run_init_flag.py

import inspect, os, sys, json, re
from collections import OrderedDict

filename = inspect.getframeinfo(inspect.currentframe()).filename
sys.path.append(os.path.dirname(os.path.realpath(filename)))

from VLBI_pipe_functions import *

try:
	# CASA 6
	import casatools
	from casatasks import *
	casalog.showconsole(True)
	casa6=True
except:
	# CASA 5
	from casac import casac as casatools
	from taskinit import casalog
	casa6=False
casalog.origin('vp_initial_flagging')

inputs = load_json('vp_inputs.json')
params = load_json(inputs['parameter_file_path'])
steps_run = load_json('vp_steps_run.json', Odict=True, casa6=casa6)
gaintables = load_gaintables(params, casa6=casa6)
gt_r = load_json('vp_gaintables.last.json', Odict=True, casa6=casa6)
gt_r['init_flag'] = {'gaintable':[],'gainfield':[],'spwmap':[],'interp':[]}

cwd = params['global']['cwd']
msfile= '%s.ms'%(params['global']['project_code'])
p_c=params['global']['project_code']

if os.path.exists('%s/%s_msinfo.json'%(params['global']['cwd'],params['global']['project_code']))==False:
	msinfo = get_ms_info(msfile)
	save_json(filename='%s/%s_msinfo.json'%(params['global']['cwd'],params['global']['project_code']), array=get_ms_info('%s/%s.ms'%(params['global']['cwd'],params['global']['project_code'])), append=False)
else:
	msinfo = load_json('%s/%s_msinfo.json'%(params['global']['cwd'],params['global']['project_code']))


if params['init_flag']['flag_edge_chans']['run'] == True:
	if steps_run['init_flag'] == 1:
		flagmanager(vis=msfile,
			 		mode='restore',
			 		versionname='pre_edge_chan')
	else:
		flagmanager(vis=msfile,
					mode='save',
					versionname='pre_edge_chan')

	ec=calc_edge_channels(value=params['init_flag']['flag_edge_chans']['edge_chan_flag'],
						  nspw=msinfo['SPECTRAL_WINDOW']['nspws'],
						  nchan=msinfo['SPECTRAL_WINDOW']['nchan'])

	flagdata(vis=msfile,
			 mode='manual',
			 spw=ec)

if params['init_flag']['flag_autocorrs'] == True:
	if steps_run['init_flag'] == 1:
		flagmanager(vis=msfile,
				    mode='restore',
				    versionname='autocorrelations')
	else:
		flagmanager(vis=msfile,
			        mode='save',
			        versionname='autocorrelations')
	flagdata(vis=msfile,
		     mode='manual',
		     autocorr=True)

if params['init_flag']['quack_data']['run'] == True:
	if steps_run['init_flag'] == 1:
		flagmanager(vis=msfile,
			        mode='restore',
			        versionname='quack')
	else:
		flagmanager(vis=msfile,
			        mode='save',
			        versionname='quack')
	quack_ints = params['init_flag']['quack_data']['quack_time']
	quack_mode = params['init_flag']['quack_data']['quack_mode']
	if type(quack_ints)==dict:
		for i in quack_ints.keys():
			flagdata(vis=msfile,
				     field=i,
				     mode='quack',
				     quackinterval=quack_ints[i],
				     quackmode=quack_mode)
	elif type(quack_ints)==float:
		flagdata(vis=msfile,
			     mode='quack',
			     quackinterval=quack_ints,
			     quackmode=quack_mode)
	else:
		casalog.post(priority='SEVERE',origin=filename,message='quack can either be dictionary to map antenna to quacking time or float to apply to all telescopes')
		sys.exit()

if params['init_flag']['manual_flagging']['run'] == True:
	if steps_run['init_flag'] == 1:
		flagmanager(vis=msfile,
				    mode='restore',
				    versionname='manual_flags')
	else:
		flagmanager(vis=msfile,
			        mode='save',
			        versionname='manual_flags')
	if os.path.exists('%s/%s'%(params['global']['cwd'],params['init_flag']['manual_flagging']['flag_file']))==True:
		flagdata(vis=msfile,
				 mode='list',
				 inpfile='%s/%s'%(params['global']['cwd'],params['init_flag']['manual_flagging']['flag_file']))
	else:
		casalog.post(priority='SEVERE',origin=filename,message='flag file %s/%s does not exist'%(params['global']['cwd'],params['init_flag']['manual_flagging']['flag_file']))
		sys.exit()

save_json(filename='%s/vp_gaintables.last.json'%(params['global']['cwd']), array=gt_r, append=False)
save_json(filename='%s/vp_gaintables.json'%(params['global']['cwd']), array=gaintables, append=False)
steps_run['init_flag'] = 1
save_json(filename='%s/vp_steps_run.json'%(params['global']['cwd']), array=steps_run, append=False)