def __init__(self, filename):
self.filename = filename
self.reg_list = pyregion.open(filename)
min_ra, max_ra, min_dec, max_dec = [], [], [], []
for r in self.reg_list:
# TODO: if necessary, box, ellipse and polygon can be added.
if r.name == 'circle':
c = r.coord_list # c_ra, c_dec, radius
# how much RA does the radius correspond to
radius_ra = np.rad2deg(2*np.arcsin(np.sin(np.deg2rad(c[2])/2)/np.cos(np.deg2rad(c[1]))))
min_ra.append(c[0] - radius_ra)
max_ra.append(c[0] + radius_ra)
min_dec.append(c[1] - c[2])
max_dec.append(c[1] + c[2])
elif r.name == 'polygon':
c = np.array(r.coord_list) # ra_i, dec_i, ra_i+1, dec_i+1
ra_mask = np.zeros(len(c), dtype=bool)
ra_mask[::2] = True
p_ra = c[ra_mask]
p_dec = c[~ra_mask]
min_ra.append(np.min(p_ra))
max_ra.append(np.max(p_ra))
min_dec.append(np.min(p_dec))
max_dec.append(np.max(p_dec))
else:
logger.error('Region type {} not supported.'.format(r.name))
sys.exit(1)
self.min_ra = np.min(min_ra)
self.max_ra = np.max(max_ra)
self.min_dec = np.min(min_dec)
self.max_dec = np.max(max_dec)
def __init__(self, pathsMS, scheduler, check_flags=True, check_sun=False, min_sun_dist=10):
"""
pathsMS: list of MS paths
scheduler: scheduler object
check_flag: if true ignore fully flagged ms
check_sun: if true check sun distance
min_sun_dist: if check_sun and distance from the sun < than this deg, skip
"""
self.scheduler = scheduler
# sort them, useful for some concatenating steps
if len(pathsMS) == 0:
logger.error('Cannot find MS files.')
raise('Cannot find MS files.')
self.mssListObj = []
for pathMS in sorted(pathsMS):
ms = MS(pathMS)
if check_flags and ms.isAllFlagged():
logger.warning('Skip fully flagged ms: %s' % pathMS)
elif check_sun and ms.sun_dist.deg < min_sun_dist:
logger.warning('Skip too close to sun (%.0f deg) ms: %s' % (ms.sun_dist.deg, pathMS))
else:
self.mssListObj.append(MS(pathMS))
if len(self.mssListObj) == 0:
raise('ALL MS files flagged.')
self.mssListStr = [ms.pathMS for ms in self.mssListObj]
self.resolution = self.mssListObj[0].getResolution(check_flags=False)
def check_run(self, log = "", commandType = ""):
"""
Produce a warning if a command didn't close the log properly i.e. it crashed
NOTE: grep, -L inverse match, -l return only filename
"""
if (not os.path.exists(log)):
logger.warning("No log file found to check results: " + log)
return 1
if (commandType == "DPPP"):
out = subprocess.check_output('grep -L "Finishing processing" '+log+' ; exit 0', shell = True, stderr = subprocess.STDOUT)
out += subprocess.check_output('grep -l "Segmentation fault\|Killed" '+log+' ; exit 0', shell = True, stderr = subprocess.STDOUT)
#
# out += subprocess.check_output('grep -l "Aborted (core dumped)" '+log+' ; exit 0', shell = True, stderr = subprocess.STDOUT)
out += subprocess.check_output('grep -i -l "Exception" '+log+' ; exit 0', shell = True, stderr = subprocess.STDOUT)
out += subprocess.check_output('grep -l "**** uncaught exception ****" '+log+' ; exit 0', shell = True, stderr = subprocess.STDOUT)
out += subprocess.check_output('grep -l "error" '+log+' ; exit 0', shell = True, stderr = subprocess.STDOUT)
out += subprocess.check_output('grep -l "misspelled" '+log+' ; exit 0', shell = True, stderr = subprocess.STDOUT)
elif (commandType == "CASA"):
out = subprocess.check_output('grep -l "[a-z]Error" '+log+' ; exit 0', shell = True, stderr = subprocess.STDOUT)
out += subprocess.check_output('grep -l "An error occurred running" '+log+' ; exit 0', shell = True, stderr = subprocess.STDOUT)
out += subprocess.check_output('grep -l "\*\*\* Error \*\*\*" '+log+' ; exit 0', shell = True, stderr = subprocess.STDOUT)
elif (commandType == "wsclean"):
out = subprocess.check_output('grep -l "exception occur" '+log+' ; exit 0', shell = True, stderr = subprocess.STDOUT)
out += subprocess.check_output('grep -l "Segmentation fault\|Killed" '+log+' ; exit 0', shell = True, stderr = subprocess.STDOUT)
out += subprocess.check_output('grep -l "Aborted" '+log+' ; exit 0', shell = True, stderr = subprocess.STDOUT)
out += subprocess.check_output('grep -L "Cleaning up temporary files..." '+log+' ; exit 0', shell = True, stderr = subprocess.STDOUT)
elif (commandType == "python"):
out = subprocess.check_output('grep -l "Traceback (most recent call last):" '+log+' ; exit 0', shell = True, stderr = subprocess.STDOUT)
out += subprocess.check_output('grep -l "Segmentation fault\|Killed" '+log+' ; exit 0', shell = True, stderr = subprocess.STDOUT)
out += subprocess.check_output('grep -i -l \'(?=^((?!error000).)*$).*Error.*\' '+log+' ; exit 0', shell = True, stderr = subprocess.STDOUT)
out += subprocess.check_output('grep -i -l "Critical" '+log+' ; exit 0', shell = True, stderr = subprocess.STDOUT)
out += subprocess.check_output('grep -l "ERROR" '+log+' ; exit 0', shell = True, stderr = subprocess.STDOUT)
out += subprocess.check_output('grep -l "raise Exception" '+log+' ; exit 0', shell = True, stderr = subprocess.STDOUT)
elif (commandType == "singularity"):
out = subprocess.check_output('grep -l "Traceback (most recent call last):" '+log+' ; exit 0', shell = True, stderr = subprocess.STDOUT)
out += subprocess.check_output('grep -i -l \'(?=^((?!error000).)*$).*Error.*\' '+log+' ; exit 0', shell = True, stderr = subprocess.STDOUT)
out += subprocess.check_output('grep -i -l "Critical" '+log+' ; exit 0', shell = True, stderr = subprocess.STDOUT)
elif (commandType == "general"):
out = subprocess.check_output('grep -l -i "error" '+log+' ; exit 0', shell = True, stderr = subprocess.STDOUT)
else:
logger.warning("Unknown command type for log checking: '" + commandType + "'")
return 1
if out != b'':
out = out.split(b'\n')[0].decode()
logger.error(commandType+' run problem on:\n'+out)
raise RuntimeError(commandType+' run problem on:\n'+out)
return 0
def distBrightSource(self, name):
"""
Get the distance in deg from some bright sources
"""
ateam={'CygA':{'ra':299.8679167, 'dec':40.7338889},
'CasA':{'ra':350.8583333, 'dec':58.8000000},
'TauA':{'ra':83.6333333, 'dec':22.0144444},
'VirA':{'ra':187.7058333, 'dec':12.3911111},
'3C338':{'ra':247.160333, 'dec':39.551556},
'3C380':{'ra':277.382420,'dec':48.746156}
}
if name not in ateam.keys():
logger.error('Unknown source for distance: %s' % name)
logger.error('Use: '+' '.join(ateam.keys()))
raise
coord_bright = SkyCoord(ra=ateam[name]['ra']*u.deg, dec=ateam[name]['dec']*u.deg)
ra, dec = self.getPhaseCentre()
return coord_bright.separation(SkyCoord(ra*u.deg, dec*u.deg)).deg
def check_run(self, log="", commandType=""):
"""
Produce a warning if a command didn't close the log properly i.e. it crashed
NOTE: grep, -L inverse match, -l return only filename
"""
import subprocess
if (not os.path.exists(log)):
logger.warning("No log file found to check results: " + log)
return 1
if (commandType == "BBS"):
out = subprocess.check_output('grep -L success ' + log +
' ; exit 0',
shell=False,
stderr=subprocess.STDOUT)
if out != '':
logger.error('BBS run problem on:\n' + out.split("\n")[0])
return 1
elif (commandType == "DPPP"):
out = subprocess.check_output('grep -L "Finishing processing" ' +
log + ' ; exit 0',
shell=True,
stderr=subprocess.STDOUT)
out += subprocess.check_output('grep -l "Exception" ' + log +
' ; exit 0',
shell=True,
stderr=subprocess.STDOUT)
out += subprocess.check_output(
'grep -l "**** uncaught exception ****" ' + log + ' ; exit 0',
shell=True,
stderr=subprocess.STDOUT)
out += subprocess.check_output('grep -l "error" ' + log +
' ; exit 0',
shell=True,
stderr=subprocess.STDOUT)
#out += subprocess.check_output('grep -l "misspelled" '+log+' ; exit 0', shell = True, stderr = subprocess.STDOUT)
if out != '':
logger.error('DPPP run problem on:\n' + out.split("\n")[0])
return 1
elif (commandType == "CASA"):
out = subprocess.check_output('grep -l "[a-z]Error" ' + log +
' ; exit 0',
shell=True,
stderr=subprocess.STDOUT)
out += subprocess.check_output(
'grep -l "An error occurred running" ' + log + ' ; exit 0',
shell=True,
stderr=subprocess.STDOUT)
out += subprocess.check_output('grep -l "\*\*\* Error \*\*\*" ' +
log + ' ; exit 0',
shell=True,
stderr=subprocess.STDOUT)
if out != '':
logger.error('CASA run problem on:\n' + out.split("\n")[0])
return 1
elif (commandType == "wsclean"):
out = subprocess.check_output('grep -l "exception occured" ' +
log + ' ; exit 0',
shell=True,
stderr=subprocess.STDOUT)
out = subprocess.check_output('grep -l "Segmentation fault" ' +
log + ' ; exit 0',
shell=True,
stderr=subprocess.STDOUT)
out += subprocess.check_output(
'grep -L "Cleaning up temporary files..." ' + log +
' ; exit 0',
shell=True,
stderr=subprocess.STDOUT)
if out != '':
logger.error('WSClean run problem on:\n' + out.split("\n")[0])
return 1
elif (commandType == "python"):
out = subprocess.check_output(
'grep -l "Traceback (most recent call last):" ' + log +
' ; exit 0',
shell=True,
stderr=subprocess.STDOUT)
out += subprocess.check_output(
'grep -i -l \'(?=^((?!error000).)*$).*Error.*\' ' + log +
' ; exit 0',
shell=True,
stderr=subprocess.STDOUT)
out += subprocess.check_output('grep -i -l "Critical" ' + log +
' ; exit 0',
shell=True,
stderr=subprocess.STDOUT)
if out != '':
logger.error('Python run problem on:\n' + out.split("\n")[0])
return 1
elif (commandType == "general"):
out = subprocess.check_output('grep -l -i "error" ' + log +
' ; exit 0',
shell=True,
stderr=subprocess.STDOUT)
if out != '':
logger.error('Run problem on:\n' + out.split("\n")[0])
return 1
else:
logger.warning("Unknown command type for log checking: '" +
commandType + "'")
return 1
return 0