def copy_data(self,inms):
# Create corrected data colun and Put data to corrected data column
t = pt.table(inms, readonly=False, ack=True)
data = t.getcol('DATA')
pt.addImagingColumns(inms, ack=True)
t.putcol('CORRECTED_DATA', data)
t.close()
def copy_data_invert(self,inms):
## Create corrected data colun and Put data to corrected data column
t = pt.table(inms, readonly=False, ack=True)
data = t.getcol('CORRECTED_DATA')
pt.addImagingColumns(inms, ack=True)
t.putcol('DATA', data)
t.close()
def check_imaging_weight(mslist_name):
# returns a boolean that says whether it did something
result = False
report('Checking for IMAGING_WEIGHT in input MSS')
mslist = [s.strip() for s in open(mslist_name).readlines()]
for ms in mslist:
t = pt.table(ms)
try:
dummy = t.getcoldesc('IMAGING_WEIGHT')
except RuntimeError:
dummy = None
t.close()
if dummy is not None:
warn('Table ' + ms + ' already has imaging weights')
else:
pt.addImagingColumns(ms)
result = True
return result
def addCorrected(msname):
""" Copy DATA to CORRECTED_DATA column.
Parameters
----------
* **msname** : str
Name of the Measurement Set
"""
isMS(msname)
mstable = table(msname, readonly=False)
data = mstable.getcol('DATA')
addImagingColumns(msname)
mstable.putcol('CORRECTED_DATA', data)
mstable.flush()
mstable.close()
updateHist(msname=msname,
message='CORRECTED data collumn copied from DATA')
return
#!/usr/bin/env python # Script that adds imaging columns to a MS # # File: addImagingColumns.py # Author: Sven Duscha ([email protected]) # Date: 2011-02-14 # Last change: 2011-10-29 import sys try: import pyrap.tables as pt except ImportError: print "addImagingColumns.py: could not import pyrap.tables" print "WARN: No imaging columns added" sys.exit(1) if len(sys.argv)> 2: print "addImagingColumns.py: Too many arguments" sys.exit(1) elif len(sys.argv)==1: print "addImagingColumns.py: No MS given" sys.exit(1) else: filename=sys.argv[1] # MS filename is by default first sys.argv pt.addImagingColumns(filename) # Add imaging columns sys.exit(0)
def run(self, environment, parset, working_dir, processed_ms_dir,
ndppp_executable, output_measurement_set, time_slices_per_image,
subbands_per_group, raw_ms_mapfile, asciistat_executable,
statplot_executable, msselect_executable, rficonsole_executable,
add_beam_tables):
"""
Entry point for the node recipe
"""
self.environment.update(environment)
with log_time(self.logger):
input_map = DataMap.load(raw_ms_mapfile)
#******************************************************************
# I. Create the directories used in this recipe
create_directory(processed_ms_dir)
# time slice dir_to_remove: assure empty directory: Stale data
# is problematic for dppp
time_slice_dir = os.path.join(working_dir, _time_slice_dir_name)
create_directory(time_slice_dir)
for root, dirs, files in os.walk(time_slice_dir):
for file_to_remove in files:
os.unlink(os.path.join(root, file_to_remove))
for dir_to_remove in dirs:
shutil.rmtree(os.path.join(root, dir_to_remove))
self.logger.debug("Created directory: {0}".format(time_slice_dir))
self.logger.debug("and assured it is empty")
#******************************************************************
# 1. Copy the input files
copied_ms_map = self._copy_input_files(processed_ms_dir, input_map)
#******************************************************************
# 2. run dppp: collect frequencies into larger group
time_slices_path_list = \
self._run_dppp(working_dir, time_slice_dir,
time_slices_per_image, copied_ms_map, subbands_per_group,
processed_ms_dir, parset, ndppp_executable)
# If no timeslices were created, bail out with exit status 1
if len(time_slices_path_list) == 0:
self.logger.error("No timeslices were created.")
self.logger.error("Exiting with error state 1")
return 1
self.logger.debug(
"Produced time slices: {0}".format(time_slices_path_list))
#***********************************************************
# 3. run rfi_concole: flag datapoints which are corrupted
self._run_rficonsole(rficonsole_executable, time_slice_dir,
time_slices_path_list)
#******************************************************************
# 4. Add imaging columns to each timeslice
# ndppp_executable fails if not present
for time_slice_path in time_slices_path_list:
pt.addImagingColumns(time_slice_path)
self.logger.debug(
"Added imaging columns to time_slice: {0}".format(
time_slice_path))
#*****************************************************************
# 5. Filter bad stations
time_slice_filtered_path_list = self._filter_bad_stations(
time_slices_path_list, asciistat_executable,
statplot_executable, msselect_executable)
#*****************************************************************
# Add measurmenttables
if add_beam_tables:
self.add_beam_tables(time_slice_filtered_path_list)
#******************************************************************
# 6. Perform the (virtual) concatenation of the timeslices
self._concat_timeslices(time_slice_filtered_path_list,
output_measurement_set)
#******************************************************************
# return
self.outputs["time_slices"] = \
time_slices_path_list
return 0
#!/usr/bin/env python # Script that adds imaging columns to a MS # # File: addImagingColumns.py # Author: Sven Duscha ([email protected]) # Date: 2011-02-14 # Last change: 2011-10-29 import sys try: import pyrap.tables as pt except ImportError: print "addImagingColumns.py: could not import pyrap.tables" print "WARN: No imaging columns added" sys.exit(1) if len(sys.argv) > 2: print "addImagingColumns.py: Too many arguments" sys.exit(1) elif len(sys.argv) == 1: print "addImagingColumns.py: No MS given" sys.exit(1) else: filename = sys.argv[1] # MS filename is by default first sys.argv pt.addImagingColumns(filename) # Add imaging columns sys.exit(0)
def run(self, environment, parset, working_dir, processed_ms_dir,
ndppp_executable, output_measurement_set, subbandgroups_per_ms,
subbands_per_subbandgroup, ms_mapfile, asciistat_executable,
statplot_executable, msselect_executable, rficonsole_executable,
add_beam_tables, globalfs, final_output_path):
"""
Entry point for the node recipe
"""
self.environment.update(environment)
self.globalfs = globalfs
with log_time(self.logger):
input_map = DataMap.load(ms_mapfile)
#******************************************************************
# I. Create the directories used in this recipe
create_directory(processed_ms_dir)
create_directory(working_dir)
# time slice dir_to_remove: assure empty directory: Stale data
# is problematic for dppp
time_slice_dir = os.path.join(working_dir, _time_slice_dir_name)
create_directory(time_slice_dir)
for root, dirs, files in os.walk(time_slice_dir):
for file_to_remove in files:
os.unlink(os.path.join(root, file_to_remove))
for dir_to_remove in dirs:
shutil.rmtree(os.path.join(root, dir_to_remove))
self.logger.debug("Created directory: {0}".format(time_slice_dir))
self.logger.debug("and assured it is empty")
#******************************************************************
# 1. Copy the input files
processed_ms_map = self._copy_input_files(processed_ms_dir,
input_map)
#******************************************************************
# 2. run dppp: collect frequencies into larger group
time_slices_path_list = \
self._run_dppp(working_dir, time_slice_dir,
subbandgroups_per_ms, processed_ms_map, subbands_per_subbandgroup,
processed_ms_dir, parset, ndppp_executable)
# If no timeslices were created, bail out with exit status 1
if len(time_slices_path_list) == 0:
self.logger.error("No timeslices were created.")
self.logger.error("Exiting with error state 1")
return 1
self.logger.debug(
"Produced time slices: {0}".format(time_slices_path_list))
#***********************************************************
# 3. run rfi_concole: flag datapoints which are corrupted
if False:
self._run_rficonsole(rficonsole_executable, time_slice_dir,
time_slices_path_list)
#******************************************************************
# 4. Add imaging columns to each timeslice
# ndppp_executable fails if not present
for time_slice_path in time_slices_path_list:
pt.addImagingColumns(time_slice_path)
self.logger.debug(
"Added imaging columns to time_slice: {0}".format(
time_slice_path))
#*****************************************************************
# 5. Filter bad stations
#if not(asciistat_executable == "" or
# statplot_executable == "" or
# msselect_executable == "" or True):
if False:
time_slice_filtered_path_list = self._filter_bad_stations(
time_slices_path_list, asciistat_executable,
statplot_executable, msselect_executable)
else:
# use the unfiltered list
time_slice_filtered_path_list = time_slices_path_list
#*****************************************************************
# 6. Add measurmenttables
if add_beam_tables:
self.add_beam_tables(time_slice_filtered_path_list)
#******************************************************************
# 7. Perform Convert polarization:
self._convert_polarization(time_slice_filtered_path_list)
#******************************************************************
# 8. Perform the (virtual) concatenation of the timeslices
self._concat_timeslices(time_slice_filtered_path_list,
output_measurement_set)
#*****************************************************************
# 9. Use table.copy(deep=true) to copy the ms to the correct
# output location: create a new measurement set.
self._deep_copy_to_output_location(output_measurement_set,
final_output_path)
# Write the actually used ms for the created dataset to the input
# mapfile
processed_ms_map.save(ms_mapfile)
#******************************************************************
# return
self.outputs["time_slices"] = \
time_slices_path_list
return 0
def run(self, environment, parset, working_dir, processed_ms_dir,
ndppp_executable, output_measurement_set,
subbandgroups_per_ms, subbands_per_subbandgroup, ms_mapfile,
asciistat_executable, statplot_executable, msselect_executable,
rficonsole_executable, add_beam_tables, globalfs, final_output_path):
"""
Entry point for the node recipe
"""
self.environment.update(environment)
self.globalfs = globalfs
with log_time(self.logger):
input_map = DataMap.load(ms_mapfile)
#******************************************************************
# I. Create the directories used in this recipe
create_directory(processed_ms_dir)
create_directory(working_dir)
create_directory(os.path.dirname(output_measurement_set))
create_directory(os.path.dirname(final_output_path))
# time slice dir_to_remove: assure empty directory: Stale data
# is problematic for dppp
time_slice_dir = os.path.join(working_dir, _time_slice_dir_name)
create_directory(time_slice_dir)
for root, dirs, files in os.walk(time_slice_dir):
for file_to_remove in files:
os.unlink(os.path.join(root, file_to_remove))
for dir_to_remove in dirs:
shutil.rmtree(os.path.join(root, dir_to_remove))
self.logger.debug("Created directory: {0}".format(time_slice_dir))
self.logger.debug("and assured it is empty")
#******************************************************************
# 1. Copy the input files
processed_ms_map = self._copy_input_files(
processed_ms_dir, input_map)
#******************************************************************
# 2. run dppp: collect frequencies into larger group
time_slices_path_list = \
self._run_dppp(working_dir, time_slice_dir,
subbandgroups_per_ms, processed_ms_map, subbands_per_subbandgroup,
processed_ms_dir, parset, ndppp_executable)
# If no timeslices were created, bail out with exit status 1
if len(time_slices_path_list) == 0:
self.logger.error("No timeslices were created.")
self.logger.error("Exiting with error state 1")
return 1
self.logger.debug(
"Produced time slices: {0}".format(time_slices_path_list))
#***********************************************************
# 3. run rfi_concole: flag datapoints which are corrupted
if False:
self._run_rficonsole(rficonsole_executable, time_slice_dir,
time_slices_path_list)
#******************************************************************
# 4. Add imaging columns to each timeslice
# ndppp_executable fails if not present
for time_slice_path in time_slices_path_list:
pt.addImagingColumns(time_slice_path)
self.logger.debug(
"Added imaging columns to time_slice: {0}".format(
time_slice_path))
#*****************************************************************
# 5. Filter bad stations
#if not(asciistat_executable == "" or
# statplot_executable == "" or
# msselect_executable == "" or True):
if False:
time_slice_filtered_path_list = self._filter_bad_stations(
time_slices_path_list, asciistat_executable,
statplot_executable, msselect_executable)
else:
# use the unfiltered list
time_slice_filtered_path_list = time_slices_path_list
#*****************************************************************
# 6. Add measurmenttables
if add_beam_tables:
self.add_beam_tables(time_slice_filtered_path_list)
#******************************************************************
# 7. Perform Convert polarization:
self._convert_polarization(time_slice_filtered_path_list)
#******************************************************************
# 8. Perform the (virtual) concatenation of the timeslices
self._concat_timeslices(time_slice_filtered_path_list,
output_measurement_set)
#*****************************************************************
# 9. Use table.copy(deep=true) to copy the ms to the correct
# output location: create a new measurement set.
self._deep_copy_to_output_location(output_measurement_set,
final_output_path)
# Write the actually used ms for the created dataset to the input
# mapfile
processed_ms_map.save(ms_mapfile)
#******************************************************************
# return
self.outputs["time_slices"] = \
time_slices_path_list
return 0
def run(self, environment, parset, working_dir, processed_ms_dir,
ndppp_executable, output_measurement_set,
time_slices_per_image, subbands_per_group, raw_ms_mapfile,
asciistat_executable, statplot_executable, msselect_executable,
rficonsole_executable, add_beam_tables):
"""
Entry point for the node recipe
"""
self.environment.update(environment)
with log_time(self.logger):
input_map = DataMap.load(raw_ms_mapfile)
#******************************************************************
# I. Create the directories used in this recipe
create_directory(processed_ms_dir)
# time slice dir_to_remove: assure empty directory: Stale data
# is problematic for dppp
time_slice_dir = os.path.join(working_dir, _time_slice_dir_name)
create_directory(time_slice_dir)
for root, dirs, files in os.walk(time_slice_dir):
for file_to_remove in files:
os.unlink(os.path.join(root, file_to_remove))
for dir_to_remove in dirs:
shutil.rmtree(os.path.join(root, dir_to_remove))
self.logger.debug("Created directory: {0}".format(time_slice_dir))
self.logger.debug("and assured it is empty")
#******************************************************************
# 1. Copy the input files
copied_ms_map = self._copy_input_files(
processed_ms_dir, input_map)
#******************************************************************
# 2. run dppp: collect frequencies into larger group
time_slices_path_list = \
self._run_dppp(working_dir, time_slice_dir,
time_slices_per_image, copied_ms_map, subbands_per_group,
processed_ms_dir, parset, ndppp_executable)
# If no timeslices were created, bail out with exit status 1
if len(time_slices_path_list) == 0:
self.logger.error("No timeslices were created.")
self.logger.error("Exiting with error state 1")
return 1
self.logger.debug(
"Produced time slices: {0}".format(time_slices_path_list))
#***********************************************************
# 3. run rfi_concole: flag datapoints which are corrupted
self._run_rficonsole(rficonsole_executable, time_slice_dir,
time_slices_path_list)
#******************************************************************
# 4. Add imaging columns to each timeslice
# ndppp_executable fails if not present
for time_slice_path in time_slices_path_list:
pt.addImagingColumns(time_slice_path)
self.logger.debug(
"Added imaging columns to time_slice: {0}".format(
time_slice_path))
#*****************************************************************
# 5. Filter bad stations
time_slice_filtered_path_list = self._filter_bad_stations(
time_slices_path_list, asciistat_executable,
statplot_executable, msselect_executable)
#*****************************************************************
# Add measurmenttables
if add_beam_tables:
self.add_beam_tables(time_slice_filtered_path_list)
#******************************************************************
# 6. Perform the (virtual) concatenation of the timeslices
self._concat_timeslices(time_slice_filtered_path_list,
output_measurement_set)
#******************************************************************
# return
self.outputs["time_slices"] = \
time_slices_path_list
return 0
for bandi in range(allms.shape[1]):
mergems = '{outmsroot}_BAND{ii:03d}.ms'.format(ii=bandi,
outmsroot=outmsroot)
if os.path.isdir(mergems):
if args.noclobber == False:
print('removing existing ms: ' + mergems)
os.system('rm -rf ' + mergems)
else:
print('ms ' + mergems +
' exists and noclobber is set True')
sys.exit()
print('concatenating in time')
print(mergems + ': ' + ','.join(allms[:, bandi]))
if not args.dryrun:
t = pt.table(allms[:, bandi])
t.sort('TIME,ANTENNA1,ANTENNA2').copy(mergems, deep=True)
print('concatenating done')
print('add imaging columns')
pt.addImagingColumns(mergems)
# remove the intermediate files unless asked to keep them
if not args.keepfiles:
for ms in allms[:, bandi]:
print('removing ' + ms)
os.system('rm -rf ' + ms)
def __init__(self, msname, slvr_cfg):
super(MeasurementSetManager, self).__init__()
self._msname = msname
# Create dictionary of tables
self._tables = { k: open_table(msname, k) for k in SUBTABLE_KEYS }
if not pt.tableexists(msname):
raise ValueError("'{ms}' does not exist "
"or is not a Measurement Set!".format(ms=msname))
# Add imaging columns, just in case
pt.addImagingColumns(msname, ack=False)
# Open the main measurement set
ms = open_table(msname)
# Access individual tables
ant, spec, ddesc, pol, field = (self._tables[k] for k in SUBTABLE_KEYS)
# Sanity check the polarizations
if pol.nrows() > 1:
raise ValueError("Multiple polarization configurations!")
self._npol = npol = pol.getcol('NUM_CORR')[0]
if npol != 4:
raise ValueError('Expected four polarizations')
# Number of channels per band
chan_per_band = spec.getcol('NUM_CHAN')
# Require the same number of channels per band
if not all(chan_per_band[0] == cpb for cpb in chan_per_band):
raise ValueError('Channels per band {cpb} are not equal!'
.format(cpb=chan_per_band))
if ddesc.nrows() != spec.nrows():
raise ValueError("DATA_DESCRIPTOR.nrows() "
"!= SPECTRAL_WINDOW.nrows()")
# Hard code auto-correlations and field_id 0
self._auto_correlations = auto_correlations = slvr_cfg['auto_correlations']
self._field_id = field_id = 0
# Create a view over the MS, ordered by
# (1) time (TIME)
# (2) baseline (ANTENNA1, ANTENNA2)
# (3) band (SPECTRAL_WINDOW_ID via DATA_DESC_ID)
ordering_query = " ".join((
"SELECT FROM $ms",
"WHERE FIELD_ID={fid}".format(fid=field_id),
"" if auto_correlations else "AND ANTENNA1 != ANTENNA2",
orderby_clause(MS_DIM_ORDER)
))
# Ordered Measurement Set
oms = pt.taql(ordering_query)
montblanc.log.debug("MS ordering query is '{o}'."
.format(o=ordering_query))
# Measurement Set ordered by unique time and baseline
otblms = pt.taql("SELECT FROM $oms {c}".format(
c=orderby_clause(UVW_DIM_ORDER, unique=True)))
# Store the main table
self._tables[MAIN_TABLE] = ms
self._tables[ORDERED_MAIN_TABLE] = oms
self._tables[ORDERED_UVW_TABLE] = otblms
self._column_descriptors = {col: ms.getcoldesc(col) for col in SELECTED}
# Count distinct timesteps in the MS
t_orderby = orderby_clause(['ntime'], unique=True)
t_query = "SELECT FROM $otblms {c}".format(c=t_orderby)
self._tables[ORDERED_TIME_TABLE] = ot = pt.taql(t_query)
self._ntime = ntime = ot.nrows()
# Count number of baselines in the MS
bl_orderby = orderby_clause(['nbl'], unique=True)
bl_query = "SELECT FROM $otblms {c}".format(c=bl_orderby)
self._tables[ORDERED_BASELINE_TABLE] = obl = pt.taql(bl_query)
self._nbl = nbl = obl.nrows()
# Number of channels per band
self._nchanperband = chan_per_band[0]
self._nchan = nchan = sum(chan_per_band)
self._nbands = nbands = len(chan_per_band)
self._npolchan = npolchan = npol*nchan
self._nvis = nvis = ntime*nbl*nchan
# Update the cube with dimension information
# obtained from the MS
updated_sizes = [ntime, nbl, ant.nrows(),
sum(chan_per_band), len(chan_per_band), npol,
npolchan, nvis]
self._dim_sizes = dim_sizes = { dim: size for dim, size
in zip(UPDATE_DIMENSIONS, updated_sizes) }
shape = tuple(dim_sizes[d] for d in MS_DIM_ORDER)
expected_rows = np.product(shape)
if not expected_rows == oms.nrows():
dim_desc = ", ".join('(%s,%s)' % (d, s) for
d, s in zip(MS_DIM_ORDER, shape))
row_desc = " x ".join('%s' % s for s in shape)
montblanc.log.warn("Encountered '{msr}' rows in '{ms}' "
"but expected '{rd} = {er}' after finding the following "
"dimensions by inspection: [{d}]. Irregular Measurement Sets "
"are not fully supported due to the generality of the format.".format(
msr=oms.nrows(), ms=msname,
er=expected_rows, rd=row_desc, d=dim_desc))