import os
import sys
import logging
import Crasa.Crasa as crasa
sys.path.append("/scratch/stimela")
utils = __import__('utils')
CONFIG = os.environ["CONFIG"]
INPUT = os.environ["INPUT"]
OUTPUT = os.environ["OUTPUT"]
MSDIR = os.environ["MSDIR"]
cab = utils.readJson(CONFIG)
args = {}
for param in cab['parameters']:
name = param['name']
value = param['value']
if value is None:
continue
args[name] = value
task = crasa.CasaTask(cab["binary"], crash_on_severe=True, **args)
task.run()
# -*- coding: future_fstrings -*-
import Crasa.Crasa as crasa
from scabha import config, parameters_dict, prun
import os
print(f"Running CASA task '{config.binary}'")
save_result = parameters_dict.pop("save_result", None)
overwrite = parameters_dict.pop("overwrite", False)
fluxtable = parameters_dict['fluxtable']
if overwrite:
os.system(f"rm -fr {fluxtable}")
task = crasa.CasaTask(config.binary, save_result=save_result, **parameters_dict)
task.run()
with open(CONFIG, "r") as _std:
cab = yaml.safe_load(_std)
junk = cab["junk"]
args = {}
for param in cab['parameters']:
name = param['name']
value = param['value']
if value is None:
continue
args[name] = value
task = crasa.CasaTask(cab["binary"], **args)
try:
task.run()
finally:
for item in junk:
for dest in [OUTPUT, MSDIR]: # these are the only writable volumes in the container
items = glob.glob("{dest}/{item}".format(**locals()))
for f in items:
if os.path.isfile(f):
os.remove(f)
elif os.path.isdir(f):
shutil.rmtree(f)
# Leave other types
gtab = args["caltable"]
# -*- coding: future_fstrings -*-
import Crasa.Crasa as crasa
from scabha import config, parameters_dict, prun
print(f"Running CASA task '{config.binary}'")
task = crasa.CasaTask(config.binary, **parameters_dict)
task.run()
name = param['name']
value = param['value']
if value is None:
continue
if name in ['threshold', 'inpimage', 'output']:
if name in ['threshold']:
im_value = ' iif( IM0 >=%s, IM0, 0.0) ' % value
im_name = 'expr'
if name in ['output']:
im_value = '%s_thresh' % value
im_name = 'outfile'
if name in ['inpimage']:
im_value = value
im_name = 'imagename'
immath_args[im_name] = im_value
if name in ['mode', 'inpimage', 'inpmask', 'output', 'overwrite']:
makemask_args[name] = value
if 'expr' in immath_args:
task = crasa.CasaTask("immath", **immath_args)
task.run()
if 'inpmask' not in makemask_args:
makemask_args['inpmask'] = immath_args['outfile']
task = crasa.CasaTask(cab["binary"], **makemask_args)
task.run()
for param in cab['parameters']:
name = param['name']
value = param['value']
if value is None:
continue
args[name] = value
prefix = args['imagename']
port2fits = args.pop('port2fits', True)
keep_casa_images = args.pop("keep_casa_images", False)
sys.stdout.write(repr(args))
task = crasa.CasaTask(cab["binary"], **args)
task.run()
nterms = args.get("nterms", 1)
images = ["flux", "model", "residual", "psf", "image"]
STD_IMAGES = images[:4]
convert = []
if port2fits:
for image in images:
img ="{:s}.{:s}".format(prefix, image)
if image == 'flux':
_images = [img]
elif nterms>1:
_images = ["%s.tt%d"%(img,d) for d in range(nterms)]
if image=="image":
for param in cab['parameters']:
name = param['name']
value = param['value']
if value is None:
continue
if name in unstack_params:
unstack_args[name] = value
else:
immath_args[name] = value
unstack = unstack_args.pop(cab["binary"], False)
if not unstack:
task = crasa.CasaTask("immath", **immath_args)
task.run()
else:
images = immath_args['imagename']
for image in images:
for i in range(unstack_args['nchans']):
ext = image.split('.')[-1]
chan_num = str(i)
outfile = '{:s}-{:s}.{:s}'.format(immath_args['outfile'], chan_num,
ext)
run_immath_args = immath_args.copy()
run_immath_args['imagename'] = image
run_immath_args['outfile'] = outfile
run_immath_args['chans'] = chan_num
task = crasa.CasaTask(cab["binary"], **run_immath_args)
task.run()
makemask_args = {}
immath_args = {}
for name, value in parameters_dic.items():
if value is None:
continue
if name in ['threshold', 'inpimage', 'output']:
if name in ['threshold']:
im_value = ' iif( IM0 >=%s, IM0, 0.0) ' % value
im_name = 'expr'
if name in ['output']:
im_value = '%s_thresh' % value
im_name = 'outfile'
if name in ['inpimage']:
im_value = value
im_name = 'imagename'
immath_args[im_name] = im_value
if name in ['mode', 'inpimage', 'inpmask', 'output', 'overwrite']:
makemask_args[name] = value
if 'expr' in immath_args:
task = crasa.CasaTask("immath", **immath_args)
task.run()
if 'inpmask' not in makemask_args:
makemask_args['inpmask'] = immath_args['outfile']
task = crasa.CasaTask(config.binary, **makemask_args)
task.run()
