if o in ("-H", "--Help"):
usage()
os._exit(0)
if o in ("-l", "--list"):
list_tests()
os._exit(0)
if o in ("-s", "--classes"):
testnames.append(a)
getclasses(testnames)
os._exit(0)
if o in ("-m", "--mem"):
# run specific tests in mem mode
MEM = 1
elif o in ("-g", "--debug"):
# Set the casalog to DEBUG
casalog.filter("DEBUG")
elif o in ("-d", "--datadir"):
# This will create an environmental variable called
# TEST_DATADIR that can be read by the tests to use
# an alternative location for the data. This is used
# to test tasks with MMS data
# directory with test data
datadir = a
if not os.path.isdir(datadir):
raise Exception, "Value of --datadir is not a directory -> " + datadir
# Set an environmental variable for the data directory
settestdir(datadir)
if not os.environ.has_key("TEST_DATADIR"):
raise Exception, "Could not create environmental variable TEST_DATADIR"
def run():
# Set CASA_ENGINGE env. variable so that:
# - taskinit does not initialize the viewer
# - taskmanmager is not initialized
os.environ['CASA_ENGINE'] = "YES"
# Initialize MPI environment
from mpi4casa.MPIEnvironment import MPIEnvironment
# Initialize MPICommunicator singleton
from mpi4casa.MPICommunicator import MPICommunicator
communicator = MPICommunicator()
# Wait to receive start service signal from MPI client processor
start_service_signal_available = False
while not start_service_signal_available:
start_service_signal_available = communicator.control_service_request_probe(
)
if start_service_signal_available:
# Receive CASA global dictionary
request = communicator.control_service_request_recv()
else:
time.sleep(MPIEnvironment.mpi_start_service_sleep_time)
# Check if request is start or stop signal
if request['signal'] == 'start':
# Get CASA environment dictionary
global casa
casa = request['casa']
global _casa_top_frame_
_casa_top_frame_ = True
# Re-set log file
if request['logmode'] == 'separated' or request[
'logmode'] == 'redirect':
casa['files']['logfile'] = '%s-server-%s-host-%s-pid-%s' % (
casa['files']['logfile'], str(
MPIEnvironment.mpi_processor_rank),
str(MPIEnvironment.hostname), str(MPIEnvironment.mpi_pid))
# Import logger, logfile is set at taskinit retrieving from the casa dict. from the stack
from taskinit import casalog
# Set log origin so that the processor origin is updated
casalog_call_origin = "mpi4casapy"
casalog.origin(casalog_call_origin)
# If log mode is separated activate showconsole to have all logs sorted by time at the terminal
if request['logmode'] == 'redirect':
casalog.showconsole(True)
# Install filter to remove MSSelectionNullSelection errors
casalog.filter('NORMAL1')
casalog.filterMsg('MSSelectionNullSelection')
casalog.filterMsg('non-existent spw')
# Post MPI welcome msg
casalog.post(MPIEnvironment.mpi_info_msg, "INFO", casalog_call_origin)
# Initialize MPICommandServer and start serving
from mpi4casa.MPICommandServer import MPICommandServer
server = MPICommandServer()
server.serve()
else:
MPIEnvironment.finalize_mpi_environment()
def run():
# Set CASA_ENGINGE env. variable so that:
# - taskinit does not initialize the viewer
# - taskmanmager is not initialized
os.environ['CASA_ENGINE']="YES"
# Initialize MPI environment
from mpi4casa.MPIEnvironment import MPIEnvironment
# Initialize MPICommunicator singleton
from mpi4casa.MPICommunicator import MPICommunicator
communicator = MPICommunicator()
# Wait to receive start service signal from MPI client processor
start_service_signal_available = False
while not start_service_signal_available:
start_service_signal_available = communicator.control_service_request_probe()
if start_service_signal_available:
# Receive CASA global dictionary
request = communicator.control_service_request_recv()
else:
time.sleep(MPIEnvironment.mpi_start_service_sleep_time)
# Check if request is start or stop signal
if request['signal'] == 'start':
# Get CASA environment dictionary
global casa
casa = request['casa']
global _casa_top_frame_
_casa_top_frame_ = True
# Re-set log file
if request['logmode'] == 'separated' or request['logmode'] == 'redirect':
casa['files']['logfile'] = '%s-server-%s-host-%s-pid-%s' % (casa['files']['logfile'],
str(MPIEnvironment.mpi_processor_rank),
str(MPIEnvironment.hostname),
str(MPIEnvironment.mpi_pid))
# Import logger, logfile is set at taskinit retrieving from the casa dict. from the stack
from taskinit import casalog
# Set log origin so that the processor origin is updated
casalog_call_origin = "mpi4casapy"
casalog.origin(casalog_call_origin)
# If log mode is separated activate showconsole to have all logs sorted by time at the terminal
if request['logmode'] == 'redirect':
casalog.showconsole(True)
# Install filter to remove MSSelectionNullSelection errors
casalog.filter('NORMAL1')
casalog.filterMsg('MSSelectionNullSelection')
casalog.filterMsg('non-existent spw')
# Post MPI welcome msg
casalog.post(MPIEnvironment.mpi_info_msg,"INFO",casalog_call_origin)
# Initialize MPICommandServer and start serving
from mpi4casa.MPICommandServer import MPICommandServer
server = MPICommandServer()
server.serve()
else:
MPIEnvironment.finalize_mpi_environment()
def run():
# Set CASA_ENGINGE env. variable so that:
# - taskinit does not initialize the viewer
# - taskmanmager is not initialized
os.environ['CASA_ENGINE'] = "YES"
# Initialize MPI environment
from mpi4casa.MPIEnvironment import MPIEnvironment
# Initialize MPICommunicator singleton
from mpi4casa.MPICommunicator import MPICommunicator
communicator = MPICommunicator()
# Wait to receive start service signal from MPI client processor
start_service_signal_available = False
while not start_service_signal_available:
start_service_signal_available = communicator.control_service_request_probe(
)
if start_service_signal_available:
# Receive CASA global dictionary (filtered)
request = communicator.control_service_request_recv()
else:
time.sleep(MPIEnvironment.mpi_start_service_sleep_time)
# Check if request is start or stop signal
if request['signal'] == 'start':
cli_logfile_name, logmode_name = 'casa_filtered', 'logmode'
for entry_name in [cli_logfile_name, logmode_name]:
if entry_name not in request:
raise RuntimeError(
'A \'start\' MPI request must have a {0} entry but it '
'was not found. Host name: {1}. MPI rank: {2}, '.format(
entry_name, MPIEnvironment.hostname,
MPIEnvironment.mpi_processor_rank))
# Get CASA environment dictionary
global casa
casa_filtered = request['casa_filtered']
casa.update(casa_filtered)
global _casa_top_frame_
_casa_top_frame_ = True
# Re-set log file
if request[logmode_name] == 'separated' or request[
logmode_name] == 'redirect':
casa['files']['logfile'] = (
'{0}-server-{1}-host-{2}-pid-{3}'.format(
casa['files']['logfile'],
MPIEnvironment.mpi_processor_rank, MPIEnvironment.hostname,
MPIEnvironment.mpi_pid))
# Import logger, logfile is set at taskinit retrieving from the casa dict. from the stack
from taskinit import casalog
# Set log origin so that the processor origin is updated
casalog_call_origin = "mpi4casapy"
casalog.origin(casalog_call_origin)
# If log mode is separated activate showconsole to have all logs sorted by time at the terminal
if request[logmode_name] == 'redirect':
casalog.showconsole(True)
# Install filter to remove MSSelectionNullSelection errors
casalog.filter('NORMAL1')
casalog.filterMsg('MSSelectionNullSelection')
casalog.filterMsg('non-existent spw')
# Post MPI welcome msg
casalog.post(MPIEnvironment.mpi_info_msg, "INFO", casalog_call_origin)
# Initialize MPICommandServer and start serving
from mpi4casa.MPICommandServer import MPICommandServer
server = MPICommandServer()
server.serve()
else:
MPIEnvironment.finalize_mpi_environment()
class sdimaging_worker(sdutil.sdtask_template_imaging):
def __init__(self, **kwargs):
super(sdimaging_worker, self).__init__(**kwargs)
self.imager_param = {}
self.sorted_idx = []
def parameter_check(self):
# outfile check
sdutil.assert_outfile_canoverwrite_or_nonexistent(
self.outfile, 'im', self.overwrite)
sdutil.assert_outfile_canoverwrite_or_nonexistent(
self.outfile + '.weight', 'im', self.overwrite)
# fix spw
if type(self.spw) == str:
self.spw = self.__format_spw_string(self.spw)
# check unit of start and width
# fix default
if self.mode == 'channel':
if self.start == '': self.start = 0
if self.width == '': self.width = 1
else:
if self.start == 0: self.start = ''
if self.width == 1: self.width = ''
# fix unit
if self.mode == 'frequency':
myunit = 'Hz'
elif self.mode == 'velocity':
myunit = 'km/s'
else: # channel
myunit = ''
for name in ['start', 'width']:
param = getattr(self, name)
new_param = self.__format_quantum_unit(param, myunit)
if new_param == None:
raise ValueError, "Invalid unit for %s in mode %s: %s" % \
(name, self.mode, param)
setattr(self, name, new_param)
casalog.post("mode='%s': start=%s, width=%s, nchan=%d" % \
(self.mode, self.start, self.width, self.nchan))
# check length of selection parameters
if is_string_type(self.infiles):
nfile = 1
self.infiles = [self.infiles]
else:
nfile = len(self.infiles)
for name in ['field', 'spw', 'antenna', 'scanno']:
param = getattr(self, name)
if not self.__check_selection_length(param, nfile):
raise ValueError, "Length of %s != infiles." % (name)
# set convsupport default
if self.convsupport >= 0 and self.gridfunction.upper() != 'SF':
casalog.post("user defined convsupport is ignored for %s kernel" %
self.gridfunction,
priority='WARN')
self.convsupport = -1
def __format_spw_string(self, spw):
"""
Returns formatted spw selection string which is accepted by imager.
"""
if type(spw) != str:
raise ValueError, "The parameter should be string."
if spw.strip() == '*': spw = ''
# WORKAROUND for CAS-6422, i.e., ":X~Y" fails while "*:X~Y" works.
if spw.startswith(":"): spw = '*' + spw
return spw
def __format_quantum_unit(self, data, unit):
"""
Returns False if data has an unit which in not a variation of
input unit.
Otherwise, returns input data as a quantum string. The input
unit is added to the return value if no unit is in data.
"""
my_qa = qatool()
if data == '' or my_qa.compare(data, unit):
return data
if my_qa.getunit(data) == '':
casalog.post("No unit specified. Using '%s'" % unit)
return '%f%s' % (data, unit)
return None
def __check_selection_length(self, data, nfile):
"""
Returns true if data is either a string, an array with length
1 or nfile
"""
if not is_string_type(data) and len(data) not in [1, nfile]:
return False
return True
def get_selection_param_for_ms(self, fileid, param):
"""
Returns valid selection string for a certain ms
Arguments
fileid : file idx in infiles list
param : string (array) selection value
"""
if is_string_type(param):
return param
elif len(param) == 1:
return param[0]
else:
return param[fileid]
def get_selection_idx_for_ms(self, file_idx):
"""
Returns a dictionary of selection indices for i-th MS in infiles
Argument: file idx in infiles list
"""
if file_idx < len(self.infiles) and file_idx > -1:
vis = self.infiles[file_idx]
field = self.get_selection_param_for_ms(file_idx, self.field)
spw = self.get_selection_param_for_ms(file_idx, self.spw)
spw = self.__format_spw_string(spw)
antenna = self.get_selection_param_for_ms(file_idx, self.antenna)
if antenna == -1: antenna = ''
scan = self.get_selection_param_for_ms(file_idx, self.scanno)
intent = self.get_selection_param_for_ms(file_idx, self.intent)
my_ms = gentools(['ms'])[0]
sel_ids = my_ms.msseltoindex(vis=vis,
spw=spw,
field=field,
baseline=antenna,
scan=scan)
fieldid = list(
sel_ids['field']) if len(sel_ids['field']) > 0 else -1
baseline = self.format_ac_baseline(sel_ids['antenna1'])
scanid = list(sel_ids['scan']) if len(sel_ids['scan']) > 0 else ""
# SPW (need to get a list of valid spws instead of -1)
if len(sel_ids['channel']) > 0:
spwid = [chanarr[0] for chanarr in sel_ids['channel']]
elif spw == "": # No spw selection
my_ms.open(vis)
try:
spwinfo = my_ms.getspectralwindowinfo()
except:
raise
finally:
my_ms.close()
spwid = [int(idx) for idx in spwinfo.keys()]
else:
raise RuntimeError("Invalid spw selction, %s ,for MS %d" (
str(spw), file_idx))
return {
'field': fieldid,
'spw': spwid,
'baseline': baseline,
'scan': scanid,
'intent': intent,
'antenna1': sel_ids['antenna1']
}
else:
raise ValueError, ("Invalid file index, %d" % file_idx)
def format_ac_baseline(self, in_antenna):
""" format auto-correlation baseline string from antenna idx list """
# exact match string
if is_string_type(in_antenna):
if (len(in_antenna) != 0) and (in_antenna.find('&') == -1) \
and (in_antenna.find(';')==-1):
in_antenna = + '&&&'
return in_antenna
# single integer -> list of int
if type(in_antenna) == int:
if in_antenna >= 0:
in_antenna = [in_antenna]
else:
return -1
# format auto-corr string from antenna idices.
baseline = ''
for idx in in_antenna:
if len(baseline) > 0: baseline += ';'
if idx >= 0:
baseline += (str(idx) + '&&&')
return baseline
def compile(self):
# imaging mode
self.imager_param['mode'] = self.mode
# Work on selection of the first table in sorted list
# to get default restfreq and outframe
imhelper = cleanhelper(self.imager, self.infiles, casalog=casalog)
imhelper.sortvislist(self.spw, self.mode, self.width)
self.sorted_idx = imhelper.sortedvisindx
selection_ids = self.get_selection_idx_for_ms(self.sorted_idx[0])
self.__update_subtable_name(self.infiles[self.sorted_idx[0]])
# field
fieldid = selection_ids['field'][0] if type(
selection_ids['field']) != int else selection_ids['field']
sourceid = -1
self.open_table(self.field_table)
source_ids = self.table.getcol('SOURCE_ID')
self.close_table()
if self.field == '' or fieldid == -1:
sourceid = source_ids[0]
elif fieldid >= 0 and fieldid < len(source_ids):
sourceid = source_ids[fieldid]
else:
raise ValueError, "No valid field in the first MS."
# restfreq
if self.restfreq == '' and self.source_table != '':
self.open_table(self.source_table)
source_ids = self.table.getcol('SOURCE_ID')
for i in range(self.table.nrows()):
if sourceid == source_ids[i] \
and self.table.iscelldefined('REST_FREQUENCY',i) \
and (selection_ids['spw'] == -1 or \
self.table.getcell('SPECTRAL_WINDOW_ID', i) in selection_ids['spw']):
rf = self.table.getcell('REST_FREQUENCY', i)
if len(rf) > 0:
self.restfreq = self.table.getcell(
'REST_FREQUENCY', i)[0]
break
self.close_table()
casalog.post("restfreq set to %s" % self.restfreq, "INFO")
# REST_FREQUENCY column is optional (need retry if not exists)
self.imager_param['restfreq'] = self.restfreq
#
# spw (define representative spw id = spwid_ref)
spwid_ref = selection_ids['spw'][0] if type(
selection_ids['spw']) != int else selection_ids['spw']
# Invalid spw selection should have handled at msselectiontoindex().
# -1 means all spw are selected.
self.open_table(self.spw_table)
if spwid_ref < 0:
for id in range(self.table.nrows()):
if self.table.getcell('NUM_CHAN', id) > 0:
spwid_ref = id
break
if spwid_ref < 0:
self.close_table()
msg = 'No valid spw id exists in the first table'
raise ValueError, msg
self.allchannels = self.table.getcell('NUM_CHAN', spwid_ref)
freq_chan0 = self.table.getcell('CHAN_FREQ', spwid_ref)[0]
freq_inc0 = self.table.getcell('CHAN_WIDTH', spwid_ref)[0]
# in case rest frequency is not defined yet.
if self.restfreq == '':
self.restfreq = '%fHz' % self.table.getcell(
'CHAN_FREQ', spwid_ref).mean()
self.imager_param['restfreq'] = self.restfreq
casalog.post(
"Using mean freq of spw %d as restfreq: %s" %
(spwid_ref, self.restfreq), "INFO")
self.close_table()
self.imager_param['spw'] = -1 #spwid_ref
# outframe (force using the current frame)
self.imager_param['outframe'] = self.outframe
if self.outframe == '':
if len(self.infiles) > 1:
# The default will be 'LSRK'
casalog.post(
"Multiple MS inputs. The default outframe is set to 'LSRK'"
)
self.imager_param['outframe'] = 'LSRK'
else:
# get from MS
my_ms = gentools(['ms'])[0]
my_ms.open(self.infiles[0])
spwinfo = my_ms.getspectralwindowinfo()
my_ms.close()
del my_ms
for key, spwval in spwinfo.items():
if spwval['SpectralWindowId'] == spwid_ref:
self.imager_param['outframe'] = spwval['Frame']
casalog.post("Using frequency frame of MS, '%s'" %
self.imager_param['outframe'])
break
if self.imager_param['outframe'] == '':
raise Exception, "Internal error of getting frequency frame of spw=%d." % spwid_ref
else:
casalog.post("Using frequency frame defined by user, '%s'" %
self.imager_param['outframe'])
# # antenna
# in_antenna = self.antenna # backup for future use
# if type(self.antenna)==int:
# if self.antenna >= 0:
# self.antenna=str(self.antenna)+'&&&'
# else:
# if (len(self.antenna) != 0) and (self.antenna.find('&') == -1) \
# and (self.antenna.find(';')==-1):
# self.antenna = self.antenna + '&&&'
def _configure_map_property(self):
selection_ids = self.get_selection_idx_for_ms(self.sorted_idx[0])
# stokes
if self.stokes == '':
self.stokes = 'I'
self.imager_param['stokes'] = self.stokes
# gridfunction
# outfile
if os.path.exists(self.outfile) and self.overwrite:
os.system('rm -rf %s' % (self.outfile))
if os.path.exists(self.outfile + '.weight') and self.overwrite:
os.system('rm -rf %s' % (self.outfile + '.weight'))
# cell
cell = self.cell
if cell == '' or cell[0] == '':
# Calc PB
grid_factor = 3.
casalog.post(
"The cell size will be calculated using PB size of antennas in the first MS"
)
qPB = self._calc_PB(selection_ids['antenna1'])
cell = '%f%s' % (qPB['value'] / grid_factor, qPB['unit'])
casalog.post("Using cell size = PB/%4.2F = %s" %
(grid_factor, cell))
(cellx, celly) = sdutil.get_cellx_celly(cell, unit='arcmin')
self.imager_param['cellx'] = cellx
self.imager_param['celly'] = celly
# Calculate Pointing center and extent (if necessary)
# return a dictionary with keys 'center', 'width', 'height'
#imsize = self.imsize
imsize = sdutil._to_list(self.imsize, int) or \
sdutil._to_list(self.imsize, numpy.integer)
if imsize is None:
imsize = self.imsize if hasattr(self.imsize,
'__iter__') else [self.imsize]
imsize = [int(numpy.ceil(v)) for v in imsize]
casalog.post(
"imsize is not integers. force converting to integer pixel numbers.",
priority="WARN")
casalog.post("rounded-up imsize: %s --> %s" %
(str(self.imsize), str(imsize)))
phasecenter = self.phasecenter
if self.phasecenter == "" or \
len(imsize) == 0 or imsize[0] < 1:
map_param = self._get_pointing_extent()
# imsize
if len(imsize) == 0 or imsize[0] < 1:
imsize = self._get_imsize(map_param['width'],
map_param['height'], cellx, celly)
if self.phasecenter != "":
casalog.post(
"You defined phasecenter but not imsize. The image will cover as wide area as pointing in MS extends, but be centered at phasecenter. This could result in a strange image if your phasecenter is a part from the center of pointings",
priority='WARN')
if imsize[0] > 1024 or imsize[1] > 1024:
casalog.post(
"The calculated image pixel number is larger than 1024. It could take time to generate the image depending on your computer resource. Please wait...",
priority='WARN')
# phasecenter
# if empty, it should be determined here...
if self.phasecenter == "":
phasecenter = map_param['center']
# imsize
(nx, ny) = sdutil.get_nx_ny(imsize)
self.imager_param['nx'] = nx
self.imager_param['ny'] = ny
# phasecenter
self.imager_param['phasecenter'] = phasecenter
self.imager_param['movingsource'] = self.ephemsrcname
# channel map
imhelper = cleanhelper(self.imager, self.infiles, casalog=casalog)
imhelper.sortvislist(self.spw, self.mode, self.width)
spwsel = str(',').join([str(spwid) for spwid in selection_ids['spw']])
srestf = self.imager_param['restfreq'] if is_string_type(
self.imager_param['restfreq']
) else "%fHz" % self.imager_param['restfreq']
(imnchan, imstart, imwidth) = imhelper.setChannelizeDefault(
self.mode, spwsel, self.field, self.nchan, self.start, self.width,
self.imager_param['outframe'], self.veltype,
self.imager_param['phasecenter'], srestf)
del imhelper
# start and width
if self.mode == 'velocity':
startval = [self.imager_param['outframe'], imstart]
widthval = imwidth
elif self.mode == 'frequency':
startval = [self.imager_param['outframe'], imstart]
widthval = imwidth
else: #self.mode==channel
startval = int(self.start)
widthval = int(self.width)
if self.nchan < 0: self.nchan = self.allchannels
self.imager_param['start'] = startval
self.imager_param['step'] = widthval
self.imager_param['nchan'] = imnchan #self.nchan
def execute(self):
# imaging
casalog.post("Start imaging...", "INFO")
if len(self.infiles) == 1:
self.open_imager(self.infiles[0])
selection_ids = self.get_selection_idx_for_ms(0)
spwsel = self.get_selection_param_for_ms(0, self.spw)
if spwsel.strip() in ['', '*']: spwsel = selection_ids['spw']
### TODO: channel selection based on spw
ok = self.imager.selectvis(
field=selection_ids['field'],
#spw=selection_ids['spw'],
spw=spwsel,
nchan=-1,
start=0,
step=1,
baseline=selection_ids['baseline'],
scan=selection_ids['scan'],
intent=selection_ids['intent'])
if not ok:
raise ValueError, "Selection is empty: you may want to review this MS selection"
else:
self.close_imager()
#self.sorted_idx.reverse()
for idx in self.sorted_idx.__reversed__():
name = self.infiles[idx]
selection_ids = self.get_selection_idx_for_ms(idx)
spwsel = self.get_selection_param_for_ms(idx, self.spw)
if spwsel.strip() in ['', '*']: spwsel = selection_ids['spw']
### TODO: channel selection based on spw
self.imager.selectvis(
vis=name,
field=selection_ids['field'],
#spw=selection_ids['spw'],
spw=spwsel,
nchan=-1,
start=0,
step=1,
baseline=selection_ids['baseline'],
scan=selection_ids['scan'],
intent=selection_ids['intent'])
# need to do this
self.is_imager_opened = True
# it should be called after infiles are registered to imager
self._configure_map_property()
casalog.post(
"Using phasecenter \"%s\"" % (self.imager_param['phasecenter']),
"INFO")
self.imager.defineimage(**self.imager_param) #self.__get_param())
self.imager.setoptions(ftmachine='sd', gridfunction=self.gridfunction)
self.imager.setsdoptions(pointingcolumntouse=self.pointingcolumn,
convsupport=self.convsupport,
truncate=self.truncate,
gwidth=self.gwidth,
jwidth=self.jwidth,
minweight=0.,
clipminmax=self.clipminmax)
self.imager.makeimage(type='singledish', image=self.outfile)
weightfile = self.outfile + ".weight"
self.imager.makeimage(type='coverage', image=weightfile)
self.close_imager()
if not os.path.exists(self.outfile):
raise RuntimeError, "Failed to generate output image '%s'" % self.outfile
if not os.path.exists(weightfile):
raise RuntimeError, "Failed to generate weight image '%s'" % weightfile
# Convert output images to proper output frame
my_ia = gentools(['ia'])[0]
my_ia.open(self.outfile)
csys = my_ia.coordsys()
csys.setconversiontype(spectral=csys.referencecode('spectra')[0])
my_ia.setcoordsys(csys.torecord())
my_ia.close()
# Mask image pixels whose weight are smaller than minweight.
# Weight image should have 0 weight for pixels below < minweight
casalog.post("Start masking the map using minweight = %f" % \
self.minweight, "INFO")
my_ia.open(weightfile)
try:
stat = my_ia.statistics(mask="'" + weightfile + "' > 0.0",
robust=True)
valid_pixels = stat['npts']
except RuntimeError, e:
if e.message.find('No valid data found.') >= 0:
valid_pixels = [0]
else:
raise e
if len(valid_pixels) == 0 or valid_pixels[0] == 0:
my_ia.close()
casalog.post(
"All pixels weight zero. This indicates no data in MS is in image area. Mask will not be set. Please check your image parameters.",
"WARN")
return
median_weight = stat['median'][0]
weight_threshold = median_weight * self.minweight
casalog.post("Median of weight in the map is %f" % median_weight, \
"INFO")
casalog.post("Pixels in map with weight <= median(weight)*minweight = %f will be masked." % \
(weight_threshold),"INFO")
###Leaving the original logic to calculate the number of masked pixels via
###product of median of and min_weight (which i don't understand the logic)
### if one wanted to find how many pixel were masked one could easily count the
### number of pixels set to false
### e.g after masking self.outfile below one could just do this
### nmasked_pixels=tb.calc('[select from "'+self.outfile+'"/mask0'+'" giving [nfalse(PagedArray )]]')
my_tb = gentools(['tb'])[0]
nmask_pixels = 0
nchan = stat['trc'][3] + 1
casalog.filter('ERROR') ### hide the useless message of tb.calc
### doing it by channel to make sure it does not go out of memory
####tab.calc try to load the whole chunk in ram
for k in range(nchan):
nmask_pixels += my_tb.calc('[select from "' + weightfile +
'" giving [ntrue(map[,,,' + str(k) +
'] <=' +
str(median_weight * self.minweight) +
')]]')['0'][0]
casalog.filter() ####set logging back to normal
casalog.filter() ####set logging back to normal
imsize = numpy.product(my_ia.shape())
my_ia.close()
# Modify default mask
my_ia.open(self.outfile)
my_ia.calcmask("'%s'>%f" % (weightfile, weight_threshold),
asdefault=True)
my_ia.close()
masked_fraction = 100. * (
1. - (imsize - nmask_pixels) / float(valid_pixels[0]))
casalog.post("This amounts to %5.1f %% of the area with nonzero weight." % \
( masked_fraction ),"INFO")
casalog.post("The weight image '%s' is returned by this task, if the user wishes to assess the results in detail." \
% (weightfile), "INFO")
# Calculate theoretical beam size
casalog.post("Calculating image beam size.")
if self.gridfunction.upper() not in ['SF']:
casalog.post(
"Beam size definition for '%s' kernel is experimental." %
self.gridfunction,
priority='WARN')
casalog.post(
"You may want to take careful look at the restoring beam in the image.",
priority='WARN')
my_msmd = gentools(['msmd'])[0]
# antenna diameter and blockage
ref_ms_idx = self.sorted_idx[0]
ref_ms_name = self.infiles[ref_ms_idx]
selection_ids = self.get_selection_idx_for_ms(ref_ms_idx)
ant_idx = selection_ids['antenna1']
diameter = self._get_average_antenna_diameter(ant_idx)
my_msmd.open(ref_ms_name)
ant_name = my_msmd.antennanames(ant_idx)
my_msmd.close()
is_alma = False
for name in ant_name:
if name[0:2] in ["PM", "DV", "DA", "CM"]:
is_alma = True
break
blockage = "0.75m" if is_alma else "0.0m" # unknown blockage diameter
# output reference code
my_ia.open(self.outfile)
csys = my_ia.coordsys()
my_ia.close()
outref = csys.referencecode('direction')[0]
cell = list(csys.increment(type='direction', format='s')['string'])
# pointing sampling
ref_ms_spw = self.get_selection_param_for_ms(ref_ms_idx, self.spw)
ref_ms_field = self.get_selection_param_for_ms(ref_ms_idx, self.field)
ref_ms_scan = self.get_selection_param_for_ms(ref_ms_idx, self.scanno)
# xSampling, ySampling, angle = sdutil.get_ms_sampling_arcsec(ref_ms_name, spw=ref_ms_spw,
# antenna=selection_ids['baseline'],
# field=ref_ms_field,
# scan=ref_ms_scan,#timerange='',
# outref=outref)
# obtain sampling interval for beam calculation.
self.open_imager(ref_ms_name)
ok = self.imager.selectvis(
field=ref_ms_field,
#spw=selection_ids['spw'],
spw=ref_ms_spw,
nchan=-1,
start=0,
step=1,
baseline=selection_ids['baseline'],
scan=ref_ms_scan,
intent=selection_ids['intent'])
if len(ant_idx) > 1:
casalog.post(
"Using only antenna %s to calculate sampling interval" %
ant_name[0])
ptg_samp = self.imager.pointingsampling(
pattern='raster',
ref=outref,
movingsource=self.ephemsrcname,
pointingcolumntouse=self.pointingcolumn,
antenna=('%s&&&' % ant_name[0]))
self.close_imager()
my_qa = qatool()
xSampling, ySampling = my_qa.getvalue(
my_qa.convert(ptg_samp['sampling'], 'arcsec'))
angle = my_qa.getvalue(my_qa.convert(ptg_samp['angle'], "deg"))[0]
casalog.post("Detected raster sampling = [%f, %f] arcsec" %
(xSampling, ySampling))
# handling of failed sampling detection
valid_sampling = True
sampling = [xSampling, ySampling]
if abs(xSampling) < 2.2e-3 or not numpy.isfinite(xSampling):
casalog.post(
"Invalid sampling=%s arcsec. Using the value of orthogonal direction=%s arcsec"
% (xSampling, ySampling),
priority="WARN")
sampling = [ySampling]
angle = 0.0
valid_sampling = False
if abs(ySampling) < 1.0e-3 or not numpy.isfinite(ySampling):
if valid_sampling:
casalog.post(
"Invalid sampling=%s arcsec. Using the value of orthogonal direction=%s arcsec"
% (ySampling, xSampling),
priority="WARN")
sampling = [xSampling]
angle = 0.0
valid_sampling = True
# reduce sampling and cell if it's possible
if len(sampling) > 1 and abs(sampling[0] -
sampling[1]) <= 0.01 * abs(sampling[0]):
sampling = [sampling[0]]
angle = 0.0
if cell[0] == cell[1]: cell = [cell[0]]
if valid_sampling:
# actual calculation of beam size
bu = sdbeamutil.TheoreticalBeam()
bu.set_antenna(diameter, blockage)
bu.set_sampling(sampling, "%fdeg" % angle)
bu.set_image_param(cell, self.restfreq, self.gridfunction,
self.convsupport, self.truncate, self.gwidth,
self.jwidth, is_alma)
bu.summary()
imbeam_dict = bu.get_beamsize_image()
casalog.post("Setting image beam: major=%s, minor=%s, pa=%s" % (
imbeam_dict['major'],
imbeam_dict['minor'],
imbeam_dict['pa'],
))
# set beam size to image
my_ia.open(self.outfile)
my_ia.setrestoringbeam(**imbeam_dict)
my_ia.close()
else:
#BOTH sampling was invalid
casalog.post(
"Could not detect valid raster sampling. Exitting without setting beam size to image",
priority='WARN')
if o in ("-H", "--Help"):
usage()
os._exit(0)
if o in ("-l", "--list"):
list_tests()
os._exit(0)
if o in ("-s", "--classes"):
testnames.append(a)
getclasses(testnames)
os._exit(0)
if o in ("-m", "--mem"):
# run specific tests in mem mode
MEM = 1
elif o in ("-g", "--debug"):
#Set the casalog to DEBUG
casalog.filter('DEBUG')
elif o in ("-d", "--datadir"):
# This will create an environmental variable called
# TEST_DATADIR that can be read by the tests to use
# an alternative location for the data. This is used
# to test tasks with MMS data
# directory with test data
datadir = a
if not os.path.isdir(datadir):
raise Exception, 'Value of --datadir is not a directory -> ' + datadir
# Set an environmental variable for the data directory
settestdir(datadir)
if not os.environ.has_key('TEST_DATADIR'):
raise Exception, 'Could not create environmental variable TEST_DATADIR'
median_weight = stat['median'][0]
weight_threshold = median_weight * minweight
casalog.post("Median of weight in the map is %f" % median_weight, \
"INFO")
casalog.post("Pixels in map with weight <= median(weight)*minweight = %f will be masked." % \
(weight_threshold),"INFO")
###Leaving the original logic to calculate the number of masked pixels via
###product of median of and min_weight (which i don't understand the logic)
### if one wanted to find how many pixel were masked one could easily count the
### number of pixels set to false
### e.g after masking self.outfile below one could just do this
### nmasked_pixels=tb.calc('[select from "'+self.outfile+'"/mask0'+'" giving [nfalse(PagedArray )]]')
my_tb = gentools(['tb'])[0]
nmask_pixels = 0
nchan = stat['trc'][3] + 1
casalog.filter('ERROR') ### hide the useless message of tb.calc
### doing it by channel to make sure it does not go out of memory
####tab.calc try to load the whole chunk in ram
for k in range(nchan):
nmask_pixels += my_tb.calc('[select from "' + weightimage +
'" giving [ntrue(map[,,,' + str(k) +
'] <=' + str(median_weight * minweight) +
')]]')['0'][0]
casalog.filter() ####set logging back to normal
# Modify default mask
with open_ia(imagename) as ia:
imsize = numpy.product(ia.shape())
ia.calcmask("'%s'>%f" % (weightimage, weight_threshold),
asdefault=True)
if o in ("-H", "--Help"):
usage()
os._exit(0)
if o in ("-l", "--list"):
list_tests()
os._exit(0)
if o in ("-s", "--classes"):
testnames.append(a)
getclasses(testnames)
os._exit(0)
if o in ("-m", "--mem"):
# run specific tests in mem mode
MEM = 1
elif o in ("-g", "--debug"):
#Set the casalog to DEBUG
casalog.filter('DEBUG')
elif o in ("-d", "--datadir"):
# This will create an environmental variable called
# TEST_DATADIR that can be read by the tests to use
# an alternative location for the data. This is used
# to test tasks with MMS data
# directory with test data
datadir = a
if not os.path.isdir(datadir):
raise Exception, 'Value of --datadir is not a directory -> '+datadir
# Set an environmental variable for the data directory
settestdir(datadir)
if not os.environ.has_key('TEST_DATADIR'):
raise Exception, 'Could not create environmental variable TEST_DATADIR'