Collection of scripts and small programs used by the EVN Support Scientists at JIVE during the regular data processing of EVN observations.
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#!/usr/bin/env python3
Flag visibilities with weights below the provided threshold.
Usage: msdata threshold
msdata : str MS data set containing the data to be flagged.
threshold : float Visibilities with a weight below the specified
value will be flagged. Must be positive.
Version: 1.4
Date: Nov 2018
Written by Benito Marcote (
version 1.4 changes
- Now it also reports the percentage or data that were different from
zero and will be flagged (not only the total data as before).
version 1.3 changes
- Minor fixes (prog name in optparse info).
version 1.2 changes
- Minor fixes.
version 1.1 changes
- Added option -v that allows you to just get how many visibilities will
be flagged (but without actually flagging the data).
from pyrap import tables as pt
import numpy as np
import sys
help_msdata = 'Measurement set containing the data to be corrected.'
help_threshold = 'Visibilities with a weight below this value will be flagged. Must be positive.'
help_v = 'Only checks the visibilities to flag (do not flag the data).'
usage = "%(prog)s [-h] <measurement set> <weight threshold>"
description="""Flag visibilities with weights below the provided threshold.
import argparse
parser = argparse.ArgumentParser(description=description, prog='', usage=usage)
parser.add_argument('msdata', type=str, help=help_msdata)
parser.add_argument('threshold', type=float, help=help_threshold)
parser.add_argument('--version', action='version', version='%(prog)s 1.4')
parser.add_argument("-v", "--verbose", default=True, action="store_false" , help=help_v)
arguments = parser.parse_args()
#print('The arguments ', arguments)
verbose = arguments.verbose
msdata = arguments.msdata[:-1] if arguments.msdata[-1]=='/' else arguments.msdata
threshold = arguments.threshold
except ImportError:
usage = "%prog [-h] [-v] <measurement set> <weight threshold>"
description="""Flag visibilities with weights below the provided threshold.
# Compatibility with Python 2.7 in eee
import optparse
parser = optparse.OptionParser(usage=usage, description=description, prog='', version='%prog 1.3')
parser.add_option("-v", action="store_false", dest="verbose", default=True, help=help_v)
theparser = parser.parse_args()
verbose = theparser[0].verbose
arguments = theparser[1]
#arguments = parser.parse_args()[1]
if len(arguments) != 2:
print('Two arguments must be provided: [-h] [-v] <measurement set> <weight threshold>')
print('Use -h to get help.')
msdata = arguments[0][:-1] if arguments[0][-1]=='/' else arguments[0]
threshold = float(arguments[1])
assert threshold > 0.0
with pt.table(msdata, readonly=False, ack=False) as ms:
weights = ms.getcol("WEIGHT")
print('Got {0:9} weights'.format(weights.size))
indexes = np.where(weights < threshold)
indexes2 = np.where((weights < threshold) & (weights > 0.0))
print('Got {0:9} bad points'.format(indexes[0].size))
print('{0:04.3}% of the total visibilities to flag'.format(100.0*indexes[0].size/weights.size))
print('{0:04.3}% of actual data (non-zero) to flag\n'.format(100.0*indexes2[0].size/weights.size))
if verbose:
weights[indexes] = -np.abs(weights[indexes])
ms.putcol("WEIGHT", weights)
print('Flag has not been applied.')