def get_scantimes(ms):
# Open the MS
tbHandle = casac.table()
tbHandle.open(ms)
# Get the time and scan columns
times = tbHandle.getcol('TIME')
scans = tbHandle.getcol('SCAN_NUMBER')
# Assign each time to the proper scan
d = dict()
for r in range(tbHandle.nrows()):
if not d.has_key(scans[r]): d[scans[r]] = list()
d[scans[r]].append(times[r])
tbHandle.close()
del tbHandle
# Get the minimum and maximum time for each scan
scanTimes = dict()
for k in d.keys():
scanTimes[k] = dict()
scanTimes[k]['min'] = numpy.min(d[k])
scanTimes[k]['max'] = numpy.max(d[k])
# Return the minimum and maximum time for each scan
return scanTimes
def pixelmask2cleanmask(imagename='',
maskname='mask0',
maskimage='',
usemasked=False):
"""
convert pixel(T/F) mask (in a CASA image) to a mask image (1/0)
used for clean
imagename - input imagename that contain a mask to be used
maskname - mask name in the image (default: mask0)
maskimage - output mask image name
usemasked - if True use masked region as a valid region
"""
ia = casac.image()
ia.open(imagename)
masks = ia.maskhandler('get')
ia.close()
inmaskname = ''
if type(masks) != list:
masks = [masks]
for msk in masks:
if maskname == msk:
inmaskname = msk
break
if inmaskname == '':
raise Exception, "mask %s does not exist. Available masks are: %s" % (
maskname, masks)
tb = casac.table()
tb.open(imagename + '/' + maskname)
dat0 = tb.getcol('PagedArray')
tb.close()
#os.system('cp -r %s %s' % (imagename, maskimage))
shutil.copytree(imagename, maskimage)
ia.open(maskimage)
# to unset mask
ia.maskhandler('set', [''])
# make all valid
if (usemasked):
ia.set(1)
else:
ia.set(0)
ia.close()
#
tb.open(maskimage, nomodify=False)
imd = tb.getcol('map')
# maybe shape check here
#by default use True part of bool mask
masked = 1
if (usemasked): masked = 0
imd[dat0] = masked
tb.putcol('map', imd)
tb.close()
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 get_polbasis(ms):
# Open the MS
tbHandle = casac.table()
tbHandle.open(ms + '/FEED')
# Get the POLARIZATION_TYPE column
pt = tbHandle.getcol('POLARIZATION_TYPE')
# Determine the polarization basis
if pt[0, :][0] == 'R' or pt[1, :][0] == 'R':
polBasis = 'CIRCULAR'
else:
polBasis = 'LINEAR'
# Return the polarization basis
return polBasis
def get_polbasis(ms):
# Open the MS
tbHandle = casac.table()
tbHandle.open(ms + "/FEED")
# Get the POLARIZATION_TYPE column
pt = tbHandle.getcol("POLARIZATION_TYPE")
# Determine the polarization basis
if pt[0, :][0] == "R" or pt[1, :][0] == "R":
polBasis = "CIRCULAR"
else:
polBasis = "LINEAR"
# Return the polarization basis
return polBasis
def addCorrectedData(msname):
""" Add CORRECTED_DATA column to an MS.
"""
tb = casac.table()
# Open the MS
tb.open(msname, nomodify=False)
cnames = tb.colnames()
# Get the description of the DATA column.
try:
cdesc = tb.getcoldesc('DATA')
except:
raise ValueError('Column DATA does not exist')
hasTiled = False
# Determine if the DATA storage specification is tiled.
hasTiled = False
try:
dminfo = None
for rec in tb.getdminfo("DATA"):
if recs[rec]['COLUMNS'][0] == 'DATA':
dminfo = recs[rec]
if dminfo['TYPE'][:5] == 'Tiled':
hasTiled = True
except:
hasTiled = False
# Use TiledShapeStMan if needed.
if not hasTiled:
dminfo = {'TYPE': 'TiledShapeStMan', 'SPEC': {'DEFAULTTILESHAPE':[4,32,128]}}
# Add the columns (if not existing). Use the description of the DATA column.
if 'CORRECTED_DATA' in cnames:
print("Column CORRECTED_DATA not added; it already exists")
else:
dminfo['NAME'] = 'correcteddata'
cdesc['comment'] = 'The corrected data column'
tb.addcols({'CORRECTED_DATA': cdesc}, dminfo)
# Flush the table to make sure it is written.
tb.flush()
def get_scantimes(ms):
# Open the MS
tbHandle = casac.table()
tbHandle.open(ms)
# Get the time and scan columns
times = tbHandle.getcol("TIME")
scans = tbHandle.getcol("SCAN_NUMBER")
# Assign each time to the proper scan
d = dict()
for r in range(tbHandle.nrows()):
if not d.has_key(scans[r]):
d[scans[r]] = list()
d[scans[r]].append(times[r])
tbHandle.close()
del tbHandle
# Get the minimum and maximum time for each scan
scanTimes = dict()
for k in d.keys():
scanTimes[k] = dict()
scanTimes[k]["min"] = numpy.min(d[k])
scanTimes[k]["max"] = numpy.max(d[k])
# Return the minimum and maximum time for each scan
return scanTimes
from casac import casac
import utils
tb = casac.table()
def formatTable(tname):
tb.open(tname)
times = [utils.render_time(t) for t in tb.getcol('TIME')]
ants = tb.getcol('ANTENNA1')
swids = tb.getcol('SPECTRAL_WINDOW_ID')
flags = list(tb.getcol('FLAG').squeeze().transpose().all(axis=1))
params = list(tb.getcol("FPARAM").squeeze())
fs = "{:20} {:3} {:2} " + 6 * "{:>15.8g} "
s = "\n".join(
fs.format(*r[1:]) for r in zip(flags, times, ants, swids, *params)
if not r[0])
tb.close()
return s
# jagonzal: Import tasks but don't load task manager and dbus os.environ['CASA_ENGINE']="YES" from tasks import * casalog = casac.logsink() casalog.setglobal(True) quanta = casac.quanta() measures = casac.measures() imager = casac.imager() calibrater = casac.calibrater() ms = casac.ms() tableplot = casac.tableplot() msplot = casac.msplot() calplot = casac.calplot() table = casac.table() #flagger = casac.flagger() agentflagger = casac.agentflagger() image = casac.image() imagepol = casac.imagepol() simulator = casac.simulator() componentlist = casac.componentlist() coordsys = casac.coordsys() regionmanager = casac.regionmanager() spectralline = casac.spectralline() utils = casac.utils() deconvolver = casac.deconvolver() vpmanager = casac.vpmanager() vlafillertask = casac.vlafillertask() atmosphere = casac.atmosphere() cu = casac.utils()
def convert_gaincurve(antab, gc, min_elevation=0.0, max_elevation=90.0):
tb = casatools.table()
outfp = tempfile.NamedTemporaryFile('w')
t = time.strptime("2000y01d00h00m00s", "%Yy%jd%Hh%Mm%Ss")
btime = time.mktime(t) + 40587.0 * 86400
t = time.strptime("2100y01d00h00m00s", "%Yy%jd%Hh%Mm%Ss")
etime = time.mktime(t) + 40587.0 * 86400
keys = StringIO()
fp = open(antab, 'r')
for line in fp:
if line.startswith('!'):
continue
keys.write(line)
if line.strip().endswith('/'):
keys.seek(0)
gain = key.read_keyfile(keys)
# Standard ANTAB
if gain and gain[0] and gain[0][0][0] == 'GAIN':
antenna = find_antenna(gain[0], keyin_keys)
gain = dict(gain[0])
try:
bfreq = gain['FREQ'][0] * 1e6
except:
bfreq = 0
pass
try:
efreq = gain['FREQ'][1] * 1e6
except:
efreq = 1e12
pass
gain_common(gain, antenna, "C", bfreq, efreq, btime, etime,
min_elevation, max_elevation, outfp)
# VLBA gains file
elif gain and gain[0] and gain[0][0][0] == 'BAND':
antenna = gain[0][8][0]
gain = dict(gain[0])
timerange = gain['TIMERANG']
btime = parse_timerange(timerange[0:])
etime = parse_timerange(timerange[4:])
band = gain['BAND']
try:
freq = vlba_freqs[band]
bfreq = freq[0] * 1e9
efreq = freq[1] * 1e9
except:
freq = gain['FREQ']
bfreq = freq - freq / 4
efreq = freq + freq / 4
pass
gain_common(gain, antenna, band, bfreq, efreq, btime, etime,
min_elevation, max_elevation, outfp)
elif gain and gain[0] and gain[0][0][0] == 'TSYS':
skip_values(fp)
pass
keys = StringIO()
continue
continue
outfp.flush()
tb.fromascii(gc, asciifile=outfp.name, sep=' ',
columnnames=columnnames, datatypes=datatypes)
outfp.close()
fp.close()
return
def importasdm(
asdm=None,
vis=None,
createmms=None,
separationaxis=None,
numsubms=None,
corr_mode=None,
srt=None,
time_sampling=None,
ocorr_mode=None,
compression=None,
lazy=None,
asis=None,
wvr_corrected_data=None,
scans=None,
ignore_time=None,
process_syspower=None,
process_caldevice=None,
process_pointing=None,
process_flags=None,
tbuff=None,
applyflags=None,
savecmds=None,
outfile=None,
flagbackup=None,
verbose=None,
overwrite=None,
showversion=None,
useversion=None,
bdfflags=None,
with_pointing_correction=None,
remove_ref_undef=None,
convert_ephem2geo=None,
polyephem_tabtimestep=None
):
"""Convert an ALMA Science Data Model observation into a CASA visibility file (MS) or single-dish data format (Scantable).
The conversion of the ALMA SDM archive format into a measurement set. This version
is under development and is geared to handling many spectral windows of different
shapes.
Keyword arguments:
asdm -- Name of input ASDM file (directory)
default: none; example: asdm='ExecBlock3'
vis -- Root ms or scantable name, note a prefix (.ms or .asap) is NOT appended to this name
default: none
createmms -- Create a Multi-MS
default: False
corr_mode -- correlation mode to be considered on input. Could
be one or more of the following, ao, co, ac, or all
default: all
srt -- spectral resolution type. Could be one or more of
the following, fr, ca, bw, or all
default: all
time_sampling -- specifies the time sampling, INTEGRATION and/or
SUBINTEGRATION. could be one or more of the following
i, si, or all.
default: all
ocorr_mode -- output data for correlation mode AUTO_ONLY
(ao) or CROSS_ONLY (co) or CROSS_AND_AUTO (ca)
default: ca
compression -- produces comrpressed columns in the resulting measurement set.
default: False
lazy -- Make the MS DATA column read the ASDM Binary data directly
(faster import, smaller MS)
default: False
asis -- creates verbatim copies of the ASDM tables in
the output measurement set. The value given to
this option must be a list of table names separated
by space characters; the wildcard character '*' is
allowed in table names.
wvr_corrected_data -- specifies wich values are considered in the
ASDM binary data to fill the DATA column in
the MAIN table of the MS. Expected values for
this option are 'no' for the uncorrected data
(this is the default), 'yes' for the corrected
data and 'both' for corrected and uncorrected
data. In the latter case, two measurement sets
are created, one containing the uncorrected
data and the other one, whose name is suffixed
by '-wvr-corrected', containing the corrected
data.
scans -- processes only the scans specified in the option's value. This value is a semicolon
separated list of scan specifications. A scan specification consists in an exec bock index
followed by the character ':' followed by a comma separated list of scan indexes or scan
index ranges. A scan index is relative to the exec block it belongs to. Scan indexes are
1-based while exec blocks's are 0-based. "0:1" or "2:2~6" or "0:1,1:2~6,8;2:,3:24~30" "1,2"
are valid values for the option. "3:" alone will be interpreted as 'all the scans of the
exec block#3'. An scan index or a scan index range not preceded by an exec block index will
be interpreted as 'all the scans with such indexes in all the exec blocks'. By default
all the scans are considered.
ignore_time -- All the rows of the tables Feed, History, Pointing, Source, SysCal, CalDevice, SysPower,
and Weather are processed independently of the time range of the selected exec block / scan.
process_syspower -- The SysPower table is processed if and only if this parameter is set to True.
default: True
process_caldevice -- The CalDevice table is processed if and only if this parameter is set to True.
default: True
process_pointing -- The Pointing table is processed if and only if this parameter is set to True.
If the parameter is set to False the resulting MS will have an empty POINTING table.
default: True
process_flags -- Process the online flags and save them to the FLAG_CMD sub-table.
default: True
>>> process_flags expandable parameter
tbuff -- Time padding buffer (in seconds).
default: 0.0
applyflags -- Apply the online flags to the MS.
default: False
savecmds -- Save the online flags to an ASCII file.
default: False
outfile -- Filename to save the online flags.
default: ''
flagbackup -- Backup the FLAG column in the .flagversions.
default: True
verbose -- produce log output as asdm2MS is being run.
overwrite -- Over write an existing MS.
showversion -- report the version of the asdm2MS being used.
useversion -- Selects the version of asdm2MS to be used (presently only \'v3\' is available).
default: v3
bdfflags -- Set the MS FLAG column according to the ASDM _binary_ flags
default: false
with_pointing_correction -- add (ASDM::Pointing::encoder - ASDM::Pointing::pointingDirection)
to the value to be written in MS::Pointing::direction
default: false
remove_ref_undef -- if set to True then apply fixspwbackport on the resulting MSes.
convert_ephem2geo -- if True, convert any attached ephemerides to the GEO reference frame
polyephem_tabtimestep -- Timestep (days) for the tabulation of polynomial ephemerides. A value <= 0 disables tabulation.
Presently, VLA data can contain polynomial ephemerides. ALMA data uses tabulated values.
default: 0.
"""
# Python script
# make agentflagger tool local
aflocal = casac.agentflagger()
# make table tool local
tblocal = casac.table()
try:
casalog.origin('importasdm')
viso = ''
visoc = '' # for the wvr corrected version, if needed
if len(vis) > 0:
viso = vis
tmps = vis.rstrip('.ms')
if tmps == vis:
visoc = vis + '-wvr-corrected'
else:
visoc = tmps + '-wvr-corrected.ms'
else:
viso = asdm.rstrip("/") + '.ms'
visoc = asdm.rstrip("/") + '-wvr-corrected.ms'
vis = asdm.rstrip("/")
useversion = 'v3'
theexecutable = 'asdm2MS'
execute_string = theexecutable + ' --icm "' + corr_mode \
+ '" --isrt "' + srt + '" --its "' + time_sampling \
+ '" --ocm "' + ocorr_mode + '" --wvr-corrected-data "' \
+ wvr_corrected_data + '" --asis "' + asis \
+ '" --logfile "' + casalog.logfile() + '"'
if len(scans) > 0:
execute_string = execute_string + ' --scans ' + scans
if ignore_time:
execute_string = execute_string + ' --ignore-time'
if useversion == 'v3':
if not process_syspower:
execute_string = execute_string + ' --no-syspower'
if not process_caldevice:
execute_string = execute_string + ' --no-caldevice'
if not process_pointing:
execute_string = execute_string + ' --no-pointing'
if compression:
execute_string = execute_string + ' --compression'
elif lazy:
execute_string = execute_string + ' --lazy'
if verbose:
execute_string = execute_string + ' --verbose'
# if not overwrite and os.path.exists(viso):
# raise Exception, \
# 'You have specified an existing MS and have indicated you do not wish to overwrite it'
# Compression
if compression:
# viso = viso + '.compressed'
viso = viso.rstrip('.ms') + '.compressed.ms'
visoc = visoc.rstrip('.ms') + '.compressed.ms'
vistoproc = [] # the output MSs to post-process
if wvr_corrected_data == 'no' or wvr_corrected_data == 'both':
vistoproc.append(viso)
if (wvr_corrected_data == 'yes' or wvr_corrected_data == 'both') :
vistoproc.append(visoc)
for ff in vistoproc:
if not overwrite and os.path.exists(ff):
raise Exception, \
'You have specified an existing MS and have indicated you do not wish to overwrite it: %s'%ff
# If viso+".flagversions" then process differently depending on the value of overwrite..
#
if flagbackup:
for myviso in vistoproc:
dotFlagversion = myviso + '.flagversions'
if os.path.exists(dotFlagversion):
if overwrite:
casalog.post("Found '" + dotFlagversion
+ "' . It'll be deleted before running the filler."
)
os.system('rm -rf %s' % dotFlagversion)
else:
casalog.post("Found '%s' but can't overwrite it."
% dotFlagversion)
raise Exception, "Found '%s' but can't overwrite it." \
% dotFlagversion
# Make outfile always a list
if isinstance(outfile, str):
if outfile == '':
outfile = []
else:
noutfile = [outfile]
outfile = noutfile
if savecmds:
if len(outfile) == 0:
# Create default names for the online flags
for myviso in vistoproc:
outfile.append(myviso.replace('.ms','_cmd.txt'))
elif len(outfile) != len(vistoproc):
casalog.post('List of outfile names does not match list of MSs','WARN')
casalog.post('Will save online flags to temporary filenames', 'WARN')
outfile = []
for myviso in vistoproc:
online_file = myviso.replace('.ms','_TEMP_cmd.txt')
outfile.append(online_file)
if not overwrite:
for of in outfile:
if os.path.exists(of):
raise Exception, "Cannot overwrite online flags file '%s'; overwrite is set to False."% of
execute_string = execute_string + ' ' + asdm + ' ' + viso
if showversion:
casalog.post("You set option \'showversion\' to True. Will just output the version information and then terminate."
, 'WARN')
execute_string = theexecutable + ' --revision'
if with_pointing_correction:
execute_string = execute_string + ' --with-pointing-correction'
if (polyephem_tabtimestep!=None) and (type(polyephem_tabtimestep)==int or type(polyephem_tabtimestep)==float):
if polyephem_tabtimestep>0:
casalog.post('Will tabulate all attached polynomial ephemerides with a time step of '
+str(polyephem_tabtimestep)+' days.')
if polyephem_tabtimestep>1.:
casalog.post('A tabulation timestep of <= 1 days is recommended.', 'WARN')
execute_string = execute_string + ' --polyephem-tabtimestep '+str(polyephem_tabtimestep)
casalog.post('Running ' + theexecutable
+ ' standalone invoked as:')
# print execute_string
casalog.post(execute_string)
exitcode = os.system(execute_string)
if exitcode != 0:
if not showversion:
casalog.post(theexecutable
+ ' terminated with exit code '
+ str(exitcode), 'SEVERE')
raise Exception, \
'ASDM conversion error. Please check if it is a valid ASDM and that data/alma/asdm is up to date.'
if showversion:
return
#
# Possibly remove the name of the measurement set expected to contain the corrected data from the list of of produced measurement
# sets if it appears the filler did not find any corrected data.
#
if not os.path.exists(visoc):
vistoproc = [myviso for myviso in vistoproc if myviso != visoc]
# CAS-7369. HISTORY should be written after createmms is tested
#
# Populate the HISTORY table of the MS with information about the context in which it's been created
#
try:
mslocal = mstool()
param_names = importasdm.func_code.co_varnames[:importasdm.func_code.co_argcount]
param_vals = [eval(p) for p in param_names]
for myviso in vistoproc:
write_history(mslocal, myviso, 'importasdm', param_names,
param_vals, casalog)
except Exception, instance:
casalog.post("*** Error \'%s\' updating HISTORY" % (instance),
'WARN')
return False
if mslocal:
mslocal = None
#
# Do we apply fixspwbackport
if remove_ref_undef :
casalog.post('remove_ref_undef=True: fixspwbackport will be applied ...')
for myviso in vistoproc:
cmd = 'fixspwbackport ' + myviso
casalog.post('Running fixspwbackport standalone invoked as:')
casalog.post(cmd)
cmdexitcode = os.system(cmd)
if cmdexitcode != 0:
casalog.post(cmd
+ ' terminated with exit code '
+ str(cmdexitcode), 'SEVERE')
raise Exception, 'fixspwbackport error.'
# Binary Flag processing
if bdfflags:
casalog.post('Parameter bdfflags==True: flags from the ASDM binary data will be used to set the MS flags ...')
bdffexecutable = 'bdflags2MS '
bdffexecstring_base = bdffexecutable + ' -f ALL' + ' --ocm "' + ocorr_mode \
+ '" --logfile "' + casalog.logfile() + '"'
if len(scans) > 0:
bdffexecstring_base = bdffexecstring_base + ' --scans ' + scans
if lazy and not compression:
bdffexecstring_base = bdffexecstring_base + ' --lazy=true'
for myviso in vistoproc:
if myviso.find("wvr-corrected") != -1:
options = " --wvr-corrected=True "
else:
options = " "
bdffexecstring = bdffexecstring_base + options + asdm + ' ' + myviso
casalog.post('Running '+bdffexecutable+' standalone invoked as:')
casalog.post(bdffexecstring)
bdffexitcode = os.system(bdffexecstring)
if bdffexitcode != 0:
casalog.post(bdffexecutable
+ ' terminated with exit code '
+ str(bdffexitcode), 'SEVERE')
raise Exception, \
'ASDM binary flags conversion error. Please check if it is a valid ASDM and that data/alma/asdm is up to date.'
theephemfields = ce.findattachedephemfields(myviso,field='*')
if len(theephemfields)>0:
# until asdm2MS does this internally: recalc the UVW coordinates for ephem fields
imt = imtool()
imt.open(myviso, usescratch=False)
imt.calcuvw(theephemfields, refcode='J2000', reuse=False)
imt.close()
if convert_ephem2geo:
for myviso in vistoproc:
ce.convert2geo(myviso, '*') # convert any attached ephemerides to GEO
if len(theephemfields)>0:
# also set the direction column in the SOURCE table
tblocal.open(myviso+'/FIELD', nomodify=False)
sourceids = tblocal.getcol('SOURCE_ID')
ftimes = tblocal.getcol('TIME')
ftimekw = tblocal.getcolkeywords('TIME')
tmpa = tblocal.getcol('PHASE_DIR')
origphasedir = tmpa
affectedsids = []
thesamplefields = []
for fld in theephemfields: # determine all source ids used by the ephem fields
if not (sourceids[fld] in affectedsids): # this source id wasn't handled yet
affectedsids.append(sourceids[fld])
thesamplefields.append(fld)
# need to temporarily change the offset (not all mosaics have an element at (0,0))
tmpa[0][0][fld]=0.
tmpa[1][0][fld]=0.
#endif
#endfor
tblocal.putcol('PHASE_DIR', tmpa)
tblocal.close()
tblocal.open(myviso+'/SOURCE')
sourceposref = tblocal.getcolkeywords('DIRECTION')['MEASINFO']['Ref']
tblocal.close()
directions = []
msmdlocal = casac.msmetadata()
msmdlocal.open(myviso)
for fld in thesamplefields:
thedirmeas = msmdlocal.phasecenter(fld)
if thedirmeas['refer']!=sourceposref:
casalog.post('Ephemeris is in '+thedirmeas['refer']+' instead of '+sourceposref
+' frame.\nEntry in SOURCE table will be converted to '+sourceposref, 'WARN')
melocal = metool()
melocal.doframe(thedirmeas)
thedirmeas = melocal.measure(thedirmeas, sourceposref)
directions.append([thedirmeas['m0']['value'], thedirmeas['m1']['value']])
thetime = me.epoch(v0=str(ftimes[fld])+'s', rf=ftimekw['MEASINFO']['Ref'])
casalog.post("Will set SOURCE direction for SOURCE_ID "+str(sourceids[fld])
+" to ephemeris phase center for time "+str(thetime['m0']['value'])+" "+thetime['m0']['unit']+" "+thetime['refer'])
#endfor
msmdlocal.close()
# restore original PHASE_DIR
tblocal.open(myviso+'/FIELD', nomodify=False)
tblocal.putcol('PHASE_DIR', origphasedir)
tblocal.close()
# write source directions
tblocal.open(myviso+'/SOURCE', nomodify=False)
ssourceids = tblocal.getcol('SOURCE_ID')
sdirs = tblocal.getcol('DIRECTION')
for row in xrange(0,len(ssourceids)):
for i in xrange(0,len(affectedsids)):
if ssourceids[row]==affectedsids[i]:
sdirs[0][row] = directions[i][0]
sdirs[1][row] = directions[i][1]
break
#endfor
#endfor
tblocal.putcol('DIRECTION', sdirs) # write back corrected directions
tblocal.close()
#end if
##############################################################################################3
# CAS-7369 - Create an output Multi-MS (MMS)
if createmms:
# Get the default parameters of partition
from tasks import partition
fpars = partition.parameters
for mypar in fpars.keys():
fpars[mypar] = partition.itsdefault(mypar)
# Call the cluster for each MS
for myviso in vistoproc:
casalog.origin('importasdm')
# Move original MS to tempdir
tempname = myviso+'.temp.ms'
outputmms = myviso
shutil.move(myviso, tempname)
# Get the proper column
datacolumn = 'DATA'
dcols = ['DATA', 'FLOAT_DATA']
for dc in dcols:
if len(th.getColDesc(tempname, dc)) > 0:
datacolumn = dc
break
fpars['datacolumn'] = datacolumn
casalog.post('Will create a Multi-MS for: '+myviso)
fpars['vis'] = tempname
fpars['flagbackup'] = False
fpars['outputvis'] = outputmms
fpars['separationaxis'] = separationaxis
fpars['numsubms'] = numsubms
pdh = ParallelDataHelper('partition', fpars)
# Get a cluster
pdh.setupCluster(thistask='partition')
try:
pdh.go()
# Remove original MS
shutil.rmtree(tempname)
except Exception, instance:
# Restore MS in case of error in MMS creation
shutil.move(tempname, myviso)
casalog.post('%s'%instance,'ERROR')
return False
casalog.origin('importasdm')
def caltab_convert2(caltabold, ms, pType, caltabnew=''):
# Check the inputs
if not os.path.exists(caltabold):
raise IOError('Invalid old-format caltable.')
if not os.path.exists(ms):
raise IOError('Invalid visibility file (MS).')
pTypeTemp = pType.strip().lower()
if (pTypeTemp != 'complex' and pTypeTemp != 'float'):
raise Exception('Invalid parameter type ("complex" or "float").')
if caltabnew == '': caltabnew = caltabold + '.new'
if os.path.exists(caltabnew):
raise IOError('New-format caltable already exists.')
# Open the old-format caltable and get the number of rows
tbOld = casac.table()
tbOld.open(caltabold)
nRow = tbOld.nrows()
# Get spwid map from old CAL_DESC subtable
tbCD = casac.table()
tbCD.open(caltabold + '/CAL_DESC')
spwmap = tbCD.getcol('SPECTRAL_WINDOW_ID')[0, :]
tbCD.close()
# Create the empty new-format caltable with the correct number of rows
tbNew = casac.table()
tbNew.create(caltabnew, desc_new(pTypeTemp))
tbNew.addrows(nRow)
# Transfer most column information from the old-format caltable to the
# new-format caltable. NB: The REF_ANT column in the old-format
# caltable (analogous to the ANTENNA2 column in the new-format caltable)
# is messed up, which means that I fill ANTENNA2 with -1.
tbNew.putcol('ANTENNA1', tbOld.getcol('ANTENNA1'))
tbNew.putcol('ANTENNA2', -1.0 * numpy.ones(nRow, dtype='int'))
tbNew.putcol('FIELD_ID', tbOld.getcol('FIELD_ID'))
tbNew.putcol('FLAG', tbOld.getcol('FLAG'))
tbNew.putcol('INTERVAL', tbOld.getcol('INTERVAL'))
tbNew.putcol('SNR', tbOld.getcol('SNR'))
# Map CAL_DESC_ID to SPECTRAL_WINDOW_ID:
tbNew.putcol('SPECTRAL_WINDOW_ID', spwmap[tbOld.getcol('CAL_DESC_ID')])
tbNew.putcol('TIME', tbOld.getcol('TIME'))
tbNew.putcol('WEIGHT', tbOld.getcol('FIT_WEIGHT'))
# Transfer the parameter column from the old-format caltable to the
# new-format caltable, taking the type into account. No parameter
# errors are present in the old-format caltable, so they are set to
# 1.0 (+j0.0).
param = tbOld.getcol('GAIN')
if pTypeTemp == 'float':
param = param.real
tbNew.putcol('FPARAM', param)
else:
tbNew.putcol('CPARAM', param)
tbNew.putcol('PARAMERR', -1.0 * numpy.ones(param.shape, dtype='float'))
# Determine the scans and put them into the new-format caltable
scanTimes = get_scantimes(ms)
keys = scanTimes.keys()
times = tbOld.getcol('TIME')
scans = numpy.zeros(0, dtype='int')
for t in times.tolist():
flag = False
for i in range(len(keys)):
k = keys[i]
if t >= scanTimes[k]['min'] and t < scanTimes[k]['max']:
flag = True
scans = numpy.append(scans, k)
break
if i == len(keys) - 1: break
l = keys[i + 1]
if t >= scanTimes[k]['max'] and t < scanTimes[l]['min']:
flag = True
scans = numpy.append(scans, l)
break
if not flag: scans = numpy.append(scans, -1)
tbNew.putcol('SCAN_NUMBER', scans)
# Copy the appropriate subcaltables from the MS to the new-format
# caltable
arg = 'cp -r ' + ms + '/ANTENNA ' + caltabnew
os.system(arg)
arg = 'cp -r ' + ms + '/FIELD ' + caltabnew
os.system(arg)
# arg = 'cp -r ' + caltabold + '/CAL_HISTORY ' + caltabnew + '/HISTORY'
# os.system( arg )
tbHis = casac.table()
tbHis.open(ms + '/HISTORY')
tbHis.copy(newtablename=caltabnew + '/HISTORY',
deep=True,
valuecopy=True,
norows=True)
tbHis.close()
del tbHis
arg = 'cp -r ' + ms + '/SPECTRAL_WINDOW ' + caltabnew \
+ '/SPECTRAL_WINDOW'
os.system(arg)
# Add the info and keywords to the main table of the new-format caltable
tabinfo = tbOld.info()
tbNew.putinfo(tabinfo)
if (pTypeTemp == 'complex'):
tbNew.putkeyword('ParType', 'Complex')
if (pTypeTemp == 'float'):
tbNew.putkeyword('ParType', 'Float')
tbNew.putkeyword('MSName', ms)
tbNew.putkeyword('VisCal', tabinfo['subType'])
polBasis = get_polbasis(ms)
tbNew.putkeyword('PolBasis', polBasis)
tbNew.putkeyword('ANTENNA', 'Table: ' + caltabnew + '/ANTENNA')
tbNew.putkeyword('FIELD', 'Table: ' + caltabnew + '/FIELD')
tbNew.putkeyword('HISTORY', 'Table: ' + caltabnew + '/HISTORY')
tbNew.putkeyword('SPECTRAL_WINDOW',
'Table: ' + caltabnew + '/SPECTRAL_WINDOW')
# Add the column keywords to the main table of the new-format caltable
colList = ['INTERVAL', 'TIME']
for col in colList:
colKeys = tbOld.getcolkeywords(col)
if colKeys != {}: tbNew.putcolkeywords(col, colKeys)
# Close the old- and new- format caltables
tbOld.close()
del tbOld
tbNew.close()
del tbNew
# Get the channel ranges from the CAL_DESC subtable of the old-format
# caltable
tbDesc = casac.table()
tbDesc.open(caltabold + '/CAL_DESC')
nDesc = tbDesc.nrows()
rDesc = range(nDesc)
spwMap = tbDesc.getcol('SPECTRAL_WINDOW_ID')[0]
chanMin = numpy.zeros(nDesc, dtype='int')
chanMax = numpy.zeros(nDesc, dtype='int')
for d in rDesc:
chanRange = tbDesc.getcol('CHAN_RANGE', startrow=d, nrow=1)
chanMin[d] = numpy.min(chanRange[0, :, :, :][0, :, 0])
chanMax[d] = numpy.max(chanRange[1, :, :, :][0, :, 0])
if numpy.all(chanMax - chanMin + 1 == 1):
gain = True
else:
gain = False
tbDesc.close()
del tbDesc
# Modify the columns of the new-format caltable according to the
# channel ranges
tbSPW = casac.table()
tbSPW.open(caltabnew + '/SPECTRAL_WINDOW', nomodify=False)
for d in rDesc:
s = int(spwMap[d])
nChan = int(chanMax[d] - chanMin[d] + 1)
tbSPW.putcell('NUM_CHAN', s, nChan)
chanFreq = tbSPW.getcell('CHAN_FREQ', s)
if gain:
chanFreq = numpy.median(chanFreq)
else:
chanFreq = chanFreq[chanMin[d]:chanMax[d] + 1]
tbSPW.putcell('CHAN_FREQ', s, chanFreq)
chanWidth = tbSPW.getcell('CHAN_WIDTH', s)
if gain:
chanWidth = numpy.sum(chanWidth)
else:
chanWidth = chanWidth[chanMin[d]:chanMax[d] + 1]
tbSPW.putcell('CHAN_WIDTH', s, chanWidth)
tbSPW.putcell('EFFECTIVE_BW', s, chanWidth)
tbSPW.putcell('RESOLUTION', s, chanWidth)
totalBandwidth = numpy.sum(chanWidth)
tbSPW.putcell('TOTAL_BANDWIDTH', s, totalBandwidth)
tbSPW.close()
del tbSPW
# Return True
return True
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()
def compVarColTables(referencetab, testtab, varcol, tolerance=0.):
'''Compare a variable column of two tables.
referencetab --> a reference table
testtab --> a table to verify
varcol --> the name of a variable column (str)
Returns True or False.
'''
retval = True
tb2 = casac.table()
tb.open(referencetab)
cnames = tb.colnames()
tb2.open(testtab)
col = varcol
if tb.isvarcol(col) and tb2.isvarcol(col):
try:
# First check
if tb.nrows() != tb2.nrows():
print 'Length of %s differ from %s, %s!=%s'%(referencetab,testtab,len(rk),len(tk))
retval = False
else:
for therow in xrange(tb.nrows()):
rdata = tb.getcell(col,therow)
tdata = tb2.getcell(col,therow)
# if not (rdata==tdata).all():
if not rdata.all()==tdata.all():
if (tolerance>0.):
differs=False
for j in range(0,len(rdata)):
### if (type(rdata[j])==float or type(rdata[j])==int):
if ((isinstance(rdata[j],float)) or (isinstance(rdata[j],int))):
if (abs(rdata[j]-tdata[j]) > tolerance*abs(rdata[j]+tdata[j])):
# print 'Column ', col,' differs in tables ', referencetab, ' and ', testtab
# print therow, j
# print rdata[j]
# print tdata[j]
differs = True
### elif (type(rdata[j])==list or type(rdata[j])==np.ndarray):
elif (isinstance(rdata[j],list)) or (isinstance(rdata[j],np.ndarray)):
for k in range(0,len(rdata[j])):
if (abs(rdata[j][k]-tdata[j][k]) > tolerance*abs(rdata[j][k]+tdata[j][k])):
# print 'Column ', col,' differs in tables ', referencetab, ' and ', testtab
# print therow, j, k
# print rdata[j][k]
# print tdata[j][k]
differs = True
if differs:
print 'ERROR: Column %s of %s and %s do not agree within tolerance %s'%(col,referencetab, testtab, tolerance)
retval = False
break
else:
print 'ERROR: Column %s of %s and %s do not agree.'%(col,referencetab, testtab)
print 'ERROR: First row to differ is row=%s'%therow
retval = False
break
finally:
tb.close()
tb2.close()
else:
print 'Columns are not varcolumns.'
retval = False
if retval:
print 'Column %s of %s and %s agree'%(col,referencetab, testtab)
return retval
def compTables(referencetab, testtab, excludecols, tolerance=0.001, mode="percentage", startrow = 0, nrow = -1, rowincr = 1):
"""
compTables - compare two CASA tables
referencetab - the table which is assumed to be correct
testtab - the table which is to be compared to referencetab
excludecols - list of column names which are to be ignored
tolerance - permitted fractional difference (default 0.001 = 0.1 percent)
mode - comparison is made as "percentage", "absolute", "phaseabsdeg" (for complex numbers = difference of the phases in degrees)
"""
rval = True
tb2 = casac.table()
tb.open(referencetab)
cnames = tb.colnames()
tb2.open(testtab)
try:
for c in cnames:
if c in excludecols:
continue
print "\nTesting column " + c
a = 0
try:
a = tb.getcol(c,startrow=startrow,nrow=nrow,rowincr=rowincr)
except:
rval = False
print 'Error accessing column ', c, ' in table ', referencetab
print sys.exc_info()[0]
break
b = 0
try:
b = tb2.getcol(c,startrow=startrow,nrow=nrow,rowincr=rowincr)
except:
rval = False
print 'Error accessing column ', c, ' in table ', testtab
print sys.exc_info()[0]
break
if not (len(a)==len(b)):
print 'Column ',c,' has different length in tables ', referencetab, ' and ', testtab
print a
print b
rval = False
break
else:
differs = False
if not (a==b).all():
for i in range(0,len(a)):
if (isinstance(a[i],float)):
if ((mode=="percentage") and (abs(a[i]-b[i]) > tolerance*abs(a[i]))) or ((mode=="absolute") and (abs(a[i]-b[i]) > tolerance)):
print "Column " + c + " differs"
print "Row=" + str(i)
print "Reference file value: " + str(a[i])
print "Input file value: " + str(b[i])
if (mode=="percentage"):
print "Tolerance is {0}%; observed difference was {1} %".format (tolerance * 100, 100*abs(a[i]-b[i])/abs(a[i]))
else:
print "Absolute tolerance is {0}; observed difference: {1}".format (tolerance, (abs(a[i]-b[i])))
differs = True
rval = False
break
elif (isinstance(a[i],int) or isinstance(a[i],np.int32)):
if (abs(a[i]-b[i]) > 0):
print "Column " + c + " differs"
print "Row=" + str(i)
print "Reference file value: " + str(a[i])
print "Input file value: " + str(b[i])
if (mode=="percentage"):
print "tolerance in % should be " + str(100*abs(a[i]-b[i])/abs(a[i]))
else:
print "absolute tolerance should be " + str(abs(a[i]-b[i]))
differs = True
rval = False
break
elif (isinstance(a[i],str) or isinstance(a[i],np.bool_)):
if not (a[i]==b[i]):
print "Column " + c + " differs"
print "Row=" + str(i)
print "Reference file value: " + str(a[i])
print "Input file value: " + str(b[i])
if (mode=="percentage"):
print "tolerance in % should be " + str(100*abs(a[i]-b[i])/abs(a[i]))
else:
print "absolute tolerance should be " + str(abs(a[i]-b[i]))
differs = True
rval = False
break
elif (isinstance(a[i],list)) or (isinstance(a[i],np.ndarray)):
for j in range(0,len(a[i])):
if differs: break
if ((isinstance(a[i][j],float)) or (isinstance(a[i][j],int))):
if ((mode=="percentage") and (abs(a[i][j]-b[i][j]) > tolerance*abs(a[i][j]))) or ((mode=="absolute") and (abs(a[i][j]-b[i][j]) > tolerance)):
print "Column " + c + " differs"
print "(Row,Element)=(" + str(j) + "," + str(i) + ")"
print "Reference file value: " + str(a[i][j])
print "Input file value: " + str(b[i][j])
if (mode=="percentage"):
print "Tolerance in % should be " + str(100*abs(a[i][j]-b[i][j])/abs(a[i][j]))
else:
print "Absolute tolerance should be " + str(abs(a[i][j]-b[i][j]))
differs = True
rval = False
break
elif (isinstance(a[i][j],list)) or (isinstance(a[i][j],np.ndarray)):
for k in range(0,len(a[i][j])):
if differs: break
if ( ((mode=="percentage") and (abs(a[i][j][k]-b[i][j][k]) > tolerance*abs(a[i][j][k]))) \
or ((mode=="absolute") and (abs(a[i][j][k]-b[i][j][k]) > tolerance)) \
or ((mode=="phaseabsdeg") and (phasediffabsdeg(a[i][j][k],b[i][j][k])>tolerance)) \
):
print "Column " + c + " differs"
print "(Row,Channel,Corr)=(" + str(k) + "," + str(j) + "," + str(i) + ")"
print "Reference file value: " + str(a[i][j][k])
print "Input file value: " + str(b[i][j][k])
if (mode=="percentage"):
print "Tolerance in % should be " + str(100*abs(a[i][j][k]-b[i][j][k])/abs(a[i][j][k]))
elif (mode=="absolute"):
print "Absolute tolerance should be " + str(abs(a[i][j][k]-b[i][j][k]))
elif (mode=="phaseabsdeg"):
print "Phase tolerance in degrees should be " + str(phasediffabsdeg(a[i][j][k],b[i][j][k]))
else:
print "Unknown comparison mode: ",mode
differs = True
rval = False
break
else:
print "Unknown data type: ",type(a[i])
differs = True
rval = False
break
if not differs: print "Column " + c + " PASSED"
finally:
tb.close()
tb2.close()
return rval
def compVarColTables(referencetab, testtab, varcol, tolerance=0.):
'''Compare a variable column of two tables.
referencetab --> a reference table
testtab --> a table to verify
varcol --> the name of a variable column (str)
Returns True or False.
'''
retval = True
tb2 = casac.table()
tb.open(referencetab)
cnames = tb.colnames()
tb2.open(testtab)
col = varcol
if tb.isvarcol(col) and tb2.isvarcol(col):
try:
# First check
if tb.nrows() != tb2.nrows():
print 'Length of %s differ from %s, %s!=%s' % (
referencetab, testtab, len(rk), len(tk))
retval = False
else:
for therow in xrange(tb.nrows()):
rdata = tb.getcell(col, therow)
tdata = tb2.getcell(col, therow)
# if not (rdata==tdata).all():
if not rdata.all() == tdata.all():
if (tolerance > 0.):
differs = False
for j in range(0, len(rdata)):
### if (type(rdata[j])==float or type(rdata[j])==int):
if ((isinstance(rdata[j], float))
or (isinstance(rdata[j], int))):
if (abs(rdata[j] - tdata[j]) > tolerance *
abs(rdata[j] + tdata[j])):
# print 'Column ', col,' differs in tables ', referencetab, ' and ', testtab
# print therow, j
# print rdata[j]
# print tdata[j]
differs = True
### elif (type(rdata[j])==list or type(rdata[j])==np.ndarray):
elif (isinstance(rdata[j],
list)) or (isinstance(
rdata[j], np.ndarray)):
for k in range(0, len(rdata[j])):
if (abs(rdata[j][k] - tdata[j][k]) >
tolerance * abs(rdata[j][k] +
tdata[j][k])):
# print 'Column ', col,' differs in tables ', referencetab, ' and ', testtab
# print therow, j, k
# print rdata[j][k]
# print tdata[j][k]
differs = True
if differs:
print 'ERROR: Column %s of %s and %s do not agree within tolerance %s' % (
col, referencetab, testtab, tolerance)
retval = False
break
else:
print 'ERROR: Column %s of %s and %s do not agree.' % (
col, referencetab, testtab)
print 'ERROR: First row to differ is row=%s' % therow
retval = False
break
finally:
tb.close()
tb2.close()
else:
print 'Columns are not varcolumns.'
retval = False
if retval:
print 'Column %s of %s and %s agree' % (col, referencetab, testtab)
return retval
def importasdm(asdm=None,
vis=None,
createmms=None,
separationaxis=None,
numsubms=None,
corr_mode=None,
srt=None,
time_sampling=None,
ocorr_mode=None,
compression=None,
lazy=None,
asis=None,
wvr_corrected_data=None,
scans=None,
ignore_time=None,
process_syspower=None,
process_caldevice=None,
process_pointing=None,
process_flags=None,
tbuff=None,
applyflags=None,
savecmds=None,
outfile=None,
flagbackup=None,
verbose=None,
overwrite=None,
showversion=None,
useversion=None,
bdfflags=None,
with_pointing_correction=None,
remove_ref_undef=None,
convert_ephem2geo=None,
polyephem_tabtimestep=None):
"""Convert an ALMA Science Data Model observation into a CASA visibility file (MS) or single-dish data format (Scantable).
The conversion of the ALMA SDM archive format into a measurement set. This version
is under development and is geared to handling many spectral windows of different
shapes.
Keyword arguments:
asdm -- Name of input ASDM file (directory)
default: none; example: asdm='ExecBlock3'
vis -- Root ms or scantable name, note a prefix (.ms or .asap) is NOT appended to this name
default: none
createmms -- Create a Multi-MS
default: False
corr_mode -- correlation mode to be considered on input. Could
be one or more of the following, ao, co, ac, or all
default: all
srt -- spectral resolution type. Could be one or more of
the following, fr, ca, bw, or all
default: all
time_sampling -- specifies the time sampling, INTEGRATION and/or
SUBINTEGRATION. could be one or more of the following
i, si, or all.
default: all
ocorr_mode -- output data for correlation mode AUTO_ONLY
(ao) or CROSS_ONLY (co) or CROSS_AND_AUTO (ca)
default: ca
compression -- produces comrpressed columns in the resulting measurement set.
default: False
lazy -- Make the MS DATA column read the ASDM Binary data directly
(faster import, smaller MS)
default: False
asis -- creates verbatim copies of the ASDM tables in
the output measurement set. The value given to
this option must be a list of table names separated
by space characters; the wildcard character '*' is
allowed in table names.
wvr_corrected_data -- specifies wich values are considered in the
ASDM binary data to fill the DATA column in
the MAIN table of the MS. Expected values for
this option are 'no' for the uncorrected data
(this is the default), 'yes' for the corrected
data and 'both' for corrected and uncorrected
data. In the latter case, two measurement sets
are created, one containing the uncorrected
data and the other one, whose name is suffixed
by '-wvr-corrected', containing the corrected
data.
scans -- processes only the scans specified in the option's value. This value is a semicolon
separated list of scan specifications. A scan specification consists in an exec bock index
followed by the character ':' followed by a comma separated list of scan indexes or scan
index ranges. A scan index is relative to the exec block it belongs to. Scan indexes are
1-based while exec blocks's are 0-based. "0:1" or "2:2~6" or "0:1,1:2~6,8;2:,3:24~30" "1,2"
are valid values for the option. "3:" alone will be interpreted as 'all the scans of the
exec block#3'. An scan index or a scan index range not preceded by an exec block index will
be interpreted as 'all the scans with such indexes in all the exec blocks'. By default
all the scans are considered.
ignore_time -- All the rows of the tables Feed, History, Pointing, Source, SysCal, CalDevice, SysPower,
and Weather are processed independently of the time range of the selected exec block / scan.
process_syspower -- The SysPower table is processed if and only if this parameter is set to True.
default: True
process_caldevice -- The CalDevice table is processed if and only if this parameter is set to True.
default: True
process_pointing -- The Pointing table is processed if and only if this parameter is set to True.
If the parameter is set to False the resulting MS will have an empty POINTING table.
default: True
process_flags -- Process the online flags and save them to the FLAG_CMD sub-table.
default: True
>>> process_flags expandable parameter
tbuff -- Time padding buffer (in seconds).
default: 0.0
applyflags -- Apply the online flags to the MS.
default: False
savecmds -- Save the online flags to an ASCII file.
default: False
outfile -- Filename to save the online flags.
default: ''
flagbackup -- Backup the FLAG column in the .flagversions.
default: True
verbose -- produce log output as asdm2MS is being run.
overwrite -- Over write an existing MS.
showversion -- report the version of the asdm2MS being used.
useversion -- Selects the version of asdm2MS to be used (presently only \'v3\' is available).
default: v3
bdfflags -- Set the MS FLAG column according to the ASDM _binary_ flags
default: false
with_pointing_correction -- add (ASDM::Pointing::encoder - ASDM::Pointing::pointingDirection)
to the value to be written in MS::Pointing::direction
default: false
remove_ref_undef -- if set to True then apply fixspwbackport on the resulting MSes.
convert_ephem2geo -- if True, convert any attached ephemerides to the GEO reference frame
polyephem_tabtimestep -- Timestep (days) for the tabulation of polynomial ephemerides. A value <= 0 disables tabulation.
Presently, VLA data can contain polynomial ephemerides. ALMA data uses tabulated values.
default: 0.
"""
# Python script
# make agentflagger tool local
aflocal = casac.agentflagger()
# make table tool local
tblocal = casac.table()
try:
casalog.origin('importasdm')
viso = ''
visoc = '' # for the wvr corrected version, if needed
if len(vis) > 0:
viso = vis
tmps = vis.rstrip('.ms')
if tmps == vis:
visoc = vis + '-wvr-corrected'
else:
visoc = tmps + '-wvr-corrected.ms'
else:
viso = asdm.rstrip("/") + '.ms'
visoc = asdm.rstrip("/") + '-wvr-corrected.ms'
vis = asdm.rstrip("/")
useversion = 'v3'
theexecutable = 'asdm2MS'
execute_string = theexecutable + ' --icm "' + corr_mode \
+ '" --isrt "' + srt + '" --its "' + time_sampling \
+ '" --ocm "' + ocorr_mode + '" --wvr-corrected-data "' \
+ wvr_corrected_data + '" --asis "' + asis \
+ '" --logfile "' + casalog.logfile() + '"'
if len(scans) > 0:
execute_string = execute_string + ' --scans ' + scans
if ignore_time:
execute_string = execute_string + ' --ignore-time'
if useversion == 'v3':
if not process_syspower:
execute_string = execute_string + ' --no-syspower'
if not process_caldevice:
execute_string = execute_string + ' --no-caldevice'
if not process_pointing:
execute_string = execute_string + ' --no-pointing'
if compression:
execute_string = execute_string + ' --compression'
elif lazy:
execute_string = execute_string + ' --lazy'
if verbose:
execute_string = execute_string + ' --verbose'
# if not overwrite and os.path.exists(viso):
# raise Exception, \
# 'You have specified an existing MS and have indicated you do not wish to overwrite it'
# Compression
if compression:
# viso = viso + '.compressed'
viso = viso.rstrip('.ms') + '.compressed.ms'
visoc = visoc.rstrip('.ms') + '.compressed.ms'
vistoproc = [] # the output MSs to post-process
if wvr_corrected_data == 'no' or wvr_corrected_data == 'both':
vistoproc.append(viso)
if (wvr_corrected_data == 'yes' or wvr_corrected_data == 'both'):
vistoproc.append(visoc)
for ff in vistoproc:
if not overwrite and os.path.exists(ff):
raise Exception, \
'You have specified an existing MS and have indicated you do not wish to overwrite it: %s'%ff
# If viso+".flagversions" then process differently depending on the value of overwrite..
#
if flagbackup:
for myviso in vistoproc:
dotFlagversion = myviso + '.flagversions'
if os.path.exists(dotFlagversion):
if overwrite:
casalog.post(
"Found '" + dotFlagversion +
"' . It'll be deleted before running the filler.")
os.system('rm -rf %s' % dotFlagversion)
else:
casalog.post("Found '%s' but can't overwrite it." %
dotFlagversion)
raise Exception, "Found '%s' but can't overwrite it." \
% dotFlagversion
# Make outfile always a list
if isinstance(outfile, str):
if outfile == '':
outfile = []
else:
noutfile = [outfile]
outfile = noutfile
if savecmds:
if len(outfile) == 0:
# Create default names for the online flags
for myviso in vistoproc:
outfile.append(myviso.replace('.ms', '_cmd.txt'))
elif len(outfile) != len(vistoproc):
casalog.post(
'List of outfile names does not match list of MSs', 'WARN')
casalog.post('Will save online flags to temporary filenames',
'WARN')
outfile = []
for myviso in vistoproc:
online_file = myviso.replace('.ms', '_TEMP_cmd.txt')
outfile.append(online_file)
if not overwrite:
for of in outfile:
if os.path.exists(of):
raise Exception, "Cannot overwrite online flags file '%s'; overwrite is set to False." % of
execute_string = execute_string + ' ' + asdm + ' ' + viso
if showversion:
casalog.post(
"You set option \'showversion\' to True. Will just output the version information and then terminate.",
'WARN')
execute_string = theexecutable + ' --revision'
if with_pointing_correction:
execute_string = execute_string + ' --with-pointing-correction'
if (polyephem_tabtimestep !=
None) and (type(polyephem_tabtimestep) == int
or type(polyephem_tabtimestep) == float):
if polyephem_tabtimestep > 0:
casalog.post(
'Will tabulate all attached polynomial ephemerides with a time step of '
+ str(polyephem_tabtimestep) + ' days.')
if polyephem_tabtimestep > 1.:
casalog.post(
'A tabulation timestep of <= 1 days is recommended.',
'WARN')
execute_string = execute_string + ' --polyephem-tabtimestep ' + str(
polyephem_tabtimestep)
casalog.post('Running ' + theexecutable + ' standalone invoked as:')
# print execute_string
casalog.post(execute_string)
exitcode = os.system(execute_string)
if exitcode != 0:
if not showversion:
casalog.post(
theexecutable + ' terminated with exit code ' +
str(exitcode), 'SEVERE')
raise Exception, \
'ASDM conversion error. Please check if it is a valid ASDM and that data/alma/asdm is up to date.'
if showversion:
return
#
# Possibly remove the name of the measurement set expected to contain the corrected data from the list of of produced measurement
# sets if it appears the filler did not find any corrected data.
#
if not os.path.exists(visoc):
vistoproc = [myviso for myviso in vistoproc if myviso != visoc]
# CAS-7369. HISTORY should be written after createmms is tested
#
# Populate the HISTORY table of the MS with information about the context in which it's been created
#
try:
mslocal = mstool()
param_names = importasdm.func_code.co_varnames[:importasdm.
func_code.
co_argcount]
param_vals = [eval(p) for p in param_names]
for myviso in vistoproc:
write_history(mslocal, myviso, 'importasdm', param_names,
param_vals, casalog)
except Exception, instance:
casalog.post("*** Error \'%s\' updating HISTORY" % (instance),
'WARN')
return False
if mslocal:
mslocal = None
#
# Do we apply fixspwbackport
if remove_ref_undef:
casalog.post(
'remove_ref_undef=True: fixspwbackport will be applied ...')
for myviso in vistoproc:
cmd = 'fixspwbackport ' + myviso
casalog.post('Running fixspwbackport standalone invoked as:')
casalog.post(cmd)
cmdexitcode = os.system(cmd)
if cmdexitcode != 0:
casalog.post(
cmd + ' terminated with exit code ' + str(cmdexitcode),
'SEVERE')
raise Exception, 'fixspwbackport error.'
# Binary Flag processing
if bdfflags:
casalog.post(
'Parameter bdfflags==True: flags from the ASDM binary data will be used to set the MS flags ...'
)
bdffexecutable = 'bdflags2MS '
bdffexecstring_base = bdffexecutable + ' -f ALL' + ' --ocm "' + ocorr_mode \
+ '" --logfile "' + casalog.logfile() + '"'
if len(scans) > 0:
bdffexecstring_base = bdffexecstring_base + ' --scans ' + scans
if lazy and not compression:
bdffexecstring_base = bdffexecstring_base + ' --lazy=true'
for myviso in vistoproc:
if myviso.find("wvr-corrected") != -1:
options = " --wvr-corrected=True "
else:
options = " "
bdffexecstring = bdffexecstring_base + options + asdm + ' ' + myviso
casalog.post('Running ' + bdffexecutable +
' standalone invoked as:')
casalog.post(bdffexecstring)
bdffexitcode = os.system(bdffexecstring)
if bdffexitcode != 0:
casalog.post(
bdffexecutable + ' terminated with exit code ' +
str(bdffexitcode), 'SEVERE')
raise Exception, \
'ASDM binary flags conversion error. Please check if it is a valid ASDM and that data/alma/asdm is up to date.'
theephemfields = ce.findattachedephemfields(myviso, field='*')
if len(theephemfields) > 0:
# until asdm2MS does this internally: recalc the UVW coordinates for ephem fields
imt = imtool()
imt.open(myviso, usescratch=False)
imt.calcuvw(theephemfields, refcode='J2000', reuse=False)
imt.close()
if convert_ephem2geo:
for myviso in vistoproc:
ce.convert2geo(myviso,
'*') # convert any attached ephemerides to GEO
if len(theephemfields) > 0:
# also set the direction column in the SOURCE table
tblocal.open(myviso + '/FIELD', nomodify=False)
sourceids = tblocal.getcol('SOURCE_ID')
ftimes = tblocal.getcol('TIME')
ftimekw = tblocal.getcolkeywords('TIME')
tmpa = tblocal.getcol('PHASE_DIR')
origphasedir = tmpa
affectedsids = []
thesamplefields = []
for fld in theephemfields: # determine all source ids used by the ephem fields
if not (sourceids[fld]
in affectedsids): # this source id wasn't handled yet
affectedsids.append(sourceids[fld])
thesamplefields.append(fld)
# need to temporarily change the offset (not all mosaics have an element at (0,0))
tmpa[0][0][fld] = 0.
tmpa[1][0][fld] = 0.
#endif
#endfor
tblocal.putcol('PHASE_DIR', tmpa)
tblocal.close()
tblocal.open(myviso + '/SOURCE')
sourceposref = tblocal.getcolkeywords(
'DIRECTION')['MEASINFO']['Ref']
tblocal.close()
directions = []
msmdlocal = casac.msmetadata()
msmdlocal.open(myviso)
for fld in thesamplefields:
thedirmeas = msmdlocal.phasecenter(fld)
if thedirmeas['refer'] != sourceposref:
casalog.post(
'Ephemeris is in ' + thedirmeas['refer'] +
' instead of ' + sourceposref +
' frame.\nEntry in SOURCE table will be converted to '
+ sourceposref, 'WARN')
melocal = metool()
melocal.doframe(thedirmeas)
thedirmeas = melocal.measure(thedirmeas, sourceposref)
directions.append(
[thedirmeas['m0']['value'], thedirmeas['m1']['value']])
thetime = me.epoch(v0=str(ftimes[fld]) + 's',
rf=ftimekw['MEASINFO']['Ref'])
casalog.post("Will set SOURCE direction for SOURCE_ID " +
str(sourceids[fld]) +
" to ephemeris phase center for time " +
str(thetime['m0']['value']) + " " +
thetime['m0']['unit'] + " " + thetime['refer'])
#endfor
msmdlocal.close()
# restore original PHASE_DIR
tblocal.open(myviso + '/FIELD', nomodify=False)
tblocal.putcol('PHASE_DIR', origphasedir)
tblocal.close()
# write source directions
tblocal.open(myviso + '/SOURCE', nomodify=False)
ssourceids = tblocal.getcol('SOURCE_ID')
sdirs = tblocal.getcol('DIRECTION')
for row in xrange(0, len(ssourceids)):
for i in xrange(0, len(affectedsids)):
if ssourceids[row] == affectedsids[i]:
sdirs[0][row] = directions[i][0]
sdirs[1][row] = directions[i][1]
break
#endfor
#endfor
tblocal.putcol('DIRECTION',
sdirs) # write back corrected directions
tblocal.close()
#end if
##############################################################################################3
# CAS-7369 - Create an output Multi-MS (MMS)
if createmms:
# Get the default parameters of partition
from tasks import partition
fpars = partition.parameters
for mypar in fpars.keys():
fpars[mypar] = partition.itsdefault(mypar)
# Call the cluster for each MS
for myviso in vistoproc:
casalog.origin('importasdm')
# Move original MS to tempdir
tempname = myviso + '.temp.ms'
outputmms = myviso
shutil.move(myviso, tempname)
# Get the proper column
datacolumn = 'DATA'
dcols = ['DATA', 'FLOAT_DATA']
for dc in dcols:
if len(th.getColDesc(tempname, dc)) > 0:
datacolumn = dc
break
fpars['datacolumn'] = datacolumn
casalog.post('Will create a Multi-MS for: ' + myviso)
fpars['vis'] = tempname
fpars['flagbackup'] = False
fpars['outputvis'] = outputmms
fpars['separationaxis'] = separationaxis
fpars['numsubms'] = numsubms
pdh = ParallelDataHelper('partition', fpars)
# Get a cluster
pdh.setupCluster(thistask='partition')
try:
pdh.go()
# Remove original MS
shutil.rmtree(tempname)
except Exception, instance:
# Restore MS in case of error in MMS creation
shutil.move(tempname, myviso)
casalog.post('%s' % instance, 'ERROR')
return False
casalog.origin('importasdm')
def caltab_convert2(caltabold, ms, pType, caltabnew=""):
# Check the inputs
if not os.path.exists(caltabold):
raise IOError("Invalid old-format caltable.")
if not os.path.exists(ms):
raise IOError("Invalid visibility file (MS).")
pTypeTemp = pType.strip().lower()
if pTypeTemp != "complex" and pTypeTemp != "float":
raise Exception('Invalid parameter type ("complex" or "float").')
if caltabnew == "":
caltabnew = caltabold + ".new"
if os.path.exists(caltabnew):
raise IOError("New-format caltable already exists.")
# Open the old-format caltable and get the number of rows
tbOld = casac.table()
tbOld.open(caltabold)
nRow = tbOld.nrows()
# Get spwid map from old CAL_DESC subtable
tbCD = casac.table()
tbCD.open(caltabold + "/CAL_DESC")
spwmap = tbCD.getcol("SPECTRAL_WINDOW_ID")[0, :]
tbCD.close()
# Create the empty new-format caltable with the correct number of rows
tbNew = casac.table()
tbNew.create(caltabnew, desc_new(pTypeTemp))
tbNew.addrows(nRow)
# Transfer most column information from the old-format caltable to the
# new-format caltable. NB: The REF_ANT column in the old-format
# caltable (analogous to the ANTENNA2 column in the new-format caltable)
# is messed up, which means that I fill ANTENNA2 with -1.
tbNew.putcol("ANTENNA1", tbOld.getcol("ANTENNA1"))
tbNew.putcol("ANTENNA2", -1.0 * numpy.ones(nRow, dtype="int"))
tbNew.putcol("FIELD_ID", tbOld.getcol("FIELD_ID"))
tbNew.putcol("FLAG", tbOld.getcol("FLAG"))
tbNew.putcol("INTERVAL", tbOld.getcol("INTERVAL"))
tbNew.putcol("SNR", tbOld.getcol("SNR"))
# Map CAL_DESC_ID to SPECTRAL_WINDOW_ID:
tbNew.putcol("SPECTRAL_WINDOW_ID", spwmap[tbOld.getcol("CAL_DESC_ID")])
tbNew.putcol("TIME", tbOld.getcol("TIME"))
tbNew.putcol("WEIGHT", tbOld.getcol("FIT_WEIGHT"))
# Transfer the parameter column from the old-format caltable to the
# new-format caltable, taking the type into account. No parameter
# errors are present in the old-format caltable, so they are set to
# 1.0 (+j0.0).
param = tbOld.getcol("GAIN")
if pTypeTemp == "float":
param = param.real
tbNew.putcol("FPARAM", param)
else:
tbNew.putcol("CPARAM", param)
tbNew.putcol("PARAMERR", -1.0 * numpy.ones(param.shape, dtype="float"))
# Determine the scans and put them into the new-format caltable
scanTimes = get_scantimes(ms)
keys = scanTimes.keys()
times = tbOld.getcol("TIME")
scans = numpy.zeros(0, dtype="int")
for t in times.tolist():
flag = False
for i in range(len(keys)):
k = keys[i]
if t >= scanTimes[k]["min"] and t < scanTimes[k]["max"]:
flag = True
scans = numpy.append(scans, k)
break
if i == len(keys) - 1:
break
l = keys[i + 1]
if t >= scanTimes[k]["max"] and t < scanTimes[l]["min"]:
flag = True
scans = numpy.append(scans, l)
break
if not flag:
scans = numpy.append(scans, -1)
tbNew.putcol("SCAN_NUMBER", scans)
# Copy the appropriate subcaltables from the MS to the new-format
# caltable
arg = "cp -r " + ms + "/ANTENNA " + caltabnew
os.system(arg)
arg = "cp -r " + ms + "/FIELD " + caltabnew
os.system(arg)
# arg = 'cp -r ' + caltabold + '/CAL_HISTORY ' + caltabnew + '/HISTORY'
# os.system( arg )
tbHis = casac.table()
tbHis.open(ms + "/HISTORY")
tbHis.copy(newtablename=caltabnew + "/HISTORY", deep=True, valuecopy=True, norows=True)
tbHis.close()
del tbHis
arg = "cp -r " + ms + "/SPECTRAL_WINDOW " + caltabnew + "/SPECTRAL_WINDOW"
os.system(arg)
# Add the info and keywords to the main table of the new-format caltable
tabinfo = tbOld.info()
tbNew.putinfo(tabinfo)
if pTypeTemp == "complex":
tbNew.putkeyword("ParType", "Complex")
if pTypeTemp == "float":
tbNew.putkeyword("ParType", "Float")
tbNew.putkeyword("MSName", ms)
tbNew.putkeyword("VisCal", tabinfo["subType"])
polBasis = get_polbasis(ms)
tbNew.putkeyword("PolBasis", polBasis)
tbNew.putkeyword("ANTENNA", "Table: " + caltabnew + "/ANTENNA")
tbNew.putkeyword("FIELD", "Table: " + caltabnew + "/FIELD")
tbNew.putkeyword("HISTORY", "Table: " + caltabnew + "/HISTORY")
tbNew.putkeyword("SPECTRAL_WINDOW", "Table: " + caltabnew + "/SPECTRAL_WINDOW")
# Add the column keywords to the main table of the new-format caltable
colList = ["INTERVAL", "TIME"]
for col in colList:
colKeys = tbOld.getcolkeywords(col)
if colKeys != {}:
tbNew.putcolkeywords(col, colKeys)
# Close the old- and new- format caltables
tbOld.close()
del tbOld
tbNew.close()
del tbNew
# Get the channel ranges from the CAL_DESC subtable of the old-format
# caltable
tbDesc = casac.table()
tbDesc.open(caltabold + "/CAL_DESC")
nDesc = tbDesc.nrows()
rDesc = range(nDesc)
spwMap = tbDesc.getcol("SPECTRAL_WINDOW_ID")[0]
chanMin = numpy.zeros(nDesc, dtype="int")
chanMax = numpy.zeros(nDesc, dtype="int")
for d in rDesc:
chanRange = tbDesc.getcol("CHAN_RANGE", startrow=d, nrow=1)
chanMin[d] = numpy.min(chanRange[0, :, :, :][0, :, 0])
chanMax[d] = numpy.max(chanRange[1, :, :, :][0, :, 0])
if numpy.all(chanMax - chanMin + 1 == 1):
gain = True
else:
gain = False
tbDesc.close()
del tbDesc
# Modify the columns of the new-format caltable according to the
# channel ranges
tbSPW = casac.table()
tbSPW.open(caltabnew + "/SPECTRAL_WINDOW", nomodify=False)
for d in rDesc:
s = int(spwMap[d])
nChan = int(chanMax[d] - chanMin[d] + 1)
tbSPW.putcell("NUM_CHAN", s, nChan)
chanFreq = tbSPW.getcell("CHAN_FREQ", s)
if gain:
chanFreq = numpy.median(chanFreq)
else:
chanFreq = chanFreq[chanMin[d] : chanMax[d] + 1]
tbSPW.putcell("CHAN_FREQ", s, chanFreq)
chanWidth = tbSPW.getcell("CHAN_WIDTH", s)
if gain:
chanWidth = numpy.sum(chanWidth)
else:
chanWidth = chanWidth[chanMin[d] : chanMax[d] + 1]
tbSPW.putcell("CHAN_WIDTH", s, chanWidth)
tbSPW.putcell("EFFECTIVE_BW", s, chanWidth)
tbSPW.putcell("RESOLUTION", s, chanWidth)
totalBandwidth = numpy.sum(chanWidth)
tbSPW.putcell("TOTAL_BANDWIDTH", s, totalBandwidth)
tbSPW.close()
del tbSPW
# Return True
return True
def compTables(referencetab,
testtab,
excludecols,
tolerance=0.001,
mode="percentage",
startrow=0,
nrow=-1,
rowincr=1):
"""
compTables - compare two CASA tables
referencetab - the table which is assumed to be correct
testtab - the table which is to be compared to referencetab
excludecols - list of column names which are to be ignored
tolerance - permitted fractional difference (default 0.001 = 0.1 percent)
mode - comparison is made as "percentage", "absolute", "phaseabsdeg" (for complex numbers = difference of the phases in degrees)
"""
rval = True
tb2 = casac.table()
tb.open(referencetab)
cnames = tb.colnames()
tb2.open(testtab)
try:
for c in cnames:
if c in excludecols:
continue
print "\nTesting column " + c
a = 0
try:
a = tb.getcol(c, startrow=startrow, nrow=nrow, rowincr=rowincr)
except:
rval = False
print 'Error accessing column ', c, ' in table ', referencetab
print sys.exc_info()[0]
break
b = 0
try:
b = tb2.getcol(c,
startrow=startrow,
nrow=nrow,
rowincr=rowincr)
except:
rval = False
print 'Error accessing column ', c, ' in table ', testtab
print sys.exc_info()[0]
break
if not (len(a) == len(b)):
print 'Column ', c, ' has different length in tables ', referencetab, ' and ', testtab
print a
print b
rval = False
break
else:
differs = False
if not (a == b).all():
for i in range(0, len(a)):
if (isinstance(a[i], float)):
if ((mode == "percentage") and
(abs(a[i] - b[i]) > tolerance * abs(a[i]))
) or ((mode == "absolute") and
(abs(a[i] - b[i]) > tolerance)):
print "Column " + c + " differs"
print "Row=" + str(i)
print "Reference file value: " + str(a[i])
print "Input file value: " + str(b[i])
if (mode == "percentage"):
print "Tolerance is {0}%; observed difference was {1} %".format(
tolerance * 100,
100 * abs(a[i] - b[i]) / abs(a[i]))
else:
print "Absolute tolerance is {0}; observed difference: {1}".format(
tolerance, (abs(a[i] - b[i])))
differs = True
rval = False
break
elif (isinstance(a[i], int)
or isinstance(a[i], np.int32)):
if (abs(a[i] - b[i]) > 0):
print "Column " + c + " differs"
print "Row=" + str(i)
print "Reference file value: " + str(a[i])
print "Input file value: " + str(b[i])
if (mode == "percentage"):
print "tolerance in % should be " + str(
100 * abs(a[i] - b[i]) / abs(a[i]))
else:
print "absolute tolerance should be " + str(
abs(a[i] - b[i]))
differs = True
rval = False
break
elif (isinstance(a[i], str)
or isinstance(a[i], np.bool_)):
if not (a[i] == b[i]):
print "Column " + c + " differs"
print "Row=" + str(i)
print "Reference file value: " + str(a[i])
print "Input file value: " + str(b[i])
if (mode == "percentage"):
print "tolerance in % should be " + str(
100 * abs(a[i] - b[i]) / abs(a[i]))
else:
print "absolute tolerance should be " + str(
abs(a[i] - b[i]))
differs = True
rval = False
break
elif (isinstance(a[i], list)) or (isinstance(
a[i], np.ndarray)):
for j in range(0, len(a[i])):
if differs: break
if ((isinstance(a[i][j], float))
or (isinstance(a[i][j], int))):
if ((mode == "percentage") and
(abs(a[i][j] - b[i][j]) >
tolerance * abs(a[i][j]))) or (
(mode == "absolute") and
(abs(a[i][j] - b[i][j]) >
tolerance)):
print "Column " + c + " differs"
print "(Row,Element)=(" + str(
j) + "," + str(i) + ")"
print "Reference file value: " + str(
a[i][j])
print "Input file value: " + str(
b[i][j])
if (mode == "percentage"):
print "Tolerance in % should be " + str(
100 * abs(a[i][j] - b[i][j]) /
abs(a[i][j]))
else:
print "Absolute tolerance should be " + str(
abs(a[i][j] - b[i][j]))
differs = True
rval = False
break
elif (isinstance(a[i][j],
list)) or (isinstance(
a[i][j], np.ndarray)):
it = xrange(0, len(a[i][j]))
if mode == "percentage":
diff = np.abs(
np.subtract(a[i][j], b[i][j])
) > tolerance * np.abs(a[i][j])
it = np.where(diff)[0]
elif (mode == "absolute"):
diff = np.abs(
np.subtract(a[i][j],
b[i][j])) > tolerance
it = np.where(diff)[0]
for k in it:
if differs: break
if ( ((mode=="percentage") and (abs(a[i][j][k]-b[i][j][k]) > tolerance*abs(a[i][j][k]))) \
or ((mode=="absolute") and (abs(a[i][j][k]-b[i][j][k]) > tolerance)) \
or ((mode=="phaseabsdeg") and (phasediffabsdeg(a[i][j][k],b[i][j][k])>tolerance)) \
):
print "Column " + c + " differs"
print "(Row,Channel,Corr)=(" + str(
k) + "," + str(j) + "," + str(
i) + ")"
print "Reference file value: " + str(
a[i][j][k])
print "Input file value: " + str(
b[i][j][k])
if (mode == "percentage"):
print "Tolerance in % should be " + str(
100 * abs(a[i][j][k] -
b[i][j][k]) /
abs(a[i][j][k]))
elif (mode == "absolute"):
print "Absolute tolerance should be " + str(
abs(a[i][j][k] -
b[i][j][k]))
elif (mode == "phaseabsdeg"):
print "Phase tolerance in degrees should be " + str(
phasediffabsdeg(
a[i][j][k],
b[i][j][k]))
else:
print "Unknown comparison mode: ", mode
differs = True
rval = False
break
else:
print "Unknown data type: ", type(a[i])
differs = True
rval = False
break
if not differs: print "Column " + c + " PASSED"
finally:
tb.close()
tb2.close()
return rval
def importasdm(
asdm=None,
vis=None,
createmms=None,
separationaxis=None,
numsubms=None,
singledish=None,
antenna=None,
corr_mode=None,
srt=None,
time_sampling=None,
ocorr_mode=None,
compression=None,
lazy=None,
asis=None,
wvr_corrected_data=None,
scans=None,
ignore_time=None,
process_syspower=None,
process_caldevice=None,
process_pointing=None,
process_flags=None,
tbuff=None,
applyflags=None,
savecmds=None,
outfile=None,
flagbackup=None,
verbose=None,
overwrite=None,
showversion=None,
useversion=None,
bdfflags=None,
with_pointing_correction=None,
remove_ref_undef=None,
convert_ephem2geo=None
):
"""Convert an ALMA Science Data Model observation into a CASA visibility file (MS) or single-dish data format (Scantable).
The conversion of the ALMA SDM archive format into a measurement set. This version
is under development and is geared to handling many spectral windows of different
shapes.
Keyword arguments:
asdm -- Name of input ASDM file (directory)
default: none; example: asdm='ExecBlock3'
vis -- Root ms or scantable name, note a prefix (.ms or .asap) is NOT appended to this name
default: none
createmms -- Create a Multi-MS
default: False
singledish -- Set True to write data as single-dish format (Scantable)
default: False singledish expandable parameter
antenna -- antenna name or id.
corr_mode -- correlation mode to be considered on input. Could
be one or more of the following, ao, co, ac, or all
default: all
srt -- spectral resolution type. Could be one or more of
the following, fr, ca, bw, or all
default: all
time_sampling -- specifies the time sampling, INTEGRATION and/or
SUBINTEGRATION. could be one or more of the following
i, si, or all.
default: all
ocorr_mode -- output data for correlation mode AUTO_ONLY
(ao) or CROSS_ONLY (co) or CROSS_AND_AUTO (ca)
default: ca
compression -- produces comrpressed columns in the resulting measurement set.
default: False
lazy -- Make the MS DATA column read the ASDM Binary data directly
(faster import, smaller MS)
default: False
asis -- creates verbatim copies of the ASDM tables in
the output measurement set. The value given to
this option must be a list of table names separated
by space characters; the wildcard character '*' is
allowed in table names.
wvr_corrected_data -- specifies wich values are considered in the
ASDM binary data to fill the DATA column in
the MAIN table of the MS. Expected values for
this option are 'no' for the uncorrected data
(this is the default), 'yes' for the corrected
data and 'both' for corrected and uncorrected
data. In the latter case, two measurement sets
are created, one containing the uncorrected
data and the other one, whose name is suffixed
by '-wvr-corrected', containing the corrected
data.
scans -- processes only the scans specified in the option's value. This value is a semicolon
separated list of scan specifications. A scan specification consists in an exec bock index
followed by the character ':' followed by a comma separated list of scan indexes or scan
index ranges. A scan index is relative to the exec block it belongs to. Scan indexes are
1-based while exec blocks's are 0-based. "0:1" or "2:2~6" or "0:1,1:2~6,8;2:,3:24~30" "1,2"
are valid values for the option. "3:" alone will be interpreted as 'all the scans of the
exec block#3'. An scan index or a scan index range not preceded by an exec block index will
be interpreted as 'all the scans with such indexes in all the exec blocks'. By default
all the scans are considered.
ignore_time -- All the rows of the tables Feed, History, Pointing, Source, SysCal, CalDevice, SysPower,
and Weather are processed independently of the time range of the selected exec block / scan.
process_syspower -- The SysPower table is processed if and only if this parameter is set to True.
default: True
process_caldevice -- The CalDevice table is processed if and only if this parameter is set to True.
default: True
process_pointing -- The Pointing table is processed if and only if this parameter is set to True.
If the parameter is set to False the resulting MS will have an empty POINTING table.
default: True
process_flags -- Process the online flags and save them to the FLAG_CMD sub-table.
default: True
>>> process_flags expandable parameter
tbuff -- Time padding buffer (in seconds).
default: 0.0
applyflags -- Apply the online flags to the MS.
default: False
savecmds -- Save the online flags to an ASCII file.
default: False
outfile -- Filename to save the online flags.
default: ''
flagbackup -- Backup the FLAG column in the .flagversions.
default: True
verbose -- produce log output as asdm2MS is being run.
overwrite -- Over write an existing MS.
showversion -- report the version of the asdm2MS being used.
useversion -- Selects the version of asdm2MS to be used (presently only \'v3\' is available).
default: v3
bdfflags -- Set the MS FLAG column according to the ASDM _binary_ flags
default: false
with_pointing_correction -- add (ASDM::Pointing::encoder - ASDM::Pointing::pointingDirection)
to the value to be written in MS::Pointing::direction
default: false
remove_ref_undef -- if set to True then apply fixspwbackport on the resulting MSes.
convert_ephem2geo -- if True, convert any attached ephemerides to the GEO reference frame
"""
# Python script
# make agentflagger tool local
aflocal = casac.agentflagger()
# make table tool local
tblocal = casac.table()
try:
casalog.origin('importasdm')
viso = ''
visoc = '' # for the wvr corrected version, if needed
# -----------------------------------------
# beginning of importasdm_sd implementation
# -----------------------------------------
if singledish:
theexecutable = 'asdm2ASAP'
# if useversion == 'v2':
# theexecutable = 'oldasdm2ASAP'
if compression:
casalog.post('compression=True has no effect for single-dish format.')
cmd = 'which %s > /dev/null 2>&1' % theexecutable
ret = os.system(cmd)
if ret == 0:
import commands
casalog.post('found %s' % theexecutable)
if showversion:
execute_string = theexecutable + ' --help'
else:
execute_string = theexecutable + ' -asdm ' + asdm
if len(vis) != 0:
execute_string += ' -asap ' + vis.rstrip('/')
execute_string += ' -antenna ' + str(antenna) \
+ ' -apc ' + wvr_corrected_data \
+ ' -time-sampling ' + time_sampling.lower() \
+ ' -overwrite ' + str(overwrite)
if corr_mode == 'all':
execute_string += \
' -corr-mode ao,ca -ocorr-mode ao'
else:
execute_string += ' -corr-mode ' \
+ corr_mode.replace(' ', ',') \
+ ' -ocorr-mode ao'
if srt == 'all':
execute_string += ' -srt ' + srt
else:
execute_string += ' -srt ' + srt.replace(' ',
',')
execute_string += ' -logfile ' + casalog.logfile()
casalog.post('execute_string is')
casalog.post(' ' + execute_string)
ret = os.system(execute_string)
if ret != 0 and not showversion:
casalog.post(theexecutable
+ ' terminated with exit code '
+ str(ret), 'SEVERE')
# raise Exception, "ASDM conversion error, please check if it is a valid ASDM and/or useversion='%s' is consistent with input ASDM."%(useversion)
raise Exception, \
'ASDM conversion error, please check if it is a valid ASDM.'
else:
casalog.post('You have to build ASAP to be able to create single-dish data.'
, 'SEVERE')
# implementation of asis option using tb.fromASDM
if asis != '':
import commands
asdmTables = commands.getoutput('ls %s/*.xml'
% asdm).split('\n')
asdmTabNames = []
for tab in asdmTables:
asdmTabNames.append(tab.split('/')[-1].rstrip('.xml'
))
if asis == '*':
targetTables = asdmTables
targetTabNames = asdmTabNames
else:
targetTables = []
targetTabNames = []
tmpTabNames = asis.split()
for i in xrange(len(tmpTabNames)):
tab = tmpTabNames[i]
try:
targetTables.append(asdmTables[asdmTabNames.index(tab)])
targetTabNames.append(tab)
except:
pass
outTabNames = []
outTables = []
for tab in targetTabNames:
out = 'ASDM_' + tab.upper()
outTabNames.append(out)
outTables.append(vis + '/' + out)
tblocal.open(vis, nomodify=False)
wtb = casac.table()
for i in xrange(len(outTables)):
wtb.fromASDM(outTables[i], targetTables[i])
tblocal.putkeyword(outTabNames[i], 'Table: %s'
% outTables[i])
tblocal.flush()
tblocal.close()
return
# -----------------------------------
# end of importasdm_sd implementation
# -----------------------------------
if len(vis) > 0:
viso = vis
tmps = vis.rstrip('.ms')
if tmps == vis:
visoc = vis + '-wvr-corrected'
else:
visoc = tmps + '-wvr-corrected.ms'
if singledish:
viso = vis.rstrip('/') + '.importasdm.tmp.ms'
else:
viso = asdm.rstrip("/") + '.ms'
visoc = asdm.rstrip("/") + '-wvr-corrected.ms'
vis = asdm.rstrip("/")
if singledish:
viso = asdm.rstrip('/') + '.importasdm.tmp.ms'
vis = asdm.rstrip('/') + '.asap'
useversion = 'v3'
theexecutable = 'asdm2MS'
execute_string = theexecutable + ' --icm "' + corr_mode \
+ '" --isrt "' + srt + '" --its "' + time_sampling \
+ '" --ocm "' + ocorr_mode + '" --wvr-corrected-data "' \
+ wvr_corrected_data + '" --asis "' + asis \
+ '" --logfile "' + casalog.logfile() + '"'
if len(scans) > 0:
execute_string = execute_string + ' --scans ' + scans
if ignore_time:
execute_string = execute_string + ' --ignore-time'
if useversion == 'v3':
if not process_syspower:
execute_string = execute_string + ' --no-syspower'
if not process_caldevice:
execute_string = execute_string + ' --no-caldevice'
if not process_pointing:
execute_string = execute_string + ' --no-pointing'
if compression:
execute_string = execute_string + ' --compression'
elif lazy:
execute_string = execute_string + ' --lazy'
if verbose:
execute_string = execute_string + ' --verbose'
# if not overwrite and os.path.exists(viso):
# raise Exception, \
# 'You have specified an existing MS and have indicated you do not wish to overwrite it'
# Compression
if compression:
# viso = viso + '.compressed'
viso = viso.rstrip('.ms') + '.compressed.ms'
visoc = visoc.rstrip('.ms') + '.compressed.ms'
vistoproc = [] # the output MSs to post-process
if wvr_corrected_data == 'no' or wvr_corrected_data == 'both':
vistoproc.append(viso)
if (wvr_corrected_data == 'yes' or wvr_corrected_data == 'both') :
vistoproc.append(visoc)
for ff in vistoproc:
if not overwrite and os.path.exists(ff):
raise Exception, \
'You have specified an existing MS and have indicated you do not wish to overwrite it: %s'%ff
# If viso+".flagversions" then process differently depending on the value of overwrite..
#
if flagbackup:
for myviso in vistoproc:
dotFlagversion = myviso + '.flagversions'
if os.path.exists(dotFlagversion):
if overwrite:
casalog.post("Found '" + dotFlagversion
+ "' . It'll be deleted before running the filler."
)
os.system('rm -rf %s' % dotFlagversion)
else:
casalog.post("Found '%s' but can't overwrite it."
% dotFlagversion)
raise Exception, "Found '%s' but can't overwrite it." \
% dotFlagversion
# Make outfile always a list
if isinstance(outfile, str):
if outfile == '':
outfile = []
else:
noutfile = [outfile]
outfile = noutfile
if savecmds:
if len(outfile) == 0:
# Create default names for the online flags
for myviso in vistoproc:
outfile.append(myviso.replace('.ms','_cmd.txt'))
elif len(outfile) != len(vistoproc):
casalog.post('List of outfile names does not match list of MSs','WARN')
casalog.post('Will save online flags to temporary filenames', 'WARN')
outfile = []
for myviso in vistoproc:
online_file = myviso.replace('.ms','_TEMP_cmd.txt')
outfile.append(online_file)
if not overwrite:
for of in outfile:
if os.path.exists(of):
raise Exception, "Cannot overwrite online flags file '%s'; overwrite is set to False."% of
execute_string = execute_string + ' ' + asdm + ' ' + viso
if showversion:
casalog.post("You set option \'showversion\' to True. Will just output the version information and then terminate."
, 'WARN')
execute_string = theexecutable + ' --revision'
if with_pointing_correction:
execute_string = execute_string + ' --with-pointing-correction'
casalog.post('Running ' + theexecutable
+ ' standalone invoked as:')
# print execute_string
casalog.post(execute_string)
exitcode = os.system(execute_string)
if exitcode != 0:
if not showversion:
casalog.post(theexecutable
+ ' terminated with exit code '
+ str(exitcode), 'SEVERE')
raise Exception, \
'ASDM conversion error. Please check if it is a valid ASDM and that data/alma/asdm is up to date.'
if showversion:
return
#
# Possibly remove the element the name of the measurement set expected to contain the corrected data from the list of of produced measurement
# sets if it appears the filler did not find any corrected data.
#
if not os.path.exists(visoc):
vistoproc = [myviso for myviso in vistoproc if myviso != visoc]
# CAS-7369. HISTORY should be written after createmms is tested
#
# Populate the HISTORY table of the MS with information about the context in which it's been created
#
try:
mslocal = mstool()
param_names = importasdm.func_code.co_varnames[:importasdm.func_code.co_argcount]
param_vals = [eval(p) for p in param_names]
for myviso in vistoproc:
write_history(mslocal, myviso, 'importasdm', param_names,
param_vals, casalog)
except Exception, instance:
casalog.post("*** Error \'%s\' updating HISTORY" % (instance),
'WARN')
return False
if mslocal:
mslocal = None
#
# Do we apply fixspwbackport
if remove_ref_undef :
casalog.post('remove_ref_undef=True: fixspwbackport will be applied ...')
for myviso in vistoproc:
cmd = 'fixspwbackport ' + myviso
casalog.post('Running fixspwbackport standalone invoked as:')
casalog.post(cmd)
cmdexitcode = os.system(cmd)
if cmdexitcode != 0:
casalog.post(cmd
+ ' terminated with exit code '
+ str(cmdexitcode), 'SEVERE')
raise Exception, 'fixspwbackport error.'
# Binary Flag processing
if bdfflags:
casalog.post('Parameter bdfflags==True: flags from the ASDM binary data will be used to set the MS flags ...')
bdffexecutable = 'bdflags2MS '
bdffexecstring_base = bdffexecutable+' -f ALL'
if len(scans) > 0:
bdffexecstring_base = bdffexecstring_base + ' --scans ' + scans
for myviso in vistoproc:
if myviso.find("wvr-corrected") != -1:
options = " --wvr-corrected=True "
else:
options = " "
bdffexecstring = bdffexecstring_base + options + asdm + ' ' + myviso
casalog.post('Running '+bdffexecutable+' standalone invoked as:')
casalog.post(bdffexecstring)
bdffexitcode = os.system(bdffexecstring)
if bdffexitcode != 0:
casalog.post(bdffexecutable
+ ' terminated with exit code '
+ str(bdffexitcode), 'SEVERE')
raise Exception, \
'ASDM binary flags conversion error. Please check if it is a valid ASDM and that data/alma/asdm is up to date.'
for myviso in vistoproc:
if os.path.exists(myviso) and flagbackup==True:
aflocal.open(myviso)
aflocal.saveflagversion('Original',
comment='Original flags at import into CASA',
merge='save')
aflocal.done()
# Importasdm Flag Parsing
if os.access(asdm + '/Flag.xml', os.F_OK):
# Find Flag.xml
casalog.post('Found Flag.xml in SDM')
# Find Antenna.xml
if os.access(asdm + '/Antenna.xml', os.F_OK):
casalog.post('Found Antenna.xml in SDM')
else:
raise Exception, 'Failed to find Antenna.xml in SDM'
# Find SpectralWindow.xml
if os.access(asdm + '/SpectralWindow.xml', os.F_OK):
casalog.post('Found SpectralWindow.xml in SDM')
else:
raise Exception, \
'Failed to find SpectralWindow.xml in SDM'
#
# Parse Flag.xml into flag dictionary
#
if process_flags:
flagcmds = fh.parseXML(asdm, float(tbuff))
onlinekeys = flagcmds.keys()
nflags = onlinekeys.__len__()
# Apply flags to the MS
if nflags > 0:
idx = 0
for myviso in vistoproc:
if applyflags:
# Open the MS and attach it to the tool
aflocal.open(myviso)
# Select the data
aflocal.selectdata()
# Setup the agent's parameters
fh.parseAgents(aflocal, flagcmds, [], True, True, '')
# Initialize the agents
aflocal.init()
# Run the tool
aflocal.run(True, True)
casalog.post('Applied %s flag commands to %s'%(nflags,myviso))
# Destroy the tool and de-attach the MS
aflocal.done()
# Save to FLAG_CMD table. APPLIED is set to True.
fh.writeFlagCommands(myviso, flagcmds, True, '', '', True)
else:
casalog.post('Will not apply flags to %s (apply_flags=False), use flagcmd to apply'%myviso)
# Write to FLAG_CMD, APPLIED is set to False
fh.writeFlagCommands(myviso, flagcmds, False, '', '', True)
# Save the flag cmds to an ASCII file
if savecmds:
# Save to standard filename
fh.writeFlagCommands(myviso, flagcmds, False, '', outfile[idx], False)
casalog.post('Saved %s flag commands to %s'%(nflags,outfile[idx]))
idx += 1
else:
casalog.post('There are no flag commands to process')
else:
casalog.post('There is no Flag.xml in ASDM', 'WARN')
import recipes.ephemerides.convertephem as ce
theephemfields = ce.findattachedephemfields(myviso,field='*')
if len(theephemfields)>0: # temporary fix until asdm2MS does this internally: recalc the UVW coordinates for ephem fields
imt = imtool()
imt.open(myviso, usescratch=False)
imt.calcuvw(theephemfields, refcode='J2000', reuse=False)
imt.close()
if convert_ephem2geo:
for myviso in vistoproc:
ce.convert2geo(myviso, '*') # convert any attached ephemerides to GEO
# CAS-7369 - Create an output Multi-MS (MMS)
if createmms:
# Get the default parameters of partition
from tasks import partition
fpars = partition.parameters
for mypar in fpars.keys():
fpars[mypar] = partition.itsdefault(mypar)
# Call the cluster for each MS
for myviso in vistoproc:
casalog.origin('importasdm')
outputmms = myviso.replace('.ms','.mms')
# Get the proper column
datacolumn = 'DATA'
dcols = ['DATA', 'FLOAT_DATA']
for dc in dcols:
if len(th.getColDesc(myviso, dc)) > 0:
datacolumn = dc
break
fpars['datacolumn'] = datacolumn
casalog.post('Will create a Multi-MS for: '+myviso)
fpars['vis'] = myviso
fpars['flagbackup'] = False
fpars['outputvis'] = outputmms
fpars['separationaxis'] = separationaxis
fpars['numsubms'] = numsubms
pdh = ParallelDataHelper('partition', fpars)
# Get a cluster
pdh.setupCluster(thistask='partition')
try:
pdh.go()
# Rename MMS to MS
shutil.rmtree(myviso)
shutil.move(outputmms, myviso)
except Exception, instance:
casalog.post('%s'%instance,'ERROR')
return False
casalog.origin('importasdm')
return