def _run_rficonsole(self, rficonsole_executable, time_slice_dir,
time_slices):
"""
_run_rficonsole runs the rficonsole application on the supplied
timeslices in time_slices.
"""
# loop all measurement sets
rfi_temp_dir = os.path.join(time_slice_dir, "rfi_temp_dir")
create_directory(rfi_temp_dir)
try:
rfi_console_proc_group = SubProcessGroup(self.logger)
for time_slice in time_slices:
# Each rfi console needs own working space for temp files
temp_slice_path = os.path.join(rfi_temp_dir,
os.path.basename(time_slice))
create_directory(temp_slice_path)
# construct copy command
self.logger.info(time_slice)
command = [rficonsole_executable, "-indirect-read", time_slice]
self.logger.info("executing rficonsole command: {0}".format(
" ".join(command)))
# Add the command to the process group
rfi_console_proc_group.run(command, cwd=temp_slice_path)
# wait for all to finish
if rfi_console_proc_group.wait_for_finish() != None:
raise Exception("an rfi_console_proc_group run failed!")
finally:
shutil.rmtree(rfi_temp_dir)
def _write_datamap_to_file(self, datamap, mapfile_name, message = ""):
"""
Write the suplied the suplied map to the mapfile.
directory in the jobs dir with the filename suplied in mapfile_name.
Return the full path to the created file.
If suplied data is None then the file is touched if not existing, but
existing files are kept as is
"""
mapfile_dir = os.path.join(
self.config.get("layout", "job_directory"), "mapfiles")
# create the mapfile_dir if it does not exist
create_directory(mapfile_dir)
# write the content to a new parset file
mapfile_path = os.path.join(mapfile_dir,
"{0}.map".format(mapfile_name))
# display a debug log entrie with path and message
if datamap != None:
datamap.save(mapfile_path)
self.logger.debug(
"Wrote mapfile <{0}>: {1}".format(mapfile_path, message))
else:
if not os.path.exists(mapfile_path):
DataMap().save(mapfile_path)
self.logger.debug(
"Touched mapfile <{0}>: {1}".format(mapfile_path, message))
return mapfile_path
def _write_datamap_to_file(self, datamap, mapfile_name, message=""):
"""
Write the suplied the suplied map to the mapfile.
directory in the jobs dir with the filename suplied in mapfile_name.
Return the full path to the created file.
If suplied data is None then the file is touched if not existing, but
existing files are kept as is
"""
mapfile_dir = os.path.join(self.config.get("layout", "job_directory"),
"mapfiles")
# create the mapfile_dir if it does not exist
create_directory(mapfile_dir)
# write the content to a new parset file
mapfile_path = os.path.join(mapfile_dir,
"{0}.map".format(mapfile_name))
# display a debug log entrie with path and message
if datamap != None:
datamap.save(mapfile_path)
self.logger.debug("Wrote mapfile <{0}>: {1}".format(
mapfile_path, message))
else:
if not os.path.exists(mapfile_path):
DataMap().save(mapfile_path)
self.logger.debug("Touched mapfile <{0}>: {1}".format(
mapfile_path, message))
return mapfile_path
def _prepare_steps(self, **kwargs):
"""
Prepare for running the NDPPP program. This means, for one thing,
patching the parsetfile with the correct input/output MS names,
start/end times if availabe, etc. If a demixing step must be performed,
some extra work needs to be done.
Returns: patch dictionary that must be applied to the parset.
"""
self.logger.debug("Time interval: %s %s" %
(kwargs['start_time'], kwargs['end_time']))
# Create output directory for output MS.
create_directory(os.path.dirname(kwargs['tmpfile']))
patch_dictionary = {
'msin': kwargs['infile'],
'msout': kwargs['tmpfile'],
'uselogger': 'True'
}
if kwargs['start_time']:
patch_dictionary['msin.starttime'] = kwargs['start_time']
if kwargs['end_time']:
patch_dictionary['msin.endtime'] = kwargs['end_time']
# If we need to do a demixing step, we have to do some extra work.
# We have to read the parsetfile to check this.
parset = parameterset(kwargs['parsetfile'])
for step in parset.getStringVector('steps'):
if parset.getString(step + '.type', '').startswith('demix'):
patch_dictionary.update(
self._prepare_demix_step(step, **kwargs))
# Return the patch dictionary that must be applied to the parset.
return patch_dictionary
def run(self, infile, outfile, executable, environment, sigma,
use_parmexportcal):
self.environment.update(environment)
if os.path.exists(infile):
self.logger.info("Processing {0}".format(infile))
else:
self.logger.error(
"Instrument model file %s does not exist" % infile
)
return 1
# Create output directory (if it doesn't already exist)
create_directory(os.path.dirname(outfile))
# Remove the target outfile if there: parexportcall fail otherwise
if os.path.exists(outfile):
shutil.rmtree(outfile)
# ********************************************************************
# 1. Select correction method
if not use_parmexportcal:
# ****************************************************************
# 3. use gainoutliercorrect from Swinbank
self.logger.info(
"Using the gainoutlier correction based on editparmdb")
self._filter_stations_parmdb(infile, outfile, sigma)
return 0
# else:
if not os.access(executable, os.X_OK):
self.logger.error(
"Could not find parmexport call executable at: {0}".format(
executable))
self.logger.error("bailing out!")
return 1
# ********************************************************************
# 2. Call parmexportcal for gain correction
self.logger.info(
"Using the gainoutlier correction based on parmexportcal")
try:
temp_dir = tempfile.mkdtemp()
with CatchLog4CPlus(
temp_dir,
self.logger.name + '.' + os.path.basename(infile),
os.path.basename(executable)
) as logger:
cmd = [executable, '-in', infile, '-out', outfile]
self.logger.debug(
"Parmexportcal call: {0} ".format(" ".join(cmd)))
catch_segfaults(
cmd,
temp_dir,
self.environment,
logger
)
except Exception, excp:
self.logger.error(str(excp))
return 1
def run(self, infile, outfile, executable, environment, sigma,
use_parmexportcal):
self.environment.update(environment)
if os.path.exists(infile):
self.logger.info("Processing {0}".format(infile))
else:
self.logger.error(
"Instrument model file %s does not exist" % infile
)
return 1
# Create output directory (if it doesn't already exist)
create_directory(os.path.dirname(outfile))
# Remove the target outfile if there: parexportcall fail otherwise
if os.path.exists(outfile):
shutil.rmtree(outfile)
# ********************************************************************
# 1. Select correction method
if not use_parmexportcal:
# ****************************************************************
# 3. use gainoutliercorrect from Swinbank
self.logger.info(
"Using the gainoutlier correction based on editparmdb")
self._filter_stations_parmdb(infile, outfile, sigma)
return 0
# else:
if not os.access(executable, os.X_OK):
self.logger.error(
"Could not find parmexport call executable at: {0}".format(
executable))
self.logger.error("bailing out!")
return 1
# ********************************************************************
# 2. Call parmexportcal for gain correction
self.logger.info(
"Using the gainoutlier correction based on parmexportcal")
try:
temp_dir = tempfile.mkdtemp(suffix=".%s" % (os.path.basename(__file__),))
with CatchLog4CPlus(
temp_dir,
self.logger.name + '.' + os.path.basename(infile),
os.path.basename(executable)
) as logger:
cmd = [executable, '-in', infile, '-out', outfile]
self.logger.debug(
"Parmexportcal call: {0} ".format(" ".join(cmd)))
catch_segfaults(
cmd,
temp_dir,
self.environment,
logger
)
except Exception, excp:
self.logger.error(str(excp))
return 1
def test_filter_stations_parmdb(self):
file_path_in = os.path.join(self.tempDir, "input")
create_directory(file_path_in)
file_path_out = os.path.join(self.tempDir, "fullName")
GainOutlierDetection = GainOutlierCorrectionWrapper()
# Call the major function
# No errors should be thrown...
parmdb = GainOutlierDetection._filter_stations_parmdb(file_path_in,
file_path_out, 2)
def test_filter_stations_parmdb(self):
file_path_in = os.path.join(self.tempDir, "input")
create_directory(file_path_in)
file_path_out = os.path.join(self.tempDir, "fullName")
GainOutlierDetection = GainOutlierCorrectionWrapper()
# Call the major function
# No errors should be thrown...
parmdb = GainOutlierDetection._filter_stations_parmdb(
file_path_in, file_path_out, 2)
def _copy_single_file_using_rsync(self, source_node, source_path,
target_path):
# assure that target dir exists (rsync creates it but..
# an error in the python code will throw a nicer error
message = "No write acces to target path: {0}".format(
os.path.dirname(target_path))
# If not existing try to create dir catch no permission
try:
create_directory(os.path.dirname(target_path))
except OSError, e:
if e.errno == 13: # No permision
self.logger.error(message)
raise IOError(message)
else:
raise e
def _copy_single_file_using_rsync(self, source_node, source_path,
target_path):
# assure that target dir exists (rsync creates it but..
# an error in the python code will throw a nicer error
message = "No write acces to target path: {0}".format(
os.path.dirname(target_path))
# If not existing try to create dir catch no permission
try:
create_directory(os.path.dirname(target_path))
except OSError, e:
if e.errno == 13: # No permision
self.logger.error(message)
raise IOError(message)
else:
raise e
def run(self, concatenated_measurement_set, sourcedb_target_path,
monet_db_hostname, monet_db_port, monet_db_name, monet_db_user,
monet_db_password, assoc_theta, parmdb_executable, slice_paths,
parmdb_suffix, environment, working_directory, makesourcedb_path,
source_list_path_extern, major_cycle):
self.logger.info("Starting imager_create_dbs Node")
self.environment.update(environment)
#******************************************************************
# 0. Create the directories used in this recipe
create_directory(working_directory)
#*******************************************************************
# 1. get a sourcelist: from gsm or from file
source_list, append = self._create_source_list(
source_list_path_extern,sourcedb_target_path,
concatenated_measurement_set,monet_db_hostname,
monet_db_port, monet_db_name, monet_db_user,
monet_db_password, assoc_theta)
#*******************************************************************
# 2convert it to a sourcedb (casa table)
if self._create_source_db(source_list, sourcedb_target_path,
working_directory, makesourcedb_path,
append) == None:
self.logger.error("failed creating sourcedb")
return 1
#*******************************************************************
# 3. Create a empty parmdb for each timeslice\
parmdbs = self._create_parmdb_for_timeslices(parmdb_executable,
slice_paths, parmdb_suffix)
if parmdbs == None:
self.logger.error("failed creating paramdb for slices")
return 1
# *******************************************************************
# Add the create databases to the measurments set,
self._add_dbs_to_ms(concatenated_measurement_set, sourcedb_target_path,
parmdbs, major_cycle)
#*******************************************************************
# 5. Assign the outputs
self.outputs["sourcedb"] = sourcedb_target_path
self.outputs["parmdbs"] = parmdbs
return 0
def copy(path_from, dir_to, clobber, use_symlinks=False):
"""
Copy a file or directory
Parameters
----------
path_from : str
Input file or directory
dir_to : str
Output directory
clobber : bool
Clobber existing file or directory?
use_symlinks : bool, optional
Use symlinks instead of copying files?
"""
if not os.path.exists(path_from):
log.warning('{} not found. Please check the '
'working directory'.format(path_from))
return
path_to = os.path.join(dir_to, os.path.basename(path_from))
if os.path.exists(path_to):
if not clobber:
log.warning(' Destination "{}" exists and clobber = False. '
'Skipping it...'.format(path_to))
return
else:
create_directory(dir_to)
if use_symlinks:
if os.path.exists(path_to):
p = subprocess.Popen('rm -rf {0}'.format(path_to),
shell=True,
stdout=subprocess.PIPE)
r = p.communicate()
os.symlink(path_from, path_to)
else:
p = subprocess.Popen('rsync -a {0} {1}'.format(path_from, dir_to),
shell=True,
stdout=subprocess.PIPE)
r = p.communicate()
if p.returncode != 0:
log.critical(
'rsync exited abnormally when attempting to archive {}'.format(
path_from))
sys.exit(1)
def run(self, concatenated_measurement_set, sourcedb_target_path,
monet_db_hostname, monet_db_port, monet_db_name, monet_db_user,
monet_db_password, assoc_theta, parmdb_executable, slice_paths,
parmdb_suffix, environment, working_directory, makesourcedb_path,
source_list_path_extern, major_cycle):
self.logger.info("Starting imager_create_dbs Node")
self.environment.update(environment)
#******************************************************************
# 0. Create the directories used in this recipe
create_directory(working_directory)
#*******************************************************************
# 1. get a sourcelist: from gsm or from file
source_list, append = self._create_source_list(
source_list_path_extern, sourcedb_target_path,
concatenated_measurement_set, monet_db_hostname, monet_db_port,
monet_db_name, monet_db_user, monet_db_password, assoc_theta)
#*******************************************************************
# 2convert it to a sourcedb (casa table)
if self._create_source_db(source_list, sourcedb_target_path,
working_directory, makesourcedb_path,
append) == None:
self.logger.error("failed creating sourcedb")
return 1
#*******************************************************************
# 3. Create a empty parmdb for each timeslice\
parmdbs = self._create_parmdb_for_timeslices(parmdb_executable,
slice_paths,
parmdb_suffix)
if parmdbs == None:
self.logger.error("failed creating paramdb for slices")
return 1
# *******************************************************************
# Add the create databases to the measurments set,
self._add_dbs_to_ms(concatenated_measurement_set, sourcedb_target_path,
parmdbs, major_cycle)
#*******************************************************************
# 5. Assign the outputs
self.outputs["sourcedb"] = sourcedb_target_path
self.outputs["parmdbs"] = parmdbs
return 0
def test__create_parmdb_missing_exec(self):
"""
Test the correct functioning of the create parmdbs function
"""
path_to_create = os.path.join(self.test_path, "testParmdb")
create_directory(path_to_create)
parmdb_output = os.path.join(path_to_create, "parmdbs")
parmdb_executable = "/opt/cep/LofIm/daily/lofar/bin/incorrectExecutable"
self.assertTrue(1 == self.imager_create_dbs._create_parmdb(parmdb_executable,
parmdb_output),
self.imager_create_dbs.logger.last())
self.assertFalse(os.path.exists(parmdb_output), "target dir to be"
"created by parmdb does exist, while it should not")
shutil.rmtree(path_to_create)
def copy(path_from, dir_to, clobber, use_symlinks=False):
"""
Copy a file or directory
Parameters
----------
path_from : str
Input file or directory
dir_to : str
Output directory
clobber : bool
Clobber existing file or directory?
use_symlinks : bool, optional
Use symlinks instead of copying files?
"""
if not os.path.exists(path_from):
log.warning('{} not found. Please check the '
'working directory'.format(path_from))
return
path_to = os.path.join(dir_to, os.path.basename(path_from))
if os.path.exists(path_to):
if not clobber:
log.warning(' Destination "{}" exists and clobber = False. '
'Skipping it...'.format(path_to))
return
else:
create_directory(dir_to)
if use_symlinks:
if os.path.exists(path_to):
p = subprocess.Popen('rm -rf {0}'.format(path_to), shell=True,
stdout=subprocess.PIPE)
r = p.communicate()
os.symlink(path_from, path_to)
else:
p = subprocess.Popen('rsync -a {0} {1}'.format(path_from, dir_to),
shell=True, stdout=subprocess.PIPE)
r = p.communicate()
if p.returncode != 0:
log.critical('rsync exited abnormally when attempting to archive {}'.format(path_from))
sys.exit(1)
def _save_active_mapfiles(self, cycle_idx, mapfile_dir, mapfiles = {}):
"""
receives a dict with active mapfiles, var name to path
Each mapfile is copier to a seperate directory and saved
THis allows us to exit the last succesfull run
"""
# create a directory for storing the saved mapfiles, use cycle idx
mapfile_for_cycle_dir = os.path.join(mapfile_dir, "cycle_" + str(cycle_idx))
create_directory(mapfile_for_cycle_dir)
saved_mapfiles = {}
for (var_name,mapfile_path) in list(mapfiles.items()):
shutil.copy(mapfile_path, mapfile_for_cycle_dir)
# save the newly created file, get the filename, and append it
# to the directory name
saved_mapfiles[var_name] = os.path.join(mapfile_for_cycle_dir,
os.path.basename(mapfile_path))
return saved_mapfiles
def test__create_parmdb_missing_exec(self):
"""
Test the correct functioning of the create parmdbs function
"""
path_to_create = os.path.join(self.test_path, "testParmdb")
create_directory(path_to_create)
parmdb_output = os.path.join(path_to_create, "parmdbs")
parmdb_executable = "/opt/cep/LofIm/daily/lofar/bin/incorrectExecutable"
self.assertTrue(
1 == self.imager_create_dbs._create_parmdb(parmdb_executable,
parmdb_output),
self.imager_create_dbs.logger.last())
self.assertFalse(
os.path.exists(parmdb_output), "target dir to be"
"created by parmdb does exist, while it should not")
shutil.rmtree(path_to_create)
def _write_parset_to_file(self, parset, parset_name, message):
"""
Write the suplied the suplied parameterset to the parameter set
directory in the jobs dir with the filename suplied in parset_name.
Return the full path to the created file.
"""
parset_dir = os.path.join(self.config.get("layout", "job_directory"),
"parsets")
# create the parset dir if it does not exist
create_directory(parset_dir)
# write the content to a new parset file
parset_path = os.path.join(parset_dir,
"{0}.parset".format(parset_name))
parset.writeFile(parset_path)
# display a debug log entrie with path and message
self.logger.debug("Wrote parset to path <{0}> : {1}".format(
parset_path, message))
return parset_path
def _write_parset_to_file(self, parset, parset_name, message):
"""
Write the suplied the suplied parameterset to the parameter set
directory in the jobs dir with the filename suplied in parset_name.
Return the full path to the created file.
"""
parset_dir = os.path.join(
self.config.get("layout", "job_directory"), "parsets")
# create the parset dir if it does not exist
create_directory(parset_dir)
# write the content to a new parset file
parset_path = os.path.join(parset_dir,
"{0}.parset".format(parset_name))
parset.writeFile(parset_path)
# display a debug log entrie with path and message
self.logger.debug("Wrote parset to path <{0}> : {1}".format(
parset_path, message))
return parset_path
def go(self):
self.logger.info("Starting CEP-II datamapper run")
super(cep2_datamapper, self).go()
if self.inputs['parset']:
datamap = self._read_files()
elif self.inputs['observation_dir']:
datamap = self._search_files()
else:
self.logger.error("Either observation_dir or parset must be given")
return 1
self.logger.info("Found %i datasets to process." % len(datamap))
self.logger.debug("datamap = %s" % datamap)
# Write datamap-file
create_directory(os.path.dirname(self.inputs['mapfile']))
store_data_map(self.inputs['mapfile'], datamap)
self.logger.debug("Wrote mapfile: %s" % self.inputs['mapfile'])
self.outputs['mapfile'] = self.inputs['mapfile']
return 0
def test__create_parmdb_for_timeslices_except(self):
"""
Test the errorous functioning of the _create_parmdb_for_timeslices
with missing executable should return 1 and no created directories
"""
path_to_create = os.path.join(self.test_path, "testParmdb")
parmdb_ms_output = os.path.join(path_to_create, "parmdbs")
create_directory(parmdb_ms_output)
parmdb_executable = "/opt/cep/LofIm/daily/lofar/bin/missingExcecutable"
#Create a number of paths to supply to the create function
ms_paths = []
for idx in range(5):
ms_paths.append(os.path.join(parmdb_ms_output, str(idx)))
self.assertTrue(
self.imager_create_dbs._create_parmdb_for_timeslices(
parmdb_executable, ms_paths, ".parmdb") == None,
self.imager_create_dbs.logger.last())
final_ms_path = os.path.join(parmdb_ms_output,
"time_slice_8.dppp.ms.parmdb")
self.assertFalse(os.path.exists(final_ms_path))
def test__create_parmdb_for_timeslices_except(self):
"""
Test the errorous functioning of the _create_parmdb_for_timeslices
with missing executable should return 1 and no created directories
"""
path_to_create = os.path.join(self.test_path, "testParmdb")
parmdb_ms_output = os.path.join(path_to_create, "parmdbs")
create_directory(parmdb_ms_output)
parmdb_executable = "/opt/cep/LofIm/daily/lofar/bin/missingExcecutable"
#Create a number of paths to supply to the create function
ms_paths = []
for idx in range(5):
ms_paths.append(os.path.join(parmdb_ms_output, str(idx)))
self.assertTrue(
self.imager_create_dbs._create_parmdb_for_timeslices(parmdb_executable,
ms_paths, ".parmdb") == None,
self.imager_create_dbs.logger.last())
final_ms_path = os.path.join(parmdb_ms_output, "time_slice_8.dppp.ms.parmdb")
self.assertFalse(os.path.exists(final_ms_path))
def go(self):
self.logger.info("Starting CEP-II datamapper run")
super(cep2_datamapper, self).go()
if self.inputs['parset']:
datamap = self._read_files()
elif self.inputs['observation_dir']:
datamap = self._search_files()
else:
self.logger.error("Either observation_dir or parset must be given")
return 1
self.logger.info("Found %i datasets to process." % len(datamap))
self.logger.debug("datamap = %s" % datamap)
# Write datamap-file
create_directory(os.path.dirname(self.inputs['mapfile']))
store_data_map(self.inputs['mapfile'], datamap)
self.logger.debug("Wrote mapfile: %s" % self.inputs['mapfile'])
self.outputs['mapfile'] = self.inputs['mapfile']
return 0
def run_rficonsole(rficonsole_executable, temp_dir,
input_ms_list, logger, resourceMonitor):
"""
_run_rficonsole runs the rficonsole application on the supplied
timeslices in time_slices.
This functionality has also been implemented in BBS.
"""
# loop all measurement sets
rfi_temp_dir = os.path.join(temp_dir, "rfi_temp_dir")
create_directory(rfi_temp_dir)
try:
rfi_console_proc_group = SubProcessGroup(logger=logger,
usageStats=resourceMonitor)
for time_slice in input_ms_list:
# Each rfi console needs own working space for temp files
temp_slice_path = os.path.join(rfi_temp_dir,
os.path.basename(time_slice))
create_directory(temp_slice_path)
# construct copy command
logger.info(time_slice)
command = [rficonsole_executable, "-indirect-read",
time_slice]
logger.info("executing rficonsole command: {0}".format(
" ".join(command)))
# Add the command to the process group
rfi_console_proc_group.run(command, cwd = temp_slice_path)
# wait for all to finish
if rfi_console_proc_group.wait_for_finish() != None:
raise Exception("an rfi_console_proc_group run failed!")
finally:
shutil.rmtree(rfi_temp_dir)
def go(self):
self.logger.info("Starting storagemapper run")
super(storagemapper, self).go()
# We read the storage node name out of the path
# and append the local filename (ie, on the storage node) to the map
# ----------------------------------------------------------------------
data = defaultdict(list)
for filename in self.inputs['args']:
host = filename.split(os.path.sep)[3]
data[host].append(filename.split(host)[-1])
# Dump the generated mapping to a parset
# ----------------------------------------------------------------------
parset = Parset()
for host, filenames in data.iteritems():
parset.addStringVector(host, filenames)
create_directory(os.path.dirname(self.inputs['mapfile']))
parset.writeFile(self.inputs['mapfile'])
self.outputs['mapfile'] = self.inputs['mapfile']
return 0
def go(self):
self.logger.info("Starting storagemapper run")
super(storagemapper, self).go()
# We read the storage node name out of the path
# and append the local filename (ie, on the storage node) to the map
# ----------------------------------------------------------------------
data = defaultdict(list)
for filename in self.inputs['args']:
host = filename.split(os.path.sep)[3]
data[host].append(filename.split(host)[-1])
# Dump the generated mapping to a parset
# ----------------------------------------------------------------------
parset = Parset()
for host, filenames in data.iteritems():
parset.addStringVector(host, filenames)
create_directory(os.path.dirname(self.inputs['mapfile']))
parset.writeFile(self.inputs['mapfile'])
self.outputs['mapfile'] = self.inputs['mapfile']
return 0
def _copy_instrument_files(self, mapfile_dir):
# For the copy recipe a target mapfile is needed
# create target map based on the node and the dir in the input data map
# with the filename based on the
copier_map_path = os.path.join(mapfile_dir, "copier")
create_directory(copier_map_path)
target_map = self._create_target_map_for_instruments()
#Write the two needed maps to file
source_path = os.path.join(copier_map_path, "source_instruments.map")
self.input_data['instrument'].save(source_path)
target_path = os.path.join(copier_map_path, "target_instruments.map")
target_map.save(target_path)
copied_files_path = os.path.join(copier_map_path, "copied_instruments.map")
# The output of the copier is a mapfile containing all the host, path
# of succesfull copied files.
copied_instruments_mapfile = self.run_task("copier",
mapfile_source=source_path,
mapfile_target=target_path,
mapfiles_dir=copier_map_path,
mapfile=copied_files_path,
allow_move=False)['mapfile_target_copied']
# Some copy action might fail; the skip fields in the other map-files
# need to be updated these to reflect this.
self.input_data['instrument'] = DataMap.load(copied_instruments_mapfile)
for data, inst, outp in zip(
self.input_data['data'],
self.input_data['instrument'],
self.output_data['data']
):
data.skip = inst.skip = outp.skip = (
data.skip or inst.skip or outp.skip
)
def _copy_instrument_files(self, mapfile_dir):
# For the copy recipe a target mapfile is needed
# create target map based on the node and the dir in the input data map
# with the filename based on the
copier_map_path = os.path.join(mapfile_dir, "copier")
create_directory(copier_map_path)
target_map = self._create_target_map_for_instruments()
#Write the two needed maps to file
source_path = os.path.join(copier_map_path, "source_instruments.map")
self.input_data['instrument'].save(source_path)
target_path = os.path.join(copier_map_path, "target_instruments.map")
target_map.save(target_path)
copied_files_path = os.path.join(copier_map_path, "copied_instruments.map")
# The output of the copier is a mapfile containing all the host, path
# of succesfull copied files.
copied_instruments_mapfile = self.run_task("copier",
mapfile_source=source_path,
mapfile_target=target_path,
mapfiles_dir=copier_map_path,
mapfile=copied_files_path,
allow_move=False)['mapfile_target_copied']
# Some copy action might fail; the skip fields in the other map-files
# need to be updated these to reflect this.
self.input_data['instrument'] = DataMap.load(copied_instruments_mapfile)
for data, inst, outp in zip(
self.input_data['data'],
self.input_data['instrument'],
self.output_data['data']
):
data.skip = inst.skip = outp.skip = (
data.skip or inst.skip or outp.skip
)
def run_rficonsole(rficonsole_executable, temp_dir, input_ms_list, logger,
resourceMonitor):
"""
_run_rficonsole runs the rficonsole application on the supplied
timeslices in time_slices.
This functionality has also been implemented in BBS.
"""
# loop all measurement sets
rfi_temp_dir = os.path.join(temp_dir, "rfi_temp_dir")
create_directory(rfi_temp_dir)
try:
rfi_console_proc_group = SubProcessGroup(logger=logger,
usageStats=resourceMonitor)
for time_slice in input_ms_list:
# Each rfi console needs own working space for temp files
temp_slice_path = os.path.join(rfi_temp_dir,
os.path.basename(time_slice))
create_directory(temp_slice_path)
# construct copy command
logger.info(time_slice)
command = [rficonsole_executable, "-indirect-read", time_slice]
logger.info("executing rficonsole command: {0}".format(
" ".join(command)))
# Add the command to the process group
rfi_console_proc_group.run(command, cwd=temp_slice_path)
# wait for all to finish
if rfi_console_proc_group.wait_for_finish() != None:
raise Exception("an rfi_console_proc_group run failed!")
finally:
shutil.rmtree(rfi_temp_dir)
def _run_rficonsole(self, rficonsole_executable, time_slice_dir,
time_slices):
"""
_run_rficonsole runs the rficonsole application on the supplied
timeslices in time_slices.
"""
# loop all measurement sets
rfi_temp_dir = os.path.join(time_slice_dir, "rfi_temp_dir")
create_directory(rfi_temp_dir)
try:
rfi_console_proc_group = SubProcessGroup(self.logger)
for time_slice in time_slices:
# Each rfi console needs own working space for temp files
temp_slice_path = os.path.join(rfi_temp_dir,
os.path.basename(time_slice))
create_directory(temp_slice_path)
# construct copy command
self.logger.info(time_slice)
command = [rficonsole_executable, "-indirect-read",
time_slice]
self.logger.info("executing rficonsole command: {0}".format(
" ".join(command)))
# Add the command to the process group
rfi_console_proc_group.run(command, cwd = temp_slice_path)
# wait for all to finish
if rfi_console_proc_group.wait_for_finish() != None:
raise Exception("an rfi_console_proc_group run failed!")
finally:
shutil.rmtree(rfi_temp_dir)
def _prepare_steps(self, **kwargs):
"""
Prepare for running the NDPPP program. This means, for one thing,
patching the parsetfile with the correct input/output MS names,
start/end times if availabe, etc. If a demixing step must be performed,
some extra work needs to be done.
Returns: patch dictionary that must be applied to the parset.
"""
self.logger.debug(
"Time interval: %s %s" % (kwargs['start_time'], kwargs['end_time'])
)
# Create output directory for output MS.
create_directory(os.path.dirname(kwargs['tmpfile']))
patch_dictionary = {
'msin': kwargs['infile'],
'msout': kwargs['tmpfile'],
'uselogger': 'True'
}
if kwargs['start_time']:
patch_dictionary['msin.starttime'] = kwargs['start_time']
if kwargs['end_time']:
patch_dictionary['msin.endtime'] = kwargs['end_time']
# If we need to do a demixing step, we have to do some extra work.
# We have to read the parsetfile to check this.
parset = parameterset(kwargs['parsetfile'])
for step in parset.getStringVector('steps'):
if parset.getString(step + '.type', '').startswith('demix'):
patch_dictionary.update(
self._prepare_demix_step(step, **kwargs)
)
# Return the patch dictionary that must be applied to the parset.
return patch_dictionary
def pipeline_logic(self):
"""
Define the individual tasks that comprise the current pipeline.
This method will be invoked by the base-class's `go()` method.
"""
# *********************************************************************
# 1. Prepare phase, collect data from parset and input mapfiles.
py_parset = self.parset.makeSubset(
self.parset.fullModuleName('PythonControl') + '.')
# Get input/output-data products specifications.
self._get_io_product_specs()
job_dir = self.config.get("layout", "job_directory")
parset_dir = os.path.join(job_dir, "parsets")
mapfile_dir = os.path.join(job_dir, "mapfiles")
# Create directories for temporary parset- and map files
create_directory(parset_dir)
create_directory(mapfile_dir)
# Write input- and output data map-files
input_data_mapfile = os.path.join(mapfile_dir, "input_data.mapfile")
self.input_data.save(input_data_mapfile)
output_data_mapfile = os.path.join(mapfile_dir, "output_data.mapfile")
self.output_data.save(output_data_mapfile)
if len(self.input_data) == 0:
self.logger.warn("No input data files to process. Bailing out!")
return 0
self.logger.debug("Processing: %s" %
', '.join(str(f) for f in self.input_data))
# *********************************************************************
# 2. Create VDS-file and databases. The latter are needed when doing
# demixing within DPPP.
with duration(self, "vdsmaker"):
gvds_file = self.run_task("vdsmaker", input_data_mapfile)['gvds']
# Read metadata (start, end times, pointing direction) from GVDS.
with duration(self, "vdsreader"):
vdsinfo = self.run_task("vdsreader", gvds=gvds_file)
# Create a parameter database that will be used by the NDPPP demixing
with duration(self, "setupparmdb"):
parmdb_mapfile = self.run_task(
"setupparmdb", input_data_mapfile,
mapfile=os.path.join(mapfile_dir, 'dppp.parmdb.mapfile'),
suffix='.dppp.parmdb'
)['mapfile']
# Create a source database from a user-supplied sky model
# The user-supplied sky model can either be a name, in which case the
# pipeline will search for a file <name>.skymodel in the default search
# path $LOFARROOT/share/pipeline/skymodels; or a full path.
# It is an error if the file does not exist.
skymodel = py_parset.getString('PreProcessing.SkyModel')
if not os.path.isabs(skymodel):
skymodel = os.path.join(
# This should really become os.environ['LOFARROOT']
self.config.get('DEFAULT', 'lofarroot'),
'share', 'pipeline', 'skymodels', skymodel + '.skymodel'
)
if not os.path.isfile(skymodel):
raise PipelineException("Skymodel %s does not exist" % skymodel)
with duration(self, "setupsourcedb"):
sourcedb_mapfile = self.run_task(
"setupsourcedb", input_data_mapfile,
mapfile=os.path.join(mapfile_dir, 'dppp.sourcedb.mapfile'),
skymodel=skymodel,
suffix='.dppp.sourcedb',
type='blob'
)['mapfile']
# *********************************************************************
# 3. Average and flag data, using NDPPP.
ndppp_parset = os.path.join(parset_dir, "NDPPP.parset")
py_parset.makeSubset('DPPP.').writeFile(ndppp_parset)
# Run the Default Pre-Processing Pipeline (DPPP);
with duration(self, "ndppp"):
self.run_task("ndppp",
(input_data_mapfile, output_data_mapfile),
data_start_time=vdsinfo['start_time'],
data_end_time=vdsinfo['end_time'],
demix_always=
py_parset.getStringVector('PreProcessing.demix_always'),
demix_if_needed=
py_parset.getStringVector('PreProcessing.demix_if_needed'),
parset=ndppp_parset,
parmdb_mapfile=parmdb_mapfile,
sourcedb_mapfile=sourcedb_mapfile
)
# *********************************************************************
# 6. Create feedback file for further processing by the LOFAR framework
# (MAC)
# Create a parset-file containing the metadata for MAC/SAS
with duration(self, "get_metadata"):
self.run_task("get_metadata", output_data_mapfile,
parset_file=self.parset_feedback_file,
parset_prefix=(
self.parset.getString('prefix') +
self.parset.fullModuleName('DataProducts')),
product_type="Correlated")
return 0
def pipeline_logic(self):
"""
Define the individual tasks that comprise the current pipeline.
This method will be invoked by the base-class's `go()` method.
"""
# *********************************************************************
# 1. Get input from parset, validate and cast to pipeline 'data types'
# Only perform work on existing files
# Created needed directories
# Create a parameter-subset containing only python-control stuff.
py_parset = self.parset.makeSubset(
self.parset.fullModuleName('PythonControl') + '.')
# Get input/output-data products specifications.
self._get_io_product_specs()
job_dir = self.config.get("layout", "job_directory")
parset_dir = os.path.join(job_dir, "parsets")
mapfile_dir = os.path.join(job_dir, "mapfiles")
# Create directories for temporary parset- and map files
create_directory(parset_dir)
create_directory(mapfile_dir)
# Write input- and output data map-files
input_correlated_mapfile = os.path.join(mapfile_dir,
"input_correlated.mapfile")
output_correlated_mapfile = os.path.join(mapfile_dir,
"output_correlated.mapfile")
output_instrument_mapfile = os.path.join(mapfile_dir,
"output_instrument.mapfile")
self.input_data['correlated'].save(input_correlated_mapfile)
self.output_data['correlated'].save(output_correlated_mapfile)
self.output_data['instrument'].save(output_instrument_mapfile)
if len(self.input_data['correlated']) == 0:
self.logger.warn("No input data files to process. Bailing out!")
return 0
self.logger.debug(
"Processing: %s" %
', '.join(str(f) for f in self.input_data['correlated']))
# *********************************************************************
# 2. Create database needed for performing work:
# Vds, descibing data on the nodes
# sourcedb, For skymodel (A-team)
# parmdb for outputtting solutions
# Produce a GVDS file describing the data on the compute nodes.
with duration(self, "vdsmaker"):
gvds_file = self.run_task("vdsmaker",
input_correlated_mapfile)['gvds']
# Read metadata (start, end times, pointing direction) from GVDS.
with duration(self, "vdsreader"):
vdsinfo = self.run_task("vdsreader", gvds=gvds_file)
# Create an empty parmdb for DPPP
with duration(self, "setupparmdb"):
parmdb_mapfile = self.run_task("setupparmdb",
input_correlated_mapfile,
mapfile=os.path.join(
mapfile_dir,
'dppp.parmdb.mapfile'),
suffix='.dppp.parmdb')['mapfile']
# Create a sourcedb to be used by the demixing phase of DPPP
# The user-supplied sky model can either be a name, in which case the
# pipeline will search for a file <name>.skymodel in the default search
# path $LOFARROOT/share/pipeline/skymodels; or a full path.
# It is an error if the file does not exist.
skymodel = py_parset.getString('PreProcessing.SkyModel')
if not os.path.isabs(skymodel):
skymodel = os.path.join(
# This should really become os.environ['LOFARROOT']
self.config.get('DEFAULT', 'lofarroot'),
'share',
'pipeline',
'skymodels',
skymodel + '.skymodel')
if not os.path.isfile(skymodel):
raise PipelineException("Skymodel %s does not exist" % skymodel)
with duration(self, "setupsourcedb"):
sourcedb_mapfile = self.run_task("setupsourcedb",
input_correlated_mapfile,
mapfile=os.path.join(
mapfile_dir,
'dppp.sourcedb.mapfile'),
skymodel=skymodel,
suffix='.dppp.sourcedb',
type='blob')['mapfile']
# *********************************************************************
# 3. Run NDPPP to demix the A-Team sources
# TODOW: Do flagging?
# Create a parameter-subset for DPPP and write it to file.
ndppp_parset = os.path.join(parset_dir, "NDPPP.parset")
py_parset.makeSubset('DPPP.').writeFile(ndppp_parset)
# Run the Default Pre-Processing Pipeline (DPPP);
with duration(self, "ndppp"):
dppp_mapfile = self.run_task(
"ndppp",
input_correlated_mapfile,
data_start_time=vdsinfo['start_time'],
data_end_time=vdsinfo['end_time'],
demix_always=py_parset.getStringVector(
'PreProcessing.demix_always'),
demix_if_needed=py_parset.getStringVector(
'PreProcessing.demix_if_needed'),
parset=ndppp_parset,
parmdb_mapfile=parmdb_mapfile,
sourcedb_mapfile=sourcedb_mapfile)['mapfile']
# *********************************************************************
# 4. Run BBS with a model of the calibrator
# Create a parmdb for calibration solutions
# Create sourcedb with known calibration solutions
# Run bbs with both
# Create an empty parmdb for BBS
with duration(self, "setupparmdb"):
parmdb_mapfile = self.run_task("setupparmdb",
dppp_mapfile,
mapfile=os.path.join(
mapfile_dir,
'bbs.parmdb.mapfile'),
suffix='.bbs.parmdb')['mapfile']
# Create a sourcedb based on sourcedb's input argument "skymodel"
with duration(self, "setupsourcedb"):
sourcedb_mapfile = self.run_task(
"setupsourcedb",
input_correlated_mapfile,
skymodel=os.path.join(
self.config.get('DEFAULT', 'lofarroot'), 'share',
'pipeline', 'skymodels',
py_parset.getString('Calibration.SkyModel') + '.skymodel'),
mapfile=os.path.join(mapfile_dir, 'bbs.sourcedb.mapfile'),
suffix='.bbs.sourcedb')['mapfile']
# Create a parameter-subset for BBS and write it to file.
bbs_parset = os.path.join(parset_dir, "BBS.parset")
py_parset.makeSubset('BBS.').writeFile(bbs_parset)
# Run BBS to calibrate the calibrator source(s).
with duration(self, "bbs_reducer"):
bbs_mapfile = self.run_task(
"bbs_reducer",
dppp_mapfile,
parset=bbs_parset,
instrument_mapfile=parmdb_mapfile,
sky_mapfile=sourcedb_mapfile)['data_mapfile']
# *********************************************************************
# 5. Perform gain outlier correction on the found calibration solutions
# Swapping outliers in the gains with the median
# Export the calibration solutions using gainoutliercorrection and store
# the results in the files specified in the instrument mapfile.
export_instrument_model = py_parset.getBool(
'Calibration.exportCalibrationParameters', False)
with duration(self, "gainoutliercorrection"):
self.run_task("gainoutliercorrection",
(parmdb_mapfile, output_instrument_mapfile),
sigma=1.0,
export_instrument_model=export_instrument_model
) # TODO: Parset parameter
# *********************************************************************
# 6. Copy corrected MS's to their final output destination.
with duration(self, "copier"):
self.run_task("copier",
mapfile_source=bbs_mapfile,
mapfile_target=output_correlated_mapfile,
mapfiles_dir=mapfile_dir,
mapfile=output_correlated_mapfile)
# *********************************************************************
# 7. Create feedback file for further processing by the LOFAR framework
# a. get metadata of the measurement sets
# b. get metadata of the instrument models
# c. join the two files and write the final feedback file
correlated_metadata = os.path.join(parset_dir, "correlated.metadata")
instrument_metadata = os.path.join(parset_dir, "instrument.metadata")
with duration(self, "get_metadata"):
self.run_task(
"get_metadata",
output_correlated_mapfile,
parset_file=correlated_metadata,
parset_prefix=(self.parset.getString('prefix') +
self.parset.fullModuleName('DataProducts')),
product_type="Correlated")
with duration(self, "get_metadata"):
self.run_task(
"get_metadata",
output_instrument_mapfile,
parset_file=instrument_metadata,
parset_prefix=(self.parset.getString('prefix') +
self.parset.fullModuleName('DataProducts')),
product_type="InstrumentModel")
parset = parameterset(correlated_metadata)
parset.adoptFile(instrument_metadata)
parset.writeFile(self.parset_feedback_file)
return 0
# Extract runtime, working, results directories from input parset
runtime_directory = input_parset.getString("ObsSW.Observation.ObservationControl.PythonControl.runtimeDirectory")
working_directory = input_parset.getString("ObsSW.Observation.ObservationControl.PythonControl.workingDirectory")
results_directory = input_parset.getString("ObsSW.Observation.ObservationControl.PythonControl.resultDirectory")
# Set up configuration for later processing stages
config = ConfigParser({
"job_name": tree_id,
"cwd": os.getcwd(),
"start_time": start_time,
})
config.read(config_file)
config.set('DEFAULT', 'runtime_directory', runtime_directory)
config.set('DEFAULT', 'default_working_directory', working_directory)
# Extract input file list from parset
to_process = input_parset.getStringVector('ObsSW.Observation.DataProducts.measurementSets')
# Read config file to establish location of parset directory to use
parset_directory = config.get("layout", "parset_directory")
create_directory(parset_directory)
# For each task (currently only ndppp), extract and write parset
tasks = ConfigParser(config.defaults())
tasks.read(string_to_list(config.get("DEFAULT", "task_files")))
ndppp_parset_location = tasks.get("ndppp", "parset")
input_parset.makeSubset("ObsSW.Observation.ObservationControl.PythonControl.DPPP.").writeFile(ndppp_parset_location)
# Run pipeline & wait for result
subprocess.check_call(['python', pipeline_definition, '-j', tree_id, '-d', '--config', config_file, '--runtime-directory', runtime_directory, '--default-working-directory', working_directory, '--start-time', start_time])
def run(self, input_image, bdsm_parameter_run1_path,
bdsm_parameter_run2x_path, catalog_output_path, image_output_path,
sourcedb_target_path, environment, working_directory,
create_sourcdb_exec):
"""
:param input_image: image to look for sources in
:param bdsm_parameter_run1_path: parset with bdsm parameters for the
first run
:param bdsm_parameter_run2x_path: second ron bdsm parameters
:param catalog_output_path: Path to full list of sources found
:param image_output_path: Path to fits image with all sources
substracted
:param sourcedb_target_path: Path to store the sourcedb created from
containing all the found sources
:param environment: environment for runwithlog4cplus
:param working_directory: Working dir
:param create_sourcdb_exec: Path to create sourcedb executable
:rtype: self.outputs['source_db'] sourcedb_target_path
"""
#******************************************************************
# 0. Create the directories used in this recipe
create_directory(working_directory)
import lofar.bdsm as bdsm#@UnresolvedImport
self.logger.info("Starting imager_source_finding")
self.environment.update(environment)
# default frequency is None (read from image), save for later cycles.
# output of pybdsm forgets freq of source image
frequency = None
# Output of the for loop: n iterations and any source found
n_itter_sourcefind = None
sources_found = False
max_sourcefind_itter = 5 # TODO: maximum itter is a magic value
for idx in range(max_sourcefind_itter):
# ******************************************************************
# 1. Select correct input image
# The first iteration uses the input image, second and later use the
# output of the previous iteration. The 1+ iteration have a
# seperate parameter set.
if idx == 0:
input_image_local = input_image # input_image_cropped
image_output_path_local = image_output_path + "_0"
bdsm_parameter_local = parameterset(bdsm_parameter_run1_path)
else:
input_image_local = image_output_path + "_{0}".format(
str(idx - 1))
image_output_path_local = image_output_path + "_{0}".format(
str(idx))
bdsm_parameter_local = parameterset(bdsm_parameter_run2x_path)
# *****************************************************************
# 2. parse the parameters and convert to python if possible
# this is needed for pybdsm
bdsm_parameters = {}
for key in bdsm_parameter_local.keys():
parameter_value = bdsm_parameter_local.getStringVector(key)[0]
try:
parameter_value = eval(parameter_value)
except:
pass #do nothing
bdsm_parameters[key] = parameter_value
# pybdsm needs its filename here, to derive the log location
bdsm_parameters["filename"] = input_image_local
# *****************************************************************
# 3. Start pybdsm
self.logger.debug(
"Starting sourcefinder bdsm on {0} using parameters:".format(
input_image_local))
self.logger.debug(repr(bdsm_parameters))
img = bdsm.process_image(bdsm_parameters, frequency = frequency)
# Always export the catalog
img.write_catalog(
outfile = catalog_output_path + "_{0}".format(str(idx)),
catalog_type = 'gaul', clobber = True,
format = "bbs", force_output = True)
# If no more matching of sources with gausians is possible (nsrc==0)
# break the loop
if img.nsrc == 0:
n_itter_sourcefind = idx
break
# We have at least found a single source!
self.logger.debug("Number of source found: {0}".format(
img.nsrc))
# *****************************************************************
# 4. export the image
self.logger.debug("Wrote list of sources to file at: {0})".format(
catalog_output_path))
img.export_image(outfile = image_output_path_local,
img_type = 'gaus_resid', clobber = True,
img_format = "fits")
self.logger.debug("Wrote fits image with substracted sources"
" at: {0})".format(image_output_path_local))
# Save the frequency from image header of the original input file,
# This information is not written by pybdsm to the exported image
frequency = img.frequency
# if not set the maximum number of itteration us performed
if n_itter_sourcefind == None:
n_itter_sourcefind = max_sourcefind_itter
# ********************************************************************
# 5. The produced catalogs now need to be combined into a single list
# Call with the number of loops and the path to the files, only combine
# if we found sources
self.logger.debug(
"Writing source list to file: {0}".format(catalog_output_path))
self._combine_source_lists(n_itter_sourcefind, catalog_output_path)
# *********************************************************************
# 6. Convert sourcelist to sourcedb
self._create_source_db(catalog_output_path, sourcedb_target_path,
working_directory, create_sourcdb_exec, False)
# Assign the outputs
self.outputs["catalog_output_path"] = catalog_output_path
self.outputs["source_db"] = sourcedb_target_path
return 0
def pipeline_logic(self):
"""
Define the individual tasks that comprise the current pipeline.
This method will be invoked by the base-class's `go()` method.
"""
self.logger.info("Starting imager pipeline")
# Define scratch directory to be used by the compute nodes.
self.scratch_directory = os.path.join(
self.inputs['working_directory'], self.inputs['job_name'])
# Get input/output-data products specifications.
self._get_io_product_specs()
# remove prepending parset identifiers, leave only pipelinecontrol
full_parset = self.parset
self.parset = self.parset.makeSubset(
self.parset.fullModuleName('PythonControl') + '.') # remove this
# Create directories to store communication and data files
job_dir = self.config.get("layout", "job_directory")
self.parset_dir = os.path.join(job_dir, "parsets")
create_directory(self.parset_dir)
self.mapfile_dir = os.path.join(job_dir, "mapfiles")
create_directory(self.mapfile_dir)
# *********************************************************************
# (INPUT) Get the input from external sources and create pipeline types
# Input measure ment sets
input_mapfile = os.path.join(self.mapfile_dir, "uvdata.mapfile")
self.input_data.save(input_mapfile)
# storedata_map(input_mapfile, self.input_data)
self.logger.debug(
"Wrote input UV-data mapfile: {0}".format(input_mapfile))
# Provides location for the scratch directory and concat.ms location
target_mapfile = os.path.join(self.mapfile_dir, "target.mapfile")
self.target_data.save(target_mapfile)
self.logger.debug(
"Wrote target mapfile: {0}".format(target_mapfile))
# images datafiles
output_image_mapfile = os.path.join(self.mapfile_dir, "images.mapfile")
self.output_data.save(output_image_mapfile)
self.logger.debug(
"Wrote output sky-image mapfile: {0}".format(output_image_mapfile))
# TODO: This is a backdoor option to manually add beamtables when these
# are missing on the provided ms. There is NO use case for users of the
# pipeline
add_beam_tables = self.parset.getBool(
"Imaging.addBeamTables", False)
# ******************************************************************
# (1) prepare phase: copy and collect the ms
concat_ms_map_path, timeslice_map_path, ms_per_image_map_path, \
processed_ms_dir = self._prepare_phase(input_mapfile,
target_mapfile, add_beam_tables)
number_of_major_cycles = self.parset.getInt(
"Imaging.number_of_major_cycles")
# We start with an empty source_list map. It should contain n_output
# entries all set to empty strings
source_list_map_path = os.path.join(self.mapfile_dir,
"initial_sourcelist.mapfile")
source_list_map = DataMap.load(target_mapfile) # copy the output map
for item in source_list_map:
item.file = "" # set all to empty string
source_list_map.save(source_list_map_path)
for idx_loop in range(number_of_major_cycles):
# *****************************************************************
# (2) Create dbs and sky model
parmdbs_path, sourcedb_map_path = self._create_dbs(
concat_ms_map_path, timeslice_map_path,
source_list_map_path = source_list_map_path,
skip_create_dbs = False)
# *****************************************************************
# (3) bbs_imager recipe.
bbs_output = self._bbs(timeslice_map_path, parmdbs_path,
sourcedb_map_path, skip = False)
# TODO: Extra recipe: concat timeslices using pyrap.concatms
# (see prepare)
# *****************************************************************
# (4) Get parameters awimager from the prepare_parset and inputs
aw_image_mapfile, maxbaseline = self._aw_imager(concat_ms_map_path,
idx_loop, sourcedb_map_path,
skip = False)
# *****************************************************************
# (5) Source finding
sourcelist_map, found_sourcedb_path = self._source_finding(
aw_image_mapfile, idx_loop, skip = False)
# should the output be a sourcedb? instead of a sourcelist
# TODO: minbaseline should be a parset value as is maxbaseline..
minbaseline = 0
# *********************************************************************
# (6) Finalize:
placed_data_image_map = self._finalize(aw_image_mapfile,
processed_ms_dir, ms_per_image_map_path, sourcelist_map,
minbaseline, maxbaseline, target_mapfile, output_image_mapfile,
found_sourcedb_path)
# *********************************************************************
# (7) Get metadata
# create a parset with information that is available on the toplevel
toplevel_meta_data = parameterset()
toplevel_meta_data.replace("numberOfMajorCycles",
str(number_of_major_cycles))
# Create a parset containing the metadata for MAC/SAS at nodes
metadata_file = "%s_feedback_SkyImage" % (self.parset_file,)
self.run_task("get_metadata", placed_data_image_map,
parset_prefix = (
full_parset.getString('prefix') +
full_parset.fullModuleName('DataProducts')
),
product_type = "SkyImage",
metadata_file = metadata_file)
self.send_feedback_processing(toplevel_meta_data)
self.send_feedback_dataproducts(parameterset(metadata_file))
return 0
def archive(parset_file, directions, dir_output, full=False, archive_subdata=False,
archive_state=False, archive_misc=True, archive_images=True,
archive_inst=False, archive_pipestate=False, archive_models=False,
archive_plots=True, clobber=False):
"""
Archives data from a Factor run
Parameters
----------
parset_file : str
Filename of Factor parset for run of interest
directions : list of str
List of direction names for which to archive the calibrated data
dir_output : str
Name of output directory where archived data will be stored
full : bool, optional
Make a full archive suitable for resuming?
archive_subdata : bool, optional
Archive the subtracted data MS files?
archive_state : bool, optional
Archive the state files?
archive_misc : bool, optional
Archive miscelaneous files?
archive_images : bool, optional
Archive the facet and field images?
archive_inst : bool, optional
Archive the instrument tables?
archive_pipestate : bool, optional
Archive the pipeline state files?
archive_models : bool, optional
Archive the sky models?
archive_plots : bool, optional
Archive the selfcal plots?
clobber : bool, optional
Clobber existing files in output directory?
"""
# Read in parset and get directions
all_directions, parset = load_directions(parset_file)
if len(all_directions) == 0:
log.error('No directions found in Factor working directory. Please check '
'the parset')
sys.exit(1)
all_names = [d.name for d in all_directions]
if len(directions) != 0:
if directions[0].lower() == 'all':
directions = all_names
for dname in directions:
if dname not in all_names:
log.warning('Direction {} not found. Skipping it...'.format(dname))
if full:
# Archive everything
archive_subdata = True
archive_state = True
archive_misc = True
archive_images = True
archive_inst = True
archive_pipestate = True
archive_models = True
archive_plots = True
working_dir = all_directions[0].working_dir
if archive_subdata:
log.info('Archiving subtracted data files...')
chunks_dir = os.path.join(working_dir, 'chunks')
copy(chunks_dir, dir_output, clobber)
if archive_state:
log.info('Archiving state files...')
state_dir = os.path.join(working_dir, 'state')
copy(state_dir, dir_output, clobber)
if archive_misc:
log.info('Archiving miscelaneous files...')
misc_dir = os.path.join(dir_output, 'misc')
if 'directions_file' in parset['direction_specific']:
directions_file = parset['direction_specific']['directions_file']
else:
directions_file = os.path.join(working_dir, 'factor_directions.txt')
file_list = [directions_file,
parset_file,
'{}/factor.log'.format(working_dir),
'{}/regions/facets_ds9.reg'.format(working_dir),
'{}/regions/calimages_ds9.reg'.format(working_dir)]
for f in file_list:
copy(f, misc_dir, clobber)
if archive_images:
log.info('Archiving field images...')
file_list = glob.glob(os.path.join(working_dir, 'results',
'field*', 'field', '*.fits'))
if len(file_list) == 0:
log.warning('No field images found.')
else:
for i, f in enumerate(file_list):
log.info(' Archiving image {0} of {1}...'.format(i+1, len(file_list)))
subdir = f.split('/')[-3]
image_dir = os.path.join(dir_output, 'images', 'field', subdir)
copy(f, image_dir, clobber)
if archive_models:
log.info('Archiving direction-independent sky models...')
band_state_files = glob.glob(os.path.join(working_dir, 'state',
'Band_*'))
file_list = []
band_list = []
for bf in band_state_files:
try:
with open(bf, 'r') as f:
b = pickle.load(f)
file_list.append(b['skymodel_dirindep'])
band_list.append(b['name'])
except:
pass
for i, f in enumerate(file_list):
skymodel_dir = os.path.join(dir_output, 'chunks', band_list[i])
log.info(' Copying sky model file {0} of {1}...'.format(i+1, len(file_list)))
copy(f, skymodel_dir, clobber)
for d in all_directions:
if archive_images:
log.info('Archiving facet images for direction {}...'.format(d.name))
file_list = glob.glob(os.path.join(working_dir, 'results',
'facetimage*', d.name, '*full2*image.fits'))
if len(file_list) == 0:
log.warning('No facet images found for direction {}.'.format(d.name))
else:
for i, f in enumerate(file_list):
subdir = f.split('/')[-3]
image_dir = os.path.join(dir_output, 'images', d.name, subdir)
copy(f, image_dir, clobber)
if archive_models:
log.info('Archiving sky models for direction {}...'.format(d.name))
if hasattr(d, 'sourcedb_new_facet_sources'):
file_list = check_existing_files(d.sourcedb_new_facet_sources)
else:
file_list = []
if len(file_list) == 0:
log.warning('No sky models found for direction {}.'.format(d.name))
else:
sourcedb_dir = os.path.join(dir_output, 'sky_models', d.name)
for i, f in enumerate(file_list):
log.info(' Copying sky model file {0} of {1}...'.format(i+1, len(file_list)))
copy(f, sourcedb_dir, clobber)
if archive_inst:
log.info('Archiving instrument tables for direction {}...'.format(d.name))
if hasattr(d, 'preapply_h5parm_mapfile'):
file_list.append(check_existing_files(d.preapply_parmdb_mapfile))
if len(file_list) == 0:
log.warning('No h5parms found for direction {}.'.format(d.name))
else:
inst_table_dir = os.path.join(dir_output, 'h5parms', d.name)
for i, f in enumerate(file_list):
log.info(' Copying h5parm file {0} of {1}...'.format(i+1, len(file_list)))
copy(f, inst_table_dir, clobber)
if archive_plots:
log.info('Archiving plots for direction {}...'.format(d.name))
file_list = glob.glob(os.path.join(working_dir, 'results', 'facetselfcal', d.name, '*png'))
if len(file_list) == 0:
file_list = glob.glob(os.path.join(working_dir, 'results', 'facetpeel', d.name, '*png'))
if len(file_list) == 0:
file_list = glob.glob(os.path.join(working_dir, 'results', 'outlierpeel', d.name, '*png'))
if len(file_list) == 0:
log.warning('No plots found for direction {}.'.format(d.name))
else:
plot_dir = os.path.join(dir_output, 'plots', d.name)
for i, f in enumerate(file_list):
copy(f, plot_dir, clobber)
if archive_pipestate:
log.info('Archiving pipeline state files for direction {}...'.format(d.name))
file_list = glob.glob(os.path.join(working_dir, 'results', 'facetselfcal', d.name, 'mapfiles', '*'))
op_name = 'facetselfcal'
if len(file_list) == 0:
file_list = glob.glob(os.path.join(working_dir, 'results', 'facetpeel', d.name, 'mapfiles', '*'))
op_name = 'facetpeel'
if len(file_list) == 0:
file_list = glob.glob(os.path.join(working_dir, 'results', 'outlierpeel', d.name, 'mapfiles', '*'))
op_name = 'outlierpeel'
if len(file_list) == 0:
log.warning('No pipeline state files found for direction {}.'.format(d.name))
else:
mapfile_dir = os.path.join(dir_output, 'pipeline_state', d.name, op_name)
for f in file_list:
copy(f, mapfile_dir, clobber)
# Also archive "final_image" mapfile for facetimage (needed for mosaicking)
file_list = glob.glob(os.path.join(working_dir, 'results',
'facetimage*', d.name, 'mapfiles', 'final_image.mapfile'))
if len(file_list) > 0:
for i, f in enumerate(file_list):
subdir = f.split('/')[-4]
mapfile_dir = os.path.join(dir_output, 'pipeline_state', d.name, subdir)
copy(f, mapfile_dir, clobber)
if d.name in directions:
log.info('Archiving calibrated data for direction {}...'.format(d.name))
if hasattr(d, 'image_data_mapfile'):
file_list = check_existing_files(d.image_data_mapfile)
else:
file_list = []
if len(file_list) == 0:
log.warning('No data found for direction {}. Skipping it...'.format(d.name))
continue
# Make the output directory
cal_data_dir = os.path.join(dir_output, 'calibrated_data', d.name)
create_directory(cal_data_dir)
# Sort the files into time chunks
data_mapfile = d.name+'_calibrated_data.mapfile'
sort_times_into_freqGroups.main(file_list, filename=data_mapfile,
mapfile_dir=cal_data_dir)
# Read the new, grouped file lists
datamap = DataMap.load(os.path.join(cal_data_dir, data_mapfile))
# Run DPPP to concatenate each time chunk in frequency
nchunks = len(datamap)
for i, item in enumerate(datamap):
log.info(' Concatenating files for time chunk {0} of {1}...'.format(i+1, nchunks))
outfile = os.path.join(cal_data_dir, '{0}_calibrated_data_chunk{1}.ms'.format(d.name, i))
if os.path.exists(outfile):
if not clobber:
log.warning(' Output file for this chuck exists and clobber = False. Skipping it...')
continue
else:
os.system('rm -rf {0}'.format(outfile))
dppp_concat(item.file, outfile)
# Clean up
os.system('rm -f {0}'.format(os.path.join(cal_data_dir, data_mapfile)))
os.system('rm -f {0}_groups'.format(os.path.join(cal_data_dir, data_mapfile)))
log.info('Archiving complete.')
def go(self):
self.logger.info("Starting BBS run")
super(new_bbs, self).go()
# Check for relevant input parameters in the parset-file
# ---------------------------------------------------------------------
self.logger.debug("Reading parset from %s" % self.inputs['parset'])
self.parset = parameterset(self.inputs['parset'])
self._set_input('db_host', 'BBDB.Host')
self._set_input('db_user', 'BBDB.User')
self._set_input('db_name', 'BBDB.Name')
self._set_input('db_key', 'BBDB.Key')
#self.logger.debug("self.inputs = %s" % self.inputs)
# Clean the blackboard database
# ---------------------------------------------------------------------
self.logger.info(
"Cleaning BBS database for key '%s'" % (self.inputs['db_key'])
)
command = ["psql",
"-h", self.inputs['db_host'],
"-U", self.inputs['db_user'],
"-d", self.inputs['db_name'],
"-c", "DELETE FROM blackboard.session WHERE key='%s';" %
self.inputs['db_key']
]
self.logger.debug(command)
if subprocess.call(command) != 0:
self.logger.warning(
"Failed to clean BBS database for key '%s'" %
self.inputs['db_key']
)
# Create a bbs_map describing the file mapping on disk
# ---------------------------------------------------------------------
if not self._make_bbs_map():
return 1
# Produce a GVDS file, describing the data that must be processed.
gvds_file = self.run_task(
"vdsmaker",
self.inputs['data_mapfile'],
gvds=self.inputs['gvds']
)['gvds']
# Construct a parset for BBS GlobalControl by patching the GVDS
# file and database information into the supplied template
# ------------------------------------------------------------------
self.logger.debug("Building parset for BBS control")
# Create a location for parsets
job_directory = self.config.get(
"layout", "job_directory")
parset_directory = os.path.join(job_directory, "parsets")
create_directory(parset_directory)
# patch the parset and copy result to target location remove tempfile
try:
bbs_parset = utilities.patch_parset(
self.parset,
{
'Observation': gvds_file,
'BBDB.Key': self.inputs['db_key'],
'BBDB.Name': self.inputs['db_name'],
'BBDB.User': self.inputs['db_user'],
'BBDB.Host': self.inputs['db_host'],
#'BBDB.Port': self.inputs['db_name'],
}
)
bbs_parset_path = os.path.join(parset_directory,
"bbs_control.parset")
shutil.copyfile(bbs_parset, bbs_parset_path)
self.logger.debug("BBS control parset is %s" % (bbs_parset_path,))
finally:
# Always remove the file in the tempdir
os.remove(bbs_parset)
try:
# When one of our processes fails, we set the killswitch.
# Everything else will then come crashing down, rather than
# hanging about forever.
# --------------------------------------------------------------
self.killswitch = threading.Event()
self.killswitch.clear()
signal.signal(signal.SIGTERM, self.killswitch.set)
# GlobalControl runs in its own thread
# --------------------------------------------------------------
run_flag = threading.Event()
run_flag.clear()
bbs_control = threading.Thread(
target=self._run_bbs_control,
args=(bbs_parset, run_flag)
)
bbs_control.start()
run_flag.wait() # Wait for control to start before proceeding
# We run BBS KernelControl on each compute node by directly
# invoking the node script using SSH
# Note that we use a job_server to send out job details and
# collect logging information, so we define a bunch of
# ComputeJobs. However, we need more control than the generic
# ComputeJob.dispatch method supplies, so we'll control them
# with our own threads.
# --------------------------------------------------------------
command = "python %s" % (self.__file__.replace('master', 'nodes'))
jobpool = {}
bbs_kernels = []
with job_server(self.logger, jobpool, self.error) as(jobhost,
jobport):
self.logger.debug("Job server at %s:%d" % (jobhost, jobport))
for job_id, details in enumerate(self.bbs_map):
host, files = details
jobpool[job_id] = ComputeJob(
host, command,
arguments=[
self.inputs['kernel_exec'],
files,
self.inputs['db_key'],
self.inputs['db_name'],
self.inputs['db_user'],
self.inputs['db_host']
]
)
bbs_kernels.append(
threading.Thread(
target=self._run_bbs_kernel,
args=(host, command, job_id, jobhost, str(jobport))
)
)
self.logger.info("Starting %d threads" % len(bbs_kernels))
for thread in bbs_kernels:
thread.start()
self.logger.debug("Waiting for all kernels to complete")
for thread in bbs_kernels:
thread.join()
# When GlobalControl finishes, our work here is done
# ----------------------------------------------------------
self.logger.info("Waiting for GlobalControl thread")
bbs_control.join()
finally:
os.unlink(bbs_parset)
if self.killswitch.isSet():
# If killswitch is set, then one of our processes failed so
# the whole run is invalid
# ----------------------------------------------------------
return 1
self.outputs['mapfile'] = self.inputs['data_mapfile']
return 0
config = ConfigParser({
"job_name": tree_id,
"cwd": os.getcwd(),
"start_time": start_time,
})
config.read(config_file)
config.set('DEFAULT', 'runtime_directory', runtime_directory)
config.set('DEFAULT', 'default_working_directory', working_directory)
# Extract input file list from parset
to_process = input_parset.getStringVector(
'ObsSW.Observation.DataProducts.measurementSets')
# Read config file to establish location of parset directory to use
parset_directory = config.get("layout", "parset_directory")
create_directory(parset_directory)
# For each task (currently only ndppp), extract and write parset
tasks = ConfigParser(config.defaults())
tasks.read(string_to_list(config.get("DEFAULT", "task_files")))
ndppp_parset_location = tasks.get("ndppp", "parset")
input_parset.makeSubset(
"ObsSW.Observation.ObservationControl.PythonControl.DPPP.").writeFile(
ndppp_parset_location)
# Run pipeline & wait for result
subprocess.check_call([
'python', pipeline_definition, '-j', tree_id, '-d', '--config',
config_file, '--runtime-directory', runtime_directory,
'--default-working-directory', working_directory, '--start-time',
start_time
def _filter_bad_stations(self, time_slice_path_list, asciistat_executable,
statplot_executable, msselect_executable):
"""
A Collection of scripts for finding and filtering of bad stations:
1. First a number of statistics with regards to the spread of the data
is collected using the asciistat_executable.
2. Secondly these statistics are consumed by the statplot_executable
which produces a set of bad stations.
3. In the final step the bad stations are removed from the dataset
using ms select
REF: http://www.lofar.org/wiki/lib/exe/fetch.php?media=msss:pandeymartinez-week9-v1p2.pdf
"""
# run asciistat to collect statistics about the ms
self.logger.info("Filtering bad stations")
self.logger.debug("Collecting statistical properties of input data")
asciistat_output = []
asciistat_proc_group = SubProcessGroup(self.logger)
for ms in time_slice_path_list:
output_dir = ms + ".filter_temp"
create_directory(output_dir)
asciistat_output.append((ms, output_dir))
cmd_string = "{0} -i {1} -r {2}".format(asciistat_executable, ms,
output_dir)
asciistat_proc_group.run(cmd_string)
if asciistat_proc_group.wait_for_finish() != None:
raise Exception("an ASCIIStats run failed!")
# Determine the station to remove
self.logger.debug("Select bad stations depending on collected stats")
asciiplot_output = []
asciiplot_proc_group = SubProcessGroup(self.logger)
for (ms, output_dir) in asciistat_output:
ms_stats = os.path.join(output_dir,
os.path.split(ms)[1] + ".stats")
cmd_string = "{0} -i {1} -o {2}".format(statplot_executable,
ms_stats, ms_stats)
asciiplot_output.append((ms, ms_stats))
asciiplot_proc_group.run(cmd_string)
if asciiplot_proc_group.wait_for_finish() != None:
raise Exception("an ASCIIplot run failed!")
# remove the bad stations
self.logger.debug("Use ms select to remove bad stations")
msselect_output = {}
msselect_proc_group = SubProcessGroup(self.logger)
for ms, ms_stats in asciiplot_output:
# parse the .tab file containing the bad stations
station_to_filter = []
file_pointer = open(ms_stats + ".tab")
for line in file_pointer.readlines():
# skip headed line
if line[0] == "#":
continue
entries = line.split()
# if the current station is bad (the last entry on the line)
if entries[-1] == "True":
# add the name of station
station_to_filter.append(entries[1])
# if this measurement does not contain baselines to skip do not
# filter and provide the original ms as output
if len(station_to_filter) == 0:
msselect_output[ms] = ms
continue
ms_output_path = ms + ".filtered"
msselect_output[ms] = ms_output_path
# use msselect to remove the stations from the ms
msselect_baseline = "!{0}".format(",".join(station_to_filter))
cmd_string = "{0} in={1} out={2} baseline={3} deep={4}".format(
msselect_executable, ms, ms_output_path, msselect_baseline,
"False")
msselect_proc_group.run(cmd_string)
if msselect_proc_group.wait_for_finish() != None:
raise Exception("an MSselect run failed!")
filtered_list_of_ms = []
# The order of the inputs needs to be preserved when producing the
# filtered output!
for input_ms in time_slice_path_list:
filtered_list_of_ms.append(msselect_output[input_ms])
return filtered_list_of_ms
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
def run(self, executable, environment, parset, working_directory,
output_image, concatenated_measurement_set, sourcedb_path,
mask_patch_size, autogenerate_parameters, specify_fov, fov):
"""
:param executable: Path to awimager executable
:param environment: environment for catch_segfaults (executable runner)
:param parset: parameters for the awimager,
:param working_directory: directory the place temporary files
:param output_image: location and filesname to story the output images
the multiple images are appended with type extentions
:param concatenated_measurement_set: Input measurement set
:param sourcedb_path: Path the the sourcedb used to create the image
mask
:param mask_patch_size: Scaling of the patch around the source in the
mask
:param autogenerate_parameters: Turns on the autogeneration of:
cellsize, npix, wprojplanes, wmax, fov
:param fov: if autogenerate_parameters is false calculate
imageparameter (cellsize, npix, wprojplanes, wmax) relative to this
fov
:rtype: self.outputs["image"] The path to the output image
"""
self.logger.info("Start imager_awimager node run:")
log4_cplus_name = "imager_awimager"
self.environment.update(environment)
with log_time(self.logger):
# Read the parameters as specified in the parset
parset_object = get_parset(parset)
# *************************************************************
# 1. Calculate awimager parameters that depend on measurement set
# and the parset
cell_size, npix, w_max, w_proj_planes = \
self._get_imaging_parameters(
concatenated_measurement_set,
parset,
autogenerate_parameters,
specify_fov,
fov)
self.logger.info("Using autogenerated parameters; ")
self.logger.info(
"Calculated parameters: cell_size: {0}, npix: {1}".format(
cell_size, npix))
self.logger.info("w_max: {0}, w_proj_planes: {1} ".format(
w_max, w_proj_planes))
# ****************************************************************
# 2. Get the target image location from the mapfile for the parset.
# Create target dir if it not exists
image_path_head = os.path.dirname(output_image)
create_directory(image_path_head)
self.logger.debug("Created directory to place awimager output"
" files: {0}".format(image_path_head))
# ****************************************************************
# 3. Create the mask
mask_file_path = self._create_mask(npix, cell_size, output_image,
concatenated_measurement_set, executable,
working_directory, log4_cplus_name, sourcedb_path,
mask_patch_size, image_path_head)
# *****************************************************************
# 4. Update the parset with calculated parameters, and output image
patch_dictionary = {'uselogger': 'True', # enables log4cpluscd log
'ms': str(concatenated_measurement_set),
'cellsize': str(cell_size),
'npix': str(npix),
'wmax': str(w_max),
'wprojplanes': str(w_proj_planes),
'image': str(output_image),
'maxsupport': str(npix),
# 'mask':str(mask_file_path), #TODO REINTRODUCE
# MASK, excluded to speed up in this debug stage
}
# save the parset at the target dir for the image
calculated_parset_path = os.path.join(image_path_head,
"parset.par")
try:
temp_parset_filename = patch_parset(parset, patch_dictionary)
# Copy tmp file to the final location
shutil.copyfile(temp_parset_filename, calculated_parset_path)
self.logger.debug("Wrote parset for awimager run: {0}".format(
calculated_parset_path))
finally:
# remove temp file
os.remove(temp_parset_filename)
# *****************************************************************
# 5. Run the awimager with the updated parameterset
cmd = [executable, calculated_parset_path]
try:
with CatchLog4CPlus(working_directory,
self.logger.name + "." +
os.path.basename(log4_cplus_name),
os.path.basename(executable)
) as logger:
catch_segfaults(cmd, working_directory, self.environment,
logger)
# Thrown by catch_segfault
except CalledProcessError, exception:
self.logger.error(str(exception))
return 1
except Exception, exception:
self.logger.error(str(exception))
return 1
def run(self, awimager_output, ms_per_image, sourcelist, target,
output_image, minbaseline, maxbaseline, processed_ms_dir,
fillrootimagegroup_exec, environment, sourcedb, concat_ms,
correlated_output_location, msselect_executable):
self.environment.update(environment)
"""
:param awimager_output: Path to the casa image produced by awimager
:param ms_per_image: The X (90) measurements set scheduled to
create the image
:param sourcelist: list of sources found in the image
:param target: <unused>
:param minbaseline: Minimum baseline used for the image
:param maxbaseline: largest/maximum baseline used for the image
:param processed_ms_dir: The X (90) measurements set actually used to
create the image
:param fillrootimagegroup_exec: Executable used to add image data to
the hdf5 image
:rtype: self.outputs['hdf5'] set to "succes" to signal node succes
:rtype: self.outputs['image'] path to the produced hdf5 image
"""
with log_time(self.logger):
ms_per_image_map = DataMap.load(ms_per_image)
# *****************************************************************
# 1. add image info
# Get all the files in the processed measurement dir
file_list = os.listdir(processed_ms_dir)
processed_ms_paths = []
ms_per_image_map.iterator = DataMap.SkipIterator
for item in ms_per_image_map:
ms_path = item.file
processed_ms_paths.append(ms_path)
#add the information the image
try:
self.logger.debug("Start addImage Info")
addimg.addImagingInfo(awimager_output, processed_ms_paths,
sourcedb, minbaseline, maxbaseline)
except Exception, error:
self.logger.warn("addImagingInfo Threw Exception:")
self.logger.warn(error)
# Catch raising of already done error: allows for rerunning
# of the recipe
if "addImagingInfo already done" in str(error):
self.logger.warn("addImagingInfo already done, continue")
pass
else:
raise Exception(error)
#The majority of the tables is updated correctly
# ***************************************************************
# 2. convert to hdf5 image format
output_directory = None
pim_image = pim.image(awimager_output)
try:
self.logger.info("Saving image in HDF5 Format to: {0}" .format(
output_image))
# Create the output directory
output_directory = os.path.dirname(output_image)
create_directory(output_directory)
# save the image
pim_image.saveas(output_image, hdf5=True)
except Exception, error:
self.logger.error(
"Exception raised inside pyrap.images: {0}".format(
str(error)))
raise error
def pipeline_logic(self):
"""
Define the individual tasks that comprise the current pipeline.
This method will be invoked by the base-class's `go()` method.
"""
# *********************************************************************
# 1. Prepare phase, collect data from parset and input mapfiles.
py_parset = self.parset.makeSubset(
self.parset.fullModuleName('PythonControl') + '.')
# Get input/output-data products specifications.
self._get_io_product_specs()
job_dir = self.config.get("layout", "job_directory")
parset_dir = os.path.join(job_dir, "parsets")
mapfile_dir = os.path.join(job_dir, "mapfiles")
# Create directories for temporary parset- and map files
create_directory(parset_dir)
create_directory(mapfile_dir)
# Write input- and output data map-files
input_data_mapfile = os.path.join(mapfile_dir, "input_data.mapfile")
self.input_data.save(input_data_mapfile)
output_data_mapfile = os.path.join(mapfile_dir, "output_data.mapfile")
self.output_data.save(output_data_mapfile)
if len(self.input_data) == 0:
self.logger.warn("No input data files to process. Bailing out!")
return 0
self.logger.debug("Processing: %s" %
', '.join(str(f) for f in self.input_data))
# *********************************************************************
# 2. Create VDS-file and databases. The latter are needed when doing
# demixing within DPPP.
with duration(self, "vdsmaker"):
gvds_file = self.run_task("vdsmaker", input_data_mapfile)['gvds']
# Read metadata (start, end times, pointing direction) from GVDS.
with duration(self, "vdsreader"):
vdsinfo = self.run_task("vdsreader", gvds=gvds_file)
# Create a parameter database that will be used by the NDPPP demixing
with duration(self, "setupparmdb"):
parmdb_mapfile = self.run_task(
"setupparmdb", input_data_mapfile,
mapfile=os.path.join(mapfile_dir, 'dppp.parmdb.mapfile'),
suffix='.dppp.parmdb'
)['mapfile']
# Create a source database from a user-supplied sky model
# The user-supplied sky model can either be a name, in which case the
# pipeline will search for a file <name>.skymodel in the default search
# path $LOFARROOT/share/pipeline/skymodels; or a full path.
# It is an error if the file does not exist.
skymodel = py_parset.getString('PreProcessing.SkyModel')
if not os.path.isabs(skymodel):
skymodel = os.path.join(
# This should really become os.environ['LOFARROOT']
self.config.get('DEFAULT', 'lofarroot'),
'share', 'pipeline', 'skymodels', skymodel + '.skymodel'
)
if not os.path.isfile(skymodel):
raise PipelineException("Skymodel %s does not exist" % skymodel)
with duration(self, "setupsourcedb"):
sourcedb_mapfile = self.run_task(
"setupsourcedb", input_data_mapfile,
mapfile=os.path.join(mapfile_dir, 'dppp.sourcedb.mapfile'),
skymodel=skymodel,
suffix='.dppp.sourcedb',
type='blob'
)['mapfile']
# *********************************************************************
# 3. Average and flag data, using NDPPP.
ndppp_parset = os.path.join(parset_dir, "NDPPP.parset")
py_parset.makeSubset('DPPP.').writeFile(ndppp_parset)
# Run the Default Pre-Processing Pipeline (DPPP);
with duration(self, "ndppp"):
output_data_mapfile = self.run_task("ndppp",
(input_data_mapfile, output_data_mapfile),
data_start_time=vdsinfo['start_time'],
data_end_time=vdsinfo['end_time'],
demix_always=
py_parset.getStringVector('PreProcessing.demix_always'),
demix_if_needed=
py_parset.getStringVector('PreProcessing.demix_if_needed'),
parset=ndppp_parset,
parmdb_mapfile=parmdb_mapfile,
sourcedb_mapfile=sourcedb_mapfile
)['mapfile']
# *********************************************************************
# 6. Create feedback file for further processing by the LOFAR framework
# Create a parset containing the metadata
metadata_file = "%s_feedback_Correlated" % (self.parset_file,)
with duration(self, "get_metadata"):
self.run_task("get_metadata", output_data_mapfile,
parset_prefix=(
self.parset.getString('prefix') +
self.parset.fullModuleName('DataProducts')),
product_type="Correlated",
metadata_file=metadata_file)
self.send_feedback_processing(parameterset({'feedback_version': feedback_version}))
self.send_feedback_dataproducts(parameterset(metadata_file))
return 0
def pipeline_logic(self):
"""
Define the individual tasks that comprise the current pipeline.
This method will be invoked by the base-class's `go()` method.
"""
# *********************************************************************
# 1. Prepare phase, collect data from parset and input mapfiles
# Create a parameter-subset containing only python-control stuff.
py_parset = self.parset.makeSubset(
'ObsSW.Observation.ObservationControl.PythonControl.')
# Get input/output-data products specifications.
self._get_io_product_specs()
# Create some needed directories
job_dir = self.config.get("layout", "job_directory")
mapfile_dir = os.path.join(job_dir, "mapfiles")
create_directory(mapfile_dir)
parset_dir = os.path.join(job_dir, "parsets")
create_directory(parset_dir)
# *********************************************************************
# 2. Copy the instrument files to the correct node
# The instrument files are currently located on the wrong nodes
# Copy to correct nodes and assign the instrument table the now
# correct data
# Copy the instrument files to the corrent nodes: failures might happen
# update both intrument and datamap to contain only successes!
self._copy_instrument_files(mapfile_dir)
# Write input- and output data map-files.
data_mapfile = os.path.join(mapfile_dir, "data.mapfile")
self.input_data['data'].save(data_mapfile)
copied_instrument_mapfile = os.path.join(mapfile_dir,
"copied_instrument.mapfile")
self.input_data['instrument'].save(copied_instrument_mapfile)
self.logger.debug("Wrote input data mapfile: %s" % data_mapfile)
# Save copied files to a new mapfile
corrected_mapfile = os.path.join(mapfile_dir, "corrected_data.mapfile")
self.output_data['data'].save(corrected_mapfile)
self.logger.debug("Wrote output corrected data mapfile: %s" %
corrected_mapfile)
# Validate number of copied files, abort on zero files copied
if len(self.input_data['data']) == 0:
self.logger.warn("No input data files to process. Bailing out!")
return 0
self.logger.debug("Processing: %s" %
', '.join(str(f) for f in self.input_data['data']))
# *********************************************************************
# 3. Create database needed for performing work:
# - GVDS, describing data on the compute nodes
# - SourceDB, for skymodel (A-team)
# - ParmDB for outputtting solutions
with duration(self, "vdsmaker"):
gvds_file = self.run_task("vdsmaker", data_mapfile)['gvds']
# Read metadata (e.g., start- and end-time) from the GVDS file.
with duration(self, "vdsreader"):
vdsinfo = self.run_task("vdsreader", gvds=gvds_file)
# Create an empty parmdb for DPPP
with duration(self, "setupparmdb"):
parmdb_mapfile = self.run_task("setupparmdb",
data_mapfile)['mapfile']
# Create a sourcedb to be used by the demixing phase of DPPP
# The user-supplied sky model can either be a name, in which case the
# pipeline will search for a file <name>.skymodel in the default search
# path $LOFARROOT/share/pipeline/skymodels; or a full path.
# It is an error if the file does not exist.
skymodel = py_parset.getString('PreProcessing.SkyModel')
if not os.path.isabs(skymodel):
skymodel = os.path.join(
# This should really become os.environ['LOFARROOT']
self.config.get('DEFAULT', 'lofarroot'),
'share',
'pipeline',
'skymodels',
skymodel + '.skymodel')
if not os.path.isfile(skymodel):
raise PipelineException("Skymodel %s does not exist" % skymodel)
with duration(self, "setupsourcedb"):
sourcedb_mapfile = self.run_task("setupsourcedb",
data_mapfile,
skymodel=skymodel,
suffix='.dppp.sourcedb',
type='blob')['mapfile']
# *********************************************************************
# 4. Run NDPPP to demix the A-Team sources
# Create a parameter-subset for DPPP and write it to file.
ndppp_parset = os.path.join(parset_dir, "NDPPP.parset")
py_parset.makeSubset('DPPP.').writeFile(ndppp_parset)
# Run the Default Pre-Processing Pipeline (DPPP);
with duration(self, "ndppp"):
dppp_mapfile = self.run_task(
"ndppp",
data_mapfile,
data_start_time=vdsinfo['start_time'],
data_end_time=vdsinfo['end_time'],
demix_always=py_parset.getStringVector(
'PreProcessing.demix_always'),
demix_if_needed=py_parset.getStringVector(
'PreProcessing.demix_if_needed'),
parset=ndppp_parset,
parmdb_mapfile=parmdb_mapfile,
sourcedb_mapfile=sourcedb_mapfile,
mapfile=os.path.join(mapfile_dir, 'dppp.mapfile'))['mapfile']
# ********************************************************************
# 5. Run bss using the instrument file from the target observation
# Create an empty sourcedb for BBS
with duration(self, "setupsourcedb"):
sourcedb_mapfile = self.run_task("setupsourcedb",
data_mapfile)['mapfile']
# Create a parameter-subset for BBS and write it to file.
bbs_parset = os.path.join(parset_dir, "BBS.parset")
py_parset.makeSubset('BBS.').writeFile(bbs_parset)
# Run BBS to calibrate the target source(s).
with duration(self, "bbs_reducer"):
bbs_mapfile = self.run_task(
"bbs_reducer",
dppp_mapfile,
parset=bbs_parset,
instrument_mapfile=copied_instrument_mapfile,
sky_mapfile=sourcedb_mapfile)['data_mapfile']
# *********************************************************************
# 6. Copy the MS's to their final output destination.
# When the copier recipe has run, the map-file named in
# corrected_mapfile will contain an updated map of output files.
with duration(self, "copier"):
self.run_task("copier",
mapfile_source=bbs_mapfile,
mapfile_target=corrected_mapfile,
mapfiles_dir=mapfile_dir,
mapfile=corrected_mapfile)
# *********************************************************************
# 7. Create feedback for further processing by the LOFAR framework
metadata_file = "%s_feedback_Correlated" % (self.parset_file, )
with duration(self, "get_metadata"):
self.run_task(
"get_metadata",
corrected_mapfile,
parset_prefix=(self.parset.getString('prefix') +
self.parset.fullModuleName('DataProducts')),
product_type="Correlated",
metadata_file=metadata_file)
self.send_feedback_processing(parameterset())
self.send_feedback_dataproducts(parameterset(metadata_file))
return 0
def __init__(self, parset, bands, direction, name=None):
self.parset = parset.copy()
self.bands = bands
self.name = name.lower()
self.parset['op_name'] = name
self.direction = direction
_logging.set_level(self.parset['logging_level'])
self.log = logging.getLogger('factor:{0}'.format(self.name))
self.hostname = socket.gethostname()
self.node_list = parset['cluster_specific']['node_list']
# Working directory
self.factor_working_dir = parset['dir_working']
# Pipeline runtime and working dirs (pipeline makes subdir here with
# name of direction)
self.pipeline_runtime_dir = os.path.join(self.factor_working_dir, 'results',
self.name)
self.pipeline_working_dir = self.pipeline_runtime_dir
create_directory(self.pipeline_runtime_dir)
# Directory that holds the mapfiles
self.pipeline_mapfile_dir = os.path.join(self.pipeline_runtime_dir,
self.direction.name, 'mapfiles')
create_directory(self.pipeline_mapfile_dir)
# Directory in the runtime dir that holds parset and config files (also
# the results of the pipeline)
self.pipeline_parset_dir = os.path.join(self.pipeline_runtime_dir,
self.direction.name)
create_directory(self.pipeline_parset_dir)
# Directory that holds the mapfiles
self.pipeline_mapfile_dir = os.path.join(self.pipeline_runtime_dir,
self.direction.name, 'mapfiles')
create_directory(self.pipeline_mapfile_dir)
# Local scratch directory and corresponding node recipes
if self.parset['cluster_specific']['dir_local'] is None:
# Not specified, specify scratch directory in normal work directory
self.local_scratch_dir = os.path.join(self.pipeline_working_dir,
self.direction.name)
self.dppp_nodescript = 'executable_args'
elif self.parset['cluster_specific']['clusterdesc_file'].lower() == 'pbs':
# PBS = "system in Hamburg" -> use special NDPPP nodescript
self.local_scratch_dir = self.parset['cluster_specific']['dir_local']
self.dppp_nodescript = 'dppp_scratch'
else:
# other: use given scratch directory an standard nodescrit
self.local_scratch_dir = self.parset['cluster_specific']['dir_local']
self.dppp_nodescript = 'executable_args'
# Directory that holds logs in a convenient place
self.log_dir = os.path.join(self.factor_working_dir, 'logs', self.name)
create_directory(self.log_dir)
# Log name used for logs in log_dir
self.logbasename = os.path.join(self.log_dir, self.direction.name)
# Below are paths for scripts, etc. in the Factor install directory
self.factor_root_dir = os.path.split(DIR)[0]
self.factor_pipeline_dir = os.path.join(self.factor_root_dir, 'pipeline')
self.factor_script_dir = os.path.join(self.factor_root_dir, 'scripts')
self.factor_parset_dir = os.path.join(self.factor_root_dir, 'parsets')
self.factor_skymodel_dir = os.path.join(self.factor_root_dir, 'skymodels')
# Below are the templates and output paths for the pipeline parset and
# config files. These may need to be re-defined in the subclasses
# if the operation has non-standard template names
self.pipeline_parset_template = '{0}_pipeline.parset'.format(self.name)
self.pipeline_parset_file = os.path.join(self.pipeline_parset_dir,
'pipeline.parset')
self.pipeline_config_template = 'pipeline.cfg'
self.pipeline_config_file = os.path.join(self.pipeline_parset_dir,
'pipeline.cfg')
# Define parameters needed for the pipeline config.
self.cfg_dict = {'lofarroot': parset['lofarroot'],
'pythonpath': parset['lofarpythonpath'],
'factorroot': self.factor_root_dir,
'pipeline_working_dir': self.pipeline_working_dir,
'pipeline_runtime_dir': self.pipeline_runtime_dir,
'casa_executable': parset['casa_executable'],
'wsclean_executable': parset['wsclean_executable'],
'image2fits_executable': parset['image2fits_executable'],
'dppp_nodescript': self.dppp_nodescript}
# Define global parameters needed by all pipeline parsets. Other,
# pipeline-specific, parameters should be defined in the subclasses by
# updating this dictionary
self.parms_dict = {'parset_dir': self.factor_parset_dir,
'skymodel_dir': self.factor_skymodel_dir,
'mapfile_dir': self.pipeline_mapfile_dir,
'pipeline_dir': self.factor_pipeline_dir,
'script_dir': self.factor_script_dir,
'local_dir': self.local_scratch_dir,
'hosts': self.node_list}
# Update the dictionaries with the attributes of the operation's
# direction object. Any attributes set in the direction object that are
# also in the parms_dict will be set to those of the direction object
# (e.g., 'max_cpus_per_node', which is set in the direction object by
# factor.cluster.divide_nodes() will override the value set above)
self.cfg_dict.update(self.direction.__dict__)
self.parms_dict.update(self.direction.__dict__)
# Add cluster-related info
if self.parset['cluster_specific']['clustertype'] == 'local':
self.cfg_dict['remote'] = '[remote]\n'\
+ 'method = local\n'\
+ 'max_per_node = {0}\n'.format(self.cfg_dict['max_cpus_per_node'])
elif self.parset['cluster_specific']['clustertype'] == 'juropa_slurm':
self.cfg_dict['remote'] = '[remote]\n'\
+ 'method = slurm_srun\n'\
+ 'max_per_node = {0}\n'.format(self.cfg_dict['max_cpus_per_node'])
elif self.parset['cluster_specific']['clustertype'] == 'pbs':
self.cfg_dict['remote'] = ''
else:
self.log.error('Could not determine the nature of your cluster!')
sys.exit(1)
# an absolute path in ...['clusterdesc'] will overrule the the "working_dir"
self.cfg_dict['clusterdesc'] = os.path.join(self.factor_working_dir,
self.parset['cluster_specific']['clusterdesc'])
def go(self):
"""
Contains functionality of the vdsmaker
"""
super(vdsmaker, self).go()
# **********************************************************************
# 1. Load data from disk create output files
args = self.inputs['args']
self.logger.debug("Loading input-data mapfile: %s" % args[0])
data = DataMap.load(args[0])
# Skip items in `data` that have 'skip' set to True
data.iterator = DataMap.SkipIterator
# Create output vds names
vdsnames = [
os.path.join(self.inputs['directory'],
os.path.basename(item.file) + '.vds') for item in data
]
# *********************************************************************
# 2. Call vdsmaker
command = "python %s" % (self.__file__.replace('master', 'nodes'))
jobs = []
for inp, vdsfile in zip(data, vdsnames):
jobs.append(
ComputeJob(inp.host,
command,
arguments=[
inp.file,
self.config.get('cluster', 'clusterdesc'),
vdsfile, self.inputs['makevds']
]))
self._schedule_jobs(jobs, max_per_node=self.inputs['nproc'])
vdsnames = [
vds for vds, job in zip(vdsnames, jobs)
if job.results['returncode'] == 0
]
if not vdsnames:
self.logger.error("All makevds processes failed. Bailing out!")
return 1
# *********************************************************************
# 3. Combine VDS files to produce GDS
failure = False
self.logger.info("Combining VDS files")
executable = self.inputs['combinevds']
gvds_out = self.inputs['gvds']
# Create the gvds directory for output files, needed for combine
create_directory(os.path.dirname(gvds_out))
try:
command = [executable, gvds_out] + vdsnames
combineproc = subprocess.Popen(command,
close_fds=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
sout, serr = combineproc.communicate()
log_process_output(executable, sout, serr, self.logger)
if combineproc.returncode != 0:
raise subprocess.CalledProcessError(combineproc.returncode,
command)
self.outputs['gvds'] = gvds_out
self.logger.info("Wrote combined VDS file: %s" % gvds_out)
except subprocess.CalledProcessError, cpe:
self.logger.exception("combinevds failed with status %d: %s" %
(cpe.returncode, serr))
failure = True
def pipeline_logic(self):
"""
Define the individual tasks that comprise the current pipeline.
This method will be invoked by the base-class's `go()` method.
"""
self.logger.info("Starting imager pipeline")
# Define scratch directory to be used by the compute nodes.
self.scratch_directory = os.path.join(
self.inputs['working_directory'], self.inputs['job_name'])
# Get input/output-data products specifications.
self._get_io_product_specs()
# remove prepending parset identifiers, leave only pipelinecontrol
full_parset = self.parset
self.parset = self.parset.makeSubset(
self.parset.fullModuleName('PythonControl') + '.') # remove this
# Create directories to store communication and data files
job_dir = self.config.get("layout", "job_directory")
self.parset_dir = os.path.join(job_dir, "parsets")
create_directory(self.parset_dir)
self.mapfile_dir = os.path.join(job_dir, "mapfiles")
create_directory(self.mapfile_dir)
# *********************************************************************
# (INPUT) Get the input from external sources and create pipeline types
# Input measure ment sets
input_mapfile = os.path.join(self.mapfile_dir, "uvdata.mapfile")
self.input_data.save(input_mapfile)
# storedata_map(input_mapfile, self.input_data)
self.logger.debug(
"Wrote input UV-data mapfile: {0}".format(input_mapfile))
# Provides location for the scratch directory and concat.ms location
target_mapfile = os.path.join(self.mapfile_dir, "target.mapfile")
self.target_data.save(target_mapfile)
self.logger.debug(
"Wrote target mapfile: {0}".format(target_mapfile))
# images datafiles
output_image_mapfile = os.path.join(self.mapfile_dir, "images.mapfile")
self.output_data.save(output_image_mapfile)
self.logger.debug(
"Wrote output sky-image mapfile: {0}".format(output_image_mapfile))
# Location of the output measurement set
output_correlated_mapfile = os.path.join(self.mapfile_dir,
"correlated.mapfile")
self.output_correlated_data.save(output_correlated_mapfile)
self.logger.debug(
"Wrote output correlated mapfile: {0}".format(output_correlated_mapfile))
# Get pipeline parameters from the toplevel recipe
# TODO: This is a backdoor option to manually add beamtables when these
# are missing on the provided ms. There is NO use case for users of the
# pipeline
add_beam_tables = self.parset.getBool(
"Imaging.addBeamTables", False)
number_of_major_cycles = self.parset.getInt(
"Imaging.number_of_major_cycles")
# Almost always a users wants a partial succes above a failed pipeline
output_result_of_last_succesfull_cycle = self.parset.getBool(
"Imaging.output_on_error", True)
if number_of_major_cycles < 3:
self.logger.error(
"The number of major cycles must be 3 or higher, correct"
" the key: Imaging.number_of_major_cycles")
raise PipelineException(
"Incorrect number_of_major_cycles in the parset")
# ******************************************************************
# (1) prepare phase: copy and collect the ms
concat_ms_map_path, timeslice_map_path, ms_per_image_map_path, \
processed_ms_dir = self._prepare_phase(input_mapfile,
target_mapfile, add_beam_tables)
# We start with an empty source_list map. It should contain n_output
# entries all set to empty strings
source_list_map_path = os.path.join(self.mapfile_dir,
"initial_sourcelist.mapfile")
source_list_map = DataMap.load(target_mapfile) # copy the output map
for item in source_list_map:
item.file = "" # set all to empty string
source_list_map.save(source_list_map_path)
succesfull_cycle_mapfiles_dict = None
for idx_cycle in range(number_of_major_cycles):
try:
# *****************************************************************
# (2) Create dbs and sky model
parmdbs_path, sourcedb_map_path = self._create_dbs(
concat_ms_map_path, timeslice_map_path, idx_cycle,
source_list_map_path = source_list_map_path,
skip_create_dbs = False)
# *****************************************************************
# (3) bbs_imager recipe.
bbs_output = self._bbs(concat_ms_map_path, timeslice_map_path,
parmdbs_path, sourcedb_map_path, idx_cycle, skip = False)
# TODO: Extra recipe: concat timeslices using pyrap.concatms
# (see prepare) redmine issue #6021
# Done in imager_bbs.p at the node level after calibration
# *****************************************************************
# (4) Get parameters awimager from the prepare_parset and inputs
aw_image_mapfile, maxbaseline = self._aw_imager(concat_ms_map_path,
idx_cycle, sourcedb_map_path, number_of_major_cycles,
skip = False)
# *****************************************************************
# (5) Source finding
source_list_map_path, found_sourcedb_path = self._source_finding(
aw_image_mapfile, idx_cycle, skip = False)
# should the output be a sourcedb? instead of a sourcelist
# save the active mapfiles: locations and content
# Used to output last succesfull cycle on error
mapfiles_to_save = {'aw_image_mapfile':aw_image_mapfile,
'source_list_map_path':source_list_map_path,
'found_sourcedb_path':found_sourcedb_path,
'concat_ms_map_path':concat_ms_map_path}
succesfull_cycle_mapfiles_dict = self._save_active_mapfiles(idx_cycle,
self.mapfile_dir, mapfiles_to_save)
# On exception there is the option to output the results of the
# last cycle without errors
except KeyboardInterrupt as ex:
raise ex
except Exception as ex:
self.logger.error("Encountered an fatal exception during self"
"calibration. Aborting processing and return"
" the last succesfull cycle results")
self.logger.error(str(ex))
# if we are in the first cycle always exit with exception
if idx_cycle == 0:
raise ex
if not output_result_of_last_succesfull_cycle:
raise ex
# restore the mapfile variables
aw_image_mapfile = succesfull_cycle_mapfiles_dict['aw_image_mapfile']
source_list_map_path = succesfull_cycle_mapfiles_dict['source_list_map_path']
found_sourcedb_path = succesfull_cycle_mapfiles_dict['found_sourcedb_path']
concat_ms_map_path = succesfull_cycle_mapfiles_dict['concat_ms_map_path']
# set the number_of_major_cycles to the correct number
number_of_major_cycles = idx_cycle - 1
max_cycles_reached = False
break
else:
max_cycles_reached = True
# TODO: minbaseline should be a parset value as is maxbaseline..
minbaseline = 0
# *********************************************************************
# (6) Finalize:
placed_data_image_map, placed_correlated_map = \
self._finalize(aw_image_mapfile,
processed_ms_dir, ms_per_image_map_path, source_list_map_path,
minbaseline, maxbaseline, target_mapfile, output_image_mapfile,
found_sourcedb_path, concat_ms_map_path, output_correlated_mapfile)
# *********************************************************************
# (7) Get metadata
# create a parset with information that is available on the toplevel
self._get_meta_data(number_of_major_cycles, placed_data_image_map,
placed_correlated_map, full_parset,
max_cycles_reached)
return 0
def pipeline_logic(self):
"""
Define the individual tasks that comprise the current pipeline.
This method will be invoked by the base-class's `go()` method.
"""
self.logger.info("Starting imager pipeline")
# Define scratch directory to be used by the compute nodes.
self.scratch_directory = os.path.join(self.inputs['working_directory'],
self.inputs['job_name'])
# Get input/output-data products specifications.
self._get_io_product_specs()
# remove prepending parset identifiers, leave only pipelinecontrol
full_parset = self.parset
self.parset = self.parset.makeSubset(
self.parset.fullModuleName('PythonControl') + '.') # remove this
# Create directories to store communication and data files
job_dir = self.config.get("layout", "job_directory")
self.parset_dir = os.path.join(job_dir, "parsets")
create_directory(self.parset_dir)
self.mapfile_dir = os.path.join(job_dir, "mapfiles")
create_directory(self.mapfile_dir)
# *********************************************************************
# (INPUT) Get the input from external sources and create pipeline types
# Input measure ment sets
input_mapfile = os.path.join(self.mapfile_dir, "uvdata.mapfile")
self.input_data.save(input_mapfile)
# storedata_map(input_mapfile, self.input_data)
self.logger.debug(
"Wrote input UV-data mapfile: {0}".format(input_mapfile))
# Provides location for the scratch directory and concat.ms location
target_mapfile = os.path.join(self.mapfile_dir, "target.mapfile")
self.target_data.save(target_mapfile)
self.logger.debug("Wrote target mapfile: {0}".format(target_mapfile))
# images datafiles
output_image_mapfile = os.path.join(self.mapfile_dir, "images.mapfile")
self.output_data.save(output_image_mapfile)
self.logger.debug(
"Wrote output sky-image mapfile: {0}".format(output_image_mapfile))
# ******************************************************************
# (1) prepare phase: copy and collect the ms
concat_ms_map_path, timeslice_map_path, ms_per_image_map_path, \
processed_ms_dir = self._prepare_phase(input_mapfile,
target_mapfile)
number_of_major_cycles = self.parset.getInt(
"Imaging.number_of_major_cycles")
# We start with an empty source_list map. It should contain n_output
# entries all set to empty strings
source_list_map_path = os.path.join(self.mapfile_dir,
"initial_sourcelist.mapfile")
source_list_map = DataMap.load(target_mapfile) # copy the output map
for item in source_list_map:
item.file = "" # set all to empty string
source_list_map.save(source_list_map_path)
for idx_loop in range(number_of_major_cycles):
# *****************************************************************
# (2) Create dbs and sky model
parmdbs_path, sourcedb_map_path = self._create_dbs(
concat_ms_map_path,
timeslice_map_path,
source_list_map_path=source_list_map_path,
skip_create_dbs=False)
# *****************************************************************
# (3) bbs_imager recipe.
bbs_output = self._bbs(timeslice_map_path,
parmdbs_path,
sourcedb_map_path,
skip=False)
# TODO: Extra recipe: concat timeslices using pyrap.concatms
# (see prepare)
# *****************************************************************
# (4) Get parameters awimager from the prepare_parset and inputs
aw_image_mapfile, maxbaseline = self._aw_imager(concat_ms_map_path,
idx_loop,
sourcedb_map_path,
skip=False)
# *****************************************************************
# (5) Source finding
sourcelist_map, found_sourcedb_path = self._source_finding(
aw_image_mapfile, idx_loop, skip=False)
# should the output be a sourcedb? instead of a sourcelist
# TODO: minbaseline should be a parset value as is maxbaseline..
minbaseline = 0
# *********************************************************************
# (6) Finalize:
placed_data_image_map = self._finalize(
aw_image_mapfile, processed_ms_dir, ms_per_image_map_path,
sourcelist_map, minbaseline, maxbaseline, target_mapfile,
output_image_mapfile, found_sourcedb_path)
# *********************************************************************
# (7) Get metadata
# Create a parset containing the metadata for MAC/SAS
metadata_file = "%s_feedback_SkyImage" % (self.parset_file, )
self.run_task(
"get_metadata",
placed_data_image_map,
parset_prefix=(full_parset.getString('prefix') +
full_parset.fullModuleName('DataProducts')),
product_type="SkyImage",
metadata_file=metadata_file)
self.send_feedback_processing(parameterset())
self.send_feedback_dataproducts(parameterset(metadata_file))
return 0
def pipeline_logic(self):
"""
Define the individual tasks that comprise the current pipeline.
This method will be invoked by the base-class's `go()` method.
Note: return 0 on success, 1 on failure.
"""
# *********************************************************************
# 1. Prepare phase, collect data from parset and input mapfiles.
#
# Note that PULP will read many of these fields directly. That makes
# the following fields, and possibly others, part of the API towards
# PULP:
#
# self.config
# self.logger
# self.input_data
# self.output_data
# self.parset_feedback_file
# self.job_dir
# Get input/output-data products specifications.
self._get_io_product_specs()
self.job_dir = self.config.get("layout", "job_directory")
parset_dir = os.path.join(self.job_dir, "parsets")
mapfile_dir = os.path.join(self.job_dir, "mapfiles")
# Create directories for temporary parset- and map files
create_directory(parset_dir)
create_directory(mapfile_dir)
# Write input- and output data map-files
# Coherent Stokes
self.input_CS_mapfile = os.path.join(mapfile_dir, "input_CS_data.mapfile")
self.input_data['coherent'].save(self.input_CS_mapfile)
# Incoherent Stokes
self.input_IS_mapfile = os.path.join(mapfile_dir, "input_IS_data.mapfile")
self.input_data['incoherent'].save(self.input_IS_mapfile)
# Output data
self.output_data_mapfile = os.path.join(mapfile_dir, "output_data.mapfile")
self.output_data['data'].save(self.output_data_mapfile)
if len(self.input_data) == 0:
self.logger.warn("No input data files to process. Bailing out!")
return 0
self.pulsar_parms = self.parset.makeSubset(self.parset.fullModuleName('Pulsar') + '.')
pulsar_parset = os.path.join(parset_dir, "Pulsar.parset")
self.pulsar_parms.writeFile(pulsar_parset)
self.logger.debug("Processing: %s" %
', '.join(str(f) for f in self.input_data))
# Rebuilding sys.argv without the options given automatically by framework
# --auto = automatic run from framework
# -q = quiet mode, no user interaction
sys.argv = ['pulp.py', '--auto', '-q']
if (not self.coherentStokesEnabled):
sys.argv.extend(["--noCS", "--noCV", "--noFE"])
if (not self.incoherentStokesEnabled):
sys.argv.append("--noIS")
# Tell PULP where to write the feedback to
self.parset_feedback_file = "%s_feedback" % (self.parset_file,)
# Run the pulsar pipeline
self.logger.debug("Starting pulp with: " + join(sys.argv))
p = pulp.pulp(self) # TODO: MUCK self to capture the API
# NOTE: PULP returns 0 on SUCCESS!!
if p.go():
self.logger.error("PULP did not succeed. Bailing out!")
return 1
# Read and forward the feedback
try:
metadata = parameterset(self.parset_feedback_file)
except IOError, e:
self.logger.error("Could not read feedback from %s: %s" % (metadata_file,e))
return 1
def run(self, executable, environment, parset, working_directory,
output_image, concatenated_measurement_set, sourcedb_path,
mask_patch_size, autogenerate_parameters, specify_fov, fov,
major_cycle, nr_cycles, perform_self_cal):
"""
:param executable: Path to awimager executable
:param environment: environment for catch_segfaults (executable runner)
:param parset: parameters for the awimager,
:param working_directory: directory the place temporary files
:param output_image: location and filesname to story the output images
the multiple images are appended with type extentions
:param concatenated_measurement_set: Input measurement set
:param sourcedb_path: Path the the sourcedb used to create the image
mask
:param mask_patch_size: Scaling of the patch around the source in the
mask
:param autogenerate_parameters: Turns on the autogeneration of:
cellsize, npix, wprojplanes, wmax, fov
:param fov: if autogenerate_parameters is false calculate
imageparameter (cellsize, npix, wprojplanes, wmax) relative to this
fov
:param major_cycle: number of the self calibration cycle to determine
the imaging parameters: cellsize, npix, wprojplanes, wmax, fov
:param nr_cycles: The requested number of self cal cycles
:param perform_self_cal: Bool used to control the selfcal functionality
or the old semi-automatic functionality
:rtype: self.outputs["image"] The path to the output image
"""
self.logger.info("Start selfcal_awimager node run:")
log4_cplus_name = "selfcal_awimager"
self.environment.update(environment)
with log_time(self.logger):
# Read the parameters as specified in the parset
parset_object = get_parset(parset)
# *************************************************************
# 1. Calculate awimager parameters that depend on measurement set
# and the parset
if perform_self_cal:
# Calculate awimager parameters that depend on measurement set
# and the parset
self.logger.info(
"Calculating selfcalibration parameters ")
cell_size, npix, w_max, w_proj_planes, \
UVmin, UVmax, robust, threshold =\
self._get_selfcal_parameters(
concatenated_measurement_set,
parset, major_cycle, nr_cycles)
self._save_selfcal_info(concatenated_measurement_set,
major_cycle, npix, UVmin, UVmax)
else:
self.logger.info(
"Calculating parameters.. ( NOT selfcalibration)")
cell_size, npix, w_max, w_proj_planes = \
self._get_imaging_parameters(
concatenated_measurement_set,
parset,
autogenerate_parameters,
specify_fov,
fov)
self.logger.info("Using autogenerated parameters; ")
self.logger.info(
"Calculated parameters: cell_size: {0}, npix: {1}".format(
cell_size, npix))
self.logger.info("w_max: {0}, w_proj_planes: {1} ".format(
w_max, w_proj_planes))
# ****************************************************************
# 2. Get the target image location from the mapfile for the parset.
# Create target dir if it not exists
image_path_head = os.path.dirname(output_image)
create_directory(image_path_head)
self.logger.debug("Created directory to place awimager output"
" files: {0}".format(image_path_head))
# ****************************************************************
# 3. Create the mask
#mask_file_path = self._create_mask(npix, cell_size, output_image,
# concatenated_measurement_set, executable,
# working_directory, log4_cplus_name, sourcedb_path,
# mask_patch_size, image_path_head)
# *****************************************************************
# 4. Update the parset with calculated parameters, and output image
patch_dictionary = {'uselogger': 'True', # enables log4cpluscd log
'ms': str(concatenated_measurement_set),
'cellsize': str(cell_size),
'npix': str(npix),
'wmax': str(w_max),
'wprojplanes': str(w_proj_planes),
'image': str(output_image),
'maxsupport': str(npix)
# 'mask':str(mask_file_path), #TODO REINTRODUCE
# MASK, excluded to speed up in this debug stage
}
# Add some aditional keys from the self calibration method
if perform_self_cal:
self_cal_patch_dict = {
'weight': 'briggs',
'padding': str(1.18),
'niter' : str(1000000),
'operation' : 'mfclark',
'timewindow' : '300',
'fits' : '',
'threshold' : str(threshold),
'robust' : str(robust),
'UVmin' : str(UVmin),
'UVmax' : str(UVmax),
'maxbaseline' : str(10000000),
'select' : str("sumsqr(UVW[:2])<1e12"),
}
patch_dictionary.update(self_cal_patch_dict)
# save the parset at the target dir for the image
calculated_parset_path = os.path.join(image_path_head,
"parset.par")
try:
temp_parset_filename = patch_parset(parset, patch_dictionary)
# Copy tmp file to the final location
shutil.copyfile(temp_parset_filename, calculated_parset_path)
self.logger.debug("Wrote parset for awimager run: {0}".format(
calculated_parset_path))
finally:
# remove temp file
os.remove(temp_parset_filename)
# *****************************************************************
# 5. Run the awimager with the parameterset
cmd = [executable, calculated_parset_path]
self.logger.debug("Parset used for awimager run:")
self.logger.debug(cmd)
try:
with CatchLog4CPlus(working_directory,
self.logger.name + "." +
os.path.basename(log4_cplus_name),
os.path.basename(executable)
) as logger:
catch_segfaults(cmd, working_directory, self.environment,
logger, usageStats=self.resourceMonitor)
# Thrown by catch_segfault
except CalledProcessError, exception:
self.logger.error(str(exception))
return 1
except Exception, exception:
self.logger.error(str(exception))
return 1
def run(self, executable, environment, parset, working_directory,
output_image, concatenated_measurement_set, sourcedb_path,
mask_patch_size, autogenerate_parameters, specify_fov, fov,
major_cycle, nr_cycles, perform_self_cal):
"""
:param executable: Path to awimager executable
:param environment: environment for catch_segfaults (executable runner)
:param parset: parameters for the awimager,
:param working_directory: directory the place temporary files
:param output_image: location and filesname to story the output images
the multiple images are appended with type extentions
:param concatenated_measurement_set: Input measurement set
:param sourcedb_path: Path the the sourcedb used to create the image
mask
:param mask_patch_size: Scaling of the patch around the source in the
mask
:param autogenerate_parameters: Turns on the autogeneration of:
cellsize, npix, wprojplanes, wmax, fov
:param fov: if autogenerate_parameters is false calculate
imageparameter (cellsize, npix, wprojplanes, wmax) relative to this
fov
:param major_cycle: number of the self calibration cycle to determine
the imaging parameters: cellsize, npix, wprojplanes, wmax, fov
:param nr_cycles: The requested number of self cal cycles
:param perform_self_cal: Bool used to control the selfcal functionality
or the old semi-automatic functionality
:rtype: self.outputs["image"] The path to the output image
"""
self.logger.info("Start selfcal_awimager node run:")
log4_cplus_name = "selfcal_awimager"
self.environment.update(environment)
with log_time(self.logger):
# Read the parameters as specified in the parset
parset_object = get_parset(parset)
# *************************************************************
# 1. Calculate awimager parameters that depend on measurement set
# and the parset
if perform_self_cal:
# Calculate awimager parameters that depend on measurement set
# and the parset
self.logger.info(
"Calculating selfcalibration parameters ")
cell_size, npix, w_max, w_proj_planes, \
UVmin, UVmax, robust, threshold =\
self._get_selfcal_parameters(
concatenated_measurement_set,
parset, major_cycle, nr_cycles)
self._save_selfcal_info(concatenated_measurement_set,
major_cycle, npix, UVmin, UVmax)
else:
self.logger.info(
"Calculating parameters.. ( NOT selfcalibration)")
cell_size, npix, w_max, w_proj_planes = \
self._get_imaging_parameters(
concatenated_measurement_set,
parset,
autogenerate_parameters,
specify_fov,
fov)
self.logger.info("Using autogenerated parameters; ")
self.logger.info(
"Calculated parameters: cell_size: {0}, npix: {1}".format(
cell_size, npix))
self.logger.info("w_max: {0}, w_proj_planes: {1} ".format(
w_max, w_proj_planes))
# ****************************************************************
# 2. Get the target image location from the mapfile for the parset.
# Create target dir if it not exists
image_path_head = os.path.dirname(output_image)
create_directory(image_path_head)
self.logger.debug("Created directory to place awimager output"
" files: {0}".format(image_path_head))
# ****************************************************************
# 3. Create the mask
#mask_file_path = self._create_mask(npix, cell_size, output_image,
# concatenated_measurement_set, executable,
# working_directory, log4_cplus_name, sourcedb_path,
# mask_patch_size, image_path_head)
# *****************************************************************
# 4. Update the parset with calculated parameters, and output image
patch_dictionary = {'uselogger': 'True', # enables log4cpluscd log
'ms': str(concatenated_measurement_set),
'cellsize': str(cell_size),
'npix': str(npix),
'wmax': str(w_max),
'wprojplanes': str(w_proj_planes),
'image': str(output_image),
'maxsupport': str(npix)
# 'mask':str(mask_file_path), #TODO REINTRODUCE
# MASK, excluded to speed up in this debug stage
}
# Add some aditional keys from the self calibration method
if perform_self_cal:
self_cal_patch_dict = {
'weight': 'briggs',
'padding': str(1.18),
'niter' : str(1000000),
'operation' : 'mfclark',
'timewindow' : '300',
'fits' : '',
'threshold' : str(threshold),
'robust' : str(robust),
'UVmin' : str(UVmin),
'UVmax' : str(UVmax),
'maxbaseline' : str(10000000),
'select' : str("sumsqr(UVW[:2])<1e12"),
}
patch_dictionary.update(self_cal_patch_dict)
# save the parset at the target dir for the image
calculated_parset_path = os.path.join(image_path_head,
"parset.par")
try:
temp_parset_filename = patch_parset(parset, patch_dictionary)
# Copy tmp file to the final location
shutil.copyfile(temp_parset_filename, calculated_parset_path)
self.logger.debug("Wrote parset for awimager run: {0}".format(
calculated_parset_path))
finally:
# remove temp file
os.remove(temp_parset_filename)
# *****************************************************************
# 5. Run the awimager with the parameterset
cmd = [executable, calculated_parset_path]
self.logger.debug("Parset used for awimager run:")
self.logger.debug(cmd)
try:
with CatchLog4CPlus(working_directory,
self.logger.name + "." +
os.path.basename(log4_cplus_name),
os.path.basename(executable)
) as logger:
catch_segfaults(cmd, working_directory, self.environment,
logger, usageStats=self.resourceMonitor)
# Thrown by catch_segfault
except CalledProcessError as exception:
self.logger.error(str(exception))
return 1
except Exception as exception:
self.logger.error(str(exception))
return 1
# *********************************************************************
# 6. Return output
# Append static .restored: This might change but prob. not
# The actual output image has this extention always, default of
# awimager
self.outputs["image"] = output_image + ".restored"
return 0
def pipeline_logic(self):
"""
Define the individual tasks that comprise the current pipeline.
This method will be invoked by the base-class's `go()` method.
"""
# *********************************************************************
# 1. Prepare phase, collect data from parset and input mapfiles
# Create a parameter-subset containing only python-control stuff.
py_parset = self.parset.makeSubset(
'ObsSW.Observation.ObservationControl.PythonControl.')
# Get input/output-data products specifications.
self._get_io_product_specs()
# Create some needed directories
job_dir = self.config.get("layout", "job_directory")
mapfile_dir = os.path.join(job_dir, "mapfiles")
create_directory(mapfile_dir)
parset_dir = os.path.join(job_dir, "parsets")
create_directory(parset_dir)
# *********************************************************************
# 2. Copy the instrument files to the correct node
# The instrument files are currently located on the wrong nodes
# Copy to correct nodes and assign the instrument table the now
# correct data
# Copy the instrument files to the corrent nodes: failures might happen
# update both intrument and datamap to contain only successes!
self._copy_instrument_files(mapfile_dir)
# Write input- and output data map-files.
data_mapfile = os.path.join(mapfile_dir, "data.mapfile")
self.input_data['data'].save(data_mapfile)
copied_instrument_mapfile = os.path.join(mapfile_dir, "copied_instrument.mapfile")
self.input_data['instrument'].save(copied_instrument_mapfile)
self.logger.debug(
"Wrote input data mapfile: %s" % data_mapfile
)
# Save copied files to a new mapfile
corrected_mapfile = os.path.join(mapfile_dir, "corrected_data.mapfile")
self.output_data['data'].save(corrected_mapfile)
self.logger.debug(
"Wrote output corrected data mapfile: %s" % corrected_mapfile
)
# Validate number of copied files, abort on zero files copied
if len(self.input_data['data']) == 0:
self.logger.warn("No input data files to process. Bailing out!")
return 0
self.logger.debug("Processing: %s" %
', '.join(str(f) for f in self.input_data['data'])
)
# *********************************************************************
# 3. Create database needed for performing work:
# - GVDS, describing data on the compute nodes
# - SourceDB, for skymodel (A-team)
# - ParmDB for outputtting solutions
with duration(self, "vdsmaker"):
gvds_file = self.run_task("vdsmaker", data_mapfile)['gvds']
# Read metadata (e.g., start- and end-time) from the GVDS file.
with duration(self, "vdsreader"):
vdsinfo = self.run_task("vdsreader", gvds=gvds_file)
# Create an empty parmdb for DPPP
with duration(self, "setupparmdb"):
parmdb_mapfile = self.run_task("setupparmdb", data_mapfile)['mapfile']
# Create a sourcedb to be used by the demixing phase of DPPP
# The user-supplied sky model can either be a name, in which case the
# pipeline will search for a file <name>.skymodel in the default search
# path $LOFARROOT/share/pipeline/skymodels; or a full path.
# It is an error if the file does not exist.
skymodel = py_parset.getString('PreProcessing.SkyModel')
if not os.path.isabs(skymodel):
skymodel = os.path.join(
# This should really become os.environ['LOFARROOT']
self.config.get('DEFAULT', 'lofarroot'),
'share', 'pipeline', 'skymodels', skymodel + '.skymodel'
)
if not os.path.isfile(skymodel):
raise PipelineException("Skymodel %s does not exist" % skymodel)
with duration(self, "setupsourcedb"):
sourcedb_mapfile = self.run_task(
"setupsourcedb", data_mapfile,
skymodel=skymodel,
suffix='.dppp.sourcedb',
type='blob'
)['mapfile']
# *********************************************************************
# 4. Run NDPPP to demix the A-Team sources
# Create a parameter-subset for DPPP and write it to file.
ndppp_parset = os.path.join(parset_dir, "NDPPP.parset")
py_parset.makeSubset('DPPP.').writeFile(ndppp_parset)
# Run the Default Pre-Processing Pipeline (DPPP);
with duration(self, "ndppp"):
dppp_mapfile = self.run_task("ndppp",
data_mapfile,
data_start_time=vdsinfo['start_time'],
data_end_time=vdsinfo['end_time'],
demix_always=
py_parset.getStringVector('PreProcessing.demix_always'),
demix_if_needed=
py_parset.getStringVector('PreProcessing.demix_if_needed'),
parset=ndppp_parset,
parmdb_mapfile=parmdb_mapfile,
sourcedb_mapfile=sourcedb_mapfile,
mapfile=os.path.join(mapfile_dir, 'dppp.mapfile')
)['mapfile']
# ********************************************************************
# 5. Run bss using the instrument file from the target observation
# Create an empty sourcedb for BBS
with duration(self, "setupsourcedb"):
sourcedb_mapfile = self.run_task(
"setupsourcedb", data_mapfile
)['mapfile']
# Create a parameter-subset for BBS and write it to file.
bbs_parset = os.path.join(parset_dir, "BBS.parset")
py_parset.makeSubset('BBS.').writeFile(bbs_parset)
# Run BBS to calibrate the target source(s).
with duration(self, "bbs_reducer"):
bbs_mapfile = self.run_task("bbs_reducer",
dppp_mapfile,
parset=bbs_parset,
instrument_mapfile=copied_instrument_mapfile,
sky_mapfile=sourcedb_mapfile
)['data_mapfile']
# *********************************************************************
# 6. Copy the MS's to their final output destination.
# When the copier recipe has run, the map-file named in
# corrected_mapfile will contain an updated map of output files.
with duration(self, "copier"):
self.run_task("copier",
mapfile_source=bbs_mapfile,
mapfile_target=corrected_mapfile,
mapfiles_dir=mapfile_dir,
mapfile=corrected_mapfile
)
# *********************************************************************
# 7. Create feedback file for further processing by the LOFAR framework
# (MAC)
# Create a parset-file containing the metadata for MAC/SAS
with duration(self, "get_metadata"):
self.run_task("get_metadata", corrected_mapfile,
parset_file=self.parset_feedback_file,
parset_prefix=(
self.parset.getString('prefix') +
self.parset.fullModuleName('DataProducts')
),
product_type="Correlated")
return 0
def pipeline_logic(self):
"""
Define the individual tasks that comprise the current pipeline.
This method will be invoked by the base-class's `go()` method.
Note: return 0 on success, 1 on failure.
"""
# *********************************************************************
# 1. Prepare phase, collect data from parset and input mapfiles.
#
# Note that PULP will read many of these fields directly. That makes
# the following fields, and possibly others, part of the API towards
# PULP:
#
# self.config
# self.logger
# self.input_data
# self.output_data
# self.parset_feedback_file
# self.job_dir
# Get input/output-data products specifications.
self._get_io_product_specs()
self.job_dir = self.config.get("layout", "job_directory")
self.globalfs = self.config.has_option("remote", "globalfs") and self.config.getboolean("remote", "globalfs")
parset_dir = os.path.join(self.job_dir, "parsets")
mapfile_dir = os.path.join(self.job_dir, "mapfiles")
# Create directories for temporary parset- and map files
create_directory(parset_dir)
create_directory(mapfile_dir)
# Write input- and output data map-files
# Coherent Stokes
self.input_CS_mapfile = os.path.join(mapfile_dir, "input_CS_data.mapfile")
self.input_data['coherent'].save(self.input_CS_mapfile)
# Incoherent Stokes
self.input_IS_mapfile = os.path.join(mapfile_dir, "input_IS_data.mapfile")
self.input_data['incoherent'].save(self.input_IS_mapfile)
# Output data
self.output_data_mapfile = os.path.join(mapfile_dir, "output_data.mapfile")
self.output_data['data'].save(self.output_data_mapfile)
if len(self.input_data) == 0:
self.logger.warn("No input data files to process. Bailing out!")
return 0
self.pulsar_parms = self.parset.makeSubset(self.parset.fullModuleName('Pulsar') + '.')
pulsar_parset = os.path.join(parset_dir, "Pulsar.parset")
if self.globalfs:
# patch for Pulp in case of DOCKER
for k in [x for x in self.pulsar_parms.keys() if x.endswith("_extra_opts")]:
self.pulsar_parms.replace(k, self.pulsar_parms[k].getString().replace(" ","\\\\ "))
self.pulsar_parms.writeFile(pulsar_parset)
self.logger.debug("Processing: %s" %
', '.join(str(f) for f in self.input_data))
# Rebuilding sys.argv without the options given automatically by framework
# --auto = automatic run from framework
# -q = quiet mode, no user interaction
sys.argv = ['pulp.py', '--auto', '-q']
if self.globalfs:
project = self.parset.getString(self.parset.fullModuleName('Campaign') + '.name')
sys.argv.extend(['--slurm', '--globalfs', '--docker', '--docker-container=lofar-pulp:%s' % os.environ.get("LOFAR_TAG"), '--raw=/data/projects/%s' % project])
else:
sys.argv.append("--auto")
if (not self.coherentStokesEnabled):
sys.argv.extend(["--noCS", "--noCV", "--noFE"])
if (not self.incoherentStokesEnabled):
sys.argv.append("--noIS")
# Tell PULP where to write the feedback to
self.parset_feedback_file = "%s_feedback" % (self.parset_file,)
# Run the pulsar pipeline
self.logger.debug("Starting pulp with: " + join(sys.argv))
self.logger.debug("Calling pulp.pulp(self) with self = %s", pprint.pformat(vars(self)))
p = pulp.pulp(self) # TODO: MUCK self to capture the API
# NOTE: PULP returns 0 on SUCCESS!!
if p.go():
self.logger.error("PULP did not succeed. Bailing out!")
return 1
# Read and forward the feedback
try:
metadata = parameterset(self.parset_feedback_file)
except IOError, e:
self.logger.error("Could not read feedback from %s: %s" % (metadata_file,e))
return 1
def pipeline_logic(self):
"""
Define the individual tasks that comprise the current pipeline.
This method will be invoked by the base-class's `go()` method.
"""
self.logger.info("Starting longbaseline pipeline")
# Define scratch directory to be used by the compute nodes.
self.scratch_directory = os.path.join(self.inputs['working_directory'],
self.inputs['job_name'])
# Get input/output-data products specifications.
self._get_io_product_specs()
# remove prepending parset identifiers, leave only pipelinecontrol
full_parset = self.parset
self.parset = self.parset.makeSubset(
self.parset.fullModuleName('PythonControl') + '.') # remove this
# Create directories to store communication and data files
job_dir = self.config.get("layout", "job_directory")
self.parset_dir = os.path.join(job_dir, "parsets")
create_directory(self.parset_dir)
self.mapfile_dir = os.path.join(job_dir, "mapfiles")
create_directory(self.mapfile_dir)
# *********************************************************************
# (INPUT) Get the input from external sources and create pipeline types
# Input measure ment sets
input_mapfile = os.path.join(self.mapfile_dir, "uvdata.mapfile")
self.input_data.save(input_mapfile)
## ***************************************************************
#output_mapfile_path = os.path.join(self.mapfile_dir, "output.mapfile")
#self.output_mapfile.save(output_mapfile_path)
# storedata_map(input_mapfile, self.input_data)
self.logger.debug(
"Wrote input UV-data mapfile: {0}".format(input_mapfile))
# Provides location for the scratch directory and concat.ms location
target_mapfile = os.path.join(self.mapfile_dir, "target.mapfile")
self.target_data.save(target_mapfile)
self.logger.debug("Wrote target mapfile: {0}".format(target_mapfile))
# images datafiles
output_ms_mapfile = os.path.join(self.mapfile_dir, "output.mapfile")
self.output_data.save(output_ms_mapfile)
self.logger.debug(
"Wrote output sky-image mapfile: {0}".format(output_ms_mapfile))
# TODO: This is a backdoor option to manually add beamtables when these
# are missing on the provided ms. There is NO use case for users of the
# pipeline
add_beam_tables = self.parset.getBool("Imaging.addBeamTables", False)
# ******************************************************************
# (1) prepare phase: copy and collect the ms
concat_ms_map_path, timeslice_map_path, ms_per_image_map_path, \
processed_ms_dir = self._long_baseline(input_mapfile,
target_mapfile, add_beam_tables, output_ms_mapfile)
# *********************************************************************
# (7) Get metadata
# create a parset with information that is available on the toplevel
toplevel_meta_data = parameterset(
{'feedback_version': feedback_version})
# get some parameters from the imaging pipeline parset:
subbandgroups_per_ms = self.parset.getInt(
"LongBaseline.subbandgroups_per_ms")
subbands_per_subbandgroup = self.parset.getInt(
"LongBaseline.subbands_per_subbandgroup")
toplevel_meta_data.replace("subbandsPerSubbandGroup",
str(subbands_per_subbandgroup))
toplevel_meta_data.replace("subbandGroupsPerMS",
str(subbandgroups_per_ms))
# Create a parset-file containing the metadata for MAC/SAS at nodes
metadata_file = "%s_feedback_Correlated" % (self.parset_file, )
self.run_task(
"get_metadata",
output_ms_mapfile,
parset_prefix=(full_parset.getString('prefix') +
full_parset.fullModuleName('DataProducts')),
product_type="Correlated",
metadata_file=metadata_file)
self.send_feedback_processing(toplevel_meta_data)
self.send_feedback_dataproducts(parameterset(metadata_file))
return 0
def pipeline_logic(self):
"""
Define the individual tasks that comprise the current pipeline.
This method will be invoked by the base-class's `go()` method.
"""
# *********************************************************************
# 1. Get input from parset, validate and cast to pipeline 'data types'
# Only perform work on existing files
# Created needed directories
# Create a parameter-subset containing only python-control stuff.
py_parset = self.parset.makeSubset(
self.parset.fullModuleName('PythonControl') + '.')
# Get input/output-data products specifications.
self._get_io_product_specs()
job_dir = self.config.get("layout", "job_directory")
parset_dir = os.path.join(job_dir, "parsets")
mapfile_dir = os.path.join(job_dir, "mapfiles")
# Create directories for temporary parset- and map files
create_directory(parset_dir)
create_directory(mapfile_dir)
# Write input- and output data map-files
input_correlated_mapfile = os.path.join(
mapfile_dir, "input_correlated.mapfile"
)
output_correlated_mapfile = os.path.join(
mapfile_dir, "output_correlated.mapfile"
)
output_instrument_mapfile = os.path.join(
mapfile_dir, "output_instrument.mapfile"
)
self.input_data['correlated'].save(input_correlated_mapfile)
self.output_data['correlated'].save(output_correlated_mapfile)
self.output_data['instrument'].save(output_instrument_mapfile)
if len(self.input_data['correlated']) == 0:
self.logger.warn("No input data files to process. Bailing out!")
return 0
self.logger.debug("Processing: %s" %
', '.join(str(f) for f in self.input_data['correlated']))
# *********************************************************************
# 2. Create database needed for performing work:
# Vds, descibing data on the nodes
# sourcedb, For skymodel (A-team)
# parmdb for outputtting solutions
# Produce a GVDS file describing the data on the compute nodes.
with duration(self, "vdsmaker"):
gvds_file = self.run_task(
"vdsmaker", input_correlated_mapfile
)['gvds']
# Read metadata (start, end times, pointing direction) from GVDS.
with duration(self, "vdsreader"):
vdsinfo = self.run_task("vdsreader", gvds=gvds_file)
# Create an empty parmdb for DPPP
with duration(self, "setupparmdb"):
parmdb_mapfile = self.run_task(
"setupparmdb", input_correlated_mapfile,
mapfile=os.path.join(mapfile_dir, 'dppp.parmdb.mapfile'),
suffix='.dppp.parmdb'
)['mapfile']
# Create a sourcedb to be used by the demixing phase of DPPP
# The user-supplied sky model can either be a name, in which case the
# pipeline will search for a file <name>.skymodel in the default search
# path $LOFARROOT/share/pipeline/skymodels; or a full path.
# It is an error if the file does not exist.
skymodel = py_parset.getString('PreProcessing.SkyModel')
if not os.path.isabs(skymodel):
skymodel = os.path.join(
# This should really become os.environ['LOFARROOT']
self.config.get('DEFAULT', 'lofarroot'),
'share', 'pipeline', 'skymodels', skymodel + '.skymodel'
)
if not os.path.isfile(skymodel):
raise PipelineException("Skymodel %s does not exist" % skymodel)
with duration(self, "setupsourcedb"):
sourcedb_mapfile = self.run_task(
"setupsourcedb", input_correlated_mapfile,
mapfile=os.path.join(mapfile_dir, 'dppp.sourcedb.mapfile'),
skymodel=skymodel,
suffix='.dppp.sourcedb',
type='blob'
)['mapfile']
# *********************************************************************
# 3. Run NDPPP to demix the A-Team sources
# TODOW: Do flagging?
# Create a parameter-subset for DPPP and write it to file.
ndppp_parset = os.path.join(parset_dir, "NDPPP.parset")
py_parset.makeSubset('DPPP.').writeFile(ndppp_parset)
# Run the Default Pre-Processing Pipeline (DPPP);
with duration(self, "ndppp"):
dppp_mapfile = self.run_task(
"ndppp", input_correlated_mapfile,
data_start_time=vdsinfo['start_time'],
data_end_time=vdsinfo['end_time'],
demix_always=
py_parset.getStringVector('PreProcessing.demix_always'),
demix_if_needed=
py_parset.getStringVector('PreProcessing.demix_if_needed'),
parset=ndppp_parset,
parmdb_mapfile=parmdb_mapfile,
sourcedb_mapfile=sourcedb_mapfile
)['mapfile']
# *********************************************************************
# 4. Run BBS with a model of the calibrator
# Create a parmdb for calibration solutions
# Create sourcedb with known calibration solutions
# Run bbs with both
# Create an empty parmdb for BBS
with duration(self, "setupparmdb"):
parmdb_mapfile = self.run_task(
"setupparmdb", dppp_mapfile,
mapfile=os.path.join(mapfile_dir, 'bbs.parmdb.mapfile'),
suffix='.bbs.parmdb'
)['mapfile']
# Create a sourcedb based on sourcedb's input argument "skymodel"
with duration(self, "setupsourcedb"):
sourcedb_mapfile = self.run_task(
"setupsourcedb", input_correlated_mapfile,
skymodel=os.path.join(
self.config.get('DEFAULT', 'lofarroot'),
'share', 'pipeline', 'skymodels',
py_parset.getString('Calibration.SkyModel') +
'.skymodel'),
mapfile=os.path.join(mapfile_dir, 'bbs.sourcedb.mapfile'),
suffix='.bbs.sourcedb')['mapfile']
# Create a parameter-subset for BBS and write it to file.
bbs_parset = os.path.join(parset_dir, "BBS.parset")
py_parset.makeSubset('BBS.').writeFile(bbs_parset)
# Run BBS to calibrate the calibrator source(s).
with duration(self, "bbs_reducer"):
bbs_mapfile = self.run_task(
"bbs_reducer", dppp_mapfile,
parset=bbs_parset,
instrument_mapfile=parmdb_mapfile,
sky_mapfile=sourcedb_mapfile
)['data_mapfile']
# *********************************************************************
# 5. Perform gain outlier correction on the found calibration solutions
# Swapping outliers in the gains with the median
# Export the calibration solutions using gainoutliercorrection and store
# the results in the files specified in the instrument mapfile.
export_instrument_model = py_parset.getBool(
'Calibration.exportCalibrationParameters', False)
with duration(self, "gainoutliercorrection"):
self.run_task("gainoutliercorrection",
(parmdb_mapfile, output_instrument_mapfile),
sigma=1.0,
export_instrument_model=export_instrument_model) # TODO: Parset parameter
# *********************************************************************
# 6. Copy corrected MS's to their final output destination.
with duration(self, "copier"):
self.run_task("copier",
mapfile_source=bbs_mapfile,
mapfile_target=output_correlated_mapfile,
mapfiles_dir=mapfile_dir,
mapfile=output_correlated_mapfile
)
# *********************************************************************
# 7. Create feedback file for further processing by the LOFAR framework
# a. get metadata of the measurement sets
# b. get metadata of the instrument models
# c. join the two files and write the final feedback file
correlated_metadata = os.path.join(parset_dir, "correlated.metadata")
instrument_metadata = os.path.join(parset_dir, "instrument.metadata")
with duration(self, "get_metadata"):
self.run_task("get_metadata", output_correlated_mapfile,
parset_file=correlated_metadata,
parset_prefix=(
self.parset.getString('prefix') +
self.parset.fullModuleName('DataProducts')),
product_type="Correlated")
with duration(self, "get_metadata"):
self.run_task("get_metadata", output_instrument_mapfile,
parset_file=instrument_metadata,
parset_prefix=(
self.parset.getString('prefix') +
self.parset.fullModuleName('DataProducts')),
product_type="InstrumentModel")
parset = parameterset(correlated_metadata)
parset.adoptFile(instrument_metadata)
parset.writeFile(self.parset_feedback_file)
return 0
def pipeline_logic(self):
try:
parset_file = os.path.abspath(self.inputs['args'][0])
except IndexError:
return self.usage()
try:
if self.parset.keys == []:
self.parset.adoptFile(parset_file)
self.parset_feedback_file = parset_file + "_feedback"
except RuntimeError:
print >> sys.stderr, "Error: Parset file not found!"
return self.usage()
self._replace_values()
# just a reminder that this has to be implemented
validator = GenericPipelineParsetValidation(self.parset)
if not validator.validate_pipeline():
self.usage()
exit(1)
if not validator.validate_steps():
self.usage()
exit(1)
#set up directories
job_dir = self.config.get("layout", "job_directory")
parset_dir = os.path.join(job_dir, "parsets")
mapfile_dir = os.path.join(job_dir, "mapfiles")
# Create directories for temporary parset- and map files
create_directory(parset_dir)
create_directory(mapfile_dir)
# *********************************************************************
# maybe we dont need a subset but just a steplist
# at the moment only a list with stepnames is given for the pipeline.steps parameter
# pipeline.steps=[vdsmaker,vdsreader,setupparmdb1,setupsourcedb1,ndppp1,....]
# the names will be the prefix for parset subsets
pipeline_args = self.parset.makeSubset(
self.parset.fullModuleName('pipeline') + '.')
pipeline_steps = self.parset.makeSubset(
self.parset.fullModuleName('steps') + '.')
# *********************************************************************
# forward declaration of things. just for better overview and understanding whats in here.
# some of this might be removed in upcoming iterations, or stuff gets added.
step_name_list = pipeline_args.getStringVector('steps')
# construct the step name list if there were pipeline.steps.<subset>
for item in pipeline_steps.keys():
if item in step_name_list:
loc = step_name_list.index(item)
step_name_list[loc:loc] = pipeline_steps.getStringVector(item)
step_name_list.remove(item)
step_control_dict = {}
step_parset_files = {}
step_parset_obj = {}
activeloop = ['']
# construct the list of step names and controls
self._construct_steps(step_name_list, step_control_dict, step_parset_files, step_parset_obj, parset_dir)
# initial parameters to be saved in resultsdict so that recipes have access to this step0
# double init values. 'input' should be considered deprecated
# self.name would be consistent to use in subpipelines
input_dictionary = {
'parset': parset_file,
'parsetobj': self.parset,
'parset_dir': parset_dir,
'mapfile_dir': mapfile_dir}
resultdicts = {}
for section in self.config.sections():
tmp_dict = {}
for entry in self.config.items(section):
input_dictionary[entry[0]] = entry[1]
tmp_dict[entry[0]] = entry[1]
resultdicts.update({section: copy.deepcopy(tmp_dict)})
resultdicts.update({'input': input_dictionary})
resultdicts.update({self.name: input_dictionary})
if 'pipeline.mapfile' in self.parset.keywords():
resultdicts['input']['mapfile'] = str(self.parset['pipeline.mapfile'])
resultdicts[self.name]['mapfile'] = str(self.parset['pipeline.mapfile'])
# *********************************************************************
# main loop
# there is a distinction between recipes and plugins for user scripts.
# plugins are not used at the moment and might better be replaced with master recipes
while step_name_list:
stepname = step_name_list.pop(0)
self.logger.info("Beginning step %s" % (stepname,))
step = step_control_dict[stepname]
#step_parset = step_parset_obj[stepname]
inputdict = {}
inputargs = []
resultdict = {}
# default kind_of_step to recipe.
try:
kind_of_step = step.getString('kind')
except:
kind_of_step = 'recipe'
try:
typeval = step.getString('type')
except:
typeval = ''
adds = None
if stepname in step_parset_obj:
adds = self._construct_step_parset(inputdict,
step_parset_obj[stepname],
resultdicts,
step_parset_files[stepname],
stepname)
# stepname not a valid input for old recipes
if kind_of_step == 'recipe':
if self.task_definitions.get(typeval, 'recipe') == 'executable_args':
inputdict['stepname'] = stepname
if adds:
inputdict.update(adds)
self._construct_cmdline(inputargs, step, resultdicts)
if stepname in step_parset_files:
inputdict['parset'] = step_parset_files[stepname]
self._construct_input(inputdict, step, resultdicts)
# hack, popping 'type' is necessary, why? because you deleted kind already in parsets
try:
inputdict.pop('type')
except:
pass
try:
inputdict.pop('kind')
except:
pass
# \hack
# more hacks. Frameworks DictField not properly implemented. Construct your own dict from input.
# python buildin functions cant handle the string returned from parset class.
if 'environment' in inputdict.keys():
val = inputdict['environment'].rstrip('}').lstrip('{').replace(' ', '')
splitval = str(val).split(',')
valdict = {}
for item in splitval:
valdict[item.split(':')[0]] = item.split(':')[1]
inputdict['environment'] = valdict
# subpipeline. goal is to specify a pipeline within a pipeline.
# load other existing pipeline parset and add them to your own.
if kind_of_step == 'pipeline':
subpipeline_parset = Parset()
subpipeline_parset.adoptFile(typeval)
submapfile = ''
subpipeline_steplist = subpipeline_parset.getStringVector('pipeline.steps')
if 'pipeline.mapfile' in subpipeline_parset.keywords():
submapfile = subpipeline_parset['pipeline.mapfile']
subpipeline_parset.remove('pipeline.mapfile')
if 'mapfile_in' in inputdict.keys():
submapfile = inputdict.pop('mapfile_in')
resultdicts.update({os.path.splitext(os.path.basename(typeval))[0]: {
'parset': typeval,
'mapfile': submapfile,
}})
#todo: take care of pluginpathes and everything other then individual steps
# make a pipeline parse methods that returns everything needed.
# maybe as dicts to combine them to one
subpipeline_parset.remove('pipeline.steps')
if 'pipeline.pluginpath' in subpipeline_parset.keywords():
subpipeline_parset.remove('pipeline.pluginpath')
checklist = copy.deepcopy(subpipeline_steplist)
for k in self._keys(subpipeline_parset):
if 'loopsteps' in k:
for item in subpipeline_parset.getStringVector(k):
checklist.append(item)
# *********************************************************************
# master parset did not handle formatting and comments in the parset.
# proper format only after use of parset.makesubset. then it is a different object
# from a different super class :(. this also explains use of parset.keys and parset.keys()
# take the parset from subpipeline and add it to the master parset.
# UPDATE: do not use .keys on master parset. use .keywords(), then comments are filtered.
# *********************************************************************
# replace names of steps with the subpipeline stepname to create a unique identifier.
# replacement values starting with ! will be taken from the master parset and overwrite
# the ones in the subpipeline. only works if the ! value is already in the subpipeline
for k in self._keys(subpipeline_parset):
val = subpipeline_parset[k]
if not str(k).startswith('!') and not str(k).startswith('pipeline.replace.'):
for item in checklist:
if item+".output" in str(val):
val = str(val).replace(item, stepname + '-' + item)
self.parset.add(stepname + '-' + k, str(val))
else:
# remove replacements strings to prevent loading the same key twice
if k in self._keys(self.parset):
self.parset.remove(k)
self.parset.add(k, str(val))
for i, item in enumerate(subpipeline_steplist):
subpipeline_steplist[i] = stepname + '-' + item
for item in step_parset_obj[stepname].keys():
for k in self._keys(self.parset):
if str(k).startswith('!') and item == str(k).strip("! ") or str(k).startswith('pipeline.replace.') and item == str(k)[17:].strip():
self.parset.remove(k)
self.parset.add('! ' + item, str(step_parset_obj[stepname][item]))
self._replace_values()
self._construct_steps(subpipeline_steplist, step_control_dict, step_parset_files, step_parset_obj, parset_dir)
for j in reversed(subpipeline_steplist):
name = j
step_control_dict[name] = step_control_dict[j]
step_name_list.insert(0, name)
# loop
if kind_of_step == 'loop':
# remember what loop is running to stop it from a conditional step
if activeloop[0] is not stepname:
activeloop.insert(0, stepname)
# prepare
counter = 0
breakloop = False
if stepname in resultdicts:
counter = int(resultdicts[stepname]['counter']) + 1
breakloop = resultdicts[stepname]['break']
loopsteps = step.getStringVector('loopsteps')
# break at max iteration or when other step sets break variable
if counter is step.getInt('loopcount'):
breakloop = True
if not breakloop:
# add loop steps to the pipeline including the loop itself
step_name_list.insert(0, stepname)
self._construct_steps(loopsteps, step_control_dict, step_parset_files, step_parset_obj, parset_dir)
for j in reversed(loopsteps):
name = j
step_control_dict[name] = step_control_dict[j]
step_name_list.insert(0, name)
# results for other steps to check and write states
resultdict = {'counter': counter, 'break': breakloop}
else:
# reset values for second use of the loop (but why would you do that?)
resultdict = {'counter': -1, 'break': False}
activeloop.pop(0)
# recipes
if kind_of_step == 'recipe':
with duration(self, stepname):
resultdict = self.run_task(
typeval,
inputargs,
**inputdict
)
# plugins
if kind_of_step == 'plugin':
bla = str(self.config.get('DEFAULT', 'recipe_directories'))
pluginpath = bla.rstrip(']').lstrip('[').split(',')
for i, item in enumerate(pluginpath):
pluginpath[i] = os.path.join(item, 'plugins')
if 'pluginpath' in pipeline_args.keys():
pluginpath.append(pipeline_args.getString('pluginpath'))
with duration(self, stepname):
resultdict = loader.call_plugin(typeval, pluginpath,
inputargs,
**inputdict)
resultdicts[stepname] = resultdict
# breaking the loopstep
# if the step has the keyword for loopbreaks assign the value
if activeloop[0] in resultdicts and resultdict is not None and 'break' in resultdict:
resultdicts[activeloop[0]]['break'] = resultdict['break']
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