from __future__ import absolute_import
import os
import shutil
# get is_CASA6 and is_python3
from casatasks.private.casa_transition import *
if is_CASA6:
from casatasks import casalog
from casatools import table, agentflagger, ms, imager, measures, msmetadata, sdm
from .mstools import write_history
from . import flaghelper as fh
from . import convertephem as ce
from .parallel.parallel_data_helper import ParallelDataHelper
else:
from taskinit import *
from mstools import write_history
import flaghelper as fh
from casac import casac
from parallel.parallel_data_helper import ParallelDataHelper
import recipes.ephemerides.convertephem as ce
agentflagger = casac.agentflagger
table = casac.table
msmetadata = casac.msmetadata
imager = imtool
measures = metool
ms = mstool
_tb = table()
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,
bdfflags=None,
with_pointing_correction=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 which 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.
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
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
casalog.origin('importasdm')
# fill in empty vis parameter
if vis is None or type(vis) is str and len(vis) == 0:
vis = asdm+".ms"
# make local sdm tool - CASA6 only, CASA5 uses asdm2MS executable
if is_CASA6:
sdmlocal = sdm(asdm)
# make agentflagger tool local
aflocal = agentflagger()
# make table tool local
tblocal = table()
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("/")
# 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 RuntimeError("Cannot overwrite online flags file '%s'; overwrite is set to False."% of)
# assemble the asdm2MS executable for CASA5
if not is_CASA6:
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 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'
execute_string = execute_string + ' ' + asdm + ' ' + viso
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')
# one more addition to the asdm2MS execution string
if not is_CASA6:
execute_string = execute_string + ' --polyephem-tabtimestep '+str(polyephem_tabtimestep)
if is_CASA6:
exitcode = sdmlocal.toms( vis, createmms, separationaxis, numsubms, corr_mode, srt, time_sampling,
ocorr_mode, compression, lazy, asis, wvr_corrected_data, scans,
ignore_time, process_syspower, process_caldevice, process_pointing,
process_flags, tbuff, applyflags, savecmds, outfile, flagbackup,
verbose, overwrite, bdfflags,
with_pointing_correction, convert_ephem2geo,
polyephem_tabtimestep )
if exitcode != True:
casalog.post("initial creation of the measurement set failed", 'SEVERE')
raise Exception('ASDM conversion error. Please check if it is a valid ASDM and that data/alma/asdm is up to date.')
else:
casalog.post('Running ' + theexecutable
+ ' standalone invoked as:')
# print execute_string
casalog.post(execute_string)
exitcode = os.system(execute_string)
if exitcode != 0:
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.')
#
# 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]
# this is only necessary for CASA5, for CASA6 these steps are handled by the toms method in sdm
if not is_CASA6:
# 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.')
if convert_ephem2geo:
for myviso in vistoproc:
ce.convert2geo(myviso, '*') # convert any attached ephemerides to GEO
for myviso in vistoproc:
theephemfields = ce.findattachedephemfields(myviso,field='*')
if len(theephemfields)>0:
# until asdm2MS or sdm.toms does this internally: recalc the UVW coordinates for ephem fields
imt = imager()
imt.open(myviso, usescratch=False)
imt.calcuvw(theephemfields, refcode='J2000', reuse=False)
imt.close()
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 = []
melocal = measures()
msmdlocal = 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.doframe(thedirmeas)
thedirmeas = melocal.measure(thedirmeas, sourceposref)
directions.append([thedirmeas['m0']['value'], thedirmeas['m1']['value']])
thetime = melocal.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 range(0,len(ssourceids)):
for i in range(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
#end for
##############################################################################################3
# CAS-7369 - Create an output Multi-MS (MMS)
if createmms:
fpars = { }
if is_CASA6:
# Get the default parameters of partition
import inspect
from casatasks import partition as pt
for k,v in inspect.signature(pt).parameters.items( ):
fpars[k] = v.default
else:
# 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']
_tb.open(tempname)
for dc in dcols:
if dc in _tb.colnames( ):
datacolumn = dc
break
_tb.close( )
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
# Run partition only at the MPIServers
pdh = ParallelDataHelper('partition', fpars)
# Get a cluster
pdh.setupCluster(thistask='partition')
try:
pdh.go()
# Remove original MS
shutil.rmtree(tempname)
except Exception as instance:
# Restore MS in case of error in MMS creation
shutil.move(tempname, myviso)
raise
casalog.origin('importasdm')
# Create a .flagversions for the MS or MMS
if flagbackup:
for myviso in vistoproc:
if os.path.exists(myviso):
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')
# 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 = ms()
param_names = importasdm.__code__.co_varnames[:importasdm.__code__.co_argcount]
if is_python3:
vars = locals( )
param_vals = [vars[p] for p in param_names]
else:
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 as instance:
casalog.post("*** Error \'%s\' updating HISTORY" % (instance),'WARN')
finally:
if mslocal:
mslocal = None