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run_prepare_data.py
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run_prepare_data.py
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import inspect, os, sys, json
filename = inspect.getframeinfo(inspect.currentframe()).filename
sys.path.append(os.path.dirname(os.path.realpath(filename)))
from casavlbitools.fitsidi import append_tsys, convert_flags, append_gc
from casavlbitools.casa import convert_gaincurve
from VLBI_pipe_functions import *
mpipath = os.path.dirname(os.path.realpath(filename))
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_prepare_data')
try:
if casa6 == True:
from casampi.MPICommandClient import MPICommandClient
else:
from mpi4casa.MPICommandClient import MPICommandClient
client = MPICommandClient()
client.set_log_mode('redirect')
client.start_services()
parallel=True
cmd = []
except:
parallel=False
try:
from astropy.io import fits
except:
import pyfits as fits
casalog.origin('prepare_data')
casalog.post("")
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)
gt_r = load_json('vp_gaintables.last.json', Odict=True, casa6=casa6)
casalog.post(origin=filename,message='Searching for location of fitsidifiles')
## Set location of fitsidifiles
if params['global']['fitsidi_path'] == "":
params['global']['fitsidi_path'] = params['global']['cwd']
casalog.post(origin=filename,message='Fitsidifile path not set ... assuming they are in the current working directory',priority='WARN')
casalog.post(origin=filename,message='Fitsidifiles to be located in %s'%params['global']['fitsidi_path'])
## Find fitsfiles
if params['global']['fitsidi_files'] == ["auto"]:
idifiles = find_fitsidi(idifilepath=params['global']['fitsidi_path'],\
cwd=params['global']['cwd'])
idifiles= natural_sort(idifiles)
else:
casalog.post(origin=filename,message='Using idifiles specified in parameter file')
casalog.post(origin=filename,message='Checking whether specified idifiles exist')
idifiles = params['global']['fitsidi_files']
for i,j in enumerate(idifiles):
fullidi = "%s/%s"%(params['global']['fitsidi_path'],j)
idifiles[i] = fullidi
if os.path.exists(fullidi) == False:
casalog.post(priority='SEVERE',origin=filename,message='Fitsidifile %s does not exist ... exiting'%fullidi)
sys.exit()
## Copy idifiles to cwd if not originally there
if params['global']['fitsidi_path'] != params['global']['cwd']:
casalog.post(origin=filename,message='Fitsidifiles in different directory. Moving to cwd.',priority='INFO')
for j,i in enumerate(idifiles):
rmfiles(['%s/%s'%(params['global']['cwd'],i.split(params['global']['fitsidi_path']+'/')[1])])
os.system('rsync --progress %s %s'%(i,params['global']['cwd']))
if os.path.exists('%s/%s'%(params['global']['cwd'],i.split(params['global']['fitsidi_path']+'/')[1])) == False:
os.system('cp %s %s'%(i,params['global']['cwd']))
if os.path.exists('%s/%s'%(params['global']['cwd'],i.split(params['global']['fitsidi_path']+'/')[1])) == False:
casalog.post(origin=filename,message='Could not move files with rsync or cp ... exiting',priority='SEVERE')
sys.exit()
idifiles[j] = '%s/%s'%(params['global']['cwd'],i.split(params['global']['fitsidi_path']+'/')[1])
telescop = []
for i in idifiles:
hdu = fits.open(i)
telescop.append(hdu['ARRAY_GEOMETRY'].header['ARRNAM'])
hdu.close()
if telescop.count(telescop[0]) == len(telescop):
telescop = telescop[0]
casalog.post(origin=filename,message='All fits files from same array i.e. %s'%telescop,priority='INFO')
else:
casalog.post(origin=filename,message='Fits files from different arrays :( please clean your fits file directory'%telescop,priority='SEVERE')
sys.exit()
## Find antab file (typical EVN antab files are <project_code>.antab)
if telescop == 'EVN':
if params['prepare_data']['antab_file'] == 'auto':
if os.path.exists('%s.antab'%params['global']['project_code']) == True:
antabfile='%s.antab'%params['global']['project_code']
casalog.post(origin=filename,message='Antab file found - %s.antab'%params['global']['project_code'],priority='INFO')
elif os.path.exists('%s_1.antab'%params['global']['project_code']) == True:
antabfile='%s_1.antab'%params['global']['project_code']
casalog.post(origin=filename,message='Antab file found - %s_1.antab'%params['global']['project_code'],priority='INFO')
else:
casalog.post(origin=filename,message='Auto set antab file %s.antab does not exist ... exiting'%params['global']['project_code'],priority='SEVERE')
sys.exit()
else:
if os.path.exists('%s'%params['prepare_data']['antab']) == False:
casalog.post(origin=filename,message='Antab file %s does not exist, please correct ... exiting'%params['prepare_data']['antab'],priority='SEVERE')
sys.exit()
else:
antabfile='%s'%params['prepare_data']['antab']
ts_fits = check_fits_ext(idifiles=idifiles,ext='SYSTEM_TEMPERATURE',del_ext=params['prepare_data']['replace_antab'])
if (params['prepare_data']['replace_antab'] == True)|(ts_fits==False):
casalog.post(origin=filename,message='Appending TSYS information onto idifiles',priority='INFO')
for i in idifiles:
if parallel == True:
cmd1 = "import inspect, os, sys; sys.path.append('%s'); from casavlbitools.fitsidi import append_tsys; append_tsys(antabfile='%s', idifiles='%s')"%(mpipath,antabfile,i)
cmdId = client.push_command_request(cmd1,block=False)
cmd.append(cmdId[0])
else:
casalog.post(origin=filename,message='Appending to %s'%i)
append_tsys(antabfile=antabfile, idifiles=i)
if parallel == True:
resultList = client.get_command_response(cmd,block=True)
else:
casalog.post(origin=filename,message='System temperature information already exists in the idifile',priority='INFO')
### Convert gaincurve
gc_fits = check_fits_ext(idifiles=idifiles,ext='GAIN_CURVE',del_ext=params['prepare_data']['replace_antab'])
if (params["prepare_data"]["replace_antab"] == True)|(gc_fits==False):
rmdirs(['%s/%s.gc'%(params['global']['cwd'],params['global']['project_code'])])
casalog.post(origin=filename,message='Generating gaincurve information - %s.gc'%params['global']['project_code'],priority='INFO')
if telescop == 'EVN':
convert_gaincurve(antab=antabfile, gc='%s/%s.gc'%(params['global']['cwd'],params['global']['project_code']), min_elevation=params['prepare_data']['gaincurve']['min_elevation'], max_elevation=params['prepare_data']['gaincurve']['max_elevation'])
elif telescop == 'VLBA':
convert_gaincurve(antab='%s/%s/data/VLBA_gains/vlba_gains.key'%(params['global']['cwd'],params['global']['vlbipipe_path']), gc='%s/%s.gc'%(params['global']['cwd'],params['global']['project_code']), min_elevation=params['prepare_data']['gaincurve']['min_elevation'], max_elevation=params['prepare_data']['gaincurve']['max_elevation'])
else:
casalog.post(origin=filename,message='Unknown array!'%params['global']['project_code'],priority='INFO')
sys.exit()
else:
casalog.post(origin=filename,message='Gain curve information already exists in the idifile',priority='INFO')
#for i in idifiles:
# append_gc(antabfile=antabfile, idifile=i)
if params["prepare_data"]["flag_file"] != "none":
casalog.post(origin=filename,message='Generating CASA-compatable observatory flags',priority='INFO')
if params["prepare_data"]["flag_file"] == "auto":
if telescop == 'EVN':
flagfile="%s/%s.uvflg"%(params['global']['cwd'],params['global']['project_code'])
if os.path.exists(flagfile) == False:
flagfile="%s/%s_1.uvflg"%(params['global']['cwd'],params['global']['project_code'])
if os.path.exists(flagfile) == False:
casalog.post(origin=filename,message='Flag file - %s - does not exist, please correct ... exiting'%flagfile,priority='SEVERE')
sys.exit()
elif telescop == 'VLBA':
flagfile="%s/%s.flag"%(params['global']['cwd'],params['global']['project_code'])
if os.path.exists(flagfile) == False:
casalog.post(origin=filename,message='Flag file - %s - does not exist, please correct ... exiting'%flagfile,priority='SEVERE')
sys.exit()
else:
casalog.post(origin=filename,message='Cannot find flags automatically for array %s'%telescop,priority='SEVERE')
sys.exit()
else:
flagfile="%s"%(params['prepare_data']['flag_file'])
if os.path.exists(flagfile) == False:
casalog.post(origin=filename,message='Flag file - %s - does not exist, please correct ... exiting'%flagfile,priority='SEVERE')
sys.exit()
convert_flags(infile=flagfile, idifiles=idifiles, outfp=sys.stdout, outfile='%s_casa.flags'%params['global']['project_code'])
gt_r['prepare_data'] = {}
for k in ['gaintable','gainfield','spwmap','interp']:
gt_r['prepare_data'][k] = []
save_json(filename='%s/vp_gaintables.last.json'%(params['global']['cwd']), array=gt_r, append=False)
steps_run['prepare_data'] = 1
save_json(filename='%s/vp_steps_run.json'%(params['global']['cwd']), array=steps_run, append=False)