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Exclude parameter added to

Benito Marcote 4 years ago
  1. 66


@ -21,21 +21,10 @@ version 2.0 changes
import os
import sys
# import stat
import glob
import argparse
#from import ascii
# if len(sys.argv) != 3: #or sys.argv[1] == '-h':
# print(' <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 = """Create the * script that runs j2ms2 to create a MS file from all the *cor files.
@ -48,13 +37,13 @@ If no parameters are provided (apart of the mandatory, experiment name), then it
help_cals = """Should the calibrators be included in all measurement sets? (in the different phase centers)
By default they are included. If you set this option then they will be removed in all but the first pha. centers.
By default they are included. If you set this option then they will be removed in all but the first phase center.
help_centers = """Phase-center source names. Provide a list (comma-separated, without spaces) of all the phase centers that have been produced and need to be included in the final dataset. NO NEEDED IF --BASE-NAME IS SET.
help_exclude = """Phase-center source names to be excluded for the final dataset. Provide a list (comma-separated, without spaces) of those phase centers to be ignored (optional).
help_exclude = """Phase-center source names to be excluded from the final dataset. Provide a list (comma-separated, without spaces) of those phase centers to be ignored (optional).
# help_base_name = """Target name (without phase center suffixes).
@ -70,10 +59,10 @@ help_ref_station = """If you want to include the line eo_setup_ref_station:XX in
parser = argparse.ArgumentParser(description=help_script)
parser.add_argument('-i', '--include-cals', default=True, dest='cals_on', action='store_false', help=help_cals)
# parser.add_argument('-c', '--phase-centers', type=str, default=None, dest='centers', help=help_centers)
parser.add_argument('-e', '--exclude', type=str, default=[], dest='exclude', help=help_exclude)
parser.add_argument('-e', '--exclude', type=str, default=None, dest='exclude', help=help_exclude)
parser.add_argument('-l', '--lis', type=str, default=None, dest='lisfile', help=help_lisfile)
# parser.add_argument('-t', '--base-name', type=str, default=None, dest='basename', help=help_base_name)
parser.add_argument('-r', '--ref-station', type=str, default=None, dest='refstation', help=help_ref_station)
parser.add_argument('-r', '--ref-station', type=str, default=None, dest='ref_station', help=help_ref_station)
parser.add_argument('expname', type=str, default=None, help='Experiment name')
args = parser.parse_args()
@ -104,14 +93,23 @@ with open(lisfile, 'r') as the_lisfile:
def get_j2ms2_line(outputfile, corfile, ref_station=None):
if ref_station is not None:
return "j2ms2 eo:setup_ref_station={ref_station} -o {outputfile} {corfile}\n"
return "j2ms2 eo:setup_ref_station={} -o {} {}\n".format(ref_station, outputfile, corfile)
return "j2ms2 -o {outputfile} {corfile}\n"
return "j2ms2 -o {} {}\n".format(outputfile, corfile)
if args.exclude is not None:
args.exclude = args.exclude.split(',')
# Get all the cor files (including all phase-centers) ordered by scan
for a_scan in scans_to_include:
scanfiles = glob.glob('./*/*{}.cor*'.format(a_scan))
# Remove the phase centers to exclude
if args.exclude is not None:
for a_scanfile in scanfiles.copy():
if a_scanfile.split('_')[-1] in args.exclude:
if len(scanfiles) > max_number_of_phase_centers:
max_number_of_phase_centers = len(scanfiles)
@ -120,10 +118,27 @@ for a_scan in scans_to_include:
print('WARNING: Scan {} listed in the lis file has not been found.'.format(a_scan))
# Create all necessary lists of j2ms2 lines for each phase-center
class Group:
center = ''
files = []
"""Simple class that defines a center name and a list of files.
def __init__(self):
self._centername = ''
self._centerlist = []
self.files = []
def center(self):
return self._centername
def center(self, name):
# Do not add the name is it is already in the self._centerlist
if name not in self._centerlist:
self._centername = '_'.join(self._centerlist)
# Each group is defined as all the j2ms2 lines that will go to the same output (to the 'center'
# source), by reading all the cor files listed in 'files'
@ -135,15 +150,14 @@ for a_file in files_to_include:
# Include calibrators in all groups or only in the first one?
if args.cals_on:
for a_group in groups_j2ms2:
# a scan with phase-centers
for i, a_center in enumerate(a_file):
# a scan with phase-centers, can be eny length <= max_number_of_phase_centers
for i, a_center in enumerate(sorted(a_file)):
if groups_j2ms2[i].center == '':
groups_j2ms2[i].center = a_center.split('_')[-1]
groups_j2ms2[i].center = a_center.split('_')[-1]
# Prepare the final sh file!
@ -154,7 +168,7 @@ with open(expname+'', 'w') as shfile:
shfile.write('echo "Doing phase center {}"\n'.format(
outfile = expname + '.ms_' +
for an_entry in a_group.files:
shfile.write(get_j2ms2_line(outfile, an_entry, args.refstation))
shfile.write(get_j2ms2_line(outfile, an_entry, args.ref_station))
#os.chmod(a_file, stat.S_IREAD | stat.S_IWUSR | stat.S_IEXEC)