Minor updates

multiphase_sfxc2ms.py

@@ -0,0 +1,102 @@
+#!/usr/bin/python3
+"""Takes the default {exp}_sfxc2ms.sh file produced by the
+sfxc2ms.pl script and adds the _SRCname to the .cor files.
+
+Generates different {exp}_sfxc2ms_SRCname.sh files for the
+different phase centers (detailed in SRCname).
+
+
+Benito Marcote
+January 2018
+JIVE
+"""
+import os
+import sys
+import stat
+import glob
+import argparse
+#from astropy.io import ascii
+
+# if len(sys.argv) != 3: #or sys.argv[1] == '-h':
+#     print('multiphase_sfxc2ms.py <expname> <targetname>')
+#     print('You need to specify the experiment name and the target source name')
+#     print('as it is without the multi-phase center labeling')
+#     print('(i.e. write only the text common to all the phase centers)')
+#     sys.exit(1)
+
+# expname = sys.argv[1].lower()
+# target = sys.argv[2]
+
+
+help_script = """Takes the default {exp}_sfxc2ms.sh file produced by the
+sfxc2ms.pl script and adds the _SRCname to the .cor file names.
+
+Generates different {exp}_sfxc2ms_{n-phasecenter}.sh files for the
+different phase centers (detailed in SRCname).
+"""
+help_cals = """Should the calibrators be included in all measurement sets? (in the different phase centers)
+By default they are include. If you set this option then they will be removed in all but the first pha. centers.
+"""
+
+parser = argparse.ArgumentParser(description=help_script)
+parser.add_argument('-c', '--include-cals', default=True, dest='cals_on', action='store_false', help=help_cals)
+parser.add_argument('expname', type=str, default=None, help='Experiment name')
+parser.add_argument('target', type=str, default=None, help='Target name (without phase center suffixes)')
+
+args = parser.parse_args()
+
+expname = args.expname.lower()
+target = args.target
+
+#### NO NEED FOR THIS ANY MORE
+# with open(expname+'.vxsm', 'r') as vexsumfile:
+# The format is always (must be) ScanNo Time1 - Time2 0.0000 SRCname Stations
+#vexsumfile = ascii.read(expname+'.vxsm')
+#scans2src = {} # In the form {'No0001': 'SRCname'}
+#for aline in vexsumfile:
+#    scans2src[aline[0]] = aline[5]
+
+# Gets all the names received by the target source for the different phase-centers
+# Stranger: do not look at this line please
+phc_names = list(set([i.split('_')[-1] for i in glob.glob('./*/*.cor_'+target+'*')]))
+phc_suffixes = [i.replace(target, '') for i in phc_names]
+
+with open(expname+'_sfxc2ms.sh', 'r') as shfile:
+    # Create a file per phase center
+    final_sh_files = [open(expname+'_sfxc2ms'+suff+'.sh', 'w') for suff in phc_suffixes]
+    shlines = shfile.readlines()
+    for ashline in shlines:
+        if ashline[:4] == 'j2ms':
+            tempfile = ashline.split(' ')
+            corfile = tempfile[-1]
+            corfile_existing = glob.glob(corfile[:-2]+'*')
+	    #print(corfile)
+	    #print(tempfile)
+	    #print(corfile_existing)
+            if len(corfile_existing) == 0:
+		pass
+	    
+	    elif len(corfile_existing) == 1:
+                for a_sh_file in final_sh_files:
+                    a_sh_file.write(' '.join(tempfile[:-1])+' '+corfile_existing[0]+'\n')
+
+            else:
+                # This is the target, multiple phase centers.
+                for i in range(len(phc_suffixes)):
+                    final_sh_files[i].write(ashline[:-1]+'_'+target+phc_suffixes[i]+'\n')
+
+        else:
+            for a_sh_file in final_sh_files:
+                a_sh_file.write(ashline)
+
+
+for a_sh_file in final_sh_files:
+    a_sh_file.close()
+
+# Make the files executable
+files = [expname+'_sfxc2ms'+suff+'.sh' for suff in phc_suffixes]
+for a_file in files:
+    #os.chmod(a_file, stat.S_IREAD | stat.S_IWUSR | stat.S_IEXEC)
+    os.chmod(a_file, 0o755)
+
+

polswap.py

@@ -0,0 +1,80 @@
+#! /usr/bin/python
+"""
+Swap polarizations for specified antennas in specified subbands
+
+Usage: polswap.py msdata antennas [-sb SUBBANDS]
+Options:
+    msdata : str          MS data set containing the data to be swapged.
+    antennas : str        Antenna or list of antennas that require to be
+                          swapped. Use the two-letter name (e.g. Ef, Mc,
+                          or Jb2). In case of more than one station, please
+                          use either string 'Ef, Mc' or a non-spaced str:
+                          Ef,Mc,Ys.
+
+Version: 0.0a
+Date: Dec 2017
+Written by Benito Marcote (marcote@jive.eu)
+"""
+
+from pyrap import tables as pt
+import numpy as np
+import sys
+
+# TO CHANGE
+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).'
+
+try:
+    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='flag_weights.py', 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 1.2')
+    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='ysfocus.py', version='%prog 1.2')
+    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: flag_weights.py [-h] [-v] <measurement set> <weight threshold>')
+        print('Use -h to get help.')
+        sys.exit(1)
+
+    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) as ms:
+    weights = ms.getcol("WEIGHT")
+    print('Got {0:9} weights'.format(weights.size))
+    indexes = np.where(weights < threshold)
+    print('Got {0:9} bad points'.format(indexes[0].size))
+    print('{0:04.3}% of the visibilities to flag\n'.format(100.0*indexes[0].size/weights.size))
+    if verbose:
+        weights[indexes] = -np.abs(weights[indexes])
+        ms.putcol("WEIGHT", weights)
+        print('Done.')
+    else:
+        print('Flag has not been applied')
+    ms.close()
+
+