved 2010-version component list instead
#cl2010='mod_setjy_spw0_Titan_230.543GHz55674.1d.cl'
#print "Using complist=",cl2010
#self.im.ft(complist=cl2010)
#if cleanupcomps:
# shutil.rmtree(clname)
#self.clnamelist.append(clname)
self.clnamelist.append(clname)
msg="Using channel dependent " if scalebychan else "Using spw dependent "
if clrecs=={}:
raise Exception, "No componentlist is generated."
self._casalog.post(msg+" flux densities")
#self._reportoLog(clrecs,self._casalog)
self._reportoLog2(clrecs,self._casalog)
#self._updateHistory(clrecs,self.vis)
self._updateHistory2(clrecs,self.vis)
# dictionary of dictionary for each field
retdict[vfid]=clrecs
# ==== end of for loop over fields
#output=self._makeRetFluxDict(retdict)
output=self._makeRetFluxDict2(retdict)
#return retval
return output
from casac import casac
import os
import numpy as np
import pdb
iaim = casac.image()
iamask = casac.image()
qa = casac.quanta()
rg = casac.regionmanager()
def automask(image='',
maskimage='',
fracofpeak=0,
rmsthresh=3.0,
resolution=None,
twopass=False):
"""
image : dirty image or residual to mask
maskimage: name of mask to create. If already existant has to be same shape
and coordsys as image
fracofpeak : Fraction of peak to use as masking threshold (a number between 0 and 1)
if 0 then rmsthresh or a value based on the rms of the image is used
rmsthresh : Threshold in sigma to use; default is 3 sigma
resolution: if image has no restoring beam ..this value is used for resolution of
image (e.g '4arcsec')
twopass: set to True if faint fluffy stuff is wanted else false if a less agressive masking
is needed especially a multi pass masking after some cleaning
"""
# print '2pass ', twopass
iaim.open(image)
from casac import casac
import os
import numpy as np
import pdb
iaim=casac.image()
iamask=casac.image()
qa=casac.quanta()
rg=casac.regionmanager()
def automask(image='', maskimage='', fracofpeak=0, rmsthresh=3.0, resolution=None, twopass=False):
"""
image : dirty image or residual to mask
maskimage: name of mask to create. If already existant has to be same shape
and coordsys as image
fracofpeak : Fraction of peak to use as masking threshold (a number between 0 and 1)
if 0 then rmsthresh or a value based on the rms of the image is used
rmsthresh : Threshold in sigma to use; default is 3 sigma
resolution: if image has no restoring beam ..this value is used for resolution of
image (e.g '4arcsec')
twopass: set to True if faint fluffy stuff is wanted else false if a less agressive masking
is needed especially a multi pass masking after some cleaning
"""
# print '2pass ', twopass
iaim.open(image)
stat=iaim.statistics(mask='abs("'+image+'") > 0.0')
csys=iaim.coordsys()
rb=iaim.restoringbeam()
numpix=10
shp=iaim.shape()
resol=qa.quantity(resolution, 'arcsec')
from casac import casac
from locatescript import copydata
quantity = casac.quanta()
im = casac.imager()
ia = casac.image()
def data():
return ['ic2233_1.ms']
def run(fetch=False):
#####fetch data
if fetch:
for f in data():
copydata(f, os.getcwd())
im.open('ic2233_1.ms')
npix = 1024
im.selectvis(spw='0', nchan=[6], start=[0], step=[1])
im.defineimage(nx=npix,
ny=npix,
cellx='3.0arcsec',
celly='3.0arcsec',
stokes="IV",
spw=[0])
im.weight(type='briggs', robust=0.7)
im.setoptions(imagetilevol=-1000000)
im.setvp(dovp=bool(1),
def setSolarObjectJy(self,
field,
spw,
scalebychan,
timerange,
observation,
scan,
intent,
useephemdir,
usescratch=False):
"""
Set flux density of a solar system object using Bryan Butler's new
python model calculation code.
A single time stamp (first time stamp of MS after selections are applied) is
currently used per execution. For flux observation done in a long time span
may need to run multiple setjy with selections by time range (or scans).
"""
#retval = True
output = {}
cleanupcomps = True # leave generated cl files
#from taskinit import *
from taskinit import gentools
qa = casac.quanta()
(myms, mytb, mycl, myme, mycb,
mymsmd) = gentools(['ms', 'tb', 'cl', 'me', 'cb', 'msmd'])
# prepare parameters need to pass to the Bryan's code
# make ms selections
# get source name
# get time ranges
# get spwused and get frequency ranges
sel = {}
sel['field'] = field
sel['spw'] = spw
sel['timerange'] = timerange
sel['observation'] = str(observation)
sel['scan'] = scan
sel['scanintent'] = intent
measframes = [
'REST', 'LSRK', 'LSRD', 'BARY', 'GEO', 'TOPO', 'GALACTO', 'LGROUP',
'CMB'
]
myms.open(self.vis)
myms.msselect(sel, False)
scansummary = myms.getscansummary()
nscan = len(scansummary.keys())
selectedids = myms.msselectedindices()
fieldids = selectedids['field']
obsids = selectedids['observationid']
myms.close()
mytb.open(self.vis + '/OBSERVATION')
if len(obsids) == 0:
getrow = 0
else:
getrow = obsids[0]
observatory = mytb.getcell('TELESCOPE_NAME', getrow)
mytb.close()
mytb.open(self.vis + '/FIELD')
colnames = mytb.colnames()
if len(fieldids) == 0:
fieldids = range(mytb.nrows())
# frame reference for field position
phdir_info = mytb.getcolkeyword("PHASE_DIR", "MEASINFO")
if phdir_info.has_key('Ref'):
fieldref = phdir_info['Ref']
elif phdir_info.has_key('TabRefTypes'):
colnames = mytb.colnames()
for col in colnames:
if col == 'PhaseDir_Ref':
fieldrefind = mytb.getcell(col, fieldids[0])
fieldref = phdir_info['TabRefTypes'][fieldrefind]
else:
fieldref = ''
srcnames = {}
fielddirs = {}
ftimes = {}
ephemid = {}
for fid in fieldids:
#srcnames.append(mytb.getcell('NAME',int(fid)))
srcnames[fid] = (mytb.getcell('NAME', int(fid)))
#fielddirs[fid]=(mytb.getcell('PHASE_DIR',int(fid)))
ftimes[fid] = (mytb.getcell('TIME', int(fid)))
if colnames.count('EHPHEMERIS_ID'):
ephemid[fid] = (mytb.getcell('EPHEMERIS_ID', int(fid)))
else:
ephemid[fid] = -1
mytb.close() # close FIELD table
# need to get a list of time
# but for now for test just get a time centroid of the all scans
# get time range
# Also, this needs to be done per source
# gather freq info from Spw table
mytb.open(self.vis + '/SPECTRAL_WINDOW')
nspw = mytb.nrows()
freqcol = mytb.getvarcol('CHAN_FREQ')
freqwcol = mytb.getvarcol('CHAN_WIDTH')
fmeasrefcol = mytb.getcol('MEAS_FREQ_REF')
reffreqs = mytb.getcol('REF_FREQUENCY')
mytb.close()
# store all parameters need to call solar_system_fd for all sources
inparams = {}
validfids = [
] # keep track of valid fid that has data (after selection)
# if same source name ....need handle this...
for fid in fieldids:
sel['field'] = str(fid)
myms.open(self.vis)
#reset the selection
try:
status = myms.msselect(sel)
except:
#skip this field
continue
if not status:
continue
validfids.append(fid)
trange = myms.range('time')
#if not inparams.has_key(srcnames[fid]):
# inparams[srcnames[fid]]={}
if not inparams.has_key(fid):
inparams[fid] = {}
inparams[fid]['fieldname'] = srcnames[fid]
#tc = (trange['time'][0]+trange['time'][1])/2. #in sec.
# use first timestamp to be consistent with the ALMA Control
# old setjy (Butler-JPL-Horizons 2010) seems to be using
# time in FIELD... but here is first selected time in main table
if ephemid[fid] == -1: # keep old behavior
tc = trange['time'][0] #in sec.
tmsg = "Time used for the model calculation (=first time stamp of the selected data) for field "
else: # must have ephem table attached...
tc = ftimes[fid] #in sec.
tmsg = "Time used for the model calculation for field "
#if inparams[srcnames[fid]].has_key('mjd'):
# inparams[srcnames[fid]]['mjds'][0].append([myme.epoch('utc',qa.quantity(tc,'s'))['m0']['value']])
#else:
# inparams[srcnames[fid]]['mjds']=[myme.epoch('utc',qa.quantity(tc,'s'))['m0']['value']]
if inparams[fid].has_key('mjd'):
inparams[fid]['mjds'][0].append(
[myme.epoch('utc', qa.quantity(tc, 's'))['m0']['value']])
else:
inparams[fid]['mjds'] = [
myme.epoch('utc', qa.quantity(tc, 's'))['m0']['value']
]
usedtime = qa.time(qa.quantity(tc, 's'), form='ymd')[0]
self._casalog.post(tmsg + str(fid) + ":" + usedtime)
# get a correct direction measure
mymsmd.open(self.vis)
dirdic = mymsmd.phasecenter(int(fid))
mymsmd.close()
# check if frame is J2000 and if not do the transform
if dirdic['refer'] != 'J2000':
myme.doframe(myme.observatory(observatory))
myme.doframe(myme.epoch('utc', qa.quantity(tc, 's')))
azeldir = myme.measure(dirdic, 'AZELGEO')
dirdic = myme.measure(azeldir, 'J2000')
fielddirs[fid] = (numpy.array([[dirdic['m0']['value']],
[dirdic['m1']['value']]]))
# somehow it gives you duplicated ids .... so need to uniquify
selspws = list(set(myms.msselectedindices()['spw']))
# make sure it is int rather than numpy.int32, etc.
selspws = [int(ispw) for ispw in selspws]
#inparams[srcnames[fid]]['spwids']= selspws if len(selspws)!=0 else range(nspw)
inparams[fid]['spwids'] = selspws if len(selspws) != 0 else range(
nspw)
#create a list of freq ranges with selected spws
# should worry about freq order???
freqlist = []
freqlistraw = []
framelist = []
#for idx in inparams[srcnames[fid]]['spwids']:
for idx in inparams[fid]['spwids']:
freqs = freqcol['r' + str(idx + 1)]
freqws = freqwcol['r' + str(idx + 1)]
fmeasref = fmeasrefcol[idx]
#if scalebychan=T, this has to be min, max determined from
# chan_freq(channel center)+/- chan width.
if scalebychan:
# pack into list of list of list (freqlist[nf][nspw])
perspwfreqlist = []
for nf in range(len(freqs)):
fl = freqs[nf][0] - freqws[nf][0] / 2.
fh = freqs[nf][0] + freqws[nf][0] / 2.
perspwfreqlist.append([fl, fh])
freqlist.append(perspwfreqlist)
else:
if (len(freqs) == 1):
fl = freqs[0][0] - freqws[0][0] / 2.
fh = freqs[0][0] + freqws[0][0] / 2.
freqlist.append([float(fl), float(fh)])
else:
freqlist.append([float(min(freqs)), float(max(freqs))])
framelist.append(measframes[fmeasref])
freqlistraw.append(
freqs.transpose()[0].tolist()) # data chanfreq list
#inparams[srcnames[fid]]['freqlist']=freqlist
#inparams[srcnames[fid]]['freqlistraw']=freqlistraw
#inparams[srcnames[fid]]['framelist']=framelist
#inparams[srcnames[fid]]['reffreqs']=reffreqs
inparams[fid]['freqlist'] = freqlist
inparams[fid]['freqlistraw'] = freqlistraw
inparams[fid]['framelist'] = framelist
inparams[fid]['reffreqs'] = reffreqs
myms.close()
# call Bryan's code
# errcode: list of list - inner list - each values for range of freqs
# flluxes: list of list
# fluxerrs:
# size: [majoraxis, minoraxis, pa]
# direction: direction for each time stamp
#
#import solar_system_setjy as ss_setjy
import solar_system_setjy as SSsetjy
retdict = {} # for returning flux densities?
ss_setjy = SSsetjy.solar_system_setjy()
#for src in srcnames:
self.clnamelist = []
for vfid in validfids:
src = srcnames[vfid]
#mjds=inparams[src]['mjds']
mjds = inparams[vfid]['mjds']
fluxes = []
# call solar_system_fd() per spw (for scalebychan freqlist has an extra dimention)
#nspwused=len(inparams[src]['freqlist'])
nspwused = len(inparams[vfid]['freqlist'])
# warning for many channels but it is really depends on the source
if scalebychan:
maxnf = 0
for ispw in range(nspwused):
#nf = len(inparams[src]['freqlist'][ispw])
nf = len(inparams[vfid]['freqlist'][ispw])
maxnf = max(nf, maxnf)
if maxnf >= 3840 and src.upper(
) != "MARS": # mars shoulde be ok
self._casalog.post(
"Processing %s spw(s) and at least some of them are a few 1000 channels or more. This may take \
many minutes (>3min per spw for 3840 channels) in some cases. Please be patient."
% nspwused, "WARN")
for i in range(nspwused): # corresponds to n spw
if type(freqlist[0][0]) == list:
#infreqs=inparams[src]['freqlist'][i]
infreqs = inparams[vfid]['freqlist'][i]
else:
#infreqs=[inparams[src]['freqlist'][i]]
infreqs = [inparams[vfid]['freqlist'][i]]
self._casalog.post(
"Calling solar_system_fd: %s(%s) for spw%s freqs=%s" %
(src, vfid, i, freqlist[i]), 'DEBUG1')
(errcodes, subfluxes, fluxerrs, sizes, dirs)=\
ss_setjy.solar_system_fd(source_name=src, MJDs=mjds, frequencies=infreqs, observatory=observatory, casalog=self._casalog)
# for old code
#(errcodes, subfluxes, fluxerrs, sizes, dirs)=\
# ss_setjy.solar_system_fd(source_name=src, MJDs=mjds, frequencies=infreqs, casalog=self._casalog)
# for nf freq ranges, nt mjds
# errcodes[nf][nt], subfluxes[nf][nt], fluxerrs[nf][nt], sizes[nt], dirs[nt]
self._casalog.post(
"+++++ solar_system_fd() returned values +++++", 'DEBUG1')
self._casalog.post(" fluxes(fds)=%s" % subfluxes, 'DEBUG1')
self._casalog.post(" sizes=%s" % sizes, 'DEBUG1')
self._casalog.post(" directions=%s\n" % dirs, 'DEBUG1')
# packed fluxes for all spws
fluxes.append(subfluxes)
# fluxes has fluxesi[nspw][nf][nt]
# ------------------------------------------------------------------------
# For testing with hardcoded values without calling solar_system_fd()...
#errcodes=[[0,0,0,0,0]]
#fluxes=[[26.40653147,65.23839313,65.23382757,65.80638802,69.33396562]]
#fluxerrs=[[0.0,0.0,0.0,0.0,0.0]]
#sizes=[[3.6228991032674371,3.6228991032674371,0.0]]
#dirs=[{'m0': {'unit': 'rad', 'value': 0.0}, 'm1': {'unit': 'rad', 'value': 0.0}, 'refer': 'J2000', 'type': 'direction'}]
# ------------------------------------------------------------------------
# local params for selected src
#framelist=inparams[src]['framelist']
#freqlist=inparams[src]['freqlist']
#freqlistraw=inparams[src]['freqlistraw']
#reffreqs=inparams[src]['reffreqs']
#spwids=inparams[src]['spwids']
framelist = inparams[vfid]['framelist']
freqlist = inparams[vfid]['freqlist']
freqlistraw = inparams[vfid]['freqlistraw']
reffreqs = inparams[vfid]['reffreqs']
spwids = inparams[vfid]['spwids']
clrecs = odict.odict()
labels = []
# loop for over for multiple directions (=multiple MJDs) for a given src
for i in range(
len(dirs)
): # this is currently only length of 1 since no multiple timestamps were used
# check errcode - error code would be there per flux per time (dir)
reterr = testerrs(errcodes[i], src)
if reterr == 2:
continue
#dirstring = [dirs[i]['refer'],qa.tos(dirs[i]['m0']),qa.tos(dirs[i]['m1'])]
if useephemdir:
dirstring = [
dirs[i]['refer'],
qa.tos(dirs[i]['m0']),
qa.tos(dirs[i]['m1'])
]
else:
#dirstring = [fieldref, str(fielddirs[fieldids[0]][0][0])+'rad', str(fielddirs[fieldids[0]][1][0])+'rad']
# extract field direction of first id of the selected field ids
#dirstring = [fieldref, "%.18frad" % (fielddirs[fieldids[0]][0][0]), "%.18frad" % (fielddirs[fieldids[0]][1][0])]
dirstring = [
fieldref,
"%.18frad" % (fielddirs[vfid][0][0]),
"%.18frad" % (fielddirs[vfid][1][0])
]
#print "dirstring=",dirstring
# setup componentlists
# need to set per dir
# if scalebychan=F, len(freqs) corresponds to nspw selected
# Need to put in for-loop to create cl for each time stamp? or scan?
#clpath='/tmp/'
clpath = './'
# construct cl name (multiple spws in one componentlist table)
selreffreqs = [reffreqs[indx] for indx in spwids]
minfreq = min(selreffreqs)
maxfreq = max(selreffreqs)
freqlabel = '%.3f-%.3fGHz' % (minfreq / 1.e9, maxfreq / 1.e9)
#tmlabel = '%.1fd' % (tc/86400.)
mjd = inparams[vfid]['mjds'][0]
tmlabel = '%.1fd' % (mjd)
#clabel = src+'_spw'+str(spwids[j])+'_'+freqlabel+'_'+tmlabel
#clabel0 = src+'_'+freqlabel+'_'+tmlabel
#pid=str(os.getpid())
#clname = clpath+clabel0+"_"+pid+'.cl'
clabel0 = src + '_' + freqlabel + '_' + tmlabel + "_" + os.path.basename(
self.vis)
clname = clpath + clabel0 + '.cl'
#debug
self._casalog.post(
"Create componentlist: %s for vfid=%s" % (clname, vfid),
'DEBUG1')
if (os.path.exists(clname)):
shutil.rmtree(clname)
iiflux = []
iinfreq = []
# for logging/output dict - pack each freq list for each spw
freqsforlog = []
for j in range(len(freqlist)): # loop over nspw
freqlabel = '%.3fGHz' % (reffreqs[int(spwids[j])] / 1.e9)
clabel = src + '_spw' + str(
spwids[j]) + '_' + freqlabel + '_' + tmlabel
#print "addcomponent...for spw=",spwids[j]," i=",i," flux=",fluxes[j][i]
if scalebychan:
index = 2.0
sptype = 'spectral index'
else:
index = 0.0
sptype = 'constant'
# adjust to change in returned flux shape. An extra [] now seems to be gone. 2012-09-27
iflux = fluxes[j][i][0]
#print "addcomponent with flux=%s at frequency=%s" %\
# (iflux,str(reffreqs[int(spwids[j])]/1.e9)+'GHz')
# i - time stamps = 0 for now, j = a freq range
infreq = freqlist[j][0][0] if type(
freqlist[j][0]) == list else freqlist[j][0]
# for a single CL with multple spws
if j == 0: infreq0 = infreq
# --- version for 'multi-spws in a single comp single CL'
# accumulate all frequencies from all spws to a list
#if not scalebychan:
#freqlist[j] for j spw should contain a list with two freqs (min and max of
# of the spw and the same fluxes should be set for the freqs so that cl.setspectrum
# with tabular would not interpolate inside each spw
##iinfreq.extend(freqlist[j])
# nch = len(freqlistraw[j])
# iinfreq.extend(freqlistraw[j])
# assigning the same flux to the two freqs
##iiflux.extend([iflux,iflux])
# for ich in range(nch):
# iiflux.extend([iflux])
#else:
# iiflux.extend(fluxes[j][i])
# if type(freqlist[j][0])==list and len(freqlist[j][0])>1:
# for fr in freqlist[j]:
# iinfreq.append((fr[1]+fr[0])/2)
# else:
# if type(freqlist[j])==list:
# iinfreq.append((freqlist[j][1]+freqlist[j][0])/2)
# else:
# iinfreq.append(freqlist[j])
# freqsforlog.append(iinfreq)
# -----------------------------------------------------------------------------------
self._casalog.post("addcomponent with flux=%s at frequency=%s" %\
# (fluxes[j][i][0],str(reffreqs[int(spwids[j])]/1.e9)+'GHz'), 'INFO1')
(iflux,str(reffreqs[int(spwids[j])]/1.e9)+'GHz'), 'INFO1')
#
mycl.addcomponent(iflux,
fluxunit='Jy',
polarization="Stokes",
dir=dirstring,
shape='disk',
majoraxis=str(sizes[i][0]) + 'arcsec',
minoraxis=str(sizes[i][1]) + 'arcsec',
positionangle=str(sizes[i][2]) + 'deg',
freq=[framelist[0],
str(infreq) + 'Hz'],
spectrumtype=sptype,
index=index,
label=clabel)
if scalebychan:
# use tabular form to set flux for each channel
# This may be redundant
if type(fluxes[j][i]) == list and len(
fluxes[j][i]) > 1:
if type(freqlist[j][0]) == list and len(
freqlist[j][0]) > 1:
freqs = []
for fr in freqlist[j]:
freqs.append((fr[1] + fr[0]) / 2)
clind = mycl.length() - 1
mycl.setspectrum(which=clind,
type='tabular',
tabularfreqs=freqs,
tabularflux=fluxes[j][0],
tabularframe=framelist[j])
### === per spw process end here
# - version that put all spws into a component -
# set a single component freq set at the the lower edge of first spw
#mycl.addcomponent(iiflux[0],fluxunit='Jy', polarization="Stokes", dir=dirstring,
# shape='disk', majoraxis=str(sizes[i][0])+'arcsec', minoraxis=str(sizes[i][1])+'arcsec',
# positionangle=str(sizes[i][2])+'deg', freq=[framelist[0],str(infreq0)+'Hz'],
# spectrumtype=sptype, index=index, label=clabel)
# if it's list of fluxes try to put in tabular form
#if type(fluxes[j][i]) ==list and len(fluxes[j][i])> 1:
# if len(iiflux)> 1:
#print "framelist[j]=",framelist[j]
#if type(freqlist[j][0])==list and len(freqlist[j][0])>1:
# freqs=[]
# for fr in freqlist[j]:
# freqs.append((fr[1]+fr[0])/2)
#else:
# freqs=freqlist[j]
#clind = mycl.length() - 1
# mycl.setspectrum(which=clind, type='tabular', tabularfreqs=freqs, tabularflux=fluxes[j][0],
#tabularframe=framelist[j])
# mycl.setspectrum(which=clind, type='tabular', tabularfreqs=iinfreq, tabularflux=iiflux,
# tabularframe=framelist[0])
#mycl.rename(clname)
#put in a record for log output
#clrecs[clabel] = mycl.torecord()
clrecs[clabel0] = mycl.torecord()
clrecs[clabel0]['allfluxinfo'] = fluxes
clrecs[clabel0]['allfreqinfo'] = freqsforlog
clrecs[clabel0]['spwids'] = spwids
mycl.rename(clname) # - A CL per field
mycl.close(False) # False for not to send a warning message
mycl.done()
# if scratch=F check if the virtual model already exist
# for the field if it is clear it.
# if j==0 and (not usescratch):
# mytb.open(self.vis, nomodify=False)
# kwds = mytb.getkeywords()
# modelkwd='definedmodel_field_'+str(vfid)
# if kwds.has_key(modelkwd):
# clmodname=kwds[modelkwd]
# mytb.removekeyword(clmodname)
# mytb.removekeyword(modelkwd)
# mytb.close()
mycb.open(self.vis, addcorr=False, addmodel=False)
mycb.delmod(otf=True, field=str(vfid), spw=spwids, scr=False)
mycb.close()
# finally, put the componentlist as model
#tqlstr=''
#if intent!='':
# tqlstr='any(STATE_ID=='+str(stateids.tolist())+')'
# Currently still need to do per spw (see the comment below...)
# assuming CL contains nrow = nspw components
mycl.open(clname)
clinrec = mycl.torecord()
mycl.close(False)
mycl.done()
ncomp = clinrec['nelements']
if ncomp != len(spwids):
raise Exception, "Inconsistency in generated componentlist...Please submit a bug report."
for icomp in range(ncomp):
#self.im.selectvis(spw=spwids[icomp],field=field,observation=observation,time=timerange,intent=intent)
ok = self.im.selectvis(spw=spwids[icomp],
field=vfid,
observation=observation,
time=timerange,
intent=intent)
# for MMS, particular subms may not contain the particular spw, so skip for such a case
if ok:
newclinrec = {}
newclinrec['nelements'] = 1
newclinrec['component0'] = clinrec['component' +
str(icomp)]
mycl.fromrecord(newclinrec)
cdir = os.getcwd()
if os.access(cdir, os.W_OK):
tmpclpath = cdir + "/"
elif os.access("/tmp", os.W_OK):
tmpclpath = "/tmp/"
#tmpclpath=tmpclpath+"_tmp_setjyCLfile_"+pid
tmpclpath = tmpclpath + os.path.basename(
self.vis) + "_tmp_setjyCLfile"
self._casalog.post("tmpclpath=" + tmpclpath)
if os.path.exists(tmpclpath):
shutil.rmtree(tmpclpath)
mycl.rename(tmpclpath)
mycl.close(False)
self._casalog.post("Now tmpclpath=" + tmpclpath)
self.im.ft(complist=tmpclpath)
# --------------------------------------------------------------------------------------------
# Currently this does not work properly for some case. Need ft can handle multi-component CL
# with the way to map which component apply to which spw
# Unable when such functionality is implemented in im.ft()
#self.im.selectvis(spw=spwids,field=field,observation=observation,time=timerange,intent=intent)
#self.im.ft(complist=clname) <= e.g. im.ft(comprec) where comrec = {'spw-mapping':[...],comprecs}..
# --------------------------------------------------------------------------------------------
#debug: set locally saved 2010-version component list instead
#cl2010='mod_setjy_spw0_Titan_230.543GHz55674.1d.cl'
#print "Using complist=",cl2010
#self.im.ft(complist=cl2010)
#if cleanupcomps:
# shutil.rmtree(clname)
#self.clnamelist.append(clname)
self.clnamelist.append(clname)
msg = "Using channel dependent " if scalebychan else "Using spw dependent "
if clrecs == {}:
raise Exception, "No componentlist is generated."
self._casalog.post(msg + " flux densities")
#self._reportoLog(clrecs,self._casalog)
self._reportoLog2(clrecs, self._casalog)
#self._updateHistory(clrecs,self.vis)
self._updateHistory2(clrecs, self.vis)
# dictionary of dictionary for each field
retdict[vfid] = clrecs
# ==== end of for loop over fields
#output=self._makeRetFluxDict(retdict)
output = self._makeRetFluxDict2(retdict)
#return retval
return output
from casac import casac
from locatescript import copydata
quantity=casac.quanta()
im = casac.imager()
ia = casac.image()
def data():
return ['ic2233_1.ms']
def run(fetch=False) :
#####fetch data
if fetch:
for f in data( ):
copydata( f, os.getcwd( ) )
im.open('ic2233_1.ms')
npix=1024
im.selectvis(spw='0', nchan=[6], start=[0], step=[1])
im.defineimage(nx=npix, ny=npix, cellx='3.0arcsec', celly='3.0arcsec', stokes="IV", spw=[0])
im.weight(type='briggs', robust=0.7)
im.setoptions(imagetilevol=-1000000);
im.setvp(dovp=bool(1), usedefaultvp=bool(1), dosquint=bool(1),
parangleinc='5.0deg')
im.make('squint_corr')
im.clean(algorithm='mfhogbom', niter=1000, model=['squint_corr'], residual=['squint_corr.residual'], image=['squint_corr.restored'], threshold='0Jy')
im.done()
return ['squint_corr.restored']
def __init__(self,
imageName,
write=True,
resultDir='WEBPAGES/imageTest/',
imDir='IMAGES/'):
import shutil
self.imTool = casac.image()
self.imTool.open(imageName) #open('tables/squint_corr.restored')
# fix up images that don't have CASA-canonical stokes and spec:
# assume for now that direction is in 01 at least,
mycs = self.imTool.coordsys()
findstok = mycs.findcoordinate("stokes")
if not findstok['return']:
myImagename = imageName + ".k"
self.imTool.adddegaxes(stokes=True,
outfile=myImagename,
overwrite=True)
mystokpix = self.imTool.summary()['ndim'] # ct from 0
self.imTool.close()
shutil.rmtree(imageName)
shutil.move(myImagename, imageName)
self.imTool.open(imageName)
mycs.done()
mycs = self.imTool.coordsys()
else:
mystokpix = findstok['pixel']
findspec = mycs.findcoordinate("spectral")
if not findspec['return']:
myImagename = imageName + ".s"
self.imTool.adddegaxes(spectral=True,
outfile=myImagename,
overwrite=True)
myspecpix = self.imTool.summary()['ndim'] # ct from 0
self.imTool.close()
shutil.rmtree(imageName)
shutil.move(myImagename, imageName)
self.imTool.open(imageName)
mycs.done()
mycs = self.imTool.coordsys()
else:
myspecpix = findspec['pixel']
curr_order = [mystokpix, myspecpix]
if curr_order != [2, 3]:
myImagename = imageName + ".t"
self.imTool.transpose(order="01%1i%1i" % (mystokpix, myspecpix),
outfile=myImagename,
overwrite=True)
shutil.rmtree(imageName)
shutil.move(myImagename, imageName)
self.imTool.open(imageName)
self.rgTool = casac.regionmanager()
self.qaTool = casac.quanta()
self.getArr() #instead make explicit call to getArr()
self.write = write
self.imageName = imageName
self.iterate = 0 #for multiple cubeFit() tests
if self.write:
self.resultDir = resultDir + strftime('/%Y_%m_%d/')
if os.access(self.resultDir, os.F_OK) is False:
print self.resultDir + ' directory DNE, so am making one!'
os.mkdir(self.resultDir)
else:
print self.resultDir + ' directory exists; will add to it!'
self.imDir = imDir
if os.access(imDir, os.F_OK) is False:
print imDir + ' directory DNE, so am making one!'
os.mkdir(imDir)
else:
print imDir + ' directory exists; will add to it!'
t = localtime(time())
self.fname = 'Regression-%s-%s-%s-%s-%s-%s.html' % (
t[0], t[1], t[2], t[3], t[4], t[5])
self.html = self.resultDir + self.fname
self.body1 = []
self.body2 = []
self.htmlPub = htmlPub(self.html, 'Image tests')
else:
print 'stats-only mode; will not write to html file!'
def __init__(self, imageName, write=True,
resultDir='WEBPAGES/imageTest/',
imDir='IMAGES/'):
import shutil
self.imTool=casac.image()
self.imTool.open(imageName) #open('tables/squint_corr.restored')
# fix up images that don't have CASA-canonical stokes and spec:
# assume for now that direction is in 01 at least,
mycs=self.imTool.coordsys()
findstok=mycs.findcoordinate("stokes")
if not findstok['return']:
myImagename=imageName+".k"
self.imTool.adddegaxes(stokes=True,outfile=myImagename,overwrite=True)
mystokpix=self.imTool.summary()['ndim'] # ct from 0
self.imTool.close()
shutil.rmtree(imageName)
shutil.move(myImagename,imageName)
self.imTool.open(imageName)
mycs.done()
mycs=self.imTool.coordsys()
else:
mystokpix=findstok['pixel']
findspec=mycs.findcoordinate("spectral")
if not findspec['return']:
myImagename=imageName+".s"
self.imTool.adddegaxes(spectral=True,outfile=myImagename,overwrite=True)
myspecpix=self.imTool.summary()['ndim'] # ct from 0
self.imTool.close()
shutil.rmtree(imageName)
shutil.move(myImagename,imageName)
self.imTool.open(imageName)
mycs.done()
mycs=self.imTool.coordsys()
else:
myspecpix=findspec['pixel']
curr_order=[mystokpix,myspecpix]
if curr_order != [2,3]:
myImagename=imageName+".t"
self.imTool.transpose(order="01%1i%1i" % (mystokpix,myspecpix),outfile=myImagename,overwrite=True)
shutil.rmtree(imageName)
shutil.move(myImagename,imageName)
self.imTool.open(imageName)
self.rgTool=casac.regionmanager()
self.qaTool=casac.quanta()
self.getArr() #instead make explicit call to getArr()
self.write=write
self.imageName=imageName
self.iterate=0 #for multiple cubeFit() tests
if self.write:
self.resultDir=resultDir+strftime('/%Y_%m_%d/')
if os.access(self.resultDir,os.F_OK) is False:
print self.resultDir+' directory DNE, so am making one!'
os.mkdir(self.resultDir)
else:
print self.resultDir+' directory exists; will add to it!'
self.imDir=imDir
if os.access(imDir,os.F_OK) is False:
print imDir+' directory DNE, so am making one!'
os.mkdir(imDir)
else:
print imDir+' directory exists; will add to it!'
t=localtime( time() )
self.fname='Regression-%s-%s-%s-%s-%s-%s.html'%(t[0],t[1],t[2],t[3],t[4],t[5])
self.html=self.resultDir+self.fname
self.body1=[]
self.body2=[]
self.htmlPub=htmlPub(self.html,'Image tests')
else:
print 'stats-only mode; will not write to html file!'
def _muellerModelDataReader(self):
"""
read flux density from the asteroid models by
Mueller
"""
from casac import casac
qa = casac.quanta()
reffreq = None
refflux = None
date = qa.time(str(self.mjd) + 'd', form='ymd')[0]
yr = date.split('/')[0]
# ------------------------------
# Following section should only to read the data initially and keep the data and only scan the new model data file
# when the mjd is outside of the current data...
#
#if int(yr) < 2015: yr = '2015'
if self.src in self.knownsrcdict.keys():
filename = self.datapath + self.src + "_ALMA_TPMprediction_" + yr + "_" + self.knownsrcdict[
self.src]['interval'] + ".txt"
if (self.openedFile != filename):
# read a new file
self.openedFile = filename
import glob
flist = glob.glob(filename)
if len(flist) == 1:
self._casalog.post("Reading model data: " + flist[0])
with open(flist[0], "r") as f:
self.data = f.readlines()
elif len(flist) == 0:
raise IOError("Cannot find the model file for " +
self.src + " for date=" + date + ".")
# else:
# self._casalog.post("use the file already read..self.openedFile="+self.openedFile)
freqs = self._checkheader(self.data)
if len(freqs) == 0:
raise IOError("Problem in reading model data file!")
i = np.abs(freqs - self.freq).argmin()
reffreq = freqs[i]
#self._casalog.post("self.freq= %s i=%s reffreq=%s" % (self.freq, i, reffreq))
#print "self.freq= %s i=%s reffreq=%s" % (self.freq, i, reffreq)
maindata = []
mjds = []
fluxes = []
for line in self.data[8:]:
if line.find('----') < 0:
maindata.append(line)
mjds.append(float(line.split()[5]))
# i th flux (0 based)
fluxes.append(float(line.split()[(i + 1) + 5]))
mjdarr = np.array(mjds)
flxarr = np.array(fluxes)
# ---------------------
# find flux density of nearest in time
t = np.abs(mjdarr - self.mjd).argmin()
refflux = flxarr[t]
#print "flxarr=",flxarr
#print "freq, mjd=",self.freq,self.mjd
#print "refflux@reffreq=%s@%s at %s" % (refflux,reffreq,mjdarr[t])
#self._casalog.post("refflux@reffreq=%s@%s at %s" % (refflux,reffreq,mjdarr[t]),"DEBUG1")
return (reffreq, refflux)
def field2skycat(msname='', skycat='', fieldpattern=''):
"""
Converts field table in ms to skycatalog
allow overlay on image in the viewer
"""
enumTypes = [
'J2000', 'JMEAN', 'JTRUE', 'APP', 'B1950', 'B1950_VLA', 'BMEAN',
'BTRUE', 'GALACTIC', 'HADEC', 'AZEL', 'AZELSW', 'AZELGEO', 'AZELSWGEO',
'JNAT', 'ECLIPTIC', 'MECLIPTIC', 'TECLIPTIC', 'SUPERGAL', 'ITRF',
'TOPO', 'ICRS'
]
qa = casac.quanta()
tb = casac.table()
tb.open(msname + '/FIELD')
dir = tb.getcol('PHASE_DIR')
nam = tb.getcol('NAME')
nfield = tb.nrows()
n = 0
for k in range(nfield):
if (re.match(fieldpattern, nam[k]) != None):
n = n + 1
eltype = []
if (tb.getcolkeyword('PHASE_DIR', 'MEASINFO').has_key('VarRefCol')):
typeid = tb.getcol(
tb.getcolkeyword('PHASE_DIR', 'MEASINFO')['VarRefCol'])
for k in range(nfield):
if (re.match(fieldpattern, nam[k]) != None):
eltype.append(enumTypes[typeid[k]])
else:
eltype = [tb.getcolkeyword('PHASE_DIR', 'MEASINFO')['Ref']] * nfield
unitra = tb.getcolkeyword('PHASE_DIR', 'QuantumUnits')[0]
unitdec = tb.getcolkeyword('PHASE_DIR', 'QuantumUnits')[1]
tb.done()
des = {}
des['Type'] = {'valueType': 'string'}
des['Long'] = {'valueType': 'double'}
des['Lat'] = {'valueType': 'double'}
des['FIELD_NAME'] = {'valueType': 'string'}
des['FIELD_ID'] = {'valueType': 'string'}
des['RA'] = {'valueType': 'string'}
des['DEC'] = {'valueType': 'string'}
tb.create(tablename=skycat, tabledesc=des, nrow=n)
tb.putcol('Type', eltype)
lati = np.zeros((n, ))
longi = np.zeros((n, ))
RA = []
DEC = []
fid = []
fieldname = []
n = 0
for k in range(nfield):
if (re.match(fieldpattern, nam[k]) != None):
longi[n] = qa.convert(qa.quantity(dir[0, 0, k], unitra),
'deg')['value']
lati[n] = qa.convert(qa.quantity(dir[1, 0, k], unitdec),
'deg')['value']
RA.append(qa.time(qa.quantity(dir[0, 0, k], unitra), prec=10))
DEC.append(qa.angle(qa.quantity(dir[1, 0, 0], unitdec), prec=10))
fid.append(str(k))
fieldname.append(nam[k])
n = n + 1
tb.putcol('RA', RA)
tb.putcol('DEC', DEC)
# tb.putcol('FIELD_NAME', nam)
tb.putcol('FIELD_NAME', fieldname)
tb.putcol('FIELD_ID', fid)
tb.putcol('Long', longi)
tb.putcol('Lat', lati)
tb.putcolkeyword(columnname='Long', keyword='UNIT', value='deg')
tb.putcolkeyword(columnname='Lat', keyword='UNIT', value='deg')
tb.putinfo({'type': 'Skycatalog'})
tb.done()
